Journals must expand access to peer review data

Empirical studies on peer review bias are primarily conducted by people from privileged groups and with affiliations with the journals studied. Data access is one major barrier to conducting peer review research. Accordingly, we propose pathways to broaden access to peer review data to people from more diverse backgrounds.

Integrated community models: A framework combining multispecies data sources to estimate the status, trends and dynamics of biodiversity

Data deficiencies among rare or cryptic species preclude assessment of community-level processes using many existing approaches, limiting our understanding of the trends and stressors for large numbers of species. Yet evaluating the dynamics of whole communities, not just common or charismatic species, is critical to understanding and the responses of biodiversity to ongoing environmental pressures. A recent surge in both public science and government-funded data collection efforts has led to a wealth of biodiversity data. However, these data collection programmes use a wide range of sampling protocols (from unstructured, opportunistic observations of wildlife to well-structured, design-based programmes) and record information at a variety of spatiotemporal scales. As a result, available biodiversity data vary substantially in quantity and information content, which must be carefully reconciled for meaningful ecological analysis. Hierarchical modelling, including single-species integrated models and hierarchical community models, has improved our ability to assess and predict biodiversity trends and processes. Here, we highlight the emerging 'integrated community modelling' framework that combines both data integration and community modelling to improve inferences on species- and community-level dynamics. We illustrate the framework with a series of worked examples. Our three case studies demonstrate how integrated community models can be used to extend the geographic scope when evaluating species distributions and community-level richness patterns; discern population and community trends over time; and estimate demographic rates and population growth for communities of sympatric species. We implemented these worked examples using multiple software methods through the R platform via packages with formula-based interfaces and through development of custom code in JAGS, NIMBLE and Stan. Integrated community models provide an exciting approach to model biological and observational processes for multiple species using multiple data types and sources simultaneously, thus accounting for uncertainty and sampling error within a unified framework. By leveraging the combined benefits of both data integration and community modelling, integrated community models can produce valuable information about both common and rare species as well as community-level dynamics, allowing for holistic evaluation of the effects of global change on biodiversity.

Deep learning with citizen science data enables estimation of species diversity and composition at continental extents

Effective solutions to conserve biodiversity require accurate community- and species-level information at relevant, actionable scales and across entire species' distributions. However, data and methodological constraints have limited our ability to provide such information in robust ways. Herein we employ a Deep-Reasoning Network implementation of the Deep Multivariate Probit Model (DMVP-DRNets), an end-to-end deep neural network framework, to exploit large observational and environmental data sets together and estimate landscape-scale species diversity and composition at continental extents. We present results from a novel year-round analysis of North American avifauna using data from over nine million eBird checklists and 72 environmental covariates. We highlight the utility of our information by identifying critical areas of high species diversity for a single group of conservation concern, the North American wood warblers, while capturing spatiotemporal variation in species' environmental associations and interspecific interactions. In so doing, we demonstrate the type of accurate, high-resolution information on biodiversity that deep learning approaches such as DMVP-DRNets can provide and that is needed to inform ecological research and conservation decision-making at multiple scales.

Search for Evidence of Baryogenesis and Dark Matter in B^{+}→ψ_{D}+p Decays at BABAR

A new dark sector antibaryon, denoted ψ_{D}, could be produced in decays of B mesons. This Letter presents a search for B^{+}→ψ_{D}+p (and the charge conjugate) decays in e^{+}e^{-} annihilations at 10.58 GeV, using data collected in the BABAR experiment. Data corresponding to an integrated luminosity of 398  fb^{-1} are analyzed. No evidence for a signal is observed. Branching fraction upper limits in the range from 10^{-7}-10^{-5} are obtained at 90% confidence level for masses of 1.0 Collapse

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Peer review perpetuates barriers for historically excluded groups

Peer review is central to the scientific process and scientists' career advancement, but bias at various stages of the review process disadvantages some authors. Here we use peer review data from 312,740 biological sciences manuscripts across 31 studies to (1) examine evidence for differential peer review outcomes based on author demographics, (2) evaluate the efficacy of solutions to reduce bias and (3) describe the current landscape of peer review policies for 541 ecology and evolution journals. We found notably worse review outcomes (for example, lower overall acceptance rates) for authors whose institutional affiliations were in Asia, for authors whose country's primary language is not English and in countries with relatively low Human Development Indices. We found few data evaluating efficacy of interventions outside of reducing gender bias through double-blind review or diversifying reviewer/editorial boards. Despite evidence for review outcome gaps based on author demographics, few journals currently implement policies intended to mitigate bias (for example, 15.9% of journals practised double-blind review and 2.03% had reviewer guidelines that mentioned social justice issues). The lack of demographic equity signals an urgent need to better understand and implement evidence-based bias mitigation strategies.

Challenges and opportunities for using natural history collections to estimate insect population trends

Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable. However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector-specific biases that can impose severe limitations to using NHC data for evaluating population trajectories. Here we review the challenges associated with using museum records to track long-term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities. Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long-term trends of insect populations and identify cases where that is not possible using existing data sources.

Disentangling direct and indirect effects of extreme events on coastal wetland communities

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population- and community-level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions. We extended static structural equation modelling approaches to incorporate system dynamics in a multi-year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system. We used data from an 8-year study (2009-2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species-specific and community-level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands. We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non-lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland-specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland-breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change. Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.

Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

Search for an Axionlike Particle in B Meson Decays

Axionlike particles (ALPs) are predicted in many extensions of the standard model, and their masses can naturally be well below the electroweak scale. In the presence of couplings to electroweak bosons, these particles could be emitted in flavor-changing B meson decays. We report herein a search for an ALP, a, in the reaction B^{±}→K^{±}a, a→γγ using data collected by the BABAR experiment at SLAC. No significant signal is observed, and 90% confidence level upper limits on the ALP coupling to electroweak bosons are derived as a function of ALP mass, improving current constraints by several orders of magnitude in the range 0.175  GeV<m_{a}<4.78  GeV.

Search for Lepton Flavor Violation in ϒ(3S)→e^{±}μ^{∓}

We report on the first search for electron-muon lepton flavor violation (LFV) in the decay of a b quark and b antiquark bound state. We look for the LFV decay ϒ(3S)→e^{±}μ^{∓} in a sample of 118 million ϒ(3S) mesons from 27  fb^{-1} of data collected with the BABAR detector at the SLAC PEP-II e^{+}e^{-} collider operating with a 10.36 GeV center-of-mass energy. No evidence for a signal is found, and we set a limit on the branching fraction B[ϒ(3S)→e^{±}μ^{∓}]<3.6×10^{-7} at 90% C. L. This result can be interpreted as a limit Λ_{NP}/g_{NP}^{2}>80  TeV on the energy scale Λ_{NP} divided by the coupling-squared g_{NP}^{2} of relevant new physics (NP).

Search for Darkonium in e^{+}e^{-} Collisions

Collider searches for dark sectors, new particles interacting only feebly with ordinary matter, have largely focused on identifying signatures of new mediators, leaving much of dark sector structures unexplored. In particular, the existence of dark matter bound states (darkonia) remains to be investigated. This possibility could arise in a simple model in which a dark photon (A^{'}) is light enough to generate an attractive force between dark fermions. We report herein a search for a J^{PC}=1^{--} darkonium state, the ϒ_{D}, produced in the reaction e^{+}e^{-}→γϒ_{D}, ϒ_{D}→A^{'}A^{'}A^{'}, where the dark photons subsequently decay into pairs of leptons or pions, using 514  fb^{-1} of data collected with the BABAR detector. No significant signal is observed, and we set bounds on the γ-A^{'} kinetic mixing as a function of the dark sector coupling constant for 0.001<m_{A^{'}}<3.16  GeV and 0.05<m_{ϒ_{D}}<9.5  GeV.

Iterative community-driven development of a SARS-CoV-2 tissue simulator

The 2019 novel coronavirus, SARS-CoV-2, is a pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral transport, and emergent tissue-scale viral propagation is limited. Moreover, little is known about immune system-virus-tissue interactions and how these can result in low-level (asymptomatic) infections in some cases and acute respiratory distress syndrome (ARDS) in others, particularly with respect to presentation in different age groups or pre-existing inflammatory risk factors. Given the nonlinear interactions within and among each of these processes, multiscale simulation models can shed light on the emergent dynamics that lead to divergent outcomes, identify actionable "choke points" for pharmacologic interventions, screen potential therapies, and identify potential biomarkers that differentiate patient outcomes. Given the complexity of the problem and the acute need for an actionable model to guide therapy discovery and optimization, we introduce and iteratively refine a prototype of a multiscale model of SARS-CoV-2 dynamics in lung tissue. The first prototype model was built and shared internationally as open source code and an online interactive model in under 12 hours, and community domain expertise is driving regular refinements. In a sustained community effort, this consortium is integrating data and expertise across virology, immunology, mathematical biology, quantitative systems physiology, cloud and high performance computing, and other domains to accelerate our response to this critical threat to international health. More broadly, this effort is creating a reusable, modular framework for studying viral replication and immune response in tissues, which can also potentially be adapted to related problems in immunology and immunotherapy.

COVID-19 virtual patient cohort suggests immune mechanisms driving disease outcomes

To understand the diversity of immune responses to SARS-CoV-2 and distinguish features that predispose individuals to severe COVID-19, we developed a mechanistic, within-host mathematical model and virtual patient cohort. Our results suggest that virtual patients with low production rates of infected cell derived IFN subsequently experienced highly inflammatory disease phenotypes, compared to those with early and robust IFN responses. In these in silico patients, the maximum concentration of IL-6 was also a major predictor of CD8+ T cell depletion. Our analyses predicted that individuals with severe COVID-19 also have accelerated monocyte-to-macrophage differentiation mediated by increased IL-6 and reduced type I IFN signalling. Together, these findings suggest biomarkers driving the development of severe COVID-19 and support early interventions aimed at reducing inflammation.

COVID-19 virtual patient cohort reveals immune mechanisms driving disease outcomes

To understand the diversity of immune responses to SARS-CoV-2 and distinguish features that predispose individuals to severe COVID-19, we developed a mechanistic, within-host mathematical model and virtual patient cohort. Our results indicate that virtual patients with low production rates of infected cell derived IFN subsequently experienced highly inflammatory disease phenotypes, compared to those with early and robust IFN responses. In these in silico patients, the maximum concentration of IL-6 was also a major predictor of CD8 + T cell depletion. Our analyses predicted that individuals with severe COVID-19 also have accelerated monocyte-to-macrophage differentiation that was mediated by increased IL-6 and reduced type I IFN signalling. Together, these findings identify biomarkers driving the development of severe COVID-19 and support early interventions aimed at reducing inflammation.

AUTHOR SUMMARY

Understanding of how the immune system responds to SARS-CoV-2 infections is critical for improving diagnostic and treatment approaches. Identifying which immune mechanisms lead to divergent outcomes can be clinically difficult, and experimental models and longitudinal data are only beginning to emerge. In response, we developed a mechanistic, mathematical and computational model of the immunopathology of COVID-19 calibrated to and validated against a broad set of experimental and clinical immunological data. To study the drivers of severe COVID-19, we used our model to expand a cohort of virtual patients, each with realistic disease dynamics. Our results identify key processes that regulate the immune response to SARS-CoV-2 infection in virtual patients and suggest viable therapeutic targets, underlining the importance of a rational approach to studying novel pathogens using intra-host models.

Precision Measurement of the Ratio B(ϒ(3S)→τ^{+}τ^{-})/B(ϒ(3S)→μ^{+}μ^{-})

We report on a precision measurement of the ratio R_{τμ}^{ϒ(3S)}=B(ϒ(3S)→τ^{+}τ^{-})/B(ϒ(3S)→μ^{+}μ^{-}) using data collected with the BABAR detector at the SLAC PEP-II e^{+}e^{-} collider. The measurement is based on a 28  fb^{-1} data sample collected at a center-of-mass energy of 10.355 GeV corresponding to a sample of 122 million ϒ(3S) mesons. The ratio is measured to be R_{τμ}^{ϒ(3S)}=0.966±0.008_{stat}±0.014_{syst} and is in agreement with the standard model prediction of 0.9948 within 2 standard deviations. The uncertainty in R_{τμ}^{ϒ(3S)} is almost an order of magnitude smaller than the only previous measurement.

Search for a Dark Leptophilic Scalar in e^{+}e^{-} Collisions

Many scenarios of physics beyond the standard model predict the existence of new gauge singlets, which might be substantially lighter than the weak scale. The experimental constraints on additional scalars with masses in the MeV to GeV range could be significantly weakened if they interact predominantly with leptons rather than quarks. At an e^{+}e^{-} collider, such a leptophilic scalar (ϕ_{L}) would be produced predominantly through radiation from a τ lepton. We report herein a search for e^{+}e^{-}→τ^{+}τ^{-}ϕ_{L}, ϕ_{L}→ℓ^{+}ℓ^{-} (ℓ=e, μ) using data collected by the BABAR experiment at SLAC. No significant signal is observed, and we set limits on the ϕ_{L} coupling to leptons in the range 0.04<m_{ϕ_{L}}<7.0  GeV. These bounds significantly improve upon the current constraints, excluding almost entirely the parameter space favored by the observed discrepancy in the muon anomalous magnetic moment below 4 GeV at 90% confidence level.

Measurements of the Absolute Branching Fractions of B^{±}→K^{±}X_{cc[over ¯]}

A study of the two-body decays B^{±}→X_{cc[over ¯]}K^{±}, where X_{cc[over ¯]} refers to one charmonium state, is reported by the BABAR Collaboration using a data sample of 424  fb^{-1}. The absolute determination of branching fractions for these decays are significantly improved compared to previous BABAR measurements. Evidence is found for the decay B^{+}→X(3872)K^{+} at the 3σ level. The absolute branching fraction B[B^{+}→X(3872)K^{+}]=[2.1±0.6(stat)±0.3(syst)]×10^{-4} is measured for the first time. It follows that B[X(3872)→J/ψπ^{+}π^{-}]=(4.1±1.3)%, supporting the hypothesis of a molecular component for this resonance.

Search for Rare or Forbidden Decays of the D^{0} Meson

We present a search for nine lepton-number-violating and three lepton-flavor-violating neutral charm decays of the type D^{0}→h^{'-}h^{-}ℓ^{'+}ℓ^{+} and D^{0}→h^{'-}h^{+}ℓ^{'±}ℓ^{∓}, where h and h^{'} represent a K or π meson and ℓ and ℓ^{'} an electron or muon. The analysis is based on 468  fb^{-1} of e^{+}e^{-} annihilation data collected at or close to the ϒ(4S) resonance with the BABAR detector at the SLAC National Accelerator Laboratory. No significant signal is observed for any of the twelve modes, and we establish 90% confidence level upper limits on the branching fractions in the range (1.0-30.6)×10^{-7}. The limits are between 1 and 3 orders of magnitude more stringent than previous measurements.

Extraction of form Factors from a Four-Dimensional Angular Analysis of B[over ¯]→D^{*}ℓ^{-}ν[over ¯]_{ℓ}

An angular analysis of the decay B[over ¯]→D^{*}ℓ^{-}ν[over ¯]_{ℓ}, ℓ∈{e,μ}, is reported using the full e^{+}e^{-} collision data set collected by the BABAR experiment at the ϒ(4S) resonance. One B meson from the ϒ(4S)→BB[over ¯] decay is fully reconstructed in a hadronic decay mode, which constrains the kinematics and provides a determination of the neutrino momentum vector. The kinematics of the semileptonic decay is described by the dilepton mass squared, q^{2}, and three angles. The first unbinned fit to the full four-dimensional decay rate in the standard model is performed in the so-called Boyd-Grinstein-Lebed approach, which employs a generic q^{2} parametrization of the underlying form factors based on crossing symmetry, analyticity, and QCD dispersion relations for the amplitudes. A fit using the more model-dependent Caprini-Lellouch-Neubert (CLN) approach is performed as well. Our form factor shapes show deviations from previous fits based on the CLN parametrization. The latest form factors also provide an updated prediction for the branching fraction ratio R(D^{*})≡B(B[over ¯]→D^{*}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^{*}ℓ^{-}ν[over ¯]_{ℓ})=0.253±0.005. Finally, using the well-measured branching fraction for the B[over ¯]→D^{*}ℓ^{-}ν[over ¯]_{ℓ} decay, a value of |V_{cb}|=(38.36±0.90)×10^{-3} is obtained that is consistent with the current world average for exclusive B[over ¯]→D^{(*)}ℓ^{-}ν[over ¯]_{ℓ} decays and remains in tension with the determination from inclusive semileptonic B decays to final states with charm.

