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At least 649 records · Page 36Linked to original sources
PubMed2026

Proteomic insights into Helicobacter pylori infection in stomach cells, revealing host response and host-targeted therapeutics repurposing.

BACKGROUND: Helicobacter pylori (H. pylori) is a globally prevalent gastric pathogen strongly associated with chronic gastritis, peptic ulcers, and gastric cancer. While bacterial factors have been extensively studied, host proteomic responses and their therapeutic potential remain largely underexplored. RESEARCH DESIGN AND METHODS: Current analyses employed a systematic proteomics-based data integration and harmonization approach (retrospective qualitative cohort study) to identify important differentially regulated host proteins. Proteomic datasets were curated from in vitro studies and analyzed for functional enrichment, protein-protein interaction networks, and hub protein identification. To explore therapeutic repurposing, drug repositioning was performed using the DrugBank database. RESULTS: Data summation describing protein differential regulation in human gastric cells as a result of the infection revealed 1672 perturbed host proteins. Bioinformatics analysis revealed 11 proteins including CSK, MET, RELA, MARK2, GRB2, FTO, PLCG1, CRKL, RPS5, RPS9, and RPS27A to be ideal host targets for therapeutic repurposing. Clinically approved drugs such as Dasatinib (targeting CSK) and Crizotinib (targeting MET) emerged as promising candidates due to favorable pharmacokinetics and known bioactivity. CONCLUSIONS: Host-directed therapeutics could offer alternative strategies to conventional antibiotic therapy, addressing challenges such as resistance and infection recurrence, providing a foundation for future experimental validation and development of host-targeted interventions for infection control.

Humans↗
PubMed1993

Technical note: the development of quality assurance for Sheffield's radiotherapy treatment planning systems.

Quality assurance procedures have been defined and implemented for the treatment planning systems at Weston Park Hospital. The programme of tests and checks covers both hardware and software: hardware checks are concerned with the input and output performance of the system's peripheral devices; the software checks involve testing system data integrity, and testing the algorithms used for planning external photon and electron beams. Beam measurements from an ionization chamber scanned in water and air were compared with calculations from two independent treatment planning systems. Following the implementation of these quality assurance procedures, some improvements have been made to the system data used and changes have been introduced to planning practice.

Algorithms↗
PubMed2004

Measuring outbreak-detection performance by using controlled feature set simulations.

INTRODUCTION: The outbreak-detection performance of a syndromic surveillance system can be measured in terms of its ability to detect signal (i.e., disease outbreak) against background noise (i.e., normally varying baseline disease in the region). Such benchmarking requires training and the use of validation data sets. Because only a limited number of persons have been infected with agents of biologic terrorism, data are generally unavailable, and simulation is necessary. An approach for evaluation of outbreak-detection algorithms was developed that uses semisynthetic data sets to provide real background (which effectively becomes the noise in the signal-to-noise problem) with artificially injected signal. The injected signal is defined by a controlled feature set of variable parameters, including size, shape, and duration. OBJECTIVES: This report defines a flexible approach to evaluating public health surveillance systems for early detection of outbreaks and provides examples of its use. METHODS: The stages of outbreak detection are described, followed by the procedure for creating data sets for benchmarking performance. Approaches to setting parameters for simulated outbreaks by using controlled feature sets are detailed, and metrics for detection performance are proposed. Finally, a series of experiments using semisynthetic data sets with artificially introduced outbreaks defined with controlled feature sets is reviewed. RESULTS: These experiments indicate the flexibility of controlled feature set simulation for evaluating outbreak-detection sensitivity and specificity, optimizing attributes of detection algorithms (e.g., temporal windows), choosing approaches to syndrome groupings, and determining best strategies for integrating data from multiple sources. CONCLUSIONS: The use of semisynthetic data sets containing authentic baseline and simulated outbreaks defined by a controlled feature set provides a valuable means for benchmarking the detection performance of syndromic surveillance systems.

Disease Outbreaks↗
PubMed2006

Clinical evidence and evidence-based dental treatment of special populations: patients with Alzheimer's disease.

