Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant succination of proteins in fumarate hydratase‐deficient mice and HLRCC patients is a robust biomarker of mutation status

Germline mutations in the FH gene encoding the Krebs cycle enzyme fumarate hydratase predispose to hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome. FH‐deficient cells and tissues accumulate high levels of fumarate, which may act as an oncometabolite and contribute to tumourigenesis. A recently proposed role for fumarate in the covalent modification of cysteine residues to S‐(2‐succinyl) cysteine (2SC) (termed protein succination) prompted us to assess 2SC levels in our existing models of HLRCC. Herein, using a previously characterized antibody against 2SC, we show that genetic ablation of FH causes high levels of protein succination. We next hypothesized that immunohistochemistry for 2SC would serve as a metabolic biomarker for the in situ detection of FH‐deficient tissues. Robust detection of 2SC was observed in Fh1 (murine FH)‐deficient renal cysts and in a retrospective series of HLRCC tumours (n = 16) with established FH mutations. Importantly, 2SC was undetectable in normal tissues (n = 200) and tumour types not associated with HLRCC (n = 1342). In a prospective evaluation of cases referred for genetic testing for HLRCC, the presence of 2SC‐modified proteins (2SCP) correctly predicted genetic alterations in FH in every case. In two series of unselected type II papillary renal cancer (PRCC), prospectively analysed by 2SCP staining followed by genetic analysis, the biomarker accurately identified previously unsuspected FH mutations (2/33 and 1/36). The investigation of whether metabolites in other tumour types produce protein modification signature(s) that can be assayed using similar strategies will be of interest in future studies of cancer. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Bacterial carbon dynamics on marine snow

We studied the biomass and production of heterotrophic bacteria on several types of marine snow including those composed predominantly of &atoms, fecal pellets, larvacean house mucus, or miscellaneous detrital components at 8 stations in the Pacific Ocean off California. We concurrently measured photoautotrophic biomass and production, and particulate organic carbon (POC) on marine snow to examine the quantitative significance of bacterial processes in carbon flow pathways in different types of marine snow Although a typical marine snow floc contained about 106 bacteria, the bacterial carbon (BOC) and phytoplankton carbon (PhytoC) were each < 13 % of total POC. Most of the floc carbon therefore consisted of detritus, unlike whole seawater samples (in other studies) where BOC + PhytoC generally comprises about 50 % of the POC. PhytoC on marine snow and in the surrounding water was generally similar to BOC (except at one station). Floc POC turnover time based on bacterial carbon demand. assuming a 30 O/ O carbon assimilation efficiency, was 20 to 100 d. This was comparable to the POC residence time reported for the Southern California Bight. Bacterial specific growth rates on flocs varied greatly between stations (0.06 to 0.96 d-l) with highest values at stations with diatom flocs where they were comparable to growth rates of free-living bacteria in mesotrophic waters. The ratio of bacterial carbon production to primary production on marine snow was typical of seawater samples from other studies. Bacterial carbon production was measured by the leucine incorporation method while bacterial cell production (and growth rate) was measured by the thymidlne incorporation method simultaneously on the same marine snow floc. We could thus calculate bacterial carbon per-new-cell (C,) and compare it with the microscopy-based average carbon per cell (C,,) to test the hypothesis that new cells reflect the average carbon content of the parent assemblage (bacteria on marine snow were much larger than those in the surrounding water). In 73 % of our samples the carbon content of the new daughter cells was within a factor of 1.5 of the carbon content of the parent cells.
Differential Response of High-Elevation Planktonic Bacterial Community Structure and Metabolism to Experimental Nutrient Enrichment

Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and emphasize that evaluation of eutrophication in these habitats should incorporate heterotrophic microbial communities and processes.
Research of GrabCut algorithm for single camera video synopsis

In this paper, the GrabCut segmentation algorithm is used for the moving object matting in single camera surveillance video. In the case of the general location of the moving object has been drawn, we can get more accurate segmentation result and the process of user interaction is simplified. At the same time, the segmentation results are placed into one background image to concentrate the surveillance video in time and space and a single camera surveillance video synopsis can be formed. The implementation result shows that video synopsis is an effective way to compress the video and the browsing efficiency is improved in large extent.
Are calcium and fiber beneficial for poorly controlled diabetic patients?

