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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]

The cost of specialized scientific equipment can be high and with limited funding resources, researchers and students are often unable to access or purchase the ideal equipment for their projects. In the fields of materials science and mechanical engineering, fundamental equipment such as tensile testing devices can cost tens to hundreds of thousands of dollars. While a research lab often has access to a large-scale testing machine suitable for conventional samples, loading devices for meso- and micro-scale samples for in-situ testing with the myriad of microscopy tools are often hard to source and cost prohibitive. Open-source software has allowed for great strides in the reduction of costs associated with software development and open-source hardware and additive manufacturing have the potential to similarly reduce the costs of scientific equipment and increase the accessibility of scientific research. To investigate the feasibility of open-source hardware, a micro-tensile tester was designed with a freely accessible computer-aided design package and manufactured with a desktop 3D-printer and off-the-shelf components. To our knowledge this is one of the first demonstrations of a tensile tester with additively manufactured components for scientific research. The capabilities of the tensile tester were demonstrated by investigating the mechanical properties of Graphene Oxide (GO) paper and thin films. A 3D printed tensile tester was successfully used in conjunction with an atomic force microscope to provide one of the first quantitative measurements of GO thin film buckling under compression. The tensile tester was also used in conjunction with an atomic force microscope to observe the change in surface topology of a GO paper in response to increasing tensile strain. No significant change in surface topology was observed in contrast to prior hypotheses from the literature. Based on this result obtained with the new open source tensile stage we propose an alternative hypothesis we term ‘superlamellae consolidation’ to explain the initial deformation of GO paper. The additively manufactured tensile tester tested represents cost savings of >99% compared to commercial solutions in its class and offers simple customization. However, continued development is needed for the tensile tester presented here to approach the technical specifications achievable with commercial solutions. [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]

Reading primary research literature is an essential skill for all scientists and students on science degree programmes, however little is known about how researchers at different career stages interact with and interpret scientific papers. To explore this, we conducted a survey of 260 undergraduate students and researchers in Biological Sciences at a research intensive UK university. Responses to Likert scale questions demonstrated increases in confidence and skill with reading the literature between individuals at each career stage, including between postdoctoral researchers and faculty academics. The survey indicated that individuals at different career stages valued different sections of scientific papers, and skill in reading the results section develops slowly over the course of an academic career. Inexperienced readers found the methods and results sections of research papers the most difficult to read, and undervalued the importance of the results section and critical interpretation of data. These data highlight a need for structured support with reading scientific literature at multiple career stages, and for senior academics to be aware that junior colleagues may prioritise their reading differently. We propose a model for the development of literature processing skills, and consider the need for training strategies to help inexperienced readers engage with primary literature, and therefore develop important skills that underpin scientific careers. We also encourage researchers to be mindful of language used when writing papers, and to be more inclusive of diverse audiences when disseminating their work. [ABSTRACT FROM AUTHOR]

The present work was focused to design a cheap, rapid, portable and easy to use filter paper based assay for the qualitative and quantitate analysis of acetone. Sodium alginate gel was loaded with the acetone specific optical signal probe, and subsequently coated onto filter paper surface to design portable colorimetric assays for acetone monitoring. The color of the paper sensor strip was observed to change from dark yellow to light yellowish in the presence of varying concentrations of acetone. Three different color analyzing models including RGB, HSV, and LAB were employed to probe the output optical signal, and their performance was compared in terms of better interpretation of the generated signal. The LAB model was found to provide better analytical figures of merit with a linear response for the acetone concentration ranging from 2.5 to 1500 ppm, and a limit of detection of 0.5 ppm. Furthermore, the specificity of the designed filter paper based sensor was demonstrated against different common interfering compounds. The results demonstrated the potential of our proposed filter paper based sensor as a novel tool for the analysis of acetone. [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]

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]

With the rapid development of information technology, scientific social networks (SSNs) have become the fastest and most convenient way for researchers to communicate with each other. Many published papers are shared via SSNs every day, resulting in the problem of information overload. How to appropriately recommend personalized and highly valuable papers for researchers is becoming more urgent. However, when recommending papers in SSNs, only a small amount of positive instances are available, leaving a vast amount of unlabelled data, in which negative instances and potential unseen positive instances are mixed together, which naturally belongs to One-Class Collaborative Filtering (OCCF) problem. Therefore, considering the extreme data imbalance and data sparsity of this OCCF problem, a hybrid approach of Social and Content aware One-class Recommendation of Papers in SSNs, termed SCORP, is proposed in this study. Unlike previous approaches recommended to address the OCCF problem, social information, which has been proved playing a significant role in performing recommendations in many domains, is applied in both the profiling of content-based filtering and the collaborative filtering to achieve superior recommendations. To verify the effectiveness of the proposed SCORP approach, a real-life dataset from CiteULike was employed. The experimental results demonstrate that the proposed approach is superior to all of the compared approaches, thus providing a more effective method for recommending papers in SSNs. [ABSTRACT FROM AUTHOR]

Microbial fuel cells (MFCs) can evolve in a viable technology if environmentally sound materials are developed and became available at low cost for these devices. This is especially important not only for the designing of large wastewater treatment systems, but also for the fabrication of low-cost, single-use devices. In this work we synthesized membranes by a simple procedure involving easily-biodegradable and economic materials such as poly (vinyl alcohol) (PVA), chitosan (CS) and the composite PVA:CS. Membranes were chemical and physically characterized and compared to Nafion®. Performance was studied using the membrane as separator in a typical H-Type MFCs showing that PVA:CS membrane outperform Nafion® 4 times (power production) while being 75 times more economic. We found that performance in MFC depends over interactions among several membrane characteristics such as oxygen permeability and ion conductivity. Moreover, we design a paper-based micro-scale MFC, which was used as a toxicity assay using 16 μL samples containing formaldehyde as a model toxicant. The PVA:CS membrane presented here can offer low environmental impact and become a very interesting option for point of need single-use analytical devices, especially in low-income countries where burning is used as disposal method, and toxic fluoride fumes (from Nafion®) can be released to the environment. [ABSTRACT FROM AUTHOR]

