32,690 results
Search Results
202. Cardiovascular risk prediction models for women in the general population: A systematic review.
- Author
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Baart, Sara J., Dam, Veerle, Scheres, Luuk J. J., Damen, Johanna A. A. G., Spijker, René, Schuit, Ewoud, Debray, Thomas P. A., Fauser, Bart C. J. M., Boersma, Eric, Moons, Karel G. M., van der Schouw, Yvonne T., and null, null
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CARDIOVASCULAR diseases risk factors ,VASCULAR medicine ,BLOOD pressure ,AMNIOTES ,EPIDEMIOLOGY - Abstract
Aim: To provide a comprehensive overview of cardiovascular disease (CVD) risk prediction models for women and models that include female-specific predictors. Methods: We performed a systematic review of CVD risk prediction models for women in the general population by updating a previous review. We searched Medline and Embase up to July 2017 and included studies in which; (a) a new model was developed, (b) an existing model was validated, or (c) a predictor was added to an existing model. Results: A total of 285 prediction models for women have been developed, of these 160 (56%) were female-specific models, in which a separate model was developed solely in women and 125 (44%) were sex-predictor models. Out of the 160 female-specific models, 2 (1.3%) included one or more female-specific predictors (mostly reproductive risk factors). A total of 591 validations of sex-predictor or female-specific models were identified in 206 papers. Of these, 333 (56%) validations concerned nine models (five versions of Framingham, SCORE, Pooled Cohort Equations and QRISK). The median and pooled C statistics were comparable for sex-predictor and female-specific models. In 260 articles the added value of new predictors to an existing model was described, however in only 3 of these female-specific predictors (reproductive risk factors) were added. Conclusions: There is an abundance of models for women in the general population. Female-specific and sex-predictor models have similar predictors and performance. Female-specific predictors are rarely included. Further research is needed to assess the added value of female-specific predictors to CVD models for women and provide physicians with a well-performing prediction model for women. [ABSTRACT FROM AUTHOR]
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- 2019
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203. A large-scale analysis of bioinformatics code on GitHub.
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Russell, Pamela H., Johnson, Rachel L., Ananthan, Shreyas, Harnke, Benjamin, and Carlson, Nichole E.
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COMPUTER software development ,BIOINFORMATICS software ,INSTITUTIONAL repositories ,COMPUTATIONAL biology ,REPRODUCIBLE research - Abstract
In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the state of source code in the bioinformatics community, specifically looking at relationships between code properties, development activity, developer communities, and software impact. To investigate these issues, we curated a list of 1,720 bioinformatics repositories on GitHub through their mention in peer-reviewed bioinformatics articles. Additionally, we included 23 high-profile repositories identified by their popularity in an online bioinformatics forum. We analyzed repository metadata, source code, development activity, and team dynamics using data made available publicly through the GitHub API, as well as article metadata. We found key relationships within our dataset, including: certain scientific topics are associated with more active code development and higher community interest in the repository; most of the code in the main dataset is written in dynamically typed languages, while most of the code in the high-profile set is statically typed; developer team size is associated with community engagement and high-profile repositories have larger teams; the proportion of female contributors decreases for high-profile repositories and with seniority level in author lists; and, multiple measures of project impact are associated with the simple variable of whether the code was modified at all after paper publication. In addition to providing the first large-scale analysis of bioinformatics code to our knowledge, our work will enable future analysis through publicly available data, code, and methods. Code to generate the dataset and reproduce the analysis is provided under the MIT license at . Data are available at . [ABSTRACT FROM AUTHOR]
- Published
- 2018
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204. Effect of Cellulases and Xylanases on Refining Process and Kraft Pulp Properties
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Kamila Przybysz Buzała, Halina Kalinowska, Małgorzata Derkowska, and Piotr Przybysz
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0106 biological sciences ,lcsh:Medicine ,02 engineering and technology ,Biochemistry ,01 natural sciences ,chemistry.chemical_compound ,Filter Paper ,Cellulases ,Electron Microscopy ,lcsh:Science ,Microscopy ,Multidisciplinary ,biology ,Organic Compounds ,Hydrolysis ,Pulp (paper) ,021001 nanoscience & nanotechnology ,Pulp and paper industry ,Enzyme structure ,Enzymes ,Laboratory Equipment ,Chemistry ,Xylosidases ,Aspergillus ,Kraft process ,Physical Sciences ,Xylanase ,Engineering and Technology ,Scanning Electron Microscopy ,Alternative Energy ,Cellular Structures and Organelles ,0210 nano-technology ,Kraft paper ,Research Article ,Paper ,Equipment ,Cellulase ,engineering.material ,Research and Analysis Methods ,010608 biotechnology ,Cellulose ,Filter paper ,business.industry ,Organic Chemistry ,lcsh:R ,Organisms ,Fungi ,Chemical Compounds ,Biology and Life Sciences ,Proteins ,Cell Biology ,Pinus ,Molds (Fungi) ,Biotechnology ,Energy and Power ,chemistry ,Enzyme Structure ,Enzymology ,engineering ,biology.protein ,lcsh:Q ,business - Abstract
Samples of bleached kraft pine cellulosic pulp, either treated with an enzyme preparation (a Thermomyces lanuginosus xylanase, an Aspergillus sp. cellulase, and a multienzyme preparation NS-22086 containing both these activities) or untreated, were refined in a laboratory PFI mill. The treatment with cellulases contained in the last two preparations significantly improved the pulp’s susceptibility to refining (the target freeness value of 30°SR was achieved in a significantly shorter time), increased water retention value (WRV) and fines contents while the weighted average fiber length was significantly reduced. These changes of pulp parameters caused deterioration of paper strength properties. The treatment with the xylanase, which partially hydrolyzed xylan, small amounts of which are associated with cellulose fibers, only slightly loosened the structure of fibers. These subtle changes positively affected the susceptibility of the pulp to refining (refining energy was significantly reduced) and improved the static strength properties of paper. Thus, the treatment of kraft pulps with xylanases may lead to substantial savings of refining energy without negative effects on paper characteristics.
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- 2016
205. Network representations of angular regions for electromagnetic scattering.
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Daniele, Vito G., Lombardi, Guido, and Zich, Rodolfo S.
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ELECTROMAGNETIC wave scattering ,WIENER-Hopf operators ,SPECTRUM analysis ,WAVE equation ,KERNEL (Mathematics) ,COEFFICIENTS (Statistics) - Abstract
Network modeling in electromagnetics is an effective technique in treating scattering problems by canonical and complex structures. Geometries constituted of angular regions (wedges) together with planar layers can now be approached with the Generalized Wiener-Hopf Technique supported by network representation in spectral domain. Even if the network representations in spectral planes are of great importance by themselves, the aim of this paper is to present a theoretical base and a general procedure for the formulation of complex scattering problems using network representation for the Generalized Wiener Hopf Technique starting basically from the wave equation. In particular while the spectral network representations are relatively well known for planar layers, the network modelling for an angular region requires a new theory that will be developed in this paper. With this theory we complete the formulation of a network methodology whose effectiveness is demonstrated by the application to a complex scattering problem with practical solutions given in terms of GTD/UTD diffraction coefficients and total far fields for engineering applications. The methodology can be applied to other physics fields. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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206. A technique for lyopreservation of Clostridium ljungdahlii in a biocomposite matrix for CO absorption.
- Author
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Schulte, Mark J., Solocinski, Jason, Wang, Mian, Kovacs, Michelle, Kilgore, Ryan, Osgood, Quinn, Underwood, Lukas, Flickinger, Michael C., and Chakraborty, Nilay
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CLOSTRIDIUM biotechnology ,COMPOSITE materials ,CARBON monoxide ,BIOCATALYSIS ,CRYOGENICS - Abstract
A system capable of biocatalytic conversion of distributed sources of single carbon gases such as carbon monoxide into hydrocarbons can be highly beneficial for developing commercially viable biotechnology applications in alternative energy. Several anaerobic bacterial strains can be used for such conversion. The anaerobic carbon monoxide-fixing bacteria Clostridium ljungdahlii OTA1 is a model CO assimilating microorganism that currently requires cryogenic temperature for storage of the viable strains. If these organisms can be stabilized and concentrated in thin films in advanced porous materials, it will enable development of high gas fraction, biocomposite absorbers with elevated carbon monoxide (CO) mass transfer rate, that require minimal power input and liquid, and demonstrate elevated substrate consumption rate compared to conventional suspended cell bioreactors. We report development of a technique for dry-stabilization of C. ljungdahlii OTA1 on a paper biocomposite. Bacterial samples coated onto paper were desiccated in the presence of trehalose using convective drying and stored at 4°C. Optimal dryness was ~1g H
2 O per gram of dry weight (gDW ). CO uptake directly following biocomposite rehydration steadily increases over time indicating immediate cellular metabolic recovery. A high-resolution Raman microspectroscopic hyperspectral imaging technique was employed to spatially quantify the residual moisture content. We have demonstrated for the first time that convectively dried and stored C. ljungdahlii strains were stabilized in a desiccated state for over 38 days without a loss in CO absorbing reactivity. The Raman hyperspectral imaging technique described here is a non-invasive characterization tool to support development of dry-stabilization techniques for microorganisms on inexpensive porous support materials. The present study successfully extends and implements the principles of dry-stabilization for preservation of strictly anaerobic bacteria as an alternative to lyophilization or spray drying that could enable centralized biocomposite biocatalyst fabrication and decentralized bioprocessing of CO to liquid fuels or chemicals. [ABSTRACT FROM AUTHOR]- Published
- 2017
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207. Questionable science and reproducibility in electrical brain stimulation research.
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Héroux, Martin E., Loo, Colleen K., Taylor, Janet L., and Gandevia, Simon C.
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BRAIN physiology ,BRAIN function localization ,NEUROLOGY ,PATHOLOGICAL psychology ,STATISTICS - Abstract
Electrical brain stimulation (EBS) is a trendy new technique used to change brain function and treat neurological, psychiatric and psychological disorders. We were curious whether the published literature, which is dominated by positive results, reflects the experience of researchers using EBS. Specifically, we wanted to know whether researchers are able to reproduce published EBS effects and whether they engage in, but fail to report, questionable research practices. We invited 976 researchers to complete an online survey. We also audited 100 randomly-selected published EBS papers. A total of 154 researchers completed the survey. Survey respondents had a median of 3 [1 to 6, IQR] published EBS papers (1180 total) and 2 [1 to 3] unpublished ones (380 total). With anodal and cathodal EBS, the two most widely used techniques, 45–50% of researchers reported being able to routinely reproduce published results. When asked about how study sample size was determined, 69% of respondents reported using the sample size of published studies, while 61% had used power calculations, and 32% had based their decision on pilot data. In contrast, our audit found only 6 papers where power calculations were used and a single paper in which pilot data was used. When asked about questionable research practices, survey respondents were aware of other researchers who selectively reported study outcomes (41%) and experimental conditions (36%), adjusted statistical analysis to optimise results (43%), and engaged in other shady practices (20%). Fewer respondents admitted to engaging in these practices themselves, although 25% admitted to adjusting statistical analysis to optimize results. There was strong agreement that such practices should be reported in research papers; however, our audit found only two such admissions. The present survey confirms that questionable research practices and poor reproducibility are present in EBS studies. The belief that EBS is effective needs to be replaced by a more rigorous approach so that reproducible brain stimulation methods can be devised and applied. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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208. The influence of journal submission guidelines on authors' reporting of statistics and use of open research practices.
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Giofrè, David, Cumming, Geoff, Fresc, Luca, Boedker, Ingrid, and Tressoldi, Patrizio
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EXPERIMENTAL psychology ,CONFIDENCE intervals ,PSYCHOLOGY of authors ,META-analysis ,COMPARATIVE studies - Abstract
From January 2014, Psychological Science introduced new submission guidelines that encouraged the use of effect sizes, estimation, and meta-analysis (the “new statistics”), required extra detail of methods, and offered badges for use of open science practices. We investigated the use of these practices in empirical articles published by Psychological Science and, for comparison, by the Journal of Experimental Psychology: General, during the period of January 2013 to December 2015. The use of null hypothesis significance testing (NHST) was extremely high at all times and in both journals. In Psychological Science, the use of confidence intervals increased markedly overall, from 28% of articles in 2013 to 70% in 2015, as did the availability of open data (3 to 39%) and open materials (7 to 31%). The other journal showed smaller or much smaller changes. Our findings suggest that journal-specific submission guidelines may encourage desirable changes in authors’ practices. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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209. A review of patient and carer participation and the use of qualitative research in the development of core outcome sets.
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Jones, Janet E., Jones, Laura L., Keeley, Thomas J. H., Calvert, Melanie J., and Mathers, Jonathan
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MEDICAL care ,MEDICAL personnel ,STAKEHOLDERS ,MEDICAL economics ,ACQUISITION of data - Abstract
Background: To be meaningful, a core outcome set (COS) should be relevant to all stakeholders including patients and carers. This review aimed to explore the methods by which patients and carers have been included as participants in COS development exercises and, in particular, the use and reporting of qualitative methods. Methods: In August 2015, a search of the Core Outcomes Measures in Effectiveness Trials (COMET) database was undertaken to identify papers involving patients and carers in COS development. Data were extracted to identify the data collection methods used in COS development, the number of health professionals, patients and carers participating in these, and the reported details of qualitative research undertaken. Results: Fifty-nine papers reporting patient and carer participation were included in the review, ten of which reported using qualitative methods. Although patients and carers participated in outcome elicitation for inclusion in COS processes, health professionals tended to dominate the prioritisation exercises. Of the ten qualitative papers, only three were reported as a clear pre-designed part of a COS process. Qualitative data were collected using interviews, focus groups or a combination of these. None of the qualitative papers reported an underpinning methodological framework and details regarding data saturation, reflexivity and resource use associated with data collection were often poorly reported. Five papers reported difficulty in achieving a diverse sample of participants and two reported that a large and varied range of outcomes were often identified by participants making subsequent rating and ranking difficult. Conclusions: Consideration of the best way to include patients and carers throughout the COS development process is needed. Additionally, further work is required to assess the potential role of qualitative methods in COS, to explore the knowledge produced by different qualitative data collection methods, and to evaluate the time and resources required to incorporate qualitative methods into COS development. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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210. Modelling Creativity: Identifying Key Components through a Corpus-Based Approach.
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Jordanous, Anna and Keller, Bill
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CREATIVE ability ,NATURAL language processing ,ONTOLOGY ,MATHEMATICAL analysis ,QUANTITATIVE research - Abstract
Creativity is a complex, multi-faceted concept encompassing a variety of related aspects, abilities, properties and behaviours. If we wish to study creativity scientifically, then a tractable and well-articulated model of creativity is required. Such a model would be of great value to researchers investigating the nature of creativity and in particular, those concerned with the evaluation of creative practice. This paper describes a unique approach to developing a suitable model of how creative behaviour emerges that is based on the words people use to describe the concept. Using techniques from the field of statistical natural language processing, we identify a collection of fourteen key components of creativity through an analysis of a corpus of academic papers on the topic. Words are identified which appear significantly often in connection with discussions of the concept. Using a measure of lexical similarity to help cluster these words, a number of distinct themes emerge, which collectively contribute to a comprehensive and multi-perspective model of creativity. The components provide an ontology of creativity: a set of building blocks which can be used to model creative practice in a variety of domains. The components have been employed in two case studies to evaluate the creativity of computational systems and have proven useful in articulating achievements of this work and directions for further research. [ABSTRACT FROM AUTHOR]
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- 2016
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211. Evaluation of a Silver-Embedded Ceramic Tablet as a Primary and Secondary Point-of-Use Water Purification Technology in Limpopo Province, S. Africa
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James A. Smith, Amidou Samie, Veronica Son, Chloe T. Rento, Beeta Ehdaie, Rebecca Dillingham, and Sydney S. Turner
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Ceramics ,Sanitization ,0208 environmental biotechnology ,Marine and Aquatic Sciences ,lcsh:Medicine ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,law.invention ,Turbidity ,South Africa ,Materials Physics ,Specimen Storage ,law ,Water Quality ,Natural Resources ,Medicine and Health Sciences ,Public and Occupational Health ,Ceramic ,lcsh:Science ,Multidisciplinary ,Physics ,Mineralogy ,Pulp and paper industry ,6. Clean water ,3. Good health ,Chemistry ,Infectious Diseases ,Ceramic water filter ,visual_art ,Physical Sciences ,Water Resources ,visual_art.visual_art_medium ,Water treatment ,Water Microbiology ,Research Article ,Chemical Elements ,Tablets ,Silver ,Infectious Disease Control ,Materials by Structure ,Materials Science ,Portable water purification ,Research and Analysis Methods ,Water Purification ,Humans ,Filtration ,Clay Mineralogy ,0105 earth and related environmental sciences ,Ecology and Environmental Sciences ,lcsh:R ,020801 environmental engineering ,Health Care ,Disinfection ,Water resources ,Storage and Handling ,Earth Sciences ,Environmental science ,lcsh:Q ,Preventive Medicine ,Water quality ,Disinfectants - Abstract
The World Health Organization (WHO) recognizes point-of-use water treatment (PoUWT) technologies as effective means to improve water quality. This paper investigates long-term performance and social acceptance of a novel PoUWT technology, a silver-infused ceramic tablet, in Limpopo Province, South Africa. When placed in a water storage container, the silver-embedded ceramic tablet releases silver ions into water, thereby disinfecting microbial pathogens and leaving the water safe for human consumption. As a result of its simplicity and efficiency, the silver-embedded ceramic tablet can serve as a stand-alone PoUWT method and as a secondary PoUWT to improve exisitng PoUWT methods, such as ceramic water filters. In this paper, three PoUWT interventions were conducted to evaluate the silver-embedded ceramic tablet: (1) the silver-embedded ceramic tablet as a stand-alone PoUWT method, (2) ceramic water filters stand-alone, and (3) a filter-tablet combination. The filter-tablet combination evaluates the silver-embedded ceramic tablet as a secondary PoUWT method when placed in the lower reservoir of the ceramic water filter system to provide residual disinfection post-filtration. Samples were collected from 79 households over one year and analyzed for turbidity, total silver levels and coliform bacteria. Results show that the silver-embedded ceramic tablet effectively reduced total coliform bacteria (TC) and E. coli when used as a stand-alone PoUWT method and when used in combination with ceramic water filters. The silver-embedded ceramic tablet's performance as a stand-alone PoUWT method was comparable to current inexpensive, single-use PoUWT methods, demonstrating 100% and 75% median reduction in E. coli and TC, respectively, after two months of use. Overall, the the filter-tablet combination performed the best of the three interventions, providing a 100% average percent reduction in E. coli over one year. User surveys were also conducted and indicated that the silver-embedded ceramic tablet was simple to use and culturally appropriate. Also, silver levels in all treated water samples remained below 20 μg/L, significantly lower than the drinking water standard of 100 μg/L, making it safe for consumption. Long-term data demonstrates that the silver-embedded ceramic tablet has beneficial effects even after one year of use. This study demonstrates that the silver-embedded ceramic tablet can effectively improve water quality when used alone, or with ceramic water filters, to reduce rates of recontamination. Therefore, the tablet has the potential to provide a low-cost means to purify water in resource-limited settings.
- Published
- 2017
212. Longitudinal assessment of anti-PGL-I serology in contacts of leprosy patients in Bangladesh
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Anouk van Hooij, Linda Oskam, Jan Hendrik Richardus, Annemieke Geluk, David Pahan, Louis Wilson, Susan J. F. van den Eeden, Konrad van der Zwet, Renate A. Richardus, Khorshed Alam, Roel Faber, and Public Health
- Subjects
Male ,Bacterial Diseases ,Delayed Diagnosis ,Disease ,Pathology and Laboratory Medicine ,Biochemistry ,Serology ,Cohort Studies ,Geographical Locations ,0302 clinical medicine ,Filter Paper ,Medicine and Health Sciences ,Longitudinal Studies ,Prospective Studies ,030212 general & internal medicine ,Enzyme-Linked Immunoassays ,Child ,Mycobacterium leprae ,Bangladesh ,education.field_of_study ,biology ,Transmission (medicine) ,lcsh:Public aspects of medicine ,Antibodies, Bacterial ,Mycobacterium Leprae ,3. Good health ,Actinobacteria ,Laboratory Equipment ,Infectious Diseases ,Child, Preschool ,Engineering and Technology ,Biomarker (medicine) ,Female ,Leprosy ,Research Article ,Neglected Tropical Diseases ,Cohort study ,Adult ,medicine.medical_specialty ,Asia ,lcsh:Arctic medicine. Tropical medicine ,Adolescent ,lcsh:RC955-962 ,030231 tropical medicine ,Population ,Equipment ,Research and Analysis Methods ,Young Adult ,03 medical and health sciences ,Diagnostic Medicine ,Internal medicine ,medicine ,Humans ,Immunoassays ,education ,Antigens, Bacterial ,Bacteria ,business.industry ,Organisms ,Public Health, Environmental and Occupational Health ,Infant ,Biology and Life Sciences ,lcsh:RA1-1270 ,Tropical Diseases ,biology.organism_classification ,medicine.disease ,Immunoglobulin M ,Immunoglobulin G ,People and Places ,Immunologic Techniques ,Glycolipids ,business ,Biomarkers - Abstract
Background Despite elimination efforts, the number of Mycobacterium leprae (M. leprae) infected individuals who develop leprosy, is still substantial. Solid evidence exists that individuals living in close proximity to patients are at increased risk to develop leprosy. Early diagnosis of leprosy in endemic areas requires field-friendly tests that identify individuals at risk of developing the disease before clinical manifestation. Such assays will simultaneously contribute to reduction of current diagnostic delay as well as transmission. Antibody (Ab) levels directed against the M.leprae-specific phenolic glycolipid I (PGL-I) represents a surrogate marker for bacterial load. However, it is insufficiently defined whether anti-PGL-I antibodies can be utilized as prognostic biomarkers for disease in contacts. Particularly, in Bangladesh, where paucibacillary (PB) patients form the majority of leprosy cases, anti-PGL-I serology is an inadequate method for leprosy screening in contacts as a directive for prophylactic treatment. Methods Between 2002 and 2009, fingerstick blood from leprosy patients’ contacts without clinical signs of disease from a field-trial in Bangladesh was collected on filter paper at three time points covering six years of follow-up per person. Analysis of anti-PGL-I Ab levels for 25 contacts who developed leprosy during follow-up and 199 contacts who were not diagnosed with leprosy, was performed by ELISA after elution of bloodspots from filter paper. Results Anti-PGL-I Ab levels at intake did not significantly differ between contacts who developed leprosy during the study and those who remained free of disease. Moreover, anti-PGL-I serology was not prognostic in this population as no significant correlation was identified between anti-PGL-I Ab levels at intake and the onset of leprosy. Conclusion In this highly endemic population in Bangladesh, no association was observed between anti-PGL-I Ab levels and onset of disease, urging the need for an extended, more specific biomarker signature for early detection of leprosy in this area. Trial registration ClinicalTrials.gov ISRCTN61223447, Author summary Leprosy is an infectious disease caused by the bacterium Mycobacterium leprae, which causes skin and nerve damage. Despite worldwide efforts to eliminate leprosy, the number of infected individuals who develop leprosy, is still substantial. Household contacts of new leprosy patients are especially at risk. Early diagnosis of leprosy is key in preventing lifelong handicaps as well as transmission. This requires field-friendly tests that identify individuals at risk of developing the disease before they develop clinical symptoms so that they can receive (prophylactic) treatment. Measuring antibody levels directed against the M.leprae-specific phenolic glycolipid I (PGL-I) provides an indication of the bacterial load. To identify whether anti-PGL-I Ab levels correlate with the development of leprosy in contacts of newly diagnosed leprosy cases, we analyzed these levels in 25 contacts who developed leprosy during 6 years of follow-up and 199 contacts who were not diagnosed with leprosy at 3 time points in 6 years. This study showed that anti-PGL-I Ab levels at intake did not significantly differ between contacts who developed leprosy during the study and those who remained free of disease. Therefore, anti-PGL-I Ab levels alone do not represent a practical tool for prediction of which household contacts will develop leprosy in an endemic area such as Bangladesh, with high levels of patients with paucibacillary leprosy. This stresses the need for a diagnostic test composed of a biomarker signature consisting of multiple biomarkers.
- Published
- 2017
213. A two-stage filter for removing salt-and-pepper noise using noise detector based on characteristic difference parameter and adaptive directional mean filter
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Yufeng Nie and Hongjin Ma
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Computer and Information Sciences ,Imaging Techniques ,Computer science ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Equipment ,Color ,lcsh:Medicine ,Transportation ,Image Analysis ,02 engineering and technology ,Digital Imaging ,Research and Analysis Methods ,Infographics ,Mathematical and Statistical Techniques ,Filter Paper ,Image Interpretation, Computer-Assisted ,Computer Science::Multimedia ,Photography ,0202 electrical engineering, electronic engineering, information engineering ,Median filter ,lcsh:Science ,Multidisciplinary ,Pixel ,Data Visualization ,Applied Mathematics ,Simulation and Modeling ,Detector ,lcsh:R ,Digital imaging ,020206 networking & telecommunications ,Salt-and-pepper noise ,White noise ,Filter (signal processing) ,Image Enhancement ,Charts ,Boats ,Laboratory Equipment ,Noise ,Computer Science::Computer Vision and Pattern Recognition ,Physical Sciences ,Engineering and Technology ,020201 artificial intelligence & image processing ,lcsh:Q ,Mathematical Functions ,Algorithm ,Mathematics ,Algorithms ,Research Article - Abstract
In this paper, a two-stage filter for removing salt-and-pepper noise using noise detector based on characteristic difference parameter and adaptive directional mean filter is proposed. The first stage firstly detects the noise corrupted pixels by combining characteristic difference parameter and gray level extreme, then develops an improved adaptive median filter to firstly restore them. The second stage introduces a restoration scheme to further restore the noise corrupted pixels, which firstly divides them into two types and then applies different restoration skills for the pixels based on the classification result. One type of pixels is restored by the mean filter and the other type of pixels is restored by the proposed adaptive directional mean filter. The new filter firstly adaptively selects the optimal filtering window and direction template, then replaces the gray level of noise corrupted pixel by the mean value of pixels on the optimal template. Experimental results show that the proposed filter outperforms many existing main filters in terms of noise suppression and detail preservation.
- Published
- 2018
214. From waste to food: Optimising the breakdown of oil palm waste to provide substrate for insects farmed as animal feed
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Marc Parker, James Donarski, Maureen Wakefield, Mark Harrison, Elizabeth Dickinson, Adrian J. Charlton, Michael Dickinson, Aida Rafat, Julie Wilson, Florence J. V. Gschwend, Jason P. Hallett, Rosie Nolan, and Royal Academy Of Engineering
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Life Cycles ,Insecta ,Proton Magnetic Resonance Spectroscopy ,Biomass ,Biogas ,02 engineering and technology ,010501 environmental sciences ,Palm Oil ,Spectrum analysis techniques ,01 natural sciences ,Lignin ,Biochemistry ,Larvae ,0202 electrical engineering, electronic engineering, information engineering ,Metabolites ,Bioenergy ,Oil Palm ,Anaerobiosis ,Materials ,Principal Component Analysis ,Multidisciplinary ,food and beverages ,Eukaryota ,Plants ,Pulp and paper industry ,Insects ,Chemistry ,Data Acquisition ,Biofuel ,Digestate ,Physical Sciences ,Metabolome ,Medicine ,Engineering and Technology ,Research Article ,Computer and Information Sciences ,Arthropoda ,General Science & Technology ,Animal feed ,Science ,020209 energy ,Materials Science ,Steaming ,Fuels ,NMR spectroscopy ,Animals ,0105 earth and related environmental sciences ,Waste Products ,Chemical Compounds ,Organisms ,Biology and Life Sciences ,Pressure cooking ,Feeding Behavior ,Animal Feed ,Invertebrates ,Energy and Power ,Research and analysis methods ,Anaerobic digestion ,Metabolism ,Biofuels ,Environmental science ,Developmental Biology - Abstract
Waste biomass from the palm oil industry is currently burned as a means of disposal and solutions are required to reduce the environmental impact. Whilst some waste biomass can be recycled to provide green energy such as biogas, this investigation aimed to optimise experimental conditions for recycling palm waste into substrate for insects, farmed as a sustainable high-protein animal feed. NMR spectroscopy and LC-HRMS were used to analyse the composition of palm empty fruit bunches (EFB) under experimental conditions optimised to produce nutritious substrate rather than biogas. Statistical pattern recognition techniques were used to investigate differences in composition for various combinations of pre-processing and anaerobic digestion (AD) methods. Pre-processing methods included steaming, pressure cooking, composting, microwaving, and breaking down the EFB using ionic liquids. AD conditions which were modified in combination with pre-processing methods were ratios of EFB:digestate and pH. Results show that the selection of pre-processing method affects the breakdown of the palm waste and subsequently the substrate composition and biogas production. Although large-scale insect feeding trials will be required to determine nutritional content, we found that conditions can be optimised to recycle palm waste for the production of substrate for insect rearing. Pre-processing EFB using ionic liquid before AD at pH6 with a 2:1 digestate:EFB ratio were found to be the best combination of experimental conditions.
- Published
- 2019
215. Development of highly efficient protocols for extraction and amplification of cytomegalovirus DNA from dried blood spots for detection and genotyping of polymorphic immunomodulatory genes
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Christian Berg, Thomas Benfield, Mette M. Rosenkilde, Thomas Sundelin, Lene Rostgaard Nielsen, Martin Barfred Friis, and Hans R. Lüttichau
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0301 basic medicine ,Human cytomegalovirus ,Male ,Cytomegalovirus Infection ,Viral Diseases ,Genotyping Techniques ,Physiology ,Cytomegalovirus ,Artificial Gene Amplification and Extension ,medicine.disease_cause ,Pathology and Laboratory Medicine ,Polymerase Chain Reaction ,Biochemistry ,law.invention ,0302 clinical medicine ,Filter Paper ,law ,Nucleic Acids ,Medicine and Health Sciences ,030212 general & internal medicine ,Pathogen ,DNA extraction ,Polymerase chain reaction ,Multidisciplinary ,virus diseases ,Viral Load ,Body Fluids ,Laboratory Equipment ,Titer ,Infectious Diseases ,Blood ,Medical Microbiology ,Viral Pathogens ,Cytomegalovirus Infections ,Viruses ,Medicine ,Human Cytomegalovirus ,Engineering and Technology ,Female ,Receptors, Chemokine ,Pathogens ,Anatomy ,Chemokines, CXC ,Research Article ,Herpesviruses ,Science ,030106 microbiology ,Equipment ,Biology ,Research and Analysis Methods ,Microbiology ,03 medical and health sciences ,Viral Proteins ,Extraction techniques ,medicine ,Genetics ,Humans ,Molecular Biology Techniques ,Genotyping ,Gene ,Molecular Biology ,Microbial Pathogens ,Retrospective Studies ,Polymorphism, Genetic ,Infant, Newborn ,Organisms ,Gene Amplification ,Biology and Life Sciences ,DNA ,medicine.disease ,Virology ,Dried Blood Spot Testing ,DNA viruses - Abstract
Congenital cytomegalovirus (CMV) infection is a major cause of birth defects ranging from developmental disorders to stillbirth. Most newborns affected by CMV do not present with symptoms at birth but are at risk of sequelae at later stages of their childhood. Stored dried blood spots (DBS) taken at birth can be used for retrospective diagnosis of hereditary diseases, but detection of pathogens is challenged by potentially low pathogen concentrations in the small blood volume available in a DBS. Here we test four different extraction methods for optimal recovery of CMV DNA from DBS at low to high CMV titers. The recovery efficiencies varied widely between the different extractions (from 3% to 100%) with the most efficient method extracting up to 113-fold more CMV DNA than the least efficient and 8-fold more than the reference protocol. Furthermore, we amplified four immunomodulatory CMV genes from the extracted DNA: the UL40 and UL111A genes which occur as functional knockouts in some circulating CMV strains, and the highly variable UL146 and US28 genes. The PCRs specifically amplified the CMV genes at all tested titers with sufficient quality for sequencing and genotyping. In summary, we here report an extraction method for optimal recovery of CMV DNA from DBSs that can be used for both detection of CMV and for genotyping of polymorphic CMV genes in congenital CMV infection.
- Published
- 2019
216. Root-endophytic Chaetomium cupreum chemically enhances aluminium tolerance in Miscanthus sinensis via increasing the aluminium detoxicants, chlorogenic acid and oosporein
- Author
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Kazuyoshi Ogawa, Hayato Masuya, Toshikatsu Haruma, Naofumi Kozai, Keiko Yamaji, and Yurina Sekine
- Subjects
0106 biological sciences ,0301 basic medicine ,Siderophore ,Fungal Structure ,Miscanthus sinensis ,Plant Science ,Chaetomium ,Heavy Metals ,Toxicology ,Pathology and Laboratory Medicine ,Plant Roots ,01 natural sciences ,chemistry.chemical_compound ,Filter Paper ,Medicine and Health Sciences ,Benzoquinones ,Toxins ,Food science ,Mycelium ,Multidisciplinary ,biology ,Eukaryota ,Plants ,Equipment Sterilization ,Laboratory Equipment ,Chemistry ,Physical Sciences ,Engineering and Technology ,Medicine ,Cellular Structures and Organelles ,Plant Cell Walls ,Cellular Types ,Chlorogenic Acid ,Citric acid ,Research Article ,Chemical Elements ,Equipment Preparation ,Plant Cell Biology ,Science ,Toxic Agents ,Equipment ,Mycology ,Research and Analysis Methods ,Poaceae ,Citric Acid ,Cell wall ,03 medical and health sciences ,Cell Walls ,Chlorogenic acid ,Plant Cells ,Filter Sterilization ,Organisms ,Chemical Compounds ,Biology and Life Sciences ,Cell Biology ,biology.organism_classification ,030104 developmental biology ,chemistry ,Seedlings ,Seedling ,Malic acid ,Acids ,Aluminum ,010606 plant biology & botany - Abstract
Miscanthus sinensis Andersson is a pioneer plant species that grows naturally at mining sites. Miscanthus sinensis can detoxify aluminium (Al) by producing phytosiderophores, such as chlorogenic acid, citric acid, and malic acid, and localizing Al in cell walls. Root-endophytic Chaetomium cupreum, which produces microbial siderophores, enhances Al tolerance in M. sinensis. However, we could not determine whether the siderophores produced by C. cupreum actually enhance Al tolerance in M. sinensis, because the microbial siderophores have not yet been identified in previous research. The purpose of this study was to clarify how C. cupreum chemically increases Al tolerance in M. sinensis under acidic mining site conditions, especially considering siderophores. Using instrumental analyses, the siderophore produced by C. cupreum was identified as oosporein. Comparison of the stability constant between Al and phytosiderophores and oosporein indicated that oosporein could detoxify Al similarly to chlorogenic acid, which shows higher stability constant than citric acid and malic acid. Inoculation test of C. cupreum onto M. sinensis in acidic mine soil showed that C. cupreum promoted seedling growth, and enhanced Al tolerance via inducing chlorogenic-acid production and producing oosporein. These results suggested that C. cupreum could chemically enhance Al tolerance and might promote growth via reducing excessive Al in cell walls, the main site of Al accumulation. In addition, the chemical enhancement of Al tolerance by C. cupreum might be important for M. sinensis to adapt to acidic mining sites.
- Published
- 2019
217. A popular Indian clove-based mosquito repellent is less effective against Culex quinquefasciatus and Aedes aegypti than DEET
- Author
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Walter S. Leal, Gabriel B. Faierstein, Kaiming Tan, Pingxi Xu, Rosângela Maria Rodrigues Barbosa, Garrison K. Buss, and Hwang, Jiang-Shiou
- Subjects
0301 basic medicine ,Time Factors ,Xenopus ,Syzygium ,Disease Vectors ,Receptors, Odorant ,Mosquitoes ,Biochemistry ,Toxicology ,DEET ,chemistry.chemical_compound ,0302 clinical medicine ,Filter Paper ,Aedes ,Receptors ,Medicine and Health Sciences ,Active ingredient ,Multidisciplinary ,biology ,Organic Compounds ,Eukaryota ,Animal Models ,Lipids ,3. Good health ,Insects ,Laboratory Equipment ,Eugenol ,Chemistry ,Culex ,Infectious Diseases ,Odorant ,Experimental Organism Systems ,Xenopus Oocytes ,Vertebrates ,Physical Sciences ,Frogs ,Engineering and Technology ,Medicine ,Research Article ,animal structures ,Arthropoda ,General Science & Technology ,First line ,Science ,030231 tropical medicine ,Equipment ,Aedes aegypti ,Aedes Aegypti ,Research and Analysis Methods ,Culex Quinquefasciatus ,Amphibians ,03 medical and health sciences ,Model Organisms ,Animals ,REPELENTES ,Ethanol ,Extramural ,Plant Extracts ,Organic Chemistry ,fungi ,Organisms ,Chemical Compounds ,Biology and Life Sciences ,biology.organism_classification ,Invertebrates ,Culex quinquefasciatus ,Insect Vectors ,Vector-Borne Diseases ,Species Interactions ,Emerging Infectious Diseases ,030104 developmental biology ,chemistry ,Alcohols ,Odorant Receptor ,Insect Repellents ,Animal Studies ,Oocytes ,Oils - Abstract
Insect repellents are widely used as the first line of defense against mosquito bites and transmission of disease-causing agents. However, the cost of daily applications of even the most affordable and the gold standard of insect repellents, DEET, is still high for low-income populations where repellents are needed the most. An Indian clove-based homemade recipe has been presented as a panacea. We analyzed this homemade repellent and confirmed by behavioral measurements and odorant receptor responses that eugenol is the active ingredient in this formulation. Prepared as advertised, this homemade repellent is ineffective, whereas 5x more concentrated extracts from the brand most enriched in eugenol showed moderate repellency activity against Culex quinquefasciatus and Aedes aegypti. DEET showed higher performance when compared to the 5x concentrated formulation and is available in the same market at a lower price than the cost of the ingredients to prepare the homemade formulation.
- Published
- 2019
218. Multifaceted analyses disclose the role of fruit size and skin-russeting in the accumulation pattern of phenolic compounds in apple
- Author
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Fabrizio Costa, Nicola Busatto, Daiki Matsumoto, Urska Vrhovsek, and Alice Tadiello
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0106 biological sciences ,Metabolite ,Fruit development ,Phytochemicals ,Fruit Crops ,Gene Expression ,01 natural sciences ,Antioxidants ,Catechin ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Medicine and Health Sciences ,Procyanidin B2 ,0303 health sciences ,Principal Component Analysis ,Multidisciplinary ,biology ,Pulp (paper) ,food and beverages ,Eukaryota ,Agriculture ,Plants ,Quality ,Horticulture ,Chemistry ,Malus ,Physical Sciences ,Medicine ,Quercetin ,Anatomy ,Research Article ,Skin Tissue ,Science ,Animal Types ,Crops ,engineering.material ,Research and Analysis Methods ,Fruits ,03 medical and health sciences ,Nutraceutical ,Phenols ,Genetics ,Apples ,Biflavonoids ,Animals ,Proanthocyanidins ,Domestic Animals ,Molecular Biology Techniques ,Molecular Biology ,030304 developmental biology ,Gene Expression Profiling ,fungi ,Organisms ,Chemical Compounds ,Biology and Life Sciences ,biology.organism_classification ,Phlorhizin ,Biological Tissue ,chemistry ,Polyphenol ,Fruit ,engineering ,Settore AGR/03 - ARBORICOLTURA GENERALE E COLTIVAZIONI ARBOREE ,Zoology ,010606 plant biology & botany ,Cloning ,Crop Science - Abstract
Fruits are nowadays considered important suppliers of anti-oxidant molecules. Apples are particularly rich in phenolic compounds, non-nutritional phytochemicals that play active roles in controlling severe chronic diseases. In this work, 19 phenolic compounds were investigated in both skin and pulp tissues of seven apple accessions across the Malus genus collected at two stages: during fruit development and at harvest. The primary difference in phenolic concentration between wild and domesticated accessions, especially in the pulp, could be explained by the larger growth rate of the domesticated varieties. The proposed dilution effect was also confirmed through the observation of the increased content of procyanidin B2+B4 and phloridzin in russet-skinned apples, known to have higher concentrations of these compounds. The metabolite screening was also accompanied by the expression analysis of 16 polyphenolic genes showing, for nine elements, a higher expression at harvest than during fruit development. Finally, a polyphenolic comparison with red-fleshed apples was also carried out, underlying a larger amount of procyanidins and quercetin-3rhamnoside in the white-fleshed accessions. The results presented and discussed in this work suggest that specific white-fleshed apples, especially with russeted-skin, may play an important role in ameliorating the nutraceutical potential of apple fruit.
- Published
- 2019
219. Is periodontitis a risk indicator for cancer? A meta-analysis.
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Corbella, Stefano, Veronesi, Paolo, Galimberti, Viviana, Weinstein, Roberto, Del Fabbro, Massimo, and Francetti, Luca
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PERIODONTITIS ,CANCER risk factors ,TUMOR growth ,PANCREATIC cancer ,META-analysis - Abstract
Background: The aim of the present systematic review was to evaluate the hypothesis of an association between periodontitis and the development of cancer. Methods: Two reviewers independently screened electronic and manual sources for pertinent articles. Primary outcome measures were the occurrence of neoplasm diagnosis in exposed and non-exposed groups, reported to evaluate association between cancer and periodontitis. Results: Of the 490 initially retrieved papers 10 were included in the qualitative synthesis and eight in the quantitative synthesis; the eight papers covered six studies. Considering hazard ratios, a statistically significant association was found for all cancers studied (1.14; CI 95%: 1.04, 1.24), digestive tract cancer (1.34; CI 95%: 1.05, 1.72), pancreatic cancer (1.74; CI 95%: 1.21, 2.52), prostate cancer (1.25; CI 95%: 1.04, 1.51), breast cancer (1.11; CI 95%: 1.00, 1.23), corpus uteri cancer (2.20; CI 95%: 1.16, 4.18), lung cancer (1.24; CI 95%: 1.06, 1.45), hematological cancer (1.30; CI 95%: 1.11, 1.53), esophagus / oropharyngeal cancer pooled together (2.25; CI 95%: 1.30, 3.90) and Non-Hodgkin lymphoma (1.30; CI 95%: 1.11, 1.52). Conclusions: Despite the sparse scientific evidence and considering the low statistical power of the results, this systematic review revealed a substantial lack of studies with standardized and comparable methods to speculate about the association between periodontitis and cancer; more studies are need in order to explore further the scientific evidence of such correlation. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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220. Characterizing the field of Atomic Layer Deposition: Authors, topics, and collaborations.
