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At least 631 records · Page 35Linked to original sources
PubMed1996

Linking patient medication data with laboratory information system.

Dozens of new drugs are taken into clinical use each year. Even if the clinicians were able to learn the most important therapeutic effects of the drugs they prescribe, they would still be unable to remember all of their minor effects. After storing patient related medication data on computerized patient records it is possible to build decision support modules which automatically remind of possible drug influences on laboratory tests and cause alarms or alerts of drug interactions. Medication profiles coded using the Anatomical Therapeutic Chemical-code (ATC-code) constitutes a valuable part of an Electronic Patient Record (EPR). In this paper, we describe the benefits of our system. By building links to commercially available drug and laboratory databases we can automatically inform clinicians on clinically relevant drug influences on laboratory test results.

Clinical Laboratory Information Systems↗
PubMed1986

The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition.

Organisms which have evolved on this earth are governed by multitudes of periodicities; tomorrow is another today, and the next year is going to be much like this year. Accordingly, the principle of repetitious recurrence pervades every aspect of life on this earth. Thus, individual genes in the genome have been duplicated and triplicated often to the point of redundancy, and each coding sequence consists of numerous variously truncated as well as variously base-substituted copies of the original primordial building block base oligomers and their allies. This principle even appears to govern the manifestations of human intellect; musical compositions also rely on this principle of repetitious recurrence. Accordingly, coding base sequences can be transformed into musical scores using one set rule. Conversely, musical scores can be transcribed to coding base sequences of long open reading frames.

Animals↗
PubMed1990

Attenuation correction in SPECT based on transmission studies and Monte Carlo simulations of build-up functions.

The quantitative information in SPECT images is distorted by photon attenuation and contribution of photons scattered in the object. It is, therefore, important to know the distribution of different attenuating tissues in order to be able to perform a proper attenuation correction. A correction method, based on correcting one pixel at a time by using density maps and build-up functions, has been developed. The density map has been produced by transmission measurements of the object using an external, solid 57Co flood source mounted on the scintillation camera head. The outline of the object is accurately defined by the map since the density values outside the object are very close to zero. The build-up of photons scattered in the object has been simulated by a Monte-Carlo code. SPECT-studies with 99mTc, 201T1 and 111In line sources in different parts of a non homogeneous Alderson phantom have been performed. The emission images have been corrected for photon attenuation using the measured density maps and the simulated build-up functions. The results show that quantitative measurements of the radioactivity in nonhomogeneous area can be accomplished to within +/- 10% for different radionuclides by using the attenuation correction described.

Algorithms↗
PubMed2005

Building medical ontologies based on terminology extraction from texts: an experimentation in pneumology.

Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri do not fit computer processing. We think the automation of the coding task requires a conceptual modelling of medical items: an ontology. Our objective is to help pneumologists code acts and diagnoses with a software that represents medical knowledge by an ontology of the concerned specialty. The main research hypothesis is to apply natural language processing tools to corpora to develop the resources needed to build the ontology. In this paper, our objective is twofold: we have to build the ontology of pneumology and we want to develop a methodology for the knowledge engineer to build various types of medical ontologies based on terminology extraction from texts.

Humans↗
PubMedDate not supplied

Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations.

An algorithm for encoding long strings of building blocks, like 4 DNA bases (adenine-A, cytosine-C, thymine-T, and guanidine-G), 20 natural amino acids (from Alanine Ala to Valine-Val, plus the stop triplet), or all 64 possible base triplets (from AAA to TTT), into "zigzag" or "spectrum-like" representations is suggested. The new encoding scheme can be derived in the 3-, 2-, or 1-dimensional form depending on the user's wishes. The only information, besides the string for which the "spectrum-like" representation is sought, is the initial positioning of the complete set of units from which the string is composed, i.e., four positions for A, C, G, and T, or 20 positions for natural amino acids plus stop, etc. This initial positioning can be initialized in either the 3-, 2-, or 1-D form. As an illustration of the suggested encoding scheme of the visual and chemometric comparison of the first 10 exon strings of the beta globin gene of 10 different species, each string consisting of about 100 basic amino acids long is shown.

Algorithms↗
PubMed1993

VISTAnet: interactive real-time calculation and display of 3-dimensional radiation dose: an application of gigabit networking.

Three-dimensional treatment planning can allow the clinician to create plans that are highly individualized for each patient. However, in lifting the constraints traditionally imposed by 2-dimensional planning, the clinician is faced with the need to compare a much larger number of plans. Although methods to automate that process are being developed, it is not yet clear how well they will perform. VISTAnet is a 3 year collaborative effort between the Departments of Radiation Oncology and Computer Science at the University of North Carolina, the North Carolina Supercomputing Center, BellSouth, and GTE with the medical goal of providing real-time 3-dimensional radiation dose calculation and display. With VISTAnet technology and resources, the user can inspect 3-dimensional treatment plans in real-time along with the associated dose volume histograms and can fine tune these plans in real-time with regard to beam position, weighting, wedging, and shape. Thus VISTAnet provides an alternate and, possibly, complementary approach to computerized searches for optimal radiation treatment plans. Building this system has required the development of very fast radiation dose code, methods for simultaneously manipulating and modifying multiple radiation beams, and new visualizations of 3-dimensional dose distributions.

Computer Communication Networks↗
PubMed2003

From humble neural beginnings comes knowledge of numbers.

Following a recent report that monkey prefrontal cortex contains cells that represent number concepts, Nieder and Miller investigated the scale used to code numbers. In this issue of Neuron, they report that prefrontal cells use the same scale (Weber's Law) used by sensory neurons to code stimulus intensity, suggesting how abstract cognitive operations may arise from simpler building blocks that humans share with other animals.

Animals↗
PubMed2000

The role of male partners in women's decision making regarding hysterectomy.

Although hysterectomy is a frequently performed surgical procedure, little is known about how women make decisions regarding hysterectomy. This report details the women's perceptions of male partners' knowledge and attitudes about hysterectomy and the role women expect or allow men to play in their decision-making process. Seventeen focus groups were conducted with a total of 82 African American and Caucasian women aged 30-65 years in two coastal counties of South Carolina. Transcripts were coded and analyzed using the nonnumerical unstructured data indexing searching and theory building (QSR NUD*IST) software program. Results indicate that women perceive men to be not well informed or knowledgeable about hysterectomy, to be concerned about the quality of sexual relations after hysterectomy, and, in some cases, to be neutral about hysterectomy. African American women reported that men hold more negative perceptions about hysterectomized women. Caucasian women stressed men's inability to understand what a woman is going through and men's concern with the hysterectomy's effect on their own egos. Nonhysterectomized women felt that men would be more bothered by a surgical procedure that left more visible effects (such as mastectomy). These women defined a limited role for men in their decision making regarding hysterectomy, consisting of discussion and offering of support/sympathy, but they reserved the actual decision for themselves. In a few instances, women accorded men a role in the hysterectomy decision based on a religious interpretation of marriage. Intervention programs are recommended that target women and their partners together, using hysterectomized women and their partners as peer educators.

Adult↗
PubMed2026

Pretraining improves prediction of genomic datasets across species.

MOTIVATION: Recent studies suggest that deep neural network models trained on thousands of human genomic datasets can accurately predict genomic features, including gene expression and chromatin accessibility. However, training these models is computation- and time-intensive, and datasets of comparable size do not exist for most other organisms. RESULTS: Here, we identify modifications to an existing state-of-the-art model that improve model accuracy while reducing training time and computational cost. Using this streamlined model architecture, we investigate the ability of models pretrained on human genomic datasets to transfer performance to a variety of different tasks. Models pretrained on human data but fine-tuned on genomic datasets from diverse tissues and species achieved significantly higher prediction accuracy while significantly reducing training time compared to models trained from scratch, with Pearson correlation coefficients between experimental results and predictions as high as 0.8. Further, we found that including excessive training tasks decreased model performance and that this decrease could be partially but not completely rescued by fine-tuning. Thus, simplifying model architecture, applying pretrained models, and carefully considering the number of training tasks may be effective and economical techniques for building new models across data types, tissues, and species. AVAILABILITY AND IMPLEMENTATION: Code is available on GitHub and Figshare: https://github.com/optimizedlearning/genomicsML, https://doi.org/10.6084/m9.figshare.31796116.

Genomics↗
PubMed1988

Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.

Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has provided useful structural information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinases to provide a structurally based sequence alignment: alpha-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat mast cell protease 2 (RMCP2). The root mean square differences in alpha-carbon atom positions among these four structures when compared in a pairwise fashion range from 0.79 to 0.97 A for structurally equivalent residues. The sequences of the two lymphocyte enzymes were then aligned to these proteinases using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. With RMCP2 as a template for CCP1 and the two enzymes RMCP2 and BT as templates for HF, the molecular models were constructed. Intramolecular steric clashes that resulted from the replacement of amino acid side chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angles in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginine residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 position of the substrate. Both CCP1 and HF have a free cysteine in the segment of polypeptide 88 to 93.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2006

Driving out errors through tight integration between software and automation.

A clear case has been made for using clinical IT to improve medication safety, particularly bar-code point-of-care medication administration and computerized practitioner order entry (CPOE) with clinical decision support. The equally important role of automation has been overlooked. When the two are tightly integrated, with pharmacy information serving as a hub, the distinctions between software and automation become blurred. A true end-to-end medication management system drives out errors from the dockside to the bedside. Presbyterian Healthcare Services in Albuquerque has been building such a system since 1999, beginning by automating pharmacy operations to support bar-coded medication administration. Encouraged by those results, it then began layering on software to further support clinician workflow and improve communication, culminating with the deployment of CPOE and clinical decision support. This combination, plus a hard-wired culture of safety, has resulted in a dramatically lower mortality and harm rate that could not have been achieved with a partial solution.

Humans↗
PubMed2004

Single-trabecula building block for large-scale finite element models of cancellous bone.

Recent development of high-resolution imaging of cancellous bone allows finite element (FE) analysis of bone tissue stresses and strains in individual trabeculae. However, specimen-specific stress/strain analyses can include effects of anatomical variations and local damage that can bias the interpretation of the results from individual specimens with respect to large populations. This study developed a standard (generic) 'building-block' of a trabecula for large-scale FE models. Being parametric and based on statistics of dimensions of ovine trabeculae, this building block can be scaled for trabecular thickness and length and be used in commercial or custom-made FE codes to construct generic, large-scale FE models of bone, using less computer power than that currently required to reproduce the accurate micro-architecture of trabecular bone. Orthogonal lattices constructed with this building block, after it was scaled to trabeculae of the human proximal femur, provided apparent elastic moduli of approximately 150 MPa, in good agreement with experimental data for the stiffness of cancellous bone from this site. Likewise, lattices with thinner, osteoporotic-like trabeculae could predict a reduction of approximately 30% in the apparent elastic modulus, as reported in experimental studies of osteoporotic femora. Based on these comparisons, it is concluded that the single-trabecula element developed in the present study is well-suited for representing cancellous bone in large-scale generic FE simulations.

Animals↗
PubMed1997

Toward building an international consensus in professional values.

Although the importance of professional values has been espoused and national codes for nurses exist, there is a lack of systematic study to ascertain the commonalities of values among professional nurses. As part of a larger international study of professional values, nursing students from England and the USA (n = 130) were surveyed to determine congruence of values. The Professional Values Scale (PVS) instrument was used to collect data. Results showed a high degree of congruence among nursing students. The incongruencies found may be related to cultural differences in education and practice.

Adult↗
PubMed2005

Benchmarking of MCNP for calculating dose rates at an interim storage facility for nuclear waste.

During the operation of research facilities at Research Centre Jülich, Germany, nuclear waste is stored in drums and other vessels in an interim storage building on-site, which has a concrete shielding at the side walls. Owing to the lack of a well-defined source, measured gamma spectra were unfolded to determine the photon flux on the surface of the containers. The dose rate simulation, including the effects of skyshine, using the Monte Carlo transport code MCNP is compared with the measured dosimetric data at some locations in the vicinity of the interim storage building. The MCNP data for direct radiation confirm the data calculated using a point-kernel method. However, a comparison of the modelled dose rates for direct radiation and skyshine with the measured data demonstrate the need for a more precise definition of the source. Both the measured and the modelled dose rates verified the fact that the legal limits (<1 mSv a(-1)) are met in the area outside the perimeter fence of the storage building to which members of the public have access. Using container surface data (gamma spectra) to define the source may be a useful tool for practical calculations and additionally for benchmarking of computer codes if the discussed critical aspects with respect to the source can be addressed adequately.

