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PubMed2006

Visualisation and interaction design solutions to address specific demands in shared home care.

UNLABELLED: When care professionals from different organisations are involved in patient care, their different views on the care process may not be meaningfully integrated. OBJECTIVE: To use visualisation and interaction design solutions addressing the specific demands of shared care in order to support a collaborative work process. METHODS: Participatory design, comprising interdisciplinary seminar series with real users and iterative prototyping, was applied. RESULTS: A set of interaction and visualisation design solutions to address care professionals' requirements in shared home care is presented, introducing support for identifying origin of information, holistic presentation of information, user group specific visualisation, avoiding cognitive overload, coordination of work and planning, and quick overviews. The design solutions are implemented in an integrated virtual health record system supporting cooperation and coordination in shared home care for the elderly. The described requirements are, however, generalized to comprise all shared care work. CONCLUSION: The presented design considerations allow healthcare professionals in different organizations to share patient data on mobile devices. Visualization and interaction design facilitates specific work situations and assists in handling specific demands in shared care. The user interface is adapted to different user groups with similar yet distinct needs. Consequently different views supporting cooperative work and presenting shared information in holistic overviews are developed.

Delivery of Health Care, Integrated↗
PubMed2005

Multiple locus linkage analysis of genomewide expression in yeast.

With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of transcriptional regulation and protein abundance are likely to be complex, meaning that genetic variation at multiple loci will influence these phenotypes. Several recent studies have investigated the role of genetic variation in transcription by applying traditional linkage analysis methods to genomewide expression data, where each gene expression level was treated as a quantitative trait and analyzed separately from one another. Here, we develop a new, computationally efficient method for simultaneously mapping multiple gene expression quantitative trait loci that directly uses all of the available data. Information shared across gene expression traits is captured in a way that makes minimal assumptions about the statistical properties of the data. The method produces easy-to-interpret measures of statistical significance for both individual loci and the overall joint significance of multiple loci selected for a given expression trait. We apply the new method to a cross between two strains of the budding yeast Saccharomyces cerevisiae, and estimate that at least 37% of all gene expression traits show two simultaneous linkages, where we have allowed for epistatic interactions. Pairs of jointly linking quantitative trait loci are identified with high confidence for 170 gene expression traits, where it is expected that both loci are true positives for at least 153 traits. In addition, we are able to show that epistatic interactions contribute to gene expression variation for at least 14% of all traits. We compare the proposed approach to an exhaustive two-dimensional scan over all pairs of loci. Surprisingly, we demonstrate that an exhaustive two-dimensional scan is less powerful than the sequential search used here. In addition, we show that a two-dimensional scan does not truly allow one to test for simultaneous linkage, and the statistical significance measured from this existing method cannot be interpreted among many traits.

Chromosome Mapping↗
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↗
PubMed2002

Cervical biopsy/cytology correlation data can be collected prospectively and shared clinically.

Cervical cytology (Cy) and biopsy (Bx) correlation is used by institutions for the evaluation of their cytodiagnostic capabilities as a part of overall laboratory quality improvement (QI). However, the data obtained from correlation are not routinely included in most surgical pathology (SP) reports. Our laboratory's procedure is to include the correlation of the patient's previous (most recent) cytology smear in the surgical pathology report of all/any gynecologic surgical pathology specimens. We reviewed this process for the time period between July 1998-June 1999. Any noncorrelating cases were assigned a correlation review code by the reviewing cytopathologist: major Cy diagnostic error (DE1), minor Cy diagnostic error (DE2), Cy sampling error (Cy SE), or biopsy sampling error (Bx SE). Of 3,486 cases reviewed, 3,229 cases were satisfactory for correlation studies. Concordant results were found in 86.9%. Cy DE1 due to either Cy screening or interpretation errors or both were found in 0.2% (n = 7) of all cases, while Cy DE2 due to the same were found in 1% (n = 32). Bx SE accounted for discrepancies in 6.8% (n = 220) of all cases, while 5.1% (n = 164) of the total cases were discrepancies due to Cy SE. Follow-up Bx was available in 97.2% (n = 214) of the Bx SE, and showed 16.4% (n = 35) to be major discrepancies and 83.6% (n = 179) to be minor discrepancies. Cervical Cy/Bx correlation is useful for the evaluation of a laboratory's QI. It is also useful for the identification of either Cy or Bx SE. While QI data exist as "internal use only" documents, SE data (as part of the CC (correlation comment) included in SP reports) are vital to a specific/given patient. Bx SE was identified in 6.3% of our patients, indicating a possible need for rebiopsy. This type of QI data may be shared clinically, and may direct the management for maximum diagnostic and patient benefit.

