Showing papers by "Trinity College, Dublin published in 1989"
TL;DR: A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer based on progressively aligning sequences according to the branching order in an initial phylogenetic tree.
Abstract: A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program described can handle up to 100 sequences of 1200 residues each. The approach is based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. The results obtained using the package appear to be as sensitive as those from any other available method.
1,609 citations
Book•
01 Nov 1989TL;DR: The Multimethod Approach and its Promises A Healthy Skepticism about Theory and Method Formulating Research Problems Collecting Data with Multiple Methods Finding the Objects to Study Measuring Concepts and Assessing Measurement Validity Explaining Social Phenomena Causally A Postscript on Postmodernism Making Research Public: The Social Context of Multimodal Research as mentioned in this paper
Abstract: The Multimethod Approach and Its Promises A Healthy Skepticism About Theory and Method Formulating Research Problems Collecting Data with Multiple Methods Finding the Objects to Study Measuring Concepts and Assessing Measurement Validity Explaining Social Phenomena Causally A Postscript on Postmodernism Making Research Public: The Social Context of Multimethod Research
1,348 citations
TL;DR: It is proposed that the differences arising because mutation patterns vary with the timing of replication of different chromosomal regions in the germline can account for both the origin of isochores in mammalian genomes and the observation that silent nucleotide substitutions in different mammalian genes do not have the same molecular clock.
Abstract: In the traditional view of molecular evolution, the rate of point mutation is uniform over the genome of an organism and variation in the rate of nucleotide substitution among DNA regions reflects differential selective constraints1,2. Here we provide evidence for significant variation in mutation rate among regions in the mammalian genome. We show first that substitutions at silent (degenerate) sites in protein-coding genes in mammals seem to be effectively neutral (or nearly so) as they do not occur significantly less frequently than substitutions in pseudogenes. We then show that the rate of silent substitution varies among genes and is correlated with the base composition of genes and their flanking DNA. This implies that the variation in both silent substitution rate and base composition3 can be attributed to systematic differences in the rate and pattern of mutation over regions of the genome. We propose that the differences arise because mutation patterns vary with the timing of replication of different chromosomal regions in the germline. This hypothesis can account for both the origin of isochores in mammalian genomes4 and the observation5 that silent nucleotide substitutions in different mammalian genes do not have the same molecular clock.
594 citations
TL;DR: The absolute rate of substitution at silent sites in nuclear genes in Drosophila is about three times hihger than the average silent rate in mammals.
Abstract: Analysis of the rate of nucleotide substitution at silent sites inDrosophila genes reveals three main points. First, the silent rate varies (by a factor of two) among nuclear genes; it is inversely related to the degree of codon usage bias, and so selection among synonymous codons appears to constrain the rate of silent substitution in some genes. Second, mitochondrial genes may have evolved only as fast as nuclear genes with weak codon usage bias (and two times faster than nuclear genes with high codon usage bias); this is quite different from the situation in mammals where mitochondrial genes evolve approximately 5–10 times faster than nuclear genes. Third, the absolute rate of substitution at silent sites in nuclear genes inDrosophila is about three times hihger than the average silent rate in mammals.
289 citations
TL;DR: In a study to discover the nature and incidence of bullying in Dublin primary schools 783 children (285 boys and 498 girls) between 7 and 13 years of age in four National Schools in Dublin were questioned about their experiences of being bullied and bullying others as mentioned in this paper.
Abstract: In a study to discover the nature and incidence of bullying in Dublin primary schools 783 children (285 boys and 498 girls) between 7 and 13 years of age in four National Schools in Dublin were questioned about their experiences of being bullied and bullying others. The most common types of bullying reported were: teasing, being hit and kicked, being ‘picked on’ and rejection. Overall, 10.5% of the children reported they were involved in serious bullying, either as the bully or the victim. These figures indicate an incidence that is twice as high as in some North European countries, such as Norway, where a 5% incidence inspired their Department of Education to launch a national campaign to combat bullying in schools.
242 citations
TL;DR: Members of a large pedigree of Irish origin presenting with early onset Type I autosomal dominant retinitis pigmentosa (ADRP) have been typed for D3S47 (C17), a polymorphic marker from the long arm of chromosome 3, hence localizing the ADRP gene (RP1) segregating in this pedigree to 3q.
237 citations
01 Jan 1989
236 citations
TL;DR: An estimated absolute silent substitution rate of 6 × 10−9 substitutions per site per year that falls within the range of average rates seen in different mammalian nuclear genomes.
Abstract: The rate of synonymous nucleotide substitution in nuclear genes of higher plants has been estimated. The rate varies among genes by a factor of up to two, in a manner that is not immediately explicable in terms of base composition or codon usage bias. The average rate, in both monocots and dicots, is about four times higher than that in chloroplast genes. This leads to an estimated absolute silent substitution rate of 6 × 10−9 substitutions per site per year that falls within the range of average rates (2−8 × 10−9) seen in different mammalian nuclear genomes.
184 citations
TL;DR: Codon usage in D. discoideum can be explained by a balance between the forces of mutational bias and translational selection, and a particular subset of codons, many of which are C-ending, are identified as optimal codons.
Abstract: Codon usage patterns in the slime mould Dictyostelium discoideum have been re-examined (a total of 58 genes have been analysed). Considering the extreme A + T-richness of this genome (G + C = 22%), there is a surprising degree of codon usage variation among genes. For example, G + C content at silent sites varies from less than 10% to greater than 30%. It was previously suggested [Warrick, H.M. and Spudich, J.A. (1988) Nucleic Acids Res. 16: 6617-6635] that highly expressed genes contain fewer 'optimal' codons than genes expressed at lower levels. However, it appears that the optimal codons were misidentified. Multivariate statistical analysis shows that the greatest variation among genes is in relative usage of a particular subset of codons (about one per amino acid), many of which are C-ending. We have identified these as optimal codons, since (i) their frequency is positively correlated with gene expression level, and (ii) there is a strong mutation bias in this genome towards A and T nucleotides. Thus, codon usage in D. discoideum can be explained by a balance between the forces of mutational bias and translational selection.
169 citations
TL;DR: In this article, the binding properties of ruthenium polypyridyl complexes were studied by absorption and emission spectroscopy, DNA melting techniques, and emission lifetime measurements.
Abstract: The nature of the binding of several ruthenium polypyridyl complexes containing 2, 2`-bipyridine (bipy), 4, 4`-dimethyl-2, 2`-bipyridine (DMB), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline(DPP), 2, 2`, 2`-terpyridine (terpy), 2, 2`-biquinoline (biq), 1,4,5,8-tetraazaphen-anthrene (TAP) and 1,4,5,8,9,12-hexaazatriphenylene (HAT), with calf thymus DNA, poly[d(A-T)] and poly[d(G-C)] were studied by absorption and emission spectroscopy, DNA melting techniques, and emission lifetime measurements. In low ionic strength phosphate buffer, spectroscopic changes and DNA stabilization depended on the polypyridyl ligands present, and indicated binding that varied from substantially electrostatic to intercalative. Ru(bipy)2(HAT)2+ and Ru(phen)32+, which bind by partial intercalation, also show a strong preference for poly[d(A-T)]. The emission quantum yields for most complexes were increased in the presence of DNA. An exception was Ru(TAP)32+ which has a markedly reduced emission quantum yield and lifetime in the presence of poly[d(G-C)] or CT-DNA, due to photoredox interaction with guanines. Emission decays of the complexes generally showed multiexponential behaviour. The ability of the ruthenium complexes to sensitise DNA cleavage was determined using pBR322 plasmid DNA. Ru(TAP)32+ is the most efficient sensitiser while uncharged complexes and complexes with very short-lived excited states do not cleave DNA.
169 citations
TL;DR: An ulcerative colitis activity index that correlates significantly with microscopic and macroscopic scores, using both clinical symptoms and laboratory findings, is proposed.
Abstract: The diagnosis of inflammatory bowel disease is usually made on a combination of clinical, radiologic, endoscopic, and histologic grounds. In the differential diagnosis, endoscopy and histologic evaluation of biopsy specimens can help to make a specific diagnosis. Site of disease is important in documentation and can determine drug choice and clinical course. Disease activity indices are important to assess a patient objectively, particularly in multicentre studies. There is poor correlation between disease activity indices and macroscopic and histologic findings. The Severity Activity Index for Crohn's disease has both clinical and laboratory variables and is a valuable tool for the definition of Crohn's disease. An ulcerative colitis activity index that correlates significantly with microscopic and macroscopic scores, using both clinical symptoms and laboratory findings, is proposed.
TL;DR: In this article, the Francis scale of attitude towards Christianity, Form ASC4B, was completed by 3600 pupils attending non-church-related state maintained schools in England from the first year of the junior school through the fifth year of secondary school.
01 Jan 1989
Abstract: © Springer-Verlag, Berlin Heidelberg New York, 1989, tous droits réservés. L’accès aux archives du séminaire de probabilités (Strasbourg) (http://portail. mathdoc.fr/SemProba/) implique l’accord avec les conditions générales d’utilisation (http://www.numdam.org/legal.php). Toute utilisation commerciale ou impression systématique est constitutive d’une infraction pénale. Toute copie ou impression de ce fichier doit contenir la présente mention de copyright.
TL;DR: Evidence was obtained for predisposition of individuals to heavy or light infection with A. lumbricoides and the influence of host age and sex on infection levels, and the relationship between parasite fecundity and worm burden was investigated.
Abstract: An epidemiological survey of intestinal helminthiases was conducted on 766 primary school children aged 5-16 years from Ile-Ife, Nigeria. On the basis of stool examinations, the prevalence of Ascaris lumbricoides, Trichuris trichiura, hookworm and Strongyloides stercoralis was 88.5, 84.5, 33.1 and 3% respectively. Intensity of infection was measured indirectly by egg counts for each species of helminth and also by counting worms passed after chemotherapy in the case of A. lumbricoides. The influence of host age and sex on infection levels was assessed. Relationships between the intensities of A. lumbricoides, T. trichiura and hookworm in individual children were identified. After anthelmintic treatment with levamisole, the frequency distribution of A. lumbricoides per host and the relationship between parasite fecundity and worm burden were investigated. Reinfection patterns of A. lumbricoides were assessed at two 6-monthly intervals and even within the narrow age range described, differences were found. In addition, evidence was obtained for predisposition of individuals to heavy or light infection with A. lumbricoides.
TL;DR: The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered.
Abstract: The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.
01 Jan 1989
TL;DR: The South Mayo flysch with its ophiolitic detritus is typical of Caledonian flysch sequences which pre-date the mid-Ordovician Taconic deformation, but differs in character from those of late Ordovician age as discussed by the authors.
Abstract: Sandstones from Ordovician sediments of the South Mayo Trough, western Irish Caledonides, show marked stratigraphic variation in their major and trace element geochemistry. High Cr, Ni, and Mg concentrations of ultramafic derivation succeed high Ti and Fe concentrations of mafic provenance This sequence is interpreted as the result of the progressive unroofing of an ophiolite. A possible sedimentary linkage with ophiolite lithologies in the Clew Bay Domain to the north would indicate minimal post-Arenig transcurrent displacement. The South Mayo flysch with its ophiolitic detritus is typical of Caledonian flysch sequences which pre-date the mid-Ordovician Taconic deformation, but differs in character from those of late Ordovician age.
TL;DR: The percentage reduction in menstrual blood loss was significantly greater in the danazol group than in the mefenamic acid group, but the adverse sideeffects occurred significantly more often in the Danazol Group.
TL;DR: The effects of stimulus intensity and the N-methyl-D-aspartate (NMDA) antagonist 2-amino-5-phosphonovalerate (AP5) were studied on the induction of short-term potentiation (STP) and long-term potency (LTP) in CA1 of the rat hippocampal slice.
TL;DR: These results clearly demonstrate that both forms of T. brucei can metabolize glucose via the oxidative segment of the classical pentose phosphate pathway in order to produce d‐ribose‐5‐phosphate for the synthesis of nucleic acids and reduced NADP for other synthetic reactions.
TL;DR: A more complete account of the heterogeneous nature of depression is now required, and two new investigations are presented which suggest the existence of 'non-hopeless' depression.
Abstract: In both Beck's cognitive theory of depression and Brown & Harris's sociopsychological model, hopelessness is given unwarranted universality and centrality. Empirical evidence contradicting this element of the two theories has been ignored, and two new investigations are presented which suggest the existence of 'non-hopeless' depression. A more complete account of the heterogeneous nature of depression is now required.
TL;DR: The positive relationship between religiosity and Eysenckian lie scale scores consistently identified by previous research has been interpreted in a variety of ways according to whether the lie scale is considered to measure actual lying, lack of insight or social conformity as mentioned in this paper.
TL;DR: Screening for carcinoma of the cervix by cervical smears satisfies none of the criteria which would provide its justification, and is an expensive contribution to ill health because the harms exceed the possible benefits by a substantial margin.
TL;DR: In this paper, the accelerator-mass spectrometer (AMS) 14C dates of hand-picked organic material from Ballybetagh were reported, which indicated that the Rumex-Salix zone, which represents the initial establishment of vegetation following deglaciation, began about 12,600 yr B.P.
TL;DR: It is suggested that in otherwise physically healthy patients who are tricyclic nonresponders, the addition of U may be a more rapid treatment than the use of ECT.
Abstract: Thirty severely depressed patients who were resistant to tricyclic antidepressant therapy were randomly allocated to treatment either with electroconvulsive therapy (ECT) or addition of lithium (Li) to the tricyclic. Twenty-one of the 30 patients significantly improved at the end of 3 weeks of treatment. There were no differences in improvement rates between the two groups. However, the patients treated with a Li/tricyclic combination improved more rapidly, showing significant alterations in mental state by day 7. It is suggested that in otherwise physically healthy patients who are tricyclic nonresponders, the addition of Li may be a more rapid treatment than the use of ECT.
TL;DR: In this article, the rate of charge transport through [Os(bipy)2(PVP)10Cl]Cl films has been investigated using chronoamperometry, chronocoulometry and cyclic voltammetry.
TL;DR: A cryptic plasmid, pBAA1, was identified in an industrial Bacillus strain and belongs to the group of small gram-positive plasmids which replicate by a rolling cycle-type mechanism.
Abstract: A cryptic plasmid, pBAA1, was identified in an industrial Bacillus strain. The plasmid is 6.8 kilobases in size and is present in cells at a copy number of approximately 5 per chromosome equivalent. The plasmid has been maintained under industrial fermentation conditions without apparent selective pressure and so is assumed to be partition proficient. The minimal replicon was localized to a 1.4-kilobase fragment which also contains the functions required for copy number control. The very low level of segregational instability of the minimal replicon suggests that it also contains functions involved in plasmid maintenance. Comparison with other plasmids indicates that pBAA1 belongs to the group of small gram-positive plasmids which replicate by a rolling cycle-type mechanism. A sequence was identified which is required for the efficient conversion of the single plus strand to the double-stranded form during plasmid replication. Deletion of this sequence resulted in a low level of segregational plasmid instability.
TL;DR: The absorption of nicotine delivered by a transdermal delivery system was investigated in two separate studies, a dose proportionality study and a multiple dose study, and the levels achieved were in the same range as reported in smokers, following absorption from nicotine chewing gum.
Abstract: The absorption of nicotine delivered by a transdermal delivery system (TDS) was investigated in two separate studies, (A) a dose proportionality study and (B) a multiple dose study. In the dose range of 15-60 mg nicotine, the AUC and Cmax values were proportional to the dose. The levels achieved were in the same range as reported in smokers, following absorption from nicotine chewing gum. The TDS used in the present study produced sustained levels of nicotine for 24 h. No significant accumulation of nicotine was evident as a result of multiple dose administration using a 30-mg nicotine patch. Absorption of nicotine from the TDS was 80-90% and the rate of delivery was similar during both studies.