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We describe herein a method of recharging used commercial spin columns or assembling homemade spin columns using filter paper as binding material for cost-effective, low throughput nucleic acid purification. The efficiency of filter paper-based spin columns was evaluated for purification of nucleic acids from various sources. Following protocols of commercial kits, we found filter paper to be a useful binding material for purification of nucleic acids, including plant genomic DNA, plant total RNA, PCR products, and DNA from agarose gels. However, filter paper has a weak binding affinity to plasmid DNA in tested miniprep protocols. Protocols for the use of filter paper recharged spin columns or homemade spin columns for low throughput purification of plant genomic DNA and total RNA with unused commercial kit buffers or less expensive homemade buffers are presented. [ABSTRACT FROM AUTHOR]

Background: Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately provide new information to shape public policy response on cholera control and elimination. Methodology/Principal findings: Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor. Conclusions: WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers this provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas. [ABSTRACT FROM AUTHOR]

Background: The use of filter paper as a simple, inexpensive tool for storage and transportation of blood, ‘Dried Blood Spots’ or Guthrie cards, for diagnostic assays is well-established. In contrast, there are a paucity of diagnostic evaluations of dried cerebrospinal fluid (CSF) spots. These have potential applications in low-resource settings, such as Laos, where laboratory facilities for central nervous system (CNS) diagnostics are only available in Vientiane. In Laos, a major cause of CNS infection is Japanese encephalitis virus (JEV). We aimed to develop a dried CSF spot protocol and to evaluate its diagnostic performance using the World Health Organisation recommended anti-JEV IgM antibody capture enzyme-linked immunosorbent assay (JEV MAC-ELISA). Methodology and Principal Findings: Sample volumes, spotting techniques and filter paper type were evaluated using a CSF-substitute of anti-JEV IgM positive serum diluted in Phosphate Buffer Solution (PBS) to end-limits of detection by JEV MAC-ELISA. A conventional protocol, involving eluting one paper punch in 200μl PBS, did not detect the end-dilution, nor did multiple punches utilising diverse spotting techniques. However, pre-cut filter paper enabled saturation with five times the volume of CSF-substitute, sufficiently improving sensitivity to detect the end-dilution. The diagnostic accuracy of this optimised protocol was compared with routine, neat CSF in a pilot, retrospective study of JEV MAC-ELISA on consecutive CSF samples, collected 2009–15, from three Lao hospitals. In comparison to neat CSF, 132 CSF samples stored as dried CSF spots for one month at 25–30°C showed 81.6% (65.7–92.3 95%CI) positive agreement, 96.8% (91.0–99.3 95%CI) negative agreement, with a kappa coefficient of 0.81 (0.70–0.92 95%CI). Conclusions/Significance: The novel design of pre-cut filter paper saturated with CSF could provide a useful tool for JEV diagnostics in settings with limited laboratory access. It has the potential to improve national JEV surveillance and inform vaccination policies. The saturation of filter paper has potential use in the wider context of pathogen detection, including dried spots for detecting other analytes in CSF, and other body fluids. [ABSTRACT FROM AUTHOR]

Background: Paper mulberry (Broussonetia papyrifera (L.) L'Hér. ex Vent) is a dioecious tree native to East Asia and mainland Southeast-Asia, introduced prehistorically to Polynesia as a source of bark fiber by Austronesian-speaking voyagers. In Oceania, trees are coppiced and harvested for production of bark-cloth, so flowering is generally unknown. A survey of botanical records of paper mulberry revealed a distributional disjunction: the tree is apparently absent in Borneo and the Philippines. A subsequent study of chloroplast haplotypes linked paper mulberry of Remote Oceania directly to a population in southern Taiwan, distinct from known populations in mainland Southeast-Asia. Methodology: We describe the optimization and use of a DNA marker designed to identify sex in paper mulberry. We used this marker to determine the sex distribution in selected localities across Asia, Near and Remote Oceania. We also characterized all samples using the ribosomal internal transcribed spacer sequence (ITS) in order to relate results to a previous survey of ITS diversity. Results: In Near and Remote Oceania, contemporary paper mulberry plants are all female with the exception of Hawaii, where plants of both sexes are found. In its natural range in Asia, male and female plants are found, as expected. Male plants in Hawaii display an East Asian ITS genotype, consistent with modern introduction, while females in Remote Oceania share a distinctive variant. Conclusions: Most paper mulberry plants now present in the Pacific appear to be descended from female clones introduced prehistorically. In Hawaii, the presence of male and female plants is thought to reflect a dual origin, one a prehistoric female introduction and the other a modern male introduction by Japanese/Chinese immigrants. If only female clones were dispersed from a source-region in Taiwan, this may explain the absence of botanical records and breeding populations in the Philippines and Borneo, and Remote Oceania. [ABSTRACT FROM AUTHOR]

