bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in Expression of Genes Related to Steroidgenesis in Abdominal Subcutaneous Adipose Tissue of Pregnant Women with and without PCOS
Authors: Emami Neda , Moini Ashraf , Yaghmaei Parichehreh , Akbarinejad Vahid , Shahhoseini Maryam , Alizadeh AliReza 
Published: October 2020

Abstract
Background: It was hypothesized that steroid-related gene expressions in the adipose tissue (AT) of women are different between women with and without polycystic ovary syndrome (PCOS). However, little information exists regarding pregnant women suffering from PCOS when interrelationships among maternal PCOS, patient’s quality of life and offspring’s health is a consideration issue in health and diseases. Our objectives were to compare the mRNA expression levels of key steroid-converting enzymes in subcutaneous AT of PCOS vs. non-PCOS pregnant women.Methods: The subjects were 48 pregnant women (12 PCOS and 36 non–PCOS women) undergoing cesarean section, from whom abdominal subcutaneous AT samples were retrieved. Expressions of fifteen genes related to steriodogenesis were investigated using quantitative real-time PCR. Results: No significant differences were found with respect to age, BMI (before pregnancy and at delivery day), gestational period and parity among non-PCOS and PCOS pregnant women. Most of the sex steroid-converting genes except 17β-Hydroxysteroid dehydrogenases2 (17BHSD2), were highly expressed on the day of delivery in subcutaneous AT. PCOS patients showed significantly higher mRNA levels of steroidgenic acute regulator (STAR; P<0.001), cytochrome P450 monooxygenase (CYP11A1; P<0.05), 17α-hydroxylase (CYP17A1; P<0.05), and 11β-Hydroxysteroid dehydrogenase (11BHSD1-2; P<0.05). The expression of steroid 21-hydroxylase (CYP21) in non-PCOS women was 4-fold higher than for PCOS women (P < 0.001). There were no significant differences between relative expression of aromatase cytochrome P450 (CYP19A1), 3β-hydroxysteroid dehydrogenase1-2 (3BHSD1-2), and 17BHSD family (1, 3, 5, 7, and 12) between the two groups.Conclusion: The expression levels of genes related to sex steroids metabolism were similar in age-matched and BMI- matched non-PCOS and PCOS pregnant women at delivery day. However, the alterations in gene expressions involved in glucocorticoids and mineralocorticoid metabolism was shown which warrants further studies regards functional activity. More attention should be given to AT of PCOS mothers that was previously ignored.
Adaptive sample size determination for the development of clinical prediction models
Authors: Christodoulou Evangelia , Smeden Maarten van , Edlinger Michael , Timmerman Dirk , Wanitschek Maria , Steyerberg Ewout W , Calster Ben Van 
Published: October 2020

Abstract
Background: We suggest an adaptive sample size calculation method for developing clinical prediction models, in which model performance is monitored sequentially as new data comes in. Methods: We illustrate the approach using data for the diagnosis of ovarian cancer (n=5914, 33% event fraction) and obstructive coronary artery disease (CAD; n=4888, 44% event fraction). We used logistic regression to develop a prediction model consisting only of a-priori selected predictors and assumed linear relations for continuous predictors. We mimicked prospective patient recruitment by developing the model on 100 randomly selected patients, and we used bootstrapping to internally validate the model. We sequentially added 50 random new patients until we reached a sample size of 3000, and re-estimated model performance at each step. We examined the required sample size for satisfying the following stopping rule: obtaining a calibration slope ≥0.9 and optimism in the c-statistic (ΔAUC) <=0.02 at two consecutive sample sizes. This procedure was repeated 500 times. We also investigated the impact of alternative modeling strategies: modeling nonlinear relations for continuous predictors, and applying Firth’s bias correction.Results: Better discrimination was achieved in the ovarian cancer data (c-statistic 0.9 with 7 predictors) than in the CAD data (c-statistic 0.7 with 11 predictors). Adequate calibration and limited optimism in discrimination was achieved after a median of 450 patients (interquartile range 450-500) for the ovarian cancer data (22 events per parameter (EPP), 20-24), and 750 patients (700-800) for the CAD data (30 EPP, 28-33). A stricter criterion, requiring ΔAUC <=0.01, was met with a median of 500 (23 EPP) and 1350 (54 EPP) patients, respectively. These sample sizes were much higher than the well-known 10 EPP rule of thumb and slightly higher than a recently published fixed sample size calculation method by Riley et al. Higher sample sizes were required when nonlinear relationships were modeled, and lower sample sizes when Firth’s correction was used. Conclusions: Adaptive sample size determination can be a useful supplement to a priori sample size calculations, because it allows to further tailor the sample size to the specific prediction modeling context in a dynamic fashion.
Influence of Convalescent Plasma Therapy on the Mortality in COVID-19 Patients: A Meta-Analysis
Authors: Liu Xingxiang , Wu Jing , Zhang Yuanyuan , Dong Chen 
Published: October 2020

