bluuebunny/crossref_metadata_2025 huggingface dataset:
Supervised dimension reduction for large-scale “omics” data with censored survival outcomes under possible non-proportional hazards
Authors: Spirko-Burns Lauren , Devarajan Karthik
Published: March 2019

The past two decades have witnessed significant advances in high-throughput “omics” technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive “omics” profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential time-varying effects of features, and methods for handling them have been lacking. In this paper, we propose supervised methods for feature selection and survival prediction that simultaneously deal with both issues. Our approach utilizes continuum power regression (CPR) - a framework that includes a variety of regression methods - in conjunction with the parametric or semi-parametric accelerated failure time (AFT) model. Both CPR and AFT fall within the linear models framework and, unlike black-box models, the proposed prognostic index has a simple yet useful interpretation. We demonstrate the utility of our methods using simulated and publicly available cancer genomics data.
Neuroanatomical Correlates in Bilinguals: The Case of Children and Elderly
Authors: García-Pentón Lorna , Fernández Yuriem , Duñabeitia Jon Andoni , Pérez Alejandro , Carreiras Manuel
Published: March 2019

How bilingualism modulates brain areas beyond the language regions is still controversial. Through a comprehensive set of analyses on brain structure, we investigated brain differences between Basque-Spanish bilinguals and monolinguals in children and the elderly, the most sensitive target groups to detect potential brain differences. In particular, we employed Diffusion MRI in combination with T1-MRI, network-based statistics and a graph-theoretical approach to investigate differences between bilinguals and monolinguals in structural connectivity and topological properties of brain networks. Additionally, regional grey and white matter structural differences between groups were examined. The findings suggest that the effects of bilingualism on brain structure are not solid but unstable. However, lifetime experience of active bilingualism may lead to increased neural reserve in ageing, since better global network graph-efficiency has been observed in the elderly lifelong bilinguals compared to monolinguals.
Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13
Authors: Kandathil Shaun M. , Greener Joe G. , Jones David T.
Published: March 2019

In this article, we describe our efforts in contact prediction in the CASP13 experiment. We employed a new deep learning-based contact prediction tool, DeepMetaPSICOV (or DMP for short), together with new methods and data sources for alignment generation. DMP evolved from MetaPSICOV and DeepCov and combines the input feature sets used by these methods as input to a deep, fully convolutional residual neural network. We also improved our method for multiple sequence alignment generation and included metagenomic sequences in the search. We discuss successes and failures of our approach and identify areas where further improvements may be possible. DMP is freely available at:https://github.com/psipred/DeepMetaPSICOV.
Progressive recruitment of distal MEC-4 channels determines touch response strength inC. elegans
Authors: Katta S. , Sanzeni A. , Das A. , Vergassola M. , Goodman M.B.
Published: March 2019

Touch deforms, or strains, the skin beyond the immediate point of contact. The spatiotemporal nature of the touch-induced strain fields depend on the mechanical properties of the skin and the tissues below. Somatosensory neurons that sense touch branch out within the skin and rely on a set of mechano-electrical transduction channels distributed within their dendrites to detect mechanical stimuli. Here, we sought to understand how tissue mechanics shape touch-induced mechanical strain across the skin over time and how individual channels located in different regions of the strain field contribute to the overall touch response. We leveragedC. elegans’touch receptor neurons (TRNs) as a simple model amenable toin vivowhole-cell patch clamp recording and an integrated experimental-computational approach to dissect the mechanisms underlying the spatial and temporal dynamics that we observed. Consistent with the idea that strain is produced at a distance, we show that delivering strong stimuli outside the anatomical extent of the neuron is sufficient to evoke MRCs. The amplitude and kinetics of the MRCs depended on both stimulus displacement and speed. Finally, we found that the main factor responsible for touch sensitivity is the recruitment of progressively more distant channels by stronger stimuli, rather than modulation of channel open probability. This principle may generalize to somatosensory neurons with more complex morphologies.

Through experiment and simulation, Kattaet al. reveal that pushing faster and deeper recruits more and more distant mechano-electrical transduction channels during touch. The net result is a dynamic receptive field whose size and shape depends on tissue mechanics, stimulus parameters, and channel distribution within sensory neurons.
Genomic landscape of the global oak phylogeny
Authors: Hipp Andrew L. , Manos Paul S. , Hahn Marlene , Avishai Michael , Bodénès Cathérine , Cavender-Bares Jeannine , Crowl Andrew , Deng Min , Denk Thomas , Fitz-Gibbon Sorel , Gailing Oliver , González-Elizondo M. Socorro , González-Rodríguez Antonio , Grimm Guido W. , Jiang Xiao-Long , Kremer Antoine , Lesur Isabelle , McVay John D. , Plomion Christophe , Rodríguez-Correa Hernando , Schulze Ernst-Detlef , Simeone Marco C. , Sork Victoria L. , Valencia-Avalos Susana
Published: March 2019

The tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.

