bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytochemical screening ofColocasia giganteaandColocasia affinis(Family: Araceae) using1H-NMR and13C-NMR techniques
Authors: Alam Safaet , Haque Mohammad Rashedul 
Published: October 2020

AbstractColocasia affinisandColocasia giganteaare two of commonly found species underColocasiagenus. Folkloric use of these plants ascertains their ethnopharmacological importance and these plants are eaten as vegetables in several regions all around the world whileColocasia giganteahas planted as an ornamental plant too. Phytochemical screening of dichloromethane fractions of these plants using several separation techniques along followed by1H-NMR and13C-NMR techniques provide flavonoids and some other phyto compounds. However, in total 7 compounds were isolated from these plants i.e. penduletin (1), 7,8 -(3”,3”-dimethyl-pyrano)-4’-hydroxy flavonol (2), mixture of 7,8 -(3’’,3’’-dimethyl-pyrano)-4’-hydroxy flavonol fromC. affinisand mixture of α-amyrin and β-amyrin (3), penduletin (5), monoglyceride of stearic acid (6) fromC. gigantea.
Differentiation of Human induced Pluripotent Stem Cells to Authentic Macrophages using Fully Defined, Serum Free, Open Source Media
Authors: Vaughan-Jackson Alun , Stodolak Szymon , Ebrahimi Kourosh H. , Browne Cathy , Reardon Paul K. , Pires Elisabete , Gilbert-Jaramillo Javier , Cowley Sally A. , James William S. 
Published: October 2020

SummaryHuman iPSC and macrophages derived from them are increasingly popular tools for research into both infectious and degenerative diseases. However, as the field strives for greater modelling accuracy, it is becoming ever more challenging to justify the use of undefined and proprietary media for the culture of these cells. We describe here two fully defined, serum-free, open-source media for the culture of iPSC and differentiation of iPSC-derived macrophages. These media are equally capable of maintaining these cells compared to commercial alternatives. The macrophages differentiated in these defined media display improved terminally differentiated cell characteristics, reduced basal expression of induced anti-viral response genes, and improved polarisation capacity. We conclude that cells cultured in these media are an appropriate and malleable model for tissue resident macrophages, on which future differentiation techniques can be built.
SplineDist: Automated Cell Segmentation With Spline Curves
Authors: Mandal Soham , Uhlmann Virginie 
Published: October 2020

ABSTRACTWe present SplineDist, an instance segmentation convolutional neural network for bioimages extending the popular StarDist method. While StarDist describes objects as star-convex polygons, SplineDist uses a more flexible and general representation by modelling objects as planar parametric spline curves. Based on a new loss formulation that exploits the properties of spline constructions, we can incorporate our new object model in StarDist’s architecture with minimal changes. We demonstrate in synthetic and real images that SplineDist produces segmentation outlines of equal quality than StarDist with smaller network size and accurately captures non-star-convex objects that cannot be segmented with StarDist.
Single-cell RNA-seq analysis of human coronary arteries using an enhanced workflow reveals SMC transitions and candidate drug targets
Authors: Ma Wei Feng , Hodonsky Chani J. , Turner Adam W. , Wong Doris , Song Yipei , Barrientos Nelson B. , Mosquera Jose Verdezoto , Miller Clint L. 
Published: October 2020

AbstractBackground and AimsThe atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability or other plaque phenotypes are not yet available. We sought to investigate the human atherosclerotic cellular environment using scRNA-seq to uncover potential therapeutic approaches. We aimed to make our workflow user-friendly, reproducible, and applicable to other disease-specific scRNA-seq datasets.MethodsHere we incorporate automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into an enhanced and reproducible scRNA-seq analysis workflow. Notably, we also developed an R Shiny based interactive web application to enable further exploration and analysis of the scRNA dataset.ResultsWe applied this analysis workflow to a human coronary artery scRNA dataset and revealed distinct derivations of chondrocyte-like and fibroblast-like cells from smooth muscle cells (SMCs), and show the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several attractive avenues for future pharmacological repurposing in precision medicine. Further, our interactive web application,PlaqView(www.plaqview.com), allows other researchers to easily explore this dataset and benchmark applicable scRNA-seq analysis tools without prior coding knowledge.ConclusionsThese results suggest novel effects of chemotherapeutics on the atherosclerotic cellular environment and provide future avenues of studies in precision medicine. This publicly available workflow will also allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems.PlaqViewallows for rapid visualization and analysis of atherosclerosis scRNA-seq datasets without the need of prior coding experience. Future releases ofPlaqViewwill feature additional larger scRNA-seq and scATAC-seq atherosclerosis-related datasets, thus providing a critical resource for the field by promoting data harmonization and biological interpretation.
Learning and motor inhibitory control in crows and domestic chickens
Authors: Wascher Claudia A.F. , Allen Katie , Szipl Georgine 
Published: October 2020

