bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Reamer Drilling Performance in Deepwater Gulf of Mexico Wells
Authors: Soares Cesar , Armenta Miguel , Panchal Neilkunal 
Published: March 2020

SummaryReamers are an integral part of deepwater Gulf of Mexico (GOM) drilling and their performance significantly impacts the economics of well construction. This paper presents a novel programmatic approach to model rate of penetration (ROP) for reamers and improve drilling efficiency. Three field implementations demonstrate value added by the reamer drilling optimization (RDO) methodology.Facilitated by user interface panels, the RDO workflow consists of surface and downhole drilling data filtering and visualization, detection of rock formation boundaries, frictional torque (FTRQ) and aggressiveness estimation, ROP modeling with analytical equations and machine learning (ML) algorithms [regression, random forests, support vector machines (SVMs), and neural networks], and optimization of drilling parameters. ROP model coefficients and bit and reamer aggressiveness are dependent on lithology and computed from offset well data. Subsequently, when planning a nearby well, bottomhole assembly (BHA) designs are evaluated on the basis of drilling performance and weight and torque distributions between cutting structures to avoid early reamer wear and dysfunctions. Geometric programming establishes optimal drilling parameter roadmaps according to operational limits, downhole tool ratings, rig equipment power constraints, and adequate hole cleaning.Separate ROP models are trained for reamer-controlled and bit-controlled ROP zones, defined by the proportion of surface weight on bit (WOB) applied at the reamer, in every rock formation. This novel concept enables ROP prediction with the appropriate model for each well segment depending on which cutting structure limits drilling speed. In the first of the three RDO applications with field data from deepwater GOM wells, optimal bit-reamer distances are determined by analyzing reamer weight load in uniform salt sections. Next, ROP modeling for the addition or removal of a reamer from the BHA is used in contrasting well designs to conceivably alleviate a USD 16 million casing inventory surplus. Finally, active optimization constraints are investigated to reveal drilling performance limiters, justifying equipment upgrades for a future deepwater GOM well.The proposed innovative workflow and methodology apply to any drilling optimization scenario. They benefit the practicing engineer interested in drilling performance optimization by providing insights on how different cutting structure sizes affect ROP behavior and ultimately aiding in the selection of appropriate bit and reamer diameters and optimal operational parameters.
Busulfan systemic exposure and its relationship with efficacy and safety in hematopoietic stem cell transplantation in children: A meta-analysis
Authors: Feng Xinying , Wu Yunjiao , Zhang Jingru , Li Jiapeng , Zhu Guanghua , FAN Duanfang , Yang Changqing , Zhao Libo 
Published: March 2020

Abstract

Background: Busulfan (Bu) is a key component of several conditioning regimens used before hematopoietic stem cell transplantation (HSCT). However, the optimum systemic exposure (expressed as the area under the concentration-time curve [AUC]) of Bu for clinical outcome in children is controversial. Methods: Research on pertinent literature was carried out at PubMed, EMBASE, ClinicalTrials.gov and the Cochrane Library. Observational studies were included, which compared clinical outcomes above and below the area under the concentration-time curve (AUC) cut-off value, which we set as 800, 900, 1000, 1125, 1350, and 1500 µM × min. The primary efficacy outcome was notable in the rate of graft failure. In the safety outcomes, incidents of veno-occlusive disease (VOD) were recorded, as well as other adverse events. Results: Thirteen studies involving 548 pediatric patients (aged 0.3-18 years) were included. Pooled results showed that, compared with the mean Bu AUC (i.e., the average value of AUC measured multiple times for each patient) of > 900 µM × min, the mean AUC value of <900 µM × min significantly increased the incidence of graft failure (RR=3.666, 95% CI:1.419, 9.467). The incidence of VOD was significantly decreased with the mean AUC <1350 µM × min (RR=0.370, 95% CI: 0.205-0.666) and <1500 µM × min (RR=0.409, 95% CI: 0182-0.920). Conclusions: In children, Bu mean AUC above the cut-off value of 900 µM × min (after every 6-hour dosing) was associated with decreased rates of graft failure, while the cut-off value of 1350 µM × min were associated with increased risk of VOD in children, particularly for the patients without VOD prophylaxis therapy. Further well-designed prospective and multi centric randomized controlled trials with larger sample size are necessary before putting our result into clinical practices.
Combined use of apatinib mesylate and vinorelbine versus vinorelbine alone in recurrent or metastatic triple-negative breast cancer: study protocol for a randomized controlled clinical trial
Authors: Wu Shuo , Zhang Liang , Li Huan , Xu Junnan , Jiang Cui , Sun Tao 
Published: March 2020