Recent studies have reported incipient morphological caste dimorphism in the Van der Vecht organ size of some temperate Polistes paper wasps. Whether species other than the temperate ones show a similar pattern remains elusive. Here, we have studied some Neotropical Polistes species. By comparing females collected through the year, we showed caste related differences in the size of the Van der Vecht organ in P. ferreri (body size corrected Van der Vech organ size of queens = 0.45 ± 0.06, workers = 0.38 ± 0.07 mm2, p = 0.0021), P. versicolor (body size corrected Van der Vech organ size of queens = 0.54 ± 0.11, workers = 0.46 ± 0.09 mm2, p = 0.010), but not P. simillimus (body size corrected Van der Vech organ size of queens = 0.52 ± 0.05, workers = 0.49 ± 0.06 mm2, p = 0.238). Therefore, it seems that queens and workers of some Neotropical Polistes have diverged in their ontogenic trajectory of the Van der Vecht organ size, providing clear evidence for incipient morphological caste dimorphism. As Polistes are distributed mostly in the tropics, we propose that physical caste differences may be widespread in the genus. Also, we highlight that morphological divergence in the queen–worker phenotypes may have started through differential selection of body structures, like the Van der Vecht organ. [ABSTRACT FROM AUTHOR]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

Early industrialization and the development of cheap production processes for paper have led to an exponential accumulation of paper-based documents during the last two centuries. Archives and libraries harbor vast amounts of ancient and modern documents and have to undertake extensive endeavors to protect them from abiotic and biotic deterioration. While services for mechanical preservation such as ex post de-acidification of historic documents are already commercially available, the possibilities for long-term protection of paper-based documents against fungal attack (apart from temperature and humidity control) are very limited. Novel processes for mechanical enhancement of damaged cellulosic documents use Ionic Liquids (IL) as essential process components. With some of these ILs having azole-functionalities similar to well-known fungicides such as Clotrimazole, the possibility of antifungal activities of these ILs was proposed but has not yet been experimentally confirmed. We evaluated the potency of four ILs with potential application in paper restoration for suppression of fungal growth on five relevant paper-infesting molds. The results revealed a general antifungal activity of all ILs, which increased with the size of the non-polar group. Physiological experiments and ultimate elemental analysis allowed to determine the minimal inhibitory concentration of each IL as well as the residual IL concentration in process-treated paper. These results provide valuable guidelines for IL-applications in paper restoration processes with antifungal activity as an added benefit. With azoles remaining in the paper after the process, simultaneous repair and biotic protection in treated documents could be facilitated. [ABSTRACT FROM AUTHOR]

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry. [ABSTRACT FROM AUTHOR]

Background: The lack of information regarding the burden of acute bacterial meningitis in Latin America leads to a reduction in the estimated incidence rates of the disease, and impairs public health decisions on the use and follow-up of preventive interventions, particularly, the evaluation of existing vaccination policies. The use of the real-time PCR in diagnostic routine procedures has resulted in a substantial increase in confirmed bacterial meningitis cases. However, in resource-poor countries, these assays are only available in reference laboratories. Sample transportation to these laboratories is a critical constraint, as it requires specialized, high cost courier services. To overcome this barrier we evaluated the use of FTATM Elute filter paper cards for the conservation and processing of samples under normal environmental conditions, as they would be when transported from remote and under-equipped healthcare facilities to the reference centers. A total of 401 samples received in 2015 as part of Sao Paulo’s national surveillance for routine diagnosis were selected for this study. Methods: The sensitivity and specificity of real-time PCR were evaluated using fresh serum and cerebrospinal fluid (CSF) samples processed using our laboratory’s standard DNA extraction, and processing the same samples after being dried and stored on FTATM card, and DNA extracted following the manufacturer’s instructions. Results: The sensitivities for detection of Neisseria meningitidis, Streptococcus pneumoniae, and Haemophilus influenzae from CSF dried and stored on FTATM cards were 98%, 92%, and 100%, respectively, and with serum samples were 73%, 88%, and 100%, respectively. When compared to our laboratory’s standard methodology, results showed high concordance, with Kappa index ranges of 0.9877–1.00 for CSF, and 0.8004–1.00 for serum samples. Conclusion: The use of FTATM cards for CSF and serum conservation and transport represents a rapid, reliable, and cost-effective alternative that will allow obtaining valuable epidemiological information that would otherwise be lost. [ABSTRACT FROM AUTHOR]