Biopsy↗
PubMed2006

Privacy protection in HealthGrid: distributing encryption management over the VO.

Grid technologies have proven to be very successful in tackling challenging problems in which data access and processing is a bottleneck. Notwithstanding the benefits that Grid technologies could have in Health applications, privacy leakages of current DataGrid technologies due to the sharing of data in VOs and the use of remote resources, compromise its widespreading. Privacy control for Grid technology has become a key requirement for the adoption of Grids in the Healthcare sector. Encrypted storage of confidential data effectively reduces the risk of disclosure. A self-enforcing scheme for encrypted data storage can be achieved by combining Grid security systems with distributed key management and classical cryptography techniques. Virtual Organizations, as the main unit of user management in Grid, can provide a way to organize key sharing, access control lists and secure encryption management. This paper provides programming models and discusses the value, costs and behavior of such a system implemented on top of one of the latest Grid middlewares. This work is partially funded by the Spanish Ministry of Science and Technology in the frame of the project Investigación y Desarrollo de Servicios GRID: Aplicación a Modelos Cliente-Servidor, Colaborativos y de Alta Productividad, with reference TIC2003-01318.

Databases as Topic↗
PubMed2004

Measuring effectiveness of drugs in observational databanks: promises and perils.

Observational databanks have inherent strengths and shortcomings. As in randomized controlled trials, poor design of these databanks can either exaggerate or reduce estimates of drug effectiveness and can limit generalizability. This commentary highlights selected aspects of study design, data collection and statistical analysis that can help overcome many of these inadequacies. An international metaRegister and a formal mechanism for standardizing and sharing drug data could help improve the utility of databanks. Medical journals have a vital role in enforcing a quality checklist that improves reporting.

Antirheumatic Agents↗
PubMed1993

Hydra: a C-language environment for real-time DOS multitasking at the bedside.

Patient monitoring at the bedside is an inherently parallel job, best handled by multiple individual tasks running concurrently. Cost and diffusion considerations strongly favor the use of PC's at the bedside, but their most widespread operating system, DOS, is not built for multitasking. Hence, a software platform in C language has been prepared, allowing the intermediate programmer to easily write independent modules which will then run simultaneously without conflicts. Such a platform aims at allowing effortless sharing of data among concurrently running processes, while providing strong insulation between tasks, enough to allow multiple copies of any one task to run simultaneously unknown to each other. A cooperative, memory sharing multitasking paradigm has been chosen, which offers fine granularity of timeslicing and low execution overhead at the price of some loss in generality of design. Speed, data exchange capability and number of stackable windows are greater than with commercial packages like Windows or LabWindows. Dynamical reprioritization of tasks is built in, allowing the computerized monitor to focus its attention and resources on urgent tasks.

Algorithms↗
PubMed1995

Predicted disulfide-bonded structures for three uniquely related proteins of Plasmodium falciparum, Pfs230, Pfs48/45 and Pf12.

