Time series transcriptome analysis implicates the circadian clock in the Drosophila melanogaster female's response to sex peptide.

Sex peptide (SP), a seminal fluid protein of Drosophila melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses including increased egg laying, activity, and food intake and a decreased remating rate. While it is known that SP achieves this, at least in part, by altering neuronal signaling in females, the genetic architecture and temporal dynamics of the female's response to SP remain elusive. We used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 h after mating to learn about the genetic architecture, at the gene and exon levels, of the female's response to SP. We find that SP is not essential to trigger early aspects of a virgin-to-mated transcriptional switch, which includes changes in a metabolic gene regulatory network. However, SP is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that SP alters rhythmic gene expression in females and suggests that SP's disruption of the female's circadian rhythm might be key to its widespread effects.

Fragility indices for only sufficiently likely modifications.

The fragility index is a clinically meaningful metric based on modifying patient outcomes that is increasingly used to interpret the robustness of clinical trial results. The fragility index relies on a concept that explores alternative realizations of the same clinical trial by modifying patient measurements. In this article, we propose to generalize the fragility index to a family of fragility indices called the incidence fragility indices that permit only outcome modifications that are sufficiently likely and provide an exact algorithm to calculate the incidence fragility indices. Additionally, we introduce a far-reaching generalization of the fragility index to any data type and explain how to permit only sufficiently likely modifications for nondichotomous outcomes. All of the proposed methodologies follow the fragility index concept.

Assessing the robustness of results from clinical trials and meta-analyses with the fragility index.

The fragility index has been increasingly used to assess the robustness of the results of clinical trials since 2014. It aims at finding the smallest number of event changes that could alter originally statistically significant results. Despite its popularity, some researchers have expressed several concerns about the validity and usefulness of the fragility index. It offers a comprehensive review of the fragility index's rationale, calculation, software, and interpretation, with emphasis on application to studies in obstetrics and gynecology. This article presents the fragility index in the settings of individual clinical trials, standard pairwise meta-analyses, and network meta-analyses. Moreover, this article provides worked examples to demonstrate how the fragility index can be appropriately calculated and interpreted. In addition, the limitations of the traditional fragility index and some solutions proposed in the literature to address these limitations were reviewed. In summary, the fragility index is recommended to be used as a supplemental measure in the reporting of clinical trials and a tool to communicate the robustness of trial results to clinicians. Other considerations that can aid in the fragility index's interpretation include the loss to follow-up and the likelihood of data modifications that achieve the loss of statistical significance.

On Graphical Models and Convex Geometry.

A mixture-model of beta distributions framework is introduced to identify significant correlations among P features when P is large. The method relies on theorems in convex geometry, which are used to show how to control the error rate of edge detection in graphical models. The proposed 'betaMix' method does not require any assumptions about the network structure, nor does it assume that the network is sparse. The results hold for a wide class of data-generating distributions that include light-tailed and heavy-tailed spherically symmetric distributions. The results are robust for sufficiently large sample sizes and hold for non-elliptically-symmetric distributions.

Two-sample inference procedures under nonproportional hazards.

We introduce a new two-sample inference procedure to assess the relative performance of two groups over time. Our model-free method does not assume proportional hazards, making it suitable for scenarios where nonproportional hazards may exist. Our procedure includes a diagnostic tau plot to identify changes in hazard timing and a formal inference procedure. The tau-based measures we develop are clinically meaningful and provide interpretable estimands to summarize the treatment effect over time. Our proposed statistic is a U-statistic and exhibits a martingale structure, allowing us to construct confidence intervals and perform hypothesis testing. Our approach is robust with respect to the censoring distribution. We also demonstrate how our method can be applied for sensitivity analysis in scenarios with missing tail information due to insufficient follow-up. Without censoring, Kendall's tau estimator we propose reduces to the Wilcoxon-Mann-Whitney statistic. We evaluate our method using simulations to compare its performance with the restricted mean survival time and log-rank statistics. We also apply our approach to data from several published oncology clinical trials where nonproportional hazards may exist.

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response.

