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PubMed1996

Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis.

The simultaneous presence of multiple HIV-1 subtypes has become common in communities with the growth of the pandemic. As a consequence, the potentiality for an increased frequency of HIV-1 mixed infections caused by viruses of distinct subtypes could be expected. Thus, there is a need to estimate the prevalence and geographic distribution of infections caused by viruses of a singular subtype as well as coinfections caused by two or more HIV-1 strains of distinct subtypes. To address this need, we have developed a genetic method based on restriction fragment length polymorphism (RFLP) to screen for these two types of infections within infected populations. In this assay, restriction enzymes may be used to predict the phylogroup of HIV-1 infected samples. A 297 bp pol fragment spanning the entire viral protease gene and a 311 bp fragment of the p24 gag region are used for this analysis. The viral regions are amplified by nested PCR using DNA templates from uncultured peripheral blood mononuclear cells (PBMC) or virus culture. Classification of HIV-1 strains to well defined subtypes B, D, F, and A/C is done by sequential endonuclease restriction analysis of a PCR amplified-protease gene followed by analysis of the p24 gag region. The electrophoretic migration patterns visualized by ethidium bromide staining or by radiolabeled probes are then determined on a 10% polyacrylamide gel. In infections caused by viruses of a singular subtype, a single restriction pattern is detected, whereas in multiple infections caused by two or more viral strains of different subtypes, the combination of different digestion patterns are observed in infected individuals. Using this methodology we have screened for genetic variations in HIV-1 proviral DNA from thirty-three Brazilian samples. Our RFLP procedure classified thirty-two samples as single infections caused by viruses of subtypes B (31) and F (1), and one sample as dual infection caused by distinct viral strains. Subsequent sequence and phylogenetic analysis of the viral protease gene in lymphocytes of all these patients confirmed our RFLP findings in single infections, and demonstrated the existence of two distinct HIV-1 strains of subtypes F and D in a patient which lymphocytes showed the simultaneous presence of two different digestion patterns. As up to now, single infections caused by subtype D variants were not identified in Brazil, our data provide the first evidence of subtype D HIV-1 in this country. Because sequencing of HIV proviral DNA is not particularly practical for large-scale molecular epidemiological studies, the protease/gag-based RFLP screening method will be useful to predict the phylogroup of HIV-1, and to identify multiple infections caused by HIV-1 strains of distinct subtypes. We believe that this information is crucial for both evaluation of the HIV-1/AIDS pandemic and intervention strategies.

Adult↗

PubMedDate not supplied

Classification and analysis of fetal deaths in Massachusetts.

Fetal deaths, in contrast to infant deaths, have been subject to epidemiologic analysis infrequently. We characterized 574 Massachusetts resident fetal deaths from 1982 and assessed the accuracy of cause-of-death information available from vital records compared with that from corresponding fetal autopsies. The fetal death rate exceeded the neonatal mortality rate. Fetal mortality was higher among black, unmarried, and older mothers. Fetuses of multiple-gestation pregnancies had an unusually high risk of fetal death. Autopsy reports were obtained for 61% of fetal deaths. The underlying cause of death from the fetal death record differed from that on the autopsy report in 55% of cases. Systematic collection of population-based autopsy data is a useful approach for improving the quality and accuracy of mortality statistics on fetal deaths. Many stillbirths remain unexplained, however, and research is needed to identify pathological markers that might reduce the heterogeneity within the fetal deaths currently ascribed to unknown causes.

Adult↗

PubMed1996

Gastric remnant carcinoma after partial gastrectomy for benign and malignant gastric lesions.