Pyocyanin is a toxin produced by Pseudomonas aeruginosa. Here we describe a novel paper-based electrochemical sensor for pyocyanin detection, manufactured with a simple and inexpensive approach based on electrode printing on paper. The resulting sensors constitute an effective electrochemical method to quantify pyocyanin in bacterial cultures without the conventional time consuming pretreatment of the samples. The electrochemical properties of the paper-based sensors were evaluated by ferri/ferrocyanide as a redox mediator, and showed reliable sensing performance. The paper-based sensors readily allow for the determination of pyocyanin in bacterial cultures with high reproducibility, achieving a limit of detection of 95 nM and a sensitivity of 4.30 μA/μM in standard culture media. Compared to the similar commercial ceramic based sensors, it is a 2.3-fold enhanced performance. The simple in-house fabrication of sensors for pyocyanin quantification allows researchers to understand in vitro adaptation of P. aeruginosa infections via rapid screenings of bacterial cultures that otherwise are expensive and time-consuming. [ABSTRACT FROM AUTHOR]

Author congratulates David Gems and co-authors on a brilliant discovery — direct proof of acute phenoptosis in the nematode — but argues that the authors underappreciate the significance of their work by suggesting that phenoptosis is a rare natural phenomenon not typically observed in mammals. [ABSTRACT FROM AUTHOR]

Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of ‘superfolder’ green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 μg/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens. [ABSTRACT FROM AUTHOR]

Amphimeriasis, a fish-borne zoonotic disease caused by the liver fluke Amphimerus spp., has recently been reported as an emerging disease affecting an indigenous Ameridian group, the Chachi, living in Ecuador. The only method for diagnosing amphimeriasis was the microscopic detection of eggs from the parasite in patients' stool samples with very low sensitivity. Our group developed an ELISA technique for detection of anti-Amphimerus IgG in human sera and a molecular method based on LAMP technology (named LAMPhimerus) for specific and sensitive parasite DNA detection. The LAMPhimerus method showed to be much more sensitive than classical parasitological methods for amphimeriasis diagnosis using human stool samples for analysis. The objective of this work is to demonstrate the feasibility of using dried stool samples on filter paper as source of DNA in combination with the effectiveness of our previously designed LAMPhimerus assay for successfully Amphimerus sp. detection in clinical stool samples. A total of 102 untreated and undiluted stool samples collected from Chachi population were spread as thin layer onto common filter paper for easily transportation to our laboratory and stored at room temperature for one year until DNA extraction. When LAMPhimerus method was applied for Amphimerus sp. DNA detection, a higher number of positive results was detected (61/102; 59.80%) in comparison to parasitological methods (38/102; 37.25%), including 28/61 (45.90%) microscopy-confirmed Amphimerus sp. infections. The diagnostic parameters for the sensitivity and specificity werecalculated for our LAMPhimerus assay, which were 79.17% and 65.98%, respectively. We demonstrate, for the first time, that common filter paper is useful for easy collection and long-term storage of human stool samples for later DNA extraction and molecular analysis of human-parasitic trematode eggs. This simple, economic and easily handling method combined with the specific and sensible LAMPhimerus assay has the potential to beused as an effective molecular large-scale screening test for amphimeriasis-endemic areas. [ABSTRACT FROM AUTHOR]

Pigmentation of paper induced by fungi is one of the most complex phenomenons because it involves living organisms growing on a heterogeneous paper substrate. A novel approach to the study of interfaces of fungi and paper in black stains produced by pigmented Dematiaceous fungi with meristematic growth was undertaken applying surface metrology techniques: confocal laser SCANNING 36:76-85, 2014. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

