bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of long-term anti-seizure medication monotherapy on all-cause death in patients with post-stroke epilepsy: a nationwide population-based study in Taiwan
Authors: Hsu Chia-Yu , Cheng Chun-Yu , Lee Jiann-Der , Lee Meng , Ovbiagele Bruce 
Published: June 2021

Abstract
Objective
We aim to compare the effect of long-term anti-seizure medication (ASM) monotherapy on the risk of death and new ischemic stroke in patients with post-stroke epilepsy (PSE).

Patients and methods
We identified all hospitalized patients (≥ 20 years) with a primary diagnosis of ischemic or hemorrhagic stroke from 2001 to 2012 using the National Health Insurance Research Database in Taiwan. The PSE cohort were defined as the stroke patients (1) who had no epilepsy and no ASMs use before the index stroke, and (2) who had epilepsy and ASMs use after 14 days from the stroke onset. The patients with PSE receiving ASM monotherapy were enrolled and were categorized into phenytoin, valproic acid, carbamazepine, and new ASM groups. We employed the Cox regression model to estimate the unadjusted and adjusted hazard ratios (HRs) with 95 % confidence intervals (CIs) of death and new ischemic stroke within 5 years across all groups, using the new ASM group as the reference.

Results
Of 6962 patients with PSE using ASM monotherapy, 3917 (56 %) were on phenytoin, 1623 (23 %) on valproic acid, 457 (7 %) on carbamazepine, and 965 (14 %) on new ASMs. After adjusting for confounders, compared with new ASM users, phenytoin users had a higher risk of death in 5 years (HR: 1.64; 95 % CI: 1.06–2.55). On the other hand, all ASM groups showed a similar risk of new ischemic stroke in 5 years.

Conclusions
Among patients with PSE on first-line monotherapy, compared to new ASMs, use of phenytoin was associated with a higher risk of death in 5 years.
Local Random Pattern Flap Coverage for Implant Exposure following Open Reduction Internal Fixation via Extensile Lateral Approach to the Calcaneus
Authors: Liu Yingjie , Cai Peihua , Cheng Liang , Li Yanfeng 
Published: June 2021

AbstractBackgroundSkin necrosis and implant exposure most often appear at the corner of Extensile Lateral Approach for open reduction and internal fixation (ORIF) for displaced intra-articular fracture of the calcaneus. Flap transfer is often used for coverage of this implant exposure. We introduced a new simple local random pattern flap to cover the implant exposure.MethodsFrom March 2017 to March 2020, 12 patients with implant exposure after ORIF for displaced intra-articular fracture of the calcaneus were treated with this procedure. The sizes of the defects ranged from 2 × 2 cm2to 5 × 2 cm2. A local random pattern flap was designed according to the defect size. The lower edge of the flap was along with the wound upper edge and extended distally. The upper horizontal incision of the flap was made at the lateral malleolus level with a length of 5–7 cm depending on the wound defect. Then the random pattern flap was elevated and transferred to cover the defect area.ResultsThe mean follow-up duration was 6.3 months (ranging 4–13 months). All 12 flaps were uneventfully healed and all patients were able to wear shoes, and no debulking procedures were required.ConclusionThe local random pattern flap could be a choice for surgeons when implant exposure at the corner of Extensile Lateral Approach to the Calcaneus occurs.
Does vitamin D supplementation improve ovarian reserve in women with diminished ovarian reserve and vitamin D deficiency: a before-and-after intervention study
Authors: Aramesh Shahintaj , Alifarja Touran , Jannesar Ramin , Ghaffari Parvin , Vanda Raziyeh , Bazarganipour Fatemeh 
Published: June 2021

Abstract
Objective
Evaluation of vitamin D supplementation on ovarian reserve in women with diminished ovarian reserve and vitamin D deficiency.

Methods
The study is a before-and-after intervention study that was performed on women with diminished ovarian reserve referred to Shahid Mofteh Clinic in Yasuj, Iran. Eligible women were prescribed vitamin D tablets at a dose of 50,000 units weekly for up to 3 months. Serum levels of vitamin D and AMH were evaluated at the end of 3 months. Significance level was also considered P ≤ 0.05.

