Ensemble methods of rank-based trees for single sample classification with gene expression profiles

Building Single Sample Predictors (SSPs) from gene expression profiles presents challenges, notably due to the lack of calibration across diverse gene expression measurement technologies. However, recent research indicates the viability of classifying phenotypes based on the order of expression of multiple genes. Existing SSP methods often rely on Top Scoring Pairs (TSP), which are platform-independent and easy to interpret through the concept of "relative expression reversals". Nevertheless, TSP methods face limitations in classifying complex patterns involving comparisons of more than two gene expressions. To overcome these constraints, we introduce a novel approach that extends TSP rules by constructing rank-based trees capable of encompassing extensive gene-gene comparisons. This method is bolstered by incorporating two ensemble strategies, boosting and random forest, to mitigate the risk of overfitting. Our implementation of ensemble rank-based trees employs boosting with LogitBoost cost and random forests, addressing both binary and multi-class classification problems. In a comparative analysis across 12 cancer gene expression datasets, our proposed methods demonstrate superior performance over both the k-TSP classifier and nearest template prediction methods. We have further refined our approach to facilitate variable selection and the generation of clear, precise decision rules from rank-based trees, enhancing interpretability. The cumulative evidence from our research underscores the significant potential of ensemble rank-based trees in advancing disease classification via gene expression data, offering a robust, interpretable, and scalable solution. Our software is available at https://CRAN.R-project.org/package=ranktreeEnsemble .

Computing within-study covariances, data visualization, and missing data solutions for multivariate meta-analysis with metavcov

Multivariate meta-analysis (MMA) is a powerful statistical technique that can provide more reliable and informative results than traditional univariate meta-analysis, which allows for comparisons across outcomes with increased statistical power. However, implementing appropriate statistical methods for MMA can be challenging due to the requirement of various specific tasks in data preparation. The metavcov package aims for model preparation, data visualization, and missing data solutions to provide tools for different methods that cannot be found in accessible software. It provides sufficient constructs for estimating coefficients from other well-established packages. For model preparation, users can compute both effect sizes of various types and their variance-covariance matrices, including correlation coefficients, standardized mean difference, mean difference, log odds ratio, log risk ratio, and risk difference. The package provides a tool to plot the confidence intervals for the primary studies and the overall estimates. When specific effect sizes are missing, single imputation is available in the model preparation stage; a multiple imputation method is also available for pooling the results in a statistically principled manner from models of users' choice. The package is demonstrated in two real data applications and a simulation study to assess methods for handling missing data.

Efficacy of a growth hormone-releasing hormone agonist in a murine model of cardiometabolic heart failure with preserved ejection fraction

Heart failure (HF) with preserved ejection fraction (HFpEF) represents a major unmet medical need owing to its diverse pathophysiology and lack of effective therapies. Potent synthetic, agonists (MR-356 and MR-409) of growth hormone-releasing hormone (GHRH) improve the phenotype of models of HF with reduced ejection fraction (HFrEF) and in cardiorenal models of HFpEF. Endogenous GHRH exhibits a broad range of regulatory influences in the cardiovascular (CV) system and aging and plays a role in several cardiometabolic conditions including obesity and diabetes. Whether agonists of GHRH can improve the phenotype of cardiometabolic HFpEF remains untested and unknown. Here we tested the hypothesis that MR-356 can mitigate/reverse the cardiometabolic HFpEF phenotype. C57BL6N mice received a high-fat diet (HFD) plus the nitric oxide synthase inhibitor (l-NAME) for 9 wk. After 5 wk of HFD + l-NAME regimen, animals were randomized to receive daily injections of MR-356 or placebo during a 4-wk period. Control animals received no HFD + l-NAME or agonist treatment. Our results showed the unique potential of MR-356 to treat several HFpEF-like features including cardiac hypertrophy, fibrosis, capillary rarefaction, and pulmonary congestion. MR-356 improved cardiac performance by improving diastolic function, global longitudinal strain (GLS), and exercise capacity. Importantly, the increased expression of cardiac pro-brain natriuretic peptide (pro-BNP), inducible nitric oxide synthase (iNOS), and vascular endothelial growth factor-A (VEGF-A) was restored to normal levels suggesting that MR-356 reduced myocardial stress associated with metabolic inflammation in HFpEF. Thus, agonists of GHRH may be an effective therapeutic strategy for the treatment of cardiometabolic HFpEF phenotype.NEW & NOTEWORTHY This randomized study used rigorous hemodynamic tools to test the efficacy of a synthetic GHRH agonist to improve cardiac performance in a cardiometabolic HFpEF. Daily injection of the GHRH agonist, MR-356, reduced the HFpEF-like effects as evidenced by improved diastolic dysfunction, reduced cardiac hypertrophy, fibrosis, and pulmonary congestion. Notably, end-diastolic pressure and end-diastolic pressure-volume relationship were reset to control levels. Moreover, treatment with MR-356 increased exercise capacity and reduced myocardial stress associated with metabolic inflammation in HFpEF.

