Nevin Manimala

Bioinformatics. 2024 Jun 28;40(Supplement_1):i548-i557. doi: 10.1093/bioinformatics/btae242.

ABSTRACT

SUMMARY: Spatial omics technologies are increasingly leveraged to characterize how disease disrupts tissue organization and cellular niches. While multiple methods to analyze spatial variation within a sample have been published, statistical and computational approaches to compare cell spatial organization across samples or conditions are mostly lacking. We present GraphCompass, a comprehensive set of omics-adapted graph analysis methods to quantitatively evaluate and compare the spatial arrangement of cells in samples representing diverse biological conditions. GraphCompass builds upon the Squidpy spatial omics toolbox and encompasses various statistical approaches to perform cross-condition analyses at the level of individual cell types, niches, and samples. Additionally, GraphCompass provides custom visualization functions that enable effective communication of results. We demonstrate how GraphCompass can be used to address key biological questions, such as how cellular organization and tissue architecture differ across various disease states and which spatial patterns correlate with a given pathological condition. GraphCompass can be applied to various popular omics techniques, including, but not limited to, spatial proteomics (e.g. MIBI-TOF), spot-based transcriptomics (e.g. 10× Genomics Visium), and single-cell resolved transcriptomics (e.g. Stereo-seq). In this work, we showcase the capabilities of GraphCompass through its application to three different studies that may also serve as benchmark datasets for further method development. With its easy-to-use implementation, extensive documentation, and comprehensive tutorials, GraphCompass is accessible to biologists with varying levels of computational expertise. By facilitating comparative analyses of cell spatial organization, GraphCompass promises to be a valuable asset in advancing our understanding of tissue function in health and disease.

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PMID:38940138 | DOI:10.1093/bioinformatics/btae242

Behav Ther. 2024 Jul;55(4):680-697. doi: 10.1016/j.beth.2024.01.010. Epub 2024 Feb 13.

ABSTRACT

Adolescents with attention-deficit/hyperactivity disorder (ADHD) experience significant academic, behavioral, and social skill difficulties including underachievement, risk for school dropout, poor peer relations, and emotion dysregulation. Although stimulant medication reduces ADHD symptoms, psychosocial and educational interventions are necessary to address functional impairments. We examined the nature and predictors of academic, behavioral, and social skills trajectories in response to multicomponent organizational and interpersonal skills training in 92 high school students with ADHD. Latent trajectory class analyses revealed positive treatment response ranging from 61.5% (report card grades) to 100% (inattention symptoms, organizational skills, social skills). Organizational skill and academic grade treatment response trajectories were predicted by assigned sex, pretreatment anxiety, and treatment dosage, while improvement in behavioral and social functioning was associated with better emotion regulation and family relations prior to treatment along with stronger working alliance with treatment coach at midtreatment. Multicomponent organizational and interpersonal skills training appears effective for most high school students with ADHD and the degree treatment-induced change is associated with multiple malleable factors can be leveraged to enhance intervention response.

PMID:38937043 | DOI:10.1016/j.beth.2024.01.010

Arch Med Res. 2024 Jun;55(4):103017. doi: 10.1016/j.arcmed.2024.103017.

ABSTRACT

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editorial Board of the Archives of Medical Research after receiving a complaint reporting that the article was based on an unreliable or non-existent statistical method. After analyzing the complaint and carefully reviewing the article, the Editorial Board contacted the corresponding author following due process and received no response. The Editorial Board no longer has confidence in the article and therefore decided to retract the article. Apologies are offered to readers of the journal that this was not detected during the review process.

PMID:38937005 | DOI:10.1016/j.arcmed.2024.103017

J Nucl Med. 2024 Jun 27:jnumed.124.267626. doi: 10.2967/jnumed.124.267626. Online ahead of print.

