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PubMed2001

EMR to the rescue. An ambulatory care pilot project shows that data sharing equals cost shaving.

PROBLEM: Inefficiencies in managing office practices and costs. SOLUTION: Installation of an EMR in ambulatory practices to integrate clinical data from patient visits and use it to improve efficiencies "downstream". RESULTS: Marked reduction in costs of ambulatory practice management and major improvements in revenue capture, improved patient satisfaction. KEYS TO SUCCESS: Analysis of workflow, documentation of progress with benchmarking.

Academic Medical Centers↗
PubMed1996

A multimedia perioperative record keeper for clinical research.

OBJECTIVE: To develop a multimedia perioperative recordkeeper that provides: 1. synchronous, real-time acquisition of multimedia data, 2. on-line access to the patient's chart data, and 3. advanced data analysis capabilities through integrated, multimedia database and analysis applications. DESIGN: To minimize cost and development time, the system design utilized industry standard hardware components and graphical. software development tools. The system was configured to use a Pentium PC complemented with a variety of hardware interfaces to external data sources. These sources included physiologic monitors with data in digital, analog, video, and audio as well as paper-based formats. DEVELOPMENT: The development process was guided by trials in over 80 clinical cases and by the critiques from numerous users. As a result of this process, a suite of custom software applications were created to meet the design goals. The Perioperative Data Acquisition application manages data collection from a variety of physiological monitors. The Charter application provides for rapid creation of an electronic medical record from the patient's paper-based chart and investigator's notes. The Multimedia Medical Database application provides a relational database for the organization and management of multimedia data. The Triscreen application provides an integrated data analysis environment with simultaneous, full-motion data display. CONCLUSION: With recent technological advances in PC power, data acquisition hardware, and software development tools, the clinical researcher now has the ability to collect and examine a more complete perioperative record. It is hoped that the description of the MPR and its development process will assist and encourage others to advance these tools for perioperative research.

Database Management Systems↗
PubMed2005

Intraoperative landmarking of vascular anatomy by integration of duplex and Doppler ultrasonography in image-guided surgery. Technical note.

BACKGROUND: The integration of ultrasound technology into neuronavigation systems has recently been the subject of reports by several groups. This article describes our preliminary findings with regard to the integration of data derived from intraoperative duplex (color mode) and Doppler ultrasonography into a neuronavigational data set. It was the aim of the study to investigate (1) whether the intraoperative landmarking of vessels that are outlined with ultrasound technology is possible and (2) whether such a technique might be of clinical interest for neurosurgical interventions. METHODS: The video image of an ultrasound plane (Toshiba, Powervision 6000 SSA-370A, Tokyo, Japan) was integrated into our neuronavigation system (VectorVision2, BrainLab, Heimstetten, Germany). For calibration of the ultrasound plane, an instrument adapter was fixed to the ultrasound probe and then calibrated using a special, predefined calibration phantom. RESULTS: Accordingly, the system supported a combination of the ultrasound plane functionality with the preoperatively acquired neuronavigational data. The duplex and Doppler mode of the ultrasound system displayed the intraoperative vascular anatomy. Once a vessel was outlined during surgery, it could be landmarked by touching the navigation screen. These landmarks were integrated automatically into the neuronavigational data set and could be used to provide intraoperative image updates of the vascular anatomy. This technique was successful in 45 of 47 (95.7%) surgical interventions. CONCLUSIONS: Both image-guided ultrasound and duplex-guided integration of vascular anatomy into the neuronavigational data set are technically possible. In the future, this technology may provide useful intraoperative information during surgery of complex cerebral pathologies.

Blood Vessels↗
PubMed1996

A high resolution CEPH crossover mapping panel and integrated map of chromosome 11.

High resolution (0.1 cM) CEPH crossover mapping panels were constructed for chromosome 11. These panels will facilitate a transition from top-down physical and genetic mapping strategies to integrated breakpoint mapping strategies. Novel methods, which differ from other methods in overcoming the limitations of incomplete heterozygosity and variable marker density, were developed for creating the panels and integrated maps. This made it possible to identify and sublocalize the majority of crossovers in 61 families. The panels were used to map 139 microsatellite markers. A semi-integrated map and a fully-integrated map were constructed by combining these data with data from CEPH 7.1 and then integrating data from the radiation hybrid (RH) map. Genetic lengths estimated from the mapping panels were similar to the estimates obtained when all recombinant and non-recombinant offspring were included (189.4 cM in females and 126.1 cM in males), indicating that genetic distances are stable at this high marker density. The maps have a cM density of 0.62. The distance between ordered markers is 1.39-2.92 cM depending on the criterion for order and the extent of map integration. The 2D maps provide the resolution and flexibility needed to enhance current applications such as positional cloning and mapping complex disorders; while the mapping panels will greatly improve the resolution, reliability and efficiency of future genetic mapping.

