bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation
Authors: Hu Ercha , Meng Yuan , Ma Ying , Song Ruiqi , Hu Zhengxiang , Li Min , Hao Yunwei , Fan Xinli , Wei Liting Wei , Fan Shilong , Chen Songqin , Zhai Xuejie , Li Yongchang , Wei Zhang , Zhang Yang , Guo Qingyong , Bayin Chahan 
Published: September 2020

Abstract
Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.
Is the perceived neighborhood built environment associated with domain-specific physical activity in Latin American adults? An eight-country observational study
Authors: Ferrari Gerson , Werneck André O. , Silva Danilo Rodrigues , Kovalskys Irina , Gómez Georgina , Rigotti Attilio , Sanabria Lilia Yadira Cortés , García Martha Cecilia Yépez , Pareja Rossina G. , Herrera-Cuenca Marianella , Zimberg Ioná Zalcman , Guajardo Viviana , Pratt Michael , Cristi-Montero Carlos , Rodríguez-Rodríguez Fernando , Marques Adilson , Cerin Ester , Dyck Delfien Van , Pires Carlos André Miranda , Fisberg Mauro 
Published: September 2020

Abstract
Background: Characteristics of the neighborhood built environment are associated with physical activity (PA). However, few studies with representative samples have examined environmental correlates of domain-specific PA in Latin America. We examined the associations of the perceived neighborhood built environment with domain-specific PA in a large sample of adults from eight Latin American countries.Methods: This study examined data from 8185 adults (aged 18–65 years) from eight Latin American countries. The Neighbourhood Environment Walkability Survey - Abbreviated (NEWS-A) scale was used to assess perceptions of land use mix–diversity, land use mix-access, street connectivity, walking/cycling facilities, aesthetics, safety from traffic, and safety from crime. Perceived proximity from home to public open spaces (metropolitan parks, playgrounds, public squares) and to shopping centers was also measured. Transport-related and leisure-time PA were assessed using the long form of the International Physical Activity Questionnaire. Both logistic and linear regression models were estimated on pooled data.Results: Perceptions of higher land use mix-access (OR: 1.40; 95% CI: 1.22,1.61), the existence of many alternative routes in the neighbourhood (1.12; 1.04,1.20), slow speed of traffic (1.19; 1.03,1.35) and few drivers exceeding the speed limits (1.09; 1.03,1.15) were associated with greater odds of reporting at least 10 min/week of transport-related PA. Perceptions of higher levels of land use mix-diversity, better aesthetics and greater safety from crime, the presence of crosswalks and pedestrian signals, and greater proximity of shopping centers were associated with more min/week of transport-related PA. Perceptions of higher land use mix-diversity (1.12; 1.05,1.20), higher land use mix-access (1.27; 1.13,1.43), more walking/cycling facilities (1.18; 1.09,1.28), and better aesthetics (1.10; 1.02,1.18) were associated with greater odds of engaging in at least 10 min/week of leisure-time PA versus none. Perceptions of higher land use mix-diversity were associated with more min/week of leisure PA.Conclusions: Different perceived neighborhood built environment characteristics were associated with domain-specific PA among adults from Latin America countries. Interventions designed to modify perceptions of the neighbourhood built environment might influence initiation or maintenance of domain-specific PA.Trial registration: ClinicalTrials.Gov NCT02226627. Retrospectively registered on August 27, 2014.
Unilateral synchronous papillary renal neoplasm with reverse polarity and clear cell renal cell carcinoma: a case report with KRAS and PIK3CA mutations
Authors: Lee Hyun Jung , Shin Dong Hoon , Park Joon Young , Kim So Young , Hwang Chung Su , Lee Jung Hee , Kim Jee Yeon , Sol Mee Young , Nam Jong Kil 
Published: September 2020

