Automatic Dream Sentiment Analysis

In this position paper, we propose a first step toward automatic analysis of sentiments in dreams. 100 dreams were sampled from a dream bank created for a normative study of dreams. Two human judges assigned a score to describe dream sentiments. We ran four baseline algorithms in an attempt to automate the rating of sentiments in dreams. Particularly, we compared the General Inquirer (GI) tool, the Linguistic Inquiry and Word Count (LIWC), a weighted version of the GI lexicon and of the HM lexicon and a standard bag-of-words. We show that machine learning allows automating the human judgment with accuracy superior to majority class choice

Real-time monitoring of cellular dynamics using a microfluidic cell culture system with integrated electrode array and potentiostat

A versatile microfluidic, multichamber cell culture and analysis system with an integrated electrode array and potentiostat suitable for electrochemical detection and microscopic imaging is presented in this paper. The system, which allows on-line electrode cleaning and modification, was developed for real-time monitoring of cellular dynamics, exemplified in this work by monitoring of redox metabolism inside living yeast cells and dopamine release from PC12 cell

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends

In yeast, Rif1 is part of the telosome, where it inhibits telomerase and checkpoint signaling at chromosome ends. In mammalian cells, Rif1 is not telomeric, but it suppresses DNA end resection at chromosomal breaks, promoting repair by nonhomologous end joining (NHEJ). Here, we describe crystal structures for the uncharacterized and conserved ∼125-kDa N-terminal domain of Rif1 from Saccharomyces cerevisiae (Rif1-NTD), revealing an α-helical fold shaped like a shepherd's crook. We identify a high-affinity DNA-binding site in the Rif1-NTD that fully encases DNA as a head-to-tail dimer. Engagement of the Rif1-NTD with telomeres proved essential for checkpoint control and telomere length regulation. Unexpectedly, Rif1-NTD also promoted NHEJ at DNA breaks in yeast, revealing a conserved role of Rif1 in DNA repair. We propose that tight associations between the Rif1-NTD and DNA gate access of processing factors to DNA ends, enabling Rif1 to mediate diverse telomere maintenance and DNA repair functions

Novel Phosphorylation Sites in the S. cerevisiae Cdc13 Protein Reveal New Targets for Telomere Length Regulation

The S. cerevisiae Cdc13 is a multifunctional protein with key roles in regulation of telomerase, telomere end protection, and conventional telomere replication, all of which are cell cycle-regulated processes. Given that phosphorylation is a key mechanism for regulating protein function, we identified sites of phosphorylation using nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS). We also determined phosphorylation abundance on both wild type (WT) and a telomerase deficient form of Cdc13, encoded by the cdc13-2 allele, in both G1 phase cells, when telomerase is not active, and G2/M phase cells, when it is. We identified 21 sites of in vivo phosphorylation, of which only five had been reported previously. In contrast, phosphorylation of two in vitro targets of the ATM-like Tel1 kinase, S249 and S255, was not detected. This result helps resolve conflicting data on the importance of phosphorylation of these residues in telomerase recruitment. multiple residues showed differences in their cell cycle pattern of modification. For example, phosphorylation of S314 was significantly higher in the G2/M compared to the G1 phase and in WT versus mutant Cdc13, and a S314D mutation negatively affected telomere length. Our findings provide new targets in a key telomerase regulatory protein for modulation of telomere dynamics. [Image: see text

The Role of Paracrine and Autocrine Signaling in the Early Phase of Adipogenic Differentiation of Adipose-derived Stem Cells.

INTRODUCTION: High cell density is known to enhance adipogenic differentiation of mesenchymal stem cells, suggesting secretion of signaling factors or cell-contact-mediated signaling. By employing microfluidic biochip technology, we have been able to separate these two processes and study the secretion pathways. METHODS AND RESULTS: Adipogenic differentiation of human adipose-derived stem cells (ASCs) cultured in a microfluidic system was investigated under perfusion conditions with an adipogenic medium or an adipogenic medium supplemented with supernatant from differentiating ASCs (conditioned medium). Conditioned medium increased adipogenic differentiation compared to adipogenic medium with respect to accumulation of lipid-filled vacuoles and gene expression of key adipogenic markers (C/EBPα, C/EBPβ, C/EBPδ, PPARγ, LPL and adiponectin). The positive effects of conditioned medium were observed early in the differentiation process. CONCLUSIONS: Using different cell densities and microfluidic perfusion cell cultures to suppress the effects of cell-released factors, we have demonstrated the significant role played by auto- or paracrine signaling in adipocyte differentiation. The cell-released factor(s) were shown to act in the recruitment phase of the differentiation process

Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay

DNA microarrays have become one of the most powerful tools in the field of genomics and medical diagnosis. Recently, there has been increased interest in combining microfluidics with microarrays since this approach offers advantages in terms of portability, reduced analysis time, low consumption of reagents, and increased system integration. Polymers are widely used for microfluidic systems, but fabrication of microarrays on such materials often requires complicated chemical surface modifications, which hinders the integration of microarrays into microfluidic systems. In this paper, we demonstrate that simple UV irradiation can be used to directly immobilize poly(T)poly(C)-tagged DNA oligonucleotide probes on many different types of plastics without any surface modification. On average, five- and fourfold improvement in immobilization and hybridization efficiency have been achieved compared to surface-modified slides with aminated DNA probes. Moreover, the TC tag only costs 30% of the commonly used amino group modifications. Using this microarray fabrication technique, a portable cyclic olefin copolymer biochip containing eight individually addressable microfluidic channels was developed and used for rapid and parallel identification of Avian Influenza Virus by DNA hybridization. The one-step, cost-effective DNA-linking method on non-modified polymers significantly simplifies microarray fabrication procedures and permits great flexibility to plastic material selection, thus making it convenient to integrate microarrays into plastic microfluidic systems

The Canadian microsimulation model (LSD-C): Content, modules, and some preliminary results

This document provides an overview of how the LSD-C projection model works. LSD-C is a microsimulation demographic projection model designed to project the Canadian population according to various characteristics. LSD-C stands for Laboratoire de Simulations Démographiques-Canada. The model has been developed by the authors at the Institut national de la recherche scientifique (INRS) in Montreal, Canada. More precisely, the LSD-C model simultaneously projects demographic (age, sex, place of residence, place of birth, generation and immigrant status), ethnocultural (mother tongue, language spoken at home, knowledge of official languages, visible minority status, religion) and socioeconomic (education, labour force participation) characteristics of the Canadian population. It allows for changes in individual characteristics over the life course as well as for intergenerational transfers of some characteristics from the mother to her child. This document describes the base population, data sources and methods for every projection modules contained in the model. The conceptualisation of the model events and the derivation of the corresponding parameters are also described. This document provides is a technical supplement to analytical reports and papers published in peer-reviewed journals presenting results generated by LSD-C. ===== RÉSUMÉ ===== Le présent document donne un aperçu du fonctionnement du modèle de projections LSD-C. Il s’agit d’un modèle de projections démographiques par microsimulation conçu pour projeter la population canadienne selon plusieurs caractéristiques. LSD-C signifie Laboratoire de Simulations Démographiques-Canada. Le modèle est développé par les auteurs à l’Institut national de la recherche scientifique (INRS) à Montréal, Canada Précisément, le modèle LSD-C projette la population canadienne selon des variables démographiques (âge, sexe, lieu de résidence, lieu de naissance, statut de génération et statut d’immigration), ethnoculturelles (langue maternelle, langue le plus souvent parlée à la maison, connaissance des langues officielles, groupes de minorités visibles, religion) et socio-économiques (éducation, statut d’activité sur le marché du travail). En cours de simulation, le modèle permet des faire évoluer les différentes caractéristiques des cas simulés et permet les transferts intergénérationnels de certaines caractéristiques de la mère à ses enfants. Ce document décrit la population de base du modèle, les sources de données et la méthodologie utilisée pour chacun des modules de projection contenus dans le modèle. La conceptualisation des événements, des états dérivés et les paramètres utilisés pour la modélisation sont également décrits. Ce document constitue un document technique aux rapports d’analyses et aux articles publiés dans les revues scientifiques qui présentent des résultats de projections générés par LSD-C