bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative epidemiology of five waves of COVID-19 in Mexico, March 2020–August 2022
Authors: Ascencio-Montiel Iván de Jesús , Ovalle-Luna Oscar David , Rascón-Pacheco Ramón Alberto , Borja-Aburto Victor Hugo , Chowell Gerardo 
Published: October 2022

Abstract
Background
The Mexican Institute of Social Security (IMSS) is the largest health care provider in Mexico, covering about 48% of the Mexican population. In this report, we describe the epidemiological patterns related to confirmed cases, hospitalizations, intubations, and in-hospital mortality due to COVID-19 and associated factors, during five epidemic waves recorded in the IMSS surveillance system.

Methods
We analyzed COVID-19 laboratory-confirmed cases from the Online Epidemiological Surveillance System (SINOLAVE) from March 29th, 2020, to August 27th, 2022. We constructed weekly epidemic curves describing temporal patterns of confirmed cases and hospitalizations by age, gender, and wave. We also estimated hospitalization, intubation, and hospital case fatality rates. The mean days of in-hospital stay and hospital admission delay were calculated across five pandemic waves. Logistic regression models were employed to assess the association between demographic factors, comorbidities, wave, and vaccination and the risk of severe disease and in-hospital death.

Results
A total of 3,396,375 laboratory-confirmed COVID-19 cases were recorded across the five waves. The introduction of rapid antigen testing at the end of 2020 increased detection and modified epidemiological estimates. Overall, 11% (95% CI 10.9, 11.1) of confirmed cases were hospitalized, 20.6% (95% CI 20.5, 20.7) of the hospitalized cases were intubated, and the hospital case fatality rate was 45.1% (95% CI 44.9, 45.3). The mean in-hospital stay was 9.11 days, and patients were admitted on average 5.07 days after symptoms onset. The most recent waves dominated by the Omicron variant had the highest incidence. Hospitalization, intubation, and mean hospitalization days decreased during subsequent waves. The in-hospital case fatality rate fluctuated across waves, reaching its highest value during the second wave in winter 2020. A notable decrease in hospitalization was observed primarily among individuals ≥ 60 years. The risk of severe disease and death was positively associated with comorbidities, age, and male gender; and declined with later waves and vaccination status.

Conclusion
During the five pandemic waves, we observed an increase in the number of cases and a reduction in severity metrics. During the first three waves, the high in-hospital fatality rate was associated with hospitalization practices for critical patients with comorbidities.
Oncologist approaches to communicating uncertain disease status in pediatric cancer: a qualitative study
Authors: Porter Amy S. , Woods Cameka , Stall Melanie , Velrajan Srilakshmi , Baker Justin N. , Mack Jennifer W. , Kaye Erica C. 
Published: October 2022

Abstract
Background
Most patients with cancer and their caregivers desire honest, clear prognostic communication, yet oncologists often disclose prognosis inconsistently. Prognostic communication becomes even more challenging when disease progression is unclear or equivocal. Presently, oncologist approaches for discussing uncertain disease findings are poorly understood.

Methods
In this prospective, longitudinal study, we audio-recorded serial disease reevaluation conversations between children with high-risk cancer, their families, and their primary oncologists over 24 months and conducted content analysis at recorded timepoints when oncologists categorized disease progression as equivocal.

Results
Of the 265 medical discussions recorded across the illness course for 33 patient-parent dyads, a total of 40 recorded discussions took place at equivocal timepoints, comprising > 500 min of medical dialogue. Prognosis talk encompassed < 3% of dialogue and was absent in nearly half of equivocal discussions (17/40, 42.5%). Curability statements were identified in only two conversations. Inductive content analysis of dialogue revealed four distinct patterns for communicating equivocal disease status: (1) up-front reassurance, (2) softening the message, (3) describing possible disease progression without interpretation, (4) expressing uncertainty without discussing the bigger picture.

