bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of three widely used multi‐GNSS real‐time single‐frequency precise point positioning models using the International GNSS Service real‐time service
Authors: Wang Ahao , Chen Junping , Zhang Yize , Wang Jiexian 
Published: September 2020

Real‐time single‐frequency precise point positioning (RT‐SFPPP) of low‐cost has been attracting increasing attention in numerous global navigation satellite system (GNSS) applications. Nowadays, three multi‐GNSS RT‐SFPPP models are widely applied, i.e. ionosphere‐corrected (IC), ionospherefree (IF) and ionosphere‐weighted (IW) models. A comprehensive evaluation of the three models using CLK93 products is performed in the aspect of observation residuals, positioning accuracy and convergence. Data sets with quad‐system are collected from 16 multi‐GNSS experiments (MGEX) stations and are analysed in the simulated kinematic precise point positioning (PPP). Besides, kinematic PPP for a 5‐h shipborne data set is also conducted. Experimental results show that the positioning accuracy of IW model using MGEX data is better than that of both IC and IF models. Regarding the kinematic shipborne test, positioning accuracy of IF/IW model is of 0.27/0.26, 0.21/0.26 and 0.49/0.48 m for the N, E and U components, respectively, which is much better than that of IC model. As for average convergence time, IW model shows the best performance, which is at least 25% faster than the IF model. Different from both IF and IW models, the amplification of ionospheric errors has some impact on the positioning performance of the IC model at different frequencies.
Is There a Role for Cerebral Ultrasonography in Near-Term/Term Neonates Following Assisted Vaginal Delivery? A Prospective, Single-Center Study
Authors: Poryo Martin , Zimmer Anika , Hamza Amr , Wagenpfeil Stefan , Zemlin Michael , Geipel Martina , Löffler Günther , Meyer Sascha , Tutdibi Erol 
Published: September 2020

Abstract
Aim To evaluate the role of cerebral ultrasonography studies (CUSS) in detecting intracerebral and cranial pathologies (hemorrhages, ischemia, skull fractures) in near-term and term neonates following assisted vaginal delivery.
Patients and Methods Prospective single-center study (11/2017–11/2018) at the University Children’s Hospital of Saarland, Homburg, Germany including newborns with a gestational age ≥ 36 weeks born by assisted vaginal delivery. In all newborns, a standardized CUSS was performed within the first three days of life prior to discharge.
Results 200 neonates (43.0 % female, 57.0 % male; gestational age 39.6 ± 1.3 weeks) were included in this study (birth weight 3345.6 ± 450.6 g, body length 51.7 ± 2.5 cm, head circumference 35.0 ± 1.5 cm). 67 (33.5 %) neonates had minor external injuries of the scalp. 5 children showed clinical neurologic abnormalities: 4 (2.0 %) seizures and 1 facial palsy (0.5 %). In 34 (17.0 %) patients, minor incidental intracranial abnormalities unrelated to mode of delivery were detected on CUSS. No intracerebral, cranial pathologies or skull fractures were seen on routine CUSS.
Conclusion Routine CUSS in newborns after assisted vaginal delivery did not yield clinically relevant results in our cohort. Clinical observation and selective CUSS in symptomatic newborns might be more efficient than routine CUSS.
High Transaminases Following Cardiac Surgery: A Narrative Review
Authors: Omar Amr S. , Taha Adel , Al-Khulaifi Abdulaziz 
Published: September 2020

AbstractElevation of liver enzymes after cardiac surgery is encountered infrequently. Acute heart failure during and after surgery may be the culprit responsible for liver dysfunction. However, it may create clinical confusion whether acute liver dysfunction could induce some sort of cardiac dysfunction through mechanisms similar to those encountered in chronic liver disease. We searched through the Medline, Cochrane, and Embase databases up to January 2018. We included review articles, meta-analyses, and original trials on the elevation of liver enzymes after cardiac surgery, and combined the following MESH terms: “intensive care, “cardiac surgery,” “high liver enzymes,” “ischemia,” “left ventricular dysfunction,” and “critical illness.” Case reports were excluded. Language restrictions were not applied. References were examined for other potentially useful articles. We did not find any articles that supported the cardiac decompensation phenomenon after acute liver injury. In contrast, low-hepatic flow, hypoxemia, or pump-induced inflammation could induce hepatic dysfunction in acute settings after cardiac surgery. In conclusion, a rise in the transaminases following cardiac surgery would favor an ischemic etiology for the condition.
Yield and Safety of Transjugular Versus Percutaneous Liver Biopsies in Suspected Cases of Diffuse Liver Disease and Correlation of Yield of Transjugular Liver Biopsy with Hepatic Venous Pressure Gradient
Authors: Dey Mousam , Das Simi , Chatterjee Argha , Dutta Agnibha , Ghosh Ranajoy , Dasgupta Jayanta 
Published: September 2020

Abstract
Background Liver biopsy is indicated in both diagnosis and prognosis of diffuse liver diseases. Conventionally, percutaneous liver biopsy (PLB) is used, as it is easily available, affordable and has a shorter procedure time, whereas transjugular liver biopsy (TJLB) is used in the setting of ascites and coagulopathy. Our aim is to evaluate the diagnostic yield of TJLB in comparison to PLB with tract embolization. Our secondary aims were to evaluate whether there is any difference in rate of major and minor complications between the two procedures and evaluate whether there is any correlation between diagnostic yield of TJLB and hepatic venous pressure gradient (HVPG).
Methods In this retrospective study, we included a total of consecutive 123 patients who underwent liver biopsy through percutaneous (n = 97) and transjugular route (n = 26). We compared the yield of the specimen based on the number of complete portal tracts (CPT).
Results There was no significant difference between mean CPT in TJLB and PLB specimens (mean CPT of TJLB and PLB were 10.9 ± 2.7 and 11.6 ±2.5, respectively [p = 0.566]). There was a moderate but significant negative correlation between the total number of CPT and HVPG in the TJLB group (Spearman’s rho − 0.58) (p = 0.002). There was no statistically significant difference in minor complication between the two procedures. Only one patient who underwent PLB developed major complication and none of TLJB procedure had any major complication.
Conclusion Yield of tissue and complication rates are comparable in TJLB and PLB groups. Yield of tissue in TJLB have intermediate but significant negative correlation with HVPG.
Making an efficient but cost-effective automated goniometric device for a light-scattering study
Authors: Deb Dwaipayan 
Published: September 2020

Abstract
A goniometer is an instrument which is frequently used in optics and other branches of physics. It enables the study of light scattered in various directions from a solid, liquid or powdered sample. The goniometric instruments that are already available on the market are designed for a specific purpose and are quite costly. Fully-computerized devices—which automatically acquire data and control the positions of the light source and detector—are even more expensive. In this work, the instrumentation of a self-fabricated, low cost, but fully computerized goniometric instrument designed for studying a light-scattering problem in planetary science is described in detail. This device uses Arduino microcontroller boards for acquiring data, and stepper motors are employed for automated control of the positions of the light source and detector. A low-cost but high-intensity laser diode was used as the light source, and a very sensitive photodiode integrated circuit was used as the light detector. This work has a pedagogical value in the sense that the reader will benefit from learning about the techniques used, the components and their calibration, the software, etc. More importantly, the cost-effectiveness of this work may be beneficial to many experimentalists and instrument designers working in this field, to control their project budgets.
Cation interstitial diffusion in lead telluride and cadmium telluride studied by means of neural network potential based molecular dynamics simulations
Authors: Mińkowski Marcin , Hummer Kerstin , Dellago Christoph 
Published: September 2020

Abstract
Using a recently developed approach to represent ab initio based force fields by a neural network potential, we perform molecular dynamics simulations of lead telluride and cadmium telluride crystals. In particular, we study the diffusion of a single cation interstitial in these two systems. Our simulations indicate that the interstitials migrate via two distinct mechanisms: through hops between interstitial sites and through exchanges with lattice atoms. We extract activation energies for both of these mechanisms and show how the temperature dependence of the total diffusion coefficient deviates from Arrhenius behaviour. The accuracy of the neural network approach is estimated by comparing the results for three different independently trained potentials.
Modeling the electron acceleration in relativistic channels for space irradiation applications
Authors: Budrigă O , Ticoş C M 
Published: September 2020

Abstract
We study the interaction of an intense short laser pulse (duration > 100 fs) with a helium gas jet (with a pressure from 1–80 bar) by performing two-dimensional particle-in-cell (PIC) simulations. The parameters of the existing setups at the CETAL PW facility are used in PIC simulations. The mechanisms of the relativistic laser channeling such as filamentary bifurcation, long-wavelength hosing, bifurcation due to long-wavelength hosing and refractive bifurcation are shown. We also findthe optimum parameters of the laser pulse and the helium gas jet for which electrons are accelerated in the direct laser acceleration regime. We obtained electrons with energies higher than 100 MeV and broad electron energy spectra features that are very useful for space irradiation simulations.
Singularity confinement in delay-differential Painlevé equations
Authors: Stokes Alexander 
Published: September 2020

Abstract
We study singularity confinement phenomena in examples of delay-differential Painlevé equations, which involve shifts and derivatives with respect to a single independent variable. We propose a geometric interpretation of our results in terms of mappings between jet spaces, defining certain singularities analogous to those of interest in the singularity analysis of discrete systems, and what it means for them to be confined. For three previously studied examples of delay-differential Painlevé equations, we describe all such singularities and show they are confined in the sense of our geometric description.
Luminous properties of recycling luminous materials SrAl2O4:Eu2+, Dy3+ based on luminous polyester fabric
Authors: Zhu Yanan , Yu Qincen , Zheng Liubin , Pang Zengyuan , Ge Mingqiao 
Published: September 2020

Abstract
The recycling luminous materials SrAl2O4:Eu2+, Dy3+ is a kind of long afterglow phosphor, prepared based on the alcoholysis of luminous polyester fabric, which has excellent characteristics like high lightness and long afterglow time. However, for that the luminous materials SrAl2O4:Eu2+, Dy3+ are recycling, and the process on the alcoholysis of luminous polyester fabric may affect its performance. Hence, in this study a couple of luminous materials SrAl2O4:Eu2+, Dy3+ were recycled from luminous polyester fabric based on the method of alcoholysis, the phase structure and luminescent properties of the fibers were characterized by scanning electron microscopy (SEM), x-ray diffractometer (XRD), fluorescence spectrometer and afterglow luminance meter. The results deduced that under a certain condition, the luminous polyester fabric can be basically degraded, and the recovered luminescent materials can be obtained at a high purity. Our research supplies a strategy to recycle luminous phosphors as well as other functional materials, and hopefully it could inspire development for luminous materials and fibers.
Early Vascular Aging and Risk Factors Among a Population Aged 50 and Below in Kailuan Study
Authors: Zheng Meng-yi , Zhao Quan-hui , Liu Ying-chi , Song Yong-jian , Zhao Mao-xiang , Ma Yi-han , Huang Jian-huan , Chen Ze-kai , Wu Shou-ling 
Published: September 2020

Abstract

Background
To examine the frequency of early vascular aging and risk factors in an adult population with age ≤50 years old in Kailuan.

Methods
A total of 21,952 subjects aged ≤50 years without previous history of cardiovascular and cerebrovascular diseases and having completed brachial-ankle pulse wave velocity test in 2010–2016 were recruited. The mean plus 2 standard deviations (mean + 2SD) of brachial-ankle pulse wave velocity in 1,813 healthy population without hypertension, diabetes, dyslipidemia, and smoking were calculated and used as the reference value for early vascular aging. The stepwise regression multivariate logistic regression model was used to analyze the influencing factors for early vascular aging in different age and gender groups.

Results
The average detection rate of early vascular aging in this population was 15.0% with 12.9% in 30 years or less, 14.8% between 30 and 40 years, and 15.6% between 40 and 50 years. Furthermore, age, male, resting heart rate, high sensitivity C-reactive protein, smoking, hypertension, and diabetes were risk factors for early vascular aging with odds ratio values (95% confidence interval) of 1.02 (1.01–1.03), 2.51 (2.10–3.00), 1.04 (1.03–1.04), 1.09 (1.05–1.13), 1.11 (1.04–1.20), 1.05 (1.00–1.11), 3.55 (3.13–4.03), and 1.69 (1.38–2.08), respectively. The risk factors for early vascular aging in women with gestational hypertension were 4.27 times higher than those in women without (95% confidence interval 1.34–13.53).