Background: The European & Developing Countries Clinical Trials Partnership (EDCTP), like many other research funders, requires its grantees to make papers available via open access (OA). This article investigates the effect of publishing in OA journals and international collaboration within and between European and sub-Saharan African countries on citation impact and likelihood of falling into the top 1% and top 10% most cited papers in poverty-related disease (PRD) research. Methods: Disease-specific research publications were identified in the Web of Science™ and MEDLINE using Medical Subject Heading (MeSH) terms. Data on the open accessibility of scientific literature were derived from 1science oaFindr. Publication data, including relative citation counts, were extracted for 2003–2015. Regression models were applied to quantify the relationship between relative citations and presence in the 1% and top 10% most cited papers versus OA and international collaboration. Results: The results show that since 2003 papers on PRDs have become increasingly available in OA. Among all PRD areas, malaria research is most frequently published in OA and in international collaboration. The adjusted regression analyses show that holding other factors constant, publishing research in OA and in international collaboration has a significant and meaningful citation advantage over non-OA or non-international collaborative research. Publishing papers as part of a European-wide or European- sub-Saharan African collaboration increases research impact. In contrast, such collaboration advantage is not observed for research output involving sub-Saharan Africa only which seems to decrease research impact. Conclusions: Our results indicate that there is a real, measurable citation advantage for publishing PRD research in OA and international collaboration. However, the international collaboration advantage seems to be region-specific with increased research impact for European-wide and European-sub-Saharan African collaborations but a decrease in research impact of collaborations confined to sub-Saharan African research institutions. Further research is required to further verify this finding and to understand the underlying factors related to this observed decrease in research impact. To target future research capacity building activities in sub-Saharan Africa it is important to assess whether the observed decreased impact reflects the scientific competencies and geographic distribution of individual researchers or institutional-, national- or funder-specific research requirements. [ABSTRACT FROM AUTHOR]

Quantifying the impact of a scholarly paper is of great significance, yet the effect of geographical distance of cited papers has not been explored. In this paper, we examine 30,596 papers published in Physical Review C, and identify the relationship between citations and geographical distances between author affiliations. Subsequently, a relative citation weight is applied to assess the impact of a scholarly paper. A higher-order weighted quantum PageRank algorithm is also developed to address the behavior of multiple step citation flow. Capturing the citation dynamics with higher-order dependencies reveals the actual impact of papers, including necessary self-citations that are sometimes excluded in prior studies. Quantum PageRank is utilized in this paper to help differentiating nodes whose PageRank values are identical. [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]

The article presents several rules for restructuring papers to avoid losing readers. Authors are instructed to focus their papers on a central contribution and to concentrate on the context-content-conclusion (C-C-C) scheme. They are also advised to optimize a paper's logical flow by avoiding zig-zag and using parallelism and to include complete story in the abstract.

Many complex physical systems exhibit a rich variety of discrete behavioural modes. Often, the system complexity limits the applicability of standard modelling tools. Hence, understanding the underlying physics of different behaviours and distinguishing between them is challenging. Although traditional machine learning techniques could predict and classify behaviour well, typically they do not provide any meaningful insight into the underlying physics of the system. In this paper we present a novel method for extracting physically meaningful clusters of discrete behaviour from limited experimental observations. This method obtains a set of physically plausible functions that both facilitate behavioural clustering and aid in system understanding. We demonstrate the approach on the V-shaped falling paper system, a new falling paper type system that exhibits four distinct behavioural modes depending on a few morphological parameters. Using just 49 experimental observations, the method discovered a set of candidate functions that distinguish behaviours with an error of 2.04%, while also aiding insight into the physical phenomena driving each behaviour. [ABSTRACT FROM AUTHOR]

The UK is one of the largest funders of health research in the world, but little is known about how health funding is spent. Our study explores whether major UK public and charitable health research funders support the research of UK-based scientists producing the most highly-cited research. To address this question, we searched for UK-based authors of peer-reviewed papers that were published between January 2006 and February 2018 and received over 1000 citations in Scopus. We explored whether these authors have held a grant from the National Institute for Health Research (NIHR), the Medical Research Council (MRC) and the Wellcome Trust and compared the results with UK-based researchers who serve currently on the boards of these bodies. From the 1,370 papers relevant to medical, biomedical, life and health sciences with more than 1000 citations in the period examined, we identified 223 individuals from a UK institution at the time of publication who were either first/last or single authors. Of those, 164 are still in UK academic institutions, while 59 are not currently in UK academia (have left the country, are retired, or work in other sectors). Of the 164 individuals, only 59 (36%; 95% CI: 29–43%) currently hold an active grant from one of the three funders. Only 79 (48%; 95% CI: 41–56%) have held an active grant from any of the three funders between 2006–2017. Conversely, 457 of the 664 board members of MRC, Wellcome Trust, and NIHR (69%; 95% CI: 65–72%) have held an active grant in the same period by any of these funders. Only 7 out of 655 board members (1.1%) were first, last or single authors of an extremely highly-cited paper. There are many reasons why the majority of the most influential UK authors do not hold a grant from the country’s major public and charitable funding bodies. Nevertheless, the results are worrisome and subscribe to similar patterns shown in the US. We discuss possible implications and suggest ways forward. [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]

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]

Bisphenol A (BPA) is an endocrine disrupting chemical used in a wide range of consumer products including photoactive dyes used in thermal paper. Recent studies have shown that dermal absorption of BPA can occur when handling these papers. Yet, regulatory agencies have largely dismissed thermal paper as a major source of BPA exposure. Exposure estimates provided by agencies such as the European Food Safety Authority (EFSA) are based on assumptions about how humans interact with this material, stating that ‘typical’ exposures for adults involve only one handling per day for short periods of time (<1 minute), with limited exposure surfaces (three fingertips). The objective of this study was to determine how individuals handle thermal paper in one common setting: a cafeteria providing short-order meals. We observed thermal paper handling in a college-aged population (n = 698 subjects) at the University of Massachusetts’ dining facility. We find that in this setting, individuals handle receipts for an average of 11.5 min, that >30% of individuals hold thermal paper with more than three fingertips, and >60% allow the paper to touch their palm. Only 11% of the participants we observed were consistent with the EFSA model for time of contact and dermal surface area. Mathematical modeling based on handling times we measured and previously published transfer coefficients, concentrations of BPA in paper, and absorption factors indicate the most conservative estimated intake from handling thermal paper in this population is 51.1 ng/kg/day, similar to EFSA’s estimates of 59 ng/kg/day from dermal exposures. Less conservative estimates, using published data on concentrations in thermal paper and transfer rates to skin, indicate that exposures are likely significantly higher. Based on our observational data, we propose that the current models for estimating dermal BPA exposures are not consistent with normal human behavior and should be reevaluated. [ABSTRACT FROM AUTHOR]

