Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer

Abstract Gastric cancer (GC) is one of the most common cancers with high incidence and mortality worldwide. Recently, RNA-binding proteins (RBPs) have drawn more and more attention for its role in cancer pathophysiology. However, the function and clinical implication of RBPs in GC have not been fully elucidated. RNA sequencing data along with the corresponding clinical information of GC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA-binding proteins (DERBPs) between tumor and normal tissues were identified by “limma” package. Functional enrichment analysis and the protein-protein interaction (PPI) network were harnessed to explore the function and interaction of DERBPs. Next, univariate and multiple Cox regression were applied to screen prognosis-related hub RBPs and to construct a signature for GC. Meanwhile, a nomogram was built on the basis of the independent factors. A total of 296 DERBPs were found, and most of them mainly related to post-transcriptional regulation of RNA and ribonucleoprotein. A PPI network of DERBPs was constructed, consisting of 262 nodes and 2567 edges. A prognostic signature was built depending on 7 prognosis-related hub RBPs that could divide GC patients into high-risk and low-risk groups. Survival analysis showed that high-risk group had a worse prognosis compared with the low-risk group and the time-dependent receiver operating characteristic (ROC) curves suggested that signature existed moderate predictive capacities of survival for GC patients. Similar results were obtained from another independent set GSE62254, confirming the robustness of signature. Besides, the genetic variation and immune heterogeneity differences were identified between the high-risk and low-risk groups by bioinformatics methods. These findings would provide evidence of the effect of RBPs and offer a novel potential biomarker in prognostic prediction and clinical decision for GC.
Unmet needs for HIV ancillary care services by healthcare coverage and Ryan White HIV/AIDS program assistance

Objective: To investigate unmet needs for HIV ancillary care services by healthcare coverage type and Ryan White HIV/AIDS Program (RWHAP) assistance among adults with HIV. Design: We analyzed data using the 2017–2019 cycles of the CDC Medical Monitoring Project, an annual, cross-sectional study designed to produce nationally representative estimates of characteristics among adults with diagnosed HIV. Methods: Unmet need was defined as needing, but not receiving, one or more HIV ancillary care services. We estimated prevalence ratios (PRs) and 95% confidence intervals (CIs) using predicted marginal means to examine associations between healthcare coverage type and unmet needs for HIV ancillary care services, adjusting for age. Associations were stratified by receipt of RWHAP assistance. Results: Unmet needs for HIV ancillary care services were highest among uninsured persons (58.7%) and lowest among those with private insurance living with at least 400% of the federal poverty level (FPL; 21.7%). Uninsured persons who received RWHAP assistance were less likely than those who did not receive RWHAP assistance to have unmet needs for HIV clinical support services (aPR: 0.21; 95% CI: 0.16–0.28) and other medical services (aPR: 0.75; 95% CI: 0.59–0.96), but not subsistence services (aPR: 0.97; 95% CI: 0.74–1.27). Unmet needs for other medical services and subsistence services did not differ by RWHAP assistance among those with Medicaid, Medicare, or other healthcare coverage. Conclusions: RWHAP helped reduce some needs for uninsured persons. However, with growing socioeconomic inequities following the coronavirus disease 2019 pandemic, expanding access to needed services for all people with HIV could improve key outcomes.
High incidence of proliferative and membranous nephritis in SLE patients with low proteinuria in the Accelerating Medicines Partnership.

OBJECTIVE Delayed detection of lupus nephritis associates with worse outcomes. There are conflicting recommendations regarding a threshold level of proteinuria at which biopsy will likely yield actionable management. This study addressed the association of urine protein creatinine ratios (UPCR) with clinical characteristics and investigated the incidence of proliferative and membranous histology in patients with a UPCR between 0.5 and 1. METHODS 275 SLE patients (113 first biopsy, 162 repeat) were enrolled in the multicentre multi-ethnic/racial Accelerating Medicines Partnership across 15 U.S. sites at the time of a clinically indicated renal biopsy. Patients were followed for 1 year. RESULTS At biopsy, 54 patients had UPCR <1 and 221 had UPCR >1. Independent of UPCR or biopsy number, a majority (92%) of patients had class III, IV, V or mixed histology. Moreover, patients with UPCR <1 and class III, IV, V, or mixed had a median activity index of 4.5 and chronicity index of 3, yet 39% of these patients had an inactive sediment. Neither anti-dsDNA nor low complement distinguished class I or II from III, IV, V, or mixed in patients with UPCR <1. Of 29 patients with baseline UPCR <1 and class III, IV, V or mixed, 23 (79%) had a UPCR <0.5 at one year. CONCLUSION In this prospective study three quarters of patients with UPCR <1 had histology showing class III, IV, V or mixed with accompanying activity and chronicity despite an inactive sediment or normal serologies. These data support renal biopsy at thresholds lower than a UPCR of 1.
Resilience in the Face of Pandemic: The Impact of COVID-19 on the Psychologic Morbidity and Health-Related Quality of Life Among Women With Ovarian Cancer