BACKGROUND: Immune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. On the level of transcription, studies have shown that this balancing act is reflected in tight control of the initiation kinetics and shutdown dynamics of specific immune genes. RESULTS: To investigate genome-wide expression dynamics and trade-offs after infection at a high temporal resolution, we performed an RNA-seq time course on D. melanogaster with 20 time points post Imd stimulation. A combination of methods, including spline fitting, cluster analysis, and Granger causality inference, allowed detailed dissection of expression profiles, lead-lag interactions, and functional annotation of genes through guilt-by-association. We identified Imd-responsive genes and co-expressed, less well characterized genes, with an immediate-early response and sustained up-regulation up to 5 days after stimulation. In contrast, stress response and Toll-responsive genes, among which were Bomanins, demonstrated early and transient responses. We further observed a strong trade-off with metabolic genes, which strikingly recovered to pre-infection levels before the immune response was fully resolved. CONCLUSIONS: This high-dimensional dataset enabled the comprehensive study of immune response dynamics through the parallel application of multiple temporal data analysis methods. The well annotated data set should also serve as a useful resource for further investigation of the D. melanogaster innate immune response, and for the development of methods for analysis of a post-stress transcriptional response time-series at whole-genome scale.

On clinical trial fragility due to patients lost to follow up.

BACKGROUND: Clinical trials routinely have patients lost to follow up. We propose a methodology to understand their possible effect on the results of statistical tests by altering the concept of the fragility index to treat the outcomes of observed patients as fixed but incorporate the potential outcomes of patients lost to follow up as random and subject to modification. METHODS: We reanalyse the statistical results of three clinical trials on coronary artery bypass grafting (CABG) to study the possible effect of patients lost to follow up on the treatment effect statistical significance. To do so, we introduce the LTFU-aware fragility indices as a measure of the robustness of a clinical trial's statistical results with respect to patients lost to follow up. RESULTS: The analyses illustrate that clinical trials can either be completely robust to the outcomes of patients lost to follow up, extremely sensitive to the outcomes of patients lost to follow up, or in an intermediate state. When a clinical trial is in an intermediate state, the LTFU-aware fragility indices provide an interpretable measure to quantify the degree of fragility or robustness. CONCLUSIONS: The LTFU-aware fragility indices allow researchers to rigorously explore the outcomes of patients who are lost to follow up, when their data is the appropriate kind. The LTFU-aware fragility indices are sensitivity measures in a way that the original fragility index is not.

Interventions to Support Behavioral Self-Management of Chronic Diseases.

A majority of the US adult population has one or more chronic conditions that require medical intervention and long-term self-management. Such conditions are among the 10 leading causes of mortality; an estimated 86% of the nation's $2.7 trillion in annual health care expenditures goes toward their treatment and management. Patient self-management of chronic diseases is increasingly essential to improve health behaviors, health outcomes, and quality of life and, in some cases, has demonstrated effectiveness for reducing health care utilization and the societal cost burden of chronic conditions. This review synthesizes the current state of the science of chronic disease self-management interventions and the evidence for their effectiveness, especially when applied with a systematic application of theories or models that account for a wide range of influences on behavior. Our analysis of selected outcomes from randomized controlled trials of chronic disease self-management interventions contained in 10 Cochrane systematic reviews provides additional evidence to demonstrate that self-management can improve quality of life and reduce utilization across several conditions.

Functional variation in the gut microbiome of wild Drosophila populations.

Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations, and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium.

Assessment and risk analysis of casing and cement impairment in oil and gas wells in Pennsylvania, 2000-2012.

Casing and cement impairment in oil and gas wells can lead to methane migration into the atmosphere and/or into underground sources of drinking water. An analysis of 75,505 compliance reports for 41,381 conventional and unconventional oil and gas wells in Pennsylvania drilled from January 1, 2000-December 31, 2012, was performed with the objective of determining complete and accurate statistics of casing and cement impairment. Statewide data show a sixfold higher incidence of cement and/or casing issues for shale gas wells relative to conventional wells. The Cox proportional hazards model was used to estimate risk of impairment based on existing data. The model identified both temporal and geographic differences in risk. For post-2009 drilled wells, risk of a cement/casing impairment is 1.57-fold [95% confidence interval (CI) (1.45, 1.67); P < 0.0001] higher in an unconventional gas well relative to a conventional well drilled within the same time period. Temporal differences between well types were also observed and may reflect more thorough inspections and greater emphasis on finding well leaks, more detailed note taking in the available inspection reports, or real changes in rates of structural integrity loss due to rushed development or other unknown factors. Unconventional gas wells in northeastern (NE) Pennsylvania are at a 2.7-fold higher risk relative to the conventional wells in the same area. The predicted cumulative risk for all wells (unconventional and conventional) in the NE region is 8.5-fold [95% CI (7.16, 10.18); P < 0.0001] greater than that of wells drilled in the rest of the state.

Impact of Early Detection of Respiratory Viruses by Multiplex PCR Assay on Clinical Outcomes in Adult Patients.

