Fractal measures of video-recorded trajectories can classify motor subtypes in Parkinson’s disease

[Abstract] Parkinson’s Disease is one of the most prevalent neurodegenerative diseases in the world and affects millions of individuals worldwide. The clinical criteria for classification of motor subtypes in Parkinson’s Disease are subjective and may be misleading when symptoms are not clearly identifiable. A video recording protocol was used to measure hand tremor of 14 individuals with Parkinson’s Disease and 7 healthy subjects. A method for motor subtype classification was proposed based on the spectral distribution of the movement and compared with the existing clinical criteria. Box-counting dimension and Hurst Exponent calculated from the trajectories were used as the relevant measures for the statistical tests. The classification based on the power-spectrum is shown to be well suited to separate patients with and without tremor from healthy subjects and could provide clinicians with a tool to aid in the diagnosis of patients in an early stage of the disease.Brasil. Conselho Nacional de Desenvolvimento Científico e Tecnológico; 306571/2011-0Brasil. Conselho Nacional de Desenvolvimento Científico e Tecnológico; 481414/2012-

Event-related desynchronization during movement attempt and execution in severely paralyzed stroke patients: An artifact removal relevance analysis

The electroencephalogram (EEG) constitutes a relevant tool to study neural dynamics and to develop brain-machine interfaces (BMI) for rehabilitation of patients with paralysis due to stroke. However, the EEG is easily contaminated by artifacts of physiological origin, which can pollute the measured cortical activity and bias the interpretations of such data. This is especially relevant when recording EEG of stroke patients while they try to move their paretic limbs, since they generate more artifacts due to compensatory activity. In this paper, we study how physiological artifacts (i.e., eye movements, motion artifacts, muscle artifacts and compensatory movements with the other limb) can affect EEG activity of stroke patients. Data from 31 severely paralyzed stroke patients performing/attempting grasping movements with their healthy/paralyzed hand were analyzed offline. We estimated the cortical activation as the event-related desynchronization (ERD) of sensorimotor rhythms and used it to detect the movements with a pseudo-online simulated BMI. Automated state-of-the-art methods (linear regression to remove ocular contaminations and statistical thresholding to reject the other types of artifacts) were used to minimize the influence of artifacts. The effect of artifact reduction was quantified in terms of ERD and BMI performance. The results reveal a significant contamination affecting the EEG, being involuntary muscle activity the main source of artifacts. Artifact reduction helped extracting the oscillatory signatures of motor tasks, isolating relevant information from noise and revealing a more prominent ERD activity. Lower BMI performances were obtained when artifacts were eliminated from the training datasets. This suggests that artifacts produce an optimistic bias that improves theoretical accuracy but may result in a poor link between task-related oscillatory activity and BMI peripheral feedback. With a clinically relevant dataset of stroke patients, we evidence the need of appropriate methodologies to remove artifacts from EEG datasets to obtain accurate estimations of the motor brain activity.This study was funded by the fortüne-Program of the University of Tübingen (2422-0-1 and 2452-0-0), the Bundesministerium für Bildung und Forschung BMBF MOTORBIC (FKZ 13GW0053) and AMORSA (FKZ 16SV7754), the Deutsche Forschungsgemeinschaft (DFG), the Basque Government Science Program (EXOTEK: KK 2016/00083). The work of A. Insausti-Delgado was supported by the Basque Government's scholarship for predoctoral students

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

ERICA: prevalência de tabagismo em adolescentes brasileiros

OBJECTIVE To estimate the prevalences of tobacco use, tobacco experimentation, and frequent smoking among Brazilian adolescents. METHODS We evaluated participants of the cross-sectional, nation-wide, school-based Study of Cardiovascular Risks in Adolescents (ERICA), which included 12- to 17-year-old adolescents from municipalities of over 100 thousand inhabitants. The study sample had a clustered, stratified design and was representative of the whole country, its geographical regions, and all 27 state capitals. The information was obtained with self-administered questionnaires. Tobacco experimentation was defined as having tried cigarettes at least once in life. Adolescents who had smoked on at least one day over the previous 30 days were considered current cigarette smokers. Having smoked cigarettes for at least seven consecutive days was an indicator for regular consumption of tobacco. Considering the complex sampling design, prevalences and 95% confidence intervals were estimated according to sociodemographic and socio-environmental characteristics. RESULTS We evaluated 74,589 adolescents. Among these, 18.5% (95%CI 17.7-19.4) had smoked at least once in life, 5.7% (95%CI 5.3-6.2) smoked at the time of the research, and 2.5% (95%CI 2.2-2.8) smoked often. Adolescents aged 15 to 17 years had higher prevalences for all indicators than those aged 12 to 14 years. The prevalences did not differ significantly between sexes. The highest prevalences were found in the South region and the lowest ones, in the Northeast region. Regardless of sex, the prevalences were found to be higher for adolescents who had had paid jobs, who lived with only one parent, and who reported having been in contact with smokers either inside or outside their homes. Female public school adolescents were found to smoke more than the ones from private schools. CONCLUSIONS Tobacco use among adolescents is still a challenge. Intending to reduce the prevalence of tobacco use among young people, especially the ones under socioeconomic vulnerability conditions, Brazil must consolidate and increase effective public health care measures.OBJETIVO Estimar as prevalências de tabagismo, experimentação e fumo frequente em adolescentes brasileiros. MÉTODOS Foram avaliados os participantes do Estudo de Riscos Cardiovasculares em Adolescentes (ERICA), estudo transversal de base escolar e abrangência nacional. Participaram adolescentes de 12 a 17 anos de municípios com mais de 100 mil habitantes. A amostra foi estratificada e conglomerada e tem representatividade nacional, regional e para as 27 capitais. As informações foram obtidas usando-se questionário autopreenchível. Experimentação foi definida como: ter experimentado cigarros alguma vez na vida. Foram considerados fumantes atuais de cigarros aqueles que fumaram pelo menos um dia nos últimos 30 dias. Utilizou-se como indicador de uso frequente de tabaco ter fumado cigarros por pelo menos sete dias seguidos. Considerando-se o desenho complexo da amostra, prevalências e intervalos de confiança de 95% foram estimados segundo características sociodemográficas e socioambientais. RESULTADOS Foram avaliados 74.589 adolescentes; dentre esses, 18,5% (IC95% 17,7-19,4) fumaram pelo menos uma vez na vida, 5,7% (IC95% 5,3-6,2) fumavam no momento da pesquisa e 2,5% (IC95% 2,2-2,8) fumavam com frequência. Adolescentes de 15 a 17 anos tiveram prevalências mais elevadas de todos os indicadores comparados aos de 12 a 14 anos. As prevalências não apresentaram diferenças significativas entre sexos. Maiores prevalências foram observadas na região Sul e menores na região Nordeste. Independentemente de sexo, as prevalências foram maiores para adolescentes que tinham tido trabalho remunerado, nos que não moravam com os dois pais e que referiram ter tido contato com fumante em casa ou fora. Adolescentes do sexo feminino de escolas públicas fumavam mais do que as de escolas privadas. CONCLUSÕES O tabagismo entre adolescentes ainda é um desafio. Visando a redução da prevalência de tabagismo entre jovens, em especial os que se encontram em situação de vulnerabilidade socioeconômica, o Brasil deve consolidar e ampliar medidas de saúde pública efetivas

Biogeographical ancestry is associated with socioenvironmental conditions and infections in a Latin American urban population.

Racial inequalities are observed for different diseases and are mainly caused by differences in socioeconomic status between ethnoracial groups. Genetic factors have also been implicated, and recently, several studies have investigated the association between biogeographical ancestry (BGA) and complex diseases. However, the role of BGA as a proxy for non-genetic health determinants has been little investigated. Similarly, studies comparing the association of BGA and self-reported skin colour with these determinants are scarce. Here, we report the association of BGA and self-reported skin colour with socioenvironmental conditions and infections. We studied 1246 children living in a Brazilian urban poor area. The BGA was estimated using 370,539 genome-wide autosomal markers. Standardised questionnaires were administered to the children's guardians to evaluate socioenvironmental conditions. Infection (or pathogen exposure) was defined by the presence of positive serologic test results for IgG to seven pathogens (Toxocara spp, Toxoplasma gondii, Helicobacter pylori, and hepatitis A, herpes simplex, herpes zoster and Epstein-Barr viruses) and the presence of intestinal helminth eggs in stool samples (Ascaris lumbricoides and Trichiuris trichiura). African ancestry was negatively associated with maternal education and household income and positively associated with infections and variables, indicating poorer housing and living conditions. The self-reported skin colour was associated with infections only. In stratified analyses, the proportion of African ancestry was associated with most of the outcomes investigated, particularly among admixed individuals. In conclusion, BGA was associated with socioenvironmental conditions and infections even in a low-income and highly admixed population, capturing differences that self-reported skin colour miss. Importantly, our findings suggest caution in interpreting significant associations between BGA and diseases as indicative of the genetic factors involved

Behavior of the thermal diffusivity of native and oxidized human low-density lipoprotein solutions studied by the Z-scan technique

Modifications in low-density lipoprotein (LDL) have emerged as a major pathogenic factor of atherosclerosis, which is the main cause of morbidity and mortality in the western world. Measurements of the heat diffusivity of human LDL solutions in their native and in vitro oxidized states are presented by using the Z-Scan (ZS) technique. Other complementary techniques were used to obtain the physical parameters necessary to interpret the optical results, e. g., pycnometry, refractometry, calorimetry, and spectrophotometry, and to understand the oxidation phase of LDL particles. To determine the sample's thermal diffusivity using the thermal lens model, an iterative one-parameter fitting method is proposed which takes into account several characteristic ZS time-dependent and the position-dependent transmittance measurements. Results show that the thermal diffusivity increases as a function of the LDL oxidation degree, which can be explained by the increase of the hydroperoxides production due to the oxidation process. The oxidation products go from one LDL to another, disseminating the oxidation process and caring the heat across the sample. This phenomenon leads to a quick thermal homogenization of the sample, avoiding the formation of the thermal lens in highly oxidized LDL solutions. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.JBO.17.10.105003]National Counsel for Scientific and Technological Development (CNPq)National Counsel for Scientific and Technological Development (CNPq)Sao Paulo Research Foundation (FAPESP)Sao Paulo Research Foundation (FAPESP)National Institute of Science and Technology of Complex Fluid (INCTFCx)National Institute of Science and Technology of Complex Fluid (INCT-FCx)Redoxoma (INCT-Redoxoma)Redoxoma (INCTRedoxoma

KALE SEEDLINGS PRODUCTION IN DIFFERENT SUBSTRATES, CELL VOLUMES AND PROTECTED ENVIRONMENTS

ABSTRACT: The kale is a brassica, this vegetable presents importance on nutritional and economic patterns. The present study aimed to evaluate the effect of different substrates, trays and protected environment in the formation of kale seedlings. The experiment was conducted in two greenhouses located at the State University of Mato Grosso do Sul -MS. The first environment consisted of an agricultural greenhouse with polyethylene film cover, while the second was an agricultural nursery with monofilament screen and mesh to offer 50% of shading. In each protected environment were used 72 and 128 cells tray and six different compositions of substrates with organic material based on cassava branches (CB) and cattle manure (CM): 1) 100% CM; 2) 20% CM + 80% CB; 3) 40% CB + 60% CM; 4) 60% CB + 40% CM; 5) 80% CB + 20% and CM; 6) 100% CB. The seedlings were evaluated according to the parameters: dry mass of seedlings, stem diameter and plant height. The agricultural nursery was the most suitable for the formation of kale seedlings, with 72 cells tray and the substrate composed of organic matter with 20% of cassava branches and 80% of cattle manure

Advantages of treating sponge-gourd waste by mechanical refining on the properties of fiber-based poly(butylene adipate-co-terephthalate)/polylactide biocomposites

