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At least 379 records · Page 21Linked to original sources
PubMed2005

A portable device for continuous analysis of dissolved gaseous mercury in natural waters.

A fully automatic device for continuous analysis of DGM (Dissolved Gaseous Mercury) concentration in natural waters, controlled by a Notebook, with a resolution time of 10-15 min, equipped with an Atomic Absorption Spectrometer with a detection limit of 0.5 pg, is described. A particular feature of this instrument is the portability, making its use suitable in remote locations by means of a car battery. Comparison of the results obtained using the device in the continuous mode and in the discrete mode shows good agreement taking into consideration that water samples were collected with shifting sampling times. To compare samples collected at the same time, a second analytical device, running in the discrete mode, was used. In this case results show that measurements performed with the discrete mode are slightly higher than the continuous one. Avoiding the sample handling it was possible to reduce the contamination from external sources and to achieve low instrumental blank values (1-2 pg). The field performance of this portable instrument was tested on seawater and lagoon water, where the DGM daily behaviour was measured. In agreement with several authors, a time shifting between DGM and solar radiation intensity higher than the instrumental resolution time was noted.

Environmental Monitoring↗
PubMed2000

Computer-aided video exposure monitoring.

A computer-aided video exposure monitoring system was used to record exposure information. The system comprised a handheld camcorder, portable video cassette recorder, radio-telemetry transmitter/receiver, and handheld or notebook computers for remote data logging, photoionization gas/vapor detectors (PIDs), and a personal aerosol monitor. The following workplaces were surveyed using the system: dry cleaning establishments--monitoring tetrachoroethylene in the air and in breath; printing works--monitoring white spirit type solvent; tire manufacturing factory--monitoring rubber fume; and a slate quarry--monitoring respirable dust and quartz. The system based on the handheld computer, in particular, simplified the data acquisition process compared with earlier systems in use by our laboratory. The equipment is more compact and easier to operate, and allows more accurate calibration of the instrument reading on the video image. Although a variety of data display formats are possible, the best format for videos intended for educational and training purposes was the review-preview chart superimposed on the video image of the work process. Recommendations for reducing exposure by engineering or by modifying work practice were possible through use of the video exposure system in the dry cleaning and tire manufacturing applications. The slate quarry work illustrated how the technique can be used to test ventilation configurations quickly to see their effect on the worker's personal exposure.

Aerosols↗
PubMed2002

Design and performance of the UCLH mark 1b 64 channel electrical impedance tomography (EIT) system, optimized for imaging brain function.

The UCLH Mark 1b is a portable EIT system that can address up to 64 electrodes, which has been designed for imaging brain function with scalp electrodes. It employs a single impedance-measuring circuit and multiplexer so that electrode combinations may be addressed flexibly using software. It operates in the relatively low frequency band between 225 Hz and 77 kHz, as lower frequencies produce larger changes during brain activity, and has a videocassette-sized headbox on a lead 10 m long, connected to a base box the size of a video recorder, and notebook PC, so that recordings may be made in ambulant subjects. Its performance was assessed using a resistor-capacitor network, and two saline-filled tanks-a cylindrical Perspex one and a latex one which contained a human skull. System signal-to-noise ratio was better than 50 dB and the maximum reciprocity error less than 10% for most frequencies. The CMMR was better than 80 dB at 38 kHz and a sponge, 20 mm across, which caused a local 12% impedance increase, was correctly localized in images. This suggests that the system has adequate performance to image impedance changes of 5-50% known to occur in the brain during normal activity, epilepsy or stroke; clinical trials to image these conditions are in progress.

Brain↗
PubMed2003

BioSPICE: access to the most current computational tools for biologists.

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Computational Biology↗
PubMed2006

The da Vinci robot.

