bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on the Genetic Differentiation of Geographic Populations of Calliptamus italicus (Orthoptera: Acrididae) in Sino-Kazakh Border Areas Based on Mitochondrial COI and COII Genes
Authors: Xu Ye , Mai Ji-wei , Yu Bing-jie , Hu Hong-xia , Yuan Liang , Jashenko Roman , Ji Rong 
Published: April 2019

AbstractCalliptamus italicus L. is an important pest on the desert and semidesert steppes along the Sino-Kazakh border. To elucidate the molecular mechanism of its continuous outbreaks, we studied 11 different geographic populations of C. italicus to determine: 1) the complete sequences of the entire mitochondrial cytochrome oxidase subunit I (COI) and mitochondrial cytochrome oxidase subunit II (COII) genes, and 2) performed genetic diversity, differentiation, gene flow, and molecular variation analyses. Of the 11 populations, the Yining County (YNX) population had the highest haplotype diversity and Pi values. There are significant differences in Tajima’s D and Fu’s Fs (P < 0.05). The fixation index Fst values of the total C. italicus population were 0.03352, and its gene flow Nm values of the total C. italicus population were 15.32. Taken together, there were five main findings: 1) the current genetic differentiation of C. italicus arose within populations; 2) genetic exchange levels were high between geographical populations; 3) genetic variation level was low; 4) C. italicus populations likely expanded in recently, and 5) there was no significant correlation between genetic distance and geographic distance for any geographic population. Findings from this study indicate that frequent gene exchange between populations may enhance the adaptability of C. italicus along the Sino-Kazakh border, leading to frequent outbreaks.
Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes
Authors: Abrusán György , Marsh Joseph A 
Published: April 2019

Abstract
The structure of ligand-binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multichain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologs, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand-binding-site structure shapes allosteric signal transduction pathways, and whether the structural similarity of binding sites influences the evolution of allostery. Our analyses show that: 1) allostery is more frequent among MBS complexes than in SBS complexes, particularly in homomers; 2) in MBS homomers, semirigid communities and critical residues frequently connect interfaces and thus they are characterized by signal transduction pathways that cross protein–protein interfaces, whereas SBS homomers usually not; 3) ligand binding alters community structure differently in MBS and SBS homomers; and 4) except MBS homomers, allosteric proteins are more likely to have homologs with similar binding site than nonallosteric proteins, suggesting that binding site similarity is an important factor driving the evolution of allostery.
Is Attentional Filtering Impaired in Schizophrenia?
Authors: Luck Steven J , Leonard Carly J , Hahn Britta , Gold James M 
Published: April 2019

Abstract
Recent evidence suggests that schizophrenia involves hyperfocusing, an unusually narrow but intense focusing of processing resources. This appears to contradict the classic idea that schizophrenia involves an impairment in the ability to focus on relevant information and filter irrelevant information. Here, we review one set of studies suggesting that attentional filtering is impaired in people with schizophrenia and another set of studies suggesting that attentional filtering is unimpaired or even enhanced in these individuals. Considerable evidence supports both conclusions, and we propose 3 potential ways of reconciling the conflicting evidence. First, impaired attentional filtering may occur primarily during periods of active psychosis, with hyperfocusing being a part of the broad pattern of cognitive impairment that persists independent of the level of positive symptoms. Second, schizophrenia may involve hyperfocusing in the visual modality and impaired attentional filtering in the auditory modality. Third, attention may be directed toward irrelevant inputs as a result of impaired executive control, and hyperfocusing on those inputs may be functionally equivalent to a failure of attentional filtering. Given the widespread clinical observations and first-person reports of impaired attentional filtering in schizophrenia, it will be important for future research to test these possibilities.
Reach of a low-intensity, multicomponent childhood overweight and obesity intervention delivered in an integrated primary care setting
Authors: Raynor Hollie A , Barroso Cristina , Propst Sara , Berlin Kristoffer , Robson Shannon , Khatri Parinda 
Published: April 2019

AbstractReach (i.e., proportion and representativeness of participants) of low-intensity, multicomponent childhood overweight/obesity interventions delivered in primary care settings with low-income and/or minority families is unknown. The purpose of this research is to describe the reach of a low-intensity, multicomponent childhood overweight/obesity intervention delivered in an integrated primary care setting in a federally qualified health center (FQHC). Eligibility criteria included children aged 4–10 years with a body mass index (BMI) ≥85th percentile, with a female caregiver. Using the electronic health record (EHR) and release forms, families were broadly categorized into groupings from recruitment flow, with differing proportions calculated from these groupings. Representativeness was determined using EHR data from families who were informed about the program (n = 963). Three calculated reach rates ranged from 54.9% to 3.9%. Lower reach rates were calculated using the number of families randomized (n = 73) as the numerator and the children from families who were informed about the program (n = 963) or all eligible children in the FQHC attending appointments (n = 1,864) as denominators. The first two steps in recruitment, informing families about the program and families initiating participation, were where the largest decreases in reach occurred. Children who were randomized were older, had a higher BMI, had a greater number of medical diagnoses indicating overweight or obesity, and were Hispanic. Reach of the intervention was low. Strategies that assist with reducing time for informing families of treatment and increasing families’ awareness of their child’s weight status should assist with enhancing reach.
Apoptosis Resistance in Fibroblasts Precedes Progressive Scarring in Pulmonary Fibrosis and Is Partially Mediated by Toll-Like Receptor 4 Activation
Authors: Hanson Kelly M , Hernady Eric B , Reed Christina K , Johnston Carl J , Groves Angela M , Finkelstein Jacob N 
Published: April 2019

Abstract
Inhalation of environmental toxicants such as cigarette smoke, metal or wood dust, silica, or asbestos is associated with increased risk for idiopathic pulmonary fibrosis (IPF). IPF involves progressive scarring of lung tissue, which interferes with normal respiration and is ultimately fatal; however, the complex cellular mechanisms of IPF pathogenesis remain unclear. Fibroblast apoptosis is essential in normal wound healing but is dysregulated in IPF. Recent studies suggest that Toll-like receptor 4 (TLR4) is key in the onset of IPF. Here, radiation-induced PF was used as a model for IPF because it very closely mimics the progressive and intractable nature of IPF. Female C57BL/6J (C57) and C57BL/6J TLR4−/− mice were exposed to a single dose of 13 Gy whole-thorax ionizing radiation. Although both strains showed similar levels of immediate radiation-induced damage, C57 mice exhibited more extensive fibrosis at 22-week postirradiation (PI) than TLR4−/− mice. Isolated C57 primary 1° MLFs showed decreased apoptosis susceptibility as early as 8-week postirradiation, a phenotype that persisted for the remainder of the radiation response. TLR4−/− 1° mouse lung fibroblasts did not exhibit significant apoptosis resistance at any point. Systemic release of high mobility group box 1, a TLR4 agonist, during the pneumonitis phase of the radiation response may act through TLR4 to contribute to fibroblast apoptosis resistance and thus interfere with wound resolution. These findings demonstrate that apoptosis resistance occurs earlier in pulmonary fibrosis pathogenesis than previously assumed, and that TLR4 signaling is a key mediator in this process.
Reappraisal of the morphology and phylogenetic relationships of the alligatoroid crocodylian Diplocynodon hantoniensis from the late Eocene of the United Kingdom
Authors: Rio Jonathan P , Mannion Philip D , Tschopp Emanuel , Martin Jeremy E , Delfino Massimo 
Published: April 2019

