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3,172 results for “public”
Data from: Publication reform to safeguard wildlife from researcher harm
Despite abundant focus on responsible care of laboratory animals, we argue that inattention to the maltreatment of wildlife constitutes an ethical blind spot in contemporary animal research. We begin by reviewing significant shortcomings in legal and institutional oversight, arguing for the relatively rapid and transformational potential of editorial oversight at journals in preventing harm to vertebrates studied in the field and outside the direct supervision of institutions. Straightforward changes to animal care policies in journals, which our analysis of 206 journals suggests are either absent (34%), weak, incoherent, or neglected by researchers, could provide a practical, effective, and rapidly imposed safeguard against unnecessary suffering. The ARROW (Animal Research: Reporting on Wildlife) guidelines we propose here, coupled with strong enforcement, could result in significant changes to how animals involved in wildlife research are treated. The research process would also benefit. Sound science requires animal subjects to be physically, physiologically, and behaviorally unharmed. Accordingly, publication of methods that contravenes animal welfare principles risks perpetuating inhumane approaches and bad science.
Data from: The location of the citation: changing practices in how publications cite original data in the Dryad Digital Repository
While stakeholders in scholarly communication generally agree on the importance of data citation, there is not consensus on where those citations should be placed within the publication – particularly when the publication is citing original data. Recently, CrossRef and the Digital Curation Center (DCC) have recommended as a best practice that original data citations appear in the works cited sections of the article. In some fields, such as the life sciences, this contrasts with the common practice of only listing data identifier(s) within the article body (intratextually). We inquired whether data citation practice has been changing in light of the guidance from CrossRef and the DCC. We examined data citation practices from 2011 to 2014 in a corpus of 1,125 articles associated with original data in the Dryad Digital Repository. The percentage of articles that include no reference to the original data has declined each year, from 31% in 2011 to 15% in 2014. The percentage of articles that include data identifiers intratextually has grown from 69% to 83%, while the percentage that cite data in the works cited section has grown from 5% to 8%. If the proportions continue to grow at the current rate of 19-20% annually, the proportion of articles with data citations in the works cited section will not exceed 90% until 2030.
Data from: Public sharing of research datasets: a pilot study of associations
The public sharing of primary research datasets potentially benefits the research community but is not yet common practice. In this pilot study, we analyzed whether data sharing frequency was associated with funder and publisher requirements, journal impact factor, or investigator experience and impact. Across 397 recent biomedical microarray studies, we found investigators were more likely to publicly share their raw dataset when their study was published in a high-impact journal and when the first or last authors had high levels of career experience and impact. We estimate the USA's National Institutes of Health (NIH) data sharing policy applied to 19% of the studies in our cohort; being subject to the NIH data sharing plan requirement was not found to correlate with increased data sharing behavior in multivariate logistic regression analysis. Studies published in journals that required a database submission accession number as a condition of publication were more likely to share their data, but this trend was not statistically significant. These early results will inform our ongoing larger analysis, and hopefully contribute to the development of more effective data sharing initiatives. **Earlier version presented at ASIS&T and ISSI Pre-Conference: Symposium on Informetrics and Scientometrics 2009**
Data from: The assessment of science: the relative merits of post-publication review, the impact factor and the number of citations
Background: The assessment of scientific publications is an integral part of the scientific process. Here we investigate three methods of assessing the merit of a scientific paper: subjective post-publication peer review, the number of citations gained by a paper and the impact factor of the journal in which the article was published. Methodology/principle findings: We investigate these methods using two datasets in which subjective post-publication assessments of scientific publications have been made by experts. We find that there are moderate, but statistically significant, correlations between assessor scores, when two assessors have rated the same paper, and between assessor score and the number of citations a paper accrues. However, we show that assessor score depends strongly on the journal in which the paper is published, and that assessors tend to over-rate papers published in journals with high impact factors. If we control for this bias, we find that the correlation between assessor scores and between assessor score and the number of citations is weak, suggesting that scientists have little ability to judge either the intrinsic merit of a paper or its likely impact. We also show that the number of citations a paper receives is an extremely error-prone measure of scientific merit. Finally, we argue that the impact factor is likely to be a poor measure of merit, since it depends on subjective assessment. Conclusions: We conclude that the three measures of scientific merit considered here are poor; in particular subjective assessments are an error-prone, biased and expensive method by which to assess merit. We argue that the impact factor may be the most satisfactory of the methods we have considered, since it is a form of pre-publication review. However, we emphasise that it is likely to be a very error-prone measure of merit that is qualitative, not quantitative.