- Author
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Alvaro, Elsa and Yanguas-Gil, Angel
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ATOMIC layer deposition ,SCIENTIFIC community ,SCIENTIFIC literature ,SCIENTIFIC development ,BIBLIOMETRICS - Abstract
This paper describes how Atomic Layer Deposition (ALD) has evolved over time using a combination of bibliometric, social network, and text analysis. We examined the rate of knowledge production as well as changes in authors, journals, and collaborators, showing a steady growth of ALD research. The study of the collaboration network of ALD scientists over time points out that the ALD research community is becoming larger and more interconnected, with a largest connected component that spans 90% of the authors in 2015. In addition, the evolution of network centrality measures (degree and betweenness centrality) and author productivity revealed the central figures in ALD over time, including new “stars” appearing in the last decade. Finally, the study of the title words in our dataset is consistent with a shift in focus on research topics towards energy applications and nanotechnology. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
221. Linguistic Traces of a Scientific Fraud: The Case of Diederik Stapel.
- Author
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Markowitz, David M. and Hancock, Jeffrey T.
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FRAUD in science ,PSYCHOLOGISTS ,LINGUISTICS ,PUBLICATIONS ,AUTHORSHIP collaboration - Abstract
When scientists report false data, does their writing style reflect their deception? In this study, we investigated the linguistic patterns of fraudulent (N = 24; 170,008 words) and genuine publications (N = 25; 189,705 words) first-authored by social psychologist Diederik Stapel. The analysis revealed that Stapel's fraudulent papers contained linguistic changes in science-related discourse dimensions, including more terms pertaining to methods, investigation, and certainty than his genuine papers. His writing style also matched patterns in other deceptive language, including fewer adjectives in fraudulent publications relative to genuine publications. Using differences in language dimensions we were able to classify Stapel's publications with above chance accuracy. Beyond these discourse dimensions, Stapel included fewer co-authors when reporting fake data than genuine data, although other evidentiary claims (e.g., number of references and experiments) did not differ across the two article types. This research supports recent findings that language cues vary systematically with deception, and that deception can be revealed in fraudulent scientific discourse. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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222. Estimates of the Continuously Publishing Core in the Scientific Workforce.
- Author
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Ioannidis, John P. A., Boyack, Kevin W., and Klavans, Richard
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PUBLICATIONS ,INFORMATION science ,INFORMATION technology ,PHYSICAL sciences ,BIBLIOMETRICS ,SCIENTISTS - Abstract
Background: The ability of a scientist to maintain a continuous stream of publication may be important, because research requires continuity of effort. However, there is no data on what proportion of scientists manages to publish each and every year over long periods of time. Methodology/Principal Findings: Using the entire Scopus database, we estimated that there are 15,153,100 publishing scientists (distinct author identifiers) in the period 1996–2011. However, only 150,608 (<1%) of them have published something in each and every year in this 16-year period (uninterrupted, continuous presence [UCP] in the literature). This small core of scientists with UCP are far more cited than others, and they account for 41.7% of all papers in the same period and 87.1% of all papers with >1000 citations in the same period. Skipping even a single year substantially affected the average citation impact. We also studied the birth and death dynamics of membership in this influential UCP core, by imputing and estimating UCP-births and UCP-deaths. We estimated that 16,877 scientists would qualify for UCP-birth in 1997 (no publication in 1996, UCP in 1997–2012) and 9,673 scientists had their UCP-death in 2010. The relative representation of authors with UCP was enriched in Medical Research, in the academic sector and in Europe/North America, while the relative representation of authors without UCP was enriched in the Social Sciences and Humanities, in industry, and in other continents. Conclusions: The proportion of the scientific workforce that maintains a continuous uninterrupted stream of publications each and every year over many years is very limited, but it accounts for the lion’s share of researchers with high citation impact. This finding may have implications for the structure, stability and vulnerability of the scientific workforce. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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223. The Trajectory of Dispersal Research in Conservation Biology. Systematic Review.
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Driscoll, Don A., Banks, Sam C., Barton, Philip S., Ikin, Karen, Lentini, Pia, Lindenmayer, David B., Smith, Annabel L., Berry, Laurence E., Burns, Emma L., Edworthy, Amanda, Evans, Maldwyn J., Gibson, Rebecca, Heinsohn, Rob, Howland, Brett, Kay, Geoff, Munro, Nicola, Scheele, Ben C., Stirnemann, Ingrid, Stojanovic, Dejan, and Sweaney, Nici
- Subjects
CONSERVATION biology ,META-analysis ,CLIMATE change ,ECOLOGICAL restoration monitoring ,DISPERSAL (Ecology) ,ACQUISITION of data - Abstract
Dispersal knowledge is essential for conservation management, and demand is growing. But are we accumulating dispersal knowledge at a pace that can meet the demand? To answer this question we tested for changes in dispersal data collection and use over time. Our systematic review of 655 conservation-related publications compared five topics: climate change, habitat restoration, population viability analysis, land planning (systematic conservation planning) and invasive species. We analysed temporal changes in the: (i) questions asked by dispersal-related research; (ii) methods used to study dispersal; (iii) the quality of dispersal data; (iv) extent that dispersal knowledge is lacking, and; (v) likely consequences of limited dispersal knowledge. Research questions have changed little over time; the same problems examined in the 1990s are still being addressed. The most common methods used to study dispersal were occupancy data, expert opinion and modelling, which often provided indirect, low quality information about dispersal. Although use of genetics for estimating dispersal has increased, new ecological and genetic methods for measuring dispersal are not yet widely adopted. Almost half of the papers identified knowledge gaps related to dispersal. Limited dispersal knowledge often made it impossible to discover ecological processes or compromised conservation outcomes. The quality of dispersal data used in climate change research has increased since the 1990s. In comparison, restoration ecology inadequately addresses large-scale process, whilst the gap between knowledge accumulation and growth in applications may be increasing in land planning. To overcome apparent stagnation in collection and use of dispersal knowledge, researchers need to: (i) improve the quality of available data using new approaches; (ii) understand the complementarities of different methods and; (iii) define the value of different kinds of dispersal information for supporting management decisions. Ambitious, multi-disciplinary research programs studying many species are critical for advancing dispersal research. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
224. Nucleic acid purification from plants, animals and microbes in under 30 seconds.
- Author
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Zou, Yiping, Mason, Michael Glenn, Wang, Yuling, Wee, Eugene, Turni, Conny, Blackall, Patrick J., Trau, Matt, and Botella, Jose Ramon
- Subjects
NUCLEIC acids ,DNA ,RNA ,EXTRACTION (Chemistry) ,NUCLEIC acid amplification techniques ,MOLECULAR diagnosis - Abstract
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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225. Can editors save peer review from peer reviewers?
- Author
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D’Andrea, Rafael and O’Dwyer, James P.
- Subjects
PROFESSIONAL peer review ,JOB performance ,EDITORS ,PUBLISHING ,STANDARDS - Abstract
Peer review is the gold standard for scientific communication, but its ability to guarantee the quality of published research remains difficult to verify. Recent modeling studies suggest that peer review is sensitive to reviewer misbehavior, and it has been claimed that referees who sabotage work they perceive as competition may severely undermine the quality of publications. Here we examine which aspects of suboptimal reviewing practices most strongly impact quality, and test different mitigating strategies that editors may employ to counter them. We find that the biggest hazard to the quality of published literature is not selfish rejection of high-quality manuscripts but indifferent acceptance of low-quality ones. Bypassing or blacklisting bad reviewers and consulting additional reviewers to settle disagreements can reduce but not eliminate the impact. The other editorial strategies we tested do not significantly improve quality, but pairing manuscripts to reviewers unlikely to selfishly reject them and allowing revision of rejected manuscripts minimize rejection of above-average manuscripts. In its current form, peer review offers few incentives for impartial reviewing efforts. Editors can help, but structural changes are more likely to have a stronger impact. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
226. Decontamination of N95 masks for re-use employing 7 widely available sterilization methods
- Author
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Barret Rush, Kevin Hills, Kimberly Malo, Gloria Vazquez-Grande, Paul Z. Chen, Samantha B Kasloff, Anders Leung, Sylvain A. Lother, James E. Strong, Jay Krishnan, Todd Cutts, Frank X. Gu, Ryan Zarychanski, and Anand Kumar
- Subjects
Ethylene Oxide ,RNA viruses ,business.product_category ,Plasma Gases ,Light ,Sanitization ,Coronaviruses ,02 engineering and technology ,Respirators ,Autoclave ,law.invention ,chemistry.chemical_compound ,Medical Conditions ,law ,Peracetic acid ,Medicine and Health Sciences ,Public and Occupational Health ,Respirator ,Decontamination ,Pathology and laboratory medicine ,Virus Testing ,0303 health sciences ,Multidisciplinary ,Physics ,Oxides ,Human decontamination ,Medical microbiology ,021001 nanoscience & nanotechnology ,Pulp and paper industry ,Peroxides ,Equipment Sterilization ,Physical sciences ,Chemistry ,Infectious Diseases ,Vesicular Stomatitis Virus ,Viruses ,Medicine ,Engineering and Technology ,SARS CoV 2 ,Pathogens ,0210 nano-technology ,Research Article ,Biotechnology ,Equipment Preparation ,Ultraviolet radiation ,Materials science ,Infectious Disease Control ,SARS coronavirus ,N95 Respirators ,Ultraviolet Rays ,Science ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Bioengineering ,Research and Analysis Methods ,Microbiology ,Rhabdoviruses ,03 medical and health sciences ,Electromagnetic radiation ,Diagnostic Medicine ,Equipment Reuse ,Humans ,Peracetic Acid ,Personal protective equipment ,Filtration ,Biology and life sciences ,SARS-CoV-2 ,030306 microbiology ,Organisms ,Viral pathogens ,Chemical Compounds ,COVID-19 ,Hydrogen Peroxide ,Vesiculovirus ,Microbial pathogens ,Health Care ,Autoclaving ,chemistry ,Medical Devices and Equipment ,Preventive Medicine ,Ultraviolet C ,business - Abstract
The response to the COVID-19 epidemic is generating severe shortages of personal protective equipment around the world. In particular, the supply of N95 respirator masks has become severely depleted, with supplies having to be rationed and health care workers having to use masks for prolonged periods in many countries. We sought to test the ability of 7 different decontamination methods: autoclave treatment, ethylene oxide gassing (ETO), low temperature hydrogen peroxide gas plasma (LT-HPGP) treatment, vaporous hydrogen peroxide (VHP) exposure, peracetic acid dry fogging (PAF), ultraviolet C irradiation (UVCI) and moist heat (MH) treatment to decontaminate a variety of different N95 masks following experimental contamination with SARS-CoV-2 or vesicular stomatitis virus as a surrogate. In addition, we sought to determine whether masks would tolerate repeated cycles of decontamination while maintaining structural and functional integrity. All methods except for UVCI were effective in total elimination of viable virus from treated masks. We found that all respirator masks tolerated at least one cycle of all treatment modalities without structural or functional deterioration as assessed by fit testing; filtration efficiency testing results were mostly similar except that a single cycle of LT-HPGP was associated with failures in 3 of 6 masks assessed. VHP, PAF, UVCI, and MH were associated with preserved mask integrity to a minimum of 10 cycles by both fit and filtration testing. A similar result was shown with ethylene oxide gassing to the maximum 3 cycles tested. Pleated, layered non-woven fabric N95 masks retained integrity in fit testing for at least 10 cycles of autoclaving but the molded N95 masks failed after 1 cycle; filtration testing however was intact to 5 cycles for all masks. The successful application of autoclaving for layered, pleated masks may be of particular use to institutions globally due to the virtually universal accessibility of autoclaves in health care settings. Given the ability to modify widely available heating cabinets on hospital wards in well-resourced settings, the application of moist heat may allow local processing of N95 masks.
- Published
- 2020
227. Experimental Evolution of Trichoderma citrinoviride for Faster Deconstruction of Cellulose
- Author
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Romas J. Kazlauskas, Michael Travisano, and Hui Lin
- Subjects
0301 basic medicine ,Fungal Structure ,Transcription, Genetic ,Molecular biology ,Physiology ,lcsh:Medicine ,Biochemistry ,chemistry.chemical_compound ,Sequencing techniques ,Filter Paper ,Gene Expression Regulation, Fungal ,Fungal Evolution ,Medicine and Health Sciences ,Cellulases ,lcsh:Science ,Genetics ,Trichoderma ,Experimental evolution ,Fungal protein ,Multidisciplinary ,Organic Compounds ,RNA sequencing ,Enzymes ,Laboratory Equipment ,Chemistry ,Metabolic Engineering ,Enzyme Induction ,Physical Sciences ,Engineering and Technology ,Research Article ,030106 microbiology ,DNA transcription ,Equipment ,Cellulase ,Mycology ,Biology ,Metabolic engineering ,Fungal Proteins ,03 medical and health sciences ,Extracellular ,RNA, Messenger ,Cellulose ,Gene ,Secretion ,Mycelium ,Sequence Analysis, RNA ,lcsh:R ,Organic Chemistry ,Chemical Compounds ,Biology and Life Sciences ,Proteins ,RNA, Fungal ,biology.organism_classification ,Research and analysis methods ,030104 developmental biology ,Molecular biology techniques ,chemistry ,biology.protein ,Enzymology ,lcsh:Q ,Gene expression ,Directed Molecular Evolution ,Physiological Processes - Abstract
Engineering faster cellulose deconstruction is difficult because it is a complex, cooperative, multi-enzyme process. Here we use experimental evolution to select for populations of Trichoderma citrinoviride that deconstruct up to five-fold more cellulose. Ten replicate populations of T. citrinoviride were selected for growth on filter paper by serial culture. After 125 periods of growth and transfer to fresh media, the filter paper deconstruction increased an average of 2.5 fold. Two populations were examined in more detail. The activity of the secreted cellulase mixtures increased more than two-fold relative to the ancestor and the largest increase was in the extracellular β-glucosidase activity. qPCR showed at least 16-fold more transcribed RNA for egl4 (endoglucanase IV gene), cbh1 (cellobiohydrolase I gene) and bgl1 (extracellular β-glucosidase I gene) in selected populations as compared to the ancestor, and earlier peak expressions of these genes. Deep sequencing shows that the regulatory strategies used to alter cellulase secretion differ in the two strains. The improvements in cellulose deconstruction come from earlier expression of all cellulases and increased relative amount of β-glucosidase, but with small increases in the total secreted protein and therefore little increase in metabolic cost.
- Published
- 2016
228. Using rapid diagnostic tests as a source of viral RNA for dengue serotyping by RT-PCR : a novel epidemiological tool
- Author
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Paul N. Newton, Onanong Sengvilaipaseuth, Narisara Chantratita, Audrey Dubot-Pérès, Koukeo Phommasone, Xavier de Lamballerie, Sommay Keomany, Stuart D. Blacksell, Sue J. Lee, Nathamon Kosoltanapiwat, Mayfong Mayxay, Manivanh Vongsouvath, and Wills, B
- Subjects
RNA viruses ,0301 basic medicine ,Serotype ,Time Factors ,Physiology ,Artificial Gene Amplification and Extension ,Dengue virus ,Pathology and Laboratory Medicine ,medicine.disease_cause ,Polymerase Chain Reaction ,Chromatography, Affinity ,Dengue fever ,Dengue ,0302 clinical medicine ,Filter Paper ,Chlorocebus aethiops ,Epidemiology ,Medicine and Health Sciences ,Reverse Transcriptase Polymerase Chain Reaction ,lcsh:Public aspects of medicine ,Hematology ,Body Fluids ,3. Good health ,Laboratory Equipment ,RNA isolation ,Blood ,Infectious Diseases ,Real-time polymerase chain reaction ,Vietnam ,Medical Microbiology ,Viral Pathogens ,Viruses ,Engineering and Technology ,RNA, Viral ,RNA extraction ,Anatomy ,Pathogens ,Research Article ,medicine.medical_specialty ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,030106 microbiology ,030231 tropical medicine ,Equipment ,Cold storage ,Biology ,Biomolecular isolation ,Microbiology ,Virus ,03 medical and health sciences ,Extraction techniques ,parasitic diseases ,medicine ,Animals ,Humans ,Serotyping ,Molecular Biology Techniques ,Molecular Biology ,Microbial Pathogens ,Vero Cells ,Flaviviruses ,Organisms ,Public Health, Environmental and Occupational Health ,Biology and Life Sciences ,lcsh:RA1-1270 ,Reverse Transcriptase-Polymerase Chain Reaction ,Dengue Virus ,medicine.disease ,Virology ,Research and analysis methods ,Reagent Kits, Diagnostic - Abstract
Background Dengue virus infection causes major public health problems in tropical and subtropical areas. In many endemic areas, including the Lao PDR, inadequate access to laboratory facilities is a major obstacle to surveillance and study of dengue epidemiology. Filter paper is widely used for blood collection for subsequent laboratory testing for antibody and nucleic acid detection. For the first time, we demonstrate that dengue viral RNA can be extracted from dengue rapid diagnostic tests (RDT) and then submitted to real-time RT-PCR for serotyping. Methodology/Principal Findings We evaluated the Standard Diagnostics (SD) Bioline Dengue Duo RDT, a commonly used test in dengue endemic areas. First, using the QIAamp RNA kit, dengue RNA was purified from the sample pad of the NS1 RDT loaded with virus isolates of the four serotypes, then quantified by RT-PCR. We observed greater recovery of virus, with a mean of 27 times more RNA recovered from RDT, than from filter paper. Second, we evaluated dengue NS1 RDTs from patients at Mahosot Hospital, Vientiane, (99 patients) and from rural Salavan Provincial Hospital (362 patients). There was good agreement between dengue RT-PCR from NS1 RDT with RT-PCR performed on RNA extracted from patient sera, either using RDT loaded with blood (82.8% and 91.4%, in Vientiane and Salavan, respectively) or serum (91.9% and 93.9%). There was 100% concordance between RDT and serum RT-PCR of infecting dengue serotype. Conclusions/Significance Therefore, the collection of NS1 positive RDTs, which do not require cold storage, may be a novel approach for dengue serotyping by RT-PCR and offers promising prospects for the collection of epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions., Author Summary Dengue fever, caused by a virus transmitted by mosquitoes, is a public health problem in tropical and subtropical regions. Dengue Rapid Diagnostic Tests, in which a drop of blood is loaded onto a paper strip in a plastic cassette, are simple to use and have good diagnostic accuracy. They are becoming the test of choice for the management of dengue epidemics, especially in rural areas without laboratory facilities. However, four types of dengue virus circulate in most tropical areas and their patterns of circulation are of epidemiological importance since they play a role in the severity and propagation of the disease. We show, for the first time, that molecular amplification permitting dengue virus detection and typing can be performed directly from used positive RDTs, that can easily be transported. This novel approach has promising prospects for the collection of dengue epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions.
- Published
- 2016
229. Using Rapid Diagnostic Tests as a Source of Viral RNA for Dengue Serotyping by RT-PCR - A Novel Epidemiological Tool.
- Author
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Vongsouvath, Manivanh, Phommasone, Koukeo, Sengvilaipaseuth, Onanong, Kosoltanapiwat, Nathamon, Chantratita, Narisara, Blacksell, Stuart D., Lee, Sue J., de Lamballerie, Xavier, Mayxay, Mayfong, Keomany, Sommay, Newton, Paul N., and Dubot-Pérès, Audrey
- Subjects
ROUTINE diagnostic tests ,DENGUE ,DIAGNOSIS of fever ,RNA analysis ,BLOOD sampling ,SEROTYPING ,EPIDEMIOLOGY ,REVERSE transcriptase polymerase chain reaction - Abstract
Background: Dengue virus infection causes major public health problems in tropical and subtropical areas. In many endemic areas, including the Lao PDR, inadequate access to laboratory facilities is a major obstacle to surveillance and study of dengue epidemiology. Filter paper is widely used for blood collection for subsequent laboratory testing for antibody and nucleic acid detection. For the first time, we demonstrate that dengue viral RNA can be extracted from dengue rapid diagnostic tests (RDT) and then submitted to real-time RT-PCR for serotyping. Methodology/Principal Findings: We evaluated the Standard Diagnostics (SD) Bioline Dengue Duo RDT, a commonly used test in dengue endemic areas. First, using the QIAamp RNA kit, dengue RNA was purified from the sample pad of the NS1 RDT loaded with virus isolates of the four serotypes, then quantified by RT-PCR. We observed greater recovery of virus, with a mean of 27 times more RNA recovered from RDT, than from filter paper. Second, we evaluated dengue NS1 RDTs from patients at Mahosot Hospital, Vientiane, (99 patients) and from rural Salavan Provincial Hospital (362 patients). There was good agreement between dengue RT-PCR from NS1 RDT with RT-PCR performed on RNA extracted from patient sera, either using RDT loaded with blood (82.8% and 91.4%, in Vientiane and Salavan, respectively) or serum (91.9% and 93.9%). There was 100% concordance between RDT and serum RT-PCR of infecting dengue serotype. Conclusions/Significance: Therefore, the collection of NS1 positive RDTs, which do not require cold storage, may be a novel approach for dengue serotyping by RT-PCR and offers promising prospects for the collection of epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
230. The Increasing Importance of Gene-Based Analyses.
- Author
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Cirulli, Elizabeth T.
- Subjects
PLETHORA (Pathology) ,NUCLEOTIDE sequencing ,EXOMES ,HUMAN genetic variation ,GUIDELINES - Abstract
In recent years, genome and exome sequencing studies have implicated a plethora of new disease genes with rare causal variants. Here, I review 150 exome sequencing studies that claim to have discovered that a disease can be caused by different rare variants in the same gene, and I determine whether their methods followed the current best-practice guidelines in the interpretation of their data. Specifically, I assess whether studies appropriately assess controls for rare variants throughout the entire gene or implicated region as opposed to only investigating the specific rare variants identified in the cases, and I assess whether studies present sufficient co-segregation data for statistically significant linkage. I find that the proportion of studies performing gene-based analyses has increased with time, but that even in 2015 fewer than 40% of the reviewed studies used this method, and only 10% presented statistically significant co-segregation data. Furthermore, I find that the genes reported in these papers are explaining a decreasing proportion of cases as the field moves past most of the low-hanging fruit, with 50% of the genes from studies in 2014 and 2015 having variants in fewer than 5% of cases. As more studies focus on genes explaining relatively few cases, the importance of performing appropriate gene-based analyses is increasing. It is becoming increasingly important for journal editors and reviewers to require stringent gene-based evidence to avoid an avalanche of misleading disease gene discovery papers. [ABSTRACT FROM AUTHOR]
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- 2016
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231. Children Reading to Dogs: A Systematic Review of the Literature.
- Author
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Hall, Sophie Susannah, Gee, Nancy R., and Mills, Daniel Simon
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HUMAN-animal communication ,MENTAL health ,EVIDENCE-based medicine ,SYSTEMATIC reviews ,ANIMAL psychology - Abstract
Background: Despite growing interest in the value of human-animal interactions (HAI) to human mental and physical health the quality of the evidence on which postulated benefits from animals to human psychological health are based is often unclear. To date there exist no systematic reviews on the effects of HAI in educational settings specifically focussing on the perceived benefits to children of reading to dogs. With rising popularity and implementation of these programmes in schools, it is essential that the evidence base exploring the pedagogic value of these initiatives is well documented. Methods: Using PRISMA guidelines we systematically investigated the literature reporting the pedagogic effects of reading to dogs. Because research in this area is in the early stages of scientific enquiry we adopted broad inclusion criteria, accepting all reports which discussed measurable effects related to the topic that were written in English. Multiple online databases were searched during January-March 2015; grey literature searches were also conducted. The search results which met the inclusion criteria were evaluated, and discussed, in relation to the Oxford Centre for Evidence Based Medicine levels of evidence; 27 papers were classified as Level 5, 13 as Level 4, 7 as Level 2c and 1 as Level 2b. Conclusion: The evidence suggests that reading to a dog may have a beneficial effect on a number of behavioural processes which contribute to a positive effect on the environment in which reading is practiced, leading to improved reading performance. However, the evidence base on which these inferences are made is of low quality. There is a clear need for the use of higher quality research methodologies and the inclusion of appropriate controls in order to draw causal inferences on whether or how reading to dogs may benefit children’s reading practices. The mechanisms for any effect remain a matter of conjecture. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
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232. Spaceborne SAR Imaging Algorithm for Coherence Optimized.
- Author
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Qiu, Zhiwei, Yue, Jianping, Wang, Xueqin, and Yue, Shun
- Subjects
SYNTHETIC aperture radar ,COHERENCE (Optics) ,SIGNAL-to-noise ratio ,INTERFEROMETRY ,COMPUTER algorithms ,SIGNAL processing - Abstract
This paper proposes SAR imaging algorithm with largest coherence based on the existing SAR imaging algorithm. The basic idea of SAR imaging algorithm in imaging processing is that output signal can have maximum signal-to-noise ratio (SNR) by using the optimal imaging parameters. Traditional imaging algorithm can acquire the best focusing effect, but would bring the decoherence phenomenon in subsequent interference process. Algorithm proposed in this paper is that SAR echo adopts consistent imaging parameters in focusing processing. Although the SNR of the output signal is reduced slightly, their coherence is ensured greatly, and finally the interferogram with high quality is obtained. In this paper, two scenes of Envisat ASAR data in Zhangbei are employed to conduct experiment for this algorithm. Compared with the interferogram from the traditional algorithm, the results show that this algorithm is more suitable for SAR interferometry (InSAR) research and application. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
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233. Peer Review Quality and Transparency of the Peer-Review Process in Open Access and Subscription Journals.
- Author
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Wicherts, Jelte M.
- Subjects
PROFESSIONAL peer review ,SUBSCRIPTIONS to serial publications ,OPEN access publishing ,PUBLISHING ,ACADEMIC libraries - Abstract
Background: Recent controversies highlighting substandard peer review in Open Access (OA) and traditional (subscription) journals have increased the need for authors, funders, publishers, and institutions to assure quality of peer-review in academic journals. I propose that transparency of the peer-review process may be seen as an indicator of the quality of peer-review, and develop and validate a tool enabling different stakeholders to assess transparency of the peer-review process. Methods and Findings: Based on editorial guidelines and best practices, I developed a 14-item tool to rate transparency of the peer-review process on the basis of journals’ websites. In Study 1, a random sample of 231 authors of papers in 92 subscription journals in different fields rated transparency of the journals that published their work. Authors’ ratings of the transparency were positively associated with quality of the peer-review process but unrelated to journal’s impact factors. In Study 2, 20 experts on OA publishing assessed the transparency of established (non-OA) journals, OA journals categorized as being published by potential predatory publishers, and journals from the Directory of Open Access Journals (DOAJ). Results show high reliability across items (α = .91) and sufficient reliability across raters. Ratings differentiated the three types of journals well. In Study 3, academic librarians rated a random sample of 140 DOAJ journals and another 54 journals that had received a hoax paper written by Bohannon to test peer-review quality. Journals with higher transparency ratings were less likely to accept the flawed paper and showed higher impact as measured by the h5 index from Google Scholar. Conclusions: The tool to assess transparency of the peer-review process at academic journals shows promising reliability and validity. The transparency of the peer-review process can be seen as an indicator of peer-review quality allowing the tool to be used to predict academic quality in new journals. [ABSTRACT FROM AUTHOR]
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- 2016
- Full Text
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234. Application of enhanced assimilable organic carbon method across operational drinking water systems
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Graeme Moore, Joby Boxall, Catherine A. Biggs, Frances C. Pick, Katherine E. Fish, and Jonathan P. Moses
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Environmental Engineering ,Water Management ,Science ,Cell Enumeration Techniques ,0208 environmental biotechnology ,02 engineering and technology ,010501 environmental sciences ,Bacterial growth ,Research and Analysis Methods ,Pseudomonas fluorescens ,01 natural sciences ,Water Purification ,Distribution system ,Spectrum Analysis Techniques ,Natural Resources ,Water Quality ,Organic Chemicals ,0105 earth and related environmental sciences ,Total organic carbon ,Multidisciplinary ,Bacteria ,Drinking Water ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,Total Cell Counting ,Reproducibility of Results ,Spirillum ,Flow Cytometry ,Pulp and paper industry ,Carbon ,020801 environmental engineering ,Chemistry ,Spectrophotometry ,Physical Sciences ,Water Resources ,Engineering and Technology ,Medicine ,Environmental science ,Water treatment ,Cytophotometry ,Water quality ,Chlorine ,Water Microbiology ,Research Article ,Chemical Elements - Abstract
Assimilable organic carbon (AOC) is known to correlate with microbial growth, which can consequently degrade drinking water quality. Despite this, there is no standardised AOC test that can be applied to drinking water distribution systems (DWDS). Herein we report the development of a quick, robust AOC that incorporates known strains Pseudomonas fluorescens strain P-17 and Spirillum strain NOX, a higher inoculum volume and enumeration using flow cytometry to generate a quicker (total test time reduced from 14 to 8 days), robust method. We apply the developed AOC test to twenty drinking water treatment works (WTW) to validate the method reproducibility and resolution across a wide range of AOC concentrations. Subsequently, AOC was quantified at 32 sample points, over four DWDS, for a year in order to identify sinks and sources of AOC in operative networks. Application of the developed AOC protocol provided a previously unavailable insight and novel evidence of pipes and service reservoirs exhibiting different AOC and regrowth behaviour. Observed correlations between AOC and microbial growth highlight the importance of monitoring AOC as an integral part of managing drinking water quality at the consumers tap.
- Published
- 2019
235. Assessment of malaria real-time PCR methods and application with focus on low-level parasitaemia
- Author
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Kurt Hanevik, Bjørn Blomberg, Stein Christian Mohn, Gro Elizabeth Ann Strøm, Christel Gill Haanshuus, Nina Langeland, and Kristine Mørch
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0301 basic medicine ,Plasmodium ,Focus (geometry) ,Physiology ,Pcr cloning ,Genes, Protozoan ,Artificial Gene Amplification and Extension ,Parasitemia ,Polymerase Chain Reaction ,law.invention ,0302 clinical medicine ,Filter Paper ,law ,Medicine and Health Sciences ,Organic Chemicals ,Polymerase chain reaction ,Protozoans ,Multidisciplinary ,Malarial Parasites ,Eukaryota ,Drugs ,Cytochromes b ,Body Fluids ,Laboratory Equipment ,Real-time polymerase chain reaction ,Blood ,Child, Preschool ,Quinolines ,Medicine ,Engineering and Technology ,Anatomy ,Research Article ,Science ,030106 microbiology ,030231 tropical medicine ,Plasmodium falciparum ,Equipment ,Computational biology ,Biology ,Diamines ,Real-Time Polymerase Chain Reaction ,Research and Analysis Methods ,Sensitivity and Specificity ,03 medical and health sciences ,Antimalarials ,Parasite Groups ,medicine ,Parasitic Diseases ,Humans ,Benzothiazoles ,Molecular Biology Techniques ,Molecular Biology ,Pharmacology ,Infant, Newborn ,Organisms ,Infant ,Reproducibility of Results ,Biology and Life Sciences ,Patient data ,DNA, Protozoan ,medicine.disease ,Tropical Diseases ,Parasitic Protozoans ,Highly sensitive ,Malaria ,Clinical diagnosis ,Parasitology ,Apicomplexa - Abstract
In epidemiological surveys and surveillance the application of molecular tools is essential in detecting submicroscopic malaria. A genus-specific conventional cytochrome b (cytb) PCR has shown high sensitivity in field studies, detecting 70% submicroscopic malaria. The main objective of this study was to assess the conversion from conventional to real-time PCR testing both SYBR and probe protocols, and including quantitative (q) PCR. The protocols were assessed applying well-defined clinical patient material consisting of 33 positive and 80 negative samples. Sequencing of positive PCR products was performed. In addition, a sensitivity comparison of real-time PCR methods was done by including five relevant assays investigating the effect of amplification target and platform. Sensitivity was further examined using field material consisting of 111 P.falciparum positive samples from Tanzanian children (< 5 years), as well as using related patient data to assess the application of q-PCR with focus on low-level parasitaemia. Both the cytb SYBR and probe PCR protocols showed as high sensitivity and specificity as their conventional counterpart, except missing one P. malariae sample. The SYBR protocol was more sensitive and specific than using probe. Overall, choice of amplification target applied is relevant for achieving ultra-sensitivity, and using intercalating fluorescence dye rather than labelled hydrolysis probes is favourable. Application of q-PCR analysis in field projects is important for the awareness and understanding of low-level parasitaemia. For use in clinical diagnosis and epidemiological studies the highly sensitive and user-friendly cytb SYBR q-PCR method is a relevant tool. The genus-specific method has the advantage that species identification by sequencing can be performed as an alternative to species-specific PCR. publishedVersion
- Published
- 2018
236. Thermogravimetric analysis of the co-combustion of coal and polyvinyl chloride
- Author
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Hongbin Gao and Jingkuan Li
- Subjects
Fossil Fuels ,Polymers ,Combustion ,Social Sciences ,Astronomical Sciences ,02 engineering and technology ,Exothermic Reactions ,law.invention ,chemistry.chemical_compound ,Mathematical and Statistical Techniques ,law ,Medicine and Health Sciences ,0202 electrical engineering, electronic engineering, information engineering ,Psychology ,Polyvinyl Chloride ,Materials ,Multidisciplinary ,Thermochemical Conversion ,Chemical Reactions ,Activation Energy ,Space Exploration ,Pulp and paper industry ,Curve Fitting ,Thermogravimetry ,Chemistry ,Coal ,Macromolecules ,Physical Sciences ,Engineering and Technology ,Medicine ,Organic Materials ,Pyrolysis ,Research Article ,Thermogravimetric analysis ,Materials science ,Science ,020209 energy ,Materials Science ,Psychological Stress ,Activation energy ,Fuels ,Research and Analysis Methods ,020401 chemical engineering ,Mental Health and Psychiatry ,0204 chemical engineering ,Weightlessness ,business.industry ,Biology and Life Sciences ,Spaceflight ,Polymer Chemistry ,Energy and Power ,Ignition system ,Polyvinyl chloride ,chemistry ,Heat of combustion ,business ,Mathematical Functions - Abstract
Coal gangue has the shortcomings of low calorific value and refractory burnout, while polyvinyl chloride has the advantages of a long combustion process and high calorific value. In order to make up for these shortcomings of coal gangue, the possibility of a treatment method based on co-combustion of coal gangue with polyvinyl chloride, which can be centrally recovered from municipal solid waste, is proposed. In order to analyze the combustion effect of a mixture of these two substances, experimental samples were prepared by mixing these two substances in three different ratios, and they were tested by thermogravimetric analysis. The experimental results were compared, analyzed and evaluated. The effects of the proportion of polyvinyl chloride in the mixture on the temperature parameters, activation energy, and interaction during co-combustion were analyzed. In order to analyze the interaction during co-combustion of the two, a coupling analysis method for mixed combustion is presented, and the effectiveness of this method is verified by comparing with the correlation analysis results of co-combustion. The results show that co-combustion can mitigate the ignition difficulty and burnout of coal gangue. When the proportion of polyvinyl chloride in the mixture was increased from 20% to 80%, the maximum weightlessness rate of the first stage rapidly increased from 4.5%/min to 15.6%/min; however, that of the second stage slowly increased from 3.7%/min to 4.2%/min. A 20% proportion of polyvinyl chloride showed the most significant promotion of co-combustion, with a maximum coupling coefficient of 0.00318, which was 1.11 and 1.35 times greater than that of 50% and 80% proportions, respectively. Co-combustion can reduce the activation energy of coal gangue during the initial and end stages. Therefore, co-combustion is helpful to improve the problems of low calorific value and refractory burnout of coal gangue.
- Published
- 2019
237. Dynamic changes in the physicochemical properties of fresh-cut produce wash water as impacted by commodity type and processing conditions
- Author
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Jie Li, Shih Chi Weng, Ellen R. Turner, Bryan T. Vinyard, Bin Zhou, Zi Teng, and Yaguang Luo
- Subjects
Food Safety ,Chemical Phenomena ,Food Handling ,Chemical Oxygen Demand ,Biological Oxygen Demand Analysis ,Physical Chemistry ,Turbidity ,Mathematical and Statistical Techniques ,Materials Physics ,Water Quality ,Vegetables ,Flowering Plants ,Total organic carbon ,Multidisciplinary ,Physics ,Statistics ,Chemical oxygen demand ,Eukaryota ,Lettuce ,Plants ,Pulp and paper industry ,Daucus carota ,Chemistry ,Physicochemical Properties ,Physical Sciences ,Medicine ,Chlorine ,Research Article ,Chemical Elements ,Science ,Materials Science ,chemistry.chemical_element ,Food Contamination ,Research and Analysis Methods ,Humans ,Statistical Methods ,Total suspended solids ,Total Dissolved Solids ,Ecology and Environmental Sciences ,Organisms ,Water ,Biology and Life Sciences ,Total dissolved solids ,Disinfection ,Physical Properties ,Chemical Properties ,chemistry ,Food Microbiology ,Environmental science ,Water quality ,Mathematics ,Disinfectants ,Forecasting - Abstract
Organic materials in fresh-cut produce wash water deplete free chlorine that is required to prevent pathogen survival and cross-contamination. This research evaluated water quality parameters frequently used to describe organic load for their fitness to predict chlorine demand (CLD) and chemical oxygen demand (COD), which are major needs identified by the industry-led produce food safety taskforce. Batches of romaine lettuce, iceberg lettuce, or carrot of different cut sizes and shapes were washed in 40 liters of water. Physicochemical properties of wash water including CLD, COD, total organic carbon (TOC), total suspended solids (TSS), total dissolved solids (TDS), turbidity, total sugar content, and pH, were monitored. Results indicate that pH is primarily commodity dependent, while organic load is additionally impacted by cutting and washing conditions. Significant linear increases in COD, TOC, CLD, TDS, and turbidity resulted from increasing product-to-water ratio, and decreasing cut size. Physicochemical parameters, excluding pH, showed significant positive correlation across different cut sizes within a commodity. High correlations were obtained between CLD and COD and between COD and TOC for pooled products. The convenient measurement of TDS, along with its strong correlation with COD and CLD, suggests the potential of TDS for predicting organic load and chlorine reactivity. Finally, the potential application and limitation of the proposed models in practical produce processing procedures are discussed extensively.
