bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving hospital quality risk-adjustment models using interactions identified by hierarchical group lasso regularisation
Authors: Ray Monika , Zhao Sharon , Wang Sheng , Bohl Alex , Romano Patrick S. 
Published: December 2023

AbstractBackgroundRisk-adjustment (RA) models are used to account for severity of illness in comparing patient outcomes across hospitals. Researchers specify covariates as main effects, but they often ignore interactions or use stratification to account for effect modification, despite limitations due to rare events and sparse data. Three Agency for Healthcare Research and Quality (AHRQ) hospital-level Quality Indicators currently use stratified models, but their variable performance and limited interpretability motivated the design of better models.MethodsWe analysed patient discharge de-identified data from 14 State Inpatient Databases, AHRQ Healthcare Cost and Utilization Project, California Department of Health Care Access and Information, and New York State Department of Health. We used hierarchical group lasso regularisation (HGLR) to identify first-order interactions in several AHRQ inpatient quality indicators (IQI) - IQI 09 (Pancreatic Resection Mortality Rate), IQI 11 (Abdominal Aortic Aneurysm Repair Mortality Rate), and Patient Safety Indicator 14 (Postoperative Wound Dehiscence Rate). These models were compared with stratum-specific and composite main effects models with covariates selected by least absolute shrinkage and selection operator (LASSO).ResultsHGLR identified clinically meaningful interactions for all models. Synergistic IQI 11 interactions, such as between hypertension and respiratory failure, suggest patients who merit special attention in perioperative care. Antagonistic IQI 11 interactions, such as between shock and chronic comorbidities, illustrate that naïve main effects models overestimate risk in key subpopulations. Interactions for PSI 14 suggest key subpopulations for whom the risk of wound dehiscence is similar between open and laparoscopic approaches, whereas laparoscopic approach is safer for other groups. Model performance was similar or superior for composite models with HGLR-selected features, compared to those with LASSO-selected features.ConclusionsIn this application to high-profile, high-stakes risk-adjustment models, HGLR selected interactions that maintained or improved model performance in populations with heterogeneous risk, while identifying clinically important interactions. The HGLR package is scalable to handle a large number of covariates and their interactions and is customisable to use multiple CPU cores to reduce analysis time. The HGLR method will allow scholars to avoid creating stratified models on sparse data, improve model calibration, and reduce bias. Future work involves testing using other combinations of risk factors, such as vital signs and laboratory values. Our study focuses on a real-world problem of considerable importance to hospitals and policy-makers who must use RA models for statutorily mandated public reporting and payment programmes.
Managing comorbidities in chronic kidney disease reduces utilization and costs
Authors: Li Yong , Barve Kanchan , Cockrell Meghan , Agarwal Amal , Casebeer Adrianne , Dixon Suzanne W. , Poonawalla Insiya 
Published: December 2023

Abstract
Background
Effective management of comorbid diabetes and hypertension in patients with chronic kidney disease (CKD) is important for optimal outcomes. However, little is known about this relationship from a health plan perspective. The objective of this study was to evaluate the association of effective management of comorbid diabetes and/or hypertension with healthcare resource utilization (HCRU) in patients with chronic kidney disease (CKD).

Methods
This retrospective cohort study used the Humana Research Database to identify patients with CKD Stage ≥ 3a in 2017. Eligible patients were enrolled in a Medicare Advantage Prescription Drug plan for ≥ 12 months before and after the index date (first observed evidence of CKD). Patients with end-stage renal disease, kidney transplant, or hospice election preindex were excluded. Recommended comorbid disease management included hemoglobin A1c monitoring; adherence to glucose-lowering, cardiovascular, and angiotensin-converting enzyme inhibitors/angiotensin receptor blocker medications; and nephrologist/primary care provider (PCP) visits. HCRU was evaluated for 12 months postindex.

Results
The final cohort of 241,628 patients was 55% female and 77% White, with an average age of 75 years. Approximately 90% of patients had Stage 3 CKD. Half had both diabetes and hypertension, and most of the remaining half had hypertension without diabetes. Patients meeting the criteria for good disease management, compared with patients not meeting those criteria, were less likely to experience an inpatient hospitalization, by as much as 40% depending on the criterion and the comorbidities present, or an emergency department visit, by as much as 30%. Total monthly healthcare costs were as much as 17% lower.

Conclusions
Management of comorbid diabetes and hypertension in patients with CKD was associated with lower HCRU and costs. Care coordination programs targeting patients with CKD must give careful attention to glucose and blood pressure control.

