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Following the fast spread of the coronavirus (Covid-19) across Europe and North America in March 2020, many people started stockpiling commodities like toilet paper. Despite the high relevance for public authorities to adequately address stockpiling behavior, empirical studies on the psychological underpinnings of toilet paper stockpiling are still scarce. In this study, we investigated the relation between personality traits, perceived threat of Covid-19, and stockpiling of toilet paper in an online survey (N = 996) across 22 countries. Results suggest that people who felt more threatened by Covid-19 stockpiled more toilet paper. Further, a predisposition towards Emotionality predicted the perceived threat of Covid-19 and affected stockpiling behavior indirectly. Finally, Conscientiousness was related to toilet paper stockpiling, such that individuals higher in Conscientiousness tended to stockpile more toilet paper. These results emphasize the importance of clear communication by public authorities acknowledging anxiety and, at the same time, transmitting a sense of control.

Social interactions have large effects on individual physiology and fitness. In the immediate sense, social stimuli are often highly salient and engaging. Over longer time scales, competitive interactions often lead to distinct social ranks and differences in physiology and behavior. Understanding how initial responses lead to longer-term effects of social interactions requires examining the changes in responses over time. Here we examined the effects of social interactions on transcriptomic signatures at two times, at the end of a 45-minute interaction and 4 hours later, in female Polistes fuscatus paper wasp foundresses. Female P. fuscatus have variable facial patterns that are used for visual individual recognition, so we separately examined the transcriptional dynamics in the optic lobe and the non-visual brain. Results demonstrate much stronger transcriptional responses to social interactions in the non-visual brain compared to the optic lobe. Differentially regulated genes in response to social interactions are enriched for memory-related transcripts. Comparisons between winners and losers of the encounters revealed similar overall transcriptional profiles at the end of an interaction, which significantly diverged over the course of 4 hours, with losers showing changes in expression levels of genes associated with aggression and reproduction in paper wasps. On nests, subordinate foundresses are less aggressive, do more foraging and lay fewer eggs compared to dominant foundresses and we find losers shift expression of many genes in the non-visual brain, including vitellogenin, related to aggression, worker behavior, and reproduction within hours of losing an encounter. These results highlight the early neurogenomic changes that likely contribute to behavioral and physiological effects of social status changes in a social insect., Author summary Aggressive interactions often create inequalities–some individuals win while others lose. Winning versus losing can lead to large physiological differences between individuals, including different neurogenomic profiles between winners and losers. How this information about contest outcome leads to distinct neurogenomic profiles is poorly understood. Here we examine gene expression in response to aggressive social encounters in paper wasps, which naturally form dominance hierarchies on their nests in the wild. Shortly following encounters winners and losers have similar expression profiles, likely because similar mechanisms are engaged by social experiences. Four hours later, we find divergent neurogenomic profiles between winners and losers, with losers showing larger shifts in expression compared to winners. Many of the most dynamically expressed genes have been previously associated with dominance and caste differences in paper wasps showing how a single interaction can engage many of the same genomic networks that are involved in mediating more dramatic differences in queen-worker behavioral differences are also involved in responses shortly following social interactions.

Paracrine and endocrine roles have increasingly been ascribed to extracellular vesicles (EVs) generated by multicellular organisms. Central to the biogenesis, content, and function of EVs are their delimiting lipid bilayer membranes. To evaluate research progress on membranes and EVs, the International Society for Extracellular Vesicles (ISEV) conducted a workshop in March 2018 in Baltimore, Maryland, USA, bringing together key opinion leaders and hands-on researchers who were selected on the basis of submitted applications. The workshop was accompanied by two scientific surveys and covered four broad topics: EV biogenesis and release; EV uptake and fusion; technologies and strategies used to study EV membranes; and EV transfer and functional assays. In this ISEV position paper, we synthesize the results of the workshop and the related surveys to outline important outstanding questions about EV membranes and describe areas of consensus. The workshop discussions and survey responses reveal that while much progress has been made in the field, there are still several concepts that divide opinion. Good consensus exists in some areas, including particular aspects of EV biogenesis, uptake and downstream signalling. Areas with little to no consensus include EV storage and stability, as well as whether and how EVs fuse with target cells. Further research is needed in these key areas, as a better understanding of membrane biology will contribute substantially towards advancing the field of extracellular vesicles. Fil: Russell, Ashley E.. University Johns Hopkins; Estados Unidos Fil: Sneider, Alexandra. University Johns Hopkins; Estados Unidos Fil: Witwer, Kenneth W.. University Johns Hopkins; Estados Unidos Fil: Bergese, Paolo. Università Degli Studi Di Brescia; Italia Fil: Bhattacharyya, Suvendra N.. Indian Institute of Chemical Biology; India Fil: Cocks, Alexander. Cardiff University; Reino Unido Fil: Cocucci, Emanuele. Ohio State University; Estados Unidos Fil: Erdbrügger, Uta. University of Virginia; Estados Unidos Fil: Falcon Perez, Juan M.. Ikerbasque Basque Foundation for Science; España Fil: Freeman, David W.. National Institute On Aging National Institute for Helth ; Estados Unidos Fil: Gallagher, Thomas M.. Loyola University Of Chicago; Estados Unidos Fil: Hu, Shuaishuai. Technological University Dublin; Irlanda Fil: Huang, Yiyao. University Johns Hopkins; Estados Unidos. Southern Medical University; China Fil: Jay, Steven M.. University of Maryland; Estados Unidos Fil: Kano, Shin-ichi. The University of Alabama at Birmingham School of Medicine; Estados Unidos Fil: Lavieu, Gregory. Institut Curie; Francia Fil: Leszczynska, Aleksandra. University of California at San Diego; Estados Unidos Fil: Llorente, Alicia M.. Oslo University Hospital; Noruega Fil: Lu, Quan. Harvard University. Harvard School of Public Health; Estados Unidos Fil: Mahairaki, Vasiliki. University Johns Hopkins; Estados Unidos Fil: Muth, Dillon C.. University Johns Hopkins; Estados Unidos Fil: Noren Hooten, Nicole. National Institute On Aging National Institute for Helth ; Estados Unidos Fil: Ostrowski, Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Prada, Ilaria. Consiglio Nazionale delle Ricerche; Italia Fil: Sahoo, Susmita. Icahn School of Medicine at Mount Sinai ; Estados Unidos Fil: Schøyen, Tine Hiorth. Uit The Arctic University Of Norway; Noruega. University Johns Hopkins; Estados Unidos Fil: Sheng, Lifuy. University of Washington. School of Medicine; Estados Unidos Fil: Tesch, Deanna. Shaw University; Estados Unidos Fil: Van Niel, Guillaume. No especifíca; Fil: Vandenbroucke, Roosmarijn E.. University of Ghent; Bélgica Fil: Verweij, Frederik J.. No especifíca; Fil: Villar, Ana V.. Universidad de Cantabria; España Fil: Wauben, Marca. University of Utrecht; Países Bajos Fil: Wehman, Ann M.. Universität Würzburg; Alemania Fil: Ardavan, Arzhang. Peking University; ; China Fil: Carter, David Raul Francisco. Oxford Brookes University; Reino Unido Fil: Vader, Pieter. University Medical Center Utrecht; Países Bajos

