cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinct Cytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introduce cyTRON, a stand-alone Cytoscape app, and cyTRON/JS, a web application which employs the functionalities of Cytoscape/JS. cyTRON was developed in Java; the code is available at https://github.com/BIMIB-DISCo/cyTRON and on the Cytoscape App Store http://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available at https://github.com/BIMIB-DISCo/cyTRON-js and the tool is accessible from https://bimib.disco.unimib.it/cytronjs/welcome

Loxosceles gaucho spider venom and its sphingomyelinase fraction trigger the main functions of human and rabbit platelets

Loxosceles venoms can promote severe local and systemic damages. We have previously reported that Loxosceles gaucho spider venom causes a severe early thrombocytopenia in rabbits. Herein, we investigated the in vitro effects of this venom and its sphingomyelinase fraction on the main functions of platelets. Whole venom and its fraction induced aggregation of both human and rabbit platelets. Aggregation was dependent of plasma component(s) but independent of venom-induced lysophosphatidic acid generation. There was no increase in the levels of lactate dehydrogenase during platelet aggregation, ruling out the possibility of platelet lysis. The increased expression of ligand-induced binding site 1 (LIBS1) induced by L. gaucho venom and its sphingomyelinase fraction, as well as of P-selectin by the whole venom, evidenced the activation state of both human and rabbit platelets. Adhesion assays showed an irregular response when platelets were exposed to the whole venom, whereas the sphingomyelinase fraction induced a dose-dependent increase in the platelet adhesion to collagen. These findings evidence that L. gaucho venom and its sphingomyelinase fraction trigger adhesion, activation, and aggregation of both human and rabbit platelets. Thus, this work justifies the use of rabbits to investigate Loxosceles venom-induced platelet disturbances, and it also supports research on the role of platelets in the pathogenesis of loxoscelism.Fil: Tavares, Flávio L.. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Peichoto, María Elisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Rangel, Danieli de Morais. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Barbaro, Kátia Cristina. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Cirillo, Maria Cristina. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Santoro, Marcelo Larami. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; BrasilFil: Sano Martins, Ida S.. Governo do Estado de Sao Paulo. Secretaria da Saude. Instituto Butantan; Brasi

Double In Situ Approach for the Preparation of Polymer Nanocomposite with Multi-functionality

A novel one-step synthetic route, the double in situ approach, is used to produce both TiO2nanoparticles and polymer (PET), and simultaneously forming a nanocomposite with multi-functionality. The method uses the release of water during esterification to hydrolyze titanium (IV) butoxide (Ti(OBu)4) forming nano-TiO2in the polymerization vessel. This new approach is of general significance in the preparation of polymer nanocomposites, and will lead to a new route in the synthesis of multi-functional polymer nanocomposites

Detalhamento de fitofisionomias do bioma Cerrado a partir de imagens contraste sazonal MODIS EVI.

Diante da necessidade de se conhecer em maior detalhe as variações fitofisionômicas do bioma Cerrado, para, entre outros, quantificarmos variações na sua biomassa e, em particular, determinar estoques de CO2 na cobertura vegetal natural, este trabalho teve por objetivo detalhar possíveis variações na classe Savana Arborizada, a qual, além de ser a de maior representatividade, apresenta elevada complexidade estrutural e funcional. Especificamente, avaliamos a resposta sazonal das imagens MODIS EVI (enhanced vegetation index), tendo por base a hipótese de que diferentes fácies da fitofisionomia Savana Arborizada respondem de forma distinta a conspícua sazonalidade do bioma Cerrado, i.e. quanto maior a densidade arbórea, menor o contraste sazonal nos valores índices de vegetação.Na publicação: Laerte Guimarães Ferreira

IL-4-secreting CD4+ T cells are crucial to the development of CD8+ T-cell responses against malaria liver stages.

CD4+ T cells are crucial to the development of CD8+ T cell responses against hepatocytes infected with malaria parasites. In the absence of CD4+ T cells, CD8+ T cells initiate a seemingly normal differentiation and proliferation during the first few days after immunization. However, this response fails to develop further and is reduced by more than 90%, compared to that observed in the presence of CD4+ T cells. We report here that interleukin-4 (IL-4) secreted by CD4+ T cells is essential to the full development of this CD8+ T cell response. This is the first demonstration that IL-4 is a mediator of CD4/CD8 cross-talk leading to the development of immunity against an infectious pathogen

Properties of the chiral spin liquid state in generalized spin ladders

We study zero temperature properties of a system of two coupled quantum spin chains subject to fields explicitly breaking time reversal symmetry and parity. Suitable choice of the strength of these fields gives a model soluble by Bethe Ansatz methods which allows to determine the complete magnetic phase diagram of the system and the asymptotics of correlation functions from the finite size spectrum. The chiral properties of the system for both the integrable and the nonintegrable case are studied using numerical techniques.Comment: 19 pages, 9eps figures, Late

The Heisenberg model on the 1/5-depleted square lattice and the CaV4O9 compound

We investigate the ground state structure of the Heisenberg model on the 1/5-depleted square lattice for arbitrary values of the first- and second-neighbor exchange couplings. By using a mean-field Schwinger-boson approach we present a unified description of the rich ground-state diagram, which include the plaquette and dimer resonant-valence-bond phases, an incommensurate phase and other magnetic orders with complex magnetic unit cells. We also discuss some implications of ours results for the experimental realization of this model in the CaV4O9 compound.Comment: 4 pages, Latex, 7 figures included as eps file

Implantação e ativação de viveiro na comunidade Água Boa 2, município de Rio Pardo de Minas, MG.

Resumo - A evasão sazonal de filhos de agricultores é um evento frequente na comunidade de Água Boa 2 na busca de trabalho fora do município de Rio Pardo de Minas, como colhedores de café no Sul de Minas e no Estado de São Paulo ou em eucaliptais na própria região. Tendo uma área de cultivo de cerca de três hectares, a agricultura não é mais suficiente para gerar alimento e sustento da família, obrigando a busca de outras fontes de renda. O extrativismo de fibras, frutos, artesanato, além do carvão vegetal é também uma alternativa de renda. Algumas mulheres preferem não ter entes da família afastados por meses para trabalhar, enquanto outras acompanham os maridos com seus filhos para o trabalho em outras regiões a fim de reforçar a renda familiar, no período de maio a agosto. A renda certa é ensejada por jovens também, para aquisição de bens como celular, eletro-portátil ou moto, notando que oportunidades são restritas quando permanecem na comunidade, comercializando os produtos da roça ou do extrativismo ou como assalariado local. Este relato trata do início da construção do segundo viveiro em março de 2012 e de sua ativação em janeiro de 2014 como uma alternativa de emprego e renda que a comunidade vislumbrou, planejou e se capacitou a partir de 2007. O primeiro viveiro construído com recurso de doação de bazares, com o objetivo de obter renda, produzir mudas para reflorestar nascentes e obter mudas para plantio nos quintais, foi inativado devido insegurança, falta de registro e de responsável técnico. As dificuldades de instalação de um sistema de abastecimento de água para irrigação foi, dentre outras, a causa do atraso na ativação do segundo viveiro e do grupo de jovens. Por outro lado, em meio às dificuldades e entraves, a comunidade vem crescendo e sendo fortalecido pelo movimento de união em defesa da nascente. Abstract - The seasonal evasion of farmers? sons is a frequent event within the Community of Agua Boa 2, seeking for job outside the municipality of Rio Pardo de Minas, as, coffee harvesters in the South of Minas Gerais and São Paulo State or eucalyptus plantation. Having about three hectares for cultivation area, agriculture is not enough for feeding and supporting the family, forcing to search for other means for their income. The extraction of fiber, fruits, handicrafts, besides charcoal from native vegetation is also an alternative for survival. Some women prefer not to have ones from the family away for months to work, while others follow their husbands with their children to work in other regions to reinforce family income during the period May to August. An assured income is also desired by young people to purchase goods such as mobile phones, portable devices or motorcycles, noting that opportunities are scarce by staying in the community, selling the products from the country or extractivism, or as a local employee. This report deals with the start of construction of the second nursery in March 2012 and its activation in January 2014 as an alternative employment and income that the community glimpsed, planned and trained since 2007. The first nursery built using donations of bazaars, with the aim to earn an income, produce seedlings for reforestation springs and get seedlings for planting in backyards, was inactivated due to insecurity, lack of registration and technical officer. The problem of installing a system of water supply for irrigation was, among others, the cause of the delay in the activation of the second nursery and the youth group. On the other hand, in the midst of difficulties and obstacles, the community is growing and being strengthened by the union movement in defense of the springs

Técnicas avançadas de sensoriamento remoto aplicadas ao estudo de mudanças climáticas e ao funcionamento dos ecossistemas amazônicos.

Este artigo se propõe a apresentar exemplos de questões científicas que puderam ser respondidas no contexto do Projeto LBA (Large Sale Biosphere-Atmosphere Experiment in Amazonia) graças à contribuição de informações derivadas de sensoriamento remoto. Os métodos de sensoriamento remoto permitem integrar informações sobre os vários processos físicos e biológicos em diferentes escalas de tempo e espaço. Nesse artigo, são enfatizados aqueles avanços de conhecimento que jamais seriam alcançados sem a concorrência da informação derivada de sensoriamento