Rapid and definitive diagnosis of viral respiratory infections is imperative in patient triage and management. We compared the outcomes for adult patients with positive tests for respiratory viruses at a tertiary care center across two consecutive influenza seasons (winters of 2010-2011 and 2012). Infections were diagnosed by conventional methods in the first season and by multiplex PCR (FilmArray) in the second season. FilmArray decreased the time to diagnosis of influenza compared to conventional methods (median turnaround times of 1.7 h versus 7.7 h, respectively; P = 0.015); FilmArray also decreased the time to diagnosis of non-influenza viruses (1.5 h versus 13.5 h, respectively; P < 0.0001). Multivariate logistic regression found that a diagnosis of influenza by FilmArray was associated with significantly lower odds ratios (ORs) for admission (P = 0.046), length of stay (P = 0.040), duration of antimicrobial use (P = 0.032), and number of chest radiographs (P = 0.005), when controlling for potential confounders. We conclude that the rapid turnaround time, multiplex nature of the test (allowing simultaneous detection of an array of viruses), and superior sensitivity of FilmArray may improve the evaluation and management of patients suspected of having respiratory virus infections.

Nocturnal systemic hypotension increases the risk of glaucoma progression.

OBJECTIVE: The objective of this prospective, longitudinal study of patients with normal-tension glaucoma (NTG) was to determine whether patients with nocturnal hypotension are at greater risk for visual field (VF) loss over 12 months than those without nocturnal hypotension. DESIGN: Prospective, longitudinal study. PARTICIPANTS: Consecutive patients with NTG with at least 5 prior VF tests were screened for eligibility. METHODS: The baseline evaluation assessed demographic and clinical characteristics, covering systemic comorbid conditions, including systemic hypertension. All oral and ophthalmologic medications were recorded. A complete ophthalmological examination was performed at baseline and follow-up. Patients had their blood pressure (BP) monitored every 30 minutes for 48 hours with an ambulatory recording device at baseline and 6 and 12 months. MAIN OUTCOME MEASURES: The primary outcome was based on the global rates of VF progression by linear regression of the mean VF threshold sensitivity over time (decibels/year). RESULTS: Eighty-five patients with NTG (166 eyes; mean age, 65 years; 67% were women) were included. Of the 85 patients, 29% had progressed in the 5 VFs collected before study enrollment. The nocturnal mean arterial pressure (MAP) was compared with the daytime MAP. Multivariate analysis showed that the total time that sleep MAP was 10 mmHg below the daytime MAP was a significant predictor of subsequent VF progression (P<0.02). CONCLUSIONS: Cumulative nocturnal hypotension predicted VF loss in this cohort. Our data suggest that the duration and magnitude of decrease in nocturnal blood pressure below the daytime MAP, especially pressures that are 10 mmHg lower than daytime MAP, predict progression of NTG. Low nocturnal blood pressure, whether occurring spontaneously or as a result of medications, may lead to worsening of VF defects.

Financial exploitation of older adults: a population-based prevalence study.

BACKGROUND: Financial exploitation is the most common and least studied form of elder abuse. Previous research estimating the prevalence of financial exploitation of older adults (FEOA) is limited by a broader emphasis on traditional forms of elder mistreatment (e.g., physical, sexual, emotional abuse/neglect). OBJECTIVES: 1) estimate the one-year period prevalence and lifetime prevalence of FEOA; 2) describe major FEOA types; and 3) identify factors associated with FEOA. DESIGN: Prevalence study with a random, stratified probability sample. PARTICIPANTS: Four thousand, one hundred and fifty-six community-dwelling, cognitively intact adults age ≥ 60 years. SETTING: New York State. MAIN MEASURES: Comprehensive tool developed for this study measured five FEOA domains: 1) stolen or misappropriated money/property; 2) coercion resulting in surrendering rights/property; 3) impersonation to obtain property/services; 4) inadequate contributions toward household expenses, but respondent still had enough money for necessities and 5) respondent was destitute and did not receive necessary assistance from family/friends. KEY RESULTS: One-year period FEOA prevalence was 2.7% (95% CI, 2.29-3.29) and lifetime prevalence was 4.7% (95% CI, 4.05-5.34). Greater relative risk (RR) of one-year period prevalence was associated with African American/black race (RR, 3.80; 95 % CI, 1.11-13.04), poverty (RR, 1.72; 95 % CI, 1.09-2.71), increasing number of non-spousal household members (RR, 1.16; 95 % CI, 1.06-1.27), and ≥ 1 instrumental activity of daily living (IADL) impairments (RR, 1.69; 95 % CI, 1.12-2.53). Greater RR of lifetime prevalence was associated with African American/black race (RR, 2.61; 95 % CI, 1.37-4.98), poverty (RR, 1.47; 95 % CI, 1.04-2.09), increasing number of non-spousal household members (RR, 1.16; 95 % CI, 1.12-1.21), and having ≥1 IADL (RR, 1.45; 95 % CI, 1.11-1.90) or ≥1 ADL (RR, 1.52; 95 % CI, 1.06-2.18) impairment. Living with a spouse/partner was associated with a significantly lower RR of lifetime prevalence (RR, 0.39; 95 % CI, 0.26-0.59) CONCLUSIONS: Financial exploitation of older adults is a common and serious problem. Elders from groups traditionally considered to be economically, medically, and sociodemographically vulnerable are more likely to self-report financial exploitation.

A higher maternal choline intake among third-trimester pregnant women lowers placental and circulating concentrations of the antiangiogenic factor fms-like tyrosine kinase-1 (sFLT1).

This study investigated the influence of maternal choline intake on the human placental transcriptome, with a special interest in its role in modulating placental vascular function. Healthy pregnant women (n=26, wk 26-29 gestation) were randomized to 480 mg choline/d, an intake level approximating the adequate intake of 450 mg/d, or 930 mg/d for 12 wk. Maternal blood and placental samples were retrieved at delivery. Whole genome expression microarrays were used to identify placental genes and biological processes impacted by maternal choline intake. Maternal choline intake influenced a wide array of genes (n=166) and biological processes (n=197), including those related to vascular function. Of special interest was the 30% down-regulation (P=0.05) of the antiangiogenic factor and preeclampsia risk marker fms-like tyrosine kinase-1 (sFLT1) in the placenta tissues obtained from the 930 vs. 480 mg/d choline intake group. Similar decreases (P=0.04) were detected in maternal blood sFLT1 protein concentrations. The down-regulation of sFLT1 by choline treatment was confirmed in a human trophoblast cell culture model and may be related to enhanced acetylcholine signaling. These findings indicate that supplementing the maternal diet with extra choline may improve placental angiogenesis and mitigate some of the pathological antecedents of preeclampsia.

Medicaid managed care: how to target efforts to reduce costs.

BACKGROUND: To be successful, cost control efforts must target Medicaid Managed Care (MMC) beneficiaries likely to incur high costs. The critical question is how to identify potential high cost beneficiaries with simple, reproducible, transparent, auditable criteria. Our objective in this analysis was to evaluate whether the total burden of comorbidity, assessed by the Charlson comorbidity index, could identify MMC beneficiaries who incurred high health care costs. METHODS: The MetroPlus MMC claims database was use to analyze six months of claims data from 07/07-12/07; the analysis focused on the total amount paid. Age, gender, Charlson comorbidity score, serious mental illness and pregnancy were analyzed as predictors of total costs. RESULTS: We evaluated the cost profile of 4,614 beneficiaries enrolled at MetroPlus, an MMC plan. As hypothesized, the comorbidity index was a key correlate of total costs (p < .01). Yearly costs were more related to the total burden of comorbidity than any specific comorbid disease. For adults, in addition to comorbidity (p < .01) both serious mental illness (p < .01) and pregnancy (p < .01) were also related to total costs, while age, drug addiction and gender were not. The model with age, gender, comorbidity, serious mental illness, pregnancy and addiction explained 20% of the variance in total costs. In children, comorbidity (p < .01), serious mental illness (p < .01), addiction (p < .03) and pregnancy (p < .01) were associated with log cost; the model with those variables explained 6% of the variance in costs. CONCLUSIONS: Comorbidity can be used to identify MMC beneficiaries most likely to have high costs.

United States Provider Experiences with Telemedicine for Hepatitis C Treatment: A Nationwide Survey.

