bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians
Authors: Portik Daniel M. , Bell Rayna C. , Blackburn David C. , Bauer Aaron M. , Barratt Christopher D. , Branch William R. , Burger Marius , Channing Alan , Colston Timothy J. , Conradie Werner , Dehling J. Maximillian , Drewes Robert C. , Ernst Raffael , Greenbaum Eli , Gvoždík Václav , Harvey James , Hillers Annika , Hirschfeld Mareike , Jongsma Gregory F.M. , Kielgast Jos , Kouete Marcel T. , Lawson Lucinda P. , Leaché Adam D. , Loader Simon P. , Lötters Stefan , Meijden Arie van der , Menegon Michele , Müller Susanne , Nagy Zoltán T. , Ofori-Boateng Caleb , Ohler Annemarie , Papenfuss Theodore J. , Rößler Daniela , Sinsch Ulrich , Rödel Mark-Oliver , Veith Michael , Vindum Jens , Zassi-Boulou Ange-Ghislain , McGuire Jimmy A. 
Published: July 2018

ABSTRACTTheory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across both micro- and macroevolutionary timescales.
TCRex: detection of enriched T cell epitope specificity in full T cell receptor sequence repertoires
Authors: Gielis Sofie , Moris Pieter , Bittremieux Wout , De Neuter Nicolas , Ogunjimi Benson , Laukens Kris , Meysman Pieter 
Published: July 2018

ABSTRACTHigh-throughput T cell receptor (TCR) sequencing allows the characterization of an individual’s TCR repertoire and directly query their immune state. However, it remains a non-trivial task to couple these sequenced TCRs to their antigenic targets. In this paper, we present a novel strategy to annotate full TCR sequence repertoires. The strategy is based on a machine learning algorithm to learn the TCR patterns common to the recognition of a specific epitope. These results are then combined with a statistical analysis to evaluate the occurrence of specific epitope-reactive TCR sequences per epitope in repertoire data. In this manner, we can directly study the capacity of full TCR repertoires to target specific epitopes of the relevant vaccines or pathogens. We demonstrate the usability of this approach on three independent datasets related to vaccine monitoring and infectious disease diagnostics by independently identifying the epitopes that are targeted by the TCR repertoire. The developed method is freely available as a web tool for academic use at tcrex.biodatamining.be.
Spectral fingerprints or spectral tilt? Evidence for distinct oscillatory signatures of memory formation
Authors: Fellner Marie-Christin , Gollwitzer Stephanie , Rampp Stefan , Kreiselmeyr Gernot , Bush Daniel , Diehl Beate , Axmacher Nikolai , Hamer Hajo , Hanslmayr Simon 
Published: July 2018

AbstractDecreases in low frequency power (2-30 Hz) alongside high frequency power increases (>40 Hz) have been demonstrated to predict successful memory formation. Parsimoniously this change in the frequency spectrum can be explained by one factor, a change in the tilt of the power spectrum (from steep to flat) indicating engaged brain regions. A competing view is that the change in the power spectrum contains several distinct brain oscillatory fingerprints, each serving different computations. Here, we contrast these two theories in a parallel MEG-intracranial EEG study where healthy participants and epilepsy patients, respectively, studied either familiar verbal material, or unfamiliar faces. We investigated whether modulations in specific frequency bands can be dissociated in time, space and by experimental manipulation. Both, MEG and iEEG data, show that decreases in alpha/beta power specifically predicted the encoding of words, but not faces, whereas increases in gamma power and decreases in theta power predicted memory formation irrespective of material. Critically, these different oscillatory signatures of memory encoding were evident in different brain regions. Moreover, high frequency gamma power increases occurred significantly earlier compared to low frequency theta power decreases. These results speak against a “spectral tilt” and demonstrate that brain oscillations in different frequency bands serve different functions for memory encoding.
Natural variation inC. elegansarsenic toxicity is explained by differences in branched chain amino acid metabolism
Authors: Zdraljevic Stefan , Fox Bennett W. , Strand Christine , Panda Oishika , Tenjo Francisco J. , Brady Shannon C. , Crombie Tim A. , Doench John G. , Schroeder Frank C. , Andersen Erik C. 
Published: July 2018

AbstractWe find that variation in thedbt-1gene underlies natural differences inCaenorhabditis elegansresponses to the toxin arsenic. This gene encodes the E2 subunit of the branched-chain α-keto acid dehydrogenase (BCKDH) complex, a core component of branched-chain amino acid (BCAA) metabolism. We causally linked a non-synonymous variant in the conserved lipoyl domain of DBT-1 to differential arsenic responses. Using targeted metabolomics and chemical supplementation, we demonstrate that differences in responses to arsenic are caused by variation in iso-branched chain fatty acids. Additionally, we show that levels of branched chain fatty acids in human cells are perturbed by arsenic treatment. This finding has broad implications for arsenic toxicity and for arsenic-focused chemotherapeutics across human populations. Our study implicates the BCKDH complex and BCAA metabolism in arsenic responses, demonstrating the power ofC. elegansnatural genetic diversity to identify novel mechanisms by which environmental toxins affect organismal physiology.
Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins
Authors: Childs Dorothee , Bach Karsten , Franken Holger , Anders Simon , Kurzawa Nils , Bantscheff Marcus , Savitski Mikhail , Huber Wolfgang 
Published: July 2018

AbstractDetecting the targets of drugs and other molecules in intact cellular contexts is a major objective in drug discovery and in biology more broadly. Thermal proteome profiling (TPP) pursues this aim at proteome-wide scale by inferring target engagement from its effects on temperature-dependent protein denaturation. However, a key challenge of TPP is the statistical analysis of the measured melting curves with controlled false discovery rates at high proteome coverage and detection power. We present non-parametric analysis of response curves (NPARC), a statistical method for TPP based on functional data analysis and nonlinear regression. We evaluate NPARC on five independent TPP datasets and observe that it is able to detect subtle changes in any region of the melting curves, reliably detects the known targets, and outperforms a melting point-centric, single-parameter fitting approach in terms of specificity and sensitivity. NPARC can be combined with established analysis of variance (ANOVA) statistics and enables flexible, factorial experimental designs and replication levels. To facilitate access to a wide range of users, a freely available software implementation of NPARC is provided.
Formulation, Evaluation and Antibacterial Efficiency of water-based herbal Hand Sanitizer Gel
Authors: Acharya Shri Balakrishna , Ghosh Saradindu , Yadav Giriraj , Sharma Kavita , Ghosh Sirsendu , Joshi Sushil 
Published: July 2018

ABSTRACTHands are the primary mode of transmission of microbes and infections. Hand-washing is critical in food production, food service and also important in healthcare setting, homes and day care preparations. The present research was aimed to evaluate the antibacterial efficacy of various herbal oils such as Cinnamon oil, Eucalyptus oil, menthol oil and lavender oil and found that cinnamon oil showed better antibacterial activity. Also the research was carried out to formulate and evaluate the poly herbal Hand wash gel containing Azadirachta indica, Ocimum sanctum and Citrus limon extracts. The anti-microbial activity of the formulated herbal hand wash gel was tested against Escherichia coli, Staphylococcus aureus and Salmonella by spread plate techniques and the results obtained were compared with commercial antibacterial standards. Also the efficiency was checked by using the hand wash gel on volunteers. The results from the present work suggest and support the incorporation and utilization of herbs in the formulations to give better effect.
The landscape of coadaptation in Vibrio parahaemolyticus
Authors: Cui Yujun , Yang Chao , Qiu Hongling , Wang Hui , Yang Ruifu , Falush Daniel 
Published: July 2018

AbstractInvestigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups involving 1,560 coding genes. 82 of these interaction groups are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 interaction groups involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. Preliminary experiments imply that the strategies influence biofilm formation and bacterial growth rate in vitro. One strategy involves a divergent profile in multiple genome regions, implying that strains have irreversibly specialized, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.
Web-based design and analysis tools for CRISPR base editing
Authors: Hwang Gue-Ho , Park Jeongbin , Lim Kayeong , Kim Sunghyun , Yu Jihyeon , Kim Sang-Tae , Eils Roland , Kim Jin-Soo , Bae Sangsu 
Published: July 2018

AbstractBackgroundAs a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.ResultsWe present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (>100MB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/bedesigner/ and http://www.rgenome.net/be-analyzer/respectivelyConclusionWe develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.
Components of Executive Function Predict Regional Prefrontal Volumes
Authors: Mace Ryan A. , Waters Abigail B. , Sawyer Kayle S. , Turrisi Taylor , Gansler David A. 
Published: July 2018