Conclusion
Oncologists rarely discuss prognosis with children with high-risk cancer and their families at timepoints when disease progression is not definitive. Formal guidance is needed to better support oncologists in navigating uncertainty while sharing honest, person- and family-centered information about prognosis.
A predictive model based on site-specific risk factors of recurrence regions in endometrial cancer patients
Authors: Shin Wonkyo , Yang Seong J. , Park Sang-Yoon , Kang Sokbom , Lee Dong Ock , Lim Myong Cheol , Seo Sang-Soo 
Published: October 2022

Abstract
Objective
This study investigated site-specific differences in clinical factors for recurrence in patients who were newly diagnosed and treated for endometrial cancer. A model for predicting recurrence sites was generated.

Methods
Electronic medical records’ data were retrieved from January 2006 to December 2018 for patients who were diagnosed with endometrial cancer at the National cancer center in Korea. Recurrence sites were classified as local, regional, or distant. We used multinomial logistic regression models that modeled the log-odds for the three recurrence sites relative to non-recurrence as a linear combination of possible risk factors for the recurrence of endometrial cancer.

Results
The data of 611 patients were selected for analysis; there were 20, 12, and 25 cases of local, regional, and distant recurrence, respectively, and 554 patients had no recurrence. High-grade disease was associated with local recurrence; non-endometrioid histology and parametrial invasion were risk factors for regional recurrence; additionally, parametrial invasion and no lymphadenectomy were associated with distant metastasis.

Conclusion
We identified different risk factors specific for each type of recurrence site. Using these risk factors, we suggest that individually tailored adjuvant treatments be introduced for patients.
Multimorbidity is associated with TV-viewing, but not with other types of screen-based behaviors in Brazilian adults
Authors: Barboza Luciana L. S. , Werneck André O , Araujo Raphael H O , Porto Luiz G G , Silva Danilo R 
Published: October 2022

Abstract
Background
The presence of multimorbidity increases the risk of mortality, and identifying correlates of multimorbidity can direct interventions by targeting specific modifiable correlates. Here we aimed to investigate the association between two types of screen-based behaviors and multimorbidity.

Methods
We used data from 87,678 Brazilian adults from the National Health Survey (2019). Multimorbidity (presence of two or more chronic conditions among 12 possibilities), TV-viewing, and time on other types of screens (computer, tablet, or cell phone), were self-reported. Crude and adjusted binary and multinominal logistic regression models were performed stratified by sex, age group, and the number of chronic conditions.

Results
Considering adjusted values, 2 h/day as a reference, and reporting values in odds ratio (OR) and prevalence ratio (PR) with 95% confidence intervals (95%CI), multimorbidity presented associations with TV-viewing in general [from OR (95%CI) 1.10 (1.03–1.18) in 2 to < 3 h/d, to OR (95%CI) 1.57 (1.40–1.76) in ≥ 6 h/d], except in 2 to < 3 h/d time category for male and 35 to 49 years, and all time categories for 18 to 34 years. In addition, TV-viewing was associated with an increasing number of chronic conditions, all greater in ≥ 6 h/d [2 conditions - PR (95%CI) 1.24 (1.08–1.43); 3 conditions - PR (95%CI) 1.74 (1.45–2.08); 4 or more conditions - PR (95%CI) 2.29 (1.93–2.73)], except in 2 conditions on 2 to < 3 h/d. Other types of screen-based behaviors were only associated with multimorbidity among males [≥ 6 h/d: OR (95%CI) 1.22 (1.01–1.48)] and older individuals (65 years) in some time categories [3 to < 6 h/d: OR (95%CI) 1.98 (1.42–2.77) and ≥ 6 h/d: OR (95%CI) 1.73 (1.06–2.84)].

Conclusion
Intervention strategies for reducing screen time in Brazilian adults should focus mainly on TV-viewing, which seems to be associated with more harmful conditions than time on other types of screen-based behaviors.
Association of triglyceride levels and prostate cancer: a Mendelian randomization study
Authors: Zhu Shusheng , Hu Xia , Fan Yanpeng 
Published: October 2022

Abstract
Background
The association between triglyceride and prostate cancer (PCa) has been reported in observational studies. However, the causality from triglyceride on PCa remained unknown.