We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.

Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.

The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
On Transformative Adaptive Activation Functions in Neural Networks for Gene Expression Inference
Authors: Kunc Vladimír , Kléma Jiří
Published: March 2019

Motivation

Gene expression profiling was made cheaper by the NIH LINCS program that profiles only ~1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D–GEX method employs neural networks to infer the whole profile. However, the original D–GEX can be further significantly improved.

Results

We have analyzed the D–GEX method and determined that the inference can be improved using a logistic sigmoid activation function instead of the hyperbolic tangent. Moreover, we propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves average mean absolute error of 0.1340 which is a significant improvement over our reimplementation of the original D–GEX which achieves average mean absolute error 0.1637
Cell BLAST: Searching large-scale scRNA-seq databases via unbiased cell embedding
Authors: Cao Zhi-Jie , Wei Lin , Lu Shen , Yang De-Chang , Gao Ge
Published: March 2019

An effective and efficient cell-querying method is critical for integrating existing scRNA-seq data and annotating new data. Herein, we present Cell BLAST, an accurate and robust cell-querying method. Powered by a well-curated reference database and a user-friendly Web server, Cell BLAST (http://cblast.gao-lab.org) provides a one-stop solution for real-world scRNA-seq cell querying and annotation.
Estimating and accounting for genotyping errors in RAD-seq experiments
Authors: Bresadola Luisa , Link Vivian , Buerkle C. Alex , Lexer Christian , Wegmann Daniel
Published: March 2019

In non-model organisms, evolutionary questions are frequently addressed using reduced representation sequencing techniques due to their low cost, ease of use, and because they do not require genomic resources such as a reference genome. However, evidence is accumulating that such techniques may be affected by specific biases, questioning the accuracy of obtained genotypes, and as a consequence, their usefulness in evolutionary studies. Here we introduce three strategies to estimate genotyping error rates from such data: through the comparison to high quality genotypes obtained with a different technique, from individual replicates, or from a population sample when assuming Hardy-Weinberg equilibrium. Applying these strategies to data obtained with Restriction site Associated DNA sequencing (RAD-seq), arguably the most popular reduced representation sequencing technique, revealed per-allele genotyping error rates that were much higher than sequencing error rates, particularly at heterozygous sites that were wrongly inferred as homozygous. As we exemplify through the inference of genome-wide and local ancestry of well characterized hybrids of two Eurasian poplar (Populus) species, such high error rates may lead to wrong biological conclusions. By properly accounting for these error rates in downstream analyses, either by incorporating genotyping errors directly or by recalibrating genotype likelihoods, we were nevertheless able to use the RAD-seq data to support biologically meaningful and robust inferences of ancestry among Populus hybrids. Based on these findings, we strongly recommend carefully assessing genotyping error rates in reduced representation sequencing experiments, and to properly account for these in downstream analyses, for instance using the tools presented here.
Whisker map organization in somatosensory cortex of awake, behaving mice
Authors: Wang Han Chin , LeMessurier Amy M. , Feldman Daniel E.
Published: March 2019

The whisker map in rodent somatosensory cortex is well characterized under anesthesia, but its organization during awake sensation, when cortical coding can differ strongly, is unknown. Using a novel behavioral task, we measured whisker receptive fields and maps in awake mice with 2-photon calcium imaging in vivo. During a whisker-attentive task, layer 2/3 pyramidal neurons were sharply tuned, with cells tuned to different whiskers intermixed in each column. This salt-and-pepper organization consisted of small clusters of similarly-tuned neurons superimposed on a mean subcolumnar map. Parvalbumin interneurons had broader tuning, and were more homogeneously tuned to the columnar whisker. During a sound-attentive task, whisker tuning of pyramidal cells was less heterogeneous in each column, and firing correlations increased. Thus, behavioral demands modulate fine-scale map structure, and decorrelate the whisker map during whisker-attentive behavior.
Inter-subject pattern analysis: a straightforward and powerful scheme for group-level MVPA
Authors: Wang Qi , Cagna Bastien , Chaminade Thierry , Takerkart Sylvain
Published: March 2019

