MODBASE, a database of annotated comparative protein structure models and associated resources.

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)

Distinct mechanisms govern recalibration to audio-visual discrepancies in remote and recent history

To maintain perceptual coherence, the brain corrects for discrepancies between the senses. If, for example, lights are consistently offset from sounds, representations of auditory space are remapped to reduce this error (spatial recalibration). While recalibration effects have been observed following both brief and prolonged periods of adaptation, the relative contribution of discrepancies occurring over these timescales is unknown. Here we show that distinct multisensory recalibration mechanisms operate in remote and recent history. To characterise the dynamics of this spatial recalibration, we adapted human participants to audio-visual discrepancies for different durations, from 32 to 256 seconds, and measured the aftereffects on perceived auditory location. Recalibration effects saturated rapidly but decayed slowly, suggesting a combination of transient and sustained adaptation mechanisms. When long-term adaptation to an audio-visual discrepancy was immediately followed by a brief period of de-adaptation to an opposing discrepancy, recalibration was initially cancelled but subsequently reappeared with further testing. These dynamics were best fit by a multiple-exponential model that monitored audio-visual discrepancies over distinct timescales. Recent and remote recalibration mechanisms enable the brain to balance rapid adaptive changes to transient discrepancies that should be quickly forgotten against slower adaptive changes to persistent discrepancies likely to be more permanent

Anaesthesia for serial whole-lung lavage in a patient with severe pulmonary alveolar proteinosis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Pulmonary alveolar proteinosis is a rare condition that requires treatment by whole-lung lavage. We report a case of severe pulmonary alveolar proteinosis and discuss a safe and effective strategy for the anaesthetic management of patients undergoing this complex procedure.</p> <p>Case presentation</p> <p>A 34-year-old Caucasian man was diagnosed with severe pulmonary alveolar proteinosis. He developed severe respiratory failure and subsequently underwent serial whole-lung lavage. Our anaesthetic technique included the use of pre-oxygenation, complete lung separation with a left-sided double-lumen endotracheal tube, one-lung ventilation with positive end-expiratory pressure, appropriate ventilatory monitoring, cautious use of positional manoeuvres and single-lumen endotracheal tube exchange for short-term postoperative ventilation.</p> <p>Conclusion</p> <p>Patients with pulmonary alveolar proteinosis may present with severe respiratory failure and require urgent whole-lung lavage. We have described a safe and effective strategy for anaesthesia for whole-lung lavage. We recommend our anaesthetic technique for patients undergoing this complex and uncommon procedure.</p

Revitalizing the South End - The Gateway for Downtown Springfield

This studio report explores a service learning strategy in the context of the Graduate Urban Design Studio taught in the Department of Landscape Architecture and Regional Planning at the University of Massachusetts Amherst. The primary goal of this project is to design the South End as the future gateway for downtown Springfield that will help to transform it into a vibrant urban community. Green design strategies, improvement of services and businesses for residents and the employees of local businesses, and new housing opportunities will enhance the vibrancy, resilience, and quality of life of this disadvantaged urban community. Revitalizing the South End - The Gateway for Downtown Springfield proposes improved parks, boulevards and Main Street as a mixed-use spine that will improve the neighborhood in a physical, cultural, and social sense. Six sustainable learning and planning principles have emerged from this studio: 1. Green infrastructure - Green streets as networks and structural framework 2. Sustainable urban form – Mixed use and pedestrian friendly neighborhoods 3. Community-building art - Expression of place and peopl

The Effect of Perceptual Learning on Face Recognition in Individuals with Central Vision Loss

Purpose: To examine whether perceptual learning could improve face discrimination and recognition in older adults with central vision loss. Methods: Ten participants with age-related macular degeneration (ARMD) received 5 days of training on a face discrimination task (mean age: 78±10 years). We measured the magnitude of improvements (i.e., a reduction in threshold size at which faces were able to be discriminated) and whether they generalised to an untrained face recognition task. Measurements of visual acuity, fixation stability, and preferred retinal locus were taken before and after training to contextualize learning-related effects. The performance of the ARMD training group was compared to nine untrained age-matched controls (8=ARMD, 1=juvenile macular degeneration; mean age: 77±10 years). Results: Perceptual learning on the face discrimination task reduced threshold size for face discrimination performance in the trained group (mean change(SD): -32.7%(+15.9%)). The threshold for performance on the face recognition task also reduced (mean change(SD): - 22.4%(+2.31%)). These changes were independent of changes in visual acuity, fixation stability, or preferred retinal locus. Untrained participants showed no statistically significant reduction in threshold size for face discrimination (mean change(SD): -8.3%(+10.1%) or face recognition (mean change(SD): +2.36%(-5.12%)).” Conclusions: This study shows that face discrimination and recognition can be reliably improved in ARMD using perceptual learning. The benefits point to considerable perceptual plasticity in higher-level cortical areas involved in face-processing. This novel finding highlights that a key visual difficulty in those suffering from ARMD is readily amenable to rehabilitation

MODBASE: a database of annotated comparative protein structure models and associated resources

MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, )

SOCIAL DESIRABILITY AND CYNICISM: BRIDGING THE ATTITUDE-BEHAVIOR GAP IN CSR SURVEYS

Many consumer-focused corporate social responsibility (CSR) studies suggest a positive link between the responsibility demonstrated by a company and consumers’ intention to favor the company in their purchases. Yet an analogous causal effect between corporate social and financial performances is not evident. This chapter conceptualizes how social desirability and cynicism contribute to the discrepancy between consumers’ attitudes and their actual purchase behavior, and analyzes why consumer choices indicated in surveys do not consistently convert into actions

Epidemic processes in complex networks

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The theoretical analysis of epidemic spreading in heterogeneous networks requires the development of novel analytical frameworks, and it has produced results of conceptual and practical relevance. A coherent and comprehensive review of the vast research activity concerning epidemic processes is presented, detailing the successful theoretical approaches as well as making their limits and assumptions clear. Physicists, mathematicians, epidemiologists, computer, and social scientists share a common interest in studying epidemic spreading and rely on similar models for the description of the diffusion of pathogens, knowledge, and innovation. For this reason, while focusing on the main results and the paradigmatic models in infectious disease modeling, the major results concerning generalized social contagion processes are also presented. Finally, the research activity at the forefront in the study of epidemic spreading in coevolving, coupled, and time-varying networks is reported.Comment: 62 pages, 15 figures, final versio