Comparing ICA-based and single-trial topographic ERP analyses.

Single-trial analysis of human electroencephalography (EEG) has been recently proposed for better understanding the contribution of individual subjects to a group-analysis effect as well as for investigating single-subject mechanisms. Independent Component Analysis (ICA) has been repeatedly applied to concatenated single-trial responses and at a single-subject level in order to extract those components that resemble activities of interest. More recently we have proposed a single-trial method based on topographic maps that determines which voltage configurations are reliably observed at the event-related potential (ERP) level taking advantage of repetitions across trials. Here, we investigated the correspondence between the maps obtained by ICA versus the topographies that we obtained by the single-trial clustering algorithm that best explained the variance of the ERP. To do this, we used exemplar data provided from the EEGLAB website that are based on a dataset from a visual target detection task. We show there to be robust correspondence both at the level of the activation time courses and at the level of voltage configurations of a subset of relevant maps. We additionally show the estimated inverse solution (based on low-resolution electromagnetic tomography) of two corresponding maps occurring at approximately 300 ms post-stimulus onset, as estimated by the two aforementioned approaches. The spatial distribution of the estimated sources significantly correlated and had in common a right parietal activation within Brodmann's Area (BA) 40. Despite their differences in terms of theoretical bases, the consistency between the results of these two approaches shows that their underlying assumptions are indeed compatible.

Absence of association between specific common variants of the obesity-related FTO gene and psychological and behavioral eating disorder phenotypes.

Extensive population-based genome-wide association studies have identified an association between the FTO gene and BMI; however, the mechanism of action is still unknown. To determine whether FTO may influence weight regulation through psychological and behavioral factors, seven single-nucleotide polymorphisms (SNPs) of the FTO gene were genotyped in 1,085 individuals with anorexia nervosa (AN) and 677 healthy weight controls from the international Price Foundation Genetic Studies of Eating Disorders. Each SNP was tested in association with eating disorder phenotypes and measures that have previously been associated with eating behavior pathology: trait anxiety, harm-avoidance, novelty seeking, impulsivity, obsessionality, compulsivity, and concern over mistakes. After appropriate correction for multiple comparisons, no significant associations between individual FTO gene SNPs and eating disorder phenotypes or related eating behavior pathology were identified in cases or controls. Thus, this study found no evidence that FTO gene variants associated with weight regulation in the general population are associated with eating disorder phenotypes in AN participants or matched controls. © 2011 Wiley-Liss, Inc.

Multiway Array Decomposition Analysis of EEGs in Alzheimer’s Disease

Methods for the extraction of features from physiological datasets are growing needs as clinical investigations of Alzheimer’s disease (AD) in large and heterogeneous population increase. General tools allowing diagnostic regardless of recording sites, such as different hospitals, are essential and if combined to inexpensive non-invasive methods could critically improve mass screening of subjects with AD. In this study, we applied three state of the art multiway array decomposition (MAD) methods to extract features from electroencephalograms (EEGs) of AD patients obtained from multiple sites. In comparison to MAD, spectral-spatial average filter (SSFs) of control and AD subjects were used as well as a common blind source separation method, algorithm for multiple unknown signal extraction (AMUSE). We trained a feed-forward multilayer perceptron (MLP) to validate and optimize AD classification from two independent databases. Using a third EEG dataset, we demonstrated that features extracted from MAD outperformed features obtained from SSFs AMUSE in terms of root mean squared error (RMSE) and reaching up to 100% of accuracy in test condition. We propose that MAD maybe a useful tool to extract features for AD diagnosis offering great generalization across multi-site databases and opening doors to the discovery of new characterization of the disease.

An efficient algorithm to perform multiple testing in epistasis screening

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn’s disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron(tm) Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn’s disease (CD) data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn’s disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations.

A Canonical Genetic Algorithm for Blind Inversion of Linear Channels

It is well known the relationship between source separation and blind deconvolution: If a filtered version of an unknown i.i.d. signal is observed, temporal independence between samples can be used to retrieve the original signal, in the same manner as spatial independence is used for source separation. In this paper we propose the use of a Genetic Algorithm (GA) to blindly invert linear channels. The use of GA is justified in the case of small number of samples, where other gradient-like methods fails because of poor estimation of statistics.

