bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhizosphere microbes and host plant genotype influence the plant metabolome and reduce insect herbivory
Authors: Hubbard Charley J. , Li Baohua , McMinn Robby , Brock Marcus T. , Maignien Lois , Ewers Brent E. , Kliebenstein Daniel , Weinig Cynthia 
Published: April 2018

SummaryRhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense remains unclear.In Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites.Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae, and the population with lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.) attack; no effect was observed of GLS on damage by a second herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (intact vs. disrupted) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted rhizosphere microbiome treatment, and distinct (as estimated from 16s rRNA amplicon sequencing) intact native microbiomes also differed in their effects on herbivore damage. These differences may be attributable to shifts in primary metabolic pathways.The findings suggest that rhizosphere microbes can play a greater role than plant genotype in defense against insect herbivores, and act through mechanisms independent of plant genotype.
Mendelian randomization does not support serum calcium in prostate cancer risk
Authors: Yarmolinsky James , Berryman Katie , Langdon Ryan , Bonilla Carolina ,   the PRACTICAL consortium, Smith George Davey , Martin Richard M , Lewis Sarah J 
Published: April 2018

AbstractBackground: Observational studies suggest that dietary and serum calcium are risk factors for prostate cancer. However, such studies suffer from residual confounding (due to unmeasured or imprecisely measured confounders), undermining causal inference. Mendelian randomization uses randomly assigned (hence unconfounded and pre-disease onset) germline genetic variation to proxy for phenotypes and strengthen causal inference in observational studies.Objective: We tested the hypothesis that serum calcium is associated with an increased risk of overall and advanced prostate cancer.Design: A genetic instrument was constructed using 5 single nucleotide polymorphisms robustly associated with serum calcium in a genome-wide association study (N ≤ 61,079). This instrument was then used to test the effect of a 0.5 mg/dL increase (1 standard deviation, SD) in serum calcium on risk of prostate cancer in 72,729 men in the PRACTICAL (Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome) Consortium (44,825 cases, 27,904 controls) and risk of advanced prostate cancer in 33,498 men (6,263 cases, 27,235 controls).Results: We found weak evidence for a protective effect of serum calcium on prostate cancer risk (odds ratio [OR] per 0.5 mg/dL increase in calcium: 0.83, 95% CI: 0.63-1.08; P=0.12). We did not find strong evidence for an effect of serum calcium on advanced prostate cancer (OR per 0.5 mg/dL increase in calcium: 0.98, 95% CI: 0.57-1.70; P=0.93).Conclusions: Our Mendelian randomization analysis does not support the hypothesis that serum calcium increases risk of overall or advanced prostate cancer.
A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events
Authors: Jaillard Magali , Lima Leandro , Tournoud Maud , Mahé Pierre , Belkum Alex van , Lacroix Vincent , Jacob Laurent 
Published: April 2018

AbstractMotivationGenome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or fine-assessment of marker effect. Recently, alignment-free methods based on kmer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are hard to interpret.MethodsHere, we introduce DBGWAS, an extended kmer-based GWAS method producing interpretable genetic variants associated with pheno-types. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes identified by the association model into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is fast, alignment-free and only requires a set of contigs and phenotypes. It produces annotated subgraphs representing local polymorphisms as well as mobile genetic elements (MGE) and offers a graphical framework to interpret GWAS results.ResultsWe validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa – along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature.ConclusionOur novel method proved its efficiency to retrieve any type of phenotype-associated genetic variant without prior knowledge. All experiments were computed in less than two hours and produced a compact set of meaningful subgraphs, thereby outperforming other GWAS approaches and facilitating the interpretation of the results.AvailabilityOpen-source tool available at https://gitlab.com/leoisl/dbgwas
Long-read sequence capture of the hemoglobin gene clusters across species
Authors: Hoff Siv Nam Khang , Baalsrud Helle T. , Tooming-Klunderud Ave , Skage Morten , Richmond Todd , Obernosterer Gregor , Shirzadi Reza , Tørresen Ole Kristian , Jakobsen Kjetill S. , Jentoft Sissel 
Published: April 2018

AbstractCombining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genetic organization and synteny of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.
Androgen Promotes Differentiation of PLZF+Spermatogonia pool via Indirect Regulatory Pattern
Authors: Wang Jingjing , Li Jinmei , Gu Yunzhao , Xia Qin , Song Weixiang , Zhang Xiaoyu , Yang Yang , Wang Wei , Li Hua , Zou Kang 
Published: April 2018

AbstractAndrogen signaling plays a pivotal role in spermatogenesis, but the molecular mechanisms underlying androgen action in this process are unclear. Specifically, it is unknown if the androgen receptor (AR) is expressed in germ cells. Thus it’s interesting to reveal how androgen induces differentiation of spermatogonial progenitor cells (SPCs) in the niche. Here we observed the AR is primarily expressed in pre-spermatogonia of mice 2 days post partum (dpp), absent before spermatogenesis onset, and then expressed in surrounding Sertoli cells. Then we examined a regulatory role of the AR in spermatogenesis using a SPCs-Sertoli cells co-culture system, and demonstrated that androgen negatively regulatedPlzf(the gene for stemness maintenance of SPCs). Additionally, we identified Gata2 as a target of AR in Sertoli cells, and demonstrated that Wilms tumor 1 (WT1) and β1-integrin as two putative intermediate molecules to transfer differentiation signals to SPCs, which was further verified using androgen pharmacological-deprivation mice model. These results demonstrate a regulatory pattern of androgen in SPCs niche in an indirect way via multiple steps of signal transduction.
Systematically investigating the key features of the nuclease deactivated Cpf1 for tunable multiplex genetic regulation
Authors: Miao Chensi , Zhao Huiwei , Qian Long , Lou Chunbo 
Published: April 2018

AbstractWith a unique crRNA processing capability, the CRISPR associated Cpf1 protein holds great potential for multiplex gene regulation. Unlike the well-studied Cas9 protein, however, conversion of Cpf1 to a transcription regulator and its related properties have not been systematically explored yet. In this study, we investigated the mutation schemes and crRNA requirements for the nuclease deactivated Cpf1 (dCpf1). By shortening the direct repeat sequence, we obtained genetically stable crRNA co-transcripts and improved gene repression with multiplex targeting. A screen of diversity-enriched PAM library was designed to investigate the PAM-dependency of gene regulation by dCpf1 from Francisella novicida and Lachnospiraceae bacterium. We found novel PAM patterns that elicited strong or medium gene repressions. Using a computational algorithm, we predicted regulatory outputs for all possible PAM sequences, which spanned a large dynamic range that could be leveraged for regulatory purposes. These newly identified features will facilitate the efficient design of CRISPR-dCpf1 based systems for tunable multiplex gene regulation.
Oxidative Stress Mediates UVC-Induced Increases in Epidermal Autofluorescence of C57 Mouse Ears
Authors: Zhang Mingchao , Maharjan Dhruba Tara , Li Yujia , Ying Weihai 
Published: April 2018

AbstractOur recent study has reported that UV-induced epidermal autofluorescence (AF) can be used as a novel biomarker for predicting UV-induced skin damage, which is originated from UV-induced, cysteine protease-mediated keratin 1 degradation. A key question regarding these findings is: Does oxidative stress play a significant role in the UV-induced epidermal AF and keratin 1 proteolysis? In our current study, we administered the widely used antioxidant N-acetyl cysteine (NAC) into the skin of mouse ears to test our hypothesis that oxidative stress mediates UV-induced increases in the epidermal AF and keratin 1 degradation. Our study has shown that NAC administration can significantly attenuate the UVC-induced AF increases. The NAC administration can also significantly decrease the UVC-induced keratin 1 degradation. Collectively, our findings have indicated that the oxidative stress induced by UVC is causative to the UVC-induced increases in epidermal AF and keratin 1 proteolysis. Moreover, since oxidative stress is significantly increased in multiple regions of the body in several major diseases, the oxidative stress-induced increases in epidermal AF may become a novel biomarker for diagnosis of major diseases.
Increased green autofluorescence is a marker for non-invasive prediction of H2O2-induced cell death and decreases in the intracellular ATP of HaCaT cells
Authors: Xu Jie , Ying Weihai 
Published: April 2018