Observation of the Decay D^{0}→K^{-}π^{+}e^{+}e^{-}

We report the observation of the rare charm decay D^{0}→K^{-}π^{+}e^{+}e^{-}, based on 468  fb^{-1} of e^{+}e^{-} annihilation data collected at or close to the center-of-mass energy of the ϒ(4S) resonance with the BABAR detector at the SLAC National Accelerator Laboratory. We find the branching fraction in the invariant mass range 0.675<m(e^{+}e^{-})<0.875  GeV/c^{2} of the electron-positron pair to be B(D^{0}→K^{-}π^{+}e^{+}e^{-})=(4.0±0.5±0.2±0.1)×10^{-6}, where the first uncertainty is statistical, the second systematic, and the third due to the uncertainty in the branching fraction of the decay D^{0}→K^{-}π^{+}π^{+}π^{-} used as a normalization mode. The significance of the observation corresponds to 9.7 standard deviations including systematic uncertainties. This result is consistent with the recently reported D^{0}→K^{-}π^{+}μ^{+}μ^{-} branching fraction, measured in the same invariant mass range, and with the value expected in the standard model. In a set of regions of m(e^{+}e^{-}), where long-distance effects are potentially small, we determine a 90% confidence level upper limit on the branching fraction B(D^{0}→K^{-}π^{+}e^{+}e^{-})<3.1×10^{-6}.

Search for a Stable Six-Quark State at BABAR

Recent investigations have suggested that the six-quark combination uuddss could be a deeply bound state (S) that has eluded detection so far, and a potential dark matter candidate. We report the first search for a stable, doubly strange six-quark state in ϒ→SΛ[over ¯]Λ[over ¯] decays based on a sample of 90×10^{6}ϒ(2S) and 110×10^{6}ϒ(3S) decays collected by the BABAR experiment. No signal is observed, and 90% confidence level limits on the combined ϒ(2S,3S)→SΛ[over ¯]Λ[over ¯] branching fraction in the range (1.2-1.4)×10^{-7} are derived for m_{S}<2.05  GeV. These bounds set stringent limits on the existence of such exotic particles.

First Evidence for cos2β>0 and Resolution of the Cabibbo-Kobayashi-Maskawa Quark-Mixing Unitarity Triangle Ambiguity

We present first evidence that the cosine of the CP-violating weak phase 2β is positive, and hence exclude trigonometric multifold solutions of the Cabibbo-Kobayashi-Maskawa (CKM) Unitarity Triangle using a time-dependent Dalitz plot analysis of B^{0}→D^{(*)}h^{0} with D→K_{S}^{0}π^{+}π^{-} decays, where h^{0}∈{π^{0},η,ω} denotes a light unflavored and neutral hadron. The measurement is performed combining the final data sets of the BABAR and Belle experiments collected at the ϒ(4S) resonance at the asymmetric-energy B factories PEP-II at SLAC and KEKB at KEK, respectively. The data samples contain (471±3)×10^{6}BB[over ¯] pairs recorded by the BABAR detector and (772±11)×10^{6}BB[over ¯] pairs recorded by the Belle detector. The results of the measurement are sin2β=0.80±0.14(stat)±0.06(syst)±0.03(model) and cos2β=0.91±0.22(stat)±0.09(syst)±0.07(model). The result for the direct measurement of the angle β of the CKM Unitarity Triangle is β=[22.5±4.4(stat)±1.2(syst)±0.6(model)]°. The measurement assumes no direct CP violation in B^{0}→D^{(*)}h^{0} decays. The quoted model uncertainties are due to the composition of the D^{0}→K_{S}^{0}π^{+}π^{-} decay amplitude model, which is newly established by performing a Dalitz plot amplitude analysis using a high-statistics e^{+}e^{-}→cc[over ¯] data sample. CP violation is observed in B^{0}→D^{(*)}h^{0} decays at the level of 5.1 standard deviations. The significance for cos2β>0 is 3.7 standard deviations. The trigonometric multifold solution π/2-β=(68.1±0.7)° is excluded at the level of 7.3 standard deviations. The measurement resolves an ambiguity in the determination of the apex of the CKM Unitarity Triangle.

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.

Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally.

Use of field-portable ultrasonography reveals differences in developmental phenology and maternal egg provisioning in two sympatric viviparous snakes

A thorough understanding of the life cycles underlying the demography of wild species is limited by the difficulty of observing hidden life‐history traits, such as embryonic development. Major aspects of embryonic development, such as the rate and timing of development, and maternal–fetal interactions can be critical features of early‐life fitness and may impact population trends via effects on individual survival. While information on development in wild snakes and lizards is particularly limited, the repeated evolution of viviparity and diversity of reproductive mode in this clade make it a valuable subject of study. We used field‐portable ultrasonography to investigate embryonic development in two sympatric garter snake species, Thamnophis sirtalis and Thamnophis elegans in the Sierra Nevada mountains of California. This approach allowed us to examine previously hidden reproductive traits including the timing and annual variation in development and differences in parental investment in young. Both species are viviparous, occupy similar ecological niches, and experience the same annual environmental conditions. We found that T. sirtalis embryos were more developmentally advanced than T. elegans embryos during June of three consecutive years. We also found that eggs increased in volume more substantially across developmental stages in T. elegans than in T. sirtalis, indicating differences in maternal provisioning of embryos via placental transfer of water. These findings shed light on interspecific differences in parental investment and timing of development within the same environmental context and demonstrate the value of field ultrasonography for pursuing questions relating to the evolution of reproductive modes, and the ecology of development.

A clinically parameterized mathematical model of Shigella immunity to inform vaccine design

We refine and clinically parameterize a mathematical model of the humoral immune response against Shigella, a diarrheal bacteria that infects 80-165 million people and kills an estimated 600,000 people worldwide each year. Using Latin hypercube sampling and Monte Carlo simulations for parameter estimation, we fit our model to human immune data from two Shigella EcSf2a-2 vaccine trials and a rechallenge study in which antibody and B-cell responses against Shigella′s lipopolysaccharide (LPS) and O-membrane proteins (OMP) were recorded. The clinically grounded model is used to mathematically investigate which key immune mechanisms and bacterial targets confer immunity against Shigella and to predict which humoral immune components should be elicited to create a protective vaccine against Shigella. The model offers insight into why the EcSf2a-2 vaccine had low efficacy and demonstrates that at a group level a humoral immune response induced by EcSf2a-2 vaccine or wild-type challenge against Shigella′s LPS or OMP does not appear sufficient for protection. That is, the model predicts an uncontrolled infection of gut epithelial cells that is present across all best-fit model parameterizations when fit to EcSf2a-2 vaccine or wild-type challenge data. Using sensitivity analysis, we explore which model parameter values must be altered to prevent the destructive epithelial invasion by Shigella bacteria and identify four key parameter groups as potential vaccine targets or immune correlates: 1) the rate that Shigella migrates into the lamina propria or epithelium, 2) the rate that memory B cells (B_M) differentiate into antibody-secreting cells (ASC), 3) the rate at which antibodies are produced by activated ASC, and 4) the Shigella-specific B_M carrying capacity. This paper underscores the need for a multifaceted approach in ongoing efforts to design an effective Shigella vaccine.

Measurement of the D^{*}(2010)^{+}-D^{+} Mass Difference

We measure the mass difference, Δm_{+}, between the D^{*}(2010)^{+} and the D^{+} using the decay chain D^{*}(2010)^{+}→D^{+}π^{0} with D^{+}→K^{-}π^{+}π^{+}. The data were recorded with the BABAR detector at center-of-mass energies at and near the ϒ(4S) resonance, and correspond to an integrated luminosity of approximately 468  fb^{-1}. We measure Δm_{+}=(140 601.0±6.8[stat]±12.9[syst])  keV. We combine this result with a previous BABAR measurement of Δm_{0}≡m(D^{*}(2010)^{+})-m(D^{0}) to obtain Δm_{D}=m(D^{+})-m(D^{0})=(4824.9±6.8[stat]±12.9[syst])  keV. These results are compatible with and approximately five times more precise than the Particle Data Group averages.

Search for Invisible Decays of a Dark Photon Produced in e^{+}e^{-} Collisions at BaBar

We search for single-photon events in 53  fb^{-1} of e^{+}e^{-} collision data collected with the BABAR detector at the PEP-II B-Factory. We look for events with a single high-energy photon and a large missing momentum and energy, consistent with production of a spin-1 particle A^{'} through the process e^{+}e^{-}→γA^{'}; A^{'}→invisible. Such particles, referred to as "dark photons," are motivated by theories applying a U(1) gauge symmetry to dark matter. We find no evidence for such processes and set 90% confidence level upper limits on the coupling strength of A^{'} to e^{+}e^{-} in the mass range m_{A^{'}}≤8  GeV. In particular, our limits exclude the values of the A^{'} coupling suggested by the dark-photon interpretation of the muon (g-2)_{μ} anomaly, as well as a broad range of parameters for the dark-sector models.

Search for B^{+}→K^{+}τ^{+}τ^{-} at the BaBar Experiment

We search for the rare flavor-changing neutral current process B^{+}→K^{+}τ^{+}τ^{-} using data from the BABAR experiment. The data sample, collected at the center-of-mass energy of the ϒ(4S) resonance, corresponds to a total integrated luminosity of 424  fb^{-1} and to 471×10^{6}  BB[over ¯] pairs. We reconstruct one B meson, produced in the ϒ(4S)→B^{+}B^{-} decay, in one of many hadronic decay modes and search for activity compatible with a B^{+}→K^{+}τ^{+}τ^{-} decay in the rest of the event. Each τ lepton is required to decay leptonically into an electron or muon and neutrinos. Comparing the expected number of background events with the data sample after applying the selection criteria, we do not find evidence for a signal. The resulting upper limit, at the 90% confidence level, is B(B^{+}→K^{+}τ^{+}τ^{-})<2.25×10^{-3}.

Species interactions and the effects of climate variability on a wetland amphibian metacommunity

Disentangling the role that multiple interacting factors have on species responses to shifting climate poses a significant challenge. However, our ability to do so is of utmost importance to predict the effects of climate change on species distributions. We examined how populations of three species of wetland-breeding amphibians, which varied in life history requirements, responded to a six-year period of extremely variable precipitation. This interval was punctuated by both extensive drought and heavy precipitation and flooding, providing a natural experiment to measure community responses to environmental perturbations. We estimated occurrence dynamics using a discrete hidden Markov modeling approach that incorporated information regarding habitat state and predator-prey interactions. This approach allowed us to measure how metapopulation dynamics of each amphibian species was affected by interactions among weather, wetland hydroperiod, and co-occurrence with fish predators. The pig frog, a generalist, proved most resistant to perturbations, with both colonization and persistence being unaffected by seasonal variation in precipitation or co-occurrence with fishes. The ornate chorus frog, an ephemeral wetland specialist, responded positively to periods of drought owing to increased persistence and colonization rates during periods of low-rainfall. Low probabilities of occurrence of the ornate chorus frog in long-duration wetlands were driven by interactions with predators due to low colonization rates when fishes were present. The mole salamander was most sensitive to shifts in water availability. In our study area, this species never occurred in short-duration wetlands and persistence probabilities decreased during periods of drought. At the same time, negative effects occurred with extreme precipitation because flooding facilitated colonization of fishes to isolated wetlands and mole salamanders did not colonize wetlands once fishes were present. We demonstrate that the effects of changes in water availability depend on interactions with predators and wetland type and are influenced by the life history of each of our species. The dynamic species occurrence modeling approach we used offers promise for other systems when the goal is to disentangle the complex interactions that determine species responses to environmental variability.