- Published
- 2019
238. Fecal indicator bacteria and virus removal in stormwater biofilters: Effects of biochar, media saturation, and field conditioning
- Author
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Alexandria B. Boehm, Benjamin P. Kranner, A. R. M. Nabiul Afrooz, and Nicole J. M. Fitzgerald
- Subjects
Statistical methods ,Rain ,Marine and Aquatic Sciences ,02 engineering and technology ,Wastewater ,010501 environmental sciences ,Pathology and Laboratory Medicine ,01 natural sciences ,Feces ,Biomimetics ,Contaminants ,Limnology ,Biochar ,Medicine and Health Sciences ,020701 environmental engineering ,Materials ,Multidisciplinary ,biology ,Statistics ,Pulp and paper industry ,Pollution ,6. Clean water ,Bacterial Pathogens ,Monte Carlo method ,Physical sciences ,Medical Microbiology ,Charcoal ,Biofilter ,Medicine ,Engineering and Technology ,Seasons ,Pathogens ,Research Article ,Science ,Materials Science ,Stormwater ,0207 environmental engineering ,Amendment ,Indicator bacteria ,Bioengineering ,Coliphages ,Microbiology ,Water Purification ,Escherichia coli ,Coliphage ,Cities ,Microbial Pathogens ,Effluent ,0105 earth and related environmental sciences ,Bacteria ,Ecology and Environmental Sciences ,Water Pollution ,Organisms ,Biology and Life Sciences ,Bacteriology ,biology.organism_classification ,Research and analysis methods ,13. Climate action ,Biofilms ,Earth Sciences ,Mathematical and statistical techniques ,Environmental science ,Bacterial Biofilms ,Filtration ,Enterococcus ,Mathematics - Abstract
Stormwater biofilters are used to attenuate the flow and volume of runoff and reduce pollutant loading to aquatic systems. However, the capacity of biofilters to remove microbial contaminants remains inadequate. While biochar has demonstrated promise as an amendment to improve microbial removal in laboratory-scale biofilters, it is uncertain if the results are generalizable to the field. To assess biochar performance in a simulated field setting, sand and biochar-amended sand biofilters were periodically dosed with natural stormwater over a 61-week conditioning phase. Impact of media saturation was assessed by maintaining biofilters with and without a saturated zone. Biochar-amended biofilters demonstrated improved Escherichia coli removal over sand biofilters during the first 31 weeks of conditioning though media type did not impact E. coli removal during the last 30 weeks of conditioning. Presence of a saturated zone was not a significant factor influencing E. coli removal across the entire conditioning phase. Following conditioning, biofilters underwent challenge tests using stormwater spiked with wastewater to assess their capacity to remove wastewater-derived E. coli, enterococci, and male-specific (F+) coliphage. In challenge tests, biochar-amended biofilters demonstrated enhanced removal of all fecal indicators relative to sand biofilters. Additionally, saturated biofilters demonstrated greater removal of fecal indicators than unsaturated biofilters for both media types. Discrepant conclusions from the conditioning phase and challenge tests may be due to variable influent chemistry, dissimilar transport of E. coli indigenous to stormwater and those indigenous to wastewater, and differences in E. coli removal mechanisms between tests. Mobilization tests conducted following challenge tests showed minimal (
- Published
- 2019
239. Development and characterisation of charcoal briquettes from water hyacinth (Eichhornia crassipes)-molasses blend
- Author
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Naomi P. Carnaje, Kalpit Shah, Romel B. Talagon, Jorge Paz-Ferreiro, and Jose P Peralta
- Subjects
Eichhornia crassipes ,Time Factors ,Calorific Value ,Combustion ,Biomass ,lcsh:Medicine ,02 engineering and technology ,010501 environmental sciences ,Exothermic Reactions ,Physical Chemistry ,01 natural sciences ,Starches ,Materials Testing ,Spectroscopy, Fourier Transform Infrared ,0202 electrical engineering, electronic engineering, information engineering ,Molasses ,Electron Microscopy ,Charcoal ,lcsh:Science ,Materials ,Microscopy ,Multidisciplinary ,biology ,Organic Compounds ,Chemistry ,Carbonization ,Hyacinth ,Temperature ,Chemical Reactions ,Eukaryota ,Plants ,Pulp and paper industry ,Eichhornia ,visual_art ,Physical Sciences ,visual_art.visual_art_medium ,Engineering and Technology ,Scanning Electron Microscopy ,Research Article ,Briquette ,020209 energy ,Materials Science ,Carbohydrates ,Fuels ,Research and Analysis Methods ,Fires ,Surface Water ,Binders ,0105 earth and related environmental sciences ,Cassava ,Organic Chemistry ,lcsh:R ,Chemical Compounds ,Organisms ,Biology and Life Sciences ,biology.organism_classification ,Solid fuel ,Carbon ,Energy and Power ,Chemical Properties ,Biofuels ,Microscopy, Electron, Scanning ,Earth Sciences ,Heat of combustion ,lcsh:Q ,Shrubs ,Hydrology - Abstract
Charcoal briquettes are inexpensive solid fuels made from carbonized biomass. The potential of converting water hyacinth (Eichhornia crassipes) charcoal into briquettes with molasses as binder was investigated in this study. Dried water hyacinth was carbonized at a temperature between 350°C to 500°C in a fabricated fine biomass carbonizer. A solution containing 80% by weight molasses was used in the production of briquettes having different charcoal/molasses ratios of 40:60, 30:70, and 20:80. Each briquette was characterized in terms of bulk density, calorific value, compressive strength, proximate analysis and micro-structure by Scanning Electron Microscopy. Charcoal briquettes were tested for their flammable characteristics through their burning rates and ignition time. Altering the molasses to charcoal ratio affected the quality and characteristics of the briquettes. Volatile combustible matter and fixed carbon increased with increasing amount of binder while ash content decreased. The 30:70 charcoal/molasses ratio produced the highest calorific value (16.6 MJ/kg) and compressive strength (19.1 kg/cm2). The results have shown the potential of converting water hyacinth into an alternative fuel source.
- Published
- 2018
240. Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor
- Author
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Joseph Brown, Stephen J. Callister, Birgitte Kiær Ahring, Amy A. Boaro, Richard A. White, Lee Ann McCue, and Brian L. LaMarche
- Subjects
Proteomics ,0301 basic medicine ,Molecular biology ,Proteomes ,Microbial metabolism ,lcsh:Medicine ,Acetates ,Biochemistry ,chemistry.chemical_compound ,Bioreactors ,DNA library construction ,RNA, Ribosomal, 16S ,Anaerobiosis ,lcsh:Science ,Protein Metabolism ,Multidisciplinary ,Ecology ,Organic Compounds ,Chemistry ,Genomics ,Genomic Library Construction ,Pulp and paper industry ,Community Ecology ,Physical Sciences ,Carbohydrate Metabolism ,Energy source ,Research Article ,DNA, Bacterial ,Rumen ,Hydraulic retention time ,DNA construction ,DNA, Ribosomal ,03 medical and health sciences ,Bacterial Proteins ,Genetics ,Bioreactor ,Animals ,Metabolomics ,Cellulose ,Caproates ,Community Structure ,Bacteria ,Ecology and Environmental Sciences ,Organic Chemistry ,lcsh:R ,Chemical Compounds ,Biology and Life Sciences ,Proteins ,Research and analysis methods ,Metabolism ,Molecular biology techniques ,030104 developmental biology ,Microbial population biology ,Fermentation ,Cattle ,lcsh:Q ,Metagenomics ,Propionates - Abstract
Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.
- Published
- 2018
241. Co-fermentation of cellobiose and xylose by mixed culture of recombinant Saccharomyces cerevisiae and kinetic modeling
- Author
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Na Wei, Guanyu Zhang, Baotong Zhu, Yingying Chen, and Ying Wu
- Subjects
Metabolic Processes ,0301 basic medicine ,Cellobiose ,Cellulosic sugars ,Density ,Biomass ,lcsh:Medicine ,Yeast and Fungal Models ,Xylose ,Biochemistry ,chemistry.chemical_compound ,Xylose metabolism ,Materials Physics ,Bioenergy ,lcsh:Science ,Multidisciplinary ,Organic Compounds ,Simulation and Modeling ,Physics ,Monosaccharides ,Eukaryota ,food and beverages ,Pulp and paper industry ,Chemistry ,Metabolic Engineering ,Experimental Organism Systems ,Cell Processes ,Cellulosic ethanol ,Physical Sciences ,Engineering and Technology ,Research Article ,Materials Science ,Material Properties ,Carbohydrates ,Lignocellulosic biomass ,Saccharomyces cerevisiae ,Fuels ,Research and Analysis Methods ,Models, Biological ,Cell Growth ,Saccharomyces ,03 medical and health sciences ,Model Organisms ,Materials by Attribute ,Ethanol ,Organic Chemistry ,lcsh:R ,Chemical Compounds ,Organisms ,Fungi ,Biology and Life Sciences ,Cell Biology ,Coculture Techniques ,Yeast ,Energy and Power ,Kinetics ,Metabolism ,030104 developmental biology ,chemistry ,Biofuels ,Alcohols ,Fermentation ,lcsh:Q - Abstract
Efficient conversion of cellulosic sugars in cellulosic hydrolysates is important for economically viable production of biofuels from lignocellulosic biomass, but the goal remains a critical challenge. The present study reports a new approach for simultaneous fermentation of cellobiose and xylose by using the co-culture consisting of recombinant Saccharomyces cerevisiae specialist strains. The co-culture system can provide competitive advantage of modularity compared to the single culture system and can be tuned to deal with fluctuations in feedstock composition to achieve robust and cost-effective biofuel production. This study characterized fermentation kinetics of the recombinant cellobiose-consuming S. cerevisiae strain EJ2, xylose-consuming S. cerevisiae strain SR8, and their co-culture. The motivation for kinetic modeling was to provide guidance and prediction of using the co-culture system for simultaneous fermentation of mixed sugars with adjustable biomass of each specialist strain under different substrate concentrations. The kinetic model for the co-culture system was developed based on the pure culture models and incorporated the effects of product inhibition, initial substrate concentration and inoculum size. The model simulations were validated by results from independent fermentation experiments under different substrate conditions, and good agreement was found between model predictions and experimental data from batch fermentation of cellobiose, xylose and their mixtures. Additionally, with the guidance of model prediction, simultaneous co-fermentation of 60 g/L cellobiose and 20 g/L xylose was achieved with the initial cell densities of 0.45 g dry cell weight /L for EJ2 and 0.9 g dry cell weight /L SR8. The results demonstrated that the kinetic modeling could be used to guide the design and optimization of yeast co-culture conditions for achieving simultaneous fermentation of cellobiose and xylose with improved ethanol productivity, which is critically important for robust and efficient renewable biofuel production from lignocellulosic biomass.
- Published
- 2018
242. Bio-hydrogen production by co-digestion of domestic wastewater and biodiesel industry effluent
- Author
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In-Won Kim, Sanjay K.S. Patel, Rakesh Sharma, Vipin Chandra Kalia, and Jyotsana Prakash
- Subjects
Glycerol ,Metabolic Processes ,0106 biological sciences ,Bacillus Thuringiensis ,lcsh:Medicine ,Bacillus ,Wastewater ,010501 environmental sciences ,Pathology and Laboratory Medicine ,Lignin ,Biochemistry ,01 natural sciences ,chemistry.chemical_compound ,Bioreactors ,Medicine and Health Sciences ,lcsh:Science ,education.field_of_study ,Biodiesel ,Multidisciplinary ,Sewage ,biology ,Cells, Immobilized ,Pulp and paper industry ,Pollution ,Continuous Cultures ,Bacterial Pathogens ,Physical sciences ,Chemistry ,Waste treatment ,Biodegradation, Environmental ,Batch Cell Culture Techniques ,Medical Microbiology ,Engineering and Technology ,Biological Cultures ,Pathogens ,Research Article ,Chemical Elements ,Cell Culturing Techniques ,Environmental Engineering ,Bacillus amyloliquefaciens ,Hydraulic retention time ,Population ,Monomers (Chemistry) ,Research and Analysis Methods ,Microbiology ,010608 biotechnology ,Humans ,Polymer chemistry ,education ,Microbial Pathogens ,Effluent ,0105 earth and related environmental sciences ,Bacteria ,Water Pollution ,lcsh:R ,Organisms ,Biology and Life Sciences ,biology.organism_classification ,Kinetics ,Metabolism ,chemistry ,Biofuels ,Biofilms ,Fermentation ,Environmental science ,lcsh:Q ,Hydrogen - Abstract
The increasing water crisis makes fresh water a valuable resource, which must be used wisely. However, with growing population and inefficient waste treatment systems, the amount of wastewater dispelled in rivers is increasing abominably. Utilizing this freely available waste-water along with biodiesel industry waste- crude glycerol for bio-hydrogen production is being reported here. The bacterial cultures of Bacillus thuringiensis strain EGU45 and Bacillus amyloliquefaciens strain CD16 produced2.4–3.0 L H2/day/L feed during a 60 days continuous culture system at hydraulic retention time of 2 days. An average H2 yield of 100–120 L/L CG was reported by the two strains. Recycling of the effluent by up to 25% resulted in up to 94% H2 production compared to control.
- Published
- 2018
243. Chemical compounds from Dictyostelium discoideum repel a plant-parasitic nematode and can protect roots
- Author
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Yumiko F. Saito, Yukiko Nagamatsu, Tamao Saito, Derek Bartlem, and Saki H. Miyazaki
- Subjects
0301 basic medicine ,Dictyosteliomycota ,lcsh:Medicine ,Plant Science ,Plant Roots ,Dictyostelium discoideum ,Dictyostelium Growth and Development ,Filter Paper ,Microbial Physiology ,Medicine and Health Sciences ,Dictyostelium ,Nematode Infections ,lcsh:Science ,Soil Microbiology ,Rhizosphere ,Dictyostelium Slug ,Multidisciplinary ,Antiparasitic Agents ,biology ,Dictyostelium Discoideum ,Microbial Growth and Development ,Eukaryota ,food and beverages ,Protists ,Soil Ecology ,Laboratory Equipment ,Chemistry ,Sympatry ,Experimental Organism Systems ,Slime Molds ,Close relationship ,Physical Sciences ,Engineering and Technology ,Soil microbiology ,Research Article ,Equipment ,Soil Science ,Research and Analysis Methods ,Microbiology ,03 medical and health sciences ,Model Organisms ,Botany ,Parasitic Diseases ,Slime mold ,Animals ,Fruiting Bodies, Fungal ,Tylenchoidea ,Plant Diseases ,Protozoan Models ,Ecology and Environmental Sciences ,fungi ,lcsh:R ,Organisms ,Chemical Compounds ,Biology and Life Sciences ,Interspecific competition ,Plant Pathology ,biology.organism_classification ,030104 developmental biology ,Nematode ,Lotus ,lcsh:Q ,Developmental Biology - Abstract
Slime mold species in the genus Dictyostelium are considered to have a close relationship with non-parasitic nematodes; they are sympatric in soils and can exhibit interspecific competition for food. We investigated whether this relationship extends to a plant-parasitic nematode that is active in the rhizosphere and has broad host specificity, damaging crops worldwide. Using a novel assay to examine the interaction between the cellular slime mold, Dictyostelium discoideum, and the plant-parasitic nematodes, Meloidogyne spp., we found that cellular slime molds can repel plant parasitic nematodes. Specifically, the repulsion activity was in response to chemical compounds released by cellular slime mold fruiting bodies. Under laboratory conditions, these soluble chemical extracts from fruiting bodies of D. discoideum showed repulsion activity strong enough to protect plant roots. The fruiting body cell extracts repelled but were not toxic to the plant-parasitic nematodes.
