bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of transcriptional regulation and functional genes induced by alkaline salt stress in roots of two switchgrass (Panicum virgatum L.) genotypes
Authors: Zhang Pan , Duo Tianqi , Wang Fengdan , Zhang Xunzhong , Yang Zouzhuan , Hu Guofu 
Published: August 2020

Abstract
Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here, we investigated the physiological responses and transcriptome changes in the roots of two switchgrass genotypes under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: The alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene transcription and regulation induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.
Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits
Authors: Yi Xinxin , Liu Jing , Chen Shengcai , Wu Hao , Liu Min , Xu Qing , Lei Lingshan , Lee Seunghee , Zhang Bao , Kudrna Dave , Fan Wei , Wing Rod , Yang Chunyan , Zhang Mengchen , Zhang Jianwei , Wang Xuelu , Chen Nansheng 
Published: August 2020

Abstract
BackgroundCultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.ConclusionsWe reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.
Telepsychiatry Adoption Across Hospitals in the United States: A Cross-Sectional Study
Authors: Li Zhong , Harrison Sayward E. , Li Xiaoming , Hung Peiyin 
Published: August 2020

Abstract
Background Access to psychiatric care is critical for patients discharged from hospital psychiatric units to ensure continuity of care. When face-to-face follow-up is unavailable or undesirable, telepsychiatry becomes a promising alternative. This study aimed to investigate hospital- and county-level characteristics associated with telepsychiatry adoption.Methods Cross-sectional national data of 3,475 acute care hospitals were derived from the 2017 American Hospital Association Annual Survey. Generalized linear regression models were used to identify characteristics associated with telepsychiatry adoption. Results About one-sixth (548 [15.8%]) reported having telepsychiatry. Rural noncore hospitals were less likely to adopt telepsychiatry (8.3%) than hospitals in rural micropolitan (13.6%) and urban counties (19.4%), with a wide variation across states. Hospitals with both outpatient and inpatient psychiatric care services (marginal difference [95% CI]: 16.0% [12.1% to 19.9%]) and hospitals only with outpatient psychiatric services (6.5% [3.7% to 9.4%]) were more likely to have telepsychiatry than hospitals with neither psychiatric services. Federal hospitals (48.9% [32.5% to 65.3%]), system-affiliated hospitals (3.9% [1.2% to 6.6%]), hospitals with larger bed size (Quartile IV vs. I: 6.2% [0.7% to 11.6%]), and hospitals with greater ratio of Medicaid inpatient days to total inpatient days (Quartile IV vs. I: 4.9% [0.3% to 9.4%]) were more likely to have telepsychiatry than their counterparts. Private non-profit hospitals (-6.9% [-11.7% to -2.0%]) and hospitals in counties designated as whole mental health professional shortage areas (-6.6% [-12.7% to -0.5%]) were less likely to have telepsychiatry. Conclusions Telepsychiatry adoption was low in US hospitals in 2017 with substantial variations by urban and rural status and by state. It raises concerns about access to psychiatric services and continuity of care for patients discharged from hospitals.
Patients Age is a Critical Factor in Determining the Severity of Osteoarthritis of the Shoulder
Authors: Märtens Nicole , Maerz Vincent , Bertrand Jessica , Lohmann Christoph H , Berth Alexander 
Published: August 2020

