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Nevin Manimala Statistics

The practice and promise of temporal genomics for measuring evolutionary responses to global change

Mol Ecol Resour. 2023 Mar 24. doi: 10.1111/1755-0998.13789. Online ahead of print.

ABSTRACT

Understanding the evolutionary consequences of anthropogenic change is imperative for estimating long-term species resilience. While contemporary genomic data can provide us with important insights into recent demographic histories, investigating past change using present genomic data alone has limitations. In comparison, temporal genomics studies, defined herein as those that incorporate time series genomic data, leverage museum collections and repeated field sampling to directly examine evolutionary change. As temporal genomics is applied to more systems, species, and questions, best practices can be helpful guides to make the most efficient use of limited resources. Here, we conduct a systematic literature review to synthesize the effects of temporal genomics methodology on our ability to detect evolutionary changes. We focus on studies investigating recent change within the past 200 years, highlighting evolutionary processes that have occurred during the past two centuries of accelerated anthropogenic pressure. We first identify the most frequently studied taxa, systems, questions, and drivers, before highlighting overlooked areas where further temporal genomic studies may be particularly enlightening. Then, we provide guidelines for future study and sample designs while identifying key considerations that may influence statistical and analytical power. Our aim is to provide recommendations to a broad array of researchers interested in using temporal genomics in their work.

PMID:36961384 | DOI:10.1111/1755-0998.13789

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Nevin Manimala Statistics

Trends and Outcomes of Salvage Lobectomy for Early-stage Non-Small Cell Lung Cancer

Am J Clin Oncol. 2023 Mar 24. doi: 10.1097/COC.0000000000001001. Online ahead of print.

ABSTRACT

OBJECTIVES: There is little data describing the outcomes for patients who develop local recurrences after stereotactic body radiation therapy (SBRT), a standard-of-care treatment for patients with early-stage non-small cell lung cancer. One emerging option is salvage lobectomy. We investigated trends in the use of salvage lobectomy after SBRT and described patient outcomes using a nationally representative sample.

METHODS: This is a retrospective study using the National Cancer Database of patients with non-small cell lung cancer diagnosed from 2004 to 2017. We used descriptive statistics to describe patients who underwent salvage lobectomy. Kaplan-Meier analysis was used to estimate overall survival (OS). Cox proportional modeling was used to identify factors associated with OS.

RESULTS: We identified 276 patients who underwent salvage lobectomy. Ninety-day mortality was 0%. The median survival time for the cohort was 50 months (95% CI, 44 to 58). Median follow-up was 65 months (Interquartile Range: 39 to 96). The factors associated with decreased OS include squamous cell histology (hazard ratio (HR)=1.72, P=0.005) and high grade (1.50, P=0.038). Increased OS was associated with lobectomy performed between 3 and 6 months after SBRT (HR=0.53, P=0.021), lobectomy performed >6 months after SBRT (HR=0.59, P=0.015), and female sex (HR=0.56, P=0.004).

CONCLUSIONS: Salvage lobectomy after local failures of SBRT was associated with no perioperative mortality and favorable long-term outcomes. Our data suggest that lobectomy performed within 3 months of SBRT is associated with worse OS.

PMID:36961366 | DOI:10.1097/COC.0000000000001001

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Nevin Manimala Statistics

Trauma across the lifespan and multisystem morbidity in women with HIV

Psychosom Med. 2023 Mar 15. doi: 10.1097/PSY.0000000000001192. Online ahead of print.

ABSTRACT

OBJECTIVE: Sexual and physical abuse are highly prevalent among women living with HIV (WLWH) and are risk factors for development of mental health and substance use disorders (MHDs, SUDs), and cognitive and medical co-morbidities. We examined empirically-derived patterns of trauma, MHD, and SUD, and associations with later cognitive and health outcomes.

METHODS: 1027 WLWH (average age = 48.6 years) in the Women’s Interagency HIV Study completed the World Mental Health-Composite International Diagnostic Interview during 2010-2013 to identify MHDs, SUDs, and age at onset of sexual and physical abuse. Then, cognitive impairment, cardiovascular/metabolic conditions, and HIV disease outcomes were assessed for up to 8.8 years. Latent class analysis (LCA) identified patterns of co-occurring trauma, MHDs, and/or SUDs. Generalized estimating equations determined associations between these patterns and mid-life cognitive and medical outcomes.

RESULTS: Six distinct profiles emerged: no/negligible sexual/physical trauma, MHD, or SUD (39%); preadolescent/adolescent sexual trauma with anxiety and SUD (22%); SUD only (16%); MHD + SUD only (12%); early childhood sexual/physical trauma only (6%); and early childhood sexual/physical trauma with later MHD + SUD (4%). Profiles including early childhood trauma had the largest number of mid-life conditions (i.e., cognitive, cardiovascular, HIV-related). Preadolescent/adolescent sexual trauma with anxiety and SUD predicted both global and domain-specific cognitive decline. Only SUD without trauma predicted lower CD4, while childhood trauma with MHD + SUD predicted increased CD8.

CONCLUSIONS: WLWH have complex multisystem profiles of abuse, MHD, and/or SUD that predict midlife cognitive, metabolic/cardiovascular, and HIV outcomes. Understanding the interplay between these factors over time can identify risks and personalize preventative and treatment interventions.

PMID:36961349 | DOI:10.1097/PSY.0000000000001192

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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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Nevin Manimala Statistics

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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Nevin Manimala Statistics

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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Nevin Manimala Statistics

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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Nevin Manimala Statistics

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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Nevin Manimala Statistics

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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Nevin Manimala Statistics

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