AbstractCognitive abilities allow animals to navigate through complex, fluctuating environments. In the present study, we tested the performance of a captive group of eight crows,Corvus corone, and ten domestic chickens,Gallus gallus domesticus, in the cylinder task, as a test of motor inhibitory control, and reversal learning as a measure of learning ability and behavioural flexibility. Four crows and nine chickens completed the cylinder task, eight crows and six chickens completed the reversal learning experiment. Crows performed better in the cylinder task compared to chickens. In the reversal learning experiment, species did not significantly differ in the number of trials until learning criterion was reached. Performance in the reversal learning experiment did not correlate with performance in the cylinder task in chickens. Our results suggest crows to possess better motor inhibitory control compared to chickens. In contrast, learning performance in a reversal learning task did not differ between the species, indicating similar levels of behavioural flexibility. Interestingly, we describe notable individual differences in performance. We stress the importance not only to compare cognitive performance between species but also between individuals of the same species when investigating the evolution of cognitive skills.
Genomic Analyses of New Genes and Their Phenotypic Effects Reveal Rapid Evolution of Essential Functions in Drosophila Development
Authors: Xia Shengqian , VanKuren Nicholas W. , Chen Chunyan , Zhang Li , Kemkemer Clause , Shao Yi , Jia Hangxing , Lee UnJin , Advani Alexander S. , Gschwend Andrea , Vibranovski Maria , Chen Sidi , Zhang Yong E. , Long Manyuan 
Published: October 2020

ABSTRACTIt is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development ofDrosophila. The recent progress in the analyses of gene effects and improvements in the computational identification of new genes, which has led to large sample sizes of new genes, open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including the dating of gene ages, the interpretation of RNAi data that may confuse false positive/false negative rates, and the potential confounding impact of compensation and developmental effects that were not considered during previous CRISPR knockout experiments. We further analyzed new data from knockdowns of 702 new genes (~66% of total 1,070Drosophila melanogasternew genes), revealing a similarly high proportion of essential genes from recent evolution, compared to those found in distant ancestors ofD. melanogaster. Knockout of a few young genes detected analogous essentiality. Furthermore, our experimentally determined distribution and comparison of knockdown efficiency in different RNAi libraries provided valuable data for general functional analyses of genes. Taken together, these data, along with an improved understanding of the phenotypic effect analyses of new genes, provide further evidence to the conclusion that new genes inDrosophilaquickly evolved essential functions in viability during development.
DNA damage-signaling, homologous recombination and genetic mutation induced by 5-azacytidine and DNA-protein crosslinks inEscherichia coli
Authors: Klaric Julie A. , Glass David J. , Perr Eli L. , Reuven Arianna D. , Towne Mason J. , Lovett Susan T. 
Published: October 2020

ABSTRACTCovalent linkage between DNA and proteins produces highly toxic lesions and can be caused by commonly used chemotherapeutic agents, by internal and external chemicals and by radiation. In this study, usingEscherichia coli, we investigate the consequences of 5-azacytidine (5-azaC), which traps covalent complexes between itself and the Dcm cytosine methyltransferase protein. DNA protein crosslink-dependent effects can be ascertained by effects that arise in wild-type but not indcmΔ strains. We find that 5-azaC induces the bacterial DNA damage response and stimulates homologous recombination, a component of which is Dcm-dependent. Template-switching at an imperfect inverted repeat (“quasipalindrome”, QP) is strongly enhanced by 5-azaC and this enhancement was entirely Dcm-dependent. The SOS response helps ameliorate the mutagenic effect of 5-azaC but unbalanced expression of the SOS-induced DNA polymerases, especially PolIV, stimulates QP-associated mutagenesis. In the absence of Lon protease, Dcm-dependent QP-mutagenesis is elevated, suggesting it may play a role in 5-azaC tolerance. Deletions at short tandem repeats, which occur likewise by a replication template-switch, are elevated, but only modestly, by 5-azaC. We see evidence for Dcm-dependent and-independent killing by 5-azaC in sensitive mutants, such asrecA,recB, andlon; homologous recombination and deletion mutations are also stimulated in part by a Dcm-independent effect of 5-azaC. Whether this occurs by a different protein/DNA crosslink or by an alternative form of DNA damage is unknown.Highlights5-azacytidine is broadly mutagenic and recombinogenicIn E. coli, 5-azaC promotes genetic instability through Dcm methyltransferase.There are other, unknown lesions induced by 5-azaC besides Dcm/DNA crosslinks5-azaC induces the SOS response, protecting cells from killing and genetic instability
Tuning intrinsic disorder predictors for virus proteins
Authors: Almog Gal , Olabode Abayomi S , Poon Art FY 
Published: October 2020

