bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevention of all-terrain vehicle injuries: A systematic review from The Eastern Association for the Surgery of Trauma
Authors: Rattan Rishi , Joseph D’Andrea K. , Dente Christopher J. , Klein Eric N. , Kimbrough Mary K. , Nguyen Jonathan , Simmons Jon D. , O’Keeffe Terence , Crandall Marie 
Published: January 2018

BACKGROUND
Despite increasing usage since their introduction, there exist no evidence-based guidelines on all-terrain vehicles (ATVs) and injury prevention. While the power and speed of these vehicles has increased over time, advancements in ATV safety have been rare.

METHODS
A priori questions about ATV injury pattern and the effect of helmet and safety equipment use and legislation mandating use were developed. A query of MEDLINE, PubMed, Cochrane Library, and Embase for all-terrain vehicle injury was performed. Letters to the editor, case reports, book chapters, and review articles were excluded. Grading of Recommendations Assessment, Development, and Evaluation methodology was used to perform a systematic review and create recommendations.

RESULTS
Twenty-eight studies were included. Helmet use reduced traumatic brain injury (TBI). However, studies examining whether legislation mandating helmet use reduced TBI had mixed results. When ATV safety legislation was enforced, overall injury rates and mortality decreased. However, enforcement varied widely and lack of enforcement led to decreased compliance with legislation and mixed results. There was not enough evidence to determine the effectiveness of non–helmet-protective equipment.

CONCLUSION
Helmet use when riding an ATV reduced the rate of TBI. ATV safety legislation, when enforced, also reduced morbidity and mortality. Compliance with laws is often low, however, possibly due to poor enforcement. We recommend helmet use when riding on an ATV to reduce TBI. We conditionally recommend implementing ATV safety legislation as a means to reduce ATV injuries, noting that enforcement must go hand in hand with enactment to ensure compliance.
Behavioral and neuroanatomical approaches in models of neurodevelopmental disorders: opportunities for translation
Authors: Silverman Jill L. , Ellegood Jacob 
Published: January 2018

Purpose of reviewThis review highlights the invaluable contribution of in-vivo rodent models in dissecting the underlying neurobiology for numerous neurodevelopmental disorders. Currently, models are routinely generated with precision genomics and characterized for research on neurodevelopmental disorders. In order to impact translation, outcome measures that are translationally relevant are essential. This review emphasizes the importance of accurate neurobehavioral and anatomical analyses.Recent findingsNumerous well validated assays for testing alterations across behavioral domains with sensitivity and throughput have become important tools for studying the effects of genetic mutations on neurodevelopment. Recent work has highlighted relationships and links between behavioral outcomes and various anatomical metrics from neuroimaging via magnetic resonance. These readouts are biological markers and outcome measures for translational research and will be have important roles for genetic or pharmacologic intervention strategies.SummaryCombinatorial approaches that leverage translationally relevant behavior and neuroanatomy can be used to develop a platform for assessment of cutting edge preclinical models. Reliable, robust behavioral phenotypes in preclinical model systems, with clustering of brain disease will lead to well informed, precise biochemical mechanistic hypotheses. Ultimately, these steadfast workhorse techniques will accelerate the progress of developing and testing targeted treatments for multiple neurodevelopmental disorders.
Motor development and delay: advances in assessment of motor skills in autism spectrum disorders
Authors: Wilson Rujuta B. , Enticott Peter G. , Rinehart Nicole J. 
Published: January 2018

Purpose of review
Motor impairments in neurodevelopmental disorders, specifically autism spectrum disorder (ASD), are prevalent and pervasive. Moreover, motor impairments may be the first sign of atypical development in ASD and likely contribute to abnormalities in social communication. However, measurement of motor function in ASD has lagged behind other behavioral phenotyping. Quantitative and neurodiagnostic measures of motor function can help identify specific motor impairments in ASD and the underlying neural mechanisms that might be implicated. These findings can serve as markers of early diagnosis, clinical stratification, and treatment targets.

Recent findings
Here, we briefly review recent studies on the importance of motor function to other developmental domains in ASD. We then highlight studies that have applied quantitative and neurodiagnostic measures to better measure motor impairments in ASD and the neural mechanisms that may contribute to these abnormalities.

Summary
Information from advanced quantitative and neurodiagnostic methods of motor function contribute to a better understanding of the specific and subtle motor impairments in ASD, and the relationship of motor function to language and social development. Greater utilization of these methods can assist with early diagnosis and development of targeted interventions. However, there remains a need to utilize these approaches in children with neurodevelopmental disorders across a developmental trajectory and with varying levels of cognitive function.
A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits
Authors: Hibrand Saint-Oyant L. , Ruttink T. , Hamama L. , Kirov I. , Lakwani D. , Zhou N.-N. , Bourke P.M. , Daccord N. , Leus L. , Schulz D. , Van de Geest H. , Hesselink T. , Van Laere K. , Balzergue S. , Thouroude T. , Chastellier A. , Jeauffre J. , Voisine L. , Gaillard S. , Borm T.J.A. , Arens P. , Voorrips R.E. , Maliepaard C. , Neu E. , Linde M. , Le Paslier M.C. , Bérard A. , Bounon R. , Clotault J. , Choisne N. , Quesneville H. , Kawamura K. , Aubourg S. , Sakr S. , Smulders M.J.M. , Schijlen E. , Bucher E. , Debener T. , De Riek J. , Foucher F. 
Published: January 2018

ABSTRACTRose is the world’s most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genusRosaby sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.We produced a haploid rose line fromR. chinensis‘Old Blush’ and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eightRosaspecies. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A roseAPETALA2homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny acrossRosaceae.
EEG-based personal identification: comparison of different functional connectivity metrics
Authors: Fraschini Matteo , Didaci Luca , Marcialis Gian Luca 
Published: January 2018

ABSTRACTGrowing interest is devoted to understanding how brain signals recorded from scalp electroencephalography (EEG) may represent unique fingerprints of individual neural activity. In this context, the present paper aims to investigate the impact of some of the most commonly used techniques to estimate functional connectivity on the ability to unveil personal distinctive patterns of inter-regional interactions. Different metrics, commonly used to estimate functional connectivity and derived centrality measures, were compared in terms of equal error rate. It is widely accepted that each metric carries specific information in respect to the underlying interactions network. Nevertheless, the reason why these metrics convey different subject specific information has not been investigated yet. Experimental results on two publicly available datasets suggest that different functional connectivity metrics define a peculiar subjective profile of connectivity and have different mechanisms to detect subject-specific patterns of inter-channel interactions. It is important to consider the effects that frequency content and spurious connectivity values may play in determining subject-specific characteristics.
FlowPot axenic plant growth system for microbiota research
Authors: Kremer James M. , Paasch Bradley C. , Rhodes David , Thireault Caitlin , Froehlich John E. , Schulze-Lefert Paul , Tiedje James M. , He Sheng Yang 
Published: January 2018

AbstractThe presence of resident microbiota on and inside plants is hypothesized to influence many phenotypic attributes of the host. Likewise, host factors and microbe-microbe interactions are believed to influence microbial community assembly. Rigorous testing of these hypotheses necessitates the ability to grow plants in the absence or presence of resident or defined microbiota. To enable such experiments, we developed the scalable and inexpensive FlowPot growth platform. FlowPots have a sterile peat substrate amenable to colonization by microbiota, and the platform supports growth of the model plant Arabidopsis thaliana in the absence or presence of soil-derived microbial communities. Mechanically, the FlowPot system is unique in that it allows for total-saturation of the sterile substrate by “flushing” with water and/or nutrient solution via an irrigation port. The irrigation port also facilitates passive drainage of the substrate, preventing root anoxia. Materials to construct an individual FlowPot total ∼$2. A simple experiment with 12 FlowPots requires ∼4.5 h of labor following peat and seed sterilization. Plants are grown on FlowPots within a standard tissue culture microbox after inoculation, thus the Flowpot system is modular and does not require a sterile growth chamber. Here, we provide a detailed assembly and microbiota inoculation protocol for the FlowPot system. Collectively, this standardized suite of tools and colonization protocols empowers the plant microbiome research community to conduct harmonized experiments to elucidate the rules microbial community assembly, the impact of microbiota on host phenotypes, and mechanisms by which host factors influence the structure and function of plant microbiota.
Imputation of posterior linkage probability relations reveals a significant influence of structural 3D constraints on linkage disequilibrium
Authors: Gerber Susanne , Fournier David , Hewel Charlotte , Horenko Illia 
Published: January 2018

Genetic association studies have become increasingly important in unraveling the genetics of diseases or complex traits. Despite their value for modern genetics, conflicting conclusions often arise through the difficulty of confirming and replicating experimental results. We argue that this problem is largely based on the application of statistical relation measures that are not appropriate for genomic data analysis and demonstrate that the standard measures used for Genome-wide association studies or genomics linkage analysis bear a statistic bias. This may come from the violation of underlying assumptions (such as independence or stationarity) as well as from other conceptual limitations in the measures or relations, such as missing invariance with respect to coding or the inability to reflect latent factors. Attempts to introduce unbiased relation measures that avoid these limitations are usually computationally expensive and do not scale for large data sizes being typical for genomics applications.To tackle these problems, we propose a straightforwardly computable relation measure called Linkage Probability (LP). This measure provides the posterior probability of a relation between two categorical data sets and considers potential biases from latent variables. We compare several aspects of popular relation measures through an illustrative example and human genomics data. We demonstrate that the application ofLPto the analysis of Single Nucleotide Polymorphisms (SNP) reveals latent 3D steric effects within 1D SNP data, that approximate to chromatin loops captured by high resolution Hi-C maps.
iTAP, a novel iRhom interactor, controls TNF secretion by policing the stability of iRhom/TACE
Authors: Oikonomidi Ioanna , Burbridge Emma , Cavadas Miguel , Sullivan Graeme , Clancy Danielle , Collis Blanka , Brezinova Jana , Humpolickova Jana , Hu Tianyi , Bileck Andrea , Gerner Christopher , Bolado Alfonso , von Kriegsheim Alex , Strisovsky Kvido , Martin Seamus J. , Adrain Colin 
Published: January 2018