ABSTRACT

This study aimed to evaluate the prognostic value of ¹⁸F-FDG PET/CT qualitative assessment in terms of recurrence-free survival (RFS), colostomy-free survival (CFS), and overall survival (OS) after radiation therapy (RT) of squamous cell carcinoma of the anus (SCCA). Secondary objectives were to evaluate the prognostic value of baseline and posttherapeutic quantitative ¹⁸F-FDG PET/CT parameters in terms of RFS, CFS, and OS. Methods: We included all consecutive patients from the French multicentric cohort FFCD-ANABASE who had undergone ¹⁸F-FDG PET/CT at baseline and 4-6 mo after RT or chemoradiotherapy for a localized SCCA. Qualitative assessments separated patients with complete metabolic response (CMR) and non-CMR. Quantitative parameters were measured on baseline and posttreatment ¹⁸F-FDG PET/CT. RFS, CFS, and OS were analyzed using the Kaplan-Meier method. Associations among qualitative assessments, quantitative parameters, and RFS, CFS, and OS were analyzed using univariate and multivariate Cox regression. Results: Among 1,015 patients treated between January 2015 and April 2020, 388 patients (300 women and 88 men) from 36 centers had undergone ¹⁸F-FDG PET/CT at diagnosis and after treatment. The median age was 65 y (range, 32-90 y); 147 patients (37.9%) had an early-stage tumor and 241 patients (62.1%) had a locally advanced-stage tumor; 59 patients (15.2%) received RT, and 329 (84.8%) received chemoradiotherapy. The median follow-up was 35.5 mo (95% CI, 32.8-36.6 mo). Patients with CMR had better 3-y RFS, CFS, and OS, at 84.2% (95% CI, 77.8%-88.9%), 84.7% (95% CI, 77.2%-89.3%), and 88.6% (95% CI, 82.5%-92.7%), respectively, than did non-CMR patients, at 42.1% (95% CI, 33.4%-50.6%), 47.9% (95% CI, 38.1%-56.8%), and 63.5 (95% CI, 53.2%-72.1%), respectively (P < 0.0001). Quantitative parameters were available for 154 patients from 3 centers. The following parameters were statistically significantly associated with 3-y RFS: baseline SUV_max (primitive tumor [T]) (hazard ratio [HR], 1.05 [95% CI, 1.01-1.1; P = 0.018]), SUV_peak (T) (HR, 1.09 [95% CI, 1.02-1.15; P = 0.007]), MTV 41% (T) (HR, 1.02 [95% CI, 1-1.03; P = 0.023]), MTV 41% (lymph node [N]) (HR, 1.06 [95% CI, 1.03-1.1; P < 0.001]), MTV 41% (T + N) (HR, 1.02 [95% CI, 1-1.03; P = 0.005]), and posttreatment SUV_max (HR, 1.21 [95% CI, 1.09-1.34; P < 0.001]). Conclusion: Treatment response assessed by ¹⁸F-FDG PET/CT after RT for SCCA has a significant prognostic value.¹⁸F-FDG PET/CT could be useful for adapting follow-up, especially for patients with locally advanced-stage tumors. Quantitative parameters could permit identification of patients with a worse prognosis but should be evaluated in further trials.

PMID:38936973 | DOI:10.2967/jnumed.124.267626

BMJ Support Palliat Care. 2024 Jun 27:spcare-2023-004657. doi: 10.1136/spcare-2023-004657. Online ahead of print.

ABSTRACT

OBJECTIVES: Lower rates of goals of care (GOC) conversations have been observed in non-white hospitalised patients, which may contribute to racial disparities in end-of-life care. We aimed to assess how a targeted initiative to increase GOC documentation rates is associated with GOC documentation by race.

METHODS: We retrospectively assessed GOC documentation during a targeted GOC initiative for adult patients with an artificial intelligence predicted elevated risk of mortality. Patients were admitted to an urban academic medical centre in Pittsburgh, Pennsylvania between July 2021 and 31 December 2022.

RESULTS: The 3643 studied patients had a median age of 72 (SD 13.0) and were predominantly white (87%) with 42% admitted to an intensive care unit and 15% dying during admission. GOC documentation was completed for 28% (n=1019/3643). By race, GOC was documented for 30% black (n=105/351), 28% white (n=883/3161) and 24% other (n=31/131) patients (p=0.3933). There was no statistical difference in the rate of documented GOC among races over time (p=0.5142).

CONCLUSIONS: A targeted initiative to increase documented GOC conversations for hospitalised patients with an elevated risk of mortality is associated with similar documentation rates across racial groups. Further research is needed to assess whether this initiative may promote racial equity in GOC documentation in other settings.

PMID:38936969 | DOI:10.1136/spcare-2023-004657

BMJ. 2024 Jun 27;385:q1436. doi: 10.1136/bmj.q1436.

NO ABSTRACT

PMID:38936955 | DOI:10.1136/bmj.q1436

In Vivo. 2024 Jul-Aug;38(4):1829-1833. doi: 10.21873/invivo.13635.

ABSTRACT

BACKGROUND/AIM: Vildagliptin is one of the dipeptidyl peptidase-4 (DPP-4) inhibitors that have been shown to improve hyperglycemia in clinical trials among patients with type 2 diabetes. However, few studies have examined the efficacy of vildagliptin in patients with diabetic kidney disease (DKD).

PATIENTS AND METHODS: Eight patients with DKD received oral vildagliptin 50-100 mg/day. The duration of diabetes was 6.7±5.9 years and observation period was 23.6±9.8 months. Changes in fasting blood glucose, and hemoglobin A1c (HbA1c), estimated glomerular filtration rate (eGFR), and urine protein-to-creatinine ratio (UPCR) were studied before and after the administration of vildagliptin.

RESULTS: Vildagliptin treatment significantly decreased fasting blood glucose and HbA1c, compared to baseline (132±56 mg/dl, p=0.036, 6.0±0.3, p=0.041, respectively). UPCR tended to be decreased, albeit without statistical significance. However, eGFR was decreased after the administration of vildagliptin. No significant adverse effects were observed in all patients during the study.

CONCLUSION: Although the sample size was limited and the observation period was brief, vildagliptin was found to be an effective and reasonably well-tolerated treatment for patients with DKD.

PMID:38936943 | DOI:10.21873/invivo.13635

In Vivo. 2024 Jul-Aug;38(4):1557-1570. doi: 10.21873/invivo.13606.

