bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of a novel mutation G511T in the 530 loop in 16S rRNA in multi drugs resistant Mycobacterium tuberculosis isolated from Sudanese patients
Authors: Alfatih Yousif Mohammed , Idris Abeer Babiker , Hassan Hadeel Gassim , Nour Eman O M , Elhaj Nihad M A , El-Zaki Salah-Eldin , Eldirdery Muataz M , Ali Rahma H , Ibrahim Nuha Y , Elegail Asrar M , Salih Mohamed Ahmed
Published: December 2018

Background: Tuberculosis (TB) is a bacterial disease considered as a global public health emergency by the World Health Organization (WHO) since 1993. In Sudan, MDR-TB represents a growing threat and one of the most important challenges that faced national tuberculosis program to establish a comprehensive multidrug-resistant tuberculosis management system.
Objective: To characterize the diversity and frequency of mutations in Sudanese MDR-TB strains isolated from Wad Madani, Al-Gadarif and Khartoum using 16S rRNA and phylogeny approach.
Material and Methods: A total of 60 MDR-TB isolates from Wad-Madani, Al-Gadarif and Khartoum were tested with molecular LPA (Genotype MTBDR plus) and GeneXpert MTB/RIF assay and Spoligotyping to confirm their resistance to RIF and INH. Sequencing and phylogenetic analysis was carried out using in silico tools.
Result: This study revealed the circulation of different Sudanese MDR-TB strains isolated from Wad Madani and Al-Gadarif belonging to two distinct common ancestors. Two isolates from Wad Madani (isolate3 and isolate11) found in one main group which characterized by a novel mutation G511T in the 530 loop.
Conclusion: The recurrence of C217A mutation in Wad Madani (isolate11) indicates the spread of this mutation in Sudanese MDR-TB strains and the diversity of this inheritance leading to generate new G511T novel mutation. So, understanding the molecular characterization of resistance mechanisms in MD-TB can facilitate the early detection of resistance, the choice of appropriate treatment and ultimately the management of MD-TB transmission. Bioinformatics approaches provide helpful tools for analyzing molecular mechanisms of resistance in pathogens.
Multivariate consistency of resting-state fMRI connectivity maps acquired on a single individual over 2.5 years, 13 sites and 3 vendors
Authors: Badhwar AmanPreet , Collin-Verreault Yannik , Orban Pierre , Urchs Sebastian , Chouinard Isabelle , Vogel Jacob , Potvin Olivier , Duchesne Simon , Bellec Pierre
Published: December 2018

Studies using resting-state functional magnetic resonance imaging (rsfMRI) are increasingly collecting data at multiple sites in order to speed up recruitment or increase sample size. The main objective of this study was to assess the long-term consistency of rsfMRI connectivity maps derived at multiple sites and vendors using the Canadian Dementia Imaging Protocol (CDIP, www.cdip-pcid.ca). Nine to ten minutes of functional BOLD images were acquired from an adult cognitively healthy volunteer scanned repeatedly at 13 Canadian sites on three scanner makes (General Electric, Philips and Siemens) over the course of 2.5 years. The consistency (spatial Pearson correlation) of rsfMRI connectivity maps for seven canonical networks ranged from about 0.4-0.8 (intra-site) to 0.3-0.8 (inter-vendor), with a negligible effect of time. We noted systematic differences in data quality across vendors, which may also explain some of these results. We also pooled the long-term longitudinal data with a single-site, short-term (1 month) data sample acquired on 26 subjects (10 scans per subject), called HNU1. Using randomly selected pairs of scans from each subject, we quantified the ability of a data-driven unsupervised cluster analysis to match two scans of the same subjects. In this fingerprinting experiment, we found that scans from the Canadian subject (Csub) could be matched with high accuracy intra-site (>95% for some networks), but that the accuracy decreased substantially for scans drawn from different sites and vendors, while still remaining in the range of accuracies observed in HNU1. Overall, our results demonstrate good multivariate stability of rsfMRI measures over several years, but substantial impact of scanning site and vendors. How detrimental these effects are will depend on the application, yet improving methods for harmonizing multisite analysis is an important area for future work.
High Dimensional Mediation Analysis with Applications to Causal Gene Identification
Authors: Zhang Qi
Published: December 2018