The Semantic Link Network is a general semantic model for modeling the structure and the evolution of complex systems. Various semantic links play different roles in rendering the semantics of complex system. One of the basic semantic links represents cause-effect relation, which plays an important role in representation and understanding. This paper verifies the role of the Semantic Link Network in representing the core of text by investigating the contribution of cause-effect link to representing the core of scientific papers. Research carries out with the following steps: (1) Two propositions on the contribution of cause-effect link in rendering the core of paper are proposed and verified through a statistical survey, which shows that the sentences on cause-effect links cover about 65% of key words within each paper on average. (2) An algorithm based on syntactic patterns is designed for automatically extracting cause-effect link from scientific papers, which recalls about 70% of manually annotated cause-effect links on average, indicating that the result adapts to the scale of data sets. (3) The effects of cause-effect link on four schemes of incorporating cause-effect link into the existing instances of the Semantic Link Network for enhancing the summarization of scientific papers are investigated. The experiments show that the quality of the summaries is significantly improved, which verifies the role of semantic links. The significance of this research lies in two aspects: (1) it verifies that the Semantic Link Network connects the important concepts to render the core of text; and, (2) it provides an evidence for realizing content services such as summarization, recommendation and question answering based on the Semantic Link Network, and it can inspire relevant research on content computing. [ABSTRACT FROM AUTHOR]

Poor research reporting is a major contributing factor to low study reproducibility, financial and animal waste. The ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines were developed to improve reporting quality and many journals support these guidelines. The influence of this support is unknown. We hypothesized that papers published in journals supporting the ARRIVE guidelines would show improved reporting compared with those in non-supporting journals. In a retrospective, observational cohort study, papers from 5 ARRIVE supporting (SUPP) and 2 non-supporting (nonSUPP) journals, published before (2009) and 5 years after (2015) the ARRIVE guidelines, were selected. Adherence to the ARRIVE checklist of 20 items was independently evaluated by two reviewers and items assessed as fully, partially or not reported. Mean percentages of items reported were compared between journal types and years with an unequal variance t-test. Individual items and sub-items were compared with a chi-square test. From an initial cohort of 956, 236 papers were included: 120 from 2009 (SUPP; n = 52, nonSUPP; n = 68), 116 from 2015 (SUPP; n = 61, nonSUPP; n = 55). The percentage of fully reported items was similar between journal types in 2009 (SUPP: 55.3 ± 11.5% [SD]; nonSUPP: 51.8 ± 9.0%; p = 0.07, 95% CI of mean difference -0.3–7.3%) and 2015 (SUPP: 60.5 ± 11.2%; nonSUPP; 60.2 ± 10.0%; p = 0.89, 95%CI -3.6–4.2%). The small increase in fully reported items between years was similar for both journal types (p = 0.09, 95% CI -0.5–4.3%). No paper fully reported 100% of items on the ARRIVE checklist and measures associated with bias were poorly reported. These results suggest that journal support for the ARRIVE guidelines has not resulted in a meaningful improvement in reporting quality, contributing to ongoing waste in animal research. [ABSTRACT FROM AUTHOR]

In this study, we address the question whether (and to what extent, respectively) altmetrics are related to the scientific quality of papers (as measured by peer assessments). Only a few studies have previously investigated the relationship between altmetrics and assessments by peers. In the first step, we analyse the underlying dimensions of measurement for traditional metrics (citation counts) and altmetrics–by using principal component analysis (PCA) and factor analysis (FA). In the second step, we test the relationship between the dimensions and quality of papers (as measured by the post-publication peer-review system of F1000Prime assessments)–using regression analysis. The results of the PCA and FA show that altmetrics operate along different dimensions, whereas Mendeley counts are related to citation counts, and tweets form a separate dimension. The results of the regression analysis indicate that citation-based metrics and readership counts are significantly more related to quality, than tweets. This result on the one hand questions the use of Twitter counts for research evaluation purposes and on the other hand indicates potential use of Mendeley reader counts. [ABSTRACT FROM AUTHOR]

Before organizing mixed-mode data collection for the self-administered questionnaire of the Belgian Health Interview Survey, measurement effects between the paper-and-pencil and the web-based questionnaire were evaluated. A two-period cross-over study was organized with a sample of 149 employees of two Belgian research institutes (age range 22–62 years, 72% female). Measurement agreement was assessed for a diverse range of health indicators related to general health, mental and psychosocial health, health behaviors and prevention with kappa coefficients and intraclass correlation (ICC). The quality of the data collected by both modes was evaluated by quantifying the missing, ‘don’t know’ and inconsistent values and data entry mistakes. Good to very good agreement was found for all categorical indicators with kappa coefficients superior to 0.60, except for two mental and psychosocial health indicators namely the presence of a sleeping disorder and of a depressive disorder (kappa≥0.50). For the continuous indicators high to acceptable agreement was observed with ICC superior to 0.70. Inconsistent answers and data-entry mistakes were only occurring in the paper-and-pencil mode. There were no less missing values in the web-based mode compared to the paper-and-pencil mode. The study supports the idea that web-based modes provide, in general, equal responses to paper-and-pencil modes. However, health indicators based upon factual and objective items tend to have higher measurement agreement than indicators requiring an assessment of personal subjective feelings. A web-based mode greatly facilitates the data-entry process and guides the completing of a questionnaire. However, item non-response was not positively affected. [ABSTRACT FROM AUTHOR]

