bluuebunny/crossref_metadata_2025_split huggingface dataset:
Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression
Authors: Tang Kujin , Ren Jie , Sun Fengzhu 
Published: December 2019

AbstractAlignment-free methods, more time and memory efficient than alignment-based methods, have been widely used for comparing genome sequences or raw sequencing samples without assembly. However, in this study, we show that alignment-free dissimilarity calculated based on sequencing samples can be overestimated compared with the dissimilarity calculated based on their genomes, and this bias can significantly decrease the performance of the alignment-free analysis. Here, we introduce a new alignment-free tool, Alignment-Free methods Adjusted by Neural Network (Afann) that successfully adjusts this bias and achieves excellent performance on various independent datasets. Afann is freely available at https://github.com/GeniusTang/Afann.
Update to the Vitamin C, Thiamine and Steroids in Sepsis (VICTAS) protocol: statistical analysis plan for a prospective, multicenter, double-blind, adaptive sample size, randomized, placebo-controlled, clinical trial
Authors: Lindsell Christopher J. , McGlothlin Anna , Nwosu Samuel , Rice Todd W. , Hall Alex , Bernard Gordon R. , Busse Laurence W. , Ely E. Wesley , Fowler Alpha A. , Gaieski David F. , Hinson Jeremiah S. , Hooper Michael H. , Jackson James C. , Kelen Gabor D. , Levine Mark , Martin Greg S. , Rothman Richard E. , Sevransky Jonathan E. , Viele Kert , Wright David W. , Hager David N. 
Published: December 2019

Abstract
Background
Observational research suggests that combined therapy with Vitamin C, thiamine and hydrocortisone may reduce mortality in patients with septic shock.

Methods and design
The Vitamin C, Thiamine and Steroids in Sepsis (VICTAS) trial is a multicenter, double-blind, adaptive sample size, randomized, placebo-controlled trial designed to test the efficacy of combination therapy with vitamin C (1.5 g), thiamine (100 mg), and hydrocortisone (50 mg) given every 6 h for up to 16 doses in patients with respiratory or circulatory dysfunction (or both) resulting from sepsis. The primary outcome is ventilator- and vasopressor-free days with mortality as the key secondary outcome. Recruitment began in August 2018 and is ongoing; 501 participants have been enrolled to date, with a planned maximum sample size of 2000. The Data and Safety Monitoring Board reviewed interim results at N = 200, 300, 400 and 500, and has recommended continuing recruitment. The next interim analysis will occur when N = 1000.
This update presents the statistical analysis plan. Specifically, we provide definitions for key treatment and outcome variables, and for intent-to-treat, per-protocol, and safety analysis datasets. We describe the planned descriptive analyses, the main analysis of the primary end point, our approach to secondary and exploratory analyses, and handling of missing data. Our goal is to provide enough detail that our approach could be replicated by an independent study group, thereby enhancing the transparency of the study.

Trial registration
ClinicalTrials.gov, NCT03509350. Registered on 26 April 2018.
Progressive structural bone changes and their relationship with treatment in patients with psoriatic arthritis: a longitudinal HR-pQCT study
Authors: Wu Dongze , Griffith James F. , Lam Steven H. M. , Wong Priscilla C. H. , Shi Lin , Li Edmund K. , Cheng Isaac T. , Li Tena K. , Hung Vivian W. , Qin Ling , Tam Lai-Shan 
Published: December 2019