BACKGROUND: A retrospective study was designed to evaluate the clinicopathologic characteristics and prognosis of gastric stump carcinoma (GSC) after gastrectomy for gastric adenocarcinoma. STUDY DESIGN: A comparison of the clinicopathologic features was made between 12 cases of GSC and 27 cases of remnant carcinoma (RC) following gastrectomy for adenocarcinoma. The various factors influencing survival of both groups of patients were evaluated separately and by multivariate analysis. RESULTS: Gastric stump carcinoma emerges late after initial gastrectomy and has a significant tendency toward lymph node metastasis. No difference was observed between the survival curves for patients with GSC or RC after gastrectomy for malignancy. Serosal invasion was the factor most affecting survival. CONCLUSIONS: Early diagnosis is most important for management of the disease, and only patients with T2 staged GSC according to the Union Internationale Contre le Cancer classification system might benefit from extensive lymphadenectomies.

Adenocarcinoma↗

PubMed1991

Prognostic factors in multiple myeloma.

The pretreatment characteristics of 265 multiple myeloma patients treated between 1977 and 1983 were evaluated as potential prognostic factors for survival. Patients whose diagnosis was based on bone marrow plasmacytosis (greater than 30%) were noticed to have poorer survival (P less than 0.001). Although classification of patients according to stage has traditionally been used to identify prognostic groups, differences in survival were noted only between Stage III and Stage I or II patients using one of two common staging systems. Multivariate analysis using Cox's proportional hazards model identified the following prognostic factors in order of importance: plasmacytosis (hazard ratio [HR] = 2.2, 95% confidence interval [CI] = 1.49 to 3.27), hypercalcemia (HR = 1.68, CI = 1.22 to 2.32), hypoalbuminemia (HR = 1.51, CI = 1.15 to 1.99), alkaline phosphatase (HR = 1.62, CI = 1.18 to 2.23), hyperuricemia (HR = 1.46, CI = 1.09 to 1.96), and renal insufficiency (HR = 1.48, CI = 1.08 to 2.04). All patients were followed from 2 to 7.5 years and 130 (49%) survived over 2 years. Logistic regression analysis demonstrated that hyperuricemia, hypoalbuminemia, renal insufficiency, plasmacytosis, gender, alkaline phosphatase, and hypercalcemia were significant predictors of 2-year survival. Knowledge of these factors could be of value in predicting prognosis and planning therapy in patients with multiple myeloma.

Adult↗

PubMed1989

Prognostic factors in primary gastrointestinal non-Hodgkin's lymphoma. A multivariate analysis, report of 106 cases, and review of the literature.

The authors have reviewed 106 cases of primary gastrointestinal non-Hodgkin's lymphoma (GI-NHL) treated at the Institut Gustave-Roussy (IGR), France, between 1975 and 1986. The occurrence was 55 in the stomach, 26 in the small intestine, ten ileocecal, seven in the large intestine, and eight patients had multiple involvement. Patients were clinically staged according to the Ann Arbor staging system using the modification of Musshoff for Stage IIE. All histologic material of the 106 patients were reviewed and graded according to the Working Formulation (WF) and the Kiel classifications. Most patients received combination chemotherapy as part or all of their primary treatment program (95 patients, 90%). Seventy five patients (71%) had a multimodality treatment. The overall 5-year survival rate was 60%. Sixteen variables were tested by univariate analyses for prognostic influence on survival. Of these, only clinical stage (P less than 0.001), the achievement of initial complete remission (CR) (P less than 0.001), erythrocyte sedimentation rate (ESR) (P = 0.01), mesenteric involvement (P = 0.03), and serosal infiltration (P = 0.05) were significant prognostic factors. Important variables were tested by a multivariate analysis using the Cox model taking into account different treatment modalities. Only three variables entered the regression analysis at a significant level: clinical stage (P = 0.02), surgical resection (P = 0.03), and histologic grade (Kiel) (P = 0.04). When the achievement of initial CR was introduced into the model, it was the most significant variable (P less than 0.001) whereas all other variables became nonsignificant except for the histologic grade (Kiel) (P = 0.004). Based on results of the multivariate analyses we propose two prognostic classifications of patients: one at the initial evaluation depending on clinical stage, surgical resectability, and histologic grade (Kiel); the other at the end of primary treatment depending on the achievement or not of CR and the histologic grade.

