bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative analysis of population-scale family trees using millions of relatives
Authors: Kaplanis Joanna , Gordon Assaf , Wahl Mary , Gershovits Michael , Markus Barak , Sheikh Mona , Gymrek Melissa , Bhatia Gaurav , MacArthur Daniel G. , Price Alkes L. , Erlich Yaniv 
Published: February 2017

AbstractFamily trees have vast applications in multiple fields from genetics to anthropology and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. Here, we collected 86 million profiles from publicly-available online data from genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of longevity by inspecting millions of relative pairs and to provide insights to population genetics theories on the dispersion of families. We also report a simple digital procedure to overlay other datasets with our resource in order to empower studies with population-scale genealogical data.One Sentence SummaryUsing massive crowd-sourced genealogy data, we created a population-scale family tree resource for scientific studies.
Optimal Response Vigor and Choice Under Non-stationary Outcome Values
Authors: Dezfouli Amir , Balleine Bernard W. , Nock Richard 
Published: February 2017

AbstractWithin a rational framework a decision-maker selects actions based on the reward-maximisation principle which stipulates they acquire outcomes with the highest values at the lowest cost. Action selection can be divided into two dimensions: selecting an action from several alternatives, and choosing its vigor, i.e., how fast the selected action should be executed. Both of these dimensions depend on the values of the outcomes, and these values are often affected as more outcomes are consumed, and so are the actions. Despite this, previous works have addressed the computational substrates of optimal actions only in the specific condition that the values of outcomes are constant, and it is still unknown what the optimal actions are when the values of outcomes are non-stationary. Here, based on an optimal control framework, we derive a computational model for optimal actions under non-stationary outcome values. The results imply that even when the values of outcomes are changing, the optimal response rate is constant rather than decreasing. This finding shows that, in contrast to previous theories, the commonly observed changes in the actions cannot be purely attributed to the changes in the outcome values. We then prove that this observation can be explained based on the uncertainty about temporal horizons; e.g., in the case of experimental protocols, the session duration. We further show that when multiple outcomes are available, the model explains probability matching as well as maximisation choice strategies. The model provides, therefore, a quantitative analysis of optimal actions and explicit predictions for future testing.
Synaptic input sequence discrimination on behavioral time-scales mediated by reaction-diffusion chemistry in dendrites
Authors: Bhalla Upinder Singh 
Published: February 2017

AbstractSequences of events are ubiquitous in sensory, motor, and cognitive function. Key computational operations, including pattern recognition, event prediction, and plasticity, involve neural discrimination of spatio-temporal sequences. Here we show that synaptically-driven reaction-diffusion pathways on dendrites can perform sequence discrimination on behaviorally relevant time-scales. We used abstract signaling models to show that this selectivity arises when inputs at successive locations are aligned with, and amplified by, propagating chemical waves triggered by previous inputs. We incorporated biological detail using sequential synaptic input onto spines in morphologically, electrically, and chemically detailed pyramidal neuronal models. Again, sequences were recognized, and local channel modulation on the length-scale of sequence input could elicit changes in neuronal firing. We predict that dendritic sequence-recognition zones occupy 5 to 20 microns and recognize time-intervals of 0.2 to 5s. We suggest that this mechanism provides highly parallel and selective neural computation in a functionally important time range.
High rates of human faecal carriage ofmcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families
Authors: Zhong Lan-Lan , Phan Hang TT , Huang Xi , Doris-Vihta Karina , Sheppard Anna E , Zeng Kun-Jiao , Li Hong-Yu , Zhang Xue-Fei , Patil Sandip , Zhang Yan-Fen , Shen Cong , Crook Derrick W , Walker A Sarah , Xing Yong , Chen Qian-yi , Lin Jia-lin , Feng Lian-Qiang , Doi Yohei , Stoesser Nicole , Tian Guo-Bao 
Published: February 2017