Method
Two-sample Mendelian randomization (MR) was performed with triglyceride genome-wide association study (GWAS) data from 177,861 individuals and GWAS summary statistics of PCa from 463,010 individuals. Then, 48 single nucleotide polymorphisms (SNPs) of triglyceride were used as instrumental variables (IVs) to conduct MR analysis on PCa. Inverse‐variance weighted (IVW), Weighted median, MR‐Egger regression, Simple mode and Weighted mode were used for MR analysis. To verify the sensitivity of the data, heterogeneity test, pleiotropy test and leave-one-out sensitivity test were performed.

Results
Association for an effect of triglyceride on PCa risk was found in IVW (odds ratio [OR]: 1.002, 95% confidence interval (CI): 1.000–1.004, p = 0.016). However, opposing results were observed using the weighted median (OR: 1.001, 95% CI: 0.999–1.003, p = 0.499) and MR‐Egger (OR: 0.999, 95% CI: 0.995–1.002, p = 0.401) approach. After MRPRESSO, the same result was obtained by using IVW method (OR: 1.002, 95% CI: 1.001–1.004, p = 0.004).

Conclusions
The large MR analysis indicated that the potential causal effect of triglyceride on PCa. The odds of PCa would increase with high levels of triglyceride.
Integrated analysis and exploration of potential shared gene signatures between carotid atherosclerosis and periodontitis
Authors: Zeng Youjie , Cao Si , Chen Minghua 
Published: October 2022

Abstract
Background
Increasing evidence has suggested an association between carotid atherosclerosis (CAS) and periodontitis (PD); however, the mechanisms have not been fully understood. This study aims to investigate the shared genes and molecular mechanisms underlying the co-pathogenesis of CAS and PD.

Methods
Gene Expression Omnibus (GEO) datasets GSE100927 and GSE10334 were downloaded, and differentially expressed genes (DEGs) shared by both datasets were identified. The functional enrichment analysis of these overlapping DEGs was then conducted. A protein-protein interaction (PPI) network was created using the STRING database and Cytoscape software, and PPI key genes were identified using the cytoHubba plugin. Then, weighted gene co-expression network analysis (WGCNA) was performed on GSE100927 and GSE10334, and the gene modules most correlated with CAS and PD were identified as key modules. The genes in key modules overlapping with PPI key genes were determined to be the key crosstalk genes. Subsequently, the key crosstalk genes were validated in three independent external datasets (GSE43292 [CAS microarray dataset], GSE16134 [PD microarray dataset], and GSE28829 [CAS microarray dataset]). In addition, the immune cell patterns of PD and CAS were evaluated by single-sample gene set enrichment analysis (ssGSEA), and the correlation of key crosstalk genes with each immune cell was calculated. Finally, we investigated the transcription factors (TFs) that regulate key crosstalk genes using NetworkAnalyst 3.0 platform.

Results
355 overlapping DEGs of CAS and PD were identified. Functional enrichment analysis highlighted the vital role of immune and inflammatory pathways in CAS and PD. The PPI network was constructed, and eight PPI key genes were identified by cytoHubba, including CD4, FCGR2A, IL1B, ITGAM, ITGAX, LCK, PTPRC, and TNF. By WGCNA, the turquoise module was identified as the most correlated module with CAS, and the blue module was identified as the most correlated module with PD. Ultimately, ITGAM and LCK were identified as key crosstalk genes as they appeared both in key modules and PPI key genes. Expression levels of ITGAM and LCK were significantly elevated in the case groups of the test datasets (GSE100927 and GSE10334) and validation datasets (GSE43292, GSE16134, and GSE28829). In addition, the expression of multiple immune cells was significantly elevated in PD and CAS compared to controls, and the two key crosstalk genes were both significantly associated with CD4 T cells. Finally, SPI1 was identified as a potential key TF, which regulates the two key crosstalk genes.