Adolescent↗

PubMed2003

[Pelvic fracture. Diagnostics and current treatment options].

Pelvic fracture, especially in combination with multiple trauma, can still lead to life-threatening situations. Only clear inclusion criteria and decisions can ensure the survival of the patient, the key task being mechanical stabilization using external fixators or pelvic clamps with or without surgical intervention for hemostasis. The basis for problem-oriented management is a precise classification, which is based on conventional X-rays in emergency situations and detailed analysis of computed tomography for the planning of definitive surgical interventions. The classification groups postulated are stable pelvic fractures (type A), rotational unstable pelvic fractures (type B--partial stability of the posterior pelvic ring present), and translational instabilities (type C--with a complete disruption of the anterior and posterior pelvic ring). This classification leads to clear indications for pelvic ring stabilization as surgical interventions are only exceptionally indicated in type A fractures, stabilization of the anterior ring is sufficient for type B fractures, and combined posterior and anterior stabilization is necessary for treatment of type C fractures. Following these concepts and by using standardized procedures and implants, the high rate of enclosed anatomical healing can be achieved even after type C injuries. Nevertheless, the role of concomitant soft tissue injuries and scar formation is not clear as the origin of the frequently observed long-term clinical impairments even after anatomical reconstruction of the osteoligamentous structures.

Adolescent↗

PubMed1977

[Genetic syndromes of multiple congenital developmental defects].

Analysis of developmental defects in 615 children who had died in hospitals in Minsk during the 5-year period (1971--1975)showed that in 274 children defects were multiple. This number includes 78 children with chromosomal diseases and 37 children with genic syndromes of multiple congenital malformations (MCM). The total number of genic syndromes of MCM is extremely great, at present over 250 of them are known. Analysis of the available literature and the authors' own findings made it possible to develop criteria of morphological diagnosis of genic syndromes of MCM with due account for different diagnostic significance of various defects. Genealogical studies and estimation of population incidence of individual malformations are also necessary for diagnosis of genic syndromes of MCM and identification of new syndromes. An etiological classification of MCM and that of genic syndromes of MCM are considered on the basis of isolation of similar clinical forms, which are of important for differential diagnosis.

Abnormalities, Multiple↗

PubMedDate not supplied

Slow progression of periampullary neoplasia in familial adenomatous polyposis.

Variable endoscopic surveillance protocols and treatment strategies have been proposed for periampullary neoplasia in familial adenomatous polyposis (FAP), primarily because of the lack of long-term, prospective natural history data. A total of 115 patients with FAP were followed prospectively for 10 years with periodic side-viewing upper gastrointestinal endoscopy by a single surgeon. The appearance of the duodenum was classified as stages 1 to 5. Statistical analysis included one-way analysis of variance for age comparisons between stage groupings and Kaplan-Meier analysis for the lifetime risks of having a particular stage of duodenal polyposis. Eighty-seven patients had multiple endoscopies over an average of 6.6 years. Thirty-three subjects had a change in stage, within an average time of 3.9 years at an average age of 41 years. The risk of having stage 3 or 4 duodenal neoplasia increased exponentially after the age of 40. The degree of dysplasia did not correlate with stage at initial classification. Progression of neoplasia in the duodenum of patients with FAP is slow. The severity of duodenal polyposis increases with age and is not influenced by the initial stage. The average time for progression of adenoma to carcinoma is likely long.

Adenomatous Polyposis Coli↗

PubMed2006

Functional specialization within rostral prefrontal cortex (area 10): a meta-analysis.

One of the least well understood regions of the human brain is rostral prefrontal cortex, approximating Brodmann's area 10. Here, we investigate the possibility that there are functional subdivisions within this region by conducting a meta-analysis of 104 functional neuroimaging studies (using positron emission tomography/functional magnetic resonance imaging). Studies involving working memory and episodic memory retrieval were disproportionately associated with lateral activations, whereas studies involving mentalizing (i.e., attending to one's own emotions and mental states or those of other agents) were disproportionately associated with medial activations. Functional variation was also observed along a rostral-caudal axis, with studies involving mentalizing yielding relatively caudal activations and studies involving multiple-task coordination yielding relatively rostral activations. A classification algorithm was trained to predict the task, given the coordinates of each activation peak. Performance was well above chance levels (74% for the three most common tasks; 45% across all eight tasks investigated) and generalized to data not included in the training set. These results point to considerable functional segregation within rostral prefrontal cortex.

