miRQuest: integration of tools on a Web server for microRNA research.

This report describes the miRQuest - a novel middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification that use different programming languages and methods to realize this task. It is difficult to understand each tool and apply it to diverse datasets and organisms available for miRNA analysis. miRQuest can easily be used by biologists and researchers with limited experience with bioinformatics. We built it using the middleware architecture on a Web platform for miRNA research that performs two main functions: i) integration of different miRNA prediction tools for miRNA identification in a user-friendly environment; and ii) comparison of these prediction tools. In both cases, the user provides sequences (in FASTA format) as an input set for the analysis and comparisons. All the tools were selected on the basis of a survey of the literature on the available tools for miRNA prediction. As results, three different cases of use of the tools are also described, where one is the miRNA identification analysis in 30 different species. Finally, miRQuest seems to be a novel and useful tool; and it is freely available for both benchmarking and miRNA identification at http://mirquest.integrativebioinformatics.me/.

Serum tryptase concentrations in beekeepers with and without Hymenoptera venom allergy.

BACKGROUND: Increased tryptase concentrations are a risk marker for the severity of reactions to Hymenoptera stings or venom immunotherapy OBJECTIVE: To investigate serum tryptase concentrations in beekeepers with and without Hymenoptera venom allergy (HVA). METHODS: Serum tryptase concentrations were measured in adult patients with HVA (n = 91, 37 of whom were beekeepers), beekeepers without HVA (n = 152), and control individuals from the general adult population (n = 246). RESULTS: Multivariate analyses revealed that serum tryptase levels were positively associated with beekeeping activities (P < .001) and HVA (P < .001). Tryptase levels were also positively associated with age (P < .001) and male'sex (P = .02), and negatively associated with alcoho consumption (P = .002). CONCLUSIONS: Beekeeping and HVA are independently associated with increased concentrations of serum tryptase.

Relation of pretreatment sequence diversity in NS5A region of HCV genotype 1 with immune response between pegylated-INF/ribavirin therapy outcomes.

Hepatitis C virus (HCV) infection frequently persists despite substantial virus-specific immune responses and the combination of pegylated interferon (INF)-α and ribavirin therapy. Major histocompatibility complex class I restricted CD8(+) T cells are responsible for the control of viraemia in HCV infection, and several studies suggest protection against viral infection associated with specific HLAs. The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Escape mutations in response to cytotoxic T lymphocyte are widely described; however, its influence in the treatment outcome is ill understood. Here, we investigate the differences in CD8 epitopes frequencies from the Los Alamos database between groups of patients that showed distinct response to pegylated α-INF with ribavirin therapy and test evidence of natural selection on the virus in those who failed treatment, using five maximum likelihood evolutionary models from PAML package. The group of sustained virological responders showed three epitopes with frequencies higher than Non-responders group, all had statistical support, and we observed evidence of selection pressure in the last group. No escape mutation was observed. Interestingly, the epitope VLSDFKTWL was 100% conserved in SVR group. These results suggest that the response to treatment can be explained by the increase in immune pressure, induced by interferon therapy, and the presence of those epitopes may represent an important factor in determining the outcome of therapy.

Granulomatous rosacea in infants. Report of three cases and discussion of the differential diagnosis.

Granulomatous rosacea is a variant of rosacea characterized by hard cutaneous papules and nodules in relatively normal-appearing skin that is rarely diagnosed in childhood. The differential diagnosis essentially includes perioral dermatitis and sarcoidosis. Despite the differences in clinical presentation and histopathology, there is similar responses to the same therapies used in rosacea. Therapeutic failure should lead to the investigation of other rare and controversial conditions, such as acne agminata.

[A multidisciplinary consultation for children with brain tumors]. / Une consultation multidisciplinaire pour les enfants traités pour une tumeur cérébrale.