Mediation analysis has been a popular framework for elucidating the mediating mechanism of the exposure effect on the outcome. Previous literature in causal mediation primarily focused on the classical settings with univariate exposure and univariate mediator, with recent growing interests in high dimensional mediator. In this paper, we study the mediation model with high dimensional exposure and high dimensional mediator, and introduce two procedures for mediator selection, MedFix and MedMix. MedFix is our new application of adaptive lasso with one additional tuning parameter. MedMix is a novel mediation model based on high dimensional linear mixed model, for which we also develop a new variable selection algorithm. Our study is motivated by the causal gene identification problem, where causal genes are defined as the genes that mediate the genetic effect. For this problem, the genetic variants are the high dimensional exposure, the gene expressions the high dimensional mediator, and the phenotype of interest the outcome. We evaluate the proposed methods using a mouse f2 dataset for diabetes study, and extensive real data driven simulations. We show that the mixed model based approach leads to higher accuracy in mediator selection and mediation effect size estimation, and is more reproducible across independent measurements of the response and more robust against model misspecification. The source R code will be made available on Githubhttps://github.com/QiZhangStat/highMedupon the publication of this paper.
Simphony: simulating large-scale, rhythmic data
Authors: Singer Jordan M , Fu Darwin Y , Hughey Jacob J
Published: December 2018

Simulated data are invaluable for assessing a computational method's ability to distinguish signal from noise. Although many biological systems show rhythmicity, there is no general-purpose tool to simulate large-scale, rhythmic data. Here we present Simphony, an R package for simulating data from experiments in which the abundances of rhythmic and non-rhythmic features (e.g., genes) are measured at multiple time points in multiple conditions. Simphony has parameters for specifying experimental design and each feature's rhythmic properties (e.g., shape, amplitude, and phase). In addition, Simphony can sample measurements from Gaussian and negative binomial distributions, the latter of which approximates read counts from next-generation sequencing data. We show an example of using Simphony to benchmark a method for detecting rhythms. Our results suggest that Simphony can aid experimental design and computational method development. Simphony is thoroughly documented and freely available at https://github.com/hugheylab/simphony.
Optical Co-registration of MRI and On-scalp MEG
Authors: Zetter Rasmus , Iivanainen Joonas , Parkkonen Lauri
Published: December 2018

Objective: To estimate the neural current distribution underlying magnetoencephalographic (MEG) signals and to link such estimates to brain anatomy, MEG data have to be co-registered with an anatomical image, typically an MR image. Optically-pumped magnetometers (OPMs) enable the construction of on-scalp MEG systems providing higher sensitivity and spatial resolution than conventional SQUID-based MEG systems. Here, we present a co-registration method that can be applied to on-scalp MEG systems, regardless of the number of channels. Methods: We apply a structured-light 3D scanner to create a surface mesh of the subject's head and the sensor array, which we fit to the MR image. To assess accuracy, we quantified the reproducibility of the surface mesh and localized current dipoles embedded in a phantom. Finally, we measured somatosensory evoked fields (SEF) to median nerve stimulation and compared their source estimates with those obtained with a SQUID-based MEG system. Results: The structured-light scanner reproduced the head surface with < 1 mm error. Phantom dipoles were localized with a mean error of 2.14 mm. The difference in SEF dipole positions between OPMs and SQUIDs were 5.0, 0.9, and 1.6 mm for N20m, P35m and P60m response peaks, respectively. Conclusion: The developed co-registration is inexpensive, fast and can easily be applied to on-scalp MEG. It is also more convenient to use than traditional co-registration methods while also being more accurate. Significance: We developed and validated a co-registration method that can be applied to on-scalp MEG systems. The method enables accurate source estimation with these novel MEG systems.
A high-throughput fluorescence-based assay for rapid identification of petroleum degrading bacteria
Authors: French K. E. , Terry N.
Published: December 2018

Over the past 100 years, oil spills and long-term waste deposition from oil refineries have significantly polluted the environment. These contaminants have widespread negative effects on human health and ecosystem functioning. Natural attenuation of long chain and polyaromatic hydrocarbons is slow and often incomplete. Bioaugmentation of polluted soils with indigenous bacteria that naturally consume petroleum hydrocarbons could speed up this process. However, the characterization of bacterial crude oil degradation efficiency—which often relies upon expensive, highly specialized gas-chromatography mass spectrometry analyses--can present a substantial bottleneck in developing and implementing these bioremediation strategies. Here, we develop a low-cost, rapid, high-throughput fluorescence-based assay for identifying wild-type bacteria that degrade crude oil using the dye Nile Red. We show that Nile Red fluoresces when in contact with crude oil and developed a robust linear model to calculate crude oil content in liquid cell cultures based on fluorescence intensity (FI). To test whether this assay could identify bacteria with enhanced metabolic capacities to break down crude oil, we screened bacteria isolated from a former Shell Oil refinery in Bay Point, CA and identified one strain (Cupriavidussp. OPK) with superior crude oil depletion efficiencies (up to 83%) in only three days. We further illustrate that this assay can be combined with fluorescence microscopy to study how bacteria interact with crude oil and the strategies they use to degrade this complex substance. We show for the first time that bacteria use three key strategies for degrading crude oil: biofilm formation, direct adherence to oil droplets, and vesicle encapsulation of oil. We propose that the quantitative and qualitative data from this assay can be used to develop new bioremediation strategies based on bioaugmentation and/or biomimetic materials that imitate the natural ability of bacteria to degrade crude oil.
PRDM9 forms an active trimer mediated by its repetitive zinc finger array
Authors: Schwarz Theresa , Striedner Yasmin , Haase Karin , Kemptner Jasmin , Zeppezauer Nicole , Hermann Phillip , Tiemann-Boege Irene
Published: December 2018