Benchmarking↗
PubMed2000

Smoke knows no boundaries: legal strategies for environmental tobacco smoke incursions into the home within multi-unit residential dwellings.

OBJECTIVE: To describe legal theories that non-smoking residents of multiple occupancy buildings may employ when affected by environmental tobacco smoke (ETS) from neighbouring units. DESIGN: Legal research was conducted in several US states. Research was performed among statutes and regulations. State health regulations were examined as well as common law claims of nuisance, warranties of habitability, and the right of quiet enjoyment. RESULTS: Through the use of state regulations, such as a sanitary code, several states provide general language for protecting the health of residents in multi-unit buildings. State law also supports more traditional claims of nuisance, warranties of habitability, and the right of quiet enjoyment. CONCLUSIONS: The use of state regulations has the potential to provide an effective, existing vehicle for resolution of ETS incursion problems. The general health protection language of the regulations, in conjunction with the latest evidence of the harmful effects of ETS, gives state agencies authority to regulate environmental tobacco smoke incursions among apartments in multi-unit dwellings. Where state regulations are not available, other common law legal remedies may be available.

Air Pollution, Indoor↗
PubMed1983

Recurrence of 49-base decamers, nonomers, and octamers within mouse C mu gene of Ig heavy chain and its primordial building block.

Within the published 2,168-base-long mouse C mu gene of Ig heavy chain consisting of four coding and four noncoding segments, 2 base decamers, 8 nonomers, and 39 octamers recurred. Recurring base heptamers (about 100) and hexamers (about 350) were simply too numerous to merit individual identification. In spite of extensive overlaps between these recurring base decamers to hexamers, they occupied nearly the entire length of mouse Ig C mu gene. As with other genes of the beta-sheet-forming beta 2-microglobulin family, the Ig C mu gene (flanking and intervening noncoding sequences included) is not a unique sequence but rather it is degenerate repeats of the 45-base-long primordial building-block sequence uniquely its own. This primordial building block must originally have specified the 15-amino-acid-residue-long primordial arm of beta-sheet-forming loops, the characteristics of the beta 2-microglobulin family of polypeptides.

Amino Acid Sequence↗
PubMed2004

Effects of treatment distance and field size on build-up characteristics of Monte Carlo calculated absorbed dose for electron irradiation.

Surface, build-up and depth dose characteristics of a monoenergetic electron point source simulated by Monte Carlo code MCNP4c for varying field size and SSD are extensively studied in this paper. MCNP4c (Monte Carlo N-Particle Transport Code System) has been extensively used in clinical dose simulation for its versatility and powerful geometrical coding tool. A sharp increase in PDD is seen with the Monte Carlo Modelling immediately at the surface within the first 0.2 mm. This effect cannot be easily measured by experimental instruments for electron contamination, and may lead to a clinical underdosing of the basal cell layer, which is one of the most radiation sensitive layers and the main target for skin carcinogenesis. A high percentage build-up dose for electron irradiation was shown. No significant effects in surface PDDs were modelled with different SSD values from 95 cm to 125 cm. Three depths were studied in detail, these being 0.05 mm, the lower depth of the basal cell layer; 0.95 mm, the lower depth of the dermal layer; and 0.95 cm, a position within the subcutaneous tissue. Results showed only small surface PDD differences were modelled for SSD variations from 95 cm to 125 cm and field sizes variation from the values between 5 cm and 10 cm squares to 25 cm. When the field side length is smaller than this, the surface dose shows an increasing trend by about 7% at 5 x 5 cm2.

Body Burden↗
PubMed2002

Parallelizing a DNA simulation code for the Cray MTA-2.

The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer. Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA. We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.

Algorithms↗