Abstract
Background: The presence of histologically different neoplasms in the same organ is rare in pathologic practice. We report the first case of synchronous clear cell renal cell carcinoma (clear cell RCC) and papillary renal neoplasm with reverse polarity (PRNRP) with comprehensive immunohistochemical and molecular characterization using next-generation sequencing (NGS). Case presentation: A 61-year-old man was incidentally found to have a left renal mass on imaging studies performed for workup of left back pain and urine color change for one week. A laparoscopic left radical nephrectomy was performed. Gross examination showed lobulated masses measuring 5.6 × 4.0 × 3.3 cm in the upper to mid pole and 1.1 × 1.0 × 1.0 cm in the lower pole. Microscopic findings revealed these to be two different separate masses of clear cell renal cell carcinoma and papillary renal neoplasm with reverse polarity. NGS analyses revealed KRAS gene mutation (c.35G>T/p.G12V in exon 2) in the papillary renal neoplasm with reverse polarity, with PIK3CA gene mutation restricted to the clear cell renal cell carcinoma (c.1624G>A/p.E542K in exon 10).Conclusions: We report here an extraordinarily rare case of synchronous renal tumors of papillary renal neoplasm with reverse polarity and clear cell renal cell carcinoma. We identified simultaneous KRAS and PIK3CA mutations in two different renal masses in the same kidney for the first time. New pathologic assessment with comparative molecular analysis of mutational profiles may be helpful for tumor studies.
Baseline Thrombopoietin Level is Associated with Platelet Count Improvement in Thrombocytopenic Chronic Hepatitis C Patients After Direct-Acting Antiviral Agent Therapy
Authors: Chen Yen-Chun , Ko Ping-Hung , Lee Chi-Che , Tseng Chih-Wei , Tseng Kuo-Chih 
Published: September 2020

Abstract
Background
Thrombocytopenia can rapidly improve in chronic hepatitis C (CHC) patients receiving direct-acting antiviral agents (DAA). The role of baseline (BL) thrombopoietin (TPO) in this phenomenon is unclear.
Methods
From June 2016 to February 2019, a total of 104 CHC patients receiving DAA, with a sustained virologic response and BL thrombocytopenia, at Dalin Tzu Chi Hospital, were enrolled in this retrospective study. Significant platelet count improvement and platelet count improvement ratio were analyzed for correlation with BL TPO.
Results
This cohort included 40 men (38.5%). Seventy-two (69.2%) patients had advanced fibrosis. The platelet count [median (range)] increased from 110.5 (32–149) × 103/µL at BL to 116.5 (40–196) and 118.0 (35–275) × 103/µL at end of treatment (EOT) and 12 weeks after EOT (P12), respectively, (EOT vs. BL, P < 0.001; P12 vs. BL, P < 0.001).BL TPO was positively correlated with significant platelet count improvement (P < 0.001), platelet count improvement ratio at EOT (P = 0.004), and P12 (P < 0.001). The area under the receiver operating characteristic curve and optimal cutoffs (pg/ml) were 0.77 (95% confidence interval, 0.67–0.86) and 120, respectively, for significant platelet count improvement prediction. The sensitivity, specificity, and accuracy were 88.6%, 71.7%, and 78.8%, respectively.
Conclusions
BL TPO level might be a useful marker for predicting significant platelet count improvement in thrombocytopenic patients after successful DAA therapy.
Deep Active Learning for Classifying Cancer Pathology Reports
Authors: De Angeli Kevin , Gao Shang , Alawad Mohammed , Yoon Hong-Jun , Schaefferkoetter Noah , Wu Xiao-Cheng , Durbin Eric B , Doherty Jennifer , Stroup Antoinette , Coyle Linda , Penberthy Lynne , Tourassi Georgia 
Published: September 2020

Abstract
Background: Automated text classiﬁcation has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often diﬃcult and expensive. Active learning techniques may mitigate this challenge by reducing the amount of labelled data required to eﬀectively train a model. In this study, we analyze the eﬀectiveness of eleven active learning algorithms on classifying subsite and histology from cancer pathology reports using a Convolutional Neural Network (CNN) as the text classiﬁcation model. Results: We compare the performance of each active learning strategy using two diﬀerently sized datasets and two diﬀerent classiﬁcation tasks. Our results show that on all tasks and dataset sizes, all active learning strategies except diversity-sampling strategies outperformed random sampling, i.e., no active learning. On our large dataset (15K initial labelled samples, adding 15K additional labelled samples each iteration of active learning), there was no clear winner between the diﬀerent active learning strategies. On our small dataset (1K initial labelled samples, adding 1K additional labelled samples each iteration of active learning), marginal and ratio uncertainty sampling performed better than all other active learning techniques. We found that compared to random sampling, active learning strongly helps performance on rare classes by focusing on underrepresented classes. Conclusions: Active learning can save annotation cost by helping human annotators eﬃciently and intelligently select which samples to label. Our results show that a dataset constructed using eﬀective active learning techniques requires less than half the amount of labelled data to achieve the same performance as a dataset that constructed using random sampling.
The Perception and Disposal Practices of Unused And Expired Medicines By Households In an Urban Municipality, Southwest Nigeria: A Comparative Cross-Sectional Study.
Authors: Aluko Olufemi O. , Imbianozor G. T , Jideama C. O. , Ogundele O. V. , Fapetu T. E , Afolabi Olusegun T. 
Published: September 2020

Abstract
Background: Medicines are formulations for the prevention and treatment of diseases and symptoms. Pharmaceutical wastes are products of unused, damaged, and expired medicines (UEMs) which pose a disposal challenge globally. Previous studies have shown that environmental disposal of medicines has health and environmental consequences. Hence, this study aims to determine and compare the management of household UEMs in a heterogeneous municipality in southwest Nigeria.Methods: The study was comparative, cross-sectional in design. Multi-stage sampling identified respondents, who are females, experienced in the handling and safekeeping of medicines. The study sample was 404 and recorded a 93% response rate. Data were analysed by IBM-SPSS, version 20. Continuous and categorical variables were presented in tables as mean(±SD), proportions (%) while bar charts highlight salient findings. Differences between LDS and HDS values were determined by 𝝌2(Pα>0.05).Results: 53.4% and 71.2% of respondents respectively had good knowledge and positive attitudes to safe disposal of UEMs. At least 31.5% households do not stock medicines in homes while 1-2 sachets of antimalarial (57.3%), analgesics (52.7%) and antibiotics (49.7%) medicines were inventoried in households and significantly different between low-density (LD) and high-density (HD) settlements. 72.9% and 67.8%; 47.9% and 55.6% respondents in LD and HD settlements respectively disposed of household solid and liquid UEMs in thrash-bins, though 34.9% (LDS) and 16.7% (HDS) disposed of liquid UEMs in the toilet/sink. There were significant differences in medicines abundance and disposal practices between LD and HD settlements for solid and liquid medications. 37.1% of respondents perceived consequences for the current methods of disposing of UEMs, which include accidental ingestion (76.6% vs 26.7%) and land pollution (69.6% vs 36.7%) and water pollution (72.4% vs 32.8%) and drugs toxicity (58.3% vs 32.8%), respectively in LD and HD settlements.Conclusions: Respondents good knowledge and positive attitudes contrasted the poor UEMs disposal practice. Most of the households’ medicines were antimalaria and analgesics and there were disparities in the disposal of solid and liquid medicines, between LD and HD settlements, respectively. Appropriate legislation, compliance monitoring and enforcement are drivers to incentive-driven, sound recovery systems for UEMs to alleviate the consequences of current disposal practices in Nigeria.
Resources-based Strategies for Health Promotion of Students With Different General Conditions and Different Origins
Authors: Böckelmann Irina , Darius Sabine , Thielmann Beatrice 
Published: September 2020