PRDM9 has been identified as a meiosis-specific protein that plays a key role in determining the location of meiotic recombination hotspots. Although it is well-established that PRDM9 is a trans-acting factor directing the double strand break machinery necessary for recombination to its DNA binding site, the details of PRDM9 binding and complex formation are not well known. It has been suggested in several instances that PRDM9 acts as a multimer in vivo; however, there is little understanding about the protein stoichiometry or the components inducing PRDM9 multimerization. In this work, we used in vitro binding studies and mass spectrometry to characterize the size of the PRDM9 multimer within the active DNA-protein complex of two different murine PRDM9 alleles, PRDM9Cst and PRDM9Dom2. For this purpose, we developed a strategy to infer the molecular weight of the PRDM9-DNA complex from native gel electrophoresis based on gel shift assays (EMSAs). Our results show that PRDM9 binds as a trimer with the DNA. This multimerization is catalysed by the long ZnF array (ZnF) at the C-terminus of the protein and 11, 10, 7 or 5 ZnFs are already sufficient to form a functional trimer. Finally, we also show that only one ZnF-array within the PRDM9 trimer actively binds to the DNA, while the remaining two ZnF-arrays likely maintain the multimer by ZnF-ZnF interactions. Our results have important implications in terms of PRDM9 dosage, which determines the number of active hotspots in meiotic cells, and contribute to elucidate the molecular interactions of PRDM9 with other components of the meiotic initiation machinery.
Live imaging the Foreign Body Response reveals how dampening inflammation reduces fibrosis
Authors: Gurevich David B. , French Kathryn E. , Collin John D. , Cross Stephen J. , Martin Paul
Published: December 2018

Implanting biomaterials such as surgical sutures leads to wound inflammation and a Foreign Body Response (FBR), which can result in scarring and ultimately biomaterial rejection. To investigate the cell and signalling events that underlie FBR, we use live imaging of zebrafish reporter lines to observe how inflammation and angiogenesis differ between a healthy acute wound versus suture implantation. We observe inflammation extending from the suture margins and correlates with subsequent avascular and fibrotic encapsulation zones: sutures that induce more inflammation result in increased zones of avascularity and fibrosis. Moreover, we capture macrophages as they fuse to become multinucleate foreign body giant cells (FBGCs) adjacent to the most pro-inflammatory sutures. Both genetic and pharmacological dampening of the inflammatory response minimises the FBR (including FBGC generation) and normalises the status of the tissue surrounding these sutures. This new model of FBR in adult zebrafish allows us, for the first time, to live image the process and to modulate it in ways that may lead us towards new strategies to ameliorate and circumvent FBR in humans.
Host evolutionary history predicts virus prevalence across bumblebee species
Authors: Pascall David J. , Tinsley Matthew C. , Obbard Darren J. , Wilfert Lena
Published: December 2018

Why a pathogen associates with one host but not another is one of the most important questions in disease ecology. Here we use transcriptome sequencing of wild-caught bumblebees from 13 species to describe their natural viruses, and to quantify the impact of evolutionary history on the realised associations between viruses and their pollinator hosts. We present 37 novel virus sequences representing at least 30 different viruses associated with bumblebees. We verified 17 of them by PCR and estimate their prevalence across species in the wild. Through small RNA sequencing, we demonstrate that at least 10 of these viruses form active infections in wild individuals. Using a phylogenetic mixed model approach, we show that the evolutionary history of the host shapes the current distribution of virus/bumblebee associations. Specifically, we find that related hosts share viral assemblages, viruses differ in their prevalence averaged across hosts and the prevalence of infection in individual virus-host pairings depends on precise characteristics of that pairing.

