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PubMed2004

Analyzing irregular working hours: lessons learned in the development of RAS 1.0--The Representation and Analysis Software.

Actual working hours of employees vary widely, especially in the transportation industry. We developed a tool, the RAS (Representation and Analysis Software), to ease the assessment of such irregular hours and the transfer of existing knowledge of proper schedule design to the problem of irregular hours. This article discusses several critical design questions that were addressed during software development in order for it to assess irregular work patterns, including the (1) importance, in spite of a lack of established definitions, of basic concepts like, e.g., night shift, (2) difficulty of modeling and adapting existing knowledge on proper design, and (3) large number of analytical methods and additional data beyond company schedule that are necessary to meet the needs of various research groups. This article describes how the RAS addresses these three issues by illustrating its application to the work schedule of a train driver involved in the Hinton train disaster.

Employment↗
PubMedDate not supplied

Wireless local area network for the dental office.

Dental offices are no exception to the implementation of new and advanced technology, especially if it enhances productivity. In a rapidly transforming digital world, wireless technology has a special place, as it has truly "retired the wire" and contributed to the ease and efficient access to patient data and other software-based applications for diagnosis and treatment. If the office or the clinic is networked, access to patient management software, imaging software and treatment planning tools is enhanced. Access will be further enhanced and unrestricted if the entire network is wireless. As with any new, emerging technology, there will be issues that should be kept in mind before adapting to the wireless environment. Foremost is the network security involved in the installation and use of these wireless networks. This short, technical manuscript deals with standards and choices in wireless technology currently available for implementation within a dental office. The benefits of each network security protocol available to protect patient data and boost the efficiency of a modern dental office are discussed.

Computer Security↗
PubMed1996

Prism: a new approach to radiotherapy planning software.

PURPOSE: We describe the capabilities and performance of Prism, an innovative new radiotherapy planning system with unusual features and design. The design and implementation strategies are intended to assure high quality and clinical acceptability. The features include Artificial Intelligence tools and special support for multileaf collimator (MLC) systems. The design provides unusual flexibility of operation and ease of expansion. METHODS AND MATERIALS: We have implemented Prism, a three-dimensional (3D) radiotherapy treatment-planning system on standard commercial workstations with the widely available X window system. The design and implementation use ideas taken from recent software engineering research, for example, the use of behavioral entity-relationship modeling and the "Mediator Method" instead of ad-hoc programming. The Prism system includes the usual features of a 3D planning system, including Beam's Eye View and the ability to simulate any treatment geometry possible with any standard radiotherapy accelerator. It includes a rule-based expert system for automated generation of the planning target volume as defined in ICRU Report 50. In addition, it provides special support for planning treatments with a multileaf collimator (MLC). We also implemented a Radiotherapy Treatment Planning Tools Foundation for Prism, so that we are able to use software tools form other institutions without any source code modification. RESULTS: The Prism system has been in clinical operation at the University of Washington since July 1994 and has been installed at several other clinics. The system is run simultaneously by several users, each with their own workstation operating from a common networked database and software. In addition to the dosimetrists, the system is used by radiation oncologists to define tumor and target volumes and by radiation therapists to select treatment setups to load into a computer controlled accelerator. CONCLUSIONS: Experience with the installation and operation has shown the design to be effective as both a clinical and research tool. Integration of software tools has eased the development and significantly enhanced the clinical usability of the system. The design has been shown to be a sound basis for further innovation in radiation treatment planning software and for research in the treatment planning process.

Computer Communication Networks↗
PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗
PubMed2006

Application of an interactive computer program to manage a problem-based dental curriculum.