UNLABELLED No nutritional protocol for poorly controlled diabetic patients receiving well-managed drug treatment is currently available. OBJECTIVE Aims were to compare dietary consumption of calcium and fibers with lipid profile and glycosilated hemoglobin HbA1c. METHODOLOGY This was a prospective observational study. Patients with poorly controlled diabetes were consecutively recruited. A food-frequency questionnaire and tests for lipid profile, HbA1c, and C reactive protein were collected, along with clinical and anthropometric assessment. RESULTS Patients (N = 114, age 65.7 ± 6.5 years, 75.4% females, BMI 29.0 ± 5.3 kg/m²) were often insulin-dependent (32.5%) and with systemic inflammation (C-reactive protein 4.2 ± 3.9 mg/L). Diet was energy restricted (1,365 ± 565 kcal/day) and mostly adequate but with suboptimal fiber (15.4 ± 8.6 g/day) and very low calcium (592.4 ± 204.4 mg/day). Calcium and fiber in the diet correlated with serum lipids, whereas fiber alone displayed a protective association regarding diabetes (HBA1c, insulin use) and arterial hypertension. CONCLUSIONS Calcium and fiber ingestion exhibited correlations with important markers of metabolic status and cardiovascular risk. Future studies should address enhancement of these ingredients by means of dietary changes and supplements.
Time ordered perturbation theory for non-local interactions; applications to NCQFT

In the past decades, time ordered perturbation theory was very successful in describing relativistic scattering processes. It was developed for local quantum field theories. However, there are field theories which are governed by non-local interactions, for example non-commutative quantum field theory (NCQFT). Filk [1] first studied NCQFT perturbatively obtaining the usual Feynman propagator and additional phase factors as the basic elements of perturbation theory. However, this treatment is only applicable for cases, where the deformation of space-time does not involve time. Thus, we generalize Filk's approach in two ways: First, we study non-local interactions of a very general type able to embed NCQFT. And second, we also include the case, where non-locality involves time. A few applications of the obtained formalism will also be discussed.
UOW-SHEF: SimpLex – Lexical Simplicity Ranking based on Contextual and Psycholinguistic Features

This paper describes SimpLex, a Lexical Simplification system that participated in the English Lexical Simplification shared task at SemEval-2012. It operates on the basis of a linear weighted ranking function composed of context sensitive and psycholinguistic features. The system outperforms a very strong baseline, and ranked first on the shared task.
A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots

Malaria transmission is spatially heterogeneous. This reduces the efficacy of control strategies, but focusing control strategies on clusters or ‘hotspots’ of transmission may be highly effective. Among 1500 homesteads in coastal Kenya we calculated (a) the fraction of febrile children with positive malaria smears per homestead, and (b) the mean age of children with malaria per homestead. These two measures were inversely correlated, indicating that children in homesteads at higher transmission acquire immunity more rapidly. This inverse correlation increased gradually with increasing spatial scale of analysis, and hotspots of febrile malaria were identified at every scale. We found hotspots within hotspots, down to the level of an individual homestead. Febrile malaria hotspots were temporally unstable, but 4 km radius hotspots could be targeted for 1 month following 1 month periods of surveillance. DOI: http://dx.doi. org/10.7554/eLife.02130. 001
ANTracks 2.0 - Generative Music on Multiple Multitouch Devices Categories and Subject Descriptors

In this paper we describe work in progress on generative music generation on multi-touch devices. Our goal is to create a musical application framework for multiple casual users that use state of the art multitouch devices. We choose the metaphor of ants moving on a hexagonal grid to interact with a pitch pattern. The set of devices used includes a custom built multitouch table and a number of iPhones to jointly create musical expressions.
Toward a Unifying Ontology Dealing with Both User–Defined Periodicity and Temporal Constraints About Repeated Events

This article proposes a first–order logic axiomatic description of some basic ontological notions underlying the meaning of different types of temporal constraints about repeated events. The article also shows that such an ontology provides an homogeneous framework that can be used to model and compare the intended meaning of different formalisms in the artificial intelligence and temporal databases literature which deal with user–defined calendar dates and/or qualitative and quantitative constraints between different types of repeated events.
Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome

Ribosome Rescue Ribosomes stall when they reach the end of defective messenger RNAs (mRNAs). In bacteria, the most-studied ribosomal rescue pathway involves a ribonucleoprotein complex comprising tmRNA (which acts as both transfer RNA and mRNA) and the protein SmpB. In an alternative pathway, some Gram-negative bacteria contain proteins that achieve tmRNA-independent rescue. Now, Neubauer et al. (p. 1366) present the structure of the Thermus thermophilus ribosome bound to a fragment of tmRNA, SmpB, and elongation factor Tu, and Gagnon et al. (p. 1370) report the structure of the T. thermophilus ribosome in complex with an initiator tRNA, a short mRNA fragment, and the rescue factor YaeJ. Though the two rescue systems are very different, both involve a protein tail that binds in the mRNA channel. This orients the rescue apparatus to facilitate switching translation to a different message in the tmRNA system or hydrolysis of peptidyl tRNA by YaeJ. Two crystal structures show the molecular bases for two pathways that rescue ribosomes that have stalled on defective messenger RNAs. In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.
An evaluation of two‐photon excitation versus confocal and digital deconvolution fluorescence microscopy imaging in xenopus morphogenesis

The ability to visualize cell motility occurring deep in the context of opaque tissues will allow many currently intractable issues in developmental biology and organogenesis to be addressed. In this study, we compare two‐photon excitation with laser scanning confocal and conventional digital deconvolution fluorescence microscopy, using the same optical configuration, for their ability to resolve cell shape deep in Xenopus gastrula and neurula tissues. The two‐photon microscope offers better depth penetration and less autofluorescence compared to confocal and conventional deconvolution imaging. Both two‐photon excitation and confocal microscopy also provide improved rejection of “out‐of‐focus” noise and better lateral and axial resolution than conventional digital deconvolution microscopy. Deep Xenopus cells are best resolved by applying the digital deconvolution method on the two‐photon images. We have also found that the two‐photon has better depth penetration without any degradation in the image quality of interior sections compared to the other two techniques. Also, we have demonstrated that the quality of the image changes at different depths for various excitation powers. Microsc. Res. Tech. 47:172–181, 1999. © 1999 Wiley‐Liss, Inc.
Division Algorithms and Implementations

Many algorithms have been developed for implementing division in hardware. These algorithms differ in many aspects, including quotient convergence rate, fundamental hardware primitives, and mathematical formulations. The paper presents a taxonomy of division algorithms which classifies the algorithms based upon their hardware implementations and impact on system design. Division algorithms can be divided into five classes: digit recurrence, functional iteration, very high radix, table look-up, and variable latency. Many practical division algorithms are hybrids of several of these classes. These algorithms are explained and compared. It is found that, for low-cost implementations where chip area must be minimized, digit recurrence algorithms are suitable. An implementation of division by functional iteration can provide the lowest latency for typical multiplier latencies. Variable latency algorithms show promise for simultaneously minimizing average latency while also minimizing area.
Rapid prototyping of a transfer-based Hebrew-to-English machine translation system

We describe the rapid development of a preliminary Hebrew-to-English Machine Translation system under a transfer-based framework specifically designed for rapid MT prototyping for languages with limited linguistic resources. The task is particularly challenging due to two main reasons: the high lexical and morphological ambiguity of Hebrew and the dearth of available resources for the language. Existing, publicly available resources were adapted in novel ways to support the MT task. The methodology behind the system combines two separate modules: a transfer engine which produces a lattice of possible translation segments, and a decoder which searches and selects the most likely translation according to an English language model. We demonstrate that a small manually crafted set of transfer rules suffices to produce legible translations. Performance results are evaluated using state of the art measures and are shown to be encouraging.
Weak Lensing with Sloan Digital Sky Survey Commissioning Data: The Galaxy-Mass Correlation Function to 1 h−1 Mpc

