A Bayesian model averaging approach to the quantification of overlapping peptides in an MALDI-TOF mass spectrum.

In a high-resolution MALDI-TOF mass spectrum, a peptide produces multiple peaks, corresponding to the isotopic variants of the molecules. An overlap occurs when two peptides appear in the vicinity of the mass coordinate, resulting in the difficulty of quantifying the relative abundance and the exact masses of these peptides. To address the problem, two factors need to be considered: (1) the variability pertaining to the abundances of the isotopic variants (2) extra information content needed to supplement the information contained in data. We propose a Bayesian model for the incorporation of prior information. Such information exists, for example, for the distribution of the masses of peptides and the abundances of the isotopic variants. The model we develop allows for the correct estimation of the parameters of interest. The validity of the modeling approach is verified by a real-life case study from a controlled mass spectrometry experiment and by a simulation study

A summer with genes: Simple disease classification from microarray data

In this article we report on the work carried out within the framework of a summer project, part-funded by an IMA small grant, in which an undergraduate student (the second author of this manuscript) developed and implemented methodology for disease classification from gene expression microarray data. While the original motivation for this study was the development of a correlation threshold for gene filtering, a general outcome of this research was that, using very simple statistical techniques (essentially at undergraduate level) but solid state-of--the-art validation routines, good classification accuracies can be obtained using relatively small-sized gene signatures. We applied the techniques on expression data for breast cancer tumour subtype classification, as well as for prediction of the presence or absence of Irritable Bowel Syndrome (IBS)

Cutting care clusters: the creation of an inverse pharmacy care law? An area-level analysis exploring the clustering of community pharmacies in England

Objectives To (1) explore the clustering of community pharmacies in England and (2) determine the relationship between community pharmacy clustering, urbanity and deprivation. Design An area-level analysis spatial study. Setting England. Primary and secondary outcome measures Community pharmacy clustering determined as a community pharmacy located within 10 min walking distance to another community pharmacy. Participants Addresses and postal codes of each community pharmacy in England were used in the analysis. Each pharmacy postal code was assigned to a lower layer super output area, which was then matched to urbanity (urban, town and fringe or village, hamlet and isolated dwellings) and deprivation decile (using the Index of Multiple Deprivation score). Results 75% of community pharmacies in England were located in a ‘cluster’ (within 10 min walking distance of another pharmacy): 19% of community pharmacies were in a cluster of two, while 56% of community pharmacies were in clusters of three or more. There was a linear relationship between community pharmacy clustering and social deprivation—with clustering more prevalent in areas of higher deprivation: for community pharmacies located in areas of lowest deprivation (decile 1), there was a significantly lower risk of clustering compared with community pharmacies located in areas of highest deprivation (relative risk 0.12 (95% CI 0.10 to 0.16)). Conclusions Clustering of community pharmacies in England is common, although there is a positive trend between community pharmacy clustering and social deprivation, whereby clustering is more significant in areas of high deprivation. Arrangements for future community pharmacy funding should not solely focus on distance from one pharmacy to another as means of determining funding allocation, as this could penalise community pharmacies in our most deprived communities, and potentially have a negative effect on other healthcare providers, such as general practitioner and accident and emergency services

An Empirical Unraveling of Lord's Paradox

Lord's Paradox occurs when a continuous covariate is statistically controlled for and the relationship between a continuous outcome and group status indicator changes in both magnitude and direction. This phenomenon poses a challenge to the notion of evidence-based policy, where data are supposed to be self-evident. We examined 50 effect size estimates from 34 large-scale educational interventions and found that impact estimates are affected in magnitude, with or without reversal in sign, when there is substantial baseline imbalance. We also demonstrated that multilevel modeling can ameliorate the divergence in sign and/or magnitude of effect estimation, which, together with project specific knowledge, promises to help those who are presented with conflicting or confusing evidence in decision-making

Multi-state models for the analysis of time-to-treatment modification among HIV patients under highly active antiretroviral therapy in Southwest Ethiopia

