bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel software for automated morphometric analysis of stented arteries
Authors: Resnick Aviel , Hooshdaran Bahman , Pressly Benjamin B. , Guerrero David T. , Alferiev Ivan S. , Chorny Michael , Levy Robert J. , Fishbein Ilia 
Published: February 2020

AbstractMorphometric analysis of explanted arteries remains the gold standard in assessing pathological mechanisms of arterial disease, and the efficacy of therapeutic interventions. Software currently used for morphometric analysis (ImageJ, ImagePro, etc.) requires manual tracing of each region of interest by the user to obtain direct and derived data needed for analysis. Manual segmentation of borders between differently stained arterial compartments is time-consuming and prone to bias, even when the operator is blind to the treatment type. Here, we report newly designed morphometric software, floodSeg, which greatly aids analysis through semiautomated segmentation, followed by automated computation and data entry. The program includes tools for both rapid component selection, and precision user-controlled contour correction. In practice, segmentation occurs following the selection of seed points and corresponding threshold values, for each desired component. The flood fill algorithm is used to map out components, followed by Sklansky’s convex-hull algorithm to obtain the outer contours. If necessary, convexity defects can be overcome through manual point placement on top of existing points, and regeneration of the contour. floodSeg was tested using a set of non-uniformly stained stented rat arteries, and compared against manually obtained results. The accuracy of the resulting measurements was within the expected limit based on repeated manual measurements by the same operator, and did not exceed 3%. Most notably, the duration for data acquisition using floodSeg was less than 20% of the time required for manual measurements by an experienced operator. Thus, our contribution is an improvement on widely used software, with significant potential for application in a multitude of areas of pathology practice.
Characterization and Mitigation of Fragmentation Enzyme-Induced Dual Stranded Artifacts
Authors: Gregory C. Thomas , Ngankeu Apollinaire , Orwick Shelley , Kautto Esko , Woyach Jennifer A. , Byrd John C. , Blachly James S. 
Published: February 2020

AbstractHigh-throughput short-read sequencing relies on fragmented DNA for optimal sampling of input nucleic acid. Several vendors now offer proprietary enzyme cocktails as a cheaper and more streamlined method of fragmentation when compared to acoustic shearing. We have discovered that these enzymes induce the formation of library molecules containing regions of nearby DNA from opposite strands. Sequencing reads derived from these molecules can lead to artifact-derived variant calls appearing at variant allele frequencies less than 5%. We present Fragmentation Artifact Detection and Elimination (FADE), software to remove these artifacts from mapped reads and mitigate artifact-related effects on downstream analysis. We find that the artifacts principally affect downstream analyses that are sensitive to a 1-3% artifact bias in the sequencing reads, such as targeted resequencing and rare variant discovery.AvailabilityData are deposited at SRA under accession No. PRJNA602687 Software described in this manuscript is freely available athttps://github.com/blachlylab/fade
Pial surface CSF-contacting texture, subpial and funicular plexus in the thoracic spinal cord in monkey: NADPH diaphorase histological configuration
Authors: Li Yinhua , Hou Wei , Jia Yunge , Wen Xiaoxin , Rao Chenxu , Xu Ximeng , Wei Zichun , Bai Lu , Tan Huibing 
Published: February 2020