UNLABELLED: School achievement of children with brain tumors is hampered by progressive neurologic and cognitive sequelae. To help the children and their family, we have created in 1997 a multidisciplinary consultation together with Necker's hospital. MATERIAL AND METHODS: The study describes the organization of the consultation and analyses the files of 69 children seen between September 2001 and June 2002. RESULTS AND CONCLUSION: The authors conclude that this consultation is an irreplaceable mean to coordinate the complex rehabilitation process of a child treated for a brain tumor.

The Discrepancy between Performance-Based Measures and Questionnaires when Assessing Clinical Outcomes and Quality of Life in Pediatric Patients with Neurological Disorders.

In clinical outcome assessment, the relation between performance-based measures and questionnaire ratings of the same domain is weak, but correlations between questionnaires proposed for the evaluation of different domains are strong. The present study aims to illustrate these phenomena in a group of patients with neurofibromatosis type 1 (NF1) and to propose an explanatory hypothesis. A single neuropsychologist interviewed the parents about the child's situation and current difficulties and then assessed this parental view as overall positive or overall negative. The same assessor then administered the Wechsler Intelligence Scales and neuropsychological tests to 78 children and adolescents with NF1 (5-18 years). Parents then completed the Child Behavioral Checklist (CBCL), the Conners' Parent Rating Scale, the Behavior Rating Inventory of Executive Function (BRIEF), as well as questionnaires assessing quality of life, impact of the medical disorder, and their own difficulties. All questionnaires were inter-correlated (r = 0.29 - 0.84) and associated with the overall positive or negative parental view of the child's progress (effect size = 0.41-1.46). Conversely, questionnaires were weakly or not significantly related to intelligence, cognitive measures, or clinical severity. In conclusion, the parental view of the child's progress was related to the answers to questionnaires assessing quality of life or strengths and difficulties of patients with a neurological disorder. This factor should be assessed independently and taken into account when assessing clinical outcome.

Neuropsychological evaluation and parental assessment of behavioral and motor difficulties in children with neurofibromatosis type 1.

Neurofibromatosis type 1 (NF1) is an autosomal dominant multisystem disorder, with large inter and intrafamilial clinical variability and uncertain prognosis. In children with NF1 cognitive disorders, learning difficulties and behavioral problems are common. The present study aims to establish the neuropsychological and behavioral profiles of 78 patients with NF1, aged between 5 and 18 years, and to examine the relationship between these profiles and the transmission of NF1 (sporadic vs. familial), clinical manifestations, and environmental factors. We used several questionnaires completed by parents and neuropsychological tests. The results confirmed specific neuropsychological disabilities in children with NF1, especially involving visuospatial and fine motor skills, learning difficulties and behavioral problems. Cognitive difficulties were significantly more frequent in patients with familial than in those with sporadic NF1. All parental questionnaires were correlated with each other, but parental reports were not associated with FSIQ, SES, school status, and clinical manifestations of the disease. Neuropsychological tests were poorly related to parental reports of cognitive and behavioral difficulties.

Role of glutamate receptors and nitric oxide in the rostral ventromedial medulla in visceral hyperalgesia.

The present study was undertaken to examine the involvement of descending pain modulatory systems from the brainstem rostral ventromedial medulla (RVM) in modulating visceral hyperalgesia produced by intracolonic instillation of zymosan. Three hours after intracolonic zymosan, the visceromotor response (VMR) to noxious colorectal distension (CRD, 80 mmHg, 20s) was increased significantly. This hyperalgesia was attenuated in a dose-dependent manner by the selective NMDA receptor antagonist APV (10-30 fmol, 1 microl) microinjected into the RVM. The hyperalgesia was also attenuated by intra-RVM administration of the nitric oxide synthase (NOS) inhibitor L-NAME. In support, there was a significant increase in the number of cells in the RVM labeled for NADPH diaphorase (NADPH-d) or neuronal NOS (nNOS) in zymosan-treated rats. In contrast to the effects of APV and L-NAME, administration of the non-NMDA receptor antagonist DNQX into the RVM further enhanced the already facilitated VMR to CRD in zymosan-treated rats. Taken together, these data suggest that zymosan-produced visceral hyperalgesia is influenced by two descending pain modulatory systems: a facilitatory system mediated by activation of NMDA receptors in the RVM and production of nitric oxide, and an inhibitory system mediated by activity at non-NMDA receptors in the RVM. The unmasking of one system by selective blockade of the other suggests simultaneous activation of both by colonic inflammation.

Immunocytochemical study of Peyer's patches follicular-associated epithelium in the marsupial, Didelphis albiventris.

The lack of probes defining leukocyte subpopulations has restricted ontogenetic studies of the opossum gut. We report for the first time the organization of the gut cellular immune components using species cross-reactive antibodies. Mouse monoclonal antibodies against human HLA-DR were used together with immunocytochemistry to demonstrate MHC class II-like antigens in the opossum Peyer's patches (PP). Positive staining was obtained in the M cell and enterocytes comprising the follicular-associated epithelium (FAE). Rabbit polyclonal antibody against human CD3 stained opossum thymocytes and T-cell dependent areas of spleen, lymph node, and PP interfollicular zones, but failed to stain intraepithelial lymphocytes in the FAE. In contrast rabbit polyclonal antibody against human IgA stained B-cell immunocytes and plasma cells present in the M-cell lateral invaginations. It is surmised that B-cell activation could occur in the opossum M-cell niches by thymus independent antigens, bypassing T-helper-cell function.

Intra-abdominal sepsis: an immunocytochemical study of the small intestine mucosa.

AIM: To investigate immunocytochemical changes in intestinal tissues from patients with intra-abdominal sepsis, and to relate the changes to the possibility of enhanced bacterial adhesion and translocation. METHODS: Tissues from 17 patients suffering from intra-abdominal sepsis and from controls were sectioned and stained immunocytochemically for IgA, IgM, secretory component, J chain, and HLA-DR. Differences in the distribution and characteristics of positively staining cells between the patient groups were assessed. RESULTS: Patients with intra-abdominal sepsis had noticeable reductions in numbers of IgA and IgM plasma cells, reduced J chain staining, and had little immunoglobulin on the surfaces of enterocytes. In contrast, HLA-DR positive cells were increased in the sepsis compared with the control group. The plasma cells present showed cytological changes suggestive of apoptosis. CONCLUSIONS: Stress associated with sepsis and its immediate causes might result in increased plasma glucocorticoid levels that bring about apoptosis of mucosal plasma cells (or their precursors). The consequent reduction in expression of IgA and IgM may favour bacterial adhesion to the enterocytes and facilitate bacterial translocation into the tissues.

Absence of lysozyme (muramidase) in the intestinal Paneth cells of newborn infants with necrotising enterocolitis.

AIM: To determine immunocytochemically whether preterm and newborn infants with necrotising enterocolitis (NEC) show differences in numbers of lysozyme positive Paneth cells compared with normal controls, and to relate the findings to the possibility that lysozyme deficiency may facilitate the bacterial infections thought to be associated with this condition. METHODS: Tissues from 10 infants with NEC and from 11 matched controls were sectioned and stained immunocytochemically for lysozyme. Differences in the numbers of Paneth cells and degree of lysozyme positivity in the tissues were assessed. RESULTS: Tissues from NEC patients showed no, or very few, lysozyme positive Paneth cells, whereas controls showed strong positive staining. CONCLUSIONS: A deficiency or developmental defect in Paneth cells, resulting in an absence of lysozyme, may render the intestine more susceptible to bacterial infection, allowing organisms to adhere and translocate across the mucosa. Such enhancement of infection may contribute to the pathogenesis of NEC.

Immunocytochemistry of mucosal changes in patients infected with the intestinal nematode Strongyloides stercoralis.

AIM: To investigate the immunopathological changes in duodenal tissues induced by strongyloidiasis and to relate these to degrees of clinical severity. METHODS: Tissues taken from 21 patients showing mild, moderate or severe symptoms of strongyloidiasis, and from non-infected controls, were sectioned and stained immunocytochemically for IgA, secretory component (SC) and HLA-DR. Immunopathology was assessed by changes in numbers, intensity and distribution of stained cells. RESULTS: Parasitised individuals showed villous atrophy and crypt hyperplasia. There was notable infiltration of the lamina propria by IgA positive plasma cells and of the epithelium by intraepithelial lymphocytes. Infection was also associated with increased expression of SC and decreased expression of HLA-DR in epithelial cells. Changes in all parameters correlated with degree of clinical severity. CONCLUSIONS: Profound mucosal changes are induced by strongyloidiasis. Some are analogous to those seen in coeliac disease, but others seem quite unusual. It is likely that these changes are functionally related to the immunopathophysiological consequences of infection seen in patients with severe disease.

Combined method for simultaneous morphology, immunophenotype and karyotype (MAC) in leukemias.

In the present study, a combined method (CM) for attaining simultaneous identification of leukemic cell morphology, karyotype and immunophenotype has been evaluated in 21 patients with acute leukemia and 1 with CML in blast crisis were studied for morphology, citochemistry, immunophenotype and karyotype. Karyotype was performed in a bone marrow sample by using conventional techniques. In each case, direct method (DM) and/or three cultures were tried. The CM consisted in separating a small part of the material resulting from any of the cultures or DM, preparing slides through cytospin and immunophenotyping through APAAP method using the same monoclonal antibodies (MoAb) as for diagnosis. In 14 cases, the metaphases proved positive to the MoAb: in 4, the cells with abnormality had their origin defined; in other 4 the karyotype was normal preventing any identification; 6 cases had minimal abnormalities not visible through CM; and in two cases abnormal karyotypes were detected only in the cultures with GM-CSF. This study showed that CM is feasible in cases where evident numerical or structural chromosomal abnormalties are present.

Relation of pretreatment sequence diversity in NS5A region ofHCV genotype 1 with immune response between pegylated- INF/ribavirin therapy outcomes

Hepatitis C virus (HCV) infection frequently persists despite substantial virus-specific immune responsesand the combination of pegylated interferon (INF)-a and ribavirin therapy. Major histocompatibility complex class Irestricted CD8+ T cells are responsible for the control of viraemia in HCV infection, and several studies suggestprotection against viral infection associated with specific HLAs. The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Escape mutations in response to cytotoxic T lymphocyte are widely described; however, its influence in the treatment outcome is ill understood. Here, we investigate the differences in CD8 epitopes frequencies from the Los Alamos database between groups of patients that showed distinct response to pegylated a-INF with ribavirin therapy and test evidence of natural.

Functional topology of the mossy fibre-granule cell--Purkinje cell system revealed by imaging of intrinsic fluorescence in mouse cerebellum.

We report an activity-induced green fluorescence signal observed when mouse cerebellar slices were illuminated with blue light and parallel fibre-Purkinje cell synapses were activated. The optical signal consisted of an initial increase in fluorescence that peaked within 1-2 s after the onset of stimulation, followed by a long lasting (40 s) transient decrease in fluorescence. Single or tetanic electrical stimuli applied to the molecular layer elicited 'beam-shaped' fluorescence changes along the trajectory of parallel fibres. These signals reported activation of Purkinje cells as they were depressed by antagonists of ionotropic and metabotropic glutamate receptors at Purkinje cells and correlated with Purkinje cell spiking activity. Optical responses induced by direct pharmacological activation of glutamate receptors were reduced by a calcium-free extracellular medium, consistent with the hypothesis that they reflect metabolic activity due to an increased intracellular calcium load associated with neuronal activation. We used these intrinsic fluorescence signals to address the question of whether granule cells excite Purkinje cells only locally via the ascending branches of their axons, or more widespread along the parallel fibre trajectory. White matter stimulation of the mossy fibres also elicited a beam-like fluorescence change along the trajectory of parallel fibres. Simultaneous imaging and extracellular recording demonstrated the association between the beam-like fluorescence signal and Purkinje cell spiking. This non-invasive imaging technique supports the notion that parallel fibre activity, evoked either locally or through the mossy fibre-granule cell pathway, can activate postsynaptic Purkinje cells along more than 3 mm of the parallel fibre trajectory.

Effects of hydrocortisone acetate treatment on the small intestine of the lactent marsupial Didelphis albiventris.

When hydrocortisone acetate was administered subcutaneously to the lactent Brazilian white belly opossum, it induced precocious intestinal maturation. Histological features of the small intestine were reminiscent of those seen in human protein-caloric malnutrition. There were also indications that the glucocorticoid acted as an inducer of the differentiation of Paneth, goblet and granulomucous cells within the small intestinal epithelium. In the lactent opossum the small intestine is lined by an epithelium containing cells which exhibit intense endocytic activity (Krause et al. 1977; Santiago et al. 1983; H.B. Coutinho, Beck--unpublished) verified that subcutaneous injections of hydrocortisone acetate could determine intestinal closure in lactent opossums. Krause et al. and Santiago et al. have reported that in Didelphis virginiana and Didelphis albiventris, respectively, the goblet cells and Paneth cells differentiate lately in the development of pouch opossum young. Freitas et al. (1982) mentioned that the plasma cortisol level was very low in lactent white belly opossum, but preceding weaning there was an abrupt increase of the plasma cortisol reaching levels comparable to that obtained in adult animals. These facts suggested the need for investigations to clarify if cortisol could act as an inductive agent for the differentiation of goblet cells and Paneth cells in the lactent D. albiventris.

Simplified method for the analysis of cellular karyotype and phenotype in leukemias.

The objective of this study was to develop a simplified method for the simultaneous analysis of cellular karyotype and phenotype which would permit the identification of cell origin. We studied 6 patients with AML, 3 with CML (one of which was in blastic transformation) and one ALL. We used a method in which the suspension of bone marrow cells was incubated in TC 199 medium with colchicine and with hypotonic solution formed from glycerol, NaCl, KCl, CaCl2, MgCl2 and sucrose. The slides were prepared from this cell suspension by cytospin and stained for peroxidase, PAS, esterases and iron. The karyotype was studied by direct method and culture. It was possible to relate the cytogenetic marker with cytochemistry characteristics in the same cell in 3 cases, showing the feasibility of cytochemistry techniques in cytogenetical preparations. The best preparations were found through peroxidase. The presence of iron granules allowed identification of erythroblastic lineage in the combined staining. Mitosis with a marker chromosome of leukemic clone in an AML cell with negative peroxidase probably showed a proliferation of more primitive precursor not sufficiently differentiated to show markers.

Cytogenetic studies in malignant lymphomas: a study of 8 cases.

Chromosome studies were carried out, by a direct method, in 28 subjects with malignant lymphomas. Lymph node cells were analysed in 24, ascitic fluid sediments in 3 and bone marrow cells in 1. Chromosome abnormalities, both numerical and structural, were found in 12 of 14 cases of well differentiated and poorly differentiated lymphocytic lymphomas, and reticulum cell sarcomas, and in 8 of 14 cases with Hodgkin's disease. The karyotypes were different from case to case and there was no correlation with the histology. In individual cases the abnormalities followed a clonal pattern indicating a common precursor for the abnormal cells. The modal number of chromosomes was near-diploid in the lymphocytic lymphomas and reticulum cell sarcomas.Hodgkin's disease showed two main features; a predominant population of cells with normal karyotype accompanied by a small number of cells of an abnormal clone with a predominantly hypertriploid number of chromosomes. It is suggested that the first population represents mitoses in the surrounding lymphocytes. Its cytogenetic normality is an argument against its neoplastic origin, and they could be components of an inflammatory reaction, the true neoplastic cells being the abnormal reticulum cells.

Immunocytochemical demonstration of insulin in the mesonephros and metanephros of the Brazilian opossum Didelphis albiventris).

The presence of insulin the brush border and apical pole of the cells lining the pouch opossum mesonephric and metanephric proximal tubules was demonstrated by immunofluorescence and immunoperoxidase techniques. Positive result for insulin was also observed in the tufts of capillaries of some metanephric corpuscles.