India has the highest burden of Tuberculosis (TB) and multidrug-resistant TB (MDR-TB) worldwide. Innovative technology is the need of the hour to identify these cases that remain either undiagnosed or inadequately diagnosed due to the unavailability of appropriate tools at primary healthcare settings. We developed and evaluated 3 kits, namely ‘TB Detect’ (containing BioFM-Filter device), ‘TB Concentration and Transport’ (containing Trans-Filter device) and ‘TB DNA Extraction’ kits. These kits enable bio-safe equipment-free concentration of sputum on filters and improved fluorescence microscopy at primary healthcare centres, ambient temperature transport of dried inactivated sputum filters to central laboratories and molecular detection of drug resistance by PCR and DNA sequencing (Mol-DST). In a 2-site evaluation (n = 1190 sputum specimens) on presumptive TB patients, BioFM-Filter smear exhibited a significant increase in positivity of 7% and 4% over ZN smear and LED-FM smear (p<0.05), respectively and an increment in smear grade status (1+ or 2+ to 3+) of 16% over ZN smear and 20% over LED-FM smear. The sensitivity of Mol-DST in presumptive MDR-TB and XDR-TB cases (n = 148) was 90% for Rifampicin (95% confidence interval [CI], 78–96%), 84% for Isoniazid (95% CI, 72–92%), 83% for Fluoroquinolones (95% CI, 66–93%) and 75% for Aminoglycosides (95% CI, 35–97%), using phenotypic DST as the reference standard. Test specificity was 88–93% and concordance was ~89–92% (κ value 0.8–0.9). The patient-friendly kits described here address several of the existing challenges and are designed to provide ‘Universal Access’ to rapid TB diagnosis, including drug-resistant disease. Their utility was demonstrated by application to sputum at 2 sites in India. Our findings pave the way for larger studies in different point-of-care settings, including high-density urban areas and remote geographical locations. [ABSTRACT FROM AUTHOR]

The rapid, selective, and sensitive determination of cyanide anion ( CN−) using a simple paper strip is highly attractive because cyanide is acutely lethal to living organisms via all routes of administration, including alcohol consumption and inhaling cigarette smoke. Here, a synthetic probe ( 1) was designed for the selective determination of cyanide. The probe displays rapid and large blue spectral change (Δλabs =148 nm, Δλem = 165 nm) with respect to target recognition. Probe 1 exhibits a strong push-pull electronic effect and comprises a dimethylaminoaryl group as a donor and malononitrile as an acceptor; the π-conjugation system can be destroyed by the Michael-type addition of cyanide at the electrophilic β-positions of the nitrile groups, resulting in the marked emergence of a peak at λem = 515 nm. The developed probe was successfully applied to a paper test strip because of its noticeable optical changes upon reaction with cyanide. The fabricated dumbbell-shaped paper strip with an internal reference allowed the cyanide detection, which is indispensable for quantitative analysis in point-of-care testing. The paper strip test showed selective response to cyanide, with a linear correlation in the range of 0-25 mM in a simple and cost-effective manner. [ABSTRACT FROM AUTHOR]

It is important to implement detection and assessment of plant diseases based on remotely sensed data for disease monitoring and control. Hyperspectral data of healthy leaves, leaves in incubation period and leaves in diseased period of wheat stripe rust and wheat leaf rust were collected under in-field conditions using a black-paper-based measuring method developed in this study. After data preprocessing, the models to identify the diseases were built using distinguished partial least squares (DPLS) and support vector machine (SVM), and the disease severity inversion models of stripe rust and the disease severity inversion models of leaf rust were built using quantitative partial least squares (QPLS) and support vector regression (SVR). All the models were validated by using leave-one-out cross validation and external validation. The diseases could be discriminated using both distinguished partial least squares and support vector machine with the accuracies of more than 99%. For each wheat rust, disease severity levels were accurately retrieved using both the optimal QPLS models and the optimal SVR models with the coefficients of determination (R2) of more than 0.90 and the root mean square errors (RMSE) of less than 0.15. The results demonstrated that identification and severity evaluation of stripe rust and leaf rust at the leaf level could be implemented based on the hyperspectral data acquired using the developed method. A scientific basis was provided for implementing disease monitoring by using aerial and space remote sensing technologies. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the extent of contamination of some of the most used paper denominations of the Egyptian currency (25 PT). Sixty-nine bills in circulation were collected from November 2003 through January 2004. A swab from each bill was cultured on nutrient agar and incubated at 37°C for 48?h. Results showed that over 65% of these bills had a bacterial count above 5.0?cm 2 . A preliminary identification of organisms present on these paper notes was done using selected Petri dishes with well-defined colonies. [ABSTRACT FROM AUTHOR]

