bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestication ofCampylobacter jejuniNCTC 11168
Authors: Pascoe Ben , Williams Lisa K. , Calland Jessica K. , Méric Guillaume , Hitchings Matthew D. , Dyer Myles , Ryder Joseph , Shaw Sophie , Lopes Bruno S. , Chintoan-Uta Cosmin , Allan Elaine , Vidal Ana , Fearnley Catherine , Everest Paul , Pachebat Justin A. , Cogan Tristan A. , Stevens Mark P. , Humphrey Thomas J. , Wilkinson Thomas S. , Cody Alison J. , Colles Frances M. , Jolley Keith A. , Maiden Martin C. J. , Strachan Norval , Pearson Bruce M. , Linton Dennis , Wren Brendan W. , Parkhill Julian , Kelly David J. , van Vliet Arnoud H. M. , Forbes Ken J. , Sheppard Samuel K. 
Published: April 2019

AbstractReference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics.Campylobacter jejunistrain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the firstCampylobacterfor which the complete genome was published (in 2000). In this study, we collected 23C. jejuniNCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37°C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change amongC. jejuniisolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.Impact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 referenceCampylobactergenomes and compare them with observable differences in common laboratory phenotypes.Data summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).All assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact:https://microreact.org/project/NCTC11168.RepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467;Table S1).The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Analyses of rare and common alleles in parent-proband trios implicate rare missense variants in SLC6A1 in schizophrenia and confirm the involvement of loss of function intolerant and neurodevelopmental disorder genes
Authors: Rees Elliott , Han Jun , Morgan Joanne , Carrera Noa , Escott-Price Valentina , Pocklington Andrew J. , Duffield Madeleine , Hall Lynsey , Legge Sophie E. , Pardiñas Antonio F. , Richards Alexander L. , Roth Julian , Lezheiko Tatyana , Kondratyev Nikolay , Golimbet Vera , Parellada Mara , González-Peñas Javier , Arango Celso ,   GROUP Investigators, Gawlik Micha , Kirov George , Walters James T. R. , Holmans Peter , O’Donovan Michael C. , Owen Michael J. 
Published: April 2019

AbstractSchizophrenia is a highly polygenic disorder with important contributions coming from both common and rare risk alleles, the latter including CNVs and rare coding variants (RCVs), sometimes occurring as de novo variants (DNVs). We performed DNV analysis in whole exome-sequencing data obtained from a new sample of 613 schizophrenia trios, and combined this with published data for a total of 3,444 trios. Loss-of-function (LoF) DNVs were significantly enriched among 3,488 LoF intolerant genes in our new trio data (rate ratio (RR) (95% CI) = 2.23 (1.31, 3.79); p = 2.2 × 10−3), supporting previous findings. In the full dataset, genes associated with neurodevelopmental disorders (NDD; n=160) were significantly enriched for LoF DNVs (RR (95% CI) = 3.32 (2.0, 5.21); p = 7.4 × 10−6). Within this set of NDD genes, SLC6A1, encoding a gamma-aminobutyric acid transporter, was associated with missense-damaging DNVs (p = 5.2 × 10−5). Using data from a subset of 1,122 trios for which we had genome-wide common variant data, schizophrenia polygenic risk was significantly over-transmitted to probands (p = 2.6 × 10−60), as was bipolar disorder common variant polygenic risk (p = 5.7 × 10−17). We defined carriers of candidate schizophrenia-related DNVs as those with LoF or deletion DNVs in LoF intolerant or NDD genes. These individuals had significantly less over-transmission of common risk alleles than non-carriers (p = 3.5 × 10−4), providing robust support for the hypothesis that this set of DNVs is enriched for those related to schizophrenia.
No evidence forWolbachiaas a nutritional co-obligate endosymbiont in the aphidPentalonia nigronervosa
Authors: Manzano-Marín Alejandro 
Published: April 2019