Conclusion
This study identified the key crosstalk genes and TF in PD and CAS, which provides new insights for further studies on the co-morbidity mechanisms of CAS and PD from an immune and inflammatory perspective.
CD44 is a prognostic biomarker and correlated with immune infiltrates in gastric cancer
Authors: Hou Weiyan , Kong Lingwei , Hou Zhiping , Ji Hairu 
Published: October 2022

AbstractObjectiveGastric carcinoma is the most common malignant tumour of the human digestive system worldwide. CD44 serves as a marker for several tumour stem cells, including gastric cancer. However, the prognostic value of CD44 and its correlation with immune infiltration in gastric cancer remain unclear.MethodsThe relative expression level of CD44 RNA in gastric cancer was analysed in the TCGA and GEPIA2 databases and validated in the GEO database. Differences in CD44 between gastric cancer cell lines and normal cells were detected by real-time PCR, and the HPA database was used to analyse the differential expression of CD44 protein in gastric cancer and normal tissues. The effect of CD44 on the proliferation and migration of gastric cancer cells was detected by CCK8 and transwell assays. UALCAN was used to analyse the relationship between CD44 expression and clinical parameters, and the Kaplan‒Meier Plotter was used to evaluate the prognostic value, including overall survival (OS), progression-free survival (PFS) and post-progression survival (PPS). The CD44 gene and protein interaction network was constructed by using the Linked Omics, GeneMANIA, STRING and DisGeNET databases. GO and KEGG analyses and GSEA of CD44 were performed by using R language. The correlation between CD44 and immune infiltration was explored by using the TIMER, CIBERSORT and GEPIA databases.ResultsCD44 is highly expressed in gastric cancer compared with normal tissues. Inhibition of proliferation and migration of gastric cancer cells after CD44 knockdown was observed. The UALCAN database showed that CD44 was independent of sex in gastric cancer but correlated with cancer stage and lymph node metastasis. Kaplan‒Meier Plotter online analysis showed that OS, PFS and PPS were prolonged in the CD44 low-expression group. GO and KEGG analyses and GSEA results showed that CD44 was mainly located in the endoplasmic reticulum and the extracellular matrix containing collagen, which was mainly involved in protein digestion and absorption. TIMER, CIBERSORT and GEPIA showed that CD44 was associated with infiltrating immune cells and thereby affected survival prognosis.ConclusionCD44 is highly expressed in gastric cancer and is an independent prognostic factor associated with immune invasion, which can be used as a candidate prognostic biomarker to determine the prognosis associated with gastric immune invasion.
Lung perfusion assessed by SPECT/CT after a minimum of three months anticoagulation therapy in patients with SARS-CoV-2-associated acute pulmonary embolism: a retrospective observational study
Authors: Berghaus Thomas M. , Bader Stefanie , Faul Christian , Haberl Sabine , Schwarz Florian , Liebich Alessandro , Dierks Alexander , Kircher Malte , Lapa Constantin , Pfob Christian H. 
Published: October 2022

Abstract
Background
Anticoagulant treatment is recommended for at least three months after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related acute pulmonary embolism (PE), but the persistent pulmonary clot burden after that time is unknown.

Methods
Lung perfusion was assessed by ventilation-perfusion (V/Q) SPECT/CT in 20 consecutive patients with SARS-CoV-2-associated acute PE after a minimum of three months anticoagulation therapy in a retrospective observational study.

Results
Remaining perfusion defects after a median treatment period of six months were observed in only two patients. All patients (13 men, seven women, mean age 55.6 ± 14.5 years) were on non-vitamin K direct oral anticoagulants (DOACs). No recurrent venous thromboembolism or anticoagulant-related bleeding complications were observed. Among patients with partial clinical recovery, high-risk PE and persistent pulmonary infiltrates were significantly more frequent (p < 0.001, respectively).