Trial registration
Not applicable.
SARSCoV-2 antibody prevalence and titers in persons living with HIV cared for at a large tertiary reference center in Mexico City
Authors: Soto-Nava Maribel , Dávila-Conn Vanessa , Venancio-Rocha Juan P. , García-Esparza Pedro , Tapia-Trejo Daniela , Hernández-Juan Ramón , Zarza-Sánchez Eduardo , Murakami-Ogasawara Akio , Ávila-Ríos Santiago 
Published: December 2023

Abstract
Objective
To assess SARS-CoV-2 antibody prevalence and titers in people living with HIV (PLWHIV) on antiretroviral treatment (ART) enrolled at a tertiary reference hospital in Mexico.

Methods
Two plasma aliquots per person, used for HIV viral load follow-up between 01/2020 and 09/2021, were used to assess total anti-N and neutralizing SARS-CoV-2 antibodies. Sociodemographic, clinical, and SARS-CoV-2 exposure risk information were collected. The risk associated with SARS-CoV-2 exposure and associations with antibody titers were analyzed with logistic, Cox, and linear multivariable models.

Results
803 PLWHIV participated; 233 had detectable SARS-CoV-2 antibodies (prevalent cases), and 132 seroconverted (incident cases). Overall, the adjusted prevalence was 46.45%, with an incidence rate of 3.78 cases/100 person-months. Factors associated with prevalent cases included lower age, location (western zone of Mexico City and the neighboring Mexico State), use of public transport, attendance at meetings without social distancing, and higher CD4 + T cell counts (p < 0.05; multivariable logistic model). BNT162b2 vaccination reduced incident cases (Cox adjusted HR = 0.4; p = 0.013). Notably, previously infected and vaccinated individuals showed maximization of neutralizing activity (p < 0.001). No associations between SARS-CoV-2 neutralization and HIV-related variables (CD4 + T cell counts, viral load, number of years in viral suppression, ART regimen) were found in multivariable analysis.

Conclusions
SARS-CoV-2 infection was associated with community risk rather than HIV-associated variables in PLWH on ART and clinical follow-up. Antibody neutralization activity in vaccinated participants was maximized with previous SARS-CoV-2 infection.
A review of foot-and-mouth disease in Ethiopia: epidemiological aspects, economic implications, and control strategies
Authors: Zewdie Girma , Akalu Mirtneh , Tolossa Wondwossen , Belay Hassen , Deresse Getaw , Zekarias Mariamawit , Tesfaye Yeneneh 
Published: December 2023

AbstractFoot-and-mouth disease (FMD) is a contagious viral disease that affects the livelihoods and productivity of livestock farmers in endemic regions. It can infect various domestic and wild animals with cloven hooves and is caused by a virus belonging to the genus Aphthovirus and family Picornaviridae, which has seven different serotypes: A, O, C, SAT1, SAT2, SAT3, and Asia-1. This paper aims to provide a comprehensive overview of the molecular epidemiology, economic impact, diagnosis, and control measures of FMD in Ethiopia in comparison with the global situation. The genetic and antigenic diversity of FMD viruses requires a thorough understanding for developing and applying effective control strategies in endemic areas. FMD has direct and indirect economic consequences on animal production. In Ethiopia, FMD outbreaks have led to millions of USD losses due to the restriction or rejection of livestock products in the international market. Therefore, in endemic areas, disease control depends on vaccinations to prevent animals from developing clinical disease. However, in Ethiopia, due to the presence of diverse antigenic serotypes of FMD viruses, regular and extensive molecular investigation of new field isolates is necessary to perform vaccine-matching studies to evaluate the protective potential of the vaccine strain in the country.
CD146-positive adipose-derived stem cells subpopulation enriched by albumin magnetic sphere ameliorates knee osteoarthritis pain and promotes cartilage repair
Authors: Wu Lianghao , Zhang Xu , Yi Chengqing , Ren Hanru 
Published: December 2023

Abstract
Background
The use of adipose stem cell (ADSCs) subpopulations in cartilage repair remains poorly characterized. In this study, we constructed an albumin magnetic sphere with specific targeting of CD146 (CD146-AMs) for sorting a subpopulation of CD146-positive ADSCs (CD146 + ADSCs) and explored the role of CD146 + ADSCs on joint pain and cartilage repair in rats with knee osteoarthritis (KOA).

Methods
CD146-AMs were prepared and analyzed in materialistic characterization tests. Subpopulations of CD146 + ADSCs were sorted using CD146-AMs. Surface labeling, viability, and proliferation of a subpopulation of CD146 + ADSCs were evaluated in vitro. Molecular characterization of mRNA and protein expression profiles was analyzed by microarray. A rat KOA pain model was established by the iodoacetic acid method, and KOA pain and the promotion of cartilage repair were assessed after treatment with bilateral joint cavity injections of CD146 + ADSCs.