Author’s Summary

Despite the importance of disease in the regulation of animal populations, our understanding of the distribution of pathogen burden across wild communities remains in its infancy. In this study, we investigated the distribution of viruses across natural populations of 13 different bumblebee species in Scotland. We first searched for viruses using a metatranscriptomic approach, finding at least 30 new viruses of bumblebees, and assayed a subset of them for their presence and absence in different host species. Then, in the first application of these methods to an animal-virus system, we used co-phylogenetic mixed models to investigate the factors that lead to species being having different prevalences for a subset of these viruses. While much of the variation in the prevalence of the viruses can be explained by the idiosyncrasies of individual bumblebee-virus pairings, there is a phylogenetic signal with related bumblebee species being infected at similar frequencies by the same sets of viruses. Consistent with previous work, our study indicates that, while in general the interaction between a host and a virus may be unpredictable, closely related species are more likely to exhibit similar patterns of infection.
A non-parametric method to compute protein-protein and protein-ligands interfaces. Application to HIV-2 protease-inhibitors complexes
Authors: Laville Pierre , Martin Juliette , Launay Guillaume , Regad Leslie , Camproux Anne-Claude , de Vries Sjoerd , Petitjean Michel
Published: December 2018

Motivation: The accurate description of interfaces is needed to identify which residues interact with another molecule or macromolecule. In addition, a data structure is required to compare interfaces within or between families of protein-protein or protein-ligands complexes. In order to avoid many unwanted comparisons, we looked for a parameter free computation of interfaces. This need appeared at the occasion of bioinformatics studies by our research team focusing on HIV-2 protease (PR2) resistance to its inhibitors.
Results: We designed the PPIC software (Protein Protein Interface Computation). It offers three methods of computation of interfaces: (1) our original parameter free method, (2) the Voronoi tessellation approach, and (3) the cutoff distance method. For the latter, we suggest on the basis of 1050 dimers protein-protein interfaces that the optimal cutoff distance is 3.7 Å, or 3.6 Å for a set of 18 PR2-ligand interfaces. We found at most 17 contact residues with PR2 ligands.
Availability: Free binaries and documentation are available through a software repository located at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
Bayesian inference and comparison of stochastic transcription elongation models
Authors: Douglas Jordan , Kingston Richard , Drummond Alexei J.
Published: December 2018

Transcription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations.

We have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes ofE. coli, S. cerevisiaeand Bacteriophage T7.

Our analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared toE. coliRNAP andS. cerevisiaepol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets.

Author summary

Transcription is a critical biological process which occurs in all living organisms. It involves copying the organism’s genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques (see reviews: [1, 2]). Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.
In vivomeasurements reveal a single 5’ intron is sufficient to increase protein expression level inC. elegans
Authors: Crane Matthew M. , Sands Bryan , Battaglia Christian , Johnson Brock , Yun Soo , Kaeberlein Matt , Brent Roger , Mendenhall Alex
Published: December 2018

Introns can increase gene expression levels using a variety of mechanisms collectively referred to as Intron Mediated Enhancement (IME). To date, the magnitude of IME has been quantified in human cell culture and plant models by comparing intronless reporter gene expression levels to those of intron-bearing reporter genesin vitro(mRNA, Western Blots, protein activity), using genome editing technologies that lacked full control of locus and copy number. Here, for the first time, we quantified IMEin vivo, in terms of protein expression levels, using fluorescent reporter proteins expressed from a single, defined locus inCaenorhabditis elegans. To quantify the magnitude of IME, we developed a microfluidic chip-based workflow to mount and image individual animals, including software for operation and image processing. We used this workflow to systematically test the effects of position, number and sequence of introns on two different proteins, mCherry and mEGFP, driven by two different promoters,vit-2andhsp-90. We found the three canonical synthetic introns commonly used inC. eleganstransgenes increased mCherry protein concentration by approximately 50%. The naturally-occurring introns found inhsp-90also increased mCherry expression level by about 50%. Furthermore, and consistent with prior results examining mRNA levels, protein activity or phenotypic rescue, we found that a single, natural or synthetic, 5’ intron was sufficient for the full IME effect while a 3’ intron was not. IME was also affected by protein coding sequence (50% for mCherry and 80% for mEGFP) but not strongly affected by promoter 46% forhsp-90and 54% for the strongervit-2. Our results show that IME of protein expression inC. elegansis affected by intron position and contextual coding sequence surrounding the introns, but not greatly by promoter strength. Our combined controlled transgenesis and microfluidic screening approach should facilitate screens for factors affecting IME and other intron-dependent processes.
Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs
Authors: Ramdhani Satesh , Navarro Elisa , Udine Evan , Schilder Brian M. , Parks Madison , Raj Towfique
Published: December 2018