Multivariate pattern analysis (MVPA) has become vastly popular for analyzing functional neuroimaging data. At the group level, two main strategies are used in the literature. The standard one is hierarchical, combining the outcomes of within-subject decoding results in a second-level analysis. The alternative one, inter-subject pattern analysis, directly works at the group-level by using, e.g, a leave-one-subject-out cross-validation. This study provides a thorough comparison of these two group-level decoding schemes, using both a large number of artificial datasets where the size of the multivariate effect and the amount of inter-individual variability are parametrically controlled, as well as two real fMRI datasets comprising respectively 15 and 39 subjects. We show that these two strategies uncover distinct significant regions with partial overlap, and that inter-subject pattern analysis is able to detect smaller effects and to facilitate the interpretation. The core source code and data are openly available, allowing to fully reproduce most of these results.
Information decomposition of multichannel EMG to map functional interactions in the distributed motor system
Authors: Boonstra Tjeerd W , Faes Luca , Kerkman Jennifer N , Marinazzo Daniele
Published: March 2019

The central nervous system needs to coordinate multiple muscles during postural control. Functional coordination is established through the neural circuitry that interconnects different muscles. Here we used multivariate information decomposition of multichannel EMG acquired from 14 healthy participants during postural tasks to investigate the neural interactions between muscles. A set of information measures were estimated from an instantaneous linear regression model and a time-lagged VAR model fitted to the EMG envelopes of 36 muscles. We used network analysis to quantify the structure of functional interactions between muscles and compared them across experimental conditions. Conditional mutual information and transfer entropy revealed sparse networks dominated by local connections between muscles. We observed significant changes in muscle networks across postural tasks localized to the muscles involved in performing those tasks. Information decomposition revealed distinct patterns in task-related changes: unimanual and bimanual pointing were associated with reduced transfer to the pectoralis major muscles, but an increase in total information compared to no pointing, while postural instability resulted in increased information, information transfer and information storage in the abductor longus muscles compared to normal stability. These findings show robust patterns of directed interactions between muscles that are task-dependent and can be assessed from surface EMG recorded during static postural tasks. We discuss directed muscle networks in terms of the neural circuitry involved in generating muscle activity and suggest that task-related effects may reflect gain modulations of spinal reflex pathways.
A new cryo-EM system for electron 3D crystallography by eEFD
Authors: Yonekura Koji , Ishikawa Tetsuya , Maki-Yonekura Saori
Published: March 2019

A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200 kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.
Inter-joint and temporal coordination change in very slow walking
Authors: Little Virginia L. , McGuirk Theresa E. , Patten Carolynn
Published: March 2019

Purpose

Very slow walking has been suggested to be a distinctively different motor behavior than walking at comfortable gait speeds. While kinematic and spatiotemporal gait parameters are known to scale with gait speed, inter-joint coordination during swing remains consistent, at least across comfortable speeds. The purpose of this study was to determine whether coordination patterns serving limb clearance and shortening differ with very slow walking, providing additional support for the premise that very slow walking represents a unique motor behavior.

Methods

We assessed nine healthy adults walking overground at their self-selected speed and two-to-three progressively slower speeds. We collected lower extremity kinematics with 3D motion analysis and quantified joint motion contributions to limb clearance and shortening. We investigated changes in coordination using linear mixed models to determine magnitude and timing differences of joint influence across walking speeds.

Results

Hip and knee influences serving limb clearance reduced considerably with slower walking speeds. Similarly, knee influence on limb shortening reduced with very slow walking. Importantly, ankle influence remained unchanged across gait speeds for limb shortening and reduced subtly for limb clearance. Temporally, joint influences on limb clearance varied across walking speeds. Specifically, the temporal order of peak hip and knee influences reversed between comfortable and very slow walking. For limb shortening the timing of ankle influence remained unchanged while the timing of knee influence occurred later in the gait cycle for slower walking speeds.

Conclusions

Our results demonstrate temporal coordination and the relative joint contributions serving limb clearance and shortening differ with very slow walking providing additional evidence that slow walking may be a behavior distinct from walking at comfortable speeds.
Segregation of floricolous ants along latitudinal and urbanization gradients
Authors: Vergnes Alan , Rome Quentin , Gayral Inès , Fontaine Colin
Published: March 2019

Recent call has been made to study the biogeography of species interactions in order to better understand ecosystems’ states and processes, as well as their response to global anthropogenic disturbances. Ants (Formicidae) are a dominant group of arthropods with a central role in ecosystem functioning. Many ant species, those feeding on liquids, are floricolous and consume nectar. The biogeography of ant-flower interactions is still poorly studied and especially in temperate area. Here we quantify variations in ant-flower interaction frequency in response to latitudinal and urbanization gradients at a country scale.

We used data from a flower-visitor monitoring program that includes pictures on 2511 flower plants across Continental France (Mainland) and over 4 years. We analysed the occurrence of the ant-flower interactions along two gradients: latitude and urbanization, this for 10 ant taxa corresponding to different taxonomical level (from family to species).

Ants visited 26 % of the sampled plants. Most of the observed ant-flower interaction involved the subfamily Formicinae (82.1 %), followed by Myrmicinae and Dolichoderinae (6.9 % and 4.6 % respectively). Globally, (i) the probability of occurrence was negatively related to latitudes (ii) and to urbanization at lower latitude. (iii) Responses to latitude among sub families, genus and species level responses were segregated and taxonomically aggregated.

At lower taxonomic levels we found clear latitudinal niche partitioning among ant taxa suggesting that competition, on both evolutionary and ecological time scales, is a major process structuring ant communities. Finally, our results highlight that the effects of large scale perturbation like urbanization can vary and affect latitudinal gradient.
Neutral genomic signatures of host-parasite coevolution
Authors: Živković Daniel , John Sona , Verin Mélissa , Stephan Wolfgang , Tellier Aurélien
Published: March 2019

Coevolution is a selective process of reciprocal adaptation between antagonistic or mutualistic symbionts and their host. Classic population genetics theory predicts the signatures of selection at the interacting loci but not the neutral genome-wide polymorphism patterns. We here build a coevolutionary model with cyclic changes in the host and parasite population sizes. Using an analytical framework, we investigate if and when these population size changes can be observed in the neutral site frequency spectrum of the host and parasite full genome data. We show that polymorphism data sampled over time can capture the changes in the population size of the parasite but not of the host because genetic drift and mutations occur on different time scales in the coevolving species. This is due to the small parasite population size at the onset of the coevolutionary history subsequently undergoing a series of strong bottlenecks. We also show that tracking coevolutionary cycles is more likely for a small amount of parasite per host and for multiple parasite generations per host generation. Our results demonstrate that time sampling of host and parasite full genome data are crucial to infer the co-demographic history of interacting species.
A seventeenth-centuryMycobacterium tuberculosisgenome supports a Neolithic emergence of theMycobacterium tuberculosiscomplex
Authors: Sabin Susanna , Herbig Alexander , Vågene Åshild J. , Ahlström Torbjörn , Bozovic Gracijela , Arcini Caroline , Kühnert Denise , Bos Kirsten I.
Published: March 2019

Background

Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modernMycobacterium tuberculosiscomplex (MTBC) genomes suggests their most recent common ancestor (MRCA) followed human migrations out of Africa ~70,000 years before present (BP). However, studies using ancient genomes as calibration points have yielded much younger MRCA dates of less than 6,000 years. Here we aim to address this discrepancy through the analysis of the highest-coverage and highest quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605 – d. 1697).

Results

A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Subsequent genomic enrichment enabled the reconstruction of a 141-fold coverageM. tuberculosisgenome. In utilizing this high-quality, high-coverage 17thcenturyM. tuberculosisgenome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.

Conclusions

The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate an MRCA date for the MTBC of 3683 BP (2253-5821 BP) and for Lineage 4 of 1651 BP (946-2575 BP) using multiple models, confirming a Neolithic emergence for the MTBC.
Cytosolic termini of the FurE transporter regulate endocytosis, pH-dependent gating and specificity
Authors: Papadaki Georgia F. , Lambrinidis George , Zamanos Andreas , Mikros Emmanuel , Diallinas George
Published: March 2019

FurE, a member of the NCS1 family, is anAspergillus nidulanstransporter specific for uracil, allantoin and uric acid. Recently we showed that C- or N-terminally truncated FurE versions are blocked for endocytosis and, surprisingly, show modified substrate specifities. Bifluorescence complementation assays and genetic analyses supported that the C- and N-termini interact dynamically and through this interaction regulate selective substrate translocation. Here we functionally dissect and delimit distinct motifs crucial for endocytosis, transport activity, substrate specificity and folding, in both cytosolic termini of FurE. Subsequently, we obtain novel genetic andin silicoevidence supporting that the molecular dynamics of specific N- and C-terminal regions affect allosterically the gating mechanism responsible for substrate selection, via pH-dependent interactions with other internal cytosolic loops and membrane lipids. Our work shows that elongated cytoplasmic termini, acquired through evolution mostly in eukaryotic transporters, provide novel specific functional roles.
De novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus for molecular analysis of aestivation
Authors: Yoshida Naoki , Kaito Chikara
Published: March 2019

