bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Event Based Topic Learning Pipeline for Neuroimaging Literature Mining
Authors: Chen Lihong , Yan Jianzhuo , Chen Jianhui , Sheng Ying , Xu Zhe , Mahmud Mufti 
Published: October 2020

Abstract
Neuroimaging text mining extracts knowledge from neuroimaging text and has received widespread attention. Topic learning is an important research focus of neuroimaging text mining. However, current neuroimaging topic learning researches mainly use traditional probability topic models to extract topics from literature and cannot obtain high-quality neuroimaging topics. The existing topic learning methods cannot meet the requirements of topic learning oriented to full-text neuroimaging literature. In this paper, three types of neuroimaging research topic events are defined to describe the process and result of neuroimaging research. An event based topic learning pipeline, called neuroimaging Event-BTM, is proposed to realize knowledge extraction from full-text neuroimaging literature. The experimental results on the PLoS One data set show that the accuracy and completeness of proposed method are significantly better than the existing main topic learning methods.
Molecular Subtypes Based on DNA Methylation Profiles can Predict the Prognosis of Patients with Laryngeal Cancer
Authors: Yang YingPo , Li Qiang , Song Jukun , An Wei , Liu Zhaohui 
Published: October 2020

Abstract
Background: Laryngeal cancer is a common malignant tumor, with the highest mortality rate and lymph node metastasis rate among cancers. Although laryngeal cancer subtypes have been defined for clinical relevance, there are few studies on the molecular characteristics of laryngeal cancer subtypes.Methods: DNA methylation profiles of laryngeal cancer were downloaded from The Cancer Genome Atlas database. The univariate Cox regression analysis and multivariate Cox regression analysis was employed to screen the prognosis-related DNA methylation site. Meanwhile, we performed unsupervised clustering using prognostic DNA methylation data to identify the molecular characteristics of laryngeal cancer. We also explored the correlation between Differences in DNA methylation levels and differences in T, N, and M category, age, stage, and prognosis. Functional enrichment analysis was conducted in each molecular subtype. A risk model was constructed via prognostic DNA methylation levels. Results: DNA methylation data in 123 laryngeal cancer samples were obtained. Through univariate Cox regression analysis, the 17,751 DNA methylation sites were defined as prognostic CpG sites with the threshold of P value less than 0.05. Then, the multivariate Cox regression analysis was further screen the prognosis-related DNA methylation sites. Five subgroups were identified based on consensus clustering using 455 prognostic CpG sites that were significantly associated with patient’s survival. We built a prediction model and used it to classify the samples.Conclusion: The unsupervised clustering was performed using prognostic DNA methylation data and described the seven laryngeal cancer molecular subtypes. Our results provide novel insights into mechanisms and more effective personalized treatments of laryngeal cancer.
Ontogenetic Shifts in Home Range Size of a Top Predatory Reef-associated Fish (Caranx ignobilis): Implications for Conservation.
Authors: Daly Ryan , Filmalter John David , Peel Lauren R , Mann Bruce Quinten , Lea James , Clarke Christopher R , Cowley Paul D 
Published: October 2020

Abstract
Defining the home range of vulnerable species is critical for designing effective spatial management strategies. However, animal home ranges often change with ontogeny and quantifying the associated temporal and spatial changes is particularly challenging for mobile marine species. Here, we investigate how the space use of a top predatory reef-associated fish (Caranx ignobilis) scales with body size. We tagged 17 individuals, representing a wide range of sizes (40.5 – 120 cm fork length (FL)), with acoustic transmitters, and passively tracked them for over 3 years at a tropical island and atoll in the Republic of Seychelles, Western Indian Ocean. We found that a sheltered atoll environment was critical for juvenile fish (< 60 cm FL) that exhibited a shift in home range location and area as they matured into adults. Small (60 – 100 cm FL) and large (> 100 cm FL) adult fish appeared to favour shallow coral reefs and associated reef drop offs whilst sharing a similar core home range location. Large adult fish, however, utilized a greater diversity of habitat types and had significantly (p < 0.05) greater annual dispersal distances (mean = 35.29 km, max = 91.32 km) than small adults (mean = 13.72 km, max = 21.55 km). Additionally, the home range (represented by minimum convex polygons) of large adults (mean = 209.74 km2) was significantly (p < 0.05) larger than that of juveniles (mean = 38.73 km2) and small adults (77.32 km2) and there was a significant (p = 0.02) relationship between fish length and home range size, with fish length accounting for 32% of the home range size variance. Furthermore, tagged fish took up to 34 months (mean = 18.54) to utilize the full extent of their home range. The habitat shift and expansion in home range size throughout ontogeny exhibited by C. ignobilis in this study should be taken into account when designing effective spatial management plans for the species.
CRISPR/Cas9-mediated Tryptophan Hydroxylase 1 Knockout Decreases Calcium Transportation in Goat Mammary Epithelial Cells
Authors: Zhang Zhifei , Tian Huibin , Chen Xiaoying , Zhao Haiying , Du Wei , Gao Huijie , Luo Jun , Zheng Huiling 
Published: October 2020

Abstract
Background: Calcium is one of the major mineral nutrients in goat milk. Tryptophan hydroxylase1 (TPH1) is a rate-limiting enzyme catalyzing hydroxylation of L-tryptophan into 5-hydroxytryptamine (5-HT) essential for maintaining calcium homeostasis. The function of TPH1 and 5-HT in goat mammary calcium homeostasis is not well known.Methods: The CRISPR/Cas9-meidated TPH1 knockout goat mammary epithelial cells (GMEC) were constructed firstly. Then the content of 5-HT, intracellular calcium level and abundance of key genes related to calcium transportation were evaluated and compared in wild-type GMEC, TPH1 knockout GMEC, to explore the impact of TPH1 on calcium transportation, respectively. Wild-type GMEC and TPH1 knockout GMEC were further treated with exogenous 5-HTP to confirm the role of TPH1 in regulating calcium homeostasis in GMEC. 5-HT concentration was measured by enzyme-linked immunosorbent assay and fluo-3 staining was used to determine intracellular calcium content.Results: The TPH1 knockout GMEC heterozygous clone with no off-target effects was obtained after transfection of the Cas9/sgRNA expression vector. The 5-HT synthesis and intracellular calcium level decreased in TPH1 gene knockout GMEC. The mRNA abundance of secretory-pathway Ca2+ -ATPase1 (SPCA1) and plasma membrane Ca2+-ATPase1 (PMCA1) were up-regulated while the mRNA abundance of secretory-pathway Ca2+ -ATPase2 (SPCA2) was down-regulated in TPH1 knockout GMEC. Up-regulation of parathyroid hormone-related peptide (PTHrP), a key regulator of mammary calcium metabolism, induced by 5-HTP were blocked by TPH1 gene knockout. The TPH1 knockout GMEC showed a lower sensitivity to 5-HTP induced elevation of calcium content.Conclusion: Results suggested that TPH1 plays an important role in regulating calcium homeostasis via PTHrP and calcium transportation related factors in GMEC.
An Augmented Multilingual Twitter Dataset for Studying the COVID-19 Infodemic
Authors: Lopez Christian E. , Gallemore Caleb 
Published: October 2020

Abstract
We present an openly available dataset to facilitate researchers’ exploration of popular discourse about the COVID-19 pandemic. The dataset, whose collection is ongoing, currently consists of over 780 million tweets, from all over the world, in multiple languages. Tweets start from 22 January 2020, when the total cases of reported COVID-19 were below 600 worldwide. The dataset was collected using the Twitter API and by rehydrating tweets from another openly available database. To facilitate access for other researchers, the English-language tweet data has been augmented by state-of-the-art Twitter sentiment and named entity recognition algorithms. The dataset and the summary files we provide allow researchers to avoid some computationally intensive analyses, facilitating more widespread use of social media data to gain insights on issues such as (mis)information diffusion, semantic networks, sentiment, and the evolution of COVID-19 discussions. The insights extracted from such analyses could help inform policy and advocacy work amid the current and future pandemics.
WITHDRAWN: LncRNA RP3-326I13.1&nbsp;Promoted Cisplatin Resistance of Lung Adenocarcinoma by Collaborating RNA&nbsp;Binding Protein HSP90B&nbsp;and Upregulating Downstream Molecule MMP13&nbsp;
Authors: Zhou Huixin , Xu Shihao , Shi Wenjing , Huang Xiaolu , Chen Jie , Huang Kate , wang Yumin 
Published: October 2020