Effect of solidification rate on microstructure evolution in dual phase microalloyed steel

In steels the dependence of ambient temperature microstructure and mechanical properties on solidification rate is not well reported. In this work we investigate the microstructure and hardness evolution for a low C low Mn NbTi-microalloyed steel solidified in the cooling rate range of 1–50 Cs⁻¹. The maximum strength was obtained at the intermediate solidification rate of 30 Cs⁻¹. This result has been correlated to the microstructure variation with solidification rate.

Observation of B→D(*) π^(+)π^(-)ℓ^(-)ν Decays in e^(+)e^(-) Collisions at the Υ(4S) Resonance

We report on measurements of the decays of B¯ mesons into the semileptonic final states B¯→D^(*)π^(+)π^(-)ℓ^(-)ν¯, where D^(*) represents a D or D^(*) meson and ℓ^(-) is an electron or a muon. These measurements are based on 471×10^(6) BB ¯ pairs recorded with the BABAR detector at the SLAC asymmetric B factory PEP-II. We determine the branching fraction ratios R_{π^{+}π^{-}}^{(*)}=B(B[over ¯]→D^{(*)}π^{+}π^{-}ℓ^{-}ν[over ¯])/B(B[over ¯]→D^{(*)}ℓ^{-}ν[over ¯]) using events in which the second B meson is fully reconstructed. We find R_{π^{+}π^{-}}=0.067±0.010±0.008 and R_{π^{+}π^{-}}^{*}=0.019±0.005±0.004, where the first uncertainty is statistical and the second is systematic. Based on these results and assuming isospin invariance, we estimate that B[over ¯]→D^{(*)}ππℓ^{-}ν[over ¯] decays, where π denotes either a π^{±} and π^{0} meson, account for up to half the difference between the measured inclusive semileptonic branching fraction to charm hadrons and the corresponding sum of previously measured exclusive branching fractions.

Liver enzymes and clustering cardiometabolic risk factors in European adolescents: the HELENA study

OBJECTIVES

This study aimed to explore the associations of liver biomarkers with cardiometabolic risk factors and their clustering, and to provide reference values (percentiles) and cut-off points for liver biomarkers associated with high cardiometabolic risk in European adolescents.

METHODS

Alanine aminotransferase (ALT), gamma-glutamyltransferase (GGT), aspartate aminotransferase to ALT ratio (AST/ALT), waist circumference, blood pressure, triglycerides, high-density lipoprotein cholesterol and insulin were measured in 1084 adolescents. We computed a continuous cardiometabolic risk score and defined the high cardiometabolic risk.

RESULTS

Higher ALT and GGT and lower AST/ALT were associated with adiposity and with the number of adverse cardiometabolic risk factors (Ps < 0.05). Higher GGT and lower AST/ALT were associated with higher cardiometabolic risk score (Ps < 0.001) in males and females, and ALT only in males (Ps < 0.001). Gender- and age-specific percentiles for liver biomarkers were provided. Receiver operating characteristic analyses showed a significant discriminatory accuracy of AST/ALT in identifying the low/high cardiometabolic risk (Ps < 0.01) and thresholds were provided.

CONCLUSIONS

Higher GGT and lower AST/ALT are associated with higher cardiometabolic risk factors and their clustering in male and female European adolescents, whereas the associations of ALT were gender dependent. Our results suggest the usefulness of AST/ALT as a screening test in the assessment of adolescents with high cardiometabolic risk and provide gender- and age-specific thresholds that might be of clinical interest.

First Observation of CP Violation in B[over ¯]^{0}→D_{CP}^{(*)}h^{0} Decays by a Combined Time-Dependent Analysis of BABAR and Belle Data

We report a measurement of the time-dependent CP asymmetry of B[over ¯]^{0}→D_{CP}^{(*)}h^{0} decays, where the light neutral hadron h^{0} is a π^{0}, η, or ω meson, and the neutral D meson is reconstructed in the CP eigenstates K^{+}K^{-}, K_{S}^{0}π^{0}, or K_{S}^{0}ω. The measurement is performed combining the final data samples collected at the ϒ(4S) resonance by the BABAR and Belle experiments at the asymmetric-energy B factories PEP-II at SLAC and KEKB at KEK, respectively. The data samples contain (471±3)×10^{6} BB[over ¯] pairs recorded by the BABAR detector and (772±11)×10^{6} BB[over ¯] pairs recorded by the Belle detector. We measure the CP asymmetry parameters -η_{f}S=+0.66±0.10(stat)±0.06(syst) and C=-0.02±0.07(stat)±0.03(syst). These results correspond to the first observation of CP violation in B[over ¯]^{0}→D_{CP}^{(*)}h^{0} decays. The hypothesis of no mixing-induced CP violation is excluded in these decays at the level of 5.4 standard deviations.