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. Fil: Gonzalez Pabon, Maria Jesus. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Figueredo, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Martínez Casillas, Diana Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Corton, Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.

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. © 2019 Howison et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Author summary Conferences are great venues for disseminating algorithmic bioinformatics results, but they unfortunately do not offer an opportunity to make major revisions in the way that journals do. As a result, it is not possible for authors to fix mistakes that might be easily correctable but nevertheless can cause the paper to be rejected. As a reviewer, I wish that I had the opportunity to tell the authors, “Hey, you forgot to do this really important thing, without which it is hard to accept the paper, but if you could go back and fix it, you might have a great paper for the conference.” This lack of a back and forth can be especially problematic for first-time submitters or those from outside the field, e.g., biologists. In this article, I outline Ten Simple Rules to follow when writing an algorithmic bioinformatics conference paper to avoid having it rejected.

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.

“There is no problem that a library card can't solve” according to author Eleanor Brown [1]. This advice is sound, probably for both life and science, but even the best tool (like the library) is most effective when accompanied by instructions and a basic understanding of how and when to use it. For many budding scientists, the first day in a new lab setting often involves a stack of papers, an email full of links to pertinent articles, or some promise of a richer understanding so long as one reads enough of the scientific literature. However, the purpose and approach to reading a scientific article is unlike that of reading a news story, novel, or even a textbook and can initially seem unapproachable. Having good habits for reading scientific literature is key to setting oneself up for success, identifying new research questions, and filling in the gaps in one’s current understanding; developing these good habits is the first crucial step. Advice typically centers around two main tips: read actively and read often. However, active reading, or reading with an intent to understand, is both a learned skill and a level of effort. Although there is no one best way to do this, we present 10 simple rules, relevant to novices and seasoned scientists alike, to teach our strategy for active reading based on our experience as readers and as mentors of undergraduate and graduate researchers, medical students, fellows, and early career faculty. Rules 1–5 are big picture recommendations. Rules 6–8 relate to philosophy of reading. Rules 9–10 guide the “now what?” questions one should ask after reading and how to integrate what was learned into one’s own science.

In our planned study, we shall empirically study the assessment of cited papers within the framework of the anchoring-and-adjustment heuristic. We are interested in the question whether citation decisions are (mainly) driven by the quality of cited references. The design of our study is oriented towards the study by Teplitskiy, Duede [10]. We shall undertake a survey of corresponding authors with an available email address in the Web of Science database. The authors are asked to assess the quality of papers that they cited in previous papers. Some authors will be assigned to three treatment groups that receive further information alongside the cited paper: citation information, information on the publishing journal (journal impact factor), or a numerical access code to enter the survey. The control group will not receive any further numerical information. In the statistical analyses, we estimate how (strongly) the quality assessments of the cited papers are adjusted by the respondents to the anchor value (citation, journal, or access code). Thus, we are interested in whether possible adjustments in the assessments can not only be produced by quality-related information (citation or journal), but also by numbers that are not related to quality, i.e. the access code. The results of the study may have important implications for quality assessments of papers by researchers and the role of numbers, citations, and journal metrics in assessment processes.

Science is increasingly done in large teams, making it more likely that papers will be written by several authors from different institutes, disciplines, and cultural backgrounds. A small number of “Ten simple rules” papers have been written on collaboration and on writing but not on combining the two. Collaborative writing with multiple authors has additional challenges, including varied levels of engagement of coauthors, provision of fair credit through authorship or acknowledgements, acceptance of a diversity of work styles, and the need for clear communication. Miscommunication, a lack of leadership, and inappropriate tools or writing approaches can lead to frustration, delay of publication, or even the termination of a project. To provide insight into collaborative writing, we use our experience from the Global Lake Ecological Observatory Network (GLEON) to frame 10 simple rules for collaboratively writing a multi-authored paper. We consider a collaborative multi-authored paper to have three or more people from at least two different institutions. A multi-authored paper can be a result of a single discrete research project or the outcome of a larger research program that includes other papers based on common data or methods. The writing of a multi-authored paper is embedded within a broader context of planning and collaboration among team members. Our recommended rules include elements of both the planning and writing of a paper, and they can be iterative, although we have listed them in numerical order. It will help to revisit the rules frequently throughout the writing process. With the 10 rules outlined below, we aim to provide a foundation for writing multi-authored papers and conducting exciting and influential science.

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. ispartof: PLOS ONE vol:13 issue:5 ispartof: location:United States status: published

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.

