bluuebunny/crossref_metadata_2025 huggingface dataset:
Empirical links between natural mortality and recovery in marine fishes
Authors: Hutchings Jeffrey A. , Kuparinen Anna
Published: June 2017

Probability of species recovery is thought to be correlated with specific aspects of organismal life history, such as age at maturity and longevity, and how these affect rates of natural mortality (M) and maximumper capitapopulation growth (rmax). Despite strong theoretical underpinnings, these correlates have been based on predicted rather than realized population trajectories following threat mitigation. Here, we examine the level of empirical support for postulated links between a suite of life-history traits (related to maturity, age, size and growth) and recovery in marine fishes. Following threat mitigation (medium time since cessation of overfishing = 20 years), 71% of 55 temperate populations had fully recovered, the remainder exhibiting, on average, negligible change (impaired recovery). Singly, life-history traits did not influence recovery status. In combination, however, those that jointly reflect length-based mortality at maturity,Mα, revealed that recovered populations have higherMα, which we hypothesize to reflect local adaptations associated with greaterrmax. But, within populations, the smaller sizes at maturity generated by overfishing are predicted to increaseMα, slowing recovery and increasing its uncertainty. We conclude that recovery potential is greater for populations adapted to highMbut that temporal increases inMconcomitant with smaller size at maturity will have the opposite effect. The recovery metric documented here (Mα) has a sound theoretical basis, is significantly correlated with direct estimates ofMthat directly reflectrmax, is not reliant on data-intensive time series, can be readily estimated, and offers an empirically defensible correlate of recovery, given its clear links to the positive and impaired responses to threat mitigation that have been observed in fish populations over the past three decades.
Biological markets in cooperative breeders: quantifying outside options
Authors: Grinsted Lena , Field Jeremy
Published: June 2017

A major aim in evolutionary biology is to understand altruistic help and reproductive partitioning in cooperative societies, where subordinate helpers forego reproduction to rear dominant breeders' offspring. Traditional models of cooperation in these societies typically make a key assumption: that the only alternative to staying and helping is solitary breeding, an often unfeasible task. Using large-scale field experiments on paper wasps (Polistes dominula), we show that individuals have high-quality alternative nesting options available that offer fitness payoffs just as high as their actual chosen options, far exceeding payoffs from solitary breeding. Furthermore, joiners could not easily be replaced if they were removed experimentally, suggesting that it may be costly for dominants to reject them. Our results have implications for expected payoff distributions for cooperating individuals, and suggest that biological market theory, which incorporates partner choice and competition for partners, is necessary to understand helping behaviour in societies like that ofP. dominula. Traditional models are likely to overestimate the incentive to stay and help, and therefore the amount of help provided, and may underestimate the size of reproductive concession required to retain subordinates. These findings are relevant for a wide range of cooperative breeders where there is dispersal between social groups.
Topological features of a gene co-expression network predict patterns of natural diversity in environmental response
Authors: Des Marais David L. , Guerrero Rafael F. , Lasky Jesse R. , Scarpino Samuel V.
Published: June 2017

Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors—drought and cold—in
Arabidopsis thaliana
. Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE. We suggest that the observed topologies reflect different constraints on the genetic pathways involved in environmental response. The approach presented here may inform predictive models linking genetic variation in molecular signalling networks with phenotypic variation, specifically traits involved in environmental response.
Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island
Authors: Sarovich Derek S. , Chapple Stephanie N. J. , Price Erin P. , Mayo Mark , Holden Matthew T. G. , Peacock Sharon J. , Currie Bart J.
Published: June 2017

Melioidosis is a tropical disease caused by the bacterium Burkholderia pseudomallei. Outbreaks are uncommon and can generally be attributed to a single point source and strain. We used whole-genome sequencing to analyse B. pseudomallei isolates collected from an historical 2-year long case cluster that occurred in a remote northern Australian indigenous island community, where infections were previously linked to a contaminated communal water supply. We analysed the genome-wide relatedness of the two most common multilocus sequence types (STs) involved in the outbreak, STs 125 and 126. This analysis showed that although these STs were closely related on a whole-genome level, they demonstrated evidence of multiple recombination events that were unlikely to have occurred over the timeframe of the outbreak. Based on epidemiological and genetic data, we also identified two additional patients not previously associated with this outbreak. Our results confirm the previous hypothesis that a single unchlorinated water source harbouring multiple B. pseudomallei strains was linked to the outbreak, and that increased melioidosis risk in this community was associated with Piper methysticum root (kava) consumption.
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
Authors: Bolouri Hamid , Farrar Jason E. , Triche Timothy , Ries Rhonda E. , Lim Emilia L. , Alonzo Todd A. , Ma Yussanne , Moore Richard , Mungall Andrew J. , Marra Marco A. , Zhang Jinghui , Ma Xiaotu , Liu Yu , Liu Yanling , Guidry Auvil Jaime M. , Davidsen Tanja M. , Gesuwan Patee , Hermida Leandro C. , Salhia Bodour , Capone Stephen , Ramsingh Giridharan , Zwaan Christian Michel , Noort Sanne , Piccolo Stephen R. , Kolb E. Anders , Gamis Alan S. , Smith Malcolm A. , Gerhard Daniela S. , Meshinchi Soheil
Published: June 2017