This paper presents the novel domain of evidence-based research in the context of treating the dental needs of patients with special needs. A contrast is made between evidence-based dentistry and traditional dentistry, which is based on the evidence obtained by the dentist, with respect to the needs and the wants of the patient, and from the pertinent and accessible literature. By contrast, evidence-based dentistry is focused on integrating traditional dentistry with "the best available" research evidence. The aim of evidence-based dentistry is to improve clinical decision-making by its reliance on a critical analysis of the entire body of the published pertinent literature. It is a system of information management, and a system of data integration that assist clinicians in the process of meshing systemic clinical expertise, evidence provided by the patient, and the best literature evidence to enhance treatment outcomes. Evidence-based dentistry emphasizes rigorous analysis of evidence from clinical research, as the basis of sound dental practice, while discouraging intuitive and unsystematic approaches and promoting the systematic analysis and appraisal of the literature to determine the best treatment alternatives. In the case of patients with special needs, it is critical whether the dentist practices traditional dentistry or evidence-based dentistry to evaluate whether or not the patient is capable of expressing his or her needs/wants, unless, as in the more severe cases, he/she is accompanied by the caregiver. The purpose of this paper is to demonstrate the use of a simple in-house questionnaire for evaluating the patient's ability to tell the dentist his or her needs and wants accurately. In this context, the paper examines the dental needs of patients with dementia of the Alzheimer's type, DAT.

Aged↗
PubMed2004

Diagnosis and testing in bronchiolitis: a systematic review.

BACKGROUND: The diagnosis of bronchiolitis is based on typical history and results of a physical examination. The indications for and utility of diagnostic and supportive laboratory testing (eg, chest x-ray films, complete blood cell counts, and respiratory syncytial virus testing) are unclear. OBJECTIVES: To review systematically the data on diagnostic and supportive testing in the management of bronchiolitis and to assess the utility of such testing. DESIGN: In conjunction with an expert panel, we generated admissibility criteria and derived relevant terms to search the literature published from 1980 to November 2002 in MEDLINE and the Cochrane Collaboration Database of Controlled Clinical Trials. Trained abstractors completed detailed data collection forms for each article. We summarized the data in tables after performing data integrity checks. RESULTS: Of the 797 abstracts identified, we present evidence from 82 trials that met our inclusion criteria (17 are primary articles on diagnosis of bronchiolitis and 65are reports of treatment or prevention trials). Numerous studies demonstrate that rapid respiratory syncytial virus tests have acceptable sensitivity and specificity, but no data show that respiratory syncytial virus testing affects clinical outcomes in typical cases of the disease. Seventeen studies presented chest x-ray film data. Abnormalities on chest x-ray films ranged from 20% to 96%. Insufficient data exist to show that chest x-ray films reliably distinguish between viral and bacterial disease or predict severity of disease. Ten studies included complete blood cell counts, but most did not present specific results. In one study, white blood cell counts correlated with radiologically defined disease categories of bronchiolitis. CONCLUSIONS: A large number of studies include diagnostic and supportive testing data. However, these studies do not define clear indications for such testing or the impact of testing on relevant patient outcomes. Given the high prevalence of this disease, prospective studies of the utility of such testing are needed and feasible.

Bronchiolitis↗
PubMed1997

Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection.

In this work we propose a reconstruction algorithm (ART with blobs) that has not been previously used in electron Tomography and we compare it with the standard method in the field (weighted back projection, WBP). We assume that only a limited set of very noisy images, collected around a single axis tilt, is available; which is a typical situation in Electron Tomography. In general, the reconstruction problem is underdetermined (due to the limited number of projections) and the data are inconsistent (due to the high level of noise). The evaluation of the results is performed in a rigorous way by a task-oriented approach which makes use of numerical observers. ART with blobs outperforms WBP for a number of key tasks. Results are presented both for simplified line integral data and for realistic simulations of macromolecular structures embedded in amorphous ice.

Algorithms↗
PubMedDate not supplied

Health care executive's guidebook to automation in the 1980s: health care information systems and DRGs.

The key to effective decision-making in health care institutions--now and in the future--is data: accurate, reliable, well-understood information about your patients and about your institution's operations. Much of the data you need for decision support are now available in your financial, patient information, and departmental systems. To put it to work in ways that will meet the challenges of the 1980s, you need to develop more effective ways to use this information. A decision-support system requires, above all, integrated data, flexible access, and the capability to extract and summarize relevant information from a mass of detail. Effective decision-support systems require powerful hardware and sophisticated software. Even more, they require planning and self-education on your part. You must understand your current system and your future needs. You must also educate yourself about the computer market-place and the many systems options available to you. Read books and magazines, attend conferences, contact vendors. Above all, talk to users of any system you are considering for your institution. The resources in this Guidebook can start you on your way.

Computers↗
PubMed2003

Combining multiple microarray studies and modeling interstudy variation.