A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium., Author summary A game of rock-paper-scissors is more than just a children’s game. This type of interactions is often used to describe competition among animals or humans. A special feature of such an interaction is that none of the pure strategies dominates, resulting in a cyclic pattern. However, in wild communities such interactions are rarely observed by biologists. Our results suggest that this lack of cyclicity may stem from imperfectness of interacting individuals. In other words, we show analytically that heterogeneity in behavioural patterns may break a cyclic relationship and lead to a stable equilibrium in pure or mixed strategies.

Objective To survey the knowledge, attitude, and practices of Vietnamese pharmacists regarding the COVID-19 pandemic. Method This cross-sectional, paper-based study was conducted from June to August 2020. A validated questionnaire (Cronbach’s alpha = 0.84) was used to interview 1,023 pharmacists in nine provinces of Vietnam. Analysis of covariance was employed to identify factors associated with the knowledge of pharmacists. The best model was chosen by using the Bayesian Model Averaging method in R software version 4.0.4. Results The mean knowledge score was 12.02 ± 1.64 (range: 6–15), which indicated that 93.4% of pharmacists had good knowledge of COVID-19. There was no difference in the average score between males and females (p > 0.05). The multivariate linear regression model revealed that the knowledge was significantly associated with pharmacists’ age, education level, and residence (p < 0.001). About attitude and practices, pharmacists daily sought and updated information on the COVID-19 pandemic through mass media and the internet (social network and online newspapers). Nearly 48% of them conceded that they communicated with customers when at least one person did not wear a face mask at the time of the COVID-19 outbreak. At medicine outlets, many measures were applied to protect pharmacists and customers, such as equipping pharmacists with face masks and hand sanitizers (95.0%), using glass shields (83.0%), and maintaining at least one-meter distance between two people (85.2%). Conclusion The pharmacists’ knowledge of COVID-19 transmission, symptoms, and prevention was good. Many useful measures against the spread of this perilous virus were applied in medicine outlets. However, pharmacists should restrict forgetting to wear face masks in communication with medicine purchasers. The government and health agencies should have practical remedies to reduce the significant differences in the COVID-19 knowledge of pharmacists among provinces and education-level groups.

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.

We propose to use Twitter data as social-spatial sensors. This study deals with the question whether research papers on certain diseases are perceived by people in regions (worldwide) that are especially concerned by these diseases. Since (some) Twitter data contain location information, it is possible to spatially map the activity of Twitter users referring to certain papers (e.g., dealing with tuberculosis). The resulting maps reveal whether heavy activity on Twitter is correlated with large numbers of people having certain diseases. In this study, we focus on tuberculosis, human immunodeficiency virus (HIV), and malaria, since the World Health Organization ranks these diseases as the top three causes of death worldwide by a single infectious agent. The results of the social-spatial Twitter maps (and additionally performed regression models) reveal the usefulness of the proposed sensor approach. One receives an impression of how research papers on the diseases have been perceived by people in regions that are especially concerned by these diseases. Our study demonstrates a promising approach for using Twitter data for research evaluation purposes beyond simple counting of tweets.

Papers describing software are an important part of computational fields of scientific research. These “software papers” are unique in a number of ways, and they require special consideration to improve their impact on the scientific community and their efficacy at conveying important information. Here, we discuss 10 specific rules for writing software papers, covering some of the different scenarios and publication types that might be encountered, and important questions from which all computational researchers would benefit by asking along the way., Author summary Computational researchers have a responsibility to ensure that the software they write stands up to the same scientific scrutiny as traditional research studies. These 10 simple rules make doing so easier by enhancing usability, reproducibility, transparency, and other crucial characteristics that aren’t taught in most computer science or research methods curricula.

In this paper, we present a facile and cost-effective method to obtain superhydrophobic filter paper and demonstrate its application for efficient water/oil separation. By coupling structurally distinct organosilane precursors (e.g., octadecyltrichlorosilane and methyltrichlorosilane) to paper fibers under controlled reaction conditions, we have formulated a simple, inexpensive, and efficient protocol to achieve a desirable superhydrophobic and superoleophilic surface on conventional filter paper. The silanized superhydrophobic filter paper showed nanostructured morphology and demonstrated great separation efficiency (up to 99.4%) for water/oil mixtures. The modified filter paper is stable in both aqueous solutions and organic solvents, and can be reused multiple times. The present study shows that our newly developed binary silanization is a promising method of modifying cellulose-based materials for practical applications, in particular the treatment of industrial waste water and ecosystem recovery.

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

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.

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.

Background Physical inactivity is an important cause of noncommunicable diseases. Interventions can increase short-term physical activity (PA), but health benefits require maintenance. Few interventions have evaluated PA objectively beyond 12 months. We followed up two pedometer interventions with positive 12-month effects to examine objective PA levels at 3–4 years. Methods and findings Long-term follow-up of two completed trials: Pedometer And Consultation Evaluation-UP (PACE-UP) 3-arm (postal, nurse support, control) at 3 years and Pedometer Accelerometer Consultation Evaluation-Lift (PACE-Lift) 2-arm (nurse support, control) at 4 years post-baseline. Randomly selected patients from 10 United Kingdom primary care practices were recruited (PACE-UP: 45–75 years, PACE-Lift: 60–75 years). Intervention arms received 12-week walking programmes (pedometer, handbooks, PA diaries) postally (PACE-UP) or with nurse support (PACE-UP, PACE-Lift). Main outcomes were changes in 7-day accelerometer average daily step counts and weekly time in moderate-to-vigorous PA (MVPA) in ≥10-minute bouts in intervention versus control groups, between baseline and 3 years (PACE-UP) and 4 years (PACE-Lift). PACE-UP 3-year follow-up was 67% (681/1,023) (mean age: 59, 64% female), and PACE-Lift 4-year follow-up was 76% (225/298) (mean age: 67, 53% female). PACE-UP 3-year intervention versus control comparisons were as follows: additional steps/day postal +627 (95% CI: 198–1,056), p = 0.004, nurse +670 (95% CI: 237–1,102), p = 0.002; total weekly MVPA in bouts (minutes/week) postal +28 (95% CI: 7–49), p = 0.009, nurse +24 (95% CI: 3–45), p = 0.03. PACE-Lift 4-year intervention versus control comparisons were: +407 (95% CI: −177–992), p = 0.17 steps/day, and +32 (95% CI: 5–60), p = 0.02 minutes/week MVPA in bouts. Neither trial showed sedentary or wear-time differences. Main study limitation was incomplete follow-up; however, results were robust to missing data sensitivity analyses. Conclusions Intervention participants followed up from both trials demonstrated higher levels of objectively measured PA at 3–4 years than controls, similar to previously reported 12-month trial effects. Pedometer interventions, delivered by post or with nurse support, can help address the public health physical inactivity challenge. Trial registrations PACE-UP isrctn.com ISRCTN98538934; PACE-Lift isrctn.com ISRCTN42122561., In this follow-up of participants from two completed trials of pedometer-based walking interventions, Tess Harris and colleagues present evidence that increases in physical activity levels seen at 12 months are still present 3-4 years later., Author summary Why was this study done? Brisk walking for 30 minutes or more daily on most days of the week can help adults and older adults to achieve moderate-to-vigorous physical activity (MVPA) guidelines for health benefits, yet many do not achieve these levels. Previous pedometer-based walking studies have shown positive effects on increased step counts and time in MVPA for up to 12 months. For sustained health benefits, increased physical activity levels need to be maintained, yet there is a lack of data from interventions assessed using objectively measured physical activity levels beyond 12 months. What did the researchers do and find? We followed up participants from two primary care 12-week pedometer-based walking trials, including both nurse-supported and postal pedometer arms, to establish whether objectively measured physical activity increases seen at 12 months were sustained at 3–4 years. PACE-UP followed up 45–75-year-olds 3 years post-baseline and showed that both nurse-supported and postal pedometer interventions continued to have higher physical activity levels compared to the control group (approximately an extra 28 and 24 minutes/week, respectively, of MVPA in bouts and an extra 670 and 630 steps/day, respectively). PACE-Lift results were very similar. In 60–75-year-olds followed up at 4 years post-baseline, the nurse-supported pedometer intervention group spent about 33 minutes/week more time in MVPA in bouts compared to the control group. What do these findings mean? These findings suggest that adult and older adult participants receiving 12-week pedometer-based walking interventions, provided either by post or with nurse support, are still doing more physical activity 3–4 years later. Pedometer interventions can help address the public health physical inactivity challenge.

The need to complete multiple tasks concurrently is a common occurrence both daily life and in occupational activities, which can often include simultaneous cognitive and physical demands. As one example, there is increasing availability of head-worn display technologies that can be employed when a user is mobile (e.g., while walking). This new method of information presentation may, however, introduce risks of adverse outcomes such as a decrement to gait performance. The goal of this study was thus to quantify the effects of a head-worn display (i.e., smart glasses) on motor variability during gait and to compare these effects with those of other common information displays (i.e., smartphone and paper-based system). Twenty participants completed four walking conditions, as a single task and in three dual-task conditions (three information displays). In the dual-task conditions, the information display was used to present several cognitive tasks. Three different measures were used to quantify variability in gait parameters for each walking condition (using the cycle-to-cycle standard deviation, sample entropy, and the “goal-equivalent manifold” approach). Our results indicated that participants used less adaptable gait strategies in dual-task walking using the paper-based system and smartphone conditions compared with single-task walking. Gait performance, however, was less affected during dual-task walking with the smart glasses. We conclude that the risk of an adverse gait event (e.g., a fall) in head-down walking conditions (i.e., the paper-based system and smartphone conditions) were higher than in single-task walking, and that head-worn displays might help reduce the risk of such events during dual-task gait conditions.

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.

Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper’s contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and typically get little training in paper writing. Focusing on how readers consume information, we present a set of 10 simple rules to help you get across the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.

Here we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.

In this months editorial, the PLOS Medicine Editors announce an upcoming Special Issue and call for papers, with Guest Editors Carol Brayne and Bruce Miller, on dementia across the lifespan and around the globe.

In this month’s editorial, the PLOS Medicine Editors announce an upcoming Special Issue, with Guest Editors Elaine Mardis and Marc Ladanyi, on actionable advances in research on the cancer genome.

Made available in DSpace on 2018-11-26T16:33:10Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-11 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) 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 mm(2), p = 0.0021), P. versicolor (body size corrected Van der Vech organ size of queens = 0.54 +/- 0.11, workers = 0.46 +/- 0.09 mm(2), 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 mm(2), 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. Univ Fed Vicosa, Dept Entomol, BR-36570000 Vicosa, MG, Brazil Univ Florence, Dipartimento Biol Evoluzionist Leo Pardi, Via Romana 17, I-50125 Florence, Italy Univ Fed Vicosa, Dept Biol Geral, BR-36570000 Vicosa, MG, Brazil Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Zool & Bot, BR-15054000 Sao Paulo, Brazil Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Zool & Bot, BR-15054000 Sao Paulo, Brazil CNPq: 143246/2011-9

Nicola Low and colleagues announce a call for research papers on sexually transmitted infections, to accompany a Collection on the topic.

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.

