bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle
Authors: Sun Hui-Zeng , Zhao Ke , Zhou Mi , Chen Yanhong , Guan Le Luo 
Published: October 2018

Abstract

Motivation
Feed efficiency is an important trait for sustainable beef production that is regulated by the complex biological process, but the mode of action behinds it has not been clearly defined. Here, we aimed to elucidate the regulatory mechanisms of this trait through studying the landscape of the genome-wide gene expression of rumen, liver, muscle and backfat tissues, the key ones involved in the energy metabolism.

Results
The transcriptome of 189 samples across four tissues from 48 beef steers with varied feed efficiency were generated using Illumina HiSeq4000. The analysis of global gene expression profiles of four tissues, functional analysis of tissue-shared and -unique genes, co-expressed network construction of tissue-shared genes, weighted correlations analysis between gene modules and feed efficiency-related traits in each tissue were performed. Among four tissues, the transcriptome of muscle tissue was distinctive from others, while those of rumen and backfat tissues were similar. The associations between co-expressed genes and feed efficiency related traits at single or all tissues level exhibited that the gene expression in the rumen, liver, muscle and backfat were the most correlated with feed conversion ratio, dry matter intake, average daily gain and residual feed intake, respectively. The 19 overlapped genes identified from the strongest module–trait relationships in four tissues are potential generic gene markers for feed efficiency.

Availability and implementation
The distribution of gene expression data can be accessed at https://www.cattleomics.com/transcriptome.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mendelian randomization analysis of C-reactive protein on colorectal cancer risk
Authors: Wang Xiaoliang , Dai James Y , Albanes Demetrius , Arndt Volker , Berndt Sonja I , Bézieau Stéphane , Brenner Hermann , Buchanan Daniel D , Butterbach Katja , Caan Bette , Casey Graham , Campbell Peter T , Chan Andrew T , Chen Zhengyi , Chang-Claude Jenny , Cotterchio Michelle , Easton Douglas F , Giles Graham G , Giovannucci Edward , Grady William M , Hoffmeister Michael , Hopper John L , Hsu Li , Jenkins Mark A , Joshi Amit D , Lampe Johanna W , Larsson Susanna C , Lejbkowicz Flavio , Li Li , Lindblom Annika , Le Marchand Loic , Martin Vicente , Milne Roger L , Moreno Victor , Newcomb Polly A , Offitt Kenneth , Ogino Shuji , Pharoah Paul D P , Pinchev Mila , Potter John D , Rennert Hedy S , Rennert Gad , Saliba Walid , Schafmayer Clemens , Schoen Robert E , Schrotz-King Petra , Slattery Martha L , Song Mingyang , Stegmaier Christa , Weinstein Stephanie J , Wolk Alicja , Woods Michael O , Wu Anna H , Gruber Stephen B , Peters Ulrike , White Emily 
Published: October 2018

Abstract

Background
Chronic inflammation is a risk factor for colorectal cancer (CRC). Circulating C-reactive protein (CRP) is also moderately associated with CRC risk. However, observational studies are susceptible to unmeasured confounding or reverse causality. Using genetic risk variants as instrumental variables, we investigated the causal relationship between genetically elevated CRP concentration and CRC risk, using a Mendelian randomization approach.

Methods
Individual-level data from 30 480 CRC cases and 22 844 controls from 33 participating studies in three international consortia were used: the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colorectal Transdisciplinary Study (CORECT) and the Colon Cancer Family Registry (CCFR). As instrumental variables, we included 19 single nucleotide polymorphisms (SNPs) previously associated with CRP concentration. The SNP-CRC associations were estimated using a logistic regression model adjusted for age, sex, principal components and genotyping phases. An inverse-variance weighted method was applied to estimate the causal effect of CRP on CRC risk.

Results
Among the 19 CRP-associated SNPs, rs1260326 and rs6734238 were significantly associated with CRC risk (P = 7.5 × 10–4, and P = 0.003, respectively). A genetically predicted one-unit increase in the log-transformed CRP concentrations (mg/l) was not associated with increased risk of CRC [odds ratio (OR) = 1.04; 95% confidence interval (CI): 0.97, 1.12; P = 0.256). No evidence of association was observed in subgroup analyses stratified by other risk factors.

Conclusions
In spite of adequate statistical power to detect moderate association, we found genetically elevated CRP concentration was not associated with increased risk of CRC among individuals of European ancestry. Our findings suggested that circulating CRP is unlikely to be a causal factor in CRC development.
GSDMB promotes non-canonical pyroptosis by enhancing caspase-4 activity
Authors: Chen Qin , Shi Peiliang , Wang Yufang , Zou Dayuan , Wu Xiuwen , Wang Dingyu , Hu Qiongyuan , Zou Yujie , Huang Zan , Ren Jianan , Lin Zhaoyu , Gao Xiang 
Published: October 2018

Abstract
Gasdermin B (GSDMB) has been reported to be associated with immune diseases in humans, but the detailed molecular mechanisms remain unsolved. The N-terminus of GSDMB by itself, unlike other gasdermin family proteins, does not induce cell death. Here, we show that GSDMB is highly expressed in the leukocytes of septic shock patients, which is associated with increased release of the gasdermin D (GSDMD) N-terminus. GSDMB expression and the accumulation of the N-terminal fragment of GSDMD are induced by the activation of the non-canonical pyroptosis pathway in a human monocyte cell line. The downregulation of GSDMB alleviates the cleavage of GSDMD and cell death. Consistently, the overexpression of GSDMB promotes GSDMD cleavage, accompanied by increased LDH release. We further found that GSDMB promotes caspase-4 activity, which is required for the cleavage of GSDMD in non-canonical pyroptosis, by directly binding to the CARD domain of caspase-4. Our study reveals a GSDMB-mediated novel regulatory mechanism for non-canonical pyroptosis and suggests a potential new strategy for the treatment of inflammatory diseases.
Riding the Waves of Work and Life: Explaining Long-Term Experiences with Work Hour Mismatches
Authors: Reynolds Jeremy , McKinzie Ashleigh Elain 
Published: October 2018

AbstractPaid work has become more precarious in the recent decades, prompting many conflicts between employers and employees, including struggles over work hours. To better understand these struggles, we provide the first examination of long-term experiences with work hour mismatches (i.e., gaps between the number of hours people prefer to work per week and the number of hours they actually work). Using sequence analysis and nearly two decades of data from the British Household Panel Study, we find heterogeneous but patterned experiences. Nearly everyone has an hour mismatch eventually (typically overemployment), and most people oscillate between having and not having hour mismatches. Existing theoretical accounts anticipate some hour mismatch sequences, but the data contradict several key predictions. Moreover, no account predicts the most dominant pattern: oscillating overemployment. We thus offer a new explanation, which proposes that hour mismatches usually come in waves but can be generated in different ways. Sometimes mismatches are caused by unstable work schedules. Other times, mismatches stem from inflexible work hours or job demands that intentionally or unintentionally prevent employees from altering their work hours to accommodate changing personal needs.
Activation of Parabrachial Nucleus Glutamatergic Neurons Accelerates Reanimation from Sevoflurane Anesthesia in Mice
Authors: Wang Tian-Xiao , Xiong Bo , Xu Wei , Wei Hao-Hua , Qu Wei-Min , Hong Zong-Yuan , Huang Zhi-Li 
Published: October 2018

Abstract

EDITOR’S PERSPECTIVE

What We Already Know about This Topic
The parabrachial nucleus is a brainstem region involved in arousal.
Brain regions involved in arousal regulate anesthetic induction and emergence.

What This Article Tells Us That Is New
Using chemogenetic techniques, activation of parabrachial nucleus glutamatergic neurons prolonged anesthetic induction and hastened emergence in mice. Inhibition of these neurons provided opposite effects.
Modulating the activity of arousal centers may provide an approach to controlling the duration of general anesthesia.

Background
The parabrachial nucleus (PBN), which is a brainstem region containing glutamatergic neurons, is a key arousal nucleus. Injuries to the area often prevent patient reanimation. Some studies suggest that brain regions that control arousal and reanimation are a key part of the anesthesia recovery. Therefore, we hypothesize that the PBN may be involved in regulating emergence from anesthesia.

Methods
We investigated the effects of specific activation or inhibition of PBN glutamatergic neurons on sevoflurane general anesthesia using the chemogenetic “designer receptors exclusively activated by designer drugs” approach. Optogenetic methods combined with polysomnographic recordings were used to explore the effects of transient activation of PBN glutamatergic neuron on sevoflurane anesthesia. Immunohistochemical techniques are employed to reveal the mechanism by which PBN regulated sevoflurane anesthesia.

Results
Chemogenetic activation of PBN glutamatergic neurons by intraperitoneal injections of clozapine-N-oxide decreased emergence time (mean ± SD, control vs. clozapine-N-oxide, 55 ± 24 vs. 15 ± 9 s, P = 0.0002) caused by sevoflurane inhalation and prolonged induction time (70 ± 15 vs. 109 ± 38 s, n = 9, P = 0.012) as well as the ED50 of sevoflurane (1.48 vs. 1.60%, P = 0.0002), which was characterized by a rightward shift of the loss of righting reflex cumulative curve. In contrast, chemogenetic inhibition of PBN glutamatergic neurons slightly increased emergence time (56 ± 26 vs. 87 ± 26 s, n = 8, P = 0.034). Moreover, instantaneous activation of PBN glutamatergic neurons expressing channelrhodopsin-2 during steady-state general anesthesia with sevoflurane produced electroencephalogram evidence of cortical arousal. Immunohistochemical experiments showed that activation of PBN induced excitation of cortical and subcortical arousal nuclei during sevoflurane anesthesia.

Conclusions
Activation of PBN glutamatergic neurons is helpful to accelerate the transition from general anesthesia to an arousal state, which may provide a new strategy in shortening the recovery time after sevoflurane anesthesia.
Estrogen Deficiency Exacerbates Intervertebral Disc Degeneration Induced by Spinal Instability in Rats
Authors: Liu Qi , Wang Xiaomeng , Hua Yue , Kong Ganggang , Wu Xiuhua , Huang Zhiping , Huang Zucheng , Liu Junhao , Yang Zhou , Zhu Qingan 
Published: October 2018

Study Design.
An experimental animal study of osteoporosis (OP) and intervertebral disc degeneration (IDD).

Objective.
The aim of this study was to clarify the effects of estrogen deficiency and supplement on cervical IDD induced by bilateral facetectomy in rats.

Summary of Background Data.
The relationship between IDD and OP is still controversy with the wide prevalence in aged people.

Methods.
Seventy-two Sprague–Dawley female rats were randomly divided into ovariectomy (OVX) group, facet joints resection of C4-6 (FR), FR–OVX group, estrogen replacement therapy (ERT, based on the FR-OVX group) group, and sham group. Specimens of C4-6 segment were harvested at 12 and 24 weeks. The microstructures of C5 vertebrae, vertebral endplate lesions and calcification, and IDD of C5/6 disc were evaluated by micro-computed tomography (micro-CT) and histology. The protein and gene levels of aggrecan, Col2α1, matrix metalloprotease (MMP)-3, and MMP-13 in the C5/6 and C4/5 discs were measured.

Results.
Microstructures of C5 vertebral body were weakened significantly after ovariectomy, while restored effectively with estradiol supplementation. The facetectomy led to significant IDD, and the IDD was aggravated when combined with OVX. The IDD of the ERT group was alleviated effectively and similar to that of the FR group in intervertebral disc height, vertebral endplate lesions and calcification, and disc degeneration scores. In addition, the estrogen supplement maintained the extracellular matrix by decreasing MMP-3 and MMP-13, and increasing aggrecan and Col2α1 expression.

Conclusion.
The present study demonstrated that estrogen deficiency exacerbated IDD induced by spinal instability, while estrogen supplementation alleviated the progression of disc degeneration related to osteoporosis.

