[A rare interstitital lung disease in two smokers]

Pulmonary Langerhans-cell histiocytosis should be suspected in patients with nodular or cystic changes in the upper pulmonary lobes. Patients with Langerhans-cell histiocytosis usually have a history of smoking; lack of nicotine exposure or an age over 60 years makes the diagnosis unlikely. The diagnostic work-up should include a high-resolution CT of the chest as well as a bronchoalveolar lavage, bronchoscopic and/or surgical lung biopsy. Smoking cessation is the essential part of the treatment.

[Dance therapeutic workshop for elderly people living in a home]

Elderly persons are often depressive; thus they are in loss of desire and motivation. They don't take care anymore of themselves and seem disembodied. It is exactly on this loss of desire that arts therapies have an impact. This involvement of the body facilitates the awareness of one's often unexploited capacities but also allows the emergence of pleasure and finally desire. Arts therapies are based on the conscience of here and now, with the perspective to become a creative being. It is the matter of helping people to recognize their own creativity that was underestimated by themselves up to here. These sessions allow the patients to go out of their room while bringing them a sensation of relaxation and well-being. They are proud to produce something by themselves and recover thus a certain self-esteem. And, through this activity, they are able to express what they feel. The statistical computations are made with the data of 10 elderly persons aged 77 to 95 years. We analyze the rating scales for self-expression through movement during 10 sessions. The subjects also filled in the Campbell's Index of Well-being in T1 and T2. Arts therapies improve in a significant way the cognitive functioning and the psychological well-being of elderly persons, as well as their quality of life.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

The identification of orthologous relationships forms the basis for most comparative genomics studies. Here, we present the second version of the eggNOG database, which contains orthologous groups (OGs) constructed through identification of reciprocal best BLAST matches and triangular linkage clustering. We applied this procedure to 630 complete genomes (529 bacteria, 46 archaea and 55 eukaryotes), which is a 2-fold increase relative to the previous version. The pipeline yielded 224 847 OGs, including 9724 extended versions of the original COG and KOG. We computed OGs for different levels of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional descriptions, protein domains, and functional categories as defined initially for the COG/KOG database. In-depth analysis is facilitated by precomputed high-quality multiple sequence alignments and maximum-likelihood trees for each of the available OGs. Altogether, eggNOG covers 2 242 035 proteins (built from 2 590 259 proteins) and provides a broad functional description for at least 1 966 709 (88%) of them. Users can access the complete set of orthologous groups via a web interface at: http://eggnog.embl.de.

An investigation on the Culicoides species composition at seven sites in southern Switzerland

In the past decade, there have been regular outbreaks of bluetongue (BT) in many parts of Europe. Owing to the presence of BT disease and its vectors in countries adjacent to Switzerland, an initial entomological survey was conducted in 2003, which established the presence of several midges of the genus Culicoides (Diptera: Ceratopogonidae). Subsequently, a sentinel herd monitoring system was established with the primary entomological aim being the determination and further study of Culicoides population compositions. Insects were collected in 2005 and 2006 at seven sentinel herd sites in the south of Switzerland (canton of Ticino) near the border of Italy, using Onderstepoort-type light traps. This region is botanically and zoologically similar to the Mediterranean and is one of the warmest and most humid areas of the country, hence it is considered a potential access path for BT disease into Switzerland. Collections were made at four cattle farms, two equestrian centres and one goat farm. Sites were sampled four times per month from June to October. Traps were operated from dusk until dawn and samples were collected monthly for analysis through microscopy as well as a Culicoides imicola-specific PCR. Results confirmed the absence of C. imicola (Kieffer) and demonstrated that the potential BT virus vectors are highly abundant, notably: Culicoides obsoletus (Meigen), Culicoides scoticus (Downes & Kettle) and Culicoides dewulfi (Goetghebuer) subgenus Avaritia and Culicoides pulicaris (Linnaeus) subgenus Culicoides. These findings expand the current knowledge of Culicoides population composition in the southern part of the Switzerland. Culicoides cataneii (Clastrier), Culicoides flavipulicaris (Dzhafarov), Culicoides indistinctus (Khalaf), Culicoides nubeculosus (Meigen) and species of the Grisescens complex were reported for the first time in Switzerland.

OnTheFly: a tool for automated document-based text annotation, data linking and network generation

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database.

Availability:http://onthefly.embl.de,http://onthefly.embl.de/FAQ.html

Contact:pavlopou@embl.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Particulate matter inhalation during hay storing activity induces systemic inflammation and platelet aggregation

The aim of this study was to investigate possible pathomechanisms behind the cardiovascular morbidity caused by inhalation of particulate matter (PM(10)). For that purpose, healthy volunteers were exposed to high PM(10) concentrations during a 2 h hay storing activity. Blood was drawn in the evening before and after PM(10) exposure and in the morning and evening of the day after exposure. The leukocyte count increased after PM(10) exposure with an initial increase of segmented neutrophils followed by banded forms. C-reactive protein increased over time. Fibrinogen and plasma viscosity became increased in the evening of the day after PM(10) exposure. Platelet aggregation was increased in the evening after PM(10) exposure. At the same time von Willebrand factor and factor VIII were increased, reflecting endothelial activation. These results confirm that acute inhalative exposure to high PM(10) concentrations during hay storage activity leads to a systemic inflammatory reaction, endothelial activation, and platelet aggregation.

