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At least 991 records · Page 55Linked to original sources
PubMed2005

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level.

The Silicon Cell initiative aims to understand cellular systems on the basis of the characteristics of their components. As a tool to achieve this, detailed kinetic models at the network reaction level are being constructed. Such detailed kinetic models are extremely useful for medical and biotechnological applications and form strong tools for fundamental studies. Several recently constructed detailed kinetic models on metabolism (glycolysis), signal transduction (EGF receptor), and the eukaryotic cell cycle (Saccharomyces cerevisiae) have been used to exemplify the Silicon Cell project. These models are stored and made accessible via the JWS Online Cellular Systems Modeling project, a web-based repository of kinetic models. Using a web-browser the models can be interrogated via a user-friendly graphical interface. The goal of the two projects is to combine models on parts of cellular systems and ultimately to construct detailed kinetic models at the cellular level.

Carbon↗
PubMed2026

Computational metabolomics at scale: from open data to insight.

Metabolomics data are currently generated at scale thanks to the evolution of technologies that have led to marked improvements in the number of metabolites detected, spanning all chemical classes. These data are increasingly submitted to public repositories for data reuse, integration, and interpretation. Despite the availability of public resources and associated computational tools, the field still lacks a widely adopted, consistent data and analytics infrastructure capable of transforming this wealth of information into scientific insight. Indeed, the metabolomics field is just now scratching the surface of being able to harness the power of new computational technologies. In this review, we summarize discussions from the "Dagstuhl-Seminar 24181 Computational Metabolomics: Towards Molecules, Models, and their Meaning" with a focus on public data availability, open data standards, data and knowledge integration, and education. Our goal is to raise awareness and adoption of the latest open science resources while highlighting key areas needing further development.

Metabolomics↗
PubMedDate not supplied

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↗
PubMedDate not supplied

CIBEX: center for information biology gene expression database.

We describe the current status of the gene expression database CIBEX (Center for Information Biology gene EXpression database, http://cibex.nig.ac.jp), with a data retrieval system in compliance with MIAME, a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. CIBEX serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.

Computational Biology↗
PubMed2004

Toxic metals in aquatic plants surviving in surface water polluted by copper mining industry.

Concentrations of the metals Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, V, and Zn, as well as the macronutrients N, P, K, Ca, Mg, and S were measured in water, sediments, and the aquatic macrophytes Potamogeton pectinatus and Myriophyllum spicatum, growing in surface water receiving sewages and solid wastes from a copper smelter and a copper ore processing factory located in the Legnica-Glogow copper district in Southwest Poland. The deposition of mineral wastes in this area belong to the largest repository in Europe. The plants were able to survive at heavily contaminated sites. The concentrations of Cd (up to 0.6-1.7 microg/L in water and up to 10.1-12.9 mg/kg in sediments), Cu (up to 29-48 microg/L in water and up to 4.6-5.6g/kg in sediments), Pb (up to 1.5-2.2 g/kg in sediments), and Zn (up to 167-200 microg/L in water and up to 1.4-1.8 g/kg in sediments) seriously exceeded background values. P. pectinatus was able to survive tissue concentrations (in mg/kg) of up to 920 Cu, 6240 Mn, 98 Co, and 59 Ni, while M. spicatum survived tissue concentrations up to 1040 Cu, 6660 Mn, and 57 Co for. Enrichment ratios of elements in plant tissue and in water were much higher than those between plant tissue and sediments.

Environmental Monitoring↗
PubMed2006

TuBaFrost 6: virtual microscopy in virtual tumour banking.

Many systems have already been designed and successfully used for sharing histology images over large distances, without transfer of the original glass slides. Rapid evolution was seen when digital images could be transferred over the Internet. Nowadays, sophisticated Virtual Microscope systems can be acquired, with the capability to quickly scan large batches of glass slides at high magnification and compress and store the large images on disc, which subsequently can be consulted through the Internet. The images are stored on an image server, which can give simple, easy to transfer pictures to the user specifying a certain magnification on any position in the scan. This offers new opportunities in histology review, overcoming the necessity of the dynamic telepathology systems to have compatible software systems and microscopes and in addition, an adequate connection of sufficient bandwidth. Consulting the images now only requires an Internet connection and a computer with a high quality monitor. A system of complete pathology review supporting bio-repositories is described, based on the implementation of this technique in the European Human Frozen Tumor Tissue Bank (TuBaFrost).

Computer Simulation↗
PubMed2026

Early proteomic and metabolic signatures of liver and eye in OAT-deficient mice.

Ornithine aminotransferase (OAT) deficiency causes hyperornithinemia and gyrate atrophy (GA) of the choroid and retina, a rare inherited retinal degeneration. To understand the early molecular changes that make the eye susceptible to damage, we performed quantitative proteomic and metabolomic profiling of liver, retina, and retinal pigment epithelium and choroid (RPE/Cho) from OAT-deficient (Oatrhg) mice prior to detectable vision impairment. In addition to reduced OAT expression and elevated ornithine, methylation-related metabolites such as N(6)-methyl-lysine were altered in all examined tissues of Oatrhg mice. In the liver, excess ornithine was directed into urea cycle metabolism, together with altered expression of detoxification enzymes and histone H2B proteins. In contrast, the retina showed minimal proteomic changes but pronounced alterations in amino acid pathways that support glutamate homeostasis. The RPE/Cho demonstrated the most extensive proteomic changes, particularly in mitochondrial metabolism, cytoskeleton, and extracellular matrix, along with changes in metabolites involved in lysine metabolism, energy metabolism, and antioxidant capacity. Incubation with 13C lysine demonstrated that lysine was primarily degraded in RPE/Cho but not the retina, and ornithine enhanced lysine degradation in an OAT-dependent manner. Together, these findings highlight common and tissue-specific impacts of OAT on the liver and ocular tissues and provide insight into early molecular changes that contribute to the selective vulnerability of the eye in GA. Proteomics data are available via ProteomeXchange (PXD063614) and metabolomics data via MassIVE repository (MSV000101103).

Animals↗
PubMed2006

Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.

Recently the genome sequences of several filamentous fungi have become available, providing the opportunity for large-scale functional analysis including genome-wide expression analysis. We report the design and validation of the first Affymetrix GeneChip microarray based on the entire genome of a filamentous fungus, the ascomycetous plant pathogen Fusarium graminearum. To maximize the likelihood of representing all putative genes (approximately 14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the online F. graminearum Genome DataBase. From these gene sets, a subset of calls was manually annotated and a non-redundant extract of all calls together with additional EST sequences and controls were submitted for GeneChip design. Experiments were conducted to test the performance of the F. graminearum GeneChip. Hybridization experiments using genomic DNA demonstrated the usefulness of the array for experimentation with F. graminearum and at least four additional pathogenic Fusarium species. Differential transcript accumulation was detected using the F. graminearum GeneChip with treatments derived from the fungus grown in culture under three nutritional regimes and in comparison with fungal growth in infected barley. The ability to detect fungal genes in planta is surprisingly sensitive even without efforts to enrich for fungal transcripts. The Plant Expression Database (PLEXdb, http://www.plexdb.org) will be used as a public repository for raw and normalized expression data from the F. graminearum GeneChip. The F. graminearum GeneChip will help to accelerate exploration of the pathogen-host pathways that may involve interactions between pathogenicity genes in the fungus and disease response in the plant.

Computational Biology↗
PubMed2006

Concepts and possibilities in forensic intelligence.

Forensic intelligence can be viewed as comprising two parts, one directly concerning intelligence delivery in forensic casework, the other considering performance aspects of forensic work, loosely termed here as business intelligence. Forensic casework can be viewed as processes that produce an intelligence product useful to police investigations. Traditionally, forensic intelligence production has been confined to discipline-specific activity. This paper examines the concepts, processes and intelligence products delivered in forensic casework, the information repositories available from forensic examinations, and ways to produce within- and across-discipline casework correlations by using information technology to capitalise on the information sets available. Such analysis presents opportunities to improve forensic intelligence services as well as challenges for technical solutions to deliver appropriate data-mining capabilities for available information sets, such as digital photographs. Business intelligence refers primarily to examination of efficiency and effectiveness of forensic service delivery. This paper discusses measures of forensic activity and their relationship to crime outcomes as a measure of forensic effectiveness.

Data Collection↗
PubMed2004

Digital three-dimensional models of Drosophila development.

Digital models of organs, cells and subcellular structures have become important tools in biological and medical research. Reaching far beyond their traditional widespread use as didactic tools, computer-generated models serve as electronic atlases to identify specific elements in complex patterns, and as analytical tools that reveal relationships between such pattern elements that would remain obscure in two-dimensional sections. Digital models also offer the unique opportunity to store and display gene-expression patterns, and pilot studies have been made in several genetic model organisms, including mouse, Drosophila and Caenorhabditis elegans, to construct digital graphic databases intended as repositories for gene-expression data.

