bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging analysis of 13 rare cases of renal collecting (Bellini) duct carcinoma patients in northern China: a case series and literature review.
Authors: Lyu Zhehao , Liu Lili , Li Huimin , Wang Haibo , Liu Qi , Chen Tingting , Xu Meiling , Tian Lin , Fu Peng 
Published: October 2020

Abstract
Background: Collective duct carcinoma (CDC) is a highly malignant kidney tumor which is rare in clinical. We report our 12-year experience of Collecting (Bellini) duct carcinoma (CDC) and retrospectively analyzed patients and tumour characteristics, clinical manifestations, different imaging characteristics including CT, MRI and PET/CT. Methods: From January 2007 to December 2019, we retrospectively examined all renal tumors and identifed 13 cases of CDC from 3 medical centers in the northern China. All 13 patients underwent CT scan, 8 of whom underwent dynamic enhanced CT scan, 2 underwent PET/CT scan and 1 underwent MRCP examination. The lesions were divided into nephritis type and mass type according to the morphology of the tumors.Results: The study group included 10 men and 3 women, with an average age of 64.23±10.74 years old. Of these 13 patients, the main clinical manifestations include gross hematuria, flank pain or waist discomfort. The mean tumour size was 8.48 ± 2.48 cm. In this group of cases, 6 (46.2%) cases are cortical-medullary involved type, 7 (53.8%) cases are cortex-medullary-pelvis involved type. 11 (84.6%) cases were nephritis type and 2 (15.4%) cases were mass type. The lesions appeared solid or complex solid and cystic on CT and MRI. The parenchymal part of 13 CDC tumors showed isodensity or slightly higher density on unenhanced CT scan. the parenchymal part of 13 CDC tumors showed isodensity or slightly higher density on unenhanced CT scan. Two patients with PET/CT showed increased radioactivity intake. Evidence of intra-abdominal metastatic disease was present on CT in 9 ( 69.2% ) cases. The incidence of metastasis reached 69%.Conclusions: The Collecting (Bellini) duct carcinoma has its certain imaging characteristics which were different from the other renal cell carcinoma. A renal tumor should be considered as CDC when it locates in the junction zone of the renal cortex and medulla, with unclear border, slight enhancement and metastases in early stage. PET/CT can greatly enrich the key information of diagnosis, surgery and treatment options, which provide significant help to the clinic.
Repetitive Transcranial Magnetic Stimulation on Chronic Tinnitus: A Systematic Review and Meta-Analysis
Authors: Liang Zhengrong , Cheng Gui , Huang Lingfei , Zhang Tao , Yang Haidi , Jia Haiying 
Published: October 2020

Abstract
Background: Although the clinical efficacy and safety of repetitive transcranial magnetic stimulation (rTMS) in the treatment of chronic tinnitus have been frequently examined, the results remain controversial. Therefore, we systematically meta-classified clinical trials concerning the effects of rTMS to evaluate its clinical efficacy and safety. Methods: Studies of rTMS for chronic tinnitus were retrieved in PubMed, Embase, and Cochrane Library due April 2020. Review Manager 5.3 software was employed for data synthesis and Stata 13.0 software for analyses of publication bias and sensitivity. Results: Twenty-nine randomized studies representing 1,228 chronic tinnitus patients were included. Compared with sham-rTMS, rTMS exhibited significant improvements in the tinnitus handicap inventory (THI) score 1-week (mean difference [MD] -7.92, 95% confidence interval [CI] -14.18,-1.66), 1-month (MD -8.52, 95% CI -12.49, -4.55), and 6-month post-intervention (MD -6.53, 95% CI -11.406,-1.66), the mean change in THI scores 1- (MD -14.86, 95% CI -21.42,-8.29) and 6-month post-intervention (MD -16.37, 95% CI -20.64,-12.11), and the tinnitus questionnaire (TQ) score 1-week post-intervention (MD -8.54, 95% CI -15.56,-1.52). Non-significant efficacy of rTMS was found concerning the THI score 2-week post-intervention (MD -1.51, 95% CI -13.42,-10.40), the mean change in TQ scores 1-month post-intervention (MD -3.67, 95% CI -8.56,1.22), the TQ score 1- (MD -8.97, 95% CI -20.41,2.48) and 6-month post-intervention (MD -7.02, 95% CI -18.18,4.13), and adverse events (odds ratios [OR] 1.11, 95% CI 0.51,2.42). The Egger's and Begg's tests indicated no publication bias ( P = 0.925). Conclusion: This meta-analysis demonstrates that rTMS is effective for chronic tinnitus; however, its safety needs more validations. Restrained by the limited number of included studies and the small sample size, more large randomized double-blind multi-center trials are needed for further verification.
Prevalence and associated factors of undernutrition among pregnant women vising ANC clinics in Silte zone, southern Ethiopia
Authors: Muze Mohammed , Yesse Mubarek , Kedir Shemsu , Mustefa Abdilmejid 
Published: October 2020