Chemistry researchers are frequently evaluated on the perceived significance of their work with the citation count as the most commonly-used metric for gauging this property. Recent studies have called for a broader evaluation of significance that includes more nuanced bibliometrics as well as altmetrics to more completely evaluate scientific research. To better understand the relationship between metrics and peer judgements of significance in chemistry, we have conducted a survey of chemists to investigate their perceptions of previously published research. Focusing on a specific issue of the Journal of the American Chemical Society published in 2003, respondents were asked to select which articles they thought best matched importance and significance given several contexts: highest number of citations, most significant (subjectively defined), most likely to share among chemists, and most likely to share with a broader audience. The answers to the survey can be summed up in several observations. The ability of respondents to predict the citation counts of established research is markedly lower than the ability of those counts to be predicted by the h-index of the corresponding author of each article. This observation is conserved even when only considering responses from chemists whose expertise falls within the subdiscipline that best describes the work performed in an article. Respondents view both cited papers and significant papers differently than papers that should be shared with chemists. We conclude from our results that peer judgements of importance and significance differ from metrics-based measurements, and that chemists should work with bibliometricians to develop metrics that better capture the nuance of opinions on the importance of a given piece of research. [ABSTRACT FROM AUTHOR]

Introduction: Data collection using paper-based questionnaires can be time consuming and return errors affect data accuracy, completeness, and information quality in health surveys. We compared smartphone and paper-based data collection systems in the Burden of Obstructive Lung Disease (BOLD) study in rural Sudan. Methods: This exploratory pilot study was designed to run in parallel with the cross-sectional household survey. The Open Data Kit was used to programme questionnaires in Arabic into smartphones. We included 100 study participants (83% women; median age = 41.5 ± 16.4 years) from the BOLD study from 3 rural villages in East-Gezira and Kamleen localities of Gezira state, Sudan. Questionnaire data were collected using smartphone and paper-based technologies simultaneously. We used Kappa statistics and inter-rater class coefficient to test agreement between the two methods. Results: Symptoms reported included cough (24%), phlegm (15%), wheezing (17%), and shortness of breath (18%). One in five were or had been cigarette smokers. The two data collection methods varied between perfect to slight agreement across the 204 variables evaluated (Kappa varied between 1.00 and 0.02 and inter-rater coefficient between 1.00 and -0.12). Errors were most commonly seen with paper questionnaires (83% of errors seen) vs smartphones (17% of errors seen) administered questionnaires with questions with complex skip-patterns being a major source of errors in paper questionnaires. Automated checks and validations in smartphone-administered questionnaires avoided skip-pattern related errors. Incomplete and inconsistent records were more likely seen on paper questionnaires. Conclusion: Compared to paper-based data collection, smartphone technology worked well for data collection in the study, which was conducted in a challenging rural environment in Sudan. This approach provided timely, quality data with fewer errors and inconsistencies compared to paper-based data collection. We recommend this method for future BOLD studies and other population-based studies in similar settings. [ABSTRACT FROM AUTHOR]

Background: There is widespread evidence that statistical methods play an important role in original research articles, especially in medical research. The evaluation of statistical methods and reporting in journals suffers from a lack of standardized methods for assessing the use of statistics. The objective of this study was to develop and evaluate an instrument to assess the statistical intensity in research articles in a standardized way. Methods: A checklist-type measure scale was developed by selecting and refining items from previous reports about the statistical contents of medical journal articles and from published guidelines for statistical reporting. A total of 840 original medical research articles that were published between 2007–2015 in 16 journals were evaluated to test the scoring instrument. The total sum of all items was used to assess the intensity between sub-fields and journals. Inter-rater agreement was examined using a random sample of 40 articles. Four raters read and evaluated the selected articles using the developed instrument. Results: The scale consisted of 66 items. The total summary score adequately discriminated between research articles according to their study design characteristics. The new instrument could also discriminate between journals according to their statistical intensity. The inter-observer agreement measured by the ICC was 0.88 between all four raters. Individual item analysis showed very high agreement between the rater pairs, the percentage agreement ranged from 91.7% to 95.2%. Conclusions: A reliable and applicable instrument for evaluating the statistical intensity in research papers was developed. It is a helpful tool for comparing the statistical intensity between sub-fields and journals. The novel instrument may be applied in manuscript peer review to identify papers in need of additional statistical review. [ABSTRACT FROM AUTHOR]

Research paper recommenders emerged over the last decade to ease finding publications relating to researchers’ area of interest. The challenge was not just to provide researchers with very rich publications at any time, any place and in any form but to also offer the right publication to the right researcher in the right way. Several approaches exist in handling paper recommender systems. However, these approaches assumed the availability of the whole contents of the recommending papers to be freely accessible, which is not always true due to factors such as copyright restrictions. This paper presents a collaborative approach for research paper recommender system. By leveraging the advantages of collaborative filtering approach, we utilize the publicly available contextual metadata to infer the hidden associations that exist between research papers in order to personalize recommendations. The novelty of our proposed approach is that it provides personalized recommendations regardless of the research field and regardless of the user’s expertise. Using a publicly available dataset, our proposed approach has recorded a significant improvement over other baseline methods in measuring both the overall performance and the ability to return relevant and useful publications at the top of the recommendation list. [ABSTRACT FROM AUTHOR]

Background: Identification of the source of mosquito blood meals is an important component for disease control and surveillance. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an effective tool for mosquito blood meal identification, using the abdomens of freshly engorged mosquitoes. In the field, mosquito abdomens are crushed on Whatman filter papers to determine the host feeding patterns by identifying the origin of their blood meals. The aim of this study was to test whether crushing engorged mosquito abdomens on Whatman filter papers was compatible with MALDI-TOF MS for mosquito blood meal identification. Both laboratory reared and field collected mosquitoes were tested. Material and methods: Sixty Anopheles gambiae Giles were experimentally engorged on the blood of six distinct vertebrate hosts (human, sheep, rabbit, dog, chicken and rat). The engorged mosquito abdomens were crushed on Whatman filter papers for MALDI-TOF MS analysis. 150 Whatman filter papers, with mosquitoes engorged on cow and goat blood, were preserved. A total of 77 engorged mosquito abdomens collected in the Comoros Islands and crushed on Whatman filter papers were tested with MALDI-TOF MS. Results: The MS profiles generated from mosquito engorged abdomens crushed on Whatman filter papers exhibited high reproducibility according to the original host blood. The blood meal host was correctly identified from mosquito abdomens crushed on Whatman filter papers by MALDI-TOF MS. The MS spectra obtained after storage were stable regardless of the room temperature and whether or not they were frozen. The MS profiles were reproducible for up to three months. For the Comoros samples, 70/77 quality MS spectra were obtained and matched with human blood spectra. This was confirmed by molecular tools. Conclusion: The results demonstrated that MALDI-TOF MS could identify mosquito blood meals from Whatman filter papers collected in the field during entomological surveys. The application of MALDI-TOF MS has proved to be rapid and successful, making it a new and efficient tool for mosquito-borne disease surveillance. [ABSTRACT FROM AUTHOR]