Chromosome Mapping↗
PubMed2000

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group.

The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www. informatics.jax.org). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional information about the laboratory mouse. MGD scientists and annotators work cooperatively with the research community to provide an integrated, consensus view of the mouse genome while also providing experimental data including data conflicting with the consensus representation. Recent improvements focus on the representation of phenotypic information and the enhancement of gene and allele descriptions.

Animals↗
PubMed2006

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data.

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15N-T1 and -T2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15N-T1, -T2, and {1H}-15N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.

Anisotropy↗
PubMed2006

Integral-based identification of patient specific parameters for a minimal cardiac model.

A minimal cardiac model has been developed which accurately captures the essential dynamics of the cardiovascular system (CVS). However, identifying patient specific parameters with the limited measurements often available, hinders the clinical application of the model for diagnosis and therapy selection. This paper presents an integral-based parameter identification method for fast, accurate identification of patient specific parameters using limited measured data. The integral method turns a previously non-linear and non-convex optimization problem into a linear and convex identification problem. The model includes ventricular interaction and physiological valve dynamics. A healthy human state and four disease states, valvular stenosis, pulmonary embolism, cardiogenic shock and septic shock are used to test the method. Parameters for the healthy and disease states are accurately identified using only discretized flows into and out of the two cardiac chambers, the minimum and maximum volumes of the left and right ventricles, and the pressure waveforms through the aorta and pulmonary artery. These input values can be readily obtained non-invasively using echo-cardiography and ultra-sound, or invasively via catheters that are often used in Intensive Care. The method enables rapid identification of model parameters to match a particular patient condition in clinical real time (3-5 min) to within a mean value of 4-10% in the presence of 5-15% uniformly distributed measurement noise. The specific changes made to simulate each disease state are correctly identified in each case to within 10% without false identification of any other patient specific parameters. Clinically, the resulting patient specific model can then be used to assist medical staff in understanding, diagnosis and treatment selection.

Algorithms↗
PubMed2003

A task framework for the web interface W2H.

SUMMARY: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta-data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user. AVAILABILITY: Within the HUSAR environment at DKFZ http://genome.dkfz-heidelberg.de/

Database Management Systems↗
PubMed2005

Evaluation of a classroom program of creative expression workshops for refugee and immigrant children.

OBJECTIVE: This evaluative study assessed the effect of a creative expression program designed to prevent emotional and behavioral problems and to enhance self-esteem in immigrant and refugee children attending multiethnic schools. METHOD: The 12-week program involved 138 children, aged 7 to 13, registered in both integration classes designed for immigrant children and regular classes at two elementary schools. Pretest and posttest data were collected from the children themselves and from their teacher. Teachers used Achenbach's Teacher's Report Form to assess the emotional and behavioral symptoms of their pupils whereas children self-reported their symptoms with the Dominic, a computerized questionnaire. Self-esteem was measured with the Piers-Harris Self-Concept Scale administered by interviewers to the children. RESULTS: At the end of the program, the children in the experimental groups reported lower mean levels of internalizing and externalizing symptoms and higher mean levels of feelings of popularity and satisfaction than the children in the control groups, when controlling for baseline data. In integration classes, the effect on self-esteem was especially notable in boys. The intervention's effect on internalizing and externalizing symptoms was not modified by gender, age or fluency in the mainstream language. CONCLUSION: The study provides some evidence that creative workshops in the classroom can have a beneficial effect on the self-esteem and symptomatology of immigrant and refugee children from various cultures and backgrounds. These quantitative results support previous qualitative analysis showing that the workshops participate in the reconstruction of a meaningful personal world while simultaneously strengthening the link of the child to the group. They also transform the teachers' perceptions of newcomers by placing an emphasis on their strength and their resilience, while not negating their vulnerabilities.

Adaptation, Psychological↗
PubMed2002

DNA-PK and ATM are required for radiation-enhanced integration.