Pfs230 is a surface protein of the gametes of Plasmodium falciparum and has been demonstrated to be a target of malaria transmission-blocking antibodies; it is an important candidate antigen for a transmission-blocking vaccine. The target epitopes of transmission-blocking antibodies against Pfs230 are almost all reduction sensitive suggesting that disulfide bonds are critical for folding the native molecule. Following the cloning of the Pfs230 gene attempts are now underway to express subunits of the protein for use in vaccine trials. It will be important to understand the disulfide-bond structure of the Pfs230 to achieve this goal. In this paper we present a model for this structure based on the observation that the Pfs230 molecule contains a series of regularly repeated cysteine-containing motifs. Four such motifs have been identified, together with a fifth cysteineless motif, which occur in the same relative order, with regular alternating omission of specific motifs, 14 times throughout the length of the protein. Each of the 14 sets of motifs contains an even number of cysteine residues (2, 4 or 6). We postulate that each set folds into a separate disulfide-bonded domain in which corresponding pairs of cysteines form an equivalent disulfide bond in every such domain. The postulated bonding arrangements in the different domains are mutually confirmatory throughout the sequence of Pfs230. We have identified two other malaria proteins, Pfs48/45 and Pf12, which share the same arrangements of motifs and conform to the same disulfide-bond structure proposed for Pfs230; no other proteins in the sequence data base share these characteristics.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Establishing mechanisms to conduct multi-institutional research--fatigue in patients with cancer: an exercise intervention.

PURPOSES/OBJECTIVES: To describe the process of establishing a multi-institutional interdisciplinary team of oncology researchers and conducting a pilot study of an exercise intervention for fatigue. DATA SOURCES: Project meeting minutes and records, research team members' logs, subjects' research records, the research study proposal, and team members' individual and collective shared experiences. DATA SYNTHESIS: Site investigators established research teams at five academic medical centers. Fifty subjects were enrolled in the study and tested during their cancer treatment. Study methods, including instrumentation, were evaluated carefully and revised. CONCLUSIONS: The multi-institutional network of researchers is an effective and efficient model for testing an intervention to manage fatigue during cancer treatment. IMPLICATIONS FOR NURSING PRACTICE: Exercise is a feasible and potentially beneficial intervention to combat distressing cancer treatment-related fatigue. A pilot study is essential to determine the best methods for conducting a clinical trial and to develop the teams of researchers necessary for such a project.

Exercise Therapy↗
PubMed2003

Which comes first: employee attitudes or organizational financial and market performance?

Employee attitude data from 35 companies over 8 years were analyzed at the organizational level of analysis against financial (return on assets; ROA) and market performance (earnings per share: EPS) data using lagged analyses permitting exploration of priority in likely causal ordering. Analyses revealed statistically significant and stable relationships across various time lags for 3 of 7 scales. Overall Job Satisfaction and Satisfaction With Security were predicted by ROA and EPS more strongly than the reverse (although some of the reverse relationships were also significant); Satisfaction With Pay suggested a more reciprocal relationship with ROA and EPS. The discussion of results provides a preliminary framework for understanding issues surrounding employee attitudes, high-performance work practices, and organizational financial and market performance.

Attitude↗
PubMed2006

TRDB--the Tandem Repeats Database.

Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench. It provides user storage space and permits collaborators to privately share their data and analysis. TRDB is available at https://tandem.bu.edu/cgi-bin/trdb/trdb.exe.

Animals↗
PubMed1998

Collaborative workspace for multimedia medical conferencing.

We propose an approach for collaborative workspace management in medical conferencing. A collaborative workspace is a virtual data space shared between medical experts for working out solutions collaboratively while conferencing. Our approach provides medical users with an integrated view of various kinds of multimedia patient data and a unified control over the workspace. For data navigation and conferencing, a tree-like navigation tool, which we named the patient record tree, is provided. And we classify patient data, which is the object of medical collaborative works, into six basic types, and provide a view template for displaying each of these types.

Cooperative Behavior↗
PubMed2000

Regional and international integrated telemedicine network for organ transplant (HC 4028 & IN 4028 European Commission DGXIII).

A substantial portion of future medical practice will depend greatly on improved collaboration between the providers throughout the healthcare sector, and effective sharing of data and expertise by different healthcare professionals. In organ transplant it is a rule, donor organs are matched to recipients via national or multinational organ-sharing organizations. Only through close co-operation between transplant surgeons, immunologists, nephrologists, pathologists, radiologists and other physicians could one increase the efficiency of organ transplantation. Information technology (IT) has become an inevitable and inherent part of transplantation medicine. The RETRANSPLANT project interfaces and integrates IT from the European Union Fourth Framework projects to support the development of regional organ transplant information networks in Central Europe.

Bone Marrow Transplantation↗
PubMed2000

Information and communication technology needs for distributed communication and coordination during expedition-class spaceflight.

AO-lU. Expedition-class missions are distinct from historical human presence in space in ways that significantly affect information flow and information technology designs for such missions. The centrality of Mission Control in these missions is challenged by the distances, associated communication delays, and durations of expeditions, all of which require crews to have more local resources available to manage on-board situations. The author's current research investigates how ground controllers effectively allocate communications bandwidth, cognitive resources, and knowledge sharing skills during time critical routine and non-routine situations. The research focus is on team-based information and communication technology (ICT) use to provide recommendations for improvements to support adaptive bandwidth allocations and improved sharing of data and knowledge in Mission Control contexts. In order to further improve communication and coordination between controllers and crew, additional ICT support resources will be needed to provide shared context knowledge and dynamic assessment of costs and benefits for accessing local information vs. remote expertise. Crew members will have critical needs to understand the goals, intentions, and situational constraints associated with mission information resources in order to use them most effectively in conditions where ground-based expertise is insufficient or requires more time to access and coordinate than local task demands permit. Results of this research will serve to improve the design and implementation of ICT systems to improve human performance capabilities and system operating tolerances for exploration missions. (Specific research data were not available at the time of publication.)

Communication↗
PubMed1999

A note on issues in meta-analysis for behavioral genetic studies using categorical phenotypes.

Meta-analysis of behavioral genetic studies would provide (i) tighter confidence intervals around parameter estimates, (ii) clarification of apparently discrepant study findings, and (iii) a mechanism for analyzing systematic causes of between-study differences. We examined some key issues that arise in the meta-analysis of categorical phenotypes. Data were simulated under a multifactorial threshold model that assumed an underlying normal liability distribution, and summary statistics (probandwise concordance rate, recurrence risk ratio, odds ratio, kappa) compared for given values of the liability correlation between relatives and given population prevalence. Although the odds ratio and kappa statistic performed well at moderate to high values of the population prevalence (15-50%), at low values all of these statistics were sensitive to overall prevalence. In cases where the assumption of a multifactorial threshold model is reasonable, direct estimation of genetic and environmental parameters from the summary statistics from all studies appears to be a preferable strategy. For cases where data from non-randomly ascertained samples are used, the impact of misspecification of the model for ascertainment was examined. For some parameter values, such misspecifications led to quite serious biases to estimates of genetic and environmental parameters. These biases varied in complex ways as a function of research design and of the true causes of variation in the population, so that the same misspecification could lead to an overestimate of the importance of genetic influences in twin data but an underestimation in adoption data or to an overestimate of the importance of genetic effects from twin data if shared environmental as well as genetic influences were simulated but an underestimate of genetic effects if shared environmental effects were assumed unimportant. These complexities emphasize the importance of being sensitive to the effects of misspecifying ascertainment corrections in any meta-analysis of behavioral genetic data.

Confidence Intervals↗
PubMed2026

Detection and characterization of antiviral-resistant viruses during the influenza season of 2024-25.