SynopsisBackgroundmcr-1-mediated transmissible colistin resistance in Enterobacteriaceae is concerning, given colistin is frequently used as a treatment of last resort in multidrug-resistant Enterobacteriaceae infections. Reported rates of humanmcr-1gastrointestinal carriage have historically been low.ObjectivesTo identify trends in human gastrointestinal carriage ofmcr-1positive andmcr-1-positive/cefotaxime-resistant Enterobacteriaceae in Guangzhou, China, 2011-2016, and investigate the genetic contexts ofmcr-1in a subset ofmcr-1-positive/cefotaxime-resistant strains using whole genome sequencing (WGS).MethodsOf 8,022 faecal samples collected, 497 (6.2%) weremcr-1- positive, and 182 (2.3%)mcr-1-positive/cefotaxime-resistant. Trends in carriage were assessed using iterative sequential regression. A subset ofmcr-1-positive isolates was sequenced (Illumina), and genetic contexts ofmcr-1were characterised.ResultsWe observed marked increases inmcr-1(now ~30% prevalence) and more recent (since January 2014) increases inmcr-1-positive/third-generation cephalosporin-resistant Enterobacteriaceae human colonisation (p<0.001). Sub-culturedmcr-1-positive/third-generation cephalosporin-resistant isolates were commonly multi-drug resistant.WGS of 50mcr-1/third-generation cephalosporin-resistant isolates (49Escherichia coli; 1Klebsiella pneumoniae) demonstrated bacterial strain diversity (39E. colisequence types);mcr-1in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequentmcr-1chromosomal integration; and loss of themcr-1-associated insertion sequence ISApl1in some plasmids. Significant sequence similarity with publishedmcr-1plasmid sequences was consistent with spread amongst pig, chicken and human reservoirs.ConclusionsThe high positivity rate (~10%) ofmcr-1in multidrug-resistantE. colicolonising humans is a clinical threat; the diverse genetic mechanisms (strains/plasmids/insertion sequences) associated withmcr-1have likely contributed to its dissemination, and will facilitate its persistence.
Neural Encoding of Auditory Features during Music Perception and Imagery: Insight into the Brain of a Piano PlayerAuditory Features and Music Imagery
Authors: Martin Stephanie , Mikutta Christian , Leonard Matthew K. , Hungate Dylan , Koelsch Stefan , Chang Edward F. , Millán José del R. , Knight Robert T. , Pasley Brian N. 
Published: February 2017

AbstractIt remains unclear how the human cortex represents spectrotemporal sound features during auditory imagery, and how this representation compares to auditory perception. To assess this, we recorded electrocorticographic signals from an epileptic patient with proficient music ability in two conditions. First, the participant played two piano pieces on an electronic piano with the sound volume of the digital keyboard on. Second, the participant replayed the same piano pieces, but without auditory feedback, and the participant was asked to imagine hearing the music in his mind. In both conditions, the sound output of the keyboard was recorded, thus allowing precise time-locking between the neural activity and the spectrotemporal content of the music imagery. For both conditions, we built encoding models to predict high gamma neural activity (70-150Hz) from the spectrogram representation of the recorded sound. We found robust similarities between perception and imagery – in frequency and temporal tuning properties in auditory areas.AbbreviationsECoGelectrocorticographyHGhigh gammaIFGinferior frontal gyrusMTGmiddle temporal gyrusPost-CGpost-central gyrusPre-CGpre-central gyrusSMGsupramarginal gyrusSTGsuperior temporal gyrusSTRFspectrotemporal receptive field
BRAPH: A Graph Theory Software for the Analysis of Brain Connectivity
Authors: Mijalkov Mite , Kakaei Ehsan , Pereira Joana B. , Westman Eric , Volpe Giovanni ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2017

