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At least 685 records · Page 38Linked to original sources
PubMed2000

Proteomic databases and software on the web.

In the wake of sequencing projects, protein function analysis is evolving fast, from the careful design of assays that address specific questions to 'large-scale' proteomics technologies that yield proteome-wide maps of protein expression or interaction. As these new technologies depend heavily on information storage, representation and analysis, existing databases and software tools are being adapted, while new resources are emerging. This paper describes the proteomics databases and software available through the World-Wide Web, focusing on their present use and applicability. As the resource situation is highly transitory, trends and probable evolutions are discussed whenever applicable.

Computational Biology↗
PubMed2026

Searching the druggable genome using large language models.

SUMMARY: The druggable genome encompasses the genes that are known or predicted to interact with drugs. The Drug-Gene Interaction Database (DGIdb) provides an integrated resource for discovering and contextualizing these interactions, supporting a broad range of research and clinical applications. DGIdb is currently accessed through structured web interfaces and API calls, requiring users to translate natural-language questions into database-specific query patterns. To allow for the use of DGIdb through natural language, we developed the DGIdb Model Context Protocol (MCP) server, which allows large language models (LLMs) access to up-to-date information through the DGIdb API. We demonstrate that the MCP server improves an LLM's ability to answer questions requiring accurate, up-to-date biomedical knowledge drawn from structured external resources. AVAILABILITY AND IMPLEMENTATION: The DGIdb MCP server is detailed at https://github.com/dgidb/dgidb-mcp-server and includes instructions for accessing the server through the Claude desktop app.

Large Language Models↗
PubMed2000

DNAssist, a C++ program for editing and analysis of nucleic acid and protein sequences on PC-compatible computers running Windows 95, 98, NT4.0 or 2000.

The size of sequence databases, the rapid rate of generating sequence data and the need to routinely construct recombinant DNA molecules in molecular biological research necessitate the frequent handling and analysis of nucleotide and protein sequences on a computer. Although several console or Web-based utility programs are available, the application of these programs generally requires reformatting the data when proceeding from one such program to the next. The acquisition of elaborate, integrated program suites is financially prohibitive to smaller laboratories. Here, we report the development of DNAssist, a shareware program for editing and analysis of nucleic acid and protein sequences. It was developed as a multiple-document interface program--similar to a word processor--where sequences are entered, edited and analyzed in a single integrated environment. DNAssist can calculate the physicochemical properties of a sequence, convert between nucleic acid and protein sequences, translate DNA in multiple frames, identify open reading frames and locate ambiguous sequence patterns allowing gaps and mismatches. DNAssist also performs restriction enzyme and transcription factor-binding site analyses of DNA sequences, the multiple alignment of nucleic acid and protein sequences and the analysis of DNA sequences for nucleosome positioning sites.

Amino Acid Sequence↗
PubMed2026

Searching the Druggable Genome using Large Language Models.

SUMMARY: The druggable genome encompasses the genes that are known or predicted to interact with drugs. The Drug-Gene Interaction Database (DGIdb) provides an integrated resource for discovering and contextualizing these interactions, supporting a broad range of research and clinical applications. DGIdb is currently accessed through structured web interfaces and API calls, requiring users to translate natural-language questions into database-specific query patterns. To allow for the use of DGIdb through natural language, we developed the DGIdb Model Context Protocol (MCP) server, which allows large language models (LLMs) access to up-to-date information through the DGIdb API. We demonstrate that the MCP server greatly enhances an LLM's ability to answer questions requiring accurate, up-to-date biomedical knowledge drawn from structured external resources. AVAILABILITY AND IMPLEMENTATION: The DGIdb MCP server is detailed at https://github.com/griffithlab/dgidb-mcp-server and includes instructions for accessing the server through the Claude desktop app.

Journal Article↗
PubMedDate not supplied

A computer expert system prototype for mechanically ventilated neonates development and impact on clinical judgment and information access capability of nurses.

A computer expert system is an alternative method of training and providing real-time clinical decision support for nurses to advance their practices from a novice to a proficient level. The purpose of this study was twofold: (1) to develop a prototype of a computer expert system for mechanically ventilated neonates (ES-MVN) and (2) to assess the impact of the ES-MVN on the clinical judgment and information access capability of nurses. Five steps used in developing the prototype are described in this article. The ES-MVN is a multimedia interactive consultation-based program that contains 2 major parts: the nursing diagnosis and the knowledge base on nursing care of mechanically ventilated neonates. A rule-based (Boolean frame) was chosen for the nursing diagnosis decision model. The prototype was developed on the Web server and a combination of computer applications operated in a Microsoft Windows environment. A quasi-experimental, 1-group pretest-posttest design was used to measure the efficacy of the ES-MVN in 16 neonatal intensive care unit registered nurses. Case simulations were used to test the nurses' clinical judgment performance. The results showed a significant increase in the nurses' performance scores of diagnoses and managed care after using the ES-MVN (t[15] = 17.21, P = .0001). The nurses' scores for perceptions of their information access capability and clinical judgment ability after receiving the ES-MVN were significantly higher than before installing the ES-MVN in the neonatal intensive care unit (ts[15] = 6.91 and = 17.53, Ps = .0001, respectively). The findings suggest the usefulness of the computer expert system as an effective tool to support nurses' clinical judgment in critical care situations and to provide access to information at the practice site.