AbstractSince oxidative stress plays important pathological roles in numerous diseases, it is of both critical theoretical and clinical significance to search for the approaches for predicting oxidative damage. Cellular models have great value for studying oxidative damage, which would be significantly promoted if non-invasive approaches for predicting oxidative damage can be established without the need of exogenous probes. In our current study, we tested our hypothesis that changes of the autofluorescence (AF) of cells may be used for predicting oxidative cellular damage. Our study found that H2O2 dose-dependently increased the green AF of HaCaT keratinocyte cell line at non-nuclear regions assessed at 1 hr or 3 hrs after the H2O2 exposures, while H2O2 did not affect the green AF of other cell types tested in our study, including PC 12 cells and BV2 microglia. We further found that the increases in the AF of HaCaT cells are highly correlated with the H2O2-induced increases in early-stage apoptosis, late-stage apoptosis and necrosis assessed at 18 hrs after the H2O2 exposures, which are also negatively correlated with the intracellular ATP levels of the H2O2-treated cells assessed at 18 hrs after the H2O2 exposures. Collectively, our study has suggested that increased AF may become the first endogenous marker for non-invasive prediction of oxidative damage selectively for such cell types as HaCaT cells. Compared with traditional approaches, our method may have significant value for studying oxidative damage of keratinocytes with significantly higher efficiency and lower cost.
Genetic control of transition from juvenile to mature wood with respect to microfibril angle (MFA) in Norway spruce (Picea abies) and lodgepole pine (Pinus contorta)
Authors: Hayatgheibi Haleh , Forsberg Nils , Lundqvist Sven-Olof , Mörling Tommy , Mellerowicz Ewa J. , Karlsson Bo , Wu Harry , García Gil M Rosario 
Published: April 2018

AbstractGenetic control of microfibril angle (MFA) transition from juvenile to mature was evaluated in Norway spruce and lodgepole pine. Increment cores were collected at breast height from 5,618 trees in two 21-year-old Norway spruce progeny trials in southern Sweden, and from 823 trees in two 34-35 – year-old lodgepole pine progeny trials in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile to mature, a threshold level of MFA 20° was considered and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h2) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, whileh2were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile to mature in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (∆G) obtained in direct selection of this trait were very high in both species.
Online customer experience (OCE) in clothing e-retail
Authors: Pandey Shweta , Chawla Deepak 
Published: April 2018

Purpose
The purpose of this paper is to explore the dimensions of online customer experience (OCE) and their impact on satisfaction and loyalty in the clothing e-retail context. Furthermore, it explores the influence of gender on the OCE-satisfaction-loyalty chain.

Design/methodology/approach
OCE dimensions were drawn from the literature and then adapted and validated using two samples (217 – exploratory factor analysis, 651 – confirmatory factor analysis) of experienced online clothing shoppers in India. An analysis was done using structured equation modelling.

Findings
Six OCE psychological factors and four OCE functionality factors were revealed. Both OCE dimensions impact loyalty either directly or indirectly through satisfaction. Gender is observed to moderate the relationship among three OCE factors (e-distrust, e-negative beliefs and website interactivity) and satisfaction.

Research limitations/implications
The research results are limited to the factors related to each of the two OCE dimensions explored within the clothing e-retail context in India.

Practical implications
Clothing e-retailers need to focus on both the OCE dimensions to drive business sustenance. Furthermore, their OCE strategies should be in line with the gender-based differences highlighted by the study.

Originality/value
The study facilitates in the adaptation and validation of the OCE dimensions in the clothing e-retail category in an emerging market. While all factors associated with both OCE dimensions are important for driving satisfaction and loyalty, the study underscores the need for a higher focus on visual engagement by e-retailers in the given context. Gender moderates the OCE-satisfaction paths, but does not moderate the OCE-loyalty paths.
Community‐acquired Acute Kidney Injury Among Children Seen in the Pediatric Emergency Department
Authors: Bernardo Erika O. , Cruz Andrea T. , Buffone Gregory J. , Devaraj Sridevi , Loftis Laura L. , Arikan Ayse Akcan 
Published: April 2018

