A novel approach for protein subcellular location prediction using amino acid exposure

BACKGROUND: Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. RESULTS: Our method has two stages. For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. In stage two we use an artificial neural network (ANN) to propose a category from the scores given to the four locations in stage one. The method reaches an accuracy of 68% when using as input 3D-derived values of amino acid exposure. Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. CONCLUSIONS: In this study we explored the relationship between residue exposure and protein subcellular location. We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. Our algorithm uses a novel approach to address the multiclass classification problem. The algorithm is implemented as web server 'NYCE' and can be accessed at http://cbdm.mdc-berlin.de/~amer/nyce

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data

BACKGROUND: Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation. FINDINGS: To facilitate the application of this approach we have created the mBISON web-application. mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3'UTR length. The tool can be accessed from the following web-resource: http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home . CONCLUSION: mBISON is a web-application that helps to extract functional information about miRNAs from gene lists, which is in contrast to comparable applications easy to use by everyone and can be applied on ChIP-seq data directly

Development of a dairy fouling model to assess the efficacy of cleaning procedures using alkaline and enzymatic products

Dairy fouling is defined as the accumulation of thermally insulating materials or deposits from process fluids which are especially formed on heat transfer surfaces. The selection of suitable cleaning strategies to remove dairy fouling requires the understanding of its composition and the relationships with the surfaces where it is formed. For the industry, the development of novel strategies to test cleaning products, as well reducing water and energy consumption during the dairy processing operations is of enormous interest. The results showed the development of a laboratory-milk fouling model (MFM) with an average content of 52.8 mg/cm2 of fouling in the test coupons. Seven different cleaners were tested with a fouling removal effectiveness of between 55% and 97%. Additionally, for evaluating the cleaning process of the model, the turbidity of the cleaning solutions was assessed. We presented an enzymatic alternative to the use of traditional cleaning products, with a similar efficacy against the dairy fouling. 78% of fouling removal after the use of enzymatic solution, in comparison to the 72% of fouling removal after the use of alkaline cleaning products. A reduction in water (−33.3%) and temperature (−28.5%), as well as shorter cleaning times (−33%) than its chemical alternative, was observed.info:eu-repo/semantics/acceptedVersio

Strong lens search in the ESO public Survey KiDS

We have started a systematic search of strong lens candidates in the ESO public survey KiDS based on the visual inspection of massive galaxies in the redshift range $0.1<z<0.5$. As a pilot program we have inspected 100 sq. deg., which overlap with SDSS and where there are known lenses to use as a control sample. Taking advantage of the superb image quality of VST/OmegaCAM, the colour information and accurate model subtracted images, we have found 18 new lens candidates, for which spectroscopic confirmation will be needed to confirm their lensing nature and study the mass profile of the lensing galaxies.Comment: 4 pages, 1 figure, to appear on the refereed Proceeding of the "The Universe of Digital Sky Surveys" conference held at the INAF--OAC, Naples, on 25th-28th november 2014, to be published on Astrophysics and Space Science Proceedings, edited by Longo, Napolitano, Marconi, Paolillo, Iodic

Stokes Diagnostis of 2D MHD-simulated Solar Magnetogranulation

We study the properties of solar magnetic fields on scales less than the spatial resolution of solar telescopes. A synthetic infrared spectropolarimetric diagnostics based on a 2D MHD simulation of magnetoconvection is used for this. We analyze two time sequences of snapshots that likely represent two regions of the network fields with their immediate surrounding on the solar surface with the unsigned magnetic flux density of 300 and 140 G. In the first region we find from probability density functions of the magnetic field strength that the most probable field strength at logtau_5=0 is equal to 250 G. Weak fields (B < 500 G) occupy about 70% of the surface, while stronger fields (B 1000 G) occupy only 9.7% of the surface. The magnetic flux is -28 G and its imbalance is -0.04. In the second region, these parameters are correspondingly equal to 150 G, 93.3 %, 0.3 %, -40 G, and -0.10. We estimate the distribution of line-of-sight velocities on the surface of log tau_5=-1. The mean velocity is equal to 0.4 km/s in the first simulated region. The averaged velocity in the granules is -1.2 km/s and in the intergranules is 2.5 km/s. In the second region, the corresponding values of the mean velocities are equal to 0, -1.8, 1.5 km/s. In addition we analyze the asymmetry of synthetic Stokes-V profiles of the Fe I 1564.8 nm line. The mean values of the amplitude and area asymmetry do not exceed 1%. The spatially smoothed amplitude asymmetry is increased to 10% while the area asymmetry is only slightly varied.Comment: 24 pages, 12 figure

The satellites of the Milky Way – insights from semi-analytic modelling in a ΛCDM cosmology

We combine the six high-resolution Aquarius dark matter simulations with a semi-analytic galaxy formation model to investigate the properties of the satellites of Milky Way-like galaxies. We find good correspondence with the observed luminosity function, luminosity–metallicity relation and radial distribution of the Milky Way satellites. The star formation histories of the dwarf galaxies in our model vary widely, in accordance with what is seen observationally. Some systems are dominated by old populations, whereas others are dominated by intermediate populations; star formation histories can either be continuous or more bursty. Ram-pressure stripping of hot gas from the satellites leaves a clear imprint of the environment on the characteristics of a dwarf galaxy. We find that the fraction of satellites dominated by old populations of stars matches observations well. However, the internal metallicity distributions of the model satellites appear to be narrower than observed. This may indicate limitations in our treatment of chemical enrichment, which is based on the instantaneous recycling approximation. We find a strong correlation between the number of satellites and the dark matter mass of the host halo. Our model works best if the dark matter halo of the Milky Way has a mass of ∼8 × 1011 M⊙, in agreement with the lower estimates from observations, but about a factor of 2 lower than estimates based on the Local Group timing argument or abundance matching techniques. The galaxy that resembles the Milky Way the most also has the best-matching satellite luminosity function, although it does not contain an object as bright as the Large or Small Magellanic Cloud. Compared to other semi-analytic models and abundance matching relations we find that central galaxies reside in less massive haloes, but the halo mass–stellar mass relation in our model is consistent both with hydrodynamical simulations and with recent observations

Quantitative trait loci for bone traits segregating independently of those for growth in an F-2 broiler X layer cross

An F broiler-layer cross was phenotyped for 18 skeletal traits at 6, 7 and 9 weeks of age and genotyped with 120 microsatellite markers. Interval mapping identified 61 suggestive and significant QTL on 16 of the 25 linkage groups for 16 traits. Thirty-six additional QTL were identified when the assumption that QTL were fixed in the grandparent lines was relaxed. QTL with large effects on the lengths of the tarsometatarsus, tibia and femur, and the weights of the tibia and femur were identified on GGA4 between 217 and 249 cM. Six QTL for skeletal traits were identified that did not co-locate with genome wide significant QTL for body weight and two body weight QTL did not coincide with skeletal trait QTL. Significant evidence of imprinting was found in ten of the QTL and QTL x sex interactions were identified for 22 traits. Six alleles from the broiler line for weight- and size-related skeletal QTL were positive. Negative alleles for bone quality traits such as tibial dyschondroplasia, leg bowing and tibia twisting generally originated from the layer line suggesting that the allele inherited from the broiler is more protective than the allele originating from the layer

Phase diagram and influence of defects in the double perovskites

The phase diagram of the double perovskites of the type Sr_{2-x} La_x Fe Mo O_6 is analyzed, with and without disorder due to antisites. In addition to an homogeneous half metallic ferrimagnetic phase in the absence of doping and disorder, we find antiferromagnetic phases at large dopings, and other ferrimagnetic phases with lower saturation magnetization, in the presence of disorder.Comment: 4 pages, 3 postscript figures, some errata correcte

The extremal limits of the C-metric: Nariai, Bertotti-Robinson and anti-Nariai C-metrics

In two previous papers we have analyzed the C-metric in a background with a cosmological constant, namely the de Sitter (dS) C-metric, and the anti-de Sitter (AdS) C-metric, following the work of Kinnersley and Walker for the flat C-metric. These exact solutions describe a pair of accelerated black holes in the flat or cosmological constant background, with the acceleration A being provided by a strut in-between that pushes away the two black holes. In this paper we analyze the extremal limits of the C-metric in a background with generic cosmological constant. We follow a procedure first introduced by Ginsparg and Perry in which the Nariai solution, a spacetime which is the direct topological product of the 2-dimensional dS and a 2-sphere, is generated from the four-dimensional dS-Schwarzschild solution by taking an appropriate limit, where the black hole event horizon approaches the cosmological horizon. Similarly, one can generate the Bertotti-Robinson metric from the Reissner-Nordstrom metric by taking the limit of the Cauchy horizon going into the event horizon of the black hole, as well as the anti-Nariai by taking an appropriate solution and limit. Using these methods we generate the C-metric counterparts of the Nariai, Bertotti-Robinson and anti-Nariai solutions, among others. One expects that the solutions found in this paper are unstable and decay into a slightly non-extreme black hole pair accelerated by a strut or by strings. Moreover, the Euclidean version of these solutions mediate the quantum process of black hole pair creation, that accompanies the decay of the dS and AdS spaces

Controlled clinical trial comparing the effectiveness of a mindfulness and self-compassion 4-session programme versus an 8-session programme to reduce work stress and burnout in family and community medicine physicians and nurses: MINDUUDD study protocol

Background: Health personnel are susceptible to high levels of work stress and burnout due to the psychological and emotional demands of their work, as well as to other aspects related to the organisation of that work. This paper describes the rationale and design of the MINDUUDD study, the aim of which is to evaluate the effectiveness of a mindfulness and self-compassion 4-session programme versus the standard 8-session programme to reduce work stress and burnout in Family and Community Medicine and Nursing tutors and residents. Methods: The MINDUDD study is a multicentre cluster randomised controlled trial with three parallel arms. Six Teaching Units will be randomised to one of the three study groups: 1) Experimental Group-8 (EG8); 2) Experimental Group-4 (EG4) Control group (CG). At least 132 subjects will participate (66 tutors/66 residents), 44 in the EG8, 44 in the EG4, and 44 in the CG. Interventions will be based on the Mindfulness-Based Stress Reduction (MBSR) program, including some self-compassion practices of the Mindful Self-Compassion (MSC) programme. The EG8 intervention will be implemented during 8 weekly face-to-face sessions of 2.5 h each, while the EG4 intervention will consist of 4 sessions of 2.5 h each. The participants will have to practice at home for 30 min/day in the EG8 and 15 min/day in the EG4. The Five Facet Mindfulness Questionnaire (FFMQ), Self-Compassion Scale (SCS), Perceived Stress Questionnaire (PSQ), Maslach Burnout Inventory (MBI), Jefferson Scale of Physician Empathy (JSPE), and Goldberg Anxiety-Depression Scale (GADS) will be administered. Measurements will be taken at baseline, at the end of the programs, and at three months after completion. The effect of the interventions will be evaluated by bivariate and multivariate analyses (Multiple Linear Regression). Discussion: If the abbreviated mindfulness programme is at least as effective as the standard program, its incorporation into the curriculum and training plans will be easier and more appropriate. It will also be more easily applied and accepted by primary care professionals because of the reduced resources and means required for its implementation, and it may also extend beyond care settings to academic and teaching environments as well