Recent human genetic studies suggest that cells of the innate immune system have a primary role in the pathogenesis of neurodegenerative diseases. However, the results from these studies often do not elucidate how the genetic variants affect the biology of these cells to modulate disease risk. Here, we applied a tensor decomposition method to uncover disease-associated gene networks linked to distal genetic variation in stimulated human monocytes and macrophages gene expression profiles. We report robust evidence that some disease-associated genetic variants affect the expression of multiple genes in trans. These include a Parkinson’s disease locus influencing the expression of genes mediated by a protease that controls lysosomal function, and Alzheimer’s disease loci influencing the expression of genes involved in type 1 interferon signaling, myeloid phagocytosis, and complement cascade pathways. Overall, we uncover gene networks in induced innate immune cells linked to disease-associated genetic variants, which may help elucidate the underlying biology of disease.
The Tenets of Teneurin: Conserved Mechanisms Regulate Diverse Developmental Processes in the Drosophila Nervous System
Authors: DePew Alison T , Aimino Michael A , Mosca Timothy J
Published: December 2018

To successfully integrate a neuron into a circuit, a myriad of developmental events must occur correctly and in the correct order. Neurons must be born and grow out towards a destination, responding to guidance cues to direct their path. Once arrived, each neuron must segregate to the correct sub-region before sorting through a milieu of incorrect partners to identify the correct partner with which they can connect. Finally, the neuron must make a synaptic connection with their correct partner; a connection that needs to be broadly maintained throughout the life of the animal while remaining responsive to modes of plasticity and pruning. Though many intricate molecular mechanisms have been discovered to regulate each step, recent work showed that a single family of proteins, the Teneurins, regulates a host of these developmental steps in Drosophila - an example of biological adaptive reuse. Teneurins first influence axon guidance during early development. Once neurons arrive in their target regions, Teneurins enable partner matching and synapse formation in both the central and peripheral nervous systems. Despite these diverse processes and systems, the Teneurins use conserved mechanisms to achieve these goals, as defined by two tenets: 1) transsynaptic interactions with each other and 2) membrane stabilization via an interaction and regulation of the cytoskeleton. These processes are further distinguished by 1) the nature of the transsynaptic interaction - homophilic interactions (between the same Teneurins) to engage partner matching and heterophilic interactions (between different Teneurins) to enable synaptic connectivity and the proper apposition of pre- and postsynaptic sites and 2) the location of cytoskeletal regulation (presynaptic cytoskeletal regulation in the CNS and postsynaptic regulation of the cytoskeleton at the NMJ). Thus, both the roles and the mechanisms governing them are conserved across processes and synapses. In this review, we will highlight the contributions of Drosophila synaptic biology to our understanding of the Teneurins and discuss the mechanistic conservation that allows the Teneurins to achieve common neurodevelopmental goals. Finally, we will posit the next steps for understanding how this remarkably versatile family of proteins functions to control multiple distinct events in the creation of a nervous system.
Respiration-phased switching between sensory inputs and top-down inputs in the olfactory cortex
Authors: Narikiyo Kimiya , Manabe Hiroyuki , Yoshihara Yoshihiro , Mori Kensaku
Published: December 2018

Olfactory perception depends on respiration phases: olfactory cortex processes external odor signals during inhalation whereas it is isolated from the external odor world during exhalation. Olfactory cortex pyramidal cells receive the sensory signals via bottom-up pathways terminating on superficial layer (SL) dendrites while they receive top-down inputs on deep layer (DL) dendrites. Here we asked whether olfactory cortex pyramidal cells spontaneously change the action modes of receiving olfactory sensory inputs and receiving top-down inputs in relation to respiration phases. Current source density analysis of local field potentials recorded in three different olfactory cortex areas of waking immobile rats revealed β- and γ-range fast oscillatory current sinks and a slow current sink in the SL during inhalation, whereas it showed β- and γ-range fast oscillatory current sinks and a slow current sink in the DL during exhalation. Sensory deprivation experiments showed that inhalation-phased olfactory sensory inputs drove the inhalation-phased fast oscillatory potentials in the SL but they drove neither the inhalation-phased slow current sink in the SL nor the exhalation-phased slow current sink in the DL. The results indicate that independent of inhalation-phased olfactory sensory inputs, olfactory cortex pyramidal cells spontaneously generate a slow depolarization in the SL dendrites during inhalation, which may selectively boost the concomitant olfactory sensory inputs to elicit spike outputs. In addition, the pyramidal cells spontaneously generate slow depolarization in the DL dendrites during exhalation, which may assist top-down inputs to elicit spike outputs. We thus hypothesize that the olfactory cortical areas coordinately perform inhalation/exhalation-phased switching of input biasing: inhalation phase is the time window for external odor signals that arrive in the SL dendrites, whereas exhalation phase is assigned to boost top-down signals to the DL dendrites that originate in higher brain centers.
Experimentally induced pain does not influence updating of peripersonal space and body representations following tool-use
Authors: Vittersø Axel Davies , Halicka Monika , Buckingham Gavin , Proulx Michael J , Wilson Mark , Bultitude Janet H
Published: December 2018

