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PubMed2001

To Matrix, Network, or Hierarchy: That Is the Question.

The authors present a structural analysis of three spatial diagrams-matrices, networks, and hierarchies-that specifies 10 properties on which these diagrammatic representations are hypothesized to differ: global structure, building block, number of sets, item/link constraints, item distinguishability, link type, absence of a relation, linking relations, path, and traversal. Each property has a "value" for each diagram, and these property values constitute the applicability conditions for the representations. Twenty-three college students (computer science majors and math educators) selected the type of diagram they thought would be most efficient for organizing the information in each of 18 short scenarios and verbally justified the reasons for their selections. The verbal protocols were coded with respect to the structural analysis. Both the representation selection and verbal justification data provided strong support for the structural analysis. Additionally, a factor analysis of students' justifications indicated that the organization of their knowledge is consistent with the structural analysis. Students' use of the structural properties to select appropriate representations and to justify those selections indicates that the structural analysis has psychological force.

Cognition↗
PubMed2006

Doctor-patient communications in the Aboriginal community: towards the development of educational programs.

OBJECTIVE: Aboriginal people in Canada have poorer health than the rest of the population. Reasons for health disparities are many and include problems in communication between doctor and patient. The objective of this study was to understand doctor-patient communication in Aboriginal communities in order to design educational interventions for medical students based on the needs and experiences of patients. METHODS: Experiences of good and poor communication were studied by semi-structured interviews or focus groups with 22 Aboriginal community members, 2 community health representatives and 2 Aboriginal trainee physicians. Transcribed data were coded and subjected to thematic analysis. RESULTS: Positive and negative experiences of communicating with physicians fell into three broad and interrelated themes: their histories as First Nations citizens; the extent to which the physician was trusted; time in the medical interview. CONCLUSION: Aboriginal peoples' history affects their communication with physicians; barriers may be overcome when patients feel they have a voice and the time for it to be heard. PRACTICE IMPLICATIONS: Physicians can improve communication with Aboriginal patients by learning about their history, building trust and giving time.

Adult↗
PubMed2004

Geographic information has to be spatialized to be neglected: a representational neglect case.

A patient with unilateral neglect had to evoke mentally the map of France in two different conditions. In the first condition, he was asked to build an iconic representation of the map of France and to list all the towns that he could 'see' on this mental image within two minutes. In the second condition, he had to remember and name as many French towns as possible within two minutes, without being instructed to form a mental image. Left representational neglect was observed in the first condition only, i.e., when an iconic representation was required. These findings, which were replicated four months later, suggest a dual mode of coding, retrieval, or both, of geographic information and show that, although topographic, geographic data has to be spatialized to be neglected.

Aged↗
PubMed2002

The effect of services on the recurrence of child maltreatment.

OBJECTIVE: Building on a previous model of recurrence, this study examined the relationship of services on the hazard of child maltreatment recurrence during CPS intervention for families who were provided continuing intervention following a confirmed index report of physical abuse or neglect. METHOD: This nonconcurrent prospective study selected 434 subject families who met study eligibility requirements from 1181 families randomly selected from the 2902 families who had experienced a substantiated report of child abuse or neglect during the sampling year. Data were collected and coded from archival sources for 5 years following the index report. Each record was coded by two research analysts to increase inter-rater reliability. Data were analyzed with the Cox Proportional Regression Model. RESULTS: Case characteristics that predicted recurrence were: child vulnerability, family stress, partner abuse, and social support deficits. After examining the potential effect of nine service-related variables only attendance at services predicted recurrence while controlling for other variables in the model. Families who were noted to attend the services identified in their service plans were 33% less likely to experience a recurrence of child maltreatment while their case was active with CPS. CONCLUSIONS: Implications of this and other research suggests that actively engaging families in a helping alliance and helping them accept and receive services may reduce the likelihood of future maltreatment.

Child↗
PubMed2003

Building a computer model of the Haemobear blood pump.

Further development of the Haemobear blood pump requires theoretical predictions of the dynamic behavior of the rotor. These predictions can be used to compare different rotor geometry at desired operating conditions before a prototype is built. The study focuses on a rotor-dynamic model of the rigid rotor with six degrees of freedom (6-DoF), which is implemented using the Matlab-Simulink software package. The forces acting on the rotor are provided to Simulink in terms of constant values (e.g., gravity force), linear coefficients, or nonlinear functions. These coefficients or functions are obtained using numerical simulation results. Fluid forces and magnetic forces can be calculated using commercial software codes. The output of these codes has to be postprocessed to get the desired values for Simulink. This article will give an overview of how to implement arbitrary physical influences on the rotor in a computational model of the complete pump.