Abstract
As of August15, 2020, more than 21,155,600 people were infected and about 761,264 were expired due to SARS-CoV-2 infection worldwide. The extreme spread of the emerging virus makes the disease a serious problem for public health. However, a curative treatment or effective specific vaccine againstSARS-CoV-2 infection is unavailable. Recently, several studies have been performed to evaluate the effects of COVID-19 convalescent plasma transfusion on the clinical outcomes in patients with severe/critical COVID-19 [1-5]. However, the results from these studies aredatable, and thus its useremains investigational.
A New Optical Coherence Tomography Method for Subfoveal Choroidal Thickness Measurement: A Single-center Observational Study
Authors: Kang Kyung Tae , Jang Ji Hye , Kim Yu Cheol 
Published: October 2020

Abstract
Background: Several macular pathologies are associated with choroidal vascular supply, and thus require choroidal thickness evaluation. However, there is no standard subfoveal choroidal thickness (SFCT) measuring method. This study investigated a new method to measure the SFCT, using optical coherence tomography.Methods: This is a single-center observational study. Eighty-two senior medical students participated as observers and independently measured the SFCT on five standard optical coherence tomography images of healthy adults in a tertiary care setting. They used three different methods: (1) the observer’s own method, (2) the conventional method, perpendicular to the retinal pigment epithelium, and (3) the new method, along a virtual line connecting the umbo with the most elevated point of the ellipsoid. Additionally, the SFCT angle—the angle between the measurement line and the vertical line of the image—was measured and compared between methods. The intraclass correlation coefficient was used to determine interpersonal variability. Results: The intraclass correlation coefficients for SFCT measured by methods 1, 2, and 3 were 0.853, 0.880, and 0.896, respectively (P < 0.001 for all). It was the highest with method 3; the intraclass correlation coefficients SFCT angles were 0.647, 0.842, and 0.307, respectively (P < 0.001 for all).Conclusions: The new method showed the lowest interpersonal variability, and could therefore be a reliable standard for SFCT measurement, even in foveae with a steep slope on optical coherence tomography.Trial registration: Not applicable
Treatment of Hepatocellular Carcinoma-associated Portal Vein Tumor Thrombus Using Combination of Portal Vein Stent Insertion and Endovascular Lodine-125 Seed-strip Implantation Followed by Transcatheter Arterial Chemoembolization- Sorafenib
Authors: Li Shuangxi , Li Baohua , Li Lei , Xu Fangyu , Yang Xujun , Wang Wenhui 
Published: October 2020

Abstract
BackgroundTo evaluate the efficacy of portal vein stent (PVS) insertion and endovascular iodine-125 (125I) seed-strip implantation followed by transcatheter arterial chemoembolization (TACE)-sorafenib (PVS-125I-TACE-S) in patients with hepatocellular carcinoma (HCC)-associated portal vein tumor thrombus (PVTT).MethodsThis retrospective analysis was performed on 53 consecutive HCC patients with PVTT between May 2014 and July 2018. Twenty-eight patients were treated via PVS-125I-TACE-S, and 25 patients were treated by TACE-S. Hepatic function, disease control, and overall survival (OS) in both groups were analyzed. The Albumin-Bilirubin (ALBI) score approach was used as a means of evaluating liver function, and a Cox regression analysis was utilized to determine which factors were linked to treatment outcomes.ResultsNo preoperative differences in ALBI scores between groups (P=0.724), nor did these scores at 1-month postoperative (P=0.666). However, these scores were significantly different at 3 (P=0.007) and 6 (P=0.044) months postoperatively. PVS-125I-TACE-S exhibiting higher rates of disease control (71.4% vs. 44.0%, P=0.043) after 6 months of treatment and extended OS duration (342.0 vs 231.0 days, P=0.007). A stratified analysis revealed OS in patients with type II PVTT did not differ significantly (313.0 vs. 321.0 days, P=0.689), but OS with type III did (344.0 vs. 226.0 days, P=0.002). A multivariate analysis revealed that tumor size > 10 cm was independently predictive of poor prognosis (P=0.002), whereas PVS-125I-TACE-S was a predictor of a favorable patient prognosis (P=0.040).ConclusionPVS-125I-TACE-S represents a potentially viable strategy for improving hepatic functionality, disease control, and OS in HCC with type III PVTT.
Toe flexor strength and foot morphology in older people requiring long-term care due to changes in their means of mobilizing in daily life: a cross-sectional study
Authors: Yokozuka Mieko , Sato Sei 
Published: October 2020