Representations of the body and peripersonal space can be distorted for people with some chronic pain conditions. Experimental pain induction can give rise to similar, but transient distortions in healthy individuals. However, spatial and bodily representations are dynamic, and constantly update as we interact with objects in our environment. It is unclear whether induced pain disrupts the mechanisms involved in updating these representations. In the present study, we sought to investigate the effect of induced pain on the updating of peripersonal space and body representations during and following tool-use. We compared performance under three conditions (pain, active placebo, neutral) on a visuotactile crossmodal congruency task and a tactile distance judgement task to measure updating of peripersonal space and body representations, respectively. We induced pain by applying 1% capsaicin cream to the arm, and for placebo we used a gel that induced non-painful warming. Consistent with previous findings, the difference in crossmodal interference from visual distractors in the same compared to opposite visual field to the tactile target was less when tools were crossed than uncrossed. This suggests an extension of peripersonal space to incorporate the tips of the tools. Also consistent with previous findings, estimates of the felt distance between two points (tactile distance judgements) decreased after active tool-use. In contrast to our predictions, however, we found no evidence that pain interfered with performance on either task when compared to the control conditions. This suggests that the updating of peripersonal space and body representations is not disrupted by induced pain. Therefore, acute pain does not account for the distorted representations of the body and peripersonal space that can endure in people with chronic pain conditions.
Hypoxic Training Increases the Concentration of Serum Irisin and Reduces Weight in Diet-induced Obese Rats
Authors: li zhigang , weng xiquan , Zhao Fangfang , Song Xue , Lin Wentao
Published: December 2018

Irisin promotes browning of white fat, improves energy metabolism, and weight loss. In this study, we investigated the effects of different oxygen concentrations during hypoxic training on the serum irisin and the PGC-1α(peroxisome proliferator-activated receptor gamma coactivator 1-alpha)-FNDC5(fibronectin type III domain containing 5)-UCP1(uncoupling protein 1) signaling pathway in the skeletal muscle of obese rats. Male Sprague-Dawley Obese rats (n=80) were randomly divided into 8 groups as follows: the control group (group A, n=10); the endurance exercise group (AE group, n=10), which involved animal treadmill training at slope 0°, 20 m/min, 40 min/d, and 5 d/w; the 16.3% hypoxia exposure group (group B, n=10), 13.3% hypoxia exposure group (group C, n=10), and 11.3% hypoxia exposure group (group D, n=10), which were exposed to a low oxygen environment with oxygen concentrations of 16.3%, 13.3%, and 11.3%, respectively, for 12 h/d; and the 16.3% hypoxic training group (BE group, n=10), 13.3% hypoxic training group (CE group, n=10), and 11.3% hypoxic training group (DE group, n=10) with animal treadmill training during hypoxia exposure. After 8 weeks, the serum irisin concentrations in the AE, BE, CE, and DE groups were significantly higher than that in the A group (p<0.05). Hypoxia exposure and hypoxic training at the three different concentrations significantly increased PGC-1α and FNDC5 gene expression in the skeletal muscle. The PGC-1α and FNDC5 protein contents were significantly higher in the skeletal muscle of the obese rats in the C, AE, and DE groups than those in group A (p<0.05). UCP1 protein expression was significantly higher in groups C, CE, D, and DE than in group A (p<0.05).To conclude, training at oxygen concentrations of 13.3% and 11.3% significantly increased the serum irisin level, and 11.3% hypoxic training enhanced the effects of the PGC-1α-Irisin-UCP1 signaling pathway in skeletal muscle.
Numerical analysis of brilliance and coherent photon flux of segmented undulator radiation based on statistical optics
Authors: Luo Hao-Wen , Chung Ting-Yi , Lee Chih-Hao , Hwang Ching-Shiang
Published: December 2018

A method based on wave optics together with electron tracking is used to analyze synchrotron radiation from a segmented undulator in a double or multi mini-β function lattice storage ring. Radiation brilliance and transverse coherence features are investigated, where the former is calculated with the Wigner distribution function and the latter is evaluated by integrating the photon flux and cross-spectral density to exhibit the coherent flux and overall degree of coherence. To be specific, radiation properties for a single undulator in a typically single mini-β function and a tandem undulator in a double mini-β
y
lattice are compared in this work. As a result, both, brilliance and coherent flux can be enhanced by a second tandem undulator at the Taiwan Photon Source.
COMET: a new end-station at SOLEIL for coherent magnetic scattering in transmission
Authors: Popescu H. , Perron J. , Pilette B. , Vacheresse R. , Pinty V. , Gaudemer R. , Sacchi M. , Delaunay R. , Fortuna F. , Medjoubi K. , Desjardins K. , Luning J. , Jaouen N.
Published: December 2018

