Joint estimation of multiple related biological networks

Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to share features. Here we present a hierarchical Bayesian formulation for joint estimation of multiple networks in this nonidentically distributed setting. The approach is general: given a suitable class of graphical models, it uses an exchangeability assumption on networks to provide a corresponding joint formulation. Motivated by emerging experimental designs in molecular biology, we focus on time-course data with interventions, using dynamic Bayesian networks as the graphical models. We introduce a computationally efficient, deterministic algorithm for exact joint inference in this setting. We provide an upper bound on the gains that joint estimation offers relative to separate estimation for each network and empirical results that support and extend the theory, including an extensive simulation study and an application to proteomic data from human cancer cell lines. Finally, we describe approximations that are still more computationally efficient than the exact algorithm and that also demonstrate good empirical performance.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS761 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Upregulation of xCT by KSHV-Encoded microRNAs Facilitates KSHV Dissemination and Persistence in an Environment of Oxidative Stress

Upregulation of xCT, the inducible subunit of a membrane-bound amino acid transporter, replenishes intracellular glutathione stores to maintain cell viability in an environment of oxidative stress. xCT also serves as a fusion-entry receptor for the Kaposi's sarcoma-associated herpesvirus (KSHV), the causative agent of Kaposi's sarcoma (KS). Ongoing KSHV replication and infection of new cell targets is important for KS progression, but whether xCT regulation within the tumor microenvironment plays a role in KS pathogenesis has not been determined. Using gene transfer and whole virus infection experiments, we found that KSHV-encoded microRNAs (KSHV miRNAs) upregulate xCT expression by macrophages and endothelial cells, largely through miR-K12-11 suppression of BACH-1—a negative regulator of transcription recognizing antioxidant response elements within gene promoters. Correlative functional studies reveal that upregulation of xCT by KSHV miRNAs increases cell permissiveness for KSHV infection and protects infected cells from death induced by reactive nitrogen species (RNS). Interestingly, KSHV miRNAs simultaneously upregulate macrophage secretion of RNS, and biochemical inhibition of RNS secretion by macrophages significantly reduces their permissiveness for KSHV infection. The clinical relevance of these findings is supported by our demonstration of increased xCT expression within more advanced human KS tumors containing a larger number of KSHV-infected cells. Collectively, these data support a role for KSHV itself in promoting de novo KSHV infection and the survival of KSHV-infected, RNS-secreting cells in the tumor microenvironment through the induction of xCT

Premature atherosclerosis is associated with hypovitaminosis d and angiotensin-converting enzyme inhibitor non-use in lupus patients

The ultimate goal is to identify and target modifiable risk factors that will reduce major cardiovascular events in African American lupus patients. As a first step toward achieving this goal, this study was designed to explore risk factor models of preclinical atherosclerosis in a predominantly African American group of patients with systemic lupus erythematosus (SLE) using variables historically associated with endothelial function in nonlupus populations. Fifty-one subjects with SLE but without a history of clinical cardiovascular events were enrolled. At entry, a Framingham risk factor history and medication list were recorded. Sera and plasma samples were analyzed for lipids, lupus activity markers and total 25-hydroxyvitamin D (25 OH)D) levels. Carotid ultrasound measurements were performed to determine total plaque area (TPA) in both carotids. Cases had TPA values above age-matched controls from a vascular prevention clinic population. Logistic regression and machine learning analyses were performed to create predictive models. 25(OH)D levels were significantly lower, and SLE disease duration was significantly higher in cases. 25(OH)D levels inversely correlated with age-adjusted TPA. Angiotensin-converting enzyme (ACE) inhibitor nonuse associated with case status. Logistic regression models containing ACE inhibitor use, 25(OH)D levels and low-density lipoprotein levels had a diagnostic accuracy of 84% for predicting accelerated atherosclerosis. Similar results were obtained with machine learning models, but hydroxychlo-roquine use associated with controls in these models. This is the first study to demonstrate an association between atherosclerotic burden and 25(OH)D insufficiency or ACE inhibitor nonuse in lupus patients. These findings provide strong rationale for the study of ACE inhibitors and vitamin D replenishment as preventive therapies in this high-risk population. © Copyright 2012 Southern Society for Clinical Investigation

The Effect of Travel Burden on Depression and Anxiety in African American Women Living with Systemic Lupus

The United States has a deficit of rheumatology specialists. This leads to an increased burden in accessing care for patients requiring specialized care. Given that most rheumatologists are located in urban centers at large hospitals, many lupus patients must travel long distances for routine appointments. The present work aims to determine whether travel burden is associated with increased levels of depression and anxiety among these patients. Data for this study were collected from baseline visits of patients participating in a lupus study at MUSC. A travel/economic burden survey was assessed as well as the 8-item Patient Health Questionnaire (PHQ-8) and the 7-item Generalized Anxiety Disorder (GAD-7) survey as measures of depression and anxiety, respectively. Linear regression models were used to assess the relationship between travel burden and depression and anxiety. Frequency of healthcare visits was significantly associated with increased depression (β = 1.3, p = 0.02). Significant relationships were identified between anxiety and requiring time off from work for healthcare appointments (β = 4, p = 0.02), and anxiety and perceived difficulty in traveling to primary care providers (β = 3.1, p = 0.04). Results from this study provide evidence that travel burden can have an effect on lupus patients’ anxiety and depression levels

An empirically-based characterization and quantification of information seeking through mailing lists during Open Source developers' software evolution

Context Several authors have proposed information seeking as an appropriate perspective for studying software evolution. Empirical evidence in this area suggests that substantial time delays can accrue, due to the unavailability of required information, particularly when this information must travel across geographically distributed sites. Objective As a first step in addressing the time delays that can occur in information seeking for distributed Open Source (OS) programmers during software evolution, this research characterizes the information seeking of OS developers through their mailing lists. Method A longitudinal study that analyses 17 years of developer mailing list activity in total, over 6 different OS projects is performed, identifying the prevalent information types sought by developers, from a qualitative, grounded analysis of this data. Quantitative analysis of the number-of-responses and response time-lag is also performed. Results The analysis shows that Open Source developers are particularly implementation centric and team focused in their use of mailing lists, mirroring similar findings that have been reported in the literature. However novel findings include the suggestion that OS developers often require support regarding the technology they use during development, that they refer to documentation fairly frequently and that they seek implementation-oriented specifics based on system design principles that they anticipate in advance. In addition, response analysis suggests a large variability in the response rates for different types of questions, and particularly that participants have difficulty ascertaining information on other developer's activities. Conclusion The findings provide insights for those interested in supporting the information needs of OS developer communities: They suggest that the tools and techniques developed in support of co-located developers should be largely mirrored for these communities: that they should be implementation centric, and directed at illustrating "how" the system achieves its functional goals and states. Likewise they should be directed at determining the reason for system bugs: a type of question frequently posed by OS developers but less frequently responded to

The status of the world's land and marine mammals: diversity, threat, and knowledge

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action

Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features

The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia