BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis

Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator) in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s), there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid. BETASCAN is publicly accessible on the Web at http://betascan.csail.mit.edu.

Passive-Active Geometric Calibration for View-Dependent Projections onto Arbitrary Surfaces

In this paper we present a hybrid technique for correcting distortions that appear when projecting images onto geometrically complex, colored and textured surfaces. It analyzes the optical flow that results from perspective distortions during motions of the observer and tries to use this information for computing the correct image warping. If this fails due to an unreliable optical flow, an accurate -but slower and visiblestructured light projection is automatically triggered. Together with an appropriate radiometric compensation, view-dependent content can be projected onto arbitrary everyday surfaces. An implementation mainly on the GPU ensures fast frame rates.

NodePM: A Remote Monitoring Alert System for Energy Consumption Using Probabilistic Techniques

In this paper, we propose an intelligent method, named the Novelty Detection Power Meter (NodePM), to detect novelties in electronic equipment monitored by a smart grid. Considering the entropy of each device monitored, which is calculated based on a Markov chain model, the proposed method identifies novelties through a machine learning algorithm. To this end, the NodePM is integrated into a platform for the remote monitoring of energy consumption, which consists of a wireless sensors network (WSN). It thus should be stressed that the experiments were conducted in real environments different from many related works, which are evaluated in simulated environments. In this sense, the results show that the NodePM reduces by 13.7% the power consumption of the equipment we monitored. In addition, the NodePM provides better efficiency to detect novelties when compared to an approach from the literature, surpassing it in different scenarios in all evaluations that were carried out.

On low-dimensional projections of high-dimensional distributions

Let P be a probability distribution on q -dimensional space. The so-called Diaconis-Freedman effect means that for a fixed dimension d<projections of P look like a scale mixture of spherically symmetric Gaussian distributions. The present paper provides necessary and sufficient conditions for this phenomenon in a suitable asymptotic framework with increasing dimension q . It turns out, that the conditions formulated by Diaconis and Freedman (1984) are not only sufficient but necessary as well. Moreover, letting P ^ be the empirical distribution of n independent random vectors with distribution P , we investigate the behavior of the empirical process n √ (P ^ −P) under random projections, conditional on P ^ .

The effect of projections on dimension in the Heisenberg group

We prove analogs of classical almost sure dimension theorems for Euclidean projection mappings in the first Heisenberg group, equipped with a sub-Riemannian metric.

Correlation between broiler lameness and anatomical measurements of bone using radiographical projections with assessments of consistency across and within radiographs.

Lameness represents a major welfare and production issue in the poultry industry with a recent survey estimating 27% of birds lame and 3% unable to walk by 40 d of age. A variety of factors may induce lameness and are typically grouped into 2 broad classes on the basis of being infectious or skeletal in nature with the latter accounting for the majority of cases. The current work sought to build upon a large body of literature assessing the anatomical properties of bone in lame birds. Our specific objectives sought to identify relationships between relevant anatomical properties of the tibia and metatarsus using digital quantification from radiographs of legs and a measure of walking difficulty. Resulting output was statistically analyzed to assess 1) observer reliability for consistency in placing the leg during the radiograph procedure and quantification of the various measures within a radiograph, 2) the relationship between the various measurements of anatomical bone properties and sex, bird mass, and gait score, and 3) the relationship between each measurement and leg symmetry. Our anatomical bone measures were found to be reliable (intra-rater and test-retest reliabilities < 0.75) within radiograph for all measures and 8 of the 10 measures across radiographs. Several measures of bone properties in the tibia correlated to difficulty walking as measured by gait score (P < 0.05), indicating greater angulations with increasing lameness. Of the measures that manifested a gait score × bird mass interaction, heavier birds appeared to exhibit less angulation with increasing difficulty walking with lighter birds the opposite. These interactions suggest possibilities for influencing effects of activity or feed intake on bone mineralization with the bone angulation observed. Our efforts agree with that of others and indicate that angulation of the tibia may be related to lameness, though subsequent efforts involving comprehensive measures of bird activity, growth rates, and internal bone structure will be needed if the validity of the measures are to be accepted.

An Ensemble Kalman Filter multi-tracer assimilation: Determining uncertain ocean model parameters for improved climate-carbon cycle projections

An Ensemble Kalman Filter is applied to assimilate observed tracer fields in various combinations in the Bern3D ocean model. Each tracer combination yields a set of optimal transport parameter values that are used in projections with prescribed CO2 stabilization pathways. The assimilation of temperature and salinity fields yields a too vigorous ventilation of the thermocline and the deep ocean, whereas the inclusion of CFC-11 and radiocarbon improves the representation of physical and biogeochemical tracers and of ventilation time scales. Projected peak uptake rates and cumulative uptake of CO2 by the ocean are around 20% lower for the parameters determined with CFC-11 and radiocarbon as additional target compared to those with salinity and temperature only. Higher surface temperature changes are simulated in the Greenland–Norwegian–Iceland Sea and in the Southern Ocean when CFC-11 is included in the Ensemble Kalman model tuning. These findings highlights the importance of ocean transport calibration for the design of near-term and long-term CO2 emission mitigation strategies and for climate projections.

Oxygen and indicators of stress for marine life in multi-model global warming projections

Decadal-to-century scale trends for a range of marine environmental variables in the upper mesopelagic layer (UML, 100–600 m) are investigated using results from seven Earth System Models forced by a high greenhouse gas emission scenario. The models as a class represent the observation-based distribution of oxygen (O2) and carbon dioxide (CO2), albeit major mismatches between observation-based and simulated values remain for individual models. By year 2100 all models project an increase in SST between 2 °C and 3 °C, and a decrease in the pH and in the saturation state of water with respect to calcium carbonate minerals in the UML. A decrease in the total ocean inventory of dissolved oxygen by 2% to 4% is projected by the range of models. Projected O2 changes in the UML show a complex pattern with both increasing and decreasing trends reflecting the subtle balance of different competing factors such as circulation, production, remineralization, and temperature changes. Projected changes in the total volume of hypoxic and suboxic waters remain relatively small in all models. A widespread increase of CO2 in the UML is projected. The median of the CO2 distribution between 100 and 600m shifts from 0.1–0.2 mol m−3 in year 1990 to 0.2–0.4 mol m−3 in year 2100, primarily as a result of the invasion of anthropogenic carbon from the atmosphere. The co-occurrence of changes in a range of environmental variables indicates the need to further investigate their synergistic impacts on marine ecosystems and Earth System feedbacks.