A new instrument named COMET for COherent Magnetic scattering Experiments in Transmission using polarized soft X-rays has been designed and built. This high-vacuum setup is placed at the intermediate focal point of the elastic branch of the SEXTANTS beamline at Synchrotron SOLEIL. The main application is in solid state physics, the instrument being optimized for studying material properties using coherent scattering of soft X-rays with an emphasis on imaging, with chemical selectivity, the magnetic domains of artificially nano-structured materials. The instrument's principal features are presented and illustrated through recently performed experiments.
Structure model of γ-Al2O3based on planar defects
Authors: Rudolph Martin , Motylenko Mykhaylo , Rafaja David
Published: December 2018

The defect structure of γ-Al2O3derived from boehmite was investigated using a combination of selected-area electron diffraction (SAED) and powder X-ray diffraction (XRD). Both methods confirmed a strong dependence of the diffraction line broadening on the diffraction indices known from literature. The analysis of the SAED patterns revealed that the dominant structure defects in the spinel-type γ-Al2O3are antiphase boundaries located on the lattice planes (00l), which produce the sublattice shifts {{1}\over{4}}\langle 10{\overline 1}\rangle. Quantitative information about the defect structure of γ-Al2O3was obtained from the powder XRD patterns. This includes mainly the size of γ-Al2O3crystallites and the density of planar defects. The correlation between the density of the planar defects and the presence of structural vacancies, which maintain the stoichiometry of the spinel-type γ-Al2O3, is discussed. A computer routine running on a fast graphical processing unit was written for simulation of the XRD patterns. This routine calculates the atomic positions for a given kind and density of planar defect, and simulates the diffracted intensities with the aid of the Debye scattering equation.
Crystal structure and Hirshfeld surface analysis of 3,4-dihydro-2-(2,4-dioxo-6-methylpyran-3-ylidene)-4-(4-pyridin-4-yl)-1,5-benzodiazepine
Authors: El Ghayati Lhoussaine , Ramli Youssef , Hökelek Tuncer , Labd Taha Mohamed , Mague Joel T. , Essassi El Mokhtar
Published: December 2018

The title compound, C20H17N3O3[systematic name: 2-(6-methyl-2,4-dioxopyran-3-ylidene)-4-(pyridin-4-yl)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine], is built up from a benzodiazepine ring system linked to pyridyl and pendant dihydropyran rings, where the benzene and pyridyl rings are oriented at a dihedral angle of 43.36 (6)°. The pendant dihydropyran ring is rotationally disordered in a 90.899 (3):0.101 (3) ratio with the orientation of each component largely determined by intramolecular N—HDiazp...ODhydp(Diazp = diazepine and Dhydp = dihydropyran) hydrogen bonds. In the crystal, molecules are linked via pairs of weak intermolecular N—HDiazp...ODhydphydrogen bonds, forming inversion-related dimers withR22(26) ring motifs. The dimers are further connected along theb-axis direction by π–π stacking interactions between the pendant dihydropyran and pyridyl rings with centroid–centroid distances of 3.833 (3) Å and a dihedral angle of 14.51 (2)°. Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (50.1%), H...C/C...H (17.7%), H...O/O...H (16.8%), C...C (7.7%) and H...N/N...H (5.3%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing.
Crystal structure and Hirshfeld surface analysis of 5-[(5-nitro-1H-indazol-1-yl)methyl]-3-phenyl-4,5-dihydroisoxazole
Authors: Boulhaoua Mohammed , Kansiz Sevgi , El Hafi Mohamed , Lahmidi Sanae , Dege Necmi , Benchidmi Mohammed , Mague Joel T.
Published: December 2018

In the title compound, C17H14N4O3, the indazole unit is planar to within 0.0171 (10) Å and makes dihedral angles of 6.50 (6) and 6.79 (4)°, respectively, with the nitro and pendant phenyl groups. The conformation of the oxazole ring is best described as an envelope. In the crystal, oblique stacks along the a-axis direction are formed by π–π stacking interactions between the indazole unit and the pendant phenyl rings of adjacent molecules. The stacks are linked into pairs through C—H...O hydrogen bonds. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H...H (36.3%), O...H/H...O (23.4%), C...H/H...C (13.4%) and N...H/H...N (11.4%) interactions.
Lean service system design: a simulation-based VSM case study
Authors: Cavdur Fatih , Yagmahan Betul , Oguzcan Ece , Arslan Nazli , Sahan Nurbanu
Published: December 2018

Purpose

The purpose of this paper is to present a methodology for using simulation models together with value stream mapping (VSM) for designing lean service systems and illustrate it with a case study.