Abstract
Background: The emergence of new molecular targeted drugs provides new prospects for the treatment of advanced breast cancer; the future therapeutic trend includes chemotherapy combined with molecular targeted therapy. Apatinib mesylate, a novel, small anti-angiogenic agent, highly selectively inhibits the activity of vascular endothelial growth factor receptor-2 tyrosine kinase. Apatinib mesylate also blocks the signaling of vascular endothelial growth factor binding to its receptor, thereby strongly inhibiting tumor angiogenesis and exerting an anti-tumor effect. However, a randomized controlled clinical trial of apatinib combined with vinorelbine for triple-negative breast cancer (TNBC) has not been reported. We will compare the therapeutic effect of vinorelbine alone, or in combination with apatinib mesylate, in patients with recurrent or metastatic TNBC in North China who have received at least two drug treatments, including anthracyclines and taxanes.
Methods/analysis: This study is a triple-blind, randomized, placebo-controlled, parallel-group clinical trial. We plan to include 210 female patients with locally recurrent or metastatic TNBC, admitted at the Liaoning Cancer Hospital & Institute, Northeast China. All enrolled patients will be randomized to oral vinorelbine alone (40 mg, thrice a week [Mondays, Wednesdays, and Fridays] in each 3-week cycle), or in combination with oral apatinib mesylate (500 mg, once daily in each 3-week cycle). Radiographic assessment will be performed every 6 weeks for 36 weeks, and every 9 weeks thereafter. The primary outcome is progression-free survival, and secondary outcomes include overall survival, disease control rate, objective response rate, and incidence of adverse events at grades 3 and 4, as defined by the National Cancer Institute Common Toxicity Criteria Version 4.0. Outcome measures will be evaluated at baseline (< 2 weeks before starting treatment), every 6 weeks during treatment, and at 4 weeks and every 3 months after treatment discontinuation.
Discussion: Based on the data from this trial, we hope to identify a treatment plan that is suitable for female TNBC patients in Northeast China who have been treated with anthracyclines and taxanes.
Trial registration: ClinicalTrials.gov (identifier: NCT03932526). Registered on April 30, 2019.
Association of timed up and go test outcomes with future incidence of cardiovascular disease and mortality in adults aged 66 years: Korean national representative longitudinal study over 5.7 years
Authors: Son Ki Young , Shin Dong Wook , Lee Ji Eun , Kim Sang Hyuck , Yun Jae Moon , Cho Belong 
Published: March 2020

Abstract
Background: The timed up and go test (TUG) is one of the most widely used tests of mobility. We aimed to examine whether the TUG is associated with cardiovascular (CV) events, CV mortality, and all-cause mortality.
Methods: Subjects in the senior cohort database of the Korean National Health Insurance Service (2002–2013) who completed the TUG as part of the National Screening Program for Transitional Ages (NSPTA) during 2007–2008 were identified. An abnormal TUG result was defined as a time ≥10 seconds. Cox proportional hazard models were used to assess the associations between TUG results and CV events, CV mortality, and all-cause mortality.
Results: The mean follow-up period was 5.7 years. Incidence rates of CV events in the normal and abnormal TUG groups were 7.93 and 8.98 per 1,000 person-years, while CV mortality rates were 0.96 and 1.51 per 1,000 person-years, respectively. In a fully adjusted model, we found that abnormal TUG results were not associated with the incidences of CV events and CV mortality. However, abnormal TUG results (≥10 sec) resulted in a 2.9-fold increase in CV mortality in women (adjusted hazard ratio 2.90, 95% confidence interval 1.15 – 7.30). Further, participants lacking certain CV risk factors, such as current cigarette smoking, obesity, or diabetes, had a higher CV mortality rate when TUG results were abnormal.
Conclusions: Abnormal TUG results in subjects aged 66 years were associated with future CV mortality in women and in subjects without obesity, diabetes, or cigarette smoking. In patient with mobility impairment, physicians should consider CV disease risk, especially in women.
Cryptococcal antigenemia and its predictors among HIV infected patients in resource limited settings: a systematic review
Authors: Derbie Awoke , Mekonnen Daniel , Woldeamanuel Yimtubezinash , Abebe Tamrat 
Published: March 2020