ABSTRACTObligate symbiotic associations are present in a wide variety of animals with a nutrient-restricted diet. Aphids (hemiptera: Aphididae) almost-universally hostBuchnera aphidicolabacteria in a specialised organs (called bacteriomes). These bacteria supply the aphid with essential nutrients lacking from their diet (i.e. essential amino acids and some B vitamins). Some aphid lineages, such as species from the Lacninae subfamily, have evolved co-obligate associations with secondary endosymbionts, deriving from a loss of biotin-and riboflavin-biosynthetic genes. In this study I re-analyse previously published sequencing data from the banana aphidPentalonia nigronervosa. I show that the metabolic inference results from De Clercket al.(2015) are incorrect and possibly arise from the use of inadequate methods. Additionally, I discuss how the biased interpretation of their antibiotic treatment analyses together with the incorrect metabolic inference resulted in the erroneous suggestion “that a co-obligatory symbiosis betweenB. aphidicolaandWolbachiaoccurs in the banana aphid”.
A novel deep learning scheme for morphology-based classification of mycobacterial infection in unstained macrophages
Authors: Zhao Xinzhuo , Bao Yanqing , Wang Lin , Qian Wei , Sun Jianjun 
Published: April 2019

AbstractObjectiveMycobacterium tuberculosis (Mtb) is an airborne, contagious bacterial pathogen that causes widespread infections in humans. Using Mycobacterium marinum (Mm), a surrogate model organism for Mtb research, the present study develops a deep learning-based scheme that can classify the Mm-infected and uninfected macrophages in tissue culture solely based on morphological changes.MethodsA novel weak-and semi-supervised learning method is developed to detect and extract the cells, firstly. Then, transfer learning and fine-tuning from the CNN is built to classify the infected and uninfected cells.ResultsThe performance is evaluated by accuracy (ACC), sensitivity (SENS) and specificity (SPEC) with 10-fold cross-validation. It demonstrates that the scheme can classify the infected cells accurately and efficiently at the early infection stage. At 2 hour post infection (hpi), we achieve the ACC of 0.923 ± 0.005, SENS of 0.938 ± 0.020, and SPEC of 0.905 ± 0.019, indicating that the scheme has detected significant morphological differences between the infected and uninfected macrophages, although these differences are hardly visible to naked eyes. Interestingly, the ACC at 12 and 24 hpi are 0.749 ± 0.010 and 0.824 ± 0.009, respectively, suggesting that the infection-induced morphological changes are dynamic throughout the infection. Finally, deconvolution with guided propagation maps the key morphological features contributing to the classification.SignificanceThis proof-of-concept study provides a novel venue to investigate bacterial pathogenesis in a macroscopic level and has a great promise in diagnosis of bacterial infections.
Laminin-driven Epac/Rap1 regulation of epithelial barriers on decellularized matrix
Authors: Young Bethany M. , Shankar Keerthana , Tho Cindy K. , Pellegrino Amanda R. , Heise Rebecca L. 
Published: April 2019

ABSTRACTDecellularized tissues offer a unique tool for developing regenerative biomaterials orin vitroplatforms for the study of cell-extracellular matrix (ECM) interactions. One main challenge associated with decellularized lung tissue is that ECM components can be stripped away or altered by the detergents used to remove cellular debris. Without characterizing the composition of lung decellularized ECM (dECM) and the cellular response caused by the altered composition, it is difficult to utilize dECM for regeneration and specifically, engineering the complexities of the alveolar-capillary barrier. This study takes steps towards uncovering if dECM must be enhanced with lost ECM proteins to achieve proper epithelial barrier formation. To achieve this, epithelial barrier function was assessed on dECM coatings with and without the systematic addition of several key basement membrane proteins. After comparing barrier function on collagen, fibronectin, laminin, and dECM in varying combinations as anin vitrocoating, the alveolar epithelium exhibited superior barrier function when dECM was supplemented with laminin as evidenced by trans-epithelial electrical resistance (TEER) and permeability assays. Increased barrier resistance with laminin addition was associated with upregulation of Claudin-18, E- cadherin, and junction adhesion molecule (JAM)-A, and stabilization of zonula occludens (ZO)-1 at junction complexes. The Epac/Rap1 pathway was observed to play a role in the ECM-mediated barrier function determined by protein expression and Epac inhibition. These findings reveal potential ECM coatings and molecular therapeutic targets for improved regeneration with decellularized scaffolds or edema related pathologies.
In vivo FirreandDxz4deletion elucidates roles for autosomal gene regulation
Authors: Andergassen Daniel , Smith Zachary D. , Lewandowski Jordan P. , Gerhardinger Chiara , Meissner Alexander , Rinn John L. 
Published: April 2019