BackgroundThe objectives of the study were to develop web-based Spanish and Catalan versions of the KIDSCREEN, and to compare scores and psychometric properties with the paper version.MethodsInternet and paper Spanish and Catalan versions of the KIDSCREEN-52 were included in a cross-sectional study in school-age children. Web-based and paper Spanish or Catalan versions of the KIDSCREEN-52 were administered to students aged 8 to 18 years from primary and secondary schools in Palafolls (Barcelona, Spain, n = 923). All students completed both web-based and paper versions during school time with an interval of at least 2 hours between administrations. The order of administration was randomized. The KIDSCREEN-52, the Strengths and Difficulties Questionnaire (SDQ), and sociodemographic variables were collected. Missing values, floor and ceiling effects, and internal consistency were compared between both versions, as well as mean score differences, level of agreement, and known groups and construct validity.ResultsParticipation rate was 77% (n = 715). Web-based and paper versions showed low percentage of missing values and similar high ceiling effect (range 0 to 44%). Mean score differences showed an effect size (ES) lower than 0.2 in all dimensions. Internal consistency ranged from 0.7 to 0.88, and degree of agreement was excellent (Intraclass correlation coefficient [ICC] range 0.75 to 0.87). Expected differences were seen by sex, age, socioeconomic status and mental health status.ConclusionsThe web-based KIDSCREEN-52 showed similar scale score and reliability and validity than the paper version. It will incorporate the child population in the assessment of quality of life providing a more attractive format.

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.

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., SCOPUS: ar.j, info:eu-repo/semantics/published

Motivation The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes. Results We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget. Availability and implementation CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer. Supplementary information Supplementary data are available at Bioinformatics online.

IL-23 is a key cytokine in the pathogenesis of spondyloarthritides, including PsA and axial spondyloarthritis, as well as related conditions, such as psoriasis and IBD. Genetic associations, animal models and translational studies in humans demonstrate the key role played by IL-23, especially when coupled with downstream overexpression of IL-17 via stimulation of T helper 17 (Th17) and other cells by IL-23. Whereas IL-23 inhibition has shown clear-cut benefit in psoriasis and peripheral manifestations of PsA, trials of IL-23 inhibitors have failed in the treatment of ankylosing spondylitis. More recently, exploratory data from PsA patients with axial symptoms suggests that improvement may occur, but needs confirmation in dedicated axial spondyloarthritis (axSpA) trials. Hypotheses for these apparently conflicting findings about IL-23 inhibition in various forms of spondylitis are discussed.

Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.

Summary A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response.Treatment of plants of monocot rice and dicot tomato with nematode‐associated molecular patterns from different nematode species or bacterial pathogen‐associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5‐azacytidine.Whole‐genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA‐directed DNA methylation pathway and DECREASED DNA METHYLATION 1.We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root‐parasitic nematodes and is likely to be part of the basal pattern‐triggered immunity response in plants.

The mechanisms underlying interactions between diatoms and bacteria are crucial to understand diatom behaviour and proliferation, and can result in far‐reaching ecological consequences. Recently, 2‐alkyl‐4‐quinolones have been isolated from marine bacteria, both of which (the bacterium and isolated chemical) inhibited growth of microalgae, suggesting these compounds could mediate diatom–bacteria interactions. The effects of several quinolones on three diatom species have been investigated. The growth of all three was inhibited, with half‐maximal inhibitory concentrations reaching the sub‐micromolar range. By using multiple techniques, dual inhibition mechanisms were uncovered for 2‐heptyl‐4‐quinolone (HHQ) in Phaeodactylum tricornutum. Firstly, photosynthetic electron transport was obstructed, primarily through inhibition of the cytochrome b 6 f complex. Secondly, respiration was inhibited, leading to repression of ATP supply to plastids from mitochondria through organelle energy coupling. These data clearly show how HHQ could modulate diatom proliferation in marine environments., Double trouble: In the light, 2‐heptyl‐4‐quinolone (HHQ) primarily blocks photosynthetic electron flow at the cytochrome b 6 f complex in the diatom P. tricornutum. In darkness, HHQ inhibits mitochondrial respiration, resulting in a decreased ATP supply, which ultimately leads to a decreased electric field strength in the thylakoid membranes inside the chloroplast of diatoms.

Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. ATRT-SMARCA4 have been associated with a higher frequency of germline mutations, younger age, and an inferior prognosis in comparison to SMARCB1 mutated cases. Based on their DNA methylation profiles and transcriptomics, SMARCB1 mutated ATRTs have been divided into three distinct molecular subgroups: ATRT-TYR, ATRT-SHH, and ATRT-MYC. These subgroups differ in terms of age at diagnosis, tumor location, type of SMARCB1 alterations, and overall survival. ATRT-SMARCA4 are, however, less well understood, and it remains unknown, whether they belong to one of the described ATRT subgroups. Here, we examined 14 ATRT-SMARCA4 by global DNA methylation analyses. We show that they form a separate group segregating from SMARCB1 mutated ATRTs and from other SMARCA4-deficient tumors like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) or SMARCA4 mutated extra-cranial malignant rhabdoid tumors. In contrast, medulloblastoma (MB) samples with heterozygous SMARCA4 mutations do not group separately, but with established MB subgroups. RNA sequencing of ATRT-SMARCA4 confirmed the clustering results based on DNA methylation profiling and displayed an absence of typical signature genes upregulated in SMARCB1 deleted ATRT. In summary, our results suggest that, in line with previous clinical observations, ATRT-SMARCA4 should be regarded as a distinct molecular subgroup.

Here we have listed 36 human and yeast CENH3 interaction partners and their corn, rice, and Arabidopsis homologs that are potentially interacting with plant CENH3., The loading and maintenance of centromeric histone 3 (CENH3) at the centromere are critical processes ensuring appropriate kinetochore establishment and equivalent segregation of the homologous chromosomes during cell division. CENH3 loss of function is lethal, whereas mutations in the histone fold domain are tolerated and lead to chromosome instability and chromosome elimination in embryos derived from crosses with wild-type pollen. A wide range of proteins in yeast and animals have been reported to interact with CENH3. The histone fold domain-interacting proteins are potentially alternative targets for the engineering of haploid inducer lines, which may be important when CENH3 mutations are not well supported by a given crop. Here, we provide an overview of the corresponding plant orthologs or functional homologs of CENH3-interacting proteins. We also list putative CENH3 post-translational modifications that are also candidate targets for modulating chromosome stability and inheritance.