Type 1 diabetes (T1D) is increasing in incidence and predictable with measurement of serum islet autoantibodies (iAb) years prior to clinical disease onset. Identifying iAb positive individuals reduces diabetic ketoacidosis and identifies individuals for T1D prevention trials. However, large scale screening for iAb remains challenging as assays have varying sensitivities and specificities, insulin autoantibodies remain difficult to measure and venipuncture is generally required to obtain serum. We developed an approach to reliably measure all four major iAb, including insulin autoantibodies, from dried blood spots (DBS) on filter-paper. By spiking iAb positive serum into iAb negative whole blood in a dose titration, we optimized the conditions for autoantibody elution from filter paper as measured by fluid phase radioimmunoassays. After assessing stability of measuring iAb from DBS over time, we then screened iAb from DBS and the corresponding serum in new-onset T1D (n = 52), and controls (n = 72) which included first-degree relatives of T1D patients. iAb measured from eluted DBS in new-onset T1D strongly correlated with serum measurements (R2 = 0.96 for mIAA, GADA = 0.94, IA-2A = 0.85, ZnT8A = 0.82, p<0.01 for each autoantibody). There were no false positives in control subjects, and 5/6 with previously unknown iAb positivity in sera were detected using DBS. With further validation, measuring iAb from DBS can be a reliable method to screen for T1D risk. [ABSTRACT FROM AUTHOR]

Written communication plays a crucial role in the history of modern civilizations as manuscripts do not only exist contemporarily, but are passed on to subsequent generations. Besides a document’s content, information is stored in the materials used for its production. Analyses of the composition allow, for example, identifying the biological origins of materials, dating, and help to understand degradation patterns. A combination of microscopic and DNA approaches was applied in order to analyze various plant derived writing sheets. Given their diversity and abundance in museum collections, plant based writing supports are yet an underexplored target for DNA studies. DNA retrieval of paper is low compared to raw paper plant material, which is likely due to the loss of organic components during paper production. Optimizing DNA extraction for each respective material drastically increased DNA recovery. Finally, we present a non-invasive DNA sampling method that utilizes nylon membranes, commonly used for bacterial DNA sampling and that is applicable to delicate material. Although bacterial infestation was visible on one sample, as indicated by scanning electron microscopy, endogenous DNA was retrieved. The results presented here are promising as they extend the scope of sources for DNA analyses by demonstrating that DNA molecules can be retrieved from a variety of plant derived writing supports. In future, such analyses can help to explore the biological diversity not only of plants and of additives utilized for producing writing supports, but also of the plenty products made from paper. [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]

An editorial is presented which discusses the collaborative writing with multiple authors which has additional challenges including varied levels of engagement of coauthors, provision of fair credit through authorship or acknowledgements and acceptance of diversity of work styles. Also discussed are the 10 simple rules for collaboratively writing a multi-authored paper which include to build a writing team wisely; to create a data management plan and to jointly decide on authorship guidelines.

Moderate-to-severe psoriasis is associated with significant comorbidity, an impaired quality of life, and increased medical costs, including those associated with treatments. Systematic reviews (SRs) and meta-analyses (MAs) of randomized clinical trials are considered two of the best approaches to the summarization of high-quality evidence. However, methodological bias can reduce the validity of conclusions from these types of studies and subsequently impair the quality of decision making. As co-authorship is among the most well-documented forms of research collaboration, the present study aimed to explore whether authors’ collaboration methods might influence the methodological quality of SRs and MAs of psoriasis. Methodological quality was assessed by two raters who extracted information from full articles. After calculating total and per-item Assessment of Multiple Systematic Reviews (AMSTAR) scores, reviews were classified as low (0-4), medium (5-8), or high (9-11) quality. Article metadata and journal-related bibliometric indices were also obtained. A total of 741 authors from 520 different institutions and 32 countries published 220 reviews that were classified as high (17.2%), moderate (55%), or low (27.7%) methodological quality. The high methodological quality subnetwork was larger but had a lower connection density than the low and moderate methodological quality subnetworks; specifically, the former contained relatively fewer nodes (authors and reviews), reviews by authors, and collaborators per author. Furthermore, the high methodological quality subnetwork was highly compartmentalized, with several modules representing few poorly interconnected communities. In conclusion, structural differences in author-paper affiliation network may influence the methodological quality of SRs and MAs on psoriasis. As the author-paper affiliation network structure affects study quality in this research field, authors who maintain an appropriate balance between scientific quality and productivity are more likely to develop higher quality reviews. [ABSTRACT FROM AUTHOR]

University scientific research ability is an important indicator to express the strength of universities. In this paper, the evaluation of university scientific research ability is investigated based on the output of sci-tech papers. Four university alliances from North America, UK, Australia, and China, are selected as the case study of the university scientific research evaluation. Data coming from Thomson Reuters InCites are collected to support the evaluation. The work has contributed new framework to the issue of university scientific research ability evaluation. At first, we have established a hierarchical structure to show the factors that impact the evaluation of university scientific research ability. Then, a new MCDM method called D-AHP model is used to implement the evaluation and ranking of different university alliances, in which a data-driven approach is proposed to automatically generate the D numbers preference relations. Next, a sensitivity analysis has been given to show the impact of weights of factors and sub-factors on the evaluation result. At last, the results obtained by using different methods are compared and discussed to verify the effectiveness and reasonability of this study, and some suggestions are given to promote China’s scientific research ability. [ABSTRACT FROM AUTHOR]

Over the last few decades, the institutionalisation of quantitative research evaluations has created incentives for scholars to publish as many papers as possible. This paper assesses the effects of such incentives on individual researchers’ scientific impact, by analysing the relationship between their number of articles and their proportion of highly cited papers. In other words, does the share of an author’s top 1% most cited papers increase, remain stable, or decrease as his/her total number of papers increase? Using a large dataset of disambiguated researchers (N = 28,078,476) over the 1980–2013 period, this paper shows that, on average, the higher the number of papers a researcher publishes, the higher the proportion of these papers are amongst the most cited. This relationship is stronger for older cohorts of researchers, while decreasing returns to scale are observed for recent cohorts. On the whole, these results suggest that for established researchers, the strategy of publishing as many papers as possible did not yield lower shares of highly cited publications, but such a pattern is not always observed for younger scholars. [ABSTRACT FROM AUTHOR]

When young children do not receive adequate amounts of the micronutrient iodine in their diet, their growth and cognitive development can be impaired. Nearly every country in the world has programs in place to track iodine intake and provide supplemental iodine if needed, usually in the form of fortified salt. The iodine nutrition status of a population can be tracked by monitoring iodine levels in urine samples to see if the median value falls in the range of 100–300 micrograms of iodine per liter of urine (μg I/L), which indicates adequate or more than adequate iodine nutrition. Many low and middle-income countries (LMIC) do not have a laboratory capable of carrying out this challenging assay, so samples must be sent out for assay in external labs, which is expensive and time-consuming. In most LMIC, population iodine surveys are carried out every 5–10 years, which limits the utility of the data for program monitoring and evaluation. To solve this problem, we developed a field-friendly paper test card that uses the Sandell-Kolthoff reaction to measure urinary iodine levels. A blind internal validation study showed that 93% of samples (n = 60) of iodide in an artificial urine matrix were categorized correctly by visual analysis as deficient, adequate, or excessive for levels set forth by the World Health Organization. Quantitative measurements based on computer image analysis had an error of 40 ± 20 μg I/L (n = 35 for samples in the calibration range) and these results categorized 88% of the samples (n = 60) correctly. We employed lifecycle analysis principles to address the known toxicity of arsenic, which is an obligatory reagent in the Sandell-Kolthoff reaction. Disposal of the cards in a landfill (their most likely destination after use) could let arsenic leach into groundwater; toxicity characteristic leaching procedure (TCLP) tests showed that the level of arsenic leached from the cards was 28.78 ppm, which is above the United States Environmental Protection Agency’s limit of 5 parts per million for solid waste. We integrated a remediation module into the card. This module contains oxone, to oxidize As(III) to As(V) oxyacids, and the iron oxide goethite. TCLP testing showed that the leachable amount of arsenic was reduced by at least 97.6%—from 28.8 ppm to lower than 0.7 ± 0.7 ppm (n = 20). This upstream intervention rendered the test card suitable for landfilling while retaining its functionality to perform a critical public health evaluation. [ABSTRACT FROM AUTHOR]

Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a “dying” paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing “offspring”. Practically, this might be used to trace the successive published milestones of a research field. [ABSTRACT FROM AUTHOR]

For several decades, a leading paradigm of how to quantitatively assess scientific research has been the analysis of the aggregated citation information in a set of scientific publications. Although the representation of this information as a citation network has already been coined in the 1960s, it needed the systematic indexing of scientific literature to allow for impact metrics that actually made use of this network as a whole, improving on the then prevailing metrics that were almost exclusively based on the number of direct citations. However, besides focusing on the assignment of credit, the paper citation network can also be studied in terms of the proliferation of scientific ideas. Here we introduce a simple measure based on the shortest-paths in the paper's in-component or, simply speaking, on the shape and size of the wake of a paper within the citation network. Applied to a citation network containing Physical Review publications from more than a century, our approach is able to detect seminal articles which have introduced concepts of obvious importance to the further development of physics. We observe a large fraction of papers co-authored by Nobel Prize laureates in physics among the top-ranked publications. [ABSTRACT FROM AUTHOR]

Aims: To evaluate the relative efficiencies of five Internet-based digital and three paper-based scientific surveys and to estimate the costs for different-sized cohorts. Methods: Invitations to participate in a survey were distributed via e-mail to employees of two university hospitals (E1 and E2) and to members of a medical association (E3), as a link placed in a special text on the municipal homepage regularly read by the administrative employees of two cities (H1 and H2), and paper-based to workers at an automobile enterprise (P1) and college (P2) and senior (P3) students. The main parameters analyzed included the numbers of invited and actual participants, and the time and cost to complete the survey. Statistical analysis was descriptive, except for the Kruskal-Wallis-H-test, which was used to compare the three recruitment methods. Cost efficiencies were compared and extrapolated to different-sized cohorts. Results: The ratios of completely answered questionnaires to distributed questionnaires were between 81.5% (E1) and 97.4% (P2). Between 6.4% (P1) and 57.0% (P2) of the invited participants completely answered the questionnaires. The costs per completely answered questionnaire were $0.57–$1.41 (E1–3), $1.70 and $0.80 for H1 and H2, respectively, and $3.36–$4.21 (P1–3). Based on our results, electronic surveys with 10, 20, 30, or 42 questions would be estimated to be most cost (and time) efficient if more than 101.6–225.9 (128.2–391.7), 139.8–229.2 (93.8–193.6), 165.8–230.6 (68.7–115.7), or 188.2–231.5 (44.4–72.7) participants were required, respectively. Conclusions: The study efficiency depended on the technical modalities of the survey methods and engagement of the participants. Depending on our study design, our results suggest that in similar projects that will certainly have more than two to three hundred required participants, the most efficient way of conducting a questionnaire-based survey is likely via the Internet with a digital questionnaire, specifically via a centralized e-mail. [ABSTRACT FROM AUTHOR]

Authorship of peer-reviewed journal articles and abstracts has become the primary currency and reward unit in academia. Such a reward is crucial for students and postdocs who are often under-compensated and thus highly value authorship as an incentive. While numerous scientific and publishing organizations have written guidelines for determining author qualifications and author order, there remains much ambiguity when it comes to how these criteria are weighed by research faculty. Here, we sought to provide some initial insight on how faculty view the relative importance of 11 criteria for scientific authorship. We distributed an online survey to 564 biomedical engineering, biology, and bioengineering faculty members at 10 research institutions across the United States. The response rate was approximately 18%, resulting in a final sample of 102 respondents. Results revealed an agreement on some criteria, such as time spent conducting experiments, but there was a lack of agreement regarding the role of funding procurement. This study provides quantitative assessments of how faculty members in the biosciences evaluate authorship criteria. We discuss the implications of these findings for researchers, especially new graduate students, to help navigate the discrepancy between official policies for authorship and the contributions that faculty truly value. [ABSTRACT FROM AUTHOR]

Several network features and information retrieval methods have been proposed to elucidate the structure of citation networks and to detect important nodes. However, it is difficult to retrieve information related to trends in an academic field and to detect cutting-edge areas from the citation network. In this paper, we propose a novel framework that detects the trend as the growth direction of a citation network using network representation learning(NRL). We presume that the linear growth of citation network in latent space obtained by NRL is the result of the iterative edge additional process of a citation network. On APS datasets and papers of some domains of the Web of Science, we confirm the existence of trends by observing that an academic field grows in a specific direction linearly in latent space. Next, we calculate each node’s degree of trend-following as an indicator called the intrinsic publication year (IPY). As a result, there is a correlation between the indicator and the number of future citations. Furthermore, a word frequently used in the abstracts of cutting-edge papers (high-IPY paper) is likely to be used often in future publications. These results confirm the validity of the detected trend for predicting citation network growth. [ABSTRACT FROM AUTHOR]

The safety of chemicals, drugs, novel foods and genetically modified crops is often tested using repeat-dose sub-acute toxicity tests in rats or mice. It is important to avoid misinterpretations of the results as these tests are used to help determine safe exposure levels in humans. Treated and control groups are compared for a range of haematological, biochemical and other biomarkers which may indicate tissue damage or other adverse effects. However, the statistical analysis and presentation of such data poses problems due to the large number of statistical tests which are involved. Often, it is not clear whether a “statistically significant” effect is real or a false positive (type I error) due to sampling variation. The author's conclusions appear to be reached somewhat subjectively by the pattern of statistical significances, discounting those which they judge to be type I errors and ignoring any biomarker where the p-value is greater than p = 0.05. However, by using standardised effect sizes (SESs) a range of graphical methods and an over-all assessment of the mean absolute response can be made. The approach is an extension, not a replacement of existing methods. It is intended to assist toxicologists and regulators in the interpretation of the results. Here, the SES analysis has been applied to data from nine published sub-acute toxicity tests in order to compare the findings with those of the author's. Line plots, box plots and bar plots show the pattern of response. Dose-response relationships are easily seen. A “bootstrap” test compares the mean absolute differences across dose groups. In four out of seven papers where the no observed adverse effect level (NOAEL) was estimated by the authors, it was set too high according to the bootstrap test, suggesting that possible toxicity is under-estimated. [ABSTRACT FROM AUTHOR]

Background: Loop mediated isothermal amplification (LAMP) provides an opportunity for improved, field-friendly detection of malaria infections in endemic areas. However data on the diagnostic accuracy of LAMP for active case detection, particularly low-density parasitaemias, are lacking. We therefore evaluated the performance of a new LAMP kit compared with PCR using DNA from filter paper blood spots. Methods and Findings: Samples from 865 fever patients and 465 asymptomatic individuals collected in Zanzibar were analysed for Pan (all species) and Pf (P. falciparum) DNA with the Loopamp MALARIA Pan/Pf kit. Samples were amplified at 65°C for 40 minutes in a real-time turbidimeter and results were compared with nested PCR. Samples with discordant results between LAMP and nested PCR were analysed with real-time PCR. The real-time PCR corrected nested PCR result was defined as gold standard. Among the 117 (13.5%) PCR detected P. falciparum infections from fever patients (mean parasite density 7491/µL, range 6–782,400) 115, 115 and 111 were positive by Pan-LAMP, Pf-LAMP and nested PCR, respectively. The sensitivities were 98.3% (95%CI 94–99.8) for both Pan and Pf-LAMP. Among the 54 (11.6%) PCR positive samples from asymptomatic individuals (mean parasite density 10/µL, range 0–4972) Pf-LAMP had a sensitivity of 92.7% (95%CI 80.1–98.5) for detection of the 41 P. falciparum infections. Pan-LAMP had sensitivities of 97% (95%CI 84.2–99.9) and 76.9% (95%CI 46.2–95) for detection of P. falciparum and P. malariae, respectively. The specificities for both Pan and Pf-LAMP were 100% (95%CI 99.1–100) in both study groups. Conclusion: Both components of the Loopamp MALARIA Pan/Pf detection kit revealed high diagnostic accuracy for parasite detection among fever patients and importantly also among asymptomatic individuals of low parasite densities from minute blood volumes preserved on filter paper. These data support LAMPs potential role for improved detection of low-density malaria infections in pre-elimination settings. [ABSTRACT FROM AUTHOR]

Open access publication rates have been steadily increasing over time. In spite of this growth, academics in low income settings struggle to gain access to the full canon of research literature. While the vast majority of open access repositories and funding organizations with open access policies are based in high income countries, the geographic patterns of open access publication itself are not well characterized. In this study, we developed a computational approach to better understand the topical and geographical landscape of open access publications in the biomedical research literature. Surprisingly, we found a strong negative correlation between country per capita income and the percentage of open access publication. Open access publication rates were particularly high in sub-Saharan Africa, but vastly lower in the Middle East and North Africa, South Asia, and East Asia and the Pacific. These effects persisted when considering papers only bearing authors from within each region and income group. However, papers resulting from international collaborations did have a higher percentage of OA than single-country papers, and inter-regional collaboration increased OA publication for all world regions. There was no clear relationship between the number of open access policies in a region and the percentage of open access publications in that region. To understand the distribution of open access across topics of biomedical research, we examined keywords that were most enriched and depleted in open access papers. Keywords related to genomics, computational biology, animal models, and infectious disease were enriched in open access publications, while keywords related to the environment, nursing, and surgery were depleted in open access publications. This work identifies geographic regions and fields of research that could be priority areas for open access advocacy. The finding that open access publication rates are highest in sub-Saharan Africa and low income countries suggests that factors other than open access policy strongly influence authors’ decisions to make their work openly accessible. The high proportion of OA resulting from international collaborations indicates yet another benefit of collaborative research. Certain applied fields of medical research, notably nursing, surgery, and environmental fields, appear to have a greater proportion of fee-for-access publications, which presumably creates barriers that prevent researchers and practitioners in low income settings from accessing the literature in those fields. [ABSTRACT FROM AUTHOR]

