bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological and ecological modelling reveal diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study
Authors: Coughtrie Abigail L. , Morris Denise E. , Anderson Rebecca , Begum Nelupha , Cleary David W. , Faust Saul N. , Jefferies Johanna M. , Kraaijeveld Alex R. , Moore Michael V. , Mullee Mark A. , Roderick Paul J. , Tuck Andrew , Whittaker Robert N. , Yuen Ho Ming , Doncaster C. Patrick , Clarke Stuart C. 
Published: January 2017

ABSTRACTRespiratory tract infections (RTI) are responsible for over 4 million deaths per year worldwide with pathobiont carriage a required precursor to infection. Through a cross-sectional community-based nasal self-swabbing study we sought to determine carriage epidemiology for respiratory pathogens amongst bacteria (Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonas aeruginosaandNeisseria meningitidis) and viruses (RSV, Influenza viruses A and B, Rhinovirus/Enterovirus, Coronavirus, Parainfluenza viruses 1-3 and Adenovirus (ADV)). Carriage of bacterial and viral species was shown to vary with participant age, recent RTI and the presence of other species. The spatial structure of microbial respiratory communities was less nested (more disordered) in the young (0-4 years) and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X2= 20.42,p= 0.002), indicating spatial clumping of species consistent with facilitative relationships amongst them. Deviations from a neutral model of ecological niches were observed for samples collected in the summer and from older individuals (those aged 5-17, 18-64 and ≥65 years) but not in samples collected from winter, younger individuals (those aged 0-4 years), individuals with recent RTI and individuals without recent RTI, demonstrating the importance of both neutral and niche processes in respiratory community assembly. The application of epidemiological methods and ecological theory to sets of respiratory tract samples has yielded novel insights into the factors that drive microbial community composition, such as seasonality and age, as well as species patterns and interactions within the nose.
Using high-throughput barcode sequencing to efficiently map connectomes
Authors: Peikon Ian D , Kebschull Justus M , Vagin Vasily V , Ravens Diana I , Sun Yu-Chi , Brouzes Eric , Corrêa Ivan R , Bressan Dario , Zador Anthony 
Published: January 2017

AbstractThe function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision—a “connectome”—is based on imaging methods that are slow, labor-intensive and expensive. Here we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence—an RNA “barcode”—which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and then joined into a form suitable for sequencing. Although at present the inefficiency in our hands of barcode joining precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost.
Visual motion computation in recurrent neural networks
Authors: Pachitariu Marius , Sahani Maneesh 
Published: January 2017

AbstractPopulations of neurons in primary visual cortex (V1) transform direct thalamic inputs into a cortical representation which acquires new spatio-temporal properties. One of these properties, motion selectivity, has not been strongly tied to putative neural mechanisms, and its origins remain poorly understood. Here we propose that motion selectivity is acquired through the recurrent mechanisms of a network of strongly connected neurons. We first show that a bank of V1 spatiotemporal receptive fields can be generated accurately by a network which receives only instantaneous inputs from the retina. The temporal structure of the receptive fields is generated by the long timescale dynamics associated with the high magnitude eigenvalues of the recurrent connectivity matrix. When these eigenvalues have complex parts, they generate receptive fields that are inseparable in time and space, such as those tuned to motion direction. We also show that the recurrent connectivity patterns can be learnt directly from the statistics of natural movies using a temporally-asymmetric Hebbian learning rule. Probed with drifting grating stimuli and moving bars, neurons in the model show patterns of responses analogous to those of direction-selective simple cells in primary visual cortex. These computations are enabled by a specific pattern of recurrent connections, that can be tested by combining connectome reconstructions with functional recordings.*Author summaryDynamic visual scenes provide our eyes with enormous quantities of visual information, particularly when the visual scene changes rapidly. Even at modest moving speeds, individual small objects quickly change their location causing single points in the scene to change their luminance equally fast. Furthermore, our own movements through the world add to the velocities of objects relative to our retinas, further increasing the speed at which visual inputs change. How can a biological system process efficiently such vast amounts of information, while keeping track of objects in the scene? Here we formulate and analyze a solution that is enabled by the temporal dynamics of networks of neurons.
Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community
Authors: Saha Surya , Hosmani Prashant S , Villalobos-Ayala Krystal , Miller Sherry , Shippy Teresa , Flores Mirella , Rosendale Andrew , Cordola Chris , Bell Tracey , Mann Hannah , DeAvila Gabe , DeAvila Daniel , Moore Zachary , Buller Kyle , Ciolkevich Kathryn , Nandyal Samantha , Mahoney Robert , Voorhis Joshua Van , Dunlevy Megan , Farrow David , Hunter David , Morgan Taylar , Shore Kayla , Guzman Victoria , Izsak Allison , Dixon Danielle E , Cridge Andrew , Cano Liliana , Cao Xialong , Jiang Haobo , Leng Nan , Johnson Shannon , Cantarel Brandi L , Richardson Stephen , English Adam , Shatters Robert G , Childers Chris , Chen Mei-Ju , Hunter Wayne , Cilia Michelle , Mueller Lukas A , Munoz-Torres Monica , Nelson David , Poelchau Monica F , Benoit Joshua B , Wiersma-Koch Helen , D’elia Tom , Brown Susan J 
Published: January 2017

