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The primate brain has unique anatomical characteristics, which translate into advanced cognitive, sensory, and motor abilities. Thus, it is important that we gain insight on its structure to provide a solid basis for models that will clarify function. Here, we report on the implementation and features of the Brain/MINDS Marmoset Connectivity Resource (BMCR), a new open-access platform that provides access to high-resolution anterograde neuronal tracer data in the marmoset brain, integrated to retrograde tracer and tractography data. Unlike other existing image explorers, the BMCR allows visualization of data from different individuals and modalities in a common reference space. This feature, allied to an unprecedented high resolution, enables analyses of features such as reciprocity, directionality, and spatial segregation of connections. The present release of the BMCR focuses on the prefrontal cortex (PFC), a uniquely developed region of the primate brain that is linked to advanced cognition, including the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset. Moreover, the inclusion of tractography data from diffusion MRI allows systematic analyses of this noninvasive modality against gold-standard cellular connectivity data, enabling detection of false positives and negatives, which provide a basis for future development of tractography. This paper introduces the BMCR image preprocessing pipeline and resources, which include new tools for exploring and reviewing the data. This study presents the Brain/MINDS Marmoset Connectivity Resource, which allows the unique visualization of high-resolution marmoset brain data from multiple individuals and modalities in a common reference space, enabling in-depth analyses of connectivity patterns such as reciprocity, directionality and spatial segregation. [ABSTRACT FROM AUTHOR]

In this article the author discusses the dependability of researchers on the integrity of traditional prepublication review process that is the most relevant means in science communication. The author worries on the increase number of journals that researchers have to read. Also discussed is the article-level metrics which only chooses a set of articles to read.

Teaching -- and testing -- students creatively is a challenge, but new public databases and more accessible literature are now helping to develop the critical thinking skills of students. [ABSTRACT FROM AUTHOR]

While the malaria parasite Plasmodium falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor (approximately 10,000 to 50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red blood cell–infecting merozoites (merozoite surface proteins (MSPs)) possess exactly 2 deeply diverged lineages that have seemingly not recombined. While of considerable interest, the evolutionary origin of this phenomenon remains unknown. In this study, we analysed the genetic diversity of 2 of the most variable MSPs, DBLMSP and DBLMSP2, which are paralogs (descended from an ancestral duplication). Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to characterise as reads containing highly diverged alleles completely fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness. Using our newly- resolved sequences, we found that both genes exhibit 2 deeply diverged lineages in a specific protein domain (DBL) and that one of the 2 lineages is shared across the genes. We identified clear evidence of nonallelic gene conversion between the 2 genes as the likely mechanism behind sharing, leading us to propose that gene conversion between diverged paralogs, and not recombination suppression, can generate this surprising genealogy; a model that is furthermore consistent with high diversity levels in these 2 genes despite the strong historical P. falciparum transmission bottleneck. Merozoite surface proteins expressed by the malaria parasite Plasmodium falciparum on the surface of human red-blood-cell-infecting merozoites possess exactly two deeply-diverged lineages that have seemingly not recombined. The evolutionary origin of this phenomenon remains unknown but genomic analysis of DBLMSP and DBLMSP2 reveals the answer to this long-standing puzzle. [ABSTRACT FROM AUTHOR]

Biodiversity appears to strongly suppress pathogens and pests in many plant and animal systems. However, this "dilution effect" is not consistently detected, and when present can vary strikingly in magnitude. Here, we use forest inventory data from over 25,000 plots (>1.1 million sampled trees) to quantify the strength of the dilution effect on dozens of forest pests and clarify why some pests are particularly sensitive to biodiversity. Using Bayesian hierarchical models, we show that pest prevalence is frequently lower in highly diverse forests, but there is considerable variability in the magnitude of this dilution effect among pests. The strength of dilution was not closely associated with host specialization or pest nativity. Instead, pest prevalence was lower in forests where co-occurring tree species were more distantly related to a pest's preferred hosts. Our analyses indicate that host evolutionary history and forest composition are key to understanding how species diversity may dilute the impacts of tree pests, with important implications for predicting how future biodiversity change may affect the spread and distribution of damaging forest pests. Biodiversity appears to strongly suppress pathogens and pests in many plant and animal systems, but this 'dilution effect' can vary strikingly in magnitude. This study uses forest inventory data from over 25,000 plots to show that the prevalence of tree pests is jointly controlled by the diversity and phylogenetic composition of forests. [ABSTRACT FROM AUTHOR]

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. This Consensus View issues a call to action to accelerate the growing momentum of preprint sharing and provides recommendations to empower researchers to provide open and constructive peer review for preprints. [ABSTRACT FROM AUTHOR]

Mosquitoes of the Culex pipiens complex are worldwide vectors of arbovirus, filarial nematodes, and avian malaria agents. In these hosts, the endosymbiotic bacteria Wolbachia induce cytoplasmic incompatibility (CI), i.e., reduced embryo viability in so-called incompatible crosses. Wolbachia infecting Culex pipiens (wPip) cause CI patterns of unparalleled complexity, associated with the amplification and diversification of cidA and cidB genes, with up to 6 different gene copies described in a single wPip genome. In wPip, CI is thought to function as a toxin-antidote (TA) system where compatibility relies on having the right antidotes (CidA) in the female to bind and neutralize the male's toxins (CidB). By repeating crosses between Culex isofemale lines over a 17 years period, we documented the emergence of a new compatibility type in real time and linked it to a change in cid genes genotype. We showed that loss of specific cidA gene copies in some wPip genomes results in a loss of compatibility. More precisely, we found that this lost antidote had an original sequence at its binding interface, corresponding to the original sequence at the toxin's binding interface. We showed that these original cid variants are recombinant, supporting a role for recombination rather than point mutations in rapid CI evolution. These results strongly support the TA model in natura, adding to all previous data acquired with transgenes expression. Long-term maintenance of Culex mosquito laboratory lines allowed this study to witness the emergence of novel cytoplasmic incompatibility patterns, showing that they arose from rapid evolution of Wolbachia genomes through gene loss and recombination. [ABSTRACT FROM AUTHOR]

Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that—while beneficial to the group—decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields. Some traditional breeding approaches select for "selfish" traits that can reduce yield in high-density monocultures. This paper proposes a simple method to identify plant genotypes that express more cooperative versus more competitive traits, based on how they grow in different social environments, and applies this method to a genetic study with Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Meta-research, or the science of science, is a powerful technique that scientists can use to improve science, however most scientists are unaware that meta-research exists and courses are rare. This initiative demonstrates the feasibility of a participant-guided "learn by doing" approach, in which a multidisciplinary, global team of early career researchers learned meta-research skills by working together to design, conduct and publish a meta-research study. This Community Page article describes a participant-guided "learn by doing" initiative, in which a multidisciplinary, global team of early career researchers learned meta-research skills by working together to design, conduct and publish a meta-research (science of science) study. Participants can now apply these skills to solve problems in their own fields. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has motivated many open and collaborative analytical research projects with real-world impact. However, despite their value, such activities are generally overlooked by traditional academic metrics. Science is ultimately improved by analytical work, whether ensuring reproducible and well-documented code to accompany papers, developing and maintaining flexible tools, sharing and curating data, or disseminating analysis to wider audiences. To increase the impact and sustainability of modern science, it will be crucial to ensure these analytical activities—and the people who do them—are valued in academia. [ABSTRACT FROM AUTHOR]

The article presents an essay titled "Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word," by Janis Antonovics. It is noted that the increase in resistance of human pathogens to antimicrobial agents is one of the best-documented examples of evolution in action for it directed life-and-death consequences. In this essay, the word evolution is searched by the author through scientific journals published since 2000 for papers dealing with antimicrobial resistance.

: It is unlikely that there is any single objective measure of merit, so research assessment therefore requires new multivariate metrics that reflect the context of research, regardless of discipline. [ABSTRACT FROM AUTHOR]

Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies. Extinct and unknown species are overlooked in evolutionary studies of gene flow. This paper shows that taking such "ghost lineages" into account changes the conclusions of several studies on this subject. [ABSTRACT FROM AUTHOR]

Characterization of circadian systems at the organism level—a top-down approach—has led to definition of unifying properties, a hallmark of the science of chronobiology. The next challenge is to use a bottom-up approach to show how the molecular workings of the cellular circadian clock work as building blocks of those properties. We review new studies, including a recently published PLOS Biology paper by Nikhil and colleagues, that show how programmed but also stochastic generation of variation in cellular circadian period explain important adaptive features of entrained circadian phase. A recent PLOS Biology paper shows that clonal cell populations are themselves a collection heterogeneous cellular circadian clocks; this Primer explores the implications, proposing that the phase of entrainment of biological clocks (to time of day or to season) is granular, built from the contributions of individual cells. [ABSTRACT FROM AUTHOR]

Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a paper's social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each user's followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from nonspecialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints appear to intentionally espouse any right-wing extremist messages, cases exist in which extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing the public discourse surrounding scientific research. Analysis of Twitter data for 1,800 bioRxiv preprints to classify the online communities engaging with biological research enables the tracing of each preprint's exposure to various academic disciplines and non-specialist audiences, potentially indicating downstream scientific and societal impacts, and revealing that some preprints receive extraordinarily high engagement from white nationalist communities. [ABSTRACT FROM AUTHOR]

Many herbivorous insects are mono- or oligophagous, having evolved to select a limited range of host plants. They specifically identify host-plant leaves using their keen sense of taste. Plant secondary metabolites and sugars are thought to be key chemical cues that enable insects to identify host plants and evaluate their quality as food. However, the neuronal and behavioral mechanisms of host-plant recognition are poorly understood. Here, we report a two-factor host acceptance system in larvae of the silkworm Bombyx mori, a specialist on several mulberry species. The first step is controlled by a chemosensory organ, the maxillary palp (MP). During palpation at the leaf edge, the MP detects trace amounts of leaf-surface compounds, which enables host-plant recognition without biting. Chemosensory neurons in the MP are tuned with ultrahigh sensitivity (thresholds of attomolar to femtomolar) to chlorogenic acid (CGA), quercetin glycosides, and β-sitosterol (βsito). Only if these 3 compounds are detected does the larva make a test bite, which is evaluated in the second step. Low-sensitivity neurons in another chemosensory organ, the maxillary galea (MG), mainly detect sucrose in the leaf sap exuded by test biting, allowing larvae to accept the leaf and proceed to persistent biting (feeding). The two-factor host acceptance system reported here may commonly underlie stereotyped feeding behavior in many phytophagous insects and determine their feeding habits. Silkworm larvae are well known for their preference for mulberry leaves; this study shows that they choose their food by using a two-factor host acceptance system, deploying two different organs and sets of chemosensory neurons with differing sensitivities operating sequentially in time. [ABSTRACT FROM AUTHOR]

Qualitative assessments of researchers are resource-intensive, untenable in nonmeritocratic settings, and error-prone. Although often derided, quantitative metrics could help improve research practices if they are rigorous, field-adjusted, and centralized. Using quantitative metrics to assess researchers is often seen as a poor choice compared with using qualitative assessments. In this Perspective, the authors argue in favor of using rigorous, field-adjusted, centralized, quantitative metrics in a bid to help improve research practices as a low-cost public good. [ABSTRACT FROM AUTHOR]

Uniformly accessible DNA sequences are needed to improve experimental reproducibility and automation. Rather than descriptions of how engineered DNA is assembled, publishers should require complete and empirically validated sequences. Describing how DNA constructs were assembled is no longer necessary when it is possible to fully sequence the final results to validate them. In this Perspective, the authors suggest that outdated methods narratives should be replaced with DNA sequence files when publishing life sciences research. [ABSTRACT FROM AUTHOR]

Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron–sulfur ([Fe–S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution. The symbioses that gave rise to primary organelles are key events in the origin of Eukaryotes. This study uses a dataset of markers belonging to two conserved machineries responsible for [Fe-S] cluster biogenesis to support an early emergence of mitochondria and plastids within Alphaproteobacteria and Cyanobacteria, respectively. [ABSTRACT FROM AUTHOR]

As the UN International Day for Biological Diversity enters its twentieth year, we take stock of recent developments and trends in biodiversity research and renew the call to build a better shared future for all life. [ABSTRACT FROM AUTHOR]

Methods sections are often missing essential details. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included giving credit or specifying what was used (who or what citation) and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors', and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.

We have empirically assessed the distribution of published effect sizes and estimated power by analyzing 26,841 statistical records from 3,801 cognitive neuroscience and psychology papers published recently. The reported median effect size was D = 0.93 (interquartile range: 0.64–1.46) for nominally statistically significant results and D = 0.24 (0.11–0.42) for nonsignificant results. Median power to detect small, medium, and large effects was 0.12, 0.44, and 0.73, reflecting no improvement through the past half-century. This is so because sample sizes have remained small. Assuming similar true effect sizes in both disciplines, power was lower in cognitive neuroscience than in psychology. Journal impact factors negatively correlated with power. Assuming a realistic range of prior probabilities for null hypotheses, false report probability is likely to exceed 50% for the whole literature. In light of our findings, the recently reported low replication success in psychology is realistic, and worse performance may be expected for cognitive neuroscience. [ABSTRACT FROM AUTHOR]

In a new paper published in PLOS Biology, Dudin and colleagues evolve simple multicellularity in Sphaeroforma arctica, a unicellular relative of animals. This work establishes a new and open-ended avenue for examining the evolution of multicellularity in an important but understudied group of organisms. This Primer explores the implications of a new PLOS Biology study in which the authors evolve simple multicellularity in Sphaeroforma arctica, a unicellular relative of animals; this work establishes a new and open-ended avenue for examining the evolution of multicellularity at the base of the metazoa. [ABSTRACT FROM AUTHOR]

Ocean acidification—decreasing oceanic pH resulting from the uptake of excess atmospheric CO2—has the potential to affect marine life in the future. Among the possible consequences, a series of studies on coral reef fish suggested that the direct effects of acidification on fish behavior may be extreme and have broad ecological ramifications. Recent studies documenting a lack of effect of experimental ocean acidification on fish behavior, however, call this prediction into question. Indeed, the phenomenon of decreasing effect sizes over time is not uncommon and is typically referred to as the "decline effect." Here, we explore the consistency and robustness of scientific evidence over the past decade regarding direct effects of ocean acidification on fish behavior. Using a systematic review and meta-analysis of 91 studies empirically testing effects of ocean acidification on fish behavior, we provide quantitative evidence that the research to date on this topic is characterized by a decline effect, where large effects in initial studies have all but disappeared in subsequent studies over a decade. The decline effect in this field cannot be explained by 3 likely biological explanations, including increasing proportions of studies examining (1) cold-water species; (2) nonolfactory-associated behaviors; and (3) nonlarval life stages. Furthermore, the vast majority of studies with large effect sizes in this field tend to be characterized by low sample sizes, yet are published in high-impact journals and have a disproportionate influence on the field in terms of citations. We contend that ocean acidification has a negligible direct impact on fish behavior, and we advocate for improved approaches to minimize the potential for a decline effect in future avenues of research. [ABSTRACT FROM AUTHOR]

The United States National Institutes of Health (NIH) imposed a public access policy on all publications for which the research was supported by their grants; the policy was drafted in 2004 and took effect in 2008. The policy is now 11 years old, yet no analysis has been presented to assess whether in fact this largest-scale US-based public access policy affected the vitality of the scholarly publishing enterprise, as manifested in changed mortality or natality rates of biomedical journals. We show here that implementation of the NIH policy was associated with slightly elevated mortality rates and mildly depressed natality rates of biomedical journals, but that birth rates so exceeded death rates that numbers of biomedical journals continued to rise, even in the face of the implementation of such a sweeping public access policy. This Perspective article analyzes whether the US National Institutes of Health open access policy, which from 2008 forced open access on thousands of papers, had a detectable effect on the "demography" of biomedical journals. [ABSTRACT FROM AUTHOR]

The Internet is rapidly changing the way the results of academic research are communicated within communities and with the wider public. In a push to accelerate change and make the results of research immediately and freely available online for all to read and use, the European Commission, with support from a group of high-profile funders, has proposed a plan to influence the way academic research is published. Here, we discuss the likely impact of this plan on the publishing landscape, the potential benefits, and some possible unintended consequences. [ABSTRACT FROM AUTHOR]

AccessLabs are workshops with two simultaneous motivations, achieved through direct citizen-scientist pairings: (1) to decentralise research skills so that a broader range of people are able to access/use scientific research, and (2) to expose science researchers to the difficulties of using their research as an outsider, creating new open access advocates. Five trial AccessLabs have taken place for policy makers, media/journalists, marine sector participants, community groups, and artists. The act of pairing science academics with local community members helps build understanding and trust between groups at a time when this relationship appears to be under increasing threat from different political and economic currents in society. Here, we outline the workshop motivations, format, and evaluation, with the aim that others can build on the methods developed. [ABSTRACT FROM AUTHOR]

Annotated primary scientific literature is a teaching and learning resource that provides scaffolding for undergraduate students acculturating to the authentic scientific practice of obtaining and evaluating information through the medium of primary scientific literature. Utilizing annotated primary scientific literature as an integrated pedagogical tool could enable more widespread use of primary scientific literature in undergraduate science classrooms with minimal disruption to existing syllabi. Research is ongoing to determine an optimal implementation protocol, with these preliminary iterations presented here serving as a first look at how students respond to annotated primary scientific literature. The undergraduate biology student participants in our study did not, in general, have an abundance of experience reading primary scientific literature; however, they found the annotations useful, especially for vocabulary and graph interpretation. We present here an implementation protocol for using annotated primary literature in the classroom that minimizes the use of valuable classroom time and requires no additional pedagogical training for instructors. [ABSTRACT FROM AUTHOR]

The author reflects on success of the journal, as well as the journal's five-year anniversary. She mentions that the journal's success relies on two features, which are trust and innovation. She also talks about the journal's responsibilities in peer review and challenges, particularly when the publication reaches the public domain.

Humans are altering biological systems at unprecedented rates, and these alterations often have longer-term evolutionary impacts. Most obvious is the spread of resistance to pesticides and antibiotics. There are a wide variety of management strategies available to slow this evolution, and there are many reasons for using them. In this paper, we focus on the economic aspects of evolution management and ask: When is it economically beneficial for an individual decision-maker to invest in evolution management? We derive a simple dimensionless inequality showing that it is cost-effective to manage evolution when the percentage increase in the effective life span of the biological resource that management generates is larger than the percentage increase in annual profit that could be obtained by not managing evolution. We show how this inequality can be used to determine optimal investment choices for single decision-makers, to determine Nash equilibrium investment choices for multiple interacting decision-makers, and to examine how these equilibrium choices respond to regulatory interventions aimed at stimulating investment in evolution management. Our results are illustrated with examples involving Bacillus thuringiensis (Bt) crops and antibiotic use in fish farming. Humans are altering biological systems at unprecedented rates and these alterations often have longer-term evolutionary impacts, such as the spread of resistance to pesticides and antibiotics. In this study, a simple mathematical criterion is derived determining when it is economically beneficial to invest in strategies for controlling and managing evolutionary change. [ABSTRACT FROM AUTHOR]

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest. In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased. Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature. [ABSTRACT FROM AUTHOR]

Figures in scientific publications are critically important because they often show the data supporting key findings. Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics. We recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies. Investigators can quickly make univariate scatterplots for small sample size studies using our Excel templates. [ABSTRACT FROM AUTHOR]

Over the last three decades, evidence has emerged that low-intensity magnetic fields can influence biological systems. It is now well established that migratory birds have the capacity to detect the Earth's magnetic field; it has been reported that power lines are associated with childhood leukemia and that pulsed magnetic fields increase the production of reactive oxidative species (ROS) in cellular systems. Justifiably, studies in this field have been viewed with skepticism, as the underlying molecular mechanisms are unknown. In the accompanying paper, Sherrard and colleagues report that low-flux pulsed electromagnetic fields (PEMFs) result in aversive behavior in Drosophila larvae and ROS production in cell culture. They further report that these responses require the presence of cryptochrome, a putative magnetoreceptor. If correct, it is conceivable that carcinogenesis associated with power lines, PEMF-induced ROS generation, and animal magnetoreception share a common mechanistic basis. [ABSTRACT FROM AUTHOR]

Assessment of researchers is necessary for decisions of hiring, promotion, and tenure. A burgeoning number of scientific leaders believe the current system of faculty incentives and rewards is misaligned with the needs of society and disconnected from the evidence about the causes of the reproducibility crisis and suboptimal quality of the scientific publication record. To address this issue, particularly for the clinical and life sciences, we convened a 22-member expert panel workshop in Washington, DC, in January 2017. Twenty-two academic leaders, funders, and scientists participated in the meeting. As background for the meeting, we completed a selective literature review of 22 key documents critiquing the current incentive system. From each document, we extracted how the authors perceived the problems of assessing science and scientists, the unintended consequences of maintaining the status quo for assessing scientists, and details of their proposed solutions. The resulting table was used as a seed for participant discussion. This resulted in six principles for assessing scientists and associated research and policy implications. We hope the content of this paper will serve as a basis for establishing best practices and redesigning the current approaches to assessing scientists by the many players involved in that process. [ABSTRACT FROM AUTHOR]