Adiponectin negatively regulates pigmentation, Wnt/β-catenin and HGF/c-Met signalling within human scalp hair follicles ex vivo

Adiponectin reportedly stimulates proliferation and elongation of human scalp hair follicles (HFs) ex vivo. In the current study, we investigated how adiponectin oligomers produced by perifollicular dermal white adipose tissue (dWAT), a potent source of adiponectin isoforms, influence human HF proliferation and pigmentation. To do so, we treated microdissected, organ-cultured HFs in the presence or absence of dWAT with a recombinant human adiponectin oligomer mix, or inhibited dWAT-derived adiponectin using a neutralizing antibody. Multiplex qPCR (Fluidigm) revealed that adiponectin oligomers downregulated pigmentation genes KITLG, PMEL and TYRP1 and Wnt genes AXIN2, LEF1 and WNT10B. In situ hybridization showed that adiponectin downregulated AXIN2 and LEF1, and up-regulated DKK1 within the dermal papilla (DP), a highly unusual transcriptional profile for a putative hair growth-promoting agent. Adiponectin oligomers also downregulated protein expression of the HGF receptor c-Met within the matrix and DP. However, adiponectin did not alter hair matrix keratinocyte proliferation within 48 h ex vivo, irrespective of the presence/absence of dWAT; HF pigmentation (Masson-Fontana histochemistry, tyrosinase activity) was also unchanged. In contrast, neutralizing adiponectin isoforms within HF + dWAT increased proliferation, melanin content and tyrosinase activity but resulted in fewer melanocytes and melanocytic dendrites, as assessed by gp100 immunostaining. These seemingly contradictory effects suggest that adiponectin exerts complex effects upon human HF biology, likely in parallel with the pro-pigmentation effects of dWAT- and DP-derived HGF. Our data suggest that dWAT-derived ratios of adiponectin isoforms and the cleaved, globular version of adiponectin may in fact determine how adiponectin impacts upon follicular pigmentation and growth.

Knowledge, attitudes, and practices towards HPV vaccination among reproductive age women in a HIV hotspot in the US

BACKGROUND

Human papillomavirus (HPV) is the most common sexually transmitted infection (STI) in the US, responsible for cervical cancer and increased risk of Human Immunodeficiency Virus (HIV) acquisition. Despite an effective HPV vaccine, women's HPV vaccination coverage and rates remain far below desired levels. This study aimed to evaluate HPV knowledge, attitudes, and vaccination practices as well as factors associated with HPV vaccination among women of reproductive age living in Miami, Florida, a Southern US city with a high incidence of STIs and low HPV vaccination coverage.

METHODS

From April to June 2022, 100 HIV-negative, cisgender, sexually active women aged 18-45 years were recruited from the Miami community. Participants completed validated questionnaires using REDCap© electronic surveys, assessing socio-demographics and sexual behaviors; HPV knowledge, screening, vaccination practices; barriers and motivators to HPV vaccination. A cumulative HPV knowledge score (HPV score) was generated. Factors associated with HPV vaccination were analyzed by Chi-square, Fisher's exact test, studentized t-test, and multivariate logistic regression (MLR).

RESULTS

A total of 100 participants were enrolled, and 84 who knew their vaccination status were included in the analysis. Of these, 43 reported receiving at least 1 HPV vaccine dose (vaccinated group) and 41 reported never being vaccinated (unvaccinated group). Mean age was 24.7 (SD 4.03) years for the vaccinated group and 31.4 (SD 8.33) for the unvaccinated group. Mean HPV score was 18.9/29 (SD 6.05) for the vaccinated group and 9.1/29 (SD 8.82) for the unvaccinated group. Amongst vaccinated participants, 76.74% reported a history of HPV/Pap smear screening vs 87.80% in the unvaccinated group. Barriers to HPV vaccination included: 14.6% low-risk perception, 29.3% healthcare barriers, and 46.3% vaccine hesitancy and personal beliefs. Motivators t HPV vaccination included: risk perception and vaccine beliefs (71.42%), healthcare-related (60.71%) and social motivators (55.95%). In the first MLR, one-point increases in HPV score were significantly associated with higher odds of HPV vaccination until an HPV score of 16, and a one-year increase in age was associated with a 16% lower odds of HPV vaccination (aOR = 0.84, 95% CI [0.72, 0.99]; p = 0.035). Contraception use was also associated with HPV vaccination (aOR 8.36 (95% CI [1.41, 49.62]; p = 0.020). Race, ethnicity, college education status, and number of sexual partners were not significant predictors of HPV vaccination. In the second MLR evaluating vaccination motivators as predictors of HPV vaccination, we found that individuals who were motivated by healthcare had 3.03 (95% CI [1.02, 9.00]; p = 0.046) times the odds of HPV vaccination compared to individuals without healthcare-related motivators.

CONCLUSION

Findings suggest suboptimal HPV knowledge and low vaccination rates among women of reproductive age. Public health efforts should focus on increasing basic HPV knowledge among women with little-to-no HPV knowledge to increase vaccine uptake.

The effect of clinically elevated body mass index on physiological stress during manual lifting activities

Individuals with a body mass index (BMI) classified as obesity constitute 27.7% of U.S. workers. These individuals are more likely to experience work-related injuries. However, ergonomists still design work tasks based on the general population and normal body weight. This is particularly true for manual lifting tasks and the calculation of recommended weight limits (RWL) as per National Institute of Occupational Safety & Health (NIOSH) guidelines. This study investigates the effects of BMI on indicators of physiological stress. It was hypothesized that, for clinically elevated BMI individuals, repeated manual lifting at RWL would produce physiological stress above safety limits. A repetitive box lifting task was designed to measure metabolic parameters: volume of carbon dioxide (VCO2) and oxygen (VO2), respiratory exchange ratio (RER), heart rate (HR), and energy expenditure rate (EER). A two-way ANOVA compared metabolic variables with BMI classification and gender, and linear regressions investigated BMI correlations. Results showed that BMI classification represented a significant effect for four parameters: VCO2 (p < 0.001), VO2 (p < 0.001), HR (p = 0.012), and EER (p < 0.001). In contrast, gender only had a significant effect on VO2 (p = 0.014) and EER (p = 0.017). Furthermore, significant positive relationships were found between BMI and VCO2 (R2 = 59.65%, p < 0.001), VO2 (R2 = 45.01%, p < 0.001), HR (R2 = 21.86%, p = 0.009), and EER (R2 = 50.83%, p < 0.001). Importantly, 80% of obese subjects exceeded the EER safety limit of 4.7 kcal/min indicated by NIOSH. Indicators of physiological stress are increased in clinically elevated BMI groups and appear capable of putting these individuals at increased risk for workplace injury.

Longitudinal transactional relationships between caregiver and child mental health during the COVID-19 global pandemic

BACKGROUND

Emerging work examining the psychological impact of COVID-19 on children and families suggests that the relationship between pandemic-related stress, child psychosocial functioning, and caregiver mental health are interrelated. However, much of this research is unidirectional and thus little is known about the bidirectional cascading effects children and caregivers may experience. The current study examined the transactional relationships between caregiver and child mental health over time during the COVID-19 pandemic.