AbstractRecent evidence has determined that the conserved X chromosome “mega-structures” controlled by theFirreandDxz4alleles are not required for X chromosome inactivation (XCI) in cell lines. Here we determined thein vivocontribution of these alleles by generating mice carrying a single or double deletion ofFirreandDxz4. We found that these mutants are viable, fertile and show no defect in random or imprinted XCI. However, the lack of these elements results in many dysregulated genes on autosomes in an organ-specific manner. By comparing the dysregulated genes between the single and double deletion, we identified superloop, megadomain, andFirrelocus dependent gene sets. The largest transcriptional effect was observed in all strains lacking theFirrelocus, indicating that this locus is the main driver for these autosomal expression signatures. Collectively, these findings suggest that these X-linked loci are involved in autosomal gene regulation rather than XCI biology.
Lactobacillus rhamnosusLcr35®as an effective treatment for preventingCandida albicansinfection in preclinical models: first mechanistical insights
Authors: Poupet Cyril , Saraoui Taous , Veisseire Philippe , Bonnet Muriel , Dausset Caroline , Gachinat Marylise , Camarès Olivier , Chassard Christophe , Nivoliez Adrien , Bornes Stéphanie 
Published: April 2019

AbstractThe increased recurrence ofCandida albicansinfections is associated with greater resistance to antifungal drugs. This involves the establishment of alternative therapeutic protocols such as the probiotic microorganisms whose antifungal potential has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding the mechanisms of action of probiotic microorganisms has become a strategic need for the development of new therapeutics for humans. In this study, we investigated the prophylactic anti-Candida albicansproperties ofLactobacillus rhamnosusLcr35®using thein vitroCaco-2 cells model and thein vivo Caenorhabditis elegansmodel. On Caco-2 cells, we showed that the strain Lcr35®significantly inhibited the growth of the pathogen (~2 log CFU.mL−1) and its adhesion (150 to 6,300 times less). Moreover, on the top of having a prolongevity activity in the nematode, Lcr35®protects the animal from the fungal infection even if the yeast is still detectable in its intestine. At the mechanistic level, we noticed the repression of genes of the p38 MAPK signaling pathway and genes involved in the antifungal response induced by Lcr35®suggesting that the pathogen no longer appears to be detected by the worm immune system. However, the DAF-16 / FOXO transcription factor, implicated in the longevity and antipathogenic response ofC. elegans, is activated by Lcr35®. These results suggest that the probiotic strain acts by stimulating its host via DAF-16, but also by suppressing the virulence of the pathogen.
Droplet-based combinatorial indexing for massive scale single-cell epigenomics
Authors: Lareau Caleb A. , Duarte Fabiana M. , Chew Jennifer G. , Kartha Vinay K. , Burkett Zach D. , Kohlway Andrew S. , Pokholok Dmitry , Aryee Martin J. , Steemers Frank J. , Lebofsky Ronald , Buenrostro Jason D. 
Published: April 2019

