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PubMed2004

The periodic safety update report as a pharmacovigilance tool.

The periodic safety update report for marketed drugs (PSUR) was designed to be a stand-alone document that allows a periodic but comprehensive assessment of the worldwide safety data of a marketed drug or biological product. The PSUR can be an important source for the identification of new safety signals, a means of determining changes in the benefit-risk profile, an effective means of risk communication to regulatory authorities and an indicator for the need for risk management initiatives, as well as a tracking mechanism monitoring the effectiveness of such initiatives. For these reasons, the PSUR can be an important pharmacovigilance tool. Numerous steps are involved in the PSUR process including: intake of adverse drug reaction information, case processing, data retrieval, data analysis, and medical review and risk assessment. These processes are heavily reliant on the availability of adequate resources. An overarching principle throughout the PSUR process is the need for a proactive approach in order to identify the critical steps in the process and to have a clear understanding of the consequences of any critical 'mis-step'. With this information comes appropriate planning, building quality into each step of the PSUR process and monitoring performance will maximise the likelihood of generating a quality report. Any failure of a key PSUR process will have the opposite effect - a poor quality report that will give little insight into emerging safety signals or provide misleading information that can adversely affect public health. A pragmatic approach that will avoid or minimise these pitfalls includes the following: adequate resource planning, training, development of 'scripts' designed to maximise the capture of key information for medically important reactions, standardised and harmonised Medical Dictionary for Regulatory Activities (MedDRA) coding procedures, pre-specified search criteria for data retrieval, ongoing medical review, and metrics to evaluate the effectiveness and efficiencies of these processes. With these quality measures in place, the utility of the PSUR as an effective pharmacovigilance tool is enhanced.

Adverse Drug Reaction Reporting Systems↗
PubMed2000

Expert practice in physical therapy.

BACKGROUND AND PURPOSE: The purpose of this qualitative study was to identify the dimensions of clinical expertise in physical therapy practice across 4 clinical specialty areas: geriatrics, neurology, orthopedics, and pediatrics. SUBJECTS: Subjects were 12 peer-designated expert physical therapists nominated by the leaders of the American Physical Therapy Association sections for geriatrics, neurology, orthopedics, and pediatrics. METHODS: Guided by a grounded theory approach, a multiple case study research design was used with each of the 4 investigators studying 3 therapists working in one clinical area. Data were obtained through nonparticipant observation, interviews, review of documents, and analysis of structured tasks. Videotapes made during selected therapist-patient treatment sessions were used as a stimulus for the expert therapist interviews. Data were transcribed, coded, and analyzed through the development of 12 case reports and 4 composite case studies, one for each specialty area. RESULTS: A theoretical model of expert practice in physical therapy was developed that included 4 dimensions: (1) a dynamic, multidimensional knowledge base that is patient-centered and evolves through therapist reflection, (2) a clinical reasoning process that is embedded in a collaborative, problem-solving venture with the patient, (3) a central focus on movement assessment linked to patient function, and (4) consistent virtues seen in caring and commitment to patients. CONCLUSION AND DISCUSSION: These findings build on previous research in physical therapy on expertise. The dimensions of expert practice in physical therapy have implications for physical therapy practice, education, and continued research.

Clinical Competence↗
PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗
PubMed2004

Efforts towards the design of 'teflon' proteins: in vivo translation with trifluorinated leucine and methionine analogues.

In vivo incorporation of monofluorinated noncanonical amino acids into recombinant proteins has been well-established for decades. Proteins fluorinated in this way proved to be useful tools for many practical applications. In contrast, trifluorinated amino acids have been incorporated in only a few peptides and relatively small proteins by using expression systems in living cells. A novel class of proteins with a fluorous core can be envisaged only if full replacement of the core-building hydrophobic and aliphatic amino acids such as leucine or methionine with the related analogues trifluoromethionine and trifluoroleucine would be feasible. However, our systematic efforts to introduce these amino acids in larger proteins (over 10 Da) that contain different structural motifs clearly show that only partial substitutions are possible. The reasons are high toxicity of these substances and difficulties to accommodate them into the compact cores of natural proteins without adverse effects on their structural integrity. Therefore, engineering of such three dimensional 'Teflon'-like structures would require, besides an expansion of the amino acid repertoire of the genetic code, a de novo protein design as well.

Drug Design↗
PubMed2004

Identification of novel and rare mutations in California Hispanic and African American cystic fibrosis patients.

In ethnic heterogeneous California, complete genetic information is currently lacking to build solid population-based cystic fibrosis (CF) screening programs because a large proportion of mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR/ABCC7) are still unknown, especially in non-Caucasian patients. A total of 402 [46 African American+356 Hispanic] Hispanic and African American patients from California CF patient registry were included in this study. Patients with at least one unidentified mutant allele were asked to donate blood samples for further analysis, first by Genzyme Genetics for a panel of 87 known mutations, followed by temporal temperature gradient gel electrophoresis (TTGE) scanning of the entire coding exons of CFTR gene. A total of eight novel mutations; one missense mutation, one splice-site mutation and six frame-shift mutations were identified. In addition to the eight novel mutations, 20 [corrected] distinct rare mutations that are not in the current available commercial mutation panels were identified by TTGE. The overall detection rate was raised to 95.7% for African American and 94.5% for Hispanic. The discovery of recurrent rare and novel mutations improves the diagnosis and care of persons with CF and improves our ability to adequately and equitably provide screening and genetic counseling services to non-Caucasians.

Adolescent↗
PubMed2025

Whole-genome sequencing of 490,640 UK Biobank participants.

Whole-genome sequencing provides an unbiased and complete view of the human genome and enables the discovery of genetic variation without the technical limitations of other genotyping technologies. Here we report on whole-genome sequencing of 490,640 UK Biobank participants, building on previous genotyping effort1. This advance deepens our understanding of how genetics associates with disease biology and further enhances the value of this open resource for the study of human biology and health. Coupling this dataset with rich phenotypic data, we surveyed within- and cross-ancestry genomic associations and identified novel genetic and clinical insights. Although most associations with disease traits were primarily observed in individuals of European ancestries, strong or novel signals were also identified in individuals of African and Asian ancestries. With the improved ability to accurately genotype structural variants and exonic variation in both coding and UTR sequences, we strengthened and revealed novel insights relative to whole-exome sequencing2,3 analyses. This dataset, representing a large collection of whole-genome sequencing data that is available to the UK Biobank research community, will enable advances of our understanding of the human genome, facilitate the discovery of diagnostics and therapeutics with higher efficacy and improved safety profile, and enable precision medicine strategies with the potential to improve global health.

Humans↗
PubMed2017

Future of rAAV Gene Therapy: Platform for RNAi, Gene Editing, and Beyond.

The use of recombinant adeno-associated viruses (rAAVs) ushered in a new millennium of gene transfer for therapeutic treatment of a number of conditions, including congenital blindness, hemophilia, and spinal muscular atrophy. rAAV vectors have remarkable staying power from a therapeutic standpoint, withstanding several ebbs and flows. As new technologies such as clustered regularly interspaced short palindromic repeat genome editing emerge, it is now the delivery tool-the AAV vector-that is the stalwart. The long-standing safety of this vector in a multitude of clinical settings makes rAAV a selling point in the advancement of approaches for gene replacement, gene knockdown, gene editing, and genome modification/engineering. The research community is building on these advances to develop more tailored delivery approaches and to tweak the genome in new and unique ways. Intertwining these approaches with newly engineered rAAV vectors is greatly expanding the available tools to manipulate gene expression with a therapeutic intent.

Dependovirus↗
PubMed1995

Building zinc fingers by selection: toward a therapeutic application.

A phage display approach was utilized to modify the specificity of each of the three fingers of the murine transcription factor Zif268. Selections were performed by using the consensus binding sequence of the natural protein and a conserved sequence in the genome of the type 1 human immunodeficiency virus. By using an extensive randomization strategy, the entire 3-bp specificity of a finger has been changed. Rapid analysis of selected zinc fingers was facilitated by the development of an immunoscreening assay for DNA binding and specificity. To investigate the mechanism of binding and specificity, the binding kinetics of Zif268 and 10 selected variants were determined in real time with an assay based on surface plasmon resonance. Differential mechanisms for sequence-specific recognition were observed. No evidence in support of a single general coding relationship between zinc finger and target DNA sequence was observed. The prospects for the development of this class of proteins in human therapy are considered.

Animals↗
PubMed2005

IgE-mediated anaphylaxis caused by bites of the pigeon tick Argas reflexus: cloning and expression of the major allergen Arg r 1.

BACKGROUND: Anaphylactic reactions caused by bites of the European pigeon tick Argas reflexus are repeatedly reported. This soft-backed tick is a parasite of wild pigeons colonizing urban buildings and houses. Occasionally the ticks can bite human beings, inducing anaphylactic reactions in sensitized patients. OBJECTIVE: Our aim was to characterize the major allergen implicated in a series of anaphylactic reactions caused by Argas bites and to produce the allergen as recombinant protein for diagnostic purposes. METHODS: Protein extracts were prepared from whole A reflexus bodies, and IgE immunoblots were performed with sera from 13 patients who had an anaphylactic reaction with pigeon tick bites. A cDNA expression library was constructed from whole ticks and screened with a polyclonal rabbit antiserum raised against the major allergen. RESULTS: The cDNA coding for the dominant allergen Arg r 1 could be isolated. It encodes a protein belonging to the lipocalin family. Allergenicity of the recombinant Arg r 1 was confirmed by immunoblot, ELISA, and intradermal skin tests. CONCLUSION: The dominant allergen of A reflexus has been isolated and the corresponding cDNA cloned. The recombinant protein, a lipocalin, was expressed in Escherichia coli and was shown to be immunoreactive in vitro and in vivo. Recombinant Arg r 1 was used as a diagnostic tool in a series of anaphylactic reactions caused by pigeon tick bites.

Allergens↗
PubMed2000

Foodstuff survey around a major nuclear facility with test of satellite images application.

A foodstuff survey was performed around the Savannah River Site, Aiken, South Carolina. It included a census of buildings and fields within 5 km of the boundary and determination of the locations and amounts of crops grown within 80 km of the Savannah River Site center. Recent information for this region was collected on the amounts of meat, poultry, milk, and eggs produced, of deer hunted, and of sports fish caught. The locations and areas devoted to growing each crop were determined by the usual process of applying county agricultural statistics reported by state agencies. This process was compared to crop analysis of two LANDSAT Thematic Mapper images. For use with environmental radionuclide transfer and radiation dose calculation codes, locations within 80 km were defined for 64 sections by 16 sectors centered on the Site and by 16-km distance intervals from 16 km to 80 km. The median areas per section devoted to each of four food crops based on county agricultural statistics were about two-thirds of those based on satellite image analysis. Most locally-raised foodstuff was distributed regionally and not retained locally for consumption.

Food Contamination, Radioactive↗
PubMed2003

Shielding design for a PET imaging suite: a case study.

The introduction of positron emission tomography into the clinical environment presents the medical health physicist with another challenge to his/her shielding acumen. On one hand, elaborate models can be employed, but most of these are beyond the resources possessed by most institutions. On the other hand, one could perform the analysis using simplifying assumptions (e.g., point source geometry, with or without build-up). This kind of approach would likely overestimate the shielding requirements. Such over-design is not ALARA. In fact, over-design could place such tight engineering or cost constraints on a project as to make it untenable. Recently, this designer was faced with the need to design a PET imaging suite with both engineering and time constraints. This paper describes an approach using resources readily available to medical health physicists. By using the dimensions of the bottle manikin (BOMAB) phantom as a guide, a human-form source was developed. Combined with a point-kernel shielding code, the exposure environment was readily modeled and shielding recommendations developed. In addition, to validate the model, results from preoperational instrument surveys and integrating dosimeters are discussed.

Humans↗
PubMed2002

Comparison between a conventional treatment energy and 50 MV photons for the treatment of lung tumours.

Radiation therapy in the thoracic region is difficult due to the presence of many dose-limiting structures and the large density differences that affect the dose distribution. Conventional irradiation techniques use low-energy photon beams to avoid build-up effects superficially in the tumour and increased lateral scattering of the beams. For deep-seated tumours higher beam energies could have lung-sparing properties that would enable dose escalation. A comparison was made for a conventional low photon energy (6 MV) and 50 MV photons for the treatment of a lung tumour. A representative patient geometry was selected, consisting of a small tumour semi-enclosed in lung tissue. Treatment plans were designed using a commercial 3D-pencil beam treatment planning system. The treatment beams designed in the TPS were simulated with the Monte Carlo code EGS4/BEAM and the dose distribution in the phantom created from the patients CT-data was calculated using MCDOSE with identical beam geometry for both energies. The intrinsic difference between the two photon energies implies a sparing effect of lung that can be utilized for dose escalation. For a treatment with two beams the mean total dose to the tumour could be increased by 5.3% for 50 MV, corresponding to 3.2 Gy for a prescription dose of 60 Gy, with the same complication probability for the treated lung as for 6 MV. In conclusion, high-energy beams have qualities that can be taken advantage of for irradiation of lung tumours. Optimum solutions would probably require the use of both high- and low-energy beams.

Humans↗
PubMed2003

[Periodontal disease in Belgian adults].

BACKGROUND: To date, no epidemiological study has been published on the periodontal health of the Belgian population. The aim of this study was to rectify this situation and determine the extent of the problem in Belgium. METHODS: A prevalence survey was carried out in a representative sample of employees of the Catholic University of Louvain. A total of 402 people aged between 35 and 65 were examined. Periodontal suffering was estimated using the CPITN index (WHO), which determines the most affected sextant of a mouth in order to assign a code to the mouth as a whole. At the same time, treatment needs were evaluated. RESULTS: Only one subject was considered healthy, i.e. there was no bleeding of the gums in any part of the mouth. At the same time, 41.4% of the subjects examined exhibited a deep periodontal pocket in at least one sextant of the mouth likely to progress to the loss of the teeth. Many mouths (28.5%), which were free from moderate or deep pockets, had to be scaled and polished or to be treated in order to eliminate other factors which could lead to a build-up of tartar. CONCLUSION: In this study population representative of a socio-economically favored stratum of the Belgian population, we observed a high prevalence of periodontal diseases, grading from mild chronic gingivitis to the deep cavities which are observed when the bone supporting the tooth has been lost. At the same time, we uncovered many needs for periodontal care, ranging from instruction on how to control the dental plaque to specialized periodontal care via careful scaling and polishing.

Adult↗
PubMed1999

Monte Carlo simulation of light fluence in tissue in a cylindrical diffusing fibre geometry.

The propagation of light emitted by a linear light diffuser in a cylindrical hollow organ was investigated by means of the Monte Carlo (MC) method. The height and radius of the cavity, scattering (mu(s)) (or reduced scattering, mu'(s)) and absorption (mu(a)) coefficients, anisotropy (g), and refractive indices of the media involved (n1, n2) are required as input data by the MC code, as are characteristics of the light diffuser (length, delivered power and emission profile). Results of our MC model were tested by measuring the light fluence rate in a tissue-simulating phantom (mu(a) = 0.5 cm(-1), mu(s) = 23 cm(-1) and g = 0.75) irradiated at 633 nm with a cylindrical diffuser. Since geometric and optical parameters determine the behaviour of light propagation in tissue, MC simulations with different sets of input parameters were carried out to provide qualitative as well as quantitative data useful in planning photodynamic therapy. Data are reported on light penetration and fluence rate build-up at mu(a) and mu'(s) values ranging between 0.1 and 5 cm(-1) and 2.5 and 50 cm(-1), respectively. Furthermore, results suggest that a shift and spread could occur in the isofluence curves along the symmetry axis, which depend on the diameter of the treated lumen as well as on the emission profile of the light diffuser. Using our data it is possible to estimate how inaccuracy in knowledge of the optical coefficients can affect (i.e. usually by increasing) the light dose scheduled at a certain depth into tissue.

Anisotropy↗
PubMed2003

Occupational characteristics of cases with asbestos-related diseases in The Netherlands.