AbstractBackgroundAlthough the short-term effects of tumor necrosis factor alpha (TNF-α) and interleukin-17A (IL-17A) inhibition on the structural changes in psoriatic arthritis (PsA) using high-resolution peripheral quantitative computed tomography (HR-pQCT) have been reported, no studies have investigated the long-term structural changes in PsA patients receiving routine care. We reported longitudinal changes of erosions and enthesiophytes using HR-pQCT and their relationship with treatments in PsA patients over a 5-year period.MethodsHR-pQCT examination at the second and third metacarpal heads (MCH2 and MCH3) was performed in 60 PsA patients at baseline and after 5 years. The size of each individual lesion was quantified. Erosion and enthesiophyte progression were defined as change exceeding the smallest detectable change (SDC).ResultsA total of 108 bone erosions and 99 enthesiophytes were detected at baseline. Three new bone erosions but no new enthesiophytes were evident at 5 years. A significant increase in mean (±SD) erosion (0.58 ± 1.50 mm3,P < 0.001) and enthesiophyte (0.47 ± 0.76 mm3,P < 0.001) volume was observed. Erosion and enthesiophyte progression were found in 37/111 (33.3%) and 50/99 (50.5%) lesions, respectively. During this 5-year period, 26 (43%) out of the 60 patients achieved sustained Disease Activity index for PSoriatic Arthritis (DAPSA) low disease activity (LDA) (SDL group, defined as achieving DAPSA-LDA at both baseline and 5 years). Fourteen (23%) out of 60 patients received a TNF inhibitor throughout the 5-year period (TNFi group). Fewer erosions progressed (12/51 [23.5%] vs 25/60 [41.7%],P = 0.047) and the increased in enthesiophyte volume was significantly less (0.28 ± 0.67 vs 0.61 ± 0.80 mm3,P = 0.048) in the SDL group than in the non-SDL group. However, no significant difference between the TNFi and non-TNFi groups was detected in terms of the change in volume or progression of bone erosion and enthesiophyte.ConclusionDamage accrual in terms of bone erosion and enthesiophyte was observed in PsA patients over a period of 5 years despite receiving routine clinical care. Nonetheless, sustained control of disease activity may be able to prevent these bony damages.
Epigenetic therapy of novel tumour suppressor ZAR1 and its cancer biomarker function
Authors: Deutschmeyer Verena , Breuer Janina , Walesch Sara K. , Sokol Anna M. , Graumann Johannes , Bartkuhn Marek , Boettger Thomas , Rossbach Oliver , Richter Antje M. 
Published: December 2019

Abstract
Background
Cancer still is one of the leading causes of death and its death toll is predicted to rise further. We identified earlier the potential tumour suppressor zygote arrest 1 (ZAR1) to play a role in lung carcinogenesis through its epigenetic inactivation.

Results
We are the first to report that ZAR1 is epigenetically inactivated not only in lung cancer but also across cancer types, and ZAR1 methylation occurs across its complete CpG island. ZAR1 hypermethylation significantly correlates with its expression reduction in cancers. We are also the first to report that ZAR1 methylation and expression reduction are of clinical importance as a prognostic marker for lung cancer and kidney cancer. We further established that the carboxy (C)-terminally present zinc-finger of ZAR1 is relevant for its tumour suppression function and its protein partner binding associated with the mRNA/ribosomal network. Global gene expression profiling supported ZAR1's role in cell cycle arrest and p53 signalling pathway, and we could show that ZAR1 growth suppression was in part p53 dependent. Using the CRISPR-dCas9 tools, we were able to prove that epigenetic editing and reactivation of ZAR1 is possible in cancer cell lines.

Conclusion
ZAR1 is a novel cancer biomarker for lung and kidney, which is epigenetically silenced in various cancers by DNA hypermethylation. ZAR1 exerts its tumour suppressive function in part through p53 and through its zinc-finger domain. Epigenetic therapy can reactivate the ZAR1 tumour suppressor in cancer.
ZMYND10, an epigenetically regulated tumor suppressor, exerts tumor-suppressive functions via miR145-5p/NEDD9 axis in breast cancer
Authors: Wang Yan , Dan Liangying , Li Qianqian , Li Lili , Zhong Lan , Shao Bianfei , Yu Fang , He Sanxiu , Tian Shaorong , He Jin , Xiao Qian , Putti Thomas C. , He Xiaoqian , Feng Yixiao , Lin Yong , Xiang Tingxiu 
Published: December 2019

Abstract
Background
Recent studies suggested that ZMYND10 is a potential tumor suppressor gene in multiple tumor types. However, the mechanism by which ZMYND10 inhibits breast cancer remains unclear. Here, we investigated the role and mechanism of ZMYND10 in breast cancer inhibition.

Results
ZMYND10 was dramatically reduced in multiple breast cancer cell lines and tissues, which was associated with promoter hypermethylation. Ectopic expression of ZMYND10 in silenced breast cancer cells induced cell apoptosis while suppressed cell growth, cell migration and invasion in vitro, and xenograft tumor growth in vivo. Furthermore, molecular mechanism studies indicated that ZMYND10 enhances expression of miR145-5p, which suppresses the expression of NEDD9 protein through directly targeting the 3'-untranslated region of NEDD9 mRNA.

Conclusions
Results from this study show that ZMYND10 suppresses breast cancer tumorigenicity by inhibiting the miR145-5p/NEDD9 signaling pathway. This novel discovered signaling pathway may be a valid target for small molecules that might help to develop new therapies to better inhibit the breast cancer metastasis.
What to expect, and how to improve online discussion forums: the instructors’ perspective
Authors: de Lima Dhanielly P. R. , Gerosa Marco A. , Conte Tayana U. , de M. Netto José Francisco 
Published: December 2019

AbstractOnline discussion forums are asynchronous communication tools that are widely used in Learning Management Systems. However, instructors and students face various difficulties, and instructors lack a guide on what strategies they can use to achieve a more participatory forum environment. This work aims to identify benefits and difficulties of using online discussion forums from the instructors’ point of view, and to provide a list of strategies and improvements that can mitigate the challenges and lead to a more participatory forum. We used coding procedures to analyze data collected through semi-structured interviews. The results of our exploratory analysis are relevant to the distance learning community and can inform instructors, developers, and researchers to help them improve the quality of mediation and use of forums.
Comparison and analysis of two forms of harvesting functions in the two-prey and one-predator model
Authors: Liu Xinxin , Huang Qingdao 
Published: December 2019

AbstractA new way to study the harvested predator–prey system is presented by analyzing the dynamics of two-prey and one-predator model, in which two teams of prey are interacting with one team of predators and the harvesting functions for two prey species takes different forms. Firstly, we make a brief analysis of the dynamics of the two subsystems which include one predator and one prey, respectively. The positivity and boundedness of the solutions are verified. The existence and stability of seven equilibrium points of the three-species model are further studied. Specifically, the global stability analysis of the coexistence equilibrium point is investigated. The problem of maximum sustainable yield and dynamic optimal yield in finite time is studied. Numerical simulations are performed using MATLAB from four aspects: the role of the carrying capacity of prey, the simulation about the model equations around three biologically significant steady states, simulation for the yield problem of model system, and the comparison between the two forms of harvesting functions. We obtain that the new form of harvesting function is more realistic than the traditional form in the given model, which may be a better reflection of the role of human-made disturbance in the development of the biological system.
Diagnostic performance in T staging for patients with esophagogastric junction cancer using high-resolution MRI: a comparison with conventional MRI at 3 tesla
Authors: Yuan Yuan , Chen Luguang , Ren Shengnan , Wang Zhen , Chen Yukun , Jin Aiguo , Li Shuai , Fang Xu , Wang Tiegong , Bian Yun , Yang Qingsong , Bai Chenguang , Hao Qiang , Lu Jianping 
Published: December 2019

Abstract
Background
To investigate and compare the diagnostic performance in T staging for patients with esophagogastric junction cancer using high-resolution magnetic resonance imaging (HR MRI), as compared with conventional MRI at 3 Tesla.

Methods
A total of 118 patients with pathologically confirmed esophagogastric junction cancer were included and underwent multiparameter HR MRI (Cohort 1, 62 patients) or conventional MRI (Cohort 2, 56 patients). T2-weighted, T1-weighted, diffusion-weighted and contrast-enhanced T1-weighted images of each patient were evaluated by two radiologists who determined the preoperative T staging by consensus. Using pathologic staging as the gold standard, the consistency between HR MRI and pathology and between conventional MRI and pathology in T staging was calculated and compared. The overall accuracy, overstatement and understatement of HR MRI and conventional MRI in T staging of patients with esophagogastric junction cancer were computed and compared. Moreover, the diagnostic performance of HR MRI and conventional MRI in T staging (≤ T1 and ≥ T4) of patients with esophagogastric junction cancer were evaluated.

Results
There were no significant differences in age (p = 0.465) and sex (p = 0.175) between Cohorts 1 and 2. Excellent agreement was observed in the T staging of patients with esophagogastric junction cancer between pathology and HR MRI (kappa = 0.813), while moderate agreement was observed between pathology and conventional MRI (kappa = 0.486). Significant differences were observed in overall accuracy (88.7% vs 64.3%, p = 0.002) and understatement (1.6% vs 26.8%, p < 0.001) but not for overstatement (9.7% vs 8.9%, p = 0.889) in T staging between HR MRI and conventional MRI techniques. For differentiating the T stages of ≤ T1 from ≥ T2 and the T stages of ≤ T3 from ≥ T4, no significant differences were observed between the imaging techniques.

Conclusions
HR MRI has good diagnostic performance and may serve as an alternative technique in the T staging of patients with esophagogastric junction cancer in clinical practice.
Regeneration patterns in Mexican pine-oak forests
Authors: Alfaro Reyna Teresa , Martínez-Vilalta Jordi , Retana Javier 
Published: December 2019

Abstract
Background
Global change is causing an increase in the incidence of natural and anthropogenic disturbances on forests, which frequently interact synergistically and promote changes in forest structure, composition and functioning. In this study we evaluate the regeneration of Pinaceae and Fagaceae species in pure and mixed stands in Mexico to determine if current regeneration patterns are indicative of changes in the relative dominance of these two tree families, as observed in other temperate regions. We also identify the environmental factors that determine the regeneration patterns of Pinaceae and Fagaceae species in these forests.

Results
We use data from two consecutive surveys of the National Inventory of Forests and Soils of Mexico (INFyS), obtained in 2004–2009 and 2009–2014. Our results show that the spatial patterns of regeneration are affected by forest structure, by climate, by the type and intensity of disturbances and by land tenure. Importantly, the presence and abundance of Fagaceae regeneration is generally higher than that of Pinaceae, and tends to be favoured (relative to Pinaceae) under warmer climates and by the presence of wildfires.

Conclusions
The higher regeneration of Fagaceae relative to Pinaceae under warmer and fire-prone conditions could have important impacts on the composition and functioning of Mexican temperate forests under ongoing climate change, as well as affect their resilience to future disturbances.
IVF outcomes after hysteroscopic metroplasty in patients with T- shaped uterus
Authors: Uyar Esra , Usal Deniz , Selam Belgin , Cincik Mehmet , Bagis Tayfun 
Published: December 2019

Abstract
Background
T- shaped uterus may be associated with infertility and adverse pregnancy outcomes. Hysteroscopic metroplasty may improve the reproductivity for these cases. To our knowledge, there is no data in literature about the clinical consequences of in vitro fertilization (IVF) in patients undergoing hysteroscopic metroplasty for T-shaped uterus. The principal objective of the current study is to assess the impact of hysteroscopic metroplasty for T-shaped uterus on the reproductive outcomes of IVF.

Methods
IVF outcomes of 74 patients who underwent hysteroscopic metroplasty for T- shaped uterus and 148 patients without any uterine abnormalities and with diagnosis of unexplained infertility (control group) were retrospectively analyzed.

Results
Patients in metroplasty and control groups were comparable with respect to age, BMI, partner’s age and duration of infertility. Number of patients with a history of pregnancy beyond 20 weeks of gestation was significantly lower in the metroplasty group (4.1% vs 18.2%; p < 0.05). Number of previous unsuccessful cycles and percentage of patients with ≥3 unsuccessful IVF cycles (35.1% vs 17.6%; p < 0.05) were significantly higher in the metroplasty group. There were no significant differences in the reproductive outcomes such as the pregnancy rate, clinical pregnancy or live birth rate between the metroplasty and control groups. There were non-significant trends for higher rates of miscarriage (18.8% vs 8%, p > 0.05) and biochemical pregnancy (20.0% vs 10.7%, p > 0.05) in the metroplasty group compared to the control group.

Conclusions
Reproductive results of the IVF cycles after hysteroscopic correction of T-shaped uterus were comparable to those of the patients without any uterine abnormalities and with diagnosis of unexplained infertility. Hysteroscopic metroplasty may contribute to improved IVF outcomes in patients with T-shaped uterus.
True brachial artery aneurysm after arteriovenous fistula closure following renal transplantation: a case report and literature review
Authors: Toyota Satoshi , Inoue Kentaro , Kurose Shun , Yoshino Shinichiro , Nakayama Ken , Yamashita Sho , Morisaki Koichi , Furuyama Tadashi , Mori Masaki 
Published: December 2019

Abstract
Background
A brachial artery aneurysm (BAA) is a rare condition accounting for 5% of all peripheral arterial aneurysms. More cases of true BAAs after arteriovenous fistula (AVF) closure have been reported in the past two decades.

Case presentation
A 60-year-old man who underwent AVF closure after renal transplantation had a true BAA on his left elbow that had grown within the past 6 months. We successfully performed an open repair with end-to-end anastomosis. No complications occurred for 1 year.