Use of genetically encoded fluorescent probes to monitor self-incompatibility (SI)-induced changes in pollen of the heterologous Arabidopsis ‘SI’ system has allowed multiparameter imaging and identified the involvement of clathrin-mediated endocytosis., Pollen tube growth is essential for plant reproduction. Their rapid extension using polarized tip growth provides an exciting system for studying this specialized type of growth. Self-incompatibility (SI) is a genetically controlled mechanism to prevent self-fertilization. Mechanistically, one of the best-studied SI systems is that of Papaver rhoeas (poppy). This utilizes two S-determinants: stigma-expressed PrsS and pollen-expressed PrpS. Interaction of cognate PrpS–PrsS triggers a signalling network, causing rapid growth arrest and programmed cell death (PCD) in incompatible pollen. We previously demonstrated that transgenic Arabidopsis thaliana pollen expressing PrpS–green fluorescent protein (GFP) can respond to Papaver PrsS with remarkably similar responses to those observed in incompatible Papaver pollen. Here we describe recent advances using these transgenic plants combined with genetically encoded fluorescent probes to monitor SI-induced cellular alterations, including cytosolic calcium, pH, the actin cytoskeleton, clathrin-mediated endocytosis (CME), and the vacuole. This approach has allowed us to study the SI response in depth, using multiparameter live-cell imaging approaches that were not possible in Papaver. This lays the foundations for new opportunities to elucidate key mechanisms involved in SI. Here we establish that CME is disrupted in self-incompatible pollen. Moreover, we reveal new detailed information about F-actin remodelling in pollen tubes after SI.

In recent years, the number of reported Human African Trypanosomiasis (HAT) cases caused by Trypanosoma brucei (T.b.) gambiense has been markedly declining, and the goal of ‘elimination as a public health problem’ is within reach. For the next stage, i.e. interruption of HAT transmission by 2030, intensive screening and surveillance will need to be maintained, but with tools and strategies more efficiently tailored to the very low prevalence. We assessed the sequential use of ELISA and Immune Trypanolysis (ITL) on dried blood spot (DBS) samples as an alternative to the traditional HAT field testing and confirmation approach. A cross-sectional study was conducted in HAT endemic and previously endemic zones in Kongo Central province, and a non-endemic zone in Haut Katanga province in the Democratic Republic of the Congo (DRC). Door-to-door visits were performed to collect dried blood spot (DBS) samples on filter paper. ELISA/T.b. gambiense was conducted followed by ITL for those testing positive by ELISA and in a subset of ELISA negatives. In total, 11,642 participants were enrolled. Of these, 11,535 DBS were collected and stored in appropriate condition for ELISA testing. Ninety-seven DBS samples tested positive on ELISA. In the endemic zone, ELISA positivity was 1.34% (95%CI: 1.04–1.64). In the previously endemic zone and non-endemic zone, ELISA positivity was 0.34% (95% CI: 0.13–0.55) and 0.37% (95% CI: 0.15–0.60) respectively. Among the ELISA positives, only two samples had a positive ITL result, both from the endemic zone. One of those was from a former HAT patient treated in 2008 and the other from an individual who unfortunately had deceased prior to the follow-up visit. Our study showed that a surveillance strategy, based on DBS samples and centralized testing with retracing of patients if needed, is feasible in DRC. ELISA seems well suited as initial test with a similar positivity rate as traditional screening tests, but ITL remains complex. Alternatives for the latter, also analyzable on DBS, should be further explored., Author summary Human African Trypanosomiasis (HAT), also known as sleeping sickness is a parasitic disease, transmitted by tsetse flies, that is usually fatal if untreated. The number of cases have been rapidly declining over the past years indicating that elimination of the disease as a public health problem is within reach. To achieve the next stage, i.e. interruption of HAT transmission by 2030, intensive screening and surveillance will need to be maintained, but with tools and strategies more efficiently tailored to the very low prevalence. In contrast to the traditional approach of sending laboratory expertise to the field, we assessed an alternative approach based on the collection of dried blood samples on filter paper that were tested in a regional laboratory. Samples were taken in endemic, previously endemic and non-endemic villages and tested by ELISA and Immune Trypanolysis. The ELISA positivity rates were similar to those of other screening techniques currently used and Immune Trypanolysis was highly specific. Hence for surveillance in HAT endemic areas, collecting dried blood samples followed by centralized testing could become an alternative to the current strategy of active screening by mobile teams with on the spot confirmation. It has also potential for post-elimination surveillance to monitor resurgence and for exploratory surveillance in historic foci. Though highly specific, Immune Trypanolysis remains too complex for use in intermediate level laboratories, to further expand this strategy an alternative second step test is required.