We have established a method for systematic integration of multiple microarray datasets. The method was applied to two different sets of cancer profiling studies. The change of gene expression in cancer was expressed as 'effect size', a standardized index measuring the magnitude of a treatment or covariate effect. The effect sizes were combined to obtain the estimate of the overall mean. The statistical significance was determined by a permutation test extended to multiple datasets. It was shown that the data integration promotes the discovery of small but consistent expression changes with increased sensitivity and reliability. The effect size methods provided the efficient modeling framework for addressing interstudy variation as well. Based on the result of homogeneity tests, a fixed effects model was adopted for one set of datasets that had been created in controlled experimental conditions. By contrast, a random effects model was shown to be appropriate for the other set of datasets that had been published by independent groups. We also developed an alternative modeling procedure based on a Bayesian approach, which would offer flexibility and robustness compared to the classical procedure.

Algorithms↗
PubMed2004

National and school policies on restrictions of teacher smoking: a multilevel analysis of student exposure to teacher smoking in seven European countries.

The paper examines the association between restrictions on teacher tobacco smoking at school and student exposure to teachers who smoke during school hours. The data are taken from a European Commission-funded study 'Control of Adolescent Smoking' (the CAS study) in seven European countries. Multilevel modelling analyses were applied to investigate associations between national legislation concerning tobacco smoking in school, local school smoking restrictions and students' exposure to teachers who smoke at school. The analyses integrate data from three levels: national (types of policy and how restrictive they are), school (survey among teachers, n = 455) and student (survey among 15-year-old students, n = 10890). The results suggest that both national- and school-level policies on restriction of smoking among teachers are associated with a decreased probability of students reporting that they are exposed to teachers who smoke indoors, but an increased probability of being exposed to teachers smoking outdoors.

Adolescent↗
PubMed1995

A review of microfabricated devices for gene-based diagnostics.

The next technologic revolution may well be the miniaturization of solution phase experimentation through the marriage of microelectronics and molecular biology. Already researchers leading this rapidly emerging technology are developing prototype biochemical "microlaboratories" that offer a millionfold reduction of scale; that is, biochemical analyses are being conducted with picoliter sample volumes rather than conventional microliter formats. Such miniaturization is achieved by exploiting the well-honed tools of microelectronics that accommodate highly parallel automated assays, ultrasensitive detection, high throughput, integrated data acquisition, computation, and distributed data storage/retrieval. The subject of this paper is to survey this evolving bioelectronic miniaturization technology with applications to gene-based diagnostics. Several pioneering microchips are described and compared to traditional biochemical methods. Specifically, miniaturized examples of various diagnostic processes such as sample preparation (PCR), assays (electrophoresis and probe arrays), and detection (integrated CCDs) are presented. Although these microdevices are rather embryonic they represent the first steps toward fabricating a fully integrated diagnostic system on a microchip.

Diagnosis↗
PubMed1990

Construction of validated, non-redundant composite protein sequence databases.

A strategy has been developed for the construction of a validated, comprehensive composite protein sequence database. Entries are amalgamated from primary source data bases by a largely automated set of processes in which redundant and trivially different entries are eliminated. A modular approach has been adopted to allow scientific judgement to be used at each stage of database processing and amalgamation. Source databases are assigned a priority depending on the quality of sequence validation and commenting. Rejection of entries from the lower priority database, in each pairwise comparison of databases, is carried out according to optionally defined redundancy criteria based on sequence segment mismatches. Efficient algorithms for this methodology are embodied in the COMPO software system. COMPO has been applied for over 2 years in construction and regular updating of the OWL composite protein sequence database from the source databases NBRF-PIR, SWISS-PROT, a GenBank translation retrieved from the feature tables, NBRF-NEW, NEWAT86, PSD-KYOTO and the sequences contained in the Brookhaven protein structure databank. OWL is part of the ISIS integrated data resource of protein sequence and structure [Akrigg et al. (1988) Nature, 335, 745-746]. The modular nature of the integration process greatly facilitates the frequent updating of OWL following releases of the source databases. The extent of redundancy in these sources is revealed by the comparison process. The advantages of a robust composite database for sequence similarity searching and information retrieval are discussed.

Amino Acid Sequence↗
PubMed2006

Proteomic analysis of the mouse mammary gland is a powerful tool to identify novel proteins that are differentially expressed during mammary development.

