Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs.

Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.

Parallel computing in conceptual sewer simulations.

Integrated urban drainage modelling is used to analyze how existing urban drainage systems respond to particular conditions. Based on these integrated models, researchers and engineers are able to e.g. estimate long-term pollution effects, optimize the behaviour of a system by comparing impacts of different measures on the desired target value or get new insights on systems interactions. Although the use of simplified conceptual models reduces the computational time significantly, searching the enormous vector space that is given by comparing different measures or that the input parameters span, leads to the fact, that computational time is still a limiting factor. Owing to the stagnation of single thread performance in computers and the rising number of cores one needs to adapt algorithms to the parallel nature of the new CPUs to fully utilize the available computing power. In this work a new developed software tool named CD3 for parallel computing in integrated urban drainage systems is introduced. From three investigated parallel strategies two showed promising results and one results in a speedup of up to 4.2 on an eight-way hyperthreaded quad core CPU and shows even for all investigated sewer systems significant run-time reductions.

Function prediction of hypothetical proteins without sequence similarity to proteins of known function.

Function prediction by sequence-similarity based methods identifies only approximately 50% of the proteins deduced from newly sequenced genomes. We have developed an approach to annotate the 'leftover proteins' i.e., those which cannot be assigned function using sequence similarity. Our method (MOPS) is pan-taxonomic, predicting fine-grained molecular function (rather than a broad functional category) with high performance. In addition, we developed a validation scheme that assesses predictions using domain-specific knowledge.

Pathology databanking and biobanking in The Netherlands, a central role for PALGA, the nationwide histopathology and cytopathology data network and archive.

Since 1991, a nationwide histopathology and cytopathology network and archive is in operation in The Netherlands under the name PALGA, encompassing all sixty-four pathology laboratories in The Netherlands. The overall system comprises decentralized systems at the participating laboratories, a central databank, and a dedicated communication and information exchange tool. Excerpts of all histopathology and cytopathology reports are generated automatically at the participating laboratories and transferred to the central databank. Both the decentralized systems and the central system perform checks on the quality and completeness of excerpts. Currently, about 42 million records on almost 10 million patients are stored in the central databank. Each excerpt contains patient identifiers, including demographic data and the so-called PALGA diagnosis. The latter is structured along five classification axes: topography, morphology, function, procedure, and diseases. All data transfer and communication occurs electronically with encryption of patient and laboratory identifiers. All excerpts are continuously available to all participating pathology laboratories, thus contributing to the quality of daily patient care. In addition, external parties may obtain permission to use data from the PALGA system, either on an ongoing basis or on the basis of a specific permission. Annually, 40 to 60 applications for permission to use PALGA data are submitted. Among external users are the Dutch cancer registry, population-based screening programs for cancer of the uterine cervix and breast cancer in The Netherlands, and individual investigators addressing a range of research questions. Many scientific papers and theses incorporating PALGA data have been published already. In conclusion, the PALGA system is a unique system that requires a minimal effort on the part of the participating laboratories, while providing them a powerful tool in their daily practices.

Duodenal carcinoma in MUTYH-associated polyposis.

Bi-allelic germline mutations in the MUTYH gene give rise to multiple adenomas and an increased incidence of colorectal cancer. In addition, duodenal adenomas and other extra-colonic manifestations have been described in MUTYH-associated polyposis (MAP) patients. We describe two patients with bi-allelic MUTYH gene mutations with duodenal carcinoma. The tumour in Patient A was detected during evaluation of non-specific abdominal complaints. Patient B was already diagnosed with tens of adenomas and a colon carcinoma, when a duodenal neoplasm was detected. The identification of somatic G>T mutations in codon 12 of the K-RAS2 gene provides evidence that the duodenal lesions were induced by MUTYH deficiency. Studies in larger series of MAP patients are needed to investigate the risk of upper-gastro-intestinal malignancies and to determine further guidelines for endoscopical surveillance.

[Complications of prostaglandin E1 treatment of congenital heart disease in paediatric medical intensive care]. / Complications du traitement par prostaglandines E1 des cardiopathies congénitales en réanimation médicale pédiatrique.

The authors undertook a retrospective study of the modes of prescription, the tolerance and efficacy of prostaglandin E1 in 62 consecutive neonates with congenital heart disease (average Age 1.6 days: 35 boys: weight: 3.1 +/- 0.6 Kg) admitted to the paediatric intensive care unit of Nancy University Hospital between 1998 and 2002. The infusion time and cumulative dosage were 134 +/- 112 (6-480) hours and 111 +/- 94 (4-396) microg/Kg respectively. The side effects that were observed were: Apnoea (19%), abdominal distension (16%), bradycardia (13%), enterocolitis (6.5%), hypotension (6.5%), vomiting (5%), fever (1.6%) and skin rash (1.6%). Gastrointestinal disturbances are associated with a low body weight (p<0.04), to prolonged treatment (p<0.02) with no influence of initial or cumulative dosages (P=NS), with respiratory assistance (p<0.03) and longer hospital stay (p<0.01). Hypotension was commoner in cases of poor neonatal adaptation. Mortality was correlated with severe initial acidosis (p<0.02), a low Apgar score, the initial prolonged use of high doses of prostaglandin (p<0.04), and the presence of severe valvular aortic stenosis or hypoplasia of the left heart (p<0.002). The authors conclude that treatment with prostaglandin is effective in the majority of cases despite the use of low maintenance doses (0.01 microg/Kg/min). Gastrointestinal disturbances favourised by the perinatal context, the cardiac disease, and prolonged treatment are significant factors for morbidity and mortality. The beneficial role of early neonatal enteral feeding was not demonstrated in this high risk population.

[Feasibility and significance of a transoesophageal electrophysiological investigation in children and adolescents with Wolff-Parkinson-White syndrome]. / Faisabilité et intérêts de l'étude électrophysiologique par voie transoesophagienne dans le syndrome de Wolff-Parkinson-White de l'enfant et de l'adolescent.

UNLABELLED: An electrophysiological investigation is the most reliable means of detecting malignant forms of Wolff-Parkinson-White syndrome (WPW). However, an endocavity investigation is an invasive procedure, especially in young subjects with few symptoms. The aim of this study was to examine the feasibility and results of an electrophysiological study performed by the transoesophageal route in children with WPW. The study was performed in 70 children aged between 11 and 19 years (mean 15 +/- 3) with an obvious ECG appearance of WPW: 13 had dizziness or syncope (group I), 25 had tachycardia (group II) and 32 were asymptomatic (group III). The ages were similar in all three groups. The transoesophageal electrophysiological investigation without premedication consisted of atrial stimulation at increasing frequencies and programmed atrial stimulation using one and two extra stimuli delivered in the basal state and after infusion of 2 to 5 microg of isoproterenol. RESULTS: The investigation was completed in all the children except one in group II. A paroxysmal junctional tachycardia was induced in 7 group I children (54%), 22 in group II (92%) and 4 in group III (12.5%). Atrial fibrillation lasting more than one minute was induced in 7 group I children (54%), 6 in group II (25%) and 6 in group III (19%). The percentage of malignant forms combining rapid conduction in the bundle of Kent at a rate of more than 240/min in the basal state or more than 300/min with isoproterenol, and atrial fibrillation was 54% in group I, 21% in group II, and 22% in group III. In conclusion, a transoesophageal electrophysiological investigation was possible as an outpatient procedure in children older than 10 years, and allowed the detection of potentially serious forms whatever the indication for the investigation, with nevertheless a significantly higher incidence in those presenting with dizziness or syncope. The incidence of 22% for potentially malignant forms in asymptomatic children provides an incentive to recommend an ECG in all children older than 10 years participating in an active sport in order to detect WPW and to propose oesophageal investigation.

[Kawasaki disease in newborns and infants: refractory forms to immunoglobulin therapy]. / Maladie de Kawasaki chez le nourrisson et l'enfant: formes réfractaires aux immunoglobulines.

UNLABELLED: We studied 52 consecutive patients with Kawasaki disease hospitalized (1984 -2003) during the acute phase (mean age 2.5 + 2.4 years; range 0.3 to 16 years, 34 males, 18 cases with coronary aneurysms, median follow-up 6.7 years), and identified a subgroup presenting a refractory subtype to immunoglobulin therapy. RESULTS: forty-nine infants benefited from a first regimen of immunoglobulins, 8.4 + 6 days following the onset of symptoms. Eleven infants (1.4 + 1.2 years, range 0.3 - 4.3 years, median 1.7 years) were non-responders, with coronary aneurysms in 8 cases (giant aneurysms (>8 mm) in 4 cases). These 11 infants were treated a second time by immunoglobulins, but 6 cases (1.8 + 1.6 years, with two cases of severe ventricular dysfunction and 2 cases of fatal myocardial infarction) required an additive therapy with (oral or IV route) corticosteroids (2) and cyclophosphamide bolus (4) with or without repetitive plasmapheresis (4). Non-responder patients had their treatment onset later (p<0.0003) using higher dosages (p<0.005), a longer delay for fever or biological signs correction (p<0.02), a worsening of coronary lesions (p<0.05) with more coronary secondary aneurysms (p<.005). The aneurysms, more frequent at the second phase of the disease (p<0.0001) are associated with: a younger age (p<0.03), a lower weight (p<0.02), a later onset of treatment (p<0.03), prolonged fever or inflammatory syndrome (p<0.05), higher level of fibrinogene (p<0.02). The overall mortality (5.7%) is correlated with giant aneurysms (p<0.001), myocardial ischemia (p<0.0001), heart failure (p<0.0001), and lack of early response to treatment (p<0.003). CONCLUSION: immunoglobin therapy can be repeated. In case of severe forms, the use of corticosteroids, cyclophosphamide and plasmapheresis may be proposed.

FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis.

FLOSYS is an interactive web-accessible bioinformatics workflow system designed to assist biologists in multi-step data analyses. FLOSYS allows the user to create complex analysis pathways (protocols) graphically, similar to drawing a flowchart: icons representing particular bioinformatics tools are dragged and dropped onto a canvas and lines connecting those icons are drawn to specify the relationships between the tools. In addition, FLOSYS permits to select input-data, execute the protocol and store the results in a personal workspace. The three-tier architecture of FLOSYS has been implemented in Java and uses a relational database system together with new technologies for distributed and web computing such as CORBA, RMI, JSP and JDBC. The prototype of FLOSYS, which is part of the bioinformatics workbench AnaBench, is accessible on-line at http://malawimonas.bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching.

[Cardiac stimulation in the infant and young child]. / Stimulation cardiaque chez le nourrisson et le jeune enfant. Avantages et inconvénients respectifs de la voie endocavitaire et de la voie épicardique.

This study evaluates the problems and the evolution of cardiac stimulation in infants (aged < 3.5 years) by comparing the endocavity and epicardial routes in a retrospective series of 37 patients. Thirty seven patients aged 1.2 +/- 0.9 years treated with epicardial (n = 19) or endocavity (n = 18) stimulation were followed for 10.9 +/- 6.4 years (0.75-24). The 2 patient groups did not differ in age or weight. Four patients were lost to follow up, and 1 died. The functional duration of the first stimulator was not significantly different if the initial approach was epicardial or endocavity. The endocavity probes were introduced by venous denudation in 15 cases and by subclavian puncture in 3 cases. Fourteen of the 19 children fitted by the epicardial route went on to endocavity stimulation, of which 10 were at the first replacement. None of the 18 patients fitted by the endocavity route went on to epicardial stimulation. Out of 11 endocavity probe replacements and 9 atrialisations, the homolateral venous approach was always possible except in 2 cases. In conclusion, the results for the epicardial and endocavity routes are comparable. For technical reasons (calibre of the veins, size of the stimulator) it would appear reasonable if the endocavity route was used, making do initially with a mono chamber stimulation. The advances in the epicardial electrodes abolishes the major handicap (threshold elevation) of this approach which can be advocated when double chamber stimulation seems preferable.

The closest unicellular relatives of animals.

Molecular phylogenies support a common ancestry between animals (Metazoa) and Fungi, but the evolutionary descent of the Metazoa from single-celled eukaryotes (protists) and the nature and taxonomic affiliation of these ancestral protists remain elusive. We addressed this question by sequencing complete mitochondrial genomes from taxonomically diverse protists to generate a large body of molecular data for phylogenetic analyses. Trees inferred from multiple concatenated mitochondrial protein sequences demonstrate that animals are specifically affiliated with two morphologically dissimilar unicellular protist taxa: Monosiga brevicollis (Choanoflagellata), a flagellate, and Amoebidium parasiticum (Ichthyosporea), a fungus-like organism. Statistical evaluation of competing evolutionary hypotheses confirms beyond a doubt that Choanoflagellata and multicellular animals share a close sister group relationship, originally proposed more than a century ago on morphological grounds. For the first time, our trees convincingly resolve the currently controversial phylogenetic position of the Ichthyosporea, which the trees place basal to Choanoflagellata and Metazoa but after the divergence of Fungi. Considering these results, we propose the new taxonomic group Holozoa, comprising Ichthyosporea, Choanoflagellata, and Metazoa. Our findings provide insight into the nature of the animal ancestor and have broad implications for our understanding of the evolutionary transition from unicellular protists to multicellular animals.

Computer-based diagnostic support systems in histopathology: what should they do?

In many fields in histopathology diagnosis making is notoriously difficult. We explored the diagnostic process in the area of CL and related disorders. The field of cutaneous lymphomas (CL) and borderline lesions is complex and representative for the type of diagnostic problems encountered. A review of diagnostic support systems in diagnostic pathology revealed that the usefulness of these systems has been disappointing. We contribute this to the fact that these systems target only part of the diagnostic process. A tentative model of diagnosis making in pathology is presented. This model assumes a two-step process, from observation to feature recognition and from features to diagnosis. In a retrospective study of existing skin biopsy pathology reports we assessed detail and scope of the histological descriptions. In a second, prospective study, a pathologist panel described a set of 16 skin biopsies using a standard set of descriptors. The retrospective study showed a large variability in the nature and details of described features, whereas the prospective study showed lack of consensus regarding both feature descriptions and diagnostic category. Both studies provide an indication that lack of consensus in feature recognition may be an important contributor to lack of consensus at the diagnostic level. Diagnostic expert systems target the step from feature to diagnosis. Evidently different input into such systems produces different output. We conclude that support of the feature recognition step can contribute to better diagnostic consensus because of more uniform interpretation of observations.