Managing the change from traditional to problem-based learning (PBL) curricula is complex because PBL employs problem cases as the vehicle for learning. Each problem case covers a wide range of different learning issues across many disciplines and is coordinated by different facilitators drawn from the school's multidisciplinary pool. The objective of this project was to adapt an interactive computer program to manage a problem-based dental curriculum. Through application of a commercial database software--CATs (Curriculum Analysis Tools)--an electronic database for all modules of a five-year problem-based program was developed. This involved inputting basic information on each problem case relating to competencies covered, key words (learning objectives), participating faculty, independent study, and homework assignments, as well as inputting information on contact hours. General reports were generated to provide an overview of the curriculum. In addition, competency, key word, manpower, and clock-hour reports at three levels (individual PBL course component, yearly, and the entire curriculum) were produced. Implications and uses of such reports are discussed. The adaptation of electronic technology for managing dental curricula for use in a PBL curriculum has implications for all those involved in managing new-style PBL dental curricula and those who have concerns about managing the PBL process.

Curriculum↗
PubMed2003

Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry.

Techniques in mass spectrometry (MS) combined with chemical cross-linking have proven to be efficient tools for the rapid determination of low-resolution three-dimensional (3-D) structures of proteins. The general procedure involves chemical cross-linking of a protein followed by enzymatic digestion and MS analysis of the resulting peptide mixture. These experiments are generally fast and do not require large quantities of protein. However, the large number of peptide species created from the digestion of cross-linked proteins makes it difficult to identify relevant intermolecular cross-linked peptides from MS data. We present a method for mapping low-resolution 3-D protein structures by combining chemical cross-linking with high-resolution FTICR (Fourier transform ion-cyclotron resonance) mass spectrometry using cytochrome c and hen egg lysozyme as model proteins. We applied several homo-bifunctional, amine-reactive cross-linking reagents that bridge distances from 6 to 16 A. The non-digested cross-linking reaction mixtures were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to determine the extent of cross-linking. Enzymatically digested reaction mixtures were separated by nano-high-performance liquid chromatography (nano-HPLC) on reverse-phase columns applying water/acetonitrile gradients with flow rates of 200 nL/min. The nano-HPLC system was directly coupled to an FTICR mass spectrometer equipped with a nano-ESI (electrospray ionization) source. Cross-linking products were identified using a combination of the GPMAW software and ExPASy Proteomics tools. For correct assignment of the cross-linking products the key factor is to rely on a mass spectrometric method providing both high resolution and high mass accuracy, such as FTICRMS. By combining chemical cross-linking with FTICRMS we were able to rapidly define several intramolecular constraints for cytochrome c and lysozyme.

Animals↗
PubMed2006

Dialysis dose (Kt/V) and clearance variation sensitivity using measurement of ultraviolet-absorbance (on-line), blood urea, dialysate urea and ionic dialysance.

BACKGROUND: An on-line monitoring system for dialysis dose calculations could make it possible to provide an adequate dialysis dose that is consistently given to haemodialysis (HD) patients. The aim of this study was to compare dialysis dose (Kt/V) using four different methods and their sensitiveness to a reduction in clearance. METHODS: Six patients were monitored on-line with ultraviolet (UV)-absorbance at a wavelength of 297 nm in three consecutive dialysis sessions during 1 week. During the last treatment, the clearance was reduced by approximately 25% by decreasing the blood flow. For the determination of UV-absorbance, a spectrophotometer was connected to the fluid outlet of the dialysis machine with all spent dialysate passing through a flow cuvette. The equilibrated Kt/V (eKt/V) estimated by UV-absorbance was compared with eKt/V from the ionic dialysance method using the on-line clearance monitor (OCM) and the appurtenant software dose-calculation tool DCTool (Fresenius Medical Care, Germany), eKt/V calculated from the dialysate-urea slope and with eKt/V from pre- and post-dialysis blood-urea samples as reference. RESULTS: The study demonstrates that the sensitiveness to clearance reduction is similar in the four methods compared for eKt/V. When the different methods were compared, the mean eKt/V of UV-absorbance was 1.21 +/- 0.20, blood 1.30 +/- 0.21, dialysate 1.32 +/- 0.21 and OCM (using the DCTool) 1.31 +/- 0.21. The standard deviation was of the same magnitude. CONCLUSION: The UV-method gives a similar response to clearance reduction compared with the other methods when comparing dialysis dose. The high sampling rate by continuous monitoring of UV-absorbance allows evaluation of the clearance process during dialysis and gives immediate feedback to on-line adjustments.