Background Reduced susceptibility of mosquito vectors to currently used insecticides hampers control interventions. Recently pyriproxyfen, an insect growth regulator has been demonstrated to effectively reduce the reproductive potential in vector mosquitoes. Methods Pyriproxyfen (PPF), in different concentrations (0.75%, 0.075%, 0.0075%, and 0.00075%) was applied on papers and Indian wild type Aedes aegypti female mosquitoes (N ≥ 20 for each treatment) were exposed onto it as per WHO guidelines, to study the reproductive disruption. PPF concentration on treated papers was quantitatively cross-determined using HPLC method. Reduction in fecundity, fertility and adult emergence in exposed female Ae. aegypti was determined. Abnormal development in ovary and eggs of exposed females was studied microscopically after different time intervals. Results Eggs laid, eggs hatched, pupae formed and adults emerged per female exposed in both before blood meal and after blood meal groups declined significantly from lowest to highest concentration of PPF (F ≥ 5.2; p < 0.02). Adult emergence inhibition in females exposed to PPF before and after blood meal groups ranged from 58.8% [OR = 0.18 (95% CI = 0.09–0.36)] to 79.2% [OR = 0.04 (95% CI = 0.02–0.10)] and 64.4% [OR = 0.12 (95% CI = 0.05–0.28)] to 77.1% [OR = 0.05 (95% CI = 0.02–0.14)] respectively in different concentrations. The probit model used suggested that FI50 (50% fertility inhibition) and EI50 (50% emergence inhibition) were 0.002% (p = 0.82) and 0.0001% (p = 0.99) for females exposed before blood meal, while 0.01% (p = 0.63) and, Author summary Development of resistance against insecticides has challenged mosquito control programmes globally and prompted the research of alternative options that can complement insecticides. An insect growth regulator, pyriproxyfen (PPF) usage against mosquitoes can effectively reduce the vector population. PPF mainly inhibits the metamorphosis of mosquito larvae into pupae and prevent the adult emergence, therefore it is generally applied in mosquito breeding habitats. PPF has been shown to exhibit delayed residual effect that may impair the reproductive capacity by affecting the survival, fecundity and fertility of adult mosquito exposed through tarsal contact. Presently, the effectiveness of different concentrations of PPF intended to be delivered through contact have been evaluated against dengue vector Ae. aegypti. Results suggested that very low PPF concentration treated surfaces drastically reduce the fecundity, fertility and adult emergence in mosquitoes. Study suggests that control interventions based on PPF-treated surfaces could provide an additional route to target mosquito vector control by overall population density reduction.

Background Control of cutaneous leishmaniasis by public health systems in the Americas relies on case identification and treatment. Point-of-care diagnostics that can be performed by health workers within or near affected communities could effectively bring the health system to the resource-limited sites providing early diagnosis and treatment, reducing morbidity and the burden of disease. Methodology/principal findings A cross-sectional study was undertaken to evaluate the diagnostic test performance of Isothermal Recombinase Polymerase Amplification (RPA) targeting Leishmania kinetoplast DNA, coupled with a lateral flow (LF) immunochromatographic strip, in a field setting and a laboratory reference center. Minimally invasive swab and FTA filter paper samples were obtained by community health workers and highly trained technicians from ulcerated lesions of > 2 weeks’ evolution from 118 patients’ ≥ 2 years of age in the municipality of Tumaco, Nariño. Extracted DNA was processed by RPA-LF at a reference center or in a primary health facility in the field. Evaluation was based on a composite “gold standard” that included microscopy, culture, biopsy and real-time polymerase chain reaction detection of Leishmania 18S rDNA. Standard of care routine diagnostic tests were explored as comparators. Sensitivity and specificity of RPA-LF in the reference lab scenario were 87% (95%CI 74–94) and 86% (95%CI 74–97), respectively. In the field scenario, the sensitivity was 75% (95%CI 65–84) and specificity 89% (95%CI 78–99). Positive likelihood ratios in both scenarios were higher than 6 while negative likelihood ratios ranged to 0.2–0.3 supporting the usefulness of RPA-LF to rule-in and potentially to rule-out infection. Conclusions/significance The low complexity requirements of RPA-LF combined with non-invasive sampling support the feasibility of its utilization by community health workers with the goal of strengthening the diagnostic capacity for cutaneous leishmaniasis in Colombia. Trial registration ClinicalTrials.gov NCT04500873., Author summary Limited access to diagnosis is a critical determinant of the “neglect” that defines the so-called Neglected Tropical Diseases (NTDs) including cutaneous leishmaniasis. Diagnostic tests that can be performed close to and involve the participation of the affected communities would improve access to treatment as well as diagnosis. Using non-invasive swab and filter paper samples obtained by Community Health Workers, we evaluated the diagnostic performance of an innovative and technically simple molecular test: Isothermal Recombinase Polymerase Amplification (RPA) to detect Leishmania DNA, coupled with a lateral flow (LF) strip to read the results with the naked eye. The RPA-LF test demonstrated high sensitivity and specificity and capacity to rule in or rule out a diagnosis of cutaneous leishmaniasis in both an endemic field setting and reference laboratory. The findings encourage the further optimization of the test format for Point-of-Care diagnosis by health personnel and rural health workers in endemic settings.