Pay It Forward: Partner Institution Publication Volume
<p>These datasets include aggregated and summarized data describing the publication output of Pay It Forward project partner institutions, as well as provide some data on the characteristics of journals and sources that project partner authors publish in. Data are aggregated and summarized from Web of Science and Scopus.</p>
Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants
Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results: We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions: The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.
Data from: In an age of open access to research policies: physician and public health NGO staff research use and policy awareness
Introduction: Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods: A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the point-of-care service UpToDate, for up to one year, with their usage monitored through the tracking of web-log data. The physicians also participated in a one-month trial of relatively complete or limited access. Results: The study found that participants' research interests were not satisfied by article abstracts alone nor, in the case of the physicians, by a clinical summary service such as UpToDate. On average, a third of the physicians viewed research a little more frequently than once a week, while two-thirds of the public health NGO staff viewed more than three articles a week. Those articles were published since the 2008 adoption of the NIH Public Access Policy, as well as prior to 2008 and during the maximum 12-month embargo period. A portion of the articles in each period was already open access, but complete access encouraged a viewing of more research articles. Conclusion: Those working in health fields will utilize more research in the course of their work as a result of (a) increasing open access to research, (b) improving awareness of and preparation for this access, and (c) adjusting public and open access policies to maximize the extent of potential access, through reduction in embargo periods and access to pre-policy literature.
Data from: Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa
Public goods cooperation is common in microbes, and there is much interest in understanding how such traits evolve. Research in recent years has identified several important factors that shape the evolutionary dynamics of such systems, yet few studies have investigated scenarios involving interactions between multiple public goods. Here we offer general predictions about the evolutionary trajectories of two public goods traits having positive, negative or neutral regulatory influence on one another's expression, and we report on a test of some of our predictions in the context of Pseudomonas aeruginosa's production of two interlinked iron-scavenging siderophores. First, we confirmed that both pyoverdine and pyochelin siderophores do operate as public goods under appropriate environmental conditions. We then tracked their production in lines experimentally evolved under different iron-limitation regimes known to favour different siderophore expression profiles. Under strong iron limitation, where pyoverdine represses pyochelin, we saw a decline in pyoverdine and a concomitant increase in pyochelin – consistent with expansion of pyoverdine-defective cheats derepressed for pyochelin. Under moderate iron limitation, pyochelin declined – again consistent with an expected cheat invasion scenario – but there was no concomitant shift in pyoverdine because cross-suppression between the traits is unidirectional only. Alternating exposure to strong and moderate iron-limitation caused qualitatively similar though lesser shifts compared to the constant-environment regimes. Our results confirm that the regulatory inter-connections between public goods traits can significantly modulate the course of evolution, yet also suggest how we can start to predict the impacts such complexities will have on phenotypic divergence and community stability.
Data from: Evolution of conditional cooperation in public good games
<p class="Standard">It is observed that in a repeated public good game with same individuals, free riding by a few individuals in the initial rounds triggers free riding by others in the subsequent rounds. It is presumed that individuals tend to imitate social behaviour of successful or relatively high payoff individuals, irrespective of how the payoffs were obtained. However, humans are concerned about how the payoffs were obtained, such as whether the payoffs were obtained by cheating or good behaviour. Individuals are willing to incur certain cost in order to improve group benefits and these individuals gain prestige. In human societies individuals tend to imitate social behaviour of high prestige agents. We propose that when agents are aware of other agents' payoffs scores and their prestige, perhaps agents are more likely to imitate social behaviour of high prestige and high payoff agents. We introduce, population level affinity parameters such as affinity towards payoff and affinity towards prestige of role models. We show that, for certain affinity parameters, high levels of cooperation are established in a population consisting of heterogeneous conditional co-operators, when agents imitate social behaviour of high prestige and high payoff agents. The proposed model provides insights into why value-based societies are more successful than competitive societies in establishing cooperation.</p>
Data from: Functional amyloids promote retention of public goods in bacteria
The growth and virulence of bacteria depends upon a number of factors that are secreted into the environment. These factors can diffuse away from the producing cells, to be either lost or utilized by cells that do not produce them (cheats). Mechanisms that act to reduce the loss of secreted factors through diffusion are expected to be favoured. One such mechanism may be the production of Fap fibrils, needle-like fibres on the cell surface observed in P.aeruginosa, which can transiently bind several secreted metabolites produced by cells. We test whether Fap fibrils help retain a secreted factor, the iron-scavenging molecule pyoverdine, and hence reduce the potential for exploitation by non-producing, cheating cells. We found that: (1) wildtype cells retain more iron-chelating metabolites than fibril non-producers; (2) purified Fap fibrils can prevent the loss of the iron-chelators PQS (Pseudomonas quinolone signal) and pyoverdine; and (3) pyoverdine non-producers have higher fitness in competition with fibril non-producers than with wildtype cells. Our results suggest that by limiting the loss of a costly public good, Fap fibrils may play an important role in stabilizing cooperative production of secreted factors.
Data from: Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies
Background: Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. Results: Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite's gene repertoire. Conclusion: Our study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies.
Data from: Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa
The production of beneficial public goods is common in the microbial world, and so is cheating – the exploitation of public goods by non-producing mutants. Here, we examine co-evolutionary dynamics between cooperators and cheats and ask whether cooperators can evolve strategies to reduce the burden of exploitation, and whether cheats in turn can improve their exploitation abilities. We evolved cooperators of the bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging siderophore pyoverdine, together with cheats, defective in pyoverdine production but proficient in uptake. We found that cooperators managed to co-exist with cheats in 56% of all replicates over approximately 150 generations of experimental evolution. Growth and competition assays revealed that co-existence was fostered by a combination of general adaptions to the media and specific adaptions to the co-evolving opponent. Phenotypic screening and whole-genome re-sequencing of evolved clones confirmed this pattern, and suggest that cooperators became less exploitable by cheats because they significantly reduced their pyoverdine investment. Cheats, meanwhile, improved exploitation efficiency through mutations blocking the costly pyoverdine-signalling pathway. Moreover, cooperators and cheats evolved reduced motility, a pattern that likely represents adaptation to laboratory conditions, but at the same time also affects social interactions by reducing strain mixing and pyoverdine sharing. Overall, we observed parallel evolution, where co-existence of cooperators and cheats was enabled by a combination of adaptations to the abiotic and social environment and their interactions.
Publicly archived datasets analyzed or generated during the study.
<p> Publicly archived datasets analyzed or generated during the study.</p>
Data from: Payoff-based learning explains the decline in cooperation in public goods games
Economic games such as the public goods game are increasingly being used to measure social behaviours in humans and non-human primates. The results of such games have been used to argue that people are pro-social, and that humans are uniquely altruistic, willingly sacrificing their own welfare in order to benefit others. However, an alternative explanation for the empirical observations is that individuals are mistaken, but learn, during the game, how to improve their personal payoff. We test between these competing hypotheses, by comparing the explanatory power of different behavioural rules, in public goods games, where individuals are given different amounts of information. We find: (i) that individual behaviour is best explained by a learning rule that is trying to maximize personal income; (ii) that conditional cooperation disappears when the consequences of cooperation are made clearer; and (iii) that social preferences, if they exist, are more anti-social than pro-social.
FIGURE 4 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 4. Title page of volume 4 of the Histoire Naturelle. Insectes. Laporte separate edition.
FIGURE 2 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 2. Timeline of production for all the dictionnaires of the EM.
Data from: Evolution of music by public choice
Music evolves as composers, performers, and consumers favor some musical variants over others. To investigate the role of consumer selection, we constructed a Darwinian music engine consisting of a population of short audio loops that sexually reproduce and mutate. This population evolved for 2,513 generations under the selective influence of 6,931 consumers who rated the loops' aesthetic qualities. We found that the loops quickly evolved into music attributable, in part, to the evolution of aesthetically pleasing chords and rhythms. Later, however, evolution slowed. Applying the Price equation, a general description of evolutionary processes, we found that this stasis was mostly attributable to a decrease in the fidelity of transmission. Our experiment shows how cultural dynamics can be explained in terms of competing evolutionary forces. The audio files attached below can also be heard at .
Industrial relations in central public administration: recent trends and features
<p>This report maps current developments in industrial relations systems in the central public administration secrtor across the Member States, covering all EU Member States except Croatia, which joined the EU in mid-2013. The report explores to what extent there is formal industrial relations processes within the sector, including the organisation of unions and employer representatives, and the role of collective bargaining and consultation. It also examines the specific features of the sector in terms of both industrial relations processes and worker outcomes and charts reforms that have been carried out since 2008: changes in collective bargaining and in the balance of negotiation versus unilateral imposition of change by the employer, and the responses of trade unions. Finally, the report addresses the role of the social partners regarding the outcomes for employees of the recent austerity measures on issues such as wages, job security, working time and pensions.</p> <p>[Google](http://www.google.com)<br /> <br /> http://www.eurofound.europa.eu/eiro/studies/tn1307019s/index.htm </p>
Materials for Publication: Software Feature Request Detection in Issue Tracking Systems
<p>Additional figures, tables, experimant data, code, and results.</p> <p>See README.md for more information.</p>
kamermanpr/Resilience.HIVPain: Publication release - update
<p>Updated publication release (v0.2.0) to include bibliometric information.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.