We present measurements of galaxy-galaxy weak lensing from 225 deg2 of early commissioning imaging data from the Sloan Digital Sky Survey (SDSS). We measure a mean tangential shear around a stacked sample of foreground galaxies in three bandpasses (g′, r′, and i′) out to angular radii of 600″, detecting the shear signal at very high statistical significance. The shear profile is well described by a power law γT = γT0(1′/θ)η, with best-fit slope of η = 0.7–1.1 (95% confidence). In the range θ = 10″–600″, the mean tangential shear is approximately 6 ± 1 × 10-4 in all three bands. A variety of rigorous tests demonstrate the reality of the gravitational lensing signal and confirm the uncertainty estimates. In particular, we obtain shear measurements consistent with zero when we rotate the background galaxies by 45°, replace foreground galaxies with random points, or replace foreground galaxies with bright stars. We interpret our results by assuming that all matter correlated with galaxies belongs to the galaxies. We model the mass distributions of the foreground galaxies, which have a mean luminosity ⟨L(θ < 5″)⟩ = 8.7 ± 0.7 × 109 h-2 Lg'☉, 1.4 ± 0.12 × 1010 h-2 Lr'☉, 1.8 ± 0.14 × 1010 h-2 Li'☉, as approximately isothermal spheres characterized by a velocity dispersion σv and a truncation radius s. The velocity dispersion is constrained to be σv = 150–190 km s-1 at 95% confidence (145–195 km s-1 including systematic uncertainties), consistent with previous determinations but with smaller error bars. Our detection of shear at large angular radii sets a 95% confidence lower limit s > 140″, corresponding to a physical radius of 260 h-1 kpc, implying that the dark halos of typical luminous galaxies extend to very large radii. However, it is likely that this is being systematically biased to large value by diffuse matter in the halos of groups and clusters of galaxies. We also present a preliminary determination of the galaxy-mass correlation function, finding a correlation length similar to the galaxy autocorrelation function and consistency with a low matter density universe with modest bias. The full SDSS will cover an area 44 times larger and provide spectroscopic redshifts for the foreground galaxies, making it possible to improve greatly the precision of these constraints, to measure additional parameters such as halo shape and halo concentration, and to measure the properties of dark matter halos separately for many different classes of galaxies.
Example-based hair geometry synthesis

We present an example-based approach to hair modeling because creating hairstyles either manually or through image-based acquisition is a costly and time-consuming process. We introduce a hierarchical hair synthesis framework that views a hairstyle both as a 3D vector field and a 2D arrangement of hair strands on the scalp. Since hair forms wisps, a hierarchical hair clustering algorithm has been developed for detecting wisps in example hairstyles. The coarsest level of the output hairstyle is synthesized using traditional 2D texture synthesis techniques. Synthesizing finer levels of the hierarchy is based on cluster oriented detail transfer. Finally, we compute a discrete tangent vector field from the synthesized hair at every level of the hierarchy to remove undesired inconsistencies among hair trajectories. Improved hair trajectories can be extracted from the vector field. Based on our automatic hair synthesis method, we have also developed simple user-controlled synthesis and editing techniques including feature-preserving combing as well as detail transfer between different hairstyles.
Dopamine Modulates Risk-Taking as a Function of Baseline Sensation-Seeking Trait

Trait sensation-seeking, defined as a need for varied, complex, and intense sensations, represents a relatively underexplored hedonic drive in human behavioral neuroscience research. It is related to increased risk for a range of behaviors including substance use, gambling, and risky sexual practice. Individual differences in self-reported sensation-seeking have been linked to brain dopamine function, particularly at D2-like receptors, but so far no causal evidence exists for a role of dopamine in sensation-seeking behavior in humans. Here, we investigated the effects of the selective D2/D3 agonist cabergoline on performance of a probabilistic risky choice task in healthy humans using a sensitive within-subject, placebo-controlled design. Cabergoline significantly influenced the way participants combined different explicit signals regarding probability and loss when choosing between response options associated with uncertain outcomes. Importantly, these effects were strongly dependent on baseline sensation-seeking score. Overall, cabergoline increased sensitivity of choice to information about probability of winning; while decreasing discrimination according to magnitude of potential losses associated with different options. The largest effects of the drug were observed in participants with lower sensation-seeking scores. These findings provide evidence that risk-taking behavior in humans can be directly manipulated by a dopaminergic drug, but that the effectiveness of such a manipulation depends on baseline differences in sensation-seeking trait. This emphasizes the importance of considering individual differences when investigating manipulation of risky decision-making, and may have relevance for the development of pharmacotherapies for disorders involving excessive risk-taking in humans, such as pathological gambling.