ABSTRACTThe Asian citrus psyllid (Diaphorina citriKuwayama) is the insect vector of the bacteriumCandidatusLiberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of theD. citrigenome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that ofDrosophila melanogasterto newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles inD. citribiology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available onhttps://citrusgreening.org/.
Comparison of one-stage and two-stage genome-wide association studies
Authors: Xue Shang , Ogut Funda , Miller Zachary , Verma Janu , Bradbury Peter J. , Holland James B. 
Published: January 2017

AbstractLinear mixed models are widely used in humans, animals, and plants to conduct genome-wide association studies (GWAS). A characteristic of experimental designs for plants is that experimental units are typically multiple-plant plots of families or lines that are replicated across environments. This structure can present computational challenges to conducting a genome scan on raw (plot-level) data. Two-stage methods have been proposed to reduce the complexity and increase the computational speed of whole-genome scans. The first stage of the analysis fits raw data to a model including environment and line effects, but no individual marker effects. The second stage involves the whole genome scan of marker tests using summary values for each line as the dependent variable. Missing data and unbalanced experimental designs can result in biased estimates of marker association effects from two-stage analyses. In this study, we developed a weighted two-stage analysis to reduce bias and improve power of GWAS while maintaining the computational efficiency of two-stage analyses. Simulation based on real marker data of a diverse panel of maize inbred lines was used to compare power and false discovery rate of the new weighted two-stage method to single-stage and other two-stage analyses and to compare different two-stage models. In the case of severely unbalanced data, only the weighted two-stage GWAS has power and false discovery rate similar to the one-stage analysis. The weighted GWAS method has been implemented in the open-source software TASSEL.
Targeted capture of complete coding regions across divergent species
Authors: Schott Ryan K , Panesar Bhawandeep , Card Daren C , Preston Matthew , Castoe Todd A , Chang Belinda SW 
Published: January 2017

AbstractDespite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
Experimental inhibition of a key cellular antioxidant affects vocal communication
Authors: Messina Simone , Eens Marcel , Casasole Giulia , AbdElgawad Hamada , Asard Han , Pinxten Rianne , Costantini David 
Published: January 2017

Summary

There is substantial interest of evolutionary ecologists in the proximate mechanisms that modulate vocal communication. In recent times, there has been growing interest in the role of oxidative stress as a mediator of avian song expression.

Here, we tested whether the experimental inhibition of the synthesis of a key cellular antioxidant (glutathione) reduces song rate metrics of male European starlings (Sturnus vulgaris). We measured the effect of our treatment on total song rate and on its two components, undirected and nest‐box‐oriented song, outside the breeding season.

Treated males that did not own a nest‐box (subordinate males likely to be of lower quality) suffered increased oxidative stress relative to untreated males, while treated males that owned a nest‐box (dominant males likely to be of higher quality) did not. Treated non‐owners also reduced their undirected song rate, whereas treated nest‐box owners did not suffer any reduction in song rate.

Our results revealed that inhibition of a key cellular antioxidant results in decreased vocal communication in a social vertebrate, and that this effect is dependent on its social status (nest‐box owner vs. non‐owner).

