Hyper-Spectral Image Analysis with Partially-Latent Regression and Spatial Markov Dependencies

Hyper-spectral data can be analyzed to recover physical properties at large planetary scales. This involves resolving inverse problems which can be addressed within machine learning, with the advantage that, once a relationship between physical parameters and spectra has been established in a data-driven fashion, the learned relationship can be used to estimate physical parameters for new hyper-spectral observations. Within this framework, we propose a spatially-constrained and partially-latent regression method which maps high-dimensional inputs (hyper-spectral images) onto low-dimensional responses (physical parameters such as the local chemical composition of the soil). The proposed regression model comprises two key features. Firstly, it combines a Gaussian mixture of locally-linear mappings (GLLiM) with a partially-latent response model. While the former makes high-dimensional regression tractable, the latter enables to deal with physical parameters that cannot be observed or, more generally, with data contaminated by experimental artifacts that cannot be explained with noise models. Secondly, spatial constraints are introduced in the model through a Markov random field (MRF) prior which provides a spatial structure to the Gaussian-mixture hidden variables. Experiments conducted on a database composed of remotely sensed observations collected from the Mars planet by the Mars Express orbiter demonstrate the effectiveness of the proposed model.Comment: 12 pages, 4 figures, 3 table

A Dutch guideline for the treatment of scoliosis in neuromuscular disorders

<p>Abstract</p> <p>Background</p> <p>Children with neuromuscular disorders with a progressive muscle weakness such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy frequently develop a progressive scoliosis. A severe scoliosis compromises respiratory function and makes sitting more difficult. Spinal surgery is considered the primary treatment option for correcting severe scoliosis in neuromuscular disorders. Surgery in this population requires a multidisciplinary approach, careful planning, dedicated surgical procedures, and specialized after care.</p> <p>Methods</p> <p>The guideline is based on scientific evidence and expert opinions. A multidisciplinary working group representing experts from all relevant specialties performed the research. A literature search was conducted to collect scientific evidence in answer to specific questions posed by the working group. Literature was classified according to the level of evidence.</p> <p>Results</p> <p>For most aspects of the treatment scientific evidence is scarce and only low level cohort studies were found. Nevertheless, a high degree of consensus was reached about the management of patients with scoliosis in neuromuscular disorders. This was translated into a set of recommendations, which are now officially accepted as a general guideline in the Netherlands.</p> <p>Conclusion</p> <p>In order to optimize the treatment for scoliosis in neuromuscular disorders a Dutch guideline has been composed. This evidence-based, multidisciplinary guideline addresses conservative treatment, the preoperative, perioperative, and postoperative care of scoliosis in neuromuscular disorders.</p

Overweight and obesity in Brazilian adolescents

OBJECTIVE: This study aimed to describe the prevalence of overweight and obesity (OW+O) among Brazilian adolescents and to identify risks for subpopulations defined according to the five country macro-regions and situation (urban-rural) of the domiciles, income, years of school attendance, age and sex.DESIGN: A nationwide home-based survey representative of the Brazilian civilian noninstitutionalized population, performed in 1989.METHODS: the sampling plans followed a stratified, multistage, probability cluster design in the National Research of Health and Nutrition sample, which collected anthropometric data of 14,455 domiciles. in all, 13,715 adolescents ranging from 10 to 19 y of age were studied. the OW + O was defined from a body mass index (BMI) equal or superior to the 85th percentile of the reference population of the NCHS. the prevalences in the different studied groups were compared using the adjusted odds ratio in logistic regression models.RESULTS: the prevalence of OW + O was of 7.7%, reaching 10.6% within the female group and 4.8% within the male group. A direct relation could be established between the socioeconomic level and OW + O. Adolescents of the most industrialized region of the country presented a risk of OW + O 1.86 (95% Cl 1.51 - 2.30) times higher than that found in the least developed region. Male youngsters who lived in urban areas were more liable (OR = 1.71, 95% Cl 1.30-2.25) to overweight than their counterparts of rural areas. the occurrence of menarche increased two and a half times (OR = 2.58, 95% CI 2.11 - 3.15) the risk of OW + O within the female group of adolescents.CONCLUSIONS: the results demonstrate a low prevalence of OW + O among Brazilian adolescents when compared with adolescents of more industrialized regions. the OW + O is twice as high within the female group, which represents a much greater difference than the one encountered in industrialized countries, probably owing to the muscular work carried out preponderantly by male adolescents of lower socioeconomic levels. Higher prevalences in subpopulations of higher socioeconomic level and of more industrialized regions show the great need for differentiated actions to control overweight and obesity in the country.Univ Fed Pelotas, Fac Nutr, BR-96010900 Pelotas, RS, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Pediat, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Pediat, São Paulo, BrazilWeb of Scienc

Modelling survival : exposure pattern, species sensitivity and uncertainty

The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans

The NEWMEDS rodent touchscreen test battery for cognition relevant to schizophrenia.

RATIONALE: The NEWMEDS initiative (Novel Methods leading to New Medications in Depression and Schizophrenia, http://www.newmeds-europe.com ) is a large industrial-academic collaborative project aimed at developing new methods for drug discovery for schizophrenia. As part of this project, Work package 2 (WP02) has developed and validated a comprehensive battery of novel touchscreen tasks for rats and mice for assessing cognitive domains relevant to schizophrenia. OBJECTIVES: This article provides a review of the touchscreen battery of tasks for rats and mice for assessing cognitive domains relevant to schizophrenia and highlights validation data presented in several primary articles in this issue and elsewhere. METHODS: The battery consists of the five-choice serial reaction time task and a novel rodent continuous performance task for measuring attention, a three-stimulus visual reversal and the serial visual reversal task for measuring cognitive flexibility, novel non-matching to sample-based tasks for measuring spatial working memory and paired-associates learning for measuring long-term memory. RESULTS: The rodent (i.e. both rats and mice) touchscreen operant chamber and battery has high translational value across species due to its emphasis on construct as well as face validity. In addition, it offers cognitive profiling of models of diseases with cognitive symptoms (not limited to schizophrenia) through a battery approach, whereby multiple cognitive constructs can be measured using the same apparatus, enabling comparisons of performance across tasks. CONCLUSION: This battery of tests constitutes an extensive tool package for both model characterisation and pre-clinical drug discovery.This work was supported by the Innovative Medicine Initiative Joint Undertaking under grant agreement no. 115008 of which resources are composed of EFPIA in-kind contribution and financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013). The authors thank Charlotte Oomen for valuable comments on the manuscript.This is the author accepted manuscript. The final version is available from Springer via http://dx.doi.org/10.1007/s00213-015-4007-

Enumeration of Mycobacterium avium subsp. paratuberculosis by quantitative real-time PCR, culture on solid media and optical densitometry

<p>Abstract</p> <p>Background</p> <p>Different approaches are used for determining the number of <it>Mycobacterium avium </it>subsp. <it>paratuberculosis </it>(MAP) cells in a suspension. The majority of them are based upon culture (determination of CFU) or visual/instrumental direct counting of MAP cells. In this study, we have compared the culture method with a previously published F57 based quantitative real-time PCR (F57qPCR) method, to determine their relative abilities to count the number of three different MAP isolates in suspensions with the same optical densities (OD). McFarland turbidity standards were also compared with F57qPCR and culture, due to its frequent inclusion and use in MAP studies.</p> <p>Findings</p> <p>The numbers of MAP in two-fold serial dilutions of isolates with respective OD measurements were determined by F57qPCR and culture. It was found that culture provided lower MAP CFU counts by approximately two log₁₀, compared to F57qPCR. The McFarland standards (as defined for <it>E. coli</it>) showed an almost perfect fit with the enumeration of MAP performed by F57qPCR.</p> <p>Conclusions</p> <p>It is recommended to use culture and/or qPCR estimations of MAP numbers in experiments where all subsequent counts are performed using the same method. It is certainly not recommended the use of culture as the standard for qPCR experiments and <it>vice versa</it>.</p

Comparison of conventional direct and enrichment culture methods for Erysipelothrix spp. from experimentally and naturally infected swine

The objective of the current study was to compare the diagnostic performance of a direct isolation method for Erysipelothrix spp. with a broth-based enrichment technique. Samples were obtained from three sources: 1) experimentally inoculated pigs, 2) porcine tissue samples submitted to the Iowa State University Veterinary Diagnostic Laboratory (Ames, IA), and 3) tissues from condemned carcasses at an abattoir. Culture plates from direct isolation and broth-based technique were evaluated for growth at 24 and 48 hr. Results indicated that the broth enrichment method was markedly more sensitive for the isolation of Erysipelothrix spp. To the authors' knowledge, this is the first comparison of direct culture and broth-based enrichment methods for the isolation of Erysipelothrix spp. Interestingly, in several samples, a Gram-positive bacterium with almost identical growth characteristics to Erysipelothrix spp. was detected and identified as a Vagococcus sp. through 16S ribosomal RNA gene sequencing. The results of this study indicate that the brothbased enrichment method should be used for the isolation of Erysipelothrix spp. from clinical samples with a history suggestive of erysipelas and that Vagococcus spp. is potentially an important differential diagnosis

The Outcome of Phagocytic Cell Division with Infectious Cargo Depends on Single Phagosome Formation

Given that macrophages can proliferate and that certain microbes survive inside phagocytic cells, the question arises as to the post-mitotic distribution of microbial cargo. Using macrophage-like cells we evaluated the post-mitotic distribution of intracellular Cryptococcus yeasts and polystyrene beads by comparing experimental data to a stochastic model. For beads, the post-mitotic distribution was that expected from chance alone. However, for yeast cells the post-mitotic distribution was unequal, implying preferential sorting to one daughter cell. This mechanism for unequal distribution was phagosomal fusion, which effectively reduced the intracellular particle number. Hence, post-mitotic intracellular particle distribution is stochastic, unless microbial and/or host factors promote unequal distribution into daughter cells. In our system unequal cargo distribution appeared to benefit the microbe by promoting host cell exocytosis. Post-mitotic infectious cargo distribution is a new parameter to consider in the study of intracellular pathogens since it could potentially define the outcome of phagocytic-microbial interactions

Predictors of Bacterial Meningitis in Resource-Limited Contexts: An Angolan Case

BACKGROUND: Despite the great morbidity and mortality that childhood bacterial meningitis (BM) is experiencing in Africa, diagnosis of BM in resource-limited contexts is still a challenge. Several algorithms and clinical predictors have been proposed to help physicians in decision-making but a lot of these markers used variables that are calculable only in well-equipped laboratories. Predictors or algorithm based on parameters that can be easily performed in basic laboratories can help significantly in BM diagnosis, even in resource-limited settings, rural hospitals or health centers. RESULTS: This retrospective study examined 145 cerebral-spinal fluid (CSF) specimens from children from 2 months to 14 years. CSF specimens were divided into two groups, according to the presence or not of a clinical diagnosis of BM. For each specimen, CSF aspect, CSF white blood cells (WBC) count, CSF glucose and protein concentration were analyzed and statistical analysis were performed. CSF WBC count ≥10/µl is no more a valuable predictor of BM. CSF protein concentration ≥50 mg/dl has a better sensitivity for BM diagnosis and when used with CSF glucose concentration ≤40 mg/dl, can help to diagnose correctly almost all the BM cases. An algorithm including CSF protein concentration, glucose concentration and WBC count has been proposed to rule out BM and to correctly diagnose it. CONCLUSIONS: In resource-limited health centers, the availability of a combination of easy-to-obtain parameters can significantly help physicians in BM diagnosis. The prompt identification of a BM case can be rapid treated or transferred to adequate structures and can modify the outcome in the patient