Search for Long-Lived Particles in e+ e- Collisions

We present a search for a neutral, long-lived particle L that is produced in e+ e- collisions and decays at a significant distance from the e+ e- interaction point into various flavor combinations of two oppositely charged tracks. The analysis uses an e+ e- data sample with a luminosity of 489.1  fb(-1) collected by the BABAR detector at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and just below the ϒ(4S). Fitting the two-track mass distribution in search of a signal peak, we do not observe a significant signal, and set 90% confidence level upper limits on the product of the L production cross section, branching fraction, and reconstruction efficiency for six possible two-body L decay modes as a function of the L mass. The efficiency is given for each final state as a function of the mass, lifetime, and transverse momentum of the candidate, allowing application of the upper limits to any production model. In addition, upper limits are provided on the branching fraction B(B→XsL), where Xs is a strange hadronic system.

Study of CP asymmetry in B^{0}-B[over ¯]^{0} mixing with inclusive dilepton events

We present a measurement of the asymmetry A_{CP} between same-sign inclusive dilepton samples ℓ^{+}ℓ^{+} and ℓ^{-}ℓ^{-} (ℓ=e, μ) from semileptonic B decays in ϒ(4S)→BB[over ¯] events, using the complete data set recorded by the BABAR experiment near the ϒ(4S) resonance, corresponding to 471×10^{6} BB[over ¯] pairs. The asymmetry A_{CP} allows comparison between the mixing probabilities P(B[over ¯]^{0}→B^{0}) and P(B^{0}→B[over ¯]^{0}), and therefore probes CP and T violation. The result, A_{CP}=[-3.9±3.5(stat)±1.9(syst)]×10^{-3}, is consistent with the standard model expectation.

Search for a dark photon in e(+)e(-) collisions at BABAR

Dark sectors charged under a new Abelian interaction have recently received much attention in the context of dark matter models. These models introduce a light new mediator, the so-called dark photon (A^{'}), connecting the dark sector to the standard model. We present a search for a dark photon in the reaction e^{+}e^{-}→γA^{'}, A^{'}→e^{+}e^{-}, μ^{+}μ^{-} using 514  fb^{-1} of data collected with the BABAR detector. We observe no statistically significant deviations from the standard model predictions, and we set 90% confidence level upper limits on the mixing strength between the photon and dark photon at the level of 10^{-4}-10^{-3} for dark photon masses in the range 0.02-10.2  GeV. We further constrain the range of the parameter space favored by interpretations of the discrepancy between the calculated and measured anomalous magnetic moment of the muon.

An eight month randomized controlled exercise intervention alters resting state synchrony in overweight children

Children with low aerobic fitness have altered brain function compared to higher-fit children. This study examined the effect of an 8-month exercise intervention on resting state synchrony. Twenty-two sedentary, overweight (body mass index ≥85th percentile) children 8-11 years old were randomly assigned to one of two after-school programs: aerobic exercise (n=13) or sedentary attention control (n=9). Before and after the 8-month programs, all subjects participated in resting state functional magnetic resonance imaging scans. Independent components analysis identified several networks, with four chosen for between-group analysis: salience, default mode, cognitive control, and motor networks. The default mode, cognitive control, and motor networks showed more spatial refinement over time in the exercise group compared to controls. The motor network showed increased synchrony in the exercise group with the right medial frontal gyrus compared to controls. Exercise behavior may enhance brain development in children.

Measurement of the D*(2010)+ meson width and the D*(2010)+ - D0 mass difference

We measure the mass difference Δm0 between the D*(2010)+ and the D0 and the natural linewidth Γ of the transition D*(2010)+ → D0π+. The data were recorded with the BABAR detector at center-of-mass energies at and near the Υ(4S) resonance, and correspond to an integrated luminosity of approximately 477  fb(-1). The D0 is reconstructed in the decay modes D0 → K- π+ and D0 → K- π+ π- π+. For the decay mode D0 → K- π+ we obtain Γ = (83.4±1.7±1.5)  keV and Δm0 = (145425.6±0.6±1.7)  keV, [corrected] where the quoted errors are statistical and systematic, respectively. For the D0 → K- π+ π- π+ mode we obtain Γ = (83.2±1.5±2.6)  keV and Δm0 = (145426.6±0.5±1.9)  keV. [corrected] The combined measurements yield Γ = (83.3±1.2±1.4)  keV and Δm0 = (145425.9±0.4±1.7)  keV; the width is a factor of approximately 12 times more precise than the previous value, while the mass difference is a factor of approximately 6 times more precise.

Search for CP violation in B0-B0 mixing using partial reconstruction of B0→D*- Xℓ+ νℓ and a kaon tag

We present results of a search for CP violation in B0- B0 mixing with the BABAR detector. We select a sample of B0→D*- Xℓ+ ν decays with a partial reconstruction method and use kaon tagging to assess the flavor of the other B meson in the event. We determine the CP violating asymmetry ACP≡[N(B0B0)-N(B0B0)]/[N(B0B0)+N(B0B0)]=(0.06±0.17(-0.32)(+0.38))%, corresponding to ΔCP=1-|q/p|=(0.29±0.84(-1.61)(+1.88))×10(-3).

Applying mathematical tools to accelerate vaccine development: modeling Shigella immune dynamics

We establish a mathematical framework for studying immune interactions with Shigella, a bacteria that kills over one million people worldwide every year. The long-term goal of this novel approach is to inform Shigella vaccine design by elucidating which immune components and bacterial targets are crucial for establishing Shigella immunity. Our delay differential equation model focuses on antibody and B cell responses directed against antigens like lipopolysaccharide in Shigella’s outer membrane. We find that antibody-based vaccines targeting only surface antigens cannot elicit sufficient immunity for protection. Additional boosting prior to infection would require a four-orders-of-magnitude increase in antibodies to sufficiently prevent epithelial invasion. However, boosting anti-LPS B memory can confer protection, which suggests these cells may correlate with immunity. We see that IgA antibodies are slightly more effective per molecule than IgG, but more total IgA is required due to spatial functionality. An extension of the model reveals that targeting both LPS and epithelial entry proteins is a promising avenue to advance vaccine development. This paper underscores the importance of multifaceted immune targeting in creating an effective Shigella vaccine. It introduces mathematical models to the Shigella vaccine development effort and lays a foundation for joint theoretical/experimental/clinical approaches to Shigella vaccine design.

