bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of Cognitive Behavioral Therapy for Insomnia in Best-Practice Care for Patients With Knee Osteoarthritis and Insomnia: A Randomized Controlled Trial Protocol
Authors: Labie Céline , Runge Nils , Mairesse Olivier , Nijs Jo , Malfliet Anneleen , Verschueren Sabine , Van Assche Dieter , de Vlam Kurt , Luyten Frank , Bilterys Thomas , Cools Wilfried , De Pourcq Veerle , Delwiche Bérénice , Huysmans Eva , De Baets Liesbet 
Published: December 2023

Abstract

Objective
Knee osteoarthritis (KOA) is a common musculoskeletal problem worldwide and its key symptom is pain. Guidelines recommend incorporating comorbidity-specific therapies into patient-centered care. Patients diagnosed with KOA frequently have insomnia, which is associated with higher-pain severity. For this reason, this study protocol outlines the methodology of a randomized controlled trial (RCT) investigating the effectiveness of cognitive behavioral therapy for insomnia (CBTi) combined with best-practice KOA care (BPC) compared to best-practice KOA care and lifestyle education.

Methods
A 2-arm RCT in patients with KOA and insomnia is conducted, in which a total of 128 patients are randomly allocated to an intervention or control group. The experimental intervention consists of 12 sessions of physical therapist–led BPC with an additional 6 sessions of CBTi. The control intervention also receives BPC, which is supplemented with 6 general lifestyle information sessions. The primary outcome is the between-group difference in change in pain severity at 6 months after intervention. Secondary outcomes are pain-related outcomes, sleep-related outcomes, symptoms of anxiety and depression, level of physical activity and function, perceived global improvement, biomarkers of inflammation, and health-related quality of life. Assessments are conducted at baseline, immediately after intervention, and 3, 6, and 12 months after intervention. Furthermore, a cost-utility analysis for the proposed intervention will be performed alongside the RCT.

Impact
This is the first RCT investigating the clinical and cost-effectiveness of a physical therapist–led intervention integrating CBTi into BPC in patients with KOA and insomnia. The results of this trial will add to the growing body of evidence on the effectiveness of individualized and comorbidity-specific KOA care, which can inform clinical decision-making and assist policymakers and other relevant stakeholders in optimizing the care pathway for patients with KOA.
Computational multigene interactions in virus growth and infection spread
Authors: Schwab Bradley , Yin John 
Published: December 2023

Abstract
Viruses persist in nature owing to their extreme genetic heterogeneity and large population sizes, which enable them to evade host immune defenses, escape antiviral drugs, and adapt to new hosts. The persistence of viruses is challenging to study because mutations affect multiple virus genes, interactions among genes in their impacts on virus growth are seldom known, and measures of viral fitness are yet to be standardized. To address these challenges, we employed a data-driven computational model of cell infection by a virus. The infection model accounted for the kinetics of viral gene expression, functional gene–gene interactions, genome replication, and allocation of host cellular resources to produce progeny of vesicular stomatitis virus, a prototype RNA virus. We used this model to computationally probe how interactions among genes carrying up to eleven deleterious mutations affect different measures of virus fitness: single-cycle growth yields and multicycle rates of infection spread. Individual mutations were implemented by perturbing biophysical parameters associated with individual gene functions of the wild-type model. Our analysis revealed synergistic epistasis among deleterious mutations in their effects on virus yield; so adverse effects of single deleterious mutations were amplified by interaction. For the same mutations, multicycle infection spread indicated weak or negligible epistasis, where single mutations act alone in their effects on infection spread. These results were robust to simulation in high- and low-host resource environments. Our work highlights how different types and magnitudes of epistasis can arise for genetically identical virus variants, depending on the fitness measure. More broadly, gene–gene interactions can differently affect how viruses grow and spread.
A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data
Authors: Brait Nadja , Hackl Thomas , Morel Côme , Exbrayat Antoni , Gutierrez Serafin , Lequime Sebastian 
Published: December 2023

Abstract
Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs.
Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.
A novel lumen-apposing metal stent for endoscopic drainage of symptomatic pancreatic fluid collections: a retrospective study
Authors: Xu Ning , Li Longsong , Su Song , Zhao Danqi , Xiang Jingyuan , Wang Pengju , Cheng Yaxuan , Linghu Enqiang , Chai Ningli 
Published: December 2023

ABSTRACT

Background and Objectives
Previous studies showed that lumen-apposing metal stent (LAMS) provides a feasible route to perform direct endoscopic necrosectomy. However, the high risk of bleeding and migration induced by the placement of LAMS attracted attention. The aim of this study was to evaluate the safety and effectiveness of a novel LAMS.

Methods
In this retrospective study, we enrolled patients with symptomatic pancreatic fluid collections (PFCs) to perform EUS–guided drainage with a LAMS in our hospital. Evaluation variables included technical success rate, clinical success rate, and adverse events.

Results
Thirty-two patients with a mean age of 41.38 ± 10.72 years (53.1% males) were included in our study, and the mean size of PFC was 10.06 ± 3.03 cm. Technical success rate and clinical success rate reached 96.9% and 93.8%, respectively. Stent migration occurred in 1 patient (3.1%), and no stent-induced bleeding occurred. The outcomes of using LAMS in 10 patients with pancreatic pseudocyst and 22 patients with walled-off necrosis were comparable. Compared with pancreatic pseudocyst, walled-off necrosis needed more direct endoscopic necrosectomy times to achieve resolution (P = 0.024).

Conclusions
Our study showed that the novel LAMS is effective and safe for endoscopic drainage of PFCs with a relatively low rate of adverse events. Further large-scale multicenter studies are needed to confirm the present findings.
Colorectal Carcinoma With Sarcomatoid Components
Authors: Golconda Umamaheshwari , McHugh Kelsey E. , Allende Daniela S. , Collins Katrina , Henn Patrick , Lacambra Maribel , Bejarano Pablo A. , Groisman Gabriel M. , Loughrey Maurice B. , Monappa Vidya , Zhang Xuchen , Hornick Jason L. , Gonzalez Raul S. 
Published: December 2023

Colorectal carcinoma with sarcomatoid components (which includes so-called carcinosarcomas and sarcomatoid carcinomas) is a rare subtype with 50 reported cases in the literature and overlapping criteria with undifferentiated carcinoma. We collected and described 15 cases from 10 men and 5 women, with a mean age of 66 years. Symptoms included abdominal pain and gastrointestinal bleeding. Most tumors presented in the rectosigmoid region, with a mean size of 8.2 cm. The sarcomatoid component, on average, represented 58% of the tumors and took many forms, including spindled (10 cases), anaplastic (9 cases), and rhabdoid (3 cases); one case showed osteoid matrix. Tumor budding was usually high, and tumor-infiltrating lymphocytes were usually low. The sarcomatoid component was keratin-positive in 10 cases. One case showed loss of mismatch repair protein expression, and 2 cases showed SMARCA4 loss (1 also with SMARCA2 loss). Molecular testing identified mutations in KRAS (n=1), NRAS (n=2), BRAF (n=2), APC (n=1), and TP53 (n=1) in a few cases. Tumors often presented at advanced stage, with 11 cases pT4, 9 cases with nodal metastases, and 7 cases with distant metastases. Follow-up was available for 10 cases (median: 2 months), with 2 alive without disease, 3 alive with disease, and 5 dead. Our findings roughly corresponded with those in previously reported cases. Colorectal carcinoma with sarcomatoid components is rare and aggressive, with a poor prognosis for many patients. We suggest that spindled cells, anaplasia, heterologous elements, and/or a component with definable sarcomatous lineage be used to distinguish colorectal carcinoma with sarcomatoid components from undifferentiated carcinoma.
Strategies and Tools for electronic health records and physician workflow alignment: A scoping review protocol
Authors: Oluwole Oluwakemi O. , Haggarty Nicole , Ikenyei Uche , Tinuoye Oluwabambi , Honora Andreawan , Issakah Mohammed Abass 
Published: December 2023