AbstractThe brain is a large-scale complex network whose workings rely on the interaction between its various regions. In the past few years, the organization of the human brain network has been studied extensively using concepts from graph theory, where the brain is represented as a set of nodes connected by edges. This representation of the brain as a connectome can be used to assess important measures that reflect its topological architecture. We have developed a freeware MatLab-based software (BRAPH – BRain Analysis using graPH theory) for connectivity analysis of brain networks derived from structural magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET) and electroencephalogram (EEG) data. BRAPH allows building connectivity matrices, calculating global and local network measures, performing non-parametric permutations for group comparisons, assessing the modules in the network, and comparing the results to random networks. By contrast to other toolboxes, it allows performing longitudinal comparisons of the same patients across different points in time. Furthermore, even though a user-friendly interface is provided, the architecture of the program is modular (object-oriented) so that it can be easily expanded and customized. To demonstrate the abilities of BRAPH, we performed structural and functional graph theory analyses in two separate studies. In the first study, using MRI data, we assessed the differences in global and nodal network topology in healthy controls, patients with amnestic mild cognitive impairment, and patients with Alzheimer’s disease. In the second study, using resting-state fMRI data, we compared healthy controls and Parkinson’s patients with mild cognitive impairment.
RNPP-type quorum sensing regulates solvent formation and sporulation inClostridium acetobutylicum
Authors: Kotte Ann-Kathrin , Severn Oliver , Bean Zak , Schwarz Katrin , Minton Nigel P. , Winzer Klaus 
Published: February 2017

ABSTRACTThe strictly anaerobic bacteriumClostridium acetobutylicumis well known for its ability to convert sugars into organic acids and solvents, most notably the potential biofuel butanol. However, the regulation of its fermentation metabolism, in particular the shift from acid to solvent production, remains poorly understood. The aim of this study was to investigate whether cell-cell communication plays a role in controlling the timing of this shift or the extent of solvent formation. Analysis of the availableC. acetobutylicumgenome sequences revealed the presence of eight putative RNPP-type quorum sensing systems, here designatedqssAtoqssH, each consisting of RNPP-type regulator gene followed by a small open reading frame encoding a putative signalling peptide precursor. The identified regulator and signal peptide precursor genes were designatedqsrAtoqsrHandqspAtoqspH, respectively. Triplicate regulator mutants were generated in strain ATCC 824 for each of the eight systems and screened for phenotypic changes. TheqsrBmutants showed increased solvent formation during early solventogenesis and hence the QssB system was selected for further characterisation. Overexpression ofqsrBseverely reduced solvent and endospore formation and this effect could be overcome by adding short synthetic peptides to the culture medium representing a specific region of the QspB signalling peptide precursor. In addition, overexpression ofqspBincreased the production of acetone and butanol and the initial (48-hour) titre of heat-resistant endospores. Together, these findings establish a role for QssB quorum sensing in the regulation of early solventogenesis and sporulation inC. acetobutylicum.
Hitchhiking and epistasis give rise to cohort dynamics in adapting populations
Authors: Buskirk Sean W. , Peace Ryan Emily , Lang Gregory I. 
Published: February 2017

ABSTRACTBeneficial mutations are the driving force of adaptive evolution. In asexual populations, the identification of beneficial alleles is confounded by the presence of genetically-linked hitchhiker mutations. Parallel evolution experiments enable the recognition of common targets of selection, yet these targets are inherently enriched for genes of large target size and mutations of large effect. A comprehensive study of individual mutations is necessary to create a realistic picture of the evolutionarily significant spectrum of beneficial mutations. Here we utilize a bulk-segregant approach to identify the beneficial mutations across 11 lineages of experimentally-evolved yeast populations. We report that most genome sequence evolution is non-adaptive: nearly 80% of detected mutations have no discernable effects on fitness and less than 1% are deleterious. We determine the distribution of driver and hitchhiker mutations in 31 mutational cohorts, groups of up to ten mutations that arise synchronously from low frequency and track tightly with one another. Surprisingly, we find that one-third of cohorts lack identifiable driver mutations. In addition, we identify intra-cohort synergistic epistasis between mutations inhsl7andkel1, which arose together in a low frequency lineage.
Using trophic structure to reveal patterns of trait‐based community assembly across niche dimensions
Authors: Fitzgerald Daniel B. , Winemiller Kirk O. , Sabaj Pérez Mark H. , Sousa Leandro M. 
Published: February 2017