AbstractWhile recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution, the throughput and quality of these methods have limited the widespread adoption of these technologies. Here, we describe a droplet microfluidics platform for single-cell assay for transposase accessible chromatin (scATAC-seq) for high-throughput single-cell profiling of chromatin accessibility. We use this approach for the unbiased discovery of cell types and regulatory elements within the mouse brain. Further, we extend the throughput of this approach by pairing combinatorial indexing with droplet microfluidics, enabling single-cell studies at a massive scale. With this approach, we measure chromatin accessibility across resting and stimulated human bone marrow derived cells to reveal changes in the cis- and trans- regulatory landscape across cell types and upon stimulation conditions at single-cell resolution. Altogether, we describe a total of 502,207 single-cell profiles, demonstrating the scalability and flexibility of this droplet-based platform.
Cell-type specific concentration regulation of the basal transcription factor TFIIH
Authors: Donnio Lise-Marie , Miquel Catherine , Vermeulen Wim , Giglia-Mari Giuseppina , Mari Pierre-Olivier 
Published: April 2019

AbstractThe basal transcription/repair factor TFIIH is a ten sub-unit complex essential for RNA polymerase II (RNAP2) transcription initiation and DNA repair. In both these processes TFIIH acts as a DNA helix opener (by the enzymatic activity of the XPB and XPD helicases), required for promoter escape of RNAP2 in transcription initiation, and to set the stage for strand incision within the Nucleotide Excision Repair (NER) pathway. We generated a knock-in mouse model that endogenously expresses a fluorescent version of XPB. Here we demonstrate, via confocal imaging of ex vivo tissues and cells derived from this mouse model, that TFIIH steady state levels are tightly regulated at the single cell level, thus keeping nuclear TFIIH concentrations remarkably constant in a cell type dependent manner. Moreover, we show that individual cellular TFIIH levels are proportional to the speed of mRNA production, hence to a cell’s transcriptional activity, which we can correlate to proliferation status. Importantly, cancer tissue presents a higher TFIIH than normal healthy tissues. Taken together, these results show that TFIIH cellular concentration might be used as a bona-fide marker of transcriptional activity and proliferation.SignificanceUsing a mouse model expressing a fluorescently version of TFIIH, we showed that TFIIH concentration is tightly controlled and that this concentration is proportional to the cellular transcriptional activity and proliferation capacity.
Single-Cell Data Analysis Using MMD Variational Autoencoder for a More Informative Latent Representation
Authors: Zhang Chao 
Published: April 2019

AbstractVariational Autoencoder (VAE) is a generative model from the computer vision community; it learns a latent representation of images and generates new images in an unsupervised way. Recently, Vanilla VAE has been applied to single-cell data analysis, in the hope of harnessing the representation power of latent space to evade the “curse of dimensionality” of the original dataset. However, Vanilla VAE is suffering from the issue of less informative latent space, which raises a question concerning the reliability of Vanilla VAE latent space in representing the high-dimensional single-cell datasets. Therefore I set up such a study to examine this issue from the multiple perspectives.This paper confirms the issue of Vanilla VAE by comparing it with MMD-VAE, a variant of VAE which has claimed to have overcome this issue based on image data, across a series of single-cell RNAseq and mass cytometry datasets. The result indicates that MMD-VAE is superior to Vanilla VAE in retaining the information not only in the latent space but also the reconstruction space, which suggests that MMD-VAE be a better option for single-cell data analysis than Vanilla VAE.
Constructing social networks and mobilizing social capital
Authors: Zhang Donghui 
Published: April 2019

Purpose
The purpose of this paper is to examine the life worlds of Tibetan students who participate in China’s inland boarding programs and seek to understand the social networks they develop in the Han-culture dominant school settings.

Design/methodology/approach
This study is based on ethnographic fieldwork with two Tibetan students (Dorji and Lhamo) in a Beijing inland boarding high school.

Findings
This study found that the Tibetan students are capable social actors who construct two kinds of social networks, the “we” group (co-ethnics) vs the “they” group (cross-ethnics), and mobilize different social capitals strategically. The former provides them with emotional support, cultural affinity and a sense of belonging, while the latter helps them achieve instrumental outcomes, such as Mandarin proficiency, academic improvement and broadened horizons.

Research limitations/implications
However, the group boundary they draw between the two kinds of networks reflects the futility of government efforts to promote interethnic integration through the inland schools.