BACKGROUND: One might assume from the title of this paper that the nuances of a complex mechanical robot will be discussed, and this would be correct. On the other hand, the date of the design and possible construction of this robot was 1495, a little more than five centuries ago. The key point in the title is the lack of a trademarked name, as Leonardo was the designer of this sophisticated system. His notes from the Codex Altanticus represent the foundation of this report. METHODS: English translations of da Vinci's notebooks are currently available. Beginning in the 1950s, investigators at the University of California began to ponder the significance of some of da Vinci's markings on what appeared to be technical drawings. Such markings also occur in his Codex Atlanticus (the largest single collection of da Vinci's sheets, consisting of 1119 separate pages and 481 folios) along with a large number of other mechanical devices. Continuing research at the Instituto e Museo di Storia della Scienza in Florence has yielded a great deal of information about Leonardo's intentions with regard to his mechanical knight. RESULTS: It is now known that da Vinci's robot would have had the outer appearance of a Germanic knight. It had a complex core of mechanical devices that probably was human powered. The robot had two independent operating systems. The first had three degree-of-freedom legs, ankles, knees, and hips. The second had four degrees of freedom in the arms with articulated shoulders, elbows, wrists, and hands. A mechanical analog-programmable controller within the chest provided the power and control for the arms. The legs were powered by an external crank arrangement driving the cable, which connected to key locations near each lower extremity's joints. Da Vinci also is known to have devised a programmable front-wheel-drive automobile with rack-and-pinion suspension mechanisms at age 26. He would recall this device again, when, at age 40, he is thought to have built a programmable automated lion, but by then, he had produced his own metal springs as well as drum-containing springs called tambours. He positioned his fusee to a stationary rotating power output shaft that would be used to power his programmable automaton. CONCLUSIONS: Part of the obscurity of da Vinci's robot comes from the difficulties interpreting Leonardo's markings. His designs precede any formal method of blueprint designing. The technical aspects had to be deciphered before anyone could even attempt to reproduce his intended device. This robotic device fits together with other pieces of evidence that link 15(th) Century automatons to da Vinci's design, namely the automated Tea Servers from Spain. As with many things from da Vinci, looking backward at this master leaves one with a pronounced sense of awe at his prescient view of the world.

Animals↗
PubMed1983

Food intake measurement: problems and approaches.

Sources of variance in dietary intake records were measured and compared. Eighteen graduate students recorded self-selected food intakes during a 30-day study. Subjects were divided into two groups and on alternating 5 consecutive day periods, one group weighted all food consumed and recorded it on tape recorders while the other group recorded estimated intake in small notebooks. An average of two, 24-h dietary recalls was also obtained from each subject and compared to previously estimated intake. The major contributions to total variance were within subject and between subject variance. There was no difference in the mean protein and energy intake recorded by weighing when compared to that recorded in household measures, but there was less variability in the records obtained by weighting intake. The 95% confidence limits were calculated both for the group's and an individual's intake for each method, these demonstrated that 1-day dietary record gave a reasonable estimate (within 15%) of the usual intake of the group. However, the 1-day record, regardless of which method used, gave a meaningless estimate of an individual's usual diet. The protein/energy ratios and the coefficient of interindividual variation are also reported.

Adult↗
PubMed2000

Mathematica packages for simulation of experimental genetics.

UNLABELLED: This note describes add-on packages for the Mathematica software system (Wolfram 1996) which allow simulation and analysis of both Mendelian and complex genetic traits in experimental crosses of plants or animals. AVAILABILITY: The add-on packages are freely available at http://www.mathsource.com/cgi-bin/msitem?0209-30 4. SUPPLEMENTARY INFORMATION: A tutorial notebook file is included with the packages at the mathsource site.

Animals↗
PubMed2026

phylobar: an R package for multiresolution compositional barplots in omics studies.

SUMMARY: Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce phylobar, an R package that interactively links stacked barplots with overview phylogenetic or taxonomic hierarchies. The interface allows users to collapse or expand subtrees, paint color palettes interactively, and search for specific taxa. This allows comparison across taxonomic resolutions that are hidden in static overviews. phylobar works with any omics data with hierarchical organization, including cell type hierarchies, as we demonstrate in a case study of immune cell composition in COVID-19 patients. AVAILABILITY AND IMPLEMENTATION: phylobar is available as an R package on GitHub. It uses the htmlwidgets library to link interactive D3 visualizations with R. The interactive plots can be embedded within R Markdown or Quarto notebooks, and views can be exported as vector graphics files. The package is open source and documented at https://mkdiro-O.github.io/phylobar.

Software↗
PubMed2026

Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation.

MOTIVATION: The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used separate database instances and backend technologies to manage integrated phenotypic and genotypic data. RESULTS: We discuss the challenges encountered when integrating dispersed data to serve through a single interface such as the Plant Breeding Application Programming Interface, BrAPI. We examine how the consistent mappability of genebank data to the BrAPI model can enable the implementation of effective services. The advantages of BrAPI in transparently linking distributed data entities through embedded, unique identifiers are highlighted. We present a technical solution involving a BrAPI proxy, which combines and merges separate BrAPI endpoints. Finally, we demonstrate the AGENT BrAPI implementation with an illustrative example that validates a suggested SNP for a trait from the literature by linking phenotypic, genotypic and passport data. AVAILABILITY AND IMPLEMENTATION: The BrAPI proxy implementation and documentation is available at the Python Package Index (https://pypi.org/project/brapi-proxy) and archived in Zenodo (doi: 10.5281/zenodo.19436445). SUPPLEMENTARY INFORMATION: A Jupyter Notebook file for the validation example using a marker-trait relationship found in the literature.

Phenotype↗
PubMed2026

MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays.

MOTIVATION: Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to detect CNVs, which can be used in genetic association tests. Unlike genotypes, CNV detection in microarrays requires the use of observed intensity signals at each probe, which limits the imputability for analyses that span multiple array types. Thus far, a consensus set of probes (those present on all arrays) has been used to circumvent the problem of differing array-specific sensitivities. This has led to excessive reduction in overall sensitivity since arrays can have an undesirably low probe overlap. To overcome this limitation, we developed MarkerMatch, a proximity-based algorithm that matches probes across different genotyping microarrays to maximize the number of probes considered in the CNV calling algorithm, thereby increasing the resolution and sensitivity while preserving precision. RESULTS: By analyzing CNV calls from 4906 individuals genotyped across three different arrays, we show that the MarkerMatch approach improves sensitivity by increasing the density of probes available for CNV calling while maintaining precision or improving it relative to the current practice (e.g. use of consensus probes only). We further demonstrate that MarkerMatch matches the CNV detection from current practice in terms of F1 score and PPV for larger CNVs. We also optimize MarkerMatch parameters, DMAX and Method, and find an optimal DMAX setting at 10 kb, with no clear optimal candidate based on Method, indicating that parameters for this metric should be determined on a use case basis. AVAILABILITY: The R package for MarkerMatch is available at: https://github.com/FranjoIM/MarkerMatch. The code used for analysis and implementation is available at: https://doi.org/10.5281/zenodo.18460979. The live notebook is available at https://fivankovic.notion.site/2026-markermatch.

DNA Copy Number Variations↗
PubMed2026

PMGen: from peptide-MHC structure prediction to peptide generation.

MOTIVATION: Accurate structural modeling of peptide-major histocompatibility complex (pMHC) complexes is essential for structure-driven immunotherapy design, yet current prediction tools suffer from narrow class coverage, restricted peptide lengths, insufficient accuracy, and a lack of built-in structure-aware peptide sampling. Consequently, most mimotope and altered peptide ligand designs rely solely on sequence substitution, leaving spatial and biophysical insights from pMHC structures largely unexploited. RESULTS: We introduce peptide-MHC generator (PMGen), an integrated framework for structure prediction and structure-guided design of variable-length peptides across MHC Class I and II. PMGen enforces anchor constraints within AlphaFold2 through two complementary strategies, initial guess and template engineering, achieving state-of-the-art structural fidelity without model fine-tuning. On a comprehensive benchmark, PMGen outperforms all existing methods, yielding median peptide-core Cα RMSDs of 0.62 Å for MHC-I and 0.33 Å for MHC-II. We show that PMGen can recover incorrectly predicted anchor positions and that AlphaFold pLDDT scores enable sequence-independent binding-core identification. Applied to a published neoantigen/wild-type pair, PMGen accurately captures mutation-induced conformational changes. Beyond structure prediction, we show that ProteinMPNN sampling on PMGen-predicted backbones yields higher affinity peptides while preserving the parental 3D conformation. Using PMGen to generate 63 817 high-confidence pMHC structures as training data, we further improve ProteinMPNN's peptide sequence recovery from 0.14 to 0.64 on a test set of 85 unseen MHC-I alleles, highlighting the value of accurate predicted structures for downstream machine learning tasks. AVAILABILITY AND IMPLEMENTATION: PMGen is freely available at https://github.com/soedinglab/PMGen, with an interactive Colab notebook at https://colab.research.google.com/github/soedinglab/PMGen/blob/master/colab.ipynb.

Peptides↗
PubMed2026

EscaPRRS-ORF5: a structure-aware evolutionary framework for prioritizing immune escape-prone variants in porcine reproductive and respiratory syndrome virus.

MOTIVATION: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a rapidly evolving RNA virus causing significant economic losses, posing a formidable challenge to vaccine efficacy due to its high mutational variability and immune escape. As the viral mutants evolve, their ability to sustain in population is driven by a range of host biology factors such as receptor binding, fusion, and uncoating. Existing tools that predict viral fitness and escape propensities rely heavily on extensive, up-to-date sequence data and lack integration of biochemical host interactions, limiting mechanistic understanding of the mutational landscape. We introduce Esca, a sequence-only toolchain framework that identifies immune escape-prone residues by exhaustively scanning each residue position for all amino acid substitutions using a Bayesian Variational Autoencoder (VAE) trained on protein language model embeddings. We demonstrate Esca on the GP5(ORF5) glycoprotein of PRRSV (EscaPRRS-ORF5) by training on ESM-2 embeddings of 32 146 GP5 sequences (2015-2022) spanning 140 sub-lineages. RESULTS: Despite being trained only on GP5 sequence data, EscaPRRS-ORF5 recovered 85.7% of the surface-exposed receptor binding interfaces as escape-prone regions. We use a mutation-sensitive fitness scoring scheme that goes beyond Hamming distances, to predict antibody escape tendencies, supporting surveillance of (re) emerging PRRSV variants. We do not claim that ORF5 alone captures PRRSV evolution or serves as a surveillance endpoint; rather, Esca offers a scalable path toward whole-genome, structure-aware surveillance. AVAILABILITY AND IMPLEMENTATION: EscaPRRS-ORF5 is freely available at https://doi.org/10.6084/m9.figshare.32661033 with an interactive Colab notebook at https://colab.research.google.com/drive/1TEgzAhPwvNAZ01VXeJbIFibfri2jnDA5? usp=sharing.

Porcine respiratory and reproductive syndrome viru↗
PubMed2026

Comparison of classic statistical methods and machine learning approaches to classify readiness.

MOTIVATION: Predicting physical and cognitive readiness in warfighters is critical for mission success. These predictions can be improved by identifying key biomarkers using multiple omics modalities. The MASTR-E study conducted by McKetney and colleagues is one of the most comprehensive multi-omics studies of saliva samples collected from warfighters, which also applied classic linear statistical (CLS) techniques to discover key biomarkers of readiness. Aligning with McKetney et al.'s assumptions, we operationalize readiness as a binary proxy, where pre-mission samples are labeled as "ready" to reflect a rested, unstressed physiological baseline, while post-mission samples are labeled "not ready" to reflect cumulative physical and cognitive load from the mission. As such, readiness here is not a direct biological or physiological construct, but an inferred state likely dominated by stress-related physiological changes. This assumption and definition is discussed further in the Introduction and Limitations sections. Here, we apply machine learning (ML) analyses to better assess generalizability, consider hidden interactions, and identify nonlinear patterns in the data. We investigated whether ML approaches could predict readiness and identify relevant biomarkers. ML models were trained on proteomics-only or metabolomics-only datasets to classify participants as ready or not ready and important model features were considered as putative biomarkers. Training and testing datasets were curated for two objectives: (i) recognize biomolecular signatures indicative of readiness within the same donor and (ii) assess generalizability across warfighters by withholding donors for testing. RESULTS: Proteomics-based models achieved AUCs of 0.907 ± 0.034 and 0.860 ± 0.063 for Objectives 1 and 2, respectively. Metabolomics-based models achieved Objective 1 AUC of 0.994 ± 0.007 and Objective 2 AUC of 0.993 ± 0.010. Comparative analysis with existing literature validates the model's feature importances, but the identified putative biomarkers significantly differ from those discovered through CLS analyses, as only one ML-identified biomarker overlapping with those identified through CLS methods. We show that these ML models and identified features are more robust to noise and generalizable across participants than those identified using CLS methods. AVAILABILITY: The analysis pipelines are provided as Jupyter notebooks, including all code and documentation, and are available publicly on GitHub at {https://github.com/netrias/ReadinessClassification}.

Machine Learning↗
PubMed2000

Why do life spans differ? Partitioning mean longevity differences in terms of age-specific mortality parameters.

Populations typically differ in mean life spans because of genetic, environmental, or experimental factors. In this paper methods are presented that clarify the relationship between differences in the longevity of two populations and differences in their underlying age-specific patterns of mortality. Data are examined from rodent and fruit fly (Drosophila melanogaster) experiments that investigated the longevity effects of a variety of environmental and genetic manipulations, including temperature, dietary restriction, laboratory selection for increased longevity, and severe inbreeding. Analyses suggest that longevity differences mediated by temperature and dietary restriction result predominantly from differences in the rate of increase in mortality with age. Increases in longevity through laboratory selection result primarily from a reduction in baseline mortality and not a slowing of the rate of aging. Although the methods are applied primarily in the context of simple mathematical models of mortality (e.g., the Gompertz model), they are quite general and can be applied to mortality models of arbitrary complexity. Mathematica protocols ("notebooks") and computer software have been developed to perform all the analyses discussed and are available from the first author.

Age Factors↗
PubMed2001

Online personal medical records: are they reliable for acute/critical care?

