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At least 469 records · Page 26Linked to original sources
PubMed2002

Curative therapy of advanced essential thrombocythemia or polycythemia vera by hemopoietic stem cell transplantation.

Twenty-five patients with advanced essential thrombocythemia (ET; n = 13) or polycythemia vera (PV; n = 12) received hemopoietic stem cell transplants (HSCT) at the Fred Hutchinson Cancer Research Center. In most cases the indication to perform an HSCT was myelofibrosis with splenomegaly and peripheral blood cytopenias or the development of a myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Patients were 18-60 (median 43) years old with intervals from diagnosis to HSCT of 8-348 (median 168) months. All but five patients had been treated with cytotoxic agents, and nine patients were splenectomized before transplant. Conditioning was performed with chemotherapy only or chemotherapy plus total body irradiation regimens followed by the infusion of either marrow (n = 19) or peripheral blood stem cells (n = 6) from related (n = 16) or unrelated (n = 9) donors. All evaluable patients showed sustained neutrophil engraftment. Nine patients (seven with AML/MDS, two with myelofibrosis) died of transplant-related complications, and 16 are surviving, 14 of them in continuous unmaintained remission. With a median follow-up of 41 (range 5-116) months after transplant, survival at 3 years is 64%. These data provide evidence that HSCT can be a curative treatment for patients with advanced PV and ET.

Adolescent↗
PubMed2006

Integrating image data into biomedical text categorization.

Categorization of biomedical articles is a central task for supporting various curation efforts. It can also form the basis for effective biomedical text mining. Automatic text classification in the biomedical domain is thus an active research area. Contests organized by the KDD Cup (2002) and the TREC Genomics track (since 2003) defined several annotation tasks that involved document classification, and provided training and test data sets. So far, these efforts focused on analyzing only the text content of documents. However, as was noted in the KDD'02 text mining contest-where figure-captions proved to be an invaluable feature for identifying documents of interest-images often provide curators with critical information. We examine the possibility of using information derived directly from image data, and of integrating it with text-based classification, for biomedical document categorization. We present a method for obtaining features from images and for using them-both alone and in combination with text-to perform the triage task introduced in the TREC Genomics track 2004. The task was to determine which documents are relevant to a given annotation task performed by the Mouse Genome Database curators. We show preliminary results, demonstrating that the method has a strong potential to enhance and complement traditional text-based categorization methods.

Artificial Intelligence↗
PubMed1988

Treatment of recurrent respiratory papillomatosis with human leukocyte interferon. Results of a multicenter randomized clinical trial.

Recurrent respiratory papillomatosis is a relentless disease of viral origin in which squamous papillomas frequently obstruct the respiratory tract of children and young adults. No therapy has been proved to be curative for this process. Recent reports have suggested that interferon may cure or dramatically control airway papillomatosis. We evaluated the efficacy of human leukocyte interferon in the treatment of respiratory papillomatosis. One hundred twenty-three patients were randomly assigned to receive treatment with either surgery plus interferon or surgery alone. Interferon (2 X 10(6) IU per square meter of body-surface area) was given daily for one week, then three times per week for one year; treatment was followed by a year of observation, without the drug. Both study groups underwent serial endoscopy to remove papillomas and to document the efficacy of treatment during the two years of study. During the first six months, the growth rate of papillomas in the interferon group was significantly lower than in the control group (P = 0.0007). This difference diminished during the second six months and was no longer statistically significant (P = 0.68). Our data do not show that interferon is either curative or of substantial value as an adjunctive agent in the long-term management of recurrent respiratory papillomatosis. The initial benefit of interferon is not sustained.

Child, Preschool↗
PubMed2005

Geographical variation in incidence of prostate cancer in Sweden.

OBJECTIVE: To investigate the geographical variation in prostate cancer incidence in Sweden, in particular the incidences of screening-detected tumours and curative treatment of prostate cancer. MATERIAL AND METHODS: Data were retrieved from the National Prostate Cancer Register of Sweden for all cases of prostate cancer diagnosed in the year 2000-01. There were a total of 14 376 cases of prostate cancer and the mean total annual age-adjusted incidence was 197/100 000 men. There were 3318 cases in tumour category T1c, i.e. non-palpable tumours diagnosed during work-up for an elevated serum level of prostate-specific antigen, 1006 of which (30%) were asymptomatic and detected at a health check-up. RESULTS: The difference between the counties with the lowest and highest age-adjusted incidences per 100 000 men of total prostate cancer was almost twofold (128 vs 217). The corresponding variation in incidence of category T1c tumours was more than fourfold (13 vs 60); the difference in incidence of T1c tumours detected in asymptomatic men was up to 10-fold (2 vs 20); and there was more than a fourfold variation in incidence of curative treatment between counties (13 vs 67). Measured incidences were mostly highest in urban regions and in counties with university hospitals. CONCLUSION: There are large geographical variations in prostate cancer incidence and in the frequency of curative treatment for prostate cancer in Sweden and there appear to be large geographical variations in the uptake of prostate cancer screening.

Aged↗
PubMed2005

Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W).

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.

Computational Biology↗
PubMed2006

[Multivariate prognostic analysis for patients with curative resection of gastric cardia cancer].

OBJECTIVE: To explore the factors affecting the long-term survival of patients with curative resection of gastric cardia cancer. METHODS: The data of 108 patients who underwent radical resection of gastric cardia cancer from Jul. 1994 to Dec. 2003 in our hospital were investigated retrospectively. The Kaplan-Meier method and long-rank test were used for bivariate comparisons of survival. Multivariate analysis was done by the Cox regression model (Backward Wald). RESULTS: Survival status of the 108 patients was ascertained in Dec. 2004. Among them, 68 were Siewert type II and 40 were Siewert type III. Seventy-four patients had lymph node metastases (68.5%). The mean follow-up time was 37 months (95% CI: 29.3-44.7 months) and the middle follow-up time was 26.6 months (95% CI: 25.8-34.2 months). The 1-,3- and 5-year cumulative survival rates were 77.2%, 33.6% and 21.8%, respectively. According to the Kaplan-Meier and log-rank methods, splenectomy, lesion size, depth of tumor invasion and regional lymph node status were prognostic factors. Multivariate regression analysis indicated that only depth of tumor invasion (P=0.009) and lymph node metastases (P=0.001) were independent prognostic factors. CONCLUSION: Depth of tumor invasion and lymph node metastases have negative effects on the survival of patients with gastric cardia cancer undergoing curative resection. Splenectomy may only be appropriate for patients with direct tumor invasion to the spleen and the extent of gastric resection does not influence survival in patients with curative gastric cardia cancer.

Adult↗
PubMed1980

The curative value of irradiation in the treatment of nondisseminated breast cancer.

Data are now available from two randomized trials showing that adjuvant irradiation of the internal mammary and supraclavicular nodes following a radical or modified radical mastectomy results in increased survival rates. A retrospective analysis of 1111 patients treated at M. D. Anderson Hospital with radical mastectomies with and without irradiation to the peripheral lymphatic areas shows equal ten-year survival rates in irradiated and unirradiated patients in spite of the fact that the irradiated patients had a much higher incidence of histologically positive nodes. There is a significant percentage of patients surviving ten-years in 353 patients with locally or regionally advanced tumors treated with simple mastectomy and irradiation without chemotherapy. Radiation of gross local and regional recurrences has a high risk of failure and radiation sequelae.

Breast Neoplasms↗
PubMed1997

The SWISS-PROT protein sequence data bank and its supplement TrEMBL.

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, structure of its domains, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and the creation of TrEMBL, a computer annotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT.

Academies and Institutes↗
PubMed2026

Assessment of the impact of manual curation in BioCyc.