Results
The CD146-AMs prepared in this study had an average particle size of 242.63 ± 6.74 nm, an average potential of 33.82 ± 3.53 mv, and high CD146 targeting and low cytotoxicity. The positive rate of enriched CD146 + ADSCs was 98.21% and showed a high level of stem cell marker expression and good cell viability. Gene and protein expression profiles showed that CD146 + ADSCs have different cellular functions, especially in regulating inflammation. In the KOA model, low, medium and high concentrations of CD146 + ADSCs were able to improve KOA pain and promote cartilage repair in a concentration-dependent trend.

Conclusions
The CD146-AMs prepared in this study were able to safely and efficiently sort out the CD146 + ADSCs subpopulation. The subpopulation of CD146 + ADSCs has a unique molecular profile that ameliorates KOA pain and repairs cartilage damage in rats, providing a new idea for KOA treatment.
Correlation between ESR1 and APOE gene polymorphisms and risk of osteonecrosis of the femoral head: a case–control study
Authors: Wang Yuan , Ma Xiaoya , Guo Jinping , Li Yujie , Xiong Yuyan 
Published: December 2023

Abstract
Background
Osteonecrosis of the femoral head (ONFH) is a disease with a high disability rate, and genetic factors are closely related to its pathogenesis. This study aimed to investigate the possible correlation between ESR1 and APOE gene polymorphisms and the risk of ONFH.

Methods
In this case–control study, the potential association between three genetic variants (rs2982573 C < T, rs10872678 C < T, and rs9322332 A < C) of the ESR1 gene and two genetic variants (rs7259620 A < G and rs769446 C < T) of the APOE gene with the risk of ONFH was investigated. Correlations between gene polymorphisms and ONFH risk were assessed using logistic regression analysis, with calculation of odds ratios (ORs) and 95% confidence intervals (CIs).

Results
The overall analysis demonstrated that rs9322332 in the ESR1 gene exhibited a correlation with a decreased risk of ONFH under the homozygous (AA vs.CC: OR = 0.69, 95% CI [0.53–0.90], p = 0.006), dominant (CA + AA vs. CC: OR = 0.70, 95% CI [0.54–0.90], p = 0.006), and additive (OR = 0.79, 95% CI [0.66–0.95], p = 0.013) models. The stratification analysis revealed that rs9322332 was linked to a lower risk of ONFH in subgroups characterized by individuals aged over 51 years and non-smokers. Nevertheless, there were no notable correlations found between ESR1 rs2982573 and rs10872678, as well as APOE rs7259620 and rs769446, with the risk of ONFH.

Conclusion
ESR1-rs9322332 is closely linked to a decreased risk of ONFH, thereby enhancing our understanding of the relationship between gene polymorphisms and ONFH.
SNHG17 alters anaerobic glycolysis by resetting phosphorylation modification of PGK1 to foster pro-tumor macrophage formation in pancreatic ductal adenocarcinoma
Authors: Lin Jiayu , Liu Yihao , Liu Pengyi , Qi Wenxin , Liu Jia , He Xingfeng , Liu Qian , Liu Zehua , Yin Jingxin , Lin Jiewei , Bao Haili , Lin Jianhong 
Published: December 2023

Abstract
Background
Within the tumor immune microenvironment (TME), tumor-associated macrophages (TAMs) are crucial in modulating polarization states to influence cancer development through metabolic reprogramming. While long non-coding RNAs (lncRNAs) have been shown to play a pivotal role in the progression of various cancers, the underlying mechanisms by which lncRNAs alter M2 polarization through macrophage metabolism remodeling remain unelucidated.

Methods
RNA sequencing was used to screen for differentially expressed lncRNAs in TAMs and normal tissue-resident macrophages (NTRMs) isolated from pancreatic ductal adenocarcinoma (PDAC) tissues, whilst RT-qPCR and FISH were employed to detect the expression level of SNHG17. Moreover, a series of in vivo and in vitro experiments were conducted to assess the functions of SNHG17 from TAMs in the polarization and glycolysis of M2-like macrophages and in the proliferation and metastasis of pancreatic cancer cells (PCs). Furthermore, Western blotting, RNA pull-down, mass spectrometry, RIP, and dual-luciferase assays were utilized to explore the underlying mechanism through which SNHG17 induces pro-tumor macrophage formation.

Results
SNHG17 was substantially enriched in TAMs and was positively correlated with a worse prognosis in PDAC. Meanwhile, functional assays determined that SNHG17 promoted the malignant progression of PCs by enhancing M2 macrophage polarization and anaerobic glycolysis. Mechanistically, SNHG17 could sponge miR-628-5p to release PGK1 mRNA and concurrently interact with the PGK1 protein, activating the pro-tumorigenic function of PGK1 by enhancing phosphorylation at the T168A site of PGK1 through ERK1/2 recruitment. Lastly, SNHG17 knockdown could reverse the polarization status of macrophages in PDAC.

