bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caldicellulosiruptor besciiregulates pilus expression in response to the polysaccharide, xylan
Authors: Khan Asma M.A.M. , Hauk Valerie J. , Ibrahim Mena , Raffel Thomas R. , Blumer-Schuette Sara E. 
Published: April 2019

ABSTRACTBiological hydrolysis of cellulose above 70°C involves microorganisms that secrete free enzymes, and deploy separate protein systems to adhere to their substrate. Strongly cellulolyticCaldicellulosiruptor besciiis one such extreme thermophile, which deploys modular, multi-functional carbohydrate acting enzymes to deconstruct plant biomass. Additionally,C. besciialso encodes for non-catalytic carbohydrate binding proteins, which likely evolved as a mechanism to compete against other heterotrophs in carbon limited biotopes that these bacteria inhabit. Analysis of theCaldicellulosiruptorpangenome identified a type IV pilus (T4P) locus encoded upstream of the tāpirins, that is encoded for by allCaldicellulosiruptorspecies. In this study, we sought to determine if theC. besciiT4P plays a role in attachment to plant polysaccharides. The majorC. besciipilin (CbPilA) was identified by the presence of pilin-like protein domains, paired with transcriptomics and proteomics data. Using immuno-dot blots, we determined that the plant polysaccharide, xylan, induced production of CbPilA 10 to 14-fold higher than glucomannan or xylose. Furthermore, we are able to demonstrate that recombinant CbPilA directly interacts with xylan, and cellulose at elevated temperatures. Localization of CbPilA at the cell surface was confirmed by immunofluorescence microscopy. Lastly, a direct role for CbPilA in cell adhesion was demonstrated using recombinant CbPilA or anti-CbPilA antibodies to reduceC. besciicell adhesion to xylan and crystalline cellulose up to 4.5 and 2-fold, respectively. Based on these observations, we propose that CbPilA and by extension, the T4P, plays a role inCaldicellulosiruptorcell attachment to plant biomass.IMPORTANCEMost microorganisms are capable of attaching to surfaces in part to persist in their environment. Here, we describe that the thermophilic, plant degrading bacterium,Caldicellulosiruptor bescii, uses type IV pili to attach to carbohydrates found in plant biomass. This ability is likely key to survival in environments where carbon sources are limiting, allowingC. besciito compete against other plant degrading microorganisms. Interestingly, the carbohydrate that induced the highest expression of pilin protein was xylan, a hemicellulose that is not the majority polysaccharide in plant biomass. Not only do we demonstrate a direct interaction of the pilin with the polysaccharides, but also that cell attachment to polysaccharides can be disrupted by the addition of recombinant pilin and notably by antibody neutralization of the native pilin. This mechanism mirrors those recently described in pathogenic Gram-positive bacteria, and further supports the ancient origins of type IV pilus systems.
Enriched environmental conditions modify the gut microbiome composition and fecal markers of inflammation in Parkinson’s disease
Authors: Singh Yogesh , Hadidi Mohamed El , Matthes Jakob , Wassouf Zinah , Schulze-Hentrich Julia M. , Kohlhofer Ursula , de Fend Leticia Quintanilla-Martinez , Huson Daniel , Riess Olaf , Casadei Nicolas 
Published: April 2019

AbstractBackgroundRecent findings suggest an implication of the gut microbiome in Parkinson’s disease patients. Parkinson’s disease onset and progression has also been linked with various environmental factors such as physical activity, exposure to pesticides, head injury, nicotine, and dietary factors.ObjectivesIn this study, we used a transgenic mouse model overexpressing the complete human SNCA genes modeling familial and sporadic forms of Parkinson’s disease to study whether environmental conditions such as standard versus enriched environment changes the gut microbiome and influences disease progression.MethodsWe performed 16S rRNA DNA sequencing on fecal samples for microbiome analysis and studied fecal inflammatory calprotectin from the colon of control and transgenic mice kept under standard environment and enriched environment conditions.ResultsThe overall composition of the gut microbiota was not changed in transgenic mice compared with wild-type in enriched environment, however, individual gut bacteria at genus level such as Lactobacillus sp. were significantly changed in transgenic mice. Furthermore, enriched environment significantly reduced colon fecal inflammatory calprotectin protein in wild-type and transgenic enriched environment conditions compared to standard environment.ConclusionOur data suggest that enriched social environment has a positive effect on the induction of SNCA mediated inflammation in the intestine by changing anti-inflammatory gut bacteria.
Evaluation of Bacteria Detected in Both Urine and Open Wounds in Nursing Facility Residents
Authors: Libertucci Josie , Bassis Christine M. , Cassone Marco , Gibson Kristen , Lansing Bonnie , Mody Lona , Young Vincent B. , Meddings Jennifer 
Published: April 2019