Abstract
Background: Maternal undernutrition is highly prevalent in underdeveloped countries. Hence, this study was intended to determine the prevalence and associated factors of undernutrition among pregnant women visiting ANC follow up clinics of health facilities.Method: Facility-based cross-sectional study was conducted from July to January 2019. Systematic random sampling technique was used to select 422 study participants from 11 randomly selected health facilities. Data was collected by using a structured-interviewer administered questionnaire. Mid upper arm circumference (MUAC) was measured by standard non stretchable MUAC tape. Data was entered into a computer using Epi data 3.1 and edited, cleaned, and analyzed using SPSS version 20. Both bivariate and multiple logistic regression analyses were employed to identify factors associated with maternal undernutrition.Result: This study found 21.8% prevalence of undernutrition among study subjects. Age greater than 31 years of women (AOR=0.15; 95% CI: 0.03, 0.93), Birth intervals > 2 years (AOR= 0.18; 95% CI: 0.04, 0.76), good nutritional knowledge (AOR=0.34; 95% CI: 0.17, 0.67), and having no dietary change as a result of current pregnancy AOR=6.02; 95% CI: 2.99, 12.14) were significantly associated with undernutrition.Conclusion and recommendation: The prevalence of undernutrition among pregnant women was 21.8 % current estimate is lower than previously reported in the study area but higher than reported in developed country. Age of women, Birth intervals, and Dietary change as a result of current pregnancy and Nutrition knowledge were important risk factors/ predictors of undernutrition (MUAC < 23 cm). Interventions targeting maternal nutrition education and child spacing with giving special emphasis to adolescent pregnant women are recommended.
Draft Genome Assembly of Passalora sequoiae a Needle Blight Pathogen on Leyland Cypress
Authors: Copes Warren , Caballero Jorge Ibarra , Babiker Ebrahiem , Stewart Jane , Orner Valerie , Windham Alan , Arias Renee 
Published: October 2020

Abstract
Objective: Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the whole genome of P. sequoiae as a resource for primer development and to investigate genotype diversity. Data description: We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress 'Leighton Green' in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 x coverage and were used to confirm accuracy of the consensus sequences.
Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates
Authors: ma qiong , Zhang Qi , Yuan Youhua , Yan Wenjuan , Wang Shanmei , Xu Junhong , Zhang Jiangfeng , Wang Yuming , Li Yi 
Published: October 2020

Abstract
Background: To evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2,342 isolates were obtained from microbial cultures of clinical specimens (e.g., blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People’s Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing.Results: At the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9% and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7% and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2,342) for the Autof MS1000 and 1.5% (34/2,342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was >93%, the identification error rate was <3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification.Conclusions: The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.
Maternal syphilis treatment and pregnancy outcomes: a retrospective study in Jiangxi Province, China
Authors: Wan Zhihua , Zhang Huan , Xu Haigang , Hu Yang , Tan Cai , Tao Yuling 
Published: October 2020