AbstractMany virus-encoded proteins have intrinsically disordered regions that lack a stable folded threedimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy,e.g., a mean 36% gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to SARS-CoV-2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response.
Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell® culture inserts
Authors: Chandiramohan Abiram , Dabaghi Mohammedhossein , Aguiar Jennifer A. , Tiessen Nicholas , Stewart Mary , Cao Quynh T. , Nguyen Jenny P. , Makhdami Nima , Cox Gerard , Doxey Andrew C. , Hirota Jeremy A. 
Published: October 2020

AbstractAccessible in vitro models recapitulating the human airway that are amenable to study whole cannabis smoke exposure are needed for immunological and toxicological studies that inform public health policy and recreational cannabis use. In the present study, we developed and validated a novel 3D printed In Vitro Exposure System (IVES) that can be directly applied to study the effect of cannabis smoke exposure on primary human bronchial epithelial cells.Using commercially available design software and a 3D printer, we designed a four-chamber Transwell® insert holder for exposures to whole smoke. Software was used to model gas distribution, concentration gradients, velocity profile and shear stress within IVES. Following simulations, primary human bronchial epithelial cells cultured at air-liquid interface on Transwell® inserts were exposed to whole cannabis smoke. Following 24 hours, outcome measurements included cell morphology, epithelial barrier function, lactate dehydrogenase (LDH) levels, cytokine and gene expression.Whole smoke delivered through IVES possesses velocity profiles consistent with uniform gas distribution across the four chambers and complete mixing. Airflow velocity ranged between 1.0-1.5 μm s−1 and generated low shear stresses (<< 1 Pa). Human airway epithelial cells exposed to cannabis smoke using IVES showed changes in cell morphology and disruption of barrier function without significant cytotoxicity. Cannabis smoke elevated IL-1 family cytokines and elevated CYP1A1 and CYP1B1 expression relative to control.IVES represents an accessible, open-source, exposure system that can be used to model varying types of cannabis smoke exposures with human airway epithelial cells grown under air-liquid interface culture conditions.
Benchmarking common preprocessing strategies in early childhood functional connectivity MRI
Authors: Graff Kirk , Tansey Ryann , Ip Amanda , Rohr Christiane , Dimond Dennis , Dewey Deborah , Bray Signe 
Published: October 2020

AbstractFunctional connectivity magnetic resonance imaging (FC-MRI) has been widely used to investigate neurodevelopment. However, FC-MRI is vulnerable to head motion, which is associated with age and distorts FC estimates. Numerous preprocessing strategies have been developed to mitigate confounds, each with advantages and drawbacks. Preprocessing strategies for FC-MRI have typically been validated and compared using resting state data from adults. However, FC-MRI in young children presents a unique challenge due to relatively high head motion and a growing use of passive viewing paradigms to mitigate motion. This highlights a need to compare processing choices in pediatric samples. To this end, we leveraged longitudinal, passive viewing fMRI data collected from 4 to 8-year-old children. We systematically investigated combinations of widely used and debated preprocessing strategies, namely global signal regression, volume censoring, ICA-AROMA, and bandpass filtering. We implemented commonly used metrics of noise removal (i.e. quality control-functional connectivity), metrics sensitive to individual differences (i.e. connectome fingerprinting), and, because data was collected during a passive viewing task, we also assessed the impact on stimulus-evoked responses (i.e. intersubject correlations; ISC). We found that the most efficacious pipeline included censoring, global signal regression, bandpass filtering, and head motion parameter regression. Despite the drawbacks of noise-mitigation steps, our findings show benefits for both noise removal and information retention in a high-motion early childhood sample.Highlights- We evaluated 27 preprocessing pipelines in passive viewing data from young children- Pipelines were evaluated on noise-removed and information retained- Pipelines that included censoring and GSR outperformed alternatives across benchmarks- For high-motion scans, preprocessing choices substantially alter connectomes
Robust Encoding of Abstract Rules by Distinct Neuronal Populations in Primate Visual Cortex
Authors: Jonikaitis Donatas , Nissim Nir , Xia Ruobing , Moore Tirin 
Published: October 2020

