UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.

Motivation: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes.

Glycoprotein YKL-40: A potential biomarker of disease activity in rheumatoid arthritis during intensive treatment with csDMARDs and infliximab. Evidence from the randomised controlled NEO-RACo trial.

Objective: YKL-40, a chitinase-like glycoprotein associated with inflammation and tissue remodeling, is produced by joint tissues and recognized as a candidate auto-antigen in rheumatoid arthritis (RA). In the present study, we investigated YKL-40 as a potential biomarker of disease activity in patients with early RA at baseline and during intensive treatment aiming for early remission.

Methods: Ninety-nine patients with early DMARD-naïve RA participated in the NEO-RACo study.

Temporally versatile polarization entanglement from Bragg reflection waveguides.

Bragg reflection waveguides emitting broadband parametric downconversion (PDC) have been proven to be well suited for the on-chip generation of polarization entanglement in a straightforward fashion [Sci. Rep.3, 2314 (2013)SRWSDA2045-232210.

Three out of four disease-modifying anti-rheumatic drug-naïve rheumatoid arthritis patients meet 28-joint Disease Activity Score remission at 12 months: results from the FIN-ERA cohort.

Objective: To assess what proportion of patients with disease-modifying anti-rheumatic drug (DMARD)-naïve early rheumatoid arthritis (ERA) reach 28-joint Disease Activity Score (DAS28) remission over 1 year, and remission variability across clinics in Finland.

Method: Patients with DMARD-naïve newly diagnosed inflammatory arthritis were recruited. The proportion of patients in 28-joint Disease Activity Score with three variables (DAS28-3) remission was compared across sites.

Uncovering dispersion properties in semiconductor waveguides to study photon-pair generation.

We investigate the dispersion properties of ridge Bragg-reflection waveguides to deduce their phasematching characteristics. These are crucial for exploiting them as sources of parametric down-conversion (PDC). In order to estimate the phasematching bandwidth we first determine the group refractive indices of the interacting modes via Fabry-Perot experiments in two distant wavelength regions.

Mode-resolved Fabry-Perot experiment in low-loss Bragg-reflection waveguides.

Based on the interaction between different spatial modes, semiconductor Bragg-reflection waveguides (BRWs) provide a highly functional platform for non-linear optics. For achieving any desired quantum optical functionality, we must control and engineer the properties of each spatial mode. To reach this purpose we extend the Fabry-Perot technique and achieve a detailed linear optical characterization of dispersive multimode semiconductor waveguides.

Major histocompatibility complex associations of ankylosing spondylitis are complex and involve further epistasis with ERAP1.

Ankylosing spondylitis (AS) is a common, highly heritable, inflammatory arthritis for which HLA-B*27 is the major genetic risk factor, although its role in the aetiology of AS remains elusive. To better understand the genetic basis of the MHC susceptibility loci, we genotyped 7,264 MHC SNPs in 22,647 AS cases and controls of European descent. We impute SNPs, classical HLA alleles and amino-acid residues within HLA proteins, and tested these for association to AS status.

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.

UniProtKB/Swiss-Prot provides expert curation with information extracted from literature and curator-evaluated computational analysis. As knowledgebases continue to play an increasingly important role in scientific research, a number of studies have evaluated their accuracy and revealed various errors. While some are curation errors, others are the result of incorrect information published in the scientific literature.

Targeted treatment with a combination of traditional DMARDs produces excellent clinical and radiographic long-term outcomes in early rheumatoid arthritis regardless of initial infliximab. The 5-year follow-up results of a randomised clinical trial, the NEO-RACo trial.

Objective: To study whether adding initial infliximab to remission-targeted initial combination-DMARD treatment improves the long-term outcomes in patients with early rheumatoid arthritis (RA).

Methods: Ninety-nine patients with early, DMARD-naïve RA were treated with a triple combination of DMARDs, starting with methotrexate (max 25 mg/week), sulfasalazine (max 2 g/day), hydroxychloroquine (35 mg/kg/week), and with prednisolone (7.5 mg/day), and randomised to double blindly receive either infliximab (3 mg/kg; FIN-RACo+INFL) or placebo (FIN-RACo+PLA) infusions during the first 6 months.

Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci.

Ankylosing spondylitis is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. In addition to HLA-B*27 alleles, 12 loci have previously been identified that are associated with ankylosing spondylitis in populations of European ancestry, and 2 associated loci have been identified in Asians. In this study, we used the Illumina Immunochip microarray to perform a case-control association study involving 10,619 individuals with ankylosing spondylitis (cases) and 15,145 controls.

Gene Ontology annotations and resources.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies.

A 2D quantum walk simulation of two-particle dynamics.

Multidimensional quantum walks can exhibit highly nontrivial topological structure, providing a powerful tool for simulating quantum information and transport systems. We present a flexible implementation of a two-dimensional (2D) optical quantum walk on a lattice, demonstrating a scalable quantum walk on a nontrivial graph structure. We realized a coherent quantum walk over 12 steps and 169 positions by using an optical fiber network.

The UniProt-GO Annotation database in 2011.

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.

Impaired postural control is associated with worse scores of the Health Assessment Questionnaire disability index among women with rheumatoid arthritis.

Objective: To explore the relationship between functional status and different domains of postural control, and to make recommendations about the use of postural control tests in clinical practice among women with rheumatoid arthritis.

Subjects: A total of 91 women with rheumatoid arthritis and 110 controls. The patients were grouped according to the total score of the Health Assessment Questionnaire (HAQ):HAQ1 = 0 (good, n = 21); HAQ2 = 0.

Testing spectral filters as Gaussian quantum optical channels.

We experimentally investigate the mode characteristics of multimode radiation fields propagating through frequency-dependent Gaussian channels. After manipulating the twin beams emitted from a conventional parametric downconversion source via spectral filtering, we study the changes in their mode characteristics, utilizing the joint normalized correlation functions. While filtering reduces the number of spectral modes, it also leads to an apparent mode mismatch, which destroys the perfect photon-number correlation between the twin beams, and influences the mode properties of heralded states.

Probing the negative Wigner function of a pulsed single photon point by point.

We investigate quantum properties of pulsed light fields point by point in phase space. We probe the negative region of the Wigner function of a single photon generated by the means of waveguided parametric down conversion. This capability is achieved by employing loss-tolerant photon-number resolving detection, allowing us to directly observe the oscillations of the photon statistics in dependence of applied displacements in phase space.

Accessing higher order correlations in quantum optical states by time multiplexing.

We experimentally measured higher order normalized correlation functions (NCF) of pulsed light with a time-multiplexing detector. We demonstrate excellent performance of our device by verifying unity valued NCF up to the eighth order for coherent light and factorial dependence of the NCF for pseudothermal light. We applied our measurement technique to a type-II parametric down-conversion source to investigate mutual two-mode correlation properties and ascertain nonclassicality.

Producing high fidelity single photons with optimal brightness via waveguided parametric down-conversion.

Parametric down-conversion (PDC) offers the possibility to control the fabrication of non-Gaussian states such as Fock states. However, in conventional PDC sources energy and momentum conservation introduce strict frequency and photon number correlations, which impact the fidelity of the prepared state. In our work we optimize the preparation of single-photon Fock states from the emission of waveguided PDC via spectral filtering.

Subaxial cervical vertebrae in patients with juvenile idiopathic arthritis--something special?

Objectives: To describe the main dimensions of the cervical vertebrae and spinal canal in two groups with juvenile idiopathic arthritis (JIA) and a non-inflammatory control group.

Methods: There were altogether 158 female patients in three different groups included in the study: a group with severe, complicated JIA (sJIA), a population based JIA group (pJIA), and fibromyalgia patients as a non-inflammatory control group (pFM). The patients' clinical records and cervical spine radiographs taken in adult age (>17 years) were evaluated.

Rheumatoid atlantoaxial subluxation can be prevented by intensive use of traditional disease modifying antirheumatic drugs.

Objective: To evaluate the 5-year incidence of cervical spine disorders in patients with early rheumatoid arthritis (RA) treated by 2 different disease modifying antirheumatic drug (DMARD) strategies.

Methods: In a national, multicenter, prospective FIN-RACo-trial, a cohort of 199 patients with early, clinically active RA was randomly assigned to treatment with a combination of 3 DMARD and prednisolone (Combi group) or with a single DMARD (Single group) with or without prednisolone, aiming to induce remission. After 2 years, the DMARD therapy was unrestricted.

Photon number statistics of multimode parametric down-conversion.

We experimentally analyze the complete photon number statistics of parametric down-conversion and ascertain the influence of multimode effects. Our results clearly reveal a difference between single-mode theoretical description and the measured distributions. Further investigations assure the applicability of loss-tolerant photon number reconstruction and prove strict photon number correlation between signal and idler modes.

Toll-like receptor 4 and CD14 polymorphisms in ankylosing spondylitis: evidence of a weak association in Finns.

Objective: To investigate the association of CD14 and Toll-like receptor (TLR4) with ankylosing spondylitis (AS).

Methods: A promoter variant in CD14 and 2 coding polymorphisms in TLR4 were investigated in UK and Finnish families with AS and in a UK case-control study. A metaanalysis of published TLR4 and CD14 studies was performed.

Serum antibodies against intact human collagen IX are elevated at onset of rheumatoid arthritis but are not related to development of erosions.

Objective: To measure the presence of autoantibodies binding to intact human recombinant collagen IX and assess their usefulness as a diagnostic marker and an indicator of disease activity in rheumatoid arthritis (RA).

Methods: Recombinant human full-length collagen IX (rCIX) was produced in a baculovirus expression system and purified for use in ELISA developed to detect antibodies to native and denatured collagen IX. Fifty-three patients with recent-onset rheumatoid factor-seropositive RA were analyzed for the presence of rCIX antibodies of the IgG type at the time of initial diagnosis and after 3, 6, 12, and 24 months of followup.