We present the molecular landscape of pediatric acute myeloid leukemia (AML), characterizing nearly 1,000 participants in Children’s Oncology Group (COG) AML trials. The COG/NCI TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA, miRNA sequencing and CpG methylation profiling. Validated DNA variants revealed diverse, infrequent mutations with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including novel gene fusions and focalMBNL1,ZEB2, andELF1deletions, were disproportionately prevalent in young as compared to adult patients. Conversely,DNMT3AandTP53mutations, common in adults, are conspicuously absent from virtually all pediatric cases. NovelGATA2,FLT3, andCBLmutations, recurrentMYC-ITD, NRAS, KRAS, andWT1mutations are frequent in pediatric AML. Deletions, mutations, and promoter DNA hypermethylation convergently impact Wnt signaling, Polycomb repression, innate immune cell interactions, and a cluster of zinc finger genes associated withKMT2Arearrangements. These results highlight the need for, and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.
Non-latching positive feedback enables robust bimodality by de-coupling expression noise from the mean
Authors: Razooky Brandon S. , Cao Youfang , Perelson Alan S. , Simpson Michael L. , Weinberger Leor S.
Published: June 2017

Fundamental to biological decision-making is the ability to generate bimodal expression patterns where two alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV’s fate decision between active replication and viral latency. We find that the HIV Tat protein manipulates the intrinsic toggling of HIV’s promoter, the LTR, to generate bimodal ON-OFF expression, and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit’s non-cooperative ‘non-latching’ feedback architecture is optimized to slow the promoter’s toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that non-latching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean-expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV’s decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.
Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
Authors: Viejo Guillaume , Cortier Thomas , Peyrache Adrien
Published: June 2017

Understanding how neurons cooperate to integrate sensory inputs and guide behavior is a fundamental problem in neuroscience. A large body of methods have been developed to study neuronal firing at the single cell and population levels, generally seeking interpretability as well as predictivity. However, these methods are usually confronted with the lack of ground-truth necessary to validate the approach. Here, using neuronal data from the head-direction (HD) system, we present evidence demonstrating how gradient boosted trees, a non-linear and supervised Machine Learning tool, can learn the relationship between behavioral parameters and neuronal responses with high accuracy by optimizing the information rate. Interestingly, and unlike other classes of Machine Learning methods, the intrinsic structure of the trees can be interpreted in relation to behavior (e.g. to recover the tuning curves) or to study how neurons cooperate with their peers in the network. We show how the method, unlike linear analysis, reveals that the coordination in thalamo-cortical circuits is qualitatively the same during wakefulness and sleep, indicating a brain-state independent feed-forward circuit. Machine Learning tools thus open new avenues for benchmarking model-based characterization of spike trains.

Author summary

The thalamus is a brain structure that relays sensory information to the cortex and mediates cortico-cortical interaction. Unraveling the dialogue between the thalamus and the cortex is thus a central question in neuroscience, with direct implications on our understanding of how the brain operates at the macro scale and of the neuronal basis of brain disorders that possibly result from impaired thalamo-cortical networks, such as absent epilepsy and schizophrenia. Methods that are classically used to study the coordination between neuronal populations are usually sensitive to the ongoing global dynamics of the networks, in particular desynchronized (wakefulness and REM sleep) and synchronized (non-REM sleep) states. They thus fail to capture the underlying temporal coordination. By analyzing recordings of thalamic and cortical neuronal populations of the HD system in freely moving mice during exploration and sleep, we show how a general non-linear encoder captures a brain-state independent temporal coordination where the thalamic neurons leading their cortical targets by 20-50ms in all brain states. This study thus demonstrates how methods that do not assume any models of neuronal activity may be used to reveal important aspects of neuronal dynamics and coordination between brain regions.
vqtl: AnRpackage for Mean-Variance QTL Mapping
Authors: Corty Robert W. , Valdar William
Published: June 2017

