The genetic landscape of a cell.

A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function.

Awareness of stroke risk factors and warning signs in southern Brazil.

Objective: To evaluate the knowledge about stroke in Caxias do Sul.

Method: A closed-ended, self-administered questionnaire was used to assess the knowledge about stroke among residents of Caxias do Sul. In order to verify variables associated to lack of knowledge we defined three main end points: (1) the inability to recognize that stroke is a disease that affects the brain; (2) insufficient knowledge of risk factors; (3) insufficient knowledge of signs and symptoms of acute stroke.

Convolutional networks can learn to generate affinity graphs for image segmentation.

Many image segmentation algorithms first generate an affinity graph and then partition it. We present a machine learning approach to computing an affinity graph using a convolutional network (CN) trained using ground truth provided by human experts. The CN affinity graph can be paired with any standard partitioning algorithm and improves segmentation accuracy significantly compared to standard hand-designed affinity functions.

[A furoncular ankle cellulitis in a teenager with a difference: Dermatobia hominis].

We report a case of botfly myiasis presenting as an ankle cellulitis in a teenager returning from Guyana. Main clinical features and therapeutic approaches are described.

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation.

Next generation software for functional trend analysis.

Unlabelled: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features. For example, enrichment analysis can now be performed within multiple gene- and protein-naming systems.

Transmission dynamics and economics of rabies control in dogs and humans in an African city.

Human rabies in developing countries can be prevented through interventions directed at dogs. Potential cost-savings for the public health sector of interventions aimed at animal-host reservoirs should be assessed. Available deterministic models of rabies transmission between dogs were extended to include dog-to-human rabies transmission.

Development and validation of a simple questionnaire for the identification of hereditary breast cancer in primary care.

Background: Breast cancer is a significant public health problem worldwide and the development of tools to identify individuals at-risk for hereditary breast cancer syndromes, where specific interventions can be proposed to reduce risk, has become increasingly relevant. A previous study in Southern Brazil has shown that a family history suggestive of these syndromes may be prevalent at the primary care level. Development of a simple and sensitive instrument, easily applicable in primary care units, would be particularly helpful in underserved communities in which identification and referral of high-risk individuals is difficult.

Quantitative phenotyping via deep barcode sequencing.

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput.

Population prevalence of hereditary breast cancer phenotypes and implementation of a genetic cancer risk assessment program in southern Brazil.

In 2004, a population-based cohort (the Núcleo Mama Porto Alegre - NMPOA Cohort) was started in Porto Alegre, southern Brazil and within that cohort, a hereditary breast cancer study was initiated, aiming to determine the prevalence of hereditary breast cancer phenotypes and evaluate acceptance of a genetic cancer risk assessment (GCRA) program. Women from that cohort who reported a positive family history of cancer were referred to GCRA. Of the 9218 women enrolled, 1286 (13.

Electronic properties of potassium doped FePc from electron energy-loss spectroscopy.

We have studied the electronic structure of potassium doped iron phthalocyanine (FePc) phases using electron energy-loss spectroscopy. The electronic excitation spectrum of FePc is rather complex and comprises both pi-pi( *) transitions of the phthalocyanine ligand and transitions that involve the Fe 3d orbitals. This allows deeper insight into the orbital occupation in FePc.

Applications of responsiveness to intervention and the speech-language pathologist in elementary school settings.

This article addresses ways in which speech-language pathologists can play a proactive and substantive part in school-wide language and reading disability prevention and intervention efforts within the responsiveness to intervention framework. Within a collaborative working paradigm, specific student-focused instructional targets are presented in the areas of oral language, metacognition, and reading comprehension. A discussion of professional development focuses on enhancing teacher-student communication interaction, a critical yet often undervalued component of teacher training.

Estimates of the optimum dietary ratio of standardized ileal digestible valine to lysine for eight to twenty-five kilograms of body weight pigs.

Valine is among the limiting AA in low protein diets for pigs, but data are currently lacking for empirical requirement studies. Therefore, 2 growth assays and 1 N-balance trial were conducted to determine the Val requirement of weaned pigs (8 to 25 kg of BW) expressed as the ratio of standardized ileal digestible (SID) Val to Lys. In Exp.

Estimation of the optimum ratio of standardized ileal digestible isoleucine to lysine for eight- to twenty-five-kilogram pigs in diets containing spray-dried blood cells or corn gluten feed as a protein source.

Two growth assays and 1 N balance trial were conducted to determine the standardized ileal digestible (SID) Ile:Lys ratio in 8- to 25-kg pigs using spray-dried blood cells or corn gluten feed as a protein source. In Exp. 1, 48 individually penned pigs (initial BW = 7.

Consistency of self-reported first-degree family history of cancer in a population-based study.

The aim of this study was to assess the prevalence and consistency of self-reported family history of cancer among first-degree relatives (FDR) in a population-based study. Women at primary care units (PCU) were submitted to a questionnaire about cancer family history. Consistency of the report was determined by comparing self-reported history at the PCU to data from subsequent genetic evaluations and/or cancer confirmatory documents.

Literature-curated protein interaction datasets.

High-quality datasets are needed to understand how global and local properties of protein-protein interaction, or 'interactome', networks relate to biological mechanisms, and to guide research on individual proteins. In an evaluation of existing curation of protein interaction experiments reported in the literature, we found that curation can be error-prone and possibly of lower quality than commonly assumed.

An empirical framework for binary interactome mapping.

Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps.

An experimentally derived confidence score for binary protein-protein interactions.

Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of individual interactions reported in interaction mapping experiments. To provide a standardized confidence-scoring method that can be applied to tens of thousands of protein interactions, we have developed an interaction tool kit consisting of four complementary, high-throughput protein interaction assays.

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity.

MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks that regulate miRNA expression remain largely unexplored. Here, we present the first genome-scale Caenorhabditis elegans miRNA regulatory network that contains experimentally mapped transcriptional TF --> miRNA interactions, as well as computationally predicted post-transcriptional miRNA --> TF interactions.

Chemical substructures that enrich for biological activity.

Motivation: Certain chemical substructures are present in many drugs. This has led to the claim of 'privileged' substructures which are predisposed to bioactivity. Because bias in screening library construction could explain this phenomenon, the existence of privilege has been controversial.

Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.

Emerging metabolomic tools have created the opportunity to establish metabolic signatures of myocardial injury. We applied a mass spectrometry-based metabolite profiling platform to 36 patients undergoing alcohol septal ablation treatment for hypertrophic obstructive cardiomyopathy, a human model of planned myocardial infarction (PMI). Serial blood samples were obtained before and at various intervals after PMI, with patients undergoing elective diagnostic coronary angiography and patients with spontaneous myocardial infarction (SMI) serving as negative and positive controls, respectively.

High-quality binary protein interaction map of the yeast interactome network.

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions.