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At least 1,117 records · Page 62Linked to original sources
PubMed2001

Pex, analytical tools for PDB files. II. H-Pex: noncanonical H-bonds in alpha-helices.

We use the H-Pex (Thomas et al., this issue) to analyze the main chain interactions in 131 proteins. In antiparallel beta-sheets, the geometry of the N...O bond is: median N...O distances, 2.9 SA, C==O...N angles at 154 degrees and the C alpha--C==O...H angles are dispersed around 3 degrees. In some instances, the other side of the C==O axis is occupied by a HC alpha. As recently supported by Vargas et al. (J Am Chem Soc 2000;122:4750-4755) C alpha H...O and NH...O could cooperate to sheet stability. In alpha-helices, the main chain C==O interact with the NH of their n + 4 neighbor on one side, and with a C beta H or C gamma H on the other side. The median O...N distance (3.0 A) and C==N angle (147 degrees) suggest a canonical H-bond, but the C alpha--C==O...H dihedral angle invalidates this option, since the hydrogen attacks the oxygen at 122 degrees, i.e., between the sp(2) and pi orbitals. This supports that the H-bond is noncanonical. In many instances, the C gamma H or the C beta H of the n + 4 residue stands opposite to the NH with respect to the oxygen. Therefore, we propose that, in alpha-helices, the C gamma H or C beta H and the NH of the n + 4 residue hold the oxygen like an electrostatic pincher. Proteins 2001;43:37-44.

Algorithms↗
PubMed2006

Problems in using birth certificate files in the capture-recapture model to estimate the completeness of case ascertainment in a population-based birth defects registry in New York State.

BACKGROUND: The limitations and underlying assumptions of the capture-recapture methods have hindered their application in epidemiological settings, especially in evaluating the completeness of birth defects registries. This study explored the possibility of using birth certificates as the secondary data source in a simple two-source capture-recapture model to estimate the completeness of case ascertainment of the Congenital Malformations Registry (CMR) for selected major birth defects. METHODS: The CMR and the birth certificates were used as the primary and secondary sources, respectively. Children who were born in 1996-2001 and had selected major birth defects were identified from the two sources. The accuracy of the diagnoses was examined by comparing the individual birth defect categories of the children from the two sources. RESULTS: Discrepancies in birth defect categories in the two data sources and false positives in the birth certificates were the major problems encountered in estimating the completeness of the CMR using the simple two-source capture-recapture method. The estimated completeness for selected major birth defects was only about 71%. Stratified analyses resulted in relatively high estimated completeness for oral clefts (90%) and Down syndrome (88%). CONCLUSIONS Although the birth certificate data was not a good source for estimating the completeness of case ascertainment of the CMR using capture-recapture methods, the analyses provided reasonable estimates for some conditions that were relatively easy to identify and diagnose at birth, such as oral clefts and Down syndrome.

Birth Certificates↗
PubMed1996

Restenosis--an open file.

The main procedural drawback to percutaneous coronary angioplasty is restenosis of the treated site within 6 months. Despite advances in equipment, technique, and adjunctive therapies, restenosis has occurred in approximately one-third to one-half of all patients. The biology of restenosis can be divided into plaque persistence and recoil, thrombus formation and transformation, and cellular proliferation and vascular remodeling. Animal models of restenosis have helped to elucidate these mechanisms of restenosis and provide a means to test pharmacologic and mechanical strategies to reduce stenosis recurrence. While numerous agents have been tested in animal models, until recently none has translated into benefit in large-scale clinical trials. Two therapeutic "hopefuls" which have recently emerged in clinical practice are the potent platelet inhibitors, glycoprotein IIb/IIIa receptor antagonists, and intracoronary metallic stents. The IIb/IIIa receptor antagonists target thrombus formation at the angioplasty site, thereby minimizing abrupt vessel closure acutely and neointimal growth chronically, while intracoronary stents safely produce a large coronary arterial lumen acutely and prevent vessel recoil. Separately, these therapeutic strategies have been shown to reduce clinical restenosis 20-30% at 6-month follow-up. With these encouraging results, the future will certainly provide more pharmacologic and mechanical therapies targeting restenosis. With increased understanding of the restenotic process and continued refinement of effective treatments, it may be possible one day to prevent stenosis recurrence.

Angioplasty, Balloon, Coronary↗
PubMed2004

The Tbx-files: the truth is out there.

T-box factors are critical regulators of embryonic development and have been implicated in several human diseases. This primer describes the basics of how T-box factors work and features a discussion of the state of T-box gene research with three experts in the field.

Animals↗
PubMed1996

Functional analysis of Drosophila and mammalian cut proteins in files.