Aged↗
PubMed2005

Ribosome builder: a software project to simulate the ribosome.

The Ribosome Builder is a software project that provides tools and techniques to create dynamic models of macromolecular systems from the rapidly growing numbers of atomic structural models. It includes a computer program that allows the user to assemble the multiple molecular components within a 3D space and to define the hypothetical interactions of these components with the initial goal of understanding protein translation at an atomic level of detail. The program employs a simplified molecular dynamics forcefield that can simulate the long time-scale events, such as docking of translation factors and mRNA translocation. An embedded scripting language and Application Programming Interface (API) enable the creation of Steered Molecular Dynamics (SMD) simulations through the programmable application of external forces and torques on atoms and bonds. A graphical interface is provided for displaying and interacting with models, recording movies of molecular dynamics movements, and creating annotated 3D simulations of complex macromolecular events. Initial applications of the project include simulation of tetraloop folding, docking of an mRNA on the 30S subunit and a schematic simulation of the translation elongation cycle. The program is an open source project released under the GNU public license.

Computer Simulation↗
PubMedDate not supplied

[Early or late referral patterns of 1137 patients starting dialysis in 15 Italian dialysis centres].

INTRODUCTION: Data on referral patterns of patients with end-stage renal failure starting renal replacement therapy were collected. The participating centres used the PFA Patients Flow Analysis (R) software programme, a Baxter tool designed to help improve data collection on dialysis patients from their first visit to the centre to the start of renal replacement therapy. METHODS: Data were collected on 1137 patients from 15 dialysis centres, mainly in northern Italy, with the aim of describing a) their referral modalities; b) their eligibility to renal replacement treatments; c) the number of early and late referrals utilising a permanent PD (Peritoneal Dialysis) or HD (Haemodialysis) access at the first treatment. RESULTS: Early Referrals (ERs) (54%) are comparable in terms of their main characteristics (sex and age) to Late Referrals (LRs) but they have wider access to a PD or to the opportunity of choosing their dialysis modality. The majority (89%) of all ERs, have a permanent access at the first dialysis treatment and a larger number (44%) have a PD as permanent dialysis treatment. Centres with structured pre-dialysis educational programmes achieve better outcomes: 66.3% patients vs. 48.2% without enhanced education start the dialysis treatment with a permanent access and more patients (40% vs. 22%) receive a permanent PD. CONCLUSIONS: Comparing centres with and without timely structured educational interventions seems to confirm the effectiveness of such education on the outcomes of ESRF patients.

Aged↗
PubMed2006

The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

BACKGROUND: Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. RESULTS: The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. CONCLUSION: The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.

Humans↗
PubMed2004

Developmental gene expression profiling of mammalian, fetal orofacial tissue.

BACKGROUND: The embryonic orofacial region is an excellent developmental paradigm that has revealed the centrality of numerous genes encoding proteins with diverse and important biological functions in embryonic growth and morphogenesis. DNA microarray technology presents an efficient means of acquiring novel and valuable information regarding the expression, regulation, and function of a panoply of genes involved in mammalian orofacial development. METHODS: To identify differentially expressed genes during mammalian orofacial ontogenesis, the transcript profiles of GD-12, GD-13, and GD-14 murine orofacial tissue were compared utilizing GeneChip arrays from Affymetrix. Changes in gene expression were verified by TaqMan quantitative real-time PCR. Cluster analysis of the microarray data was done with the GeneCluster 2.0 Data Mining Tool and the GeneSpring software. RESULTS: Expression of >50% of the approximately 12,000 genes and expressed sequence tags examined in this study was detected in GD-12, GD-13, and GD-14 murine orofacial tissues and the expression of several hundred genes was up- and downregulated in the developing orofacial tissue from GD-12 to GD-13, as well as from GD-13 to GD-14. Such differential gene expression represents changes in the expression of genes encoding growth factors and signaling molecules; transcription factors; and proteins involved in epithelial-mesenchymal interactions, extracellular matrix synthesis, cell adhesion, proliferation, differentiation, and apoptosis. Following cluster analysis of the microarray data, eight distinct patterns of gene expression during murine orofacial ontogenesis were selected for graphic presentation of gene expression patterns. CONCLUSIONS: This gene expression profiling study identifies a number of potentially unique developmental participants and serves as a valuable aid in deciphering the complex molecular mechanisms crucial for mammalian orofacial development.