Abstract
Background: Cryptococcosis is an opportunistic fungal infection that primarily affects people with advanced HIV/AIDS and is an important cause of morbidity and mortality around the globe. By far the most common presentation of the disease is cryptococcal meningitis (CM), which leads to an estimated 15-20% of all HIV related deaths worldwide, 75% of which are in sub-Saharan Africa. However, to the best of our knowledge there is quite limited reviewed data that on the epidemiology of cryptococcal antigenemia in a large HIV-infected population in resource limited settings.
Methods: Articles published in English irrespective of the time of publication were systematically searched using comprehensive search strings from PubMed/Medline and SCOPUS. In addition, Google Scholar and Google databases were searched manually for grey literature. Two reviewers independently assessed study eligibility, extracted data, and assessed risk of bias. The magnitude of cryptococcal antigenemia and its predictors were presented with descriptive statistics and summary measures. The pooled prevalence of cryptococcal antigenemia was also determined with 95% confidence interval (CI).
Result: Among 2941 potential citations, we have included 22 studies with a total of 8,338 HIV positive individuals. The studies were reported in ten different countries during the year (2007-2018). Most of the articles reported the mean CD4 count of the participants <100 cells/µl. The pooled prevalence of cryptococcal antigenemia at different CD4 count and ART status was at 8% (95%CI: 6-10%) (ranged between 1.7% and 33%). Body mass index (BMI) <18.5kg/m2, CD4 count <100 cells, presenting with headache and male gender were reported by two or more articles as an important predictors of cryptococcal antigenemia.
Conclusions: Implementing a targeted screening of HIV patients with low BMI, CD4 count <100 cells, having headache and males; and treatment for asymptomatic cryptococcal disease should be considered. Additional data is needed to better define the epidemiology of cryptococcal antigenemia and its predictors in resource limited settings in order to design prevention, diagnosis, and treatment strategies.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Authors: Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A. , Dornburg Alex 
Published: March 2020

Abstract
Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource. Results We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question. Conclusions TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.
Clinical Features and Survival of Pregnancy-Associated Breast Cancer: A Retrospective Study of 203 Cases in China
Authors: Han Bo-yue , Li Xiao-guang , Zhao Hai-yun , Hu Xin , Ling Hong 
Published: March 2020

Abstract
Background: Pregnancy-associated breast cancer (PABC) is an aggressive disease, and sinceChinese authoritybegan to encourage childbearing in 2015, the incidence of PABC has increased. This study investigated the characteristics and survival of PABC patients. Methods: Patients with PABC who underwent surgery at Fudan University, Shanghai Cancer Center between 2005 and 2018 were enrolled.Data concerning the tumor characteristics, maternal state (whether first or non-first pregnancy ) and survival outcome were recorded. Pearson Chi-square tests were used to compare the characteristics of the tumors, and Kaplan-Meier methods were used to perform the survival analysis. Results: Overall, 203 PABC patients were recruited. Since 2015, 65.5% of non-first pregnant women were diagnosed with breast cancer, it’s 5.7 fold of the incidence of PABC in non-first pregnant women. No significant differences in tumor characteristics were observed between the patients who were in their first pregnancy and those in non-first pregnancy. Among the entire PABC population, luminal B breast cancer accounted for the largest proportion (38.4%), followed by triple-negative breast cancer (TNBC, 30.0%). The distribution of the molecular subtypes of PABC and non-PABC differed (P<0.001) as follows: in the PABC patients, Luminal B 38.4%, Triple negative breast cancer (TNBC) 30.1%, Human Epidermal Growth Factor Receptor 2 (HER-2) overexpression 15.8%, and Luminal A 10.8%; in the non-PABC patients, Luminal A 50.9%, Luminal B 20.1%, TNBC 17.4%, and HER-2 overexpression 8.0%. The 3-year disease free survival (DFS) of all PABC patients was 80.3%. The 3-year DFS of the patients in the first-pregnancy group was 78.4%, and that of the patients in the non-first-pregnancy group was 83.7% (P=0.325). Conclusions: Our study proved that the proportion of women who developed PABC during the second or third pregnancy was extremely high relative to the newborn populations. The patients in the PABC population tended to present more luminal B and TNBC breast cancer than the non-PABC patients.
A cross-sectional study of the relationships between different components of sarcopenia and brachial ankle pulse wave velocity in community-dwelling elderly
Authors: Rong Yu-Dong , Bian Ai-Lin , Hu Hui-Ying , Ma Yue , Zhou Xin-Zi 
Published: March 2020

Abstract
Background
Declination of skeletal muscle mass or sarcopenia is associated with the arterial stiffness. However, but it is unclear whether muscle strength and physical performance; important contributors of sarcopenia are associated with the arterial stiffness. The aim of this study was to investigate the relationship between sarcopenia, the components of sarcopenia and arterial stiffness among elderly population.
Methods
Four hundred and fifty community dwelling elderly participants (266 male, and 184 female, >65 years) were enrolled in this study. Each participant received general medical examinations in Tianjin First Center Hospital. Based on the diagnostic criteria for sarcopenia in older people developed by the Asian Working Group for Sarcopenia (AWGS), 89 participants were separated into the sarcopenia group. The living habits, disease status, general status and laboratory examinations of all participants were collected. The body composition (including appendicular skeletal muscle mass , and visceral fat area (VFA) was measured by bioimpedance analysis. Handgrip strength (HS), usual gait speed (GS), and brachial ankle pulse wave velocity (baPWV) were measured.
Results
Sarcopenia participants had higher baPWV, nutrition risk and lower appendicular skeletal muscle index(ASMI), HS, GS, body mass index(BMI), triacylglycerol(TG), serum albumin(ALB) and creatinine(Cr) than the non-sarcopenia participants; Sarcopenia participants also had higher visceral fat area (VFA)compared to non-sarcopenia participants (p<0.05). ASMI and HS were negatively associated with baPWV (t=-5.807, p=0.000 and t=-3.085, p=0.002), but the relationship between baPWV, and GS was not statistically significant (t=-0.862, p=0.389) by multivariable linear regression. After adjusting for confounders, a multivariate logistic regression analysis revealed that sarcopenia was related to age, BMI, sports and baPWV in community dwelling elderly.
Conclusions
ASMI and HS were negatively associated with baPWV in community dwelling elderly in China; and baPWV was a risk factor of sarcopenia.
Knowledge Level of Cancer Symptoms and Risk Factors in the Gaza Strip: A Cross-sectional Study
Authors: Elshami Mohamedraed , Elshami Alaa , Alshorbassi Nabeela , Alkhatib Mohammed , Ismail Iyad , Abu-Nemer Khitam , Hana Mustafa , Qandeel Ahmed , Abdelwahed Ahmed , Yazji Hamza , Abuamro Hisham , Matar Ghadeer , Alsahhar Ahmed , Abolamzi Ahmed , Baraka Obay , Elblbessy Mahmood , Samra Tahani , Bottcher Bettina 
Published: March 2020