AbstractObjectivesAcute kidney injury (AKI) is a significant risk factor for morbidity and mortality in children. Little is known about community‐acquired AKI (CA‐AKI) in the pediatric emergency department (PED). Early recognition of AKI allows for nephroprotective measures. The goal of this investigation was to determine the incidence of CA‐AKI and the frequency of clinician identified CA‐AKI to better inform future nephroprotective interventions.MethodsThis was a retrospective cross‐sectional study in the PED of a children's hospital. Children 1 month to 18 years of age seen in the PED from January 1 to December 31, 2015, and in whom at least one creatinine level was obtained were included. Patients with chronic kidney disease or end‐stage renal disease or who died in the PED were excluded. Patients had CA‐AKI based on modified Kidney Disease‐Improving Global Outcomes criteria using the creatinine obtained in the PED compared to age‐specific norms. Patients were considered identified if the PED clinician diagnosed AKI. The primary outcome was the incidence of CA‐AKI. Secondary outcomes included frequency of AKI identification, nephrotoxic medication use, hospital length of stay, renal replacement therapy, and death. Fisher exact test or Pearson's chi‐square test was used to calculate odds ratio (OR) with 95% confidence intervals (CIs); multivariable analyses were performed using logistic regression.ResultsIn 2015 there were 119,151 PED visits; 15,486 met inclusion criteria. CA‐AKI was present in 239 of 15,486 (1.5%) encounters. AKI was identified by PED clinicians in 46 of 239 (19%) of encounters and by the inpatient team in 123 of 199 (62%) of the encounters admitted. AKI was never recognized by a PED or inpatient clinician in 74 of 199 (37%) encounters. Encounters with AKI correctly diagnosed were older (13 years old vs. 10 years old, p = 0.0114), had more severe (stage 2 or 3) AKI (OR = 5.5, 95% CI = 2.6–11.8), and were more likely to be admitted (OR = 10.3, 95% CI = 1.38–77.4) than encounters with missed AKI.ConclusionsCA‐AKI remains an underrecognized entity in the PED. Better tools for early recognition of AKI in the busy PED environment are needed.
The Bursts and Lulls of Multimodal Interaction: Temporal Distributions of Behavior Reveal Differences Between Verbal and Non‐Verbal Communication
Authors: Abney Drew H. , Dale Rick , Louwerse Max M. , Kello Christopher T. 
Published: April 2018

AbstractRecent studies of naturalistic face‐to‐face communication have demonstrated coordination patterns such as the temporal matching of verbal and non‐verbal behavior, which provides evidence for the proposal that verbal and non‐verbal communicative control derives from one system. In this study, we argue that the observed relationship between verbal and non‐verbal behaviors depends on the level of analysis. In a reanalysis of a corpus of naturalistic multimodal communication (Louwerse, Dale, Bard, & Jeuniaux, ), we focus on measuring the temporal patterns of specific communicative behaviors in terms of their burstiness. We examined burstiness estimates across different roles of the speaker and different communicative modalities. We observed more burstiness for verbal versus non‐verbal channels, and for more versus less informative language subchannels. Using this new method for analyzing temporal patterns in communicative behaviors, we show that there is a complex relationship between verbal and non‐verbal channels. We propose a “temporal heterogeneity” hypothesis to explain how the language system adapts to the demands of dialog.
Association of the novel susceptible locus rs9266150 with clinical features of psoriasis vulgaris in the Chinese Han population
Authors: Wu Juan , Huang Yan , Guo Huimin , Ye Lei , Huang Yong , Huang Hequn , Qian Wenjun , Zhang Xuelei , Wang Wenjun , Zheng Xiaodong , Zhang Xuejun , Fan Xing , Liu Jianjun , Yang Sen 
Published: April 2018

AbstractPsoriasis is a chronic multifactorial disease and is considered to be strongly associated with the major histocompatibility complex (MHC) region. We have discovered an independent, novel and susceptible psoriasis risk HLA loci, rs9266150; P = 4.52 × 10−9 for the first time. In this study, we aimed to verify the relationship between the susceptible locus and the subphenotypes of psoriasis vulgaris (PV), including geographic location, gender, age of onset, family history and present skin lesion types (chronic plaque and guttate). To investigate the distribution and association of the rs9266150 gene with clinical phenotypes of PV in Chinese Han population, we conducted an analysis in case‐control and case‐only subjects in the 9906 controls and 8744 cases by MHC targeted sequencing stratified analysis in this study. Significant associations were found with a northern geographic location in the case‐only (P = 1.97 × 10−4) and the subphenotype‐control analyses (P = 5.57 × 10−5), males in the case‐only (P = 4.77 × 10−3) and the subphenotype‐control analyses (P = 7.31 × 10−4), and guttate psoriasis in the case‐only (P = 4.08 × 10−3) and the subphenotype‐control analyses (P = 1.27 × 10−3). There were no significant differences observed between the age of onset (OR = 1.062, 95% CI: 0.9725‐1.16, P = 1.8 × 10−1) and the family history of psoriasis (OR = 0.981, 95% CI: 0.9048‐1.064, P = 6.43 × 10−1). The recessive model provided the best fit for rs9266150 (P = 4.38 × 10−7). Our results implied that rs9266150 might not only play an important role in the development of psoriasis, but also be positively associated with the geographic location, gender and present skin lesion in the Chinese population.