We presentvqtl, anRpackage for mean-variance QTL mapping. This QTL mapping approach tests for genetic loci that influence the mean of the phenotype, termed mean QTL, the variance of the phenotype, termed variance QTL, or some combination of the two, termed mean-variance QTL. It is unique in its ability to correct for variance heterogeneity arising not only from the QTL itself but also from nuisance factors, such as sex, batch, or housing. This package provides functions to conduct genome scans, run permutations to assess the statistical significance, and make informative plots to communicate results. Because it is inter-operable with the popularqtlpackage and uses many of the same data structures and input patterns, it will be straightforward for geneticists to analyze future experiments withvqtlas well as re-analyze past experiments, possibly discovering new QTL.
Faster carbon accumulation in global forest soils
Authors: Zhang Weixin , Chen Yuanqi , Shi Leilei , Wang Xiaoli , Liu Yongwen , Rao Xingquan , Lin Yongbiao , Shao Yuanhu , Li Xiaobo , Liu Shengjie , Piao Shilong , Zhu Weixing , Zou Xiaoming , Fu Shenglei
Published: June 2017

Comparing soil organic carbon (SOC) stocks across space and time is a fundamental issue in global ecology. However, the conventional approach fails to determine SOC stock in an equivalent volume of mineral-soil, and therefore, SOC stock changes can be under- or overestimates if soils swell or shrink during forest development or degradation. Here, we propose to estimate SOC stock as the product of mineral-soil mass in an equivalent mineral-soil volume and SOC concentration expressed as g C Kg-1mineral-soil. This method enables researchers to compare SOC stocks across space and time. Our results show an unaccounted SOC accumulation of 2.4 - 10.1 g C m-2year-1in the 1m surface mineral-soils in global forests. This unaccounted SOC amounts to an additional C sink of 0.12 – 0.25 Pg C year-1, which equals 30 – 62% of the previously estimated annual SOC accumulation in global forests. This finding suggests that forest soils are stronger C sinks than previously recognized.
Compositional Mediation Analysis for Microbiome Studies
Authors: Sohn Michael B. , Li Hongzhe
Published: June 2017

Motivated by recent advances in causal mediation analysis and problems in the analysis of microbiome data, we consider the setting where the effect of a treatment on an outcome is transmitted through perturbing the microbial communities or compositional mediators. Compositional and high-dimensional nature of such mediators makes the standard mediation analysis not directly applicable to our setting. We propose a sparse compositional mediation model that can be used to estimate the causal direct and indirect (or mediation) effects utilizing the algebra for compositional data in the simplex space. We also propose tests of total and component-wise mediation effects using bootstrap. We conduct extensive simulation studies to assess the performance of the proposed method and apply the method to a real metagenomic dataset to investigate the effect of fat intake on body mass index mediated through the gut microbiome composition.
Phylogeographic separation and formation of sexually discrete lineages in a global population ofYersinia pseudotuberculosis
Authors: Seecharran Tristan , Kalin-Mänttäri Laura , Koskela Katja A. , Nikkari Simo , Dickins Benjamin , Corander Jukka , Skurnik Mikael , McNally Alan
Published: June 2017

Yersinia pseudotuberculosisis a Gram negative intestinal pathogen of humans and has been responsible for several nation-wide gastro-intestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenicYersinia, Y. pestisandY. enterocoliticaallowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no large-scale global population genomic analysis ofY. pseudotuberculosishas been performed. Here we present analyses of the genomes of 134 strains ofY. pseudotuberculosisisolated from around the world, from multiple ecosystems since 1960’s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.
A multi-parent advanced generation inter-cross population for genetic analysis of multiple traits in cowpea (Vigna unguiculataL. Walp.)
Authors: Huynh Bao-Lam , Ehlers Jeffrey D. , Munoz-Amatriain Maria , Lonardi Stefano , Santos Jansen R. P. , Ndeve Arsenio , Batieno Benoit J. , Boukar Ousmane , Cisse Ndiaga , Drabo Issa , Fatokun Christian , Kusi Francis , Agyare Richard Y. , Guo Yi-Ning , Herniter Ira , Lo Sassoum , Wanamaker Steve I. , Close Timothy J. , Roberts Philip A.
Published: June 2017

Development and analysis of Multiparent Advanced Generation Inter-Cross (MAGIC) populations have been conducted with several crop plants to harness the potential for dissecting the genetic structure of traits and improving breeding populations. We developed a first MAGIC population for cowpea (Vigna unguiculataL. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in sub-Saharan Africa (SSA) where cowpea is vitally important in the human diet and in local economies. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each of the founder parents, followed by single-seed descent, resulting in 365 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. This was confirmed by SNP genotyping with the cowpea Illumina 60K iSelect BeadArray. Following filtering to eliminate duplicates, sister lines and accidental selfing events, a core set of 305 F8 RILs was chosen as the primary population. The F8 lines were on average 99.74% homozygous while also diverse in agronomic traits including flowering time, growth habit, maturity, yield potential and seed characteristics across environments. Trait-associated SNPs were identified for most of the parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by genetic mapping in biparental RIL populations. The distribution of recombination frequency varied considerably between chromosomes, with recombination hotspots distributed mostly in the telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain and high-resolution genetic mapping for gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.
A systematic survey of centrality measures for protein-protein interaction networks
Authors: Ashtiani Minoo , Salehzadeh-Yazdi Ali , Razaghi-Moghadam Zahra , Hennig Holger , Wolkenhauer Olaf , Mirzaie Mehdi , Jafari Mohieddin
Published: June 2017