Design/methodology/approach

The authors propose a methodology combining simulation and VSM. Simulation models for both current and future states are developed to validate the results of the corresponding maps of current and future states, respectively.

Findings

The results illustrate the advantages of the suggested design represented by the future state map. Additionally, using simulation models together with VSM for validating current and future states also allows decision makers to perform comprehensive analyses on the system and draw statistical conclusions.

Originality/value

Although some lean applications in educational services exist in previous studies, according to the best of the authors’ knowledge, this study is the first one combining VSM and simulation for the implementation of the lean concepts in the construction and technical services of a public university.
Performance evaluation of tourism supply chain management: the case of Thailand
Authors: Palang Daraka , Tippayawong Korrakot Yaibuathet
Published: December 2018

Purpose

The purpose of this paper is to investigate and develop a framework of the performance evaluation of tourism supply chain management (SCM) for the case of Thailand.

Design/methodology/approach

The performance measurement of tourism SCM was based upon the eight dimensions of service performance, namely order process management (OPM), supplier relationship management (SRM), service performance management (SPM), capacity and resources management, customer relationship management, demand management (DM), information and technology management, tour finance supply chain. Data were collected from 195 samples of experts of each component of the supply chain to identify the weight pairwise and criteria on each tourism component. The study also adopted analytical hierarchy process (AHP) technique to rank the dimensions of service performance for searching the suitable performance measurement.

Findings

The results showed that there are both similarities and differences in each tier. Among the eight dimensions subject to this measurement, OPM, SPM and SRM are ranked as 1, 2 and 3, respectively, in tourism supply chain.

Research limitations/implications

One limitation should be considered. As the results of this performance measurement are drawn from sole perspectives of the tourism-business operators, these are probably different from those of the tourists.

Originality/value

The contribution of this study is another effective performance measurement which is expected to benefit the evaluation of tourism supply chain for Thai tourism industry.
Mature students, transformation and transition
Authors: Broadhead Samantha Jane
Published: December 2018

Purpose

The purpose of this paper is to argue for a transformative education that acknowledges and values the capacities of mature students, where higher education institutions reflect on their own assumptions and practices in order to become more inclusive and open to difference.

Design/methodology/approach

The stories told by Eliza, a mature student, are analysed through narrative inquiry; this approach uses a narrative as a means of capturing and analysing experience. In this case, Eliza’s stories about transition and transformation were collected over three years. Eliza made the transition from her “Access to HE course” to a degree programme in textiles. She was crossing a boundary between further and higher education, a time which could impact positively or negatively on her future achievements. The conclusions drawn from this study are not easily turned into generalisations or “truths” as they are contingent on the contexts in which the narratives were produced. Narrative is a representation of experience which is mediated by the social and cultural positions of the narrators and their audiences.

Findings

This study found that Eliza was confronted by many difficulties and misunderstandings around time management, pedagogy and assessment. Ineffective communication between Eliza and her tutors led to a growing frustration resulting in her considering leaving the course. Eliza’s institution sometimes seemed inflexible and was unable to respond effectively to her needs as a part-time student.

Practical implications

The implications for educators are that they should think about strategies for adapting to a diverse student body.

Originality/value

The previous experiences and backgrounds of “newcomers” should be celebrated rather than being perceived as “issues” that need to be fixed. In other words, when “non-traditional” students move through the stages of their education, their learning contexts may also need to be transformed.
Implementation of BIM technology for knowledge transfer in IBS building maintenance projects
Authors: Ismail Zul-Atfi
Published: December 2018

Purpose

The current maintenance management method affects the efficiency of the complex, high-rise industrialised building system (IBS) building maintenance management projects in Malaysia. The usage of a conventional system (paper-based reports/unsystematic database) has various drawbacks, such as IBS component aesthetic and structural defects which occur repeatedly in the building and maintenance of conventional building, lack of integration between maintenance systems and lack of the intelligent capabilities of linking defect diagnosis operations in maintenance affecting various building elements with IBS component defect knowledge. Thus, the purpose of this paper is to focus on the development of a mechanism to improve IBS component defect knowledge transfer in IBS building maintenance projects through the integration of building information modelling (BIM).

Design/methodology/approach

Eight clients/maintenance contractors were selected based on the major problems of using a conventional system to investigate the maintenance management practices in each complex and high-rise IBS building.

Findings

The findings indicated that several computerised systems such as Building Automation System and Supervisory Control and Data Acquisition System are used by a client/maintenance contractor. Moreover, BIM technology awareness was found to be limited, with no implementation in IBS building maintenance till now. The results of this case study were used as a foundation for the development of a prototype system using Computerised Maintenance Management System, Expert System and BIM.

Originality/value

The development of this new system improves IBS component diagnosis knowledge integration with the BIM technology.