Abstract
Background
In low-income settings, cancer is often diagnosed in advanced stages due to late presentation. Good public awareness of cancer signs and symptoms has a positive impact on the time patients take before they present to healthcare professionals. Therefore, this study examined public knowledge of cancer signs and symptoms as well as risk factors in Gaza.
Methods
This was a cross-sectional study. Participants were recruited from adult visitors (≥18 years) to governmental hospitals covering all five governorates of Gaza, and adolescent students (15 to 17 years) from ten high schools in corresponding locations. An Arabic version of the Cancer Awareness Measure (CAM) was completed in a face-to-face interview. It described demographic data and knowledge of: cancer prevalence, age-related risk, signs and symptoms as well as risk factors both in recall and recognition questions.
Results
Of 3033 participants invited, 2886 completed the CAM (response rate= 95.2%). Adult mean age ± standard deviation (SD) was 33.7±11.7 years and that of adolescents was 16.3±0.8 years. Half of the participants (n=1457, 50.5%) were adolescent (781 females; 53.6%) and 1429 (49.5%) were adult (702 females; 49.1%). About two thirds (n=1885) thought about cancer as unrelated to age. Only 196 participants (6.8%) identified colorectal cancer as the most common cancer among men. Awareness of cancer signs/symptoms was poor to fair, where ‘lump’ was most commonly recognized (n= 2227, 77.2%) and ‘change of bowel habit’ the least (n=670, 23.2%). Only 217 participants (7.5%) had a good level of recognizing risk factors with ‘smoking’ being the most identified and ‘eating less than five portions of fruits and vegetables a day’ the least. There was a higher likelihood for adults to identify most cancer signs/symptoms and risk factors than adolescents, except for recalling ‘unexplained pain’, ‘persistent cough/hoarseness’, ‘non-healing ulcer’, ‘smoking’, and ‘eating less than five portions of fruits and vegetables a day’.
Conclusion
Public awareness of cancer signs/symptoms and risk factors needs to improve to facilitate early presentation and diagnosis in Gaza. Combining the delivery of public campaigns with tailored education to population groups, including the youth, may increase their knowledge and maintain its impact.
Vitamin D status among postmenopausal osteoporotic women: a hospital based cross-sectional study from Northern Sri Lanka.
Authors: Suganthan Navaneethakrishnan , Kumanan Thirunavukarasu , Kesavan Vithegi , Aravinthan Mahalingam , Rajeshkannan Nadarajah 
Published: March 2020

Abstract
Background Vitamin D deficiency is common among post-menopausal women and it is important to treat vitamin D deficiency to prevent falls and fractures in patients with osteoporosis. Few studies examined the prevalence of vitamin D deficiency in general population of Sri Lanka but no studies to date done among post-menopausal women with osteoporosis. This is the first study of such kind conducted to evaluate the serum vitamin D levels and factors related to Vitamin D deficiency among postmenopausal women.Methodology Hospital based Cross -sectional study was conducted at the Endocrine Unit, Teaching Hospital from January to December 2018.During the study period 105 postmenopausal women registered for DEXA scan with Endocrine Unit were recruited to the study. Data collection was done by investigators and blood sample was taken from each participant by registered nursing officers and sample was analysed by using immunohistochemistry assays. Serum Vitamin D levels were categorized and data analysis was done using SPSS 26.Results Mean age of 105 postmenopausal women was 67.7 with minimum 33 and maximum 84 years. Mean Vitamin D levels were 27.5(range11.7-52.5ng/ml). Vitamin D levels were adequate in only 36.2% (95%CI: 27.4-45.7) of women, 44% had insufficient levels and deficiency was present in 19% (95%CI: 12.4-27.4) of participants. Among the 105 women 20% were vegetarian and 53% of them consuming milk on average 3 days per week, 76.2% consuming fish on average 2 days per week, 64.8% consuming egg on average 1 day per week. Furthermore seventy five participants (71.4%) reported adequate level of sun exposure (>30minutes).Commonly reported vitamin deficiency symptoms includes paraesthesia (57.1%),bone pain (55.2%), easy fatigability (54.3%), malaise (51.4%), muscle cramps (43.8%) and proximal myopathy (40.0%).Among 71(66.7%) completed bone density assessment,38% (27.3-49.7) of them showed osteoporosis range. Vertebral Z score showed a significant correlation with vitamin D level(r-0.252, P-0.034).Conclusion Prevalence of vitamin D deficiency is relatively high among the post-menopausal women with a provisional diagnosis of osteoporosis. It is essential to correct vitamin D deficiency with supplementation when initiating treatment for osteoporosis. So vitamin D testing is desirable in decision making to treat or not to treat.