bluuebunny/crossref_metadata_2025_split huggingface dataset:
Safety and efficacy of resmetirom in the treatment of patients with non-alcoholic steatohepatitis and liver fibrosis: a systematic review and meta-analysis
Authors: Raja Adarsh , Subhash Sagar Raja , Saeed Sadia , Zia ul haq Amna , Khan Owais , Dileep Bhimani Parshant , Raja Sandesh , Deepak Fnu , Ahmed Muhammad , Ashir Shafique Muhammad , Saqlain Mustafa Muhammad , Sohaib Asghar Muhammad , Sharma Varsha 
Published: May 2024

Introduction:
Non-alcoholic fatty liver disease (NAFLD), spanning from non-alcoholic steatohepatitis (NASH) to liver fibrosis, poses a global health challenge amid rising obesity and metabolic syndrome rates. Effective pharmacological treatments for NASH and liver fibrosis are limited.

Objective:
This study systematically reviews and meta-analyzes the safety and efficacy of resmetirom, a selective thyroid hormone receptor-β agonist, in NASH and liver fibrosis treatment. By analyzing data from clinical trials, we aim to offer evidence-based recommendations for resmetirom’s use in managing these conditions and identify avenues for future research.

Methods:
Electronic databases (PubMed, Scopus, Science Direct, Google Scholar, ClinicalTrials.gov, and Cochrane CENTRAL) were systematically searched, supplemented by manual screening of relevant sources. Only English-language randomized controlled trials were included. Data extraction, risk of bias assessment, pooled analyses, and meta-regression were performed.

Results:
Three randomized controlled trials involving 2231 participants were analyzed. Resmetirom demonstrated significant reductions in hepatic fat fraction [standardized mean difference (SMD) −4.61, 95% CI −6.77 to −2.44, P < 0.0001], NASH resolution without worsening fibrosis [risk ratio (RR) 2.51, 95% CI 1.74–3.64, P = 0.00001), and liver fibrosis improvement (RR 2.31, 95% CI 1.20–4.44, P = 0.01). Secondary outcomes showed significant improvements in lipid profiles, liver enzymes, and NASH biomarkers with resmetirom treatment. Meta-regression revealed associations between covariates and primary outcomes.

Conclusion:
Resmetirom exhibits promising efficacy in reducing hepatic fat, improving NASH resolution, and ameliorating liver fibrosis with a favorable safety profile. Further research is warranted to validate findings and optimize therapeutic strategies for NASH and liver fibrosis management.
Detection of Adverse Events With the Austrian Inpatient Quality Indicators
Authors: Schmied Marten , Buchberger Wolfgang , Perkhofer Dieter , Kvitsaridze Irma , Brunner Wolfgang , Kapferer Oliver , Siebert Uwe 
Published: May 2024

Objectives
Indicators based on routine data are considered a readily available and cost-effective method for assessing health care quality and safety. The Austrian Inpatient Quality Indicators (A-IQI) have been introduced in all Austrian public hospitals as a mandatory quality measurement. The purpose of this study was to assess the value of conspicuous A-IQI in predicting the presence of adverse events (AEs).

Methods
We conducted an exploratory study comparing all indicator-positive patient cases contributing to 18 conspicuous A-IQI indicators to randomly selected indicator-negative control cases regarding the prevalence and severity of AEs. Structured medical record review using the Institute for Healthcare Improvement Global Trigger Tool was used as the gold standard.

Results
In 421 chart reviews, we identified 158 AEs. 70.9% (n = 112) of the AEs were found in cases with a positive indicator. The relative risk of an AE occurring was 3.47 (95% confidence interval: 2.30, 5.24) in indicator-positive cases compared to indicator-negatives. The proportion of severe events (National Coordination Council for Medication Error Reporting and Prevention Index categories H and I) was 54.5% (n = 61) in indicator-positive cases and only 15.3% (n = 7) in indicator-negative cases. Overall sensitivity of the A-IQI was 68.2%, specificity 69.4%, positive predictive value 36.0%, and negative predictive value 89.6%.

