A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation

<p>Abstract</p> <p>Background</p> <p>The identification of novel genes by high-throughput studies of complex diseases is complicated by the large number of potential genes. However, since disease-associated genes tend to interact, one solution is to arrange them in modules based on co-expression data and known gene interactions. The hypothesis of this study was that such a module could be a) found and validated in allergic disease and b) used to find and validate one ore more novel disease-associated genes.</p> <p>Results</p> <p>To test these hypotheses integrated analysis of a large number of gene expression microarray experiments from different forms of allergy was performed. This led to the identification of an experimentally validated reference gene that was used to construct a module of co-expressed and interacting genes. This module was validated in an independent material, by replicating the expression changes in allergen-challenged CD4⁺cells. Moreover, the changes were reversed following treatment with corticosteroids. The module contained several novel disease-associated genes, of which the one with the highest number of interactions with known disease genes, <it>IL7R</it>, was selected for further validation. The expression levels of <it>IL7R </it>in allergen challenged CD4⁺cells decreased following challenge but increased after treatment. This suggested an inhibitory role, which was confirmed by functional studies.</p> <p>Conclusion</p> <p>We propose that a module-based analytical strategy is generally applicable to find novel genes in complex diseases.</p

The Cohen-Macaulay property of separating invariants of finite groups

In the case of finite groups, a separating algebra is a subalgebra of the ring of invariants which separates the orbits. Although separating algebras are often better behaved than the ring of invariants, we show that many of the criteria which imply that the ring of invariants is non Cohen-Macaulay actually imply that no graded separating algebra is Cohen-Macaulay. For example, we show that, over a field of positive characteristic p, given sufficiently many copies of a faithful modular representation, no graded separating algebra is Cohen-Macaulay. Furthermore, we show that, for a p-group, the existence of a Cohen-Macaulay graded separating algebra implies the group is generated by bireflections. Furthermore, we show that, for a $p$-group, the existence of a Cohen-Macaulay graded separating algebra implies the group is generated by bireflections. Additionally, we give an example which shows that Cohen-Macaulay separating algebras can occur when the ring of invariants is not Cohen-Macaulay.Comment: We removed the conjecture which appeared in previous versions: we give a counter-example. We fixed the proof of Lemma 2.2 (previously Remark 2.2). 16 page

Early and efficient detection of Mycobacterium tuberculosis in sputum by microscopic observation of broth cultures.

Early, efficient and inexpensive methods for the detection of pulmonary tuberculosis are urgently needed for effective patient management as well as to interrupt transmission. These methods to detect M. tuberculosis in a timely and affordable way are not yet widely available in resource-limited settings. In a developing-country setting, we prospectively evaluated two methods for culturing and detecting M. tuberculosis in sputum. Sputum samples were cultured in liquid assay (micro broth culture) in microplate wells and growth was detected by microscopic observation, or in Löwenstein-Jensen (LJ) solid media where growth was detected by visual inspection for colonies. Sputum samples were collected from 321 tuberculosis (TB) suspects attending Bugando Medical Centre, in Mwanza, Tanzania, and were cultured in parallel. Pulmonary tuberculosis cases were diagnosed using the American Thoracic Society diagnostic standards. There were a total of 200 (62.3%) pulmonary tuberculosis cases. Liquid assay with microscopic detection detected a significantly higher proportion of cases than LJ solid culture: 89.0% (95% confidence interval [CI], 84.7% to 93.3%) versus 77.0% (95% CI, 71.2% to 82.8%) (p = 0.0007). The median turn around time to diagnose tuberculosis was significantly shorter for micro broth culture than for the LJ solid culture, 9 days (interquartile range [IQR] 7-13), versus 21 days (IQR 14-28) (p<0.0001). The cost for micro broth culture (labor inclusive) in our study was US $4.56 per sample, versus US$11.35 per sample for the LJ solid culture. The liquid assay (micro broth culture) is an early, feasible, and inexpensive method for detection of pulmonary tuberculosis in resource limited settings

The Feasibility and Impact of Delivering a Mind-Body Intervention in a Virtual World

Introduction: Mind-body medical approaches may ameliorate chronic disease. Stress reduction is particularly helpful, but face-to-face delivery systems cannot reach all those who might benefit. An online, 3-dimensional virtual world may be able to support the rich interpersonal interactions required of this approach. In this pilot study, we explore the feasibility of translating a face-to-face stress reduction program into an online virtual setting and estimate the effect size of the intervention. Methods and Findings: Domain experts in virtual world technology joined with mind body practitioners to translate an existing 8 week relaxation response-based resiliency program into an 8-week virtual world-based program in Second Life™ (SL). Twenty-four healthy volunteers with at least one month's experience in SL completed the program. Each subject filled out the Perceived Stress Scale (PSS) and the Symptom Checklist 90- Revised (SCL-90-R) before and after taking part. Participants took part in one of 3 groups of about 10 subjects. The participants found the program to be helpful and enjoyable. Many reported that the virtual environment was an excellent substitute for the preferred face-to-face approach. On quantitative measures, there was a general trend toward decreased perceived stress, (15.7 to 15.0), symptoms of depression, (57.6 to 57.0) and anxiety (56.8 to 54.8). There was a significant decrease of 2.8 points on the SCL-90-R Global Severity Index (p<0.05). Conclusions: This pilot project showed that it is feasible to deliver a typical mind-body medical intervention through a virtual environment and that it is well received. Moreover, the small reduction in psychological distress suggests further research is warranted. Based on the data collected for this project, a randomized trial with less than 50 subjects would be appropriately powered if perceived stress is the primary outcome

Cingulate cortex hypoperfusion predicts Alzheimer's disease in mild cognitive impairment

BACKGROUND: Mild cognitive impairment (MCI) was recently described as a heterogeneous group with a variety of clinical outcomes and high risk to develop Alzheimer's disease (AD). Regional cerebral blood flow (rCBF) as measured by single photon emission computed tomography (SPECT) was used to study the heterogeneity of MCI and to look for predictors of future development of AD. METHODS: rCBF was investigated in 54 MCI subjects using Tc-99m hexamethylpropyleneamine oxime (HMPAO). An automated analysis software (BRASS) was applied to analyze the relative blood flow (cerebellar ratios) of 24 cortical regions. After the baseline examination, the subjects were followed clinically for an average of two years. 17 subjects progressed to Alzheimer's disease (PMCI) and 37 subjects remained stable (SMCI). The baseline SPECT ratio values were compared between PMCI and SMCI. Receiver operating characteristic (ROC) analysis was applied for the discrimination of the two subgroups at baseline. RESULTS: The conversion rate of MCI to AD was 13.7% per year. PMCI had a significantly decreased rCBF in the left posterior cingulate cortex, as compared to SMCI. Left posterior cingulate rCBF ratios were entered into a logistic regression model for ROC curve calculation. The area under the ROC curve was 74%–76%, which indicates an acceptable discrimination between PMCI and SMCI at baseline. CONCLUSION: A reduced relative blood flow of the posterior cingulate gyrus could be found at least two years before the patients met the clinical diagnostic criteria of AD

Caries associated with orthodontic care part 2: management

It is recognized that wearing an orthodontic appliance increases the caries risk of the individual. The prevalence of demineralization has been reported to be as high as 73%. When demineralization occurs a number of treatments exist: fluoride application, acid microabrasion, casein phosphopeptide-amorphous calcium phosphate (CCP-ACP), resin infiltration and self-assembling peptides. Of these, topical fluoride has the most evidence to support its use. CPD/Clinical Relevance: Demineralization is the most common complication of orthodontic care. The clinician should understand how to manage this when it occurs

Ethnic differences in oral health and use of dental services:cross-sectional study using the 2009 Adult Dental Health Survey

Background Oral health impacts on general health and quality of life, and oral diseases are the most common non-communicable diseases worldwide. Non-White ethnic groups account for an increasing proportion of the UK population. This study explores whether there are ethnic differences in oral health and whether these are explained by differences in sociodemographic or lifestyle factors, or use of dental services. Methods We used the Adult Dental Health Survey 2009 to conduct a cross-sectional study of the adult general population in England, Wales and Northern Ireland. Ethnic groups were compared in terms of oral health, lifestyle and use of dental services. Logistic regression analyses were used to determine whether ethnic differences in fillings, extractions and missing teeth persisted after adjustment for potential sociodemographic confounders and whether they were explained by lifestyle or dental service mediators. Results The study comprised 10,435 (94.6 %) White, 272 (2.5 %) Indian, 165 (1.5 %) Pakistani/Bangladeshi and 187 (1.7 %) Black participants. After adjusting for confounders, South Asian participants were significantly less likely, than White, to have fillings (Indian adjusted OR 0.25, 95 % CI 0.17-0.37; Pakistani/Bangladeshi adjusted OR 0.43, 95 % CI 0.26-0.69), dental extractions (Indian adjusted OR 0.33, 95 % CI 0.23-0.47; Pakistani/Bangladeshi adjusted OR 0.41, 95 % CI 0.26-0.63), and &lt;20 teeth (Indian adjusted OR 0.31, 95 % CI 0.16-0.59; Pakistani/Bangladeshi adjusted OR 0.22, 95 % CI 0.08-0.57). They attended the dentist less frequently and were more likely to add sugar to hot drinks, but were significantly less likely to consume sweets and cakes. Adjustment for these attenuated the differences but they remained significant. Black participants had reduced risk of all outcomes but after adjustment for lifestyle the difference in fillings was attenuated, and extractions and tooth loss became non-significant. Conclusions Contrary to most health inequalities, oral health was better among non-White groups, in spite of lower use of dental services. The differences could be partially explained by reported differences in dietary sugar

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

The stellar halo of the Galaxy

Stellar halos may hold some of the best preserved fossils of the formation history of galaxies. They are a natural product of the merging processes that probably take place during the assembly of a galaxy, and hence may well be the most ubiquitous component of galaxies, independently of their Hubble type. This review focuses on our current understanding of the spatial structure, the kinematics and chemistry of halo stars in the Milky Way. In recent years, we have experienced a change in paradigm thanks to the discovery of large amounts of substructure, especially in the outer halo. I discuss the implications of the currently available observational constraints and fold them into several possible formation scenarios. Unraveling the formation of the Galactic halo will be possible in the near future through a combination of large wide field photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes. Full-resolution version available at http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd

Prediction and analysis of near-road concentrations using a reduced-form emission/dispersion model

<p>Abstract</p> <p>Background</p> <p>Near-road exposures of traffic-related air pollutants have been receiving increased attention due to evidence linking emissions from high-traffic roadways to adverse health outcomes. To date, most epidemiological and risk analyses have utilized simple but crude exposure indicators, most typically proximity measures, such as the distance between freeways and residences, to represent air quality impacts from traffic. This paper derives and analyzes a simplified microscale simulation model designed to predict short- (hourly) to long-term (annual average) pollutant concentrations near roads. Sensitivity analyses and case studies are used to highlight issues in predicting near-road exposures.</p> <p>Methods</p> <p>Process-based simulation models using a computationally efficient reduced-form response surface structure and a minimum number of inputs integrate the major determinants of air pollution exposures: traffic volume and vehicle emissions, meteorology, and receptor location. We identify the most influential variables and then derive a set of multiplicative submodels that match predictions from "parent" models MOBILE6.2 and CALINE4. The assembled model is applied to two case studies in the Detroit, Michigan area. The first predicts carbon monoxide (CO) concentrations at a monitoring site near a freeway. The second predicts CO and PM_2.5concentrations in a dense receptor grid over a 1 km²area around the intersection of two major roads. We analyze the spatial and temporal patterns of pollutant concentration predictions.</p> <p>Results</p> <p>Predicted CO concentrations showed reasonable agreement with annual average and 24-hour measurements, e.g., 59% of the 24-hr predictions were within a factor of two of observations in the warmer months when CO emissions are more consistent. The highest concentrations of both CO and PM_2.5were predicted to occur near intersections and downwind of major roads during periods of unfavorable meteorology (e.g., low wind speeds) and high emissions (e.g., weekday rush hour). The spatial and temporal variation among predicted concentrations was significant, and resulted in unusual distributional and correlation characteristics, including strong negative correlation for receptors on opposite sides of a road and the highest short-term concentrations on the "upwind" side of the road.</p> <p>Conclusions</p> <p>The case study findings can likely be generalized to many other locations, and they have important implications for epidemiological and other studies. The reduced-form model is intended for exposure assessment, risk assessment, epidemiological, geographical information systems, and other applications.</p