RosettaBackrub--a web server for flexible backbone protein structure modeling and design.

The RosettaBackrub server (http://kortemmelab.ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein-protein interfaces. The three protocols have been validated on experimental data. Starting from a user-provided single input protein structure in PDB format, the server generates near-native conformational ensembles. The predicted conformations and sequences can be used for different applications, such as to guide mutagenesis experiments, for ensemble-docking approaches or to generate sequence libraries for protein design

Dynamic Unstructured Bargaining with Private Information: Theory, Experiment, and Outcome Prediction via Machine Learning

We study dynamic unstructured bargaining with deadlines and one-sided private information about the amount available to share (the “pie size”). Using mechanism design theory, we show that given the players’ incentives, the equilibrium incidence of bargaining failures (“strikes”) should increase with the pie size, and we derive a condition under which strikes are efficient. In our setting, no equilibrium satisfies both equality and efficiency in all pie sizes. We derive two equilibria that resolve the trade-off between equality and efficiency by favoring either equality or efficiency. Using a novel experimental paradigm, we confirm that strike incidence is decreasing in the pie size. Subjects reach equal splits in small pie games (in which strikes are efficient), while most payoffs are close to either the efficient or the equal equilibrium prediction, when the pie is large. We employ a machine learning approach to show that bargaining process features recorded early in the game improve out-of-sample prediction of disagreements at the deadline. The process feature predictions are as accurate as predictions from pie sizes only, and adding process and pie data together improves predictions even more

Notes on the taxonomy, iconography, and ecology of <i>Aloe pluridens</i> Haw. (Asphodelaceae: Alooideae), an endemic species from southeastern South Africa

The history of the discovery of Aloe pluridens Haw (Asphodelaceae: Alooideae) by the Kew collector James Bowie in 1822–23 in the Eastern Cape Province of South Africa and its subsequent description in 1824 is discussed. The surprising dearth of published illustrations of this long-known species is emphasised and the first known photograph dating from only 1900 is reproduced. It is also shown that a painting at Kew by George Bond that dates from 1829 does not qualify as having been associated with the species by the author of the name, Adrian Hardy Haworth and cannot supersede the specimen on which the name A. pluridens was previously effectively neo-typified. The name A. pluridens Haw. var. beckeri Schönland is lectotypified and it is shown that the name Aloe atherstonei does not have a type as it was previously typified on an apparently non-existent specimen. Additionally the species is illustrated both in habitat and in cultivation. Observations on the ecology and cultivation of the species are also included

Investigating the online and offline contexts of day-to-day democracy as participation spaces.

Citizen-led participation in democracy is explored through studying the online and offline spaces where people work together to influence those in power and improve their communities. The concept of a participation space is introduced to describe these contexts. The spatial theme guides the research, from literature, through methodology, to findings. Case studies of three community/activist groups provide the data to identify participation spaces and model these as Socio-Technical Interaction Networks (STINs) (Kling, McKim, & King, 2003). These participation spaces include social media, email, and blogs, as well as paper media and offline spaces, such as rooms. The STIN models of these participation spaces reveal that the characteristics which influence their use for participation are the same for online and offline spaces. These can be understood in terms of spatial characteristics: the spaces’ perceived boundaries and inhabitants, combined with ownership and access, including costs. As well as recording the roles of these spatial characteristics, the participation space models map the day-to-day activities of participation. Collating these activities reveals that participation primarily takes the form of communication: organising and increasing solidarity, sharing information, encouraging involvement, and trying to influence events. The models also reveal that most of these activities are non-public. This sociotechnical study describes the relationship between the activities of local, grassroots democracy and the characteristics of the online and offline spaces where it takes place

Differential gene expression in multiple neurological, inflammatory and connective tissue pathways in a spontaneous model of human small vessel stroke

Aims: Cerebral small vessel disease (SVD) causes a fifth of all strokes plus diffuse brain damage leading to cognitive decline, physical disabilities and dementia. The aetiology and pathogenesis of SVD are unknown, but largely attributed to hypertension or microatheroma. Methods: We used the spontaneously hypertensive stroke-prone rat (SHRSP), the closest spontaneous experimental model of human SVD, and age-matched control rats kept under identical, non-salt-loaded conditions, to perform a blinded analysis of mRNA microarray, qRT-PCRand pathway analysis in two brain regions (frontal and midcoronal) commonly affected by SVD in the SHRSP at age five, 16 and 21 weeks. Results: We found gene expression abnormalities, with fold changes ranging from 2.5 to 59 for the 10 most differentially expressed genes, related to endothelial tight junctions (reduced), nitric oxide bioavailability (reduced), myelination (impaired), glial and microglial activity (increased), matrix proteins (impaired), vascular reactivity (impaired) and albumin (reduced), consistent with protein expression defects in the same rats. All were present at age 5 weeks thus pre-dating blood pressure elevation. ‘Neurological’ and ‘inflammatory’ pathways were more affected than ‘vascular’ functional pathways. Conclusions: This set of defects, although individually modest, when acting in combination could explain the SHRSP's susceptibility to microvascular and brain injury, compared with control rats. Similar combined, individually modest, but multiple neurovascular unit defects, could explain susceptibility to spontaneous human SVD

Experimental approaches for 100 TeV gamma-ray astronomy

The high energy end of gamma-ray source spectra might provide important clues regarding the nature of the processes involved in gamma-ray emission. Several galactic sources with hard emission spectra extending up to more than 30TeV have already been reported. Measurements around 100TeV and above should be an important goal for the next generation of high energy gamma-ray astronomy experiments. Here we present several techniques providing the required exposure (100 km^2.h). We focus our study on three Imaging Atmospheric Cherenkov Technique (IACT) based approaches: low elevation observations, large field of view telescopes, and large telescope arrays. We comment on the advantages and disadvantages of each approach and report simulation based estimates of their energy ranges and sensitivities.Comment: 3 pages 1 figure. Proceedings of TeV particle astrophysics 2, Madison, August 2006. http://www.icecube.wisc.edu/TeV/presentations/colin_poster.pd

Review of interactive television pilot: initial report

The Scottish Executive launched a six month pilot of interactive Digital Television ( iDTV) in September 2004, in collaboration with five partner organisations - Dumfries and Galloway Council, NHS Scotland (Health Education Board), StartHere, West Lothian Council and Young Scot. The aim of this pilot was to test the feasibility of delivering electronic public services and information via digital television. The pilot service provided information on a range of public services, including information about health, youth and local and community services. Evaluation of the pilot involved analysis of usage data, interviews with representatives of the pilot partners and iDTV viewer

Review of interactive television pilot: initial report

The Scottish Executive launched a six month pilot of interactive Digital Television ( iDTV) in September 2004, in collaboration with five partner organisations - Dumfries and Galloway Council, NHS Scotland (Health Education Board), StartHere, West Lothian Council and Young Scot. The aim of this pilot was to test the feasibility of delivering electronic public services and information via digital television. The pilot service provided information on a range of public services, including information about health, youth and local and community services. Evaluation of the pilot involved analysis of usage data, interviews with representatives of the pilot partners and iDTV viewer