Abstract
Background:We previously obtained a lncRNA RP3-326I13.1, which significantly upregulated by cisplatin resistance in lung adenocarcinoma (LAD), but the biological function and molecular mechanism is unclear. Methods:Expression levels of RP3-326I13.1 and HSP90B mRNA were estimated by qPCR from 57 pairs of LAD and NT samples without and with cisplatin. Knockdown and overexpression in A549/DDP and A549 cell lines by lentiviral- mediated techniques to observe changes in tumor behavior in A549/DDP and A549 cells, as well as tumorigenicity in experimental nude mice. The ranscriptome was sequenced to obtain downstream target molecules of RP3-326I13.1 and RNA-binding proteins were obtained using RNA pulldown. Results: QPCR showed that the expression level of RP3-326I13.1 and HSP90B mRNA in A549/DDP cells, LAD tissues and progressive LAD tissues (cisplatin treatment was not effective) were tangibly higher than that of A549 cells, adjacent tissues, and complete remission (P=0.0037, P=0.0181; P=0.0027, P=0.009 and P=0.002, P=0.007). RP3-326I13.1 markedly enhanced the proliferation, migrate, invasion, clonal proliferation ability of LAD cell lines and speed and weight of tumorigenicity in nude mice experiment while increased the proportion of G1 phase cells (P=0.019). RNA-pull down and mass spectrometry obtained RNA binding protein HSP90B and HSP90B clearly decreased proliferation, invasive ability while increased the apoptosis of LAD cell lines after knocked down. We found matrix metalloproteinase-13 (MMP-13) was RP3-326I13.1 downstream target gene. Conclusions: So, RP3-326I13.1 was a drug-resistant relative lncRNA promoted cisplatin resistance of lung adenocarcinoma by collaborating RNA binding protein HSP90B and upregulating downstream target molecule MMP13.
Contextual Influences on Deliberate Self-harm Among Chinese University Undergraduates: A Representative Nationwide Study
Authors: Peng Sihui , Zhang Weifang , Yang Tingzhong , Cottrell Randall R. , Rockett Ian R.H. 
Published: October 2020

Abstract

Background: Numerous studies have identified factors associated with deliberate self-harm (DSH), but environmental influences have been largely neglected. This study explored regional and university contextual factors impacting DSH among undergraduate students in China. Methods: In this observational cross-sectional study, subjects were 5,016 undergraduate students, who were identified through multistage survey sampling in 22 Chinese universities. Individual-level data were obtained through a self-administered questionnaire, and environmental variables were extracted from the National Bureau of Statistics database. Multilevel logistic regression models were used to examine regional correlates of DSH.Results: The overall prevalence of self-reported DSH in the study sample was 7.5% (95% CI: 4.1%, 10.9%). The full multilevel logistic model showed university rank and city size were inversely associated with DSH prevalence (OR: 0.24 and 0.55). Regional unemployment rates were positively associated with DSH prevalence (OR: 1.98).Conclusion: Results yield important insights on the role of context in DSH among Chinese undergraduates, and indicate the need to consider environmental factors in order to ameliorate the problem.
SARS-CoV-2 infects cells of the human exocrine and endocrine pancreas and interferes with beta-cell function
Authors: Müller Janis A. , Groß Rüdiger , Conzelmann Carina , Krüger Jana , Koepke Lennart , Steinhart Johannes , Weil Tatjana , Bozzo Caterina Prelli , Read Clarissa , Fois Giorgio , Eiseler Tim , Gehrmann Julia , Vuuren Joanne van , Wessbecher Isabel M. , Frick Manfred , Costa Ivan G. , Breunig Markus , Schuster Michael , Liebau Stefan , Seufferlein Thomas , Stenger Steffen , Stenzinger Albrecht , MacDonald Patrick E. , Kirchhoff Frank , Sparrer Konstantin M. J. , Walther Paul , Lickert Heiko , Barth Thomas F.E. , Wagner Martin , Münch Jan , Heller Sandra , Kleger Alexander 
Published: October 2020

Abstract
Preexisting diabetes increases the risk of a severe course of the pandemic coronavirus disease 2019 (COVID-19). Vice versa, exacerbations of a preexisting diabetes as well as new-onset diabetes have been reported upon SARS-CoV-2 infection. Thus, there is an imperative need to clarify whether human pancreatic endocrine cells organized within an islet of Langerhans are permissive for and affected by SARS-CoV-2 infection, and to elucidate the mechanisms underlying the development of diabetes upon COVID-19. Here, we (i) defined ACE2 and TMPRSS2 expression patterns in human pancreatic endocrine and exocrine cell types, (ii) employed human pancreatic islet cultures to demonstrate susceptibility to SARS-CoV-2 infection and to viral replication in β-cells, (iii) showed that SARS-CoV-2 attenuates glucose-stimulated insulin secretion, and (iv) tested remdesivir as eventually effective to prevent β-cell failure. In addition, we (v) visualized viral particles replicating in endocrine pancreatic cells and define their subcellular localization patterns via transmission electron microscopy, and finally (vi) present examples of cell type specific pancreatic infection patterns of COVID-19 deceased patients. Overall, our data demonstrate that SARS-CoV-2 can infect both the exocrine and endocrine compartments of the pancreas and can perturb β-cell integrity, which might lead to an increased risk for diabetes.
Validation of a prospective urinalysis-based prediction model for ICU-resources and outcome of Covid-19 disease: A multicenter cohort study
Authors: Gross Oliver , Moerer Onnen , Rauen Thomas , Böckhaus Jan , Hoxha Elion , Jörres Achim , Kamm Matthias , Elfanish Amin , Windisch Wolfram , Dreher Michael , Floege Juergen , Kluge Stefan , Schmidt-Lauber Christian , Turner Jan-Eric , Huber Samuel , Addo Marylyn M. , Scheithauer Simone , Friede Tim , Braun Gerald S. , Huber Tobias B. , Blaschke Sabine 
Published: October 2020