Computer Simulation↗
PubMed1999

Simulation of DNA fragment distributions after irradiation with photons.

The Monte Carlo track structure code PARTRAC has been further improved by implementing electron scattering cross-sections for liquid water and by explicitly modelling the interaction of water radicals with DNA. The model of the genome inside a human cell nucleus in its interphase is based on the atomic coordinates of the DNA double helix with an additional volume for the water shell. The DNA helix is wound around histone complexes, and these nucleosomes are folded into chromatin fibres and further to fibre loops, which are interconnected to build chromosomes with a territorial organisation. Simulations have been performed for the irradiation of human fibroblast cells with carbon K and aluminium K ultrasoft x-rays, 220 kVp x-rays and 60Co gamma-rays. The ratio single-strand breaks to double-strand breaks (ssb/dsb) for both types of ultrasoft x-rays is lower than for gamma-rays by a factor of 2. The contributions of direct and indirect effects to strand break induction are almost independent of photon energy. Strand break patterns from indirect effects reflect differences in the susceptibility of the DNA helix to OH* attack inside the chromatin fibre. Distributions of small DNA fragments (<3 kbp) are determined by the chromatin fibre structure irrespective of whether direct or indirect effects are causing the breaks. In the calculated fragment size distributions for larger DNA fragments (>30 kbp), a substantial deviation from random breakage is found only for carbon K irradiation, and is attributed to its inhomogeneous dose distribution inside the cell nucleus. For the other radiation qualities, the results for larger fragments can be approximated by random breakage distributions calculated for a yield of dsb which is about 10% lower than the average for the whole genome. The excess of DNA fragments detected experimentally in the 8-300 kbp region after x-ray irradiation is not seen in our simulation results.

Chromatin↗
PubMed1998

Genetic complexity, structure, and characterization of highly active bovine intestinal alkaline phosphatases.

Mammalian alkaline phosphatases (APs) display 10-100-fold higher kcat values than do bacterial APs. To begin uncovering the critical residues that determine the catalytic efficiency of mammalian APs, we have compared the sequence of two bovine intestinal APs, i.e. a moderately active isozyme (bovine intestinal alkaline phosphatase, bIAP I, approximately 3,000 units/mg) previously cloned in our laboratory, and a highly active isozyme (bIAP II, approximately 8, 000 units/mg) of hitherto unknown sequence. An unprecedented level of complexity was revealed for the bovine AP family of genes during our attempts to clone the bIAP II cDNA from cow intestinal RNAs. We cloned and characterized two novel full-length IAP cDNAs (bIAP III and bIAP IV) and obtained partial sequences for three other IAP cDNAs (bIAP V, VI, and VII). Moreover, we identified and partially cloned a gene coding for a second tissue nonspecific AP (TNAP-2). However, the cDNA for bIAP II, appeared unclonable. The sequence of the entire bIAP II isozyme was determined instead by a classical protein sequencing strategy using trypsin, carboxypeptidase, and endoproteinase Lys-C, Asp-N, and Glu-C digestions, as well as cyanogen bromide cleavage and NH2-terminal sequencing. A chimeric bIAP II cDNA was then constructed by ligating wild-type and mutagenized fragments of bIAP I, III, and IV to build a cDNA encoding the identified bIAP II sequence. Expression and enzymatic characterization of the recombinant bIAP I, II, III, and IV isozymes revealed average kcat values of 1800, 5900, 4200, and 6100 s-1, respectively. Comparison of the bIAP I and bIAP II sequences identified 24 amino acid positions as likely candidates to explain differences in kcat. Site-directed mutagenesis and kinetic studies revealed that a G322D mutation in bIAP II reduced its kcat to 1300 s-1, while the converse mutation, i.e. D322G, in bIAP I increased its kcat to 5800 s-1. Other mutations in bIAP II had no effect on its kinetic properties. Our data clearly indicate that residue 322 is the major determinant of the high catalytic turnover in bovine IAPs. This residue is not directly involved in the mechanism of catalysis but is spatially sufficiently close to the active site to influence substrate positioning and hydrolysis of the phosphoenzyme complex.

Alkaline Phosphatase↗
PubMed1993

Institutional structure to ensure research integrity.