Background: Despite malaria, malnutrition and anaemia being major public-health challenges in Cameroon, very little has been reported on the interaction between these interconnected health determinants. This study therefore sought to investigate the relationship between malaria, anaemia, nutritional and socio-economic status amongst under—ten children living in six localities within two health districts in the North Region of Cameroon. Methods: Accordingly, a cross- sectional survey was conducted during the peak malaria season in November 2014, in Pitoa and Mayo-Oulo Health Districts. Three hundred and sixty eight children aged 6months—10 years were enrolled. Structured questionnaires were used to assess socio-economic status. Anthropometric indices were taken using standard methods and nutritional status assessed by calculating Height for Age (HA), Weight for Age (WA) and Weight for Height (WH) z-scores to determine stunting, underweight and wasting respectively. Finger-prick blood samples were used to prepare thin and thick blood smears for microscopy. Whole blood was collected to determine the PCV and blood spots on filter paper were used to extract plasmodium DNA for speciation by PCR. Results: Overall prevalence rates of malaria, malnutrition and anaemia were 32.9%, 54.1% and 20.6% respectively. Stunting, underweight and wasting were detected in 56.9%, 63.5% and 34.8% of the children respectively. There was a significant association between malaria and malnutrition [OR = 1.89, (95% CI: 1.12–3.19); (p = 0.017)]. Malnutrition was also strongly associated with malaria status [OR = 2.07, (95% CI: 1.22–3.53); (p = 0.007)]. The prevalence rates of mild, moderate and severe anaemia were 8.1%, 9.2% and 3.3% respectively. Both malaria status and anaemia correlated with development index [OR = 0.75, (95% CI: 0.58–0.99); (p = 0.042)] and [OR = 1.45, (95% CI: 1.05–2.00); (p = 0.023)] respectively. Conclusion: Our findings show a synergistic relationship between malaria and malnutrition. Effective collaboration between malaria control and nutrition intervention programmes is essential for proper case management and improved socio-economic status. [ABSTRACT FROM AUTHOR]

Our goal is to produce a rapid and accurate diagnostic tool for malaria using resonance Raman spectroscopy to detect small inclusions of haemozoin in Plasmodium falciparuminfected red blood cells. In pursuit of this aim we serendipitously discovered a partial dark-field effect generated by our experimental setup, which helps identify in thick blood films potential parasites that are normally difficult to see with conventional bright-field microscopy. The haemozoin deposits ‘light up’ and these can be selectively targeted with the Raman microscope to confirm the presence or absence of haemozoin by the strong 1569 cm−1band, which is a marker for haemozoin. With newly developed imaging Raman microscopes incorporating ultra-sensitive rapid readout CCDs it is possible to obtain spectra with a good signal-to-noise ratio in 1 second. Moreover, images from a smear of potentially infected cells can be recorded and analysed with multivariate methods. The reconstructed images show what appear to be sub-micron-inclusions of haemozoin in some cells indicating that the technique has potential to identify low pigmented forms of the parasite including early trophozoite-stage infected cells. Further work is required to unambiguously confirm the presence of such forms through systematic staining but the results are indeed promising and may lead to the development of a new Raman-based malaria diagnostic. [ABSTRACT FROM AUTHOR]

Single cells in genetically homogeneous microbial cultures exhibit marked phenotypic heterogeneity that is considered to bolster the fitness of the whole population. Heterogeneity on the single-cell level is typically masked in conventional studies of microbial populations, which rely on data averaged across thousands or millions of cells in a sample. Here we introduce confocal Raman microspectroscopy as a method for investigating and illustrating the spatial heterogeneity of microbial cell populations. By the use of three different test organisms as model systems, we show pronounced cellular heterogeneity even in colonies cultivated under laboratory conditions. [ABSTRACT FROM AUTHOR]

