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At least 1,009 records · Page 56Linked to original sources

[Experience in resection of hilar cholangiocarcinoma: a report of 54 cases].

OBJECTIVE: To summarize the experience in ameliorating curative resection rate and major postoperative complication rate for treatment of hilar cholangiocarcinoma. METHODS: Respective analysis was made on the clinical data of 54 consecutive cases who underwent resection of hilar cholangiocarcinoma from Jan. 1998 to Dec. 2004. RESULTS: In this group 54 cases received tumor resection with a resection rate of 63.5%. Combined partial hepatectomy was performed in 14 patients, while combined pancreaticoduodenectomy (Whipple) in 3 patients, and combined resection of portal vein in 2 patients and combined resection of hepatic artery in 2 patients. Thirty patients had curative resection. The curative resection rate was greatly increased from 27.0% (before 2001) to 41.7% (after 2001) in this group with well controlled perioperative mortality and postoperative complications rate (e.g. hepatic failure and major infection). The gross 1-, 2-, and 3-year survival rates for the whole group were 67.4%, 28.1% and 13.5% respectively. The 1-, 2-, and 3-year survival rates for curative resection were 87%, 36% and 24% respectively. The 1-, 2-year survival rates for palliative resection were 42% and 18%. CONCLUSIONS: Enhanced surgical technique resulted in better clinical outcomes.

Adult↗

Choice of cancer therapy varies with age of patient.

We used data on 22,899 cancer cases collected by the New Mexico Tumor Registry to examine the relationship between patient age and the use of potentially curative therapy for cancers of selected sites and acute leukemias. For cancers of most sites, either local or regional stage, the proportion of cases receiving potentially curative therapy declined with age. For local-stage cancers, the proportion not given any treatment increased with age. Overall mortality rates during the first year after diagnosis were much higher for local-stage cases without treatment than for those who received treatment. These data show that cancer therapy varies with age and suggest that decision making regarding therapy is influenced by the presence of other diseases.

Adult↗

The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks.

Chemicals in the environment play a critical role in the etiology of many human diseases. Despite their prevalence, the molecular mechanisms of action and the effects of chemicals on susceptibility to disease are not well understood. To promote understanding of these mechanisms, the Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org/) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. CTD integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. These comparisons will facilitate understanding of structure-function correlations and the genetic basis of susceptibility. Manual curation and integration of cross-species chemical-gene and chemical-protein interactions from the literature are now underway. These data will provide information for building complex interaction networks. New CTD features include (1) cross-species gene, rather than sequence, query and visualization capabilities; (2) integrated cross-links to microarray data from chemicals, genes, and sequences in CTD; (3) a reference set related to chemical-gene and protein interactions identified by an information retrieval system; and (4) a "Chemicals in the News" initiative that provides links from CTD chemicals to environmental health articles from the popular press. Here we describe these new features and our novel cross-species curation of chemical-gene and chemical-protein interactions.

Animals↗

Study on the causes of local recurrence of rectal cancer after curative resection:analysis of 213 cases.

AIM:To study the local recurrent rate and the causes of rectal cancer after surgery.METHODS:The clinicopathological data of 213 rectal cancer patients and the follow-up information were analyzed. The overall recurrent rate and the recurrent rates from different surgical appreaches were calculated. The main causes of recurrence were investigated.RESULTS:Among the 213 cases, 73 (34.27%) had local recurrence. The recurrent time ranged from 3 months to 62 months after the first operation. Most of the recurrence (65/73, 89.04%) occurred within 3 years after operation.CONCLUSION:Local recurrence had no significant correlation with surgical methods or pathological types, but closely related to Dukes' stages, location of primary tumors and the length of the distal rectum resected. Early resection and a wide tumor free resection margin are key factors to prevent local recurrence.

Journal Article↗

Adverse histopathological findings as a guide to patient management after curative resection of node-positive colonic cancer.

BACKGROUND: The aim of this study was to identify patient and tumour characteristics that might assist in developing an improved approach to patient selection for chemotherapy after resection of clinicopathological stage C colonic cancer. METHODS: Clinical, pathological and follow-up data have been collected prospectively for all patients undergoing resection for colorectal cancer at Concord Hospital since 1971. From an initial 2980 patients, after exclusions 378 remained who had a potentially curative operation for colonic cancer with nodal metastases and did not receive adjuvant chemotherapy. Associations between several pathological features and survival were examined by proportional hazards regression. RESULTS: In a multivariate model, both overall and colonic cancer-specific survival rates were negatively associated with serosal surface involvement, apical node metastasis, high histological grade and venous invasion. The survival of patients with stage C disease who had none of these adverse features was not significantly different from that of patients with stage B lesions. However, survival diminished significantly when one or more of the adverse features were present. CONCLUSION: Patients with a stage C tumour but with none of the identified adverse features experience relatively good survival and are unlikely to benefit from adjuvant chemotherapy. In this series such patients accounted for 40.5 per cent of patients with stage C disease.

Aged↗

[Quality of medical records as a basis for DRG classification in the health care system in Bosnia-Herzegovina].

Medical Record contains data about use of health care services of every member of certain population, no matter if they come from preventive or curative health care. Quality of Medical Records is very often in direct as well as indirect connection with health care quality. Better health care systems usually have better Medical Records. These are computer processed and stored on some of contemporary computer media, like: disks, microfilms, magnetic tapes and so-called "smart cards". Good Medical Record should have at least next characteristics: 1. Time dimension, which should contain chronological: past, present and future data, relevant to health care consumers. 2. It should be complete in a sense that every Medical Record must contain adequate medical and other relevant data for health care planning, organization and control. From the aspects of our research described here, it is very important that Medical Records contain all financial data. These usually are consequences of consumption of health care services from various resources of different levels. The results of our research about the application of DRG classification in B&H health system, that have been done in Tuzla University-Clinical Center, show that hospital Medical Records have many inadequacies, both in respect of medical as well as non-medical part. Physicians use very little ICD coding system. There is no uniform anamnesis, no detailed evidences about all hospital services, no adequately defined severity of disease and patient status at discharge. Due to manual based information system, there is no evidence about spending of resources per patient with financial data. The development and application of computer based health information system must go towards direction of solving these problems.

Bosnia and Herzegovina↗

Reactome: a knowledgebase of biological pathways.

Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.

Animals↗

Death from early colorectal cancer is predicted by the presence of transcripts of the REG gene family.

An intrinsic component of colorectal carcinogenesis may be the capacity to activate regenerative responses simultaneously with inhibition of apoptosis. Since apoptosis is known to be inhibited in colorectal cancer, this study sought evidence for the activation of the REG family of genes which are considered to be activated during regeneration of intestinal mucosa. Transcripts for the REG gene were found in 53% of colorectal cancers and for the PAP gene in 60% of colorectal cancers, by RT-PCR. Using in situ hybridization, the REG transcripts were found to be present in the tumour cells themselves rather than inflammatory or stromal cells. There were no significant correlations between the expression of these two genes and tumour stage, age or sex of the patient population or tumour site. However, in patients with non-metastatic disease who underwent ostensibly curative surgery, the expression of REG alone and co-expression of REG with PAP had a highly significantly adverse effect on survival. These data provide support for the concept that, in some tumours, carcinogenesis involves a regenerative process which co-exists with apoptotic inhibition and may provide a valuable selective indicator of the need for adjuvant therapy in those patients with early-stage colorectal cancer whose disease is destined to recur after curative surgery.

ADP-Ribosylation Factors↗

Ukrain - a new cancer cure? A systematic review of randomised clinical trials.

BACKGROUND: Ukrain is an anticancer drug based on the extract of the plant Chelidonium majus L. Numerous pre-clinical and clinical investigations seem to suggest that Ukrain is pharmacologically active and clinically effective. We wanted therefore to critically evaluate the clinical trial data in the form of a systematic review. METHODS: Seven electronic databases were searched for all relevant randomised clinical trials. Data were extracted and validated by both authors, tabulated and summarised narratively. The methodological quality was assessed with the Jadad score. RESULTS: Seven trials met our inclusion criteria. Without exception, their findings suggest that Ukrain has curative effects on a range of cancers. However, the methodological quality of most studies was poor. In addition, the interpretation of several trials was impeded by other problems. CONCLUSION: The data from randomised clinical trials suggest Ukrain to have potential as an anticancer drug. However, numerous caveats prevent a positive conclusion, and independent rigorous studies are urgently needed.

Alkaloids↗

Markov model recognition and classification of DNA/protein sequences within large text databases.

MOTIVATION: Short sequence patterns frequently define regions of biological interest (binding sites, immune epitopes, primers, etc.), yet a large fraction of this information exists only within the scientific literature and is thus difficult to locate via conventional means (e.g. keyword queries or manual searches). We describe herein a system to accurately identify and classify sequence patterns from within large corpora using an n-gram Markov model (MM). RESULTS: As expected, on test sets we found that identification of sequences with limited alphabets and/or regular structures such as nucleic acids (non-ambiguous) and peptide abbreviations (3-letter) was highly accurate, whereas classification of symbolic (1-letter) peptide strings with more complex alphabets was more problematic. The MM was used to analyze two very large, sequence-containing corpora: over 7.75 million Medline abstracts and 9000 full-text articles from Journal of Virology. Performance was benchmarked by comparing the results with Journal of Virology entries in two existing manually curated databases: VirOligo and the HLA Ligand Database. Performance estimates were 98 +/- 2% precision/84% recall for primer identification and classification and 67 +/- 6% precision/85% recall for peptide epitopes. We also find a dramatic difference between the amounts of sequence-related data reported in abstracts versus full text. Our results suggest that automated extraction and classification of sequence elements is a promising, low-cost means of sequence database curation and annotation. AVAILABILITY: MM routine and datasets are available upon request.

Abstracting and Indexing↗

[Prostate-specific antigen in the diagnosis of organ-confined treatable prostate carcinoma].

Prostate cancer is now the most common cancer and the second most common cause of death from cancer among men. Several studies have shown a frequency of autopsy-detected cancer of 40% in men over 50 years of age. In contrast, the lifetime probability of prostate cancer being diagnosed clinically is only 8%. Thus histologically documented prostate cancer only becomes clinically relevant if the tumors are > 0.5 cm3 and the life expectancy exceeds 10 years. Therapy with curative intention is only possible for organ confined disease. Because disease specific survival is about 80-90% after 10 years for conservative treatment of organ confined disease, early detection of prostate cancer is useful for patients with a life expectancy > 10 years. Organ confined prostate cancer is usually asymptomatic. The use of prostate specific antigen (PSA) combined with digital rectal examination (DRE) results in a 2-3 fold increase in prostatic carcinoma detection rate, especially of organ confined disease, by PSA. In men with a minimally elevated PSA-value of 4-10 ng/ml (Hybritech Assays), 25% will have a prostatic carcinoma regardless of the finding of the DRE, which would have reached clinical significance in the follow-up. The indication for biopsy should be established at an early date. There is no support for the common opinion that early detection programs detect clinically unimportant cancers. 95% of tumor volumes are > 0.5 cm3. Furthermore only 3-5% of subjects show prostate cancer in detection programs though 8% will develop clinical symptoms of prostate cancer during their lifetime. This difference is a reason for longitudinal programs with PSA and DRE control once a year, as proposed by the American Cancer Society and the American and Canadian Urological Association, in contrast to other health care organizations, which would wait with general screening until data from prospective randomized trials with beneficial effects of screening are available. To introduce prostate cancer therapy with curative intention for symptomatic patients as well, the cancer should be detected below a PSA level of 10 ng/ml. Insufficient specificity of PSA (2-4 patients have to undergo biopsies to detect one cancer patient) is still an unsolved problem.

Aged↗

Racial differences in the receipt of bowel surveillance following potentially curative colorectal cancer surgery.

OBJECTIVE: To investigate racial differences in posttreatment bowel surveillance after colorectal cancer surgery in a large population of Medicare patients. DATA SOURCES: We used a large population-based dataset: Surveillance, Epidemiology, and End Results (SEER) linked to Medicare data. STUDY DESIGN: This is a retrospective cohort study. We analyzed data from 44,768 non-Hispanic white, 2,921 black, and 4,416 patients from other racial/ethnic groups, aged 65 and older at diagnosis, who had a diagnosis of local or regional colorectal cancer between 1986 and 1996, and were followed through December 31, 1998. Cox Proportional Hazards models were used to investigate the relation of race and receipt of posttreatment bowel surveillance. DATA COLLECTION: Sociodemographic, hospital, and clinical characteristics were collected at the time of diagnosis for all members of the cohort. Surgery and bowel surveillance with colonoscopy, sigmoidoscopy, and barium enema were obtained from Medicare claims using ICD-9-CM and CPT-4 codes. PRINCIPAL FINDINGS: The chance of surveillance within 18 months of surgery was 57 percent, 48 percent, and 45 percent for non-Hispanic whites, blacks, and others, respectively. After adjusting for sociodemographic, hospital, and clinical characteristics, blacks were 25 percent less likely than whites to receive surveillance if diagnosed between 1991 and 1996 (RR = 0.75, 95 percent CI = 0.70-0.81). CONCLUSIONS: Elderly blacks were less likely than non-Hispanic whites to receive posttreatment bowel surveillance and this result was not explained by measured racial differences in sociodemographic, hospital, and clinical characteristics. More research is needed to explore the influences of patient- and provider-level factors on racial differences in posttreatment bowel surveillance.

Aftercare↗

[Surgery of loco-regional recurrences in colorectal cancer].

By the term of local recurrence (LR), after apparently curative resection of a colorectal cancer, we mean the recurrence of the disease at the site of the original tumor, in correspondence to the regional lymph nodes or to intestinal anastomosis. The frequency of LR, which differs widely from one case to another because of the unhomogenity of the samples under examination, is on average around 16%, although this figure is to be considered an underestimation since it is not supported by routine autopsies. The authors analyse, together with the data in the literature, the results of their personal experience relating to 1164 patients undergoing surgery for colorectal cancer in the space of 18 years, in order to evaluate the true effectiveness of surgery on patients affected by LR. Surgery on the original tumor had a curative aim in 791 (68%) of these cases, 33 patients died during the postoperative period and 37 were lost to follow-up. Among the remaining 721 patients, recurrence was observed in 218 cases (30.2%): in 81 of these was confirmed a LR, with simultaneous distant metastasis in 45. During the same time span, 15 patients were admitted who were affected by LR from colorectal cancers treated surgically in other hospitals. Of these, only 2 had concomitant distant metastasis. 58 of these 96 patients (60.4%) underwent surgery, which had a curative aim in 22 cases (37.9%)/ Up to present, 12 patients undergoing curative surgery are still alive, 4 (33.3%) being affected by further relapse. The data reported demonstrate that in patients with proven LR surgical intervention is widely indicated, being the only therapeutic approach able to provide tangible results. However, the choice of exeresis must be carefully weighed: surgery of LR can be said to be truly curative in few cases, and thus the operative risks may not be acceptable in situations where limited results, in terms of duration and quality, are foreseen.

Adult↗

AgBase: a functional genomics resource for agriculture.

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.

Agriculture↗

Autologous stem cell transplantation for follicular lymphoma: no benefit for early transplant?

Autologous stem cell transplantation (SCT) is widely used as salvage treatment for patients with relapsed follicular lymphoma (FL). Although SCT can induce prolonged remissions, it does not appear to be curative in the vast majority of patients. The purpose of this study was to investigate if incorporation of SCT into first-line therapy can improve its efficacy. Fifty-five patients underwent sequential high-dose therapy as up-front (n=33) or salvage treatment (n=22) for advanced stage FL at our institution. Treatment consisted of intensive chemotherapy with dexamethasone, carmustine (BCNU), etoposide, cytarabine, and melphalan (Dexa-BEAM) for mobilization of peripheral stem cells and reduction of tumor load, followed by one of three different myeloablative regimens and SCT. With a median follow-up of 4 years, projected event-free survival (EFS) and overall survival (OS) at 4 years post transplant was 59% and 84%, respectively, with no evidence of plateau in the survival curves. By univariate and multivariate analysis weighing age, sex, stage, BM and extranodal involvement, timing of transplant, ex vivo purging, and conditioning regimen [total body irradiation (TBI) vs non-TBI], the only significant factor predicting for superior EFS and OS was up-front vs salvage transplant (4-year EFS 76% vs 38%, p=0.02; 4-year OS 92% vs 73%, p=0.033). However, when calculated from diagnosis, EFS and OS of the up-front and salvage groups were virtually identical, implying that the longer survival post SCT in the up-front group was completely compensated by the longer interval between diagnosis and transplant in the salvage group. Median OS from diagnosis was 13.5 years. Except for one case of anaplastic large cell lymphoma, secondary neoplasms have not occurred to date. In conclusion, our data indicate that SCT might improve the prognosis of patients with disseminated FL, although it is probably not curative even if applied early during the course of the disease. The optimum timing of SCT remains to be determined by the ongoing randomized multicenter trial of the German Low-grade Lymphoma Study Group. The impact of radiotherapy on the success of SCT does not seem to be as essential as originally believed.

Adult↗

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development.

Bacteria↗

MetaFam: a unified classification of protein families. I. Overview and statistics.

MOTIVATION: Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects. At present, there are several independent classification methods. To aid the general classification effort, we have created a unified protein family resource, MetaFam. MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks + DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS). MetaFam's family 'supersets', as we call them, are created automatically using set-theory to compare families among the databases. Families of one database are matched to those in another when the intersection of their members exceeds all other possible family pairings between the two databases. Pairwise family matches are drawn together transitively to create a new list of protein family supersets. RESULTS: MetaFam family supersets have several useful features: (1) each superset contains more members than the families from which it is composed, because each of the component family databases only works with a subset of our full non-redundant set of proteins; (2) conflicting assignments can be pinpointed quickly, since our analysis identifies individual members that are in conflict with the majority consensus; (3) family descriptions that are absent from automated databases can frequently be assigned; (4) statistics have been computed comparing domain boundaries, family size distributions, and overall quality of MetaFam supersets; (5) the supersets have been loaded into a relational database to allow for complex queries and visualization of the connections among families in a superset and the consensus of individual domain members; and (6) the quality of individual supersets has been assessed using numerous quantitative measures such as family consistency, connectedness, and size. We anticipate this new resource will be particularly useful to genomic database curators.

Data Interpretation, Statistical↗

Leiomyosarcoma of the gastric cardia and fundus.

BACKGROUND: Gastric leiomyosarcoma is rare among gastric malignancies, and only 20% of the cases are located in the gastric cardia or fundus. It has clinical manifestations different from tumors in other sites of the stomach. We reviewed cases of leiomyosarcoma of the gastric cardia or fundus to evaluate their clinicopathologic characters and patient survival. METHODS: From May, 1981, to June, 1998, a total of 15 patients who underwent curative resection of leiomyosarcoma of the gastric cardia or fundus were retrospectively identified and studied. All the clinical and pathologic data were reviewed and recorded. RESULTS: There were 11 men and four women. Their mean age was 59.1 years (range, 37-73 years). Tarry stools and epigastric fullness and pain were the most common symptoms, followed by body weight loss. All 15 patients had submucosal tumors in the gastric cardia or fundus, as shown by endoscopy, barium contrast radiography and computerized tomography. The incidence of esophageal involvement by the tumors was quite low. The mean tumor size was 10 cm, ranging from 4 cm to 20 cm. Locoregional organs were involved in nine patients. The median and mean survivals were 17.8 months and 31.7 months, respectively (range, 10.1-80.1 months) after curative resection. The three-year and five-year survival rates were 53% and 22%, respectively. CONCLUSIONS: The definitive preoperative diagnosis of the tumor is difficult before surgery, even though imaging studies show positive findings. Surgical resection with an adequate safe margin of normal tissue is the treatment of choice. Tumor size, serosal invasion with locoregional organ involvement and high tumor grade were the prognostic factors in the study.

Adult↗