Abstract
Background: Osteoarthritis (OA) is one of the most common musculoskeletal disorders in the aging population. The correlation of radiographic OA severity, disability and pain is variable and inconsistent for the different joints. This study aims to elucidate the relationship between histological and radiological signs of shoulder OA with pain sensation and functional impairment to potentially adapt the recommendation for surgical treatment for primary total shoulder arthroplasty (TSA). Methods: Forty-four patient with shoulder OA undergoing a TSA using an anatomic stemless implant were included in this study. The radiological OA severity was scored preoperatively on true ap X-rays according to the Kellgren-Lawrence-Score (KL-Score). The histological OA severity was determined according to the OARSI-Score using bone-cartilage sections from loaded areas of the humeral head. Pain was quantified with the Visual Analog Scale (VAS). The functional status was assessed by the items “mobility” and “strength” out of the Constant-Murley-Score (CS-Score). Results: There was no correlation between radiographic and histological severity in shoulder OA. However, a correlation between age and the severity of radiological changes was observed. Further, pain did not correlate with histological or radiological scores, whereas it correlated with age. The functional shoulder status (mobility, strength) correlated with the severity of radiological changes, but not with the histologic scoring. Conclusion: This study shows that increased age is the main determinant of radiological changes in shoulder OA, as well as pain. Therefore, age and pain sensation should be considered as important parameters for the recommendation for TSA.
Can Thoracolumbar Deformity Improve if Surgery Just for Lumbar Stenois Syndrome in Degenerative Thoracolumbar Kyphosis Patients ?
Authors: Meng Fanqi , Bao Xianguo , Xu Shuai , Liang Yan , Liu Haiying 
Published: August 2020

Abstract
Background: Fusion across thoracolumbar spine or not for degenerative thoracolumbar kyphosis (DTLK) in lumbar stenois syndrome (LSS) remains controversial. The influencing factors for postoperative TLK in this group have not been determined yet. So the study was to explore whether DTLK could improve with only surgery for lumbar stenois syndrome LSS and identify influencing factors on postoperative TLK.Methods: The study was performed from January 2016 to December 2018. 69 participants (25 male) diagnosed LSS with DTLK were enrolled and surgery was only for LSS. Radiological parameters included TLK, lumbar lordosis (LL), pelvic incidence (PI), pelvic tilt (PT), sacral slope (SS) and osteoporosis. Clinical outcomes were visual analogue scale (VAS) and Oswestry disability index (ODI). According to lower instrumented vertebrae (LIV) on L5 or S1, inter-group comparisons were performed between LIV on L5 (L5 group) and S1 (S1 group).Results: Demographics was well-matched between L5 and S1 group with a mean follow-up of 24.3±12.1 (m). TLK improved with a mean of 16.2±7.6 (°) (P <0.001). It was insignificant on radiological and clinical parameters between L5 and S1 groups except a larger PT in S1 group (P=0.046). VAS (P=0.787) and ODI (P=0.530) were both indifference between normal TLK and DTLK at last (P˃0.05). Postoperative TLK was affected by osteoporosis and SS, the latter was determined by PI and PT. Osteoporosis was the risk factor for TLK correction (P=0.001, OR=9.58).Conclusions: DTLK get improved if suegery only performed for LSS. TLK and clinical outcomes are comparable between L5 and S1 groups. Severe osteoporosis can impede TLK correction.
A qualitative study on midwives’ identity and perspectives on the occurrence of disrespect and abuse in Maputo city
Authors: Galle Anna , Manaharlal Helma , Griffin Sally , Osman Nafissa , Roelens Kristien , Degomme Olivier 
Published: August 2020

Abstract
BACKGROUND
Midwifery care plays a vital role in the reduction of preventable maternal and newborn mortality and morbidity. There is a growing concern about the quality of care during facility based childbirth and the occurrence of disrespect and abuse (D&A) worldwide. While several studies have reported a high prevalence of D&A, evidence about the drivers of D&A is scarce.
AIM
This study aims to explore midwives’ professional identity and perspectives on the occurrence of D&A in urban Mozambique.
METHODS
A qualitative study took place in the central hospital of Maputo, Mozambique. Nine focus group discussions with midwives were conducted, interviewing 56 midwives. RQDA software was used for analyzing the data by open coding and thematic analysis.
RESULTS
Midwives felt proud of their profession but felt they were disrespected by the institution and wider society because of their inferior status compared to doctors. Furthermore, they felt being blamed for poor health outcomes. The occurrence of D&A seemed more likely in emergency situations but midwives tended to blame this on women being “uncooperative”. The involvement of birth companions was a protective factor against D&A together with supervision.
Conclusion
In order to improve quality of care and reduce the occurrence of D&A midwives will need to be treated with more respect within the health system. Furthermore, they should be trained in handling obstetric emergency situations with respect and dignity for the patient. Systematic and constructive supervision might be another promising strategy for preventing D&A.
The Relationship Between microRNA-195 and the Prognosis of Cervical Cancer
Authors: Cao Shuangqing , Zheng Lei 
Published: August 2020