Single-cell studies have important implications in biomedicine. An accurate investigation of biochemical behaviour and status requires a biomolecular probe such as vibrational microscopy. Amongst other approaches, synchrotron infrared microspectroscopy is an appropriate analytical tool for single-cell investigation. However, it is important to understand the precise origin of spectral differences as they are directly related to the cell biochemistry. Beside biomolecular changes, physical properties can interfere in the resulting information, and the two effects need separating. Both cells and nuclei induce Mie scattering effects due to their equivalent size with the probe wavelength. This results in a large modification of the spectra, and its precise contribution has to be determined in order to extract the true spectral information. On this basis, we carried out this study in order to evaluate the exact contribution of cell nuclei to Mie scattering. To this purpose, we isolated whole cancer cell nuclei and obtained, for the first time, their FTIR spectra with good signal to noise ratio. The synchrotron-based FTIR (S-FTIR) spectra of nuclei showed changes in lipids, proteins, and DNA absorptions when compared to spectra of whole lung cancer cells. Importantly, we estimated the Mie scattering properties of single cells and single nuclei spectra and were consequently able to separate optical and chemical properties of single cells and nuclei. This is the first study which sheds new light on the identification of the precise spectral biomarkers of a whole cell and those of the cell nucleus. [ABSTRACT FROM AUTHOR]

Basic color terms used in Mandarin Chinese have been controversial since first discussed by Berlin and Kay in 1969. Previous studies showed much inconsistency on what should be considered as basic color terms in Mandarin Chinese. In the present study, we investigated categories of color rather than merely the color terms used by Taiwanese native Mandarin speakers. Using samples conforming to the Berlin and Kay survey, various colors were chosen from a collection of Natural Color System (NCS) colored papers and mounted on a piece of neutral gray card. The card was then mounted on a touch-screen, under D65 illumination. Thirty-two single-character color related Mandarin terms were selected from a Chinese character database according to frequency of use. Participants were required to select the color sample that matched the term by pressing a virtual button on the touch screen. The results show that certain terms can be directly correlated to basic color terms in English, comparable with the results of Berlin and Kay’s original study and those that followed. However, some terms, such as Mo (墨 ink), Tie (鐵 iron), and Cai (菜vegetable), show a wide spread of term maps and inconsistent use among subjects. Principle component analysis (PCA) procedures were used to analysis the commodity of data among subjects. The findings suggest that the basic color categories among Mandarin Chinese speakers are similar to those found in the World Color Survey (WCS), but are represented by wide-spread and inconsistent color terms among speakers. [ABSTRACT FROM AUTHOR]

Abstract: The ethnographic component (traditional/indigenous therapeutic uses of plants or animals, specific contexts of use, preparation, dosage, route of administration) published in the Journal of Ethnopharmacology (JEP) has not been consistently and fully provided in the past. In an attempt to ensure the fulfillment of these criteria, hence, the fulfillment of the scope of papers published in this journal, starting with the February, 2004 issue of JEP (vol. 90, 2004), the journal provided detailed “Guide to Authors”, “Author Checklist”, and models of ethnopharmacology papers. An analysis of research papers published in JEP vols. 98 and 99 showed that these papers still have not achieved full compliance with the interdisciplinarity/multidisciplinarity nature of the journal, and the discipline. Thus, a minimum standard for the ethnographic component is set down. [Copyright &y& Elsevier]

Blockchain is a decentralized transaction and data management technology developed first for Bitcoin cryptocurrency. The interest in Blockchain technology has been increasing since the idea was coined in 2008. The reason for the interest in Blockchain is its central attributes that provide security, anonymity and data integrity without any third party organization in control of the transactions, and therefore it creates interesting research areas, especially from the perspective of technical challenges and limitations. In this research, we have conducted a systematic mapping study with the goal of collecting all relevant research on Blockchain technology. Our objective is to understand the current research topics, challenges and future directions regarding Blockchain technology from the technical perspective. We have extracted 41 primary papers from scientific databases. The results show that focus in over 80% of the papers is on Bitcoin system and less than 20% deals with other Blockchain applications including e.g. smart contracts and licensing. The majority of research is focusing on revealing and improving limitations of Blockchain from privacy and security perspectives, but many of the proposed solutions lack concrete evaluation on their effectiveness. Many other Blockchain scalability related challenges including throughput and latency have been left unstudied. On the basis of this study, recommendations on future research directions are provided for researchers. [ABSTRACT FROM AUTHOR]