Ionizing radiation is known to improve transfection of exogenous DNA, a process we have termed radiation-enhanced integration. Previous observations have demonstrated that Ku proteins are critical for radiation-enhanced integration. Since Ku proteins form the DNA-binding domain of DNA-PK and since DNA-PK is important in nonhomologous DNA end joining, it was hypothesized that DNA-PK function might be important for radiation-enhanced integration. The ATM protein has been shown to be important in the recognition of a variety of types of DNA damage and to associate with DNA-PK under certain conditions. It was thus hypothesized that ATM might also play a role in radiation-enhanced integration. To test these hypotheses, radiation-enhanced integration was measured in hamster cells that are defective in the catalytic subunit of DNA-PK and in human cells containing mutant ATM. Radiation-enhanced integration was not detected in any of the cell lines with mutant PRKDC (also known as DNA-PKcs), but it was present in cells of the same lineage with wild-type PRKDC. Radiation-enhanced integration was defective in cells lacking kinase activation. ATM-deficient cell lines also showed defective radiation-enhanced integration. These data demonstrate that DNA-PK and ATM must both be active for radiation-enhanced integration to be observed.

Animals↗
PubMed2004

Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.

Diverse datasets including genomic, proteomic, isotopomer, and DNA sequence variation are becoming available for human mitochondria. Thus there is a need to integrate these data within an in silico modeling framework where mitochondrial biology and related disorders can be studied and analyzed. This paper reports a reconstruction and characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. The 189 reactions included in this reconstruction are both elementally and charge-balanced and are assigned to their respective cellular compartments (mitochondrial, cytosol, or extracellular). The capabilities of the reconstructed network to fulfill three metabolic functions (ATP production, heme synthesis, and mixed phospholipid synthesis) were determined. Network-based analysis of the mitochondrial energy conversion process showed that the overall ATP yield per glucose is 31.5. Network flexibility, characterized by allowable variation in reaction fluxes, was evaluated using flux variability analysis and analysis of all of the possible optimal flux distributions. Results showed that the network has high flexibility for the biosynthesis of heme and phospholipids but modest flexibility for maximal ATP production. A subset of all of the optimal network flux distributions, computed with respect to the three metabolic functions individually, was found to be highly correlated, suggesting that this set may contain physiological meaningful fluxes. Examinations of optimal flux distributions also identified correlated reaction sets that form functional modules in the network.

Amino Acids↗
PubMed2003

ARAMEMNON, a novel database for Arabidopsis integral membrane proteins.

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

Amino Acid Transport Systems↗
PubMed2004

Integration of clinical and imaging data to predict the presence of coronary artery disease with the use of neural networks.

AIM: To establish proof of the principle that a computer-based neural network method can be employed that will enhance diagnostic accuracy vis-a-vis image analysis alone in the interpretation of treadmill exercise tests performed in conjunction with myocardial perfusion imaging. MATERIALS AND METHODS: One-hundred-and-two patients underwent myocardial perfusion imaging in association with the standard Bruce protocol. Twenty objective parameters describing each patient's exercise physiology, general clinical status and image appearance were used to train an artificial neural network. Classification accuracy of the neural network and clinical interpretation was determined by coronary angiography. We evaluated the ability of the neural network to integrate clinical, exercise and imaging data to determine the likelihood of coronary artery disease and compared these results with an optimized method of clinical image interpretation, which made use of all available clinical, angiographic and stress test data. RESULTS: The artificial neural network had a sensitivity of 88% and a specificity of 65% for detection of ischemic heart disease and was comparable to that of the optimized clinical method (sensitivity 80%, specificity 69%). Incorporation of clinical and exercise data significantly improved the predictive accuracy of the network compared to a network based on image data alone (P<0.05). CONCLUSION: The results show a computer-based neural network can perform as well as expert readers working under optimal conditions including full knowledge of the patient's clinical, prior angiographic and stress test data. Thus, the method is promising as a diagnostic aid to the recognition of ischemic heart disease in the clinical setting of treadmill exercise testing in conjunction with myocardial perfusion imaging.

Aged↗
PubMed2005

Communicating for a clinical purpose: strategy in interaction in healthcare consultations.

