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Nevin Manimala Statistics

HiCube: Interactive visualization of multiscale and multimodal Hi-C and 3D genome data

Bioinformatics. 2023 Mar 24:btad154. doi: 10.1093/bioinformatics/btad154. Online ahead of print.

ABSTRACT

SUMMARY: HiCube is a lightweight web application for interactive visualization and exploration of diverse types of genomics data at multiscale resolutions. Especially, HiCube displays synchronized views of Hi-C contact maps and three-dimensional (3D) genome structures with user-friendly annotation and configuration tools, thereby facilitating the study of 3D genome organization and function.

AVAILABILITY AND IMPLEMENTATION: HiCube is implemented in Javascript and can be installed via NPM. The source code is freely available at GitHub (https://github.com/wmalab/HiCube).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:36961339 | DOI:10.1093/bioinformatics/btad154

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Role of initial medical treatment and effectiveness of thoracic endovascular aortic repair for acute type a aortic dissection with thrombosed false lumen

Eur J Cardiothorac Surg. 2023 Mar 24:ezad102. doi: 10.1093/ejcts/ezad102. Online ahead of print.

ABSTRACT

OBJECTIVES: The optimal treatment for acute type A aortic dissection (AAAD) with thrombosed false lumen (T-FL) of the ascending aorta remains controversial. This study aimed to the evaluate clinical outcomes of initial medical treatment (IMT) and the effectiveness of thoracic endovascular aortic repair (TEVAR) for AAAD with T-FL.

METHODS: We retrospectively analysed 60 AAAD with T-FL patients. Emergent aortic repair was performed in 33 patients and IMT was selected in 27 uncomplicated patients with ascending aortic diameter < 50 mm and ascending T-FL thickness ≤ 10 mm.

RESULTS: Among the 27 patients who received IMT, 14 had intramural haematoma at admission; however, new ulcer-like projections appeared in 7 (50%) during hospitalization. Before discharge, 12 (44%) were treated with only medical treatment and 15 (56%) required delayed aortic repair including TEVAR in 8 and open repair in 7. The median interval from onset to delayed repair was 9 days and significantly more patients received TEVAR compared to those receiving emergent repair (53% vs 21%; P = 0.043). Between TEVAR (n = 15) and open repair (n = 33), one (7%) 30-day mortality occurred in TEVAR, whereas no in-hospital mortality occurred in open repair. During the median follow-up time of 24.8 months, no aorta-related death was observed and there were no statistically significant differences in the freedom rate from aortic events (TEVAR: 92.8%/3 years vs open repair: 88.4%/3 years; P = 0.871).

CONCLUSIONS: Our management with a combination of emergent aortic repair, IMT, and delayed aortic repair for AAAD with T-FL achieved favourable clinical outcomes. In the selected Japanese patients, IMT with repeated MDCT could detect a new intimal tear which could be closed by TEVAR in some cases and TEVAR for this pathology resulted in acceptable early and mid-term outcomes. Further investigations are required to validate the safety and efficacy of this management.

PMID:36961338 | DOI:10.1093/ejcts/ezad102

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Association between hypogammaglobulinaemia and severe infections during induction therapy in ANCA-associated vasculitis: from J-CANVAS study

Rheumatology (Oxford). 2023 Mar 24:kead138. doi: 10.1093/rheumatology/kead138. Online ahead of print.

ABSTRACT

OBJECTIVES: To investigate the association between decreased serum IgG levels caused by remission-induction immunosuppressive therapy of antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and the development of severe infections.

METHODS: We conducted a retrospective cohort study of patients with new-onset or severe relapsing AAV enrolled in the J-CANVAS registry, which was established at 24 referral sites in Japan. The minimum serum IgG levels up to 24 weeks and the incidence of severe infection up to 48 weeks after treatment initiation were evaluated. After multiple imputations for all explanatory variables, we performed the multivariate analysis using a Fine-Gray model to assess the association between low IgG (the minimum IgG levels < 500 mg/dl) and severe infections. In addition, the association was expressed as a restricted cubic spline (RCS) and analysed by treatment subgroups.

RESULTS: Of 657 included patients (microscopic polyangiitis, 392; granulomatosis with polyangiitis, 139; eosinophilic granulomatosis with polyangiitis, 126), 111 (16.9%) developed severe infections. The minimum serum IgG levels were measured in 510 patients, of whom 77 (15.1%) had low IgG. After multiple imputations, the confounder-adjusted hazard ratio of low IgG for the incidence of severe infections was 1.75 (95% confidence interval: 1.03-3.00). The RCS revealed a U-shaped association between serum IgG levels and the incidence of severe infection with serum IgG 946 mg/dl as the lowest point. Subgroup analysis showed no obvious heterogeneity between treatment regimens.

CONCLUSION: Regardless of treatment regimens, low IgG after remission-induction treatment was associated with the development of severe infections up to 48 weeks after treatment initiation.

PMID:36961329 | DOI:10.1093/rheumatology/kead138

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The effect of luteolin on spermatological parameters, apoptosis, oxidative stress rate in freezing rabbit semen

Pol J Vet Sci. 2023 Mar;26(1):91-98. doi: 10.24425/pjvs.2023.145010.

ABSTRACT

The aim of the present study was to determine the effects of Luteolin (LUT) on semen quality, oxidative stress, apoptosis, acrosomal integrity, mitochondrial membrane potential and dead sperm ratio in rabbits. Ejaculates from six New Zealand rabbits were collected, evaluated and pooled. The pooling was divided into five groups as control (no additive) LUT 25 µM, LUT 50 µM, LUT 100 µM and LUT 200 µM and LUT added. It was then filled into a falcon tube with Tris-based extender at a final concentration of approximately 35 x 106 spermatozoa. Diluated rabbit semen samples were drawn into frozen and thawed. Frozen semen straws were thawed at 37°C in 30 seconds. According to our findings, no statistical difference was found between all doses of luteolin and the control group in the CASA (computer assisted sperm analysis) analysis performed at 4°C. However, total motility, progressive motility and rapid sperm percentage were found to be higher in the frozen and thawed rabbit semen at a dose of LUT 50 µM compared to the other groups (p⟨0.05). While amplitude of lateral head displacement (ALH) and beat cross-frequency (BCF) values were found at the lowest dose of LUT 200 µM, a statistically significant difference was observed between the other groups. When the flow cytometry results were examined, no statistical difference was found between the rate of dead sperm, acrosomal integrity, mitochondrial membrane potential and apoptosis rate. Morever, the H2 O2 percentage was found to be lower in all experimental groups compared to the control group (p⟨0.001). In conclusion, the addition of LUT in long-term storage of rabbit semen provided a protective effect for spermatozoa with its antioxidative properties against damage caused by cryopreservation.

PMID:36961262 | DOI:10.24425/pjvs.2023.145010

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Estimation of species divergence times in presence of cross-species gene flow

Syst Biol. 2023 Mar 24:syad015. doi: 10.1093/sysbio/syad015. Online ahead of print.

ABSTRACT

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model, and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1,000 transcriptome loci from fourteen species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times, but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling.

PMID:36961245 | DOI:10.1093/sysbio/syad015

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The factors associated with the deterioration of activities of daily life in stroke patients: A retrospective cohort study

Top Stroke Rehabil. 2023 Mar 24:1-8. doi: 10.1080/10749357.2023.2194095. Online ahead of print.

ABSTRACT

BACKGROUND: The activities of daily life (ADL) of stroke patients generally improves after rehabilitation. However, some patients remain at risk of ADL deterioration in the future. So far, there have been few studies on the factors related to ADL deterioration in stroke patients.

OBJECTIVE: To identify the factors related to ADL deterioration in stroke patients with independent mobility after discharge.

METHODS: We assessed 336 stroke patients with independent mobility who were discharged from the rehabilitation center between January 2016 and December 2018. The primary outcome was ADL deterioration, defined as that ADL assessed at 2 years after discharge decreased more than 15 points compared with that assessed at discharge. Univariate and multivariate statistical analyses were conducted to screen for factors related to ADL deterioration.

RESULTS: Overall, 62 (18.4%) patients exhibited ADL deterioration at 2 years after discharge.Age (OR = 1.114, 95%CI = 1.045-1.188, p = 0.001), vascular risk factors>3 (OR = 3.269, 95%CI = 1.189-8.986, p = 0.022) and with post-stroke depression (OR = 2.486, 95%CI = 1.011-6.114, p = 0.047) were risk factors for ADL deterioration in stroke patients. In contrast, elevated Berg Balance Scale (BBS) scores at discharge was a protective factor for ADL deterioration (OR = 0.484, 95%CI = 0.386-0.606, p < 0.001).

CONCLUSIONS: Nearly 1 in 5 stroke patients with independent mobility experienced ADL deterioration at 2 years after discharge. Aging, vascular risk factors>3, BBS at discharge, and post-stroke depression (PSD) were identified as factors associated with ADL deterioration.

PMID:36961229 | DOI:10.1080/10749357.2023.2194095

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Does Adjunction of Autologous Osteoblastic Cells Improve the Results of Core Decompression in Early-stage Femoral Head Osteonecrosis? A Double-blind, Randomized Trial

Clin Orthop Relat Res. 2023 Mar 23. doi: 10.1097/CORR.0000000000002610. Online ahead of print.

ABSTRACT

BACKGROUND: Osteonecrosis of the femoral head (ONFH) is a disabling disease that can ultimately progress to collapse of the femoral head, often resulting in THA. Core decompression of the femoral head combined with cell therapies have shown beneficial effects in previous clinical studies in patients with early-stage (Association Research Circulation Osseous [ARCO] Stage I and II) ONFH. However, high-quality evidence confirming the efficacy of this treatment modality is still lacking.

QUESTIONS/PURPOSES: (1) Is core decompression combined with autologous osteoblastic cell transplantation superior to core decompression with placebo implantation in relieving disease-associated pain and preventing radiologic ONFH progression in patients with nontraumatic early-stage ONFH? (2) What adverse events occurred in the treatment and control groups?

METHODS: This study was a Phase III, multicenter, randomized, double-blind, controlled study conducted from 2011 to 2019 (ClinicalTrails.gov registry number: NCT01529008). Adult patients with ARCO Stage I and II ONFH were randomized (1:1) to receive either core decompression with osteoblastic cell transplantation (5 mL with 20 x 106 cells/mL in the study group) or core decompression with placebo (5 mL of solution without cells in the control group) implantation. Thirty percent (68 of 230) of the screened patients were eligible for inclusion in the study; of these, 94% (64 of 68) underwent a bone marrow harvest or sham procedure (extended safety set) and 79% (54 of 68) were treated (study group: 25 patients; control group: 29). Forty-nine patients were included in the efficacy analyses. Similar proportions of patients in each group completed the study at 24 months of follow-up (study group: 44% [11 of 25]; control: 41% [12 of 29]). The study and control groups were comparable in important ways; for example, in the study and control groups, most patients were men (79% [27 of 34] and 87% [26 of 30], respectively) and had ARCO Stage II ONFH (76% [19 of 25] and 83% [24 of 29], respectively); the mean age was 46 and 45 years in the study and control groups, respectively. The follow-up period was 24 months post-treatment. The primary efficacy endpoint was the composite treatment response at 24 months, comprising the clinical response (clinically important improvement in pain from baseline using the WOMAC VA3.1 pain subscale, defined as 10 mm on a 100-mm scale) and radiologic response (the absence of progression to fracture stage [≥ ARCO Stage III], as assessed by conventional radiography and MRI of the hips). Secondary efficacy endpoints included the percentages of patients achieving a composite treatment response, clinical response, and radiologic response at 12 months, and the percentage of patients undergoing THA at 24 months. We maintained a continuous reporting system for adverse events and serious adverse events related to the study treatment, bone marrow aspiration and sham procedure, or other study procedures throughout the study. A planned, unblinded interim analysis of efficacy and adverse events was completed at 12 months. The study was discontinued because our data safety monitoring board recommended terminating the study for futility based on preselected futility stopping rules: conditional power below 0.20 and p = 0.01 to detect an effect size of 10 mm on the 100-mm WOMAC VA3.1 pain subscale (improvement in pain) and the absence of progression to fracture (≥ ARCO Stage III) observed on radiologic assessment, reflecting the unlikelihood that statistically beneficial results would be reached at 24 months after the treatment.