Results
Our results have been showed there was a statistically significant difference in vitamin D levels of participants before [12.1(6.5)] and after [26(9.15)] the intervention (P < 0.001). Moreover, there was a statistically significant difference in serum AMH levels of participants before [0.50(0.44)] and after [0.79(0.15)] the intervention (P=0.02 ).

Conclusion
In conclusion, the results of the current study support a possible favorable effect of vitamin D on increase AMH expression by acting on the AMH gene promoter. Therefore, it is possible that vitamin D increases AMH levels without changing the antral follicle count/ovarian reserve.
Malignant transformation of hepatic endometriosis: a case report and literature review
Authors: Wang Dandan , Yang Qing , Wang Huaitao , Liu Chang 
Published: June 2021

Abstract
Background
Extrapelvic endometriosis is defined as the presence of ectopic endometrial tissue in structures outside the pelvis. Although extra-pelvic endometriosis is generally considered benign conditions, malignant potential within endometriotic foci occurs even after definitive surgery. Malignant transformation of hepatic endometriosis is extremely rare. Preoperative diagnosis of this cancer is difficult, and no guidelines on the optimal management currently exist. Here, we present a case report of malignant transformation of hepatic endometriosis and a brief literature review to highlight the current knowledge of the prevalence, clinical features, diagnosis, and management of this condition.

Case presentation
A 50-year-old woman with a 2-year duration of progressive right upper quadrant abdominal pain was admitted to the hospital. She underwent hysterectomy and bilateral salpingo-oophorectomy for benign conditions 4 years prior. Tumor markers demonstrated elevated carbohydrate antigen (CA)-199 112U/mL (normal range: 0–35U/mL) only. Radiological imaging suggested the presence of a 10.7 × 7.7-cm mass in the right lobe of the liver extending to the diaphragm. The intraoperative frozen sections suggested malignant tumor. Right hepatectomy with infiltrating diaphragm resection was performed. The final pathology with immunohistochemistry staining confirmed endometrioid adenocarcinoma in the liver originating from preexisting hepatic endometriosis. After the multidisciplinary team meeting, the consensus was surgery followed by adjuvant chemotherapy. To our knowledge, this is the first case of Chinese woman of a malignant liver tumor originating from endometriosis ever reported by reviewing the current English medical literature.

Conclusion
Though rare, extrapelvic endometriosis-associated cancers should be considered as differentiated diagnosis even after hysterectomy and bilateral salpingo-oophorectomy. This case highlights the importance of collaborative efforts across multiple disciplines for accurate diagnosis and appropriate treatment of malignant transformation of hepatic endometriosis.
Development, production and evaluation of 2-dimensional transfer tattoos to simulate skin conditions in health professions education
Authors: Bauer Daniel , Lörwald Andrea C. , Wüst Sandra , Beltraminelli Helmut , Germano Miria , Michel Adrian , Schnabel Kai P. 
Published: June 2021

Abstract
Background
Moulages can greatly extend the possibilities of simulation in teaching and assessment. Since moulages that fit an educator’s exact needs are often unavailable commercially, this paper explains how 2-dimensional transfer tattoos can be independently developed, produced, and evaluated.

Methods
From representative photographs of the specific skin condition an analogue copy of the pathological finding is drawn. Once validated by the medical expert, it can be digitized by scanning and processed using graphics software. The final digital image file is printed onto transfer paper. Once applied and fixed onto the intended wearer, usually a simulated patient, its authenticity can be confirmed, and further transfer tattoos can be produced.

Results
Using this moulage technique we produced 10 different 2-dimensional transfer tattoos to date, including hematoma, Janeway lesions and splinter nails. These moulages are used in clinical skills training, formative and high-stakes summative assessment in undergraduate medical and nursing programs.