Conclusions
The frequency of early vascular aging is 15.0% in adult population ≤50 years old. Risk factors for early vascular aging include age, male, resting heart rate, high sensitivity C-reactive protein, smoking, hypertension, diabetes, and in women, the pregnancy-induced hypertension.
Bacnet: a user-friendly platform for building multi-omics websites
Authors: Danès Loane , Tchitchek Nicolas , Bécavin Christophe 
Published: September 2020

Abstract

Summary
To face up to the exponential growth of heterogeneous datasets of various organisms, we developed a user-friendly platform for building multi-omics websites, which is named Bacnet. This platform helps bioinformaticians to construct four key web interfaces: (i) an interactive genome viewer; (ii) an expression and protein atlas; (iii) an interface for analysis of co-expression network; (iv) an interface for exploring homolog presence. We believe our platform will help the bioinformaticians to construct personalized user interfaces dedicated to biologists studying non-reference organisms.

Availability and implementation
https://github.com/becavin-lab/bacnet; Java; Eclipse RAP; Eclipse RCP.
Neighbourhoods in the yeast regulatory network in different physiological states
Authors: Lesk Arthur M , Konagurthu Arun S 
Published: September 2020

Abstract

Motivation
The gene expression regulatory network in yeast controls the selective implementation of the information contained in the genome sequence. We seek to understand how, in different physiological states, the network reconfigures itself to produce a different proteome.

Results
This article analyses this reconfiguration, focussing on changes in the local structure of the network. In particular, we define, extract and compare the 1-neighbourhoods of each transcription factor, where a 1-neighbourhood of a node in a network is the minimal subgraph of the network containing all nodes connected to the central node by an edge. We report the similarities and differences in the topologies and connectivities of these neighbourhoods in five physiological states for which data are available: cell cycle, DNA damage, stress response, diauxic shift and sporulation. Based on our analysis, it seems apt to regard the components of the regulatory network as ‘software’, and the responses to changes in state, ‘reprogramming’.
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method
Authors: Sun Shanwen , Xu Lei , Zou Quan , Wang Guohua 
Published: September 2020

Abstract

Summary
Processing raw reads of RNA-sequencing (RNA-seq) data, no matter public or newly sequenced data, involves a lot of specialized tools and technical configurations that are often unfamiliar and time-consuming to learn for non-bioinformatics researchers. Here, we develop the R package BP4RNAseq, which integrates the state-of-art tools from both alignment-based and alignment-free quantification workflows. The BP4RNAseq package is a highly automated tool using an optimized pipeline to improve the sensitivity and accuracy of RNA-seq analyses. It can take only two non-technical parameters and output six formatted gene expression quantification at gene and transcript levels. The package applies to both retrospective and newly generated bulk RNA-seq data analyses and is also applicable for single-cell RNA-seq analyses. It, therefore, greatly facilitates the application of RNA-seq.

Availability and implementation
The BP4RNAseq package for R and its documentation are freely available at https://github.com/sunshanwen/BP4RNAseq.

Supplementary information
Supplementary data are available at Bioinformatics online.
The synapse in traumatic brain injury
Authors: Jamjoom Aimun A B , Rhodes Jonathan , Andrews Peter J D , Grant Seth G N 
Published: September 2020

AbstractTraumatic brain injury (TBI) is a leading cause of death and disability worldwide and is a risk factor for dementia later in life. Research into the pathophysiology of TBI has focused on the impact of injury on the neuron. However, recent advances have shown that TBI has a major impact on synapse structure and function through a combination of the immediate mechanical insult and the ensuing secondary injury processes, leading to synapse loss. In this review, we highlight the role of the synapse in TBI pathophysiology with a focus on the confluence of multiple secondary injury processes including excitotoxicity, inflammation and oxidative stress. The primary insult triggers a cascade of events in each of these secondary processes and we discuss the complex interplay that occurs at the synapse. We also examine how the synapse is impacted by traumatic axonal injury and the role it may play in the spread of tau after TBI. We propose that astrocytes play a crucial role by mediating both synapse loss and recovery. Finally, we highlight recent developments in the field including synapse molecular imaging, fluid biomarkers and therapeutics. In particular, we discuss advances in our understanding of synapse diversity and suggest that the new technology of synaptome mapping may prove useful in identifying synapses that are vulnerable or resistant to TBI.
Psychosocial health of adolescents in relation to underweight, overweight/obese status: the EU NET ADB survey
Authors: Drosopoulou Georgia , Sergentanis Theodoros N , Mastorakos Georgios , Vlachopapadopoulou Elpis , Michalacos Stefanos , Tzavara Chara , Bacopoulou Flora , Psaltopoulou Theodora , Tsitsika Artemis 
Published: September 2020

AbstractBackgroundBoth deviations from normal weight, namely, underweight and overweight/obese status, have been inversely associated with psychosocial health in adolescents. This study aimed to examine the relationship between psychosocial health and body mass index (BMI) among adolescents in five European countries, while assessing the effect of sociodemographic variables.MethodsA cross-sectional school-based study of adolescents aged 14–17.9 years was conducted in the framework of the European Network for Adolescent Addictive Behavior survey. Self-reported questionnaires from Greece, Iceland, the Netherlands, Romania and Spain were used for the current analysis. Associations between Youth Self-Report (YSR) scales and BMI status were investigated by multiple logistic regression analysis. The effect of sociodemographic variables was also measured.ResultsΤhe sample consisted of 7005 adolescents aged 14–17.9 years. Borderline/clinical scores on some YSR scales were independently associated with overweight/obesity, specifically total problems (OR = 1.52, 95% CI: 1.18–1.96), internalizing ( OR = 1.48, 95% CI: 1.16–1.91), externalizing (OR = 1.36, 95% CI: 1.10–1.68), social (OR = 1.67, 95% CI: 1.19–2.35) and thought problems (OR = 1.62, 95% CI: 1.20–2.20). Among subscales, overweight/obesity specifically correlated with anxiety/depression (OR = 1.83, 95% CI: 1.33–2.51), withdrawal/depression (OR = 1.58, 95% CI: 1.02–2.48) and rule-breaking behavior (OR = 1.55, 95% CI: 1.15–2.08). Underweight was associated with problems on activities (OR = 1.31, 95% CI: 1.01–1.68) and withdrawal/depression (OR = 1.95, 95% CI: 1.27–3.01).ConclusionsLower levels of psychosocial health are associated with both deviations from normal weight. These findings suggest the need for health policies that target health habits and lifestyle, as well as positive attitudes towards the body image, with respect to the different psychosocial characteristics of each body weight status category.
Regulation of telomeric function by DNA methylation differs between humans and mice
Authors: Toubiana Shir , Larom Gal , Smoom Riham , Duszynski Robert J , Godley Lucy A , Francastel Claire , Velasco Guillaume , Selig Sara 
Published: September 2020

Abstract
The most distal 2 kb region in the majority of human subtelomeres contains CpG-rich promoters for TERRA, a long non-coding RNA. When the function of the de novo DNA methyltransferase DNMT3B is disrupted, as in ICF1 syndrome, subtelomeres are abnormally hypomethylated, subtelomeric heterochromatin acquires open chromatin characteristics, TERRA is highly expressed, and telomeres shorten rapidly. In this study, we explored whether the regulation of subtelomeric epigenetic characteristics by DNMT3B is conserved between humans and mice. Studying the DNA sequence of the distal 30 kb of the majority of murine q-arm subtelomeres indicated that these regions are relatively CpG-poor and do not contain TERRA promoters similar to those present in humans. Despite the lack of human-like TERRA promoters, we clearly detected TERRA expression originating from at least seven q-arm subtelomeres, and at higher levels in mouse pluripotent stem cells in comparison with mouse embryonic fibroblasts (MEFs). However, these differences in TERRA expression could not be explained by differential methylation of CpG islands present in the TERRA-expressing murine subtelomeres. To determine whether Dnmt3b regulates the expression of TERRA in mice, we characterized subtelomeric methylation and associated telomeric functions in cells derived from ICF1 model mice. Littermate-derived WT and ICF1 MEFs demonstrated no significant differences in subtelomeric DNA methylation, chromatin modifications, TERRA expression levels, telomere sister chromatid exchange or telomere length. We conclude that the epigenetic characteristics of murine subtelomeres differ substantially from their human counterparts and that TERRA transcription in mice is regulated by factors others than Dnmt3b.