bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding
Authors: Bogatyrev Said R. , Ismagilov Rustem F. 
Published: January 2020

ABSTRACTCurrent methods for detecting, accurately quantifying, and profiling complex microbial communities based on the microbial 16S rRNA marker genes are limited by a number of factors, including inconsistent extraction of microbial nucleic acids, amplification interference from contaminants and host DNA, different coverage of PCR primers utilized for quantification and sequencing, and potentially biases in PCR amplification rates among microbial taxa during amplicon barcoding. Here, we describe a single-step method that enables the quantification of microbial 16S rRNA gene DNA copies with wide dynamic range and broad microbial diversity, and simultaneous amplicon barcoding for quantitative 16S rRNA gene amplicon profiling of microbiota. The method is suitable for a variety of sample types and is robust in samples with low microbial abundance, including samples containing high levels of host mammalian DNA, as is common in human clinical samples. We demonstrate that our modification to the Earth Microbiome Project (EMP) V4 16S rRNA gene primers expands their microbial coverage while dramatically reducing non-specific mammalian mitochondrial DNA amplification, thus achieving wide dynamic range in microbial quantification and broad coverage for capturing high microbial diversity in samples with or without high host DNA background. The approach relies only on broadly available hardware (real-time PCR instruments) and standard reagents utilized for conventional 16S rRNA gene amplicon library preparation both of which make it amenable for immediate and widespread adoption. Simultaneous 16S rRNA gene DNA copy quantification and amplicon barcoding for multiplexed next-generation sequencing from the same analyzed sample, performed in a combined workflow, reduces the amount of sample needed and reduces time and reagent costs. Additionally, we demonstrate that using our modified 16S rRNA gene primers in a digital PCR (dPCR) format enables precise and exact microbial quantification in samples with very high host DNA background levels without the need for quantification standards. Potential future applications of this approach include: (1) quantitative microbiome profiling in human and animal microbiome research; (2) detection of monoinfections and profiling of polymicrobial infections in tissues, stool, and bodily fluids in human and veterinary medicine; (3) environmental sample analyses (e.g., soil and water); and (4) broad-coverage detection of microbial food contamination in products high in mammalian DNA, such as meat products. We predict that utilization of this approach primarily for quantitative microbiome profiling will be invaluable to microbiome studies, which have historically been limited to analysis of relative abundances of microbes.
Bacterial Growth Induced Biocementation Technology, ‘Space-Brick’ - A Proposal for Experiment at Microgravity and Planetary Environments
Authors: Kumar Aloke , Dikshit Rashmi , Gupta Nitin , Jain Animesh , Dey Arjun , Nandi Anuj , Venugopal I. , Viswanathan Koushik , Sridhara N. , Rajendra A. 
Published: January 2020

AbstractWe present results of our investigation of microbial induced calcite precipitation for manufacturing ‘space bricks’ and a proposal for study of this activity in low-earth orbit (LEO).Sporosarcina pasteurii, a urease producing bacterial strain was used to consolidate lunar simulant soil (LSS) in the form of a ‘brick’ with non-trivial strength properties. Potential of a naturally occurring polymer namely, guar gum, as an additive was investigated for enhancement in compressive strength of bio-consolidated samples. Experimental results of bio-brick exhibited an approximate 10-fold increase in compressive strength with guar gum supplementation in soil. We present results of microstructural analysis of the ‘space bricks’ and also propose a payload design for related experiments in LEO.
The combination of lipopolysaccharide and D-galactosamine administration show positive genotoxic effect in mice liver
Authors: Dong Wenjing , Song Erqun , Song Yang 
Published: January 2020

AbstractLipopolysaccharide (LPS)/D-galactosamine (D-GalN) co-administration induced acute liver injury (ALI) and hepatic fibrosis have been extensively studied. However, whether LPS/D-GalN show genotoxic effect is current unknown. Male mice were divided into eight groups and each group contain eight animals. For the acute administration of LPS/D-GalN, the mice were given a single intraperitoneal (i.p.) injection of LPS/D-GalN (25 μg/kg + 250 mg/kg, 25 μg/kg + 500 mg/kg, 50 μg/kg + 500 mg/kg body weight) for 6 h, respectively. The chronic administration was conduct by thei.p.injection of LPS/D-GalN (10 μg/kg + 100 mg/kg) every other day for 8 weeks. Saline solution (0.9%) and cyclophosphamide (CTX) (50 mg/kg body weight) injection were used as negative and positive control, respectively. Using single cell gel electrophoresis (SCGE) assay, we found that the acute administration of LPS/D-GalN induces severe DNA damage in mice hepatic cells, but not in brain, sperm and bone marrow cells, implied the genotoxicity of LPS/D-GalN. Interestingly, the chronic treatment of LPS/D-GalN causes significant genotoxic effect in both hepatic and brain cells, but not sperm and bone marrow cells. Histopathological examination in liver and brain section consistent with SCGE results, accordingly. Our study, for the first time, reported the genotoxic potential of LPS/D-GalN co-administration. In addition, LPS/D-GalN administration may serve as an experimental model for further genotoxic study.
Role of the medial prefrontal cortex in the effects of rapid acting antidepressants on decision-making biases in rodents
Authors: Hales CA , Bartlett JM , Arban R , Hengerer B , Robinson ESJ 
Published: January 2020

AbstractMajor Depressive Disorder is a significant and costly cause of global disability. Until the discovery of the rapid acting antidepressant (RAAD) effects of ketamine, treatments were limited to drugs that have delayed clinical benefits. The mechanism of action of ketamine is currently unclear but one hypothesis is that it may involve neuropsychological effects mediated through modulation of affective biases (where cognitive processes such as learning and memory and decision-making are modified by emotional state). Previous work has shown that affective biases in a rodent decision-making task are differentially altered by ketamine, compared to conventional, delayed onset antidepressants. This study sought to further investigate these effects by comparing ketamine with other NMDA antagonists using this decision-making task. We also investigated the subtype selective GluN2B antagonist, CP-101,606 and muscarinic antagonist scopolamine which have both been shown to have RAAD effects. Both CP-101,606 and scopolamine induced similar positive biases in decision-making to ketamine, but the same effects were not seen with other NMDA antagonists. Using targeted medial prefrontal cortex (mPFC) infusions, these effects were localised to the mPFC. In contrast, the GABAAagonist, muscimol, induced general disruptions to behaviour. These data suggest that ketamine and other RAADs mediate a specific effect on affective bias which involves the mPFC. Non-ketamine NMDA antagonists lacked efficacy and we also found that temporary inactivation of the mPFC did not fully recapitulate the effects of ketamine, suggesting a specific mechanism.
Speech-in-noise detection is related to auditory working memory precision for frequency
Authors: Lad Meher , Holmes Emma , Chu Agatha , Griffiths Timothy D 
Published: January 2020

AbstractSpeech-in-noise (SiN) perception is a critical aspect of natural listening, deficits in which are a major contributor to the hearing handicap in cochlear hearing loss. Studies suggest that SiN perception correlates with cognitive skills, particularly phonological working memory: the ability to hold and manipulate phonemes or words in mind. We consider here the idea that SiN perception is linked to a more general ability to hold sound objects in mind, auditory working memory, irrespective of whether the objects are speech sounds. This process might help combine foreground elements, like speech, over seconds to aid their separation from the background of an auditory scene.We investigated the relationship between auditory working memory precision and SiN thresholds in listeners with normal hearing. We used a novel paradigm that tests auditory working memory for non-speech sounds that vary in frequency and amplitude modulation (AM) rate. The paradigm yields measures of precision in frequency and AM domains, based on the distribution of participants’ estimates of the target. Across participants, frequency precision correlated significantly with SiN thresholds. Frequency precision also correlated with the number of years of musical training. Measures of phonological working memory did not correlate with SiN detection ability.Our results demonstrate a specific relationship between working memory for frequency and SiN. We suggest that working memory for frequency facilitates the identification and tracking of foreground objects like speech during natural listening. Working memory performance for frequency also correlated with years of musical instrument experience suggesting that the former is potentially modifiable.
Cancer-associated HIF-2α impacts trunk neural crest stemness
Authors: Mohlin Sofie , Persson Camilla U. , Fredlund Elina , Monni Emanuela , Lindvall Jessica M. , Kokaia Zaal , Hammarlund Emma , Bronner Marianne E. 
Published: January 2020