This work provides support for the hypothesis that acoustic signals may honestly convey information about the individual oxidative status and capacity to regulate the oxidative balance. Our findings raise the possibility of hitherto unexplored impacts of oxidative stress on fitness traits in social species.

A lay summary is available for this article.
The tortoise and the hare: reducing resource availability shifts competitive balance between plant species
Authors: Pearson Dean E. , Ortega Yvette K. , Maron John L. 
Published: January 2017

Summary

Determining how changes in abiotic conditions influence community interactions is a fundamental challenge in ecology. Meeting this challenge is increasingly imperative in the Anthropocene where climate change and exotic species introductions alter abiotic context and biotic composition to reshuffle natural systems.

We created plant assemblages consisting of monocultures or equal abundance of the native community dominant bluebunch wheatgrass (Pseudoroegneria spicata) and the exotic spotted knapweed (Centaurea stoebe), a co‐occurring invasive forb that has overtaken grasslands across the western United States. We subjected these composition treatments to drought (20% of average precipitation vs. average) and herbivory on C. stoebe by its biocontrol agent Cyphocleonus achates to explore how reduced precipitation might influence the effects of competition and biocontrol herbivory on C. stoebe's abundance.

At the end of 7 years, C. stoebe dominated mixed‐species plots under normal precipitation conditions, with biomass 50% greater than that of the native P. spicata. However, under drought stress, P. spicata's biomass was >200% greater than C. stoebe's. Interestingly, both species were impervious to drought in monoculture, indicating the importance of the drought by competition interaction. The biocontrol herbivore reduced C. stoebe abundance and indirectly increased P. spicata biomass in mixed‐species drought plots, but these effects were only marginally significant and relatively weak. Overall, C. stoebe abundance was primarily driven by the drought by competition interaction, with negatively additive but weak effects of the drought by herbivory interaction.

The response of the exotic to the treatments was driven by rapid changes in population density linked to its fast life‐history strategy, while the native's response was driven by changes in per capita plant biomass linked to its slower life‐history strategy. Individual plant performance metrics did not predict overall population responses for the invader, indicating the importance of longer term population measures.

Synthesis. These results demonstrate that reduced precipitation inputs linked to climate change can dramatically shift the balance of plant competition, even toggling the advantage from exotic to native dominance. They also illustrate the importance of biotic interactions in predicting species responses to abiotic change.
Comparison of Parent, Peer, Psychiatric, and Cannabis Use Influences Across Stages of Offspring Alcohol Involvement: Evidence from the COGA Prospective Study
Authors: Bucholz Kathleen K. , McCutcheon Vivia V. , Agrawal Arpana , Dick Danielle M. , Hesselbrock Victor M. , Kramer John R. , Kuperman Samuel , Nurnberger John I. , Salvatore Jessica E. , Schuckit Marc A. , Bierut Laura J. , Foroud Tatiana M. , Chan Grace , Hesselbrock Michie , Meyers Jacquelyn L. , Edenberg Howard J. , Porjesz Bernice 
Published: January 2017

BackgroundAll stages of development of alcohol use disorder (AUD) have not been equally studied. While initiation of drinking has been given considerable attention, other stages have not been as thoroughly investigated. It is not clear whether the same factors are associated consistently across early and late transitions in AUD involvement. High‐risk family samples that are enriched for AUD vulnerability and transitions in AUD development offer an opportunity to examine influences across multiple stages of AUD development.MethodsData from adolescents and young adults from high‐risk families were used to study 4 transitions in AUD development—time to first drink, first drink to first problem, first drink to first diagnosis, and first problem to first diagnosis. Cox modeling was used to compare associations of parental AUD, parental separation, peer substance use, offspring ever‐use of cannabis, trauma exposures, and internalizing and externalizing psychopathology across transitions.ResultsHazards of most transitions were elevated for those who had ever used cannabis, those who attributed substance use to their peers, those with externalizing disorders, and those with parents with AUD. Many risk factors were linked to early initiation of alcohol, particularly cannabis use. Internalizing disorders were associated with later stages. Nonassaultive trauma was associated only with early initiation; assaultive trauma was not associated with any transition.ConclusionsIn this large, ethnically diverse sample of high‐risk youth, significant influences across transitions were fairly consistent, with externalizing disorders and cannabis ever‐use elevating the likelihood of each stage, and peer and parental (and especially maternal AUD) influences linked to initiation and some later stages. Finally, in light of the increasingly permissive legal and social stances toward cannabis in the United States, the marked elevations of all alcohol outcomes observed for cannabis use underscore the importance of studying the underpinnings of this relationship.
GPs' perspectives on prescribing for older people in primary care: a qualitative study
Authors: Riordan David O. , Byrne Stephen , Fleming Aoife , Kearney Patricia M. , Galvin Rose , Sinnott Carol 
Published: January 2017

AimsThe aim of this study was firstly to reveal the determinants of GP prescribing behaviour for older adults in primary care and secondly to elicit GPs' views on the potential role for broad intervention strategies involving pharmacists and/or information technology systems in general practice.MethodsSemi‐structured qualitative interviews were carried out with a purposive sample of GPs. Three multidisciplinary researchers independently coded the interview data using a framework approach. Emerging themes were mapped to the Theoretical Domains Framework (TDF), a tool used to apply behaviour change theories.ResultsSixteen GPs participated in the study. The following domains in the TDF were identified as being important determinants of GP prescribing behaviour: ‘Knowledge’, ‘Skills’, ‘Reinforcement’, ‘Memory Attention and Decision Process’, ‘Environmental Context and Resources’, ‘Social Influences’, ‘Social/Professional Role and Identity’. Participants reported that the challenges associated with prescribing for an increasingly older population will require them to become more knowledgeable in pharmacology and drug interactions and they called for extra training in these topics. GPs viewed strategies such as academic detailing sessions delivered by pharmacists or information technology systems as having a positive role to play in optimizing prescribing.ConclusionThis study highlights the complexities of behavioural determinants of prescribing for older people in primary care and the need for additional supports to optimize prescribing for this growing cohort of patients. Interventions that incorporate, but are not limited to interprofessional collaboration with pharmacists and information technology systems, were identified by GPs as being potentially useful for improving prescribing behaviour, and therefore require further exploration.
Stereotype threat and social function in opioid substitution therapy patients
Authors: von Hippel Courtney , Henry Julie D. , Terrett Gill , Mercuri Kimberly , McAlear Karen , Rendell Peter G. 
Published: January 2017

ObjectivesPeople with a history of substance abuse are subject to widespread stigmatization. It seems likely that this societal disapproval will result in feelings of stereotype threat, or the belief that one is the target of demeaning stereotypes. If so, stereotype threat has the potential to contribute to functional difficulties including poor social outcomes.MethodsEighty drug users on opioid substitution therapy and 84 demographically matched controls completed measures of mental health and social function. The opioid substitution therapy group were additionally asked to complete a measure that focused on their feelings of stereotype threat in relation to their drug use history. Bivariate correlations and hierarchical regression analyses were conducted to establish the magnitude and specificity of the relationship between stereotype threat and social functioning.ResultsRelative to controls, the opioid substitution therapy group reported higher levels of negative affect and schizotypy, and poorer social functioning, with all three of these indices significantly correlated with their feelings of stereotype threat. The results also showed that stereotype threat contributed significant unique variance to social functioning in the opioid substitution therapy group, even after taking into account other background, clinical, and mental health variables.ConclusionsSocial functioning is an important aspect of recovery, yet these data indicate that people with a history of drug abuse who believe they are the target of stereotypical attitudes have poorer social functioning. This relationship holds after controlling for the impact of other variables on social functioning, including mental health. The theoretical and practical implications of these findings are discussed.Practitioner points

Concerns about being stereotyped can shape the social experiences of opioid substitution therapy patients.

Opioid substitution therapy patients who feel negatively stereotyped experience greater social function deficits, and this relationship emerges after controlling for important clinical and mental health variables.

Understanding the relationship between feeling stereotyped and social function may assist practitioners in their treatment.

The study is cross‐sectional, and thus, experimental or longitudinal research is required to determine the causal direction between stereotype threat and social function.