The molecular mechanisms of aestivation, a state of dormancy that occurs under dry conditions at ordinary temperature, are not yet clarified. Here, we report the first de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus, which aestivates for 6-10 months during the hot and dry season. Polyadenylated RNA from tissues was sequenced to 75,320,390 paired-end reads, and the de novo assembly generated 101,682 transcripts. Of these, 100,093 transcripts had open reading frames encoding more than 25 amino acids. BLASTx analysis against the Uniprot Xenopus tropicalis protein database revealed 64,963 transcripts having little homology with an E value higher than 1E-5 and 8,147 transcripts having no homology, indicating that the African bullfrog has many novel genes that are absent in X. tropicalis. The other 28,570 transcripts had homology with an E value lower than 1E-5 for which molecular functions were estimated by gene ontology (GO) analysis and found to contain the aestivation-related genes conserved among other aestivating organisms, including the African lungfish. This study is the first to identify a comprehensive set of genes expressed in the African bullfrog, thus providing basic information for molecular level analysis of aestivation.
Taxonomic and functional anuran beta diversity of a subtropical metacommunity respond differentially to environmental and spatial predictors
Authors: Dalmolin Diego Anderson , Tozetti Alexandro Marques , Ramos Pereira Maria João
Published: March 2019

The relative contributions of environmental and spatial predictors in the patterns of taxonomic and functional anuran beta diversity were examined in 33 ponds of a metacommunity along the coast of south Brazil. Anurans exhibit limited dispersion ability and have physiological and behavioural characteristics that narrow their relationships with both environmental and spatial predictors. So, we expected that neutral processes and, in particular, niche-based processes could have similar influence on the taxonomic and functional beta diversity patterns. Variation partitioning and distance-based methods (db-RDA) were conducted with presence/absence and abundance data to examine taxonomic and functional facets and components (total, turnover and nestedness-resultant) in relation to environmental and spatial predictors. Processes determining metacommunity structure were similar between the components of beta diversity but differed among taxonomic and functional diversity. While taxonomic beta diversity was further accounted by environmental predictors, functional beta diversity responded more strongly to spatial predictors. These patterns were more evident when assessed through abundance data. These opposing patterns were contrary to what we had predicted, suggesting that while there is a taxonomic turnover mediated by environmental filters, the spatial distance promotes the trait dissimilarity between sites. Our results reinforce the idea that studies aiming to evaluate the patterns of structure in metacommunities should include different facets of diversity so that better interpretations can be achieved.
Exploring the relationship between social inclusion and special educational needs: mainstream primary perspectives
Authors: Benstead Helen
Published: March 2019

This article explores the process by which children attending mainstream UK primary schools can achieve social inclusion. It presents the findings from a systematic literature review, followed by empirical research, exploring the concept of social inclusion with particular regard to the experiences of pupils identified with SEND. The article draws upon research conducted for the author’s doctoral study, which explored management of the role of Teaching Assistants on the social inclusion of pupils identified with SEND in mainstream primary schools. Reviewing relevant literature has informed the presentation of two researcher‐ devised models, tentatively depicting the process of social inclusion for pupils identified with SEND in mainstream primary communities, as ‘fuzzy generalizations’, to inform future research. Firstly, an ‘ideal’ model of social inclusion is presented, highlighting the likely process by which pupils may achieve the end goal of social inclusion: participation. Secondly, a ‘current’ model of social inclusion is presented, which draws upon the empirical research conducted in three mainstream primary contexts for the author’s doctoral study. The two models highlight the frequent disparity between the ‘ideal’ goal of social inclusion and the current outcome of the process of social inclusion for many pupils identified with SEND in mainstream primary contexts.
Research on body‐worn cameras
Authors: Lum Cynthia , Stoltz Megan , Koper Christopher S. , Scherer J. Amber
Published: March 2019

Research Summary

In this article, we provide the most comprehensive narrative review to date of the research evidence base for body‐worn cameras (BWCs). Seventy empirical studies of BWCs were examined covering the impact of cameras on officer behavior, officer perceptions, citizen behavior, citizen perceptions, police investigations, and police organizations. Although officers and citizens are generally supportive of BWC use, BWCs have not had statistically significant or consistent effects on most measures of officer and citizen behavior or citizens’ views of police. Expectations and concerns surrounding BWCs among police leaders and citizens have not yet been realized by and large in the ways anticipated by each. Additionally, despite the large growth in BWC research, there continues to be a lacuna of knowledge on the impact that BWCs have on police organizations and police–citizen relationships more generally.

Policy Implications

Regardless of the evidence‐base, BWCs have already rapidly diffused into law enforcement, and many agencies will continue to adopt them. Policy implications from available evidence are not clear‐cut, but most likely BWCs will not be an easy panacea for improving police performance, accountability, and relationships with citizens. To maximize the positive impacts of BWCs, police and researchers will need to give more attention to the ways and contexts (organizational and community) in which BWCs are most beneficial or harmful. They will also need to address how BWCs can be used in police training, management, and internal investigations to achieve more fundamental organizational changes with the long‐term potential to improve police performance, accountability, and legitimacy in the community.
Did de‐policing cause the increase in homicide rates?
Authors: Rosenfeld Richard , Wallman Joel
Published: March 2019

Research Summary

Widespread protests and demands for accountability in the wake of broadly publicized police killings of unarmed civilians coincided with the marked upturn in homicide levels, especially in large U.S. cities, in 2015. Many observers, including prominent political figures, claimed that de‐policing caused the homicide rate to rise: Fearing increased legal liability and publicity, the police employed less proactive enforcement and made fewer arrests, producing an increase in homicide levels. We use structural equation modeling to estimate the simultaneous relationship between arrest and homicide rates between 2010 and 2015 in 53 large cities. We find no evidence of an effect of arrest rates on city homicide rates for any offense category for any year in this period, including 2015, the year of the spike in homicide levels.

Policy Implications

The results of our analysis reveal that declining rates of arrest did not produce the rise in homicide levels. But arrests, the chief formal reaction to crime, can play an important supporting role in crime prevention. Ample research findings have demonstrated the effectiveness of proactive policing practices, such as targeted patrol, in reducing crime rates. The success of such tactics depends, in turn, on citizens’ belief that criminal offenders face an appreciable risk of arrest. It is equally important, however, that residents of communities that have experienced unwarranted police violence believe that law enforcement is fairly applied. Lack of trust and confidence in the police militates against crime prevention as a co‐production of police and community and may promote violence as a form of self‐help.
European Landscapes in Transition: Implications for Policy Integration and Landscape Governance
Authors: Primdahl Jørgen , Pinto‐Correia Teresa , Pedroli Bas
Published: March 2019

European rural landscapes are in transition due to macro changes in climate, agriculture and public policy, combined with various forms of urbanisation. These changes are affecting the resource basis of agriculture, the socio‐cultural identity of rural communities, and are challenging the policy regimes affecting European landscapes. Therefore, they demand new forms of landscape governance if the diversity and quality of the landscapes are to be protected and further developed in the future. New analytical tools supported by revised conceptual frameworks are needed to assist identification and assessment of future development options. This article is based on a book published earlier this year. It presents and discusses the current patterns of change and their implications for policy. Three major policy challenges are identified: integration of agricultural and environmental policies; pro‐active approaches to landscape change to cope with non‐agricultural demands including recreation and nature conservation; and stakeholder involvement in policy design and implementation including farmers and other primary managers, public agencies at all levels and local communities in various forms. Key points are illustrated in a case study involving the development of a landscape strategy in the Karby parish in northwest Denmark.
High kinesin family member 18A expression correlates with poor prognosis in primary lung adenocarcinoma
Authors: Li Xiaoqing , Liu Meirong , Zhang Zheng , Zhang Linlin , Liang Xingmei , Sun Linlin , Zhong Diansheng
Published: March 2019

Background

Lung adenocarcinoma (LUAD) is the most prevalent pathological subtype of lung cancer. Kinesin family member 18A (KIF18A) plays an important role in tumorigenesis. Its roles in breast cancer, colorectal cancer, and other tumors have been demonstrated; however, studies of KIF18A in LUAD are limited. This study aimed to determine the role of KIF18A in LUAD progression and prognostic prediction.

Methods

KIF18A expression was examined in LUAD cells and tissues by immunohistochemistry and Western blotting. Cell proliferation assay was performed to study the role of KIF18A in LUAD cells. Correlations between KIF18A expression and clinicopathological features were analyzed. The role of KIF18A in LUAD prognosis was evaluated using data from The Cancer Genome Atlas (TCGA).

Results

KIF18A expression was increased in tumor cells and tissues. Downregulation of KIF18A expression resulted in the suppression of cancer cell proliferation in in vitro assays, and was particularly related to poor tumor differentiation, big tumor size, lymph node metastasis, and more advanced tumor stage. In the TCGA dataset, high KIF18A messenger RNA expression was associated with poor disease‐free and overall survival in patients with LUAD. In addition, multivariate analysis indicated that KIF18A is an independent prognostic factor of disease‐free and overall survival in LUAD.

Conclusions

Collectively, our results demonstrate that KIFl8A is highly expressed in LUAD. KIFl8A plays an important role in LUAD cell proliferation, but is a poor prognostic factor.
NMNAT2‐mediated NAD+ generation is essential for quality control of aged oocytes
Authors: Wu Xinghan , Hu Feifei , Zeng Juan , Han Longsen , Qiu Danhong , Wang Haichao , Ge Juan , Ying Xiaoyan , Wang Qiang
Published: March 2019

Advanced maternal age has been reported to impair oocyte quality; however, the underlying mechanisms remain to be explored. In the present study, we identified the lowered NAD+ content and decreased expression of NMNAT2 protein in oocytes from old mice. Specific depletion of NMNAT2 in mouse oocytes disturbs the meiotic apparatus assembly and metabolic activity. Of note, nicotinic acid supplementation during in vitro culture or forced expression of NMNAT2 in aged oocytes was capable of reducing the reactive oxygen species (ROS) production and incidence of spindle/chromosome defects. Moreover, we revealed that activation or overexpression of SIRT1 not only partly prevents the deficient phenotypes of aged oocytes but also ameliorates the meiotic anomalies and oxidative stress in NMNAT2‐depleted oocytes. To sum up, our data indicate a role for NMNAT2 in controlling redox homeostasis during oocyte maturation and uncover that NMNAT2‐ NAD+‐SIRT1 is an important pathway mediating the effects of maternal age on oocyte developmental competence.
Changes in Drinking Patterns, and Attitudes Toward and Knowledge About Alcohol Consumption During Pregnancy in a Population of Pregnant Danish Women
Authors: Kesmodel Ulrik Schiøler , Urbute Aivara
Published: March 2019

Background

In 1997, The Danish Health Authority recommended that “it is safest not to drink alcohol when you are pregnant,” and in 1999 expanded recommendations. There are only a few studies evaluating the possible change of average alcohol consumption following changes in national recommendations, and no studies have been found comparing the changes in pregnant women's attitudes toward alcohol consumption during pregnancy. We aimed to evaluate the changes in drinking pattern, and knowledge about and attitudes toward alcohol consumption during pregnancy before and after the change of national recommendations.

Methods

This is a cross‐sectional interview study with a representative sample of 1,418 woman attending antenatal care at the beginning of their second trimester in Aarhus, Denmark, in the year 2000, and a comparable sample of 439 pregnant women from 1998 in Aarhus. Participants were interviewed about their average alcohol consumption, binge drinking, and attitudes toward and knowledge about alcohol consumption during pregnancy. Data collection procedures and questions were identical for both samples.

Results

There were no differences between the 2 samples in terms of average alcohol consumption before (p = 0.19) and during (p = 0.45) pregnancy, and binge drinking in early pregnancy (p = 0.47). Attitudes toward and knowledge about alcohol in pregnancy did not change either (p > 0.5). Women's knowledge about guidelines was less precise in 2000 (p < 0.001). Worse knowledge was associated with younger age considering both samples (OR = 2.63, 95% CI: 1.63 to 4.26). Most pregnant women reported that they had not been informed or advised about alcohol consumption during pregnancy, but they would like to be advised by their healthcare professionals.

Conclusions

After the changes in the national guidelines about alcohol consumption during pregnancy, there were no changes in behavior, attitudes, and knowledge of pregnant women. This would indicate that healthcare specialists should be encouraged to initiate a conversation about alcohol consumption during the first antenatal visit.
Incidence of microcracks after preparation of straight and curved root canals with three different NiTi instrumentation techniques assessed by micro‐CT
Authors: Rödig Tina , Krämer Juliane , Müller Christine , Wiegand Annette , Haupt Franziska , Rizk Marta
Published: March 2019

This study evaluated the effect of three different NiTi instrumentation techniques on the incidence of microcracks after the preparation of straight and curved root canals using micro‐CT. Roots from mandibular premolars and maxillary molars (n = 66) with the same mean canal curvatures were assigned to three groups of straight and three groups of curved roots (n = 11). After preoperative micro‐CT scans, root canals were prepared with Reciproc, OneShape and ProTaper Next to size 25. Specimens were scanned again, and pre‐ and post‐operative cross‐sectional images (n = 75 263) were screened to identify the presence of dentinal microcracks. Overall, microcracks were detected in 2.97% (n = 2236) of the cross‐sectional images. No new dentinal microcracks were observed after root canal instrumentation of straight and curved canals with the tested NiTi systems. Instrumentation with Reciproc, OneShape and ProTaper Next did not induce the formation of dentinal microcracks irrespective of canal curvature.
PRE‐OPERATIVE ULTRASOUND MEASUREMENT OF BILE DUCT DIAMETER: BASIS FOR SELECTIVE CHOLANGIOGRAPHY
Authors: HUNT D. R. , REITER L. , SCOTT A. J.
Published: March 2019

In this prospective study, prior to cholecystectomy, the diameter of the common hepatic duct was measured; duct size was then compared with probability of finding stones at operation. Of 115 patients entering the study, 36 had stones removed from the common duct at the time of cholecystectomy but only three (8%) were demonstrated by ultrasonography. No stones were found in ducts ⩽ 3 mm in size (31 % patients). Only two of 26 patients with ducts measuring 4 mm had stones. As duct size increased, so did the probability of stones and all patients with ducts ⩾ 9 mm in diameter had stones. It is concluded that pre‐operative ultrasound provides a reliable basis for a policy of selective cholangiography.
PELVIC LIPOMATOSIS WITH CYSTITIS CYSTICA, CYSTITIS GLANDULARIS AND ADENOCARCINOMA OF THE BLADDER: FIRST REPORTED CASE
Authors: GORDON NEIL S. I. , SINCLAIR ROGER A. , SNOW ROSS M.
Published: March 2019

Pelvic lipomatosis is a rare disease which may cause obstructive uropathy. It has been reported with cystitis cystica and cystitis glandularis. Cystitis cystica and cystitis glandularis have been reported previously as progressing to adenocarcinoma of the bladder. The first reported case of pelvic lipomatosis, cystitis cystica, cystitis glandularis and adenocarcinoma of the bladder is presented and the literature reviewed.
Eye Injuries across history and the evolution of eye protection
Authors: Hoskin Annette K. , Mackey David A. , Keay Lisa , Agrawal Rupesh , Watson Stephanie
Published: March 2019

Purpose

To describe the history of eye injuries and the consequent evolution of eye protection.

Methods

A comprehensive search of Medline and the grey literature using the terms ‘ocular trauma’ and ‘eye protection’ or ‘injury prevention’ and ‘history’. References were used to identify other relevant publications. Publications were classified according to the setting of eye injury: occupational, recreational or combat‐related.

Results

Eye protection has been described in a wide range of sources, including in literature and art. With advances in eye protection material and design, as well as government and societal promotion of appropriate eye protection usage in the workplace, the epidemiology of ocular trauma has changed over time. In developed countries, the use of eye protection in the workplace has reduced the proportion of occupation‐related eye injuries over the last century, with a higher proportion occurring during sports or at home. New protection devices and policies have evolved to meet this change.

Conclusion

Vision loss has broad implications for the individual and for society and despite available prevention strategies, ocular trauma is a significant cause of preventable monocular and bilateral vision loss. The use of appropriate eye protection has reduced the burden of ocular trauma. History provides lessons for informing current eye protection and eye injury prevention strategies.
Outbreak of Methicillin‐resistant Staphylococcus aureus in a Hospital Center for Children's and Women's Health in a Swedish County
Authors: Gideskog Maria , Melhus Åsa
Published: March 2019

The objective of this study was to investigate a sudden increase in methicillin‐resistant Staphylococcus aureus (MRSA) cases primarily in one maternity ward at the Center for Children's and Women's Health at Linköping University Hospital, Sweden. Approximately 300 individuals including patients, their family members, and healthcare workers were screened for MRSA. The antibiotic susceptibility was tested and isolates polymerase chain reaction (PCR)‐positive for the mecA gene were spa typed. Isolates with the same antibiogram and spa type were further whole genome sequenced. Compliance to current cleaning and hygiene routines was also controlled, and environmental samples collected. The results showed that a total of 13 individuals were involved in the outbreak. It was caused by a t386 MRSA strain (ST‐1, NCBI‐accession AB505628) with additional resistance to erythromycin and clindamycin. All cases were epidemiologically connected to the index patient, who had recently emigrated from a high‐endemic area for MRSA. With improved cleaning and better compliance to basic hygiene routines, no further cases were reported. This study demonstrates how rapid an MRSA strain can disseminate in a ward with susceptible patients and insufficient cleaning and hygiene. For a better control of MRSA, clinical cultures and screening samples need to be obtained early and more extensively than according to the current recommendations.