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The Small Subunit rRNA Modification Database.

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods.

Base Sequence↗

Biodiversity informatics.

Biodiversity informatics is an emerging field that applies information management tools to the management and analysis of species-occurrence, taxonomic character, and image data. A wide and growing range of tools is available for both curators and researchers. The development and implementation of formal data exchange standards and query protocols have made it possible to integrate data holdings from collections around the world. The current technological environment is summarized; protocols, standards, and tools for data management, sharing, and integration are reviewed; and methods and tools for analyzing species-occurrence and character data are examined. Direct access to primary data and imagery has the power to transform the means by which taxonomy is practiced and its results disseminated to the general community.

Animals↗

The health service coverage of quality-certified primary health care units in Metro-Manila, the Philippines.

INTRODUCTION: In 1998, the Philippines' Department of Health implemented the Quality Assurance Programme, known as the Sentrong Sigla (Centre of Vitality) Movement, starting with primary health care units. The Department established the National Objectives for Health in 1999, which set targets for health status and service coverage by 2004. The Movement certifies primary health care facilities that comply with its list of quality standards. Three years after implementation of the Sentrong Sigla Movement, the present study assessed it as an intervention for the delivery of health care services. Specifically, it evaluated the 2001 service coverage among certified facilities and compared it with that of non-certified facilities in the National Capital Region (Metro-Manila) of the Philippines, and related service coverage to the targets of the National Objectives for Health for 2001. METHODS: For the intervention group, the study randomly selected 82 of the 143 certified facilities (57.3%), with 88 of the 223 non-certified facilities (39.5%) serving as the control group. Using reliable and valid measurement indicator tools, data were collected on preventive health services programmes, curative programmes and monitoring programmes. To compare service coverage of the intervention and control groups, the data were analyzed using chi-squared tests, prevalence ratios, clustered sampling analysis and linear regressions of the rates. RESULTS: The overall 2001 service coverage shows that certified facilities had significantly less success in the preventive and monitoring programmes than the non-certified facilities, but were not significantly different in the curative programmes. Neither type of facility reached the targets of the 2001 National Objectives for Health for preventive programmes. After adjusting for clustering, the certified facilities showed significantly lower service coverage, compared with non-certified facilities, only for enrolling new acceptors to the Family Planning Programme and for water-supply testing in the Environmental Sanitation Programme. CONCLUSION: Unlike previous studies, the results and analysis of the present study show that, generally, the Sentrong Sigla Movement had not improved the processes required to achieve better outcomes. Factors that could have contributed to the findings are described and strategies for improvement are recommended.

Humans↗

Family history of gastric cancer: a correlation between epidemiologic findings and clinical data.

BACKGROUND: The pathogenetic mechanisms behind gastric cancer are still unclear. Its familial aggregation, on the other hand, has been very well documented by many epidemiologists. Nonetheless, only a limited number of studies have analyzed possible correlations between demographic and clinical data. METHODS: Between January 1988 and August 2004, 541 patients underwent gastric resection with a curative intent at our department; demographic information, laboratory data, imaging, operative notes, and pathology reports were available for all patients. During 2004 we conducted a series of structured interviews with the surviving patients or their closest relatives regarding oncological family history, limited to first-degree relatives. RESULTS: Family history could be obtained in 383 patients (70.8%). Gastric cancer was by far the most frequently associated tumor: 21.9% of the overall number of tumors reported in the family histories were gastric cancers. Patients were also subdivided into those having at least one other family member with stomach cancer (71 patients; 18.5%) and those with no relatives affected by gastric cancer (312 patients; 81.5%). No statistically significant differences between the groups were observed regarding the primary tumor location, size, pTNM classification, and ABO or Rh blood types. However, the intestinal histotype was significantly (P = 0.015) more frequently represented in individuals with at least one family member affected by gastric cancer compared with those with no relatives with stomach cancer (71.8% vs 55.1%, respectively). CONCLUSIONS: Stomach cancer has a relevant degree of familial aggregation and in our series of patients, this was even more pronounced for the intestinal histotype.

Adenocarcinoma↗

Human chromosome 21/Down syndrome gene function and pathway database.

Down syndrome, trisomy of human chromosome 21, is the most common genetic cause of intellectual disability. Correlating the increased expression, due to gene dosage, of the >300 genes encoded by chromosome 21 with specific phenotypic features is a goal that becomes more feasible with the increasing availability of large scale functional, expression and evolutionary data. These data are dispersed among diverse databases, and the variety of formats and locations, plus their often rapid growth, makes access and assimilation a daunting task. To aid the Down syndrome and chromosome 21 community, and researchers interested in the study of any chromosome 21 gene or ortholog, we are developing a comprehensive chromosome 21-specific database with the goals of (i) data consolidation, (ii) accuracy and completeness through expert curation, and (iii) facilitation of novel hypothesis generation. Here we describe the current status of data collection and the immediate future plans for this first human chromosome-specific database.

Base Sequence↗

Postoperative cytology for drained fluid from the pancreatic bed after "curative" resection of pancreatic cancers: does it predict both the patient's prognosis and the site of cancer recurrence?

OBJECTIVE: To evaluate the postoperative cytology of drained fluid from the pancreatic bed as a predictive indicator of local recurrence after curative (R0) resection of pancreatic cancer. SUMMARY BACKGROUND DATA: The pancreatic bed offers a common site of cancer recurrence (local recurrence), even after curative (R0) resection is performed for pancreatic cancer. If local recurrence is thereby predicted precisely, soon after surgery, we have a chance to treat it by adding radiation or some other locoregional therapy before it can grow or spread beyond the pancreatic bed. However, there have been no previous reports of cytology performed on the drained fluid after pancreatectomy. METHODS: This study includes 94 patients who had shown negative results in the peritoneal washing cytology before resection and subsequently received pancreatectomies for pancreatic tumors. They consisted of 12 benign tumors, 17 noninvasive or minimally invasive carcinomas and 65 invasive ductal carcinomas (R0 = 58; R1/2 = 7). Postoperatively, the drained fluid from the pancreatic bed was collected for 24 hours and used for cytologic examination. The cytologic results were examined in association with the histopathology of the resected tumor, patient's survival, and mode of cancer recurrence, including local recurrence. RESULTS: Patients with benign tumors or noninvasive/minimally invasive carcinomas had negative result in cytology, and none of them have died of local recurrence (limited to the pancreatic bed) to date. However, patients with invasive ductal carcinoma revealed higher cytology-positive rates: 28% (16/58) in curative (R0) resection; and 71% (5/7) in noncurative (R1/2) resection. Among 58 patients with R0 resection, the 3-year survival rate was 14% in 16 cytology-positive patients and 55% in 42 cytology-negative patients (P < 0.05). The 3-year cumulative rate of local recurrence was 85% and 23%, respectively (P < 0.05). Compared with other histopathologic parameters obtained from the resected specimens, the drain cytology was more specific in predicting the subsequent development of local recurrence. CONCLUSIONS: Drain-cytology was a quick examination that enabled us to specifically indicate both minute residual cancer and subsequent development of local recurrence even after R0 resection of pancreatic cancer.

Adenocarcinoma↗

Improving survival results after resection of hepatocellular carcinoma: a prospective study of 377 patients over 10 years.

OBJECTIVE: To investigate whether the survival results after resection of hepatocellular carcinoma (HCC) have improved within the past decade by an analysis of a prospective cohort of patients over a 10-year period. SUMMARY BACKGROUND DATA: The surgical death rate after resection of HCC has greatly improved in recent years, but the long-term prognosis remains unsatisfactory. It remains unknown whether the survival results after resection of HCC have improved within the past decade. METHODS: The clinicopathologic and follow-up data of 377 patients who underwent curative resection of HCC between January 1989 and January 1999 were prospectively collected. These patients were categorized according to two time periods: before 1994 (group 1, n = 136) and after 1994 (group 2, n = 241). The two groups were compared for clinicopathologic data and survival results. The prognostic factors for disease-free survival were further analyzed to identify the factors that might have led to improved survival outcomes. RESULTS: The overall and disease-free survival results were significantly better in group 2 compared with group 1. Patients in group 2 had significantly higher proportions of subclinical presentation, small tumors, and tumors of early pTNM stage. There were also significantly lower frequencies of histologic margin involvement, less intraoperative blood loss, and a lower transfusion rate in group 2. By multivariate analysis, early pTNM stage, subclinical HCC, and no perioperative transfusion were independent favorable prognostic factors for disease-free survival. CONCLUSIONS: Significant improvement of overall and disease-free survival results after resection of HCC has been achieved within the past decade as a result of advances in the diagnosis and surgical management of HCC. Earlier diagnosis of HCC by better imaging modalities, increased detection of subclinical HCC by screening of high-risk patients, and a reduced perioperative transfusion rate were identified as the major contributory factors for the improved outcomes.

Adult↗

High preoperative serum carcinoembryonic antigen predicts metastatic recurrence in potentially curative colonic cancer: results of a five-year study.

INTRODUCTION: Serum carcinoembryonic antigen is used mainly for tumor follow-up to detect recurrence of colonic cancer. However, raised preoperative carcinoembryonic antigen levels may be helpful for the identification of understaged cases and of patients meriting more intensive preoperative and postoperative diagnostic workup. METHODS: From a prospectively collected database, the data on 261 patients who had curative colonic carcinoma with a minimal follow-up of five years and who had preoperative carcinoembryonic antigen levels assessed were retrieved and analyzed. Outcome parameters were local and/or distant recurrence and time to recurrence. These parameters were correlated with Dukes staging and preoperative carcinoembryonic antigen levels. RESULTS: The cumulative disease-free survival of patients with a preoperative carcinoembryonic antigen level within the normal range was significantly better than that of those whose carcinoembryonic antigen was 5 ng/ml or more (P = 0.001). No patient with carcinoembryonic antigen levels less than 1 ng/ml developed metastatic recurrence. Twenty-three percent of all patients with a raised carcinoembryonic antigen above 5 ng/ml compared with 2.1 percent of patients with carcinoembryonic antigen below 5 ng/ml developed a metastasis at two years. At five years, these figures were 37.2 percent and 7.5 percent, respectively. Dukes staging and carcinoembryonic antigen levels were found to be directly correlated (P < 0.001) when all patients were included. Carcinoembryonic antigen of more of 15 ng/ml was found to be a significant adverse prognostic indicator for disease-free survival irrespective of Dukes staging (P < 0.02). Raised carcinoembryonic antigen levels predicted distant metastatic recurrence (P < 0.001) but did not predict local recurrence (P = 0.72). CONCLUSIONS: High preoperative carcinoembryonic antigen levels above 15 ng/ml predicted an increased risk of metastatic recurrence in potentially curative colonic cancer and may indicate undetectable disseminated disease. Preoperative carcinoembryonic antigen levels predict understaging and the possibility of distant recurrence. Such patients may therefore be selected for adjuvant therapy where indicated. Therefore, carcinoembryonic antigen is complementary to conventional Dukes staging for the prediction of recurrence and survival.

Aged↗

[Characteristics of metastasis and recurrence following curative resection for colonic carcinoma].

OBJECTIVE: To investigate the characteristics of metastasis and recurrence following curative resection for colonic carcinoma,and analyze the prognosis. METHODS: The clinicopathological and follow-up data of 310 patients with colon carcinoma undergoing curative resection were analyzed retrospectively. RESULTS: The recurrence rate after curative resection was 23.2% (72/310). The 5-year survival rate was 64.6%. Hepatic metastasis accounted for 38.9% of the cases. Gross classification,histological type, differentiation, lymph node metastasis were correlated with metastasis/recurrence. Univariate analysis revealed that gross classification, histological type, differentiation, lymph node metastasis, blood vessel invasion, TNM Stage, postoperative chemotherapy, portal chemotherapy were prognostic factors. Cox regression analysis revealed that only gross classification, lymph node metastasis, postoperative chemotherapy, portal chemotherapy were independent prognostic factors. CONCLUSIONS: Liver is the most common metastatic site after curative resection for colonic carcinoma. Gross classification, lymph node metastasis, postoperative chemotherapy, and portal chemotherapy are independent prognostic factors.

Adult↗

A landscape ecological approach to address scaling problems in conservation management and monitoring.

Management of many African game reserves is today often still an art based on experience and intuition, rather than a science. Decision-making is based on an informal integration of accumulated individual knowledge and keen field observations. Data are generally poorly captured and curated. Until fairly recently, denominators of biological parameters (such as the unit of land or unit of plant production used as measurement) have generally been treated as being homogenous. The patchiness of landscapes and the issue of ecological scaling were ignored, often because of a lack of appropriate technical tools. The ecological data available on the 49,000-ha Songimvelo Game Reserve (SGR) result from a number of discrete survey and monitoring projects undertaken by different researchers, with different objectives, at different spatial and temporal scales. A landscape ecological approach towards research and monitoring is appropriate for an area of the size and diversity of the SGR. A combination of a database approach and spatial representation was used to consolidate and integrate data across temporal and spatial scales. Herbivore spatial and temporal distribution patterns were explored across three spatial scales. An understanding was achieved of the importance of landscape patchiness in controlling resource availability for herbivores. This insight is important in guiding management and monitoring of the SGR by placing perceived patch overutilization in its proper landscape context. The landscape ecological approach bridges the traditional scale-independent view to a more contemporary scale-related understanding of ecosystem diversity and functioning.

Africa↗

A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies.

BACKGROUND: Large biomedical data sets have become increasingly important resources for medical researchers. Modern biomedical data sets are annotated with standard terms to describe the data and to support data linking between databases. The largest curated listing of biomedical terms is the the National Library of Medicine's Unified Medical Language System (UMLS). The UMLS contains more than 2 million biomedical terms collected from nearly 100 medical vocabularies. Many of the vocabularies contained in the UMLS carry restrictions on their use, making it impossible to share or distribute UMLS-annotated research data. However, a subset of the UMLS vocabularies, designated Category 0 by UMLS, can be used to annotate and share data sets without violating the UMLS License Agreement. METHODS: The UMLS Category 0 vocabularies can be extracted from the parent UMLS metathesaurus using a Perl script supplied with this article. There are 43 Category 0 vocabularies that can be used freely for research purposes without violating the UMLS License Agreement. Among the Category 0 vocabularies are: MESH (Medical Subject Headings), NCBI (National Center for Bioinformatics) Taxonomy and ICD-9-CM (International Classification of Diseases-9-Clinical Modifiers). RESULTS: The extraction file containing all Category 0 terms and concepts is 72,581,138 bytes in length and contains 1,029,161 terms. The UMLS Metathesaurus MRCON file (January, 2003) is 151,048,493 bytes in length and contains 2,146,899 terms. Therefore the Category 0 vocabularies, in aggregate, are about half the size of the UMLS metathesaurus.A large publicly available listing of 567,921 different medical phrases were automatically coded using the full UMLS metatathesaurus and the Category 0 vocabularies. There were 545,321 phrases with one or more matches against UMLS terms while 468,785 phrases had one or more matches against the Category 0 terms. This indicates that when the two vocabularies are evaluated by their fitness to find at least one term for a medical phrase, the Category 0 vocabularies performed 86% as well as the complete UMLS metathesaurus. CONCLUSION: The Category 0 vocabularies of UMLS constitute a large nomenclature that can be used by biomedical researchers to annotate biomedical data. These annotated data sets can be distributed for research purposes without violating the UMLS License Agreement. These vocabularies may be of particular importance for sharing heterogeneous data from diverse biomedical data sets. The software tools to extract the Category 0 vocabularies are freely available Perl scripts entered into the public domain and distributed with this article.

Algorithms↗

[Patients surviving 5 years after curative oesophagectomy for oesophageal cancer].

AIM OF THE STUDY: To analyse the clinical and pathological parameters of 5-year survival patients after curative oesophageal resection for cancer and to identify factors predictive of long-term survival. METHODS: The data of 370 patients who underwent oesophagectomy with curative intent from January 1982 for oesophageal squamous cell carcinoma (n = 320) or adenocarcinoma (n = 50) were reviewed. After excluding postoperative deaths (n = 20), these patients were surviving (S group, n = 113) or dead (NS group, n = 237) with a 60-month follow-up. Uni- and multivariate analysis allowed comparison between the two groups. RESULTS: Postoperative mortality and morbidity rates were 4.0% and 37.6%, respectively. Parameters related to 5-year survival were: absence of preoperative malnutrition or dysphagia, transhiatal resection, no reoperation, limited tumour, histological response to neoadjuvant treatment, absence of lymph node capsular invasion, number of invaded lymph nodes < or = 4, invaded lymph node ratio < or = 0.1, absence of tumour recurrence or metachronous primary cancer. On multivariate analysis, factors predictive of 5-year survival were: absence of preoperative dysphagia (P < 0.001), stage 0-I-IIA tumour (P<0.001) and absence of metachronous cancer (P = 0.016). CONCLUSION: Complete surgical resection allows 5-year survival. Factors predictive of long-term survival assessed in preoperative evaluation, dysphagia and tumour stage, should be useful to select patients for neoadjuvant treatment.

Adenocarcinoma↗

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow&#x2122; (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗

engGNN: a dual-graph neural network for omics-based disease classification and feature selection.

Omics data, such as transcriptomics, proteomics, and metabolomics, provide critical insights into disease mechanisms and clinical outcomes. However, their high dimensionality, small sample sizes, and intricate biological networks pose major challenges for reliable prediction and meaningful interpretation. Graph neural networks offer a promising way to integrate prior knowledge by encoding feature relationships as graphs. Yet, existing methods typically rely solely on either an externally curated feature graph or a data-driven generated graph, which limits their ability to capture complementary information. To address this, we propose the external and generated Graph Neural Network (engGNN), a dual-graph framework that jointly leverages both external biological networks and data-driven generated graphs. Specifically, engGNN constructs a biologically informed undirected feature graph from established network databases and complements it with a directed feature graph derived from tree-ensemble models. This dual-graph design produces more comprehensive representations, thereby improving predictive performance and interpretability. Through extensive simulation studies and real-world applications to three independent gene expression datasets, engGNN consistently demonstrates strong classification performance compared with competitive baselines. Beyond classification, engGNN provides feature- and source-level interpretability, enabling biologically meaningful analyses such as pathway enrichment analysis. Taken together, these results highlight engGNN as a robust, flexible, and interpretable framework for disease classification and biomarker discovery in high-dimensional omics contexts.

Graph Neural Networks↗

The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge.

The Pharmacogenetics and Pharmacogenomics Knowledge Base, PharmGKB (http://www.pharmgkb.org), curates pharmacogenetic and pharmacogenomic information to generate knowledge concerning the relationships among genes, drugs, and diseases, and the effects of gene variation on these relationships. PharmGKB curators collect information on genotype-phenotype relationships both from the literature and from the deposition of primary research data into our database. Their goal is to catalyze pharmacogenetic and pharmacogenomic research.

Biomedical Research↗

The progression of invasiveness regarding the role of transforming growth factor beta receptor type II in gastric cancer.

AIMS: Transforming growth factor beta (TGF beta) is a potent growth inhibitor of epithelial cells. The expression of TGF beta receptors is required for the effect of TGF beta. In this study, we used immunohistochemistry to demonstrate the roles of the expression of TGF beta type I (T beta R-I) and type II (T beta R-II) receptors in the progression of gastric carcinoma. METHODS: To evaluate the potential prognostic value of T beta R-I and T beta R-II, 158 consecutive gastric cancer tissues specimens obtained over a 3-year period were examined. RESULTS: A total of 50 (32%) and 28 (18%) patients had T beta R-I(+) and T beta R-II(+), respectively. The 5-year survival rates of the patients with T beta R-I(+) and those with T beta R-I(-) were 74% and 71%, respectively. In contrast, the 5-year survival rates of the patients with T beta R-II(+) and those with T beta R-II(-) were 57% and 75%, respectively, and the difference was statistically significant (P<0.05). The extent of T beta R-II was closely correlated to the macroscopic types based on the Borrmann classification (P<0.01), and curability (P<0.05). However, a significant difference between the 5-year survival rates of the patients with T beta R-II(+) and those with T beta R-II(-) was only obtained in advanced cases (P<0.05) not in either curative cases, non-curative cases, or early cases. CONCLUSIONS: Our data suggest that when T beta R-II expression correlates with the progression of invasiveness in gastric cancer, it may lead to a non-curative resection and a poor prognosis.

Adult↗

ArrayExpress: a public database of gene expression data at EBI.

ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress).

Computational Biology↗

Trends in the curative treatment of localized prostate cancer after the introduction of prostate-specific antigen: data from the Rotterdam Cancer Registry.

OBJECTIVE: To investigate changes in the incidence and treatment of prostate cancer over the period in which new diagnostic tools were introduced and the attitude towards treatment was changing. PATIENTS AND METHODS: Information on the extent of disease and treatment of patients diagnosed with prostate cancer within the Rotterdam region was retrieved from the Rotterdam Cancer Registry. RESULTS: In the period 1989-95, 4344 patients were diagnosed with prostate cancer and the age-standardized incidence increased from 62 to 125 per 100 000 men. This increase mainly comprised tumours localized to the prostate, while the incidence of advanced cancers remained stable. The proportion of poorly differentiated tumours decreased from 33% in 1989 to 24% in 1995. In the same period the number of patients receiving radiotherapy increased from 80 to 258, while the annual number of radical prostatectomies rose from 17 to 159. Radiotherapy was the preferred type of treatment in patients over 70 years of age, whereas radical prostatectomy was used more frequently in younger patients with localized tumours. CONCLUSION: While the value of screening for prostate cancer remains in debate, incidence and treatment patterns are changing rapidly. Information on patterns of care is needed to interpret future mortality data and to plan resources for adequate health care.

Age Distribution↗