Animals↗
PubMed2004

Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus).

The launch of large-scale chicken expressed sequence tags (EST) projects has placed the chicken in the lead for the number of EST sequences in agriculturally important animals. More than 451,000 chicken ESTs derived from over 158 libraries have been deposited in the NCBI dbEST database as of December 2003. But how many genes these ESTs represent and how they are expressed in different chicken tissues/organs remain undetermined. In the present research, we developed a human gene-based strategy for census of chicken orthologous genes and identification of their expression patterns. Among 34,157 human coding genes used in the study, BLAST analysis revealed that 11,066 genes provisionally matched 248,628 chicken ESTs. Based on the average EST abundance of the orthologous genes, the current public repository of chicken ESTs could represent approximately 20,000 provisional genes. Analysis of gene expression in 14 single tissues/organs showed that approximately 15% of genes were expressed exclusively in single tissue/organ whereas the remaining approximately 85% of genes were co-expressed in two or more tissues/organs. A majority (91.15%) of genes expressed in chicken embryos were also expressed at post-hatch stages, indicating that most genes activated in chicken embryos could serve housekeeping functions. Self-organizing maps (SOM) analysis organized 8807 provisional genes in selected chicken tissues into 98 clusters with each cluster being indicative of common regulatory factors and pathways. A total of 969 provisional orthologous genes were identified as preferentially expressed genes (PEGs) in various chicken tissues/organs (LOD>3.0). No doubt, the present study on gene expression patterns will provide insight into dynamics of metabolic pathways and tissue/organ programming and reprogramming in chickens.

Algorithms↗
PubMed2005

Utilization of colonoscopy in the United States: results from a national consortium.

BACKGROUND: To assess capacity for colonoscopy, we need to understand current utilization of colonoscopy in diverse clinical practice settings. The objective of this study was to determine the utilization of colonoscopy in diverse clinical practice settings. METHODS: The Clinical Outcomes Research Initiative (CORI) data repository, which receives endoscopy reports from 73 diverse adult practice sites in the United States was used. Colonoscopy reports from January 2000 to August 2002 were analyzed to determine the demographic characteristics of adult patients who received a colonoscopy and the procedure indication. The relationship of age, race, gender, and procedure indication was analyzed. RESULTS: Results of colonoscopies in 146,457 unique patients were analyzed. Of the reports, 68% came from nonacademic settings. Patients less than 50 years of age accounted for 20% of colonoscopies. The most common indications were rectal bleeding (33.6%), irritable bowel symptoms (23.8%), or screening because of a positive family history of colorectal cancer (22.4%) and screening with a primary colonoscopy or a fecal occult blood test (FOBT) (12.8%). In patients 50 years and older, asymptomatic screening (average-risk screening colonoscopy, positive family history, or FOBT positivity) accounted for 38.1% of all colonoscopies. Surveillance colonoscopy in patients with previous cancer or polyps accounted for 21.9% of colonoscopies performed in this age group. Differences in utilization were noted, based on gender and race. CONCLUSIONS: Colonoscopy utilization varies based on age, gender, and race. Colonoscopy often is performed in patients less than 50 years old for irritable bowel symptoms; rectal bleeding; or average-risk screening, for which benefits are uncertain. In patients older than 50 years, surveillance after polyp removal is a common indication and may be overused. Understanding utilization can lead to further study to determine outcomes, to optimize utilization, and to provide a basis for shifting limited resources.

Aged↗
PubMed2007

Endoscopic screening for varices in cirrhotic patients: data from a national endoscopic database.

BACKGROUND: The current guidelines for primary prophylaxis of variceal hemorrhage in cirrhotic patients recommend screening for varices with upper endoscopy (EGD). Utilization and outcomes of screening in clinical practice are unknown. OBJECTIVE: Our purpose was to determine the use of endoscopic variceal screening in diverse practice settings and to determine factors associated with the finding of esophageal varices. DESIGN: Endoscopic reports generated by the Clinical Outcomes Research Initiative (CORI) repository were analyzed to determine the use, changes over time, and findings of screening upper endoscopies between January 1, 2000, and December 31, 2003. SETTING: Data from 68 CORI practices (70% community/17% academic/13% Veterans Affairs Medical Center [VAMC]) were evaluated. PATIENTS: A total of 1688 of 172,854 EGDs were performed for the purpose of screening for varices. RESULTS: Overall, there was a linear increase in annual proportion of screening EGDs performed (P < .0001). A significantly greater proportion of variceal screening EGDs are performed in academic centers compared with VAMC and community practices. Varices were found in 881 screened patients (52.2%). Varices were found more often in Child-Pugh class B/C (71.9%) compared with Child-Pugh class A (42.7%) patients. Of those with varices found, patients with Child-Pugh class B/C were more likely to have large varices than were patients with Child-Pugh class A (P = .02). LIMITATIONS: A limitation of this study was the inability to determine the total number of cirrhotic patients cared for at each CORI site included in this study. CONCLUSIONS: Endoscopic screening for varices represents a small proportion of all upper endoscopies performed. This proportion increased between 2000 and 2003. Varices were found more frequently in patients with more severe liver disease.

Adult↗
PubMed2025

Substitutions of nucleotides at the 3' ends of COL6A1/2/3 exons induce exon skipping associated with collagen VI-related muscular dystrophies and therapeutic strategies.

PURPOSE: Collagen VI-related muscular dystrophies, characterized by proximal muscle weakness and joint contractures, are caused by pathogenic variants in the genes, COL6A1 to COL6A3. A monoallelic variant at the last nucleotide of a COL6A1 exon was initially classified as a missense variant but acted as a splicing variant, resulting in exon skipping. Here, we evaluated whether single-nucleotide variants at the 3'-ends of COL6A1 to COL6A3 exons cause aberrant splicing. METHODS: Ten relevant variants were identified in patients from our repository or public databases, and their muscle COL6A1 to COL6A3 transcripts were analyzed. The effects of the variants on splicing were also analyzed by minigene assay and SpliceAI in silico prediction. RESULTS: Transcripts from muscles of individuals with suspected collagen VI-related phenotypes showed exon skipping (skipping rate >12%). Findings of minigene assay and in silico prediction experiments supported these findings. Two therapeutic approaches, splicing correction of pre-messenger RNA or gene silencing of mature messenger RNA were assessed. Among them, gene silencing using short interfering RNAs targeting the skipped transcripts proved to be effective in restoring collagen VI in cells containing the pathogenic variant. CONCLUSION: Single-nucleotide variants at the 3'-ends of exons can lead to aberrant splicing, and allele-specific gene silencing targeting such variants is a promising therapeutic strategy.

Humans↗
PubMed2026

Characterization of the genotypic and phenotypic spectrum of TCF7L2-related neurodevelopmental disorder (TRND).

PURPOSE: TCF7L2 (OMIM 602228; HGNC:11641) is a transcription factor and a critical effector of the Wnt/ &#x3b2;-Catenin pathway. In 2021, 11 pediatric patients with monoallelic predicted loss-of-function (pLOF) TCF7L2 variants and syndromic features were observed. Characterization of patients with pLOF TCF7L2 variants and neurodevelopmental features-herein referred to as TCF7L2-related neurodevelopmental disorder-is urgently needed. METHODS: We leveraged multiple methods (eg, GeneMatcher, DECIPHER, literature review, and public/private repositories) to identify an international cohort of 76 patients with pLOF TCF7L2 variants and neurodevelopmental features and phenotypically characterized them. We also retrospectively searched for an independent cohort of adults with pLOF TCF7L2 variants (n = 11) from more than 60,000 PennMedicine BioBank patients. RESULTS: Among 76 patients with pLOF TCF7L2 variants, speech delay (95.3%), craniofacial dysmorphisms (73.3%), ophthalmologic conditions (65.5%), autism (62.1%), and orthopedic abnormalities (52.6%) were the most commonly observed. Phenotypic differences did not cluster by variant type or genomic locus. Among PennMedicine BioBank patients, an association of nominal significance with type 2 diabetes with renal manifestations (odds ratio = 5.8; P = .03) was detected, warranting further investigation. CONCLUSION: This study represents the most comprehensive characterization of TCF7L2-related neurodevelopmental disorder to date, a novel neurodevelopmental disorder, defining its genotypic and phenotypic spectra. We opened a Simons Searchlight natural history study that is now available for patient enrollment to enhance the understanding of this condition.

Neurodevelopmental syndrome↗
PubMed2006

MICA, MICB, and MHC beta block matching in bone marrow transplantation: relevance to transplantation outcome.