Aplicació del Value Stream Map (VSM) en un sistema de producció de feltres insonoritzants per a l'automòbil

Actualment en el sector industrial, les organitzacions tenen el repte d'optimitzar els seus sistemes productius per a millorar en quant a preu, qualitat i nivell de servei i poder adaptar-se a les exigències dels clients (excel·lència productiva). El present anàlisi, es basa en l'optimització d'una cadena de producció de feltres insonoritzants per a l'automòbil a través de l'eliminació de les pèrdues existents (operacions que no aporten valor afegit al producte final). Per dur-ho a terme, la metodologia emprada és el Value Stream Map (VSM). El VSM és una tècnica desenvolupada sota el model de gestió de la producció Lean Manufacturing, molt visual i entenedora, permet visualitzar i entendre l'estat actual d'un procés. Aquesta, abarca a tota la organització, i te per objectiu recolzar-la en el procés de redisseny dels seus entorns productius per assolir un estat futur millor que possibiliti obtenir resultats en un periode curt de temps. L'objectiu principal de l'estudi, és aplicar l'eina VSM com a mètode per a l'eliminació de les mudes o malbarataments que impedeix la consecució d'una cadena Lean amb el cas concret d'un sistema productiu de feltres insonoritzants. En la primera part del projecte s'introdueix al lector en la teoria del pensament Lean (quins principis té i quins són els objectius) com a marc teòric. Aquí es detalla el procediment, així com les característiques per a la correcta elaboració del VSM actual, per al seu corresponent anàlisi i per a la seva representació del estat futur. En una segona part del projecte, s'exposen les etapes que constitueixen la cadena de producció d'estudi i es duu a terme l'elaboració del Value Stream Map, on es posen de manifest les ineficiències del flux que conformen la línia de producció. Per últim s'analitzen els fluxes, s'identifiquen les pèrdues de la cadena, i a partir d'aquests, es dissenyen i es proposen projectes i accions que permitin establir línies d'actuació per a un millor estat futur. L'estudi ha permés demostrar la validesa del VSM com a eina per a facilitar la consecució i assoliment de millores en la productivitat, competitivitat i rendibilitat dels diferents processos de l'organització en la línia de fabricació de feltres insonoritzats.

Flea infestation reduces the life span of the common vole.

Parasitism is often a source of variation in host's fitness components. Understanding and estimating its relative importance for fitness components of hosts is fundamental from physiological, ecological and evolutionary perspectives. Host-parasite studies have often reported parasite-induced reduction of host fecundity, whereas the effect of parasitism on host survival has been largely neglected. Here, we experimentally investigated the effect of infestation by rat fleas (Nosopsyllus fasciatus) on the life span of wild-derived male common voles (Microtus arvalis) bred in captivity. We found that the mean life span of parasitized voles was reduced by 36% compared to control voles. Parasitized voles had a smaller body size, but a relatively larger heart and spleen than control voles. These results indicate an effect of flea infestation on host life span and our findings strongly suggest that ectoparasites should be taken into account in the studies of host population dynamics.

Microsatellites for genetic studies and breeding programs in common bean

Twenty microsatelitte loci were identified and characterized in common bean. Microsatellites were tested in 14 genotypes. The allele number ranged from 1 to 3, and the polymorphism information content (PIC) was between 0.14 and 0.65. These polymorphic markers are available to be used for breeding programs.

Methods for Estimating Annual Exceedance-Probability Discharges for Streams in Iowa, Based on Data through Water Year 2010, TR-519, 2013

A statewide study was performed to develop regional regression equations for estimating selected annual exceedance- probability statistics for ungaged stream sites in Iowa. The study area comprises streamgages located within Iowa and 50 miles beyond the State’s borders. Annual exceedanceprobability estimates were computed for 518 streamgages by using the expected moments algorithm to fit a Pearson Type III distribution to the logarithms of annual peak discharges for each streamgage using annual peak-discharge data through 2010. The estimation of the selected statistics included a Bayesian weighted least-squares/generalized least-squares regression analysis to update regional skew coefficients for the 518 streamgages. Low-outlier and historic information were incorporated into the annual exceedance-probability analyses, and a generalized Grubbs-Beck test was used to detect multiple potentially influential low flows. Also, geographic information system software was used to measure 59 selected basin characteristics for each streamgage. Regional regression analysis, using generalized leastsquares regression, was used to develop a set of equations for each flood region in Iowa for estimating discharges for ungaged stream sites with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities, which are equivalent to annual flood-frequency recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years, respectively. A total of 394 streamgages were included in the development of regional regression equations for three flood regions (regions 1, 2, and 3) that were defined for Iowa based on landform regions and soil regions. Average standard errors of prediction range from 31.8 to 45.2 percent for flood region 1, 19.4 to 46.8 percent for flood region 2, and 26.5 to 43.1 percent for flood region 3. The pseudo coefficients of determination for the generalized leastsquares equations range from 90.8 to 96.2 percent for flood region 1, 91.5 to 97.9 percent for flood region 2, and 92.4 to 96.0 percent for flood region 3. The regression equations are applicable only to stream sites in Iowa with flows not significantly affected by regulation, diversion, channelization, backwater, or urbanization and with basin characteristics within the range of those used to develop the equations. These regression equations will be implemented within the U.S. Geological Survey StreamStats Web-based geographic information system tool. StreamStats allows users to click on any ungaged site on a river and compute estimates of the eight selected statistics; in addition, 90-percent prediction intervals and the measured basin characteristics for the ungaged sites also are provided by the Web-based tool. StreamStats also allows users to click on any streamgage in Iowa and estimates computed for these eight selected statistics are provided for the streamgage.

