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PubMed2000

Parallel cascade identification as a means for automatically classifying protein sequences into structure/function groups.

Current methods for automatically classifying protein sequences into structure/function groups, based on their hydrophobicity profiles, have typically required large training sets. The most successful of these methods are based on hidden Markov models, but may require hundreds of exemplars for training in order to obtain consistent results. In this paper, we describe a new approach, based on nonlinear system identification, which appears to require little training data to achieve highly promising results.

Animals↗
PubMed2006

Structures and serology of the O-antigens of Proteus strains classified into serogroup O17 and former serogroup O35.

INTRODUCTION: Bacteria of the genus Proteus are facultative pathogens which commonly cause urinary tract infections. Based on the serological specificity of the O-chain polysaccharide of the lipopolysaccharide (O-polysaccharide, O-antigen), strains of P. mirabilis and P. vulgaris have been classified into 60 serogroups. Studies on the chemical structure and serological specificity of the O-antigens aim at the elucidation of the molecular basis and improvement of the serological classification of these bacteria. MATERIALS AND METHODS: The O-polysaccharide was prepared by acetic acid degradation of the lipopolysaccharide isolated from dried bacterial mass of each strain by hot phenol/water extraction. (1)H- and (13)C-NMR spectroscopy was used for structural studies. Serological studies were performed with rabbit O-antisera using enzyme immunosorbent assay, passive hemolysis test, and the inhibition of reactions in these assays as well DOC-PAGE and Western blot. RESULTS: Four Proteus strains belonging to serogroups O17 and O35 were found to possess similar O-polysaccharide structures, in particular having the same carbohydrate backbone built up of tetrasaccharide repeating units. However, they differ in the presence or absence of additional substituents, such as phosphoethanolamine in P. mirabilis O17 and glucose in P. penneri O17, as well as in the pattern and degree of O-acetylation of various monosaccharide residues. Serological studies also showed close relationships between the O-antigens studied. CONCLUSIONS: Based on these data it is proposed to reclassify strain P. mirabilis PrK 61/57, formerly representing the O35 serogroup, into the serogroup O17 in the Kauffman-Perch classification system of Proteus.

Carbohydrate Conformation↗
PubMed2003

Body mass index, waist hip ratio, and waist circumference: which measure to classify obesity?

OBJECTIVES: To determine the proportion of a representative population sample of adults in South Australia who have a body mass index (a measure of overall obesity) classified as normal or underweight, but who also have a waist circumference or waist hip ration (measures of central obesity) that indicates obesity. METHODS: A representative population sample of adults aged 18 years and over living in the north west region of Adelaide (n = 2523) were recruited to the study. Clinical measures of height, weight, waist and hip circumference were obtained and used to determine body mass index, waist hip ratio and waist circumference. RESULTS: Among women with a normal body mass index, 19.0% had a high waist circumference (> or = 80 cm) and 8.5% had a high waist hip ratio (> 0.85). Among males with a normal body mass index, 3.4% had a high waist circumference (> or = 95 cm) and 0.1% had a high waist hip ratio (> 1.0). CONCLUSIONS: Body mass index, waist hip ratio and waist circumference all have a role in the identification of those who are obese or overweight.

Adolescent↗
PubMed1998

Mutations in the hepatocyte nuclear factor-1alpha gene in Caucasian families originally classified as having Type I diabetes.

Mutations in the hepatocyte nuclear factor-1alpha (HNF-1alpha) gene are the cause of maturity-onset diabetes of the young type 3 (MODY3), which is characterised by a severe impairment of insulin secretion and an early onset of the disease. Also at onset of diabetes some MODY patients show similar clinical symptoms and signs as patients with Type I (insulin-dependent) diabetes mellitus. The objective of this study was to estimate the prevalence of MODY3 patients misclassified as Type I diabetic patients. From a large population-based sample of unrelated Danish Caucasian Type I diabetic patients with an affected first degree relative, 39 patients (6.7%) who did not carry any high-risk HLA-haplotypes, i.e. DR3 or DR4 or both were examined by single-strand conformational polymorphism scanning and direct sequencing of the coding region and the minimal promoter of the HNF-1alpha gene. Four of the 39 Type I diabetic patients (10%) were identified as carrying mutations in the HNF-1alpha gene. One patient carried a missense mutation (Glu48Lys) in exon 1, two patients carried a missense mutation (Cys241Gly) in exon 4 and one patient carried a frameshift mutation (Pro291fsdelA) in exon 4. The mutations were all identified in heterozygous form, segregated with diabetes, and were not identified in 84 unrelated, healthy subjects. Furthermore, family history in three of the four families showed diabetes in four consecutive generations, suggestive of an autosomal dominant inheritance. In conclusion, about 10% of Danish diabetic patients without a high-risk HLA-haplotype, originally classified as having Type I diabetes could have diabetes caused by mutations in the HNF-1alpha gene. Clinical awareness of family history of diabetes and mode of inheritance might help to identify and reclassify these diabetic subjects as MODY3 patients.

Adolescent↗
PubMed2006

Defining and classifying acute renal failure: from advocacy to consensus and validation of the RIFLE criteria.

Until recently, more than 30 different definitions of acute renal failure (ARF) had been used in the literature. This lack of a common reference point created confusion and made comparisons difficult. It also led to strong advocacy of a consensus definition. In response to the need for a common definition and classification of ARF, the Acute Dialysis Quality Initiative (ADQI) group of experts developed and published a consensus definition of ARF. This definition goes under the acronym of RIFLE to indicate that it classifies patients with renal dysfunction according to the degree of impairment into patients at risk (R), with injury (I), with failure (F), with sustained loss (L) and with end-stage (E) status in relation to their renal function. This editorial aims to summarize and interpret recent findings concerning the application of the RIFLE criteria to the assessment of the epidemiology and the prediction of the outcome of ARF.

Acute Kidney Injury↗
PubMed2004

The effect of novelty on amphetamine self-administration in rats classified as high and low responders.

RATIONALE: Rats categorized as high responders (HR) based on their activity in an inescapable novel environment self-administer more amphetamine than low responder (LR) rats. Previous research has also demonstrated that novel stimuli presented during the amphetamine self-administration session decreases the number of infusions earned. OBJECTIVES: This study determined whether individual differences in response to inescapable or free-choice novelty differentially predict the ability of novel stimuli to decrease amphetamine self-administration. Further, this study determined whether novel stimuli maintained the ability to reduce self-administration with repeated presentations, and whether the effect of novel stimuli varied as a function of the unit dose of amphetamine tested. METHODS: Male rats were screened for their response in inescapable and free-choice novelty tests. Following initial training using a high unit dose of amphetamine (0.1 mg/kg per infusion), the dose was reduced (0.03 mg/kg per infusion), and novel stimuli were presented in the operant conditioning chamber on four separate sessions. In experiment 2, novel stimuli were presented during several sessions at a variety of amphetamine doses (0.003, 0.01, 0.03, and 0.056 mg/kg per infusion). RESULTS: Four repeated presentations of novel stimuli reduced amphetamine self-administration with no significant loss in the effect of novel stimuli across repeated presentations. In experiment 2, novel stimuli reduced amphetamine self-administration at low unit doses (0.003 mg/kg and 0.01 mg/kg per infusion), and rats classified as HR based on their activity in inescapable novel stimuli were more disrupted by novel stimuli than LR rats. CONCLUSIONS: These results suggest that repeated presentation of novel stimuli can reduce amphetamine self-administration at low unit doses and that HR rats are more sensitive than LR rats to non-drug stimuli that compete with responding for amphetamine.

Amphetamine↗
PubMed2005

Indication of hepatectomy for cirrhotic patients with hepatocellular carcinoma classified as Child-Pugh class B.