RESULTS: There was no difference between the study and control groups in the proportion of patients who achieved a composite treatment response at 24 months (61% [14 of 23] versus 69% [18 of 26]; p = 0.54). There was no difference in the proportion of patients with a treatment response at 12 months between the study and control groups (14 of 21 versus 15 of 23; p = 0.92), clinical response (17 of 21 versus 16 of 23; p = 0.38), and radiologic response (16 of 21 versus 18 of 23; p = 0.87). With the numbers available, at 24 months, there was no difference in the proportion of patients who underwent THA between the study and control groups (24% [six of 25] versus 14% [four of 29]). There were no serious adverse events related to the study treatment, and only one serious adverse event (procedural pain in the study group) was related to bone marrow aspiration. Nonserious adverse events related to the treatment were rare in the study and control groups (4% [one of 25] versus 14% [four of 29]). Nonserious adverse events related to bone marrow or sham aspiration were reported by 15% (five of 34) of patients in the study group and 7% (two of 30) of patients in the control group.

CONCLUSION: Our study did not show any advantage of autologous osteoblastic cells to improve the results of core decompression in early-stage (precollapse) ONFH. Adverse events related to treatment were rare and generally mild in both groups, although there might have been a potential risk associated with cell expansion. Based on our findings, we do not recommend the combination of osteoblastic cells and core decompression in patients with early-stage ONFH. Further, well-designed studies should be conducted to explore whether other treatment modalities involving a biological approach could improve the overall results of core decompression.

LEVEL OF EVIDENCE: Level II, therapeutic study.

PMID:36961220 | DOI:10.1097/CORR.0000000000002610

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Assessing intentions for a third child among Chinese adults: A nationwide online survey regarding China’s 3-child policy

Medicine (Baltimore). 2023 Mar 24;102(12):e33255. doi: 10.1097/MD.0000000000033255.

ABSTRACT

Aging populations, along with low fertility rates, have become a pervasive world-wide problem. To address this challenge, China issued a universal 3-child policy on May 31, 2021. However, little is known regarding the intentions of childbearing-aged Chinese for a third child. The purpose of this study was to assess the fertility intentions of the Chinese as related to this third-child policy and identify risk factors for third-child refusal. In this cross-sectional study, a total of 2129 Chinese childbearing-aged participants were recruited nationwide from June 15 to July 22, 2021. Each participant was interviewed using questionnaires to establish their sociodemographic variables, psychosocial factors as related to third-child intentions, and reasons for third-child refusal. Finally, 2115 responses (866 men and 1249 women) were analyzed. IBM SPSS Statistical Software (version 19) was used for the statistical analyses. Multivariate logistic regression analyses were used to assess independent influences for third-child refusal. Approximately 30% of these participants reported an intention for having a third child. In those expressing a refusal for a third child, women showed a higher prevalence rate (74.1 vs 63.2%, P < .001). Results from multivariate logistic regression analyses revealed that age (P = .033), unemployment (P = .045), and currently raising 2 children (P = .017) were risk factors for third-child refusal among men, while age (P < .001), >15 years of education (P = .017), current smokers (P = .005) and residing in Northern China (P = .035) were risk factors for women. Overall, increased demands upon time and energy (41.5%), as well as economic burdens (41.4%), were the most prevalent reasons for the refusal of a third child, while achieving mutual care among siblings (52.5%) and reducing child educational costs (33.3%) were the most effective persuasions. In response to the 3-child policy, Chinese childbearing-aged adults showed low rates of intention for a third child, with women showing a higher prevalence of third-child refusal. The identification of risk factors and the reasons for third-child refusal as revealed from the results of this study provide a foundation for the development of programs needed to aid in the implementation of this 3-child policy.