Summary

Trait‐based approaches for studying community assembly have improved understanding of mechanisms; however, the challenge of interpreting process from pattern is complicated by the possibility of multiple mechanisms operating simultaneously. Different traits may influence the assembly process in different ways. Analysing patterns of functional diversity among co‐occurring species for each trait individually may aid interpretation of complex assembly processes; yet, few studies have tested whether patterns vary depending on trait function.

We used tropical fish assemblages from the Xingu River, Brazil to test whether traits associated with resource acquisition play a stronger role in niche segregation relative to other traits. First, a null modelling approach was used to determine how trait distributions within local assemblages deviated from expectations under random assembly. Then, correlations between functional traits and stable isotope ratios (δ13C, δ15N) were used as a measure of a trait's association with trophic structure. Finally, we used mixed effects models to test whether traits having higher correlations with trophic structure also had greater deviation from null expectations. In addition, we explored how well stable isotopes explain multivariate functional trait variation and compared our correlation‐based approach for organizing traits with previous categorical approaches.

A significant relationship was found between a trait's deviation from null expectations and its correlation with isotopic patterns. Traits strongly associated with trophic structure had greater dispersion from the assemblage mean and were more evenly spaced than weakly associated traits. Traits strongly associated with trophic structure also were more clustered because trophic diversification tended to occur around some basic feeding strategies, such as benthic grazing or capturing food items from the water column. Based on redundancy analysis, isotopic ratios explained a low (11·6%) but significant portion of trait variation.

In this study system, traits strongly associated with trophic ecology were more influential in niche differentiation among coexisting species compared to weakly associated traits. These results suggest that certain traits may respond to assembly mechanisms in predictable ways despite the complex, multidimensional nature of the assembly process. Methods designed to identify differential trait response will be critical to developing a general theory of trait‐based community assembly.

A lay summary is available for this article.
Resistance of plant–plant networks to biodiversity loss and secondary extinctions following simulated environmental changes
Authors: Losapio Gianalberto , Schöb Christian 
Published: February 2017

Summary

Plant interactions are fundamental processes for structuring plant communities and are an important mechanism governing the response of plant species and communities to environmental changes. Thus, understanding the role played by the interaction network in modulating the impact of environmental changes on plant community composition and diversity is crucial. Here, we aimed to develop a new analytical and conceptual framework to evaluate the responses of plant communities to environmental changes.

This framework uses functional traits as sensitivity measures for simulated environmental changes and assesses the consequences of microhabitat loss. We show here its application to an alpine plant community where we recorded functional traits [specific leaf area (SLA) and leaf dry matter content (LDMC)] of all plants associated with three foundation species or the surrounding open areas. We then simulated primary species loss based on different scenarios of environmental change and explored community persistence to the loss of foundation species.

Generally, plant community responses differed among environmental change scenarios. In a scenario of increasing drought alone (i.e. species with lower LDMC were lost first) or increasing drought with increasing temperature (i.e. species with lower LDMC and higher SLA were lost first), the plant community resisted because drought‐tolerant foundation species tolerated those deteriorating conditions. However, in scenarios with increasing nitrogen input (i.e. species having lower SLA were lost earlier), foundation species accelerated species loss due to their early primary extinctions and the corresponding secondary extinctions of species associated to their microhabitat.

The resistance of a plant community depends on the driver of environmental change, meaning that the prediction of the fate of this system is depending on the knowledge of the main driver of environmental change. Our framework provides a mechanistic understanding of an ecosystem response to such environmental changes thanks to the integration of biology‐informed criteria of species sensitivities to environmental factors into a network of interacting species.

