bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing
Authors: Anatskiy E. , Ryan D.P. , Grüning B. , Arrigoni L. , Manke T. , Bönisch U. 
Published: June 2018

AbstractSummaryThis paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples. Starting with user requests, Parkour allows tracking and assessing samples based on predefined quality criteria through different stages of the sample preparation workflow. Ideally suited for academic core laboratories, the software aims to maximize efficiency and reduce turnaround time by intelligent sample grouping and a clear assignment of staff to work units. Tools for automated invoicing, interactive statistics on facility usage and simple report generation minimize administrative tasks. Provided as a web application, Parkour is a convenient tool for both deep sequencing service users and laboratory personal. A set of web APIs allow coordinated information sharing with local and remote bioinformaticians. The flexible structure allows workflow customization and simple addition of new features as well as the expansion to other domains.Availability and implementationThe code and documentation are available at https://github.com/maxplanck-ie/parkourContactboenisch@ie-freiburg.mpg.de
TACAN is an essential component of the mechanosensitive ion channel responsible for pain sensing
Authors: Beaulieu-Laroche L. , Christin M. , Donoghue AM , Agosti F. , Yousefpour N. , Petitjean H. , Davidova A. , Stanton C. , Khan U. , Dietz C. , Faure E. , Fatima T. , MacPherson A. , Ribeiro-Da-Silva A. , Bourinet E. , Blunck R. , Sharif-Naeini R. 
Published: June 2018

SummaryMechanotransduction, the conversion of mechanical stimuli into electrical signals, is a fundamental process underlying several physiological functions such as touch and pain sensing, hearing and proprioception. This process is carried out by specialized mechanosensitive ion channels whose identities have been discovered for most functions except pain sensing. Here we report the identification of TACAN (Tmem120A), an essential subunit of the mechanosensitive ion channel responsible for sensing mechanical pain. TACAN is expressed in a subset of nociceptors, and its heterologous expression increases mechanically-evoked currents in cell lines. Purification and reconstitution of TACAN in synthetic lipids generates a functional ion channel. Finally, knocking down TACAN decreases the mechanosensitivity of nociceptors and reduces behavioral responses to mechanical but not to thermal pain stimuli, without affecting the sensitivity to touch stimuli. We propose that TACAN is a pore-forming subunit of the mechanosensitive ion channel responsible for sensing mechanical pain.
GenotypeTensors: Efficient Neural Network Genotype Callers
Authors: Cohen Joshua , Simi Manuele , Campagne Fabien 
Published: June 2018

ABSTRACTWe studied the problem of calling genotypes using neural networks. A machine learning approach to calling genotypes requires a training set, an approach to convert genomic sites into tensors and robust model development and evaluation protocols. We discuss each of these components of our approach and compare four types of neural network training protocols, two fully supervised and two semi-supervised approaches. Semi-supervised approaches use unlabeled data to supplement limited quantities of labeled data. Random hyper-parameter searches identified highly performing models that reach indel F1 of 99.4% on a chromosomes 20, 21, 22 and X of NA12878/HG001. We further validate these models by evaluating performance on HG002, an independent sample used in the PrecisionFDA challenge. We apply GenotypeTensors to evaluate the impact of (1) training with small datasets, (2) training models only with sites inside confidence regions, or (3) training with improved true label annotations. A PyTorch open-source implementation of GenotypeTensors is available at https://github.com/CampagneLaboratory/GenotypeTensors. DNANexus cloud applications are provided to help process new datasets both to train model or call genotypes with trained models.
Comparison of trimethoprim-sulfamethoxazole versus ciprofloxacin monotherapy in Stenotrophomonas maltophilia bloodstream infections in children
Authors: Aksay Ahu , Devrim İlker , Katipoğlu Nagehan , Bayram Nuri , Arslanoglu Sertaç , Çallkavur Şebnem , Gülfidan Gamze , Ceylan Gökhan , Ağın Hasan 
Published: June 2018

ABSTRACTTreatment of invasive infections caused by Stenotothromhomas maltophilia is difficult as the bacterium is frequently resistant to a wide range of commonly used antimicrobials. The aim of this retrospective study was to evaluate effectiveness of treatment with ciprofloxacin monotherapy compared to trimethoprim-sulfamethoxazole monotherapy in patients with S. maltophilia infections. We evaluated 50 patients with S. maltophilia bloodstream infections who had received monotherapy with trimethoprim-sulfamethoxazole or ciprofloxacin. Twenty-five patients (50%) received trimethoprim-sulfamethoxazole, and 25 patients (50%) received ciprofloxacin. Thirty-six (72%) patients were in the intensive care unit. All of the patients had at least one indwelling devices and approximately 25% patients had immunosuppression. Ciprofloxacin had the same clinical outcome and mortality as trimethoprim-sulfamethoxazole for the treatment of S. maltophilia bacteremia. In our study; side-effects ratio were not statistically different between ciprofloxacin and trimethoprim-sulfamethoxazole group. Ciprofloxacin could be an alternative drug of choice for treating S. maltophilia infections especially in premature infans in stead of trimethoprim-sulfamethoxazole.
The key lethal effect existed in the antibacterial behavior of short, medium, and long chain fatty acid monoglycerides onEscherichia coli
Authors: Zhang Song , Xiong Jian , Lou Wenyong , Ning Zhengxiang , Zhang Denghui , Yang Jiguo 
Published: June 2018

AbstractMonoglyceride is an amphiphilic molecule with promising antimicrobial activity for bacteria; however, the key lethal effect in its antibacterial behavior was still unknown. In the study, monobutyrate (MB), monolaurate (ML), monomyristate (MM) were selected to represent the short, medium, and long chain monoglycerides to compare their inhibitory effect againstEscherichia coli, and a new dose-dependent inhibitory mechanism was proposed by the key lethal effect. The minimal inhibitory concentration and antibacterial curve showed a huge diversity existed in biology activity of MB, ML and MM. The results in scanning electron microscopy and flow cytometry assay indicated that the interference level of MB on cell membrane was obviously weaker than that of ML and MM, while the latter two had similar performance in increasing cell permeability at low doses. The results presented in UV-Vis spectroscopy, cell cycle and biomacromolecules synthesis inhibition assay showed that the cell cycle ofEscherichia coliwas obviously affected by three monoglycerides at doses near MIC, which was therefore regarded as the key lethal effect. The reason for the better biological activity of MM than ML was the stronger interference ability on bacterial cell cycle. In addition, an expanded antibacterial mode was raised that cell permeability increase at low doses was antimicrobial basis, cell cycle arrest at medium doses played the key lethal effect, and cell lysis at high doses was the result of combined action.
Contextual influence on confidence judgments in human reinforcement learning
Authors: Lebreton Maël , Bacily Karin , Palminteri Stefano , Engelmann Jan B. 
Published: June 2018

AbstractThe ability to correctly estimate the probability of one’s choices being correct is fundamental to optimally re-evaluate previous choices or to arbitrate between different decision strategies. Experimental evidence nonetheless suggests that this metacognitive process -referred to as a confidence judgment-is susceptible to numerous biases. We investigate the effect of outcome valence (gains or losses) on confidence while participants learned stimulus-outcome associations by trial-and-error. In two experiments, we demonstrate that participants are more confident in their choices when learning to seek gains compared to avoiding losses. Importantly, these differences in confidence were observed despite objectively equal choice difficulty and similar observed performance between those two contexts. Using computational modelling, we show that this bias is driven by the context-value, a dynamically updated estimate of the average expected-value of choice options that has previously been demonstrated to be necessary to explain equal performance in the gain and loss domain. The biasing effect of context-value on confidence, also recently observed in the context of incentivized perceptual decision-making, is therefore domain-general, with likely important functional consequences.
Adversarial childhood events are associated with Sudden Infant Death Syndrome (SIDS): an ecological study
Authors: Elhaik Eran 
Published: June 2018

AbstractSudden Infant Death Syndrome (SIDS) is the most common cause of postneonatal infant death. Theallostatic load hypothesisposits that SIDS is the result of perinatal cumulative painful, stressful, or traumatic exposures that tax neonatal regulatory systems. To test it, we explored the relationships between SIDS and two common stressors, male neonatal circumcision (MNC) and prematurity, using latitudinal data from 15 countries and over 40 US states during the years 1999-2016. We used linear regression analyses and likelihood ratio tests to calculate the association between SIDS and the stressors. SIDS prevalence was significantly and positively correlated with MNC and prematurity rates. MNC explained 14.2% of the variability of SIDS’s male bias in the US, reminiscent of the Jewish myth of Lilith, the killer of infant males. Combined, the stressors increased the likelihood of SIDS. Ecological analyses are useful to generate hypotheses but cannot provide strong evidence of causality. Biological plausibility is provided by a growing body of experimental and clinical evidence linking adversary preterm and early-life events with SIDS. Together with historical evidence, our findings emphasize the necessity of cohort studies that consider these environmental stressors with the aim of improving the identification of at-risk infants and reducing infant mortality.
metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data
Authors: Olson Nathan D. , Shah Nidhi , Kancherla Jayaram , Wagner Justin , Paulson Joseph N. , Corrada-Bravo Hector 
Published: June 2018

AbstractWe developed themetagenomeFeaturesR Bioconductor package along with annotation packages for the three primary 16S rRNA databases (Greengenes, RDP, and SILVA) to facilitate working with 16S rRNA sequence databases and marker-gene survey feature data. ThemetagenomeFeaturespackage defines two classes,MgDbfor working with 16S rRNA sequence databases, andmgFeaturesfor working with marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different 16S rRNA databases facilitating database comparison and exploration. ThemgFeaturesrepresents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R.Availabilityhttps://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.htmlContactnolson@nist.gov
Functional lability of RNA-dependent RNA polymerases in animals
Authors: Pinzón Natalia , Bertrand Stéphanie , Subirana Lucie , Busseau Isabelle , Escrivá Hector , Seitz Hervé 
Published: June 2018

AbstractRNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordateBranchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from variousBranchiostomadevelopmental stages. Our results show thatBranchiostomaRdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways.Author summaryRNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (”RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.
Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies
Authors: Shivram Haridha , Iyer Vishwanath R. 
Published: June 2018

AbstractThe quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Non-specific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published datasets. We show that mispriming can occur with as little as 2 bases of complementarity at the 3’ end of the primer followed by intermittent regions of complementarity. We also provide a computational pipeline that identifies cDNA reads produced from RT mispriming, allowing users to filter them out from any aligned dataset. Using this analysis pipeline, we identify thousands of mispriming events in a dozen published datasets from diverse technologies including short RNA-seq, total/mRNA-seq, HITS-CLIP and GRO-seq. We further show how RT-mispriming can lead to misinterpretation of data. In addition to providing a solution to computationally remove RT-misprimed reads, we also propose an experimental solution to avoid RT-mispriming by performing RNA-seq using thermostable group II intron derived reverse transcriptase (TGIRT-seq).
Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations
Authors: Ranathunge Chathurani , Wheeler Gregory L. , Chimahusky Melody E. , Perkins Andy D. , Pramod Sreepriya , Welch Mark. E. 
Published: June 2018

ABSTRACTMicrosatellites are common in most species. While an adaptive role for these highly mutable regions has been considered, little is known concerning their contribution towards phenotypic variation. We used populations of the common sunflower (Helianthus annuus) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA-Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2379. The percentage of variation in gene expression explained by eSTRs ranged from 1–86% when controlling for population and allele-by-population interaction effects at the 479 eSTRs. Of these, 70.4% are in untranslated regions (UTRs). A Gene Ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis- and trans-regulatory processes. These findings suggest that a substantial number of transcribed microsatellites can influence gene expression.
Whole genome sequencing,de novoassembly and phenotypic profiling for the new budding yeast speciesSaccharomyces jurei
Authors: Naseeb Samina , Alsammar Haya , Burgis Tim , Donaldson Ian , Knyazev Norman , Knight Christopher , Delneri Daniela 
Published: June 2018

AbstractSaccharomyces sensu strictocomplex consist of yeast species, which are not only important in the fermentation industry but are also model systems for genomic and ecological analysis. Here, we present the complete genome assemblies ofSaccharomyces jurei,a newly discoveredSaccharomyces sensu strictospecies from high altitude oaks. Phylogenetic and phenotypic analysis revealed thatS. jureiis a sister-species toS. mikatae,thanS. cerevisiae,andS. paradoxus.The karyotype ofS. jureipresents two reciprocal chromosomal translocations between chromosome VI/VII and I/XIII when compared toS. cerevisiaegenome. Interestingly, while the rearrangement I/XIII is unique toS. jurei,the other is in common withS. mikataestrain IFO1815, suggesting shared evolutionary history of this species after the split betweenS. cerevisiaeandS. mikatae.The number of Ty elements differed in the new species, with a higher number of Ty elements present inS. jureithan inS. cerevisiae.Phenotypically, theS. jureistrain NCYC 3962 has relatively higher fitness than the other strain NCYC 3947Tunder most of the environmental stress conditions tested and showed remarkably increased fitness in higher concentration of acetic acid compared to the othersensu strictospecies. Both strains were found to be better adapted to lower temperatures compared toS. cerevisiae.
Nucleus reuniens is required for encoding and retrieving precise, hippocampal-dependent contextual fear memories in rats
Authors: Ramanathan Karthik R. , Ressler Reed L. , Jin Jingji , Maren Stephen 
Published: June 2018

AbstractThe nucleus reuniens (RE) is a ventral midline thalamic nucleus that interconnects the medial prefrontal cortex (mPFC) and hippocampus (HPC). Considerable data indicate that HPC-mPFC circuits are involved in contextual and spatial memory; however, it is not clear whether the RE mediates the acquisition or retrieval of these memories. To examine this question, we inactivated the RE with muscimol before either the acquisition or retrieval of Pavlovian fear conditioning in rats; freezing served as the index of fear. We found that RE inactivation before conditioning impaired the acquisition of contextual freezing, whereas inactivation of the RE prior to retrieval testing increased the generalization of freezing to a novel context; inactivation of the RE did not affect either the acquisition or expression of auditory fear conditioning. Interestingly, contextual conditioning impairments were absent when retrieval testing was also conducted after RE inactivation. Contextual memories acquired under RE inactivation were hippocampal-independent, insofar as contextual freezing in rats conditioned under RE inactivation was insensitive to intra-hippocampal infusions of the NMDA receptor antagonist, D,L-amino-5-phosophonovaleric acid (APV). Together, these data reveal that the RE supports hippocampal-dependent encoding of precise contextual memories that allow discrimination of dangerous from safe contexts. When the RE is inactive, however, alternate neural systems acquire an impoverished contextual memory that is only expressed when the RE is offline.SIGNIFICANCE STATEMENTThe midline thalamic nucleus reuniens (RE) coordinates communication between the hippocampus and medial prefrontal cortex, brain areas critical for contextual and spatial memory. Here we show that temporary pharmacological inactivation of RE impairs the acquisition and precision of contextual fear memories after Pavlovian fear conditioning in rats. However, inactivating the RE prior to retrieval testing restored contextual memory in rats conditioned after RE inactivation. Critically, we show that imprecise contextual memories acquired under RE inactivation are learned independently of the hippocampus. These data reveal that the RE is required for hippocampal-dependent encoding of precise contextual memories to support the discrimination of safe and dangerous contexts.
Site-directed mutagenesis of the 1,3-β glucan synthase catalytic subunit ofPneumocystis jiroveciiand susceptibility assays suggest its sensitivity to caspofungin
Authors: Luraschi A. , Richard S. , Hauser P. M. 
Published: June 2018

AbstractThe echinocandin caspofungin inhibits the catalytic subunit Gsc1 of the enzymatic complex synthetizing 1,3-β glucan, an essential compound of the fungal wall. Studies in rodents showed that caspofungin can treatPneumocystisinfections. However, its efficacy againstPneumocystis jirovecii, the species infecting exclusively humans, remains controversial. The aim of this study was to assess the sensitivity to caspofungin of theP. jiroveciiGsc1 subunit, as well as of those ofPneumocystis cariniiandPneumocystis murinainfecting respectively rats and mice. In absence of an establishedin vitroculture method forPneumocystisspecies, we used functional complementation of theSaccharomyces cerevisiae gsc1deletant. In the fungal pathogenCandida albicans, mutations leading to amino acid substitutions in Gsc1 confer resistance to caspofungin. We introduced the corresponding mutations into thePneumocystis gsc1genes using site-directed mutagenesis. In spot dilution tests, the sensitivity to caspofungin of the complemented strains decreased with the number of mutations introduced, suggesting that the wild-type enzymes are sensitive. The minimum inhibitory concentrations of caspofungin determined by E-test®and Yeastone®for strains complemented withPneumocystisenzymes (respectively 0.125 and 0.12 microg/ml) were identical to those upon complementation with the enzyme ofC. albicansthat is sensitive to caspofungin. However, they were lower than the MICs upon complementation with the enzyme of the resistant speciesCandida parapsilosis(0.19 and 0.25). Sensitivity levels of Gsc1 enzymes of the threePneumocystisspecies were similar. Our results suggest thatP. jiroveciiis sensitive to caspofungin during infections, asP. cariniiandP. murina.