bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic factors underlie the association between anxiety, attitudes and performance in mathematics
Authors: Malanchini Margherita , Rimfeld Kaili , Wang Zhe , Petrill Stephen A. , Tucker-Dob Elliot M. , Plomin Robert , Kovas Yulia 
Published: August 2019

AbstractStudents struggling with mathematics anxiety (MA) tend to show lower levels of mathematics self-efficacy and interest as well as lower performance. The current study addresses: (1) how MA relates to different aspects of mathematics attitudes (self-efficacy and interest), ability (understanding numbers, problem-solving ability, and approximate number sense) and achievement (exam scores); (2) to what extent these observed relations are explained by overlapping genetic and environmental factors; and (3) the role of general anxiety in accounting for these associations. The sample comprised 3,410 twin pairs aged 16-21 years, from the Twins Early Development Study. Negative associations of comparable strength emerged between MA and the two measures of mathematics attitudes, phenotypically (∼ -.45) and genetically (∼ -.70). Moderate negative phenotypic (∼ -.35) and strong genetic (∼ -.70) associations were observed between MA and measures of mathematics performance. The only exception was approximate number sense whose phenotypic (-.10) and genetic (-.31) relation with MA was weaker. Multivariate quantitative genetic analyses indicated that all mathematics related measures combined accounted for ∼75% of the genetic variance in MA and ∼20% of its environmental variance. Genetic effects were largely shared across all measures of mathematics anxiety, attitudes, abilities and achievement, with the exception of approximate number sense. This genetic overlap was not accounted for by general anxiety. These results have important implications for future genetic research concerned with identifying the genetic underpinnings of individual variation in mathematics-related traits, as well as for developmental research into how children select and modify their mathematics-related experiences partly based on their genetic predispositions.
Novel mechanisms for phosphate acquisition in abundant rhizosphere-dwellingBacteroidetes
Authors: Lidbury Ian D.E.A. , Scanlan David J. , Murphy Andrew R. J. , Bottrill Andrew , Jones Alex , Tibbett Mark , Bending Gary , Hammond John P. , Wellington Elizabeth M. H. 
Published: August 2019

AbstractGlobal food production is reliant on the application of finite phosphorus (P) fertilisers. Numerous negative consequences associated with intensive P fertilisation have resulted in a high demand to find alternative sustainable methods that will enhance crop P uptake.Bacteroidetes, primarily from the genusFlavobacterium, have recently been shown to be abundant members of the plant microbiome, but their general ecological role and potential to mobilise P in the rhizosphere remains very poorly characterised. Here, we sought to determine the P mobilisation potential ofFlavobacteriumstrains isolated from the rhizosphere of oilseed rape (Brassica napusL.). We show that theseFlavobacteriumstrains possess novel mechanisms for P mobilisation and subsequent acquisition. These include the constitutive and inducible expression of completely novel and phylogenetically distinct phosphatases, the phosphate starvation inducible expression of uncharacterised and hypothetical genes and gene clusters and, for the first time, the involvement of outer membrane SusCD transport complexes (usually associated with carbohydrate transport) in P acquisition. The genes encoding these unusual phosphate starvation inducible proteins were enriched in plant-associatedFlavobacteriumstrains suggesting that this machinery represents niche-adaptive strategies for overcoming P scarcity in this genus. We propose that abundant rhizosphere-dwellingFlavobacteriumspp. have evolved unique mechanisms for coping with Pi-stress which may provide novel solutions for future sustainable agricultural practices.
PIWIL3 forms a complex with TDRKH in mammalian oocytes
Authors: Tan Minjie , van Tol Helena T.A. , Rosenkranz David , Roovers Elke F. , Damen Mirjam J. , Stout Tom A.E. , Wu Wei , Roelen Bernard A.J. 
Published: August 2019

AbstractPIWIs are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrials-recruited three-membered complex with TDRKH and PNLDC1, and demonstrated by mutagenesis that PIWIL3 N-terminal arginine modifications are required for complex assembly. Finally we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.
Liquid biopsies for omics-based analysis in sentinel mussels
Authors: Caza France , de Boissel Philippine Granger Joly , Villemur Richard , Betoulle Stéphane , St-Pierre Yves 
Published: August 2019

AbstractLiquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in sentinel mussels to assess the quality of marine ecosystems.
Medicago truncatula possesses a single Shaker outward K+ channel: functional characterization and roles in planta
Authors: Drain Alice , Thouin Julien , Wang Limin , Pauly Nicolas , Nieves-Cordones Manuel , Boeglin Martin , Gaillard Isabelle , Véry Anne-Aliénor , Sentenac Hervé 
Published: August 2019

SUMMARYThe model legume Medicago truncatula possesses a single outward Shaker K+ channel, while Arabidopsis thaliana possesses two channels of this type, named SKOR and GORK, the former having been shown to play a major role in K+ secretion into the xylem sap in the root vasculature and the latter to mediate the efflux of K+ across the guard cell membrane upon stomatal closure. Here we show that the expression pattern of the single M. truncatula outward Shaker channel, which has been named MtGORK, includes the root vasculature, guard cells and root hairs. As shown by patch-clamp experiments on root hair protoplasts, besides the Shaker-type slowly-activating outwardly-rectifying K+ conductance encoded by MtGORK, a second K+-permeable conductance, displaying fast activation and weak rectification, can be expressed by M. truncatula. A KO mutation resulting in absence of MtGORK activity is shown to weakly reduce K+ translocation to shoots, and only in plants engaged in rhizobial symbiosis, but to strongly affect the control of stomatal aperture and transpitational water loss. In legumes, the early electrical signaling pathway triggered by Nod Factor perception is known to comprise a short transient depolarization of the root hair plasma membrane. In absence of MtGORK functional expression, while the rate of the membrane repolarization is shown to be decreased by about 3 times, this defect is without any consequence on infection thread development and nodule production, indicating that the plant capacity to engage rhizobial symbiosis does not require integrity of the early electrical signaling events.
Low-cost scalable discretization, prediction and feature selection for complex systems
Authors: Gerber S. , Pospisil L. , Navandar M. , Horenko I. 
Published: August 2019

AbstractFinding reliable discrete approximations of complex systems is a key prerequisite when applying many of the most popular modeling tools. Common discretization approaches (for example, the very popular K-means clustering) are crucially limited in terms of quality and cost. We introduce a low-cost improved-quality Scalable Probabilistic Approximation (SPA) algorithm, allowing for simultaneous data-driven optimal discretization, feature selection and prediction. Cross-validated applications of SPA to a range of large realistic data classification and prediction problems reveal drastic cost and performance improvements. For example, SPA allows the unsupervised next-day surface temperature predictions for Europe with the mean crossvalidated one-day prediction error of 0.75°C on a common PC (being around 40% better in terms of errors and five to six orders-of-magnitude cheaper than the next-day surface temperature predictions calculated on supercomputers and provided by the weather services).One Sentence SummaryIntroduced computational tool allows obtaining drastic cost and quality gains for a broad range of science applications.
Human Inference in Changing Environments with Temporal Structure
Authors: Prat-Carrabin Arthur , Wilson Robert C. , Cohen Jonathan D. , da Silveira Rava Azeredo 
Published: August 2019

AbstractTo make informed decisions in natural environments that change over time, humans must update their beliefs as new observations are gathered. Studies exploring human inference as a dynamical process that unfolds in time have focused on situations in which the statistics of observations are history-independent. Yet temporal structure is everywhere in nature, and yields history-dependent observations. Do humans modify their inference processes depending on the latent temporal statistics of their observations? We investigate this question experimentally and theoretically using a change-point inference task. We show that humans adapt their inference process to fine aspects of the temporal structure in the statistics of stimuli. As such, humans behave qualitatively in a Bayesian fashion, but, quantitatively, deviate away from optimality. Perhaps more importantly, humans behave suboptimally in that their responses are not deterministic, but variable. We show that this variability itself is modulated by the temporal statistics of stimuli. To elucidate the cognitive algorithm that yields this behavior, we investigate a broad array of existing and new models that characterize different sources of suboptimal deviations away from Bayesian inference. While models with ‘output noise’ that corrupts the response-selection process are natural candidates, human behavior is best described by sampling-based inference models, in which the main ingredient is a compressed approximation of the posterior, represented through a modest set of random samples and updated over time. This result comes to complement a growing literature on sample-based representation and learning in humans.
Taking the next-gen step: comprehensive antimicrobial resistance detection from Burkholderia pseudomallei genomes
Authors: Madden Danielle E. , Webb Jessica R. , Steinig Eike J. , Currie Bart J. , Price Erin P. , Sarovich Derek S. 
Published: August 2019

AbstractBackgroundAntimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens.MethodsUsing 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA and CARD) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei.ResultsCARD failed to identify any clinically-relevant AMR in B. pseudomallei, ARIBA cannot differentiate AMR determinants from natural genetic variation, and neither CARD or ARIBA can identify CNV or gene loss determinants. In contrast, ARDaP accurately detected all SNP, indel, CNV, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency.ConclusionsWe demonstrate that existing AMR software are inadequate for comprehensive AMR detection; ARDaP overcomes the shortcomings of existing tools. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection.
Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
Authors: Gao Bo , Baudis Michael 
Published: August 2019

AbstractCopy number variations (CNV) are regional deviations from the normal autosomal bi-allelic DNA content. While germline CNVs are a major contributor to genomic syndromes and inherited diseases, the majority of cancers accumulate extensive “somatic” CNV (sCNV or CNA) during the process of oncogenetic transformation and progression. While specific sCNV have closely been associated with tumorigenesis, intriguingly many neoplasias exhibit recurrent sCNV patterns beyond the involvement of a few cancer driver genes.Currently, CNV profiles of tumor samples are generated using genomic micro-arrays or high-throughput DNA sequencing. Regardless of the underlying technology, genomic copy number data is derived from the relative assessment and integration of multiple signals, with the data generation process being prone to contamination from several sources. Estimated copy number values have no absolute and linear correlation to their corresponding DNA levels, and the extent of deviation differs between sample profiles which poses a great challenge for data integration and comparison in large scale genome analysis.In this study, we present a novel method named Minimum Error Calibration and Normalization of Copy Numbers Analysis (Mecan4CNA). For each sCNV profile,Mecan4CNAreduces the noise level, calculates values representing the normal DNA copies (baseline) and the change of one copy (level distance), and finally normalizes all values. Experiments ofMecan4CNAon simulated data showed an overall accuracy of 93% and 91% in determining the baseline and level distance, respectively. Comparison of baseline and level distance estimation with existing methods and karyotyping data on the NCI-60 tumor cell line produced coherent results. To estimate the method’s impact on downstream analyses we performed GISTIC analyses on original andMecan4CNAdata from the Cancer Genome Atlas (TCGA) where the normalized data showed prominent improvements of both sensitivity and specificity in detecting focal regions.In general,Mecan4CNAprovides an advanced method for CNA data normalization especially in research involving data of high volume and heterogeneous quality. but with its informative output and visualization can also facilitate analysis of individual CNA profiles.Mecan4CNAis freely available as a Python package and through Github.
Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms
Authors: Andreozzi Emilio , Carannante Ilaria , D’Addio Giovanni , Cesarelli Mario , Balbi Pietro 
Published: August 2019

AbstractBackgroundComputational models of ionic channels represent the building blocks of conductance-based, biologically inspired models of neurons and neural networks. Ionic channels are still widely modelled by means of the formalism developed by the seminal work of Hodgkin and Huxley, although the electrophysiological features of the channels are currently known to be better fitted by means of kinetic (Markov-type) models.ObjectiveThe present study is aimed at showing why kinetic, simplified models are better suited to model ionic channels compared to Hodgkin and Huxley models, and how the manual optimization process is rationally carried out in practice for these two kinds of models.MethodsPreviously published experimental data on macroscopic currents of an illustrative ionic channel (NaV1.5) are exploited to develop a step by step optimization of the two models in close comparison. The proposed kinetic model is a simplified one, consisting of five states and ten transitions.ResultsA conflicting practical limitation is recognized for the Hodgkin and Huxley model, which only supplies one parameter to model two distinct electrophysiological behaviours (namely the steady-state availability and the recovery from inactivation). In addition, a step by step procedure is provided to correctly optimize the kinetic model.ConclusionSimplified kinetic models are at the moment the best option to closely approximate the known complexity of the ionic channel macroscopic currents. Their optimization is achievable by means of a rationally guided procedure, and it results in models with computational burdens comparable with those from Hodgkin and Huxley models.
A high-throughput segregation analysis identifies the sex chromosomes ofCannabis sativa
Authors: Prentout Djivan , Razumova Olga , Rhoné Bénédicte , Badouin Hélène , Henri Hélène , Feng Cong , Käfer Jos , Karlov Gennady , Marais Gabriel AB 
Published: August 2019

AbstractCannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide.C. sativais a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. TheC. sativasex chromosomes sequence would improve early sexing and better management of this crop; however, theC. sativagenome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral,C. sativasex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced aC. sativafamily (2 parents and 10 male and female offspring) and performed a segregation analysis for allC. sativagenes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to aC. sativagenome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed thatC. sativahas a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).
mDia2 formin selectively interacts with catenins and not E-cadherin to regulate Adherens Junction formation
Authors: Zhang Yuqi , Pettee Krista M. , Becker Kathryn N. , Eisenmann Kathryn M. 
Published: August 2019

AbstractBackgroundEpithelial ovarian cancer (EOC) cells disseminate within the peritoneal cavity, in part, via the peritoneal fluid as single cells, clusters, or spheroids. Initial single cell egress from a tumor can involve disruption of cell-cell adhesions as cells are shed from the primary tumor into the peritoneum. In epithelial cells, Adherens Junctions (AJs) are characterized by homotypic linkage of E-cadherins on the plasma membranes of adjacent cells. AJs are anchored to the intracellular actin cytoskeletal network through a complex involving E-cadherin, p120 catenin, β-catenin, and αE-catenin. However, the specific players involved in the interaction between the junctional E-cadherin complex and the underlying F-actin network remains unclear. Recent evidence indicates that mammalian Diaphanous-related (mDia) formins plays a key role in epithelial cell AJ formation and maintenance through generation of linear actin filaments. Binding of αE-catenin to linear F-actin inhibits association of the branched-actin nucleator Arp2/3, while favoring linear F-actin bundling. We previously demonstrated that loss of mDia2 was associated with invasive single cell egress from EOC spheroids through disruption of junctional F-actin.ResultsIn the current study, we now show that mDia2 has a role at adherens junctions (AJs) in EOC OVCA429 cells and human embryonic kidney (HEK) 293 cells through its association with αE-catenin and β-catenin. mDia2 depletion in EOC cells leads to reduction in actin polymerization and disruption of cell-cell junctions with decreased interaction between β-catenin and E-cadherin.ConclusionsOur results support a necessary role for mDia2 in AJ stability in EOC cell monolayers and indicate a critical role for mDia formins in regulating EOC AJs during invasive transitions.
jULIEs: extracellular probes for recordings and stimulation in the structurally and functionally intact mouse brain
Authors: Racz Romeo , Kollo Mihaly , Racz Gabriella , Bulz Ciprian , Ackels Tobias , Warner Tom , Wray William , Kiskin Nikolai , Chen Chi , Ye Zhiwen , de Hoz Livia , Rancz Ede , Schaefer Andreas 
Published: August 2019

AbstractHigh signal-to-noise, scalable and minimally invasive recording and stimulation of the nervous system in intact animals is of fundamental importance to advance the understanding of brain function. Extracellular electrodes are among the most powerful tools capable of interfacing with large neuronal populations1-3. Neuronal tissue damage remains a major limiting factor in scaling electrode arrays, and has been found to correlate with electrode diameter across different electrode materials, such as microfabricated Michigan and Utah-style arrays4, MEMS and microsystems5, soft polymer or tungsten electrodes6 and Parylene C probes7. Small diameter ultramicroelectrodes (UMEs), while highly desirable, pose significant technical challenges such as reaching sufficient electrolyte-electrode coupling and limiting stray signal loss. To overcome these challenges, we have designed juxtacellular Ultra-Low Impedance Electrodes (jULIEs), a scalable technique for achieving high signal-to-noise electrical recordings as well as stimulation with UMEs. jULIEs are metal-glass composite UMEs thermally drawn to outer diameters (OD) of <25 µm, with metal core diameters (ID) of as little as 1 µm. We introduce a two-step electrochemical modification strategy that reduces UME coupling impedances by two orders of magnitude. Modifications enabled high signal-to-noise neural recordings in vivo through wires with micrometer scale core diameters. Histological and imaging experiments indicated that local vascular damage is minimal. Spikes reached amplitudes over 1 mV in vivo, indicating that recordings are possible in close proximity to intact neurons. Recording sites can be arranged in arbitrary patterns tailored to various neuroanatomical target structures and allowing parallel penetrations. jULIEs thus represent a versatile platform that allows for reliable recording and manipulation of neural activity in any areas of the functionally intact mammalian brain.