METHODS

Linguistically, racially, and ethnically diverse caregivers (N = 286) of young children completed measures of caregiver mental health, caregiver pandemic-related stress, and child mental health (i.e., externalizing, internalizing, prosocial behavior) across three time points in the spring of 2020.

RESULTS

Using autoregressive cross-lagged analyses, impaired caregiver mental health at Time 1 (April 2020) predicted increased caregiver pandemic-related stress at Time 2 (May 2020). Caregiver pandemic-related stress at Time 1 predicted increased child internalizing symptoms at Time 2 which, in turn, predicted increased caregiver pandemic-related stress at Time 3 (July 2020). Lastly, impaired caregiver mental health at Time 2 (May 2020) predicted increased child externalizing symptoms at Time 3 (July 2020).

CONCLUSIONS

Assessing transactional relationships between child and caregiver mental health during the COVID-19 pandemic is important to inform models of risk and resilience. Interventions at the level of the caregiver, the child, and/or the family should be considered as a way to interrupt potential negative developmental cascades.

Gut microbial dysbiosis in individuals with Sjögren's syndrome

BACKGROUND

Autoimmune diseases have been associated with changes in the gut microbiome. In this study, the gut microbiome was evaluated in individuals with dry eye and bacterial compositions were correlated to dry eye (DE) measures. We prospectively included 13 individuals with who met full criteria for Sjögren's (SDE) and 8 individuals with features of Sjögren's but who did not meet full criteria (NDE) for a total of 21 cases as compared to 21 healthy controls. Stool was analyzed by 16S pyrosequencing, and associations between bacterial classes and DE symptoms and signs were examined.

RESULTS

Results showed that Firmicutes was the dominant phylum in the gut, comprising 40-60% of all phyla. On a phyla level, subjects with DE (SDE and NDE) had depletion of Firmicutes (1.1-fold) and an expansion of Proteobacteria (3.0-fold), Actinobacteria (1.7-fold), and Bacteroidetes (1.3-fold) compared to controls. Shannon's diversity index showed no differences between groups with respect to the numbers of different operational taxonomic units (OTUs) encountered (diversity) and the instances these unique OTUs were sampled (evenness). On the other hand, Faith's phylogenetic diversity showed increased diversity in cases vs controls, which reached significance when comparing SDE and controls (13.57 ± 0.89 and 10.96 ± 0.76, p = 0.02). Using Principle Co-ordinate Analysis, qualitative differences in microbial composition were noted with differential clustering of cases and controls. Dimensionality reduction and clustering of complex microbial data further showed differences between the three groups, with regard to microbial composition, association and clustering. Finally, differences in certain classes of bacteria were associated with DE symptoms and signs.

CONCLUSIONS

In conclusion, individuals with DE had gut microbiome alterations as compared to healthy controls. Certain classes of bacteria were associated with DE measures.

Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs

Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and infection is one of the most common reasons for diabetes-related hospitalizations and amputations. In this study, we examined how DFU microbiomes respond to initial sharp debridement and offloading and how the initial composition associates with 4 week healing outcomes. We employed 16S rRNA next generation sequencing to perform microbial profiling on 50 samples collected from 10 patients with vascularized neuropathic DFUs. Debrided wound samples were obtained at initial visit and after one week from two DFU locations, wound bed and wound edge. Samples of the foot skin outside of the wounds were also collected for comparison. We showed that DFU wound beds are colonized by a greater number of distinct bacterial phylotypes compared to the wound edge or skin outside the wound. However, no significant microbiome diversity changes occurred at the wound sites after one week of standard care. Finally, increased initial abundance of Gram-positive anaerobic cocci (GPAC), especially Peptoniphilus (p < 0.05; n = 5 subjects), was associated with impaired healing; thus, GPAC's abundance could be a predictor of the wound-healing outcome.