We clarified the indication of partial hepatectomy in hepatocellular carcinoma (HCC) patients with liver cirrhosis classified as Child-Pugh class B. Univariate analysis revealed that adverse prognostic factors were (1) the presence of ascites, (2) elevated total bilirubin (1.5 mg/dl or higher), (3) reduced choline esterase (160 IU/ or lower), (4) elevated alpha-fetoprotein (AFP) (400 ng/ml or higher), (5) microscopic vascular invasion, and (6) non-curative hepatectomy. Microvascular invasion was excluded in the multivariate analysis because this factor could not be predicted before hepatectomy. Multivariate analysis revealed that independent adverse prognostic factors were (1) elevated total bilirubin (1.5 mg/dl or higher), (2) presence of ascites, (3) elevated AFP (400 ng/ml or higher), and (4) non-curative hepatectomy. The overall 5-year survival rate of patients with none of or only one of the four adverse prognostic factors was 45.8%. The overall 5-year survival rate of patients with two or more adverse prognostic factors was only 7.0%. Partial hepatectomy is the first choice of treatment for patients with none of or only one of the four adverse prognostic factors, whereas orthotopic liver transplantation or other conservative treatment should be considered for patients with two or more adverse prognostic factors.

Adult↗
PubMed1999

Tumour characteristics and survival in patients with invasive interval breast cancer classified according to mammographic findings at the latest screening: a comparison of true interval and missed interval cancers.

The aim of this study was to investigate whether different mammographic categories of interval cancer classified according to findings at the latest screening are associated with different distributions of prognostic factors or with different survival rates. The series consisted of all patients with invasive interval cancer detected from May 1978 to August 1995 (n = 544). The tumours were evaluated with regard to age, radiological category, interval between the latest screen and diagnosis and tumour characteristics at the time of diagnosis. We investigated possible relationships between the survival rate of patients with interval cancer and the interval between the latest screen and diagnosis, tumour characteristics and radiological category of the interval tumours. The study focused on comparison of patients with true interval and missed interval cancer. Women with mammographically occult tumours were younger than those in the other radiological categories. Comparisons of true interval cancers with overlooked or misinterpreted tumours showed equal distributions of age, tumour size, TNM stage and lymph node status. The overlooked or misinterpreted tumours showed significantly higher proportions of grade-I tumours (22 vs 11 %), tumours with low S-phase fraction (SPF; 44 vs 24 %) and oestrogen receptor (ER) positive tumours (72 vs 57 %). However, analyses of survival rates disclosed no clear differences between the two radiological categories. Radiological category and interval between the latest screen and diagnosis were not genuine predictors of the prognosis in patients with invasive interval breast cancer. No certain prognostic difference existed between true interval cancers and overlooked or misinterpreted interval breast cancers, despite higher proportions of grade-I tumours, ER positive tumours and tumours with low SPF in the latter group.

Adult↗
PubMed1999

Classifying the location of osteosarcoma with reference to the epiphyseal plate helps determine the optimal skeletal resection in limb salvage procedures.

Between 1989 and 1996, 21 skeletally immature patients were treated for osteosarcoma of the extremity. Their average age was 12.6 years (range 9-16 years). We classified the location and extent of the lesion in bone on magnetic resonance imaging (MRI) with reference to the growth plate and joint margin into five subtypes. This classification served as a guide for the level of resection and the type of reconstruction required for a limb salvage procedure. All patients received neoadjuvant chemotherapy using a modified T10 protocol before the definitive operation. These patients were followed up for periods ranging from 11-86 months, with a mean of 35. 5 months. Patients were assessed for (1) local tumour recurrence, (2) metastatic disease, (3) allograft complications and (4) extremity function and joint stability. Excellent function was retained in 2, good in 13 and fair function in 6 patients. The MRI classification proved useful for the resection and provides an insight into the possible functional outcomes.

Adolescent↗
PubMed2005

Rhabdomyosarcoma: molecular diagnostics of patients classified by morphology and immunohistochemistry with emphasis on bone marrow and purged peripheral blood progenitor cells involvement.