Level of Evidence: N/A
Reconstruction of Medial Canthal Tendon Using Novel Suture Anchoring System: A Case Report
Authors: Kakudo Natsuko , Takegawa Masayasu , Hihara Masakatsu , Morimoto Naoki , Masuoka Hiromu , Kusumoto Kenji 
Published: October 2018

Summary:
For medial canthal tendon reattachment, many kinds of surgical technique have previously been reported. They are complicated and generally require technical skill and prolonged operating times. We, for the first time, describe a novel device, the Caraji Anchor Suture System, used for reattaching the medial canthal tendon to the medial orbital wall after removal of squamous cell carcinoma. The medial canthal tendon was excellently fixed with this rapid and simple method. No complications, such as local infection or exposure, have occurred up to the present. This technique appears to be safe, fast, and effective for reconstruction of the medial canthus after tendon avulsion or loss from excision of cutaneous carcinoma in plastic and reconstructive surgery.
Exploring the Hidden Functions of Nursing Bedside Shift Report
Authors: Manges Kirstin A. , Groves Patricia S. 
Published: October 2018

Background:
Implementing Nursing Bedside Shift Report (NBSR) is challenging for nurse leaders. Before implementing or improving NBSR, nurse leaders need a clear understanding of the process and functions of nursing shift report. However, the social-cultural latent functions (unrecognized or unintended uses) of NBSR are poorly understood.

Purpose:
The purpose of this qualitative study was to describe the latent functions of NBSR from the perspectives of frontline nurses.

Methods:
Thematic analysis of previously collected semistructured interviews with nurses (n = 13) about NBSR was used to explore NBSR's latent functions.

Results:
Three latent functions emerged; nurses used bedside shift report as a performance, ritual, and sensemaking opportunity. The latent functions are described, and corresponding recommendations for successful implementation of NBSR are provided.

Conclusions:
Nurse leaders can use this study's findings to inform the development or improvement of an efficient, effective, and sustainable NBSR process at their local institution.
A Prospective, Randomized, Blinded Trial Comparing Digital Simulation to Textbook for Cleft Surgery Education
Authors: Plana Natalie M. , Rifkin William J. , Kantar Rami S. , David Joshua A. , Maliha Samantha G. , Farber Scott J. , Staffenberg David A. , Grayson Barry H. , Diaz-Siso J. Rodrigo , Flores Roberto L. 
Published: October 2018

Background:
Simulation is progressively being integrated into surgical training; however, its utility in plastic surgery has not been well described. The authors present a prospective, randomized, blinded trial comparing digital simulation to a surgical textbook for conceptualization of cleft lip repair.

Methods:
Thirty-five medical students were randomized to learning cleft repair using a simulator or a textbook. Participants outlined markings for a standard cleft lip repair before (preintervention) and after (postintervention) 20 minutes of studying their respective resource. Two expert reviewers blindly graded markings according to a 10-point scale, on two separate occasions. Intrarater and interrater reliability were calculated using intraclass correlation coefficients. Paired and independent t tests were performed to compare scoring between study groups. A validated student satisfaction survey was administered to assess the two resources separately.

Results:
Intrarater grading reliability was excellent for both raters for preintervention and postintervention grading (rater 1, intraclass correlation coefficient = 0.94 and 0.95, respectively; rater 2, intraclass correlation coefficient = 0.60 and 0.92, respectively; p < 0.001). Mean preintervention performances for both groups were comparable (0.82 ± 1.17 versus 0.64 ± 0.95; p = 0.31). Significant improvement from preintervention to postintervention performance was observed in the textbook (0.82 ± 1.17 versus 3.50 ± 1.62; p < 0.001) and simulator (0.64 ± 0.95 versus 6.44 ± 2.03; p < 0.001) groups. However, the simulator group demonstrated a significantly greater improvement (5.81 ± 2.01 versus 2.68 ± 1.49; p < 0.001). Participants reported the simulator to be more effective (p < 0.001) and a clearer tool (p < 0.001), that allowed better learning (p < 0.001) than textbooks. All participants would recommend the simulator to others.