A lay summary is available for this article.
Finding the best management policy to eradicate invasive species from spatial ecological networks with simultaneous actions
Authors: Nicol Sam , Sabbadin Regis , Peyrard Nathalie , Chadès Iadine 
Published: February 2017

Summary

Spatial management of invasive species is more likely to be successful when multiple locations are treated simultaneously. However, selecting the best locations to act is difficult due to the many options available at any time.

We design a near‐optimal policy for applying multiple actions simultaneously for faster invasive species control within a network. Our method uses a recent optimisation tool, the graph‐based Markov decision process (GMDP). Since the policy can be difficult to interpret, we extracted a simpler policy using classification trees. We applied our approach to the eradication of invasive mosquitofish Gambusia holbrooki from the habitat of the red‐finned blue‐eye Scaturiginichthys vermeilipinnis, a critically endangered fish with a global population that is restricted to seven artesian springs in Queensland, Australia.

The policy returned by the GMDP was to manage springs occupied by mosquitofish and their connected neighbours, unless the neighbours were occupied by red‐finned blue‐eyes.

Simultaneous management resulted in rapid declines in simulated mosquitofish occupancy even if eradication effectiveness was low; however, the cost of simultaneous eradication was high and sustained eradication effort was necessary to maintain low mosquitofish occupancy.

Synthesis and applications. Our paper finds a near‐optimal, multi‐action control policy to remove an invasive species from a multi‐species spatial network. We introduce the graph‐based Markov decision process and apply it to a real case study – eradication of invasive mosquitofish from the habitat of the red‐finned blue‐eye. We find that the graph‐based Markov decision process can generate policies for networks with extremely large state spaces; however, it works best when nodes have fewer than five neighbours. We conclude that simultaneous eradications are effective for rapid control of invasive species; however, managers should consider the cost and time required for an effective eradication program.
The impact of subcutaneous tissue suturing at caesarean section on wound complications: a meta‐analysis
Authors: Pergialiotis V , Prodromidou A , Perrea DN , Doumouchtsis SK 
Published: February 2017

BackgroundCaesarean wound complications are frequently observed in everyday practice.ObjectivesTo study whether subcutaneous tissue closure following caesarean section results in decreased wound complications.Search strategyWe systematically searched Medline (1966–2016), Scopus (2004–2016), ClinicalTrials.gov (2008–2016) and Cochrane Central Register of Controlled Trials CENTRAL (1999–2016) databases together with reference lists from included studies.Selection criteriaRandomised and quasi‐randomised trials that investigated the impact of subcutaneous tissue suturing on wound complications following caesarean section were held eligible for inclusion. Retrospective studies and prospective nonrandomised studies were excluded from the present meta‐analysis.Data collection and analysisThe methodological quality of studies was assessed with the Jadad scale. Statistical meta‐analysis was performed with the RevMan 5.3 software.Main resultsTen studies were finally included in our meta‐analysis, which involved 3696 women delivered by caesarean section. Re‐approximation of the subcutaneous tissue significantly reduced the odds of developing any type of wound complication [3811 women, random effects model (REM), odds ratio (OR) 0.66, 95% CI 0.47–0.93]. The incidence of seroma was also decreased (1979 women, REM, OR 0.53, 95% CI 0.33–0.84). On the other hand, the incidence of haematoma remained unaffected by subcutaneous closure (1663 women, REM, OR 0.74, 95% CI 0.22–2.42) as well as the likelihood of developing a wound infection (1971 women, REM, OR 0.99, 95% CI 0.70–1.41).ConclusionsThe results of our meta‐analysis suggest that subcutaneous tissue closure may benefit women undergoing caesarean section. Current data in women with high body mass index remain very limited; hence, definitive conclusions are precluded for this specific group.Tweetable abstractSubcutaneous tissue closure may benefit women undergoing caesarean section.