Two histologically distinct subtypes of rhabdomyosarcomas (RMS), embryonal and alveolar, are different in many aspects, such as age distribution, primary site, and clinical outcome. We analyzed a group of 30 patients with RMS. The aim was to broaden the spectrum of diagnostic tools in evaluating the primary tumors, their recurrences and/or metastases, and to extend the diagnostic boundary to bone marrow and purged peripheral progenitor blood cell samples. We have performed the RT-PCR assay to analyze RMS for the presence of expression of MyoD1 gene and for the presence of chimeric transcripts PAX3/FKHR or PAX7/FKHR. MyoD1 gene expression was found in all 30 patients in samples from primary tumors. The chimeric transcripts PAX/FKHR were identified in 13 of 15 patients with alveolar RMS. Furthermore, the fusion transcript PAX7/FKHR was identified in 2 of 15 patients with RMS classified as embryonal by histology. Bone marrow samples (12) and peripheral blood progenitor cell specimens (13) in ten patients were examined by RT-PCR. We were able to identify 7 patients with bone marrow involvement and/or with contamination of peripheral blood progenitor cells by the tumor cells. We demonstrate that employing molecular diagnostics has an impact on staging, therapy monitoring and recognition of malignant cells at the tumor resection margins.

Adolescent↗
PubMed1997

Long-term follow up of children with head injuries-classified as "good recovery" using the Glasgow Outcome Scale: neurological, neuropsychological and magnetic resonance imaging results.

UNLABELLED: The primary issues addressed in this study were: (1) determination of the significance of the classification "good outcome" utilizing the Glasgow Outcome Scale (GOS) in children at least 1 year after brain injury; (2) detection of residual lesions of brain parenchyma in these children upon follow up MRI scans; and (3) detection of relationships between neuropsychological test performance and MRI results. Selection criteria included children 6-15 years of age at the time of testing who received an initial CT scan at the time of their head injury and who had been injured at least 12 months prior to the follow up test. Only children who did not demonstrate neurological disability at the time of follow up examination were selected. The children showed a status of "good outcome" as defined by the GOS. Neurological examination, neuropsychological tests and an MRI were done. The test results of 59 patients were compared to those of a matched control group. Children, after receiving head injuries, showed significantly poorer results with respect to cognitive, motor and fine motor skills. Of all MRI-scans 66% revealed pathological findings. Cortical lesions were detected on MRI in 14% of cases; subcortical injuries were detected in 12% and, deep white matter lesions in 31%. Furthermore, corpus callosum damage was observed in 26% of cases. Pathological MRI findings were also observed in children with mild head injuries. All of the children with normal MRI findings showed abilities comparable to those of children in the control group. Patients with cortical lesions exhibited only motor deficits, whereas motor and cognitive deficits were seen in patients with deep white matter lesions. Children with multiple lesions demonstrated test results in all variables 1 to 2 standard deviations below those of the control group. CONCLUSION: Children suffering a brain injury who 1 year later are classified within the "good outcome" group according to the Glasgow Outcome Scale often have significant morphological and functional brain deficits.

Adolescent↗
PubMed2005

Problems in classifying vasculitis in children.

Vasculitis is inflammation of blood vessels, which may also affect the arteries of the kidney. The definition and classification of vasculitides derive from the Chapel Hill nomenclature criteria (CHCC) and American College of Rheumatology (ACR) criteria, respectively. These criteria are not perfect, and adult literature refers to problems with misclassification and a low concordance between the two criteria. The problems associated with defining a child patient according to these criteria are even more apparent, since both sets of criteria have been based on adult data alone and have never been validated in children. When classifying their patients as having polyarteritis, paediatricians do not keep strictly to the CHCC or ACR criteria. A recent series has shown that the microscopic polyarteritis associated with MPO-ANCA and the HBs associated with classic polyarteritis nodosa are rarer in children than in adults. Paediatricians should revise the existing criteria based on registries and international consensus in the field.

Adult↗
PubMed2004

Evaluation of various species demarcation criteria in attempts to classify ten new tombusvirus isolates.