UNLABELLED: During the high severity season of 2024-25, CDC with public health partners sequenced and analyzed genomes of >10,000 influenza viruses for antiviral resistance markers. Available sequence-flagged and representative viruses were tested with antivirals using in vitro assays. In the US, three oseltamivir-resistant A(H3N2) viruses had treatment-emergent neuraminidase (NA) mutations, either E119V or R292K. Oseltamivir-resistant A(H1N1)pdm09 viruses with NA-H275Y were detected in 15 states, albeit at a low frequency (0.53%). They belonged to several phylogenetic groups, with hemagglutinin (HA) subclade D.3.1 combined with either NA subclade D.1 or D.2 being most common. Based on shared sequence data, nearly all H275Y viruses from Australia, Canada, and Chile also belonged to these HA and NA subclades. Conversely, most H275Y viruses (68/81) from China belonged to HA subclade C.1.9 and NA subclade D and shared the permissive mutation R257K. Influenza polymerase acidic (PA) mutations conferring 4- to 92-fold decreased baloxavir susceptibility were detected in nine influenza A viruses. Viruses with PA-I38T showed mild attenuation of replicative fitness in three cell lines. Based on available data, NA-H275Y and PA-I38T viruses were collected from patients with no exposure to antivirals. Baseline susceptibility to all US-approved influenza antivirals remained largely unchanged compared to previous seasons. All swine-origin viruses detected in the US had adamantane resistance-conferring marker, M2-S31N, but remained susceptible to other approved antivirals. Monitoring antiviral susceptibility has substantially improved with increased sequencing capacities and bioinformatic support at public health laboratories. Information gained through influenza surveillance has been used to guide recommendations on antiviral use. IMPORTANCE: Circulation of influenza viruses with reduced susceptibility to antivirals can diminish the usefulness of medications prescribed for influenza. This study informs on the prevalence of drug-resistant influenza viruses in the US during the high severity season of 2024-25. It provides information on susceptibility profile to all approved antiviral medications and on replicative fitness of representative drug-resistant viruses. Most drug-resistant viruses were collected from patients who were not exposed to antivirals indicating their ability to transmit from human to human. Whole-genome sequence (WGS)-based analysis is the cornerstone for surveillance, and numerous laboratories have been utilizing this approach. However, CDC laboratory is the only laboratory in the US conducting phenotypic testing of circulating viruses needed to confirm the outcomes of sequence-based analysis and to identify new molecular markers of resistance. Data gathered through virologic surveillance give much-needed information on drug susceptibility of influenza viruses which are used to guide recommendations on antiviral use.

Antiviral Agents↗
PubMed2025

OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics Data.

Cell deconvolution estimates cell type proportions from bulk omics data, enabling insights into tissue microenvironments and disease. However, practical applications are often hindered by batch effects between bulk data and referenced single-cell data, a challenge that is frequently overlooked. To address this discrepancy, we developed OmicsTweezer, a distribution-independent cell deconvolution model. By integrating optimal transport with deep learning, OmicsTweezer aligns simulated and real data in a shared latent space, effectively mitigating data shifts and inter-omics distribution differences. OmicsTweezer is versatile, capable of deconvolving bulk RNA-seq, bulk proteomics, and spatial transcriptomics. Extensive evaluations on simulated and real-world datasets demonstrate its robustness and accuracy. Furthermore, applications in prostate and colon cancer showcase OmicsTweezer's ability to identify biologically meaningful cell types. As a unified deconvolution framework for multi-omics data, OmicsTweezer offers an efficient and powerful tool for studying disease microenvironments.

Humans↗
PubMed2006

COSMIC 2005.

The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community. Over the past 25 years, approximately 350 cancer genes have been identified, of which 311 are somatically mutated. COSMIC has been expanded and now holds data previously reported in the scientific literature for 28 known cancer genes. In addition, there is data from the systematic sequencing of 518 protein kinase genes. The total gene count in COSMIC stands at 538; 25 have a mutation frequency above 5% in one or more tumour type, no mutations were found in 333 genes and 180 are rarely mutated with frequencies <5% in any tumour set. The COSMIC web site has been expanded to give more views and summaries of the data and provide faster query routes and downloads. In addition, there is a new section describing mutations found through a screen of known cancer genes in 728 cancer cell lines including the NCI-60 set of cancer cell lines.

Databases, Genetic↗