AbstractIt is widely known that neural activity in sensory representations is modulated by cognitive factors such as attention, reward value and working memory. In such cases, sensory responses are found to reflect a selection of the specific sensory information needed to achieve behavioral goals. In contrast, more abstract behavioral constraints that do not involve stimulus selection, such as task rules, are thought to be encoded by neurons at later stages. We show that information about abstract rules is encoded by neurons in primate visual cortex in the absence of sensory stimulation. Furthermore, we show that rule information is greatest among neurons with the least visual activity and the weakest coupling to local neuronal networks. Our results identify rule-specific signals within a sensory representation and suggest that distinct mechanisms exist there for mapping rule information onto sensory guided decisions.
Loss of heterochromatin and retrotransposon silencing constitute an early phase in oocyte aging
Authors: Wasserzug-Pash Peera , Rothman Rachel , Reich Eli , Schonberger Oshrat , Weiss Yifat , Srebnik Naama , Cohen-Hadad Yaara , Weintraub Amir , Ben-Ami Ido , Holzer Hananel , Klutstein Michael 
Published: October 2020

AbstractMammalian oocyte quality reduces with female age. A well-studied aspect of this deterioration is an age-associated rise in oocyte aneuploidy. We show that prior to the occurrence of significant aneuploidy (at the age of 9 months in mouse females), epigenetic changes occur and impact oocyte quality and maturation ability. At this age- we observe a reduction in heterochromatin marks in mouse oocytes. This decrease is apparent in both constitutive heterochromatin and facultative heterochromatin marks but is absent in active euchromatic marks which remain constant. A decrease of heterochromatin marks with age is also observed in human GV oocytes from IVF treatments. Heterochromatin loss with age is associated with an elevation in retrotransposon RNA transcription and processing, an elevation in retrotransposon protein expression, elevation in DNA repair proteins nuclear localization and oocyte maturation defects. Artificial inhibition of the heterochromatin machinery in young oocytes causes an elevation in retrotransposon expression and processing and oocyte maturation defects. Collectively, our work demonstrates an early stage of oocyte aging, characterized by the loss of heterochromatin associated chromatin marks and activation of retrotransposons which cause DNA damage and impair oocyte maturation. We hypothesize that this heterochromatin loss serves as an oocyte associated “epigenetic clock” and is exploited by the cell as an oocyte QC mechanism.One Sentence SummaryOocyte aging includes an early pre-aneuploidy phase when loss of repressive chromatin marks occurs as well as retrotransposon activation and egg maturation defects.
Identification of genomic regions affecting production traits in pigs divergently selected for feed efficiency
Authors: Delpuech Emilie , Aliakbari Amir , Labrune Yann , Fève Katia , Billon Yvon , Gilbert Hélène , Riquet Juliette 
Published: October 2020

AbstractBackgroundFeed efficiency is a major driver of the sustainability of pig production systems. Understanding biological mechanisms underlying these agronomic traits is an important issue whether for environment and farms economy. This study aimed at identifying genomic regions affecting residual feed intake (RFI) and other production traits in two pig lines divergently selected for RFI during 9 generations (LRFI, low RFI; HRFI, high RFI).ResultsWe built a whole dataset of 570,447 single nucleotide polymorphisms (SNPs) in 2,426 pigs with records for 24 production traits after both imputation and prediction of genotypes using pedigree information. Genome-wide association studies (GWAS) were performed including both lines (Global-GWAS) or each line independently (LRFI-GWAS and HRFI-GWAS). A total of 54 chromosomic regions were detected with the Global-GWAS, whereas 37 and 61 regions were detected in LRFI-GWAS and HRFI-GWAS, respectively. Among those, only 15 regions were shared between at least two analyses, and only one was common between the three GWAS but affecting different traits. Among the 12 QTL detected for RFI, some were close to QTL detected for meat quality traits and 9 pinpointed novel genomic regions for some harbored candidate genes involved in cell proliferation and differentiation processes of gastrointestinal tissues or lipid metabolism-related signaling pathways. Detection of mostly different QTL regions between the three designs suggests the strong impact of the dataset on the detection power, which could be due to the changes of allelic frequencies during the line selection.ConclusionsBesides efficiently detecting known and new QTL regions for feed efficiency, the combination of GWAS carried out per line or simultaneously using all individuals highlighted the identification of chromosomic regions under selection that affect various production traits.