MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.Comment: 19 pages, 5 figure

Ph-Metrie oesophagienne a double canal dans le diagnostic du reflux gastro-oesophagien Avec manifestations ORL

Objectif : Déterminer la fréquence du reflux proximal pathologique chez des patients présentant un reflux gastro-oesophagien (RgO) avec manifestations oto-rhino-laryngologiques (ORL) et explorés par une ph-métrie oesophagienne des 24 heures, utilisant une sonde à double canal, déterminer le taux de concordance entre les symptômes ORL et les épisodes de RgO proximal et enfin, rechercher des facteurs  épidémiologiques, cliniques et ph-métriques distaux associés à un plus grand risque de survenue de RgO proximal. : Nous avons revu tous les tracés et comptes rendus des phmétries oesophagiennes des 24 heures à double canal pratiquées entre 2008 et 2010, pour exploration de  manifestations ORL de RgO.Matériel et méthodes : Nous avons revu tous les tracés et comptes rendus des ph-métries oesophagiennes des 24 heures à double canal pratiquées entre 2008 et 2010, pour exploration de manifestations ORL de RgO.Résultats : il s’agissait de 33 patients, d’âge moyen de 43,2 ans (10-73 ans). Un reflux proximal pathologique a été retrouvé chez 27 patients. Il était associé à un reflux distal chez 16 patients et isolé chez 11 patients. Un reflux proximal nocturne pathologique a été retrouvé chez 13 patients. Une bonne concordance symptomatique a été retrouvée chez 9 malades. Concernant les facteurs prédictifs du reflux proximal pathologique, nous avons retrouvé une corrélation statistiquement significative avec l’existence d’un reflux distal associé et l’existence d’un reflux distal nocturne.Conclusion : en attendant le développement et la diffusion de   l’impédancemétrie oesophagienne, la ph-métrie oesophagienne utilisant une sonde à double canal doit être proposée à tous les patients souffrant d’un RgO avec manifestations ORL.Mots-clés : reflux gastro-oesophagien, ph-métrie oesophagienne des 24 heures, oto-rhino-laryngologie

Rancang Bangun Sistem Distribusi Hasil Produksi Obat untuk Menjamin Kualitas dalam Meningkatkan Pelayanan Pelanggan

Pharmaceutical companies in Indonesia that are engaged in manufacturing currently continue to develop, they process medicinal ingredients into pharmaceuticals, such as tablets, syrup, capsules and others. At present the distribution and production management system of drugs is still semi-computerized, because it still uses Ms. Excel, which can cause file-to-file buildup, besides that it is possible that the data will be lost or damaged, and when searching for data, it takes a long time. To overcome this need to be built a system to process the drug distribution and production management system, to help companies more easily access drug data to computerized travel documents, so as to increase the effectiveness and time efficiency, and get maximum work results and data accuracy in data input in the relevant section. It certainly can be found with various methods that use penuls, starting from the use of uml to provide an overview of system design, then MySql as a data processing application in thedatabase, as a programming language using php

Rancang Bangun Aplikasi Game Puzzle Berbasis Android Menggunakan Algoritma Decision Tree

The development of games today is very rapid and has become part of the lifestyle. A puzzle game is an application that can be used to hone thinking and memory skills where users have to find a way out and collect special items that have been provided at every level of the game . The player must collect all the white orb in each level to get the key to move to the next level but the player will be confronted by the constraints on how to find the key and retrieve it . The game is designed using decision tree and game algorithms designed using Game Maker Studio that is applied to Android devices

Awareness and attitude toward using dental magnification among dental students and residents at King Abdulaziz University, Faculty of Dentistry

Abstract Background The authors conducted a study aimed to assess the awareness and attitude among dental students and residents at King Abdulaziz University, Faculty of Dentistry (KAUFD) toward using dental magnification. Methods An e-questionnaire was formulated then sent to dental students and residents (n = 651). The questionnaire included questions that assessed both the awareness and attitude toward using dental magnification. Data were analyzed using IBM SPSS version 22. The chi-square test was used to establish relationships between categorical variables. Results The response rate was 69.7 % (n = 454). Of those, 78.1 % did not use magnification during dental procedures. However, 81.8 % agreed that dental magnification could enhance the accuracy and quality of their dental work. Thus, 91.6 % thought it would be useful in endodontics and 46.3 % voted for surgery. Of the 21.9 % that used magnification, dental loupes were mostly used, 55.9 %. The majority (59.4 %) of the participants believed that using dental magnification should be introduced by faculty beginning in Year I of dental school. Conclusions Among our respondents, most of the undergraduate students did not use dental magnification nor attended courses in the use of dental magnifications. However, most of the students were aware of its significance in improving the accuracy and quality of their work.http://deepblue.lib.umich.edu/bitstream/2027.42/134609/1/12903_2016_Article_254.pd

Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes

Background: miRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis. Results: Here, we have performed miRNA transcriptome profiling in human affinity-purified CD56+ myoblasts induced to differentiate in vitro. In total, we have identified 60 miRNAs differentially expressed during myogenic differentiation. Many were not known for being differentially expressed during myogenic differentiation. Of these, 14 (miR-23b, miR-28, miR-98, miR-103, miR-107, miR-193a, miR-210, miR-324-5p, miR-324-3p, miR-331, miR-374, miR-432, miR-502, and miR-660) were upregulated and 6 (miR-31, miR-451, miR-452, miR-565, miR-594 and miR-659) were downregulated. mRNA transcriptome profiling performed in parallel resulted in identification of 6,616 genes differentially expressed during myogenic differentiation. Conclusions: This simultaneous miRNA/mRNA transcriptome profiling allowed us to predict with high accuracy target genes of myogenesis-related microRNAs and to deduce their functions

Time series clustering of T cell subsets dissects heterogeneity in immune reconstitution and clinical outcomes among MUD-HCT patients receiving ATG or PTCy

IntroductionAnti-T-lymphocyte globulin (ATG) or post-transplant cyclophosphamide (PTCy) prevent graft-versus-host disease (GVHD) after hematopoietic cell transplantation (HCT), yet individual patients benefit differentially.MethodsGiven the sparse comparative data on the impact of cellular immune reconstitution in this setting, we studied flow cytometry and clinical outcomes in 339 recipients of 10/10 matched-unrelated donor (MUD) HCT using either ATG (n=304) or PTCy (n=35) for in vivo T cell manipulation along with a haploidentical PTCy control cohort (n=45). Longitudinal cellular immune reconstitution data were analyzed conventionally and with a data science approach using clustering with dynamic time warping to determine the similarity between time-series of T cell subsets.ResultsConsistent with published studies, no significant differences in clinical outcomes were observed at the cohort level between MUD-ATG and MUD-PTCy. However, cellular reconstitution revealed preferences for distinct T cell subpopulations associating with GVHD protection in each setting. Starting early after HCT, MUD-PTCy patients had higher regulatory T cell levels after HCT (p <0.0001), while MUD-ATG patients presented with higher levels of γδ T- or NKT cells (both p <0.0001). Time-series clustering further dissected the patient population’s heterogeneity revealing distinct immune reconstitution clusters. Importantly, it identified phenotypes that reproducibly associated with impaired clinical outcomes within the same in vivo T cell manipulation platform. Exemplarily, patients with lower activated- and αβ T cell counts had significantly higher NRM (p=0.032) and relapse rates (p =0.01).DiscussionThe improved understanding of the heterogeneity of cellular reconstitution in MUD patients with T cell manipulation both at the cohort and individual level may support clinicians in managing HCT complications

Pattern of disinfectants use and their adverse effects on the consumers after COVID-19 outbreak

Background and objective: The aim of this study was to investigate the pattern of disinfectants use within outbreak of COVID-19 and estimate their adverse effects on the consumer�s health. Methods: In this descriptive-analytical study, 1090 participants were entered into the study without age and gender limitations. A researcher-made electronic checklist containing 43 questions was applied to collect data. The checklist included three sections: demographic characteristics (8 questions), disinfection of body and non-living surfaces (21 questions), and adverse effects of disinfectants on health (15 questions). Results: 87 of participants used the incorrect proportions of water and alcohol to make this disinfectant available at home. The percentage of people with wrong proportion of sodium hypochlorite was 74.2. Approximately 42 of participants experienced at least one disorder on their hands, feet, eyes, respiratory or gastrointestinal systems after sequential uses of disinfectants. The most common disorders among the participants were found to be skin dryness (76.3), obsession (42.2), skin itching (41.2), coughing (41.1), and eyes irritation (39.5). The mean frequency of hand washing and hand disinfecting were 15.28 and 10.74 times per a day, respectively, and the clean-up in case of surfaces was 2.99 times a day. The frequency of hand washing and disinfecting in women group (16.4 and 11.2 times a day) were higher than in men (14.0 and 10.3 times a day) group. In addition, these self-care actions in married people (15.6 and 11.0 times a day) were higher compared to those in single people (14.0 and 10.6 times a day). Conclusion: Being unaware of participants with instruction for preparation and use disinfectants may harm their health. Therefore, it is suggested that the authorities provide the necessary training program for public through official media. © 2020, Springer Nature Switzerland AG