Staphylococci from the feces of different animal species: biotypes of Staphylococcus aureus strains of sheep and goat origin.

Staphylococcus aureus was found in 96% of the rectal swabs from 133 sheep and in 80% of the swabs from 125 goats. Seventy-seven percent of the isolates from both hosts exhibited the fibrinolytic and growth characteristics of human biotype A on human plasma and crystal violet agar, respectively, but 99% of these isolates resembled S. aureus of animal origin in their other properties. Only 21% of the sheep and 24% of the goat isolates were clearly identifiable as human biotype A and animal biotypes B and C.     

Clinical and molecular description of the prenatal diagnosis of a fetus with a maternally inherited microduplication 22q11.2 of 2.5 Mb

Microduplications of 22q11.2 have been recently characterized as a new genomic duplication syndrome showing an extremely variable phenotype ranging from normal or mild learning disability to multiple congenital defects and sharing some overlapping features with DiGeorge/Velocardiofacial syndrome (DGS/VCFS). We report on the prenatal diagnosis of a 22q11.2 microduplication in a fetus with normal development that was referred for chromosomal analysis at 17 weeks of gestation because of advanced maternal age. Pregnancy was the result of an IVF-ICSI attempt after 4 years of infertility, mainly due to severe oligoasthenoteratospermia of the father. Amniocentesis was undertaken and cytogenetic analysis revealed an apparently normal male karyotype. Multiple Ligation-dependent Probe Amplification (MLPA) revealed a microduplication in the 22q11.2 chromosome region. Parental analysis showed that the 22q11.2 microduplication has been inherited from the otherwise healthy mother. Analysis with high resolution array-CGH showed that the size of the microduplication is 2.5 Mb and revealed the genes that are duplicated, including the TBX1 gene. The parents elected to continue with the pregnancy and the infant is now five months old and shows normal development.     

Expression of the Novel Hepatitis C Virus Core+1/ARF Protein in the Context of JFH1-Based Replicons

Hepatitis C virus contains a second open reading frame within the core gene, designated core+1/ARF. Here we demonstrate for the first time expression of core+1/ARF protein in the context of a bicistronic JFH1-based replicon and report the production of two isoforms, core+1/L (long) and core+1/S (short), with different kinetics.     

Role of superoxide-nitric oxide interactions in the accelerated age-related loss of muscle mass in mice lacking Cu,Zn superoxide dismutase

Mice lacking Cu,Zn superoxide dismutase (SOD1) show accelerated, age-related loss of muscle mass. Lack of SOD1 may lead to increased superoxide, reduced nitric oxide (NO), and increased peroxynitrite, each of which could initiate muscle fiber loss. Single muscle fibers from flexor digitorum brevis of wild-type (WT) and Sod1(-/-) mice were loaded with NO-sensitive (4-amino-5-methylamino-2',7'-difluorofluorescein diacetate, DAF-FM) and superoxide-sensitive (dihydroethidium, DHE) probes. Gastrocnemius muscles were analyzed for SOD enzymes, nitric oxide synthases (NOS), and 3-nitrotyrosine (3-NT) content. A lack of SOD1 did not increase superoxide availability at rest because no increase in ethidium or 2-hydroxyethidium (2-HE) formation from DHE was seen in fibers from Sod1(-/-) mice compared with those from WT mice. Fibers from Sod1(-/-) mice had decreased NO availability (decreased DAF-FM fluorescence), increased 3-NT in muscle proteins indicating increased peroxynitrite formation and increased content of peroxiredoxin V (a peroxynitrite reductase), compared with WT mice. Muscle fibers from Sod1(-/-) mice showed substantially reduced generation of superoxide in response to contractions compared with fibers from WT mice. Inhibition of NOS did not affect DHE oxidation in fibers from WT or Sod1(-/-) mice at rest or during contractions, but transgenic mice overexpressing nNOS showed increased DAF-FM fluorescence and reduced DHE oxidation in resting muscle fibers. It is concluded that formation of peroxynitrite in muscle fibers is a major effect of lack of SOD1 in Sod1(-/-) mice and may contribute to fiber loss in this model, and that NO regulates superoxide availability and peroxynitrite formation in muscle.     

