The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Control of Proton Beam Self-Modulation for AWAKE via Initial Beam Parameters

Plasma wakefield acceleration is a promising concept in the development of a new type of electron accelerators for high-energy physics experiments. The Advanced Wakefield Experiment AWAKE is based on this concept and has been, following the first successful proof of concept Run, under continuous and carefully planned development. In the future Run 2c, the experimental setup will consist of two plasma sources in which the highly relativistic proton driver bunch will undergo seeded self-modulation in the first plasma source, and electron acceleration will be performed in the second. Self-modulation is governed by transverse wakefields which have their origin in the self-modulation instability (SMI). At AWAKE, SMI can be controlled by either laser or electron seeding, which provides a wakefield peak that defines the phase of the fields and that of the emerging micro-bunch train. Consecutive bunches appear in the periodicity given by the plasma frequency such that they coherently drive the longitudinal wakefields. When laser seeding is applied, the part of the bunch in front of the seeding does not travel through plasma. For a successful application of laser seeding, this unmodulated front must not undergo self-modulation in the second plasma source. This front part will have a transverse bunch size of about 500 μm when arriving at the second plasma source. I studied in this thesis the self-modulation of proton beams of different transverse sizes. In the experiment the transverse proton beam sizes at the plasma entrance are measured by a code I developed which provides a description of the proton beam envelope. This characterisation of the proton beam is used to determine the parameter space of the numeric simulations. A detailed explanation of the code and propositions for noise reduction are given in this work. In this thesis for the first time the self-modulation growth rate of beams with transverse sizes larger than in the baseline design will be compared. It will be demonstrated through experiment that a proton beam with a transverse size of ∼560 μm and a length of ∼6.7 cm, focused at the plasma entrance, does not self-modulate in front of the bunch centre. This beam size corresponds, when laser seeding is applied, to the size of the unmodulated front at the second plasma source in Run 2c. These important results indicate that laser seeding could be possible in Run 2c. Before this work, comparisons of experimental results with numeric simulations have only been carried out for beam sizes according to the baseline design. I will show that the simulations performed with a quasi-static PIC code show good qualitative agreement with the experiment when comparing the micro-bunch train structure for a larger beam after seeded self-modulation. It is therefore shown that numerical simulations remain also for larger beams an important tool to discover and understand trends and phenomena. Additionally, I will show a previously unseen band-like radial structure that has been observed in the transverse projections of the beams. This radial structure is observed in numerical simulations after letting the bunch propagate through 10 m of plasma and is further enhanced as the beam size is increased. This could be used for future self-modulation diagnostics

Protein microarray allergen profiling in bronchoalveolar lavage fluid and serum of horses with asthma.

BACKGROUND The diagnostic value of allergen-specific immunoglobulin E (IgE) in horses with asthma is uncertain. A recently developed protein microarray detected abnormally high latex-specific IgE concentrations in the serum of horses with severe asthma. OBJECTIVES The main objective was to characterize the IgE profiles of asthmatic horses in Switzerland using a protein microarray platform in serum and bronchoalveolar lavage fluid (BALF). The secondary objective was to determine whether serological and BALF allergen-specific IgE concentrations correlated. ANIMALS Forty-four asthmatic and 39 control horses ≥5 years of age. METHODS This prospective cross-sectional study investigated the sensitization profiles of horses with asthma compared with environmentally matched healthy controls. Both serum and BALF were analyzed using the protein microarray. Partial least square-discriminant analysis (PLS-DA) was used to identify and rank the importance of the allergens for class detection (ie, asthma vs control), with a variable influence on the projection (VIP) >1 considered significant. RESULTS The allergens that best discriminated (VIP >1) asthmatic horses from controls were proteins derived from fungi (Aspergillus fumigatus), insects (Culicoides spp.), and latex (Hevea brasiliensis). The serological model predictive ability was markedly inferior (area under the curve [AUC] 0.585, 95% confidence interval [CI]: 0.454-0.747) to that of the BALF (AUC 0.751, 95% CI: 0.582-0.866). The two models shared nine allergens, of which eight showed significant weak to moderate correlations. CONCLUSION AND CLINICAL IMPORTANCE The concentrations of several allergen-specific IgE were higher in asthmatic horses. The protein microarray performed better on BALF than serum for detection of asthma. Serological IgE concentrations do not closely correlate with BALF concentrations and should be interpreted with caution