Algorithms↗

PubMed2005

Expressed sequence tag analysis of the soybean rust pathogen Phakopsora pachyrhizi.

Soybean rust is caused by the obligate fungal pathogen Phakopsora pachyrhizi Sydow. A unidirectional cDNA library was constructed using mRNA isolated from germinating P. pachyrhizi urediniospores to identify genes expressed at this physiological stage. Single pass sequence analysis of 908 clones revealed 488 unique expressed sequence tags (ESTs, unigenes) of which 107 appeared as multiple copies. BLASTX analysis identified 189 unigenes with significant similarities (Evalue<10(-5)) to sequences deposited in the NCBI non-redundant protein database. A search against the NCBI dbEST using the BLASTN algorithm revealed 32 ESTs with high or moderate similarities to plant and fungal sequences. Using the Expressed Gene Anatomy Classification, 31.7% of these ESTs were involved in primary metabolism, 14.3% in gene/protein expression, 7.4% in cell structure and growth, 6.9% in cell division, 4.8% in cell signaling/cell communication, and 4.8% in cell/organism defense. Approximately 29.6% of the identities were to hypothetical proteins and proteins with unknown function.

Basidiomycota↗

PubMed2003

Bagging tree classifiers for laser scanning images: a data- and simulation-based strategy.

Diagnosis based on medical image data is common in medical decision making and clinical routine. We discuss a strategy to derive a classifier with good performance on clinical image data and to justify the properties of the classifier by an adapted simulation model of image data. We focus on the problem of classifying eyes as normal or glaucomatous based on 62 routine explanatory variables derived from laser scanning images of the optic nerve head. As learning sample we use a case-control study of 98 normal and 98 glaucomatous subjects matched by age and sex. Aggregating multiple unstable classifiers allows substantial reduction of misclassification error in many applications and bench mark problems. We investigate the performance of various classifiers for the clinical learning sample as well as for a simulation model of eye morphologies. Bagged classification trees (bagged-CTREE) are compared to single classification trees and linear discriminant analysis (LDA). We additionally compare three estimators of misclassification error: 10-fold cross-validation, the 0.632+ bootstrap and the out-of-bag estimate. In summary, the application of our strategy of a knowledge-based decision support shows that bagged classification trees perform best for glaucoma classification.

Case-Control Studies↗

PubMed2007

J-GFT NMR for precise measurement of mutually correlated nuclear spin-spin couplings.

G-matrix Fourier transform (GFT) NMR spectroscopy is presented for accurate and precise measurement of chemical shifts and nuclear spin-spin couplings correlated according to spin system. The new approach, named "J-GFT NMR", is based on a largely extended GFT NMR formalism and promises to have a broad impact on projection NMR spectroscopy. Specifically, constant-time J-GFT (6,2)D (HA-CA-CO)-N-HN was implemented for simultaneous measurement of five mutually correlated NMR parameters, that is, 15N backbone chemical shifts and the four one-bond spin-spin couplings 13Calpha-1Halpha, 13Calpha-13C', 15N-13C', and 15N-1HNu. The experiment was applied for measuring residual dipolar couplings (RDCs) in an 8 kDa protein Z-domain aligned with Pf1 phages. Comparison with RDC values extracted from conventional NMR experiments reveals that RDCs are measured with high precision and accuracy, which is attributable to the facts that (i) the use of constant time evolution ensures that signals do not broaden whenever multiple RDCs are jointly measured in a single dimension and (ii) RDCs are multiply encoded in the multiplets arising from the joint sampling. This corresponds to measuring the couplings multiple times in a statistically independent manner. A key feature of J-GFT NMR, i.e., the correlation of couplings according to spin systems without reference to sequential resonance assignments, promises to be particularly valuable for rapid identification of backbone conformation and classification of protein fold families on the basis of statistical analysis of dipolar couplings.

Carbon Isotopes↗

PubMed1990

Cytological grading of breast carcinoma--a feasible proposition?

Fine needle aspiration cytology (FNAC) of the breast is widely used in the diagnosis of breast carcinoma. In some centres this is sometimes the only diagnostic procedure performed prior to definitive treatment. A grading system based on cytology would be helpful in the selection of patients for appropriate therapy. The aim of this study, therefore, was to devise such a system for grading breast carcinoma based on cytological features alone. The features assessed were the degree of cell clustering, nuclear pleomorphism, nuclear diameter, the presence of multiple, easily visible nucleoli and necrosis. Cytological features were compared to the histological grade of the tumours following excision. Discriminant analysis showed that the features with the closest correlation with histological grade were nuclear diameter, nuclear pleomorphism and the presence of nucleoli. A scoring system based on these three parameters enabled the classification of tumours into high and low cytological grades which showed a close correlation with histological grade.

Biopsy, Needle↗

PubMed2026

Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminate Escherichia coli strains originating from poultry.

UNLABELLED: Escherichia coli is a highly diverse bacterial species that includes avian pathogenic E. coli (APEC), one of the most prevalent causative agents of disease in poultry worldwide. Rapid and accurate discrimination of E. coli strains is essential for outbreak management, antimicrobial resistance surveillance, and vaccine development. In this study, we compared the performance of Fourier Transform Infrared (FTIR) spectroscopy using the IR Biotyper system with Nanopore and Illumina whole-genome sequencing (WGS) for typing 200 E. coli isolates, originating from four poultry rearing farms in the Netherlands. From each farm, we sampled 10 one-day-old meat type rearing chicks, and from every chick, we isolated 5 E. coli strains. FTIR clustering showed strong concordance with WGS-based classifications, particularly serotyping and core-genome similarity determined by PopPUNK analysis (Adjusted Rand Index 0.75-0.92). While Nanopore and Illumina sequencing provided the highest genetic resolution, FTIR offered a faster (max 6 vs 12-28 days for 200 isolates) and more cost-effective alternative for assessing clonality. Across all methods, multiple strains were detected per farm, whereas most birds carried a single dominant E. coli strain. Our findings demonstrate that FTIR provides a reliable and scalable phenotypic method for rapid strain discrimination in E. coli, complementing WGS in diagnostic, surveillance, and epidemiological settings where speed and throughput are critical. IMPORTANCE: Escherichia coli is a major pathogen in poultry and a potential zoonotic risk for humans. Rapid and accurate discrimination of avian pathogenic E. coli (APEC) strains is critical for outbreak management, antimicrobial resistance surveillance, and the design of effective autogenous vaccines. In this study, we compared Fourier Transform Infrared (FTIR) spectroscopy with Nanopore and Illumina whole-genome sequencing for strain typing of E. coli isolates originating from poultry. The results show that FTIR provides comparable clustering accuracy to genomic approaches at a fraction of the time and costs. This work demonstrates that FTIR can serve as a practical, high-throughput alternative for routine monitoring of E. coli in veterinary diagnostics and food safety of poultry meat, enabling faster decision-making and more targeted interventions across the poultry production chain.

Animals↗

PubMed2005

Periacetabular limb salvage for malignant bone tumours.