Abstract
Background: Hallux valgus and lesser toe deformity reduce the strength of the toe flexors and are a cause of falls in older people. This study aimed to examine the differences in toe flexor strength and foot morphology in older people requiring long-term care due to changes in the way they mobilize in everyday life.Methods: Eighty-four people aged ≥70 without motor paralysis who are undergoing or had undergone ambulatory rehabilitation. They were divided into those who could mobilize without a wheelchair (walking group, n=54) and those who used a wheelchair to mobilize (wheelchair group, n=30). Presence of diseases, hand grip strength, toe flexor strength, and foot morphology were compared between the two groups.Results: No significant between-group difference in foot morphology was found. Factors related to differences in the means used to mobilize in daily life were a history of fracture, heart disease, and toe flexor strength. In muscle strength of the wheelchair group compared with the mean values of the walking group, the toe flexor strength was significantly more decreased in relation to hand grip strength.Conclusions: Older people who use a wheelchair to mobilize have significantly less toe flexor strength than those who do not despite having no significant difference in foot morphology. Use of a wheelchair is associated with a reduction in toe flexor strength.
Safety measures for COVID-19 do not compromise the outcomes of patients undergoing primary percutaneous coronary intervention: A single center study
Authors: Guan Xiaonan , Zhang Jianjun , Li Yanbing , Ma Ning 
Published: October 2020

Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic impacting nearly 170 countries/regions and millions of patients worldwide. Patients with acute myocardial infarction (AMI) still need to be treated at percutaneous coronary intervention (PCI) centers with relevant safety measures. This study was conducted to assess the therapeutic outcomes of PCI performed under the safety measures and normal conditions. AMI patients undergoing PCI between January 24 to April 30, 2020 were performed under safety measures for COVID-19. Patients received pulmonary computed tomography (CT) and underwent PCI in negative pressure ICU. Cardiac catheterization laboratory (CCL) staff and physicians worked with level Ⅲ personal protection. Demographic and clinical data, such as door-to-balloon (DTB) time, operation time, complications for patients in this period (NCP group) and the same period in 2019 (2019 group) were retrieved and analyzed. NCP and 2019 groups had 37 and 96 patients, respectively. There was no significant difference in age, gender, BMI and comorbidity between the two groups. DTB time and operation time were similar between the two groups (60.0 ± 12.39 vs 58.83 ± 12.85 min, p = 0.636; 61.46 ± 9.91 vs 62.55 ± 10.72 min, p = 0.592). Hospital stay time in NCP group was significantly shorter (6.78 ± 2.14 vs 8.85 ± 2.64 days, p < 0.001). The incidences of malignant arrhythmia and Takotsubo Syndrome in NCP group were higher than 2019 group significantly (16.22% vs 5.21%, p = 0.039; 10.81% vs 1.04% p = 0.008). During hospitalization and 3-month follow-up, the incidence of major adverse cardiovascular events and mortality in the two groups were statistically similar (35.13% vs 14.58%, p = 0.094; 16.22% vs 8.33%, p =0.184). Our analysis showed that safety measures undertaken in this hospital, including screening of COVID-19 infection and use of personal protection equipment for conducting PCI did not compromise the surgical outcome as compared with PCI under normal condition, although there were slight increases in incidence of malignant arrhythmia and Takotsubo Syndrome.
African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors that are associated with immunologic and infectious functions and environmental exposures
Authors: Singh Urminder , Hernandez Kyle , Aronow Bruce , Wurtele Eve 
Published: October 2020