Abstract
BackgroundStudies investigating the associations of maternal syphilis treatment with birth outcomes mainly concentrated in economically developed areas. Limited data are available in economically underdeveloped areas, such as Jiangxi Province. The study aims to investigate the impact of maternal treatment on birth outcomes in Jiangxi Province, China.MethodsData were obtained from the China’s Information System of Prevention of Mother-to-Child Transmission in Jiangxi Province. All syphilis infected pregnant women who delivered ≥28 gestational weeks and were registered in this system between 1 January 2013 and 31 December 2019 were enrolled. Pregnancy outcomes were evaluated by group-specific analyses according to their treatment status, adequacy and initiation time.Results4210 syphilis infected pregnant women were included in the analyses. Infants born to untreated mothers (n = 1364) were at significantly higher risk for stillbirth (adjusted odds ratio (aOR) = 1.74, 95% CI, 1.01-3.00, P = 0.045), preterm birth (aOR = 1.27, 95% CI, 1.02-1.59, P = 0.034) and low birth weight (LBW) (aOR = 1.44; 95% CI, 1.11-1.86, P = 0.006) than those born to treated mothers (n = 2846) after adjustment for confounding factors. A significantly higher risk of stillbirth (aOR = 3.68; 95% CI, 1.62-8.34, P = 0.002), preterm birth (aOR = 2.26; 95% CI, 1.71-3.00, P < 0.001), LBW (aOR = 2.23; 95% CI, 1.59-3.14, P < 0.001) and congenital syphilis (CS) (aOR = 3.63; 95% CI, 1.80-7.31, P < 0.001) was found in infants exposed to mothers treated inadequately (n = 1299) than those treated adequately (n = 1547). No pregnant women who initiated the treatment in the first trimester (n = 682) delivered a neonatal CS case. Compared with mothers who initiated treatment in the first trimester (n = 682), those initiated in the third trimester (n = 1234) suffered an increased risk of stillbirth (aOR = 4.48; 95% CI, 1.31-15.30, P = 0.017), preterm birth (aOR = 2.34; 95% CI, 1.61-3.40, P < 0.001) and LBW (aOR = 3.25; 95% CI, 1.97-5.37, P < 0.001). ConclusionsMaternal treatment, especially early and adequate treatment, plays a crucial role in mitigating adverse pregnancy outcomes among syphilis infected women.
­­­­­­Genomic analysis of worldwide sheep breeds reveals PDGFD as a major target of fat-tail selection in sheep
Authors: Dong Kunzhe , Yang Min , Han Jiangang , Ma Qing , Han Jilong , Song Ziyi , Luosang Cuicheng , Gorkhali Neena Amatya , Yang Bohui , He Xiaohong , Ma Yuehui , Jiang Lin 
Published: October 2020

Abstract
Background: Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this trait. Nevertheless, these studies obtained different candidates. The results of these regional studies were easily biased by the breed structures. Results: To minimize the bias and distinguish the true candidates, we used an extended data set of 968 sheep representing 18 fat-tailed breeds and 14 thin-tailed breeds from around the world, and integrated two statistical tests to detect selection signatures, including Genetic Fixation Index (FST) and difference of derived allele frequency (ΔDAF). The results showed that platelet derived growth factor D (PDGFD) exhibited the highest genetic differentiation between fat- and thin-tailed sheep breeds. Analysis of sequence variation identified that a 6.8-kb region within the first intron of PDGFD is likely the target of positive selection and contains regulatory mutation(s) in fat-tailed sheep. Histological and gene expression analyses demonstrated that PDGFD expression is associated with maturation and hemostasis of adipocytes. Further retrospective analysis of public transcriptomic datasets revealed that PDGFD expression is down-regulated during adipogenesis in both human and mouse, and is higher in fat tissues of obese individuals than that in lean individuals. Conclusions: These results reveal that PDGFD is the predominant factor for the fat tail phenotype in sheep by contributing to adiopogenesis and maintaining the hemostasis of mature adipocytes. This study provides insights into the selection of fat-tailed sheep and has important application to animal breeding, as well as obesity-related human diseases.
Bioelectrical Impedance Analysis-derived Phase Angle as a Determinant of Protein-energy Wasting and Frailty in Maintenance Hemodialysis Patients: retrospective cohort study
Authors: Saitoh Masakazu , Ogawa Masumi , Kondo Hisae , Suga Kiichi , Takahashi Tetsuya , Itoh Haruki , Tabata Yoichiro 
Published: October 2020

Abstract
Background: Phase angle (PA), measured by bioelectrical impedance analysis (BIA) has been studied as indicator of nutritional status or muscle function in hemodialysis (HD) patients. It remains unclear if the phase angle is associated protein-energy wasting (PEW) or frailty, which are common complication in hemodialysis patients. The aim of this study is to determine whether BIA-derived PA is a marker of PEW or frailty in HD patients.Methods: This retrospective observational study included 116 adult HD patients (35% female, 64 ± 12 years of age) in a single dialysis center. Patients were classified according to the PA quartiles into four groups; 1) first quartile: PA<3.7°, 2) second quartile: PA 3.7-4.1°, 3) third quartile: PA 4.2-4.9°and 4) forth quartile: PA ≥ 5.0°. International Society of Renal Nutrition and Metabolism (ISRNM) criteria and Japanese version of Cardiovascular Health Study (J-CHS) criteria were used to identify PEW and frailty.Results: The lower PA group was associated with a greater risk of PEW (35% vs. 24% vs. 21% vs. 3%; p=0.032), frailty (59% vs. 40% vs. 21% vs. 3%; p<0.001). In multivariate logistic regression analysis, the first quartile group was at a significantly greater risk of both PEW and frailty compared with the fourth quartile group after adjusting for other confounding factors. Conclusions: Lower PA was associated with a greater risk of PEW and frailty in HD patients.
Pegylated liposomal doxorubicin in patients with epithelial ovarian cancer
Authors: Yuan Zhen , Zhang Ying , Cao Dongyan , Shen Keng , Li Qingshui , Zhang Guonan , Wu Xiaohua , Cui Manhua , Yue Ying , Cheng Wenjun , Wang Li , Qu Pengpeng , Tao Guangshi , Hou Jianqing , Sun Lixin , Meng Yuanguang , Li Guiling , Li Changzhong , Shi Huirong , Chen Yaqing 
Published: October 2020

Abstract
Objective: To evaluate the efficacy and safety of PLD in treating of in patients who experience epithelial ovarian, fallopian tubal, and peritoneal cancer progression within 12 months after the first-line platinum-based therapy. Methods: This was an open-label, single-arm and multicenter clinical trial. The ORR was the interim primary objective, and the DCR, AEs and QOL were the secondary objectives. The impact of factors on efficacy outcomes, the change trend of CA125 and the artificial platinum-free interval were exploratory endpoints. Results: Totally, 115 patients were enrolled in this study and included in the ITT population. Moreover, 101 patients were included in the safety population. The median follow-up time was 4 months (IQR 2–6). In the ITT population, the confirmed ORR was 37.4% (95% CI, 28.4%-46.4%), and the DCR was 65.2% (95% CI, 56.4%-74.1%). The previous response status to platinum-based chemotherapy and baseline CA125 levels were significantly correlated with the ORR. The ORR was significantly higher in patients with a CA125 decrease after the first cycle than in the patients with a CA125 increase. The most common grade 3 or higher AE was hand-foot syndrome (3 [3.0%] of 101 patients). No statistically significant differences existed between the baseline and the postbaseline questionnaires. Conclusions: For patients who experience platinum-resistant and platinum-refractory relapse, the use of PLD may be acceptable because of the associated satisfactory efficacy, low frequency of AEs and high patient QOL. Moreover, a low CA125 level at baseline and a reduction in CA125 after the first cycle are predictive factors for satisfactory efficacy.
Nonlinear ridge regression improves robustness of cell-type-specific differential expression analysis
Authors: Takeuchi Fumihiko , Kato Norihiro 
Published: October 2020