Background: Targeting of MDSCs is a major clinical challenge in the era of immunotherapy. Antibodies which deplete MDSCs in murine models can reactivate T cell responses. In humans such approaches have not developed due to difficulties in identifying targets amenable to clinical translation. Methods: RNA-sequencing of M-MDSCs and G-MDSCs from cancer patients was undertaken. Flow cytometry and immunohistochemistry of blood and tumours determined MDSC CD33 expression. MDSCs were treated with Gemtuzumab ozogamicin and internalisation kinetics, and cell death mechanisms determined by flow cytometry, confocal microscopy and electron microscopy. Effects on T cell proliferation and CAR-T cell anti-tumour cytotoxicity were identified in the presence of Gemtuzumab ozogamicin. Findings: RNA-sequencing of human M-MDSCs and G-MDSCs identified transcriptomic differences, but that CD33 is a common surface marker. Flow cytometry indicated CD33 expression is higher on M-MDSCs, and CD33+ MDSCs are found in the blood and tumours regardless of cancer subtype. Treatment of human MDSCs leads to Gemtuzumab ozogamicin internalisation, increased p-ATM, and cell death; restoring T cell proliferation. Anti-GD2-/mesothelin-/EGFRvIII-CAR-T cell activity is enhanced in combination with the anti-MDSC effects of Gemtuzumab ozogamicin. Interpretation: The study identifies that M-MDSCs and G-MDSCs are transcriptomically different but CD33 is a therapeutic target on peripheral and infiltrating MDSCs across cancer subtypes. The immunotoxin Gemtuzumab ozogamicin can deplete MDSCs providing a translational approach to reactivate T cell and CAR-T cell responses against multiple cancers. In the rare conditions of HLH/MAS gemtuzumab ozogamicin provides a novel anti-myeloid strategy. Fund: This work was supported by Cancer Research UK, CCLG, Treating Children with Cancer, and the alumni and donors to the University of Birmingham. (c) 2019 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Background and objectives: Several sources of haematopoietic stem cells have been used for static culture of megakaryocytes to produce platelets in vitro. This study compares and characterizes platelets produced in shear flow using precursor cells from either umbilical (UCB) or adult peripheral blood (PB). Materials and methods: The efficiency of platelet production of the cultured cells was studied after perfusion in custom-built von Willebrand factor-coated microfluidic flow chambers. Platelet receptor expression and morphology were investigated by flow cytometry and microscopy, respectively. Results: Proliferation of stem cells isolated out of UCB was significantly higher (P < 0 center dot 0001) compared to PB. Differentiation of these cells towards megakaryocytes was significantly lower from PB compared to UCB where the fraction of CD42b/CD41 double positive events was 44 +/- 9% versus 76 +/- 11%, respectively (P < 0 center dot 0001). However, in vitro platelet production under hydrodynamic conditions was more efficient with 7 center dot 4 platelet-like particles per input cell from PB compared to 4 center dot 2 from UCB (P = 0 center dot 02). The percentage of events positive for CD42b, CD41 and CD61 was comparable between both stem cell sources. The mean number of receptors per platelet from UCB and PB was similar to that on blood bank platelets with on average 28 000 CD42b, 57 000 CD61 and 5500 CD49b receptors. Microscopy revealed platelets appearing similar to blood bank platelets in morphology, size and actin cytoskeleton, alongside smaller fragments and source megakaryocytes. Conclusion: This characterization study suggests that platelets produced in vitro under flow either from UCB or from PB share receptor expression and morphology with donor platelets stored in the blood bank.

International audience; In cancer, infection and inflammation, the immune system's function can be dysregulated. Instead of fighting disease, immune cells may increase pathology and suppress host-protective immune responses. Myeloid cells show high plasticity and adapt to changing conditions and pathological challenges. Despite their relevance in disease pathophysiology, the identity, heterogeneity and biology of myeloid cells is still poorly understood. We will focus on phenotypical and functional markers of one of the key myeloid regulatory subtypes, the myeloid derived suppressor cells (MDSC), in humans, mice and non-human primates. Technical issues regarding the isolation of the cells from tissues and blood, timing and sample handling of MDSC will be detailed. Localization of MDSC in a tissue context is of crucial importance and immunohistochemistry approaches for this purpose are discussed. A minimal antibody panel for MDSC research is provided as part of the Mye-EUNITER COST action. Strategies for the identification of additional markers applying state of the art technologies such as mass cytometry will be highlighted. Such marker sets can be used to study MDSC phenotypes across tissues, diseases as well as species and will be crucial to accelerate MDSC research in health and disease.

In most low-resource settings, microscopy still is the standard method for diagnosis of cutaneous leishmaniasis, despite its limited sensitivity. In Ethiopia, the more sensitive molecular methods are not yet routinely used. This study compared five PCR methods with microscopy on two sample types collected from patients with a suspected lesion to advise on optimal diagnosis of Leishmania aethiopica. Between May and July 2018, skin scrapings (SS) and blood exudate from the lesion spotted on filter paper (dry blood spot, DBS) were collected for PCR from 111 patients of four zones in Southern Ethiopia. DNA and RNA were simultaneously extracted from both sample types. DNA was evaluated by a conventional PCR targeting ITS-1 and three probe-based real-time PCRs: one targeting the SSU 18S rRNA and two targeting the kDNA minicircle sequence (the ‘Mary kDNA PCR’ and a newly designed ‘LC kDNA PCR’ for improved L. aethiopica detection). RNAs were tested with a SYBR Green-based RT-PCR targeting spliced leader (SL) RNA. Giemsa-stained SS smears were examined by microscopy. Of the 111 SS, 100 were positive with at least two methods. Sensitivity of microscopy, ITS PCR, SSU PCR, Mary kDNA PCR, LC kDNA PCR and SL RNA PCR were respectively 52%, 22%, 64%, 99%, 100% and 94%. Microscopy-based parasite load correlated well with real-time PCR Ct-values. Despite suboptimal sample storage for RNA detection, the SL RNA PCR resulted in congruent results with low Ct-values. DBS collected from the same lesion showed lower PCR positivity rates compared to SS. The kDNA PCRs showed excellent performance for diagnosis of L. aethiopica on SS. Lower-cost SL RNA detection can be a complementary high-throughput tool. DBS can be used for PCR in case microscopy is negative, the SS sample can be sent to the referral health facility where kDNA PCR method is available., Author summary Cutaneous leishmaniasis is a neglected tropical disease and causing a public health problem in Ethiopia. Microscopy is still the standard method for detection of the parasite in Ethiopia, and also in many other low resource settings. A more sensitive method is needed for timely diagnosis and treatment. In this study, we compared five molecular methods on samples collected from patients with a skin lesion suspected of cutaneous leishmaniasis to advice on optimal diagnosis of L. aethiopica. We collected two sample types from the same lesion (skin scrapings and lesion fluid on filter paper) and isolated both DNA and RNA of them. Majority (90.1%) of the samples from skin scrapings were positive in two or more methods and the molecular methods had a higher sensitivity than the conventional methods. Interestingly, we evaluated for the first time a new molecular method designed to improve L. aethiopica detection. Also, we showed that RNA detection performed well for samples that were collected under difficult field conditions. Samples collected on filter paper showed less positive results than skin scraped samples, but could still be the method of choice for easy sampling and transport in resource-limited settings as it performed better than microscopy.