Conclusions
High flow due to AVF and some collateral factors such as the use of steroids and immunosuppressants after renal transplantation, arteriosclerosis, and chronic mechanical stimulation might contribute to BAA formation.
Comparing videos and a 3D virtual environment for teaching school-related functional skills and behaviors to students with ADHD or developmental dyslexia, displaying challenging behaviors: a case study
Authors: Fokides Emmanuel , Chronopoulou Maria-Ioanna , Kaimara Polyxeni 
Published: December 2019

AbstractThe study presents the results of a comparative study in which videos and a 3D virtual environment were used for teaching school-related functional skills to students with ADHD or developmental dyslexia, displaying challenging behaviors. The participating students (sixteen 8 to 9 years old) were divided into two groups. To the first, videos were used and the second used the virtual environment. To both, a school environment was presented, students observed how they were expected to behave, and had to demonstrate what they have learned. Each student attended a total of three two-hour sessions. Data were collected by means of observations. The results indicated that students in the second group significantly improved their functional skills in terms of the number of behaviors that were retained and manifested in the real school environment. Thus, it can be argued that virtual environments are a promising tool for teaching functional skills to students with ADHD or developmental dyslexia, displaying challenging behaviors. Implications for research and practice are also discussed.
Development of the Health Awareness and Behaviour Tool (HABiT): reliability and suitability for a Canadian older adult population
Authors: Agarwal Gina , Pirrie Melissa , Angeles Ricardo , Marzanek Francine , Parascandalo Jenna 
Published: December 2019

AbstractBackgroundDetermining the effectiveness of community-based health promotion and disease prevention programs requires an appropriate data collection tool. This study aimed to develop a comprehensive health questionnaire for older adults, called the HABiT, and evaluate its reliability, content validity, and face validity in assessing individual health-related items (e.g., health status, healthcare utilization) and five specific scales: knowledge, current health behaviors (risk factors), health-related quality of life (HRQoL), perceived risk and understanding, and self-efficacy.MethodsIterative survey development and evaluation of its psychometric properties in a convenience sample of 28 older adults (≥ 55 years old), half from a low-income population. Following item generation, the questionnaire was assessed for content validity (expert panel), face validity (participant feedback), internal consistency of each scale (Cronbach’s alpha), and test-retest reliability for each item and scale (Pearson’srand phi correlations, as appropriate).ResultsQuestions were drawn from 15 sources, but primarily three surveys: Canadian Community Health Survey, Canadian Diabetes Risk Questionnaire (CANRISK), and a survey by the Canadian Hypertension Education Program. Expert consensus was attained for item inclusion and representation of the desired constructs. Participants completing the questionnaire deemed the questions to be clear and appropriate. Test-retest reliability for many individual items was moderate-to-high, with some exceptions for items that can reasonably change in a short period (e.g., perceived day-to-day stress). Of the five potential scales evaluated, two had acceptable internal consistency (Cronbach’s alpha ≥ 0.60) and a subset of one scale also had acceptable internal consistency. Test-retest reliability was high (correlation ≥ 0.80) for all scales and sub-scales.ConclusionsThe HABiT is a reliable and suitable comprehensive tool with content and face validity that can be used to evaluate health promotion and chronic disease prevention programs in older adults, including low-income older adults. Some noted limitations are discussed. Data collected using this tool also provides a diabetes risk score, health literacy score, and quality-adjusted life years (QALYs) for economic analysis.
Review of modeling and control strategy of thermostatically controlled loads for virtual energy storage system
Authors: Xie Kang , Hui Hongxun , Ding Yi 
Published: December 2019

AbstractThe increasing penetration of renewable energy sources (RESs) brings more power generation fluctuations into power systems, which puts forward higher requirement on the regulation capacities for maintaining the power balance between supply and demand. In addition to traditional generators for providing regulation capacities, the progressed information and communication technologies enable an alternative method by controlling flexible loads, especially thermostatically controlled loads (TCLs) for regulation services. This paper investigates the modeling and control strategies of aggregated TCLs as the virtual energy storage system (VESS) for demand response. First, TCLs are modeled as VESSs and compared with the traditional energy storage system (ESS) to analyze their characteristic differences. Then, the control strategies of VESS are investigated in microgrid and main grid aspects, respectively. It shows that VESS control strategies can play important roles in frequency regulation and voltage regulation for power systems’ stability. Finally, future research directions of VESS are prospected, including the schedulable potential evaluation, modeling of TCLs, hierarchical control strategies of VESS considering ESSs and RESs and reliability and fast response in frequency control for VESS.