Abstract

Purpose: Identifying preventive strategies in Covid-19 patients helps to improve ICU-resource-allocation and reduce mortality. We recently demonstrated in a post-mortem cohort that SARS-CoV-2 renal tropism was associated with kidney injury, disease severity and mortality. We also proposed an algorithm to predict the need for ICU-resources and the risk of adverse outcomes in Covid-19 patients harnessing urinalysis and protein/coagulation parameters on admission for signs of kidney injury. Here, we aimed to validate this hypothesis in a multicenter cohort. Methods: Patients hospitalized for Covid-19 at four tertiary centers were screened for an available urinalysis, serum albumin (SA) and antithrombin-III activity (AT-III) obtained prospectively within 48h upon admission. The respective presumed risk for an unfavorable course was categorized as “low”, “intermediate” or “high”, depending on a normal urinalysis, an abnormal urinalysis with SA ≥2 g/dl and AT-III ≥70%, or an abnormal urinalysis with at least one SA or AT-III abnormality. Time to ICU or death within ten days served as primary, in-hospital mortality and required organ support served as secondary endpoints.Results: Among a total of N=223 screened patients, N=145 were eligible for enrollment, falling into the low (N=43), intermediate (N=84), and high risk (N=18) categories. The risk for ICU transfer or death was 100% in the high risk group and significantly elevated in the composite of high and intermediate risk as compared to the low risk group (63.7% vs. 27.9%; HR 2.6; 95%-CI 1.4 to 4.9; P=0.0020). Having an abnormal urinalysis was associated with mortality, need for mechanical ventilation, extra-corporeal membrane oxygenation (ECMO) or renal replacement therapy (RRT). Conclusion: Our data confirm that Covid-19-associated urine abnormalities on admission predict disease aggravation and need for ICU. By engaging a simple urine dipstick on hospital admission our algorithm allows for early preventive measures and appropriate patient stratification. (ClinicalTrials.gov number NCT04347824)
Functional gall-bladder disorders and non-alcoholic fatty liver disease: clinical features and new approaches to therapy
Authors: Mekhtiev S. N. , Mekhtieva O. A. , Ibragimova Z. M. 
Published: October 2020

Introduction. Statistical data indicate a frequent combination of functional biliary disorders with non-alcoholic fatty liver disease.Aim. To study the efficacy and safety of Phosphogliv® URSO in patients with functional disorders of the gall-bladder, biliary sludge in combination with fatty hepatosis in comparison with the group receiving monotherapy ursodeoxycholic acid (UDCA).Materials and methods. The study included 30 patients with a diagnosis of functional gall-bladder disorder, biliary sludge in combination with non-alcoholic fatty liver disease. Patients of the main group received monotherapy with Phosphogliv® URSO. The comparison group received monotherapy UDCA. After three-month therapy, the dynamics of clinical symptoms, laboratory parameters, and ultrasound parameters were assessed.Results. Positive dynamics of clinical manifestations of functional disorders of the gallbladder, as well as parameters of cholestatic syndrome and bilirubin level was observed in both groups. In patients taking Phosphogliv® URSO, a significant decrease in cytolysis syndrome indicators was recorded, a significant difference was revealed in relation to an increase in HDL levels and a decrease in the atherogenic coefficient in the main group. When assessing the ultrasound parameters of the gall-bladder in patients of group 1, a significant decrease in the thickness of its wall, reverse development of biliary sludge, an improvement in the contractile function of the gall-bladder in comparison with the UDCA monotherapy group were revealed.Conclusion. The use of a combined medicine containing glycyrrhizic acid and UDCA (Phosphogliv® URSO) can be recommended for patients with functional disorders of the gallbladder, biliary sludge and non-alcoholic fatty liver disease, given its more pronounced anticytolytic effect, restoration of functional disorders of the gallbladder and resolution of biliary sludge in comparison with monotherapy UDCA.
Possibilities of ademetionine in treatment of patients with alcoholic liver disease
Authors: Maslovskiy L. V. , Bulanova M. I. , Shaposhnikova O. F. , Minushkin O. N. 
Published: October 2020