AbstractDiplocynodon is a genus of basal alligatoroid comprising nine species, which spanned the late Palaeocene to middle Miocene of Europe. Despite recent revisions of most Diplocynodon species, one of the earliest named and most complete, Diplocynodon hantoniensis, has not been re-described for over 150 years. This species is known from the remains of numerous individuals from the Priabonian (late Eocene) Headon Hill Formation, which crops out at Hordle (Hordwell) Cliff in Hampshire, United Kingdom. Here we re-describe and diagnose Diplocynodon hantoniensis, providing the first detailed description of postcranial anatomy in Diplocynodon, and indeed any basal alligatoroid. Diplocynodon hantoniensis is diagnosed by four autapomorphies, including retention of the ectopterygoid–pterygoid flexure through ontogeny and a unique anterior process of the ectopterygoid adjacent to the posteriormost maxillary alveoli. A critical review of previously referred remains from elsewhere in Europe and the USA restricts Diplocynodon hantoniensis to the late Eocene of the UK. Through comparisons with extant crocodylians, the well-preserved postcranial skeleton enables the interpretation of numerous muscle attachments in the forelimbs and hindlimbs, providing a potentially rich source of character data for future phylogenetic analyses. Based on a comparison of humeral morphology between a large sample of crocodylian species, we outline two new morphological characters in the humerus. We include D. hantoniensis in a phylogenetic analysis, including all putative Diplocynodon species (103 taxa scored for 187 characters). We use four different character-weighting schemes: equal weighting, implied weighting (k value = 8) and extended implied weighting with k-values of 4 and 8. In general, these weighted analyses produce congruent results with the equal-weights analysis, and increase the resolution within Diplocynodon. We recover a monophyletic Diplocynodon in three of the four analyses. However, the fourth analysis, with the strongest downweighting of homoplastic characters and missing data (extended implied weighting with k = 4), recovers the Palaeocene Diplocynodon remensis outside Diplocynodon. Our comprehensive revision of one of the most completely known Diplocynodon species facilitates comparisons in the genus, as well as between other basal alligatoroids, and forms the basis for comparing postcranial anatomy in other fossil crocodylians.
Halyos: A patient-facing visual EHR interface for longitudinal risk awareness
Authors: Mataraso Samson , Socrates Vimig , Lekschas Fritz , Gehlenborg Nils 
Published: April 2019

AbstractWe have developed Halyos (http://halyos.gehlenborglab.org), a visual EHR web application that complements the functionality of existing patient portals. Halyos is designed to integrate with existing EHR systems to help patients interpret their health data. The Halyos application utilizes the SMART on FHIR (Substitutable Medical Applications and Reusable Technologies on Fast Healthcare Interoperability Resources) platform to create an interoperable interface that provides interactive visualizations of clinically validated risk scores and longitudinal data derived from a patient’s clinical measurements. These visualizations allow patients to investigate the relationships between clinical measurements and risk over time. By enabling patients to set hypothetical future values for these clinical measurements, patients can see how changes in their health will impact their risks. Using Halyos, patients are provided with the opportunity to actively improve their health based on increased understanding of longitudinal information available in EHRs and to begin a dialogue with their providers.
Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants, and mutations
Authors: Gilpatrick Timothy , Lee Isac , Graham James E. , Raimondeau Etienne , Bowen Rebecca , Heron Andrew , Sedlazeck Fritz J , Timp Winston 
Published: April 2019

AbstractNanopore sequencing technology can rapidly and directly interrogate native DNA molecules. Often we are interested only in interrogating specific areas at high depth, but conventional enrichment methods have thus far proved unsuitable for long reads1. Existing strategies are currently limited by high input DNA requirements, low yield, short (<5kb) reads, time-intensive protocols, and/or amplification or cloning (losing base modification information). In this paper, we describe a technique utilizing the ability of Cas9 to introduce cuts at specific locations and ligating nanopore sequencing adaptors directly to those sites, a method we term ‘nanopore Cas9 Targeted-Sequencing’ (nCATS).We have demonstrated this using an Oxford Nanopore MinION flow cell (Capacity >10Gb+) to generate a median 165X coverage at 10 genomic loci with a median length of 18kb, representing a several hundred-fold improvement over the 2-3X coverage achieved without enrichment. We performed a pilot run on the smaller Flongle flow cell (Capacity ~1Gb), generating a median coverage of 30X at 11 genomic loci with a median length of 18kb. Using panels of guide RNAs, we show that the high coverage data from this method enables us to (1) profile DNA methylation patterns at cancer driver genes, (2) detect structural variations at known hot spots, and (3) survey for the presence of single nucleotide mutations. Together, this provides a low-cost method that can be applied even in low resource settings to directly examine cellular DNA. This technique has extensive clinical applications for assessing medically relevant genes and has the versatility to be a rapid and comprehensive diagnostic tool. We demonstrate applications of this technique by examining the well-characterized GM12878 cell line as well as three breast cell lines (MCF-10A, MCF-7, MDA-MB-231) with varying tumorigenic potential as a model for cancer.ContributionsTG and WT constructed the study. TG performed the experiments. TG, IL, and FS analyzed the data. TG, JG, ER, RB and AH and developed the method. TG and WT wrote the paper
Rapid discovery of synthetic DNA sequences to rewrite endogenous T cell circuits
Authors: Roth Theodore L. , Li P. Jonathan , Nies Jasper F. , Yu Ruby , Nguyen Michelle L.T. , Lee Youjin , Apathy Ryan , Truong Anna , Hiatt Joseph , Wu David , Nguyen David N. , Goodman Daniel , Bluestone Jeffrey A. , Roybal Kole , Shifrut Eric , Marson Alexander 
Published: April 2019

ABSTRACTGenetically-engineered immune cell therapies have been in development for decades1–3 and recently have proven effective to treat some types of cancer4. CRISPR-based genome editing methods, enabling more flexible and targeted sequence integrations than viral transduction, have the potential to extend the clinical utility of cell therapies5,6. Realization of this potential depends on improved knowledge of how coding and non-coding sites throughout the genome can be modified efficiently and on improved methods to discover novel synthetic DNA sequences that can be introduced at targeted sites to enhance critical immune cell functions. Here, we developed improved guidelines for non-viral genome targeting in human T cells and a pooled discovery platform to identify synthetic genome modifications that enhance therapeutically-relevant cell functions. We demonstrated the breadth of targetable genomic loci by performing large knock-ins at 91 different genomic sites in primary human T cells, and established the power of flexible genome targeting by generating cells with Genetically Engineered Endogenous Proteins (GEEPs) that seamlessly integrate synthetic and endogenous genetic elements to alter signaling input, output, or regulatory control of genes encoding key immune receptors. Motivated by success in introducing synthetic circuits into endogenous sites, we then developed a platform to facilitate discovery of novel multi-gene sequences that reprogram both T cell specificity and function. We knocked in barcoded pools of large DNA sequences encoding polycistronic gene programs. High-throughput pooled screening of targeted knock-ins to the endogenous T cell receptor (TCR) locus revealed a transcriptional regulator and novel protein chimeras that combined with a new TCR specificity to enhance T cell responses in the presence of suppressive conditions in vitro and in vivo. Overall, these pre-clinical studies provide flexible tools to discover complex synthetic gene programs that can be written into targeted genome sites to generate more effective therapeutic cells.
Neutrophils use selective autophagy receptor p62/SQSTM1 to targetStaphylococcus aureusfor degradationin vivoin zebrafish
Authors: Gibson Josie F , Prajsnar Tomasz K , Hill Christopher J , Tooke Amy K , Serba Justyna J , Tonge Rebecca D , Foster Simon J , Grierson Andrew J , Ingham Philip W , Renshaw Stephen A , Johnston Simon A 
Published: April 2019

AbstractAutophagy leads to degradation of cellular components and has an important role in restricting intracellular pathogens. Autophagy receptors, including p62, target invading intracellular pathogens to the autophagy pathway for degradation.Staphylococcus aureusis a significant pathogen of humans and often life-threatening in the immunocompromised. Increasing evidence demonstrates thatS. aureusis an intracellular pathogen of immune cells and may use neutrophils as proliferative niche but the intracellular fate ofS. aureusfollowing phagocytosis by neutrophils has not previously been analysedin vivo. In vitro, p62 is able to co-localise with intracellularStaphylococcus aureus, but whether p62 is beneficial or detrimental in host defence againstS. aureus in vivohad not been determined.Here we use zebrafish to determine the fate and location ofS. aureuswithin neutrophils throughout infection. We show that Lc3 and p62 recruitment to phagocytosedS. aureusis altered depending on the bacterial location within the neutrophil. We also show rapid Lc3 marking of bacterial phagosomes within neutrophils which may be associated with subsequent bacterial degradation. Finally, we find that p62 is important for controlling cytosolic bacteria demonstrating for the first time a key role of p62 in autophagic control ofS. aureusin neutrophils.
CRISPR-Cas9-assisted native end-joining editing offers a simple strategy for efficient genetic engineering in Escherichia coli
Authors: Huang Chaoyong , Ding Tingting , Wang Jingge , Wang Xueqin , Wang Jialei , Zhu Lin , Bi Changhao , Zhang Xueli , Ma Xiaoyan , Huo Yi-Xin 
Published: April 2019