Many studies of communication employ interviewing techniques and conversation analysis, particularly in situations where one participant brings specialist resources. Interviews and recorded interactions are usually handled separately: ethnographic data are introduced once conversation analysis is complete, to validate findings or illustrate their wider significance. However, integrating interview data in conversation analysis has the potential to illuminate analysts' interpretations, and to enhance professionals' contributions from analysis through to dissemination. In this study, interviews highlighted a parameter between professionals who actively used communication to manipulate the consultation's course, engaging patients at particular points and in particular ways, and professionals whose consultation management was more 'clinical' and less dependent on interaction. The different ways professionals talked in interview were paralleled by differences identified from conversation analysis of consultations. For some, 'clinical' orientation was more prevalent in the organization of their consultations than 'active' manipulation of communication, and their management of the consultation more 'unilateral'. For others, communication played a more strategic and integral part in clinical practice, and their management of the consultation was more 'bilateral'. These contrasts in professionals' descriptions of their consultation management suggest that at least some features of a 'bilateral' approach are consciously employed and may be teachable.

Anthropology, Cultural↗
PubMed2005

Biochemical clustering of monomeric GTPases of the Ras superfamily.

To date phylogeny has been used to compare entire families of proteins based on their nucleotide or amino acid sequence. Here we developed a novel analytical platform allowing a systematic comparison of protein families based on their biochemical properties. This approach was validated on the Rho subfamily of GTPases. We used two high throughput methods, referred to as AlphaScreen and FlashPlate, to measure nucleotide binding capacity, exchange, and hydrolysis activities of small monomeric GTPases. These two technologies have the characteristics to be very sensitive and to allow homogenous and high throughput assays. To analyze and integrate the data obtained, we developed an algorithm that allows the classification of GTPases according to their enzymatic activities. Integration and hierarchical clustering of these results revealed unexpected features of the small Rho GTPases when compared with primary sequence-based trees. Hence we propose a novel phylobiochemical classification of the Ras superfamily of GTPases.

Algorithms↗
PubMed2025

A decentralized future for the open-science databases.

The continuous and reliable open access to curated biological data repositories is indispensable for accelerating rigorous scientific inquiry and fostering reproducible research outcomes. However, the current paradigm, which relies heavily on centralized infrastructure for the storage and distribution of foundational biomedical datasets, inherently introduces significant vulnerabilities. This centralized model is susceptible to single points of failure, including cyberattacks, technical malfunctions, natural disasters, and even political or funding uncertainties. Such disruptions can lead to widespread data unavailability, data loss, integrity compromises, and substantial delays in critical research, ultimately impeding scientific progress. The downstream effect of such interruptions can be the widespread paralysis of diverse research activities, including computational, clinical, molecular, and climate studies. This scenario vividly illustrates the inherent dangers of consolidating essential scientific resources within a single geopolitical or institutional locus. As data generation is accelerating and the global landscape continues to fluctuate, the sustainability of centralized models must be critically re-evaluated. A shift toward federated and decentralized architectures may offer a robust and forward-looking approach to enhancing the resilience of scientific data infrastructures by reducing exposure to governance instability, infrastructural fragility, and funding volatility, while also promoting equity and global accessibility. Inspired by established models such as ELIXIR's federated infrastructure and the policy and funding frameworks developed by CODATA and the Global Biodata Coalition (GBC), emerging Decentralized Science (DeSci) initiatives can contribute to building more resilient, fair, and incentive-aligned data ecosystems. The future of open science depends on integrating these complementary approaches to establish a globally distributed, economically sustainable, and institutionally robust infrastructure that safeguards scientific data as a public good, further ensuring continued accessibility, interoperability, and preservation for generations to come. Here, we examine the structural limitations of centralized repositories, evaluate federated and decentralized models, and propose a hybrid framework for resilient, fair, and sustainable scientific data stewardship.

data accessibility↗
PubMed2005

Mercury in northeastern North America: a synthesis of existing databases.

A large number of datasets representing mercury (Hg) levels in northeastern North America were assembled in a standardized format between 2000 and 2003. Based on support from the Northeastern States Research Cooperative, scientists annually gathered and developed an operational template to collaboratively analyze and interpret these data for a series of peer-reviewed publications. The diverse group covered Hg policy connections, Hg in air, sediment and surface water, Hg in biota, and Hg collection, assessment and monitoring tools. A site-specific application of these Hg data is provided to demonstrate the importance of well-placed air monitoring stations, the need for integrative multimedia data sets, and the complexity of linking abiotic and biotic Hg compartments. Demonstrated is the ubiquitous nature of Hg and methylmercury availability and how its heterogeneous distribution is now relatively well understood for northeastern North America.

Animals↗