bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Profile Analysis of Synovial Fluid in Patients With Anterior Cruciate Ligament Tears
Authors: Brophy Robert H. , Cai Lei , Zhang Qiang , Townsend R. Reid , Rai Muhammad Farooq 
Published: August 2022

Background: Anterior cruciate ligament (ACL) tears are associated with posttraumatic osteoarthritis, but the early biological changes that initiate joint degeneration after this injury are not well characterized. ACL tears typically result in effusion in the knee, which may provide insight into the initial response of the joint to injuries. Hypothesis: Patient- and injury-specific factors are associated with the proteomics of synovial fluid in knees with ACL tears. Study Design: Descriptive laboratory study. Methods: Synovial fluid was collected from 105 patients (38 male, 67 female) with an acute traumatic ACL tear. Patient- and injury-specific factors such as age, sex, body mass index, time from injury, presence/absence of concomitant meniscal tears, and location of concomitant bone bruises (if present) were recorded. The protein concentration of synovial fluid was measured, followed by benchmarking of samples for multi-affinity high-abundance protein depletion. An isotropically labeled high-resolution nano-liquid chromatography with tandem mass spectrometry–based proteomic approach was used to determine the synovial fluid protein profile. Data were processed, quality controlled, and analyzed computationally for each patient and injury factor. Results: The proteomics of synovial fluid from ACL tears was associated with patient sex, injury pattern, and location of bone bruises but not with patient age, body mass index, or time from injury. Knees with an isolated ACL tear had higher glutathione peroxidase 1 (GPX1) and plastin 3 levels than knees with an ACL tear and meniscal tear. A bone bruise on the lateral femoral condyle was associated with elevated leptin and glucose-6-phosphate dehydrogenase (G6PD) levels. A bone bruise on the lateral tibial plateau was associated with decreased GPX1 levels. Male patients had higher matrix metalloproteinase 9 and lower G6PD levels than female patients. Conclusion: Patient sex, injury pattern, and bone bruise location were important determinants of the proteomic profile of effusion resulting from ACL tears. Clinical Relevance: Longitudinal follow-ups to see if and how proteomic differences relate to clinical outcomes and mechanistic studies to assess the role that specific proteins play in the joint are warranted. Ultimately, these investigations could lead to better approaches to predict clinical outcomes and identify possible interventions to optimize outcomes in these patients.
Legitimate Peripheral Participation by Novices in a Dungeons and Dragons Community
Authors: Giordano Michael J. 
Published: August 2022

Introduction Dungeons & Dragons (D&D) is a cooperative tabletop roleplaying game in which players gather together to tell stories. Expert players have a wealth of experiences and game knowledge from which to draw upon while playing the game. Novices, on the other hand, have little experience to depend on when navigating the first few gaming sessions. Objectives The primary objective of this investigation was to describe how different novices become socialized to the D&D culture in this small community at the beginning of a new gaming campaign. Methods The present study is a cross-sectional qualitative participant observation of D&D novice socialization through the lens of communities of practice (CoP). Observation and interviews of two experts and five novice fifth edition D&D players revealed interactions and choices made by players related to the dissemination of cultural and practical knowledge and the fluidity of player and character identity within the scope of observed gameplay. Results The results showed that for some novices explicit in-game training was required to learn their role at the table, but socialization could come more quickly for novices who took extra steps to gain experience by engaging in the wider distributed and virtual community through online forums or viewing streamed actual-play D&D games. Three interaction types—player-to-player, player-to-dungeon master (DM), and character-to-character—for three distinct purposes—understanding game mechanics, describing scenes, and interacting in narrative—were observed. Additionally, the character choices regarding gender and in-game actions were explored. Conclusion The cooperative nature of D&D can afford novices explicit training from expert players at the table. However, as was observed during the game and confirmed in the interviews, socialization into this D&D gaming community also came from legitimate peripheral participation of the novices who engaged in the wider, virtual D&D community through online forums, actual-play streams and podcasts, and general knowledge of the fantasy genre.
Preservation of the fecal microbiome is associated with reduced severity of graft-versus-host disease
Authors: Burgos da Silva Marina , Ponce Doris M. , Dai Anqi , M. Devlin Sean , Gomes Antonio L. C. , Moore Gillian , Slingerland John , Shouval Roni , Armijo Gabriel K. , DeWolf Susan , Fei Teng , Clurman Annelie , Fontana Emily , Amoretti Luigi A. , Wright Roberta J. , Andrlova Hana , Miltiadous Oriana , Perales Miguel-Angel , Taur Ying , Peled Jonathan U. , van den Brink Marcel R. M. 
Published: August 2022

Abstract
Following allogeneic hematopoietic cell transplantation (allo-HCT), the gastrointestinal (GI) tract is frequently affected by acute graft-versus-host disease (aGVHD), the pathophysiology of which is associated with a dysbiotic microbiome. Since microbial composition varies along the length of the GI tract, the authors hypothesized that microbiome features correlate with the pattern of organ involvement after allo-HCT. We evaluated 266 allo-HCT recipients from whom 1303 stool samples were profiled by 16S ribosomal gene sequencing. Patients were classified according to which organs were affected by aGVHD. In the 20 days prior to disease onset, GVHD patients had lower abundances of members of the class Clostridia, lower counts of butyrate producers, and lower ratios of strict-to-facultative (S/F) anaerobic bacteria compared with allograft recipients who were free of GVHD. GI GVHD patients showed significant reduction in microbial diversity preonset. Patients with lower GI aGVHD had lower S/F anaerobe ratios compared with those with isolated upper GI aGVHD. In the 20 days after disease onset, dysbiosis was observed only in GVHD patients with GI involvement, particularly those with lower-tract disease. Importantly, Clostridial and butyrate-producer abundance as well as S/F anaerobe ratio were predictors of longer overall survival; higher abundance of butyrate producers and higher S/F anaerobe ratio were associated with decreased risk of GVHD-related death. These findings suggest that the intestinal microbiome can serve as a biomarker for outcomes of allo-HCT patients with GVHD.
Use of penile shear wave elastosonography for the diagnosis of Peyronie’s Disease: a prospective case–control study
Authors: Trama Francesco , Illiano Ester , Iacono Fabrizio , Ruffo Antonio , di Lauro Giovanni , Aveta Achille , Crocetto Felice , Manfredi Celeste , Costantini Elisabetta 
Published: August 2022

Abstract
Background
To evaluate the stiffness of the tunica albuginea (TA), we used a new noninvasive diagnostic technique called shear wave elastography (SWE). We determined whether SWE values are correlated with the degree of penile curvature, the time of disease onset, and pain severity experienced by patients during erection. This study analyzed the elasticity of the TA of patients with Peyronie’s disease compared to that of the control group. We also analyzed any correlations between the stiffness of the cavernous bodies and the degree of curvature, time from diagnosis to curvature onset, and erectile pain severity. This was a prospective case–control study involving 100 men enrolled from September 2020 to August 2021. Participants were divided into group A (case group, n = 50), which included men with PD, with or without pain, and with penile curvature, or group B (control group, n = 50), which included healthy patients older than 18 years who visited the urology clinic for reasons other than PD. The medical history was collected for all patients who also underwent objective examination, B-mode ultrasound evaluation, and SWE. The International Index of Erectile Function (IIEF-15) visual analog scale (VAS) questionnaire was administered to all participants.

Results
There were no significant between-group differences regarding age, weight, and height (p > 0.05); however, there was a significant difference in the stiffness values (p < 0.05). An inverse correlation was observed between stiffness and the VAS score (p < 0.0001). A positive correlation was observed between the degree of curvature (p < 0.0001) and the time of curvature onset (p < 0.0001). The IIEF-15 scores were poorer in group A than in group B (p < 0.0001).

Conclusion
SWE is an inexpensive, noninvasive method that can be used to measure the stiffness of PD patients.
Evaluation of data imputation strategies in complex, deeply-phenotyped data sets: the case of the EU-AIMS Longitudinal European Autism Project
Authors: Llera A. , Brammer M. , Oakley B. , Tillmann J. , Zabihi M. , Amelink J. S. , Mei T. , Charman T. , Ecker C. , Dell’Acqua F. , Banaschewski T. , Moessnang C. , Baron-Cohen S. , Holt R. , Durston S. , Murphy D. , Loth E. , Buitelaar J. K. , Floris D. L. , Beckmann C. F. 
Published: August 2022

AbstractAn increasing number of large-scale multi-modal research initiatives has been conducted in the typically developing population, e.g. Dev. Cogn. Neur. 32:43-54, 2018; PLoS Med. 12(3):e1001779, 2015; Elam and Van Essen, Enc. Comp. Neur., 2013, as well as in psychiatric cohorts, e.g. Trans. Psych. 10(1):100, 2020; Mol. Psych. 19:659–667, 2014; Mol. Aut. 8:24, 2017; Eur. Child and Adol. Psych. 24(3):265–281, 2015. Missing data is a common problem in such datasets due to the difficulty of assessing multiple measures on a large number of participants. The consequences of missing data accumulate when researchers aim to integrate relationships across multiple measures. Here we aim to evaluate different imputation strategies to fill in missing values in clinical data from a large (total N = 764) and deeply phenotyped (i.e. range of clinical and cognitive instruments administered) sample of N = 453 autistic individuals and N = 311 control individuals recruited as part of the EU-AIMS Longitudinal European Autism Project (LEAP) consortium. In particular, we consider a total of 160 clinical measures divided in 15 overlapping subsets of participants. We use two simple but common univariate strategies—mean and median imputation—as well as a Round Robin regression approach involving four independent multivariate regression models including Bayesian Ridge regression, as well as several non-linear models: Decision Trees (Extra Trees., and Nearest Neighbours regression. We evaluate the models using the traditional mean square error towards removed available data, and also consider the Kullback–Leibler divergence between the observed and the imputed distributions. We show that all of the multivariate approaches tested provide a substantial improvement compared to typical univariate approaches. Further, our analyses reveal that across all 15 data-subsets tested, an Extra Trees regression approach provided the best global results. This not only allows the selection of a unique model to impute missing data for the LEAP project and delivers a fixed set of imputed clinical data to be used by researchers working with the LEAP dataset in the future, but provides more general guidelines for data imputation in large scale epidemiological studies.
Prediction model of delayed graft function based on clinical characteristics combined with serum IL-2 levels
Authors: Zhao Shitao , Liu Yuan , Zhou Chen , Chen Zide , Cai Zeyu , Han JiaLiang , Xiao Jiansheng , Xiao Qi 
Published: August 2022

Abstract
Background
Kidney transplantation is an effective treatment for end-stage renal disease (ESRD). Delayed graft function (DGF) is a common complication after kidney transplantation and exerts substantial effects on graft function and long-term graft survival. Therefore, the construction of an effective model to predict the occurrence of DGF is particularly important.

Methods
Seventy-one patients receiving their first kidney transplant at the First Affiliated Hospital of Nanchang University from October 2020 to October 2021 were enrolled in the discovery cohort. Based on clinical characteristics and serum markers, a logistic regression model was used to simulate the risk of DGF in the discovery cohort. The DGF prediction model was named the prediction system and was composed of risk factors related to DGF. Thirty-two patients receiving a kidney transplant at the First Affiliated Hospital of Nanchang University from October 2021 to February 2022 were enrolled in the validation cohort. The validation cohort was used to verify the accuracy and reliability of the prediction model.

Results
Cold ischemia time (CIT), donor history of diabetes mellitus, donor interleukin-2 (IL-2) level and donor terminal creatinine level constitute the prediction system. In the validation test, the area under the receiver operating characteristic curve (AUC) was 0.867 for the prediction system, and good calibration of the model was confirmed in the validation cohort.

Conclusions
This study constructed a reliable and highly accurate prediction model that provides a practical tool for predicting DGF. Additionally, IL-2 participates in the kidney injury process and may be a potential marker of kidney injury.
The Tommy’s Clinical Decision Tool, a device for reducing the clinical impact of placental dysfunction and preterm birth: protocol for a mixed-methods early implementation evaluation study
Authors: Carter Jenny , Anumba Dilly , Brigante Lia , Burden Christy , Draycott Tim , Gillespie Siobhán , Harlev-Lam Birte , Judge Andrew , Lenguerrand Erik , Sheehan Elaine , Thilaganathan Basky , Wilson Hannah , Winter Cathy , Viner Maria , Sandall Jane 
Published: August 2022

Abstract
Background

Disparities in stillbirth and preterm birth persist even after correction for ethnicity and social deprivation, demonstrating that there is wide geographical variation in the quality of care. To address this inequity, Tommy’s National Centre for Maternity Improvement developed the Tommy’s Clinical Decision Tool, which aims to support the provision of “the right care at the right time”, personalising risk assessment and care according to best evidence. This web-based clinical decision tool assesses the risk of preterm birth and placental dysfunction more accurately than current methods, and recommends best evidenced-based care pathways in a format accessible to both women and healthcare professionals. It also provides links to reliable sources of pregnancy information for women. The aim of this study is to evaluate implementation of Tommy’s Clinical Decision Tool in four early-adopter UK maternity services, to inform wider scale-up.

Methods

The Tommy’s Clinical Decision Tool has been developed involving maternity service users and healthcare professionals in partnership. This mixed-methods study will evaluate: maternity service user and provider acceptability and experience; barriers and facilitators to implementation; reach (whether particular groups are excluded and why), fidelity (degree to which the intervention is delivered as intended), and unintended consequences. Data will be gathered over 25 months through interviews, focus groups, questionnaires and through the Tommy’s Clinical Decision Tool itself. The NASSS framework (Non-adoption or Abandonment of technology by individuals and difficulties achieving Scale-up, Spread and Sustainability) will inform data analysis.

Discussion
This paper describes the intervention, Tommy’s Clinical Decision Tool, according to TiDIER guidelines, and the protocol for the early adopter implementation evaluation study. Findings will inform future scale up.

Trial registration
This study was prospectively registered on the ISRCTN registry no. 13498237, on 31st January 2022.
Triple careers of athletes: exploring the challenges of planning a pregnancy among female elite athletes using semi-structured interviews
Authors: Dietz Pavel , Legat Larissa , Sattler Matteo C. , van Poppel Mireille N. M. 
Published: August 2022

Abstract
Background
The challenging factors that elite athletes perceive for combining their sportive career with planning a pregnancy and motherhood need to be identified in order to develop supportive measures. Therefore, this phenomenological qualitative study aimed to explore challenges associated with planning a pregnancy among female, non-pregnant elite athletes.

Methods
Semi-structured skype-interviews were performed among female elite athletes (athletes competing on national or international level) aged 28 years or older. Using Mayring’s qualitative content analysis approach, anchor examples served to identify potential challenges of planning a pregnancy which were categorized independently by two researchers.

Results
Interviews of 16 elite athletes (mean age 30.7 years) entered analysis. Eleven challenges of planning a pregnancy were identified, categorized into organizational / environmental, financial, personal, and physical factors.

Conclusions
With regard to financial challenges, we propose mandatory maternity leave and continuation of the contracts and salary. Furthermore, mentoring programs may help to provide support and advice to new generations of female elite athletes and help to reduce concerns regarding the wish of becoming pregnant during a sportive career. In order to reduce physical concerns regarding pregnancy and exercise, we see a need for scientific studies investigating the association of sport discipline specific characteristics on sportive performance and the mother´s, fetus’ and child´s health. Finally, the results of the current study may be used in future quantitative studies to test specific hypotheses.
Correlation between human development index and its components with COVID-19 indices: a global level ecologic study
Authors: Mirahmadizadeh Alireza , Ghelichi-Ghojogh Mousa , Vali Mohebat , Jokari Kimia , Ghaem Haleh , Hemmati Abdolrasool , Jafari Fatemeh , Dehghani Seyed Sina , Hassani Amir Hossein , Jafari Alireza , Rezaei Fatemeh 
Published: August 2022

AbstractBackgroundGiven that COVID-19 continues to spread worldwide, attempts to restrain the virus and to prevent the effects that critically ill patients with COVID-19 have on healthcare systems, has become a public health priority. This ecological study aimed to investigate the correlation between the Human Development Index (HDI) and the epidemiological indicators of COVID-19, including the cumulative incidence rate of cases, the cumulative incidence rate of death, performed COVID-19 tests per million, recovery rate, and case fatality rate.MethodsIn this ecological study, a data set was provided, which included the epidemiologic indices of COVID-19, HDI, and its components for each country. Correlation coefficients were used to determine linear correlation. Also, the scatter plots of the HDI for the studied countries based on the epidemiologic indices of COVID-19 were drawn.ResultsThis study showed that HDI and its components had positive correlation with a cumulative incidence rate of cases, the cumulative incidence rate of death, and performed COVID-19 tests (p < 0.001). HDI and two of its components, including literacy and Gross National Income (GNI) components had negative correlation with case fatality rate (CFR). Also, HDI and two of its components, including literacy and life expectancy components had negative correlation with recovery rate.ConclusionOur study showed that the HDI and its components can affect the epidemiological status of COVID-19. As HDI increased, the cumulative incidence rate of cases, cumulative incidence rate of death, and COVID-19 tests increased as well. As HDI increased, CFR and recovery rate decreased as well. Although the HDI is higher in high-income countries, these countries may have also better reporting and surveillance systems.
BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin
Authors: Kshirsagar Meghana , Yuan Han , Ferres Juan Lavista , Leslie Christina 
Published: August 2022

AbstractWe present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can disentangle an input DNA sequence into distinct latent factors that encode cell-type specific in vivo binding signals for individual TFs, composite patterns for TFs involved in cooperative binding, and genomic context surrounding the binding sites. On the task of retrieving the motifs of expressed TFs in a given cell type, BindVAE is competitive with existing motif discovery approaches.
Application of different quantitative analytical techniques for estimation of aspirin and omeprazole in pharmaceutical preparation
Authors: Abdelazim Ahmed H. , Ramzy Sherif 
Published: August 2022

AbstractSeveral quantitative analytical methods were used to estimate aspirin and omeprazole in recently FDA-approved tablets. The first derivative of the ratio spectra was used to resolve the recorded overlapping spectra between aspirin and omeprazole. The first derivative of the ratio spectra of the studied drug mixtures was divided by a spectrum of a standard solution of omeprazole for the estimation of aspirin. Also, the first derivative of the ratio spectra of the studied drug mixtures was divided by a spectrum of the standard solution of aspirin for the estimation of omeprazole. For the simultaneous quantitative analysis of aspirin and omeprazole, the TLC densitometry technique was applied using TLC aluminum silica gel plates, toluene–acetonitrile–methanol (7:2:0.5, by volume) as the mobile phase, and UV detection at 272 nm. The advantages and disadvantages of the proposed techniques were discussed in the context of the results and the sensitivity limits of the methods. The proposed techniques were validated and successfully applied to the analysis of drugs in pure and pharmaceutical forms. A statistical comparison of the data obtained by the described methods with other data obtained by a previously published HPLC method was performed. The results agreed well with respect to the recommended statistical tests. Furthermore, the greenness of the described methods was assessed using different tools, the analytical eco-scale, the green analytical procedure index and the AGREE evaluation method. The proposed methods showed more adherence to the greenness characters in comparison to the previously reported HPLC method.