AbstractUnlike eukaryotes, bacteria are less proficient in homologous recombination (HR) and non-homologous end joining (NHEJ). All existing genomic editing methods for Escherichia coli rely on exogenous HR or NHEJ systems to repair DNA double-strand breaks (DSBs). Although an E. coli native end-joining (ENEJ) system has been reported, its potential in chromosomal engineering has not yet been explored. Here, we present a CRISPR-Cas9-assisted native end-joining editing and show that ENEJ-dependent DNA repair can be used to conduct rapid and efficient knocking-out of E. coli genomic sequence of up to 83 kb. Moreover, the positive rate and editing efficiency is independent of high-efficiency competent cells. The method requires neither exogenous DNA repair systems nor introduced editing template. The Cas9 complex is the only foreign element in this method. This study is the first successful engineering effort to utilize ENEJ mechanism in genomic editing and provides an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.SignificanceThe application in prokaryotes is difficult because of the weak homologous recombination and non-homologous end joining systems. E. coli, as the most-used prokaryote in metabolic engineering, has no NHEJ system. All existing genomic editing methods for E. coli rely on exogenous HR or NHEJ systems to repair double-strand breaks introduced by CRISPR/Cas9. In this report, we firstly demonstrate that the weak and previously ignored end-joining mechanism in E. coli can be used for efficient large-scale genetic engineering assisted by CRISPR/Cas9. Our efforts greatly simplify the genomic editing procedure of E. coli and provide an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.
Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging
Authors: Chakraborty Tonmoy , Driscoll Meghan , Murphy Malea , Roudot Philippe , Chang Bo-Jui , Vora Saumya , Wong Wen Mai , Nielson Cara , Zhang Hua , Zhemkov Vladimir , Hiremath Chitkale , De La Cruz Estanislao Daniel , Bezprozvanny Ilya , Zhao Hu , Tomer Raju , Heintzmann Rainer , Meeks Julian , Marciano Denise , Morrison Sean , Danuser Gaudenz , Dean Kevin M. , Fiolka Reto 
Published: April 2019

AbstractWe present cleared tissue Axially Swept Light-Sheet Microscopy (ctASLM), which achieves sub-micron isotropic resolution, high optical sectioning capability, and large field of view imaging (870×870 μm2) over a broad range of immersion media. ctASLM can image live, expanded, and both aqueous and organic chemically cleared tissue preparations and provides 2- to 5-fold better axial resolution than confocal or other reported cleared tissue light-sheet microscopes. We image millimeter-sized tissues with sub-micron 3D resolution, which enabled us to perform automated detection of cells and subcellular features such as dendritic spines.
Automated Reconstruction of a Serial-Section EM Drosophila Brain with Flood-Filling Networks and Local Realignment
Authors: Li Peter H. , Lindsey Larry F. , Januszewski Michał , Zheng Zhihao , Bates Alexander Shakeel , Taisz István , Tyka Mike , Nichols Matthew , Li Feng , Perlman Eric , Maitin-Shepard Jeremy , Blakely Tim , Leavitt Laramie , Jefferis Gregory S.X.E. , Bock Davi , Jain Viren 
Published: April 2019

AbstractReconstruction of neural circuitry at single-synapse resolution is a key target for improving understanding of the nervous system in health and disease. Serial section transmission electron microscopy (ssTEM) is among the most prolific imaging methods employed in pursuit of such reconstructions. We demonstrate how Flood-Filling Networks (FFNs) can be used to computationally segment a forty-teravoxel whole-brain Drosophila ssTEM volume. To compensate for data irregularities and imperfect global alignment, FFNs were combined with procedures that locally re-align serial sections as well as dynamically adjust and synthesize image content. The proposed approach produced a largely merger-free segmentation of the entire ssTEM Drosophila brain, which we make freely available. As compared to manual tracing using an efficient skeletonization strategy, the segmentation enabled circuit reconstruction and analysis workflows that were an order of magnitude faster.