In Europe, responsible research and innovation (RRI) has emerged as a science policy measure that demands the early integration of a broad range of social actors and perspectives into research and development (R&D). More collaboration of the social sciences and humanities (SSH) with science and engineering appears within this policy framework as a crucial element that will enable better technological development. However, RRI is new to both natural scientists and SSH scholars, and interdisciplinary collaborations are challenging for many reasons. In this paper, we discuss these challenges while suggesting that what RRI can be in a particular project is not a given but remains an empirical question. Natural scientists and SSH scholars need to coresearch RRI in an experimental mode. [ABSTRACT FROM AUTHOR]

Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation. This paper presents IVEN (Internal Versus External Neighbourhood), a new user-interactive tool for the quantitative description of cell environment and organismal architecture, and uses it to reveal how changes in embryo architecture relate to changes in cell neighbourhood, identifying nuanced effects of FGF treatment on embryo morphology. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented about the submission of DNA sequences to the joint databases of GenBank, EMBL, and the DNA Databank of Japan.

The widespread use of plastic packaging for storing, transporting, and conveniently preparing or serving foodstuffs is significantly contributing to the global plastic pollution crisis. This has led to many efforts directed toward amending plastic packaging's end of life, such as recycling, or alternative material approaches, like increasingly using paper for food packaging. But these approaches often neglect the critical issue of chemical migration: When contacting foodstuffs, chemicals that are present in packaging transfer into food and thus unwittingly become part of the human diet. Hazardous chemicals, such as endocrine disrupters, carcinogens, or substances that bioaccumulate, are collectively referred to as "chemicals of concern." They can transfer from plastic packaging into food, together with other unknown or toxicologically uncharacterized chemicals. This chemical transfer is scientifically undisputed and makes plastic packaging a known, and avoidable, source of human exposure to synthetic, hazardous, and untested chemicals. Here, I discuss this issue and highlight aspects in need of improvement, namely the way that chemicals present in food packaging are assessed for toxicity. Further, I provide an outlook on how chemical contamination from food packaging could be addressed in the future. Robust innovations must attempt systemic change and tackle the issue of plastic pollution and chemical migration in a way that integrates all existing knowledge. The widespread use of plastic packaging for storing, transporting, and conveniently preparing or serving foodstuffs is significantly contributing to the global plastic pollution crisis. This Essay exhorts us to change the conversation about plastic packaging and address the chemicals that migrate into food. [ABSTRACT FROM AUTHOR]

The transition from mitosis into the first gap phase of the cell cycle in budding yeast is controlled by the Mitotic Exit Network (MEN). The network interprets spatiotemporal cues about the progression of mitosis and ensures that release of Cdc14 phosphatase occurs only after completion of key mitotic events. The MEN has been studied intensively; however, a unified understanding of how localisation and protein activity function together as a system is lacking. In this paper, we present a compartmental, logical model of the MEN that is capable of representing spatial aspects of regulation in parallel to control of enzymatic activity. We show that our model is capable of correctly predicting the phenotype of the majority of mutants we tested, including mutants that cause proteins to mislocalise. We use a continuous time implementation of the model to demonstrate that Cdc14 Early Anaphase Release (FEAR) ensures robust timing of anaphase, and we verify our findings in living cells. Furthermore, we show that our model can represent measured cell–cell variation in Spindle Position Checkpoint (SPoC) mutants. This work suggests a general approach to incorporate spatial effects into logical models. We anticipate that the model itself will be an important resource to experimental researchers, providing a rigorous platform to test hypotheses about regulation of mitotic exit. This study presents a logical compartmental model of the yeast mitotic exit network (MEN) that represents spatial aspects of regulation. The model correctly predicts the majority of published MEN phenotypes and reveals both the role of the Cdc14 early anaphase release and a link between mitosis length and checkpoint competence. [ABSTRACT FROM AUTHOR]