Abstract
The COVID-19 pandemic has affected African American populations disproportionately with respect to prevalence, morbidity, and mortality. Because gene expression profiles represent combined genetic, socioenvironmental, and physiological effects, and could provide therapeutic biomarkers and environmental mitigation strategies, we undertook a large-scale assessment of differential gene expression between African Americans and European Americans. To do this, we mined RNA-Seq datasets from normal and diseased (tumor) conditions whose metadata could be used to evaluate differential patterns. We observed widespread differential expression of genes implicated in COVID-19 and integral to epithelial boundary function, inflammation, infection, and reactive oxygen stress. Notably, expression of the little-studied F8A2 gene is up to 40-fold greater in African
Americans. F8A2, like F8A1, encodes HAP40 protein, which mediates early endosome movement. African American gene expression signatures reveal increased number or activity of esophageal glandular cells and lung ACE2-positive basal keratinocytes. These findings have potential to establish prognostic signatures, refine approaches to minimizing risk of severe infection, and improve precision treatment of COVID-19.
Towards Health System Resiliency: An Agile Systems Modelling Framework for Bed Resource Planning During COVID-19
Authors: Lam Shao Wei Sean , Abdullah Hairil Rizal Bin , Pourghaderi Ahmad Reza , Nguyen Ngoc Hoang Long , Wu Jun Tian , Mohan Somesh Dev S/O , Low Seng Kee , Lee Jiunn Kee , Tan Bo Ren , Han Songhan , Chong Zhi Ying Brendan , Siddiqui Fahad Javaid , Ansah John Pastor , Low G Jenny , Matchar David Bruce , Ong Eng Hock Marcus 
Published: October 2020

Abstract
Background: We describe the development of a dynamic simulation modelling framework to support agile resource planning during the COVID-19 pandemic. The framework takes into consideration the dynamic evolution of the pandemic and the rapidly evolving policies and processes to deal with the ever-changing outbreak scenarios.Methods: A specific use case based on short-term bed resource planning is described within the proposed framework. The simulation model was calibrated against historical data for the Singapore COVID-19 situation. The time period for model calibration was from 1st April till 30th April 2020. The model was used to project for bed resource needs over the period from 1st May 2020 till 31st May 2020. Multivariate sensitivity analysis was also conducted for ICU and general isolation bed demand, length-of-stay (LOS), and age-adjusted conversion rates across different care needs. The unmet needs under various scenarios were also evaluated for planning purposes.Results: Several variants of the agile resource planning model were developed to adapt to the fast-changing COVID-19 situation in Singapore. The use case demonstrated an agile adaptation of the model to account for previously unexpected scenarios. The rapid evolution of the pandemic locally revealed streams of new infections that arose from two distinct sources. The model projections were calibrated with the latest data for short-term projections. The agility in flexing plans and collaborative management structures to rapidly deploy human and capital resources to surge the level of care during the COVID-19 pandemic have proven utility in guiding the allocation of scarce healthcare resources and helped system resiliency.Conclusions: The rapidly evolving COVID-19 pandemic in Singapore has necessitated the development of an agile and adaptable modelling framework that can be quickly calibrated to changes both from demand and supply. The modelling framework is able to deploy systems modelling concepts in a holistic manner. This facilitates the evaluation of complex cause-and-effect relationships. A robust collaborative framework, coupled with the availability of in-depth domain knowledge and accurate and updated data availability ensures a model is realistic, timely and useful.
SARS-CoV-2 historical global testing and genomic variability
Authors: Tannous Halim , Akiki Shadi , Boulos Rasha E. , Eid Charlene El Khoury , Hasbani Ghadi El , Khoueiry Lea Maria , Khoury Lynn El , Tohme Rawan , Moussa Rim , Khazen Georges 
Published: October 2020