OBJECTIVE: To provide an introduction to Internet-based Online Personal Medical Records (OPMRs), to assess their use and limitations in acute/critical care situations, and to identify potential improvements that could increase their usefulness. DESIGN: A review of publicly available Internet-based OPMRs conducted in April 2001. DATA SOURCES: Twenty-nine OPMR sites were identified in March 2000 using ten Internet search engines with the search term "Personal Medical Records." Through 2000 and 2001, an additional 37 sites were identified using lists obtained from trade journals and through the author's participation in standards-setting meetings. MEASUREMENTS: Each publicly available site was reviewed to assess suitability for acute/critical care situations using four measures developed by the author and for general use using eight measures developed in a standards-setting process described in the article. RESULTS: Of the 66 companies identified, only 16 still offer OPMRs that are available to the public on the Internet. None of these met all of the evaluation measures. Only 19% had rapid emergency access capabilities and only 63% provided medical summaries of the record. Security and confidentiality issues were well addressed in 94% of sites. Data portability was virtually nonexistent because all OPMRs lacked the ability to exchange data electronically with other OPMRs, and only two OPMRs permitted data transfer from physician electronic medical records. Controls over data accuracy were poor: 81% of sites allowed entry of dates for medical treatment before the patient's date of birth, and one site actually gave incorrect medical advice. OPMRs were periodically inaccessible because of programming deficiencies. Finally, approximately 40 sites ceased providing OPMRs in the past year, with the probable loss of patient information. CONCLUSIONS: Most OPMRs are not ready for use in acute/critical care situations. Many are just electronic versions of the paper-based health record notebooks that patients have used for years. They have, however, great promise and, with further development, could form the basis of a new medical record system that could contribute to improving the quality of medical care.

Confidentiality↗
PubMed2005

Matching point-of care devices to clinicians for positive outcomes.

Home care clinicians' use of point-of-care (POC) technology has increased 63% in the past 5 years. Although there are more POC system choices, matching the right device to each clinician's role is a challenge. This article clarifies the uses of laptop or notebook computer, personal digital assistants (PDAs), telephony, or automated telehealth, suggesting ways these technologies can result in clinical efficiencies, care coordination, and regulatory compliance.

Automation↗
PubMed2001

Enhancing an appointment diary on a pocket computer for use by people after brain injury.

People with memory loss resulting from brain injury benefit from purpose-designed memory aids such as appointment diaries on pocket computers. The present study explores the effects of extending the range of memory aids and including games. For 2 months, 12 people who had sustained brain injury were loaned a pocket computer containing three purpose-designed memory aids: diary, notebook and to-do list. A month later they were given another computer with the same memory aids but a different method of text entry (physical keyboard or touch-screen keyboard). Machine order was counterbalanced across participants. Assessment was by interviews during the loan periods, rating scales, performance tests and computer log files. All participants could use the memory aids and ten people (83%) found them very useful. Correlations among the three memory aids were not significant, suggesting individual variation in how they were used. Games did not increase use of the memory aids, nor did loan of the preferred pocket computer (with physical keyboard). Significantly more diary entries were made by people who had previously used other memory aids, suggesting that a better understanding of how to use a range of memory aids could benefit some people with brain injury.

Appointments and Schedules↗
PubMed2004

Internet-based learning.

The Internet, with established and newly appearing websites, is becoming a more integral part of orthopaedic education every day. We review some of the well-known resources on the Internet (Orthogate, OrthoNet, American Academy of Orthopaedic Surgeons site, Orthopedic Hyperguide, WorldOrtho, Wheeless's Textbook of Orthopaedics, Orthoteers, AO North America site, University of Iowa Virtual Hospital texts, and South Australian Orthopaedic Registrars' Notebook) and reports the results of a survey of 35 orthopaedic surgery residents and 24 attending orthopaedic surgeons on the use of orthopaedic knowledge resources on the World Wide Web. The top three most commonly used online sites by the residents were Wheeless's Textbook of Orthopaedics, the American Academy of Orthopaedics Surgeons website, and Orthopedics Hyperguide. According to the survey, all 35 residents used online resources for learning, giving preference to online textbooks when looking for clinical information and online practice examinations when preparing for the in-training (OITE) or board examinations. Among the attending physicians, 19 (79%) used the Internet. Their most commonly used online sites were the American Academy of Orthopaedics Surgeons website, AO North America site, and Wheeless's Textbook of Orthopaedics. The attending physicians also preferred online textbooks to other online resources. Also provided in this article is a discussion of our idea for a future comprehensive, accurate, and constantly updated orthopaedic online resource that uses already available technology.

Computer-Assisted Instruction↗