The origin and early evolution of mitochondria.

Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically alpha-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.

Influence of age on the electrophysiological mechanism of paroxysmal supraventricular tachycardias.

The purpose of this study was to evaluate the influence of age on the mechanism of paroxysmal supraventricular tachycardia (PSVT). Previous studies have shown age and sex differences between certain arrhythmias and especially changes in electrophysiological characteristics of Wolff-Parkinson-White syndrome. Four hundred and eighty five patients aged 9-86 years, with PSVT and without Wolff-Parkinson-White syndrome in sinus rhythm, were studied. The esophageal or intracardiac electrophysiological study used a standardized atrial pacing protocol. Paroxysmal junctional tachycardia was induced in 475 patients. The mechanism of tachycardia was not influenced by age and atrioventricular nodal reentrant tachycardia (AVNRT) was found as the main cause of PSVT in all ranges of age. Atrioventricular reentrant tachycardia (AVRT) using a concealed accessory pathway (AP) had a similar incidence from youth to elderly. The ratio male/female (M/F) and the inducibility of other arrhythmias (atrial flutter/fibrillation) (AF/AFl) were also found to be similar in all ranges of age. The age of the patients did not influence the mechanism of the tachycardia. Most of PVST were related to a AV nodal reentrant tachycardia. Concealed accessory pathway was identified with a similar incidence in young and old patients.

GOBASE: the organelle genome database.

GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with taxonomically broad coverage, and in furnishing data that have been exhaustively verified and completed by experts. So far, we have focused on mitochondrial data: GOBASE contains all published nucleotide and protein sequences encoded by mitochondrial genomes, selected RNA secondary structures of mitochondria-encoded molecules, genetic maps of completely sequenced genomes, taxonomic information for all species whose sequences are present in the database and organismal descriptions of key protistan eukaryotes. All of these data have been integrated and organized in a formal database structure to allow sophisticated biological queries using terms that are inherent in biological concepts. Most importantly, data have been validated, completed, corrected and standardized, a prerequisite of meaningful analysis. In addition, where critical data are lacking, such as genetic maps and RNA secondary structures, they are generated by the GOBASE team and collaborators, and added to the database. The database is implemented in a relational database management system, but features an object-oriented view of the biological data through a Web/Genera-generated World Wide Web interface. Finally, we have developed software for database curation (i.e. data updates, validation and correction), which will be described in some detail in this paper.

Familial cancer database: a clinical aide-mémoire.

Cancer is associated with a wide range of hereditary disorders. Recognizing these disorders in cancer patients may be of great importance for the medical management of both patients and their relatives. Conversely, recognizing the fact that cancer may develop in patients already diagnosed with a particular hereditary disorder may be important for the same reason. We have developed a stand-alone interactive computer program, Familial Cancer Database (FaCD), to assist the clinician in making a genetic differential diagnosis in cancer patients as well as in becoming aware of the tumour spectrum associated with a particular hereditary disorder. The program tries to match tumour and non-tumour features observed in patients and their families with any of the more than 300 disorders presently contained in its database and provides a clinical synopsis with literature references for each of these disorders. FaCD is offered free of charge in support of the Familial Cancer and Prevention project of the UICC Cancer Epidemiology and Prevention program. The software is primarily aimed at health care professionals with at least a basic knowledge of clinical cancer genetics, and can be downloaded from the internet at http://facd.uicc.org.

Prototypical profiles of the Brief Psychiatric Rating Scale.

Three prototypical profiles of the Brief Psychiatric Rating Scale (BPRS; Overall & Gorham, 1962) were isolated using a Q-type factor-analytic strategy with a sample of homeless men with mental illness (N=165). The 3 profiles--depressed, actively psychotic, and withdrawn--were used to study changes in BPRS profiles over time in a control group and a group that received assertive community treatment (ACT). Over2 time periods (inception to 12 months and 12-24 months), the 2 groups did not differ in terms of changes in profile shape, but they did differ in terms of changes in profile elevation. The ACT group evidenced a decrease in symptom severity during the last 12 months, whereas the control group showed an increase. Although changes in profile shape in both groups did occur, there was a significant tendency for the shape of the BPRS profiles to remain stable from the inception of the study to the 12-month assessment and from that time to the 24-month assessment. We describe the uses of these prototypical profiles and discuss the applicability of this analytical approach to other assessment instruments.

Early eukaryote evolution based on mitochondrial gene order breakpoints.

The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.