PURPOSE: The COVID-19 pandemic has created new challenges for ovarian cancer survivors. This study aims to evaluate the psychologic morbidity and alterations in medical care caused by the pandemic. METHODS: Advanced-stage ovarian cancer survivors at our institution were contacted for participation in a cross-sectional telephone-based quantitative survey study assessing pandemic-related psychologic morbidity. Psychologic domains using validated measures were explored: health-related quality of life (HRQOL; functional assessment of cancer therapy [FACT-G7]), anxiety (generalized anxiety disorder-7 [GAD7]), depression (Patient Health Questionnarie-2 [PHQ2]), global health Patient-Reported Outcomes Measurement Information System - Global Physical Health/Global Mental Health (PROMIS-GMH/GPH), resilience (brief resilience scale), and loneliness (English Longitudinal Study on Aging). Novel COVID-19 pandemic questions were drawn from a larger survey developed in our department. RESULTS: Fifty-nine percent (61 of 104) of contacted patients completed the survey. One quarter of respondents had high resilience, with only 10% reporting low resilience. Only one patient screened positive for depression, and two for anxiety. Increased loneliness was reported by 43% of respondents. Patients' overall HRQOL was good (median = 21; range = 6-28). Few patients experienced treatment delays, with only four experiencing chemotherapy interruption and two reporting surgical delays. Multiple regression analyses revealed that high FACT-G7 HRQOL was predicted by age > 65 years, high self-reported mental health, high resilience, and being off chemotherapy. Lower COVID-19 concern was predicted by recurrent cancer and high resilience. CONCLUSION: Despite the far-reaching impact of the COVID-19 pandemic, ovarian cancer survivors' HRQOL has been maintained. Older age, high resilience, high mental health, and being off chemotherapy predicted better HRQOL. Ovarian cancer survivors remain resilient in the face of the pandemic, and the support of clinicians to preserve this invaluable personal resource is critical for well-being. Ovarian cancer survivors’ resilience has supported their well-being during the COVID-19 pandemic
Improvements in Parental Sleep, Fear of Hypoglycemia, and Diabetes Distress With Use of an Advanced Hybrid Closed Loop System.

OBJECTIVE Parental sleep quality may contribute to glycemic control in youth with type 1 diabetes. In this article we present sleep analysis from a multicenter, randomized trial of children ages 6-13 years with type 1 diabetes evaluating the Tandem Control-IQ (CIQ) hybrid closed loop (HCL) system. RESEARCH DESIGN AND METHODS Pittsburgh Sleep Quality Index (PSQI) scores were assessed at baseline to identify parents as "poor" sleepers (PSQI >5). Glycemic and psycho-behavioral outcomes before and after CIQ use were analyzed in poor sleepers (n = 49) and their children. RESULTS Nocturnal time in range (P < 0.001) and time hyperglycemic (P < 0.001), Hypoglycemia Fear Survey for Parents score (P < 0.001), Problem Areas in Diabetes scale score (P < 0.001), PSQI score (P < 0.001), and Hypoglycemia Fear Survey for Children score (P = 0.025) significantly improved. Of poor sleepers, 27 became good sleepers (PSQI score <5). CONCLUSIONS Use of CIQ in youth with type 1 diabetes ages 6-13 years significantly improved sleep and psychosocial measures in parent poor sleepers, coinciding with improvements in child nocturnal glycemia, highlighting the relationship between HCL systems and parent sleep quality.
Effects of therapeutic exercise on disease severity, balance, and functional Independence among individuals with cerebellar ataxia: A systematic review with meta-analysis