PMID:36961189 | DOI:10.1097/MD.0000000000033255

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Completeness and quality of information about death from COVID-19 in a Brazilian state: A descriptive population-based register study

Medicine (Baltimore). 2023 Mar 24;102(12):e33343. doi: 10.1097/MD.0000000000033343.

ABSTRACT

Health information is particularly essential in times of pandemics in which rapid response is crucial for political and stakeholder decision-making processes, and therefore the availability of data as well as its quality analysis are necessary. This study aimed to describe the completeness and quality of the e-Sistema Único de Saúde (SUS) Health Surveillance database (SUS Vigilância em Saúde) of the state of Espírito Santo, Brazil, from the notification of deaths from corana virus disease 2019 (COVID-19) from January 2020 to June 2021. A descriptive population-based register study was conducted from the analysis of the completeness of secondary data from the record of deaths from COVID-19, retrieved from the e-SUS Vigilância em Saúde (Health Surveillance) (VS) database of the state of Espírito Santo, Brazil, from January 2020 to June 2021. A total of 11,359 death records from COVID-19 via e-SUS VS in the state of Espírito Santo, Brazil, were evaluated. The score used to assess incompleteness was the 1 proposed by Romero and Cunha which classifies as excellent (when < 5%), good (between 5% and 10%), regular (between 10% and 20%), poor (between 20% and 50%), and very poor (when > 50%), according to the percentage of the absence of information. Descriptive statistical analyses were conducted in the Stata program, version 15.1. “Case identification” variables, and “condition” variables were classified as excellent completeness. Among the evolution variables, only “hospitalization” was classified as regular. Among the laboratory variables, only the polymerase chain reaction presented excellent completeness, while the “rapid test” and “serologies for immunoglobulin G, and immunoglobulin M” variables were classified as good completeness. It is concluded that most of the variables available in e-SUS VS of the state of Espírito Santo, Brazil, of notification of deaths from COVID-19 in 2020 presented excellent completeness, confirming the excellent quality of the state database.

PMID:36961187 | DOI:10.1097/MD.0000000000033343

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The association between statin use and prognosis in esophageal cancer patients: A meta-analysis

Medicine (Baltimore). 2023 Mar 24;102(12):e33359. doi: 10.1097/MD.0000000000033359.

ABSTRACT

BACKGROUND: The impact of statin use on the survival of esophageal cancer patients remains unclear now. The aim of this study was to identify the relationship between statin use and the long-term survival of esophageal cancer patients.

METHODS: The PubMed, EMBASE, and Web of Science databases were searched up to August 20, 2022, for relevant studies. The endpoints included overall survival (OS), cancer-specific survival (CSS), recurrence-free survival, and hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) were pooled to assess the association between statin use and the prognosis of esophageal cancer patients. Subgroup analysis based on the pathological type (adenocarcinoma vs squamous cell carcinoma), dose of statin use and tumor stage (tumor-node-metastasis I-III vs IV) was further performed. All statistical analyses were conducted using STATA 12.0 software.

RESULTS: A total of 7 retrospective studies involving 25,711 participants were included in this meta-analysis. The pooled results indicated that statin use was significantly associated with improved OS (HR = 0.80, 95% CI: 0.74-0.87, P < .001), CSS (HR = 0.77, 95% CI: 0.74-0.89, P < .001), and recurrence-free survival (HR = 0.38, 95% CI: 0.16-0.87, P = .022). Furthermore, subgroup analysis stratified by the pathological type, dose of statin use and tumor stage for OS and CSS showed similar results and indicated the protective role of statin use in the prognosis of esophageal cancer patients.

CONCLUSION: Statin use is significantly associated with improved long-term survival of esophageal cancer patients and might serve as a promising prognostic indicator in esophageal cancer. However, more prospective high-quality studies are still needed to verify our findings.

PMID:36961185 | DOI:10.1097/MD.0000000000033359