Cerebral: visualizing multiple experimental conditions on a graph with biological context

Systems biologists use interaction graphs to model the behavior of biological systems at the molecular level. In an iterative process, such biologists obser ve the reactions of living cells under various experimental conditions, view the results in the context of the interaction graph, and then propose changes to the graph model. These graphs ser ve as a form of dynamic knowledge representation of the biological system being studied and evolve as new insight is gained from the experimental data. While numerous graph layout and drawing packages are available, these tools did not fully meet the needs of our immunologist collaborators. In this paper, we describe the data information display needs of these immunologists and translate them into design decisions. These decisions led us to create Cerebral, a system that uses a biologically guided graph layout and incor porates experimental data directly into the graph display. Small multiple views of different experimental conditions and a data-driven parallel coordinates view enable correlations between experimental conditions to be analyzed at the same time that the data is viewed in the graph context. This combination of coordinated views allows the biologist to view the data from many different perspectives simultaneously. To illustrate the typical analysis tasks performed, we analyze two datasets using Cerebral. Based on feedback from our collaboratorsweconcludethat Cerebral is a valuable tool for analyzing experimental data in the context of an interaction graph model.      

Composite rectilinear deformation for stretch and squish navigation

We present the first scalable algorithm that supports the composition of successive rectilinear deformations. Earlier systems that provided stretch and squish navigation could only handle small datasets. More recent work featuring rubber sheet navigation for large datasets has focused on rendering and on application-specific issues. However, no algorithm has yet been presented for carrying out such navigation methods; our paper addresses this problem. For maximum flexibility with large datasets, a stretch and squish navigation algorithm should allow for millions of potentially deformable regions. However, typical usage only changes the extents of a small subset k of these n regions at a time. The challenge is to avoid computations that are linear in n, because a single deformation can affect the absolute screen-space location of every deformable region. We provide an O(klogn) algorithm that supports any application that can lay out a dataset on a generic grid, and show an implementation that allows navigation of trees and gene sequences with millions of items in sub-millisecond time.     

Genetic Correlational Analyses of Ethanol Reward and Aversion Phenotypes in Short-Term Selected Mouse Lines Bred for Ethanol Drinking or Ethanol-Induced Conditioned Taste Aversion.

Short-term selective breeding created mouse lines divergent for ethanol drinking (high drinking short-term selected line [STDRHI], low drinking [STDRLO]) or ethanol-induced conditioned taste aversion (CTA; high [HTA], low [LTA]). Compared with STDRLO, STDRHI mice consumed more saccharin and less quinine, exhibited greater ethanol-induced conditioned place preference (CPP), and showed reduced ethanol stimulation and sensitization under some conditions; a line difference in ethanol-induced CTA was not consistently found. Compared with LTA, HTA mice consumed less ethanol but were similar in saccharin consumption, sensitivity to ethanol-induced CPP, and ethanol-induced locomotor stimulation and sensitization. These data suggest that ethanol drinking is genetically associated with several reward-and aversion-related traits. The interpretation of ethanol-induced CTA as more genetically distinct must be tempered by the inability to test the CTA lines beyond Selection Generation 2. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Formation of Quasicrystals and Related Structures in Systems of Aluminum with Transition Metals. Part 1. Binary Systems Formed by Aluminum with 3d Metals

Quasiperiodic phases (quasicrystals) with symmetries forbidden by classic crystallography have been observed in systems of aluminum with transition metals. In binary systems, these phases are metastable; they were obtained for the first time by rapid solidification of melts. We consider the formation of the quasicrystals and we refine the phase diagrams for binary systems A – 3d-M (from V to Ni) in which quasicrystals have been observed.     

Evidence for Oxidative Pathways in the Pathogenesis of PD: Are Antioxidants Candidate Drugs to Ameliorate Disease Progression?

