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PubMed2005

Exploring relationships and mining data with the UCSC Gene Sorter.

In parallel with the human genome sequencing and assembly effort, many tools have been developed to examine the structure and function of the human gene set. The University of California Santa Cruz (UCSC) Gene Sorter has been created as a gene-based counterpart to the chromosome-oriented UCSC Genome Browser to facilitate the study of gene function and evolution. This simple, but powerful tool provides a graphical display of related genes that can be sorted and filtered based on a variety of criteria. Genes may be ordered based on such characteristics as expression profiles, proximity in genome, shared Gene Ontology (GO) terms, and protein similarity. The display can be restricted to a gene set meeting a specific set of constraints by filtering on expression levels, gene name or ID, chromosomal position, and so on. The default set of information for each gene entry-gene name, selected expression data, a BLASTP E-value, genomic position, and a description-can be configured to include many other types of data, including expanded expression data, related accession numbers and IDs, orthologs in other species, GO terms, and much more. The Gene Sorter, a CGI-based Web application written in C with a MySQL database, is tightly integrated with the other applications in the UCSC Genome Browser suite. Available on a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set in interactive genomic exploration and analysis.

Computational Biology↗
PubMed2005

A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database.

A high-throughput proteomic approach was employed to determine the expression profile and identity of hundreds of proteins during seed filling in soybean (Glycine max) cv Maverick. Soybean seed proteins were analyzed at 2, 3, 4, 5, and 6 weeks after flowering using two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This led to the establishment of high-resolution proteome reference maps, expression profiles of 679 spots, and corresponding matrix-assisted laser desorption ionization time-of-flight mass spectrometry spectra for each spot. Database searching with these spectra resulted in the identification of 422 proteins representing 216 nonredundant proteins. These proteins were classified into 14 major functional categories. Proteins involved in metabolism, protein destination and storage, metabolite transport, and disease/defense were the most abundant. For each functional category, a composite expression profile is presented to gain insight into legume seed physiology and the general regulation of proteins associated with each functional class. Using this approach, an overall decrease in metabolism-related proteins versus an increase in proteins associated with destination and storage was observed during seed filling. The accumulation of unknown proteins, sucrose transport and cleavage enzymes, cysteine and methionine biosynthesis enzymes, 14-3-3-like proteins, lipoxygenases, storage proteins, and allergenic proteins during seed filling is also discussed. A user-intuitive database (http://oilseedproteomics.missouri.edu) was developed to access these data for soybean and other oilseeds currently being investigated.

Databases, Protein↗
PubMed2004

A wireless PDA-based physiological monitoring system for patient transport.

This paper proposes a mobile patient monitoring system, which integrates current personal digital assistant (PDA) technology and wireless local area network (WLAN) technology. At the patient's location, a wireless PDA-based monitor is used to acquire continuously the patient's vital signs, including heart rate, three-lead electrocardiography, and SpO2. Through the WLAN, the patient's biosignals can be transmitted in real-time to a remote central management unit, and authorized medical staffs can access the data and the case history of the patient, either by the central management unit or the wireless devices. A prototype of this system has been developed and implemented. The system has been evaluated by technical verification, clinical test, and user survey. The evaluation of performance yields a high degree of satisfaction (mean = 4.64, standard deviation--SD = 0.53 in a five-point Likert scale) of users who used the PDA-based system for intrahospital transport. The results also show that the wireless PDA model is superior to the currently used monitors both in mobility and in usability, and is, therefore, better suited to patient transport.

Adult↗
PubMed2003

The contribution of insurance coverage and community resources to reducing racial/ethnic disparities in access to care.

OBJECTIVE: To examine the extent to which health insurance coverage and available safety net resources reduced racial and ethnic disparities in access to care. DATA SOURCES: Nationally representative sample of 11,692 African American, 10,325 Hispanic, and 74,397 white persons. Nonelderly persons with public or private health insurance and those who were uninsured. STUDY DESIGN: Two cross-sectional surveys of households conducted during 1996-1997 and 1998-1999. DATA COLLECTION: Commonly used measures of access to and utilization of medical care were constructed for individuals. These measures include the following. (1) percent reporting unmet medical needs, (2) percent without a regular health care provider, and (3) no visit with a physician in the past year. FINDINGS: More than 6.5 percent of Hispanic and African Americans reported having unmet medical needs compared to less than 5.6 percent of white Americans. Hispanics were least likely to see the same doctor at their usual source of care (59 percent), compared to African Americans (66 percent) and whites (75 percent). Similarly, Hispanics were less likely than either African Americans or whites to have seen a doctor in the last year (65 percent compared to 76 percent or 79 percent). For Hispanics, more than 80 percent of the difference from whites was due to differences in measured characteristics (e.g., insurance coverage, income, and available safety net services). Differences in measured characteristics between African Americans and whites explained less than 80 percent of the access disparities. CONCLUSION: Lack of health insurance was the single most important factor in white-Hispanic differences for all three measures and for two of the white-African American differences. Income differences were the second most important factor, with one exception. Community characteristics generally were much less important, with one exception. The positive effects of insurance coverage in reducing disparities outweigh benefits of increasing physician charity care or access to emergency rooms.

