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Building sensory receptors on the tongue.

Neurotrophins, neurotrophin receptors and sensory neurons are required for the development of lingual sense organs. For example, neurotrophin 3 sustains lingual somatosensory neurons. In the traditional view, sensory axons will terminate where neurotrophin expression is most pronounced. Yet, lingual somatosensory axons characteristically terminate in each filiform papilla and in each somatosensory prominence within a cluster of cells expressing the p75 neurotrophin receptor (p75NTR), rather than terminating among the adjacent cells that secrete neurotrophin 3. The p75NTR on special specialized clusters of epithelial cells may promote axonal arborization in vivo since its over-expression by fibroblasts enhances neurite outgrowth from overlying somatosensory neurons in vitro. Two classical observations have implicated gustatory neurons in the development and maintenance of mammalian taste buds--the early arrival times of embryonic innervation and the loss of taste buds after their denervation in adults. In the modern era more than a dozen experimental studies have used early denervation or neurotrophin gene mutations to evaluate mammalian gustatory organ development. Necessary for taste organ development, brain-derived neurotrophic factor sustains developing gustatory neurons. The cardinal conclusion is readily summarized: taste buds in the palate and tongue are induced by innervation. Taste buds are unstable: the death and birth of taste receptor cells relentlessly remodels synaptic connections. As receptor cells turn over, the sensory code for taste quality is probably stabilized by selective synapse formation between each type of gustatory axon and its matching taste receptor cell. We anticipate important new discoveries of molecular interactions among the epithelium, the underlying mesenchyme and gustatory innervation that build the gustatory papillae, their specialized epithelial cells, and the resulting taste buds.

Animals↗

The problem of privacy in transcultural research: reflections on an ethnographic study in Sri Lanka.

Western laws and codes of ethics frequently require that private health information be treated confidentially. However, cross-cultural research shows that it is not always easy to determine what members of a culture consider to be private or how they wish private information to be handled. This article begins by presenting an ethnographic study of patient-healer relationships in Sri Lanka; researchers were surprised to find that participants' views of health and privacy differed greatly from typical Western views, and that the privacy protections they had put in place caused discomfort among participants. Building on this ethics case study, the article explores two main questions. First, can a single definition of privacy possibly do justice to the cultural variations that exist, or does a conceptual definition inevitably run the risk of ethnocentrism? Second, to what extent is strict compliance with research regulations or ethics codes ethically justifiable when following the rules will obviously cause unease in international participants?

Anthropology, Cultural↗

Fast algorithm for predicting the secondary structure of single-stranded RNA.

A computer method is presented for finding the most stable secondary structures in long single-stranded RNAs. It is 1-2 orders of magnitude faster than existing codes. The time required for its application increases as N3 for a chain N nucleotides long. As many as 1000 nucleotides can be searched in a single run. The approach is systematic and builds an optimal structure in a straightforward inductive procedure based on an exact mathematical algorithm. Two simple half-matrices are constructed and the best folded form is read directly from the second matrix by a simple back-tracking procedure. The program utilizes published values for base-pairing energies to compute one structure with the lowest free energy.

Base Sequence↗

Performance of three different unfolding procedures connected to Bonner sphere data.

This paper presents the results obtained in a comparison of three neutron spectrum unfolding procedures based on the SAND, MINCHI and UNFANA computer programs. The calculations were performed with data obtained previously from measurements using the PTB Bonner sphere spectrometer and taken from the literature; the neutron dosimetry was done with the Leake rem-meter. The evaluation of some spectrum hardness quantifiers is also reported. The codes give comparable neutron spectrum results. Relative to ambient dose equivalent derived from the Bonner sphere system, as a function of the unfolding code used, the Leake calculated readings were typically 1.16 to 1.91 and 1.58 to 2.69 times larger for the environment of a transport cask with spent fuel elements (Clab) and inside the containment building of a pressurised water reactor (Ring-G), respectively, depending on the calibration fields.

Algorithms↗

DATA PROCESSING ASPECTS OF MEDLARS.

The speed and volume requirements of MEDLARS necessitate the use of high-speed data processing equipment, including paper-tape typewriters, a digital computer, and a special device for producing photo-composed output. Input to the system is of three types: variable source data, including citations from the literature and search requests; changes to such master files as the medical subject headings list and the journal record file; and operating instructions such as computer programs and procedures for machine operators. MEDLARS builds two major stores of data on magnetic tape. The Processed Citation File includes bibliographic citations in expanded form for high-quality printing at periodic intervals. The Compressed Citation File is a coded, time-sequential citation store which is used for high-speed searching against demand request input. Major design considerations include converting variable-length, alphanumeric data to mechanical form quickly and accurately; serial searching by the computer within a reasonable period of time; high-speed printing that must be of graphic quality; and efficient maintenance of various complex computer files.

Abstracting and Indexing↗

A plant dialect of the histone language.

The genome contains all the information needed to build an organism. However, during differentiation and development, additional epigenetic information determines the functional state of cells and tissues. This epigenetic information can be introduced by cytosine methylation and by marking nucleosomal histones. The code written on histones consists of post-translational modifications, including acetylation and methylation. In contrast to the universal nature of the DNA code, the histone language and its decoding machinery differ among animals, plants and fungi. Plant cells have retained totipotency to generate the entire plant and maintained the ability to dedifferentiate, which suggests that the establishment and maintenance of epigenetic information differs from animals. Here, I aim to summarize the histone code and plant-specific aspects of setting and translating the code.

Acetylation↗

Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability.

The leuB gene from the psychrotrophic strain Vibrio sp. I5 has been cloned and sequenced. The gene codes for 3-isopropylmalate dehydrogenase, a 360-residue, dimeric enzyme involved in the biosynthesis of leucine. Three recently solved homologous isopropylmalate dehydrogenase (IPMDH) crystal structures from thermophilic and mesophilic organisms have been used to build a homology model for the psychrotrophic IPMDH and to deduce the possible structural reasons for its decreased thermostability. According to our model the psychrotrophic IPMDH contains fewer stabilizing interactions than its mesophilic and thermophilic counterparts. Elements that have been identified as destabilizing in the comparison of the psychrotrophic, mesophilic and thermophilic IPMDHs are a smaller number of salt-bridges, a reduction in aromatic-aromatic interactions, fewer proline residues and longer surface loops. In addition, there are a number of substitutions of otherwise strictly conserved residues that can be linked to thermostability.

3-Isopropylmalate Dehydrogenase↗

A profile of communication in primary care physician telephone consultations: application of the Roter Interaction Analysis System.

BACKGROUND: Telephone consultations are a part of everyday practice, there is surprisingly little research on the subject. AIM: To describe the variation of consulting skills within a body of telephone consultations in primary care, highlighting the performance of one method of assessing the process of the consultation-- the Roter Interaction Analysis System-- with telephone consultations. DESIGN OF STUDY: Cross sectional study of 43 recordings of telephone consultations with GPs. SETTING: One rural county in the Midlands. METHOD: Recordings were made of 8 GPs, purposively selected for maximum variance in one region of the UK. Forty-three consultations were coded using the Roter Interaction Analysis System. From the descriptive categories, six composite categories were compiled reflecting a number of domains of interaction in a consultation: rapport, data gathering, patient education and counselling, partnership building, doctor dominance and patient-centredness. Analysis of variance was undertaken to explain variations between consultations for the different domains. Comparison was made to findings from similar work for face-to-face consultations. RESULTS: These telephone consultations feature more biomedical information exchange than psychosocial or affective communication. Length of interaction accounts for much of the variation seen between consultations in the domains of rapport, data gathering, patient education and counselling and partnership. Male doctors are more patient centred in this study. There is the suggestion of more doctor dominance and a less patient-centred approach when comparisons are made with previous work on face-to-face consultations. CONCLUSIONS: Although the telephone is increasingly being used to provide care, this study highlights the fact that telephone consultations cannot be taken as equivalent to those conducted face to face. More work needs to be done to delineate the features of telephone consultations.

Adult↗

National survey on the natural radioactivity and 222Rn exhalation rate of building materials in The Netherlands.