Conclusions
The present study illustrated the essential role of SNHG17 and its molecular mechanism in TAMs derived from PDAC, indicating that SNHG17 might be a viable target for PDAC immunotherapy.
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases
Authors: AlAbdi Lama , Shamseldin Hanan E. , Khouj Ebtissal , Helaby Rana , Aljamal Bayan , Alqahtani Mashael , Almulhim Aisha , Hamid Halima , Hashem Mais O. , Abdulwahab Firdous , Abouyousef Omar , Jaafar Amal , Alshidi Tarfa , Al-Owain Mohammed , Alhashem Amal , Al Tala Saeed , Khan Arif O. , Mardawi Elham , Alkuraya Hisham , Faqeih Eissa , Afqi Manal , Alkhalifi Salwa , Rahbeeni Zuhair , Hagos Samya T. , Al-Ahmadi Wijdan , Nadeef Seba , Maddirevula Sateesh , Khabar Khalid S. A. , Putra Alexander , Angelov Angel , Park Changsook , Reyes-Ramos Ana M. , Umer Husen , Ullah Ikram , Driguez Patrick , Fukasawa Yoshinori , Cheung Ming Sin , Gallouzi Imed Eddine , Alkuraya Fowzan S. 
Published: December 2023

Abstract
Background
Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown.

Methods
In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform.

Results
Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level.

Conclusions
Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
Multifocal gastrointestinal stromal tumor with osseous metaplasia: a case report
Authors: Al Saleem Maryam Abdullah , Khan Nida Mirzaman , ElSharkawy Tarek Mohammad 
Published: December 2023

Abstract
Background
Gastrointestinal stromal tumor is considered the most common mesenchymal neoplasm of the gastrointestinal tract. The majority of gastrointestinal stromal tumor cases are located in the stomach and usually affects older adults. Most of gastrointestinal stromal tumor cases are sporadic; however, few have a syndromic association, including Carney triad, Carney–Stratakis syndrome, familial gastrointestinal stromal tumor syndrome, and neurofibromatosis type 1.

Case presentation
Herein, we report a rare case of a 54-year-old Middle-Eastern female with multifocal gastrointestinal stromal tumor mixed type (epithelioid and spindle cell type) with osseous metaplasia. Fluoresce in situ hybridization analysis of platelet-derived growth factor receptor alpha revealed deletion in 42% of the tumor cells studied. Interestingly, next generation sequencing revealed platelet-derived growth factor receptor alpha exon 12 mutation (p.Y555C) and exon 14 mutation (p.N659Y).

Conclusions
In conclusion, osseous metaplasia in GIST is a very rare event and only few cases are reported in the literature. The number of reported cases is inadequate to confirm the pathogenesis and the prognosis.
COVISHIELD vaccine-induced thyroiditis: a case report
Authors: Sachin J. , Shukla Ravindra , Anil Abhishek , Saravanan Aswini , Santhyavu Sanjay , Varthya Shoban Babu , Ambwani Sneha , Singh Surjit 
Published: December 2023

Abstract
Background
The rapid development of coronavirus disease 2019 vaccines during the pandemic has left their long-term effects largely unknown. Instances of autoimmune and subacute thyroiditis showing features of autoimmune/inflammatory syndrome induced by adjuvants have been reported post-vaccination. This case report aims to highlight the autoimmune/inflammatory syndrome induced by adjuvants syndrome after coronavirus disease 2019 vaccination, drawing attention to a possible connection with thyroid dysfunction and urging for further thorough research.

Case presentation
We present a case of thyroiditis induced by the COVISHIELD vaccine in a 37-year-old Indian woman. An apparently normal and healthy adult woman developed neck pain and easy fatigability 2 weeks after the second dose of COVISHIELD, which gradually increased and was associated with irritability, decreased sleep, excessive sweating, tremor, palpitation, and weight loss. She presented to the outpatient department after 1 week of symptoms and was evaluated with laboratory tests and imaging. She was diagnosed with thyroiditis due to the coronavirus disease 2019 vaccine and was treated with propranolol.

Conclusion
This case report adds to the growing evidence of coronavirus disease 2019 vaccine-related thyroid issues. The development of thyroiditis is rare and underreported post-coronavirus disease 2019 vaccination; hence, research to evaluate the association of coronavirus disease 2019 vaccines with thyroid dysfunction needs to be done in the future.
Periodic dynamics of predator-prey system with Beddington–DeAngelis functional response and discontinuous harvesting
Authors: Wang Yingying , Xia Zhinan 
Published: December 2023

AbstractThis paper investigates a delayed predator-prey model with discontinuous harvesting and Beddington–DeAngelis functional response. Using the theory of differential inclusion theory, the existence of positive solutions in the sense of Filippov is discussed. Under reasonable assumptions and periodic disturbances, the existence of positive periodic solutions of the model is studied based on the theory of Mawhin’s coincidence degree. Finally, through numerical simulation, the correctness and feasibility of the conclusions are verified.