Abstract
Background: MicroRNA-195 (miR-195), a tumor suppressor, had reported to be involved in carcinogenesis and the progression of some cancers. However, the prognostic value of miR-195 in cervical cancer remained unclear. The purpose of this study was to detect the expression of miR-195 in cervical cancer tissues and to investigate its correlation with tumor progression and prognosis.Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the relative mRNA expression of miR-195 in cervical cancer tissues and corresponding adjacent normal tissues. The relationship between miR-195 expression and clinical characteristics of patients was analyzed by chi-square test. Kaplan-Meier method was applied to compare the overall survival, and the prognostic value of miR-195 was estimated via cox regression analysis.Results: Compared with normal tissues, miR-195 expression was significantly down-regulated in cervical cancer tissues (P < 0.001). Importantly, decreased expression of miR-195 was closely associated with FIGO stage, lymph node metastasis and vascular invasion (P < 0.05). Additionally, Kaplan-Meier analysis indicated that patients with high miR-195 expression had obviously longer overall survival than those with low miR-195 expression (log rank test, P = 0.001). And miR-195 was an independent prognostic factor of cervical cancer patients via univariate and multivariate cox regression analyses.Conclusions: Decreased expression of miR-195 is associated with the progression of cervical cancer. And miR-195 may have potency to predict the prognosis of cervical cancer.
Aurora-B Knockdown Inhibits Osteosarcoma Metastasis by Inducing Autophagy via the mTOR/ULK1 Pathway
Authors: Wu Xin , Liu Jia-ming , Song Honghai , Yang Qikun , Ying Hui , Tong Weilai , Zhou Yang , Liu Zhi-li 
Published: August 2020

Abstract
Background
Autophagy plays an essential role in metastasis of malignancies. Although our studies showed that Aurora-B facilitate pulmonary metastasis in OS, the mechanism of Aurora-B kinase on autophagy and metastasis in OS has not been explored.
Methods
Clinical-pathological parameters and follow-up information was collected in OS patients. Immunohistochemical staining was performed to detect Aurora-B and LC3 protein in OS tissues. Short hairpin RNA transfection was used to silence Aurora-B in OS cells. Real-time quantitative PCR (RT-qPCR) was performed to detect Aurora-B mRNA expression in OS cells. Aurora-B and autophagy related protein were measured by Western blot. Transmission electron microscopy and laser scanning confocal microscopy were performed to observe the formation of autophagosomes and autolysosomes. Migratory and invasive ability of OS cells were measured by Wound healing and transwell assays. Orthotopic xenograft model was used to evaluate the effect of autophagy mediated by Aurora-B inhibition on pulmonary metastasis of OS.
Results
The elevated expression of Aurora-B protein in OS tissues negatively associated with the overall survival of OS patients. Further investigation has found that Aurora-B expression was negatively correlative with autophagy related protein LC3 in OS patient tissues. Knockdown Aurora-B stimulates autophagy and inhibits migratory and invasive ability of OS cells. Mechanistically, Aurora-B knockdown suppressed the mTOR/ULK1 signaling pathway and reactivation of the mTOR/ULK1 pathway decreased autophagy level. Furthermore, the inhibition effect of silencing Aurora-B on migration and invasion of OS was reversed by chloroquine and mTOR activator in vitro and vivo.
Conclusions
Our results suggest that silencing of Aurora-B stimulate autophagy via decreasing mTOR/ULK1 and result in inhibiting OS metastasis. Targeted Aurora-B/mTOR/ULK1 pathway may be a promising treatment strategy for OS patients.
Identification and Validation of a Predictive Immune-related Genes Signature for the Prognosis of Cholangiocarcinoma
Authors: Zhang Rui , Chen Chen , Li Qi , Fu Jialu , Zhang Dong , Li Wenzhi , Geng Zhimin 
Published: August 2020

Abstract
Background: Immune-related genes (IRGs) play a crucial role in the initiation and progression of cholangiocarcinoma (CCA). However, immune signatures have rarely been used to predict prognosis of CCA. The aim of this study was to construct a novel model for CCA to predict survival based on IRGs expression data.Methods: The gene expression profiles and clinical data of CCA patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were integrated to establish and validate prognostic IRG signatures. Differentially expressed immune-related genes were screened. Univariate and multivariate Cox analysis were performed to identify prognostic IRGs, and the risk model that predicts outcomes was constructed. Furthermore, receiver operating characteristic (ROC) and Kaplan-Meier curve were plotted to examine predictive accuracy of the model, and a nomogram was constructed based on IRGs signature, combining with other clinical characteristics. Finally, CIBERSORT was used to analyze the association of immune cells infiltration with risk score.Results: We identified that 223 IRGs were signiﬁcantly dysregulated in patients with CCA, among which five IRGs (AVPR1B, CST4, TDGF1, RAET1E and IL9R) were identified as robust indicators for overall survival (OS), and a prognostic model was built based on the IRGs signature. Meanwhile, patients with high risk had worse OS in training and validation cohort, and the area under the ROC was 0.898 and 0.846, respectively. Nomogram demonstrated that immune risk score contributed much more points than other clinicopathological variables, with a C-index of 0.819 (95% CI, 0.727-0.911). Finally, we found that IRGs signature was positively correlated with the proportion of CD8+ T cells, neurophils and T gamma delta, while negatively with that of CD4+ memory resting T cells.Conclusions: We established and validated an effective five IRGs-based prediction model for CCA, which could accurately classify patients into groups with low and high risk of poor prognosis.
Identification of Metabolism-associated Genes and Construction of a Prognostic Signature in Bladder Cancer
Authors: Shen Chengquan , Liu Jing , Wang Liping , Liang Zhijuan , Niu Haitao , Wang Yonghua 
Published: August 2020

Abstract
Background
Bladder cancer (BC) is a commonly diagnosed malignant tumor in the urinary system, with a high morbidity and recurrence rate. Current studies indicated that metabolism-associated genes (MAGs) having critical roles in the etiology of BC. The present study aims to identify differentially expressed MAGs and construct a MAGs prognostic risk signature in BC by using The Cancer Genome Atlas (TCGA) database and proteomics data.
Methods
RNA-sequence data from the TCGA database and proteomics were used to identify differentially expressed MAGs and construct a prognostic MAGs signature in BC. Subsequently, survival analysis and nomogram were used to evaluate the prognostic and predictive value of the MAGs model in BC. RNA isolation and reverse transcription‑quantitative PCR (RT-qPCR) was further performed to investigate the expression levels of MAGs in BC cell lines and explore the relationship between MAGs and M2 tumor associated macrophages (TAMs) secreted TGF-beta 1 in BC.
Results
A total of 23 differentially expressed MAGs were identified and five MAGs were finally used to construct a MAGs based signature. Survival analysis revealed that the MAGs based signature was closely correlated with the survival outcomes of patients with BC. A nomogram with the MAGs based signature risk score and clinical features also constructed to facilitate the individualized prediction of BC patients. RT-qPCR showed that four MAGs were significantly elevated and the expression levels of three MAGs were positively correlated with M2 TAM secreted TGF-β1 in T24 cells.
Conclusions
Our study identified novel prognostic MAGs and constructed a MAGs based signature, which can be used as an independent signature in evaluating the prognosis of patients with BC. Furthermore, M2 TAMs may promote the expression of three MAGs via TGF-β1 signaling pathway. Further clinical trials and experimental exploration are needed to validate our observations in BC.
CBX3 Regulated by miR-139 Promoted the Development of HCC by Regulating Cell Cycle Progression
Authors: Zhang Pan , Yang Xiaoyan , Zha Zhongming , Zhu Yumeng , Zhang Guoqiang , Li Guotao 
Published: August 2020