AbstractThe neural crest is a stem cell population that gives rise to sympathetic ganglia, the cell type of origin of neuroblastoma. Hypoxia Inducible Factor (HIF)-2α is associated with high risk neuroblastoma, however, little is known about its role in normal neural crest development. To address this important question, here we show that HIF-2α is expressed in trunk neural crest cells of human, murine and avian embryos. Modulating HIF-2α in vivonot only causes developmental delays but also induces proliferation and stemness of neural crest cells while altering the number of cells migrating ventrally to sympathoadrenal sites. Transcriptome changes after loss of HIF-2α reflect thein vivophenotype. The results suggest that expression levels of HIF-2α must be strictly controlled and abnormal levels increase stemness and may promote metastasis. Our findings help elucidate the role of HIF-2α during normal development with implications also in tumor initiation at the onset of neuroblastoma.
Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix
Authors: Nematbakhsh Ali , Levis Megan , Kumar Nilay , Chen Weitao , Zartman Jeremiah , Alber Mark 
Published: January 2020

AbstractEpithelial sheets play important roles in defining organ architecture during development. Here, we employed an iterative experimental and multi-scale computational modeling approach to decouple direct and indirect effects of actomyosin-generated forces, nuclear positioning, extracellular matrix (ECM), and cell-cell adhesion in shapingDrosophilawing imaginal discs, a powerful system for elucidating general principles of epithelial morphogenesis. Basally generated actomyosin forces are found to regulate apically biased nuclear positioning and are required for generating epithelial bending and cell elongation of the wing disc pouch. Surprisingly, however, short-term pharmacological inhibition of ROCK-driven actomyosin contractility does not impact the maintenance of tissue height or curved shape. In comparison, the relative tautness of the extracellular basement membrane is also patterned between regions of the wing disc. However, computational simulations show that patterning of ECM tautness provides only a minor contribution to modulating tissue shape. Instead, the buildup of a passive ECM pre-strain serves a principle role in shape maintenance. Surprisingly, this is independent from the maintenance of actomyosin contractility. Furthermore, localized apical adhesion between the two cell layers within the wing disc requires ROCK-driven actomyosin activity in the absence of the basal extracellular matrix. This apical adhesion between the two cell layers provides additional mechanical support to help maintain tissue integrity. The combined experimental and computational approach provides general insight into how the subcellular forces are generated and maintained within individual cells to induce tissue curvature and suggests an important design principle of epithelial organogenesis whereby forces generated by actomyosin followed by maintenance as pre-strain within the ECM are interconnected, but functionally separable.Significance statementA major outstanding question in developmental biology is the elucidation of general principles of organ shape formation and maintenance. Here, an iterative experimental and multi-scale computational modeling approach reveals that actomyosin contractility generates the bent profile along the anterior-posterior axis while tension within the ECM is sufficient and necessary for preserving the bent shape even in the absence of continued actomyosin contractility once the shape is generated. The mechanisms tested in this study define the necessary factors for establishing the shape of the wing disc, which later everts to form the adult wing during pupal development. The method can be extended to test novel mechanisms of other epithelial systems that consist of several cellular and ECM layers.
A Bayesian and efficient observer model explains concurrent attractive and repulsive history biases in visual perception
Authors: Fritsche Matthias , Spaak Eelke , de Lange Floris P. 
Published: January 2020

AbstractPerceptual decisions can be repelled away from (repulsive adaptation) or attracted towards recent visual experience (attractive serial dependence). It is currently unclear whether and how these repulsive and attractive biases interact during visual processing and what computational principles may underlie these history dependencies. In the current study, we disentangle repulsive and attractive biases by exploring the respective timescales over which current visual processing is influenced by previous experience. Across four experiments, we find that perceptual decisions about stimulus orientation are concurrently attracted towards the short-term perceptual history and repelled from stimuli experienced up to minutes into the past. We show that the temporal pattern of short-term attraction and long-term repulsion cannot be captured by an ideal Bayesian observer model alone. Instead, it is well captured by an ideal observer model with efficientencodingand Bayesiandecodingof visual information in a slowly changing environment. Concurrent attractive and repulsive history biases in perceptual decisions may thus be the consequence of the need for visual processing to simultaneously satisfy constraints of both efficiency and stability.
Ginseng Ameliorates Effect of Prolonged Use of Omeprazole in Rat Renal Cortex through Decreasing Inflammation, Fibrosis and Apoptosis
Authors: Abdel Dayem Dina Ali Maher , Mahmoud Ahmed Sayed , Ali Azza Hussein , El-Tahawy Nashwa Fathy Gamal 
Published: January 2020

AbstractOmeprazole is used in acid-related gastrointestinal disorders but has prolonged usage adverse effects. The aim was to study changes in renal cortex following chronic Omeprazole administration and the possible protective role of ginseng. Rats were divided into control (C-), Ginseng (G-), omeprazole (OM-), and omeprazole-ginseng (OM-G) groups. Serum urea and creatinine levels and 24-hours urine-protein were determined. Kidneys were processed for histological study. Serum urea and creatinine and 24-hours protein were significantly higher in OM-group compared to controls and significantly decreased in OM-G group comparing to OM-group. OM-group showed significant glomerular and tubulointerstitial injury with vascular congestion, inflammatory cell infiltration, partial or complete damage of apical brush border of most tubules, interrupted basement membranes of glomerular capillaries and tubules, marked increase in collagen deposition, and significant increases in COX-2 and caspase-3 immune-expression. Co-administration of ginseng with omeprazole resulted in marked and significant improvement of these morphological changes.ConclusionOmeprazole induced renal functional and morphological changes through inflammatory reaction, induction of fibrosis, cellular degeneration and apoptosis. Co-administration of ginseng ameliorated these effects through its anti-inflammatory, anti-fibrotic, and anti-apoptotic effects.
Ketamine blocks morphine-induced conditioned place preference and anxiety-like behaviors in mice
Authors: McKendrick Greer , Garrett Hannah , Jones Holly E. , McDevitt Dillon S. , Sharma Sonakshi , Silberman Yuval , Graziane Nicholas M. 
Published: January 2020

AbstractPatients suffering from opioid use disorder often relapse during periods of abstinence, which is posited to be caused by negative affective states that drive motivated behaviors. Here, we explored whether conditioning mice with morphine in a CPP training paradigm evoked anxietylike behavior during morphine abstinence. To do this, mice were conditioned with morphine (10 mg/kg, i.p.) for five days. 24 h following conditioning, anxiety levels were tested by measuring time in the open arms of the elevated plus maze. The next day, mice were placed in the three compartment chamber to measure morphine-induced conditioned place preference (CPP). Our results show that following morphine conditioning, mice spent significantly less time in the open arm of the elevated plus maze and expressed robust morphine CPP on CPP test day. Furthermore, we found that an acute treatment with (R,S)-ketamine (10 mg/kg, i.p.), a medication demonstrating promise for preventing anxiety-related phenotypes, 30 min. prior to testing on post conditioning day 1, increased time spent in the open arm of the elevated plus maze in saline- and morphine-conditioned mice. Additionally, we found that a second injection of ketamine 30 min. prior to CPP tests on post conditioning day 2 prevented morphine-induced CPP, which lasted for up to 28 d post conditioning. Furthermore, we found that conditioning mice with 10% (w/v) sucrose using an oral self-administration procedure did not evoke anxietylike behavior, but elicited robust CPP, which was attenuated by ketamine treatment 30 min. prior to CPP tests. Overall, our results suggest that the ketamine-induced block of morphine CPP may not be attributed solely to alleviating negative affective states, but potentially through impaired memory of morphine-context associations.
A new optimization model for design of traditional cockpit interfaces
Authors: Şenol Mehmet Burak 
Published: January 2020