INTRODUCTION: BioCyc is an extensive collection of databases of genomic and pathway information for microorganisms and model eukaryotes. These organismal databases integrate diverse biological data by combining computationally inferred information, data imported from other databases, and, for selected organisms, literature-based manual curation. This study investigates the magnitude and significance of annotation changes performed during the curation of 10 prokaryotic genomes to better understand the rate of erroneous annotations and the value of BioCyc curation. METHODS: We identified curation changes by finding cases where the annotation of the protein at the start of the curation process differed from its annotation at the end of the process. RESULTS: We found that across a sample of curated databases (n = 10), the annotation of 6,753, or 25.6% of the proteins in the pooled protein dataset (n = 26,126) were modified. Assessment of considerable sampling fractions of these proteins found that a median of 62% (mean of 52.9%) represented functionally informative name changes, rather than stylistic annotation changes. These results were then extrapolated to total proteins with name changes with uncertainty quantified via finite population correction, indicating that most Tier 2 Biocyc PGDBs received hundreds of functionally informative name changes during manual curation. On average 363, or13% (±5.4% SD) of the proteins encoded in each genome received functionally informative annotation changes, ranging from 5.3% (Streptococcus pneumoniae D39V) to 22.7% (Staphylococcus aureus NCTC 8325). DISCUSSION: These findings demonstrate a substantial improvement in the accuracy of manually curated BioCyc databases compared with automated annotation pipelines. This result is particularly impactful as the rate of downstream propagation of erroneous annotations across biological databases can significantly compromise scientific discovery.

annotation errors↗
PubMed1991

Excess female deaths among rural Bangladeshi children: an examination of cause-specific mortality and morbidity.

Excess female over male mortality during childhood, well known in the northern Indian subcontinent, is particularly marked in rural Bangladesh. While the determinants of this phenomenon and the respective roles of cultural and economic factors are still debated, little data exist on cause-specific mortality, to identify the specific causes of death producing this differential. In 1986-1987 in Matlab, a study area under intensive demographic surveillance in rural Bangladesh, female children aged 1 to 4 years had a risk of dying 1.8 times higher than male children (95% confidence interval: 1.5-2.1). The causes of death which contributed the most to this excess female mortality were severe malnutrition and diarrhoeal diseases. The risks of dying were 2.5 and 2.1 higher for female than for male children for these two causes, respectively. Possible mechanisms are examined using data on incidence of selected diseases and admission rates to curative facilities. There was no gender difference in incidence of severe diarrhoeal diseases, but female children with diarrhoea were taken to the hospital significantly less often than male children. In contrast, there was a higher incidence of severe malnutrition in female than male children, and a lower rate of hospital admission. The data suggest that gender differentials in mortality may not be as much affected by preventive measures against diarrhoea as by efforts to provide equivalent curative services to female and male children.

Bangladesh↗
PubMed2004

The otter annotation system.

With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly even more important, is the requirement to curate and improve this annotation in the light of future data. For this to be possible, there is a need for tools to access and manage the annotation. Ensembl provides an excellent means for storing gene structures, genome features, and sequence, but it does not support the extra textual data necessary for manual annotation. We have extended Ensembl to create the Otter manual annotation system. This comprises a relational database schema for storing the manual annotation data, an application-programming interface (API) to access it, an extensible markup language (XML) format to allow transfer of the data, and a server to allow multiuser/multimachine access to the data. We have also written a data-adaptor plugin for the Apollo Browser/Editor to enable it to utilize an Otter server. The otter database is currently used by the Vertebrate Genome Annotation (VEGA) site (http://vega.sanger.ac.uk), which provides access to manually curated human chromosomes. Support is also being developed for using the AceDB annotation editor, FMap, via a perl wrapper called Lace. The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20.

Computational Biology↗
PubMed2004

Autopsy results after surgery for non-small cell lung cancer.

OBJECTIVE: To determine the percentage of metastatic and unexpected residual lung cancer at autopsy in patients considered for curative resection of non-small cell lung cancer during a time when computed tomography was available as a preoperative staging tool. MATERIAL AND METHODS: Clinical data and surgical and autopsy slides of all patients who underwent curative resection of nonsmall cell lung cancer at the Mayo Clinic in Rochester, Minn, between 1985 and 1999 and who underwent autopsy within 30 days of surgery were reviewed retrospectively for the presence of residual or metastatic disease. RESULTS: The study group consisted of 25 men and 7 women, with a mean age of 70 years. A pulmonary metastasis was identified at surgery in 1 patient (3%). Metastases were found in an additional 5 patients (16%) at autopsy, 1 of whom had 2 sites involved. These sites included the liver in 2 and lung, epicardium, adrenal gland, and kidney in 1 each. The average diameter of metastases was 1.6 cm. No factor studied was found to be significantly associated with the presence of unrecognized metastatic disease at autopsy. CONCLUSION: The advent of computed tomography as a staging tool has decreased the percentage of patients with undiagnosed metastatic disease at surgery; however, preoperative understaging in lung cancer remains a problem.

Aged↗
PubMed2003

The Zebrafish Information Network (ZFIN): the zebrafish model organism database.

The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data. ZFIN is publicly accessible at http://zfin.org. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data. Recent enhancements to ZFIN include: (i) an anatomical dictionary that provides a controlled vocabulary of anatomical terms, grouped by developmental stages, that may be used to annotate and query gene expression data; (ii) gene expression data; (iii) expanded support for genome sequence; (iv) gene annotation using the standardized vocabulary of Gene Ontology (GO) terms that can be used to elucidate relationships between gene products in zebrafish and other organisms; and (v) collaborations with other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnections based on shared curation.

Animals↗
PubMed1984

The uptake of preventive and curative child health services in Maputo, Mozambique.

This study seeks to analyse the uptake of preventive and curative child health services in three health centres in Maputo, Mozambique. Within the context of overall social and economic change, Mozambique has given priority to Primary Health Care as the driving force of its newly developed National Health Service, with a principal focus on maternal and child health. Three health centres were selected from areas of contrasting environmental quality. Data were collected from over 6000 women attending the curative and preventive child health services at these centres. It was found that the women using curative services had significantly higher child mortality rates, had lived less time in Maputo City and had children of lower weight status than their counterparts attending for preventive care. Additionally, levels of child mortality were found to increase as environmental quality decreased. It is argued that the lower users of preventive care are, as in the U.K., precisely those who appear to have an increased risk of mortality and morbidity. It is concluded that integration between the curative and preventive health services must be increased in order to overcome the user inertia which militates against the poorer population using the facilities for prevention to the best advantage. This would fit in both with national strategies (1) and WHO recommendations (2-4) in the field of primary health care.

Age Factors↗
PubMed2006

AFP mRNA detected in bone marrow by real-time quantitative RT-PCR analysis predicts survival and recurrence after curative hepatectomy for hepatocellular carcinoma.

OBJECTIVE: To determine whether detection of hepatocellular carcinoma (HCC) cells by real-time quantitative RT-PCR targeting of alpha-fetoprotein mRNA (AFP mRNA) before or after curative hepatectomy predicts HCC recurrence and patient survival. SUMMARY BACKGROUND DATA: The presence of cancer cells in peripheral blood and/or bone marrow in patients with malignant disease has been reported to correlate with outcome. METHODS: Between July 2000 and June 2005, 136 consecutive HCC patients underwent primary curative hepatectomy. Bone marrow aspirated preoperatively, and peripheral blood samples collected before and after operation were subjected to real-time quantitative RT-PCR analysis using AFP mRNA as a target molecule. Median follow-up was 23 months (range, 6-54 months). Patient survival (PS), disease-free survival (DFS), and clinicopathologic features were compared between patients with positive and negative AFP mRNA. RESULTS: Twenty-four patients died (22 from HCC). HCC recurred in 66 patients (hepatic in 37 [56.1%]; hepatic and remote in 17 [25.8%], and remote alone in 12 [18.2%]). Bone marrow was positive for AFP mRNA in 38 patients (27.9%) and negative in 98 (72.1%). One- and 3-year PS was 96.6% and 91.4%, respectively, with negative AFP mRNA versus 86.2% and 55.5%, respectively, with positive AFP mRNA (P < 0.0001). One- and 3-year DFS were 73.2% and 44.8%, respectively, with negative AFP mRNA versus 54.5% and 25.8%, respectively, with positive AFP mRNA (P = 0.0399). Portal vascular invasion, tumor size, multiple tumors, and tumor differentiation correlated with inferior PS and DFS on univariate analysis. On multivariate analysis, positive AFP mRNA was the most important risk factor for PS (P = 0.001) and DFS (P = 0.0165). In addition, positive AFP mRNA in peripheral blood after operation tended to predict reduced DFS. CONCLUSION: AFP mRNA in the bone marrow and systemic circulation during the perioperative period predicts patient survival and recurrence after curative hepatic resection for HCC.

Biomarkers, Tumor↗
PubMed2006

The mouse genome database (MGD): new features facilitating a model system.

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

Animals↗
PubMed2004

Ectopic liver and hepatocarcinogenesis.

Hepatocellular carcinomata are relatively rare in the western hemisphere, but they are much more common in South-East Asia and sub-Saharan Africa due to high endogenous levels of hepatitis B and C. Ectopic liver tissue usually is found incidentally (frequently at cholecystectomy), but it may also be found due to neoplastic changes or compressive effects. Ectopic liver tissue has an increased neoplastic potential over orthotopic liver, which we postulate is due to compromised vascular supply and biliary drainage. These lesions may be susceptible to surgical resection, although long-term follow-up data are poor. Ectopic or accessory liver tissue is a rare condition. Most commonly, it is found incidentally, but it may also be found as a result of neoplasia or compressive effects. These lesions appear to have an increased potential for the development of hepatocellular carcinoma in the absence of malignancy in the mother liver. Due to their anatomical features, these carcinomata appear to be susceptible to curative resection, although long-term follow-up data are poor. These carcinomata have been reported more frequently from South-East Asia than from Western countries; however, the common risk factors for hepatocellular carcinoma, such as infection with hepatitis B or C and cirrhosis, appear to be less implicated than in carcinomata of the orthotopic liver. In ectopic or accessory liver tissue, development of hepatocellular carcinoma may be the result of compromised vascular supply or biliary drainage.

Carcinoma, Hepatocellular↗
PubMed2003

Risk factors for postoperative infectious complications in noncolorectal abdominal surgery: a multivariate analysis based on a prospective multicenter study of 4718 patients.

HYPOTHESIS: Infectious complications are the main causes of postoperative morbidity in abdominal surgery. Identification of risk factors, which could be avoided in the perioperative period, may reduce the rate of postoperative infectious complications. DESIGN: A database was established from 3 prospective, randomized, multicenter studies. Multivariate analysis was performed using nonconditional logistic regression expressed as an odds ratio (OR). SETTING: Multicenter studies (ie, private medical centers, institutional hospitals, and university hospitals). PATIENTS: From June 1982 to September 1996, a database was established containing the information of 4718 patients who underwent noncolorectal abdominal surgery. MAIN OUTCOME MEASURES: The dependent variables studied included surgical site infection (SSI) (divided into parietal and deep infectious complications with or without fistulas) and global infectious complications (SSI and extraparietal and abdominal infectious complications). RESULTS: The rate of global infectious complications was 13.3%; SSI, 4.05%; parietal infectious complications, 2.2%; deep infectious complications with fistulas, 2.18%; and deep infectious complications without fistulas, 1.38%. In multivariate analysis, the following 7 independent risk factors for global infectious complications have been identified: age (60-74 years, OR, 1.64; >or=75 years, OR, 1.45); being underweight (OR, 1.51); having cirrhosis (OR, 2.45), having a vertical abdominal incision (OR, 1.66); having a suture placed or an anastomis of the bowel (OR, 1.48) in the digestive tract; having a prolonged operative time (61-120 minutes, OR, 1.66; 121 minutes, OR, 2.72); and being categorized as having a class 4 surgical site (ie, obese patients or having a risk factor of a healing defect) (OR, 1.66). Ceftriaxone sodium therapy was identified as a protective factor (OR, 0.43). In multivariate analysis, the following 5 independent risk factors for SSI have been identified: the existence of a preoperative cutaneous abscess or cutaneous necrosis (OR, 4.75), having a suture placed or an anastomosis of the bowel (OR, 1.82) in the digestive tract, having postoperative abdominal drainage (OR, 2.15), undergoing a surgical procedure for the treatment of cancer (OR, 1.74), and receiving curative anticoagulant therapy (OR, 3.33) postoperatively. CONCLUSIONS: Our data show that risk factors for SSI and for global infectious complications are disparate. Indeed, only the placement of a suture or having an anastomosis of the bowel in the digestive tract is a risk factor for both SSI and global infections. Some of these factors may be modifiable before or during the surgical procedure to reduce the infection rate or to prevent postoperative complications.

Adult↗