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PubMed1995

Methadone maintenance and the likelihood of risky needle-sharing.

Survey data were used to study the association of methadone maintenance and needle-sharing. An ordinal scale of HIV risk was derived from the number of persons from whom subjects reported accepting a used needle and syringe in the 6 months prior to interview. The odds of respondents in methadone maintenance being in the higher risk group were half those of daily heroin users not in treatment for all three transitions in a four-level ordinal scale of risk (OR 0.55, 95% CL 0.33 to 0.90, ordinal logistic regression). This association disappeared when methadone patients who had not injected in the month prior to interview were excluded from the analysis. Subjects' knowledge concerning HIV and AIDS had no measurable association with the outcome. It is concluded that methadone maintenance reduces heroin addicts' risk of infection with HIV by reducing the likelihood of their injecting drugs rather than by changing their injecting behavior.

Acquired Immunodeficiency Syndrome↗
PubMed2016

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Biological Products↗
PubMed2001

Microarrays in brain research: the good, the bad and the ugly.

Making sense of microarray data is a complex process, in which the interpretation of findings will depend on the overall experimental design and judgement of the investigator performing the analysis. As a result, differences in tissue harvesting, microarray types, sample labelling and data analysis procedures make post hoc sharing of microarray data a great challenge. To ensure rapid and meaningful data exchange, we need to create some order out of the existing chaos. In these ground-breaking microarray standardization and data sharing efforts, NIH agencies should take a leading role

Animals↗
PubMed2025

The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data.

The Genome Sequence Archive family (GSA family) provides a comprehensive suite of database resources for archiving, retrieving, and sharing multi-omics data for the global academic and industrial communities. It currently comprises four distinct database members: the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa), the Genome Sequence Archive for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human), the Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix), and the Open Biomedical Imaging Archive (OBIA, https://ngdc.cncb.ac.cn/obia). Compared to its 2021 version, the GSA family has expanded significantly by introducing a new repository, the OBIA, and by comprehensively upgrading the existing databases. Notable enhancements to the existing members include broadening the range of accepted data types, strengthening quality control systems, improving the data retrieval system, and refining data-sharing management mechanisms.

Humans↗
PubMed2004

New roles for poison control centres in the developing countries.

The primary mission of poison control centres has always been an improvement in the poisoned patients' care and poison prevention. The need to reach this mission implies that many functions and roles must be accomplished. Many centres, even in developing countries, are multifunctional and provide a broad toxicological information service. However, the main challenges of poison centres in developing countries are still treatment information, formal training, laboratory services accessibility and availability of antidotes. At the same time poison centres from developing countries need to accomplish their public health mission through strengthening and expansion of some well-defined roles like toxico-surveillance and environmental health monitoring according to the prevailing and future toxicological problems. Poison control centres from developing countries continue to face old challenges but cannot ignore the new ones that appear in the globalised world. Poison centres have a vital role for environmental exposure surveillance systems for sentinel event detection. Poison centres offer real-time and continuous data needed for preparation and response during such events and also offer a means to report health concerns. Centres from South America were involved in some of the most important environmental health problems of the region e.g., lead contamination (children), children 'occupational' poisoning, and flour contamination with fusarium toxins. Furthermore, poison centres can be the markers of risk factors or identifiers of vulnerable population e.g., changes in drugs prescription patterns, unusual patterns of addiction, unexpected product uses, children abuse scenarios or undetected sources of environmental contamination. In an era of evidence-based medicine and research, toxico-vigilance based on the millions of cases registered by poison centres everyday acquires more and more importance. A new approach of the toxico-vigilance and preventive roles of poison information centres lies in their ability to contribute to risk assessment methodologies with their human data. The data routinely collected by poisons centres could contribute to risk assessment documentation and to define priorities for risk assessment of the harmful chemicals. Although there is some scepticism about the value of poison centres data, the shared volume of human data could validate this information. The international effort of the IPCS/INTOX program, on harmonisation of data collection and terminology for comparable recording of observational human data, has been a great advancement towards handling this problem.

Child↗
PubMed1996

Integrating public health information and surveillance systems.