- Published
- 2018
244. A new approach to stabilize waste biomass for valorization using an oxidative process at 90 °C
- Author
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Takanori Itoh, Kumpei Ota, and Kazunori Iwabuchi
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Atmospheric Science ,Hot Temperature ,Conservation of Energy Resources ,Biomass ,lcsh:Medicine ,02 engineering and technology ,010501 environmental sciences ,01 natural sciences ,chemistry.chemical_compound ,Waste Management ,0202 electrical engineering, electronic engineering, information engineering ,Recycling ,lcsh:Science ,Multidisciplinary ,Moisture ,Chemistry ,Commerce ,Chemical Reactions ,Agriculture ,Pulp and paper industry ,Equipment Sterilization ,Dairying ,Biofuel ,Physical Sciences ,Carbon dioxide ,Evolutionary Rate ,Engineering and Technology ,Oxidation-Reduction ,Research Article ,Chemical Elements ,Equipment Preparation ,Quality Control ,Livestock ,Evolutionary Processes ,020209 energy ,Materials Science ,chemistry.chemical_element ,Fuels ,Research and Analysis Methods ,Heating ,Greenhouse Gases ,Filter Sterilization ,Oxidation ,Animals ,Environmental Chemistry ,Desiccation ,Materials by Attribute ,0105 earth and related environmental sciences ,Decomposition ,Evolutionary Biology ,Ecology and Environmental Sciences ,lcsh:R ,Chemical Compounds ,Biology and Life Sciences ,Carbon Dioxide ,Solid fuel ,Manure ,Oxygen ,Energy and Power ,Biofuels ,Atmospheric Chemistry ,Earth Sciences ,Cattle ,Heat of combustion ,lcsh:Q ,Carbon - Abstract
This study aimed to establish a new methodology for upgrading biomass quality using low-temperature (below 100 degrees C) oxidation to achieve simultaneous drying and decomposition. Sterilized manure (63% wet basis) was heated at 90 degrees C for 49 days under an oxidative environment. The obtained solid and moisture reduction curves indicated that drying and decomposition proceeded simultaneously. The biomass was decomposed by oxidation with the release of water, carbon dioxide, and volatile fatty acids such as acetic acid. The oxidation process stopped when the biomass was dehydrated, indicating that the water originally present in the biomass governed the process. Elemental and calorific analyses revealed no remarkable increase in carbon content or increased heating value, and a slight decrease in oxygen content. Although the severity of the process was insufficient to produce an optimum solid fuel due to the low temperature used, the process would enable the stabilization of waste biomass with low energy consumption such as using waste heat.
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- 2018
245. Location of water in fresh sugarcane bagasse observed by synchrotron X-ray microtomography
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Paulo E. Mantelatto, Daison Yancy-Caballero, Carlos S. B. Dias, Nathaly L. Archilha, Carlos Driemeier, and Liu Y. Ling
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0301 basic medicine ,Atmospheric Science ,Technology ,Biomass ,Plant Science ,02 engineering and technology ,Diagnostic Radiology ,Medicine and Health Sciences ,0202 electrical engineering, electronic engineering, information engineering ,Fiber ,Multidisciplinary ,Chemistry ,Plant Anatomy ,Radiology and Imaging ,Eukaryota ,Agriculture ,Plants ,Pulp and paper industry ,Bone Imaging ,Saccharum ,Plant Physiology ,Physical Sciences ,Vascular Bundles ,Engineering and Technology ,Medicine ,Cellular Structures and Organelles ,Cellular Types ,Research Article ,Ellipsoids ,Imaging Techniques ,Plant Cell Biology ,020209 energy ,Science ,Geometry ,Equipment ,Crops ,Research and Analysis Methods ,03 medical and health sciences ,Cell Walls ,Meteorology ,Xylem ,Diagnostic Medicine ,Plant Cells ,Dry matter ,Grasses ,Cellulose ,Sugar ,Extraction (chemistry) ,Organisms ,Biology and Life Sciences ,Parenchyma Cells ,Water ,Humidity ,Cell Biology ,X-Ray Microtomography ,Sugarcane ,X-Ray Radiography ,030104 developmental biology ,Earth Sciences ,Particle Accelerators ,Bagasse ,ddc:600 ,Mathematics ,Synchrotrons ,Crop Science - Abstract
Sugarcane bagasse is a vast lignocellulosic byproduct generated in the industry with ~50% humidity (1 kg dry matter associated with 1 kg water). Although the presence of water brings deleterious consequences for combustion, storage and sugar extraction, the location of water in fresh bagasse remains unknown. In this work, we use synchrotron X-ray microtomography for non-invasive 3D imaging of fresh bagasse particles, which allows the visualization of intraparticle water. The sclerified fiber cells in the sheaths surrounding xylem vessels are often found full of water. We suggest this can be juice preserved from the native stalks as many sclerified fibers seem to keep their structural integrity despite the mechanical action during sugarcane crushing. The microtomograms of fresh bagasse also shows mineral particles adhered to biomass surfaces, with adhesion presumably favored by the presence of water. In summary, this work unveils the location of water in fresh bagasse, solving an old mystery of sugarcane technology.
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- 2018
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246. What attributes should be included in a discrete choice experiment related to health technologies? A systematic literature review.
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Trapero-Bertran, Marta, Rodríguez-Martín, Beatriz, and López-Bastida, Julio
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LITERATURE reviews ,MEDICAL technology ,META-analysis ,INDIVIDUALS' preferences ,DRUG side effects - Abstract
Discrete choice experiments (DCEs) are a way to assess priority-setting in health care provision. This approach allows for the evaluation of individuals’ preferences as a means of adding criteria to traditional quality-adjusted life year analysis. The aim of this systematic literature review was to identify attributes for designing a DCE in order to then develop and validate a framework that supports decision-making on health technologies. Our systematic literature review replicated the methods and search terms used by de Bekker-Grob et al. 2012 and Clark et al. 2014. The Medline database was searched for articles dated between 2008 and 2015. The search was limited to studies in English that reflected general preferences and were choice-based, published as full-text articles and related to health technologies. This study included 72 papers, 52% of which focused on DCEs on drug treatments. The average number of attributes used in all included DCE studies was 5.74 (SD 1.98). The most frequently used attributes in these DCEs were improvements in health (78%), side effects (57%) and cost of treatment (53%). Other, less frequently used attributes included waiting time for treatment or duration of treatment (25%), severity of disease (7%) and value for money (4%). The attributes identified might inform future DCE surveys designed to study societal preferences regarding health technologies in order to better inform decisions in health technology assessment. [ABSTRACT FROM AUTHOR]
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- 2019
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247. Treatment of HIV among tuberculosis patients: A replication study of timing of antiretroviral therapy for HIV-1-associated tuberculosis.
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Djimeu, Eric W. and Heard, Anna C.
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HIV infections ,TUBERCULOSIS patients ,MEDICAL microbiology ,ANTIRETROVIRAL agents ,VIRAL replication - Abstract
Co-diagnosis of HIV and tuberculosis presents a treatment dilemma. Starting both treatments at the same time can cause a flood of immune response called immune reconstitution inflammatory syndrome (IRIS) which can be lethal. But, how long to delay HIV treatment is less understood. In 2011, based on the conclusions of three separate studies, WHO recommended starting HIV treatment earlier for those with later HIV disease progression. This paper conducts a replication study of one of the three studies, by Havlir and colleagues. Using their publicly available data, we were able to replicate most of the results presented in the original paper. In our measurement and estimation analyses we use different estimation techniques to assess the robustness of the results. We find that adjusting for loss to follow-up does not affect the main results of the paper. However, an ANCOVA estimation and an instrumental variable model weaken the main result of the paper of better outcomes with early HIV treatment only for those who are sicker, reducing significance from the 5% to the 10% level. A change-point analysis also detects no changes in effect by timing of HIV treatment initiation or different thresholds of CD4 count for the primary outcome. This result suggests that the choice of start time for HIV treatment initiation should be based on other factors including potential drug interactions, overlapping side effects, a high pill burden and severity of illness rather than CD4 threshold and preset timeframes. While we caution against overgeneralizing, the result of this replication is aligned with more recent studies that show no evidence that early initiation of HIV treatment reduces mortality for any patients. [ABSTRACT FROM AUTHOR]
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- 2019
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248. The long run impact of early childhood deworming on numeracy and literacy: Evidence from Uganda.
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Croke, Kevin and Atun, Rifat
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LONGITUDINAL method ,PRESCHOOL children ,LITERACY ,CHILDREN ,HELMINTHIASIS - Abstract
Background: Up to 1.45 billion people currently suffer from soil transmitted helminth infection, with the largest burden occurring in Africa and Asia. Safe and cost effective deworming treatment exists, but there is a debate about mass distribution of this treatment in high prevalence settings. While the World Health Organization recommends mass administration of anthelmintic drugs for preschool and school-aged children in high (>20%) prevalence settings, and several long run follow up studies of an influential trial have suggested large benefits that persist over time, recent systematic reviews have called this recommendation into question. Methods and findings: This paper analyzes the long-term impact of a cluster-randomized trial in eastern Uganda that provided mass deworming treatment to preschool aged children from 2000 to 2003 on the numeracy and literacy skills of children and young adults living in those villages in 2010-2015. This study uses numeracy and literacy data collected seven to twelve years after the end of the deworming trial in a randomly selected subset of communities from the original trial, by an education-focused survey that had no relationship to the deworming study. Building on an earlier working paper which used data from 2010 and 2011 survey rounds, this paper uses an additional four years of numeracy and literacy data (2012, 2013, 2014, and 2015). Aggregating data from all survey rounds, the difference between numeracy scores in treatment versus control communities is 0.07 standard deviations (SD) (95% CI -0.10, 0.24, p = 0.40), the difference in literacy scores is 0.05 SD (95% CI -0.16, 0.27, p = 0.62), and the difference in total scores is 0.07 SD (95% CI -0.11, 0.25, p = 0.44). There are significant differences in program impact by gender, with numeracy and literacy differentially positively affected for girls, and by age, with treatment effects larger for the primary school aged subsample. There are also significant treatment interactions for those living in households with more treatment-eligible children. There is no evidence of differential treatment effects on age at program eligibility or number of years of program eligibility. Conclusions: Mass deworming of preschool aged children in high prevalence communities in Uganda resulted in no statistically significant gains in numeracy or literacy 7-12 years after program completion. Point estimates were positive but imprecise; the study lacked sufficient power to rule out substantial positive effects or more modest negative effects. However, there is suggestive evidence that deworming was relatively more beneficial for girls, primary school aged children, and children living in households with other treated children. Research approval: As this analysis was conducted on secondary data which is publicly available, no research approval was sought or received. All individual records were anonymized by the data provider prior to public release. [ABSTRACT FROM AUTHOR]
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- 2019
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249. An experimental study on the flocculating settling of unclassified tailings
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Hao Wang, Jiwei Bian, Chongchun Xiao, and Deming Zhang
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Fossil Fuels ,Arithmetic underflow ,Velocity ,lcsh:Medicine ,Chemical Composition ,02 engineering and technology ,Waste Disposal, Fluid ,020501 mining & metallurgy ,Mud ,lcsh:Science ,Suspended solids ,Multidisciplinary ,Physics ,Experimental Design ,Classical Mechanics ,021001 nanoscience & nanotechnology ,Pulp and paper industry ,Mineralogy ,Tailings ,Chemistry ,Coal ,0205 materials engineering ,Research Design ,Physical Sciences ,Engineering and Technology ,Organic Materials ,0210 nano-technology ,Research Article ,Flocculation ,Materials by Structure ,Materials Science ,Material Properties ,Fuels ,Research and Analysis Methods ,Mining ,Permeability ,Motion ,Flux (metallurgy) ,Settling ,Materials by Attribute ,lcsh:R ,Energy and Power ,Slurries ,Mixtures ,Slurry ,Earth Sciences ,Environmental science ,lcsh:Q ,Waste disposal - Abstract
Unclassified tailings are the main backfilling aggregates in mines and their settling is the first step in the utilization of tailings; thus, it is very important to determine their settling behavior. The aim of this study was to understand the flocculating settling behavior of unclassified tailings with different factors. The combination of property detection, laboratory experiments and industrial tests were used to assess the flocculating settling behavior of unclassified tailings; the orthogonal experimental design and the control variate method were used for an experimental design. The results show that the flocculating settling velocity of unclassified tailings decreases with the increase of slurry concentration and that this settling velocity increases first and then decreases with the increase of flocculant unit consumption. The underflow concentration is positively correlated with the slurry concentration and negatively correlated with the flocculant unit consumption and flocculant concentration. Slower feed velocity could produce higher concentration underflow but lower clarity overflow water. The greater the mud height, the higher the underflow concentration and the suspended solids concentration in the overflow water. The underflow concentration has a maximum at the rake speed of 0.3 r/min, and the rake speed has little effect on the suspended solids concentration in the overflow water. By analyzing the settling velocity, the underflow concentration, the suspended solids concentration in the overflow water and the solid flux, the following parameters of the flocculating settling experiments were determined: the flocculant type is APAM with a molecular weight of 12 million, the flocculant unit consumption is 30 g/t, the slurry concentration is 6 vol.%, the flocculant concentration is 0.1 wt.%, the rake speed is 0.3 r/min, and the feed velocity is 0.4 L/min (its solid flux is 0.523 t/(m2·h)). The industrial tests were carried out based on the laboratory settling data, and the appropriate selection parameters of the industrial tests were estimated.
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- 2017
250. Quality circles for quality improvement in primary health care: Their origins, spread, effectiveness and lacunae– A scoping review.
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Rohrbasser, Adrian, Harris, Janet, Mickan, Sharon, Tal, Kali, and Wong, Geoff
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PRIMARY health care ,COMMUNITY health services ,MEDICAL personnel ,SELF-esteem ,META-analysis - Abstract
Quality circles or peer review groups, and similar structured small groups of 6–12 health care professionals meet regularly across Europe to reflect on and improve their standard practice. There is debate over their effectiveness in primary health care, especially over their potential to change practitioners’ behaviour. Despite their popularity, we could not identify broad surveys of the literature on quality circles in a primary care context. Our scoping review was intended to identify possible definitions of quality circles, their origins, and reported effectiveness in primary health care, and to identify gaps in our knowledge. We searched appropriate databases and included any relevant paper on quality circles published until December 2017. We then compared information we found in the articles to that we found in books and on websites. Our search returned 7824 citations, from which we identified 82 background papers and 58 papers about quality circles. We found that they originated in manufacturing industry and that many countries adopted them for primary health care to continuously improve medical education, professional development, and quality of care. Quality circles are not standardized and their techniques are complex. We identified 19 papers that described individual studies, one paper that summarized 3 studies, and 1 systematic review that suggested that quality circles can effectively change behaviour, though effect sizes varied, depending on topic and context. Studies also suggested participation may affirm self-esteem and increase professional confidence. Because reports of the effect of quality circles on behaviour are variable, we recommend theory-driven research approaches to analyse and improve the effectiveness of this complex intervention. [ABSTRACT FROM AUTHOR]
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- 2018
- Full Text
- View/download PDF
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