Conclusion:
The authors present evidence from a prospective, randomized, blinded trial supporting online digital simulation as a superior educational resource for novice learners, compared with traditional textbooks.
A Case of Tophaceous Pseudogout on 18F-FDG PET/CT Imaging
Authors: Shen Guohua , Su Minggang , Liu Bin , Kuang Anren 
Published: October 2018

AbstractA 53-year-old man with a 10-year history of gout was admitted to our hospital due to chronic low back pain. Initial CT examinations showed a high-density mass with bone destruction of bilateral facet joints at the L3 to L5 level. MRI findings also revealed lesion with the dural sac compression. On PET/CT, the juxta-articular mass of bilateral L3 to L5 facet joints showed abnormal FDG uptake with an SUVmaxof 4.2. The possible diagnosis may be gouty tophi; however, the biopsy revealed the diagnosis of calcium pyrophosphate dihydrate deposition disease, also referred to as pseudogout.
A Feasibility Study of a Multifaceted Walking Intervention to Maintain the Functional Mobility, Activities of Daily Living, and Quality of Life of Nursing Home Residents With Dementia
Authors: Chu Charlene H. , Puts Martine , Brooks Dina , Parry Monica , McGilton Katherine S. 
Published: October 2018

Abstract

Purpose
The aim of the study was to evaluate the feasibility, acceptability, and efficacy of a multifaceted walking intervention (MWI) aimed to maintain the functional mobility, activities of daily living function, and quality of life of long-term care home residents with dementia.

Design/Methods
A quasiexperimental time-series design was used. The 4-month intervention provided one-on-one walking 2–4 days a week, guided by an individualized communication care plan and interviews with collaterals and staff.

Results
The MWI was feasible based on high recruitment and adherence rates (86% and 94%, respectively) and highly acceptable to stakeholders. Residents (n = 25) showed significant improvements after the intervention: Timed Up-and-Go (−8.85 seconds, p = .00), Two-Minute Walk Test (27.47 m, p = .00), Functional Independence Measure (0.72, p = .00), and Alzheimer’s Disease-Related Quality of Life (2.44, p = .05).

Conclusion
The MWI was feasible and improved functional mobility compared to usual care.

Clinical Relevance
Physical activity delivered with a person-centered care was feasible and may be beneficial to mitigate decline in long-term care home residents with dementia.
Gene Expression of Neurotrophins and Their Receptors in Keloids
Authors: Petecof Rafael de Moraes , Gragnani Alfredo , Isoldi Felipe Contoli , Munoz Gibrán Elias Harcha , de Noronha Samuel Marcos Ribeiro , Corrêa Silvana Aparecida Alves , Ferreira Lydia Masako 
Published: October 2018

Abstract
The aim of this study was to assess gene expression of neurotrophins and their receptors in keloids. Skin samples of normal skin and keloids were obtained from patients in the control (n = 12) and keloid (n = 12) groups, respectively. Ribonucleic acid was extracted from the skin specimens, purified, evaluated by spectrophotometry, and used to synthesize complementary DNA. Real-time quantitative polymerase chain reaction analysis of 84 human neurotrophin genes and their receptors was performed. Twelve genes, including heat shock 27-kDa protein 1, gastrin-releasing peptide receptor, corticotropin-releasing hormone receptor 2, neuropeptide Y Y2 receptor, interleukin 6 signal transducer, nerve growth factor, metallothionein 3, B-cell chronic lymphocytic leukemia/lymphoma 2, cholecystokinin A receptor, persephin, galanin receptor 2, and fibroblast growth factor receptor 3, were down-regulated in keloid tissue compared with normal skin. The genes 27-kDa heat shock protein 1, gastrin-releasing peptide receptor, corticotropin-releasing hormone receptor 2, nerve growth factor, metallothionein 3, B-cell chronic lymphocytic leukemia/lymphoma 2, and persephin protein were considered priority genes associated with keloid formation.
Inferring linguistic transmission between generations at the scale of individuals
Authors: Thouzeau Valentin , Affholder Antonin , Mennecier Philippe , Verdu Paul , Austerlitz Frédéric 
Published: October 2018

AbstractHistorical linguistics strongly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we developed an approach inspired from population genetics to perform historical linguistic inferences from linguistic data sampled at the individual scale, within a population. We built four within-population demographic models of linguistic transmission over generations, each differing by the number of teachers involved during the language acquisition and the relative roles of the teachers. We then compared the simulated data obtained with these models with real contemporaneous linguistic data sampled from Tajik speakers from Central Asia, an area known for its large within-population linguistic diversity, using approximate Bayesian computation methods. Under this statistical framework, we were able to select the models that best explained the data, and infer the best-fitting parameters under the selected models. This demonstrates the feasibility of using contemporaneous within-population linguistic diversity to infer historical features of human cultural evolution.