bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer illumination of TRIM gene family reveals immunology regulation and potential therapeutic implications
Authors: Gao Yueying , Pan Tao , Xu Gang , Li Si , Guo Jing , Zhang Ya , Xu Qi , Pan Jiwei , Ma Yanlin , Xu Juan , Li Yongsheng 
Published: December 2022

Abstract
Background
The tripartite motif (TRIM) proteins function as important regulators in innate immunity, tumorigenesis, cell differentiation and ontogenetic development. However, we still lack knowledge about the genetic and transcriptome alterations landscape of TRIM proteins across cancer types.

Methods
We comprehensively reviewed and characterized the perturbations of TRIM genes across > 10,000 samples across 33 cancer types. Genetic mutations and transcriptome of TRIM genes were analyzed by diverse computational methods. A TRIMs score index was calculated based on the expression of TRIM genes. The correlation between TRIMs scores and clinical associations, immune cell infiltrations and immunotherapy response were analyzed by correlation coefficients and gene set enrichment analysis.

Results
Alterations in TRIM genes and protein levels frequently emerge in a wide range of tumors and affect expression of TRIM genes. In particular, mutations located in domains are likely to be deleterious mutations. Perturbations of TRIM genes are correlated with expressions of immune checkpoints and immune cell infiltrations, which further regulated the cancer- and immune-related pathways. Moreover, we proposed a TRIMs score index, which can accurately predict the clinical outcome of cancer patients. TRIMs scores of patients are correlated with clinical survival and immune therapy response across cancer types. Identifying the TRIM genes with genetic and transcriptome alterations will directly contribute to cancer therapy in the context of predictive, preventive, and personalized medicine.

Conclusions
Our study provided a comprehensive analysis and resource for guiding both mechanistic and therapeutic analyses of the roles of TRIM genes in cancer.
Interpersonal Behaviors Questionnaire (IBQ) applied to parenting of emerging adults: dimensional structure and criterion validity
Authors: Vosylis Rimantas , Erentaitė Rasa 
Published: December 2022

Abstract
Background
The prolonged transitions to adulthood strengthen interest in parenting characteristics that can shape emerging adults’ development and progression to full-fledged adulthood. It also strengthens interest in instruments suitable for measuring such parenting characteristics. The current study contributes to this area of research by applying the Interpersonal Behavior Questionnaire (IBQ), to assess parenting behaviors that are pertinent for emerging adults’ development and wellbeing, and seeks evidence of its dimensional structure and criterion validity.

Method
The sample of the study consisted of 600 emerging adults (Mage = 24.94, SDage = 3.03, range 19–29 years; 52.3% women). The dimensionality of IBQ was assessed by testing a sequence of theoretically plausible models representing alternative factor score structures. Criterion validity was investigated by exploring the associations between the IBQ dimensions and basic psychological need satisfaction and frustration, negative affectivity, and thriving.

Results
The findings provide evidence of a hypothesized six-factor structure, but advocate for the use of exploratory structural equation as it may more accurately reflect associations between the six dimensions. Findings also provide evidence of criterion validity.

Conclusions
The findings indicate that IBQ applied to parenting targets dimensions highly relevant for EAs’ flourishing or impoverished functioning. Findings also offer evidence of structure and criterion validity for the IBQ applied to emerging adults’ parent behaviors. As such, researchers may find IBQ attractive, as it is relatively concise yet also a holistic measure that captures the behaviors that both support and thwart an emerging adult’s need for autonomy, competence, and relatedness. Findings also shed light on the process of becoming an adult, the shift in parent–child relationships during this process, and emerging adults’ wellbeing.
Potential antiviral peptides targeting the SARS-CoV-2 spike protein
Authors: Khater Ibrahim , Nassar Aaya 
Published: December 2022

Abstract
Background
The coronavirus disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection became an international pandemic and created a public health crisis. The binding of the viral Spike glycoprotein to the human cell receptor angiotensin-converting enzyme 2 (ACE2) initiates viral infection. The development of efficient treatments to combat coronavirus disease is considered essential.

