bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting species distributions: unifying model selection and scale optimization for multi‐scale occupancy models
Authors: Stevens Bryan S. , Conway Courtney J. 
Published: May 2019

AbstractGeographic distributions are a basic component of a species’ ecology, and predicting distributions is a fundamental task of conservation and resource management. Reliable prediction depends on identification of appropriate scales of effect for environmental data, and scale‐optimization techniques are thus desirable to identify optimal scales for predictor variables. Recent statistical developments have also advanced methods of model selection based explicitly on predictive ability, which differ from commonly used methods that regulate model structures via anticipated predictive performance. Such methods are beginning to permeate into species distribution models (SDMs), yet there remains no consensus methodology for developing optimally predictive multi‐scale SDMs when covariate data are collected over a range of scales. Thus, we compared the performance of common approaches for scale optimization and model selection in terms of their ability to produce optimally predictive multi‐scale Bayesian occupancy models for predicting a species distribution, using models of the breeding distribution for King Rails (Rallus elegans) as a case study. Our results demonstrate sizable gains in predictive performance for hierarchical occupancy models selected via their ability to predict out‐of‐sample data using the logarithmic scoring rule, as compared to models selected using information criteria (deviance information criteria [DIC] and Watanabe information criteria [WAIC]). Information criteria commonly selected individual covariates, as well as scales of effect for those covariates, with suboptimal predictive performance. Performance of models selected using the logarithmic scoring rule was also robust across the method of scale optimization, which was not true for models selected using DIC and WAIC. Thus, we demonstrate empirical benefits of study designs and statistical tools that enable covariate and scale selection based explicitly on predictive ability. Our results also imply that more careful consideration of what constitutes an optimal scale is warranted in many ecological applications, as the meaning of optimal is not independent of the technique used for scale selection.
Divergent memory responses driven by adenoviral vectors are impacted by epitope competition
Authors: Colston Julia M , Hutchings Claire , Chinnakannan Senthil , Highton Andrew , Perez‐Shibayama Christian , Ludewig Burkhard , Klenerman Paul 
Published: May 2019

AbstractAdenoviral vectors induce robust epitope‐specific CD8+ T cell responses. Within the repertoire of responses generated both conventional memory evolution and the phenomenon of memory inflation are seen. The rules governing which epitopes inflate are not fully known, but may include a role for both antigen processing and competition. To investigate this, we looked at memory generated from vectors targeting the Gp33‐41 (KAVYNFATC/K9C) epitope from the gp of lymphocytic choriomeningitis virus (LCMV) in mice. This well‐described epitope has both the Gp33‐41 and Gp34‐41 epitopes embedded within it. Vaccination with a full‐length gp or a minigene Ad‐Gp33/K9C vector‐induced conventional memory responses against the immunodominant Gp33/K9C epitope but a strong inflationary response against the Gp34/A8C epitope. These responses showed sustained in vivo function, with complete protection against LCMV infectious challenge. Given the unexpected competition between epitopes seen in the minigene model, we further tested epitope competition using the full‐length Ad‐LacZ (β‐galactosidase) model. Generation of an Ad‐LacZ vector with a single amino acid disruption of the inflationary β‐gal96‐103/D8V epitope transformed the β‐gal497‐504/I8V epitope from conventional to inflationary memory. This work collectively demonstrates the importance of epitope competition within adenoviral vector inserts and is of relevance to future studies using adenoviral vectored immunogens.
New statistical methods for the comparison and characterization of particle shape
Authors: Graham David J. , Gadsden Richard J. 
Published: May 2019

AbstractThis paper presents novel methods for robust statistical testing of particle shape data. Shape (the relative lengths of three orthogonal axes) is a key property of sedimentary particles, providing information on provenance, transport history and depositional environment. However, the usefulness of shape data, including the ability to make robust comparisons between samples, has been constrained by the absence of a satisfactory definition of the mean shape for a sample of particles. Such a definition is proposed and used to develop confidence regions for the population mean shape using both parametric (theoretical) and computational (bootstrap) methods. These techniques are based on a transform that permits multivariate statistical methods for the analysis of compositional data to be extended to shape. These techniques are validated with reference to a dataset of 169 clast samples and found to perform well. A statistical test on the mean – using the multivariate extension of Student's t‐test, Hotelling's T2 – is presented. The benefits of the methods presented are demonstrated with reference to a case study. © 2019 John Wiley & Sons, Ltd.
Microglia suppress the secondary progression of autoimmune encephalomyelitis
Authors: Tanabe Shogo , Saitoh Shohei , Miyajima Hisao , Itokazu Takahide , Yamashita Toshihide 
Published: May 2019