Background Highly active antiretroviral therapy (HAART) has shown a dramatic change in controlling the burden of HIV/AIDS. However, the new challenge of HAART is to allow long-term sustainability. Toxicities, comorbidity, pregnancy, and treatment failure, among others, would result in frequent initial HAART regimen change. The aim of this study was to evaluate the durability of first line antiretroviral therapy and to assess the causes of initial highly active antiretroviral therapeutic regimen changes among patients on HAART. Methods A Hospital based retrospective study was conducted from January 2007 to August 2013 at Jimma University Hospital, Southwest Ethiopia. Data on the prescribed ARV along with start date, switching date, and reason for change was collected. The primary outcome was defined as the time-to-treatment change. We adopted a multi-state survival modeling approach assuming each treatment regimen as state. We estimate the transition probability of patients to move from one regimen to another. Result A total of 1284 ART naive patients were included in the study. Almost half of the patients (41.2%) changed their treatment during follow up for various reasons; 442 (34.4%) changed once and 86 (6.69%) changed more than once. Toxicity was the most common reason for treatment changes accounting for 48.94% of the changes, followed by comorbidity (New TB) 14.31%. The HAART combinations that were robust to treatment changes were tenofovir (TDF) + lamivudine (3TC)+ efavirenz (EFV), tenofovir + lamivudine (3TC) + nevirapine (NVP) and zidovudine (AZT) + lamivudine (3TC) + nevirapine (NVP) with 3.6%, 4.5% and 11% treatment changes, respectively. Conclusion Moving away from drugs with poor safety profiles, such as stavudine(d4T), could reduce modification rates and this would improve regimen tolerability, while preserving future treatment options

beadarrayFilter : an R package to filter beads

Microarrays enable the expression levels of thousands of genes to be measured simultaneously. However, only a small fraction of these genes are expected to be expressed under different experimental conditions. Nowadays, filtering has been introduced as a step in the microarray preprocessing pipeline. Gene filtering aims at reducing the dimensionality of data by filtering redundant features prior to the actual statistical analysis. Previous filtering methods focus on the Affymetrix platform and can not be easily ported to the Illumina platform. As such, we developed a filtering method for Illumina bead arrays. We developed an R package, beadarrayFilter, to implement the latter method. In this paper, the main functions in the package are highlighted and using many examples, we illustrate how beadarrayFilter can be used to filter bead arrays

Choice of initial antiretroviral drugs and treatment outcomes among HIV-infected patients in sub-Saharan Africa: systematic review and meta-analysis of observational studies

Background: The effectiveness of antiretroviral therapy (ART) depends on the choice of regimens during initiation. Most evidences from developed countries indicated that there is difference between efavirenz (EFV) and nevirapine (NVP). However, the evidences are limited in resource poor countries particularly in Africa. Thus, this systematic review and meta-analysis was carried out to summarize reported long-term treatment outcomes among people on first line therapy in sub-Saharan Africa. Methods: Observational studies that reported odds ratio, relative risk, hazard ratio, or standardized incidence ratio to compare risk of treatment failure among HIV/AIDS patients who initiated ART with EFV versus NVP were systematically searched. Searches were conducted using the MEDLINE database within PubMed, Google Scholar, HINARI, and Research Gates between 2007 and 2016. Information was extracted using standardized form. Pooled risk ratios (RR) and 95% confidence intervals (CI) were calculated using random-effect, generic inverse variance method. Result: A total of 6394 articles were identified, of which, 29 were eligible for review and abstraction in sub-Saharan Africa. Seventeen articles were used for the meta-analysis. Of a total of 121,092 independent study participants, 76,719 (63.36%) were females. Of these, 40,480 (33.43%) initiated with NVP containing regimen. Two studies did not report the median CD4 cell counts at initiation. Patients who have low CD4 cell counts initiated with EFV containing regimen. The pooled effect size indicated that treatment failure was reduced by 15%, 0.85 (95%CI: 0.75–0.98), and non-nucleoside reverse transcriptase inhibitor (NNRTI) switch was reduced by 43%, 0.57 (95%CI: 0.37–0.89). Conclusion: The risk of treatment failure and NNRTI switch were lower in patients who initiated with EFV than NVP-containing regimen. The review suggests that initiation of patients with EFV-containing regimen will reduce treatment failure and NNRTI switch

Minding the Gap

The chapter examines inequalities in mental health in Stockton-on-Tees using data from a longitudinal household survey

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

Background: Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events do occur which have been linked to genetic disorders, such as several types of cancer and neurodegenerative diseases (Fan et al., Theor Biol Med Model 3:19, 2006). Therefore, understanding the mechanism of alternative splicing and identifying the difference in splicing events between diseased and healthy tissue is crucial in biomedical research with the potential of applications in personalized medicine as well as in drug development. Results: We propose a linear mixed model, Random Effects for the Identification of Differential Splicing (REIDS), for the identification of alternative splicing events. Based on a set of scores, an exon score and an array score, a decision regarding alternative splicing can be made. The model enables the ability to distinguish a differential expressed gene from a differential spliced exon. The proposed model was applied to three case studies concerning both exon and HTA arrays. Conclusion: The REIDS model provides a work flow for the identification of alternative splicing events relying on the established linear mixed model. The model can be applied to different types of arrays

Telomerase Activation to Reverse Immunosenescence in Elderly Patients With Acute Coronary Syndrome: Protocol for a Randomized Pilot Trial

Background: Inflammation plays a key role in the pathophysiology of coronary heart disease (CHD) and its acute manifestation, acute coronary syndrome (ACS). Aging is associated with a decline of the immune system, a process known as immunosenescence. This is characterized by an increase in highly proinflammatory T cells that are involved in CHD progression, plaque destabilization, and myocardial ischemia–reperfusion injury. Telomere dysfunction has been implicated in immunosenescence of T lymphocytes. Telomerase is the enzyme responsible for maintaining telomeres during cell divisions. It has a protective effect on cells under oxidative stress and helps regulate flow-mediated dilation in microvasculature. Objective: The TACTIC (Telomerase ACTivator to reverse Immunosenescence in Acute Coronary Syndrome) trial will investigate whether a telomerase activator, TA-65MD, can reduce the proportion of senescent T cells in patients with ACS with confirmed CHD. It will also assess the effect of TA-65MD on decreasing telomere shortening, reducing oxidative stress, and improving endothelial function. Methods: The study was designed as a single-center, randomized, double-blind, parallel-group, placebo-controlled phase II trial. Recruitment started in January 2019. A total of 90 patients, aged 65 years or older, with treated ACS who have had CHD confirmed by angiography will be enrolled. They will be randomized to one of two groups: TA-65MD oral therapy (8 mg twice daily) or placebo taken for 12 months. The primary outcome is the effect on immunosenescence determined by a decrease in the proportion of CD8+ TEMRA (T effector memory cells re-expressing CD45RA [CD45 expressing exon A]) cells at 12 months. Secondary outcomes include leukocyte telomere length, endothelial function, cardiac function as measured by echocardiography and NT-proBNP (N-terminal fragment of the prohormone brain-type natriuretic peptide), systemic inflammation, oxidative stress, and telomerase activity. Results: The study received National Health Service (NHS) ethics approval on August 9, 2018; Medicines and Healthcare products Regulatory Agency approval on October 19, 2018; and NHS Health Research Authority approval on October 22, 2018. The trial began recruiting participants in January 2019 and completed recruitment in March 2020; the trial is due to report results in 2021. Conclusions: This pilot trial in older patients with CHD will explore outcomes not previously investigated outside in vitro or preclinical models. The robust design ensures that bias has been minimized. Should the results indicate reduced frequency of immunosenescent CD8+ T cells as well as improvements in telomere length and endothelial function, we will plan a larger, multicenter trial in patients to determine if TA-65MD is beneficial in the treatment of CHD in elderly patients