Abstract
Background: The aim of this study is to investigate the study-/work-related behavior and experience patterns of students, taking into account their origins as well as the stressful general conditions. Methods: A total of 194 students (41.8% women, 58.2% men, 58.7% German and 41.3% foreign students) were evaluated to their strains during the study and study-/work-related Behavior and Experience Patterns (AVEM). Four potentially stressful conditions were taken into account.Results: For only 14% of foreign students, but 45% of German students risk patterns for work-related behavior and experience were found. Study-/work-related behaviour and experience patterns depend on the origin of the students. Resources during study were significantly higher among students of German origin. Conclusions: A study-related strengthening of resources is necessary, which can be viewed as a competitive advantage when choosing a study location.
Perspectives of Infant Active Play: A Qualitative Comparison of Working Versus Stay-at-home Parents
Authors: Snyder Kailey , Rech John P , Masuda Kim , Dinkel Danae 
Published: September 2020

Abstract
Background: Parents play a key role in infants’ development through their interactions and the type of environment they provide for their child to promote active play. The amount of time parents are able to spend with their infant is dependent on their working status, yet few studies have explored parents’ perceptions of their infants’ active play by parental working status. The purpose of this study was to explore parents’ perceptions of active play and compare responses between working and stay at home parents. Methods: Twenty-nine parents participated in this qualitative study by completing a one-time, in-person semi-structured interview based on the Theory of Planned Behavior. Themes were developed and the proportion of working and stay at home parents who responded within each theme were used to compare for differences between working status using a directed content analysis approach. Results: All parents believed active play could have a positive effect on their child’s development through physical, social and emotional, cognitive, and/or language and communication development. However, stay at home parents reported a broader impact of active play across these domains; whereas working parents most often referenced active play as impacting infant’s physical development. Social and emotional interactions were the highest reported form of active play among all parents. Additionally, all parents described similar barriers to increasing the time for active play. The most commonly reported barrier for all parents was time or schedule followed by care needs of the infant, environmental concerns, and need for restrictive devices (e.g., car seats). More stay at home parents than working parents reported the care needs of the infant as being a barrier. Recommendations for active play were not widely known amongst all parents, with a higher percentage of working parents reporting they would listen to a healthcare provider.Conclusions: Working status of parents seems to have implications on certain aspects and perceptions of active play which in turn may influence infants’ physical development. Future studies should objectively assess the impact of parents’ working status on infant development and explore how gender of the parent may serve as a confounding variable.
The germline/somatic DNA damage repair gene mutations modulate the therapeutic response in Chinese patients with advanced pancreatic ductal adenocarcinoma
Authors: Shui Lin , Li Xiaofen , Peng Yang , Tian Jiangfang , Li Shuangshuang , He Du , Li Ang , Tian Bole , Li Mao , Yi Cheng , Cao Dan 
Published: September 2020

Abstract
Background: PDAC is a fatal disease with molecular heterogeneity, inducing differences in biological behavior and therapeutic strategy. NGS profiles of pathogenic alterations in Chinese PDAC population are limited. We conducted a retrospective study to investigate the predictive role of DNA damage repair (DDR) mutations in precise medicine. Methods: NGS were performed on resected tissues or peripheral blood from 195 Chinese PDAC patients. Baseline clinical or genetic characteristics, and survival status were collected. The Kaplan–Meier survival analyses were performed by the R version 3.6.1.Results: The main driver genes were KRAS, TP53, CDKN2A, and SMAD4. Advanced patients with KRAS mutation showed worse OS than those without (p=0.048). DDR deficiency was identified in 30 (15.38%) of overall patients, mainly involving BRCA2 (n=9, 4.62%), ATM (n=8, 4.10%) and RAD50 genes (n=3, 1.54%). There was no significant improvement of OS between patients with or without DDR mutations (p=0.88). Treatment with platinum-based chemotherapy (p=0.0096) or olaparib (p=0.018) respectively improved the overall survival of patients with DDR mutation. No statistical correlation between tumor mutation burden (TMB) and DDR mutations was identified. Treatment of PD-1 blockades did not bring significiantly improved OS to DDR-mutated patients than intact DDR group (p=0.14). Conclusions: In this multi-center retrospective study, we showed the role of germline and somatic DDR mutation in predicting the efficacy of olaparib and platinum-based chemotherapy. However, DDR alteration has shown limited value in prediction of hypermutational status and the sensitivity to PD-1 blockade.
A Noninvasive Model to Predict Liver Histology for Antiviral Therapy Decision in Chronic Hepatitis B with Alanine Aminotransferase＜2 Upper Limit of Normal
Authors: Chen Shanshan , Huang Haijun 
Published: September 2020