Background

Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

Results

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

Conclusions

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.
Dissecting super-enhancer hierarchy based on chromatin interactions
Authors: Huang Jialiang , Li Kailong , Cai Wenqing , Liu Xin , Zhang Yuannyu , Orkin Stuart H. , Xu Jian , Yuan Guo-Cheng
Published: June 2017

Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.
Pleistocene climate change and the formation of regional species pools
Authors: Calatayud Joaquín , Rodríguez Miguel Ángel , Molina-Vengas Rafael , Leo María , Hórreo Jose Luís , Hortal Joaquín
Published: June 2017

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100053). Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We use a network approach to identify regional and sub-regional faunas of EuropeanCarabusbeetles, and analyse the effects of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration ofCarabusfaunas occurred during the Pleistocene. Our results show how extreme recent historical events –such as Pleistocene climate cooling, rather than just deep-time evolutionary processes, can profoundly modify the composition and structure of geographic species pools.
Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals
Authors: Getz Michael , Swanson Lee , Sahoo Debashish , Ghosh Pradipta , Rangamani Padmini
Published: June 2017

Cellular levels of the versatile second messenger, cyclic-(c)AMP are regulated by the antagonistic actions of the canonical G protein→adenylyl cyclase pathway that is initiated by G-protein-coupled receptors (GPCRs) and by phosphodiesterases (PDEs); dysregulated cAMP signaling drives many diseases, including cancers. Recently, an alternative paradigm for cAMP signaling has emerged, in which growth factor-receptor tyrosine kinases (RTKs;e.g., EGFR) access and modulate G proteins via cytosolic guanine-nucleotide exchange modulator (GEM), GIV/Girdin; dysregulation of this pathway is frequently encountered in cancers. Here we present a comprehensive network-based compartmental model for the paradigm of GEM-dependent signaling that reveals unforeseen crosstalk and network dynamics between upstream events and the various feedback-loops that fine-tune the GEM action of GIV, and captures the experimentally determined dynamics of cAMP. The model also reveals that GIV acts a tunable control-valve within the RTK→cAMP pathway; hence, it modulates cAMP via mechanisms distinct from the two most-often targeted classes of cAMP modulators, GPCRs and PDEs.
Standing balance assessment using a head-mounted wearable device
Authors: Salisbury Joseph P. , Keshav Neha U. , Sossong Anthony D. , Sahin Ned T.
Published: June 2017

Background:The presence of accelerometers in smartphones has enabled low-cost balance assessment. Smartglasses, which contain an accelerometer similar to that of smartphones, could provide a safe and engaging platform for virtual and augmented reality balance rehabilitation; however, the validity of head-mounted measurement of balance using smartglasses has not been investigated.

Objective:To perform preliminary validation of a smartglasses-based balance accelerometry measure (BAM) compared with previously validated waist-based BAM.

Methods:42 healthy individuals (26 male, 16 female; mean age ± SD = 23.8 ± 5.2 years) participated in the study. Following the BAM protocol, each subject performed two trials of six balance stances while accelerometer and gyroscope data were recorded from smartglasses (Google Glass). Test-retest reliability and correlation were determined relative to waist-based BAM as used in the NIH Standing Balance Toolbox.

Results:Balance measurements obtained using a head-mounted wearable were highly correlated with those obtained through a waist-mounted accelerometer (Spearman’s rank correlation coefficient = 0.85). Test-retest reliability was high (ICC = 0.85, 95% CI 0.81-0.88), and in good agreement with waist balance measurements (ICC = 0.84, 95% CI 0.80-0.88). Taking into account the total NPL magnitude improved inter-device correlation (0.90) while maintaining test-retest reliability (0.87, 95% CI 0.83-0.90). All subjects successfully completed the study, demonstrating the feasibility of using a head-mounted wearable to assess balance in a healthy population.

Conclusion:Balance measurements derived from the smartglasses-based accelerometer were consistent with those obtained using a waist-mounted accelerometer. Given this and the potential for smartglasses in vestibular rehabilitation, the continued development and validation of balance assessment measurements obtained via smartglasses is warranted. This research was funded in part by Department of Defense/Defense Health Program (#W81XWH-14-C-0007, SBIR Phase II contract awarded to TIAX, LLC).