AbstractSecondary progressive multiple sclerosis (SPMS) is an autoimmune disease of the central nervous system (CNS) characterized by progressive motor dysfunction, sensory deficits, and visual problems. The pathological mechanism of SPMS remains poorly understood. In this study, we investigated the role of microglia, immune cells in the CNS, in a secondary progressive form of experimental autoimmune encephalomyelitis (EAE), the mouse model of SPMS. We induced EAE in nonobese diabetic mice and treated the EAE mice with PLX3397, an antagonist of colony stimulating factor‐1 receptor, during secondary progression in order to deplete microglia. The results showed that PLX3397 treatment significantly exacerbated secondary progression of EAE and increased mortality rates. Additionally, histological analysis showed that PLX3397 treatment significantly promoted inflammation, demyelination, and axonal degeneration. Moreover, the number of CD4+ T cells in the spinal cord of EAE mice was expanded due to PLX3397‐mediated proliferation. These results suggest that microglia suppressed secondary progression of EAE by inhibiting the proliferation of CD4+ T cells in the CNS.
Patterns of care and survival impact of adjuvant chemoradiotherapy for oropharyngeal cancer with intermediate‐risk features
Authors: Goel Alexander N. , Sangar Sophia , Mukdad Laith , Heaton Chase M. , Ryan William R. , Wang Marilene B. , Long Jennifer L. , St. John Maie A. 
Published: May 2019

AbstractBackgroundSurvival outcomes for adjuvant chemoradiotherapy (aCRT) and adjuvant radiotherapy (aRT) were compared in patients with oropharyngeal squamous cell carcinoma (OPSCC) with intermediate‐risk features.MethodsWe identified 2164 patients with OPSCC in the National Cancer Database without positive margins or extracapsular extension and with at least one intermediate‐risk feature: pT3‐T4 disease, ≥two positive lymph nodes, level IV/V nodal disease, and/or lymphovascular invasion. We assessed predictors of aCRT use and covariables impacting overall survival.ResultsaCRT was commonly used for both human papillomavirus (HPV)‐positive (62.0%) and HPV‐negative (64.3%) patients with OPSCC. Higher N stage, level IV/V neck disease, and younger age strongly predicted aCRT utilization. There was no significant survival benefit associated with aCRT vs aRT in HPV‐positive (hazard ratio [HR], 0.93; 95% confidence interval [CI], 0.62‐1.38; P = .71) or HPV‐negative (HR, 0.75; 95% CI, 0.51‐1.10; P = .15) disease.ConclusionsDespite high rates of utilization, aCRT is not associated with better survival vs aRT for OPSCC with intermediate‐risk features, including HPV‐negative tumors.
Quality Measures, All‐Cause Mortality, and Health Care Use in a National Cohort of Veterans With Cirrhosis
Authors: Serper Marina , Kaplan David E. , Shults Justine , Reese Peter P. , Beste Lauren A. , Taddei Tamar H. , Werner Rachel M. 
Published: May 2019

Decompensated cirrhosis is associated with high morbidity and mortality. However, no standardized quality measures (QMs) have yet been adopted widely. The Veterans Affairs (VA) Advanced Liver Disease Technical Advisory Group recently developed a set of six internal QMs to guide quality improvement efforts in cirrhosis in the domains of access to care, hepatocellular carcinoma surveillance, variceal surveillance, quality of inpatient care for upper gastrointestinal bleeding, and cirrhosis‐related rehospitalizations. We aimed to (1) quantify adherence to cirrhosis QMs and (2) determine whether adherence was associated with all‐cause mortality and health care use within a large national cohort of veterans with cirrhosis. We performed a retrospective study using data from the Veterans Outcomes and Costs Asociated with Liver Disease cohort of 121,129 patients newly diagnosed with cirrhosis from January 1, 2008, to December 31, 2016, at 128 VA facilities. The mean follow‐up time was 2.7 years (interquartile range, 1.1‐5.1 years). Adherence to outpatient access to specialty care was 71%, variceal surveillance was 32%, and early postdischarge care was 54%. In adjusted analyses, outpatient access to specialty care (hazard ratio [HR], 0.80; 95% confidence interval [CI], 0.78‐0.82), hepatocellular carcinoma surveillance (HR, 0.92; 95% CI, 0.90‐0.95), variceal surveillance (HR, 0.93; 95% CI, 0.89‐0.99), and early postdischarge care (HR, 0.57; 95% CI, 0.54‐0.60) were associated with lower all‐cause mortality. Readmissions after 30 days (HR, 1.53; 1.46‐1.60) and 90 days (HR, 1.88; 95% CI, 1.54‐1.70) were associated with higher all‐cause mortality. Higher adherence to QMs was also associated with lower inpatient health care use. Conclusion: Five of the six proposed VA cirrhosis QMs were measurable using existing data sources, associated with mortality and health care use, and may be used to guide future quality improvement efforts in cirrhosis.
Using sediment rating parameters to evaluate the changes in sediment transport regimes in the middle Yellow River basin, China
Authors: Zhang Shiyan , Chen Dong , Chen Li , Chen Xiaobing , He Li 
Published: May 2019

AbstractThis study analyses the changes in sediment transport regimes in the middle Yellow River basin (MYRB) using sediment rating parameters. Daily streamflow and suspended sediment concentration data were collected at 35 hydrological stations from the 1950s to 2016, which can be divided into three periods based on the type and intensity of human activities: the base stage before 1970, the restraining stage from 1971 to 1989, and the restoration stage after 2002. Data within each period were fitted by log‐linear sediment rating curves and the sediment rating parameters were utilized to analyse the spatial and temporal variations in sediment transport regimes. The results show that sediment rating parameters are indicative of sediment transport regimes. In the base stage and the restraining stage, the hydrological stations can be categorized into four groups based on their locations on the rating parameter plot. The stations with small drainage basins were characterized by the highest sediment transport regime, followed by those located in the coarse‐particle zone, the loess zone, and the mountainous/forest zone. In the restoration stage, the difference in sediment transport regimes between different geomorphic zones became less distinguishable than in previous stages. During the transition from the base stage to the restraining stage, sediment rating parameters showed no significant changes in sediment transport regimes in all four geomorphic groups. During the transition from the restraining stage to the restoration stage, significant changes were observed in the coarse‐particle zone and the mountain/forest zone, indicating that the revegetation programme and large reservoirs imposed a stronger influence on sediment transport regimes in these two zones than in the rest of the MYRB. This study provides theoretical support for evaluating sediment transport regimes with sediment rating parameters.
Quantum Dots Based Photocatalytic Hydrogen Evolution
Authors: Fan Xiang‐Bing , Yu Shan , Hou Bo , Kim Jong Min 
Published: May 2019

AbstractPhotocatalytic production of hydrogen from water can directly convert solar energy into chemical energy storage, which has significant advantages and great promise. As an emerging photosensitizer, the efficiency of quantum dots (QDs) based artificial photosynthetic system have made breakthroughs. In this review, we will give a summary of the development of QDs based photocatalytic hydrogen evolution in these years. First, we highlight different types of hydrogen evolution catalyst combined with QDs; then we focus on the surface modification and heterostructure formation of QDs to improve the photocatalytic efficiency, respectively. In the end, we will propose some Cd‐free QDs and future development of photocatalytic hydrogen evolution.
Elevated BMP and Mechanical Signaling Through YAP1/RhoA Poises FOP Mesenchymal Progenitors for Osteogenesis
Authors: Stanley Alexandra , Heo Su-jin , Mauck Robert L , Mourkioti Foteini , Shore Eileen M 
Published: May 2019

ABSTRACT
Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease characterized by the formation of extraskeletal bone, or heterotopic ossification (HO), in soft connective tissues such as skeletal muscle. All familial and sporadic cases with a classic clinical presentation of FOP carry a gain-of-function mutation (R206H; c.617 G &gt; A) in ACVR1, a cell surface receptor that mediates bone morphogenetic protein (BMP) signaling. The BMP signaling pathway is recognized for its chondro/osteogenic-induction potential, and HO in FOP patients forms ectopic but qualitatively normal endochondral bone tissue through misdirected cell fate decisions by tissue-resident mesenchymal stem cells. In addition to biochemical ligand-receptor signaling, mechanical cues from the physical environment are transduced to activate intracellular signaling, a process known as mechanotransduction, and can influence cell fates. Utilizing an established mesenchymal stem cell model of mouse embryonic fibroblasts (MEFs) from the Acvr1R206H/+ mouse model that mimics the human disease, we demonstrated that activation of the mechanotransductive effectors Rho/ROCK and YAP1 are increased in Acvr1R206H/+ cells. We show that on softer substrates, a condition associated with low mechanical signaling, the morphology of Acvr1R206H/+ cells is similar to the morphology of control Acvr1+/+ cells on stiffer substrates, a condition that activates mechanotransduction. We further determined that Acvr1R206H/+ cells are poised for osteogenic differentiation, expressing increased levels of chondro/osteogenic markers compared with Acvr1+/+ cells. We also identified increased YAP1 nuclear localization in Acvr1R206H/+ cells, which can be rescued by either BMP inhibition or Rho antagonism. Our results establish RhoA and YAP1 signaling as modulators of mechanotransduction in FOP and suggest that aberrant mechanical signals, combined with and as a result of the increased BMP pathway signaling through mutant ACVR1, lead to misinterpretation of the cellular microenvironment and a heightened sensitivity to mechanical stimuli that promotes commitment of Acvr1R206H/+ progenitor cells to chondro/osteogenic lineages.
Effect of microRNA‐27a‐5p on apoptosis and inflammatory response of pancreatic acinar cells in acute pancreatitis by targeting PTEN
Authors: Kong Lei , Wu Qinghua , Zhao Liangchao , Ye Jinhua , Li Nengping , Yang Huali 
Published: May 2019