The single most important component in an institutional culture of research integrity is institutional leadership committed to ethical conduct. If the institution's leaders are committed to integrity in research and act on that commitment, the campus will follow that lead; conversely, if the perception develops that the leaders pay only lip service to ethical conduct, the campus will adopt the same attitude. An institution must pay attention to both prevention and education, and many are developing codes of conduct. Further, institutions must establish a misconduct review process that can render objective, fact-based decisions untainted by personal bias and conflicts of interest. In developing such a process, leaders must be aware of probable pitfalls, create an accessible structure, and provide for consistent assessment of allegations and complaints, focusing on facts, not personalities. Increased demands for accountability and a heightened public interest in ethical issues portend increasing pressures on institutions to monitor the conduct of their members. The institution that builds effective, credible structures for preventing and resolving ethical issues will be well equipped to cope with these external pressures. Ultimately, however, institutional structures for such monitoring accomplish far more than preserving institutional autonomy: they protect the principle of scholarly and scientific inquiry that is at the core of the institution's mission.

Academic Medical Centers↗
PubMed2004

Validation of a method to establish practice-based stroke and TIA registers.

This study compares two methods to establish stroke and transient ischaemic attack (TIA) practice-based registers, which are of particular relevance to practices with limited diagnostic coding. Both arms involved a notes review of all patients taking antiplatelets or anticoagulants, and, either a further notes review of all patients with ischaemic heart disease (IHD) or diabetes (extensive arm), or asking about a history of stroke or TIA during IHD or diabetic clinics (pragmatic arm). The extensive arm involved searching 11% of the practice notes, whereas the pragmatic arm only involved 3% and had almost as high a yield. This study suggests that the pragmatic method could be used to help build practice-based stroke and TIA registers.

Aged↗
PubMed1997

Comparative genomics of mycoplasmas.

The mycoplasmas are the smallest and simplest self-replicating organisms. The goal of defining in molecular terms the entire machinery of a living cell by using mycoplasmas as models was put forward by Harold Morowitz in 1984. The recent complete sequencing of the genomes of the human pathogens Mycoplasma genitalium and Mycoplasma pneumoniae brings us much closer to achieving this goal. The M. genitalium genome contains only 479 predicted protein coding sequences (genes) and that of M. pneumoniae 677, as compared with 1703 in Haemophilus influenzae and about 4000 in E. coli. Thus, M. genitalium is apparently the simplest organism capable of independent life with a minimal set of genes. The drastic economization in genetic information must have been associated with the parasitic mode of life of the mycoplasmas. During their reductive evolution from Gram-positive bacteria the mycoplasmas have lost the cell wall and many biosynthetic systems involved in synthesis of macromolecule building blocks provided by their host. Thus, the M. genitalium and M. pneumoniae genomes do not carry any gene involved in amino acid biosynthesis, and very few genes for vitamin, nucleic acid precursor and fatty acid biosynthesis. The mycoplasma genomes carry a minimal set of energy metabolism genes, being content with a restricted supply of ATP needed for their parasitic mode of life. Nevertheless, these minimal organisms carry the essential genes for DNA replication, transcription and translation, but even here gene saving is expressed by a minimal number of rRNA and tRNA genes. A genomic price had been paid to maintain parasitism, so that a significant number of mycoplasmal genes is devoted to adhesins, attachment organelles and variable membrane surface antigens directed towards evasion of the host immune system.

Animals↗
PubMed2002

Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron.

The intron content of plant organellar genes is a useful marker in molecular systematics and evolution. We have tested representatives of a wide range of monocotyledonous plant families for the presence of an intron (cox2 intron 1) in one of the most conservative mitochondrial genes, the cox2 locus. Almost all species analyzed were found to harbor a group II intron at a phylogenetically conserved position. The only exceptions were members of a single monocot family, the Ruscaceae: representatives of all genera in this family were found to lack cox2 intron 1, but instead harbor an intron in the 3' portion of the cox2 coding region (cox2 intron 2). The presence of cox2 intron 1 in families of monocotyledonous plants that are closely related to the Ruscaceae suggests that loss of the intron is specific to this family and may have accompanied the evolutionary appearance of the Ruscaceae. Interestingly, sequences that are highly homologous to cox2 intron 2 are found in a nuclear intron in a lineage of monocotyledonous plants, suggesting that the originally mitochondrial group II intron sequence was transferred to the nuclear genome and reused there to build a spliceosomal intron.

Amino Acid Sequence↗
PubMed2003

Developing the ontological foundations of a terminological system for end-stage diseases, organ failure, dialysis and transplantation.