ABSTRACTNursing home residents are at a greater risk of developing pressure injuries that develop into an open wound. Open wounds can be colonized with bacteria from multiple sources. Emerging evidence suggests the specific composition of the open wound microbial community can result in delayed wound healing and increased infection risk. Understanding the factors that influence microbial colonization of open wounds, can lead to the prevention of infections. The relationship between bacteria found in urine and that of open wounds, is currently unknown. Recent studies have shown that nursing home residents can harbor a urinary microbiota independent of symptoms and frequently experience urinary incontinence. To determine if the colonization of open wounds mirrors urinary colonization, we conducted a pilot study with nursing home residents, comparing bacteria present in open pressure injuries below the umbilicus and urine. To identify microbial species that were present in both urine and open wound at one timepoint, standard bacteriologic culture techniques followed by MALDI-TOF was used as well as16S rRNA-encoding gene amplicon sequencing. In this study we found that some bacteria detected in urine were also detected in open wounds in one individual at one timepoint, using both culture dependent and independent techniques. Bacterial species that were more often detected at both sites included Enterococcus faecalis, Proteus mirabilis, Escherichia coli, and Providencia stuartii. This pilot study provides evidence that urinary colonization can mirror open wound colonization. Further studies are needed to investigate if parallel colonization of these anatomical sites affect infection outcomes.
Amygdala Reward Neurons Form and Store Fear Extinction Memory
Authors: Zhang Xiangyu , Kim Joshua , Tonegawa Susumu 
Published: April 2019

SummaryThe ability to extinguish conditioned fear memory is critical for adaptive control of fear response, and its impairment is a hallmark of emotional disorders like post-traumatic stress disorder (PTSD). Fear extinction is thought to take place when animals form a new memory that suppresses the original fear memory. However, little is known about the nature and the site of formation and storage of the new extinction memory. Here, we demonstrate that a fear extinction memory engram is formed and stored in a genetically distinct basolateral amygdala (BLA) neuronal population that drive reward behaviors and antagonize the BLA’s original fear neurons. The activation of the fear extinction engram neurons and natural reward-responsive neurons overlap extensively in the BLA. Furthermore, these two neuron subsets are mutually interchangeable in driving reward behaviors and fear extinction behaviors. Thus, fear extinction memory is a newly formed reward memory.
SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq
Authors: Fang Rongxin , Preissl Sebastian , Li Yang , Hou Xiaomeng , Lucero Jacinta , Wang Xinxin , Motamedi Amir , Shiau Andrew K. , Zhou Xinzhu , Xie Fangming , Mukamel Eran A. , Zhang Kai , Zhang Yanxiao , Behrens M. Margarita , Ecker Joseph R. , Ren Bing 
Published: April 2019

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by heterogeneity of the samples. Single cell analysis of transposase-accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volumes of data could pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC can efficiently dissect cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, a sampling technique that generates the low rank embedding for large-scale dataset, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC was applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis revealed ∼370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate transcriptional regulators in each of the cell types.
Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates theTrypanosoma bruceicell cycle post-transcriptionally
Authors: Benz Corinna , Urbaniak Michael D. 
Published: April 2019

AbstractThe cell division cycle of the unicellular eukaryoteTrypanosome bruceiis tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation toT. bruceicell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of theT. bruceicell cycle.Data are available via ProteomeXchange with identifier PXD013488.
pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection
Authors: Odom Gabriel J. , Ban Yuguang , Liu Lizhong , Sun Xiaodian , Pico Alexander R. , Zhang Bing , Wang Lily , Chen Xi 
Published: April 2019