Animals↗
PubMed1991

Migrating a clinical laboratory information system between technologies.

The technical revolution that has strongly driven events in the clinical laboratory for the last thirty years is now threatening to make obsolete what has become the central pillar of operation in many laboratories, the minicomputer-based laboratory information system. Some of its functions could easily be absorbed by the personal computers which are proliferating in the laboratory, but any single step leap between systems risks replacing order with chaos. Appropriate use of networking tools, together with essential software development, can provide a systematic migrational path for both the administrative and technical computer support from one environment to another without the trauma of a massive replacement step.

Clinical Laboratory Information Systems↗
PubMed1990

Real-time multiprocessing of slit scan chromosome profiles.

The multiprocessor NERV and its application to slit scan flow cytometry is described. Up to 320 processors and 640 MBytes of RAM may be used in one VME crate, providing a computing power of less than or equal to 1300 MIPS. The multiprocessor is controlled by a host computer that provides a friendly user interface and comfortable program development tools. All hardware and software has been tested on a prototype NERV system with 5 processors. For a real-time classification/detection of normal and aberrant chromosomes, the centromeric index or the number of centromeres are computed or specifically labeled DNA sequences are detected. The program is partitioned into 60 tasks that can be executed concurrently. A total analysis time of less than 600 microseconds including system overhead will be achieved according to timing measurements which have been done for all individual tasks.

Algorithms↗
PubMed2005

Homology modelling and protein structure based functional analysis of five cucumovirus coat proteins.

Coat proteins (CP) of five cucumovirus isolates, Cucumber mosaic virus (CMV) strains R, M and Trk7, Tomato aspermy virus (TAV) strain P and Peanut stunt virus (PSV) strain Er, were constructed by homology modelling. The X-ray structure of the Fny-CMV CP subunit B was used as a template. Models of cucumovirus CPs were built by the MODELLER program. Model refinements were carried out using the Kollman molecular mechanical force field. Models were analyzed by the PROCHECK programs. Electrostatic potential calculations were applied to all models and functional site search was performed with the PROSITE software, a web based tool for searching biologically significant sites. Symptom determinants published up to the present were compared with the PROSITE hits in the light of 3D models and electrostatic information. In all cases, we analyzed the effect of mutations on the structure, electrostatic potential patterns and function of CPs, respectively. We found that high flexibility of the betaE-alphaEF loop starting with the residue 129 is required, but it is not sufficient for the symptom appearance. Furthermore, phosphorylation of the CP is prospective to be important in the host response mechanism. All analyzed mutations were related to the modifications of the predicted phosphorylation sites. Based on our conclusions we predicted the infectivity of the examined viruses.

Amino Acid Sequence↗
PubMed1996

The accuracy of measurements of three-dimensional computed tomography reconstructions.