Methods
An in silico approach was employed to design amino acid peptide inhibitor against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. The designed inhibitor (SARS-CoV-2 PEP 49) consists of amino acids with the α1 helix and the β4 - β5 sheets of ACE2. The PEP-FOLD3 web tool was used to create the 3D structures of the peptide amino acids. Analyzing the interaction between ACE2 and the RBD of the Spike protein for three protein data bank entries (6M0J, 7C8D, and 7A95) indicated that the interacting amino acids were contained inside two regions of ACE2: the α1 helical protease domain (PD) and the β4 - β5 sheets.

Results
Molecular docking analysis of the designed inhibitor demonstrated that SARS-CoV-2 PEP 49 attaches directly to the ACE2 binding site of the Spike protein with a binding affinity greater than the ACE2, implying that the SARS-CoV-2 PEP 49 model may be useful as a potential RBD binding blocker.
Tricolored bats at a southern range edge exhibit partial migration northward in autumn
Authors: Smith Lisa M. , Gore Jeffery A. , Doonan Terry J. , Campbell Caitlin J. 
Published: December 2022

AbstractBackgroundAnimal migration is a widespread global adaptation by which individuals move in response to environmental conditions to reach more favorable conditions. For bats in temperate climates, migration and hibernation are often associated with each other when these bats must migrate to reach suitable overwintering sites. However, differences in movement across the geographical range of a species and the degree to which hibernation drives migratory behavior of bats in subtropical climates, where conditions may remain warm with available prey year-round, remains incomplete. Understanding the migratory strategies of subtropical bats during winter is of increasing importance as they are threatened by stressors such as disease and environmental change.MethodsWe evaluated migration patterns of tricolored bats (Perimyotis subflavus) in Florida, USA, through analysis of stable hydrogen isotope ratios of the fur. We inferred the summer geographic origins of the fur samples and estimated the minimum distance and likely direction traveled by hibernating individuals. We used linear models to examine whether hibernation region, colony size, and an individual’s sex affected the distance traveled.ResultsWe sampled 111 bats hibernating at 40 sites and found that more than half (54.1%) of individuals were residents of the area in which they hibernated. We found that almost half of the sampled bats (43.2%) traveled from southern Florida to overwinter in North Florida. We also documented three individuals that traveled > 100 km from northerly origins, one of which had traveled an estimated minimum distance of 1382 km. We also found that tricolored bats moved farther to reach hibernacula in Northwest Florida and hibernacula with more populous colonies, with no difference in movement between sexes.ConclusionsOur results indicate a pattern of northward autumnal movements of tricolored bats in the subtropical southeastern portion of their range. We suggest that bats are differentially constrained at the edge of their geographical range, resulting in movement contrary to what is expected. Even though we found that few (2.7%) bats moved into Florida from farther north, those migrants can potentially transfer the fungus that causes the deadly white-nose syndrome, which does not currently occur in the state. Our results support the characterization of tricolored bats as flexible partial migrators, with a rarely exercised capacity for long-distance movements.
Demystifying Iranian EFL teachers’ perceptions and practices of learning-oriented assessment (LOA): challenges and prospects in focus
Authors: Derakhshan Ali , Ghiasvand Farhad 
Published: December 2022

AbstractAs a growing approach to assessment, learning-oriented assessment (LOA) has recently flourished to position learning at the center of assessment practices. It aims to unify assessment, teaching, and learning. However, little is written and known about its benefits, challenges, and practices in English as a foreign language (EFL) contexts. To shed light on these aspects, the present study was a bid to unpack Iranian EFL teachers’ perceptions about the benefits, challenges, and professional activities that facilitate LOA understanding and practice. To this end, 40 EFL teachers including both genders were invited to a semi-structured interview held in person. The results of the thematic analysis obtained by MAXQDA revealed that Iranian EFL teachers had different perceptions regarding LOA. They argued that LOA is a process-based, feedback-oriented, formative, and alternative assessment technique that foregrounds feedback and progress rather than the final outcome. Furthermore, it was identified that LOA can be practiced by using alternative assessment, performance assessment, dynamic assessment, peer assessment, self-assessment, and portfolio assessment. Likewise, the results demonstrated that LOA is beneficial in enhancing classroom interaction, collaboration, and engagement, integrating assessment, teaching, and learning, and monitoring students’ progress. However, the time budget, large classes, and teachers’ lack of knowledge and training on LOA were perceived as challenges for applying LOA. Furthermore, it was found that Iranian EFL teachers supported the use of training courses, reading articles and books, and attending assessment-related workshops, webinars, seminars, and conferences to improve LOA knowledge and skills. The study provides implications for EFL teachers and trainers, who can use different assessment techniques/practices representative of LOA.
Impact of the COVID-19 pandemic on critical care utilization in Japan: a nationwide inpatient database study
Authors: Ohbe Hiroyuki , Sasabuchi Yusuke , Matsui Hiroki , Yasunaga Hideo 
Published: December 2022

AbstractBackgroundThe coronavirus disease 2019 (COVID-19) pandemic has disrupted critical care services worldwide. Examining how critical care systems responded to the COVID-19 pandemic on a national level will be useful in setting future critical care plans. The present study aimed to describe the utilization of critical care services before and during the COVID-19 pandemic using a nationwide Japanese inpatient administrative database.MethodsAll patients admitted to an intensive care unit (ICU) or a high-dependency care unit (HDU) from February 9, 2019, to February 8, 2021, in the Japanese Diagnosis Procedure Combination inpatient database were included. February 9, 2020, was used as the breakpoint separating the periods before and during COVID-19 pandemic. Hospital and patient characteristics were compared before and during the COVID-19 pandemic. Change in ICU and HDU bed occupancy before and during the COVID-19 pandemic was evaluated using interrupted time-series analysis.ResultsThe number of ICU patients before and during the COVID-19 pandemic was 297,679 and 277,799, respectively, and the number of HDU patients was 408,005 and 384,647, respectively. In the participating hospitals (383 ICU-equipped hospitals and 460 HDU-equipped hospitals), the number of hospitals which increased the ICU and HDU beds capacity were 14 (3.7%) and 33 (7.2%), respectively. Patient characteristics and outcomes in ICU and HDU were similar before and during the COVID-19 pandemic except main etiology for admission of COVID-19. The mean ICU bed occupancy before and during the COVID-19 pandemic was 51.5% and 47.5%, respectively. The interrupted time-series analysis showed a downward level change in ICU bed occupancy during the COVID-19 pandemic (− 4.29%, 95% confidence intervals − 5.69 to − 2.88%), and HDU bed occupancy showed similar trends. Of 383 hospitals with ICUs, 232 (60.6%) treated COVID-19 patients in their ICUs. Their annual hospital case volume of COVID-19 ICU patients varied greatly, with a median of 10 (interquartile range 3–25, min 1, max 444).ConclusionsThe ICU and HDU bed capacity did not increase while their bed occupancy decreased during the COVID-19 pandemic in Japan. There was no change in clinicians’ decision-making to forego ICU/HDU care for selected patients, and there was no progress in the centralization of critically ill COVID-19 patients.
Comparable rates of secondary surgery between anterior cruciate ligament repair with suture tape augmentation and anterior cruciate ligament reconstruction
Authors: Hopper G. P. , Wilson W. T. , O’Donnell L. , Hamilton C. , Blyth M. J. G. , MacKay G. M. 
Published: December 2022

Abstract
Purpose
The aim of this study was to determine the frequency of secondary surgery following anterior cruciate ligament (ACL) repair with suture tape augmentation in comparison to conventional hamstring ACL reconstruction. We hypothesised that there would be no differences between the groups.

Methods
This was a retrospective comparison study of patients undergoing ACL surgery between September 2011 and April 2018. Two hundred and 73 patients underwent ACL reconstruction using hamstring autograft. During the same timeframe, 137 patients with an acute proximal ACL rupture underwent ACL repair with suture tape augmentation. One patient was lost to follow-up in the ACL reconstruction group leaving 272 patients (99.6%) for the final analysis. In the ACL repair group, three patients were lost to follow-up leaving 134 patents (97.8%) for the final analysis. Secondary surgery was identified by contacting the patients by email/telephone and reviewing patient notes at the time of this analysis.

Results
Re-rupture occurred in 32 patients (11.8%) in the ACL reconstruction group compared to 22 patients (16.4%) in the ACL repair group (p = 0.194). Contralateral ACL rupture occurred in four patients (1.5%) in the ACL reconstruction group compared to three patients (2.2%) in the ACL repair group (p = 0.224). In the ACL reconstruction group, nine patients (3.3%) required secondary meniscal surgery whilst five patients (3.7%) required meniscal surgery in the ACL repair group (p = 0.830). Seven other operations were performed in the ACL reconstruction group (2.6%) compared to three other operations in the ACL repair group (2.2%) (p = 0.374). The overall number of patients undergoing secondary surgery in the ACL reconstruction group was 52 (19.1%) in comparison to 30 (22.4%) in the ACL repair group (p = 0.114).

Conclusion
ACL repair with suture tape augmentation for acute proximal ruptures demonstrated comparable rates of secondary surgery with hamstring ACL reconstruction.
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
Authors: Su Min , Pan Tao , Chen Qiu-Zhen , Zhou Wei-Wei , Gong Yi , Xu Gang , Yan Huan-Yu , Li Si , Shi Qiao-Zhen , Zhang Ya , He Xiao , Jiang Chun-Jie , Fan Shi-Cai , Li Xia , Cairns Murray J. , Wang Xi , Li Yong-Sheng 
Published: December 2022

AbstractThe application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.
Modularized bioceramic scaffold/hydrogel membrane hierarchical architecture beneficial for periodontal tissue regeneration in dogs
Authors: Wei Yingming , Wang Zhongxiu , Han Jiayin , Jiang Xiaojian , Lei Lihong , Yang Xianyan , Sun Weilian , Gou Zhongru , Chen Lili 
Published: December 2022

Abstract

Background
Destruction of alveolar bone and periodontal ligament due to periodontal disease often requires surgical treatment to reconstruct the biological construction and functions of periodontium. Despite significant advances in dental implants in the past two decades, it remains a major challenge to adapt bone grafts and barrier membrane in surgery due to the complicated anatomy of tooth and defect contours. Herein, we developed a novel biphasic hierarchical architecture with modularized functions and shape based on alveolar bone anatomy to achieve the ideal outcomes.

Methods
The integrated hierarchical architecture comprising of nonstoichiometric wollastonite (nCSi) scaffolds and gelatin methacrylate/silanized hydroxypropyl methylcellulose (GelMA/Si-HPMC) hydrogel membrane was fabricated by digital light processing (DLP) and photo-crosslinked hydrogel injection technique respectively. The rheological parameters, mechanical properties and degradation rates of composite hydrogels were investigated. L-929 cells were cultured on the hydrogel samples to evaluate biocompatibility and cell barrier effect. Cell scratch assay, alkaline phosphatase (ALP) staining, and alizarin red (AR) staining were used to reveal the migration and osteogenic ability of hydrogel membrane based on mouse mandible-derived osteoblasts (MOBs). Subsequently, a critical-size one-wall periodontal defect model in dogs was prepared to evaluate the periodontal tissue reconstruction potential of the biphasic hierarchical architecture.

Results
The personalized hydrogel membrane integrating tightly with the nCSi scaffolds exhibited favorable cell viability and osteogenic ability in vitro, while the scratch assay showed that osteoblast migration was drastically correlated with Si-HPMC content in the composite hydrogel. The equivalent composite hydrogel has proven good physiochemical properties, and its membrane exhibited potent occlusive effect in vivo; meanwhile, the hierarchical architectures exerted a strong periodontal regeneration capability in the periodontal intrabony defect models of dogs. Histological examination showed effective bone and periodontal ligament regeneration in the biomimetic architecture system; however, soft tissue invasion was observed in the control group.

Conclusions
Our results suggested that such modularized hierarchical architectures have excellent potential as a next-generation oral implants, and this precisely tuned guided tissue regeneration route offer an opportunity for improving periodontal damage reconstruction and reducing operation sensitivity.

Graphical Abstract
Equiosmolar doses of hypertonic saline versus mannitol for brain relaxation in patients undergoing elective craniotomies: an updated systematic review and meta-analysis
Authors: Johansyah Theodorus Kevin Putra , Jonathan Jeremy , Yusari I. G. A. A. Andra , Nolan John , Alamsyah Alif Hakim , Ramadhana Geizar Arsika 
Published: December 2022

Abstract
Background
Hypertonic saline and mannitol are hyperosmolar agents frequently used to lower ICP and relax the brain during surgeries. Several methods have been used to achieve a good and relaxed brain, such as hyperventilation, cerebrospinal fluid drainage, head position correction, and administration of hyperosmolar agents. Comparing equiosmolar doses between hypertonic saline and mannitol in patients undergoing elective craniotomies is important to further notice the differences in several outcomes. This study aims to compare the outcome of hypertonic saline versus mannitol on brain relaxation in patients undergoing elective craniotomy.

Results
10 articles from 2007 to 2021 were included. Hypertonic saline is associated with better brain relaxation (OR  = 1.84, 95% CI 1.31–2.59; P = 0.001) but significantly increase blood natrium level, both serum and arterial (MD = 3.03, 95% CI 1.70–4.36; P =  < 0.001 and MD = 7.14, 95% CI 0.04–14.24; P =  < 0.001, respectively). Mannitol was associated with increased fluid input and urine output (SMD = − 0.56, 95% CI − 0.98 to − 0.15; P =  < 0.001 and SMD = − 0.96, 95% CI − 1.42 to − 0.50; P =  < 0.001, respectively). Serum osmolality and hemodynamic parameters difference was insignificant.

Conclusions
Hypertonic saline is associated with significantly better brain relaxation score and increased blood sodium level without increase in urine. This may prove to be clinically significant in patients with electrolyte imbalance.
Impact of direct-acting antivirals on neuropsychiatric and neurocognitive dysfunction in chronic hepatitis C patients
Authors: Shehata Ghaydaa A. , Ahmed Gellan K. , Hassan Elham Ahmed , Rehim Abeer Sharaf El-Din Abdel , Mahmoud Saad Zaky , Masoud Noha Ali , Seifeldein Gehan S. , Hassan Waleed Attia , Aboshaera Khaled O. 
Published: December 2022

Abstract
Background
Hepatitis C virus (HCV) infection is associated with psychiatric and cognitive dysfunctions. We aimed to investigate depression, anxiety, and cognitive function of chronic hepatitis C (CHC) patients before and after treatment with direct-acting antivirals (DAAs). Forty CHC patients (20 non-cirrhotic and 20 cirrhotic) who had undergone DAA treatment in our outpatient clinic and ten controls. We administered the Hospital Anxiety and Depression questionnaires to measure the anxiety and depression symptoms and the Cognitive Abilities Screening Instruments (CASI) to measure the cognitive function at the beginning and 3 months after the end of the treatment.

Results
Sustained virological response (SVR) was achieved in all patients. Post-treatment anxiety and depression scores showed a significant improvement than pre-treatment ones in CHC patients. Regarding CASI, before and after the treatment, a statistical significance was found in short-term memory (P = 0.001), concentration (P = 0.033), abstract thinking and judgment (P = 0.024), total (P = 0.001) in non-cirrhotic, Also, an improvement was seen in long-term memory (P = 0.015), short-term memory (P < 0.001), concentration (P = 0.024) and total (P = 0.01) in cirrhotic. However, these changes were still impaired in post-treated cirrhotic compared to controls.

Conclusions
CHC patients' anxiety, depression, and cognitive function partially improved after DAA therapy. Besides, improving the status of CHC, reversibility of cognitive dysfunction in non-cirrhotic patients may indicate the importance of treatment in early stages of liver disease.