Joining up health and bioinformatics: e-science meets e-health

CLEF (Co-operative Clinical e-Science Framework) is an MRC sponsored project in the e-Science programme that aims to establish methodologies and a technical infrastructure forthe next generation of integrated clinical and bioscience research. It is developing methodsfor managing and using pseudonymised repositories of the long-term patient histories whichcan be linked to genetic, genomic information or used to support patient care. CLEF concentrateson removing key barriers to managing such repositories ? ethical issues, informationcapture, integration of disparate sources into coherent ?chronicles? of events, userorientedmechanisms for querying and displaying the information, and compiling the requiredknowledge resources. This paper describes the overall information flow and technicalapproach designed to meet these aims within a Grid framework

Global copy number profiling of cancer genomes

Summary: In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the approach to the analysis of over 200 skin cancer samples, we demonstrate its utility for discovering distinct CNA events and for deriving ancillary information such as tumor purity

Use of continuous glucose monitoring in young children with type 1 diabetes: implications for behavioral research

Patton SR, Williams LB, Eder SJ, Crawford MJ, Dolan L, Powers SW. Use of continuous glucose monitoring in young children with type 1 diabetes: implications for behavioral research.Objective: This study presents data on the use of continuous glucose monitoring (CGM) in young children with type 1 diabetes mellitus (T1DM). CGM provides moment-to-moment tracking of glucose concentrations and measures of intra- and interday variability, which are particularly salient measures in young children with T1DM.Methods: Thirty-one children (mean age = 5.0 yr ) with T1DM wore the Medtronic Minimed CGM for a mean of 66.8 h. The CGM was inserted in diabetes clinics, and parents were provided brief training.Results: Few difficulties were experienced and families cited the acceptability of CGM. Participants' CGM data are compared with self-monitoring blood glucose (SMBG) data as well as data from older children with T1DM to illustrate differences in methodology and variability present in this population. CGM data are used to calculate glucose variability, which is found to be related to diabetes variables such as history of hypoglycemic seizures.Conclusions: CGM is an acceptable research tool for obtaining glucose data in young children with T1DM and has been used previously in older children and adults. CGM may be particularly useful in young children who often experience more glucose variability. Data obtained via CGM are richer and more detailed than traditional SMBG data and allow for analyses to link blood glucose with behavior.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78635/1/j.1399-5448.2010.00649.x.pd

Effects of an exercise and hypocaloric healthy eating intervention on indices of psychological health status, hypothalamic-pituitary-adrenal axis regulation and immune function after early-stage breast cancer : a randomised controlled trial

INTRODUCTION: Many women experience emotional distress, depression and anxiety after a diagnosis of breast cancer. Psychological stress and depression have been associated with hypothalamic-pituitary-adrenal (HPA) axis dysregulation that may adversely affect immune system functioning and impact upon survival. This study investigated the effects of a lifestyle intervention on indices of psychological health status, HPA axis regulation and immune function in overweight women recovering from early-stage breast cancer treatment. METHODS: A total of 85 women treated for breast cancer 3 to 18 months previously were randomly allocated to a 6-month exercise and hypocaloric healthy eating program plus usual care or usual care alone (control group). Women in the intervention group received three supervised exercise sessions per week and individualized dietary advice, supplemented by weekly nutrition seminars. Depressive symptoms (Beck Depression Inventory version II: BDI-II), perceived stress (Perceived Stress Scale: PSS), salivary diurnal cortisol rhythms; inflammatory cytokines (IL-6 and Tumor necrosis factor-α), leukocyte phenotype counts, natural killer (NK) cell cytotoxicity and lymphocyte proliferation following mitogenic stimulation were assessed at baseline and 6-month follow up. RESULTS: Compared with the control group, the intervention group exhibited a reduction in depressive symptoms (adjusted mean difference, 95% confidence intervals (95% CI): -3.12, -1.03 to -5.26; P = 0.004) at the 6-month follow-up but no significant decrease in PSS scores (-2.07, -4.96 to 0.82; P = 0.16). The lifestyle intervention also had a significant impact on diurnal salivary cortisol rhythm compared with usual care alone, as evidenced by an increase in morning salivary cortisol at the 6-month follow-up (P <0.04), indicating a change in HPA axis regulation. Women in the control group had higher total leukocyte, neutrophil and lymphocyte counts in comparison to the intervention group at the 6-month follow-up (P ≤0.05), whereas there was no difference in NK cell counts (P = 0.46), NK cell cytotoxicity (P = 0.85) or lymphocyte proliferation responses (P = 0.11) between the two groups. CONCLUSION: Our results show that the lifestyle intervention resulted in a reduction in depressive symptoms and a normalisation of HPA axis regulation. Such changes could have important implications for long-term survival in women recovering from early-breast cancer treatment. TRIAL REGISTRATION: Current Controlled Trials: ISRCTN08045231