PURPOSE: The purpose of this study was to evaluate the accuracy and reproducibility of linear measurements obtained from three-dimensional reconstructions of computed tomography (CT) scans. MATERIALS AND METHODS: Ten rectangular acrylic blocks were prepared with titanium molybdenum alloy (TMA) markers spaced from 1 to 10 mm, respectively. A plastic sphere was prepared with 10 sets of TMA markers spaced at variable intervals of 1 to 10 mm. Each object was scanned three times at 3-mm slice thicknesses and 1.5 mm with 0.5 mm overlap slice thicknesses, as well as positioned in the CT scanner in two different directions (perpendicular and parallel) to the scanning beam. Intermarker distances of the reconstructed objects were then measured using the measurement tool of the MediCAD software and compared with measurements taken by hand with a vernier caliper. RESULTS: Using the 3-mm cut protocol, the data indicated that inconsistency exists between intermarker distance in the scans when the rectangular objects were scanned parallel to the scanning beam. This finding was not seen using the 1.5-mm with 0.5-mm overlap slice thickness protocol. The intermarker distances for objects scanned perpendicular to the scanning beam were consistent but subject to demagnification in the range of 17% to 20% for both scanning protocols. CONCLUSION: The orientation of the object to the scanning beam and slice thickness protocol appear to have an impact on the accuracy and variability of linear measurements taken in the x, y, z axes.

Acrylic Resins↗
PubMedDate not supplied

Validation of the VITEK2 and the Advance Expert System with a collection of Enterobacteriaceae harboring extended spectrum or inhibitor resistant beta-lactamases.

The susceptibility testing accuracy of the VITEK2 system and the ability of the Advance Expert System (AES) to provide interpretive readings were evaluated against 86 extended spectrum (ESBL) and 6 inhibitor-resistant-TEM (IRT) beta-lactamases producing Enterobacteriaceae clinical isolates. VITEK2 MICs of 12 beta-lactams were compared with those obtained by the standard NCCLS microdilution technique. The overall essential agreement ( +/- 1 log dilution) was 87.8%. Discrepancies were mainly observed with cefepime (30.3% of total number of discrepancies), ceftazidime (21.2%), and cefotaxime (15.1%). MIC discrepancies were slightly higher in CTX-M- (14.4%) than in TEM- (12.5%) or SHV- (11.9%) type ESBL producers and were rare in IRT producers (1.4%). Overall interpretive agreement was 92.5% and minor, major, and very major errors were 5.4%, 1.7%, and 2.1%, respectively. The AES was able to identify an ESBL phenotype in 85 out of 86 isolates (98.8%) and an IRT phenotype in all 6 isolates harboring these enzymes, thus reducing very major errors to 0.9%. The VITEK2 system, in conjunction with the AES software, is a reliable tool for detection of ESBL or IRT producing Enterobacteriaceae isolates.

Anti-Bacterial Agents↗
PubMed2003

User acceptance of an anaesthesia information management system.

BACKGROUND AND OBJECTIVE: This paper describes the user acceptance of an anaesthesia information management system at the University Hospital in Giessen, Germany, after 5 yr of routine use. METHODS: A questionnaire with 75 items was distributed to all anaesthesiologists and anaesthetic nurses of the Department of Anaesthesiology. The questions were answered anonymously on a five-point Likert scale. RESULTS: The return rate was 60% (44 physicians and 24 nurses). The results indicated that the system generally met user expectations. The respondents thought that electronic record keeping improved the quality of their work, and they did not want to switch back to paper records. Problems arose with hardware placement and software features, e.g. coding tools for diagnoses and type of surgery. The perceived quality of training strongly influenced user acceptance. CONCLUSIONS: Despite the deficits revealed by the survey, the respondents did not want to switch back to manual record keeping. A structured user survey is a useful tool for the development, adaptation and implementation of an anaesthesia information management system. A training strategy that takes the needs of the users into account is recommended.

Adult↗
PubMed2005

Search for improved host architectures: application of de novo structure-based design and high-throughput screening methods to identify optimal building blocks for multidentate ethers.

This paper presents a computational approach to the deliberate design of improved host architectures. The approach, which involves the use of computer-aided design software, is illustrated by application to cation hosts containing multiple aliphatic ether oxygen binding sites. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential bidentate building block structures. Enhanced cation binding affinity can be achieved when highly organized building blocks are used to construct macrocyclic hosts.

Journal Article↗