Method for evaluation of root hairs of common bean genotypes

The objective of this work was to test a simple method for root hair evaluation of 21 common bean (Phaseolus vulgaris) genotypes, most of them used in breeding programs in Brazil. Hairs of basal and primary roots of 5-day old seedlings, produced on germination paper with no phosphorus addition, were visually evaluated by a rating scale after staining with 0.05% trypan blue. The method reveals variability among the genotypes, and the standard error of the mean is relatively low.

Low immunoglobulin levels in patients with cystic fibrosis: reduced inflammation or sign of common variable immunodeficiency syndrome?

Introduction: In children with cystic fibrosis (CF), low immunoglobulin (IgG) levels have been reported to be associated with significantly less severe lung disease. However, decreased IgG can be a sign for common variable immunodeficiency (CVID) and affect clinical outcome. The aim of this study was to analyze clinical and serological data of patients having low IgG levels in routine blood tests at annual assessment, particularly their antibody response to polysaccharide antigens. Method: Retrospective chart review of demographic data of CF patients followed at the pediatric CF clinic throughout 2009. Clinical parameters (genotype, pancreas sufficiency, FEV1), presence of Pseudomonas aeruginosa (PA) and number of exacerbations per year were correlated with immunoglobulin and vaccination antibodies levels (antibodies to pneumococcal serotypes 14, 19, 23, 1, 5 and 7F measured by enzyme-linked immune-sorbent assay). Results: 4 out of 60 patients (6.7%) had lower IgG-levels for age. Ages ranged from 1 year 8 months to 11 years, 2 boys, 2 girls. Three patients were delF508 homozygotes, one heterozygote composite delF508/G542X. All were pancreatic insufficient. FEV1 ranged from 74 to 108%. One patient never had colonization by PA, 2 had intermittent PA colonization and one was chronically infected. After conjugated vaccination all patients had protective antibodies against serotypes 14, 19, 23F. For serotypes not included in the vaccine, only one patient had protective titers for 1 out of 3 serotypes. None of the patients had received unconjugated pneumococcal vaccine. There was no significant clinical difference in FEV1, PA colonization or number of exacerbations according to IgG and vaccination antibody levels. Conclusion: Cystic Fibrosis patients with low immunoglobulin levels have normal antibody response to protein antigens. However, despite recurrent infections, there seems to be delayed or deficient antibody response to polysaccharide antigens. Prospective studies are needed to evaluate the development of polysaccharide antibody responses in CF-patients to monitor for CVID. With early detection of CF by newborn screening program, long term follow up could be started early in childhood.

Root traits of common bean genotypes used in breeding programs for disease resistance

The objective of this work was to assess root traits of 19 common bean genotypes, used in breeding programs for disease resistance. Genotypes DOR 364 and G 19833 were used as deep and shallow basal root checks, respectively. The number of whorls and basal roots were assessed on five-day old seedlings grown in germination paper. Growth pouch studies were conducted to evaluate basal root gravitropism and lateral root length from primary roots, in seven-day old seedlings. The following root gravitropic traits were estimated: basal growth angle, shallow basal root length (localized in the top 2 cm), and relative shallow basal root growth. Number of whorls varied from 1.47 to 3.07, and number of basal roots ranged from 5.67 (genotype TO) to 12.07 (cultivar Jalo MG-65). Cultivars BRS MG Talismã, Carioca, BRS Pioneiro, and Diamante Negro exhibited shallow basal roots, while genotypes Vi-10-2-1, TU, AB 136, and México 54 showed deep basal roots. Cultivar Jalo MG-65 showed more lateral roots from the primary root than the other genotypes. Genotypes used on common bean breeding programs for disease resistance have great variability on basal and primary root traits.

Liberties and constraints of the normative approach to evaluation and decision in forensic science: a discussion towards overcoming some common misconceptions

At a time when disciplined inference and decision making under uncertainty represent common aims to participants in legal proceedings, the scientific community is remarkably heterogenous in its attitudes as to how these goals ought to be achieved. Probability and decision theory exert a considerable influence, and we think by all reason rightly do so, but they go against a mainstream of thinking that does not embrace-or is not aware of-the 'normative' character of this body of theory. It is normative, in the sense understood in this article, in that it prescribes particular properties, typically (logical) coherence, to which reasoning and decision making ought to conform. Disregarding these properties can result in diverging views which are occasionally used as an argument against the theory, or as a pretext for not following it. Typical examples are objections according to which people, both in everyday life but also individuals involved at various levels in the judicial process, find the theory difficult to understand and to apply. A further objection is that the theory does not reflect how people actually behave. This article aims to point out in what sense these examples misinterpret the analytical framework in its normative perspective. Through examples borrowed mostly from forensic science contexts, it is argued that so-called intuitive scientific attitudes are particularly liable to such misconceptions. These attitudes are contrasted with a statement of the actual liberties and constraints of probability and decision theory and the view according to which this theory is normative.