Abstract This study compares the morphology, thermal, and dynamic-mechanical properties of composites based on polybutylene adipate terephthalate/polylactide biocomposites with sponge gourd waste treated code as R, and non-treated sponge gourd, coded as NR, by mechanical disc refining after milled process. Extrusion followed by compression molding was used to produce biocomposites with fiber contents of 0, 2.5, 5, 10, and 15% wt/wt for R and NR sponge gourd fibers. Scanning electron microscopy analysis reveals that NR has the morphology of a rigid tubular shape, whereas R is a thinner, twisted, and fibrillated fiber. Regardless of the type of sponge gourd fiber used, the thermal stability of the composite decreases as the sponge gourd content increases. At 25°C, the biocomposite with 10%wt/wt R fiber has the highest storage modulus value. The comparison of Tangent peak values reveals that the presence of sponge gourd fibers reduces the energy dissipation of the biocomposites. The analysis of the loss modulus at 25°C reveals that R fiber contributes more to the reduction of energy dissipation of the biocomposites than NR. Furthermore, the Cole-Cole plot shows that R and NR fibers are dispersed and do not significantly change the homogeneity of the biopolymer systems

Overexpression of KLC2 due to a homozygous deletion in the non-coding region causes SPOAN syndrome

SPOAN syndrome is a neurodegenerative disorder mainly characterized by spastic paraplegia, optic atrophy and neuropathy (SPOAN). Affected patients are wheelchair bound after 15 years old, with progressive joint contractures and spine deformities. SPOAN patients also have sub normal vision secondary to apparently non-progressive congenital optic atrophy. A potential causative gene was mapped at 11q13 ten years ago. Here we performed next-generation sequencing in SPOAN-derived samples. While whole-exome sequencing failed to identify the causative mutation, whole-genome sequencing allowed to detect a homozygous 216-bp deletion (chr11.hg19:g.66,024,557_66,024,773del) located at the non-coding upstream region of the KLC2 gene. Expression assays performed with patient’s fibroblasts and motor neurons derived from SPOAN patients showed KLC2 overexpression. Luciferase assay in constructs with 216-bp deletion confirmed the overexpression of gene reporter, varying from 48 to 74%, as compared with wild-type. Knockdown and overexpression of klc2 in Danio rerio revealed mild to severe curly-tail phenotype, which is suggestive of a neuromuscular disorder. Overexpression of a gene caused by a small deletion in the non-coding region is a novel mechanism, which to the best of our knowledge, was never reported before in a recessive condition. Although the molecular mechanism of KLC2 up-regulation still remains to be uncovered, such example adds to the importance of non-coding regions in human pathologyFil: Melo, Uira S.. Universidade de Sao Paulo; BrasilFil: Macedo Souza, Lucia I.. Universidade de Sao Paulo; BrasilFil: Figueiredo, Thalita. Federal University of Paraiba; Brasil. Paraiba State University; BrasilFil: Muotri, Alysson R. University of California at San Diego; Estados UnidosFil: Gleeson, Joseph G.. The Rockefeller University; Estados UnidosFil: Coux, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Armas, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Calcaterra, Nora Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Kitajima, João P.. Mendelics Genomic Analysis; BrasilFil: Amorim, Simone. Universidade de Sao Paulo; BrasilFil: Olávio, Thiago R.. Universidade de Sao Paulo; BrasilFil: Griesi Oliveira, Karina. Universidade de Sao Paulo; BrasilFil: Coatti, Giuliana C.. Universidade de Sao Paulo; BrasilFil: Rocha, Clarissa R.R. Universidade de Sao Paulo; BrasilFil: Martins Pinheiro, Marinalva. Universidade de Sao Paulo; BrasilFil: Menck, Carlos F.M.. Universidade de Sao Paulo; BrasilFil: Zaki, Maha S.. National Research Center. EL Cairo; EgiptoFil: Kok, Fernando. Universidade de Sao Paulo; BrasilFil: Zatz, Mayana. Universidade de Sao Paulo; BrasilFil: Santos, Silvana. Federal University of Paraiba; Brasil. Paraiba State University; Brasi