bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of glycolysis in brown adipocytes by HIF-1α
Authors: Basse Astrid L. , Isidor Marie S. , Winther Sally , Skjoldborg Nina B. , Murholm Maria , Andersen Elise S. , Pedersen Steen B. , Wolfrum Christian , Quistorff Bjørn , Hansen Jacob B. 
Published: June 2017

AbstractBrown adipose tissue takes up large amounts of glucose during cold exposure in mice and humans. Here we report an induction of glucose transporter 1 expression and increased expression of several glycolytic enzymes in brown adipose tissue from cold-exposed mice. Accordingly, these genes were also induced after β-adrenergic activation of cultured brown adipocytes, concomitant with accumulation of hypoxia inducible factor-1α (HIF-1α) protein levels. HIF-1α accumulation was dependent on uncoupling protein 1 and generation of mitochondrial reactive oxygen species. Expression of key glycolytic enzymes was reduced after knockdown of HIF-1α in mature brown adipocytes. Glucose consumption, lactate export and glycolytic capacity were reduced in brown adipocytes depleted of Hif-1α. Finally, we observed a decreased β-adrenergically induced oxygen consumption in Hif-1α knockdown adipocytes cultured in medium with glucose as the only exogenously added fuel. These data suggest that HIF-1α-dependent regulation of glycolysis is necessary for maximum glucose metabolism in brown adipocytes.
Standing wave effect and fractal structure in dislocation evolution
Authors: Li P. , Zhang Z. F. 
Published: June 2017

AbstractTheoretical model required for the evolution of regular dislocation pattern should simultaneously take into account both static distribution and dynamic evolution of dislocation pattern. In principle, there exists a stable uniformly moving dislocation with both core and far field advancing at the same constant velocity, which suggests the existence of the traveling waves representing moving dislocation. Therefore, one new term “dislocation wave” is defined by simultaneously consisting of both an elastic wave and a dislocation in each wavefront. According to the standing wave effect, the edge dislocation segments capture mutually to form the periodic ladder structures at the nodes. These persistent slip band (PSB) ladders are not only self-organized but also self-similar dislocation patterns. The fractal dimension further reveals the intrinsic nature of crack initiation and propagation along slip bands and deformation bands.
Focal Adhesion Kinase Regulates Hepatic Stellate Cell Activation and Liver Fibrosis
Authors: Zhao Xue-Ke , Yu Lei , Cheng Ming-Liang , Che Pulin , Lu Yin-Ying , Zhang Quan , Mu Mao , Li Hong , Zhu Li-Li , Zhu Juan-Juan , Hu Meng , Li Po , Liang Yue-Dong , Luo Xin-Hua , Cheng Yi-Ju , Xu Zhi-Xiang , Ding Qiang 
Published: June 2017

AbstractUnderstanding the underlying molecular mechanisms of liver fibrosis is important to develop effective therapy. Herein, we show that focal-adhesion-kinse (FAK) plays a key role in promoting hepatic stellate cells (HSCs) activation in vitro and liver fibrosis progression in vivo. FAK activation is associated with increased expression of α-smooth muscle actin (α-SMA) and collagen in fibrotic live tissues. Transforming growth factor beta-1 (TGF-β1) induces FAK activation in a time and dose dependent manner. FAK activation precedes the α-SMA expression in HSCs. Inhibition of FAK activation blocks the α-SMA and collagen expression, and inhibits the formation of stress fibers in TGF-β1 treated HSCs. Furthermore, inhibition of FAK activation significantly reduces HSC migration and small GTPase activation, and induces apoptotic signaling in TGF-β1 treated HSCs. Importantly, FAK inhibitor attenuates liver fibrosis in vivo and significantly reduces collagen and α-SMA expression in an animal model of liver fibrosis. These data demonstrate that FAK plays an essential role in HSC activation and liver fibrosis progression, and FAK signaling pathway could be a potential target for liver fibrosis.
3D Bayesian cluster analysis of super-resolution data reveals LAT recruitment to the T cell synapse
Authors: Griffié Juliette , Shlomovich Leigh , Williamson David J. , Shannon Michael , Aaron Jesse , Khuon Satya , L. Burn Garth , Boelen Lies , Peters Ruby , Cope Andrew P. , Cohen Edward A. K. , Rubin-Delanchy Patrick , Owen Dylan M. 
Published: June 2017