Human perturbation of natural systems is accelerating the emergence of infectious diseases, mandating integration of disease and ecological research. Bats have been associated with recent zoonoses, but our bibliometric analysis of coauthor relationships identified a separation of bat ecologists and infectious disease researchers with few cross-disciplinary relationships. Of 5,645 papers, true interdisciplinary collaborations occurred primarily in research focused on White Nose Syndrome (WNS). This finding is important because it illustrates how research with outcomes favoring both bat conservation and disease mitigation promotes domain integration and network connectivity. We advocate for increased engagement between ecology and infectious researchers to address such common causes and suggest that efforts focus on leveraging existing activities, building interdisciplinary projects, and networking individuals and networks to integrate domains and coordinate resources. We provide specific opportunities for pursuing these strategies through the Bat One Health Research Network (BOHRN). Limited collaboration between bat ecologists and disease researchers has precluded integrative research on disease emergence. These historical silos are now challenged by the emergence of SARS-CoV-2, which threatens both human and bat health. This Perspective article maintains that interdisciplinary research can be accelerated when disparate domains address common, foundational causes. [ABSTRACT FROM AUTHOR]

The article discusses the contribution of chemist Rosalind E. Franklin in the discovery of double helix and highlights the changes and developments in the research practices and genomic collaborations as of 2016. Topics discussed include the rise of coauthorship in scientific papers, the underrepresentation of women in terms of authorship and the differences between the propensity of men and women to collaborate in research.

Why do adult mammalian central nervous system axons not regenerate, when peripheral axons do? Two studies in PLOS Biology point to the role of 2 related ribosomal S6 kinase family members in the differences in regeneration capacity between central and peripheral axons. Why do adult mammalian central nervous system axons not regenerate? This Primer explores two recent PLOS Biology manuscripts that have revealed a role for two related ribosomal S6 kinases, RSK1 and RSK2, in the regenerative capacity of the mammalian central and peripheral nervous systems. [ABSTRACT FROM AUTHOR]

While heritable symbionts are common in insects, strains that act as male-killers are considered rare. A new study in PLOS Biology identifies a novel male-killer hidden by coinfection and host resistance, highlighting the complexity of host-microbial interactions in natural systems. While heritable symbionts are common in insects, strains that act as male-killers are considered rare. This Primer explores a new study in PLOS Biology which reveals a novel male-killer hidden by co-infection and host resistance, highlighting the complexity of host-microbial interactions in natural systems. [ABSTRACT FROM AUTHOR]

The article discusses how genes contribute to one's unique abilities, could it be cognitive or physical that differentiate them from apes. These genes that are fixed within one's lineage are those that make her up as a human. Due to recent advances in genomic sequencing and analysis, many papers had come out depending on many dimensions including detecting selection, single-gene studies and genome-wide analysis.

Access to analytical code is essential for transparent and reproducible research. We review the state of code availability in ecology using a random sample of 346 nonmolecular articles published between 2015 and 2019 under mandatory or encouraged code-sharing policies. Our results call for urgent action to increase code availability: only 27% of eligible articles were accompanied by code. In contrast, data were available for 79% of eligible articles, highlighting that code availability is an important limiting factor for computational reproducibility in ecology. Although the percentage of ecological journals with mandatory or encouraged code-sharing policies has increased considerably, from 15% in 2015 to 75% in 2020, our results show that code-sharing policies are not adhered to by most authors. We hope these results will encourage journals, institutions, funding agencies, and researchers to address this alarming situation. Publication of the analytical code underlying a scientific study is increasingly expected or even mandated by journals, allowing others to reproduce the results. However, a survey of more than 300 recently published ecology papers finds the majority have no code publicly available, handicapping efforts to improve scientific transparency. [ABSTRACT FROM AUTHOR]

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. Despite widespread endorsement by the scientific community, the impact of ARRIVE on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This explanation and elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature. This document also covers advice and best practice in the design and conduct of animal studies to support researchers in improving standards from the start of the experimental design process through to publication. The NC3Rs developed the ARRIVE guidelines in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. This article explains the rationale behind each item in the revised and updated ARRIVE guidelines 2019, clarifying key concepts and providing illustrative examples. [ABSTRACT FROM AUTHOR]

