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At least 163 records · Page 9Linked to original sources

PubMed2005

VEGA, the genome browser with a difference.

The Vertebrate Genome Annotation (Vega) database is a community resource for browsing manual annotation from a variety of vertebrate genomes of finished sequence (http://vega.sanger.ac.uk). Vega is different from other genome browsers as it has a standardised classification of genes which encompasses pseudogenes and non-coding transcripts. The data is manually curated, which is more accurate at identifying splice variants, pseudogenes poly(A) features, non-coding and complex gene structures and arrangements than current automated methods. The database also contains annotation from regions, not just whole genomes, and displays multiple species annotation (human, mouse, dog and zebrafish) for comparative analysis. Vega encourages community feedback that results in annotation updates and manual annotation of finished vertebrate sequence.

Animals↗

PubMed2003

DDBASE2.0: updated domain database with improved identification of structural domains.

MOTIVATION: Although many methods are available for the identification of structural domains from protein three-dimensional structures, accurate definition of protein domains and the curation of such data for a large number of proteins are often possible only after manual intervention. The availability of domain definitions for protein structural entries is useful for the sequence analysis of aligned domains, structure comparison, fold recognition procedures and understanding protein folding, domain stability and flexibility. RESULTS: We have improved our method of domain identification starting from the concept of clustering secondary structural elements, but with an intention of reducing the number of discontinuous segments in identified domains. The results of our modified and automatic approach have been compared with the domain definitions from other databases. On a test data set of 55 proteins, this method acquires high agreement (88%) in the number of domains with the crystallographers' definition and resources such as SCOP, CATH, DALI, 3Dee and PDP databases. This method also obtains 98% overlap score with the other resources in the definition of domain boundaries of the 55 proteins. We have examined the domain arrangements of 4592 non-redundant protein chains using the improved method to include 5409 domains leading to an update of the structural domain database. AVAILABILITY: The latest version of the domain database and online domain identification methods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html SUPPLEMENTARY INFORMATION: http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html

Amino Acid Sequence↗

PubMed2001

The ARKdb: genome databases for farmed and other animals.

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Animals↗

PubMed2003

MGD: the Mouse Genome Database.

The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental details annotated from both literature and on-line genomic data sources. MGD curates and presents the consensus representation of genotype (sequence) to phenotype information including highly detailed information about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse. Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system.

Alleles↗

PubMed2004

WormBase: a multi-species resource for nematode biology and genomics.

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.

Animals↗

PubMed2006

OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI.

Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a comparative biology resource, OMIA is a comprehensive resource of phenotypic information on heritable animal traits and genes in a strongly comparative context, relating traits to genes where possible. OMIA is modelled on and is complementary to Online Mendelian Inheritance in Man (OMIM). OMIA has been moved to a MySQL database at the Australian National Genomic Information Service (ANGIS) and can be accessed at http://omia.angis.org.au/. It has also been integrated into the Entrez search interface at the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia). Curation of OMIA data by researchers working on particular species and disorders has also been enabled.

Animals↗

PubMed1998

Atypical or worrisome features in cellular neurothekeoma: a study of 10 cases.

Cellular neurothekeoma is a recently characterized benign cutaneous neoplasm arising usually on the upper trunk or head and neck of children or young adults. Typical histology is that of a lobulated dermal tumor composed of spindle and epithelioid cells, arranged in fascicles and nests, lacking immunoreactivity for S-100 protein, but usually being NK1/C3 positive. We present 10 new cases of cellular neurothekeoma with atypical histologic features that have not been described previously and that suggested the possibility of malignancy. The age range of affected patients was 1 to 44 years (median, 20.5 years); sites included the head and neck (three cases), the upper limbs (two cases), the lower limbs (two cases), and the trunk (two cases). Atypical findings in individual cases included large size (up to 6 cm), deep penetration (extending into skeletal muscle or subcutaneous fat, or both), diffusely infiltrative borders, vascular invasion, high mitotic rate, and marked cytologic pleomorphism. Clinical follow-up was available in 7 of 10 cases. Although the atypical features raised concern about the biologic potential of these lesions, preliminary follow-up (1-5 years) has shown no recurrence and suggests that complete surgical excision of these lesions is curative. These new data expand the morphologic spectrum of cellular neurothekeoma.