Abstract
Background Hepatocellular carcinoma (HCC), comprises of the major primary liver cancer, is one of the most lethal malignancies in the world [1]. Increasing evidence has demonstrated that chromobox protein homolog 3 (CBX3) functioned as an oncogene in different cancers. However, its expression profiles and biological functions in HCC remain exactly unknown. Methods Data of CBX3 expression in HCC acquired from TCGA and GEO databases were analyzed. The biological functions of CBX3 in HCC were examined by in vitro experiments. Bioinformatics analysis, qRT-PCR and western blot were performed to explpore the mechanism of CBX3 involved in HCC. Results CBX3 mRNA was upregulated in HCC tissues, and overexpression of CBX3 mRNA was negatively correlated with malignancies and poor prognosis in HCC patients. Knocking down of CBX3 induced slower growth, less migration and fewer invasions of the HCC cells in vitro. Moreover, bioinformatics analysis and experimental observation indicated that CBX3 expression was correlated with cell cycle regulation proteins of HCC cells. Finally, Starbase predicted that the miR-139 could directly target CBX3 in HCC; Confirmatory experiments verified that miR-139 overexpression attenuated the HCC cells proliferation and migration, which could be reversed by overexpressing CBX3 concurrently. Conclusion Our results concluded that miR-139/CBX3 axis may involve in the HCC development through regulating cell cycle progression and may be a promising target in the treatment of HCC.
Patients with Pretreatment Leukoencephalopathy and Older Patients have More Cognitive Decline after Whole Brain Radiotherapy
Authors: Chan Matthew , Ferguson David , Mhurchu Elaine Ni , Yuan Ren , Gondara Lovedeep , McKenzie Michael , Olson Robert , Thiessen Brian , Lalani Nafisha , Ma Roy , Nichol Alan 
Published: August 2020

Abstract
Purpose: To investigate predictors of cognitive decline after whole brain radiotherapy (WBRT) for brain metastases. Methods: A secondary analysis of a phase 2 clinical trial was conducted in patients who received stereotactic radiosurgery for 1-10 brain metastases and WBRT (NCT01046123). The Montreal Cognitive Assessment (MoCA) was performed at baseline and every three months after WBRT. Baseline T2-weighted fluid attenuation inversion recovery magnetic resonance imaging was independently assessed by two neuroradiologists for the presence of white matter hyperintensities (WMH) using the Fazekas visual rating scale. WMH were also manually segmented for volumetric analysis. Univariable and multivariable logistic regression were used to test the association between baseline variables and MoCA score decline. Results: Forty-six patients survived ≥3 months after treatment. Age (OR 1.12 (1.04 – 1.21, p < 0.01), baseline WMH volume (OR 1.20, 95% CI 1.06 – 1.52, p = 0.02) and baseline Fazekas score ≥ 3/6 (OR 6.4, 95% CI 1.7 – 24.7, p < 0.01) were predictive of MoCA score decline. In multivariable analysis, age was the only significant predictor of MoCA decline. However, all three patients with pretreatment leukoencephalopathy (Fazekas score = 6/6) had notable adverse outcomes due to cognitive impairment: one required full-time home nursing support and two were institutionalized. Conclusion: A greater decline in cognition after WBRT was observed in older patients and patients with a higher baseline WMH burden. Although this study is small, we propose that a Fazekas score of 6 should be a relative contraindication to WBRT. Trial Registration: clinicaltrials.gov identifier NCT01046123. First posted January 11, 2010. https://clinicaltrials.gov/ct2/show/NCT01046123