AbstractTo investigate the apoptosis and inflammatory response of microRNA‐27a‐5p (miR‐27a‐5p) in pancreatic acinar cells of acute pancreatitis (AP) and its related mechanisms. Rat pancreatic acinar cell line AR42J was treated with caerulein (10nmol/L) to construct an acute pancreatitis cell model. Quantitative real‐time polymerase chain reaction was performed to measure the expression of miR‐27a‐5p; The miR‐27a‐5p mimic was transfected into cell, and the apoptosis rate of the cells was detected by flow cytometry; The levels of TNF‐α, IL‐1, and IL‐6 in the culture supernatant were determined by enzyme‐linked immunosorbent assay; TargetScans database predicted and dual luciferase reporter gene assay verified the relationship between miR‐27a‐5p and the phosphatase and tensin homolog deleted on chromosome 10 (PTEN); The recovery experiment explored the apoptosis and the effects of inflammatory responses. The expression of miR‐27a‐5p decreased gradually (P < 0.05) and the expression of PTEN increased gradually (P < 0.05) with the prolongation of acting time. Upregulation of miR‐27a‐5p significantly promoted cell apoptosis (P < 0.05) and inhibited inflammatory response (P < 0.05); The TargetScans database predicted that the 3'UTR of PTEN contains a base complementary to the miR‐27a‐5p seed region. Cotransfection of wild‐type vector (PTEN‐WT) with miR‐27a‐5p mimic or miR‐27a‐5p inhibitor significantly affected the relative activity of luciferase (P < 0.05), and no significant impact was observed in mutant PTEN‐MUT. Compared with miR‐27a‐5p + pcDNA group, transfection of miR‐27a‐5p mimic and pcDNA‐PTEN significantly increased the expression of PTEN (P < 0.05), decreased the apoptotic rate (P < 0.05), and increased the inflammatory response (P < 0.05). miR‐27a‐5p induced apoptosis and inhibited the inflammatory response of pancreatic acinar cells in AP by targeting PTEN.
Polydatin enhances the chemosensitivity of osteosarcoma cells to paclitaxel
Authors: Zhao Weijia , Chen Zonghan , Guan Meng 
Published: May 2019

AbstractDespite improvements in the prognosis of osteosarcoma patients, chemotherapy fails in a considerable number of cases due to drug resistance. The development of novel agents may enhance chemosensitivity. This study explored the anticancer function of polydatin and its ability—in combination with paclitaxel—to overcome drug resistance in human osteosarcoma U‐2OS and MG‐63 cell lines. A cell proliferation assay (celll counting kit‐8), a cell‐cycle assay, an apoptosis assay (annexin V‐fluorescein isothiocyanate/propidium iodide), and a cell migration assay (Transwell) were used to analyze cell activity. Western blot analysis and quantitative reverse‐transcription polymerase chain reaction were performed to examine function‐related mRNA and protein levels. Treatment with polydatin suppressed cell growth and migration in both cell lines. Moreover, polydatin induced cell apoptosis in both parental and paclitaxel‐resistant cells, and cell‐cycle arrest in the S phase. Furthermore, it altered the expression of various proteins associated with cell growth (Ki67, p21, cyclin A, cyclin E, and cyclin‐dependent kinase 2), migration (matrix metalloproteinase‐2 [MMP‐2], MMP‐9, and tissue inhibitor of metalloproteinase‐1), apoptosis (poly[ADP‐ribose] polymerase 1 and caspase 3), and drug resistance (p‐glycoprotein 1, lung resistance‐related protein 1, growth arrest and DNA damage‐45α, glutathione S‐transferase π, and heat shock protein 27) in paclitaxel‐resistant osteosarcoma cells. Cells transfected with myr‐Akt caused obvious upregulation and activation of Akt, which were significantly attenuated via polydatin treatment. In conclusion, polydatin may enhance the chemosensitivity of osteosarcoma cells to paclitaxel.
Whole transcriptome analysis of diabetic nephropathy in the db/db mouse model of type 2 diabetes
Authors: Wen Li , Zhang Zheng , Peng Rui , Zhang Luyu , Liu Handeng , Peng Huimin , Sun Yan 
Published: May 2019

AbstractWhole‐transcriptome analysis using RNA sequencing (RNA‐seq) affords broader insights about gene expression regulatory networks in diabetic nephropathy (DN). To better explore the molecular basis of DN, kidney tissue from db/db DN model mice and control mice were submitted to RNA‐seq analysis. Thousands of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) were found to be significantly differentially expressed in the DN group relative to the control group. To research the regulatory mechanism of these lncRNAs and mRNAs, the integrated co‐expression networks were constructed for 322 mRNAs and 27 lncRNAs that revealed significantly correlated expression patterns in DN. The potential roles of these co‐expressed mRNAs were classified by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The co‐expression networks involved 27 lncRNAs interacting with 38 key mRNAs related to metabolic processes, including ND4/4L, Ndufa2/5, Ndufb4/7, Ndufs3, Uqcrc1, Aco2, Alad, Alas1, Alpl, Atp5j2, Coq5, Coq6, Cth, and CytB, all of which are highly related to encoding subunits of the mitochondrial complexes. Thus, mitochondrial dysfunction could result in renal function decline in DN. Seven dysregulated lncRNAs and nine dysregulated mRNAs in the DN model were confirmed by quantitative real‐time polymerase chain reaction. The lncRNA‐mRNA co‐expression network provides novel evidence to support the contention that metabolic changes are associated with metabolic reprogramming in the kidneys, and that these changes play a critical role during the progression of DN.
Silencing microRNA‐221/222 cluster suppresses glioblastoma angiogenesis by suppressor of cytokine signaling‐3‐dependent JAK/STAT pathway
Authors: Xu Chun‐Hua , Liu Yue , Xiao Li‐Min , Chen Li‐Ke , Zheng Su‐Yue , Zeng Er‐Ming , Li Dong‐Hai , Li You‐Ping 
Published: May 2019

AbstractAngiogenesis is a major pathologic characteristic of glioblastoma, which is one aggressive primary brain tumor. MicroRNA‐221/222 (miR‐221/222) cluster has been previously reported to function importantly in malignant glioma biological process. The current study aims at evaluating the effects of miR‐221/222 cluster on angiogenesis of glioblastoma cells. Microarray data were analyzed to select glioblastoma‐associated differentially expressed genes, and dual‐luciferase reporter assay was performed to assess targeting correlation between miR‐221/222 cluster and suppressor of cytokine signaling‐3 (SOCS3). Subsequently, the expression patterns of miR‐221 and miR‐222 in glioblastoma cells were identified. miR‐221 and miR‐222 were overexpressed or silenced in glioblastoma cells to identify the effect of miR‐221/222 cluster in cell invasion, migration, proliferation, and angiogenesis. To define downstream pathway of miR‐221/222 cluster or SOCS3 in glioblastoma, levels of Janus kinase (JAK)/signal transducers and activators of transcription (STAT) pathway‐related proteins were assessed. Additionally, the functions of miR‐221/222 on glioblastoma cell angiogenesis were measured in vivo with microvessel density assayed. miR‐221 and miR‐222 were expressed at a high level and SOCS3 was at a low level in glioblastoma. Downregulation of the miR‐221/222 cluster diminished the invasion, migration, proliferation, and angiogenesis with reduced protein levels of matrix metalloproteinase‐2 (MMP‐2), MMP‐9, and vascular endothelial growth factor in glioblastoma cells. Also, silencing miR‐221/222 cluster reduced p‐JAK2/JAK2 and p‐STAT3/STAT3. Consistently, the inhibitory role of silencing miR‐221/222 cluster on tumorigenesis of glioblastoma cells was confirmed in vivo. Collectively, the inhibition of miR‐221/222 cluster could attenuate the glioblastoma angiogenesis through inactivation of the JAK/STAT pathway by upregulating SOCS3.