PurposeReal flight is cognitively demanding; accordingly, both indicators and display panel layout should be user-friendly to improve pilot-aircraft interaction. Poor pilot-interface interactions in aircrafts could result in accidents. Although a general reason of accidents is improper displays, relatively few studies were conducted on interfaces. This study aims to present an optimization model to create intuitively integrated user-friendly cockpit interfaces.Design/methodology/approachSubjectivity within most usability evaluation techniques could bring about interface design problems.A prioriinformation about indicator’s possible locations may be available or unavailable. Thus different analytical approaches must be applied for modifications and new interface designs. Relative layout design (RLD) model was developed and used in new interface designs to optimize locations of indicators. This model was based on layout optimization and constructed in accordance with design requirements, ergonomic considerations with the pilot preferences. RLD model optimizes interface design by deploying indicators to the best locations to improve usability of display panel, pilot-aircraft interaction and flight safety.FindingsOptimum interfaces for two problem instances were gathered by RLD model in 15.77 CPU(s) with 10 indicators and 542.51 CPU(s) with 19 indicators. A comparison between relative and existing cockpit interfaces reveals that locations of six navigation and four mechanical system indicators are different. The differences may stem from pilots’ preferences and relativity constraints. Both interfaces are more similar for the central part of the display panel. The objective function value of relative interface design (Opt: 527938) is far better than existing interface (737100). The RLD model improved usability of existing interface (28.61 per cent considering decrease in the objective function values from 737100 to 527938.Practical implicationsFuture cockpit and new helicopter interface designs may involve RLD model as an alternative interface design tool. Furthermore, other layout optimization problems, e.g. circuit boards, microchips and engines, etc. could be handled in a more realistic manner by RLD model.Originality/valueOriginality and impact of this study related to development and employment of a new optimization model (RLD) on cockpit interface design for the first time. Engineering requirements, human factors, ergonomics and pilots’ preferences are simultaneously considered in the RLD model. The subjectivity within usability evaluation techniques could be diminished in this way. The contributions of RLD model to classical facility layout models are relativity constraints with the physical constrictions and ergonomic objective function weights. Novelty of this paper is the development and employment of a new optimization model (RLD) to locate indicators.
Knowledge-based HRM practices as an antecedent to service innovative behavior
Authors: Noopur Noopur , Dhar Rajib Lochan 
Published: January 2020

Purpose
The purpose of this paper is to try to profess that human resource management and knowledge are key antecedents, the amalgamation of which helps in developing the human capital (HC) which in turn generates employee’s service innovative behavior. Previous researches have studied the combination of human resource management (HRM) and knowledge perspective but not explicitly, there remains a significant gap and the HRM-innovative behavior literature remains unexplored.

Design/methodology/approach
SPSS 21, AMOS 21 and SAS 9.1 software were used to calculate the reliability of the scales, convergent, discriminant validity and overall ﬁtness of the proposed model. SPSS macro called PROCESS was used to determine the indirect effect if any. Further, hierarchical linear modeling was performed to test the group level effect on the proposed model.

Findings
The research work confirms the role of knowledge-based human resource management (KHRM) practices as a precursor to HC, thus influencing the employee service innovative behavior when the person–organization fit is high rather than low. The literature has also elaborated on the central role of knowledge mechanisms in influencing a firm’s capability to support novel ideas and creative work patterns.

Originality/value
The present study has tried to investigate a very novel topic, i.e., KHRM practices whose literature are negligible. The research work has highlighted as to how KHRM practices which are basically non-tangible, rare, non-imitable can influence the innovative work-behavior of employees in a less knowledge-intensive industry such as the tourist hotels.