Microfabricated Inserts for Magic Angle Coil Spinning (MACS) Wireless NMR Spectroscopy

This article describes the development and testing of the first automatically microfabricated probes to be used in conjunction with the magic angle coil spinning (MACS) NMR technique. NMR spectroscopy is a versatile technique for a large range of applications, but its intrinsically low sensitivity poses significant difficulties in analyzing mass- and volume-limited samples. The combination of microfabrication technology and MACS addresses several well-known NMR issues in a concerted manner for the first time: (i) reproducible wafer-scale fabrication of the first-in-kind on-chip LC microresonator for inductive coupling of the NMR signal and reliable exploitation of MACS capabilities; (ii) improving the sensitivity and the spectral resolution by simultaneous spinning the detection microcoil together with the sample at the "magic angle" of 54.74° with respect to the direction of the magnetic field (magic angle spinning - MAS), accompanied by the wireless signal transmission between the microcoil and the primary circuit of the NMR spectrometer; (iii) given the high spinning rates (tens of kHz) involved in the MAS methodology, the microfabricated inserts exhibit a clear kinematic advantage over their previously demonstrated counterparts due to the inherent capability to produce small radius cylindrical geometries, thus tremendously reducing the mechanical stress and tearing forces on the sample. In order to demonstrate the versatility of the microfabrication technology, we have designed MACS probes for various Larmor frequencies (194, 500 and 700 MHz) testing several samples such as water, Drosophila pupae, adamantane solid and LiCl at different magic angle spinning speeds.     

Serum levels of CXCL13 are associated with ultrasonographic synovitis and predict power Doppler persistence in early rheumatoid arthritis treated with non-biological disease-modifying anti-rheumatic drugs

Introduction

Biological markers specifically reflecting pathological processes may add value in the assessment of inter-individual variations in the course of rheumatoid arthritis (RA). The current study was undertaken to investigate whether baseline serum levels of the chemokine CXCL13 might predict clinical and ultrasonographic (US) outcomes in patients with recent-onset RA.

Methods

The study included 161 early RA patients (disease duration < 12 months) treated according to a disease activity score (DAS) driven step-up protocol aiming at DAS < 2.4. Clinical disease activity measures were collected at baseline, 2, 4, 6, 9 and 12 months, and US examination of the hands was performed at baseline, 6 and 12 months. Grey-Scale (GS) and Power Doppler (PD) synovitis were scored (0 to 3), with overall scores as the sum of each joint score. CXCL13 levels were measured at baseline by enzyme-linked immunosorbent assay and evaluated in relation to the achievement of low disease activity (LDA, DAS < 2.4) and US residual inflammation (PD ≤ 1) at 12 months.

Results

Baseline levels of CXCL13 were significantly higher in RA compared to healthy controls (n = 19) (P = 0.03) and correlated with measures of synovitis, such as the swollen joint count (R 0.28, P < 0.001), the US-GS (R 0.27, P = 0.003) and US-PD (R 0.26, P = 0.005) score. Although CXCL13 did not predict the likelihood of achieving clinical LDA at 12 months within a structured treat-to-target protocol, elevated levels of CXCL13 were associated with more frequent increases of methotrexate dosage (P < 0.001). Using adjusted analyses, the highest levels of CXCL13 (> 100 pg/ml) were the only independent predictor of residual imaging inflammation (P = 0.005), irrespective of initial US-PD scores, disease activity status, acute phase reactants and autoantibodies. Among the patients in clinical LDA at 12 months, US-PD scores ≤ 1 were less frequently achieved in the high baseline CXCL13 (> 100 pg/ml) group, with an adjusted OR = 0.06 (95% CI 0.01 to 0.55, P = 0.01).

Conclusions

CXCL13 emerges as a new biological marker in early RA, accurate in assessing the severity of synovitis and the persistence of US-PD activity over time in response to conventional treatments.     

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics

Background

So far many algorithms have been proposed towards the detection of significant genes in microarray analysis problems. Several of those approaches are freely available as R-packages though their engagement in gene expression analysis by non-bioinformaticians is usually a frustrating task. Besides, only some of those packages offer a complete suite of tools starting from initial data import and ending to analysis report. Here we present an R/Bioconductor package that implements a hybrid gene selection method along with a bunch of functions to facilitate a thorough and convenient gene expression profiling analysis.

Results

mAPKL is an open-source R/Bioconductor package that implements the mAP-KL hybrid gene selection method. The advantage of this method is that selects a small number of gene exemplars while achieving comparable classification results to other well established algorithms on a variety of datasets and dataset sizes. The mAPKL package is accompanied with extra functionalities including (i) solid data import; (ii) data sampling following a user-defined proportion; (iii) preprocessing through several normalization and transformation alternatives; (iv) classification with the aid of SVM and performance evaluation; (v) network analysis of the significant genes (exemplars), including degree of centrality, closeness, betweeness, clustering coefficient as well as the construction of an edge list table; (vi) gene annotation analysis, (vii) pathway analysis and (viii) auto-generated analysis reporting.

Conclusions

Users are able to run a thorough gene expression analysis in a timely manner starting from raw data and concluding to network characteristics of the selected gene exemplars. Detailed instructions and example data are provided in the R package, which is freely available at Bioconductor under the GPL-2 or later license http://www.bioconductor.org/packages/3.1/bioc/html/mAPKL.html.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0719-5) contains supplementary material, which is available to authorized users.     

A historical perspective on the engineering ideologies of sustainability: the case of SLCA

Purpose

The 1990s produced two distinct engineering ideologies of sustainability—one emphasizing engineering innovation and the other emphasizing socio-cultural change. The technological change ideology of sustainability refers to engineering reform controlled and directed by engineers themselves—in other words, technological practices can be improved through the application of expertise. The technopolitics’ ideology of sustainability is about engineering challenge; it places more emphasis on the devolution of expertise from the existing model of engineering and society, and it questions the dominant values of engineering practice. In this article, I present a historico-philosophical perspective on the development of social life cycle assessment (SLCA) to highlight how the dialectic between sustainability and engineering has been defined largely by the ideology of technological change.

Methods

I provide original historical evidence regarding the roles of key actors and institutions in fitting the life cycle perspective and corporate social responsibility (CSR) into sustainable development. Primary data for this chapter is based on archival materials as well as on 30, in depth, semi-structured interviews with North American and European LCA and SLCA experts. Other primary data were collected from participant observation in SLCA webinars and workshops.

Results and discussion

Technology is at the heart of SLCA—it is a shared faith in technology as the solution. At the same time, there is growing appreciation amongst SLCA proponents that such technology must be construed more critically. Although it remains a subaltern current within LCA, SLCA is evidence of how technological change and technopolitics are starting to converge and influence each other—a probe toward a more reflective form of engineering discourse and toward the formation of a new hybrid sustainability ideology.

Conclusions

SLCA, I argue in this article, is an ideological hybrid where there are many spots of dissent and disagreement but also some surprising fundamental alignments between those who see engineering as techniques and those who believe that engineering needs to be socially and politically contextualized. Yet, even as the concepts of sustainable development, CSR, and LCA provide the intellectual and institutional mold within which SLCA becomes conceivable, these concepts may also obscure the historicity of sustainability engineering.

     

Cardiovascular Comorbidities Relate More than Others with Disease Activity in Rheumatoid Arthritis

Objectives

To explore the influence of comorbidities on clinical outcomes and disease activity in rheumatoid arthritis (RA).

Methods

In patients included in the cross-sectional observational multicenter international study COMORA, demographics, disease characteristics and comorbidities (hypertension, diabetes, hyperlipidemia, renal failure, ischemic heart disease, stroke, cancer, gastro-intestinal ulcers, hepatitis, depression, chronic pulmonary disease, obesity) were collected. Multivariable linear regression models explored the relationship between each comorbidity and disease activity measures: 28-swollen joint count (SJC), 28-tender joint count (TJC), erythrocyte sedimentation rate (ESR), patient’s and physician’s global assessment (PtGA, PhGA), patient reported fatigue and 28-Disease Activity Score (DAS28). Results are expressed as mean difference (MD) adjusted for the main confounders (age, gender, disease characteristics and treatment).

Results

A total of 3,920 patients were included: age (mean ±SD) 56.27 ±13.03 yrs, female 81.65%, disease duration median 7.08 yrs (IQR 2.97–13.27), DAS28 (mean ±SD) 3.74 ± 1.55. Patients with diabetes had more swollen and tender joints and worse PtGA and PhGA (MD +1.06, +0.93, +0.53 and +0.54, respectively). Patients with hyperlipidemia had a lower number of swollen and tender joints, lower ESR and better PtGA and PhGA (MD -0.77, -0.56, -3.56, -0.31 and -0.35, respectively). Patients with history of ischemic heart disease and obese patients had more tender joints (MD +1.27 and +1.07) and higher ESR levels (MD +5.64 and +5.20). DAS28 is influenced exclusively by cardiovascular comorbidities, in particular diabetes, hyperlipidemia, ischemic heart disease and obesity.

Conclusions

Cardiovascular comorbidities relate more than others with disease activity in RA. Diabetes and hyperlipidemia in particular seem associated with higher and lower disease activity respectively influencing almost all considered outcomes, suggesting a special importance of this pattern of comorbidities in disease activity assessment and clinical management.