Background: Hepatitis C virus (HCV) elimination requires treatment access expansion, especially for underserved populations. Telehealth has the potential to improve HCV treatment access, although data are limited on its incorporation into standard clinical practice. Methods: We conducted a cross-sectional, e-mail survey of 598 US HCV treatment providers who had valid email addresses and 1) were located in urban areas and had written ≥20 prescriptions for HCV treatment to US Medicare beneficiaries in 2019-20 or 2) were located in non-urban areas and wrote any HCV prescriptions in 2019-20. Through email, we notified providers of a self-administered electronic 28-item survey of clinical strategies and attitudes about telemedicine for HCV. Results: We received 86 responses (14% response rate), of which 75 used telemedicine for HCV in 2022. Of those 75, 24% were gastroenterologists/hepatologists, 23% general medicine, 17% infectious diseases, and 32% non-physicians. Most (82%) referred patients to commercial laboratories, and 85% had medications delivered directly to patients. Overwhelmingly, respondents (92%) felt that telehealth increases healthcare access, and 76% reported that it promotes or is neutral for treatment completion. Factors believed to be "extremely" or "very" important for telehealth use included patient access to technology (86%); patients' internet access (74%); laboratory access (76%); reimbursement for video visits (74%) and audio-only visits (66%). Non-physician licensing and liability statutes were rated "extremely" or "very" important by 43% and 44%, respectively. Conclusions: Providers felt that telehealth increases HCV treatment access. Major limitations were technological requirements, reimbursement, and access to ancillary services. These findings support the importance of digital equity and literacy to achieve HCV elimination goals.

Integrative Analysis of Differentially Expressed Genes in Time-Course Multi-Omics Data with MINT-DE.

Background: Time-course multi-omics experiments have been highly informative for obtaining a comprehensive understanding of the dynamic relationships between molecules in a biological process, especially if the different profiles are obtained from the same samples. A fundamental step in analyzing time-course multi-omics data involves selecting a short list of genes or gene regions ("sites") that warrant further study. Two important criteria for site selection are the magnitude of change and the temporal dynamic consistency. However, existing methods only consider one of these criteria, while neglecting the other. Results: In our study, we propose a framework called MINT-DE (Multi-omics INtegration of Time-course for Diffierential Expression analysis) to address this limitation. MINT-DE is capable of selecting sites based on summarized measures of both aforementioned aspects. We calculate evidence measures assessing the extent of differential expression for each assay and for the dynamical similarity across assays. Then based on the summary of the evidence assessment measures, sites are ranked. To evaluate the performance of MINT-DE, we apply it to analyze a time-course multi-omics dataset of Drosophila development. We compare the selection obtained from MINT-DE with those obtained from other existing methods. The analysis reveal that MINT-DE is able to identify differentially expressed time-course pairs with the highest correlations. Their corresponding genes are significantly enriched for known biological functions, as measured by gene-gene interaction networks and the Gene Ontology enrichment. Conclusions: These findings suggest the effectiveness of MINT-DE in selecting sites that are both differentially expressed within at least one assay and temporally related across assays. This highlights the potential of MINT-DE to identify biologically important sites for downstream analysis and provide a complementarity of sites that is neglected by existing methods.

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.

Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread and informing public health strategies. However, existing simulators often fail to capture the dynamic interplay between these processes, resulting in oversimplified models that do not fully reflect real-world complexities in which the pathogen's genetic evolution dynamically influences disease transmission. We introduce the epidemiological-ecological-evolutionary simulator (e3SIM), an open-source framework that concurrently models the transmission dynamics and molecular evolution of pathogens within a host population while integrating environmental factors. Using an agent-based, discrete-generation, forward-in-time approach, e3SIM incorporates compartmental models, host-population contact networks, and quantitative-trait models for pathogens. This integration allows for realistic simulations of disease spread and pathogen evolution. Key features include a modular and scalable design, flexibility in modeling various epidemiological and population-genetic complexities, incorporation of time-varying environmental factors, and a user-friendly graphical interface. We demonstrate e3SIM's capabilities through simulations of realistic outbreak scenarios with SARS-CoV-2 and Mycobacterium tuberculosis, illustrating its flexibility for studying the genomic epidemiology of diverse pathogen types.

A mixture-model approach for parallel testing for unequal variances.

Testing for unequal variances is usually performed in order to check the validity of the assumptions that underlie standard tests for differences between means (the t-test and anova). However, existing methods for testing for unequal variances (Levene's test and Bartlett's test) are notoriously non-robust to normality assumptions, especially for small sample sizes. Moreover, although these methods were designed to deal with one hypothesis at a time, modern applications (such as to microarrays and fMRI experiments) often involve parallel testing over a large number of levels (genes or voxels). Moreover, in these settings a shift in variance may be biologically relevant, perhaps even more so than a change in the mean. This paper proposes a parsimonious model for parallel testing of the equal variance hypothesis. It is designed to work well when the number of tests is large; typically much larger than the sample sizes. The tests are implemented using an empirical Bayes estimation procedure which `borrows information' across levels. The method is shown to be quite robust to deviations from normality, and to substantially increase the power to detect differences in variance over the more traditional approaches even when the normality assumption is valid.