After lactation, the mouse mammary gland undergoes apoptosis and tissue remodelling as the gland reverts to its prepregnant state. This complex change was investigated using 2-DE. An integrated database was produced from lactation and involution proteomes. Forty-four molecular cluster indexes (MCIs) that showed altered expression from lactation to involution were selected for MS analysis. Of these, 32 gave protein annotations, 18 of which were unequivocal proteins. Selected proteins were then studied across all of development, including pregnancy, using data integrated from another proteome database. Two proteins, the RNA polymerase B transcription factor 3 (BTF3) and the minichromosome maintenance protein 3 (MCM3), although initially selected on the basis of the lactation/involution criteria, had expression profiles that indicated an additional role in mammary development and were further analysed. BTF3, a transcription factor previously not described in the mammary gland, was up-regulated strongly in pregnancy, indicating an involvement in alveolar growth. MCM3's expression was greatest in pregnancy and late involution, decreasing through lactation. Immunohistochemistry localised MCM3 to the mammary epithelium, where a greater proportion of cells stained than for the proliferation marker Ki67. MCM3 expression during lactation may identify cells that are licensed to repopulate the gland during cell loss in lactation and following involution.

Animals↗
PubMed2003

Uzilla: a new tool for web usability testing.

Web usability testing and research presents challenges for accurate data collection. An instrumented browser solution, Uzilla, is compared with existing solutions, and its contributions to usability testing practice are noted. Uzilla implements a client-server architecture based on the open source Mozilla browser. Instrumentation of the browser facilitates the evaluation of Web sites and applications inside and outside of the laboratory. An integrated data collection and analysis server application decreases the effort required to understand test results and facilitates iterative testing.

Ergonomics↗
PubMedDate not supplied

Taking digital imaging to the next level: challenges and opportunities.

New medical imaging technology, such as multi-detector computed tomography (CT) scanners and positron emission tomography (PET) scanners, are creating new possibilities for non-invasive diagnosis that are leading providers to invest heavily in these new technologies. The volume of data produced by such technology is so large that it cannot be "read" using traditional film-based methods, and once in digital form, it creates a massive data integration and archiving challenge. Despite the benefits of digital imaging and archiving, there are several key challenges that healthcare organizations should consider in planning, selecting, and implementing the information technology (IT) infrastructure to support digital imaging. Decisions about storage and image distribution are essentially questions of "where" and "how fast." When planning the digital archiving infrastructure, organizations should think about where they want to store and distribute their images. This is similar to decisions that organizations have to make in regard to physical film storage and distribution, except the portability of images is even greater in a digital environment. The principle of "network effects" seems like a simple concept, yet the effect is not always considered when implementing a technology plan. To fully realize the benefits of digital imaging, the radiology department must integrate the archiving solutions throughout the department and, ultimately, with applications across other departments and enterprises. Medical institutions can derive a number of benefits from implementing digital imaging and archiving solutions like PACS. Hospitals and imaging centers can use the transition from film-based imaging as a foundational opportunity to reduce costs, increase competitive advantage, attract talent, and improve service to patients. The key factors in achieving these goals include attention to the means of data storage, distribution and protection.

Costs and Cost Analysis↗
PubMed1999

3-dimensional volume rendered computerized tomography for preoperative evaluation and intraoperative treatment of patients undergoing nephron sparing surgery.

PURPOSE: Computerized tomography (CT) is the diagnostic and staging modality of choice for renal neoplasms. Existing imaging modalities are limited by a 2-dimensional (D) format. Recent advances in computer technology now allow the production of high quality 3-D images from helical CT. Nephron sparing surgery requires a detailed understanding of renal anatomy. Preoperative evaluation must delineate the relationship of the tumor to adjacent normal structures and demonstrate the vascular supply to the tumor for the surgeon to conserve as much normal parenchyma as possible. We propose that helical CT combined with 3-D volume rendering provides all of the information required for preoperative evaluation and intraoperative management of nephron sparing surgery cases. We prospectively evaluated the role of 3-D volume rendering CT in 60 patients undergoing nephron sparing surgery for renal cell carcinoma at the Cleveland Clinic Foundation. MATERIALS AND METHODS: Triphasic spiral CT was performed preoperatively in 60 consecutive patients undergoing nephron sparing surgery for renal neoplasms. A 3 to 5-minute videotape was prepared using volume rendering software which demonstrated the position of the kidney, location and depth of extension of the tumor(s), renal artery(ies) and vein(s), and relationship of the tumor to the collecting system. These videotapes were viewed by a radiologist and urologist in the operating room at surgery, and immediately correlated with surgical findings. Corresponding renal arteriograms of 19 patients were retrospectively compared to 3-D volume rendering CT and operative findings. RESULTS: A total of 97 renal masses were identified in 60 cases evaluated with 3-D volume rendering CT before nephron sparing surgery. There were no complications related to the 3-D protocol and 3-D rendering was successful in all patients. The number and location of lesions identified by 3-D volume rendering CT were accurate in all cases, while enhancement and diagnostic characteristics were consistent with pathological findings in 95 of 97 tumors (98%). Of 77 renal arteries identified at surgery 74 were detected by 3-D volume rendering CT (96%). Helical CT missed 3 small accessory arteries, including 1 in a cross fused ectopic kidney. All major venous branches and anomalies were identified, including 3 circumaortic left renal veins. Of 69 renal veins identified at surgery 64 were detected by 3-D volume rendering CT (93%). All 5 renal veins missed by CT were small, short, duplicated right branches of the main renal vein. Renal fusion and malrotation anomalies were correctly identified in all 4 patients. CONCLUSIONS: The 3-D volume rendering CT accurately depicts the renal parenchymal and vascular anatomy in a format familiar to most surgeons. The data integrate essential information from angiography, venography, excretory urography and conventional 2-D CT into a single imaging modality, and can obviate the need for more invasive imaging. Additionally, the use of videotape in an intraoperative setting provides concise, accurate and immediate 3-D information to the surgeon, and it has become the preferred means of data display for these procedures at our center.

Adult↗
PubMed1987

Use of manpower data in an integrated database for program efficiency analysis: an example from a statewide community mental health system.

This article describes a method for systematically utilizing manpower data to analyze program efficiency of community mental health services. Examples of how analyses of performance data can be substantially enhanced by integrating manpower staffing data with other key financial, client, and service volume variables are provided.

Community Mental Health Services↗
PubMed2026

Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.

A broad spectrum of high-density genotyping approaches, including single-nucleotide polymorphism (SNP) arrays, genotyping-by-sequencing, and whole-genome reduced-representation sequencing, have been shown to perform well in strawberry (Fragaria × ananassa), despite the inherent complexity of the octoploid genome. While these approaches are effective, their routine deployment in breeding programs can be constrained by cost, computational requirements, and workflow complexity. In parallel, many breeding programs continue to rely on locus-specific assays for marker-assisted selection, resulting in fragmented and inefficient genotyping strategies. Here, we describe medium-density amplicon-based genotyping platforms for strawberry designed to provide cost-effective, turnkey solutions that integrate markers used for marker-assisted selection with genome-wide markers suitable for genomic prediction in a single laboratory assay. These platforms were developed by targeting 1,650 or 4,811 target SNPs via amplicon sequencing, and are interoperable with existing high-density genotyping resources, including a widely used 50K SNP array, thereby facilitating data integration across platforms. We benchmarked their performance relative to the 50K SNP array across breeding-relevant applications, including identity and purity testing, pedigree authentication, marker-assisted selection, and genomic selection, and further evaluated the feasibility of genotype imputation to enhance genome-wide information content. Across analyses, the 1,650- and 4,811-amplicon platforms produced results comparable to higher-density platforms while substantially reducing genotyping cost and analytical overhead. This work demonstrates that targeted amplicon-based genotyping can support efficient, scalable, and integrated genome-informed breeding, enabling the routine application of both marker-assisted and genomic selection within strawberry breeding workflows. Open-source R workflows are provided to support streamlined analyses in breeding contexts.

Fragaria↗
PubMed2001

Clinical trials integrity: a CRO perspective.

When contract research organizations (CROs) were first formed, pharmaceutical companies outsourced to them only certain aspects of the conduct of their clinical trials. At first CROs were highly specialized entities, providing, for example, either biostatistical advice, clinical research associates who monitored investigational sites for regulatory compliance, or regulatory support. Gradually, full service CROs emerged, offering a full range of services for clinical trials, including the selection of investigators and investigational sites, assistance with patient recruitment, safety surveillance and reporting, site audits, and data management and biostatistics. This evolving relationship between CROs and the pharmaceutical and medical device industries has resulted in CROs assuming more and more of the regulatory and ethical risks and responsibilities inherent in the conduct of clinical trials. In this full service role, CROs, unlike sponsors, are not interested in the outcome of study, but like sponsors, are subject to heavy regulation by the federal government, must follow applicable state laws, must respect international guidelines, and are obliged to follow their own operating procedures. Moreover, they are judged by the industry on the basis of the scope and quality of services provided, including the degree of adherence to the research protocol, regulatory requirements, and timelines; the quality of the professional working relationships with investigators and institutions, both academic and community-based; and the validity of the data. Further, CROs are subject to comprehensive audits by sponsoring companies, FDA, and other regulatory authorities. For all these reasons, CROs are being tasked with strict vigilance of all stages of the clinical trial process to ensure that the laws, regulations, and industry standards designed for the protection of human subjects and data integrity are maintained.

Advisory Committees↗