Adult↗
PubMed2002

[Microsurgical repair of syndactyly of the fingers in children].

OBJECTIVE: To evaluate the effectiveness of microsurgical technique for repairing syndactyly of the fingers in children. METHODS: Microsurgical repair of syndactyly of the fingers was performed in 32 children. The skin joining the syndactyly was incised and relaxed under microscope, and dorsal metacarpal flap of comparable size was used to repair the lateral skin defect of the finger and also to reconstruct the finger web. RESULTS: All the flaps survived without scar leaving on the lateral skin of the fingers, and the reconstruction of the finger web was satisfying. CONCLUSION: Microsurgical technique is applicable in the surgical repair of syndactyly of the fingers in children.

Child↗
PubMed1996

Double-u double-u double-u dot APIC dot org: a review of the APIC World Wide Web site.

The widespread use of the Internet and the development of the World Wide Web have led to a revolution in electronic communication and information access. The Association for Professional in Infection Control and Epidemiology (APIC) has developed a site on the World Wide Web to provide mechanisms for international on-line information access and exchange on issues related to the practice of infection control and the application of epidemiology. From the home page of the APIC Web site, users can access information on professional resources, publications, educational offering, governmental affairs, the APIC organization, and the infection control profession. Among the chief features of the site is a discussion forum for posing questions and sharing information about infection control and epidemiology. The site also contains a searchable database of practice-related abstracts and descriptions and order forms for APIC publications. Users will find continuing education course descriptions and registration forms, legislative and regulatory action alerts and a congressional mailer, chapter and committee information, and infection control information of interest to the general public. APIC is considering several potential future enhancements to their Web site and will continue to review the site's content and features to provide current and useful information to infection control professionals.

Computer Communication Networks↗
PubMed2005

Evolving telemedicine/ehealth technology.

This paper describes emerging technologies to support a rapidly changing and expanding scope of telemedicine/telehealth applications. Of primary interest here are wireless systems, emerging broadband, nanotechnology, intelligent agent applications, and grid computing. More specifically, the paper describes the changes underway in wireless designs aimed at enhancing security; some of the current work involving the development of nanotechnology applications and research into the use of intelligent agents/artificial intelligence technology to establish what are termed "Knowbots"; and a sampling of the use of Web services, such as grid computing capabilities, to support medical applications. In addition, the expansion of these technologies and the need for cost containment to sustain future health care for an increasingly mobile and aging population is discussed.

Algorithms↗
PubMed2003

PalmCIS: a wireless handheld application for satisfying clinician information needs.

Wireless handheld technology provides new ways to deliver and present information. As with any technology, its unique features must be taken into consideration and its applications designed accordingly. In the clinical setting, availability of needed information can be crucial during the decision-making process. Preliminary studies performed at New York Presbyterian Hospital (NYPH) determined that there are inadequate access to information and ineffective communication among clinicians (potential proximal causes of medical errors). In response to these findings, the authors have been developing extensions to their Web-based clinical information system including PalmCIS, an application that provides access to needed patient information via a wireless personal digital assistant (PDA). The focus was on achieving end-to-end security and developing a highly usable system. This report discusses the motivation behind PalmCIS, design and development of the system, and future directions.

Computer Communication Networks↗
PubMed2006

The Life Sciences Semantic Web is full of creeps!

The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as 'semantic creep'-timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.

Computational Biology↗
PubMed2006

Developing internet-based eHealth promotion programs: the Spiral Technology Action Research (STAR) model.

Health education and health promotion have a tradition of using information and communication technology (ICT). In recent years, the rapid growth of the Internet has created innovative opportunities for Web-based health education and behavior change applications-termed eHealth promotion. However, many eHealth promotion applications are developed without an explicit model to guide the design, evaluation, and ongoing improvement of the program. The spiral technology action research (STAR) model was developed to address this need. The model comprises five cycles (listen, plan, do, study, act) that weave together technological development, community involvement, and continuous improvement. The model is illustrated by a case study describing the development of the Smoking Zine (www.SmokingZine.org), a youth smoking prevention and cessation Web site.

Adolescent↗
PubMed2005

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.

We carry out an extensive statistical study of the applicability of normal modes to the prediction of mobile regions in proteins. In particular, we assess the degree to which the observed motions found in a comprehensive data set of 377 nonredundant motions can be modeled by a single normal-mode vibration. We describe each motion in our data set by vectors connecting corresponding atoms in two crystallographically known conformations. We then measure the geometric overlap of these motion vectors with the displacement vectors of the lowest-frequency mode, for one of the conformations. Our study suggests that the lowest mode contains useful information about the parts of a protein that move most (i.e., have the largest amplitudes) and about the direction of this movement. Based on our findings, we developed a Web tool for motion prediction (available from http://molmovdb.org/nma) and apply it here to four representative motions--from bacteriorhodopsin, calmodulin, insulin, and T7 RNA polymerase.