AbstractIn spinal cord, white matter is distinguished from grey matter in that it contains ascending and descending axonal tracts. While grey matter gets concentrated with neuronal cell bodies. Notable cell bodies and sensory modality of cerebral spinal fluid (CSF) in white matter are still elusive in certain segment of the spinal cord. Monkey Spinal cord was examined by NADPH diaphorase (NADPH-d) histochemistry. We found that NADPH-d positive neurons clustered and featured flat plane in mediolateral funiculus in caudal thoracic and rostral lumber spinal cord, especially evident in the horizontal sections. Majority of NADPH-d funicular neurons were relatively large size and moderately-or lightly-stained neurons. In horizontal section, the multipolar processes of the neurons were thicker than that of regular other neurons. The processes oriented laterally or obliquely in the lateral funiculus. Some of neuronal cell bodies and proximal processes attached NADPH-d positive buttons or puncta. The neuronal processes interlaced network medially linked to lateral horn (intermediolateral nucleus, IML) and laterally to subpial region, in which formed subpial plexus with subpial NADPH-d neurons. Subpial plexus appeared to contacting externally with CSF. The subpial plexus patterned like round brackets located in lateromarginal pial surface. Compared with sympathetic IML in rostral thoracic segments and sacral parasympathetic IML, the funicular plexus configurated a specialized neuro-texture in caudal thoracic segments. The dendritic arbor of funicular neuron featured variety geometric plane shapes. The funicular plexus oriented exclusive layered flat-plane organization between lateral horn and subpial region in caudal thoracic and rostral lumber spinal cord. The subpial plexus may work as CSF sensor outside of spinal cord. The cluster of funicular neurons may function as locomotion sensor, besides visceral regulation. Different to periventricular CSF contacting or pericentral canal structures, NADPH-d funicular neurons and subpial plexus that located in the pial surface. With advantage of NADPH-d, we found funicular neurons which termed academically as funicular plexus and specialized localization for subpial structure we termed subpial plexus. The funicular texture was regarded as neuronal bridge between the interior CSF in the central canal and external CSF out of the pial surface.
Characterization of an ECF56-family sigma factor fromStreptomyces venezuelaereveals a highly conserved regulome
Authors: Thompson Mitchell G. , Zargar Amin , Cruz-Morales Pablo , De Rond Tristan , Chang Samantha , Pearson Allison N. , Goyal Garima , Barajas Jesus F. , Blake-Hedges Jacquelyn M. , Phelan Ryan M. , Reyes-Umana Victor , Hernández Amanda C. , Hillson Nathan J. , Shih Patrick M. , Keasling Jay D. 
Published: February 2020

AbstractBacteria often possess alternative sigma factors that initiate the transcription of specific genes under environmental stresses, the largest and most diverse group being the extracytoplasmic function (ECF) sigma factors. The regulation of ECF activity is crucial for ensuring the distinct transcription of stress responsive genes only occurs under the appropriate conditions. While most ECFs are comprised of only the core σ2and σ4regions, a unique form of ECF sigma factor regulation also contains a C-terminal extension bearing homology to the NTF2 superfamily of protein domains. While previous work has shown that this NTF2 domain can affect transcriptional activityin vivoin ECF41 and ECF42, its role in the newly classified ECF56 subgroup is unknown. In this work, we show that truncation of the C-terminus of the ECF56 sigma factor SVEN_4562 ofStreptomyces venezuelaeupregulates its activity in a hybrid assay. Through transcriptomics inS. venezuelae, we found that this truncated ECF56 sigma factor has a highly conserved promoter sequencein vivo. Bioinformatic assays illustrated that deep branches of theActinobacteriaphylum contained putative ECF56 promoter motifs identical to those found in theS. venezuelaeECF56 regulon. We validated these findings throughex situhybrid assays illustrating that truncated ECF56 sigma factors from phylogenetically diverseActinobacteriaactivate transcription from these promoters. Importantly, our work shows that the genetic infrastructure of the ECF56 family of sigma factors is highly conserved and performs important functions yet to be understood inActinobacteria.ImportanceMost ECF sigma-factors rely on anti-sigma factor regulation; in contrast, the unique classes of ECF sigma-factors that contain a C-terminal extension are thought to respond directly to an environmental signal. Here we show that thecis-acting regulatory element of the ECF56 regulon is likely highly conserved in manyActinobacteria, with exact nucleotide level conservation over ~2 billion years of evolution. The high conservation of this genetic architecture, as well as a conserved gene content within the regulon, strongly point to a specialized and important role inActinobacteriabiology.
The bacterial quorum sensing signal DSF hijacksArabidopsis thalianasterol biosynthesis to suppress plant innate immunity
Authors: Tran Tuan Minh , Ma Zhiming , Triebl Alexander , Nath Sangeeta , Cheng Yingying , Gong Ben-Qiang , Han Xiao , Wang Junqi , Li Jian-Feng , Wenk Markus R. , Torta Federico , Mayor Satyajit , Yang Liang , Miao Yansong 
Published: February 2020

AbstractQuorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely under-studied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced byXanthomonas campestrispv.campestriscan suppress pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) inArabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of oligomerization states and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile ofArabidopsis, with a particular increase of the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate PAMP-triggered host immunity.SIGNIFICANCE STATEMENTBacteria rely on small signalling molecules called quorum sensing (QS) signals to communicate and coordinate their behaviors. QS is known to regulate gene expression, production of virulence factors, and biofilm formation for pathogenic bacteria to effectively colonize their hosts and cause diseases. In this work, we found a class of QS molecule called diffusible-signal factor (DSF), produced by devastating phytopathogenic bacteria such asXanthomonasspp. andXylella fastidiosa, could communicate directly with plant host and subvert plant innate immunity by inducing plant sterol production and thereby, attenuating receptor signalling through hindering the receptor clustering and plant endocytosis. The results significantly enrich our understanding of the mechanisms in the tug-of-war between bacterial pathogenesis and host immunity.
Primary Human Hepatocytes Maintain Long-term Functions in Porous Silk Scaffolds Containing Extracellular Matrix Proteins
Authors: Kukla David A. , Stoppel Whitney L. , Kaplan David L. , Khetani Salman R. 
Published: February 2020

ABSTRACTThe shortage of donor organs for transplantation has prompted the development of alternative implantable human liver tissues; however, the need for a clinically viable liver tissue that can be fabricated using physiologically-relevant primary human hepatocytes (PHHs) is unmet. Purified silk proteins provide desirable features for generating implantable tissues, such as sustainable sourcing from insects/arachnids, biocompatibility, tunable mechanical properties and degradation rates, and low immunogenicity upon implantation; however, the utility of such scaffolds to generate human liver tissues using PHHs remains unclear. Here, we show that the incorporation of type I collagen during the fabrication and/or autoclaving of silk scaffolds was necessary to enable robust PHH attachment/function. Scaffolds with small pores (73 +/- 25 µm) promoted higher PHH functions than large pores (235 +/- 84 µm). Further incorporation of growth-arrested 3T3-J2 fibroblasts into scaffolds enhanced PHH functions up to 5-fold for 5 months in culture, an unprecedented longevity, and functions were better retained than 2D configurations. Lastly, encapsulating PHHs within Matrigel™ while housed in the silk/collagen scaffold led to higher functions than Matrigel or silk/collagen alone. In conclusion, porous silk scaffolds are useful for generating long-term PHH +/- fibroblast tissues which may ultimately find applications in regenerative medicine and drug development.
JNK signaling controls branching, nucleokinesis, and positioning of centrosomes and primary cilia in migrating cortical interneurons
Authors: Smith Skye E. , Coker Nicholas K. , Tucker Eric S. 
Published: February 2020

ABSTRACTAberrant migration of inhibitory interneurons can alter the formation of cortical circuitry and lead to severe neurological disorders including epilepsy, autism, and schizophrenia. However, mechanisms involved in directing the migration of these cells remain incompletely understood. In the current study, we used live-cell confocal microscopy to explore the mechanisms by which the c-Jun NH2-terminal kinase (JNK) pathway coordinates leading process branching and nucleokinesis, two cell biological processes that are essential for the guided migration of cortical interneurons. Pharmacological inhibition of JNK signaling disrupts the kinetics of leading process branching, rate and amplitude of nucleokinesis, and leads to the rearward mislocalization of the centrosome and primary cilium to the trailing process. Genetic loss ofJnkfrom interneurons corroborates our pharmacological observations and suggests that important mechanics of interneuron migration depend on the intrinsic activity of JNK. These findings suggest that JNK signaling regulates leading process branching, nucleokinesis, and the trafficking of centrosomes and cilia during interneuron migration, and further implicates JNK signaling as an important mediator of cortical development.Summary StatementLoss of JNK signaling reduces growth cone branching frequency, limits interstitial side branch duration, alters rate and amplitude of nucleokinesis, and mislocalizes centrosomes and primary cilia in migrating cortical interneurons.
A preliminary ecological profile of Kyasanur Forest disease virus hosts among the mammalian wildlife of the Western Ghats, India
Authors: Walsh Michael G. , Mor Siobhan M. , Maity Hindol , Hossain Shah 
Published: February 2020

AbstractKyasanur Forest disease (KFD) is one of India’s severe arboviruses capable of causing prolonged debilitating disease. It has been expanding beyond its historical endemic locus at an alarming rate over the last two decades. The natural nidus of this zoonosis is located in the monsoon rainforest of the Western Ghats, India, which is one of the world’s most important biodiversity hotspots. Definitive reservoir hosts for KFD virus (KFDV) have yet to be delineated, and thus much of the infection ecology of this virus, and its consequent transmission dynamics, remains uncertain. Given its unique biogeographical context, identifying ecological parameters of KFDV relevant to the virus’ epidemiology has been complex and challenging. The challenge has been exacerbated by diminished research efforts in wildlife surveillance over the last two decades, coinciding with the expansion of the range of KFD across the region. The current investigation sought to define a preliminary ecological profile of KFDV hosts based on their life history and feeding traits to aid in re-establishing targeted wildlife surveillance and to discern those ecological traits of wildlife hosts that may improve our understanding of KFD epidemiology. The importance of fast-living among KFDV hosts was of special interest with respect to the latter aim. We compared mammalian traits between host and non-host species using general additive models and phylogenetic generalised linear models. This study found that both body mass and forest forage were strongly associated with mammalian host infection status, but that reproductive life history traits were not. These findings will help in structuring ecologically based wildlife surveillance and field investigations, while also helping to parameterise novel epidemiological models of zoonotic infection risk that incorporate species functional traits in a region where biogeography, landscape ecology, and community ecology manifest extraordinary complexity, particularly under growing anthropogenic pressure.
Prebiotics and community composition influence gas production of the human gut microbiota
Authors: Yu Xiaoqian , Gurry Thomas , Tu Nguyen Le Thanh , Richardson Hunter S. , Alm Eric J. 
Published: February 2020

AbstractPrebiotics confer benefits to human health often by promoting the growth of gut bacteria that produce metabolites valuable to the human body, such as short chain fatty acids (SCFAs). While prebiotic selection has strongly focused on maximizing the production of SCFAs, less attention has been paid to gases, a byproduct of SCFA production that also has physiological effects on the human body. Here, we investigate how the content and volume of gas production by human gut microbiota is affected by the chemical composition of the prebiotic and by the composition of the microbiota. We first constructed a linear systems model based on mass and electron balance and compared the theoretical product range of two prebiotics, inulin and pectin. Modeling shows that pectin is more restricted in product space, with less potential for H2 but more potential for CO2 production. An ex vivo experimental system showed pectin degradation produced significantly less H2 than inulin, but CO2 production fell outside the theoretical product range, suggesting fermentation of fecal debris. Microbial community composition also impacted results: methane production was dependent on the presence of Methanobacteria, while inter-individual differences in H2 production during inulin degradation was driven by a Lachnospiraceae taxon. Overall, these results suggest that both the chemistry of the prebiotic and the composition of the microbiota are relevant to gas production. Metabolic processes that are relatively prevalent in the microbiome, such as H2 production will depend more on substrate, while rare metabolisms like methanogenesis depend more strongly on microbiome composition.ImportancePrebiotic fermentation in the gut often leads to the co-production of short chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely taken into account during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic and the community composition of the human gut microbiota can affect the volume and content of gas production during prebiotic fermentation. Specifically, more prevalent metabolic processes such as hydrogen production was strongly affected by the oxidation state of the probiotic, while rare metabolisms such as methane production was less affected by the chemical nature of the substrate and entirely dependent on the presence of Methanobacteria in the microbiota.
Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability
Authors: Tsai Kevin , Vasudevan Ananda Ayyappan Jaguva , Martinez Campos Cecilia , Emery Ann , Swanstrom Ronald , Cullen Bryan R. 
Published: February 2020

AbstractCovalent modifications added to individual nucleotides on mRNAs, called epitranscriptomic modifications, have recently emerged as key regulators of both cellular and viral mRNA function1,2and RNA methylation has now been shown to enhance the replication of human immunodeficiency virus 1 (HIV-1) and several other viruses3–11. Recently, acetylation of the N4position of cytidine (ac4C) was reported to boost cellular mRNA function by increasing mRNA translation and stability12. We therefore hypothesized that ac4C and N-acetyltransferase 10 (NAT10), the cellular enzyme that adds ac4C to RNAs, might also have been subverted by HIV-1 to increase viral gene expression. We now confirm that HIV-1 transcripts are indeed modified by addition of ac4C at multiple discreet sites and demonstrate that silent mutagenesis of a subset of these ac4C addition sites inhibits HIV-1 gene expression incis. Moreover, reduced expression of NAT10, and the concomitant decrease in the level of ac4C on viral RNAs, inhibits HIV-1 replication by reducing HIV-1 RNA stability. Interestingly Remodelin, a previously reported inhibitor of NAT10 function13,14, also inhibits HIV-1 replication without affecting cell viability, thus raising the possibility that the addition of ac4C to viral mRNAs might emerge as a novel cellular target for antiviral drug development.
Homeostatic Plasticity Commonly Fails at the Intersection of Autism-Gene Mutations and a Novel Class of Common Phenotypic Modifier
Authors: Genç Özgür , An Joon Y. , Fetter Richard D. , Kulik Yelena , Zunino Giulia , Sanders Stephan J. , Davis Graeme W. 
Published: February 2020

ABSTRACTWe identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1,CHD8,CHD2,WDFY3,ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP). Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, we find that PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen,PDPK1andPPP2R5D,are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation ofCREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.