Introduction. Alcoholic liver disease (ALD) is the most common liver disease, the terminal stage of which is alcoholic liver cirrhosis (ALC), which ranks first in terms of prevalence and frequency of lethal outcomes in hospital patients. The pathogenesis of alcoholic liver disease is based on direct damage to the hepatocyte membrane, oxidative stress, hepatic parenchyma inflammation with hyperproduction of inflammatory mediators, immune mechanisms, hepatic parenchyma fibrosis. S-adenosyl-L-methionine (ademetionine) is able to affect the different parts of the pathogenesis of ALD. One of the new ademetionine drugs is Samelix (manufacturer – Canonfarma Production JSC, Russia).Aim of the study. Evaluation of Samelix efficacy and safety in patients with chronic alcoholic liver disease with cholestasis syndrome at the inpatient stage of treatment.Materials and methods. 23 patients (men – 11, women – 12) were admitted to the study. The average age was 51.8 ± 3.4 years. Duration of the disease in the remaining patients averaged 3.5 ± 1.9 years (from 0.5 to 8 years). All patients received detoxification therapy, vitamin therapy, and Verospiron was used in patients with liver cirrhosis. Within 10-12 days the therapy with Samelix was carried out: 800 mg/day intravenous drip. The dynamics of biochemical indices (ALT, AST, GGT, bilirubin, ALP); clinical manifestations; life quality according to the SF-36 questionnaire; side effects were assessed.Conclusions. There was a significant reduction in the number of patients with skin itching, increased fatigue and depressed mood, positive dynamics of biochemical indicators in the form of a decrease in AST, ALT, alkaline phosphatase, GGT, total and direct bilirubin. Thus, the therapy allows to effectively reduce symptoms in patients with alcoholic liver disease, resulting in an improvement on all scales and summary indicators – psychological and physical component of health.
State-of-the-art review on the transient flow modeling and utilization for urban water supply system (UWSS) management
Authors: Duan Huan-Feng , Pan Bin , Wang Manli , Chen Lu , Zheng Feifei , Zhang Ying 
Published: October 2020

AbstractIn the context of smart city development and rapid urbanization worldwide, urban water supply system (UWSS) has been of vital importance to this process. This paper presents a comprehensive review on the transient flow research for UWSS management. This review consists of two aspects as follows. The first aspect is about the development and progress of current transient theory, including transient flow models, unsteady friction and turbulence models, and numerical simulation methods. The other aspect is about the utilization and application of transient-based methods for effective UWSS diagnosis and management, including leakage, discrete and extended partial blockages, unknown branch, and other defects in water pipelines. A total of 228 publications have been reviewed and analyzed in this paper. In addition to the state-of-the-art progress and achievement of the research on transients, the advances and recommendations of future work in this field are also discussed for the development and management of next-generation smart UWSS in the paper.
A Case-Control Study Investigating the Effect of MTHFR C677T Variant on Performance of Elite Athletes
Authors: Nursal Ayse F. , Yigit Serbulent , Rustemoglu Husniye , Cenikli Abdullah 
Published: October 2020

Objective:
Increased level of plasma homocysteine (Hcy) is a potential risk factor for
several multi-system diseases. The Methylenetetrahydrofolate reductase (MTHFR) gene C677T
variant has been established as an important genetic determinant of hyperhomocysteinemia. There
are conflicting reports about the effects of physical activity on plasma Hcy. Therefore, the main
aim of this study was to investigate whether the MTHFR C677T variant affects elite athletic performance.

Methods:
This study was carried out on 214 individuals (114 elite athletes and 100 sedentary controls).
Genotyping was performed using PCR- RFLP method. Odds ratios (ORs) with 95% confidence
intervals (CIs) were used to assess the strength of association.

Results:
There was a significant difference between the athletes and the control group in genotype
distribution and allele frequency of the MTHFR C677T variant. MTHFR C677T CC genotype and
C allele were more prevalent in elite athletes than those in the sedentary controls (p =0.007, OR:
2.16, 95%:1.26-3.70; p=0.009, OR: 1.84, 95%:1.18-2.89, respectively). The control group had a
higher MTHFR C677T CT genotype than the athletes (p=0.019, OR: 0.51, 95%:0.30-0.88). There
was no deviation from HWE for the MTHFR C677T variant in the groups.

Conclusion:
Our findings support that there is an association between the MTHFR C677T C allele
and athletic performance among the elite Turkish athletes.