With exciting new NASA plans for a sustainable return to the moon, astronauts will once again leave Earth's protective magnetosphere only to endure higher levels of radiation from galactic cosmic radiation (GCR) and the possibility of a large solar particle event (SPE). Gateway, lunar landers, and surface habitats will be designed to protect crew against SPEs with vehicle optimization, storm shelter concepts, and/or active dosimetry; however, the ever penetrating GCR will continue to pose the most significant health risks especially as lunar missions increase in duration and as NASA sets its aspirations on Mars. The primary risks of concern include carcinogenesis, central nervous system (CNS) effects resulting in potential in-mission cognitive or behavioral impairment and/or late neurological disorders, degenerative tissue effects including circulatory and heart disease, as well as potential immune system decrements impacting multiple aspects of crew health. Characterization and mitigation of these risks requires a significant reduction in the large biological uncertainties of chronic (low-dose rate) heavy-ion exposures and the validation of countermeasures in a relevant space environment. Historically, most research on understanding space radiation-induced health risks has been performed using acute exposures of monoenergetic single-ion beams. However, the space radiation environment consists of a wide variety of ion species over a broad energy range. Using the fast beam switching and controls systems technology recently developed at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory, a new era in radiobiological research is possible. NASA has developed the "GCR Simulator" to generate a spectrum of ion beams that approximates the primary and secondary GCR field experienced at human organ locations within a deep-space vehicle. The majority of the dose is delivered from protons (approximately 65%–75%) and helium ions (approximately 10%–20%) with heavier ions (Z ≥ 3) contributing the remainder. The GCR simulator exposes state-of-the art cellular and animal model systems to 33 sequential beams including 4 proton energies plus degrader, 4 helium energies plus degrader, and the 5 heavy ions of C, O, Si, Ti, and Fe. A polyethylene degrader system is used with the 100 MeV/n H and He beams to provide a nearly continuous distribution of low-energy particles. A 500 mGy exposure, delivering doses from each of the 33 beams, requires approximately 75 minutes. To more closely simulate the low-dose rates found in space, sequential field exposures can be divided into daily fractions over 2 to 6 weeks, with individual beam fractions as low as 0.1 to 0.2 mGy. In the large beam configuration (60 × 60 cm2), 54 special housing cages can accommodate 2 to 3 mice each for an approximately 75 min duration or 15 individually housed rats. On June 15, 2018, the NSRL made a significant achievement by completing the first operational run using the new GCR simulator. This paper discusses NASA's innovative technology solution for a ground-based GCR simulator at the NSRL to accelerate our understanding and mitigation of health risks faced by astronauts. Ultimately, the GCR simulator will require validation across multiple radiogenic risks, endpoints, doses, and dose rates. This study describes how NASA's new earth-based galactic cosmic ray simulator is being used to accelerate our understanding of the effects of space radiation exposure on astronauts and to validate countermeasures for exploration missions. For the first time, research teams can study mixed field ion and dose rate effects in a simulated space environment. [ABSTRACT FROM AUTHOR]

A gene duplication can lead to all sorts of problems in a cell. However, it can also lead to all sorts of benefits. Beneficial or not, the gene duplicates might be kept in the genome because of several different reasons. For instance, if natural selection works towards optimizing one function of a gene at the expense of another, then gene duplication could resolve this conflict by separating the functions in two genes. Here, we outline evolutionary incentives to keep a duplicated gene in the genome, focusing on divergence in expression and trade-off resolution as featured in a new and exciting paper published in this edition of PLOS Biology. Gene duplication can lead to problems for a cell, but can also afford a range of opportunities. This Primer explores the evolutionary incentives to keep a duplicated gene in the genome, focusing on a recent demonstration that duplication can help resolve conflicts in gene regulation. [ABSTRACT FROM AUTHOR]

Predicting individual mental traits and behavioral dispositions from brain imaging data through machine-learning approaches is becoming a rapidly evolving field in neuroscience. Beyond scientific and clinical applications, such approaches also hold the potential to gain substantial influence in fields such as human resource management, education, or criminal law. Although several challenges render real-life applications of such tools difficult, future conflicts of individual, economic, and public interests are preprogrammed, given the prospect of improved personalized predictions across many domains. In this Perspective paper, we thus argue for the need to engage in a discussion on the ethical, legal, and societal implications of the emergent possibilities for brain-based predictions and outline some of the aspects for this discourse. Advances in machine learning on neuroimaging data have opened up the possibility of objectively predicting individual traits like intelligence, personality, or clinical risks from brain scans. This Perspective article discusses the methodological and ethical challenges arising from these advances. [ABSTRACT FROM AUTHOR]