This paper defines the best practices for documenting ocean acidification (OA) metadata and presents a framework for an OA metadata template. Metadata is structured information that describes and locates an information resource. It is the key to ensuring that a data set will survive and continue to be accessible into the future. With the rapid expansion of studies on biological responses of organisms to OA, the lack of a common metadata template to document the resulting data poses a significant hindrance to effective OA data management efforts. In this paper, we present a metadata template that can be applied to a broad spectrum of OA studies, including those studying the biological responses of organisms to OA. The "variable metadata section", which includes the variable name, observation type, whether the variable is a manipulation condition or response variable, and the biological subject on which the variable is studied, forms the core of this metadata template. Additional metadata elements, such as investigators, temporal and spatial coverage, platforms for the sampling, data citation, are essential components to complete the template. We also explain the structure of the template, and define many metadata elements that may be unfamiliar to researchers. Template availability. - Available at: http://ezid.cdlib.org/id/doi:10.7289/V5C24TCK. - DOI: 10.7289/V5C24TCK. - NOAA Institutional Repository Accession number: ocn881471371. [ABSTRACT FROM AUTHOR]

Environmental stochasticity and climate affect outcomes in evolutionary games, which can thereby affect biological diversity. Our maximum likelihood (ML) estimates of replicator dynamics for morph frequency data from control (25 years) and three experimentally perturbed populations (14 years) of side-blotched lizards yield a 3 × 3 payoff matrix in the generalized Rock-Paper-Scissors family; it has intransitive best replies, and each strategy is its own worst reply. ML estimates indicate significant interactive effects of density and temperature on morph frequency. Implied dynamics feature a powerful interior attractor and recover (for the first time) observed 4-5 year oscillations. Our evolutionary experiment on morph frequency confirms that oscillations are driven by frequency dependent selection, but climate entrains the cycles across the perturbed and control populations within 10 generations. Applying the model across the species range, we find that climate also accounts for morph fixation and mating system diversity, suggesting climate may similarly impact ecosystem diversity. [ABSTRACT FROM AUTHOR]

The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human, animal, and environmental health. While One Health has received considerable press, its benefits remain unclear because its effects have not been quantitatively described. We systematically surveyed the published literature and used social network analysis to measure interdisciplinarity in One Health studies constructing dynamic pathogen transmission models. The number of publications fulfilling our search criteria increased by 14.6% per year, which is faster than growth rates for life sciences as a whole and for most biology subdisciplines. Surveyed publications clustered into three communities: one used by ecologists, one used by veterinarians, and a third diverse-authorship community used by population biologists, mathematicians, epidemiologists, and experts in human health. Overlap between these communities increased through time in terms of author number, diversity of co-author affiliations, and diversity of citations. However, communities continue to differ in the systems studied, questions asked, and methods employed. While the infectious disease research community has made significant progress toward integrating its participating disciplines, some segregation—especially along the veterinary/ecological research interface—remains. [ABSTRACT FROM AUTHOR]

Our world is in the midst of unprecedented change—climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment. [ABSTRACT FROM AUTHOR]

Developed countries have an even distribution of published papers on the seventeen model organisms. Developing countries have biased preferences for a few model organisms which are associated with endemic human diseases. A variant of the Hirsch-index, that we call the mean moh-index (“model organism h-index”), shows an exponential relationship with the amount of papers published in each country on the selected model organisms. Developing countries cluster together with low mean moh-indexes, even those with high number of publications. The growth curves of publications on the recent model Caenorhabditis elegans in developed countries shows different formats. We also analyzed the growth curves of indexed publications originating from developing countries. Brazil and South Korea were selected for this comparison. The most prevalent model organisms in those countries show different growth curves when compared to a global analysis, reflecting the size and composition of their research communities. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Fast-moving, competitive fields often inadvertently duplicate research. In a research environment that values being first over being robust, this results in one manuscript “scooping” ongoing research from other groups. Opportunities to demonstrate the solidity of a result through coincidental reproduction are thus lost. Here, two group leaders, one the scooper and one the scoopee, discuss their experiences under PLOS Biology’s new “complementary research” policy. In this case, submission of the second article followed publication of the first by mere days. Scooper and scoopee discuss how complementary research is good for everyone by expanding the scientific reach of studies that are overlapping but not identical, demonstrating the robustness of related results, increasing readership for both authors, and making “replication” studies cost effective by creatively using resources that have already been spent. [ABSTRACT FROM AUTHOR]