Adolescent↗

PubMed1998

Reduction of peritoneal trauma by using nonsurgical gauze leads to less implantation metastasis of spilled tumor cells.

OBJECTIVES: To evaluate whether infliction of peritoneal trauma would promote tumor cell adherence to damaged peritoneal surfaces; to investigate whether peritoneal damage could promote tumor growth of extraperitoneal tumors; and to evaluate whether the amount of trauma correlated with the degree of tumor cell adherence and local and distant tumor growth. BACKGROUND DATA: After potentially curative resection of colorectal carcinoma, the most common site for recurrence is locoregional. We previously demonstrated that surgical trauma induces a cascade of events leading to adhesion formation. The same mechanisms may be responsible for improved tumor cell adherence and growth facilitation in early local recurrence. METHODS: A reproducible rat model was used in which peritoneal damage was inflicted by standardized rubbing of the peritoneum with surgical gauzes of different texture. In the first experiment, tumor cell adherence and growth at traumatized and nontraumatized peritoneal sites were assessed semiquantitatively 3 weeks after perioperative intra-abdominal injection of CC-531 tumor cells. In the second experiment, the effect of peritoneal trauma on ectopic tumor growth was investigated (CC-531 implanted under the renal capsule). In the final experiment, we evaluated how soon after peritoneal traumatization tumor cell adhesion and growth-promoting factors were active and whether they could be passively transferred to naïve nontraumatized abdominal cavities. RESULTS: A significant correlation between the amount of peritoneal trauma and the degree of tumor take at damaged peritoneal surfaces was found (p < or = 0.018). Tumor take at remote peritoneal sites not directly traumatized was also significantly higher after severe trauma than after moderate trauma of the peritoneum (p < or = 0.005). In addition, a significant correlation between the degree of peritoneal trauma and the growth of ectopic tumors under the renal capsule was observed (p < or = 0.009). The final experiment demonstrated that within a few hours after infliction of peritoneal trauma, tumor growth-promoting effects could be passively transferred to naïve recipients. CONCLUSIONS: Surgical trauma is an important factor in the promotion of local recurrence. The enhancing effect of trauma is not restricted to the inflicted site but rather has a generalized character. Avoidance of unnecessary surgical trauma by using gentle techniques and materials is therefore indicated.

Adenocarcinoma↗

PubMed2004

Prognostic impact of cysteine proteases cathepsin B and cathepsin L in pancreatic adenocarcinoma.

OBJECTIVES: The cysteine proteases cathepsin B (CTSB) and L (CTSL) have been implicated in tumor spread and metastatic formation. In pancreatic adenocarcinoma, the role of these proteases is not very well defined. To find out which cell types produce CTSB and CTSL and to evaluate the prognostic impact of these proteases, 70 specimens from curatively resected patients with pancreatic adenocarcinoma were examined by in situ hybridization and immunohisto-chemistry. METHODS: Seventy patients with ductal adenocarcinoma of the pancreas were studied after R0 resection with a follow-up of at least 3 years. CTSB and CTSL expression was performed immunohisto-chemically using polyclonal anti-CTSB and CTSL antibodies. To detect cell types involved in producing CTSB and CTSL as well as the intracellular localization of specific mRNA sequences, nonisotopic in situ hybridization was performed. The correlations among CTSB and CTSL expression, clinicopathologic parameters, and clinical outcome were analyzed. RESULTS: The immunoreactivity was 96% for CTSB and 90% for CTSL. Positive mRNA signals were obtained in the cytoplasm tumor cells, macrophages, and fibroblasts in 77% for CTSB and 81% for CTSL, respectively. Statistical analysis showed a significant correlation between CTSB/CTSL expression and tumor grading (P < 0.05) and between CTSB and lymphatic invasion (P = 0.05). Kaplan-Meier analyses revealed statistical significance for CTSB/CTSL expression with the survival after curative resection (P < 0.05). Both proteases are strong prognostic markers in multivariate analysis (P = 0.0001) beside UICC stage, nodal status, tumor size, and grading (P < 0.05). Furthermore, CTSB expression is an independent prognostic marker for cancer recurrence within 6 months after curative surgery in multivariate analysis (P = 0.0001). CONCLUSIONS: CTSB and CTSL are strong and independent prognostic markers in resectable pancreatic adenocarcinoma rather than UICC stage, TNM classification, or tumor grading. Furthermore, CTSB is a predictor for early recurrence after curative resection. These data underline the significance of tumor-associated proteolysis for cancer invasion and metastasis and may lead to defining subgroups of patients with early recurrence and poor outcome.

Adult↗

PubMed2001

GeneLynx: a gene-centric portal to the human genome.

GeneLynx is a meta-database providing an extensive collection of hyperlinks to human gene-specific information in diverse databases available on the Internet. The GeneLynx project is based on the simple notion that given any gene-specific identifier (accession number, gene name, text, or sequence), scientists should be able to access a single location that provides a set of links to all the publicly available information pertinent to the specified human gene. GeneLynx was implemented as an extensible relational database with an intuitive and user-friendly Web interface. The data are automatically extracted from more than 40 external resources, using appropriate approaches to maximize coverage of the available data. Construction and curation of the system is mediated by a custom set of software tools. An indexing utility is provided to facilitate the establishment of hyperlinks in external databases. A unique feature of the GeneLynx system is a communal curation system for user-aided annotation. GeneLynx can be accessed freely at http://www.genelynx.org.

Database Management Systems↗

PubMed2006

From information to understanding: the role of model organism databases in comparative and functional genomics.

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.

Animals↗

PubMed2005

The predicted impact of coding single nucleotide polymorphisms database.

Nonsynonymous single nucleotide polymorphisms (nsSNP) have the potential to affect the structure or function of expressed proteins and are, therefore, likely to represent modifiers of inherited susceptibility. We have classified and catalogued the predicted functionality of nsSNPs in genes relevant to the biology of cancer to facilitate sequence-based association studies. Candidate genes were identified using targeted search terms and pathways to interrogate the Gene Ontology Consortium database, Kyoto Encyclopedia of Genes and Genomes database, Iobion's Interaction Explorer PathwayAssist Program, National Center for Biotechnology Information Entrez Gene database, and CancerGene database. A total of 9,537 validated nsSNPs located within annotated genes were retrieved from National Center for Biotechnology Information dbSNP Build 123. Filtering this list and linking it to 7,080 candidate genes yielded 3,666 validated nsSNPs with minor allele frequencies > or =0.01 in Caucasian populations. The functional effect of nsSNPs in genes with a single mRNA transcript was predicted using three computational tools-Grantham matrix, Polymorphism Phenotyping, and Sorting Intolerant from Tolerant algorithms. The resultant pool of 3,009 fully annotated nsSNPs is accessible from the Predicted Impact of Coding SNPs database at http://www.icr.ac.uk/cancgen/molgen/MolPopGen_PICS_database.htm. Predicted Impact of Coding SNPs is an ongoing project that will continue to curate and release data on the putative functionality of coding SNPs.

Algorithms↗

PubMed1990

External-beam radiation for carcinoma of the prostate.

Over 14 years 111 patients with prostatic cancer underwent attempted curative radiotherapy; full data was obtained on 105 patients. The 5-year actuarial survival rate was 62%, with 54 patients still alive at the time of review. The toxicity rate was 94%, and serious late complications occurred in 4%. 40% of the patients developed symptomatic recurrence, and only 4% of the patients had local recurrence.

Aged↗

PubMed2005

Quality of life determinants in women with breast cancer undergoing treatment with curative intent.

BACKGROUND: The diagnosis of breast cancer and its subsequent treatment has significant impact on the woman's physical functioning, mental health and her well-being, and thereby causes substantial disruption to quality of life (QOL). Factors like patient education, spousal support and employment status, financial stability etc., have been found to influence QOL in the breast cancer patient. The present study attempts to identify the determinants of QOL in a cohort of Indian breast cancer patients. PATIENTS AND METHODS: Functional Assessment of Cancer Therapy-Breast (FACT-B) Version 4 Malayalam was used to assess quality of life in 502 breast cancer patients undergoing treatment with curative intent. The data on social, demographic, disease, treatment, and follow-up were collected from case records. Data was analysed using Analysis of Variance (ANOVA) and multinomial logistic regression. RESULTS: The mean age of the patients was 47.7 years with 44.6% of the women being pre-menopausal. The FACT-B mean score was 90.6 (Standard Deviation [SD] = 18.4). The mean scores of the subscales were - Physical well-being 19.6 (SD = 4.7), Social well-being 19.9 (SD = 5.3), Emotional well-being 14 (SD = 4.9), Functional well-being 13.0 (SD = 5.7), and the Breast subscale 23.8 (SD = 4.4). Younger women (< 45 years), women having unmarried children, nodal and/or metastatic disease, and those currently undergoing active treatment showed significantly poorer QOL scores in the univariate analysis. However multivariate analysis indicated that the religion, stage, pain, spouse education, nodal status, and distance travelled to reach the treatment centre as indicative of patient QOL. CONCLUSION: QOL derangements are common in breast cancer patients necessitating the provisions for patient access to psychosocial services. However, because of the huge patient load, a screening process to identify those meriting intervention over the general population would be a viable solution.

Journal Article↗

PubMed1995

Lymph node staging standards in gastric cancer.

PURPOSE: In tumor-node-metastasis (TNM) staging, no recommendations are provided on the number of lymph nodes to examine per N level. We investigated the relationship between number of nodes examined and probability of detecting metastases, and ultimately staging accuracy. PATIENTS AND METHODS: Data from 473 curatively resected gastric cancer patients, from a randomized trial that compared the Western resection with limited and the Japanese resection with extended lymphadenectomy, were used. RESULTS: Yields varied between zero to 67 in N1 and zero to 43 in N2. Yields correlated significantly with classification; the more nodes examined, the more likely the classification was N+. Calculating the probability of detecting metastases using either a likelihood-ratio estimate or an exponential model, this probability increased steeply in the lower range and more gradually in the higher range yield. CONCLUSION: To standardize treatment results, we emphasize histologic examination of a fixed number of nodes per anatomically defined N level (20 in N1 and 15 in N2), corresponding with a probability to detect metastases of 60% to 65% and 40% to 45%, respectively. These yields are feasible in all resection specimens, while the extra increase in the chance of detecting metastases by examining more nodes does not compensate the effort to increase yields further. Thus, standardization of histologic TNM staging can improve and render comparison of surgical and adjuvant treatment modalities feasible.

Humans↗

PubMed2000

Long-term disease-free survivors in metastatic undifferentiated carcinoma of nasopharyngeal type.

PURPOSE: To review incidence and analyze profile of long-term complete responders among patients with undifferentiated carcinoma of nasopharyngeal type (UCNT) treated at a single institution. PATIENTS AND METHODS: We present a cohort of 20 long-term unmaintained complete responders to chemotherapy for metastatic UCNT treated at the Institut Gustave Roussy between April 1978 and November 1996. A patient was considered a long-term survivor if he or she was disease-free for more than 36 months without treatment after obtaining a complete response by chemotherapy. Patient characteristics were as follows: sex, 17 men and three women; median age, 28 years (range, 9 to 62 years); median World Health Organization performance status, 1; and initial tumor-node-metastasis stage (International Union Against Cancer-American Joint Committee on Cancer, 1987) of T3 to T4, 60%, and of N2b to N3, 75%. Epstein-Barr virus serology was characteristic in 19 patients. Of 16 pretreated patients, 11 were pretreated by radiotherapy alone and five by chemotherapy and radiotherapy. Thirteen patients had metastatic relapses of locally controlled UCNT. Tumor sites were bone in 15 patients, lung in four, and liver (biopsy-proven) in two. Chemotherapy included the following: cisplatin, bleomycin, and fluorouracil in five patients; bleomycin, epirubicin, and cisplatin in seven patients; fluorouracil, mitomycin, epirubicin, and cisplatin in four patients; and fluorouracil, bleomycin, epirubicin, and cisplatin in one patient. Three patients were treated with platinum-based regimens before 1985. Patients received a median of six cycles (range, three to 13). Thirteen patients with bone metastases received consolidating radiotherapy. RESULTS: As of June 1999, 14 of 20 patients were still alive with no evidence of disease after treatment (disease-free survival time, 82+ to 190+ months), three patients died of other causes while in complete response at 61, 109, and 208 months after treatment, and three patients died of disease at 42, 89, and 115 months after treatment. Long-term complete responses were obtained in both bone and visceral disease. CONCLUSION: Our data support a curative role for chemotherapy in metastatic UCNT and are a major incentive to continue research for better combinations to increase the percentage of patients with metastatic UCNT who attain complete responses and long-term survival.

Adolescent↗

PubMed2005

[Childhood adrenocortical tumors].

Adrenocortical tumors (ACT) in children are uncommon. However, the incidence of these tumors in Paraná, Brazil, is 15 times higher than that worldwide. We describe the clinical, laboratory and treatment characteristics and outcome of 125 patients treated in a single institution in the State of Paraná. The median age at diagnosis was 4.3 years, with a female:male ratio of 2.6:1. The most common forms of presentation were isolated virilization (51.2%) and virilization and Cushing's syndrome (42%). Nonfunctioning tumors comprised 4.8% of the cases. Two patients (1.6%) had isolated Cushing's syndrome and 1 (0.8%) had Conn's syndrome. Fifty-six percent presented hypertension. Surgery is the only curative treatment. Our data show that disease stage 1, absence of spillage during surgery and absence of intravenous thrombus were associated with better survival rates.

Adolescent↗

PubMed2004

Effects of autacoid inhibitors and of an antagonist on malaria infection in mice.

The effects of p-chlorophenylalanine, an inhibitor of serotonin synthesis, indomethacin, an inhibitor of prostaglandin synthesis, cyproheptadine, a serotonin, bradykinin and histamine antagonist, were assessed separately and in combination with chloroquine (CQ) in Vom strains of Swiss albino mice (18-22 g) of either sex infected intraperitoneally with 1 x 10(7) Plasmodium yoelii nigeriensis-induced malaria. As prophylactic, these agents reduced from 31.9 +/- 4.5 to 16.1 +/- 8.1% the level of parasitemia relative to control but had no appreciable activity as curative agents when administered subcutaneously once daily for 4 days after 72 h of parasites innoculum in vivo. However, CQ alone and the combination of these agents with CQ in curative and prophylactic treatments significantly reduced (from 50.3 +/- 5.8 to 4.9 +/- 0.75%) the level of parasitemia (P < 0.05), which was taken only once 72 h after the parasites innoculum. The prophylactic result was shown to produce better results than the curative treatment. The data indicate that inhibitors and an antagonist can reduce the parasitemia load (the extent of damage and the severity of infection) as well as enhance the effects of CQ when combined with it for malaria therapy. The study reveals that the production of autacoids in established infection renders autacoid inhibitors and an antagonist ineffective for radical cure in malarial mice; however, selective inhibition of local hormones implicated in the pathological manifestations of malaria infection by autacoid inhibitors and an antagonist may be a possible pathway to reduce the severity of infection and the associated tissue damage and to enhance the efficacy of available anti-malarials.

Animals↗