Conclusions
By sharing our development process for 2-dimensional transfer tattoos, health profession educators can produce their own that best fit their local educational needs. Due to their high authenticity and standardization, 2-dimensional transfer tattoos are ideal for use in high-stakes assessment.
A novel approach for heart disease prediction using strength scores with significant predictors
Authors: Yazdani Armin , Varathan Kasturi Dewi , Chiam Yin Kia , Malik Asad Waqar , Wan Ahmad Wan Azman 
Published: June 2021

AbstractBackgroundCardiovascular disease is the leading cause of death in many countries. Physicians often diagnose cardiovascular disease based on current clinical tests and previous experience of diagnosing patients with similar symptoms. Patients who suffer from heart disease require quick diagnosis, early treatment and constant observations. To address their needs, many data mining approaches have been used in the past in diagnosing and predicting heart diseases. Previous research was also focused on identifying the significant contributing features to heart disease prediction, however, less importance was given to identifying the strength of these features.MethodThis paper is motivated by the gap in the literature, thus proposes an algorithm that measures the strength of the significant features that contribute to heart disease prediction. The study is aimed at predicting heart disease based on the scores of significant features using Weighted Associative Rule Mining.ResultsA set of important feature scores and rules were identified in diagnosing heart disease and cardiologists were consulted to confirm the validity of these rules. The experiments performed on the UCI open dataset, widely used for heart disease research yielded the highest confidence score of 98% in predicting heart disease.ConclusionThis study managed to provide a significant contribution in computing the strength scores with significant predictors in heart disease prediction. From the evaluation results, we obtained important rules and achieved highest confidence score by utilizing the computed strength scores of significant predictors on Weighted Associative Rule Mining in predicting heart disease.
The advanced machine learner XGBoost did not reduce prehospital trauma mistriage compared with logistic regression: a simulation study
Authors: Larsson Anna , Berg Johanna , Gellerfors Mikael , Gerdin Wärnberg Martin 
Published: June 2021

Abstract
Background
Accurate prehospital trauma triage is crucial for identifying critically injured patients and determining the level of care. In the prehospital setting, time and data are often scarce, limiting the complexity of triage models. The aim of this study was to assess whether, compared with logistic regression, the advanced machine learner XGBoost (eXtreme Gradient Boosting) is associated with reduced prehospital trauma mistriage.

Methods
We conducted a simulation study based on data from the US National Trauma Data Bank (NTDB) and the Swedish Trauma Registry (SweTrau). We used categorized systolic blood pressure, respiratory rate, Glasgow Coma Scale and age as our predictors. The outcome was the difference in under- and overtriage rates between the models for different training dataset sizes.

Results
We used data from 813,567 patients in the NTDB and 30,577 patients in SweTrau. In SweTrau, the smallest training set of 10 events per free parameter was sufficient for model development. XGBoost achieved undertriage rates in the range of 0.314–0.324 with corresponding overtriage rates of 0.319–0.322. Logistic regression achieved undertriage rates ranging from 0.312 to 0.321 with associated overtriage rates ranging from 0.321 to 0.323. In NTDB, XGBoost required the largest training set size of 1000 events per free parameter to achieve robust results, whereas logistic regression achieved stable performance from a training set size of 25 events per free parameter. For the training set size of 1000 events per free parameter, XGBoost obtained an undertriage rate of 0.406 with an overtriage of 0.463. For logistic regression, the corresponding undertriage was 0.395 with an overtriage of 0.468.

Conclusion
The under- and overtriage rates associated with the advanced machine learner XGBoost were similar to the rates associated with logistic regression regardless of sample size, but XGBoost required larger training sets to obtain robust results. We do not recommend using XGBoost over logistic regression in this context when predictors are few and categorical.
Validation of the German version of the work and social adjustment scale in a sample of depressed patients
Authors: Heissel A. , Bollmann J. , Kangas M. , Abdulla K. , Rapp M. , Sanchez A. 
Published: June 2021

Abstract
Background
Depression is one of the key factors contributing to difficulties in one’s ability to work, and serves as one of the major reasons why employees apply for psychotherapy and receive insurance subsidization of treatments. Hence, an increasing and growing number of studies rely on workability assessment scales as their primary outcome measure. The Work and Social Assessment Scale (WSAS) has been documented as one of the most psychometrically reliable and valid tools especially developed to assess workability and social functioning in patients with mental health problems. Yet, the application of the WSAS in Germany has been limited due to the paucity of a valid questionnaire in the German language. The objective of the present study was to translate the WSAS, as a brief and easy administrable tool into German and test its psychometric properties in a sample of adults with depression.

Methods
Two hundred seventy-seven patients (M = 48.3 years, SD = 11.1) with mild to moderately severe depression were recruited. A multistep translation from English into the German language was performed and the factorial validity, criterion validity, convergent validity, discriminant validity, internal consistency, and floor and ceiling effects were examined.

Results
The confirmatory factor analysis results confirmed the one-factor structure of the WSAS. Significant correlations with the WHODAS 2–0 questionnaire, a measure of functionality, demonstrated good convergent validity. Significant correlations with depression and quality of life demonstrated good criterion validity. The WSAS also demonstrated strong internal consistency (α = .89), and the absence of floor and ceiling effects indicated good sensitivity of the instrument.

Conclusions
The results of the present study demonstrated that the German version of the WSAS has good psychometric properties comparable to other international versions of this scale. The findings recommend a global assessment of psychosocial functioning with the sum score of the WSAS.

Trial registration
ISRCTN identifier: ISRCTN28972230. Date of registration June 26th 2018.
Sexually transmitted infections and semen quality from subfertile men with and without leukocytospermia
Authors: Bai Shun , Li Yuan , Wan Yangyang , Guo Tonghang , Jin Qi , Liu Ran , Tang Wenjuan , Sang Meiying , Tao Yuanyuan , Xie Baoguo , Zhao Yun , Li Wei , Xu Xiangdong , Yue Qiuling , Hu Xuechun , Xu Bo 
Published: June 2021

AbstractBackgroundThe role of sexually transmitted infections (STIs) in semen parameters and male infertility is still a controversial area. Previous studies have found bacterial infection in a minority of infertile leukocytospermic males. This study aims to investigate the prevalence of STIs in semen from subfertile men with leukocytospermia (LCS) and without leukocytospermia (non-LCS) and their associations with sperm quality.MethodsSemen samples were collected from 195 men who asked for a fertility evaluation. Infection with the above 6 pathogens was assessed in each sample. Sperm quality was compared in subfertile men with and without LCS.ResultsThe LCS group had significantly decreased semen volume, sperm concentration, progressive motility, total motility and normal morphology. The infection rates ofUreaplasma urealyticum(Uuu),Ureaplasma parvum(Uup),Mycoplasma hominis(MH),Mycoplasma genitalium(MG),Chlamydia trachomatis(CT), herpes simplex virus-2 (HSV-2) andNeisseria gonorrhoeae(NG) were 8.7 %, 21.0 %, 8.2 %, 2.1 %, 3.6 %, 1.0 and 0 %, respectively. The STI detection rates of patients with LCS were higher than those of the non-LCS group (52.3 % vs. 39.3 %), although there was no statistically significant difference between the two groups (P = 0.07). All semen parameters were not significantly different between LCS with STIs and without STIs, except the semen volume in the MG-infected patients with LCS was significantly lower than that in the noninfected group.ConclusionsLCS was associated with a reduction in semen quality, but was not associated with STIs.
Integrated multi-omics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN
Authors: Codrich Marta , Dalla Emiliano , Mio Catia , Antoniali Giulia , Malfatti Matilde Clarissa , Marzinotto Stefania , Pierobon Mariaelena , Baldelli Elisa , Di Loreto Carla , Damante Giuseppe , Terrosu Giovanni , Pucillo Carlo Ennio Michele , Tell Gianluca 
Published: June 2021

Abstract
Background
Colorectal cancer (CRC) represents the fourth leading cause of cancer-related deaths. The heterogeneity of CRC identity limits the usage of cell lines to study this type of tumor because of the limited representation of multiple features of the original malignancy. Patient-derived colon organoids (PDCOs) are a promising 3D-cell model to study tumor identity for personalized medicine, although this approach still lacks detailed characterization regarding molecular stability during culturing conditions. Correlation analysis that considers genomic, transcriptomic, and proteomic data, as well as thawing, timing, and culturing conditions, is missing.

Methods
Through integrated multi–omics strategies, we characterized PDCOs under different growing and timing conditions, to define their ability to recapitulate the original tumor.

Results
Whole Exome Sequencing allowed detecting temporal acquisition of somatic variants, in a patient-specific manner, having deleterious effects on driver genes CRC-associated. Moreover, the targeted NGS approach confirmed that organoids faithfully recapitulated patients’ tumor tissue. Using RNA-seq experiments, we identified 5125 differentially expressed transcripts in tumor versus normal organoids at different time points, in which the PTEN pathway resulted of particular interest, as also confirmed by further phospho-proteomics analysis. Interestingly, we identified the PTEN c.806_817dup (NM_000314) mutation, which has never been reported previously and is predicted to be deleterious according to the American College of Medical Genetics and Genomics (ACMG) classification.

Conclusion
The crosstalk of genomic, transcriptomic and phosphoproteomic data allowed to observe that PDCOs recapitulate, at the molecular level, the tumor of origin, accumulating mutations over time that potentially mimic the evolution of the patient’s tumor, underlining relevant potentialities of this 3D model.
Genetic correlation and causal relationships between cardio-metabolic traits and lung function impairment
Authors: Wielscher Matthias , Amaral Andre F. S. , van der Plaat Diana , Wain Louise V. , Sebert Sylvain , Mosen-Ansorena David , Auvinen Juha , Herzig Karl-Heinz , Dehghan Abbas , Jarvis Debbie L. , Jarvelin Marjo-Riitta 
Published: June 2021

Abstract
Background
Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability or are confounded by environmental factors.

Methods
We performed three analyses: (1) cardio-metabolic health to lung function association tests in Northern Finland Birth cohort 1966, (2) cross-trait linkage disequilibrium score regression (LDSC) to compare genetic backgrounds and (3) Mendelian randomisation (MR) analysis to assess the causal effect of cardio-metabolic traits and disease on lung function, and vice versa (bidirectional MR). Genetic associations were obtained from the UK Biobank data or published large-scale genome-wide association studies (N > 82,000).

Results
We observed a negative genetic correlation between lung function and cardio-metabolic traits and diseases. In Mendelian Randomisation analysis (MR), we found associations between type 2 diabetes (T2D) instruments and forced vital capacity (FVC) as well as FEV1/FVC. Body mass index (BMI) instruments were associated to all lung function traits and C-reactive protein (CRP) instruments to FVC. These genetic associations provide evidence for a causal effect of cardio-metabolic traits on lung function. Multivariable MR suggested independence of these causal effects from other tested cardio-metabolic traits and diseases. Analysis of lung function specific SNPs revealed a potential causal effect of FEV1/FVC on blood pressure.

Conclusions
The present study overcomes many limitations of observational studies by using Mendelian Randomisation. We provide evidence for an independent causal effect of T2D, CRP and BMI on lung function with some of the T2D effect on lung function being attributed to inflammatory mechanisms. Furthermore, this analysis suggests a potential causal effect of FEV1/FVC on blood pressure. Our detailed analysis of the interplay between cardio-metabolic traits and impaired lung function provides the opportunity to improve the quality of existing intervention strategies.
TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
Authors:   The TE Hub Consortium, Elliott Tyler A. , Heitkam Tony , Hubley Robert , Quesneville Hadi , Suh Alexander , Wheeler Travis J. 
Published: June 2021

AbstractTransposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework, https://tehub.org, (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform’s development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.