BioTools at UMassMed

Presentation to science librarians about the BioTools site (http://biotools.umassmed.edu/), a resource of tools for bioinformatics for the five schools of the University of Massachusetts System

Teacher Perception of School Safety Between Mississippi Secondary Schools with School Resource Officers and School Safety Officers

The purpose of the study was to determine if there was a significant difference in the perception of school safety by teachers between secondary schools that employ School Resource Officers (SROs), who are armed, and School Safety Officers (SSOs), who are unarmed or a combination of SROs and SSOs. The School Resource Officers and School Climate Teacher Survey, created by Dr. Amy Oaks (2001) was utilized to gather data. The 193 participants of the study included certified teachers at secondary schools in the Jackson Public School District, the Jackson County Public School District, and the Ocean Springs School District. A Pearson Chi-Square test was conducted to determine if there was a significant difference in the perception of safety between the two groups. In all items analyzed, it was found that there was a statistically significant difference in the perception of school safety with the SRO group perceiving their schools as being safer than the teachers in the SRO/SSO group. In an environment in which the issue of school safety is becoming an increasingly important topic, the perception of teachers working in these schools is vital

Impaired Spatial Reorientation in the 3xTg-AD Mouse Model of Alzheimer's Disease.

In early Alzheimer's disease (AD) spatial navigation is impaired; however, the precise cause of this impairment is unclear. Recent evidence suggests that getting lost is one of the first impairments to emerge in AD. It is possible that getting lost represents a failure to use distal cues to get oriented in space. Therefore, we set out to look for impaired use of distal cues for spatial orientation in a mouse model of amyloidosis (3xTg-AD). To do this, we trained mice to shuttle to the end of a track and back to an enclosed start box to receive a water reward. Then, mice were trained to stop in an unmarked reward zone to receive a brain stimulation reward. The time required to remain in the zone for a reward was increased across training, and the track was positioned in a random start location for each trial. We found that 6-month female, but not 3-month female, 6-month male, or 12-month male, 3xTg-AD mice were impaired. 6-month male and female mice had only intracellular pathology and male mice had less pathology, particularly in the dorsal hippocampus. Thus, AD may cause spatial disorientation as a result of impaired use of landmarks

Vers une résolution numérique du vent dans la couche limite atmosphérique à micro-échelle avec la méthode de simulation des grandes échelles (LES) sous OpenFOAM

À l’aide de modélisation mathématique avancée de la turbulence et de ressources informatiques modernes, une amélioration des simulations numériques des écoulements atmosphériques est envisageable. Un avancement significatif dans ce domaine aurait un impact positif sur la recherche en énergie éolienne. Afin d’y contribuer, le présent ouvrage propose de s’attarder sur la conception d’un solveur numérique micro-échelle basé sur la méthode des Simulations aux Grandes Échelles (LES) avec loi de paroi à l’aide du progiciel à code source libre OpenFOAM. Des conditions atmosphériques neutres avec frontière rigide ou avec inversion de température potentielle comme frein à la progression verticale de la couche limite, un terrain plat, un fluide incompressible, une approximation de la flottabilité par Boussinesq et une turbulence horizontalement homogène sont les hypothèses de travail. Pour y parvenir, un réaménagement important du code est proposé. De nouvelles conditions frontières de vitesse et de température potentielle, un terme source dédié à satisfaire les lois de paroi et une modification à l’algorithme de résolution PISO permettant de stabiliser la couche d’inversion de température potentielle ont entre autres été créés. Grâce à ces ajouts, le nouveau solveur conçu est en mesure d’obtenir un comportement moyen proche de la similarité de Monin-Obukhov lorsque les simulations se retrouvent dans la Zone de Haute Précision. Il se démarque par sa capacité à résoudre des cas en présence de stratification thermique tout en conservant une forte compatibilité avec les différentes librairies de la distribution officielle d’OpenFOAM. Lorsque comparé avec d’autres solveurs d’organisations professionnelles (notamment MC2), les résultats obtenus sont prometteurs. Il est néanmoins recommandé de poursuivre le raffinement du code. Il est estimé qu’un renforcement plus stricte du couplage de résolution vitesse-pression-température et qu’une correction de la discrétisation linéaire des opérateurs différentielles du champ de vitesse en région proche-paroi amélioreraient davantage la qualité des simulations

Arabidopsis thaliana computationally-generated next-state gene interaction models

The construction of gene interaction models must be a fully collaborative and intentional effort. All aspects of the research, such as growing the plants, extracting the measurements, refining the measured data, developing the statistical framework, and forming and applying the algorithmic techniques, must lend themselves to repeatable and sound practices. This paper holistically focuses on the process of producing gene interaction models based on transcript abundance data from Arabidopsis thaliana after stimulation by a plant hormone

Optimization of kinetic proofreading: A general method for derivation of the constraint relations and an exploration of a specific case

We have previously presented a general cost-accuracy relationship for a broad class of kinetic proofreading mechanisms. In this paper we present a general matrix method, based upon classical enzyme kinetics, for the derivation of the constraint relation that characterizes specific proofreading mechanisms. For purpose of illustration we present the method in the context of a conventional Michaelis-Menten mechanism with side reactions. We then explore optimization of the general cost function under a variety of different constraints that may exist for such a mechanism. In this way we are able to contrast different perspectives on the optimization of enzyme design.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24198/1/0000457.pd

Complete Sequence, Analysis and Organization of the Orgyia leucostigma Nucleopolyhedrovirus Genome

The complete genome of the Orgyia leucostigma nucleopolyhedrovirus (OrleNPV) isolated from the whitemarked tussock moth (Orgyia leucostigma, Lymantridae: Lepidoptera) was sequenced, analyzed, and compared to other baculovirus genomes. The size of the OrleNPV genome was 156,179 base pairs (bp) and had a G+C content of 39%. The genome encoded 135 putative open reading frames (ORFs), which occupied 79% of the entire genome sequence. Three inhibitor of apoptosis (ORFs 16, 43 and 63), and five baculovirus repeated ORFs (bro-a through bro-e) were interspersed in the OrleNPV genome. In addition to six direct repeat (drs), a common feature shared among most baculoviruses, OrleNPV genome contained three homologous regions (hrs) that are located in the latter half of the genome. The presence of an F-protein homologue and the results from phylogenetic analyses placed OrleNPV in the genus Alphabaculovirus, group II. Overall, OrleNPV appears to be most closely related to group II alphabaculoviruses Ectropis obliqua (EcobNPV), Apocheima cinerarium (ApciNPV), Euproctis pseudoconspersa (EupsNPV), and Clanis bilineata (ClbiNPV)

Discovery and validation of molecular biomarkers for colorectal adenomas and cancer with application to blood testing

Results: Genome-wide analysis uncovered reproducible gene expression signatures for both adenomas and cancers compared to controls. 386/489 (79%) of the adenoma and 439/529 (83%) of the adenocarcinoma biomarkers were validated in independent tissues. We also identified genes differentially expressed in adenomas compared to cancer. KIAA1199 was selected for further analysis based on consistent up-regulation in neoplasia, previous studies and its interest as an uncharacterized gene. Plasma KIAA1199 RNA levels were significantly higher in patients with either cancer or adenoma (31/ 40) compared to neoplasia-free controls (6/20).This work was co-funded by Flinders University of South Australia and the Commonwealth Scientific and Industrial Research Organisation (CSIRO) of Australia. Drs. Dunne, Molloy and Brown are employed by CSIRO. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding was also provided by Clinical Genomics Pty Ltd., a company involved in the discovery and commercialization of biomarkers for colorectal cancer. Drs. LaPointe, Pedersen, Gaur, McEvoy and Thomas are employed by Clinical Genomics Pty Ltd and Prof. Young is a paid consultant of Clinical Genomics Pty Ltd. The funder thus played roles in study design, data collection and analysis, decision to publish, and preparation of the manuscript. Mrs. Pimlott and Dr. Wattchow have nothing to disclose. This work was co-funded by Clinical Genomics Pty Ltd, a company involved in the discovery and commercialization of biomarkers for colorectal cancer. Drs. LaPointe, Pedersen, Gaur, McEvoy and Thomas are employed by Clinical Genomics Pty Ltd. Prof. Young is a paid consultant of Clinical Genomics Pty Ltd. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials