An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker.

[Mobile team of palliative care in a department of neurology: value of two multidisciplinary and professional groups fruit of a joint distribution of the palliative approach and ethical support]. / L'équipe mobile de soins palliatifs en service de neurologie : présentation de deux groupes interdisciplinaires et pluriprofessionnels fruits d'un projet commun de diffusion de la démarche palliative et d'aide à la réflexion éthique.

This article describes how a mobile team of palliative care and a department of neurology learned to cope with many complex end-of-life situations. After a brief introduction to inter-team cooperation, clinical work of the mobile team with patients and families and its cooperation with the neurology team are presented. The specificity of supportive care in neurology is also analyzed. Two interdisciplinary and multi-professional tools - the Palliative Care Resource Group and the Ethics Consultation Group - are described, with their activities and their goals. The Palliative Care Resource Group is a specific entity whose identity lies at the crossroads between commonly recognized organizational units: clinic staff, clinical practice, ethical or organizational analysis groups (Balint, 1960), discussion groups (Rusznievski, 1999), training groups. It has several objectives: 1) create a robust conceptual environment enabling the pursuit of palliative care practices without relying on the empty paradigm of stereotypical actions; if suffering cannot be avoided, psychic development and transformation can be promoted; 2) attempt to prevent caregiver burnout; 3) help support and strengthen the collective dimension of the team, learning a mode of care which goes beyond the execution of coded actions; 4) enhance the primary dimension of care, i.e. taking care, especially in clinical situations where conventional wisdom declares that "nothing more can be done."; 5) promote group work so new ideas arising from the different teams influence the behavior of all caregivers. The Ethics Consultation Group organizes its work in several steps. The first step is discernment, clearly identifying the question at hand with the clinical staff. This is followed by a consultation between the clinical team, the patient, the family and the referring physician to arrive at a motivated decision, respecting the competent patient's opinion. The final step is an evaluation of the decision and its consequences. The Ethical Consultation Group, which meets at a scheduled time at a set place, unites the different members of the neurology and palliative care teams who come to a common decision. These specific moments have an important impact on team cohesion, creating a common culture and a convergence of individual representations about making difficult decisions. Specific clinical cases are described to illustrate some of the difficulties encountered in palliative care decision-making. These cases provide insight about the decision to create a palliative care gastrostomy for a man with progressive supranuclear palsy, the suffering experienced by a medical team caring for a young woman with Creutzfeldt-Jacob encephalopathy, or a woman's experience with the post-stroke life-and-death seesaw. Theoretical divisions, illustrated with clinical stories, can be useful touchstones for neurology teams.

[Excellent performances of Wells' score and of the modified Wells' score for the diagnosis of proximal or distal deep venous thrombosis in outpatients or inpatients at Toulouse University Hospital: TVP-PREDICT study]. / Excellentes performances du score de Wells et du score de Wells modifié dans le diagnostic de thrombose veineuse profonde proximale ou distale chez des patients hospitalisés ou ambulatoires au CHU de Toulouse: étude TVP-PREDICT.

AIM OF THE STUDY: In order to validate a standardized strategy for the diagnosis of lower limb deep vein thrombosis (DVT) in the regional university hospital of Toulouse, we decided to study the performances of Wells' score and the modified Wells' score for the diagnosis of proximal and distal DVT. METHOD: Inpatients or outpatients referred to the vascular medicine department from April 2006 to March 2007 with suspected DVT were included prospectively and consecutively. Wells' score was determined for each patient and compared with the duplex ultrasound result. RESULTS: Two hundred and ninety-seven patients were included. The prevalence of DVT was 13.5%. The negative predictive values of Wells' score and the modified Wells' score were 99 and 97% respectively. Similar results were found for proximal or distal thrombosis. The performances of the modified Wells' score were not statistically better than those of the original score. In 48% of patients, the determination of the D-dimers would not have been contributory. In the group with low probability (70% of patients), the incidence of thrombosis was 0.6%. CONCLUSION: Wells' score and Wells' modified score have shown excellent performances. The value of the modified Wells' score is not superior and our preference, for practical reasons, goes to the original score. The widespread use of duplex ultrasound, the large proportion of patients in which D-dimers would not have been contributory and the excellent results of Wells score for patients with a low probability of DVT are encouraging arguments in favor of the development of an alternative strategy for these patients.

Sensory loss, pains, motor deficit and axonal regeneration in length-dependent diabetic polyneuropathy.

In order to learn more on the occurrence of pains and motor deficit in severe diabetic polyneuropathy we reviewed the data of a series of 30 diabetic patients with an uncommonly severe length-dependent diabetic polyneuropathy (LDDP). Extensive sensory loss predominated with pains and temperature sensations and affected all four limb extremities, anterior trunk in all, plus the top of the scalp in 9 patients and the cauda equina territory in 2. Twenty patients had neuropathic pains. Symptomatic autonomic dysfunction was present in 28/30 patients, mild distal motor deficit in 12 patients, severe in only one. Vibratory sensation was impaired in the lower limbs in 18 patients; position sense in 8. In the 10 nerve biopsy specimens, the density of myelinated axons was reduced to 23 % and that of unmyelinated axons to 8.5 % of control values. Regenerating axons accounted for 32.4 +/- 19.8 % of the myelinated fibres. On teased fibre preparations 13.9 % of fibres were undergoing axonal degeneration, while 29.4 % of fibres showed focal abnormalities of the myelin sheath.We conclude that distal motor deficit occurs only after major loss of sensory fibres in LDDP; the unmyelinated axons are predominantly affected; absence of clinical improvement contrasts with the high proportion of regenerating axons; detection of alteration of pain and temperature sensation in the feet seems the best method for neuropathy screening in diabetic patients.

Polymyalgia rheumatica--an underdiagnosed disease.

Characteristic features of polymyalgia rheumatica, a widely underdiagnosed disease, are described. The features of the disease are illustrated by the authors' own experience in the treated patients, and compared with literature data. According to the authors' experience, patients with polymyalgia rheumatica are mostly treated for inaccurate diagnoses such as cervicobrachial or lumbosacral syndrome, seronegative rheumatoid arthritis, unexplained febrile state, or precipitated erythrocyte sedimentation rate of unknown etiology. This results is delayed diagnosis or the accurate diagnosis is never reached at all.

Devic's neuromyelitis optica: a clinicopathological review of the literature in connection with a case showing fatal dysautonomia.

A new clinicopathological case of Devic's neuromyelitis optica, including unusual predominant clinical features (fatal dysautonomia) is described herein: pathological examination showed extensive and severe demyelination mainly involving the optic nerves, the medulla, and spinal cord, which was particularly pronounced in the thoracic segments, and thus explained the unusual vegetative symptomatology. In a review of 45 clinicopathological cases described in the literature as Devic's disease (DD), it turned out that only 22 cases, including the patient described here, fulfilled the recently defined diagnostic criteria [Devic 1980]. Among the other 23 cases, 15 did not fulfill the criteria because of the occurrence of relapses, 3 others had 2 separate pathological locations within the spinal cord, and the remaining 5 showed evidence that a disease other than DD was involved. Among the 22 cases which were definitely taken to be DD, the mean age at clinical onset was 39 years (+/- 14); it was characterized by acute bilateral visual loss and transversal myelitis which gradually led either to death or to partial or complete recovery. The pathological lesions, which mostly were located along the optic tracts and the spinal cord, were characterized by demyelination with inflammation and necrosis; in some cases the pathological process diffused into the medulla (8/22 cases) or the whole brainstem (4/22 cases). The cavitation of the spinal cord was not a key feature of the diagnosis, since it was observed on only 9/22 cases. Devic's neuromyelitis optica may be a separate nosological entity which differs from multiple sclerosis.

Severe pancreatitis as first symptom of mumps complicated with pseudocyst and abscess of pancreas.

A 22-year-old man, a refugee from Bosnia, developed serious pancreatitis complicated with pseudocyst and pancreatic abscess. Staphylococcus aureus was isolated from pus and blood cultures. On day 12 of illness, parotitis and epididymitis appeared with elevated specific IgG antibody levels to the mumps virus. Surgical drainage and antibiotics were necessary for complete recovery. According to our observations, a significant number of hospitalized refugees during the war in Croatia had impaired host defences probably due to prolonged stress. A negative influence of these circumstances and/or the virulence of the agent should be considered in our patient as well.

Gamma-GT activity in the rat epididymis: effect of LHRH agonist (D-Trp 6-LHRH).

The aim of the present study was to follow the gamma-GT activity changes in the rat epididymis after withdrawal of androgens. Treatment of adult rats with the LHRH agonist D-Trp 6-LHRH led to reduce serum testosterone concentrations below the limit of detection of the assay. In the treated rats, specific activity of gamma-GT (nmol/min mg protein-1) drastically decreased in caput epididymidis. Histochemical reactions for gamma-GT completely disappeared in the initial and proximal segments but weak activity remained on the luminal plasma membranes of middle segment of the caput. In the corpus and cauda epididymidis, residual reaction for gamma-GT could be seen on the basal part of epithelial cells and on peritubular cells: Thus gamma-GT is confirmed to be androgen-dependent, but there is a regional responsiveness to withdrawal of androgen in the epididymis.

[Typical and atypical forms of neuralgic amyotrophy of the shoulder: 86 cases]. / Formes typiques et atypiques de névralgie amyotrophiante de l'épaule: 86 cas.

Eighty-six cases of neuralgic shoulder amyotrophy are reported. Among these, 67 cases were concordant with the usual semeiological description. The other cases were atypical in their anatomical distribution (extensive or restricted to peripheral nerve rami), in their course (chronic or recurrent or alternating from one side to the other) and in their cause, notably familial forms. The continuum existing between these variants is most probably due to an immuno-allergic mechanism.

[Cardiac sarcoidosis verified histologically by endovenous myocardial biopsy]. / Sarkoidoza srca histoloski verificirana endovenskom biopsijom miokarda.

The female patient with sarcoidosis simultaneously involving the lungs, heart, liver, eyes, skin and lacrimal glands is presented. The diagnosis of this disorder was established by biopsy of the liver and skin as well as by at our institution newly introduced method of endovenous blind-myocardial biopsy. Generalized active sarcoidosis had brought the patient into a very profound cachectic state (body weight 48 kg), but her life was directly endangered by granulomatous inflammation of the myocardium with the development of cardiac decompensation, grade I and II atrioventricular conduction disturbances as well as by transitory and total AV block with frequent arrhythmias. A significant resolution of the disease occurred after the introduction of corticosteroid therapy. However, grade I AV block persisted even after one year of treatment, suggesting that the syndrome has probably proceeded from granulomatous inflammation to fibrosis. Therefore, the patient is still a potential candidate for an electrostimulator.

[Study and surgery of diseases of the middle meatus under endoscopic control]. / Exploration et chirurgie de la pathologie du méat moyen sous guidage endoscopique.

The middle meatus is the site of abnormalities which are to a great extent responsible for naso-sinus pathology. Its exploration has benefited from improvements in optical systems (microscopes and endoscopes) and radiological investigations. We present our experience with exploration and surgery of the middle meatus under endoscopic control. The medical examination (past history, allergy, etc.) combined with radio-endoscopic findings helps to define the appropriate therapy. Functional surgery is sometimes necessary. This is performed under local anesthetic, which in our experience improves the condition for the procedure and decreases the post-operative complications.