bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of spleen stiffness measurement to rule out high-risk varices in patients with porto-sinusoidal vascular disorder
Authors: Moga Lucile , Paradis Valérie , Ferreira-Silva Joel , Gudavalli Koushik , Indulti Federica , Dajti Elton , Nicoara-Farcau Oana , Tosetti Giulia , Antonenko Antonina , Fodor Andreea , Vidal-González Judit , Turco Laura , Capinha Francisco , Elkrief Laure , Monllor-Nunell Teresa , Goria Odile , Balcar Lorenz , Lannes Adrien , Mallet Vincent , Poujol-Robert Armelle , Thabut Dominique , Houssel-Debry Pauline , Wong Yu Jun , Ronot Maxime , Vilgrain Valérie , Rampally Sai Prasanth , Payancé Audrey , Castera Laurent , Reiberger Thomas , Ferrusquía-Acosta José , Noronha Ferreira Carlos , Vitale Giovanni , Simon-Talero Macarena , Procopet Bogdan , Berzigotti Annalisa , Caccia Riccardo , Turon Fanny , Schepis Filippo , Ravaioli Federico , Colecchia Antonio , Valsan Arun , Macedo Guilherme , Plessier Aurélie , Rautou Pierre-Emmanuel ,   on behalf of the ERN RARE-LIVER; a study of VALDIG, an EASL consortium
Published: July 2024

Background and Aims:
Baveno VII consensus suggests that screening endoscopy can be spared in patients with compensated cirrhosis when spleen stiffness measurement (SSM) by vibration-controlled transient elastography (VCTE) is ≤40 kPa as they have a low probability of high-risk varices (HRV). Conversely, screening endoscopy is required in all patients with porto-sinusoidal vascular disorder (PSVD). This study aimed to evaluate the performance of SSM-VCTE to rule out HRV in patients with PSVD and signs of portal hypertension.

Approach and Results:
We retrospectively included patients with PSVD, ≥1 sign of portal hypertension, without a history of variceal bleeding, who underwent an SSM-VCTE within 2 years before or after an upper endoscopy in 21 VALDIG centers, divided into a derivation and a validation cohort. One hundred fifty-four patients were included in the derivation cohort; 43% had HRV. By multivariable logistic regression analysis, SSM-VCTE >40 kPa and serum bilirubin ≥1 mg/dL were associated with HRV. SSM-VCTE ≤40 kPa combined with bilirubin <1 mg/dL had a sensitivity of 96% to rule out HRV and could spare 38% of screening endoscopies, with 4% of HRV missed, and a 95% negative predictive value. In the validation cohort, including 155 patients, SSM combined with bilirubin could spare 21% of screening endoscopies, with 4% of HRV missed and a 94% negative predictive value.

Conclusions:
This study gathering a total of 309 patients with PSVD showed that SSM-VCTE ≤40 kPa combined with bilirubin <1 mg/dL identifies patients with PSVD and portal hypertension with a probability of HRV <5%, in whom screening endoscopy can be spared.
Long-term outcomes of extensive thoracoabdominal aortic aneurysm repair utilizing normothermic iliac perfusion: a retrospective cohort study with 10-year single-center experience
Authors: Wang Luchen , Liu Yanxiang , Gao Haoyu , Xie Mingxin , Zhang Bowen , Zhou Sangyu , Qian Xiangyang , Yu Cuntao , Sun Xiaogang 
Published: July 2024

Background:
Normothermic iliac perfusion has been increasingly utilized for thoracoabdominal aortic aneurysm repair; however, the long-term outcomes in large samples are lacking. This study was designed to assess the perioperative and long-term results of thoracoabdominal aortic repair using normothermic iliac perfusion.

Methods:
The authors retrospectively analyzed 156 patients having Crawford extent II or III thoracoabdominal aortic aneurysm replacement with normothermic iliac perfusion from 2012 to 2022. Primary endpoints were composite adverse events and long-term survival, which encompassed 30-day mortality, persistent stroke, persistent paraplegia, and acute renal failure needing continuous dialysis. The cohort was divided into two subgroups based on the use of selective visceral and cold renal perfusion techniques.

Results:
The combined adverse event rate was 14.1%. Specific rates were: 30-day mortality (4.5%), persistent stroke (1.9%), persistent paraplegia (4.5%), and renal failure requiring persistent dialysis (3.2%). The median follow-up time was 67 months. Overall survival rates at 1, 3, 5, 7, and 10 years were 91.6, 90.0, 85.4, 77.6, and 69.7%, respectively. Subgroup analysis showed the visceral and renal perfusion group had a significantly reduced adverse event incidence compared to the nonperfusion group (6.5 vs. 19.1%, P=0.026). Multivariable logistic regression analysis confirmed selective visceral and cold renal perfusion techniques as protective factors against postoperative adverse events (OR 0.30, 95% CI: 0.09–0.94; P=0.038). Multivariable Cox regression analysis identified age ≥50 years (HR 2.63, 95% CI: 1.10–6.27; P=0.029) and NYHA grade ≥III (HR: 3.20, 95% CI: 1.04–9.87; P=0.043) as independent risk factors predicting overall survival.

Conclusions:
Normothermic iliac perfusion is a feasible option for thoracoabdominal aortic repair with cost benefits and simpler management, and selective visceral and cold renal perfusion techniques may further improve its safety and effectiveness. However, enhanced vigilance and meticulous care are essential, particularly for elderly patients and those with cardiac insufficiency.
Reoperation for ipsilateral local recurrence following prior nephron-sparing surgery: innovative surgical insights from a high-volume urological center with cross-sectional study
Authors: Ma Wenming , Xu Wenlong , Meng Jialin , Chen Lei , Tai Sheng , Yang Cheng , Chen Jinhu , Shi Haoqiang , Liang Chaozhao 
Published: July 2024

Background:
The main aim of this study was to examine the perioperative results of reoperations and suggest novel surgical approaches. Based on a substantial number of robotic and laparoscopic nephron-sparing surgery (NSS), the authors aim to propose novel surgical strategies that offer practical recommendations to surgeons.

Methods:
Renal cell carcinoma patients with ipsilateral recurrent tumors, without evidence of metastasis, and who underwent primary NSS at our center between 2013 and 2023 were enrolled in this study, and all received the second time surgery. The authors conducted an analysis to evaluate perioperative outcomes and observed trends over a decade. Additionally, based on the findings from this study, the authors developed our surgical strategies.

Results:
In the past decade, our center has successfully conducted a total of 2546 surgeries for renal cell carcinoma, out of which this study includes 15 patients who met the specified criteria. For reoperation, robotic-assisted surgery was applied in five cases (33.3%), laparoscopic surgery in six cases (40%), and open surgeries in four cases (26.7%). While four (26.7%) patients underwent NSS while radical nephrectomy was performed on 11 patients (73.3%). The median operative time was 215 min (IQR: 135–300), and the median estimated blood loss was 50 ml (IQR: 50–100). The median length of postoperative hospitalization was 6 days (IQR: 5–9). Furthermore, there has been a yearly increase in the application of robotic-assisted NSS at our institution.

Conclusion:
Reoperation following the pNSS is a secure and effective surgical approach. The authors introduce novel surgical strategies for primary surgery and reoperation, which offer valuable insights to surgeons in the current study.
Cross-circulation combined with rapidly deployable venovenous bypass grafts for multiorgan biosystemic support in liver failure: experimental studies
Authors: Liu Peng , Yang Lifei , Lu Qiang , Qian Yerong , Shi Aihua , Liu Xin , Wei Shasha , Fan Shujuan , Lv Yi , Xiang Junxi 
Published: July 2024

Background:
Liver failure remains a critical clinical challenge with limited treatment options. Cross-circulation, the establishment of vascular connections between individuals, has historically been explored as a potential supportive therapy but with limited success. This study investigated the feasibility of combining cross-circulation with a rapidly deployable venovenous bypass (VVB) graft for multiorgan support in a rat model of total hepatectomy, representing the most severe form of liver failure.

Materials and methods:
A Y-shaped VVB graft was fabricated using coaxial electrospinning of PLCL/heparin nanofibers and magnetic rings for rapid anastomosis. After total hepatectomy in rats, the VVB graft was implanted to divert blood flow. Cross-circulation was then established between anhepatic and normal host rats. Hemodynamics, biochemical parameters, blood gases, and survival were analyzed across three groups: hepatectomy with blocked vessels (block group), hepatectomy with VVB only (VVB group), and hepatectomy with VVB and cross-circulation (VVB/cross-circulation group).