Abstract
The world has been dealing with the COVID-19 pandemic since December 2019 and a lot of effort has focused on tracking the spread of the virus by gathering information regarding testing statistics and generating viral genomic sequences. Unfortunately, there is neither a single comprehensive resource with global historical testing data nor a centralized database with summary statistics of the identified genomic variants.We merged different pre-aggregated historical testing data and complemented them with our manually extracted ones, which consist of 6852 historical test statistics from 76 countries/states unreported in any other dataset, at the date of submission, making our dataset the most comprehensive to date. We also analyzed all publicly deposited SARS-CoV-2 genomic sequences in GISAID and annotated their variants. Both datasets can be accessed through our interactive dashboard which also provides important insights on different outbreak trends across countries and states.The dashboard is available at https://bioinfo.lau.edu.lb/gkhazen/covid19. A daily updated version of the datasets can be downloaded from github.com/KhazenLab/covid19-data.
Ultra-reduced phases in ophiolites cannot come from Earth’s mantle
Authors: Ballhaus Chris , Helmy Hassan M. , Fonseca Rául O.C. , Wirth Richard , Schreiber Anja , Jöns Niels 
Published: October 2020

Abstract
Several recent papers have purported to find ultra-reduced minerals—as natural examples—within ophiolitic mantle sections, including SiC moissanite, Fe-Si alloys, various metal carbides, nitrides, and borides. All those phases were interpreted to be mantle derived. The phases are recovered from mineral concentrates and are assigned to the deep mantle because microdiamonds and other ultrahigh-pressure (UHP) minerals are also found. Based on these findings, it is claimed that the mantle rocks of ophiolite complexes are rooted in the transition zone (TZ) or even in the lower mantle, at redox states so reduced that phases like SiC moissanite are stable.
We challenge this view. We report high-temperature experiments carried out to define the conditions under which SiC can be stable in Earth’s mantle. Mineral separates from a fertile lherzolite xenolith of the Eifel and chromite from the LG-1 seam of the Bushveld complex were reacted with SiC at 1600 K and 0.7 GPa. At high temperature, a redox gradient is quickly established between the silicate/oxide assemblage and SiC, of ~12 log-bar units in fO2.
Reactions taking place in this redox gradient allow us to derive a model composition of an ultra-reduced mantle by extrapolating phase compositions to 8 log units below the iron-wüstite equilibrium (IW-8) where SiC should be stable. At IW-8 silicate and oxide phases would be pure MgO end-members. Mantle lithologies at IW-8 would be Fe° metal saturated, would be significantly enriched in SiO2, and all transition elements with the slightest siderophile affinities would be dissolved in a metal phase. Except for the redox-insensitive MgAl2O4 end-member, spinel would be unstable. Relative to an oxidized mantle at the fayalite-magnetite-quartz (FMQ) buffer, an ultra-reduced mantle would be enriched in enstatite by factor 1.5 since the reduction of the fayalite and ferrosilite components releases SiO2. That mantle composition is unlike any natural mantle lithology ever reported in the literature. Phases as reduced as SiC or Fe-Si alloys are unstable in an FeO-bearing, hot, convecting mantle. Based on our results, we advise against questioning existing models of ophiolite genesis because of accessory diamonds and ultra-reduced phases of doubtful origin.
Impacts of bias nonstationarity of climate model outputs on hydrological simulations
Authors: Hui Yu , Xu Yuni , Chen Jie , Xu Chong-Yu , Chen Hua 
Published: October 2020

Abstract
Bias correction methods are based on the assumption of bias stationarity of climate model outputs. However, this assumption may not be valid, because of the natural climate variability. This study investigates the impacts of bias nonstationarity of climate models simulated precipitation and temperature on hydrological climate change impact studies. The bias nonstationarity is determined as the range of difference in bias over multiple historical periods with no anthropogenic climate change for four different time windows. The role of bias nonstationarity in future climate change is assessed using the signal-to-noise ratio as a criterion. The results show that biases of climate models simulated monthly and annual precipitation and temperature vary with time, especially for short time windows. The bias nonstationarity of precipitation plays a great role in future precipitation change, while the role of temperature bias is not important. The bias nonstationarity of climate model outputs is amplified when driving a hydrological model for hydrological simulations. The increase in the length of time window can mitigate the impacts of bias nonstationarity for streamflow projections. Thus, a long time period is suggested to be used to calibrate a bias correction method for hydrological climate change impact studies to reduce the influence of natural climate variability.