bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arteriovenous Fistula Stenosis: Correlating Degree of Neointimal Hyperplasia With Reduction in Volume Flow Measured on Ultrasound and Ultrasound Characterization Based on Stenosis Morphology
Authors: Clifford Thomas , Ramanarayanan Sivaramakrishnan , Nanou Rhami , Steiner Kate 
Published: October 2023

Introduction: Duplex ultrasound (DUS) is commonly used to diagnose and grade arteriovenous fistula (AVF) stenosis. Duplex ultrasound may also be used to examine stenosis type based on measurement of intimal-medial thickness (IMT). There are, as yet, no criteria in use to define the different stenosis types based on measurement of percentage IMT (%IMT). In this study, we have examined stenosis morphology using ultrasound. We have examined consecutive DUS examinations to assess the incidence and degree of IMT and correlated %IMT with volume flow as an indicator of AVF dysfunction. Methods: Duplex ultrasound was performed as per standard of care. Volume flow was measured within the ipsilateral brachial artery. Measurements of luminal diameter and vessel wall diameter were used to calculate %IMT. Results: The study group included 156 consecutive DUS examinations demonstrating a greater than 50% AVF stenosis. Mean %IMT was 45%. There were 17 (11%) lesions where there was no measurable IMT; the remainder had measurable IMT. On receiver-operating characteristic (ROC) analysis, a %IMT of 54% predicted low flow with 62.5% sensitivity and 62.7% specificity. Conclusion: Intimal-medial thickness has a moderate predictive value in predicting volume flow. Based on our results, there are 4 lesion types: (1) lesions with no measurable intimal hyperplasia, (2) a predominantly intimal hyperplastic lesion, (3) those with nonpredominant intimal hyperplasia, and (4) those with a valve type stenosis. A value based on correlation with volume flow could be considered based on our results at 54%IMT or based on morphology at 45%IMT to distinguish between predominant and nonpredominant intimal hyperplasia groups. Including measurements of %IMT in clinical trials could further our knowledge of how lesions with no measurable IMT and those with different degrees of intimal hyperplasia respond to different percutaneous interventions. This could potentially improve outcomes for patients and target more costly treatment options where there is most benefit.
Risk and Timing of Major Bleeding Complications Requiring Intervention of the Percutaneous Kidney Biopsy With a Short Observation Protocol: A Retrospective Chart Review
Authors: Schorr Melissa , Roshanov Pavel S. , Vandelinde Jeremy , House Andrew A. 
Published: October 2023

Background: We previously published a retrospective study of kidney biopsies performed in a tertiary care hospital in London, Ontario from 2012 to 2017. This study resulted in a change of practice in our institution to shorter postbiopsy monitoring for outpatients as well as the development of a risk calculator to predict serious bleeding complications. Objective: The primary objective of this study was to determine whether this shorter monitoring time is adequate in the outpatient setting. A secondary objective was to validate the bleeding risk calculator in both inpatients and outpatients. Design: This was a retrospective chart review. Setting: This study was performed at a tertiary academic hospital in London, Ontario, Canada. Participants: This was a retrospective study of 400 adult patients who underwent kidney biopsy between April 30, 2018 and February 25, 2022 at a tertiary academic hospital in London, Canada. Methods: We retrospectively assessed frequency and timing of major bleeding complications in patients who underwent kidney biopsy. In secondary analyses, we examined the prediction performance of the risk calculator in discrimination and calibration. Results: Major bleeding occurred in 7 patients (1.8%). Five of these patients required blood transfusions (1.3%) and 2 required embolization (0.5%). In the outpatient setting, any major bleeding events were identified immediately (1 patient) or on the routine 2-hour ultrasounds (1 patient). The risk calculator showed good discrimination (C-statistic, 0.91, 95% confidence interval [CI] = [0.84 to 0.95]) and calibration (slope, 1.10, 95% CI = [0.47 to 1.74]; intercept, 95% CI = −0.02 [−0.79 to 0.75]), but with much uncertainty in the estimates. Limitations: The occurrence of only a few major bleeding events limits the reliability of our assessment of our risk calculator. Conclusions: There appears to be little yield in extending observation beyond 2 hours after an outpatient kidney biopsy with the use of immediate and 2-hour postbiopsy ultrasounds. The bleeding risk calculator ( http://perioperativerisk.com/kbrc ) warrants further validation.
Disruption of Healthcare in New York City During the COVID-19 Pandemic: Findings From Residents Living in North and Central Brooklyn, the South Bronx, and East and Central Harlem
Authors: Dorvil Sheena , Nieves Christina , Pierre Jennifer , Valdez Jocelyn , Dannefer Rachel , Shiman Lauren J. , Diallo Fatoumata 
Published: October 2023

Introduction: The COVID-19 pandemic has disproportionately affected some New York City (NYC) neighborhoods that primarily consist of Black, Indigenous, and Latinx residents. In comparison to the rest of NYC, these neighborhoods experienced high hospitalization and COVID-related death rates, which has been attributed to a longstanding history of structural racism and disinvestment. While stay-at-home orders were implemented to reduce the spread of COVID-19, this may have also affected access and utilization of non-COVID related healthcare services. This study aims to assess the prevalence of and reasons for the disruption of non-COVID related healthcare services during the first 18 months of the pandemic. Methods: From September 30, 2021 to November 4, 2021, the NYC Health Department administered the COVID-19 Community Recovery Survey to a subset of residents who were part of the NYC Health Panel a probability-based survey panel. This cross-sectional survey, which included closed and open-ended questions, was either self-administered online or completed via CATI (Computer Assisted Telephone Interviewing) in English, Spanish, and Simplified Chinese. Descriptive statistics were used to summarize responses and unweighted, weighted, age-adjusted percentages, and 95% Confidence Intervals (CIs) were calculated. Results: With a response rate of 30.3% (N = 1358), more than half of participants (54%) reported disruption to either routine physical healthcare or mental health services. Concern about getting COVID-19 (61%), stay-at-home policies (40%), belief that care could safely be postponed (35%), and appointment challenges (34%) were among reasons for delaying routine healthcare. Concern about getting COVID-19 (38%) and reduced hours of service (36%) were primary reasons for delaying mental healthcare. Reported reasons for the sustained delay of care past 18 months involved COVID concerns, appointment, and insurance challenges. Conclusions: Due to the pandemic, some disruption to healthcare was expected. However, most study participants either avoided or experienced a delay in healthcare. The delay of non-COVID related healthcare throughout the pandemic may result in the further widening of the health inequity gap among NYC residents dealing with a higher chronic disease burden before the start of the COVID-19 pandemic in March 2020. Findings from this study can support equitable COVID-19 recovery, and guide efforts with health promotion.
The potential mechanism of gut microbiota-microbial metabolites-mitochondrial axis in progression of diabetic kidney disease
Authors: Ma Leilei , Zhang Li , Li Jing , Zhang Xiaotian , Xie Yiran , Li Xiaochen , Yang Bo , Yang Hongtao 
Published: October 2023

AbstractDiabetic kidney disease (DKD), has become the main cause of end-stage renal disease (ESRD) worldwide. Lately, it has been shown that the onset and advancement of DKD are linked to imbalances of gut microbiota and the abnormal generation of microbial metabolites. Similarly, a body of recent evidence revealed that biological alterations of mitochondria ranging from mitochondrial dysfunction and morphology can also exert significant effects on the occurrence of DKD. Based on the prevailing theory of endosymbiosis, it is believed that human mitochondria originated from microorganisms and share comparable biological characteristics with the microbiota found in the gut. Recent research has shown a strong correlation between the gut microbiome and mitochondrial function in the occurrence and development of metabolic disorders. The gut microbiome’s metabolites may play a vital role in this communication. However, the relationship between the gut microbiome and mitochondrial function in the development of DKD is not yet fully understood, and the role of microbial metabolites is still unclear. Recent studies are highlighted in this review to examine the possible mechanism of the gut microbiota-microbial metabolites-mitochondrial axis in the progression of DKD and the new therapeutic approaches for preventing or reducing DKD based on this biological axis in the future.
GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination
Authors: Li Dandan , Liu Kai , Zhao Chuanchao , Liang Siyi , Yang Jing , Peng Ziai , Xia Aoyun , Yang Meng , Luo Lixin , Huang Cuihong , Wang Jiafeng , Huang Ming , Xiao Wuming , Wang Hui , Su Ling , Guo Tao 
Published: October 2023

AbstractDirect seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, l-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of l-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.
Outcomes of trimethoprim/ sulfamethoxazole treatment for ocular toxoplasmosis in Congolese patients
Authors: Nsiangani Lusambo Nadine , Kaimbo Wa Kaimbo Dieudonné , Ngoyi Mumba Dieudonné Mumba , de-la-Torre Alejandra 
Published: October 2023

Abstract
Background
Ocular toxoplasmosis (OT) is the leading cause of infectious posterior uveitis in several areas worldwide. The combination of Trimethoprim/Sulfamethoxazole (TMP/SMX) has been presented as an attractive alternative to the “classic’ treatment therapy (Pyrimethamine/Sulfadiazine).

Methods
A prospective study was carried out between February 2020 and September 2021 in 2 ophthalmic centers in Kinshasa. This study aimed to describe TMP/SMX treatment outcomes for OT in a cohort of immunocompetent Congolese patients.

Results
54 patients were included, with a mean age at presentation of 37.5 ± 13.6 years old and a Male-Female ratio of 1.45:1. Three patients (5.6%) presented a recurrence during the follow-up period. At the end of the follow-up, improvement in VA and resolution of inflammation concerned 75.9% and 77.5% of patients, respectively. Cataracts (3.7%), macular scars (3.7%), and vitreous opacities (3.7%) were the principal causes of non-improvement in VA. Treatment-related adverse events were present in 10 patients (18.5%); gastrointestinal (14.8%) and dermatological (3.7%) adverse events were the most frequent. Dermatological adverse events led to discontinuation of treatment.

Conclusion
TMP/SMX regimen appears to be a safe and effective treatment for OT in Congolese patients. The low cost and the accessibility of the molecules make this regimen an option for treating OT in resource-limited countries.
Quality of life and its predictors in first-episode schizophrenia and individuals at clinical high-risk for psychosis
Authors: Mao Zhen , Tian Lu , Sun Yue , Dong Fang , Wang Chuanyue , Bo Qijing 
Published: October 2023

Abstract
Background
This is a cross-sectional study comparing the degree of subjective quality of life (QOL) impairment and its predictive factors in first-episode schizophrenia (FES) and individuals at clinical high-risk (CHR) for psychosis.

Methods
Seventy-seven FES, 59 CHR, and 64 healthy controls (HC) were included. The QOL of all participants was assessed using the World Health Organization Quality of Life (WHOQOL)-Brief Form (BREF). Psychiatric symptoms of individuals with FES were assessed with the Positive and Negative Syndrome Scale (PANSS), five factors were further identified through factor analysis; for individuals with CHR and HC, the Scale of Prodromal Symptoms (SOPS) was used.

Results
The total and four sub-domain scores of the WHOQOL-BREF in the FES and CHR groups were lower than those of the HC group. The overall and psychological health scores in the CHR group were lowest. In the FES group, after applying Bonferroni’s correction, there is a negative correlation between the total QOL scores and anxiety/depressive symptom scores (r = –0.34, P = 0.003). The stepwise multiple regression analysis showed that the QOL of both FES and CHR group were negatively affected by anxiety/depressive symptoms and unemployment (P < 0.05).

Conclusions
Compared with FES, CHR individuals are more dissatisfied with their QOL. Although diagnostic assessment of FES and CHR relies heavily on positive symptoms, the QOL is more affected by anxiety/depressive symptoms and social functioning.
Identification of potentially functional circRNAs and prediction of the circRNA-miRNA-hub gene network in mice with primary blast lung injury
Authors: Lu Qianying , Li Junfeng , Zhao Yanmei , Zhang Jianfeng , Shi Mingyu , Yu Sifan , Liang Yangfan , Fan Haojun , Meng Xiangyan 
Published: October 2023

Abstract
Objectives
Primary blast lung injury (PBLI) is the main cause of death in blast injury patients, and is often ignored due to the absence of a specific diagnosis. Circular RNAs (circRNAs) are becoming recognized as new regulators of various diseases, but the role of circRNAs in PBLI remain largely unknown. This study aimed to investigate PBLI-related circRNAs and their probable roles as new regulators in PBLI in order to provide new ideas for PBLI diagnosis and treatment.

Methods
The differentially expressed (DE) circRNA and mRNA profiles were screened by transcriptome high-throughput sequencing and validated by quantitative real-time PCR (qRT-PCR). The GO and KEGG pathway enrichment was used to investigate the potential function of DE mRNAs. The interactions between proteins were analyzed using the STRING database and hub genes were identified using the MCODE plugin. Then, Cytoscape software was used to illustrate the circRNA-miRNA-hub gene network.

Results
A total of 117 circRNAs and 681 mRNAs were aberrantly expressed in PBLI, including 64 up-regulated and 53 down-regulated circRNAs, and 315 up-regulated and 366 down-regulated mRNAs. GO and KEGG analysis revealed that the DE mRNAs might be involved in the TNF signaling pathway and Fanconi anemia pathway. Hub genes, including Cenpf, Ndc80, Cdk1, Aurkb, Ttk, Aspm, Ccnb1, Kif11, Bub1 and Top2a, were obtained using the MCODE plugin. The network consist of 6 circRNAs (chr18:21008725–21020999 + , chr4:44893533–44895989 + , chr4:56899026–56910247-, chr5:123709382–123719528-, chr9:108528589–108544977 + and chr15:93452117–93465245 +), 7 miRNAs (mmu-miR-3058-5p, mmu-miR-3063-5p, mmu-miR-668-5p, mmu-miR-7038-3p, mmu-miR-761, mmu-miR-7673-5p and mmu-miR-9-5p) and 6 mRNAs (Aspm, Aurkb, Bub1, Cdk1, Cenpf and Top2a).

Conclusions
This study examined a circRNA-miRNA-hub gene regulatory network associated with PBLI and explored the potential functions of circRNAs in the network for the first time. Six circRNAs in the circRNA-miRNA-hub gene regulatory network, including chr18:21008725–21020999 + , chr4:44893533–44895989 + , chr4:56899026–56910247-, chr5:123709382–123719528-, chr9:108528589–108544977 + and chr15:93452117–93465245 + may play an essential role in PBLI.
Assessing the safety of lipid-modifying medications among Chinese adolescents: a drug-target Mendelian randomization study
Authors: Luo Shan , Lam Hugh Simon , Chan Yap Hang , Tang Clara Sze Man , He Baoting , Kwok Man Ki , Leung Gabriel M. , Schooling C Mary , Au Yeung Shiu Lun 
Published: October 2023

Abstract
Background
With increasing hypercholesterolemia prevalence in East Asian adolescents, pharmacologic interventions (e.g., HMGCR inhibitors (statins) and PCSK9 inhibitors) may have to be considered although their longer-term safety in the general adolescent population is unclear. This study aims to investigate the longer-term safety of HMGCR inhibitors and PCSK9 inhibitors among East Asian adolescents using genetics.

Methods
A drug-target Mendelian randomization study leveraging the Global Lipid Genetics Consortium (East Asian, n = 146,492) and individual-level data from Chinese participants in the Biobank clinical follow-up of Hong Kong’s “Children of 1997” birth cohort (n = 3443, aged ~ 17.6 years). Safety outcomes (n = 100) included anthropometric and hematological traits, renal, liver, lung function, and other nuclear magnetic resonance metabolomics. Positive control outcomes were cholesterol markers from the “Children of 1997” birth cohort and coronary artery disease from Biobank Japan.

Results
Genetic inhibition of HMGCR and PCSK9 were associated with reduction in cholesterol-related NMR metabolomics, e.g., apolipoprotein B (HMGCR: beta [95% CI], − 1.06 [− 1.52 to − 0.60]; PCSK9: − 0.93 [− 1.56 to − 0.31]) and had the expected effect on the positive control outcomes. After correcting for multiple comparisons (p-value < 0.006), genetic inhibition of HMGCR was associated with lower linoleic acid − 0.79 [− 1.25 to − 0.35]. Genetic inhibition of PCSK9 was not associated with the safety outcomes assessed.

Conclusions
Statins and PCSK9 inhibitors in East Asian adolescents appeared to be safe based on the outcomes concerned. Larger studies were warranted to verify these findings. This study serves as a proof of principle study to inform the medication safety among adolescents via genetics.
HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD)
Authors: Chiu Yen-Jung , Ni Chung-En , Huang Yen-Hua 
Published: October 2023

Abstract
Background
Cell composition deconvolution (CCD) is a type of bioinformatic task to estimate the cell fractions from bulk gene expression profiles, such as RNA-seq. Many CCD models were developed to perform linear regression analysis using reference gene expression signatures of distinct cell types. Reference gene expression signatures could be generated from cell-specific gene expression profiles, such as scRNA-seq. However, the batch effects and dropout events frequently observed across scRNA-seq datasets have limited the performances of CCD methods.

Methods
We developed a deep neural network (DNN) model, HASCAD, to predict the cell fractions of up to 15 immune cell types. HASCAD was trained using the bulk RNA-seq simulated from three scRNA-seq datasets that have been normalized by using a Harmony-Symphony based strategy. Mean square error and Pearson correlation coefficient were used to compare the performance of HASCAD with those of other widely used CCD methods. Two types of datasets, including a set of simulated bulk RNA-seq, and three human PBMC RNA-seq datasets, were arranged to conduct the benchmarks.

Results
HASCAD is useful for the investigation of the impacts of immune cell heterogeneity on the therapeutic effects of immune checkpoint inhibitors, since the target cell types include the ones known to play a role in anti-tumor immunity, such as three subtypes of CD8 T cells and three subtypes of CD4 T cells. We found that the removal of batch effects in the reference scRNA-seq datasets could benefit the task of CCD. Our benchmarks showed that HASCAD is more suitable for analyzing bulk RNA-seq data, compared with the two widely used CCD methods, CIBERSORTx and quanTIseq. We applied HASCAD to analyze the liver cancer samples of TCGA-LIHC, and found that there were significant associations of the predicted abundance of Treg and effector CD8 T cell with patients’ overall survival.

Conclusion
HASCAD could predict the cell composition of the PBMC bulk RNA-seq and classify the cell type from pure bulk RNA-seq. The model of HASCAD is available at https://github.com/holiday01/HASCAD.
A computer-aided determining method for the myometrial infiltration depth of early endometrial cancer on MRI images
Authors: Xiong Liu , Chen Chunxia , Lin Yongping , Mao Wei , Song Zhiyu 
Published: October 2023

AbstractTo classify early endometrial cancer (EC) on sagittal T2-weighted images (T2WI) by determining the depth of myometrial infiltration (MI) using a computer-aided diagnosis (CAD) method based on a multi-stage deep learning (DL) model. This study retrospectively investigated 154 patients with pathologically proven early EC at the institution between January 1, 2018, and December 31, 2020. Of these patients, 75 were in the International Federation of Gynecology and Obstetrics (FIGO) stage IA and 79 were in FIGO stage IB. An SSD-based detection model and an Attention U-net-based segmentation model were trained to select, crop, and segment magnetic resonance imaging (MRl) images. Then, an ellipse fitting algorithm was used to generate a uterine cavity line (UCL) to obtain MI depth for classification. In the independent test datasets, the uterus and tumor detection model achieves an average precision rate of 98.70% and 87.93%, respectively. Selecting the optimal MRI slices method yields an accuracy of 97.83%. The uterus and tumor segmentation model with mean IOU of 0.738 and 0.655, mean PA of 0.867 and 0.749, and mean DSC of 0.845 and 0.779, respectively. Finally, the CAD method based on the calculated MI depth reaches an accuracy of 86.9%, a sensitivity of 81.8%, and a specificity of 91.7% for early EC classification. In this study, the CAD method implements an end-to-end early EC classification and is found to be on par with radiologists in terms of performance. It is more intuitive and interpretable than previous DL-based CAD methods.