bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Public Database on Traumatic Brachial Plexus Injury
Authors: Patroclo Cristiane B , Ramalho Bia L , Maia Juliana S , Rangel Maria Luíza , Torres Fernanda F , Souza Lidiane , Braghetto Kelly R , Vargas Claudia D 
Published: August 2018

AbstractWe hereby present the first worldwide public digital database centred on adult Traumatic Brachial Plexus Injury (TBPI). This initiative aims at reducing distance between clinical and experimental practice and encouraging data sharing and reuse. Detailed electronic questionnaires made with the free software LimeSurvey were designed to collect patients’ epidemiological, physical and clinical data. The freely available software Neuroscience Experiments System (NES) was employed to support data storage and management. First results of this effort concern data collected from 109 Brazilian adult TBPI patients with varying degrees of functional impairment. The sample is composed by large majority of men (84.4%), mean age of 32.1 (11.3 SD) years old, victims of motorcycle accidents (67%). The similarity of this dataset basic descriptors with those from previous reports in TBPI validates the strategies employed herein. Managing data from diverse provenance in TBPI may allow identifying functional markers related to the patients’ clinical improvement and foster the development of new investigative tools to unveil its mechanisms.
New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life
Authors: Strassert Jürgen F. H. , Jamy Mahwash , Mylnikov Alexander P. , Tikhonenkov Denis V. , Burki Fabien 
Published: August 2018

AbstractThe broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker ‘TSAR’ to accommodate this new mega-assemblage in the phylogeny of eukaryotes.
Sparse network-based regularization for the analysis of patientomics high-dimensional survival data
Authors: Veríssimo André , Carrasquinha Eunice , Lopes Marta B. , Oliveira Arlindo L. , Sagot Marie-France , Vinga Susana 
Published: August 2018

AbstractData availability by modern sequencing technologies represents a major challenge in oncological survival analysis, as the increasing amount of molecular data hampers the generation of models that are both accurate and interpretable. To tackle this problem, this work evaluates the introduction of graph centrality measures in classical sparse survival models such as the elastic net.We explore the use of network information as part of the regularization applied to the inverse problem, obtained both by external knowledge on the features evaluated and the data themselves. A sparse solution is obtained either promoting features that are isolated from the network or, alternatively, hubs,i.e., features that are highly connected within the network.We show that introducing the degree information of the features when inferring survival models consistently improves the model predictive performance in breast invasive carcinoma (BRCA) transcriptomic TCGA data while enhancing model interpretability. Preliminary clinical validation is performed using the Cancer Hallmarks Analytics Tool API and the String database.These case studies are included in the recently released glmSparseNet R package1, a flexible tool to explore the potential of sparse network-based regularizers in generalized linear models for the analysis of omics data.
Detection and Molecular Epidemiology of Human Bocavirus in Children with Acute Gastroenteritis from Brazil
Authors: Soares L.S. , Lima A. B. , Pantoja K.C. , Lobo P.S. , Cruz J.F. , Guerra S.F.S. , Bezerra D.A.M. , Bandeira R.S. , Mascarenhas J.D.P. 
Published: August 2018

SUMMARYHuman Bocavirus (HBoV) is a recently discovered virus and was first detected in the nasopharyngeal aspirate samples and after in stool samples, suggesting that HBoV may be a causative agent for human enteric infections. Due to absence of treatment options, there is a need to understand the disease-causing mechanism of these viruses. The aim of this was to demonstrate the prevalence of HBoV from children less than 10 years with acute gastroenteritis in Brazil, during November 2011 to November 2012. Stool samples from hospitalized children ≤ 10 years who presented symptoms of acute gastroenteritis were analyzed for the presence of HBoV DNA by nested-PCR. HBoV- positivity was detected in 24.0% (54/225) of samples. Two peaks of HBoV detection were observed, during November 2011 and July to September 2012. Co-infections between HBoV and rotavirus A were identified in 50.0% (27/54) of specimens. Phylogenetic analysis identified the presence of HBoV-1 (94.8%), HBoV-2 (2.6%) and HBoV-3 (2.6%) species, with only minor variations among them. Further investigations are necessary to improve the knowledge on the role of HBoV in gastrointestinal infections.
Characterization and mechanism of lead and zinc biosorption by growing Verticillium insectorum J3
Authors: Feng Chong-ling , Li Jin , Li Xue , Li Ke-lin , Luo Kun , Liao Xing-sheng , Liu Tao 
Published: August 2018

AbstractVerticillium insectorum J3 was isolated from a local lead-zinc deposit tailing, and its biosorption characteristics and reaction to the toxicities of different Pb(II) and Zn(II) concentrations were investigated. SEM, FTIR, a pH test and a desorption experiment were carried out to identify a possible mechanism. The biosorption of J3 presented an inhibition trend at low concentrations (25-75 mg L-1) and promotion at high concentrations (100-300 mg L-1). J3 absorbed Pb(II) prior to Zn(II) and produced alkaline substances, while mycelial and pellet morphology modifications were important for the removal of Pb(II) and Zn(II) under different stressful conditions (SEM results). Both intracellular accumulation and extracellular absorption may contribute to the removal of Pb(II) at lower concentrations (25-50 mg L-1), although mainly extracellular biosorption occurred at higher concentrations (75-300 mg L-1). However, Zn(II) bioaccumulation occurred at all concentrations assayed. Verticillium insectorum J3 may have evolved active defenses to alleviate the toxicity of heavy metals and proved to be a highly efficient biosorbent, especially for Pb(II) at high concentrations. This study is a useful reference for the development of biotreatment technologies to mitigate heavy metal waste.
Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, Fundulus heteroclitus
Authors: Alfieri James M. , Anderson Tavis K. 
Published: August 2018

AbstractThis study examined the relationship between urbanization and parasite community structure in the estuarine fish, Fundulus heteroclitus. We measured landscape and physicochemical factors associated with urbanization at 6 sites from 4 collection periods. Concurrently, we quantified the metazoan parasite community in F. heteroclitus collected at those sites, with 105 fish studied per site during the 4 collection periods. Parasite community composition differed between sites. Variation in the prevalence and intensity of infection of two indirect life-cycle parasites, Lasiocotus minutus and Glossocercus caribaensis, were the primary parasite species that determined this pattern. Sediment potassium and aquatic osmium were the most important physicochemical factors in structuring parasite communities, and habitat dominance was the most important landscape factor. Our data supports the hypothesis that urbanization, acting at both landscape and physicochemical scales, can have a significant impact on parasite community structure. This, however, varied by parasite life history: there was little effect of urbanization on the prevalence and intensity of direct life-cycle parasites, but significant variation was dedicated for indirect life-cycle parasites. This study demonstrates how anthropogenically driven landscape change influences fine-scale parasite population dynamics.
Systematic characterization of genome editing in primary T cells reveals proximal genomic insertions and enables machine learning prediction of CRISPR-Cas9 DNA repair outcomes
Authors: Leenay Ryan T. , Aghazadeh Amirali , Hiatt Joseph , Tse David , Hultquist Judd F. , Krogan Nevan , Wu Zhenqin , Marson Alexander , May Andrew P. , Zou James 
Published: August 2018

AbstractThe Streptococcus pyogenes Cas9 (SpCas9) nuclease has become a ubiquitous genome editing tool due to its ability to target almost any location in DNA and create a double-stranded break1,2. After DNA cleavage, the break is fixed with endogenous DNA repair machinery, either by non-templated mechanisms (e.g. non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ)), or homology directed repair (HDR) using a complementary template sequence3,4. Previous work has shown that the distribution of repair outcomes within a cell population is non-random and dependent on the targeted sequence, and only recent efforts have begun to investigate this further5–11. However, no systematic work to date has been validated in primary human cells5,7. Here, we report DNA repair outcomes from 1,521 unique genomic locations edited with SpCas9 ribonucleoprotein complexes (RNPs) in primary human CD4+ T cells isolated from multiple healthy blood donors. We used targeted deep sequencing to measure the frequency distribution of repair outcomes for each guide RNA and discovered distinct features that drive individual repair outcomes after SpCas9 cleavage. Predictive features were combined into a new machine learning model, CRISPR Repair OUTcome (SPROUT), that predicts the length and probability of nucleotide insertions and deletions with R2 greater than 0.5. Surprisingly, we also observed large insertions at more than 90% of targeted loci, albeit at a low frequency. The inserted sequences aligned to diverse regions in the genome, and are enriched for sequences that are physically proximal to the break site due to chromatin interactions. This suggests a new mechanism where sequences from three-dimensionally neighboring regions of the genome can be inserted during DNA repair after Cas9-induced DNA breaks. Together, these findings provide powerful new predictive tools for Cas9-dependent genome editing and reveal new outcomes that can result from genome editing in primary T cells.
Cryogenically preserved RBCs support gametocytogenesis ofPlasmodium falciparuminvitroand gametogenesis in mosquitoes
Authors: Pathak Ashutosh K. , Shiau Justine C. , Thomas Matthew B. , Murdock Courtney 
Published: August 2018