OBJECTIVE: To describe the occupational background of cases with an asbestos-related disease and to present overall mesothelioma risks across industries with historical exposure to asbestos. METHODS: For the period 1990-2000, cases were collected from records held by two law firms. Information on jobs held, previous employers, activities performed and specific products used were obtained from patients themselves or next of kin. Branches of industry and occupations were coded and the likelihood of asbestos exposure was assessed. For each branch of industry, the overall risk of mesothelioma was calculated from the ratio of the observed number of mesothelioma cases and the cumulative population-at-risk in the period 1947-1960. In order to compare mesothelioma risks across different industries, risk ratios were calculated for the primary asbestos industry and asbestos user industries relative to all other branches of industry. RESULTS: In total, 710 mesotheliomas and 86 asbestosis cases were available. The average latency period was approximately 40 yr and the average duration of exposure was 22 yr. Ship building and maintenance contributed the largest number of cases (27%), followed by the construction industry (14%), the insulation industry (12%), and the navy and army, primarily related to ship building and maintenance (5%). In the insulation industry, the overall risk of mesothelioma was 5 out of 100 workers, and in the ship building industry, 1 out of 100 workers. The construction industry had an overall risk comparable with many other asbestos-using industries (7 per 10,000 workers), but due to its size claimed many mesothelioma cases. CONCLUSION: The majority of cases with asbestos-related diseases had experienced their first asbestos exposure prior to 1960. For cases with first asbestos exposure after 1960, a shift was observed from the primary asbestos industry towards asbestos-using industries, such as construction, petroleum refining, and train building and maintenance. Due to the long latency period, asbestos exposure from 1960 to 1980 will cause a considerable number of mesothelioma cases in the next two decades.

Adult↗
PubMed2006

Mechanism of tRNA-dependent editing in translational quality control.

Protein synthesis requires the pairing of amino acids with tRNAs catalyzed by the aminoacyl-tRNA synthetases. The synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. The fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from tRNAs before they are delivered to the ribosome. Although editing has been described in numerous synthetases, the reaction mechanism is unknown. To define the mechanism of editing, phenylalanyl-tRNA synthetase was used to investigate different models for hydrolysis of the noncognate product Tyr-tRNA(Phe). Deprotonation of a water molecule by the highly conserved residue betaHis-265, as proposed for threonyl-tRNA synthetase, was excluded because replacement of this and neighboring residues had little effect on editing activity. Model building suggested that, instead of directly catalyzing hydrolysis, the role of the editing site is to discriminate and properly position noncognate substrate for nucleophilic attack by water. In agreement with this model, replacement of certain editing site residues abolished substrate specificity but only reduced the catalytic efficiency of hydrolysis 2- to 10-fold. In contrast, substitution of the 3'-OH group of tRNA(Phe) severely impaired editing and revealed an essential function for this group in hydrolysis. The phenylalanyl-tRNA synthetase editing mechanism is also applicable to threonyl-tRNA synthetase and provides a paradigm for synthetase editing.

Binding Sites↗
PubMed2002

Architecture of a mediator for a bioinformatics database federation.

Developments in our ability to integrate and analyze data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad hoc queries across multiple data resources and correlating data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous distributed biological databases. Our architecture makes use of the existing search capabilities and indexes of the underlying databases, without infringing on their autonomy. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation, and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in SRS.

Algorithms↗
PubMed1998

Building cross-thesauri with the support of UMLS.

The absence of a robust system of descriptors (cross-thesaurus) hampers the development of combinatorial terminological systems. We developed a tool (I-BROWSE) to produce a cross-thesaurus by analyzing terminological corpora. To facilitate the work of experts and to produce re-usable results, our application interacts via the Internet with the UMLS Knowledge Sources Server. We applied our tool on 2999 dissections on surgical procedures produced in the project GALEN-IN-USE, as a part of the internal Quality Assurance program. Support from UMLS seems mostly promising about descriptors on , , and . Additional assistance can be given to domain experts on less frequent descriptors on pervasive modifiers. We plan to apply our tool also to production of terminological standards in CEN, as a part of a worldwide process of gradual convergence and transformation of coding systems into second-generation systems and terminological services.

Artificial Intelligence↗