[Chronic facial pain due to a brainstem cavernoma]

Idiopathic trigeminal neuralgia is almost always associated with pathological nerve/vessel contact. Symptomatic forms of trigeminal neuralgia include cases of multiple sclerosis, infratentorial tumours and postherpetic neuralgia. Vascular malformations causing neuralgia have rarely been reported. We present the case of a 55-year old woman, who suffered from facial pain and ptosis on her left side. Repeated neurological examinations as well as repeated magnetic resonance imaging did not lead to a definite diagnosis or therapy. The pain suddenly stopped three weeks before admission and only a slight left sided facial hypaesthesia persisted. Reevaluating the older MRI we found a small signal alteration of 2 mm in the caudal part of the left trigeminal nucleus. A new MRI showed a subacute haemorrhage into a small brainstem cavernoma, which must have caused the pain and later on the hypaesthesia. Small vascular malformations are a rare cause of neuropathic facial pain.

Overexpression of human wildtype torsinA and human DeltaGAG torsinA in a transgenic mouse model causes phenotypic abnormalities

Primary torsion dystonia is an autosomal-dominant inherited movement disorder. Most cases are caused by an in-frame deletion (GAG) of the DYT1 gene encoding torsinA. Reduced penetrance and phenotypic variability suggest that alteration of torsinA amino acid sequence is necessary but not sufficient for development of clinical symptoms and that additional factors must contribute to the factual manifestation of the disease. We generated 4 independent transgenic mouse lines, two overexpressing human mutant torsinA and two overexpressing human wildtype torsinA using a strong murine prion protein promoter. Our data provide for the first time in vivo evidence that not only mutant torsinA is detrimental to neuronal cells but that also wildtype torsinA can lead to neuronal dysfunction when overexpressed at high levels. This hypothesis is supported by (i) neuropathological findings, (ii) neurochemistry, (iii) behavioral abnormalities and (iv) DTI-MRI analysis.

Novel approach for assessing performance of PCR cyclers used for diagnostic testing

As part of a large international project for validation and standardization of PCR, the influence of thermocyclers on PCR was tested. Six brand-new, Peltier technology-driven 96-well thermocyclers were subjected to a novel and stringent in-tube (not block) physical testing. The temperature was directly monitored in PCR tubes containing 50 microl of distilled water at 13 different block positions. The certified temperature accuracy of the measurement system was +/-0.3 degrees C. Finally, the results of the physical testing were compared to those of an amplification efficiency study running an in-house PCR assay. The cyclers did not perform within the manufacturer's specification. Premature timing, under- and overshooting, and spatial variation of heat transfer were found to be the critical factors. The physical testing allowed us to distinguish accurate from less-accurate (2/6) cyclers. The lack of thermal homogeneities became most evident at the denaturation level during the first 15 s. At the time point zero, the accurate cyclers showed temperature deviations of 0.5 to 1.5 degrees C, whereas less-accurate cyclers failed to reach the set temperature by 13 to 20 degrees C. Consequently, the two less-accurate cyclers could not gain positive PCR results by running an in-house PCR assay. However, by modifying the original temperature protocol by increasing the denaturation temperature and time, the amplification efficiency of these two cyclers could be improved significantly. The results have implication for laboratories using diagnostic PCR testing.

Automated alignment and pattern recognition of single-molecule force spectroscopy data

Recently, direct measurements of forces stabilizing single proteins or individual receptor-ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor-ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.

[Diarrhea and weight loss in common variable immunodeficiency]

A 25-year-old male was hospitalized for diarrhea and weight loss. Since childhood he had experienced recurrent episodes of pneumonia and diarrhea. Physical and laboratory findings were compatible with malabsorption. On endoscopy, nodular lymphoid hyperplasia (NLH) of the small intestine was found. Common variable immunodeficiency syndrome (CVID) was suspected and diagnosis was established by demonstrating a significant reduction of plasma gamma-globulin levels. Immediately after starting immunoglobulin treatment diarrhea stopped, and both incidence and severity of pulmonary infections were significantly reduced, while recurrent gastrointestinal infections (notably lambliasis and Campylobacter infections) continued to occur and both bronchiectases and splenomegaly were progressive over years. This case report focuses on CVID as a potential underlying cause of diarrhea. The most important complications of the disease are presented. Therapeutical options are discussed in the light of recently published data.

[The importance of a careful examination of all persons in close contact with newly diagnosed infectious tuberculosis]

The diagnosis of infectious pulmonary tuberculosis was made in a 53-year-old Macedonian man. A careful examination of all persons in close contact with him according to the guidelines of the Swiss respiratory society was performed. Pulmonary tuberculosis was diagnosed in his 22-year-old son, in his 20-year-old daughter and in his 3-year-old granddaughter. Seven persons had isoniazid preventive treatment for latent tuberculosis. These data shows very clearly that a careful examination of all persons in close contact with contagious tuberculosis is very important.