The Etablissement français des Greffes (EfG) is a state agency dealing with Public Health issues related to organ, tissue and cell transplantation in France. The evaluation of organ retrieval and transplantation activities, one of its missions, is supported by a national information system (EfG-IS). The EfG-IS is moving towards a new n-tier architecture comprising a terminology server for end-stage diseases, organ failure, dialysis and transplantation (EfG-TS). Following a preliminary audit of the existing coding system and in order to facilitate data recording, to improve the quality of information, to assume compatibility with terminological existing standards and to allow semantic interoperability with other local, national or international registries, a specific work has been conducted on the thesauri to integrate within the EfG-TS. In this paper focusing on the server's content rather than the container, we report first the functional and cognitive requirements that resulted from the preliminary audit. We then describe the methodological approach used to build the terminological server on "sound ontological foundations". We performed the semantic analysis of existing medical terms to set up disease description frame-like structures. These diseases description frames consist of a limited set of nosological discriminating slots such as etiology, semiology, pathology, evolution and associated diseases. Each relevant medical term is thus associated to a concept defined and inserted within a hierarchy according to disease description frame resulting from the semantic analysis. Last, because this terminological server is shared by various transplant and dialysis centers to record patient data at different time point, contextualization of terms appeared as one of the functional requirements. We will also point out various contexts for medical terms and how they have been taken into account.

Automation↗
PubMedDate not supplied

The minimal cellular genome of mycoplasma.

The mycoplasmas are the smallest and simplest self-replicating organisms, being built of a plasma membrane, ribosomes, and a circular double-stranded DNA molecule-the typical prokaryotic genome. The idea of using mycoplasmas as models for defining in molecular terms the entire machinery of a living cell was raised by Morowitz in 1984. The goal has been to prove the dogma of the completeness of molecular biology, that is, that the logic of life is finite, relatively simple and subject to full exploration. The recent complete sequencing of the genome of the human pathogen Mycoplasma genitalium brings us much closer to achieving this goal. The M. genitalium genome is only 580 kb long and contains only 470 predicted coding sequences(genes), as compared with 1727 in Haemophilus influenzae and about 4000 in E. coli. Thus, M. genitalium is apparently the simplest organism capable of independent life with a minimal set of genes. The drastic economization in genetic information must be associated with the parasitic mode of life of the mycoplasmas. Mycoplasmas evolved by reductive evolution from Gram-positive bacteria with low G + C genomes. During evolution the mycoplasmas have lost the cell wall and many biosynthetic systems involved in synthesis of macromolecule building blocks provided by their host. Thus, the M. genitalium genome carries only one gene involved in amino acid biosynthesis, and very few genes for vitamin and nucleic acid precursors; the lack of genes involved in fatty acid biosynthesis, leads to dependence on exogenous fatty acids, enabling the introduction of controlled variations in membrane acyl chains and the use of mycoplasmas as models in studying membrane fluidity. Moreover, the dependence of mycoplasmas on exogenous cholesterol for growth was exploited to show the role of cholesterol as a buffer of membrane fluidity. The mycoplasma genome carries the minimal set of energy metabolism genes, being content with a restricted supply of ATP needed for their parasitic mode of life. Being limited by a single permeability barrier enabled the saving of a considerable number of transport system genes. Nevertheless, these minimal organisms were shown to carry all the essential genes needed for DNA replication, transcription and translation, but even here gene saving is expressed in a minimal number of rRNA and tRNA genes. A genomic price had been paid to maintain parasitism, so that a significant number of mycoplasmal genes is devoted to adhesins, attachment organelles and variable membrane surface antigens directed towards evasion of the host immune system.

Genome, Bacterial↗
PubMedDate not supplied

Building a cytology report database: a computer-assisted system for documentation, evaluation and hospital-wide recall of haematological biopsy reports.

Owing to an increasing number of biopsies from different organ systems in our institution and referring institutions there was need to develop a computer-based system to improve documentation, analysis and reports of pathological findings, as well as speed of transmission of information in a clinical haematology/oncology unit. As terminals connected to a central minicomputer are located on all wards of our hospital, we have now provided a faster way of moving information from the cytology reporting site to all hospital departments. Using the hospital's minicomputer we developed an easy-to-use system based on five different codes for each cytological specimen: organ biopsied, quality of specimen, cytological diagnosis including information as to status of patient (i.e. pretherapy), and an additional code describing the degree of remission obtained after chemotherapy of acute leukemias. After microscopic analysis of the specimen these five codes are read into a terminal; minutes after the diagnosis is made, a short version of the report can be accessed from all wards in the hospital.

Biopsy↗
PubMed2006

From counting and pouring to caring: the empathic developmental process of community pharmacists.

BACKGROUND: Pharmacists are the most accessible health care provider. As such, they often interact with patients who, for a variety of reasons, are in some form of emotional distress. Pharmacists who can communicate empathically are able to build good patient rapport, which often translates into improved patient outcomes. OBJECTIVES: The objective of this study was to better understand the process of how experienced community pharmacists developed into highly empathic pharmacists. This study was not intended to measure empathic abilities of pharmacists as an outcome. METHODS: Using a grounded theory qualitative methodology, a purposeful sample of 20 highly empathic experienced community pharmacists was selected using explicit selection criteria. A semistructured interview was conducted with each pharmacist selected. Interview data were analyzed first through open coding, then with qualitative data analysis software. RESULTS: Two significant themes emerged from the data. Theme 1 focused on the social learning component of empathy development such as observation and imitation of others; and theme 2 centered on the role of the consistent use of self-reflective practices when pharmacists interact with a patient in distress. CONCLUSIONS: The data suggest that empathic development in pharmacists is a function of social learning and reflection in action. This interplay appears to facilitate empathic responding to patients who are experiencing physical or emotional distress.

Adult↗
PubMed1999

Isolation and characterization of the naphthocyclinone gene cluster from Streptomyces arenae DSM 40737 and heterologous expression of the polyketide synthase genes.

Streptomyces arenae produces the aromatic polyketide naphthocyclinone, which exhibits activity against Gram-positive bacteria. A cosmid clone containing the putative naphthocyclinone gene cluster was isolated from a genomic library of S. arenae by hybridization with a conserved region from the actinorhodin PKS of S. coelicolor. Sequence analysis of a 5.5-kb DNA fragment, which hybridizes with the actI probe, revealed three open reading frames coding for the minimal polyketide synthase. A strong sequence similarity was found to several previously described ketosynthases, chain length factors and acyl carrier proteins from other polyketide gene clusters. An additional open reading frame downstream of the PKS genes of S. arenae showed 53% identity to act VII probably encoding an aromatase. Another open reading frame was identified in a region of 1.436 bp upstream of the PKS genes, which, however, had no similarity to known genes in the database. Approximately 8 kb upstream of the PKS genes, a DNA fragment was identified that hybridizes to an actVII--actIV specific probe coding for a cyclase and a putative regulatory protein, respectively. Disruption of the proposed naphthocyclinone gene cluster by insertion of a thiostrepton resistance gene completely abolished production of naphthocyclinones in the mutant strain, showing that indeed the naphthocyclinone gene cluster had been isolated. Heterologous expression of the minimal PKS genes in S. coelicolor CH999 in the presence of the act ketoreductase led to the production of mutactin and dehydromutactin, indicating that the S. arenae polyketide synthase forms a C-16 backbone that is subsequently dimerized to build naphthocyclinone. The functions of the proposed cyclase and aromatase were examined by coexpression with genes from different polyketide core producers.

Amino Acid Sequence↗
PubMed2001

The impact of psychiatric diagnosis and family system relationship on problems identified by families coping with a mentally ill member.

The purpose of this study was to explore how psychiatric diagnosis and family relationships relate to problems identified by participants in three one-day public family psychoeducation workshops for families with a member with a serious mental illness. Workshop participants generated lists of problems they had faced, which were coded into eleven categories. Logistic regression models predicting listing of categories were developed based on ill member (diagnosis, sex, treatment compliance) and family member (sex, age, relationship to the ill member) characteristics. For models predicting content category from ill member characteristics, only denial/noncompliance and interpersonal/social categories were significantly predictive as dependent variables. For models predicting content categories from family member characteristics, only the resources/benefits model was predictive. The significant findings, in conjunction with the important negative results, suggest implications for further development of family intervention models. Building on previous research, groups composed of families coping with more than a single diagnosis and including a variety of family member relationships have the potential to reach consensus on curriculum topics.

Adult↗
PubMed1982

[Effect of combustion devices on the quality of indoor air].

Combustion devices and the equipment conducting their effluent gases such as ducts and chimneys are factors which might have an unreasonable or even dangerous impact on the quality of air inside buildings. There is a danger of flue gases entering the indoor environment during the heating process (a) if the air-circulation associated with the operation of a combustion device is disturbed or even interrupted, (b) if the air stream - as far as flue gases are involved - flows under elevated pressure, and (c) if the combustion device and the flue gas conducting equipment are not leak-proof. These three cases and their influence on indoor air quality are extensively discussed. In the German Combustion Device Code from 1980 care is taken to minimize the pollutant concentrations in rooms with combustion devices by setting special requirements for the room in which the device is located, and by prescribing the standardization of the technical characteristics of chimneys and combustion devices.

Air Pollutants↗