Interpretation
Temporary DOAC treatment seems to be safe and efficacious for resolving pulmonary clot burden in SARS-CoV-2-associated acute PE. Partial clinical recovery is more likely caused by prolonged SARS-CoV-2-related parenchymal lung damage rather than by persistent pulmonary perfusion defects.
Determinants of health-related quality of life in recently detoxified patients with severe alcohol use disorder
Authors: Lahbairi Najlaa , Laniepce Alice , Segobin Shailendra , Cabé Nicolas , Boudehent Céline , Vabret François , Rauchs Géraldine , Pitel Anne-Lise 
Published: October 2022

AbstractBackgroundHealth-related quality of life (HRQoL) is an important clinical outcome in Alcohol Use Disorder (AUD) and is considered as a relevant indicator of treatment success. While a better understanding of the factors affecting HRQoL would enable to adjust patients’ care to favour treatment outcome, the determinants of HRQoL in AUD remain unclear. This study aims at describing HRQoL in AUD patients and at identifying its best predictors.Methods53 recently detoxified patients with severe AUD (sAUD) underwent a cognitive assessment and filled in a HRQoL questionnaire dedicated to AUD patients (Alcohol Quality of Life Scale; AQoLS), as well as questionnaires concerning socio-demographics, alcohol history, sleep quality, depression, anxiety and impulsivity. 38 healthy controls (HC) underwent the same assessment (except AQoLS) in order to identify the altered cognitive and clinical variables that could potentially be determinants of HRQoL in sAUD.ResultssAUD patients reported that alcohol affects their HRQoL mainly in the “negative emotions”, “control”, “relationships”, and “sleep” domains. Compared to HC, they were impaired on episodic memory, working memory, executive functions, and processing speed tasks. They also reported lower sleep quality, higher depression, anxiety and impulsivity. No association was found between AQoLS total score and socio-demographics, cognitive performance, or sleep quality in patients. We found a significant correlation between HRQoL and depression/anxiety as well as impulsivity. Anxiety and impulsivity were indeed the only significant predictors of HRQoL, explaining 47.7% of the variance.ConclusionAnxiety and impulsivity are crucial determinants of HRQoL in recently detoxified sAUD patients. Since anxiety and impulsivity are frequent issues in addiction and especially in AUD, they should be particularly considered by clinicians to favour treatment outcomes.
The role of mindfulness in quality of life of persons with spinal cord injury: a cross-sectional study
Authors: Bhattarai Muna , Smedema Susan Miller , Hoyt William T. , Bishop Malachy 
Published: October 2022

Abstract
Background
Quality of life is considered the most overarching psychosocial adaptation outcome following the rehabilitation of persons with spinal cord injury. Literature suggests that the quality of life of persons with spinal cord injury is determined by many personal and psychological factors, including mindfulness. This study aimed to identify the direct and indirect effect of mindfulness on the quality of life of persons living with spinal cord injury.

Methods
Participants consisted of 231 members of three spinal cord injury organizations in the United States: United Spinal Association, North American Spinal Cord Injury Consortium, and Paralyzed Veterans of America-Wisconsin Chapter. The participants completed a set of standardized self-report questionnaires in an online Qualtrics survey. A hierarchical regression analysis was performed to identify the contribution of mindfulness to quality of life, controlling for sociodemographic and injury-related factors. A serial mediation analysis was performed to examine the indirect effect of mindfulness on quality of life.

Results
In the hierarchical regression analysis, sociodemographic and injury-related factors (i.e., age, gender, race, marital status, education, employment, level and completeness of injury, comorbidities, frequency of hospitalization, pain intensity, and functional limitation) and mindfulness explained 59% variance on quality of life of the participants with spinal cord injury. Mindfulness uniquely contributed to the higher quality of life above and beyond sociodemographic and injury-related variables. In the serial mediation analysis, pain and functional limitation did not significantly mediate the relationship between mindfulness and quality of life. However, the indirect effects of mindfulness on functional limitation and quality of life through pain were significant.

Conclusion
The findings underscore the vital role of mindfulness in improving the quality of life of persons with spinal cord injury. Implications of these findings for future research and clinical practice are discussed.