ABSTRACT

BACKGROUND/AIM: This study examined the effects of tocotrienols (TT) in conjunction with statin on glucose homeostasis, bone microstructure, gut microbiome, and systemic and liver inflammatory markers in obese C57BL/6J mice.

MATERIALS AND METHODS: Forty male C57BL/6J mice were fed a high-fat diet (HFD) and assigned into four groups in a 2 (no statin vs. 120 mg statin/kg diet)×2 (no TT vs. 400 mg TT/kg diet) factorial design for 14 weeks.

RESULTS: Statin and TT improved glucose tolerance only when each was given alone, and only statin supplementation decreased insulin resistance. Consistently, only statin supplementation decreased serum insulin levels and HOMA-IR. Pancreatic insulin was also increased with statin treatment. Statin and TT, alone or in combination, reduced the levels of serum IL-6, but only TT attenuated the increased serum leptin levels induced by a HFD. Statin supplementation increased bone area/total area and connectivity density at LV-4, while TT supplementation increased bone area/total area and trabecular number, but decreased trabecular separation at the distal femur. Statin supplementation, but not TT, reduced hepatic inflammatory cytokine gene expression. Neither TT supplementation nor statin supplementation statistically altered microbiome species evenness or richness. However, they altered the relative abundance of certain microbiome species. Most notably, both TT and statin supplementation increased the relative abundance of Lachnospiraceae UCG-006.

CONCLUSION: TT and statin collectively benefit bone microstructure, glucose homeostasis, and microbial ecology in obese mice. Such changes may be, in part, associated with suppression of inflammation in the host.

PMID:38936927 | DOI:10.21873/invivo.13606

In Vivo. 2024 Jul-Aug;38(4):1823-1828. doi: 10.21873/invivo.13634.

ABSTRACT

BACKGROUND/AIM: The number of available treatment options for urothelial carcinoma has increased recently. Upper tract urothelial carcinoma (UTUC) is relatively rare compared with bladder cancer. There are few reports on the efficacy of immune checkpoint inhibitors (ICIs) for metastatic UTUC, and ICIs may occasionally show less efficacy and cause severe side effects. Therefore, it is important to predict the treatment response and change the treatment strategy as appropriate. We investigated the prognostic factors for treatment response in patients with metastatic UTUC treated with pembrolizumab at our hospital.

PATIENTS AND METHODS: Patients who received pembrolizumab for UTUC between January 2018 and June 2023 were analyzed. Patients who presented with bladder cancer complications at initial diagnosis were excluded. The primary endpoints assessed were overall survival (OS) and progression-free survival (PFS). Statistical analyses were conducted using laboratory values obtained before and after pembrolizumab administration. The relationship between cancer and inflammation is important. Therefore, we analyzed this relationship using prognostic factors for urothelial carcinoma as previously reported. Specifically, pretreatment C-reactive protein (CRP) level, neutrophil-to-lymphocyte ratio (NLR), and NLR/albumin values were examined.

RESULTS: Forty-seven patients were analyzed. The median PFS was 66 days (24-107 days), and the median OS was 164 days (13-314 days). A CRP level <1 before the first cycle was a useful factor in the multivariate analysis for both OS and PFS [OS: p=0.004, hazard ratio (HR)=3.244, 95% confidence interval (CI)=1.464-7.104; PFS: p=0.003, HR=2.998, 95%CI=1.444-6.225].

CONCLUSION: CRP level is a prognostic factor for pembrolizumab treatment response in patients with UTUC.

PMID:38936923 | DOI:10.21873/invivo.13634

In Vivo. 2024 Jul-Aug;38(4):2016-2023. doi: 10.21873/invivo.13659.

ABSTRACT

BACKGROUND/AIM: Acute myeloid leukemia (AML) is a myeloproliferative neoplasm marked by abnormal clonal expansion of hematopoietic progenitor cells, displaying karyotypic aberrations and genetic mutations as prognostic indicators. The World Health Organization (WHO) and the European LeukemiaNet guidelines categorize BCR::ABL1 p190+ AML as high risk. This study explored the identification of the increased incidence of BCR::ABL1 p190+ in our AML population.

PATIENTS AND METHODS: This study included 96 AML patients stratified according to WHO guidelines. Subsequently, patients were screened for genetic abnormalities, such as BCR::ABL1 p 190+, PML::RARA, RUNX1::RUNX1T1, and CBFB::MYH11 by quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis.

RESULTS: Among 96 AML patients, 36 displayed BCR::ABL1 p190+, overcoming the expected global incidence. Age variations (19 to 78 years) showed no significant laboratory differences between BCR::ABL1 p190+ and non-BCR::ABL p190+ cases. The overall survival analysis revealed no statistically significant differences among the patients (p=0.786).

CONCLUSION: The analyzed population presented a higher frequency of BCR::ABL1 p190+ detection in adult AML patients when compared to what is described in the worldwide literature. Therefore, more studies are needed to establish the reason why this incidence is higher and what the best treatment approach should be in these cases.

PMID:38936913 | DOI:10.21873/invivo.13659