AbstractSingle-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10–30 nm, revealing the cell’s nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM). Also, existing methods that could be extended to 3D SMLM are usually subject to user defined analysis parameters, which remains a major drawback. Here, we present a new open source cluster analysis method for 3D SMLM data, free of user definable parameters, relying on a model-based Bayesian approach which takes full account of the individual localisation precisions in all three dimensions. The accuracy and reliability of the method is validated using simulated data sets. This tool is then deployed on novel experimental data as a proof of concept, illustrating the recruitment of LAT to the T-cell immunological synapse in data acquired by iPALM providing ~10 nm isotropic resolution.
Human endothelial cells secrete neurotropic factors to direct axonal growth of peripheral nerves
Authors: Grasman Jonathan M. , Kaplan David L. 
Published: June 2017

AbstractUnderstanding how nerves spontaneously innervate tissues or regenerate small injuries is critical to enhance material-based interventions to regenerate large scale, traumatic injuries. During embryogenesis, neural and vascular tissues form interconnected, complex networks as a result of signaling between these tissue types. Here, we report that human endothelial cells (HUVECs) secrete brain-derived neurotrophic factor (BDNF), which significantly stimulated axonal growth from chicken or rat dorsal root ganglia (DRGs). HUVEC-conditioned medium was sufficient to enhance axonal growth, demonstrating that direct cell-cell contact was not required. When BDNF was neutralized, there was a significant reduction in axonal growth when incubated in HUVEC-conditioned medium and in direct co-culture with HUVECs. These data show that HUVECs secrete neurotrophic factors that significantly enhance axonal growth, and can inform future in vivo studies to direct or pattern the angiogenic response in regenerating tissues to encourage re-innervation.
Predicting long-term mortality in hospitalized elderly patients using the new ESPEN definition
Authors: Jiang Jiaojiao , Hu Xiaoyi , Chen Jing , Wang Haozhong , Zhang Lei , Dong Birong , Yang Ming 
Published: June 2017

AbstractThe European Society of Clinical Nutrition and Metabolism (ESPEN) recently published new diagnostic criteria for malnutrition. The aim of this study was to evaluate whether malnutrition by the new ESPEN diagnostic criteria can predict long-term mortality in elderly inpatients. We conducted a prospective study in the acute geriatric wards. Malnutrition was defined according to the new ESPEN criteria and the Mini Nutritional Assessment (MNA), respectively. The survival status was determined by telephone interviews at 3-years. A total of 437 elderly adults were included. According to the new ESPEN criteria, 66 participants (15.1%) were malnourished. According to the MNA, 45 participants (10.3%) were identified as malnourished. The 3-year all-cause mortality was 41.7% in participants with malnutrition defined by the ESPEN criteria and 15.3% in participants without malnutrition (p < 0.001). After adjusting for relevant confounders, malnutrition defined by the ESPEN criteria was a significant predictor of 3-year all-cause mortality (hazard ratio [HR] 2.98, 95% confidence interval [CI] 1.87–4.86). However, malnutrition defined by the MNA was not a significant predictor of 3-year all-cause mortality (HR 1.67, 95% CI 0.89–2.31). In conclusion, the new ESPEN diagnostic criteria for malnutrition are reliable in predicting 3-year all-cause mortality among elderly inpatients.
Variants of the ABCA3 gene might contribute to susceptibility to interstitial lung diseases in the Chinese population
Authors: Zhou Wei , Zhuang Yi , Sun Jiapeng , Wang Xiaofen , Zhao Qingya , Xu Lizhi , Wang Yaping 
Published: June 2017

AbstractATP-binding cassette A3 (ABCA3) is a phospholipid carrier that is mainly expressed in the alveolar epithelium. Biallelic mutations of ABCA3 has been associated with fatal respiratory distress syndrome and interstitial lung disease (ILD) in children. However, whether variations in ABCA3 have a role in the development of adult ILD, including idiopathic pulmonary fibrosis (IPF), remains to be addressed. In this study, we screened for germline variants of ABCA3 by exons-sequencing in 30 patients with sporadic IPF and in 30 matched healthy controls. Eleven missense variants, predominantly in heterozygous, were found in 13 of these patients, but only two missenses in 2 healthy controls. We then selected four of the detected missense variants (p.L39V, p.S828F, p.V968M and p.G1205R) to performed cohort analysis in 1,024 ILD patients, containing 250 IPF and 774 connective tissue disease-ILD (CTD-ILD) patients, and 1,054 healthy individuals. Our results showed that the allele frequency of p.G1205R, but not p.L39V, was significantly higher in ILD patients than in healthy controls. However, no additional subject carrying the variant p.S828F or p.V968M was detected in the cohort analysis. These results indicate that the heterozygous ABCA3 gene variants may contribute to susceptibility to diseases in the Chinese population.
A snake venom group IIA PLA2 with immunomodulatory activity induces formation of lipid droplets containing 15-d-PGJ2 in macrophages
Authors: Giannotti Karina Cristina , Leiguez Elbio , Carvalho Ana Eduarda Zulim de , Nascimento Neide Galvão , Matsubara Márcio Hideki , Fortes-Dias Consuelo Latorre , Moreira Vanessa , Teixeira Catarina 
Published: June 2017

AbstractCrotoxin B (CB) is a catalytically active group IIA sPLA2 from Crotalus durissus terrificus snake venom. In contrast to most GIIA sPLA2s, CB exhibits anti-inflammatory effects, including the ability to inhibit leukocyte functions. Lipid droplets (LDs) are lipid-rich organelles associated with inflammation and recognized as a site for the synthesis of inflammatory lipid mediators. Here, the ability of CB to induce formation of LDs and the mechanisms involved in this effect were investigated in isolated macrophages. The profile of CB-induced 15-d-PGJ2 (15-Deoxy-Delta-12,14-prostaglandin J2) production and involvement of LDs in 15-d-PGJ2 biosynthesis were also investigated. Stimulation of murine macrophages with CB induced increased number of LDs and release of 15-d-PGJ2. LDs induced by CB were associated to PLIN2 recruitment and expression and required activation of PKC, PI3K, MEK1/2, JNK, iPLA2 and PLD. Both 15-d-PGJ2 and COX-1 were found in CB-induced LDs indicating that LDs contribute to the inhibitory effects of CB by acting as platform for synthesis of 15-d-PGJ2, a pro-resolving lipid mediator. Together, our data indicate that an immunomodulatory GIIA sPLA2 can directly induce LD formation and production of a pro-resolving mediator in an inflammatory cell and afford new insights into the roles of LDs in resolution of inflammatory processes.
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness
Authors: Liu Yue , Zhang Wenli , Zhang Kang , You Qi , Yan Hengyu , Jiao Yuannian , Jiang Jiming , Xu Wenying , Su Zhen 
Published: June 2017

AbstractLight, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis. We found that ~40% DHSs (DNaseI hypersensitive sites) were diminished under darkness. In non-TE regions, the majority of DHS-changed genes were DHS-diminished under darkness. A total of 519 down-regulated genes were associated with diminished DHSs under darkness, mainly involved in photosynthesis process and retrograde signaling, and were regulated by chloroplast maintenance master regulators such as GLK1. In TE regions, approximately half of the DHS-changed TEs were DHS-increased under darkness and were primarily associated with the LTR/Gypsy retrotransposons in the heterochromatin flanking the centromeres. In contrast, DHS-diminished TEs under darkness were enriched in Copia, LINE, and MuDR dispersed across chromosomes. Together, our results indicated that extended darkness resulted in more increased chromatin compaction in euchromatin and decompaction in heterochromatin, thus further leading to gene expression changes in Arabidopsis.
Postoperative Complications and Long-Term Results after Primary Cardiac Sarcoma Resection
Authors: Scheld Hans , Kessler Torsten , Sindermann Jürgen , Kösek Volkan , Tjan T. , Martens Sven , Hoffmeier Andreas , Kavakbasi Erhan 
Published: June 2017

Background Primary malignant cardiac tumors rarely occur in clinical care. Little is known about the impact of a parameter on postoperative survival.
Methods From May 1991 to May 2014, a total of 24 patients underwent surgical treatment of a primary cardiac sarcoma in our center. We analyzed our clinical database retrospectively for information on patient characteristics and treatment data. The follow-up could be completed to 91.7%.
Results Angiosarcoma and non-otherwise-specified sarcoma were the most common tumor entities. R0 resection was achieved in most cases. Postoperative mortality within the first 30 days was 20.8% (n = 5). In four of these five cases, postoperative low-output cardiac failure was the leading cause of death. The cumulative survival rate was 77.3% after 30 days, 68.2% after 3 months, 50.0% after 6 months, 45.0% after 12 months, and 18.0% after 24 months. The mean survival time in the whole group was 47.0 months. A low tumor differentiation was associated with low mean survival, but this was not statistically significant. Mean survival of sarcoma was higher after R0 resection. There was no significant rate of survival difference regarding the adjuvant therapy concept.
Conclusion Extended surgery alone or in combination with chemo- and/or radiotherapy may be successful in certain cases and may offer a satisfactory quality of life. The establishment of a multicenter heart tumor register in Germany is necessary to increase the number of cases in studies, get more remarkable study results, and standardize the diagnosis and therapy.
Polysomnography Applied to Patients with Tinnitus: A Review
Authors: Teixeira Liane , Granjeiro Ronaldo , Oliveira Carlos , Bahamad Júnior Fayez 
Published: June 2017

Introduction Tinnitus has been defined as an “auditory phantom perception,” meaning that tinnitus results from an abnormal activity within the nervous system, in the absence of any internal or external acoustic stimulation. About 10 to 15% of the adult population is affected by tinnitus, and a relevant percentage of tinnitus sufferers experience symptoms severe enough to significantly affect quality of life, including sleep disturbances, work impairment, and, in some cases, psychiatric distress. The self-rated complaints about tinnitus focus on emotional distress, auditory perceptual difficulties, and sleep disturbances.
Objectives To evaluate the works that show sleep disorders in patients with tinnitus, and sleep disorders assessed by polysomnography.
Data Synthesis We found four studies with polysomnography to assess sleep disorders in patients with tinnitus. The first study evaluated 80 patients who were military personnel without major psychiatric disturbances, and their tinnitus was associated with noise-induced permanent hearing. The second study was a prospective, case-control, nonrandomized study of 18 patients affected by chronic tinnitus who were compared with a homogeneous control group consisting of 15 healthy subjects. The last work evaluated questionnaires mailed to patients before their initial appointment at the Oregon Health Sciences University Tinnitus Clinic between 1994 and 1997. These questionnaires requested information pertaining to insomnia, tinnitus severity, and loudness. Follow-up questionnaires were mailed to 350 patients 1 to 4 years (mean 5 ± 2.3 years) after their initial appointment at the clinic.
Conclusion There are few studies with polysomnography for the evaluation of patients with sleep disorders caused by tinnitus. This shows the need for more studies on this subject.
Qualitative Determination of Human Chorionic Gonadotropin in Vaginal Washings for the Early Diagnosis of Premature Rupture of Fetal Membranes
Authors: Dartibale Camila Buziquia , Uchimura Nelson Shozo , Nery Luiz , Schumeish Angelita Polato , Uchimura Liza Yurie Teruya , Santana Rosangela Getirana , Uchimura Taqueco Teruya 
Published: June 2017

Purpose This study aimed to evaluate and validate the qualitative human chorionic gonadotropin β subunit (β-hCG) test of the vaginal fluid washings of pregnant women with premature rupture of fetal membranes (PROM).
Methods Cross-sectional study of pregnant women between gestational weeks 24 and 39 who underwent consultations in one of our institutions. They were divided into two groups: group A (pregnant women clinically diagnosed with PROM) and group B (pregnant women without loss of amniotic liquid). The patients were subjected to a vaginal fluid washing with 3 mL of saline solution, which was aspirated subsequently with the same syringe. The solution was immediately sent to the laboratory to perform the vaginal β-hCG test with cut-off points of 10 mIU/mL (β-hCG-10) and/or 25 mIU/mL (β-hCG-25).
Results The β-hCG-10 test of the vaginal secretion was performed in 128 cases. The chi-squared test with Yates' correction showed a statistically significant difference between the 2 groups (p = 0.0225). The sensibility, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy parameters were 77.1%, 43.6%, 52.3%; 70.4%; and 58.6% respectively. The β-hCG-25 test of the vaginal washing was performed in 49 cases. The analysis by Fisher's exact test showed a statistically significant difference between the groups (p = 0.0175). The sensibility, specificity, PPV, NPV, and accuracy parameters were 44.4%, 87.1%, 66.6%; 72.9%; and 71.4% respectively.
Conclusions The β-hCG-25 test showed better accuracy for the diagnosis of PROM, and can corroborate the early diagnosis of PROM because it is a simple and quick exam.
BioQueue: a novel pipeline framework to accelerate bioinformatics analysis
Authors: Yao Li , Wang Heming , Song Yuanyuan , Sui Guangchao 
Published: June 2017

Abstract

Motivation
With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, and dispatch jobs based on users’ experience about the resources needed by the execution of a certain step in a protocol. As a result, it is difficult for these tools to maximize the potential of computing resources, and avoid errors caused by overload, such as memory overflow.

Results
Here, we have developed BioQueue, a web-based framework that contains a checkpoint before each step to automatically estimate the system resources (CPU, memory and disk) needed by the step and then dispatch jobs accordingly. BioQueue possesses a shell command-like syntax instead of implementing a new script language, which means most biologists without computer programming background can access the efficient queue system with ease.

Availability and implementation
BioQueue is freely available at https://github.com/liyao001/BioQueue. The extensive documentation can be found at http://bioqueue.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Survival analysis of the association between antenatal care attendance and neonatal mortality in 57 low- and middle-income countries
Authors: Doku David T , Neupane Subas 
Published: June 2017

Abstract

Background
Neonatal mortality is unacceptably high in most low- and middle-income countries (LMICs). In these countries, where access to emergency obstetric services is limited, antenatal care (ANC) utilization offers improved maternal health and birth outcomes. However, evidence for this is scanty and mixed. We explored the association between attendance for ANC and survival of neonates in 57 LMICs.

Methods
Employing standardized protocols to ensure comparison across countries, we used nationally representative cross-sectional data from 57 LMICs (N = 464 728) to investigate the association between ANC visits and neonatal mortality. Cox proportional hazards multivariable regression models and meta-regression analysis were used to analyse pooled data from the countries. Kaplan-Meier survival curves were used to describe the patterns of neonatal survival in each region.

Results
After adjusting for potential confounding factors, we found 55% lower risk of neonatal mortality [hazard ratio (HR) 0.45, 95% confidence interval (CI) 0.42–0.48] among women who met both WHO recommendations for ANC (first visit within the first trimester and at least four visits during pregnancy) in pooled analysis. Furthermore, meta-analysis of country-level risk shows 32% lower risk of neonatal mortality (HR 0.68, 95% CI 0.61–0.75) among those who met at least one WHO recommendation. In addition, ANC attendance was associated with lower neonatal mortality in all the regions except in the Middle East and North Africa.

Conclusions
ANC attendance is protective against neonatal mortality in the LMICs studied, although differences exist across countries and regions. Increasing ANC visits, along with other known effective interventions, can improve neonatal survival in these countries.
Spontaneous Clearance of Hepatitis C Virus Infection Among Human Immunodeficiency Virus–Infected Men Who Have Sex With Men
Authors: Newsum Astrid M. , Schinkel Janke , van de Laar Thijs J. W. , van der Meer Jan T. M. , Prins Maria 
Published: June 2017

Abstract
We assessed spontaneous clearance in 27 human immunodeficiency virus–infected men who have sex with men (MSM) who seroconverted for hepatitis C virus (HCV). In contrast with a recent estimate of 45.8%, we found a spontaneous clearance rate of 11.1% (95% confidence interval = 2.4–29.2). This finding suggests that treatment deferral to await spontaneous clearance might not be justified for MSM with sexually acquired HCV.