Abstract
Background and Aim: Although liver biopsy is currently the gold standard to evaluate liver histology, it has many limitations, such as sampling error, cost and risk of complications. This study aims to construct a noninvasive model to predict liver histology for antiviral therapy in chronic hepatitis B (CHB) with alanine aminotransferase (ALT)＜2 times upper limit of normal(ULN).Methods: We retrospectively analyzed 577 patients with CHB who received liver biopsy and whose ALT was less than 2 ULN. Then they were randomly divided into a training group and a validation group. Through logistic regression analysis, a novel predictive model was constructed in the training group to predict significant changes in liver histology [necro-inflammatory activity grade (G) ≥2 or fibrosis stage (S) ≥2] and then validated in the validation group.Results: If liver biopsy showed moderate or severe inflammation or significant fibrosis, antiviral treatment was recommended. Aspartate aminotransferase (AST), anti-hepatitis B virus core antibody (anti-HBC) and glutamine transpeptidase (GGT) were identified as independent predictors for antiviral therapy, with area under the ROC curve (AUROC) of 0.649, 0.647 and 0.616, respectively. Our novel model index, which combined AST, anti- HBC and GGT with AUROC of 0.700 and 0.742 in estimation set and validation set.Conclusions: This study established a noninvasive model to predict liver histology for antiviral treatment decision in patients with CHB with ALT < 2 ULN, which can reduce the clinical needs of liver biopsy.
Appraisal of Long-time Outcomes After Curative Surgery in Elderly Patients with Gastric Cancer: A Propensity Score Matching Analysis
Authors: Matunaga Tomoyuki , Ishiguro Ryo , Miyauchi Wataru , Shishido Yuji , Miyatani Kozo , Yamamoto Manabu , Tokuyasu Naruo , Takano Shuichi , Sakamoto Teruhisa , Honjo Soichiro , Saito Hiroaki , Fujiwara Yoshiyuki 
Published: September 2020

Abstract
Background: This study was conducted to assess the long-term outcomes of elderly patients among propensity-score-matched gastric cancer patients after curative gastrectomy and to propose the proper management of elderly gastric cancer patients.Methods: We enrolled 626 patients with gastric cancer who underwent curative gastrectomy at our institution between January 2004 and December 2015. To minimize selection bias among 2 groups, propensity score matching was performed.Results: Patients were divided into an elderly group over 75 years old (EP group; n=186) and a non-elderly group (NEP group; n=440). After propensity score matching, patients were divided into EP group (n=186) and NEP group (n=186). Five-year overall survival was significantly lower in the EP group than in the NEP group, consistent with a subgroup analysis of each stage. However, the 5-year disease-specific survival among all enrolled patients and those with stage I and II disease did not differ significantly. Moreover, in the subgroup of stage III patients, 5-year disease-specific survival was significantly lower in the EP group (23.0%) than in the NEP group (59.4%; P=0.004). Because elderly patients with stage III disease had an extremely poor prognosis, we decided to compare the two groups with stage III. The EP group contained significantly fewer patients with D2 lymphadectomy (P=0.002) and adjuvant chemotherapy (P<0.001) than the NEP group. Multivariate analysis revealed that older age and lymphatic invasion were independent prognostic factors. C-reactive protein to albumin ratio was significantly higher in patients in the EP group than in the NEP group (P=0.046), and the prognostic nutritional index was significantly lower in EP group patients than NEP group patients (P=0.045). Conclusions: Elderly gastric cancer patients with stage III disease showed poorer disease-specific survival compared with non-elderly patients, which may be due to fewer D2 lymphadenectomies, a lack of adjuvant chemotherapy, and a poorer nutritional and inflammatory background. The safe induction of standard lymphadenectomy and adjuvant chemotherapy with perioperative aggressive nutritional support may improve the prognosis of elderly gastric cancer patients with stage III disease.