Results:
The VVB graft exhibited suitable mechanical properties and hemocompatibility. VVB rapidly restored hemodynamic stability and mitigated abdominal congestion posthepatectomy. Cross-circulation further ameliorated liver dysfunction, metabolic derangements, and coagulation disorders in anhepatic rats, significantly prolonging survival compared to the VVB group (mean 6.56±0.58 vs. 4.05±0.51 h, P<0.05) and the block group (mean 1.01±0.05 h, P<0.05).

Conclusion:
Combining cross-circulation with a rapidly deployed VVB graft provided effective multiorgan biosystemic support in a rat model of total hepatectomy, substantially improving the biochemical status and survival time. This approach holds promise for novel liver failure therapies and could facilitate liver transplantation procedures.
Using Simulation-Based Mastery Learning to Achieve Excellent Learning Outcomes in Physical Therapist Education
Authors: Tappan Rachel S. , Roth Heidi R. , McGaghie William C. 
Published: July 2024

Introduction.
The 2 aims of this observational study are (a) to describe the implementation and feasibility of a bed mobility skills simulation-based mastery learning (SBML) curricular module for physical therapist students and (b) to measure learning outcomes and student perceptions of this module.

Review of Literature.
Simulation-based mastery learning is an outcome-based educational approach that has been successful in other health professions but has not been explored in physical therapy education.

Subjects.
Eighty-seven students in a single cohort of a Doctor of Physical Therapy program.

Methods.
The SBML module in this pretest–posttest study included a pretest, instruction, initial posttest, and additional rounds of instruction and assessment as needed for all learners to achieve the minimum passing standard (MPS) set using the Mastery Angoff and Patient Safety methods. Outcome measures were bed mobility assessment pass rates and scores, additional student and faculty time compared with a traditional approach, and student perceptions of their self-confidence and the module.

Results.
All students achieved the MPS after 3 rounds of training and assessment beyond the initial posttest. Mean Total Scores improved from 67.6% (12.9%) at pretest to 91.4% (4.8%) at mastery posttest (P < .001, Cohen's d = 1.8, 95% CI [1.4–2.1]); mean Safety Scores improved from 75.2% (16.0%) at pretest to 100.0% (0.0%) at mastery posttest (P < .001, Cohen's d = 1.5, 95% CI [1.2–1.9]). Students who did not achieve the MPS at the initial posttest (n = 30) required a mean of 1.2 hours for additional instruction and assessment. Survey results revealed an increase in student confidence (P < .001) and positive student perceptions of the module.

Discussion and Conclusion.
Implementation of this SBML module was feasible and resulted in uniformly high levels of bed mobility skill acquisition. Based on rigorous learning outcomes, feasible requirements for implementation, and increased student confidence, SBML offers a promising approach for wider implementation in physical therapy education.
Urinary Incontinence Medications: Patient-Initiated Concerns in Primary Care
Authors: Neuner Joan , Schmitt Emily , Winn Aaron , Davidson Emily , O’Connor Robert C. , Marowski Sarah , Luebke Marie , Balza Joanna , Attewell Madeline , Flynn Kathryn E. 
Published: July 2024

Importance
Guideline-recommended medications for overactive bladder and urge urinary incontinence (OAB/UUI) are effective but have high costs and side effects. Little is known about patient concerns regarding these medications when prescribed by their primary care providers (PCPs).

Objective
The aim of the study was to describe PCP-patient interactions when prescribing medications for OAB/UUI, specifically clinical concerns, cost and authorization issues, and mode of communication for these interactions.

Study Design
Using electronic health records, we identified a retrospective cohort of women aged 18–89 years who were prescribed a medication for OAB/UUI during a primary care office visit from 2017 to 2018. We examined the electronic health record from initial prescription through 15 subsequent months for documentation of prior authorization requests and patient concerns about cost, side effects, or ineffectiveness. The association of patient demographics, comorbidity, and medication class with these concerns was examined with logistic regression models.

Results
Overall, 46.2% of patients (n = 123) had 1 or more OAB/UUI medication concerns, and 52 reported outside an office visit. Only higher comorbidity was associated with reduced concern of any type. Although the overall percent age of patients reporting concerns was similar by medication type, the patterns of concern type varied. Compared with those taking short-acting antimuscarinics, patients taking long-acting antimuscarinics other than oxybutynin were less likely to have side effect concerns (adjusted odds ratio 0.35, 95% CI 0.16–0.78) and more likely to have cost concerns (adjusted odds ratio 5.10, 95% CI 1.53–17.03).

Conclusions
Patient concerns regarding OAB/UUI medications were common in primary care practices and frequently reported outside of office visits. However, the patterns of concerns (cost vs side effects) varied between medication classes.
Joint exome and metabolome analysis in individuals with dyslexia: Evidence for associated dysregulations of olfactory perception and autoimmune functions
Authors: Nandakumar Rohit , Shi Xiaojian , Gu Haiwei , Kim Yookyung , Raskind Wendy H. , Peter Beate , Dinu Valentin 
Published: July 2024

AbstractDyslexia is a learning disability that negatively affects reading, writing, and spelling development at the word level in 5%-9% of children. The phenotype is variable and complex, involving several potential cognitive and physical concomitants such as sensory dysregulation and immunodeficiencies. The biological pathogenesis is not well-understood. Toward a better understanding of the biological drivers of dyslexia, we conducted the first joint exome and metabolome investigation in a pilot sample of 30 participants with dyslexia and 13 controls. In this analysis, eight metabolites of interest emerged (pyridoxine, kynurenic acid, citraconic acid, phosphocreatine, hippuric acid, xylitol, 2-deoxyuridine, and acetylcysteine). A metabolite-metabolite interaction analysis identified Krebs cycle intermediates that may be implicated in the development of dyslexia. Gene ontology analysis based on exome variants resulted in several pathways of interest, including the sensory perception of smell (olfactory) and immune system-related responses. In the joint exome and metabolite analysis, the olfactory transduction pathway emerged as the primary pathway of interest. Although the olfactory transduction and Krebs cycle pathways have not previously been described in dyslexia literature, these pathways have been implicated in other neurodevelopmental disorders including autism spectrum disorder and obsessive-compulsive disorder, suggesting the possibility of these pathways playing a role in dyslexia as well. Immune system response pathways, on the other hand, have been implicated in both dyslexia and other neurodevelopmental disorders.
Metabolic mode estimated by breathing reflects long-term motor memory
Authors: Hayashi Takuji , Nakano Nobuyasu , Washino Sohei , Murai Akihiko 
Published: July 2024

AbstractRespiration is a crucial metabolic process that converts macronutrients and oxygen (O2) into energy and carbon dioxide (CO2), supporting motor actions. In addition to the energy demands for movements, the brain is a significant energy consumer for neural activity and plasticity. However, it is not known whether breathing patterns can serve as an indicator for them as they can for movement intensity. According to computational theory, motor memory updating involves fast and slow timescales, which may correspond to neural activity and plasticity. To investigate whether breathing patterns reflect these time constants, human experiments assessed short- and long-term memories while recording the O2-CO2 gas exchange. We found that the respiratory exchange ratio (RER), an indicator of metabolic mode, was not influenced by the execution and learning of the reaching movement and was stable within individuals but diverse across individuals. Interestingly, the individual differences in the RER reflect individual variation in long-term memory rather than short-term memory. Furthermore, to manipulate the RER, we provided 200 kcal of glucose immediately before the task. Surprisingly, 24-hour retention increased by 21%. Together, the RER would serve as a remarkable proxy for long-term motor memory and ingesting glucose would shift the neurophysiological “idling state” for learning.
Cellular and Molecular Changes During Aging in MEC: Unveiling the Role of Bglap3 Neurons in Cognitive Aging
Authors: Cao Qichen , Uzeen Sorgog , Cheng Sihui , Liu Yuanjing , Liu Jiangyuan , Wen Shidan , Zhong Meng , Hao Jun , Yao Shuyang , Yang Yikai , Yan Xingyu , Guo Weixiang , Miao Chenglin 
Published: July 2024

SummaryAging-correlated cognitive declines, including deficiencies in spatial orientation and memory, may reflect dysfunction in the hippocampus and medial entorhinal cortex (MEC). However, aging-related changes in MEC at the cellular and molecular levels remain unclear. In this study, we found fewer grid cells with reduced spatial stability in old mice. We compared gene expression profiles between young and old mice using 10x Genomics Visium technology. Among 1664 differentially expressed genes, we discovered Bglap3, a marker gene for subpopulation in MEC Layer III with decreased cell number with age. Silencing of Bglap3+ neurons in young mice impaired the spatial tuning of neurons in MEC and the spatial learning of a new platform location in water maze. These findings help us to understand the cellular and molecular changes in the MEC in healthy aging animals and the changes of Bglap3+ cells in old mice indicating a possible cause of aging-related MEC deficiency.
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling
Authors: Johnston Iain G. , Diaz-Uriarte Ramon 
Published: July 2024

AbstractAccumulation models, where a system progressively acquires binary features over time, are common in the study of cancer progression, evolutionary biology, and other fields. Many approaches have been developed to infer the accumulation pathways by which features (for example, mutations) are acquired over time. However, most of these approaches do not support reversibility: the loss of a feature once it has been acquired (for example, the clearing of a mutation from a tumour or population). Here, we demonstrate how the well-established Mk model from evolutionary biology, embedded on a hypercubic transition graph, can be used to infer the dynamics of accumulation processes, including the possibility of reversible transitions, from data which may be uncertain and cross-sectional, longitudinal, or phylogenetically / phylogenomically embedded. Positive and negative interactions between arbitrary sets of features (not limited to pairwise interactions) are supported. We demonstrate this approach with synthetic datasets and real data on bacterial drug resistance and cancer progression. While this implementation is limited in the number of features that can be considered, we discuss how this limitation may be relaxed to deal with larger systems.
TEtrimmer: a novel tool to automate the manual curation of transposable elements
Authors: Qian Jiangzhao , Xue Hang , Ou Shujun , Storer Jessica , Fürtauer Lisa , Wildermuth Mary C. , Kusch Stefan , Panstruga Ralph 
Published: July 2024

ABSTRACTTransposable elements (TEs) are repetitive DNA sequences capable of moving within genomes. Accurate annotation and classification of TEs is crucial but challenging due to their sequence diversity and often fragmented occurrence. We present TEtrimmer, a novel tool to automate manual TE curation. TEtrimmer integrates multiple sequence alignment (MSA) clustering, MSA sequence extension, MSA cleaning, TE boundary definition, and TE classification, and provides report plots and a graphical user interface (GUI) application to inspect and improve results. Benchmarked on the genomes of six organisms from various kingdoms of life, TEtrimmer consistently improved the identification of intact TEs compared to established tools.
Disturbance of the Sense of Agency in Obsessive-Compulsive Disorder and its Modulation by Social Context
Authors: Roth Manuel J. , Lindner Axel , Fallgatter Andreas J. , Wittorf Andreas , Jusyte Aiste 
Published: July 2024

AbstractExecuting precise actions and perceiving them as one’s own is a fundamental ability underlying the sense of agency (SoA). The SoA thereby heavily relies on the accuracy and reliability of forward models, capturing sensory movement consequences. Impairments thereof thus represent a promising candidate mechanism contributing to cases of SoA pathogenesis. In obsessive-compulsive disorder (OCD), for example, the feeling of control over one’s actions is perturbed: Compulsive actions are often experienced as uncontrollable and performed without conscious awareness. At the same time, compulsions can be coupled with an inflated sense of illusory control for uncontrollable events. Here we studied self-action perception in virtual reality with and without veridical or rotated visual feedback about subjects’ pointing movements to test whether patients’ internal forward models are indeed less reliable compared to controls. Interestingly, OCD patients did not exhibit deficits in their accuracy and reliability of motor performance and self-action perception in the absence of visual feedback, suggesting intact forward models. Nonetheless, OCD patients weighted rotated visual action-feedback significantly stronger perceptually. Furthermore, they adapted their movement to this false feedback on a trial-by-trial basis. Finally, increasing the social relevance of action consequences led to stronger feedback weighting in all participants while this effect increased with the strength of OCD symptomatology under conditions with strongest social relevance. We suggest that internal forward models are equally reliable in OCD but their weight is pathologically decreased leading to patients’ overreliance on explicit visual action-feedback and, more generally, to their over-attribution of unrelated events to themselves.