In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus", “HIV-1” and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Then, a sub-network of the papers with the highest number of inter-citations (with a minimal in-degree of 28) was selected to perform a combination of network clustering and text mining to identify the paradigmatic research fronts and analyze their dynamics. Thirteen research fronts were identified in this sub-network. The biggest and oldest front is related to the clinical knowledge on the disease in the patient. Nine of the fronts are related to the study of specific molecular structures and mechanisms and two of these fronts are related to the development of drugs. The rest of the fronts are related to the study of the disease at the cellular level. Interestingly, the emergence of these fronts occurred in successive "waves" over the time which suggest a transition in the paradigmatic focus. The emergence and evolution of the biomedical fronts in HIV/AIDS research is explained not just by the partition of the problem in elements and interactions leading to increasingly specialized communities, but also by changes in the technological context of this health problem and the dramatic changes in the epidemiological reality of HIV/AIDS that occurred between 1993 and 1995. [ABSTRACT FROM AUTHOR]

Over the last 25 years, research on biodiversity has expanded dramatically, fuelled by increasing threats to the natural world. However, the number of published studies is heavily weighted towards certain taxa, perhaps influencing conservation awareness of and funding for less-popular groups. Few studies have systematically quantified these biases, although information on this topic is important for informing future research and conservation priorities. We investigated: i) which animal taxa are being studied; ii) if any taxonomic biases are the same in temperate and tropical regions; iii) whether the taxon studied is named in the title of papers on biodiversity, perhaps reflecting a perception of what biodiversity is; iv) the geographical distribution of biodiversity research, compared with the distribution of biodiversity and threatened species; and v) the geographical distribution of authors’ countries of origin. To do this, we used the search engine Web of Science to systematically sample a subset of the published literature with ‘biodiversity’ in the title. In total 526 research papers were screened—5% of all papers in Web of Science with biodiversity in the title. For each paper, details on taxonomic group, title phrasing, number of citations, study location, and author locations were recorded. Compared to the proportions of described species, we identified a considerable taxonomic weighting towards vertebrates and an under-representation of invertebrates (particularly arachnids and insects) in the published literature. This discrepancy is more pronounced in highly cited papers, and in tropical regions, with only 43% of biodiversity research in the tropics including invertebrates. Furthermore, while papers on vertebrate taxa typically did not specify the taxonomic group in the title, the converse was true for invertebrate papers. Biodiversity research is also biased geographically: studies are more frequently carried out in developed countries with larger economies, and for a given level of species or threatened species, tropical countries were understudied relative to temperate countries. Finally, biodiversity research is disproportionately authored by researchers from wealthier countries, with studies less likely to be carried out by scientists in lower-GDP nations. Our results highlight the need for a more systematic and directed evaluation of biodiversity studies, perhaps informing more targeted research towards those areas and taxa most depauperate in research. Only by doing so can we ensure that biodiversity research yields results that are relevant and applicable to all regions and that the information necessary for the conservation of threatened species is available to conservation practitioners. [ABSTRACT FROM AUTHOR]

Background: In economic analyses of HIV interventions, South Africa is often used as a case in point, due to the availability of good epidemiological and programme data and the global relevance of its epidemic. Few analyses however use locally relevant cost data. We reviewed available cost data as part of the South African HIV Investment Case, a modelling exercise to inform the optimal use of financial resources for the country’s HIV programme. Methods: We systematically reviewed publication databases for published cost data covering a large range of HIV interventions and summarised relevant unit costs (cost per person receiving a service) for each. Where no data was found in the literature, we constructed unit costs either based on available information regarding ingredients and relevant public-sector prices, or based on expenditure records. Results: Only 42 (5%) of 1,047 records included in our full-text review reported primary cost data on HIV interventions in South Africa, with 71% of included papers covering ART. Other papers detailed the costs of HCT, MMC, palliative and inpatient care; no papers were found on the costs of PrEP, social and behaviour change communication, and PMTCT. The results informed unit costs for 5 of 11 intervention categories included in the Investment Case, with the remainder costed based on ingredients (35%) and expenditure data (10%). Conclusions: A large number of modelled economic analyses of HIV interventions in South Africa use as inputs the same, often outdated, cost analyses, without reference to additional literature review. More primary cost analyses of non-ART interventions are needed. [ABSTRACT FROM AUTHOR]