The usefulness of various suggested species demarcation criteria was compared in attempts to determine the taxonomic status of ten new tombusvirus isolates. Five of them (Lim 1, 2, 3, 5 and 6) were obtained from different sources of commercially grown statice (Limonium sinuatum), two (Gyp 1 and 2) from different sources of commercially grown Gypsophila paniculata and three from water samples, i.e. from a small river (Schunter) in Northern Germany, from a brook (near Dossenheim) in Southern Germany and from the groundwater in a Limonium production glasshouse in the Netherlands (Lim 4). The immunoelectron microscopical decoration test allowed a quick preliminary assignment of various isolates to several known tombusviruses. A more precise analysis of the relationships was achieved by comparing the deduced amino acid sequences of the coat proteins. Sequence as well as serological data suggested that eight of the isolates should be classified as strains or variants of either Carnation Italian ringspot virus, Grapevine Algerian latent virus, Petunia asteroid mosaic virus or Sikte waterborne virus, respectively, whereas the 9th isolate (Lim 2) appears to represent a distinct new tombusvirus species. The case of the 10th isolate (Lim 5) illustrates the classification problems experienced when the properties of a virus place it close to the more or less arbitrary man-made borderline between virus species and virus strains. The coat protein gene sequences were also determined for some viruses for which these data had not yet been available, i.e. Neckar river virus, Sikte waterborne virus and Eggplant mottled crinkle virus. The sequences of the coat protein gene and also of ORF 1 of the latter virus proved to be almost identical to the corresponding genome regions of the recently described Pear latent virus, which for priority reasons should be renamed. Criteria which have been suggested in addition to serology and sequence comparisons for tombusvirus species demarcation, i.e. differences in natural and in experimental host ranges, in cytopathological features and in coat protein size, appear to be of little value for the classification of new tombusviruses.

Base Sequence↗
PubMed2006

Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform.

As the potential drug targets, G-protein coupled receptors (GPCRs) and nuclear receptors (NRs) are the focuses in pharmaceutical research. It is of great practical significance to develop an automated and reliable method to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine was proposed to classify GPCRs and NRs from the hydrophobicity of proteins. The models for all the GPCR families and NR subfamilies were trained and validated using jackknife test and the results thus obtained are quite promising. Meanwhile, the performance of the method was evaluated on GPCR and NR independent datasets with good performance. The good results indicate the applicability of the method. Two web servers implementing the prediction are available at http://chem.scu.edu.cn/blast/Pred-GPCR and http://chem.scu.edu.cn/blast/Pred-NR.

Computer Simulation↗
PubMed1999

Photic driving response in primary headache: diagnostic value tested by discriminant analysis and artificial neural network classifiers.

The aim of this study was to discriminate migraine patients (MWoA) from tension-type headache (TTH) patients and normals in order to confirm that the photic driving response in the medium frequency range is a marker of migraine and to test the hypothesis that MWoA and TTH are separate disorders based on electrophysiological pattern. We recruited 120 MWoA patients, 64 TTH patients, and 51 healthy controls without any history of headache or of migraine inheritance, according to International Headache Society (IHS) criteria. The classification method was discriminant analysis using both linear discriminant analysis with a stepwise selection of predictors and an artificial neural network classifier (NNs). The mean amplitude of the first harmonic elicited by flash stimulation in the 15-27 Hz range was significantly increased over Fp1, C3, C4, P4, O2, and O1 electrodes in MWoA and TTH patients in comparison with normal subjects. Using both classification methods, only the control subjects were correctly distinguished. When only the patient groups were matched, no significant difference was detectable. The increased brain response to visual stimulation detected in both migraine and TTH suggests a common neuronal dysfunction in the two headache subtypes.

Adolescent↗
PubMed2004

Benign/malignant classifier of soft tissue tumors using MR imaging.

UNLABELLED: This article presents a pattern-recognition approach to the soft tissue tumors (STT) benign/malignant character diagnosis using magnetic resonance (MR) imaging applied to a large multicenter database. OBJECTIVE: To develop and test an automatic classifier of STT into benign or malignant by using classical MR imaging findings and epidemiological information. MATERIALS AND METHODS: A database of 430 patients (62% benign and 38% malignant) from several European multicenter registers. There were 61 different histologies (36 with benign and 25 with malignant nature). Three pattern-recognition methods (artificial neural networks, support vector machine, k-nearest neighbor) were applied to learn the discrimination between benignity and malignancy based on a defined MR imaging findings protocol. After the systems had learned by using training samples (with 302 cases), the clinical decision support system was tested in the diagnosis of 128 new STT cases. RESULTS: An 88-92% efficacy was obtained in a not-viewed set of tumors using the pattern-recognition techniques. The best results were obtained with a back-propagation artificial neural network. CONCLUSION: Benign vs. malignant STT discrimination is accurate by using pattern-recognition methods based on classical MR image findings. This objective tool will assist radiologists in STT grading.

Algorithms↗
PubMed2003

Risk of lymph node and distant metastases in patients with early invasive colorectal cancer classified as Haggitt's level 4 invasion: image analysis of submucosal layer invasion.

PURPOSE: Tumor invasion in patients with early invasive colorectal cancer has been classified into four levels proposed by Haggitt. Level 4 invasion into the submucosa has been defined as a risk factor for lymph node metastasis; however, the false-positive rate remains high. This study was designed to determine risk factors for lymph node and distant metastases in addition to Haggitt's Level 4 invasion. METHODS: Seventy-one of 142 patients with submucosa-invasive colorectal cancer underwent intestinal resection as an initial surgical treatment between 1975 and 2000. The subjects of this study were 65 of these 71 patients, all of whom were diagnosed as having Haggitt's Level 4 invasion. The depth, width, and area of submucosal invasion were measured with an image analyzer. RESULTS: Lymph node metastasis was noted in 11 (16.9 percent) of the 65 patients. There were no significant differences in the depth or area of submucosal invasion between node-positive and node-negative patients. However, the width of submucosal invasion was significantly greater in node-positive than in node-negative patients (P = 0.001). When 5-mm-wide submucosal invasion was used as an indicator for intestinal resection, 37 patients were found to have indications for bowel resection, and 11 (29.7 percent) of the 37 had lymph node metastases. Distant metastasis was noted in five patients (7.7 percent). The depth, width, and area of submucosal invasion in patients with distant metastasis did not differ significantly from those without distant metastasis. CONCLUSION: Although further prospective investigation is required, the positive predictive value increases from 17 to 30 percent when the width of submucosal invasion is added to Haggitt's Level 4 as an indicator for bowel resection.

Adenocarcinoma↗
PubMedDate not supplied

Isolation and sequencing of a new glucoamylase gene from an Aspergillus niger aggregate strain (DSM 823) molecularly classified as Aspergillus tubingensis.

Based on morphological characteristics the taxa included in the Aspergillus aggregate can hardly be differentiated. For that reason the phylogeny of this genus was revised several times as different criteria, from morphological to later molecular, were used. We found, comparing nucleotide sequences of the ITS-region, that the strain Aspergillus niger (DSM 823) which is claimed to be identical to the strains ATCC 10577, IMI 027809, NCTC 7193 and NRRL 2322 can be molecularly classified as Aspergillus tubingensis, exhibiting 100% identity with the A. tubingensis CBS strains 643.92 and 127.49. We amplified, cloned and sequenced a new glucoamylase gene (glaA) from this strain of A. tubingensis (A. niger DSM 823) using primers derived from A. niger glucoamylase G1. The amplified cDNA fragment of 2013 bp contained an open reading frame encoding 648 amino acid residues. The calculated molecular mass of the glucoamylase, deduced from the amino acid sequence, was 68 kDa. The nucleotide sequence of glaA showed 99% similarity with glucoamylases from Aspergillus kawachii and Aspergillus shirousami, whereas the similarity with the glucoamylase G1 from A. niger was 92%

Amino Acid Sequence↗