Originality/value
The issue of minority students as active agents in constructing social networks and mobilizing social capital in unfamiliar sociocultural settings is a relatively new research area (Reynolds, 2007; Holland et al., 2007), whereas the Tibetan students in China are among the least known in the existing scholarship.
Social customer relationship management (s-CRM) among
small- and medium-sized enterprises (SMEs) in Malaysia
Authors: Hassan Siti Hasnah , Mohamed Haniba Noor Mohamed , Ahmad Noor Hazlina 
Published: April 2019

Purpose
In this twenty-first century, the emergence of social media has been integral
in business-related processes, especially in small- and medium-sized
enterprises (SMEs), which allows businesses to interact and build a
relationship with customers to improve their sustainable service quality.
Concisely, this study aims to examine the benefits of social customer
relationship management (s-CRM) performance from the perceptive of SMEs
owned by Muslims.

Design/methodology/approach
A survey method was used and the data were gathered from 135 SMEs which
participated in Halfest (Halal Fiesta Malaysia) trade show in Kuala Lumpur,
Malaysia.

Findings
Interestingly, the results revealed that the adoption of information and
communications technology (ICT) has both direct and indirect impacts on
s-CRM performance. On the other hand, the perceived value of s-CRM mediates
the relationship between customer information management and performance of
s-CRM. In this context, the perceived value was ascertained to be an
influential factor for both ICT adoption and customer information
management.

Research
limitations/implications
With a connection to the results, this study concludes that to enhance
business performance to sustain in the marketplace, the establishment of
s-CRM is crucial, as it has significant implication in marketing, customer
service and sales department of SMEs.

Originality/value
This paper provides new insight into the importance of s-CRM to SMEs to
improve interactions with the key stakeholders and convey meaningful insight
to instil customer-centric practices.
A novel alarm signal in aquatic prey: Familiar minnows coordinate group defences against predators through chemical disturbance cues
Authors: Bairos‐Novak Kevin R. , Ferrari Maud C. O. , Chivers Douglas P. 
Published: April 2019

Abstract

Animal signalling systems outside the realm of human perception remain largely understudied. These systems consist of four main components: a signalling context, a voluntary signal, receiver responses and resulting fitness benefits to both the signaller and receiver(s). It is often most difficult to determine incidental cues from voluntary signals. One example is chemical disturbance cues released by aquatic prey during predator encounters that may serve to alert conspecifics of nearby risk and initiate tighter shoaling.

We aimed to test whether disturbance cues are released incidentally (i.e. as a cue) or are produced voluntarily depending on a specific signalling context such as the audience surrounding the individual, and thus constitute a signal. We hypothesized that if receivers use disturbance cues to communicate risk among themselves, they would produce more (or more potent) disturbance cues when present in a group of conspecifics rather than when they are isolated (presence/absence of an audience) and use disturbance cues more when present alongside familiar rather than unfamiliar conspecifics (audience composition effect).

We placed fathead minnows (Pimephales promelas) in groups with familiar fish, unfamiliar fish or as isolated individuals with no audience present, and then simulated a predator chase to evoke disturbance cues. We used bioassays with independent receivers to assess whether the disturbance cues produced differed depending on the signallers’ audience.

We found evidence of voluntary signalling, as minnows responded to disturbance cues from groups of fish with tighter shoaling while disturbance cues from isolated minnows did not evoke a significant shoaling response (presence/absence audience effect). Receivers also increased shoaling, freezing and dashing more in response to disturbance cues from familiar groups compared to disturbance cues from unfamiliar groups or isolated minnows (audience composition effect).

Together, these findings support our hypothesis that disturbance cues are used as an antipredator signal to initiate coordinated group defences among familiar conspecifics involving shoaling, freezing and dashing. This study represents the strongest evidence to date that chemicals released by aquatic prey upon disturbance by predators serve as voluntary signals rather than simply cues that prey have evolved to detect when assessing their risk of predation.