Background: Sponsors that seek to commercialize new drugs apply to the Food and Drug Administration (FDA) which independently analyzes the raw data and reports the results on its website. Objectives: This study sought to determine if there are differences between the FDA assessments and journal reports on biologic agents developed for the treatment of rheumatoid arthritis. Methods: Available data on FDA-approved drugs were extracted from the website, and a systematic literature search was conducted to identify matching studies in peer-reviewed medical journals. Outcome measures were the American College of Rheumatology response criteria ACR20 (efficacy) and withdrawal due to adverse events (safety). As effect size odds ratios were estimated for each active trial arm vs. control arm (i.e. for both sources: FDA and journal report), followed by calculation of the ratios of the FDA and journal report odds ratios. A ratio of odds ratios not equal to 1 was categorized as a discrepancy. Results: FDA reports were available for 8 of 9 FDA-approved biologic agents for rheumatoid arthritis; all identified trials (34) except one were published in peer-reviewed journals. Overall, discrepancies were noted for 20 of the 33 evaluated trials. Differences in the apparent benefit reporting were found in 39% (24/61) pairwise comparisons and in 11 cases these were statistically significant; the FDA report showed greater benefit than the journal publication in 15 comparisons and lesser benefit in 9. Differences in the reported harms were found in 51% (28/55) pairwise comparisons and were statistically significant in 5. The “signal” in FDA reports showed a less harmful effect than the journal publication in 17 comparisons whereas a more harmful effect in 11. The differences were attributed to differences in analytic approach, patient inclusion, rounding effect, and counting discrepancies. However, no differences were categorized as critical. Conclusion: There was no empirical evidence to suggest biased estimates between the two sources. Increased and detailed transparency in publications would improve the understanding and credibility of published results. Further, the FDA report was found to be a useful source when data are missing in the published report (i.e. reporting bias). [ABSTRACT FROM AUTHOR]

Sexually selected signals are common in many animals, though little reported in social insects. We investigated the occurrence of male visual signals mediating the dominance relationships among males and female choice of sexual partner in the paper wasp Polistes simillimus. Males have three conspicuous, variable and sexually dimorphic traits: black pigmentation on the head, a pair of yellow abdominal spots and body size differences. By conducting behavioral assays, we found that none of the three visual traits are associated with male-male dominance relationship. However, males with higher proportion of black facial pigmentation and bigger yellow abdominal spots are more likely chosen as sexual partners. Also, after experimentally manipulating the proportion of black pigment on males' face, we found that females may evaluate male facial coloration during the choice of a sexual partner. Thus, the black pigmentation on P. simillimus male's head appears to play a role as a sexually selected visual signal. We suggest that sexual selection is a common force in Polistes and we highlight the importance of this group as a model for the study of visual communication in insects. [ABSTRACT FROM AUTHOR]

Some scholars add authors to their research papers or grant proposals even when those individuals contribute nothing to the research effort. Some journal editors coerce authors to add citations that are not pertinent to their work and some authors pad their reference lists with superfluous citations. How prevalent are these types of manipulation, why do scholars stoop to such practices, and who among us is most susceptible to such ethical lapses? This study builds a framework around how intense competition for limited journal space and research funding can encourage manipulation and then uses that framework to develop hypotheses about who manipulates and why they do so. We test those hypotheses using data from over 12,000 responses to a series of surveys sent to more than 110,000 scholars from eighteen different disciplines spread across science, engineering, social science, business, and health care. We find widespread misattribution in publications and in research proposals with significant variation by academic rank, discipline, sex, publication history, co-authors, etc. Even though the majority of scholars disapprove of such tactics, many feel pressured to make such additions while others suggest that it is just the way the game is played. The findings suggest that certain changes in the review process might help to stem this ethical decline, but progress could be slow. [ABSTRACT FROM AUTHOR]

Scientists often perceive a trade-off between quantity and quality in scientific publishing: finite amounts of time and effort can be spent to produce few high-quality papers or subdivided to produce many papers of lower quality. Despite this perception, previous studies have indicated the opposite relationship, in which productivity (publishing more papers) is associated with increased paper quality (usually measured by citation accumulation). We examine this question in a novel way, comparing members of the National Academy of Sciences with themselves across years, and using a much larger dataset than previously analyzed. We find that a member’s most highly cited paper in a given year has more citations in more productive years than in in less productive years. Their lowest cited paper each year, on the other hand, has fewer citations in more productive years. To disentangle the effect of the underlying distributions of citations and productivities, we repeat the analysis for hypothetical publication records generated by scrambling each author’s citation counts among their publications. Surprisingly, these artificial histories re-create the above trends almost exactly. Put another way, the observed positive relationship between quantity and quality can be interpreted as a consequence of randomly drawing citation counts for each publication: more productive years yield higher-cited papers because they have more chances to draw a large value. This suggests that citation counts, and the rewards that have come to be associated with them, may be more stochastic than previously appreciated. [ABSTRACT FROM AUTHOR]

Objective: Detection of vascular endothelial growth factor (VEGF) levels in ocular tissue may perhaps provide insight into the role of VEGF in the pathogenesis and progression of diabetic retinopathy (DR). The aim of this study was to evaluate the levels of VEGF in tears and serum amongst type 2 diabetes mellitus (DM) patients. Methods: A comparative cross-sectional study was conducted between August 2016 and May 2018 involving type 2 DM patients with no DR, non-proliferative DR (NPDR), and proliferative DR (PDR). Tear samples were collected using no.41 Whatman filter paper (Schirmer strips) and 5 mL blood samples were drawn by venous puncture. VEGF levels in tears and serum were measured by enzyme-linked immunosorbent assay. Results: A total of 88 type 2 DM patients (no DR: 30 patients, NPDR: 28 patients, PDR: 30 patients) were included in the study. Mean tear VEGF levels were significantly higher in the NPDR and PDR groups (114.4 SD 52.5 pg/mL and 150.8 SD 49.7 pg/mL, respectively) compared to the no DR group (40.4 SD 26.5 pg/mL, p < 0.001). There was no significant difference in the mean serum VEGF levels between the three groups. There was a fair correlation between serum and tear VEGF levels (p = 0.015, r = 0.263). Conclusion: VEGF levels in tears were significantly higher amongst diabetic patients with DR compared to those without DR and were significantly associated with the severity of DR. There was a fair correlation between serum and tear VEGF levels. Detection of VEGF in tears is a good non-invasive predictor test for the severity of DR. A large cohort study is needed for further evaluation. [ABSTRACT FROM AUTHOR]