AbstractBackgroundThe malaria Eradication Research Agenda (malERA) has identified human-to-mosquito transmission ofPlasmodium falciparumas a major target for eradication. The cornerstone for identifying and evaluating transmission in the laboratory is small membrane feeding assays (SMFAs) where mature gametocytes ofP. falciparumgeneratedin vitroare offered to mosquitoes as part of a blood-meal. However, propagation of “infectious” gametocytes requires 10-12 days with considerable physico-chemical demands imposed on host RBCs and thus, “fresh” RBCs that are ≤1-week old post-collection are generally recommended. However, in addition to the costs, physico-chemical characteristics unique to RBC donors may confound reproducibility and interpretation of SMFAs. Cryogenic storage of RBCs (cryo-preserved RBCs herein) is approved by the European and US FDAs as an alternative to refrigeration (4°C) for preserving RBC quality and while cryo-preserved RBCs have been used forin vitrocultures of otherPlasmodiaand the asexual stages ofP. falciparum, none of the studies required RBCs to support parasite development for >4 days.ResultsUsing the standard laboratory strain,P. falciparumNF54, we first demonstrate that cryo-preserved RBCs preserved in the gaseous phase of liquid nitrogen and thawed after storage for 1, 4, 8 and 12 weeks, supported gametocytogenesisin vitroand subsequent gametogenesis inAnopheles stephensimosquitoes. Using data from 11 SMFAs and RBCs from 4 separate donors with 3 donors re-tested following various periods of cryo-preservation, we show that overall levels of sporogony in the mosquito, as measured by oocyst prevalence and burdens in the midguts and sporozoites in salivary glands, were similar or better than using ≤1-week old refrigerated RBCs. Additionally, the potential for cryo-preserved RBCs to serve as a universal substrate for SMFAs is shown for a Cambodian isolate ofP. falciparum.ConclusionsConsidering the suitability of cryo-preserved RBCs forP. falciparumSMFAs, we suggest guidelines for their use and how they can be integrated into an existing laboratory/insectary framework with the potential to significantly reduce running costs and provide greater reliability. Finally, we discuss scenarios where cryo-preserved RBCs may be especially useful in enhancing our understanding and/or providing novel insights into the patterns and process underlying human-to-mosquito transmission.
KymoButler, a Deep Learning software for automated kymograph analysis
Authors: Jakobs Maximilian A. H. , Dimitracopoulos Andrea , Franze Kristian 
Published: August 2018

AbstractKymographs are graphical representations of spatial position over time, which are often used in biology to visualise the motion of fluorescent particles, molecules, vesicles, or organelles moving along a predictable path. Although in kymographs tracks of individual particles are qualitatively easily distinguished, their automated quantitative analysis is much more challenging. Kymographs often exhibit low signal-to-noise-ratios (SNRs), and available tools that automate their analysis usually require manual supervision. Here we developed KymoButler, a Deep Learning-based software to automatically track dynamic processes in kymographs. We demonstrate that KymoButler performs as well as expert manual data analysis on kymographs with complex particle trajectories from a variety of different biological systems. The software was packaged in a web-based “one-click” application for use by the wider scientific community. Our approach significantly speeds up data analysis, avoids unconscious bias, and represents another step towards the widespread adaptation of Machine Learning techniques in biological data analysis.
Looking at the map – or navigating in a virtual city interaction of visuospatial display and spatial strategies in VR
Authors: Török Zsolt Gyozo , Török Ágoston 
Published: August 2018

AbstractTo study geo-visualization processes a Cognitive Cartography Lab was established at Eötvös University, and the “Virtual Tourist” experiment was designed for the better understanding of actual map use during navigation. In this paper we present some preliminary results of the experiment. We explored the use of a static, north-oriented city map during navigation in an interactive, 3D town. Participants explored the virtual environment or followed verbal instructions before they completed spatial tasks. Their spatial behavior, verbal reactions were recorded, and also eye tracking data from 64 participants was collected. The experiment was designed by a multidisciplinary research group, including students of Eötvös Loránd University.
Crystal Structure of a Natural Light-Gated Anion Channelrhodopsin
Authors: Li Hai , Huang Chia-Ying , Govorunova Elena G. , Schafer Christopher T. , Sineshchekov Oleg A. , Wang Meitian , Zheng Lei , Spudich John L. 
Published: August 2018

ABSTRACTThe anion channelrhodopsin GtACR1 from the alga Guillardia theta is a potent neuron-inhibiting optogenetics tool. Presented here, its X-ray structure at 2.9 Å reveals a tunnel traversing the protein from its extracellular surface to a large cytoplasmic cavity. The tunnel is lined primarily by small polar and aliphatic residues essential for anion conductance. A disulfide-immobilized extracellular cap facilitates channel closing and the ion path is blocked mid-membrane by its photoactive retinylidene chromophore and further by a cytoplasmic side constriction. The structure also reveals a novel photoactive site configuration that maintains the retinylidene Schiff base protonated when the channel is open. These findings suggest a new channelrhodopsin mechanism, in which the Schiff base not only controls gating, but also serves as a direct mediator for anion flux.
miPIE: NGS-based Prediction of miRNA Using Integrated Evidence
Authors: Peace R.J. , Hassani M. Sheikh , Green J.R. 
Published: August 2018

AbstractMethods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-based methods. While miRDeep2 does examine the predicted secondary structure of putative miRNA sequences, it does not leverage many of the sequence-based features used in state-of-the-art de novo methods. Meanwhile, other NGS-based methods, such as miRanalyzer, place an emphasis on sequence-based features without leveraging advanced expression-based features reflecting miRNA biosynthesis. This represents an opportunity to combine the strengths of NGS-based analysis with recent advances in de novo sequence-based miRNA prediction. We here develop a method, microRNA Prediction using Integrated Evidence (miPIE), which integrates both expression-based and sequence-based features to achieve significantly improved miRNA prediction performance. Feature selection identifies the 20 most discriminative features, 3 of which reflect strictly expression-based information. Evaluation using precision-recall curves, for six NGS data sets representing six diverse species, demonstrates substantial improvements in prediction performance compared to miRDeep2 and miRanalyzer. The individual contributions of expression-based and sequence-based features are also examined and we demonstrate that their combination is more effective than either alone.
Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase ofStaphylococcus aureus
Authors: Monk Ian R. , Shaikh Nausad , Begg Stephanie L. , Gajdiss Mike , Lee Jean Y. H. , Pidot Sacha J. , Seemann Torsten , Kuiper Michael , Winnen Brit , Hvorup Rikki , Collins Brett M. , Bierbaum Gabriele , Howden Benjamin P. , McDevitt Christopher A. , King Glenn F. , Stinear Timothy P. 
Published: August 2018

ABSTRACTWalKR (YycFG) is the only essential two-component regulator in the human pathogenStaphylococcus aureus.WalKR regulates peptidoglycan synthesis, but this function alone appears not to explain its essentiality. To understand WalKR function we investigated a suppressor mutant that arose when WalKR activity was impaired; a single histidine to tryptophan substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introduction of the WalKH271Ymutation into wild-typeS.aureusactivated the WalKR regulon. Structural analyses of the WalK PASCYTdomain revealed a hitherto unknown metal binding site, in which a zinc ion (Zn2+) was tetrahedrally-coordinated by four amino acid residues including H271. The WallkH271Ymutation abrogated metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn2+-binding negatively regulates WalKR activity. Identification of a metal ligand sensed by the WalKR system substantially expands our understanding of this criticalS.aureusregulon.
The multi-peak adaptive landscape of crocodylomorph body size evolution
Authors: Godoy Pedro L. , Benson Roger B. J. , Bronzati Mario , Butler Richard J. 
Published: August 2018

AbstractBackgroundLittle is known about the long-term patterns of body size evolution in Crocodylomorpha, the > 200-million-year-old group that includes living crocodylians and their extinct relatives. Extant crocodylians are mostly large-bodied (3–7 m) predators. However, extinct crocodylomorphs exhibit a wider range of phenotypes, and many of the earliest taxa were much smaller (< 1.2 m). This suggests a pattern of size increase through time that could be caused by multi-lineage evolutionary trends of size increase or by selective extinction of small-bodied species. In this study, we characterise patterns of crocodylomorph body size evolution using a model fitting-approach (with cranial measurements serving as proxies). We also estimate body size disparity through time and quantitatively test hypotheses of biotic and abiotic factors as potential drivers of crocodylomorph body size evolution.ResultsCrocodylomorphs reached an early peak in body size disparity during the Late Jurassic, and underwent essentially continually decreases in disparity since then. A multi-peak Ornstein-Uhlenbeck model outperforms all other evolutionary models fitted to our data (including both uniform and non-uniform), indicating that the macroevolutionary dynamics of crocodylomorph body size are better described within the concept of an adaptive landscape, with most body size variation emerging after shifts to new macroevolutionary regimes (analogous to adaptive zones). We did not find support for a consistent evolutionary trend towards larger sizes among lineages (i.e., Cope’s rule), or strong correlations of body size with climate. Instead, the intermediate to large body sizes of some crocodylomorphs are better explained by group-specific adaptations. In particular, the evolution of a more aquatic lifestyle (especially marine) correlates with increases in average body size, though not without exceptions.ConclusionsShifts between macroevolutionary regimes provide a better explanation of crocodylomorph body size evolution than do climatic factors, suggesting a central role for lineage-specific adaptations rather than climatic forcing. Shifts leading to larger body sizes occurred in most aquatic and semi-aquatic groups. This, combined with extinctions of groups occupying smaller body size regimes (particularly during the Late Cretaceous and Cenozoic), gave rise to the upward-shifted body size distribution of extant crocodylomorphs compared to their smaller-bodied terrestrial ancestors.