The present study reports on results of a nation-wide survey on the natural radioactivity concentrations and Rn exhalation rates of the prevailing building materials in the Netherlands. In total 100 samples were taken and analyzed for the activity concentrations of Ra, Ra, Th, and K and for their Rn exhalation rate. The sampled materials consisted of gypsum products, aerated concrete, sand-lime and clay bricks, mortars and concrete, representing about 95% of the stony building materials used in the construction of Dutch homes. The laboratory analyses were performed according to two well-documented standard procedures, the interlaboratory reproducibility of which is found to be within 5% on average. The highest radionuclide concentrations were found in a porous inner wall brick to which fly ash was added. The second highest were clay bricks with average Ra and Ra levels around 40 Bq kg. Concrete and mortar show the highest exhalation rates with a fairly broad range of 1 to 13 microBq (kg s). Low natural radioactivity levels are associated with either natural gypsum (products) or gypsum from flue gas desulphurization units, and low exhalation rates with clay bricks. To evaluate the radiological impact the radioactivity concentrations in each sample were combined into a so-called dose factor, representing the absorbed dose rate in a room with a floor, walls and ceiling of 20 cm of the material in question. For that purpose, calculations with the computer codes MCNP, Marmer and MicroShield on the specific absorbed dose rates were incorporated in the paper. The results of these codes corresponded within 6% and average values were calculated at 0.90, 1.10, and 0.080 nGy h per Bq kg for the U series, the Th series, and K, respectively. Model calculations on the external dose rate, based on the incidence of the various building materials in 1,336 living rooms, are in accordance with measured data.

Air Pollutants, Radioactive↗

Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics.

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20-600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor-joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.

Animals↗

A mutation in the CLN8 gene in English Setter dogs with neuronal ceroid-lipofuscinosis.

A heritable neurodegenerative disease of English Setters has long been studied as a model of human neuronal ceroid-lipofuscinosis (NCL). Megablast searches of the first build of the canine genome for potential causative genes located the CLN8 gene near the q telomere of canine chromosome 37, close to a marker previously linked to English Setter NCL. Sequence analysis of the coding region from affected dogs revealed a T-to-C transition in the CLN8 gene that predicts a p.L164P missense mutation. Leucine 164 is conserved in four other mammalian species. The C allele co-segregated with the disease phenotype in a two-generation English Setter family in a pattern consistent with autosomal recessive inheritance. All four NCL-affected family members were C/C homozygotes and all four obligate carriers were C/T heterozygotes; whereas, 103 unrelated dogs were all T/T homozygotes. These findings indicate that the CLN8 T-to-C transition is the likely cause of English Setter NCL.

Amino Acid Sequence↗

Interventions to enhance communication among patients, providers, and families.

Whether patient suffering is caused by physical symptoms, unwanted medical intervention, or spiritual crisis, the common pathway to relief is through a provider who is able to elicit these concerns and is equipped to help the patient and family address them. This paper reviews the current state of knowledge in communication at the end of life, organized according to a framework of information gathering, information giving, and relationship building; and then focuses on interventions to enhance communication among patients, providers, and families. Several observations emerge from the existing literature. Patients have highly individualized desires for information and we cannot predict patient preferences. Communication coding methodology has advanced significantly yet the current systems remain poorly understood and largely inaccessible. Physicians and other health care providers do not discuss sufficiently treatment options, quality of life or respond to emotional cues from patients, and there is plenty of room for improvement. On the positive side, we have also learned that physicians and other health care providers can be taught to communicate better through intensive communication courses, and that communication interventions can improve some patient outcomes. Finally, huge gaps remain in our current knowledge, particularly with regard to understanding the relationship between communication style and outcomes. These findings suggest several recommendations. We should create larger and more diverse datasets; improve upon the analysis of recorded communication data; increase our knowledge about patient preferences for information; establish a stronger link between specific communication behaviors and outcomes; and identify more efficient ways to teach providers communication skills.

Family Relations↗

RBT--a tool for building refined Buneman trees.

SUMMARY: We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm--which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction--enables refined Buneman tree reconstruction on large taxa sets. AVAILABILITY: The source code for RBT, written in Java, is available under the GNU Public License (GPL) at http://www.birc.dk/Software/RBT CONTACT: besen@daimi.au.dk.

Algorithms↗

Building chromosome-wide LD maps.

SUMMARY: BMapBuilder builds maps of pairwise linkage disequilibrium (LD) in either two or three dimensions. The optimized resolution allows for graphical display of LD for single nucleotide polymorphisms (SNPs) in a whole chromosome. AVAILABILITY: The program is coded in Java, which runs on all relevant operating systems, including Windows, Mac and Unix/Linux, and is available from http://bios.ugr.es/BMapBuilder.

Chromosome Mapping↗

Rhizobium tropici genes involved in free-living salt tolerance are required for the establishment of efficient nitrogen-fixing symbiosis with Phaseolus vulgaris.

Characterization of nine transposon-induced mutants of Rhizobium tropici with decreased salt tolerance (DST) allowed the identification of eight gene loci required for adaptation to high external NaCl. Most of the genes also were involved in adaptation to hyperosmotic media and were required to overcome the toxicity of LiCl. According to their possible functions, genes identified could be classified into three groups. The first group included two genes involved in regulation of gene expression, such as ntrY, the sensor element of the bacterial ntrY/ntrX two-component regulatory system involved in regulation of nitrogen metabolism, and greA, which encodes a transcription elongation factor. The second group included genes related to synthesis, assembly, or maturation of proteins, such as alaS coding for alanine-tRNA synthetase, dnaJ, which encodes a molecular chaperone, and a nifS homolog probably encoding a cysteine desulfurase involved in the maturation of Fe-S proteins. Genes related with cellular build-up and maintenance were in the third group, such as a noeJ-homolog, encoding a mannose-1-phosphate guanylyltransferase likely involved in lipopolysaccharide biosynthesis, and kup, specifying an inner-membrane protein involved in potassium uptake. Another gene was identified that had no homology to known genes but that could be conserved in other rhizobia. When inoculated on Phaseolus vulgaris growing under nonsaline conditions, all DST mutants displayed severe symbiotic defects: ntrY and noeJ mutants were impaired in nodulation, and the remaining mutants formed symbiosis with very reduced nitrogenase activity. The results suggest that bacterial ability to adapt to hyperosmotic and salt stress is important for the bacteroid nitrogen-fixing function inside the legume nodule and provide genetic evidence supporting the suggestion that rhizobia face severe environmental changes after their release into plant cells.

Genes, Bacterial↗

Building an effective corporate compliance plan.

Corporate compliance plans are essential for healthcare organizations to cope with, and perhaps even stave off, investigations arising from allegations of illegal business practices. Initial development and implementation of a corporate compliance plan can be facilitated through four steps: determining the content of the code of conduct, determining how the code will be distributed, assigning responsibility for implementing the plan, and appointing a compliance task force to guide the implementation process. Special attention should be paid to education requirements of the United States Sentencing Guidelines to see that all employees understand and can apply provisions of the plan.

Employee Discipline↗

Cognitive design for sharing medical knowledge models.

By building a medical conceptual model inside the galen project, a methodology has been defined to deal with both operative goals and deep and unsolved problems about knowledge. This knowledge sharing oriented approach exploits existing medical coding systems such as knowledge sources and enables us to represent their concepts in a wider cognitive context referring to ontological theories. The tasks of cognitive ergonomy, quasi-naturalness of language, versatility, and flexibility seem to be supported through some functions, such as viewpoint, context, and sign, which act as spin-off points to knowledge or information which is not modeled.

Artificial Intelligence↗

Proteasomes of the yeast S. cerevisiae: genes, structure and functions.

Proteasomes are large multicatalytic protease complexes which fulfil central functions in major intracellular proteolytic pathways of the eukaryotic cell. 20S proteasomes are 700 kDa cylindrically shaped particles, found in the cytoplasm and the nucleus of all eukaryotes. They are composed of a pool of 14 different subunits (MW 22-25 kDa) arranged in a stack of 4 rings with 7-fold symmetry. In the yeast Saccharomyces cerevisiae a complete set of 14 genes coding for 20S proteasome subunits have been cloned and sequenced. 26S proteasomes are even larger proteinase complexes (about 1700 kDa) which degrade ubiquitinylated proteins in an ATP-dependent fashion in vitro. The 26S proteasome is build up from the 20S proteasome as core particle and two additional 19S complexes at both ends of the 20S cylinder. Recently existence of a 26S proteasome in yeast has been demonstrated. Several 26S proteasome specific genes have been cloned and sequenced. They share similarity with a novel defined family of ATPases. 20S and 26S proteasomes are essential for functioning of the eukaryotic cell. Chromosomal deletion of 20S and 26S proteasomal genes in the yeast S. cerevisiae caused lethality of the cell. The in vivo functions of proteasomes in major proteolytic pathways have been demonstrated by the use of 20S and 26S proteasomal mutants. Proteasomes are needed for stress dependent and ubiquitin mediated proteolysis. They are involved in the degradation of short-lived and regulatory proteins. Proteasomes are important for cell differentiation and adaptation to environmental changes. Proteasomes have also been shown to function in the control of the cell cycle.

Cysteine Endopeptidases↗