Citizen-science data provides new insight into annual and seasonal variation in migration patterns

Current rates of global environmental and climate change pose potential challenges for migratory species that must cope with or adapt to new conditions and different rates of change across broad spatial scales throughout their annual life cycle. North American migratory hummingbirds may be especially sensitive to changes in environment and climate due to their extremely small body size, high metabolic rates, and dependence on nectar as a main resource. We used occurrence information from the eBird citizen-science database to track migratory movements of five North American hummingbird species (Archilochus alexandri, A. colubris, Selasphorus calliope, S. platycercus, and S. rufus) across 6 years (2008–2013) at a daily temporal resolution to describe annual and seasonal variation in migration patterns. Our findings suggest that the timing of the onset of spring migration generally varies less than the arrival on the wintering grounds. Species follow similar routes across years, but exhibit more variation in daily longitude than latitude. Long distance migrants generally had less annual variation in geographic location and timing than shorter distance migrants. Our study is among the first to examine variation in migration routes and timing for hummingbirds, but more work is needed to understand the capacity of these species to respond to different rates of environmental change along their migratory routes

Headstrong intervention for pediatric migraine headache: a randomized clinical trial

Background The purpose of this study was to evaluate the efficacy of a self-guided CD-ROM program (“Headstrong”) containing cognitive-behavioral self-management strategies versus an educational CD-ROM program for treating headaches, headache-related disability, and quality of life. Methods Participants were 35 children ages 7–12 years with migraine recruited from one university medical center and two children’s hospital headache clinics. Participants were randomly assigned to complete the Headstrong or educational control CD-ROM program over a 4-week period. Data on headache frequency, duration, and severity, migraine-related disability, and quality of life (QOL) were obtained at baseline, post-intervention, and 3-months post-intervention. Results At post-intervention, Headstrong resulted in lower severity (on a 10-point scale) than the control group by child report (5.06 ± 1.50 SD vs. 6.25 ± 1.92 SD, p = 0.03, ES = 0.7). At 3-months post-intervention, parents reported less migraine-related disability (on the PedMIDAS) in the Headstrong group compared to the control group (1.36 ± 2.06 SD vs. 5.18 ± 6.40 SD; p = 0.04, ES = 0.8). There were no other group differences at post treatment or at 3-months post-intervention. Conclusions When compared to an educational control, Headstrong resulted in lower pain severity at post-treatment and less migraine-related disability at 3-months post-intervention, by child and parent report respectively. Headache frequency and quality of life did not change more for Headstrong versus control. Additional research is needed on the Headstrong Program to increase its efficacy and to test it with a larger sample recruited from multiple centers simultaneously.The study reported in this paper was funded by a grant from the National Institutes of Health, (National Institute of Neurological Disorders and Stroke), R01-NS046641, Michael Rapoff, Principal Investigator

Tethered Satellites as an Enabling Platform for Operational Space Weather Monitoring Systems

Tethered satellites offer the potential to be an important enabling technology to support operational space weather monitoring systems. Space weather "nowcasting" and forecasting models rely on assimilation of near-real-time (NRT) space environment data to provide warnings for storm events and deleterious effects on the global societal infrastructure. Typically, these models are initialized by a climatological model to provide "most probable distributions" of environmental parameters as a function of time and space. The process of NRT data assimilation gently pulls the climate model closer toward the observed state (e.g., via Kalman smoothing) for nowcasting, and forecasting is achieved through a set of iterative semi-empirical physics-based forward-prediction calculations. Many challenges are associated with the development of an operational system, from the top-level architecture (e.g., the required space weather observatories to meet the spatial and temporal requirements of these models) down to the individual instruments capable of making the NRT measurements. This study focuses on the latter challenge: we present some examples of how tethered satellites (from 100s of m to 20 km) are uniquely suited to address certain shortfalls in our ability to measure critical environmental parameters necessary to drive these space weather models. Examples include long baseline electric field measurements, magnetized ionospheric conductivity measurements, and the ability to separate temporal from spatial irregularities in environmental parameters. Tethered satellite functional requirements are presented for two examples of space environment observables