Abstract
Background: Epigenome-wide association studies (EWAS) and differential gene expression analyses are generally performed on tissue samples, which consist of multiple cell types. Cell-type-specific effects of a trait, such as disease, on the omics expression are of interest but difficult or costly to measure experimentally. By measuring omics data for the bulk tissue, cell type composition of a sample can be inferred statistically. Subsequently, cell-type-specific effects are estimated by linear regression that includes terms representing the interaction between the cell type proportions and the trait. This approach involves two issues, scaling and multicollinearity.Results: First, although cell composition is analyzed in linear scale, differential methylation/expression is analyzed suitably in the logit/log scale. To simultaneously analyze two scales, we applied nonlinear regression. Second, we show that the interaction terms are highly collinear, which is obstructive to ordinary regression. To cope with the multicollinearity, we applied ridge regularization. In simulated data, nonlinear ridge regression attained well-balanced sensitivity, specificity and precision. In real data, nonlinear ridge regression detected signals consistently over the examined cases.Conclusion: Nonlinear ridge regression performed cell-type-specific association test on bulk omics data more robustly than previous methods. The omicwas package for R implements nonlinear ridge regression for cell-type-specific EWAS, differential gene expression and QTL analyses. The software is freely available from https://github.com/fumi-github/omicwas
A nomogram based on pretreatment CT radiomics features for predicting complete response to chemoradiotherapy in patients with esophageal squamous cell cancer
Authors: Luo Hesan , Huang Shao-Fu , Xu Hong-Yao , Li Xu-Yuan , Wu Sheng-Xi , Wu De-Hua 
Published: October 2020

Abstract
Purpose: To develop and validate a nomogram model to predict complete response (CR) after concurrent chemoradiotherapy (CCRT) in esophageal squamous cell carcinoma (ESCC) patients using pretreatment CT radiomic features. Methods: Data of patients diagnosed as ESCC and treated with CCRT in Shantou Central Hospital during the period from January 2013 to December 2015 were retrospectively collected. Eligible patients were included in this study and randomize divided into a training set and a validation set after successive screening. The least absolute shrinkage and selection operator (LASSO) with logistic regression to select radiomics features calculating Rad-score in the training set. The logistic regression analysis was performed to identify the predictive clinical factors for developing a nomogram model. The area under the receiver operating characteristic curves (AUC) was used to assess the performance of the predictive nomogram model and decision curve was used to analyze the impact of the nomogram model on clinical treatment decisions. Results: A total of 226 patients were included and randomly divided into two groups, 160 patients in training set and 66 patients in validation set. After LASSO analysis, seven radiomics features were screened out to develop a radiomics signature Rad-score. The AUC of Rad-score was 0.812 (95%CI: 0.742-0.869, p<0.001) in the training set and 0.744 (95%CI: 0.632-0.851, p=0.003) in the validation set. Multivariate analysis showed that Rad-score and clinical staging were independent predictors of CR status, with P values of 0.035 and 0.023, respectively. A nomogram model incorporating Rad-socre and clinical staging was developed and validated, with an AUC of 0.844 (95％CI: 0.779-0.897) in the training set and 0.807 (95％CI: 0.691-0.894) in the validation set．Delong test showed that the nomogram model was significantly superior to the clinical staging, with P<0.001 in the training set and P=0.026 in the validation set. The decision curve showed that the nomogram model was superior to the clinical staging when the risk threshold was greater than 25%. Conclusion: We developed and validated a nomogram model for predicting CR status of ESCC patients after CCRT. The nomogram model was combined radiomics signature Rad-score and clinical staging. This model provided us with an economical and simple method for evaluating the response of chemoradiotherapy for patients with ESCC.