Parkinson’s disease (PD) is a progressive neurodegenerative disorder that arises due to a complex and variable interplay between elements including age, genetic, and environmental risk factors that manifest as the loss of dopaminergic neurons. Contemporary treatments for PD do not prevent or reverse the extent of neurodegeneration that is characteristic of this disorder and accordingly, there is a strong need to develop new approaches which address the underlying disease process and provide benefit to patients with this debilitating disorder. Mitochondrial dysfunction, oxidative damage, and inflammation have been implicated as pathophysiological mechanisms underlying the selective loss of dopaminergic neurons seen in PD. However, results of studies aiming to inhibit these pathways have shown variable success, and outcomes from large-scale clinical trials are not available or report varying success for the interventions studied. Overall, the available data suggest that further development and testing of novel therapies are required to identify new potential therapies for combating PD. Herein, this review reports on the most recent development of antioxidant and anti-inflammatory approaches that have shown positive benefit in cell and animal models of disease with a focus on supplementation with natural product therapies and selected synthetic drugs.     

Eco-Sustainable Silk Fibroin/Pomegranate Peel Extract Film as an Innovative Green Material for Skin Repair

Skin disorders are widespread around the world, affecting people of all ages, and oxidative stress represents one of the main causes of alteration in the normal physiological parameters of skin cells. In this work, we combined a natural protein, fibroin, with antioxidant compounds extracted in water from pomegranate waste. We demonstrate the effective and facile fabrication of bioactive and eco-sustainable films of potential interest for skin repair. The blended films are visually transparent (around 90%); flexible; stable in physiological conditions and in the presence of trypsin for 12 days; able to release the bioactive compounds in a controlled manner; based on Fickian diffusion; and biocompatible towards the main skin cells, keratinocytes and fibroblasts. Furthermore, reactive oxygen species (ROS) production tests demonstrated the high capacity of our films to reduce the oxidative stress induced in cells, which is responsible for various skin diseases.     

No evidence of citation bias as a determinant of STEM gender disparities in US biochemistry,genetics and molecular biology research

Scientometrics - The lack of females in many Science Technology, Engineering and Mathematics (STEM) subjects in the USA is an ongoing concern, with many initiatives attempting to redress this...     

Dendritic Nanotheranostic for the Delivery of Infliximab: A Potential Carrier in Rheumatoid Arthritis Therapy

Antibodies are macromolecules that specifically recognize their target, making them good candidates to be employed in various therapies. The possibility of attaching a drug to an immunoglobulin makes it possible to release it specifically into the affected tissue as long as it overexpresses the target. However, chemical coupling could affect the functionality (specificity and affinity) of the antibody. It has been observed that the use of intermediaries, such as dendrimers, could resolve this issue. Because carbosilane dendrimers have aroused great interest in the field of biomedicine, this report describes the synthesis of an anionic carbosilane dendrimer with a fluorochrome on its surface that then forms a conjugate with an antibody. It has been used as immunoglobulin and infliximab, whose target is TNF-α, which is a cytokine that is overexpressed in the inflamed area or even in the blood of patients with autoimmune diseases, such as rheumatoid arthritis. In addition, the integrity and functionality of the antibody has been studied to see if they have been affected after the chemical coupling process.     

Information Systems in Transition Economies: Does Ownership Matter?

This research investigates the moderating roles of firm ownership in managerial perceptions of information systems (IS) in transition economies. Analysis of representative survey data from 304 companies in Hungary showed that perceptions of IS are driven by organizational variables in foreign firms, and by environmental variables in domestic firms. The findings embrace a more fine-grained notion of variables affecting IS usefulness in the transition economy context by showing that those are contingent on firm ownership.     

Medical knowledge management for specific hospital departments

Medical knowledge representation and management is concerned with how to organise the often vague clinical experience of medical staff required for computable models. However, few knowledge management and acquisition tools have entered routine use, since such tools are not perceived by physicians as part of the clinical information process. An attempt to partially solve this problem, we identify two key aspects of knowledge representation and management tasks. The first is to adopt a medical knowledge standardisation to provide a consistent terminology control and to simplify the integration between knowledge management tools and the health information system. The second is to establish an effective knowledge acquisition process in specific medical fields by adapting knowledge acquisition tools. Therefore, the main goal of this work is to define computational models and to design mechanisms for the effective acquisition and management of medical knowledge in real-life hospital departments. To this end, we analyse the representation of medical knowledge (based on deep-causal models) and the development of knowledge management tools (based on ontologies), integrated within the information processing activities of the clinical user. Finally, we illustrate its applicability in the Intensive Care Unit and Pediatry scenarios.