Genetic testing of the MHC is required for selection of donors for bone marrow transplantation. The outcome of related bone marrow transplantation is usually superior to that of unrelated bone marrow transplantation. This may be the result of inaccurate or incomplete genetic testing employed for selection of donor for transplantation. Based on MHC haplotype matching, MHC block matching has been developed for selection of potential unrelated donor. Block matching has been shown previously to improve outcome when added to the conventional method of human leukocyte antigen (HLA) typing for selection of donors. In this study, we have retrospectively analyzed 44 donor recipient pairs from the Australian Bone Marrow Donor Registry Repository with respect to matching of HLA-B and HLA-Cw by sequence-based typing and MICA and MICB by polymerase chain reaction-sequence specific primer and MHC beta block matching and correlated these results with survival. Beta block matching was correlated with MIC matching (p < 0.005) and with HLA-B and HLA-Cw matching. Patients who were HLA-B and -Cw matched had significantly improved survival when they were additionally matched for MHC beta block (p(c) = 0.04) or MIC (p(c) = 0.05).

Adolescent↗
PubMed2004

A review of content-based image retrieval systems in medical applications-clinical benefits and future directions.

Content-based visual information retrieval (CBVIR) or content-based image retrieval (CBIR) has been one on the most vivid research areas in the field of computer vision over the last 10 years. The availability of large and steadily growing amounts of visual and multimedia data, and the development of the Internet underline the need to create thematic access methods that offer more than simple text-based queries or requests based on matching exact database fields. Many programs and tools have been developed to formulate and execute queries based on the visual or audio content and to help browsing large multimedia repositories. Still, no general breakthrough has been achieved with respect to large varied databases with documents of differing sorts and with varying characteristics. Answers to many questions with respect to speed, semantic descriptors or objective image interpretations are still unanswered. In the medical field, images, and especially digital images, are produced in ever-increasing quantities and used for diagnostics and therapy. The Radiology Department of the University Hospital of Geneva alone produced more than 12,000 images a day in 2002. The cardiology is currently the second largest producer of digital images, especially with videos of cardiac catheterization ( approximately 1800 exams per year containing almost 2000 images each). The total amount of cardiologic image data produced in the Geneva University Hospital was around 1 TB in 2002. Endoscopic videos can equally produce enormous amounts of data. With digital imaging and communications in medicine (DICOM), a standard for image communication has been set and patient information can be stored with the actual image(s), although still a few problems prevail with respect to the standardization. In several articles, content-based access to medical images for supporting clinical decision-making has been proposed that would ease the management of clinical data and scenarios for the integration of content-based access methods into picture archiving and communication systems (PACS) have been created. This article gives an overview of available literature in the field of content-based access to medical image data and on the technologies used in the field. Section 1 gives an introduction into generic content-based image retrieval and the technologies used. Section 2 explains the propositions for the use of image retrieval in medical practice and the various approaches. Example systems and application areas are described. Section 3 describes the techniques used in the implemented systems, their datasets and evaluations. Section 4 identifies possible clinical benefits of image retrieval systems in clinical practice as well as in research and education. New research directions are being defined that can prove to be useful. This article also identifies explanations to some of the outlined problems in the field as it looks like many propositions for systems are made from the medical domain and research prototypes are developed in computer science departments using medical datasets. Still, there are very few systems that seem to be used in clinical practice. It needs to be stated as well that the goal is not, in general, to replace text-based retrieval methods as they exist at the moment but to complement them with visual search tools.

Databases, Factual↗
PubMed2005

Bedside, classroom and bench: collaborative strategies to generate evidence-based knowledge for nursing practice.

The rise of evidence-base practice (EBP) as a standard for care delivery is rapidly emerging as a global phenomenon that is transcending political, economic and geographic boundaries. Evidence-based nursing (EBN) addresses the growing body of nursing knowledge supported by different levels of evidence for best practices in nursing care. Across all health care, including nursing, we face the challenge of how to most effectively close the gap between what is known and what is practiced. There is extensive literature on the barriers and difficulties of translating research findings into practical application. While the literature refers to this challenge as the "Bench to Bedside" lag, this paper presents three collaborative strategies that aim to minimize this gap. The Bedside strategy proposes to use the data generated from care delivery and captured in the massive data repositories of electronic health record (EHR) systems as empirical evidence that can be analysed to discover and then inform best practice. In the Classroom strategy, we present a description for how evidence-based nursing knowledge is taught in a baccalaureate nursing program. And finally, the Bench strategy describes applied informatics in converting paper-based EBN protocols into the workflow of clinical information systems. Protocols are translated into reference and executable knowledge with the goal of placing the latest scientific knowledge at the fingertips of front line clinicians. In all three strategies, information technology (IT) is presented as the underlying tool that makes this rapid translation of nursing knowledge into practice and education feasible.

Cooperative Behavior↗