Imaging interactions between the immune and cardiovascular systems in vivo by multiphoton microscopy

Several recent studies in immunology have used multiphoton laser-scanning microscopy to visualise the induction of an immune response in real time in vivo. These experiments are illuminating the cellular and molecular interactions involved in the induction, maintenance and regulation of immune responses. Similar approaches are being applied in cardiovascular research where there is an increasing body of evidence to support a significant role for the adaptive immune system in vascular disease. As such, we have begun to dissect the role of T lymphocytes in atherosclerosis in real time in vivo. Here, we provide step-by-step guides to the various stages involved in visualising the migration of T cells within a lymph node and their infiltration into inflamed tissues such as atherosclerotic arteries. These methods provide an insight into the mechanisms involved in the activation and function of immune cells in vivo

Comparison of Medicine Availability Measurements at Health Facilities: Evidence from Service Provision Assessment Surveys in Five Sub-Saharan African Countries.

With growing emphasis on health systems strengthening in global health, various health facility assessment methods have been used increasingly to measure medicine and commodity availability. However, few studies have systematically compared estimates of availability based on different definitions. The objective of this study was to compare estimates of medicine availability based on different definitions. A secondary data analysis was conducted using data from the Service Provision Assessment (SPA) - a nationally representative sample survey of health facilities - conducted in five countries: Kenya SPA 2010, Namibia SPA 2009, Rwanda SPA 2007, Tanzania SPA 2006, and Uganda SPA 2007. For 32 medicines, percent of facilities having the medicine were estimated using five definitions: four for current availability and one for six-month period availability. 'Observed availability of at least one valid unit' was used as a reference definition, and ratios between the reference and each of the other four estimates were calculated. Summary statistics of the ratios among the 32 medicines were calculated by country. The ratios were compared further between public and non-public facilities within each country. Across five countries, compared to current observed availability of at least one valid unit, 'reported availability without observation' was on average 6% higher (ranging from 3% in Rwanda to 8% in Namibia), 'observed availability where all units were valid' was 11% lower (ranging from 2% in Tanzania to 19% in Uganda), and 'six-month period availability' was 14% lower (ranging from 5% in Namibia to 25% in Uganda). Medicine availability estimates vary substantially across definitions, and need to be interpreted with careful consideration of the methods used

Improving pneumonia case-management in Benin: a randomized trial of a multi-faceted intervention to support health worker adherence to Integrated Management of Childhood Illness guidelines

<p>Abstract</p> <p>Background</p> <p>Pneumonia is a leading cause of death among children under five years of age. The Integrated Management of Childhood Illness strategy can improve the quality of care for pneumonia and other common illnesses in developing countries, but adherence to these guidelines could be improved. We evaluated an intervention in Benin to support health worker adherence to the guidelines after training, focusing on pneumonia case management.</p> <p>Methods</p> <p>We conducted a randomized trial. After a health facility survey in 1999 to assess health care quality before Integrated Management of Childhood Illness training, health workers received training plus either study supports (job aids, non-financial incentives and supervision of workers and supervisors) or "usual" supports. Follow-up surveys were conducted in 2001, 2002 and 2004. Outcomes were indicators of health care quality for Integrated Management-defined pneumonia. Further analyses included a graphical pathway analysis and multivariable logistic regression modelling to identify factors influencing case-management quality.</p> <p>Results</p> <p>We observed 301 consultations of children with non-severe pneumonia that were performed by 128 health workers in 88 public and private health facilities. Although outcomes improved in both intervention and control groups, we found no statistically significant difference between groups. However, training proceeded slowly, and low-quality care from untrained health workers diluted intervention effects. Per-protocol analyses suggested that health workers with training plus study supports performed better than those with training plus usual supports (20.4 and 19.2 percentage-point improvements for recommended treatment [p = 0.08] and "recommended or adequate" treatment [p = 0.01], respectively). Both groups tended to perform better than untrained health workers. Analyses of treatment errors revealed that incomplete assessment and difficulties processing clinical findings led to missed pneumonia diagnoses, and missed diagnoses led to inadequate treatment. Increased supervision frequency was associated with better care (odds ratio for recommended treatment = 2.1 [95% confidence interval: 1.13.9] per additional supervisory visit).</p> <p>Conclusion</p> <p>Integrated Management of Childhood Illness training was useful, but insufficient, to achieve high-quality pneumonia case management. Our study supports led to additional improvements, although large gaps in performance still remained. A simple graphical pathway analysis can identify specific, common errors that health workers make in the case-management process; this information could be used to target quality improvement activities, such as supervision (ClinicalTrials.gov number NCT00510679).</p

On the underestimation of auditory verbal learning impairments in temporal lobe epilepsy