ABSTRACTWith the advance in high-throughput technology for molecular assays, multi-omics datasets have become increasingly available. However, most currently available pathway analysis software provide little or no functionalities for analyzing multiple types of -omics data simultaneously. In addition, most tools do not provide sample-specific estimates of pathway activities, which are important for precision medicine. To address these challenges, we present pathwayPCA, a unique R package for integrative pathway analysis that utilizes modern statistical methodology including supervised PCA and adaptive elastic-net PCA for principal component analysis. pathwayPCA can analyze continuous, binary, and survival outcomes in studies with multiple covariate and/or interaction effects. We provide three case studies to illustrate pathway analysis with gene selection, integrative analysis of multi-omics datasets to identify driver genes, estimating and visualizing sample-specific pathway activities in ovarian cancer, and identifying sex-specific pathway effects in kidney cancer. pathwayPCA is an open source R package, freely available to the research community. We expect pathwayPCA to be a useful tool for empowering the wide scientific community on the analyses and interpretation of the wealth of multiomics data recently made available by TCGA, CPTAC and other large consortiums.
Lidocaine‐Propitocain Cream, a Eutectic Mixture of Local Anesthetics, Effectively Relieves Pain Associated With Vascular Access Intervention Therapy in Patients Undergoing Hemodialysis: A Placebo‐Controlled, Double‐Blind, Crossover Study
Authors: Aihara Seishi , Yamada Shunsuke , Shichijo Satoru , Fukumitsu Kento , Kondo Mika , Hirashima Yutaro , Oka Hideaki , Kamimura Taro , Harada Atsumi , Nakano Toshiaki , Tsuruya Kazuhiko , Kitazono Takanari 
Published: April 2019

AbstractVascular access intervention therapy (VAIVT) is necessary to maintain vascular access in patients undergoing hemodialysis. VAIVT‐associated vasodilatation is painful. However, few reports have focused on effective pain relief at the time of VAIVT. The present study was performed to determine whether lidocaine‐propitocain cream, a eutectic mixture of local anesthetics (EMLA), effectively reduces VAIVT‐associated pain in patients undergoing hemodialysis. This placebo‐controlled, double‐blind, crossover study was conducted in a single center. Among 210 patients who underwent a total of 437 VAIVT procedures from August 2017 to June 2018, 30 patients were randomly allocated to either the EMLA–placebo arm or placebo–EMLA arm at the time of VAIVT. EMLA application significantly reduced the visual analog scale score compared with placebo (47.0 ± 21.1 vs. 68.6 ± 20.7 mm, respectively; P < 0.05). EMLA is a safe and effective treatment for relief of VAIVT‐associated pain in patients undergoing hemodialysis.
Producing race disparities: A study of drug arrests across place and race*
Authors: Gaston Shytierra 
Published: April 2019

AbstractIn studies of race disparities in policing, scholars generally employ quantitative methodologies with the goal of determining whether race disparities exist or, in fewer instances, of ruling out correlates. Yet, lacking from theoretical and empirical efforts is an elucidation of how and why on‐the‐ground policing produces race disparities that are justified in legal, race‐neutral terms. To address this knowledge gap, I analyze officers’ self‐reported accounts of their enforcement activities, justifications, and decision‐making in a representative sample of 300 official reports of drug arrests made in St. Louis from 2009 to 2013. These accounts are analyzed across neighborhood racial contexts and arrestee race, revealing important differences that help illuminate the race disparity problem. Unlike drug arrests in White neighborhoods or of White citizens that primarily stem from reactive policing, drug arrests in Black and racially mixed neighborhoods and of Black citizens result from officers’ greater use of discretionary stops based on neighborhood conditions, suspicion of ambiguous demeanor, or minor infractions. During such stops, officers’ discovery of drug possession often results from discretionary Terry frisks or searches incident to arrests for outstanding bench warrants. These findings fill important theoretical and empirical gaps and have implications for reforms toward racially just policing.
Food Assistance Programmes and Food Insecurity in the United States
Authors: Gundersen Craig 
Published: April 2019