The Centers for Disease Control and Prevention (CDC) recognizes sound public health information is the essential ingredient of all of its work and the key to effective public health decision making. A CDC/ATSDR committee reached a consensus that CDC needed to streamline and consolidate its public health surveillance and information systems into an integrated system. With integrated systems, a wide range of diverse individual information systems will continue to exist but these systems must be coordinated, interconnected, comparable, and easy to use. The "glue" that holds these systems together consists of (1) uniform data standards, (2) communications networks, and (3) policy-level agreements regarding data access, sharing, and reduction of data collection burdens. By putting the appropriate policy-making apparatus and resources in place, CDC believes the end result will be a streamlined process that meets the information needs of CDC and its partners with less confusion and frustration.

Humans↗
PubMed2025

A Sociotechnical Approach to Genomic Data Privacy: A Comparative Analysis.

The sharing of genomic data across international borders presents significant privacy law challenges.Secured computed environments on smartphones allow the storing and processing of sensitive data without the underlying data being shared with processors.A novel technology, described here, to process genomic data within a secured computing environment seems to comport with EU and US privacy laws, despite their differing aims and rules.This technology suggests there may be technological solutions to privacy law fragmentation across jurisdictions, so long as data subjects socially trust the technology and have control over their data.

genome↗
PubMed2002

Threshold protocol for the exchange of confidential medical data.

BACKGROUND: Medical researchers often need to share clinical data without violating patient confidentiality. Threshold cryptographic protocols divide messages into multiple pieces, no single piece containing information that can reconstruct the original message. The author describes and implements a novel threshold protocol that can be used to search, annotate or transform confidential data without breaching patient confidentiality. METHODS: The basic threshold protocol is: 1) Text is divided into short phrases; 2) Each phrase is converted by a one-way hash algorithm into a seemingly-random set of characters; 3) Threshold Piece 1 is composed of the list of all phrases, with each phrase followed by its one-way hash; 4) Threshold Piece 2 is composed of the text with all phrases replaced by their one-way hash values, and with high-frequency words preserved. Neither Piece 1 nor Piece 2 contains information linking patients to their records. The original text can be re-constructed from Piece 1 and Piece 2. RESULTS: The threshold algorithm produces two files (threshold pieces). In typical usage, Piece 2 is held by the data owner, and Piece 1 is freely distributed. Piece 1 can be annotated and returned to the owner of the original data to enhance the complete data set. Collections of Piece 1 files can be merged and distributed without identifying patient records. Variations of the threshold protocol are described. The author's Perl implementation is freely available. CONCLUSIONS: Threshold files are safe in the sense that they are de-identified and can be used for research purposes. The threshold protocol is particularly useful when the receiver of the threshold file needs to obtain certain concepts or data-types found in the original data, but does not need to fully understand the original data set.

Algorithms↗
PubMed1997

Pediatric renal transplantation: a review of the UNOS data. United Network for Organ Sharing.

The UNOS Scientific Renal Transplant Registry data from October 1987 to December 1996, including information on transplants to 537 patients aged 0-2, 2399 patients aged 3-12 and 5986 patients aged 13-21, were used to examine the results of pediatric transplantation by both univariate and multivariate methods. One-year and long-term graft survival rates were adjusted for 9 covariates including donor source and age, recipient sex, race and disease, and transplant year, HLA mismatches, and transplant center. The adjusted 1- and 5-year graft survival rates were 71% and 60% for ages 0-2, 83% and 64% for ages 3-12 and 85% and 57% for ages 13-21. Except for the youngest recipients, these results compared favorably at 1 year with 86% graft survival among 78,418 adults. The projected graft half-life was highest in patients under age 2 (18 years) and lowest among teenagers (7 years) compared with adults and children (11 years). Univariate analyses revealed a significant 10% graft survival advantage with living donor kidneys for all age groups, but especially for those aged 0-2 in whom survival was 66% with a cadaver donor and 84% with a living donor. The youngest recipients experienced early rejection of the mother's kidney less often than the father's (47% vs 28% in the first 6 months, p<0.007). Results in blacks were similar to those in whites during the first year, but the 3.8 year half-life for black teenagers was the lowest among all groups. We conclude that with the exception of very young (age 2 or under) patients, 1-year pediatric renal transplant survival rates are comparable to those in adults, but in the long term, non-compliance and late acute rejection result in an accelerated graft failure rate among teenagers.

Adolescent↗
PubMed2003

Development of common data elements: the experience of and recommendations from the early detection research network.

There have been an increasing number of large research consortia in recent years funded by the National Cancer Institute (NCI) to facilitate multi-disciplinary, multi-institutional cancer research. Some of these consortia have central data collection plans similar to a multi-center clinical trial whereas others plan to store data locally and pool or share the data at a later date. Regardless of the goal of the consortium, there is a need to standardize the way certain data are collected and stored, transferred, or reported across the institutions involved. This communication is a report of the process and current status of the development of common data elements (CDEs) by the Early Detection Research Network (EDRN). The development of the CDEs involved several stages with each stage requiring input from multi-disciplinary experts in oncology, epidemiology, biostatistics, pathology, informatics, and study coordination. An effort was made to be consistent with other consortia developing similar CDEs and to follow data standards when available. Initial focus was on identifying the minimum data that would be necessary to collect on all EDRN study participants and EDRN specimens. There are currently CDEs in the development or pilot phase for eight different organ sites and 13 different types of specimen procurements and plans to develop CDEs for 12 or more additional types of specimens.

Data Collection↗
PubMed2006

The MGED Ontology: a resource for semantics-based description of microarray experiments.

MOTIVATION: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT: Stoeckrt@pcbi.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computational Biology↗
PubMed1993

Combining census, dual-system, and evaluation study data to estimate population shares.

"The 1990 [U.S.] census and Post-Enumeration Survey produced census and dual system estimates (DSE) of population by domain, together with an estimated sampling covariance matrix of the DSE. Estimates of the bias of the DSE were derived from various PES evaluation programs. Of the three sources, the unadjusted census is the least variable but is believed to be the most biased, the DSE is less biased but more variable, and the bias estimates may be regarded as unbiased but are the most variable. This article addresses methods for combining the census, the DSE, and bias estimates obtained from the evaluation programs to produce accurate estimates of population shares, as measured by weighted squared- or absolute-error loss functions applied to estimated population shares of domains."

Americas↗
PubMed2003

Web-based submission, archive, and review of radiotherapy data for clinical quality assurance: a new paradigm.

PURPOSE: To report on the implementation of a web-based system (the Resource Center for Emerging Technologies [RCET] System) that provides immediate access to the patient radiotherapy planning and delivery data for clinical quality assurance (QA) by the experts. MATERIALS AND METHODS: An infrastructure of comprehensive tools required for preparation, submission, auto-archiving, web-based review, and retrieval of diagnostic images, treatment planning images, and radiation therapy objects has been developed. These tools represent approximately 1.1 million lines of computer code development in seven languages (V, C++, Visual Basic, Java, ASP, HTML, and SQL) and consist of a secure auto-anonymizing upload and auto-archiving patient database, a web-based secure object archiving network system, a web-based rapid review tool, a web-based upload/download tool, and a personal computer client data application for data object preparation, visualization, and submission, named NetSys. The RCET system enables users to share radiotherapy data in a secure environment. This paradigm of electronic data exchange makes remote peer review very efficient and convenient. RESULTS: The RCET system can help the radiation therapy community ensure consistent evaluation of its therapies. It will encourage proactive QA. An example of proactive clinical QA would be to provide atlases of target and critical structure definitions, to serve as class solutions, as well as dose prescription, specification, and reporting examples for guidance to the radiation oncologists in the community. The web-based clinical quality assurance is ideally suited for emerging technologies in radiation therapy that generate complex and voluminous multimodality imaging and planning data. CONCLUSIONS: The RCET system enables users to share multimodality imaging data, radiation therapy planning, and delivery data on demand. Our design paradigm will allow rapid peer review of radiotherapy data through a simple personal computer-based web browser.

Humans↗
PubMed2004

Native Hawaiians mortality, morbidity, and lifestyle: comparing data from 1982, 1990, and 2000.

This paper shares 2000 data on Native Hawaiian health and compares the 2000 data with data from 1982 and 1990. The findings suggest that Native Hawaiians continue to die at younger ages than Hawai'i residents in other ethnic groups, have a higher prevalence of hypertension, diabetes, and asthma than other ethnic groups, and have higher rates of smoking, drinking, and being overweight. Compared to earlier years, however, smoking and drinking prevalence has decreased, and more Native Hawaiians are getting physical exams and other screening exams. These improvements may be related to increases in Native Hawaiian health professionals, supported by the Native Hawaiian Health Scholarship Program, and to increased access to health education and to care through outreach programs such as the Native Hawaiian Health Care Systems and the Breast and Cervical Cancer Control Program. If these programs are allowed to continue and to expand, we should see an improvement in overall health status of Native Hawaiians.

Adolescent↗
PubMed2026

Single-cell transcriptomic landscape of the southern green stink bug (Nezara viridula) midgut.

BACKGROUND: The southern green stink bug (SGSB), Nezara viridula, is a globally distributed hemipteran pest that damages many economically important crops. Its midgut supports digestion, defense, symbiosis, and interactions with orally delivered control agents, yet the cellular composition of this tissue remains poorly characterized. We therefore developed a single-cell transcriptomic atlas of the N. viridula midgut. RESULTS: Single-cell RNA sequencing of two biological replicates yielded a quality-filtered data set of 13,763 cells. Unsupervised clustering identified 12 transcriptionally distinct populations with putative annotations, including a stem cell/enteroblast (SC/EB)-like population, seven enterocyte-related populations, goblet-like cells, enteroendocrine cells, visceral muscle cells, and an extracellular-matrix-associated epithelial population. Enterocyte-related populations accounted for more than 77% of recovered cells. Putative annotations were assigned primarily from marker gene enrichment and homology to markers reported in other insects. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified population-associated functional enrichment patterns, and pseudotime analysis suggested transcriptional relationships between the SC/EB-like population and several enterocyte- and secretory-associated populations without establishing developmental lineages. Immune- and defense-associated transcripts were preferentially enriched in the pEC2 population, and genes associated with symbiont recognition, insecticide action, xenobiotic transport, and orally delivered double-stranded RNA showed population-biased expression. Descriptive comparisons with published insect midgut data sets identified shared and data-set-specific patterns among annotated populations. CONCLUSION: This atlas provides the first single-cell transcriptomic resource for a stink bug midgut and establishes a descriptive cellular framework for SGSB midgut biology. The dataset prioritizes candidate genes and cell populations for future spatial validation, functional testing, and studies of hemipteran midgut physiology, symbiosis, immunity, and pest-management-relevant traits. &#xa9; 2026 Society of Chemical Industry.

Nezara viridula↗
PubMed2003

Caring behaviors of advanced practice nursing students.

The purpose of this project was to provide advanced practice nursing (APN) students with the opportunity to enrich their aesthetic knowing and acquire the meaning of caring in their practice by reflecting on their caring narratives. Students were asked to write about a caring encounter they experienced in their practice. The instructor analyzed and organized that data from each narrative. The instructor shared the data with the students for reflection and discussion. This report focuses on the caring practices of the APN students. Nine themes that embraced physical care, communication, comfort, presence, knowing, acceptance, touch, collaboration, and encouragement were identified. The APN students demonstrated aesthetic knowing as well as other ways of knowing in their caring narratives. Through reflection on the caring experiences and discussion in class, students were able to identify the meaning of caring in their practice.

Education, Nursing, Graduate↗
PubMed2006

Advances in systems biology: measurement, modeling and representation.

Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this emerging and cross-disciplinary field by allowing researchers to explore how biological components function as a network in cells, tissues and organisms. Recently, pharmaceutical companies have begun to embrace systems approaches in an effort to better understand physiology, pathogenic processes and pharmacological responses. This review focuses on recent advances within three core areas of systems biology: data collection, data analysis, and the integration and sharing of data.

Animals↗