AbstractThe apical inflammatory cytokine TNF regulates numerous important biological processes including inflammation and cell death, and drives inflammatory diseases. TNF secretion requires ADAM17/TACE, which cleaves TNF from its transmembrane tether, releasing it for signalling. The trafficking of ADAM17/TACE to the cell surface, and stimulation of its proteolytic activity, depends on membrane proteins, called iRhoms. To delineate how the TNF/TACE/iRhom axis is regulated, we performed an immunoprecipitation/mass spectrometry screen to identify iRhom-binding proteins. Here we report a novel protein, that we name iTAP (iRhom tail-associatedprotein) that binds to iRhoms, enhancing the stability of iRhoms and TACE, preventing their degradation in lysosomes. iTAP-null primary human macrophages, or tissues from iTAP KO mice, are dramatically depleted in the levels of iRhom2 and active TACE, and are, consequently, profoundly impaired in TNF production. Our work illustrates iTAP as a physiological rheostat controlling TNF signalling and a novel target for the control of inflammation.
Binding during sequence learning does not alter cortical representations of individual actions
Authors: Beukema Patrick , Diedrichsen Jörn , Verstynen Timothy 
Published: January 2018

ABSTRACTAs a movement sequence is learned, serially ordered actions get bound together into sets in order to reduce computational complexity during planning and execution. Here we examined how the binding of serial actions alters the cortical representations of individual movements. Across five weeks of practice, healthy human subjects learned either a complex 32-item sequence of finger movements (Trained group, N=9) or randomly ordered actions (Control group, N=9). After five weeks of training, responses during sequence production in the Trained group were correlated, consistent with being bound together under a common command. These behavioral changes, however, did not coincide with plasticity in the multivariate representations of individual finger movements, assessed using fMRI, at any level of the cortical motor hierarchy. This suggests that the representations of individual actions remain stable, even as the execution of those same actions become bound together in the context of producing a well learned sequence.
Visualizing BDNF cell-to-cell transfer reveals astrocytes are the primary recipient of neuronal BDNF
Authors: Stahlberg Markus A. , Kügler Sebastian , Dean Camin 
Published: January 2018

AbstractBrain-derived neurotrophic factor (BDNF) is essential for neuronal growth, differentiation, and synaptic plasticity. Although the release and effects of BDNF have been well-studied separately, the transfer of BDNF between cells has not been investigated. Using a four-fluorophore imaging approach to identify both the cell of origin and target cells, we quantified the transfer of BDNF. Surprisingly, we found that astrocytes are the main recipient of neuronally expressed BDNF. We further found that astrocytes specifically take up mature (not pro) BDNF released by neurons. Over-expression of TrkB in neurons redirects released BDNF from astrocytes to neurons, indicating that TrkB levels determine neuronal versus astrocytic BDNF uptake. Increased neuronal activity further increased astrocytic (but not neuronal) uptake of neuronally expressed BDNF. Finally, we demonstrate that astrocytes are not simply a sink for excess BDNF, but that BDNF taken up by astrocytes mediates physiological effects on the astrocytic population by increasing astrocytic territory.
Crop domestication and pathogen virulence: Interactions of tomato andBotrytisgenetic diversity
Authors: Soltis Nicole E. , Atwell Susanna , Shi Gongjun , Fordyce Rachel , Gwinner Raoni , Gao Dihan , Shafi Aysha , Kliebenstein Daniel J. 
Published: January 2018

AbstractHuman selection during crop domestication alters numerous traits, including disease resistance. Studies of qualitative resistance to specialist pathogens typically find decreased resistance in domesticated crops in comparison to their wild relatives. However, less is known about how crop domestication affects quantitative interactions with generalist pathogens. To study how crop domestication impacts plant resistance to generalist pathogens, and correspondingly how this interacts with the pathogen’s genetics, we infected a collection of wild and domesticated tomato accessions with a genetically diverse population of the generalist pathogenBotrytis cinerea. We quantified variation in lesion size of 97B. cinereagenotypes (isolates) on 6 domesticatedSolanum lycopersicumand 6 wildS. pimpinellifoliumgenotypes. This showed that lesion size was significantly controlled by plant domestication, plant genetic variation, and the pathogen’s genotype. Overall, resistance was slightly elevated in the wild germplasm in comparison to domesticated tomato accessions. Genome-wide association (GWA) mapping inB. cinereaidentified a highly polygenic collection of genes. This suggests that breeding against this pathogen would need to utilize a diversity of isolates to capture all possible mechanisms. Critically, we identified a discrete subset ofB. cinereagenes where the allelic variation was linked to altered virulence against the wild versus domesticated tomato accessions. This indicates that this generalist pathogen already has the necessary allelic variation in place to handle the introgression of wild resistance mechanisms into the domesticated crop. Future studies are needed to assess how these observations extend to other domesticated crops and other generalist pathogens.
Lineage space and the propensity of bacterial cells to undergo growth transitions
Authors: Bandyopadhyay Arnab , Wang Huijing , Ray J. Christian J. 
Published: January 2018

AbstractThe molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity. Such regulatory mechanisms form networks that contain thresholds between phenotypes. Populations of cells can be poised near the threshold so that a subset of the population probabilistically undergoes the phenotypic transition. We sought to characterize the diversity of bacterial populations around a growth-modulating threshold via analysis of the effect of non-genetic inheritance, similar to conditions that create antibiotictolerant persister cells and other examples of bet hedging. Using simulations and experimental lineage data inEscherichia coli, we present evidence that regulation of growth amplifies the dependence of growth arrest on cellular lineage, causing clusters of related cells undergo growth arrest in certain conditions. Our simulations predict that lineage correlations and the sensitivity of growth to changes in toxin levels coincide in a critical regime. Below the critical regime, the sizes of related growth arrested clusters are distributed exponentially, while in the critical regime clusters sizes are more likely to become large. Furthermore, phenotypic diversity can be nearly as high as possible near the critical regime, but for most parameter values it falls far below the theoretical limit. We conclude that lineage information is indispensable for understanding regulation of cellular growth.Author SummaryOne of the most important characteristics of a cell is whether it is growing. Actively growing cells can multiply exponentially. In the case of infections and cancer, growth causes problems for the host organism. On the other hand, cells that have stopped growing can allocate cellular resources toward different activities, such as bacteria surviving antibiotics and tissues in multicellular organisms performing their physiological roles. Observing small bacterial colonies in a microscope over time, we have found that cells closely related to each other often have similar growth state. We were curious if lineage dependence was an intrinsic property of growth regulation or if other factors were needed to explain this effect. We therefore built a computational model of a growing and dividing cellular colony with an encoded growth regulation network. We found that regulation of growth is sufficient for lineage dependence to emerge. We next asked if lineage dependence constrains how diverse the cellular population can become. We found that cellular diversity can reach a peak that is nearly as high as possible near the conditions that have the highest lineage dependence, but that most conditions do not permit such high diversity. We conclude that lineage is an important constraint and discuss how the growth arrest transition is in some ways like a phase transition from physics, and in some ways strikingly different, making it a unique phenomenon.
DREAM-Yara: An exact read mapper for very large databases with short update time
Authors: Dadi Temesgen Hailemariam , Siragusa Enrico , Piro Vitor C. , Andrusch Andreas , Seiler Enrico , Renard Bernhard Y. , Reinert Knut 
Published: January 2018

AbstractMotivationMapping-based approaches have become limited in their application to very large sets of references since computing an FM-index for very large databases (e.g. > 10 GB) has become a bottleneck. This affects many analyses that need such index as an essential step for approximate matching of the NGS reads to reference databases. For instance, in typical metagenomics analysis, the size of the reference sequences has become prohibitive to compute a single full-text index on standard machines. Even on large memory machines, computing such index takes about one day of computing time. As a result, updates of indices are rarely performed. Hence, it is desirable to create an alternative way of indexing while preserving fast search times.ResultsTo solve the index construction and update problem we propose the DREAM (Dynamic seaRchablE pArallel coMpressed index) framework and provide an implementation. The main contributions are the introduction of an approximate search distributor directories via a novel use of Bloom filters. We combine several Bloom filters to form an interleaved Bloom filter and use this new data structure to quickly exclude reads for parts of the databases where they cannot match. This allows us to keep the databases in several indices which can be easily rebuilt if parts are updated while maintaining a fast search time. The second main contribution is an implementation of DREAM-Yara a distributed version of a fully sensitive read mapper under the DREAM framework.Contacttemesgen.dadi@fu-berlin.deAvailabilityhttps://gitlab.com/pirovc/dream_yara/