AbstractObjectiveDesigned to measure a diversity of executive functioning (EF) through classical neuropsychological tests, the Delis-Kaplan Executive Function Scale (D-KEFS) allows for the investigation of the neural architecture of EF. We examined how the D-KEFS Tower, Verbal Fluency, Design Fluency, Color–Word Interference, and Trail Making Test tasks related to regional frontal lobe volumes, quantifying how components of EF were represented in disparate neural networks.MethodAdults from the Nathan Kline Institute – Rockland Sample (NKI-RS), an open-access community study of brain development, with complete MRI (3T scanner) and D-KEFS data were selected for analysis (N = 478; ages 20-85). In a mixed-effects model predicting volume, D-KEFS task, D-KEFS score, region of interest (ROI; 13 frontal, 1 occipital control), were entered as fixed effects with intercepts for participants as random effects.Results“Unitary” EF (average of D-KEFS scores) was positively associated with superior frontal, rostral middle frontal, and lateral orbitofrontal volumes; a negative association was observed with frontal pole volume (| z-score slope | range = 0.040 to 0.051). “Diverse” EF skills (individual D-KEFS task scores) were differentially associated with two or three ROIs, respectively, but to a stronger extent (| z-score slope | range = 0.053 to 0.103).ConclusionsThe neural correlates found for the D-KEFS support the prefrontal modularity of EF at both the unitary (aspects of EF ability common to all tasks) and task (diverse EF skills) levels. The separation of task-general variance in neurocognition from task-specific variance can further evaluate neuropsychological tests as indices of brain integrity.Public Significance StatementsOur results support the relationship between larger lateral prefrontal cortex and greater executive function.A composite of executive function performance, which was broadly associated with the prefrontal cortex, may be ideal for assessing diffuse frontal lobe damage (e.g., hypoxia).Individual executive functions, which were more narrowly but strongly related to specific prefrontal regions, could be better for assessing the effects of localized brain injuries (e.g., tumor).
ROSeq: Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data
Authors: Gupta Krishan , Lalit Manan , Biswas Aditya , Maulik Ujjwal , Bandyopadhyay Sanghamitra , Ahuja Gaurav , Ghosh Abhik , Sengupta Debarka 
Published: July 2018

1AbstractSystematic delineation of complex biological systems is an ever-challenging and resource-intensive process. Single cell transcriptomics allows us to study cell-to-cell variability in complex tissues at an unprecedented resolution. Accurate modeling of gene expression plays a critical role in the statistical determination of tissue-specific gene expression patterns. In the past few years, considerable efforts have been made to identify appropriate parametric models for single cell expression data. The zero-inflated version of Poisson/Negative Binomial and Log-Normal distributions have emerged as the most popular alternatives due to their ability to accommodate high dropout rates, as commonly observed in single cell data. While the majority of the parametric approaches directly model expression estimates, we explore the potential of modeling expression-ranks, as robust surrogates for transcript abundance. Here we examined the performance of the Discrete Generalized Beta Distribution (DGBD) on real data and devised a Wald-type test for comparing gene expression across two phenotypically divergent groups of single cells. We performed a comprehensive assessment of the proposed method, to understand its advantages as compared to some of the existing best practice approaches. Besides striking a reasonable balance between Type 1 and Type 2 errors, we concluded that ROSeq, the proposed differential expression test is exceptionally robust to expression noise and scales rapidly with increasing sample size. For wider dissemination and adoption of the method, we created an R package called ROSeq, and made it available on the Bioconductor platform.
Tissue-specific actions of Pax6 on proliferation-differentiation balance in the developing forebrain are Foxg1-dependent
Authors: Quintana-Urzainqui Idoia , Kozić Zrinko , Mitra Soham , Tian Tian , Manuel Martine , Mason John O. , Price David J. 
Published: July 2018

SummaryDifferences in the growth and maturation of diverse forebrain tissues depends on region-specific transcriptional regulation. Individual transcription factors act simultaneously in multiple regions that develop very differently, raising questions about the extent to which their actions vary regionally. We found that the transcription factor Pax6 affects the transcriptomes and the balance between proliferation and differentiation in opposite directions in murine diencephalon versus cortex. We tested several possible mechanisms to explain Pax6’s tissue-specific actions and found that the presence of the transcription factor Foxg1 in cortex but not diencephalon was most influential. We found that Foxg1 is responsible for many of the differences in cell cycle gene expression between diencephalon and cortex. In cortex lacking Foxg1, Pax6’s action on the balance of proliferation versus differentiation became diencephalon-like. Our findings reveal a mechanism for generating regional forebrain diversity in which the actions of one transcription factor completely reverse the actions of another.
High-dimensional geometry of population responses in visual cortex
Authors: Stringer Carsen , Pachitariu Marius , Steinmetz Nicholas , Carandini Matteo , Harris Kenneth D. 
Published: July 2018

AbstractA neuronal population encodes information most efficiently when its activity is uncorrelated and high-dimensional, and most robustly when its activity is correlated and lower-dimensional. Here, we analyzed the correlation structure of natural image coding, in large visual cortical populations recorded from awake mice. Evoked population activity was high dimensional, with correlations obeying an unexpected power-law: the nth principal component variance scaled as 1/n. This was not inherited from the 1/f spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that the variance spectrum must decay at least this fast if a population code is smooth, i.e. if small changes in input cannot dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness represents a fundamental constraint governing correlations in neural population codes.
Domestic gardens as favorable pollinator habitats in impervious landscapes
Authors: Levé Marine , Baudry Emmanuelle , Bessa-Gomes Carmen 
Published: July 2018

AbstractUrban expansion is correlated to negative biodiversity trends. The amount of impervious surfaces in urban areas is a determinant of pollinator species assemblages. While the increase in urbanization and impervious surfaces negatively impacts pollinators, cities also encompass urban green spaces, which have a significant capacity to support biodiversity. Among them, domestic gardens that represent a non-negligible fraction of green spaces have been shown to benefit pollinators. Domestic gardens may form habitat clusters in residential areas, although their value at a landscape scale is still unknown. Here, we investigate the combined effects of impervious surfaces and domestic garden areas on pollinator richness. Due to the difficulty of accessing privately owned domestic gardens, we chose to use citizen science data from a well-established French citizen science program known as SPIPOLL. Using regression tree analysis on buffers located from 50m to 1000m around the data points, we show the importance of pollinators being in close proximity to domestic gardens as locally favorable habitats that are embedded within a landscape, in which impervious surfaces represent unfavorable areas. We highlight the inter-connection between local and landscape scales, the potential for patches of domestic gardens in residential areas, and the need to consider the potential of gardeners’ coordinated management decisions within a landscape context.HighlightsCitizen science provided access to domestic gardens, understudied urban green spacesImpervious surfaces limit pollinators presence at landscape levelSufficient critical amount of gardens increased pollinator diversity at local scaleCritical amount of gardens’ knowledge may favor coordinated decisions by gardenersPollinators may benefit from patches of domestic gardens in an urban matrix
Regression of solid breast tumours in mice by Newcastle disease virus is associated with production of apoptosis related-cytokines
Authors: Ahmad Umar , Raihan Juraimi , Yong Yoke Keong , Eshak Zolkapli , Othman Fauziah , Ideris Aini 
Published: July 2018

AbstractBackgroundDifferent strains of Newcastle disease virus (NDV) worldwide proved to have tumouricidal activity in several types of cancer cells. However, the possible anti-cancer activity of Malaysian NDV AF2240 strain and its mechanism of action remains unknown. The ability of cytokine-related apoptosis-inducing NDV AF2240 to treat breast cancer was investigated in the current study.MethodsA total of 90 mice were used and divided into 15 groups, each group comprising of 6 mice. Tumour, body weight and mortality of the mice were determined throughout the experiment, to observe the effect of NDV and NDV+Tamoxifen treatments on the mice. In addition, the toxic effect of the treatments was determined through liver function test. In order to elucidate the involvement of cytokine production induced by NDV, a total of six cytokines, i.e. IL-6, IFN-γ, MCP-1, IL-10, IL12p70 and TNF-α were measured using cytometric bead array assay (plasma) and enzyme-linked immunosorbent spot (isolated splenocytes).ResultsThe results demonstrated that 4T1 breast cancer cells in allotransplanted mice treated with AF2240 showed a noticeable inhibition in tumour growth and induce apoptotic-related cytokines.ConclusionNDV AF2240 suppression of breast tumour growth is associated with induction of apoptotic-related cytokines.