ABSTRACT Background Balance impairments are common in cerebellar ataxia. Exercises are beneficial in this population. Objective Explore the benefits of therapeutic exercises on disease severity, balance and functional independence in cerebellar ataxia. Methods Databases were searched from inception until July 2021. Methodological quality was assessed using the Physiotherapy Evidence Database (PEDro) scale and the Newcastle-Ottawa Scale (NOS); and quality of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) tool. Results Twenty-six studies were included and eight studies of low to high PEDro methodological quality were meta-analyzed. ‘Low’ to ‘moderate’ GRADE quality evidence supports the use of therapeutic exercises to reduce disease severity, assessed using the Scale for the Assessment and Rating of Ataxia [weighted mean difference (WMD): −3.3; 95% confidence interval (95%CI): −3.7, −2.8; p < . 01]; and improve balance, assessed using the Berg Balance Scale (WMD: 2.6; 95%CI: 1.1, 4.2; p < .01). The effect of therapeutic exercises on functional independence was insignificant (WMD: 1.6; 95%CI: −1.5, 4.6; p = .31). Conclusion Low to moderate evidence from studies of low to high methodological quality provides some support for therapeutic exercises for reducing disease severity among non-hereditary degenerative cerebellar ataxia and improving balance among acquired cerebellar ataxia. Exercises did not benefit functional independence. Additional studies of large sample size and high methodological quality are necessary to substantiate these findings.
A Smartphone-Based Information Communication Technology Solution for Primary Modifiable Risk Factors for Noncommunicable Diseases: Pilot and Feasibility Study in Norway

Background Cardiovascular diseases, cancers, chronic respiratory diseases, and diabetes are the 4 main noncommunicable diseases. These noncommunicable diseases share 4 modifiable risk factors (tobacco use, harmful use of alcohol, physical inactivity, and unhealthy diet). Short smartphone surveys have the potential to identify modifiable risk factors for individuals to monitor trends. Objective We aimed to pilot a smartphone-based information communication technology solution to collect nationally representative data, annually, on 4 modifiable risk factors. Methods We developed an information communication technology solution with functionalities for capturing sensitive data from smartphones, receiving, and handling data in accordance with general data protection regulations. The main survey comprised 26 questions: 8 on socioeconomic factors, 17 on the 4 risk factors, and 1 about current or previous noncommunicable diseases. For answers to the continuous questions, a keyboard was displayed for entering numbers; there were preset upper and lower limits for acceptable response values. For categorical questions, pull-down menus with response options were displayed. The second survey comprised 9 yes-or-no questions. For both surveys, we used SMS text messaging. For the main survey, we invited 11,000 individuals, aged 16 to 69 years, selected randomly from the Norwegian National Population Registry (1000 from each of the 11 counties). For the second survey, we invited a random sample of 100 individuals from each county who had not responded to the main survey. All data, except county of residence, were self-reported. We calculated the distribution for socioeconomic background, tobacco use, diet, physical activity, and health condition factors overall and by sex. Results The response rate was 21.9% (2303/11,000; women: 1397/2263; 61.7%, men: 866/2263, 38.3%; missing: 40/2303, 1.7%). The median age for men was 52 years (IQR 40-61); the median age for women was 48 years (IQR 35-58). The main reported reason for nonparticipation in the main survey was that the sender of the initial SMS was unknown. Conclusions We successfully developed and piloted a smartphone-based information communication technology solution for collecting data on the 4 modifiable risk factors for the 4 main noncommunicable diseases. Approximately 1 in 5 invitees responded; thus, these data may not be nationally representative. The smartphone-based information communication technology solution should be further developed with the long-term goal to reduce premature mortality from the 4 main noncommunicable diseases.
Using molecular epidemiology to trace the history of the injection-related HIV epidemic in New York City, 1985–2019

Objective: Unintentional drug poisoning and overdose deaths in New York City (NYC) increased 175% between 2010 and 2017, partly due to the transition from noninjectable opioids to heroin injection. This transition has led to concern of a resurgent HIV epidemic among persons who inject drugs (PWID) in NYC. Thus, we sought to characterize HIV transmission dynamics in PWID. Design: Genetic network analysis of HIV-1 public health surveillance data. Methods: We analyzed HIV diagnoses reported to public health surveillance to determine the trajectory of the HIV epidemic among PWID in NYC, from 1985 through 2019. Genetic distance-based clustering was performed using HIV-TRACE to reconstruct transmission patterns among PWID. Results: The majority of the genetic links to PWID diagnosed in the 1980s and 1990s are to other PWID. However, since 2011, there has been a continued decline in new diagnoses among PWID, and genetic links between PWID have become increasingly rare, although links to noninjecting MSM and other people reporting sexual transmission risk have become increasingly common. However, we also find evidence suggestive of a resurgence of genetic links among PWID in 2018–2019. PWID who reported male-male sexual contact were not preferentially genetically linked to PWID over the surveillance period, emphasizing their distinct risk profile from other PWID. Conclusion: These trends suggest a transition from parenteral to sexual transmission among PWID in NYC, suggesting that harm reduction, syringe exchange programs, and legalization of over-the-counter syringe sales in pharmacies have mitigated HIV risk by facilitating well tolerated injection among new PWID.
Influence of Locomotor Muscle Group III/IV Afferents on Cardiovascular and Ventilatory Responses in Human Heart Failure during Submaximal Exercise.