PURPOSE: To evaluate treatment outcomes in primary malignant periacetabular bone tumour removal and limb salvage with or without bone-graft reconstruction. METHODS: A total of 13 patients were treated for malignant periacetabular bone tumours at Siriraj Hospital, Bangkok, Thailand. The diagnoses were chondrosarcoma (n=8), Ewing's sarcoma (n=2), osteosarcoma (n=1), well-differentiated osteosarcoma (n=1), and malignant giant cell tumour (n=1). 11 patients did not undergo reconstruction following tumour resection; 2 patients received fibular bone grafts bridging the periacetabulum to the remaining sacrum. Adjuvant chemotherapy was administered for high-grade malignant tumours, and postoperative radiation therapy was performed on patients with a closed surgical margin. RESULTS: At a mean follow-up of 24.3 months (range, 8.9-43.9 months), 9 patients remained disease-free, 3 had died of the disease, and one was alive with disease. According to the Musculoskeletal Tumor Society classification system, the mean functional analysis at final follow-up was 68.7%. Patients who underwent internal hemipelvectomy experienced a subsequent leg-length discrepancy ranging from 3 to 10 cm. Four patients had complications (one each for deep wound infection, skin necrosis, seroma, and vascular spasms) and were successfully treated with multiple debridements and appropriate antibiotics. Three patients had local recurrences; one required a classic hemipelvectomy. CONCLUSION: Malignant periacetabular tumours are difficult to manage. Functional results of our patients with no reconstruction or with bone-graft bridging were fair. Patients undergoing internal hemipelvectomy may experience leg-length discrepancies, which can be balanced with shoe lifts.

Adult↗

PubMed2001

Underutilization of neuropsychology in traumatic brain injury rehabilitation: is managed care to blame?

We evaluated factors determining which individuals received neuropsychological evaluations (NPEs) following traumatic brain injury (TBI). Comprehensive records from a State-wide/sponsored Head Injury Program were followed from 1985--1995 to monitor effects of managed care on provision (or absence) of formal NPEs and ultimately on rehabilitation outcome. Only 26% of 273 individuals received NPEs (within their first three years post-injury). In the years prior to and after large changes in managed care, there were no differences in the provision of formal NPEs. Discriminant analysis identified functional status at discharge from primary rehabilitation and total number of rehabilitation facilities as the two variables that most distinguished those who had received NPEs with 69% classification accuracy. Between group analyses revealed that individuals were more likely to receive NPEs if they were young, involved in liability claims, attended multiple rehabilitation facilities, or had higher functional status at discharge from primary rehabilitation, regardless of the nature or severity of their TBI. Individuals receiving formal NPEs ultimately achieved higher levels of functional independence, suggesting a potential selection bias. Individuals were no more likely to receive NPEs according to insurance status (private versus government assisted) or as a function of the decade of their injury (1980's versus 1990's). It appears that health-care reform has had no deleterious effect on neuropsychologists' ability to provide consultative services for this population, and following TBI, only a discrete sample of individuals receive and benefit from NPEs.

Adolescent↗

PubMed2004

PPD - Proteome Profile Database.

With the complete sequencing of multiple genomes, there have been extensions in the methods of sequence analysis from single gene/protein-based to analyzing multiple genes and proteins simultaneously. Therefore, there is a demand of user-friendly software tools that will allow mining of these enormous datasets. PPD is a WWW-based database for comparative analysis of protein lengths in completely sequenced prokaryotic and eukaryotic genomes. PPD's core objective is to create protein classification tables based on the lengths of proteins by specifying a set of organisms and parameters. The interface can also generate information on changes in proteins of specific length distributions. This feature is of importance when the user's interest is focused on some evolutionarily related organisms or on organisms with similar or related tissue specificity or life-style. PPD is available at: PPD Home.

Animals↗

PubMed1992

[Estimation of genetic parameters by using analysis of variance within unit].

In the estimation of heritability, various non-genetic factors must be excluded from the variance of sire or dam. The methods of sib correlation within unit, suggested by professor Sheng Zhilian is commonly used in China. This paper will provide evidence to verify this method theoretically and discuss the application of the method to systematic classification. In addition, in this paper the author suggest some other methods to estimate heritability by using analysis of variance within unit when the blood relationship exists between sire and dam. These methods not only make the estimation procedure of hertability simple but also have the same function of analyzing variance with multiple factors.

Analysis of Variance↗