AbstractIntroductionThe rapid adoption of electronic health records (EHR) across the globe by the healthcare industry is an indication of the rising digitalization of healthcare functions. Despite the potential benefits of EHR, achieving a fit between physician workflow and EHR has posed a major challenge, with negative effects on physician wellbeing and patient outcomes. To this effect, organizations have attempted to align the EHR with physician workflow in various ways. It is important to understand the strategies and tools that have been employed and, where possible, the outcome of these engagements as a fundamental insight to resolving this issue.MethodologyThe study will employ a methodological framework developed by Arksey and O’Malley to strategically identify articles that use any type of concept for the alignment of physician workflow and EHR from Embase (OVID), MEDLINE (OVID), PubMed, CINAHL, and Scopus databases. It will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Extension for Scoping Reviews (PRISMA-ScR) checklist to report findings. The articles will be extracted into the Covidence software, screened, and relevant data will be extracted from the selected articles. A qualitative thematic approach will be used to analyze the data. No ethical approval was sought because the data were collected from sources in the public domain.ResultThe scoping review is scheduled to be completed by April 2024. The results will be presented in tabular and narrative form and published in a reputable journal and through conference presentations.ConclusionThe outcome of the review aims to provide a systematic toolkit of activities and strategies and, where possible, the corresponding effectiveness that organizations can use to optimize EHR-to-physician workflow alignment. The outcome would also help make appropriate recommendations for alignment. Subsequently, it can improve patient outcomes such as the reduction of medication errors and improvement of patient-centered, improve physician well-being and reduce burnout.
WITHDRAWN: Analysis of Pleiotropy for Testosterone and Lipid Profiles in Males and Females
Authors: Chattopadhyay Srijan , Bhattacharyya Swapnaneel , Basu Sevantee 
Published: December 2023

Withdrawal StatementThe authors have withdrawn this manuscript owing to the work having been performed in the lab of Anasuya Chakrabarty, but the mansucript being submitted without her knowledge or consent. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Study Protocol and Rationale of “The UP Project”: Evaluating the Effectiveness of Active Breaks on Health Indicators in Desk-Based Workers
Authors: Cristi-Montero Carlos , Martínez-Flores Ricardo , Espinoza-Puelles Juan Pablo , Favero-Ramirez Laura , Zurita-Corvalan Natalia , Cañete Ignacio Castillo , Leppe Jaime , Ferrari Gerson , Sadarangani Kabir , Cancino-López Jorge , Hernandez-Jaña Sam , Farias Tuillang Yuing , Lemes Vanilson Batista , Rodríguez-Rodríguez Fernando , Brand Caroline 
Published: December 2023

ABSTRACTBackgroundExcessive sedentary time has been negatively associated with several health outcomes, and physical activity alone does not seem to fully counteract these consequences. This panorama emphasizes the essential of sedentary time interruption programs. “The Up Project” seeks to assess the effectiveness of two interventions, one incorporating active breaks led by a professional and the other utilizing a computer application (self-led), of both equivalent duration and intensity. These interventions will be compared with a control group to evaluate their impact on physical activity levels, sedentary time, stress perception, occupational pain, and cardiometabolic risk factors among office workers.MethodsThis quasi-experimental study includes 60 desk-based workers from universities and educational institutes in Valparaiso, Chile, assigned to three groups: a) booster breaks led by professionals, b) computer prompts that are unled, and c) a control group. The intervention protocol for both experimental groups will last 12 weeks (only weekdays). The following measurements will be performed at baseline and post-intervention: cardiometabolic risk based on body composition (fat mass, fat-free mass, and bone mass evaluated by DXA), waist circumference, blood pressure, and resting heart rate. Physical activity and sedentary time will be self-reported and objectively assessed using accelerometry. Questionnaires will be used to determine the perception of stress and occupational pain.DiscussionGovernments worldwide are addressing health issues associated with sedentary behavior, particularly concerning individuals highly exposed to it, such as desk-based workers. Despite implementing certain strategies, there remains a noticeable gap in comprehensive research comparing diverse protocols. For instance, studies that contrast the outcomes of interventions led by professionals with those prompted by computers are scarce. This ongoing project is expected to contribute to evidence-based interventions targeting reduced perceived stress levels and enhancing desk-based employees’ mental and physical well-being. The implications of these findings could have the capacity to lay the groundwork for future public health initiatives and government-funded.
LDLR Variant Classification for Improved Cardiovascular Risk Prediction in Familial Hypercholesterolemia
Authors: Ibrahim Shirin , Hartgers Merel L. , Reeskamp Laurens F. , Zuurbier Linda , Defesche Joep , Kastelein John J.P. , Stroes Erik S.G. , Hovingh G. Kees , Huijgen Roeland 
Published: December 2023

AbstractBackgroundFamilial Hypercholesterolemia (FH) is a genetic disorder marked by high LDL cholesterol and an increased premature coronary artery disease (CAD) risk. Current dichotomous classification of LDL receptor gene (LDLR) variants may inadequately capture patient variability in LDL cholesterol levels and CAD risk. This study assessed a novel approach for assessingLDLRvariant severity using variant-specific LDL cholesterol percentiles.MethodsParticipants of the Dutch FH cascade screening program were screened for 456LDLRvariants. Sex- and age-specific LDL cholesterol percentiles were computed for eachLDLRvariant carrier. These percentiles were used to calculate the mean LDL cholesterol percentile for each variant. Based on the variant-specific LDL cholesterol percentiles, carriers were grouped into the following strata: <75th, 75th-88th, 88th-92nd, 92nd-96.5th, 96.5th-98th, and ≥98thpercentile. Additionally, variants were categorized into class 1 (LDLR deficient) and non-class 1 (often LDLR defective) variants. CAD risk between carriers in the different strata and non-carriers was compared using a Cox proportional hazard model.ResultsOut of 35,257 participants, 12,485 (36%)LDLRvariant carriers were identified. Carriers had a 5-fold higher CAD risk compared with non-carriers. Hazard ratios for CAD increased gradually from 2.2 (95%CI 0.97-5.0) to 12.0 (95%CI 5.5-24.8) across the strata. A 7.3-fold and 3.9-fold increased CAD risk was observed in carriers of class 1 and non-class 1LDLRvariants, respectively.ConclusionsThis study presents a refined approach for classifyingLDLRvariants based on their impact on LDL cholesterol levels, allowing for more precise, genotype-specific CAD risk estimation in FH patients compared with traditional methods.
Competition for resources during development drives allometric patterns in the grassSetaria
Authors: Dale Renee , Banan Darshi , Millman Britney , Leakey Andrew D.B. , Mukherji Shankar , Baxter Ivan 
Published: December 2023

AbstractGrasses grow a series of phytomers during development. The distance between successive leaves is determined by internode lengths. Grasses exhibit genetic, developmental, and environmental variability in phytomer number, but how this affects internode length, biomass, and height is unknown. We hypothesized that a generalized mathematical model of phytomer development wherein between-phytomer competition influences internode length distributions would be sufficient to explain internode length patterns in twoSetariagenotypes: weedy A10 and domesticated B100. Our model takes a novel approach that includes the vegetative growth of leaf blade, sheath, and internode at the individual phytomer level, and the shift to reproductive growth. To validate and test our mathematical model, we carried out a greenhouse experiment. We found that the rate of leaf emergence is consistent for both genotypes across development, and that the length of time spent elongating for the leaf and internode can be described as the ratio between the time of phytomer emergence and the elongation completion time. The validated model was simulated across all possible parameter values to predict the influence of phytomer number on internode length. This analysis predicts that different internode length distributions across different numbers of total phytomers are an emergent property, rather than a genotype-specific property requiring genotype-specific models. We applied the model to internode length only field data ofS. italicaaccession B100, grown under both well-watered and drought conditions. The model predicts that droughted plants reduce leaf elongation time, reduce resource allocation to the internodes, and overall experience slower growth. Together, model and data suggest that allometric patterns are driven by competition for resources among phytomer and the shift to reproductive growth inSetaria. The resulting model enables us to predict growth dynamics and final allometries at the phytomer level.
“Let's do it and not you do it”: role of mentoring in facilitating change supportive behaviour
Authors: Kurian Rona Elizabeth 
Published: December 2023

Purpose The developmental relation of informal mentoring within the organization could aid in tiding over the challenges that arise with change. The purpose is to explore the relationship between informal mentoring within the organization and change supportive behaviour to put forth a framework describing the catalytic and a priori role of informal mentoring within the organization in augmenting change readiness and facilitating change supportive behaviour for a successful organizational change.Design/methodology/approach Drawing on the appraisal theory of stress coping, the paper put forward a conceptual framework describing the mechanisms through which informal mentoring within the organization leads to change supportive behaviour among the individuals.Findings The conceptual model explains how informal mentoring within the organization develops optimism, resilience, self-efficacy and trust and facilitates change readiness among the individuals, which leads to change supportive behaviours in them. The paper also describes the influence of poor change management history and organizational identity threat on the relations.Research limitations/implications The paper explains the underexplored relationship between mentoring and change readiness. It also sheds light on the importance of exploring the micro-foundations of a macro-level phenomenon. Further research should focus on the differential effect of different forms of mentoring on change readiness.Originality/value The paper is developed based on the review of extant literature and applying the theoretical lens of appraisal theory of stress coping to the phenomenon. The paper explains the micro-foundation of the phenomenon and describes how informal mentoring would lead to a change supportive behaviour among the individuals.