PURPOSE To determine the influence of locomotor muscle group III/IV afferent inhibition on central and peripheral hemodynamics at multiple levels of submaximal cycling exercise in heart failure patients with reduced ejection fraction (HFrEF). METHODS Eleven HFrEF patients and 9 healthy matched controls were recruited. The participants performed a multiple stage (i.e. 30 W, 50%peak workload (WL), and a workload eliciting a respiratory exchange ratio (RER) of ~1.0) exercise test with lumbar intrathecal fentanyl (FENT) or placebo (PLA). Cardiac output (Q̇TOT) was measured via open-circuit acetylene wash-in technique and stroke volume was calculated. Leg blood flow (Q̇L) was measured via constant infusion thermodilution and leg vascular conductance (LVC) was calculated. Radial artery and femoral venous blood gases were measured. RESULTS For HFrEF, stroke volume was higher at the 30 W (FENT: 110±21 vs. PLA: 100±18 mL), 50%peak WL (FENT: 113±22 vs. PLA: 103±23 mL), and RER=1.0 (FENT: 119±28 vs. PLA: 110±26 mL) stages, while heart rate and systemic vascular resistance were lower with fentanyl compared to placebo (all, p<0.05). Q̇TOT in HFrEF and Q̇TOT, stroke volume, and heart rate in controls were not different between fentanyl and placebo (all, p>0.19). During submaximal exercise, controls and HFrEF patients exhibited increased LVC with fentanyl compared to placebo (all, p<0.04), while no differences were present in Q̇L or O2 delivery with fentanyl (all, p>0.20). CONCLUSION Taken together, these findings provide support for locomotor muscle group III/IV afferents playing a role in integrative control mechanisms during submaximal cycling exercise in HFrEF patients and older controls.
Upper Hemi-Sternotomy Provides Benefit for Patients with Isolated or Combined Mitral Valve Surgery

Background and objectives: Certain clinical and anatomical conditions are absolute or relative contraindications for safe mitral valve surgery via the right mini-thoracotomy access. It is uncertain whether patients with these contraindications may benefit from the less invasive approach via upper hemi-sternotomy compared to standard full sternotomy. Materials and methods: Out of 2052 mitral valve surgery patients, operated from 6/04 through 2/19, 1535 were excluded due to the different criteria for eligibility to both approaches. Out of these, 350 received full sternotomy and 167 upper hemi-sternotomy. After propensity score matching, 164 pairs were analyzed for operative variables, postoperative complications and 30-day and one-year survival. Results: Upper hemi-sternotomy was associated with a survival benefit of 30 days (99.4% vs. 82.1%; p < 0.001) and one-year (93.9% vs. 79.9% p < 0.001, HR 0.26, 95% CI 0.14–0.49). Cardiopulmonary bypass and aortic cross-clamp times were comparable in both groups. Upper hemi-sternotomy resulted in less low cardiac output syndrome (18.9% vs. 31.1%; p = 0.011); ventilation time (8 vs. 13 h; p < 0.001), length of intensive care stay (1 vs. 2 days; p < 0.001) and total hospital stay (8 vs. 9 days; p < 0.001) were shorter in the upper hemi-sternotomy group. Conclusion: In patients undergoing mitral valve surgery, upper hemi-sternotomy is associated with short- and mid-term survival benefits as well as lower postoperative complication rates compared to full sternotomy. Hence, the less invasive upper hemi-sternotomy can be a valid approach in patients with contraindications for right mini-thoracotomy.
Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents

Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.
The Influence of Perfectionism, Self-Esteem and Resilience on Young People’s Mental Health

ABSTRACT The current study explored whether maladaptive perfectionism and low self-esteem constituted reliable risk factors of student mental illness, as well as determining whether resilience moderates these predictive relationships. 434 University undergraduate students were recruited. Depression and anxiety were measured using the Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder Assessment (GAD-7). Perfectionism, self-esteem and resilience were analyzed in relation to the PHQ9 and GAD-7 scores via a regression analysis. Perfectionism discrepancy, self-esteem and resilience all significantly predicted depression and anxiety. Hierarchical regression analysis revealed a statistically significant amount of additional variance to be explained by resilience for depression and anxiety, than for perfectionism and self-esteem alone. Maladaptive perfectionism and low self-esteem predispose an individual to depression and anxiety, though resilience may act as a protective factor against development of mental illness.