SummaryA central goal of the US Department of Agriculture is to reduce food insecurity among the US population. This is pursued both by agricultural policies that focus on food supply and, arguably of greater importance, through food and nutrition programmes. The Supplemental Nutrition Assistance Program (SNAP), formerly known as the Food Stamp Program, is the largest in terms of the number of participants and annual expenditure. SNAP is particularly well‐suited to alleviating food insecurity insofar as it is designed to target those most in need, is flexible enough to address geographical variations in food insecurity, has the ability to expand in times of increased need, such as economic downturns, and gives recipients the dignity and autonomy to make their own food choices. Due to its size – about US$ 70 billion in expenditures per year – the programme has generated proposals to impose direct and indirect restrictions on recipients in order to reduce expenditure. These proposals include removing the ability of states to set higher income thresholds for eligibility, imposing work requirements, and curtailing the food choices of recipients. In contrast, other proposals would build on the perceived successes of SNAP both to expand the number of recipients and to increase benefit levels.
High Homogenization Speeds for Preparing Unstable Myofibrillar Protein–Olive Oil Emulsions
Authors: Li Ruren , He Qing , Rong Liangyan , Lin Yanting , Jia Na , Shao Junhua , Liu Dengyong 
Published: April 2019

AbstractNatural protein‐based oil‐in‐water emulsions have recently attracted a lot of attention because of their potential as a synthetic emulsifier replacer. It is, however, unclear how the emulsification process and protein concentration may affect the stability of such emulsions. Therefore, this study investigated the effects of homogenization speeds (4,000, 8,000, 12,000, and 16,000 rpm/min) and myofibrillar protein (MP) concentrations (10, 20, 30, 40, and 50 mg/mL) on the stability of MP–olive oil emulsion. The emulsifying creaming index, emulsifying activity index (EAI), droplet size, microstructure, free sulfhydryl content, and zeta potential of the emulsion were measured. The results showed that with the condition of sufficient emulsifier (at least 20 mg/mL), the EAI increased, and the droplet size and zeta potential of emulsions decreased with the increase of homogenization speed. Emulsions were stable at 4,000 and 8,000 rpm/min (20, 30, 40, and 50 mg/mL) within 48 hr, and they were unstable at 12,000 and 16,000 rpm/min (20, 30, 40, and 50 mg/mL) within 48 hr. This result is mainly attributed to the fact that sulfhydryl–disulfide interchange leads the excessive aggregate of MP at the oil–water interface.Practical ApplicationMyofibrillar protein–olive oil emulsions (oil‐in‐water) may be used to deliver nutrients into food products. In this study, myofibrillar protein–olive oil emulsions stabilized with the optimizing emulsification conditions. This study may have important implications to produce food‐grade myofibrillar protein–olive oil emulsions to deliver nutrients.
Akkermansia muciniphila is a promising probiotic
Authors: Zhang Ting , Li Qianqian , Cheng Lei , Buch Heena , Zhang Faming 
Published: April 2019

SummaryAkkermansia muciniphila (A. muciniphila), an intestinal symbiont colonizing in the mucosal layer, is considered to be a promising candidate as probiotics. A. muciniphila is known to have an important value in improving the host metabolic functions and immune responses. Moreover, A. muciniphila may have a value in modifying cancer treatment. However, most of the current researches focus on the correlation between A. muciniphila and diseases, and little is known about the causal relationship between them. Few intervention studies on A. muciniphila are limited to animal experiments, and limited studies have explored its safety and efficacy in humans. Therefore, a critical analysis of the current knowledge in A. muciniphila will play an important foundation for it to be defined as a new beneficial microbe. This article will review the bacteriological characteristics and safety of A. muciniphila, as well as its causal relationship with metabolic disorders, immune diseases and cancer therapy.
Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes
Authors: Hosoya Sho , Hirase Shotaro , Kikuchi Kiyoshi , Nanjo Kusuto , Nakamura Yohei , Kohno Hiroyoshi , Sano Mitsuhiko 
Published: April 2019

AbstractWhile various technologies for high‐throughput genotyping have been developed for ecological studies, simple methods tolerant to low‐quality DNA samples are still limited. In this study, we tested the availability of a random PCR‐based genotyping‐by‐sequencing technology, genotyping by random amplicon sequencing, direct (GRAS‐Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000–9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next‐generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation‐by‐distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS‐Di for fine‐grained genetic analysis using field samples, including mangrove fishes.