Observation of time-reversal violation in the B0 meson system

Although CP violation in the B meson system has been well established by the B factories, there has been no direct observation of time-reversal violation. The decays of entangled neutral B mesons into definite flavor states (B(0) or B(0)), and J/ψK(L)(0) or ccK(S)(0) final states (referred to as B(+) or B(-)), allow comparisons between the probabilities of four pairs of T-conjugated transitions, for example, B(0) → B(-) and B(-) → B(0), as a function of the time difference between the two B decays. Using 468 × 10(6) BB pairs produced in Υ(4S) decays collected by the BABAR detector at SLAC, we measure T-violating parameters in the time evolution of neutral B mesons, yielding ΔS(T)(+) = -1.37 ± 0.14(stat) ± 0.06(syst) and ΔS(T)(-) = 1.17 ± 0.18(stat) ± 0.11(syst). These nonzero results represent the first direct observation of T violation through the exchange of initial and final states in transitions that can only be connected by a T-symmetry transformation.

Precision measurement of the B → Xs γ photon energy spectrum, branching fraction, and direct CP asymmetry A(CP)((B → X(s+d)γ)

The photon spectrum in the inclusive electromagnetic radiative decays of the B meson, B → X(s)γ plus B → X(d)γ, is studied using a data sample of (382.8 ± 4.2) × 10(6)Υ(4S) → BB decays collected by the BABAR experiment at SLAC. The spectrum is used to extract the branching fraction B(B → X(s)γ) = (3.21 ± 0.33) × 10(-4) for E(γ) >1.8 GeV and the direct CP asymmetry A(CP) (B → X(s+d)γ) = 0.057 ± 0.063. The effects of detector resolution and Doppler smearing are unfolded to measure the photon energy spectrum in the B meson rest frame.

Simultaneous liver-kidney transplantation: a survey of US transplant centers

Consensus recommendations have been published to help better define those patients who would benefit from simultaneous liver-kidney transplantation (SLK). We conducted a survey of transplant centers that perform SLK (n = 88, 65% response rate) to determine practice patterns in the United States. The majority of centers (73%) stated that they use dialysis duration whereas only 30% of centers use acute kidney injury duration as a criterion for determining need for SLK. Dialysis duration >4 weeks was used by 32% of centers, >6 weeks by 37% and >8 weeks by 32% of centers. Glomerular filtration rate (GFR) was estimated using the modified diet in renal disease (MDRD)-4 equation in roughly half of centers whereas the MDRD-6 equation was used by only 6%. In patients with chronic kidney disease, GFR < 40 mL/min was used by 24% of centers as a criterion for SLK transplants instead of the recommended threshold of < 30 mL/min. Regional differences in practices were also observed. This survey demonstrates significant variation in the criteria used for SLK among transplant centers, with few centers following the current published recommendations, and emphasizes the need for evidence-based guidelines and uniformity in studying renal dysfunction in liver transplant candidates.

Simultaneous liver-kidney transplantation summit: current state and future directions

Although previous consensus recommendations have helped define patients who would benefit from simultaneous liver-kidney transplantation (SLK), there is a current need to reassess published guidelines for SLK because of continuing increase in proportion of liver transplant candidates with renal dysfunction and ongoing donor organ shortage. The purpose of this consensus meeting was to critically evaluate published and registry data regarding patient and renal outcomes following liver transplantation alone or SLK in liver transplant recipients with renal dysfunction. Modifications to the current guidelines for SLK and a research agenda were proposed.

Evidence for an excess of B→D*τ(-)ν(τ) decays

Based on the full BABAR data sample, we report improved measurements of the ratios R(D(*))=B(B[over ¯]→D(*)τ(-)ν[over ¯](τ))/B(B[over ¯]→D(*)ℓ(ℓ)(-)ν[over ¯](ℓ)), where ℓ is either e or μ. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure R(D)=0.440±0.058±0.042 and R(D(*))=0.332±0.024±0.018, which exceed the standard model expectations by 2.0σ and 2.7σ, respectively. Taken together, our results disagree with these expectations at the 3.4σ level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model.

A perinatal intervention program for urban american indians part 1: design, implementation, and outcomes

High infant mortality rates among American Indians are disproportionate to state statistics for other races and higher than the national average. These findings prompted a community health center in a large Midwestern city to create and provide an American Indian infant mortality reduction project in the early 1990s. Strategies for program implementation included networking with local organizations, communicating with reservation health clinics throughout the state, educating American Indian mothers and their community about factors contributing to American Indian infant mortality, and providing individual case management to American Indian women and infants. We offer this article for three reasons: This grant project was successful, disparity in rates of infant mortality among peoples of color continues, and a paucity of information exists about the health behaviors of American Indian women.

Search for low-mass dark-sector Higgs bosons

Recent astrophysical and terrestrial experiments have motivated the proposal of a dark sector with GeV-scale gauge boson force carriers and new Higgs bosons. We present a search for a dark Higgs boson using 516 fb(-1) of data collected with the BABAR detector. We do not observe a significant signal and we set 90% confidence level upper limits on the product of the standard model-dark-sector mixing angle and the dark-sector coupling constant.