bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sex and Menopause Modify the Effect of Single Nucleotide Polymorphism Genotypes on Fibrosis in NAFLD
Authors: Wegermann Kara , Garrett Melanie E. , Zheng Jiayin , Coviello Andrea , Moylan Cynthia A. , Abdelmalek Manal F. , Chow Shein‐Chung , Guy Cynthia D. , Diehl Anna Mae , Ashley‐Koch Allison , Suzuki Ayako 
Published: January 2021

The development of fibrosis in nonalcoholic fatty liver disease (NAFLD) is influenced by genetics, sex, and menopausal status, but whether genetic susceptibility to fibrosis is influenced by sex and reproductive status is unclear. Our aim was to identify metabolism‐related single nucleotide polymorphisms (SNPs), whose effect on NAFLD fibrosis is significantly modified by sex and menopausal status. We performed a cross‐sectional, proof‐of‐concept study of 616 patients in the Duke NAFLD Clinical Database and Biorepository. The primary outcome was nonalcoholic steatohepatitis–Clinical Research Network (NASH–CRN) fibrosis stage. Menopause status was self‐reported; age 51 years was used as a surrogate for menopause in patients with missing menopause data. The Metabochip was used to obtain 98,359 SNP genotypes in known metabolic pathway genes for each patient. We used additive genetic models to characterize sex and menopause‐specific effects of SNP genotypes on NAFLD fibrosis stage. In the main effects analysis, none of the SNPs were associated with fibrosis at P < 0.05 after correcting for multiple comparisons. Twenty‐five SNPs significantly interacted with sex/menopause to affect fibrosis stage (interaction P < 0.0001). After removal of loci in linkage disequilibrium, 10 independent loci were identified. Six were in the following genes: KCNIP4 (potassium voltage‐gated channel interacting protein 4), PSORS1C1 (psoriasis susceptibility 1 candidate 1), KLHL8 (Kelch‐like family member 8), GLRA1 (glycine receptor alpha 1), NOTCH2 (notch receptor 2), and PRKCH (protein kinase C eta), and four SNPs were intergenic. In stratified models, four SNPs were significant in premenopausal and postmenopausal women, three only in postmenopausal women, two in men and postmenopausal women, and one only in premenopausal women. Conclusion: We identified 10 loci with a significant sex/menopause interaction with respect to fibrosis. None of these SNPs were significant in all sex/menopause groups, suggesting modulation of genetic susceptibility to fibrosis by sex and menopause status. Future studies of genetic predictors of NAFLD progression should account for sex and menopause.
Three years’ experience of quality monitoring program on pre‐analytical errors in china
Authors: Kang Fengfeng , Li Weixing , Xia Xiaohua , Shan Zhiming 
Published: January 2021

AbstractBackgroundVarious errors in the procedure of specimen collection have been reported as the primary causes of pre‐analytical errors. The aim of this study was to monitor and assess the reasons and frequencies of rejected samples in China.MethodsA pre‐analytical external quality assessment (EQA) scheme involving six quality indicators (QIs) was conducted from 2017 to 2019. Rejection rate was calculated for each QI. The difference of the rejection rates over the time was checked by Chi‐square test. Furthermore, the 25th, 50th, and 75th percentiles of the results from total laboratories each year were calculated as optimum, desirable, and minimum level of performance specifications.ResultsIn total, 423 laboratories submitted data continuously for six EQA rounds. The overall rejection rates were 0.2042%, 0.1709%, 0.1942%, 0.1689%, 0.1593%, and 0.1491%, respectively. The most common error was sample hemolysed (0.0514%–0.0635%), and the least one was sample not received (0.0008%–0.0014%). A significant reduction in percentages was observed for all QIs. For biochemistry and immunology, hemolysis accounted for more than half of the rejection causes, while for hematology, the primary cause shifted from incorrect fill level to sample clotted. The quality specifications had improved over time, except for the optimum level.ConclusionThe significant reduction in error rates on sample rejection we observed suggested that laboratories should pay more attention to the standardized specimen collection. We also provide a benchmark for QIs performance specification to help laboratories increase awareness about the critical aspects in the need of improvement actions.
Application of Individualized PBPK Modeling of Rate Data to Evaluate the Effect of Hemodialysis on Nonrenal Clearance Pathways
Authors: Franchetti Yoko , Nolin Thomas D. 
Published: January 2021

AbstractThe aim of this study was to apply individualized, physiologically based pharmacokinetic modeling of 14CO2 production rates (iPBPK‐R) measured by the erythromycin breath test to characterize the effect of hemodialysis on the function of nonrenal clearance pathways in patients with end‐stage renal disease. Twelve patients previously received 14C‐erythromycin intravenously pre‐ and post‐hemodialysis. Serial breath samples were collected after each dose over 2 hours. Eight PBPK parameters were co‐estimated across periods, whereas activity of cytochrome P450 (CYP) 3A4 clearance was independently estimated for each period. Inhibition coefficients for organic anion transporting polypeptide (OATP), P‐glycoprotein, and multidrug resistance‐associated protein 2 activities were also estimated. Nonrenal clearance parameter estimates were explored regarding sex differences and correlations with uremic toxins and were used in hierarchical cluster analysis (HCA). Relationships between the function of nonrenal clearance pathways and uremic toxin concentrations were explored. Mean CYP 3A4 clearance increased by 2.2% post‐hemodialysis. Uptake transporter activity was highly intervariable across hemodialysis. Females had 22% and 30% higher median CYP3A4 activity than males pre‐ and post‐hemodialysis, respectively. Exploratory HCA indicated that using both CYP3A4 and OATP activity parameters at pre‐ and post‐hemodialysis best identifies heterogeneous patients. This is the first study to use the iPBPK‐R approach to simultaneously estimate multiple in vivo nonrenal elimination pathways in individual patients with kidney disease and to assess the effect of hemodialysis.
A transfer learning approach for automatic segmentation of the surgically treated anterior cruciate ligament
Authors: Flannery Sean W. , Kiapour Ata M. , Edgar David J. , Murray Martha M. , Beveridge Jillian E. , Fleming Braden C. 
Published: January 2021

AbstractQuantitative magnetic resonance imaging enables quantitative assessment of the healing anterior cruciate ligament or graft post‐surgery, but its use is constrained by the need for time consuming manual image segmentation. The goal of this study was to validate a deep learning model for automatic segmentation of repaired and reconstructed anterior cruciate ligaments. We hypothesized that (1) a deep learning model would segment repaired ligaments and grafts with comparable anatomical similarity to intact ligaments, and (2) automatically derived quantitative features (i.e., signal intensity and volume) would not be significantly different from those obtained by manual segmentation. Constructive Interference in Steady State sequences were acquired of ACL repairs (n = 238) and grafts (n = 120). A previously validated model for intact ACLs was retrained on both surgical groups using transfer learning. Anatomical performance was measured with Dice coefficient, sensitivity, and precision. Quantitative features were compared to ground truth manual segmentation. Automatic segmentation of both surgical groups resulted in decreased anatomical performance compared to intact ACL automatic segmentation (repairs/grafts: Dice coefficient = .80/.78, precision = .79/.78, sensitivity = .82/.80), but neither decrease was statistically significant (Kruskal‐Wallis: Dice coefficient p = .02, precision p = .09, sensitivity p = .17; Dunn post‐hoc test for Dice coefficient: repairs/grafts p = .054/.051). There were no significant differences in quantitative features between the ground truth and automatic segmentation of repairs/grafts (0.82/2.7% signal intensity difference, p = .57/.26; 1.7/2.7% volume difference, p = .68/.72). The anatomical similarity performance and statistical similarities of quantitative features supports the use of this automated segmentation model in quantitative magnetic resonance imaging pipelines, which will accelerate research and provide a step towards clinical applicability.
One‐year outcomes following physical therapist‐led intervention for chronic hip‐related groin pain: Ancillary analysis of a pilot multicenter randomized clinical trial
Authors: Harris‐Hayes Marcie , Steger‐May Karen , M. Bove Allyn , Mueller Michael J. , Clohisy John C. , Fitzgerald G. Kelley 
Published: January 2021

AbstractEvidence related to physical therapist‐led intervention for patients with chronic hip‐related groin pain (HRGP) is limited. The purpose was to assess sustainability of treatment effects for people with HRGP undergoing two physical therapist‐led interventions. We completed an ancillary analysis of a pilot multicenter, randomized clinical trial. Forty‐six patients with chronic HRGP, 15–40 years, were enrolled. Patients were randomized to participate in 10 sessions over 12 weeks of either movement pattern training (MoveTrain) or traditional strength/flexibility (Standard). Participants completed self‐report questionnaires before treatment and 6 and 12 months after treatment completion. Outcome measures included Hip disability and Osteoarthritis and Outcome Score (HOOS), Patient Specific Functional Scale and Numeric Pain Rating Scale for average and worst pain. Continuous data were analyzed with mixed model repeated measures analysis of variance (RM‐ANOVA) within each group. Numeric pain rating scale (NPRS) was analyzed using multinomial generalized estimating equations (GEE) with a cumulative logit. Reported p values are from statistical contrasts within the RM‐ANOVAs and GEEs testing a priori hypotheses regarding change from pretest to month 6, and pretest to month 12. A total of 43/46 (93.5%) participants completed treatment, 40 (87.0%) completed 6 and 38 (82.6%) completed 12 month questionnaires. At 6 and 12 months, both groups demonstrated clinically significant improvements, compared to pretest, in all subscales of HOOS (p < 0.01), Patient Specific Functional Scale (p < 0.001), and NPRS (p < 0.0001). Among patients with chronic HRGP, both MoveTrain and Standard resulted in improved outcomes that were sustained 12 months after treatment. Further investigation in a larger sample is needed to confirm our findings.
Using machine learning techniques predicts prognosis of patients with Ewing sarcoma
Authors: Chen Wenhao , Zhou Chaoming , Yan Zhiyu , Chen Hui , Lin Kainan , Zheng Zibing , Xu Wenchen 
Published: January 2021

AbstractEwing sarcoma is one of the most common types of malignant bone tumor in children and adolescents. However, to our limited knowledge, no study exists that uses machine learning to create algorithms for the prediction of survivorship for Ewing sarcoma. About 2332 patients with Ewing sarcoma between 1975 and 2016 in the United States were identified from Surveillance, Epidemiology, and End Results (SEER) program. All patients in the data set were randomly assigned into the training set and the testing set, at a 2:8 ratio. In the training set, boosted decision tree, support vector machine, nonparametric random forest method, and neural network models were developed to predict the 5‐year survivorship. The overall survival rate in 5‐year follow‐up of this patient cohort is 60.72%. With respect to the algorithms for both cancer specific survival and overall survival, there was slight superiority in our performance metrics favoring the random forest method over the other models for survival prediction, with 77/83% sensitivity and 91/94% specificity, respectively. The random forest method was incorporated into a freely available web‐based application. This application can be accessed through https://zryan.shinyapps.io/EwingSarcoma/. Clinical Significance: To the best of our knowledge, this is the first available predictive model for predicting survival in Ewing sarcoma based on machine‐learning algorithms. This study may provide orthopedic surgeons with an easily accessible prediction tool when dealing with patients suffering from Ewing sarcoma.
Multi‐residue extraction to determine organic pollutants in mussel hemolymph
Authors: Álvarez‐Ruiz Rodrigo , Picó Yolanda , Campo Julián 
Published: January 2021

AbstractThis study assesses the extraction of eleven pharmaceuticals, five pesticides, five perfluoroalkyl substances, and two illicit drugs in hemolymph from (Mytilus Galloprovincialis). Four extraction procedures using Phree™ Phospholipid Removal cartridges were tested using different volumes of methanol (400 and 600 μL) and acetonitrile (300 and 450 μL). The pollutants were determined by high‐performance liquid chromatography–tandem mass spectrometry. The use of methanol gave several problems during the extraction procedure, such as longer times and sample loss. Three methods (acetonitrile 300 and 450 μL; and methanol 600 μL) were validated. Recoveries at three concentration levels (5, 50, and 100 ng/mL) ranged 35.1–129.0 and 29.3–133.0% for acetonitrile 300 and 450 μL, respectively, while recoveries for methanol 600 μL ranged 52.2–166.0%. Limits of detection were < 10 ng/mL for most analytes using any of the methods. Methanol 600 μL was the only method capable to extract the illicit drug 4‐methoxyphencyclidine and provided a better peak shape and higher signal‐noise ratio. When applied to non‐spiked samples from local markets salicylic acid and diclofenac were detected at 33.50‐97.79 and 28.30‐30.31 ng/mL respectively. To our knowledge, there are no methods to determine organic contaminants in hemolymph and this is the first application of Phree™ cartridges for mussel hemolymph extraction.
Implementation of an Online Multimedia Pediatric Tracheostomy Care Module for Healthcare Providers
Authors: Ahmed Sadia T. , Yang Catherina , Deng Junwen , Bottalico Danielle M. , Matta‐Arroyo Esther , Cassel‐Choudhury Gina , Yang Christina J. 
Published: January 2021

Objectives/HypothesisTo investigate the effect of a multimedia educational module on provider attitudes toward pediatric tracheostomy care. We also describe the process of module development and dissemination at an academic children's hospital.Study DesignProspective observational study.MethodsThe pediatric airway committee at an urban tertiary care center developed a multimedia pediatric tracheostomy care module. Nurses, respiratory therapists, as well as resident, fellow, and attending physicians caring for pediatric patients with tracheostomies were eligible. Managers and clinical supervisors from various units recruited participants to complete the pediatric tracheostomy care electronic module and pre‐ and postassessment knowledge quizzes and surveys. Provider confidence was analyzed using Kruskal–Wallis H‐test and Mann–Whitney U‐test, and paired t‐test was used to compare pre‐ and postmodule quiz scores.ResultsA total of 422 participants completed the module. A total of 275 participants completed the premodule survey, 385 completed the premodule quiz, 253 completed the postmodule survey, and 233 completed the postmodule quiz. Participants included providers in the neonatal intensive care unit, pediatric intensive care unit, pediatric emergency department, and pediatric wards. Postmodule surveys demonstrated a significant reduction in the average percentage of participants indicating lack of confidence with regards to changing an established tracheostomy, responding to accidental decannulation of established tracheostomy, and responding to accidental decannulation of fresh tracheostomy (P < .001). Average quiz scores increased by 5.6 points from 83.0% to 88.6% (P < .00001).ConclusionsA multimedia educational module can improve provider perception of their knowledge and confidence surrounding pediatric tracheostomy management.Level of Evidence3 Laryngoscope, 131:1893–1901, 2021
From sensemaking to sensegiving: A discourse analysis of the scholarly communications community's public response to the global pandemic
Authors: Cuevas Shaw Lisa 
Published: January 2021

AbstractThis study examines the scholarly communications community's public response to the global pandemic. A discourse analysis was conducted of press releases, blogs, and website updates across non‐profits, commercial publishers, government agencies, technology companies, and universities to identify (1) the range of support activities immediately undertaken following the proclamation of the pandemic; (2) the language and style of public discourse used, demonstrating how different organizations characterized their responses and roles during the crisis; and (3) specific patterns that emerged among this community related to the process of organizational sensemaking. The findings show that the global community appeared highly adaptive and conceptually aligned in its initial response. Different actors within the community presented distinct identities relative to leadership, advocacy, service, or constituent orientation. More importantly, a majority of organizations demonstrated the use of sensegiving strategies to influence the future state of scholarly publishing, particularly with respect to the expressed desire for greater global collaboration, transparency, quality assurance, and openness. These findings may have implications regarding the future enactment of open and collaborative research publishing, which is especially significant at this stage of the global open science movement's development.
So, what does resilience mean for scholarly publishing?
Authors: Irfanullah Haseeb Md. 
Published: January 2021

Key points
Resilience in the publishing industry can be viewed through a framework of assessing five capitals or assets: human, social, physical, financial, and natural capital.
A resilient system requires four properties: robustness, redundancy, resourcefulness, and rapidity, and scholarly publishing can be seen to have some element of each.
The ability to thrive in adversity and bounce back is not found in all parts of the publishing system, with those in the Global South disproportionately disadvantaged.
The positive changes introduced in the past year need to be retained and elements of inequality and exclusion removed to ensure future resilience and sustainability.
Simultaneous recording of filtration and respiration in marine organisms in response to short‐term environmental variability
Authors: Vajedsamiei Jahangir , Melzner Frank , Raatz Michael , Kiko Rainer , Khosravi Maral , Pansch Christian 
Published: January 2021

AbstractClimate change imposes unusual long‐term trends in environmental conditions, plus some tremendous shifts in short‐term environmental variability, exerting additional stress on marine ecosystems. This paper describes an empirical method that aims to improve our understanding of the performance of benthic filter feeders experiencing changes in environmental conditions, such as temperature, on time scales of minutes to hours, especially during daily cycles or extreme events such as marine heatwaves or hypoxic upwelling. We describe the Fluorometer and Oximeter equipped Flow‐through Setup (FOFS), experimental design, and methodological protocols to evaluate the flood of data, enabling researchers to monitor important energy budget traits, including filtration and respiration of benthic filter‐feeders in response to fine‐tuned environmental variability. FOFS allows online recording of deviations in chlorophyll and dissolved oxygen concentrations induced by the study organism. Transparent data processing through Python scripts provides the possibility to adjust procedures to needs when working in different environmental contexts (e.g., temperature vs. pH, salinity, oxygen, biological cues) and with different filter‐feeding species. We successfully demonstrate the functionality of the method through recording responses of Baltic Sea blue mussels (Mytilus) during one‐day thermal cycles. This method practically provides a tool to help researchers exposing organisms to environmental variability for some weeks or months, to relate the observed long‐term performance responses to short‐term energy budget responses, and to explain their findings with the potential to generalize patterns. The method, therefore, allows a more detailed description of stress‐response relationships and the detection of species' tolerance limits.
Sarcopenia in Children With End‐Stage Liver Disease on the Transplant Waiting List
Authors: Woolfson Jessica P. , Perez Manuela , Chavhan Govind B. , Johara Fatema T. , Lurz Eberhard , Kamath Binita M. , Ng Vicky L. 
Published: January 2021

Sarcopenia predicts morbidity and mortality in adults with end‐stage liver disease (ESLD) and is determined by total psoas muscle area (tPMA) measurement from computed tomography (CT) imaging. Recently developed pediatric age‐ and sex‐specific tPMA growth curves provide the opportunity to ascertain prevalence and impact of sarcopenia in children awaiting liver transplantation (LT). This retrospective single‐center study evaluated sarcopenia in children between 1 and 16 years with ESLD and a clinically indicated abdominal CT less than 3 months before first isolated LT. Sarcopenia was defined as tPMA z score less than −2 measured at the intervertebral L4‐5 level. Patient demographic, biochemical, and outcome data were recorded. tPMA was compared with other measures of nutritional status using univariate and multivariate logistic analyses. Outcome measures included 1‐year morbidity events and mortality after LT. CT images from 25 (64% female) children with median age of 5.50 (interquartile range [IQR], 3.75‐11.33) years were reviewed. Ten children (40%) had a tPMA z score less than −2. Sarcopenia was associated with lower z scores for weight (odds ratio [OR], 0.38; P = 0.02), height (OR, 0.32; P = 0.03), and nutritional support before LT (OR, 12.93; P = 0.01). Sarcopenic children had a longer duration of pediatric intensive care unit (PICU) stay (3.50 [IQR, 3.00‐6.00] versus 2.00 [IQR, 2.00‐3.50] days; P = 0.03). Sarcopenia was prevalent in 40% of children with ESLD awaiting LT, and lower tPMA z score was associated with deficient anthropometrics and need for nutritional support before LT. Post‐LT PICU duration was increased in children with sarcopenia, reflecting adverse outcomes associated with muscle loss. Further studies are needed to elucidate the underlying mechanisms of sarcopenia in children with ESLD.