Adult↗
PubMed1992

Patterns of alcohol consumption in white collar-workers--a cross-sectional and longitudinal study.

A 6-year follow-up of a cohort of male and female white collar workers in whom there was baseline information on alcohol consumption and access to data on sickness absence, promotion and labour turnover, revealed that even moderate alcohol and consumption in this population was associated with social costs for the employer and the employee, particularly in terms of sickness absence. The longitudinal examination of consumption in this study suggests that early intervention in a drinking career may reduce alcohol consumption and consequently avoid years of morbidity and sickness absence, as well as having a favourable influence on promotion prospects and labour turnover.

Adult↗
PubMed2005

Conducting ethnography in medical settings.

BACKGROUND: Ethnographic research methods have a considerable history of use in medical settings. This paper provides a personal account of conducting ethnography in medical environments and focuses on some of the practical and ethical issues encountered in such settings. DISCUSSION AND CONCLUSION: The paper describes particular issues that arise when undertaking ethnographic work, such as gaining access, recording data, research roles and researching elite groups, and recounts some of the dilemmas posed by doing this type of research in a medical setting. The paper concludes by reflecting on what ethnography might offer to medicine in return for the rich data medicine provides.

Anthropology, Cultural↗
PubMed1993

Subtypes of non-transformed human mammary epithelial cells cultured in vitro: histo-blood group antigen H type 2 defines basal cell-derived cells.

Normal (non-transformed) human mammary epithelial cell lines derived from reduction mammoplasties were analyzed by immunocytochemistry with more than 80 monoclonal antibodies (mAbs) and other specific reagents to tissue-specific and developmentally regulated antigens at different passage levels. A subpopulation of poorly differentiated, proliferating epithelial cells, corresponding to the 'selected' cell type of late passages, is shown to be characterized by a new marker, the histo-blood group antigen H type 2, probably carried on a membrane-bound glycolipid. These cells also express a number of other onco-developmental carbohydrate antigens [Le(y), Le(x), sialosyl-Le(a), precursor of Thomsen Friedenreich antigen (Tn), but not Thomsen-Friedenreich antigen and sialosyl-Tn]. Their cytokeratin (CK) phenotype, as assessed by reactivity with monospecific mAbs and two-dimensional gel electrophoresis, is CK 5, 6, 14 and 17, with CK 19 being consistently absent, and varying minor amounts of CK 7, 8 and 18, as well as 15 and 16. The reactivity of these cells with a panel of 11 mAbs specific for CK 18 varies considerably even after cloning, indicating heterogeneity of epitope expression or accessibility. Our data strongly suggest that the H type 2+ cells develop from the basal cell layer of the mammary gland.

Adult↗
PubMed1993

A sporulation gene in Coxiella burnetii?

During a search for conserved target sequences on the genome of Coxiella burnetii for a diagnostic PCR a NotI/EcoRV DNA fragment was cloned and sequenced from the isolate "Nine Mile", Phase I (sequence data are registered under accession number X70045 in data bases EMBL, GENEBANK and DDBJ). On this fragment we have found a sequence of 1741 base pairs which showed an exceptionally high homology (60% on the nucleic acid level and 49.6% on the amino acid level) to the sporulation gene "spoIIIE" of the gram-positive bacterium Bacillus subtilis. This is first evidence of the molecular basis for formation of spores in Coxiella burnetii which has been postulated in the literature by electron microscopic investigations.

Amino Acid Sequence↗
PubMed2005

Worldwide access to evidence-based mental health literature: how useful is PubMed in Anglo-Saxon and non-Anglo-Saxon countries?

The aim of this study was to verify the presence of cultural variety among the psychiatric journals available on PubMed, the major online tool for accessing literature. Data for analysis were taken from a survey of the world psychiatric journals indexed in Index Medicus 1999 (IM), the alphabetical list used by PubMed, and from the mean impact factor (IF) values of the journals. Approximately 80% of international psychiatric literature available on PubMed is published in Anglo-Saxon countries, especially in the USA (59.8% of the total). The widespread use of the English language (94.9% of all the journals) further stresses the dominance of the Anglo-Saxon cultural model, as do the mean IF values of Anglo-Saxon journals compared to non-Anglo-Saxon publications (3.252 vs. 1.693; P=0.0079). The under-representation of non-Anglo-Saxon cultural models on PubMed plays a negative role for bringing about a truly multicultural literature in psychiatry.

Culture↗
PubMed1997

Laparoscopic cholecystectomy: the missed diagnosis.

BACKGROUND: All 534 laparoscopic cholecystectomies performed by five surgeons at a single institution over a 3-year period were reviewed as part of a quality assurance process. The aim of the review, which has previously been published in this journal, was to identify and quantify complications of the procedure. Five cases in this series were recognized where major intra-abdominal pathology not identified at the time of laparoscopic cholecystectomy required laparotomy shortly thereafter. These five cases are reported here because there has been little discussion in the literature of this problem associated with laparoscopic cholecystectomy. METHODS: The records of all 534 patients having a laparoscopic cholecystectomy between October 1990 and September 1993 were reviewed and entered into a computer database (Microsoft Access). This data collection and recording have subsequently become an ongoing process of quality assurance. RESULTS: Five of 534 patients treated by laparoscopic cholecystectomy failed to have resolution of their symptoms postoperatively. A laparotomy was subsequently required within 3-12 months which demonstrated causative pathology present, but not detected at, the time of laparoscopic cholecystectomy. Where possible, treatment of these laparotomy findings resolved the initial presenting symptoms of colicky epigastric pain. CONCLUSIONS: The rate of 'missed diagnosis' is found to be < 1%. Laparoscopic cholecystectomy is a therapeutic, rather than diagnostic, procedure, and pre-operative discussion should include the possibility of further procedures being required subsequently, particularly when symptoms and signs are atypical.

Adult↗
PubMed2002

Institutional research responsibilities and needed infrastructure.

PURPOSE: To describe research grantee institutions' responsibilities to the funding agencies, research participants, and investigators, and the infrastructure and resources necessary for successful completion of funded research projects. ORGANIZING FRAMEWORK: Grants management includes investigator access to institutional and school infrastructure and resources, oversight and monitoring of the implementation of the research, and strategies to maximize research yield while stretching research dollars. CONCLUSIONS: Grantee institutions are responsible for overseeing the conduct of research, protecting rights of research participants, safety of study personnel, monitoring conflict of interest, fiscal management, access to data, and disseminating study findings. Central and school departments that provide needed services are important infrastructure supports. In addition to research space and investigator time, senior research mentors and research administrators are the most valuable resources for research success.

Ethics, Institutional↗
PubMed2006

Patient's delay in oral cancer: A systematic review.

Detecting oral cancer at an early stage is the most effective means of improving survival and reducing morbidity from this disease, yet a significant proportion of patients delay seeking help after the self-discovery of symptoms of oral cancer. The literature on factors associated with patient delay was searched systematically to access relevant data published between 1975 and 2005. Eight studies met the inclusion criteria for the review. In these studies, most clinical/tumour factors, sociodemographic variables, and patient health-related behaviours were not related to the duration of patient delay. Healthcare factors and psychosocial factors may play a role but the research in this area is sparse, atheoretical and of poor quality. Patient delay is a problem in oral cancer and yet at present the reasons for such delays are poorly understood and under-researched. Systematic, high-quality and theory-driven research in this area is urgently required.

Carcinoma, Squamous Cell↗
PubMed1988

Sexual aggression in the great apes.

Species-typical frequencies of copulation during the menstrual cycle differ among common chimpanzee, orang-utan, and gorilla, but all three species exhibit a midcycle enhancement associated with estrus. Thus, in the natural habitat, chimpanzees mate for 10-14 days, orang-utans for 5-6 days, and gorillas for 2-3 days. In traditional laboratory pair-tests, however, conducted in a single cage with both animals freely accessible to each other, all three species of great apes copulate more frequently than the species-typical pattern. In all three species, moreover, the increased copulation appears to result from increased male sexual initiative (aggression), male dominance over females, and the inability of the female to avoid or escape from the male within the limited spatial conditions of the free-access test. This interpretation is supported by studies using restricted-access tests in which females control sexual access. These data suggest that male sexual aggression in our closest biological affiliates commonly occurs when females are rendered vulnerable to the male by the absence of the normal social constraints and spatial prerogatives typical of the natural habitat. The possible implications of this interpretation for a biological perspective on human sexual aggression are considered.

Aggression↗
PubMed1992

DecisionNET: database/network support for clinical decision analysts.

DecisionNET is a proposed remote database/wide-area computer network that should cultivate quantitative approaches to medicine by providing rapid access to medical facts, literature citations, decision models, and commentary of specific use to those involved with quantitative clinical decision making. Increasing accessibility to data and providing a forum for exchange of ideas should prove to be a significant asset to clinicians, either as modelers or as clients. Further work will address specific database implementation, development of a query engine, and coordination of the communications infrastructure. DecisionNET provides a unique model for the growth and maintenance of other medical knowledge bases.

Archives↗
PubMed2025

The Mycobacterium tuberculosis Transposon Sequencing Database (MtbTnDB): A Large-Scale Guide to Genetic Conditional Essentiality.

Characterizing genetic essentiality across various conditions is fundamental for understanding gene function. Transposon sequencing (TnSeq) is a powerful technique to generate genome-wide essentiality profiles in bacteria and has been extensively applied to Mycobacterium tuberculosis (Mtb). Dozens of TnSeq screens have yielded valuable insights into the biology of Mtb in&#xa0;vitro, inside macrophages, and in model host organisms. Despite their value, these Mtb TnSeq profiles have not been standardized or collated into a single, easily searchable database. This results in significant challenges when attempting to query and compare these resources, limiting our ability to obtain a comprehensive and consistent understanding of genetic conditional essentiality in Mtb. We address this problem by building a central repository of publicly available Mtb TnSeq screens, the Mtb transposon sequencing database (MtbTnDB). The MtbTnDB is a living resource that encompasses to date &#x2248;150 standardized TnSeq screens, enabling open access to data, visualizations, and functional predictions through an interactive web app (www.mtbtndb.app). We conduct several statistical analyses on the complete database, such as demonstrating that (i) genes in the same genomic neighborhood have similar TnSeq profiles, and (ii) clusters of genes with similar TnSeq profiles are enriched for genes from similar functional categories. We further analyze the performance of machine learning models trained on TnSeq profiles to predict the functional annotation of orphan genes in Mtb. By facilitating the comparison of TnSeq screens across conditions, the MtbTnDB will accelerate the exploration of conditional genetic essentiality, provide insights into the functional organization of Mtb genes, and help predict gene function in this important human pathogen.

DNA Transposable Elements↗
PubMed2004

Adaptive algebraic reconstruction technique.

Algebraic reconstruction techniques (ART) are iterative procedures for reconstructing objects from their projections. It is proven that ART can be computationally efficient by carefully arranging the order in which the collected data are accessed during the reconstruction procedure and adaptively adjusting the relaxation parameters. In this paper, an adaptive algebraic reconstruction technique (AART), which adopts the same projection access scheme in multilevel scheme algebraic reconstruction technique (MLS-ART), is proposed. By introducing adaptive adjustment of the relaxation parameters during the reconstruction procedure, one-iteration AART can produce reconstructions with better quality, in comparison with one-iteration MLS-ART. Furthermore, AART outperforms MLS-ART with improved computational efficiency.

Algorithms↗
PubMed2004

Automatic real-time surveillance of eye position and gating for stereotactic radiotherapy of uveal melanoma.

A new prototype (hardware and software) for monitoring eye movements using a noninvasive technique for gated linac-based stereotactic radiotherapy (SRT) of uveal melanoma was developed. The prototype was tested within the scope of a study for 11 patients. Eye immobilization was achieved by having the patient fixate a light source integrated into the system. The system is used in conjunction with a Head&Neck mask system for immobilization, and uses infrared tracking technology for positioning (both BrainLAB AG Heimstetten/Germany). It was used during CT and MR image acquisition as well as during all of five treatment fractions (6 MeV, 5 x 12 Gy to 80% isodose) to guarantee identical patient setup and eye rotational state during treatment planning and treatment delivery. Maximum temporal and angular deviations tolerated during treatment delivery can be chosen by the physician, the radiation then being interrupted automatically and instantaneously if those criteria are being exceeded during irradiation. A graphical user interface displays life video images of the treated eye and information about the current and previous rotational deviation of the eye from its reference treatment position. The physician thus has online access to data directly linked to the success of the treatment and possible side effects. Mean angular deviations during CT/MR scans and treatment deliveries ranged from 1.61 degrees to 3.64 degrees (standard deviations 0.87 degrees to 2.09 degrees ) which is in accordance with precision requirements for SRT. Typical situations when preset deviation criteria were exceeded are slow drifts (fatigue), sudden large eye movements (irritation), or if patients closed their eyes (fatigue). In these cases radiation was reliably interrupted by the gating system. In our clinical setup the novel system for computer-controlled eye movement gated treatments was well tolerated by all patients. The system yields quantitative real-time information about the eye's rotational state with respect to a reference position (treatment planning situation). Together with the possibility of performing movement-gated treatments of uveal melanoma, the system thus greatly improves the quality of this treatment.

Eye↗
PubMed2003

Preserving the tree of life.

Phylogenies provide new ways to measure biodiversity, to assess conservation priorities, and to quantify the evolutionary history in any set of species. Methodological problems and a lack of knowledge about most species have so far hampered their use. In the future, as techniques improve and more data become accessible, we will have an expanded set of conservation options, including ways to prioritize outcomes from evolutionary and ecological processes.

Animals↗