Databases, Protein↗
PubMed1998

Otolaryngology and the Internet. E-mail and the World Wide Web.

Computer technology and Internet-based communications are evolving at a tremendous rate. At present, most physicians either have or can easily obtain online access. E-mail represents a new method of interpersonal communication, with many useful applications in the field of clinical medicine. The World Wide Web has developed over the past few years into a vast information resource, with global reach and the ability to provide users with text and audio and video materials on every conceivable topic. These modalities are discussed in detail, stressing controversial aspects such as e-mail security, validation of content, professional liability as it relates to online comments, and the academic status of Web publishing.

Computer Communication Networks↗
PubMed2006

Next-generation applications in healthcare digital libraries using semantic service composition and coordination.

Healthcare digital libraries (DLs) increasingly make use of dedicated services to access functionality and/or data. Semantic (web) services enhance single services and facilitate compound services, thereby supporting advanced applications on top of a DL. The traditional process management approach tends to focus on process definition at build time rather than on actual service events in run time, and to anticipate failures in order to define appropriate strategies. This paper presents a novel approach where service coordination is distributed among a set of agents. A dedicated component plans compound semantic services on demand for a particular application. In failure, the planner is reinvoked to define contin- gency strategies. Finally, matchmaking is effected at runtime by choosing the appropriate service provider. These combined technologies will provide key support for highly flexible next-generation DL applications. Such technologies are under development within CASCOM.

Information Storage and Retrieval↗
PubMed2003

Emergency healthcare process automation using workflow technology and web services.

Emergency healthcare delivery involves a variety of interrelated activities performed from the time of a call to the ambulance service until the time of patient's exit from the emergency department of a hospital. As these activities can be viewed as parts of inter-organizational healthcare processes that involve at least two organizations (e.g. an ambulance service and a hospital), there is a need to provide the appropriate technological infrastructure for automating and managing these processes even in cases where the organizations involved use heterogeneous systems to support their internal services. Web-based workflow systems in conjunction with web services present a new way for service-oriented integration (SOI) of disparate systems and for developing distributed applications within and between organizations. Thus, process automation with the use of web services can provide an appropriate infrastructure for the integration of pre-hospital and in-hospital emergency healthcare. A prototype development of such a system is presented in this paper.

Ambulances↗
PubMed2004

Aquatic mesocosm assessments of a neem (azadirachtin) insecticide at environmentally realistic concentrations--2: zooplankton community responses and recovery.

A neem-based insecticide, Neemix 4.5, was applied to forest pond enclosures at environmentally realistic concentrations (i.e., below the worst-case expected environmental concentration of 35 microg L(-1)). Crustacean zooplankton communities were examined by multivariate ordination (nonmetric multidimensional scaling) and time-course analyses of population trends among indicator taxa over two field seasons to determine application effects on community structure and recovery patterns. Significant effects on zooplankton community structure were detected at all main test concentrations (n = 5) of 28, 17, and 10 microg L(-1) azadirachtin. There was also evidence of adverse effects on zooplankton communities at an auxiliary test concentration (n = 2) of 5 microg L(-1) azadirachtin. Community-level effects resulted primarily from reductions in adult copepods with short-term, reciprocal increases in cladocerans. Copepod nauplii were not significantly affected. Response patterns suggested that the reductions in adult copepods resulted from growth-regulating effects of the active ingredient azadirachtin, or other neem compounds, and not from formulation ingredients. There was no evidence of recovery among adult copepods within the season of application. At the beginning of the second sampling season, there were apparent carryover effects similar to the community responses in the previous year. By the end of the second season, there was evidence indicating recovery of community structure at the two lower test concentrations of 10 and 17 microg L(-1), but not at 28 microg L(-1). The selective toxicity to adult copepods is problematic in that this group has a relatively long life cycle (1 year), contributes a major component of zooplankton biomass and respiration, and occupies critical functional guilds within zooplankton food web structures. Mitigation measures such as reductions in application rates and efforts to avoid deposition of sprayed materials on water bodies will be required to reduce the risk of harmful effects on zooplankton communities of forest ponds and other shallow, standing-water bodies.

Animals↗
PubMed2005

A web-based remote collaborative system for visualization and assessment of semi-automatic diagnosis of liver cancer from CT images.

We propose a web-based collaborative CAD system allowing for the remote communication and data exchange between radiologists and researchers in computer vision-based software engineering. The proposed web-based interface is implemented in the Java Advanced Imaging Application Programming Interface. The different modules of the interface allow for 3D and 2D data visualization, as well as for the parametric adjustment of 3D reconstruction process. The proposed web-based CAD system was tested in a pilot study involving a limited number of liver cancer cases. The successful system validation in the feasibility stage will lead to an extended clinical study on CT and MR image databases.

Diagnosis, Computer-Assisted↗