Background: The auditory verbal learning test (AVLT) procedure is routinely deployed in neuropsychological investigations to examine learning and memory status in research and clinical cohorts. Concerns however have been raised regarding the susceptibility of the standard AVLT procedure to ceiling effects, which may have adverse consequences for psychometric properties and result in an underestimation of true potential and differences between normal and abnormal scores. Methods: We examined the performance of patients with temporal lobe epilepsy (TLE; n = 40) who had completed a standard 15-item AVLT and compared a group of TLE patients (n = 12) with healthy controls (n = 12) who completed an extended 24-item AVLT, which was designed to minimise the probability of ceiling scores. Results: Ceiling effects on at least one trial (≥ 14) was achieved by 33% of patients on the 15-item test, with 60% of patients scoring within or above the average list learning total score. Increasing the list length to 24-items reduced the percentage of TLE patients scoring within the normal range to 42%. In addition, no patients but 25% of control participants achieved a maximum score on trial A5. The performance of controls was superior to patients for the best learning trial, learning rate and total learning score. Conclusions: Increasing the list length to 24-items eliminated ceiling scores in all TLE patients and most controls and allowed the true magnitude in difference between the groups to be observed. These findings have implications for decisions relating to optimal AVLT list lengths that might be deployed for memory assessment in TLE

“Even if You Know Everything You Can Forget”: Health Worker Perceptions of Mobile Phone Text-Messaging to Improve Malaria Case-Management in Kenya

This paper presents the results of a qualitative study to investigate the perceptions and experiences of health workers involved in a a cluster-randomized controlled trial of a novel intervention to improve health worker malaria case-management in 107 government health facilities in Kenya. The intervention involved sending text-messages about paediatric outpatient malaria case-management accompanied by “motivating” quotes to health workers’ mobile phones. Ten malaria messages were developed reflecting recommendations from the Kenyan national guidelines. Two messages were delivered per day for 5 working days and the process was repeated for 26 weeks (May to October 2009). The accompanying quotes were unique to each message. The intervention was delivered to 119 health workers and there were significant improvements in correct artemether-lumefantrine (AL) management both immediately after the intervention (November 2009) and 6 months later (May 2010). In-depth interviews with 24 health workers were undertaken to investigate the possible drivers of this change. The results suggest high acceptance of all components of the intervention, with the active delivery of information in an on the job setting, the ready availability of new and stored text messages and the perception of being kept ‘up to date’ as important factors influencing practice. Applying the construct of stages of change we infer that in this intervention the SMS messages were operating primarily at the action and maintenance stages of behaviour change achieving their effect by creating an enabling environment and providing a prompt to action for the implementation of case management practices that had already been accepted as the clinical norm by the health workers. Future trials testing the effectiveness of SMS reminders in creating an enabling environment for the establishment of new norms in clinical practice as well as in providing a prompt to action for the implementation of the new case-management guidelines are justified

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

Species Specificity in Major Urinary Proteins by Parallel Evolution

Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1) diversity, to enable the signaling of multiple behaviors, 2) dynamic regulation, to indicate age and dominance, and 3) species-specificity. Recently, the major urinary proteins (Mups) have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues

Classification of HIV-1 Sequences Using Profile Hidden Markov Models

Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain. We show that a standard method that relies on the construction of a positive training set only, to capture unique features associated with a particular subtype, can accurately classify sequences belonging to all subtypes except B and D. We point out the drawbacks of the standard method; namely, an arbitrary choice of threshold to distinguish between true positives and true negatives, and the inability to discriminate between closely related subtypes. We then propose an improved classification method based on construction of a positive as well as a negative training set to improve discriminating ability between closely related subtypes like B and D. Finally, we show how the improved method can be used to accurately determine the subtype composition of Common Recombinant Forms of the virus that are made up of two or more subtypes. Our method provides a simple and highly accurate alternative to other classification methods and will be useful in accurately annotating newly sequenced HIV-1 strains

Information Discovery on Electronic Health Records Using Authority Flow Techniques

<p>Abstract</p> <p>Background</p> <p>As the use of electronic health records (EHRs) becomes more widespread, so does the need to search and provide effective information discovery within them. Querying by keyword has emerged as one of the most effective paradigms for searching. Most work in this area is based on traditional Information Retrieval (IR) techniques, where each document is compared individually against the query. We compare the effectiveness of two fundamentally different techniques for keyword search of EHRs.</p> <p>Methods</p> <p>We built two ranking systems. The traditional BM25 system exploits the EHRs' content without regard to association among entities within. The Clinical ObjectRank (CO) system exploits the entities' associations in EHRs using an authority-flow algorithm to discover the most relevant entities. BM25 and CO were deployed on an EHR dataset of the cardiovascular division of Miami Children's Hospital. Using sequences of keywords as queries, sensitivity and specificity were measured by two physicians for a set of 11 queries related to congenital cardiac disease.</p> <p>Results</p> <p>Our pilot evaluation showed that CO outperforms BM25 in terms of sensitivity (65% vs. 38%) by 71% on average, while maintaining the specificity (64% vs. 61%). The evaluation was done by two physicians.</p> <p>Conclusions</p> <p>Authority-flow techniques can greatly improve the detection of relevant information in EHRs and hence deserve further study.</p

LNCS

Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude