Climate and Developmental Plasticity: Interannual Variability in Grapevine Leaf Morphology.

The shapes of leaves are dynamic, changing over evolutionary time between species, within a single plant producing different shaped leaves at successive nodes, during the development of a single leaf as it allometrically expands, and in response to the environment. Notably, strong correlations between the dissection and size of leaves with temperature and precipitation exist in both the paleorecord and extant populations. Yet, a morphometric model integrating evolutionary, developmental, and environmental effects on leaf shape is lacking. Here, we continue a morphometric analysis of >5,500 leaves representing 270 grapevines of multiple Vitis species between two growing seasons. Leaves are paired one-to-one and vine-to-vine accounting for developmental context, between growing seasons. Linear discriminant analysis reveals shape features that specifically define growing season, regardless of species or developmental context. The shape feature, a more pronounced distal sinus, is associated with the colder, drier growing season, consistent with patterns observed in the paleorecord. We discuss the implications of such plasticity in a long-lived woody perennial, such as grapevine (Vitis spp.), with respect to the evolution and functionality of plant morphology and changes in climate.

Multiple white matter tract abnormalities underlie cognitive impairment in RRMS.

Diffusion tensor imaging (DTI) is a sensitive tool for detecting microstructural tissue damage in vivo. In this study, we investigated DTI abnormalities in individuals with relapsing remitting multiple sclerosis (RRMS) and examined the relations between imaging-based measures of white matter injury and cognitive impairment. DTI-derived metrics using tract-based spatial statistics (TBSS) were compared between 37 individuals with RRMS and 20 healthy controls. Cognitive impairment was assessed with three standard tests: the Symbol Digit Modalities Test (SDMT), which measures cognitive processing speed and visual working memory, the Rey Auditory Verbal Learning Test (RAVLT), which examines verbal memory, and the Paced Auditory Serial Addition Test (PASAT), which assesses sustained attention and working memory. Correlations between DTI-metrics and cognition were explored in regions demonstrating significant differences between the RRMS patients and the control group. Lower fractional anisotropy (FA) was found in RRMS participants compared to controls across the tract skeleton (0.40 ± 0.03 vs. 0.43 ± 0.01, p<0.01). In areas of reduced FA, mean diffusivity was increased and was dominated by increased radial diffusivity with no significant change in axial diffusivity, an indication of the role of damage to CNS myelin in MS pathology. In the RRMS group, voxelwise correlations were found between FA reduction and cognitive impairment in cognitively-relevant tracts, predominantly in the posterior thalamic radiation, the sagittal stratum, and the corpus callosum; the strongest correlations were with SDMT measures, with contributions to these associations from both lesion and normal-appearing white matter. Moreover, results using threshold-free cluster enhancement (TFCE) showed more widespread white matter involvement compared to cluster-based thresholding. These findings indicate the important role for DTI in delineating mechanisms underlying MS-associated cognitive impairment and suggest that DTI could play a critical role in monitoring the clinical and cognitive effects of the disease.

Pre-hospital delays in patients experiencing symptoms of acute stroke or transient ischaemic attack.

AIM: Delays in seeking help following stroke or transient ischaemic attack (TIA) are associated with worse outcomes and missed treatment opportunities, including stroke reperfusion therapy. This study aims to discover the reasons for these delays. METHOD: Patients admitted with stroke or TIA were eligible for inclusion. In Part A, we collected demographic data and particulars at the time of symptom onset, with data dichotomised into early (<4.5 hours) or late (≥4.5 hours) presentation times. In Part B, we collected qualitative data on cognitive factors that led to delayed admission. A standardised questionnaire was used to collect the data. RESULTS: One-half of 41 patients presented early. Living closer to hospital (36.4 vs 54.4 km, p=0.036) and early contact with healthcare services (37 vs 1382 minutes, p=0.001) were associated with early presentation; contact with emergency services within 15 minutes of symptom onset was significantly associated with treatment with thrombolytics (p<0.001). Neither patient awareness of acute stroke symptoms, having a partner present nor a history of prior stroke were associated with early presentation (all p>0.05). Themes associated with delays included: difficulty understanding symptoms, personal beliefs, minimising symptoms, the influence of others and fulfilling prior responsibilities. CONCLUSIONS: The findings of this study provide important insights that could help healthcare organisations introduce strategies to help improve access to organised stroke services.

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

MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).

Parainfectious meningo-encephalo-radiculo-myelitis (cat scratch disease, Lyme borreliosis, brucellosis, botulism, legionellosis, pertussis, mycoplasma).

Parainfectious disorders of the nervous system encompass those meningo-encephalo-radiculomyelitic conditions that are temporally associated with a systemic infection, antigenic stimuli, or toxin exposure, in the absence of evidence of direct neuronal infection or invasion of the central nervous system (CNS) or peripheral nervous system (PNS). Pathogenetic mechanisms can be due to immune-mediated processes (such as bystander activation, molecular mimicy) or the inciting insult can be due to toxic factors, as in the case of botulism. A myriad of clinical manifestations can occur including headache, seizures, and mental status changes, ranging from mood and behavioral disturbances to varying levels of alteration in consciousness. Focal neurological deficits can include aphasia, hemiparesis, or paraparesis. The PNS can also be affected leading to cranial nerve involvement, focal or multifocal neuropathies, and dysfunction of the autonomic nervous system. Diagnosis is based not only on the history, examination, laboratory, and neuroimaging data but also on epidemiological factors. The parainfectious disorders covered in this review are cat scratch disease, Lyme borreliosis, legionellosis, brucellosis, botulism, pertussis, and mycoplasma. Each is associated with a distinct organism, has both systemic and neurological manifestations, and has a different epidemiological profile.

Enhancing data sharing in collaborative research projects with DASH.

We describe a software framework, called DASH, that enables the facile access, maintenance, curation and sharing of computational biology data among collaborating research scientists. The DASH event-based framework enables members of team-based research projects to describe the multistep computational processing pipelines frequently required to generate data for sharing, monitors multiple distributed data stores for changes, and will then automatically invoke the appropriate processing pipeline(s). These pipelines can be used to communicate the results of data analyses to collaborators using mechanisms such as Web Services. We describe the overall design of the DASH system and the application of a simple DASH prototype to a collaborative pharmacogenomics research project involving several dozen researchers located at several different sites--the UCSF Pharmacogenetics of Membrane Transporters project.

UCSF Chimera--a visualization system for exploratory research and analysis.

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.