Conclusions
Our study shows that significantly more AEs and more severe AEs were found in cases with positive A-IQI than in indicator-negative control cases. However, studies with larger numbers of cases and with larger numbers of conspicuous indicators are needed for the validation of the entire A-IQI indicator set.
Identification of excessive contact pressures under hand orthosis based on finite element analysis
Authors: Tan Xinyang , Ahmed-Kristensen Saeema , Zhu Qian , Han Ting , Zhu Lei , Chen Wei , Cao Jiangang , Nanayakkara Thrishantha 
Published: May 2024

Background:
Implicit magnitudes and distribution of excessive contact pressures under hand orthoses hinder clinicians from precisely adjusting them to relieve the pressures. To address this, contact pressure under a hand orthosis were analysed using finite element method.

Methods:
This paper proposed a method to numerically predict the relatively high magnitudes and critical distribution of contact pressures under hand orthosis through finite element analysis, to identify excessive contact pressure locations. The finite element model was established consisting of the hand, orthosis and bones. The hand and bones were assumed to be homogeneous and elastic bodies, and the orthosis was considered as an isotropic and elastic shell. Two predictions were conducted by assigning either low (fat) or high (skin) material stiffness to the hand model to attain the range of pressure magnitudes. An experiment was conducted to measure contact pressures at the predicted pressure locations.

Results:
Identical pressure distributions were obtained from both predictions with relatively high pressure values disseminated at 12 anatomical locations. The highest magnitude was found at the thumb metacarpophalangeal joint with the maximum pressure range from 13 to 78 KPa. The measured values were within the predicted range of pressure magnitudes. Moreover, 6 excessive contact pressure locations were identified.

Conclusions:
The proposed method was verified by the measurement results. It renders understanding of interface conditions underneath the orthosis to inform clinicians regarding orthosis design and adjustment. It could also guide the development of 3D printed or sensorised orthosis by indicating optimal locations for perforations or pressure sensors.
A scoping review of postoperative early rehabilitation programs after dysvascular-related amputations
Authors: Wong Christopher K , Rosati Jennifer , Forbes Kaitlynne , Feng Shanshan , Donohue Aine , Beckley Akinpelumi 
Published: May 2024

Background:
After amputation, people face challenges including wound healing and decreased functional mobility. Early mobilization in acute hospital care has proved safe, improved function, and sped discharge. Still, loss of a leg complicates standing and early mobilization after amputation. Approaches to early mobilization and rehabilitation after amputation surgery have not been widely studied.

Objectives:
To map the evidence regarding early postoperative mobilization after dysvascular amputation. Specific aims included identifying research designs and populations, describing rehabilitation approaches, and identifying gaps within the literature.

Study design:
Scoping review following PRISMA-Sc guidelines.

Methods:
The a priori scoping review methodology conducted in June 2022 with English language and 20-year limits used the OVID Medline, OVID Allied and Complementary Medicine Database, Cumulative Index to Nursing and Allied Health Literature, Cochrane databases, and Journal of Prosthetics and Orthotics archive. Reviewer pairs used Covidence software to screen for inclusion (subjects with major lower limb dysvascular amputations, seen immediately postoperatively for hospital-based rehabilitation) with decisions by concurrence. Data for best practice scoping reviews were synthesized for analysis.

Results:
Two hundred ninety-six citations were screened, 13 full texts reviewed, and 8 articles included: 2 cohort studies, 3 case-control studies, 2 single-group interventional studies, and 1 case study. There were no randomized control trials or prospective comparison group trials.

Conclusions:
Few studies were identified regarding acute rehabilitation after major lower extremity amputation. The limited evidence in this review suggested that early mobilization in the days after amputation was safe with or without use of temporary prostheses, although further research is certainly warranted.
Myelodysplastic Syndrome Related to Successful Treatment With177Lu-PSMA for Metastatic Castration–Refractory Prostate Cancer
Authors: Vija Racaru Lavinia , Krim Mehdi , Rivet Valérian , Mourey Loic , Courbon Pr Frederic 
Published: May 2024

Abstract

177Lu-vipivotide tetraxetan (177Lu-PSMA-617/LuPSMA) received recent EMA approval for metastatic castration–resistant prostate cancer, with promising data for earlier stages. Secondary myeloid neoplasm following exposure to DNA-damaging therapy (therapy-related myelodysplastic syndrome [MDS]) is a rare severe complication of 177Lu-oxodotreotide. We present a 77-year-old man, with synchronous liver, bone, and lymph node metastatic prostate cancer, having developed a low-risk MDS with SF3B1 mutation, 1 month after the sixth administration of LuPSMA. Although on partial metabolic and biological response with PSA nadir at 7 months after therapy, life quality was significantly altered by MDS.
Unplanned Surgery in Dually Eligible Beneficiaries for Conditions that Should Be Treated Electively
Authors: Dualeh Shukri H.A. , Bonner Sidra N. , Kunnath Nicholas J. , Ibrahim Andrew M. 
Published: May 2024

Objective:
To evaluate the rate of unplanned surgery among dually eligible beneficiaries for surgical conditions that should be treated electively.

Summary Background Data:
Access-sensitive surgical conditions (e.g. abdominal aortic aneurysm repair, colectomy for colon cancer, ventral hernia repair) are ideally treated with elective surgery, but when left untreated have a natural history leading to unplanned surgery. Dually eligible beneficiaries may face systematic barriers to access surgical care.

Methods:
Cross-sectional retrospective study of all beneficiaries who were eligible for both Medicare and Medicaid, and underwent surgery for an access-sensitive surgical condition between 2016-2020. We compared the rate of unplanned surgery as well as 30-day mortality, complications and readmissions for dually eligible versus non-dually eligible beneficiaries. Sex, age, race/ethnicity, comorbidities, teaching status, nursing ratio, hospital region and bed size and surgery year were included in the risk-adjustment model.

Results:
Out of 853,500 beneficiaries, 118,812 were dually eligible with an average age (SD) of 75.2(7.7) years. Compared to non-dually eligible beneficiaries, dually eligible beneficiaries had a higher rates of unplanned surgery for access-sensitive surgical conditions (45.1% vs. 31.8%, P<0.001), 30-day mortality (2.9% vs. 2.6%, aOR=1.10 (1.07-1.14), P<0.001), complications (23.6% vs. 20.1%, aOR=1.23 (1.20-1.25), P<0.001), and 30-day readmissions (15.5% vs. 12.9%, aOR=1.24 (1.22-1.27), P<0.001). These differences narrowed significantly when evaluating elective procedures only.

Conclusions:
Dually eligible beneficiaries were more likely to undergo unplanned surgery for access-sensitive surgical conditions, leading to worse rates of mortality, complications and readmissions. Our findings suggest that improving rates of elective surgery for these conditions represents an actionable target to narrow the difference in post-operative outcomes between dually eligible and non-dually eligible beneficiaries.
Use of Federal Reimbursement for Living Donor Costs by Racial and Ethnic Minorities: Implications for Disparities in Access to Living Donor Transplantation
Authors: Mathur Amit K. , Goodrich Nathan , Hong Barry , Smith Abigail R. , Mandell Rebecca J. , Warren Patricia H. , Gifford Kimberly A. , Ojo Akinlolu O. , Merion Robert M. 
Published: May 2024

Background.
Minority race, ethnicity, and financial barriers are associated with lower rates of living donor (LD) kidney transplantation (LDKT). Financial reimbursement for LD costs may impact social determinants of health and, therefore, impact disparities in access to LDKT.

Methods.
Among US LDKTs, we studied associations between racial and ethnic minority status and utilization of the National Living Donor Assistance Center (NLDAC), a means-tested reimbursement program for nonmedical LD costs. We analyzed demographic, clinical, income, and survey data from NLDAC and the Scientific Registry of Transplant Recipients (January 1, 2011, to December 31, 2022) to identify predictors of NLDAC utilization.

Results.
Among 70 069 US LDKTs, 6093 NLDAC applicants were identified (9% of US LDKTs). Racial and ethnic minorities were over-represented in NLDAC-supported LDKTs compared with non-NLDAC US LDKTs (Black donors 12% versus 9%; Black recipients 15% versus 12%; Hispanic donors 21% versus 14%; Hispanic recipients 23% versus 15%; all P < 0.001). Among preemptive transplants, use of NLDAC by donors to Hispanic recipients (11%) was nearly twice as high as that of non-Hispanic recipients (6%) (P < 0.001). At time of NLDAC application, 72% stated NLDAC “will make it possible” to donate; higher proportions of minority applicants agreed (Black 80%, White 70%, P < 0.001; Hispanic 79%, non-Hispanic 70%, P < 0.001). Racial and ethnic minority-concordant transplants were significantly more likely to use NLDAC (donor/recipient: Black/Black risk-adjusted odds ratio [OR], 1.85, other/other OR 2.59, Hispanic/Hispanic OR 1.53; all P < 0.05).

Conclusions.
Reduction of LD financial barriers may increase access to LDKT, particularly in racial and ethnic minority communities.
Targeted Restoration of GPX3 Attenuates Renal Ischemia/Reperfusion Injury by Balancing Selenoprotein Expression and Inhibiting ROS-mediated Mitochondrial Apoptosis
Authors: Wu Yikun , Shi Hua , Xu Yuangao , Shu Guofeng , Xiao Yu , Hong Guangyi , Xu Shuxiong 
Published: May 2024

Background.
Renal ischemia/reperfusion (IR) injury is the leading cause of acute kidney injury in both autologous and transplanted kidneys. Low-level glutathione peroxidase 3 (GPX3) is associated with renal IR injury. The exact mechanism of targeted GPX3 restoration in renal IR injury has yet to be determined.

Methods.
The distribution of GPX3 in different tissues and organs of the body was investigated. The level of GPX3 in renal IR injury was assessed. To confirm the action of GPX3 and its mechanisms, IR models were used to introduce adeno-associated virus 9 containing GPX3, as well as hypoxia/reoxygenation-exposed normal rat kidney cells that consistently overexpressed GPX3. Reverse molecular docking was used to confirm whether GPX3 was a target of ebselen.

Results.
GPX3 is abundant in the kidneys and decreases in expression during renal IR injury. GPX3 overexpression reduced renal IR injury and protected tubular epithelial cells from apoptosis. Proteomics analysis revealed a strong link between GPX3 and mitochondrial signaling, cellular redox state, and different expression patterns of selenoproteins. GPX3 inhibited reactive oxygen species-induced mitochondrial apoptosis and balanced the disordered expression of selenoproteins. GPX3 was identified as a stable selenoprotein that interacts with ebselen. Ebselen enhanced the level of GPX3 and reduced IR-induced mitochondrial damage and renal dysfunction.

Conclusions.
Targeted restoration of GPX3 attenuates renal IR injury by balancing selenoprotein expression and inhibiting reactive oxygen species-mediated mitochondrial apoptosis, indicating that GPX3 could be a potential therapeutic target for renal IR injury.
Closing the loop between environment, brain and mental health: how far we might go in real-life assessments?
Authors: Lehmler Stephan , Siehl Sebastian , Kjelkenes Rikka , Heukamp Jannik , Westlye Lars Tjelta , Holz Nathalie , Nees Frauke 
Published: May 2024

Purpose of review
Environmental factors such as climate, urbanicity, and exposure to nature are becoming increasingly important influencers of mental health. Incorporating data gathered from real-life contexts holds promise to substantially enhance laboratory experiments by providing a more comprehensive understanding of everyday behaviors in natural environments. We provide an up-to-date review of current technological and methodological developments in mental health assessments, neuroimaging and environmental sensing.

Recent findings
Mental health research progressed in recent years towards integrating tools, such as smartphone based mental health assessments or mobile neuroimaging, allowing just-in-time daily assessments. Moreover, they are increasingly enriched by dynamic measurements of the environment, which are already being integrated with mental health assessments. To ensure ecological validity and accuracy it is crucial to capture environmental data with a high spatio-temporal granularity. Simultaneously, as a supplement to experimentally controlled conditions, there is a need for a better understanding of cognition in daily life, particularly regarding our brain's responses in natural settings.

Summary
The presented overview on the developments and feasibility of “real-life” approaches for mental health and brain research and their potential to identify relationships along the mental health-environment-brain axis informs strategies for real-life individual and dynamic assessments.
What Is Brain Damage and Does Electroconvulsive Therapy Cause It?
Authors: Swartz Conrad M. 
Published: May 2024

Abstract
Surveys show public misperceptions and confusion about brain damage and electroconvulsive therapy (ECT). Fictional movies have misrepresented ECT to suggest brain damage and to ridicule mental illness and psychiatric patients. “Brain damage” has become a colloquial expression without consistent meaning. In contrast, brain injury is the medical term for destruction of brain cells, such as from kinetic impact (concussion), hypoxia, or infection. Studies of both high-resolution magnetic resonance imaging (MRI) and enzyme assays find that causes of brain injury are accompanied by observable structural changes on MRI and elevated blood and cerebrospinal fluid levels of brain enzymes that leak from injured brain cells. Concussion is also followed by intracerebral bleeding, progressive brain atrophy, diffuse axonal injury, cranial nerve injury, and 2–4 fold increased risk for dementia. In contrast, there is no evidence that ECT produces any of these. Studies of ECT patients find no brain edema, structural change persisting 6 months, or elevated levels of leaked brain enzymes. Statistical comparisons between brain injury and ECT effects indicate no similarity (P < 0.00000001). Moreover, the kinetic, thermal, and electrical effects of ECT are far below levels that could possibly cause harm. This robust evidence shows that there is no basis to claim that ECT causes brain injury.
Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes
Authors: Jodkowska Karolina , Parteka-Tojek Zofia , Agarwal Abhishek , Denkiewicz Michał , Korsak Sevastianos , Chiliński Mateusz , Banecki Krzysztof , Plewczynski Dariusz 
Published: May 2024

AbstractChromosome Conformation Capture (3C) methods, including Hi-C (a high-throughput variation of 3C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment, which includes a chromatin immunoprecipitation step (ChIP), allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that performing cohesin HiChIP with two cross-linking agents (formaldehyde [FA] and EGS) instead of the typically used FA alone, results in a substantially better signal-to-noise ratio, higher ChIP efficiency and improved detection of chromatin loops and architectural stripes. Additionally, we propose an automated pipeline called nf-HiChIP (https://github.com/SFGLab/hichip-nf-pipeline) for processing HiChIP samples starting from raw sequencing reads data and ending with a set of significant chromatin interactions (loops), which allows efficient and timely analysis of multiple samples in parallel, without the need of additional ChIP-seq experiments. Finally, using novel approaches for biophysical modelling and stripe calling we generate accurate loop extrusion polymer models for a region of interest and a detailed picture of architectural stripes, respectively.
Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data
Authors: Kosiński Jan Grzegorz , Ranaweera Sandeepani , Chełkowska-Pauszek Agnieszka , Kashlev Mikhail , Babitzke Paul , Żywicki Marek 
Published: May 2024

ABSTRACTIn recent years, Term-seq became a standard experimental approach for high-throughput identification of 3’ ends of bacterial transcripts. It was widely adopted to study transcription termination events and 3’ maturation of bacterial RNAs. Despite widespread utilization, a universal bioinformatics toolkit for comprehensive analysis of Term-seq sequencing data is still lacking. Here, we describeTERMITe, a novel method for the identification of stable 3’ RNA ends based on bacterial Term-seq data.TERMITeworks with data obtained from both currently available Term-seq protocols and provides robust identification of the 3’ RNA termini. Unique features ofTERMITeinclude the calculation of the transcription termination efficiency using matched RNA-seq data and the comprehensive annotation of the identified 3’ RNA ends, allowing functional analysis of the results. We have appliedTERMITeto the comparative analysis of experimentally validated intrinsic terminators spanning different species across the bacterial domain of life, revealing substantial differences in their sequence and secondary structure. We also provide a complete atlas of experimentally validated intrinsic transcription termination sites for 13 bacterial species, includingEscherichia coli, Bacillus subtilis, Listeria monocytogenes, Enterococcus faecalis, Synechocystis sp.,Streptomyces clavuligerus, Streptomyces griseus, Streptomyces coelicolor, Streptomyces avermitilis, Streptomyces lividans, Streptomyces tsukubaensis, Streptomyces venezuelae, andZymomonas mobilis.
Accounting for digestion enzyme bias in Casanovo
Authors: Melendez Carlo , Sanders Justin , Yilmaz Melih , Bittremieux Wout , Fondrie Will , Oh Sewoong , Noble William Stafford 
Published: May 2024

AbstractA key parameter of any proteomics mass spectrometry experiment is the identity of the enzyme that is used to digest proteins in the sample into peptides. The Casanovode novosequencing model was trained using data that was generated with trypsin digestion; consequently, the model prefers to predict peptides that end with the amino acids “K” or “R.” This bias is desirable when the Casanovo is used to analyze data that was also generated using trypsin but can be problematic if the data was generated using some other digestion enzyme. In this work, we modify Casanovo to take as input the identify of the digestion enzyme, alongside each observed spectrum. We then train Casanovo with data generated using several different restriction enzymes, and we demonstrate that the resulting model successfully learns to capture enzyme-specific behavior. However, we find, surprisingly, that this new model does not yield a significant improvement in sequencing accuracy relative to a model trained without the enzyme information but using the same training set. This observation may have important implications for future attempts to make use of experimental metadata inde novosequencing models.