The cut locus acts as a bimodal switch controlling cell fate in the peripheral nervous system of Drosophila and is also required for the development of the wing margin. It encodes a protein, Cut, that contains an atypical homeodomain and three copies of a new motif which can bind DNA in vitro. The human protein CDP and the murine protein Cux have recently been isolated as DNA-binding activities and they are structurally related to Cut. We show that ectopic expression of Cut, CDP, or Cux similarly affects embryonic sensory organ development and can rescue a wing scalloping mutant phenotype associated with loss of cut expression along the prospective wing margins. This suggests that the function of Cut is evolutionarily conserved.

Animals↗
PubMed1982

Calculation of percentage of cases on file with an unnamed father in 100 one-man and 100 two-man cases (filiation cases) from South-West Germany in 1976-1981. Ratio of defendants to witnesses among non-excluded men in two-man cases.

Applying the formula of Schulte-Mönting and Hummel to 100 one-man affairs (filiation cases) in South-West Germany between 1979 and 1981 gave a realistic prior probability of paternity of 0.837 +/- 0.0372. This means that in approximately 83.7% of all one-man affairs the man named by the mother to be the father of her child is indeed the father. For two-man affairs a realistic prior probability of paternity of 0.863 +/- 0.0369 was calculated on the basis of 100 two-man affairs in South-West Germany between 1976 and 1981. In other words, there is a probability of about 86.3% that a non-excludable man--irrespective of other factors--in a two-man affair is the real father of the child. In approximately 13.7% of two-man affairs neither the "defendant" nor the witness is the father, but a third unknown person. In about 85.7% of the two-man affairs in which a father of the child was named the "defendant" is in fact the father and in 14.3% the "witness" is the father.

Blood Grouping and Crossmatching↗
PubMed1981

Potassium transport across rabbit descending colon in vitro: evidence for single-file diffusion through a paracellular pathway.

The results of previous studies indicate that the bidirectional fluxes of K across short-circuited rabbit descending colon are attributable to passive diffusion through paracellular pathways and that this route is ten times more permeable to K than to Na and Cl. However, transepithelial diffusion potentials in the presence of large transepithelial Na and K concentration differences are much lower than those predicted by the "constant field equation" and appear to be inconsistent with this high K selectivity. The results of the present studies, designed to resolve this apparent contradiction, indicate that: (a) The ratios of the bidirectional transepithelial fluxes of K determined over a wide range of combined chemical and electrical potential differences conform reasonably well with those predicted by the Ussing flux-ratio equation. (b) The permeability coefficient of K (PK), determined from the net fluxes in the presence of concentration differences and from unidirectional fluxes under short-circuit conditions, decreases with increasing K concentration; in the presence of low K concentrations, PK is approximately ten-times PNa, but it approaches PNa in the presence of high K concentrations. PNa is not affected under these conditions. These results provide an explanation for the failure to observe large transepithelial diffusion potentials in the presence of large transepithelial Na and K concentration differences. In addition, these results are consistent with the notion that K diffuses across this preparation through two parallel pathways, one that does not discriminate among K, Na and Cl (a "free-solution" shunt) and another that is highly K selective and involves an interaction with one, or at most two, sites along the route.

Animals↗
PubMed1996

Evidence for site selection during synaptogenesis: the surface distribution of synaptic sites in photoreceptor terminals of the files Musca and Drosophila.

1. Photoreceptor terminals in the flies Musca domestica and Drosophila melanogaster have been reconstructed in three dimensions from serial EM to reveal the surface distributions of afferent tetrad synapses. 2. The terminals are cylindrical and surround two target cells; they have synaptic sites distributed along their length and around their circumference, except for a strip along the face that lies furthest away from the target cells. 3. Over their inner faces, the terminals have presynaptic sites that are distributed evenly. 4. The distribution of sites in maps plotted from reconstructed membrane surfaces was examined by quadrat analyses. The frequency of sites per quadrat division was not Poissonian, i.e. was non-random. Thus, some form of site selection must exist during synaptogenesis. 5. The sites were shown by variance ratio analysis to be regular (evenly dispersed, not clustered). This suggests that some form of interaction exists, so as to reduce the probability that a synapse will form close to an already existing synaptic site. 6. Distances between nearest-neighbour pairs of synapses had a closest minimum spacing of about 0.8 micron in Musca that was violated by about 5% of pairs, whereas the corresponding distances were about 0.2 micron shorter in Drosophila, which had 13% of pairs situated closer together than 0.8 micron. 7. During synaptogenesis, either initially in the pupa or later in the adult, the probability that a synapse will form is therefore effectively zero within these distances from an existing synaptic site, perhaps through an inhibitory influence exerted by the latter. The nearest-neighbour distances are normally distributed. 8. Unlike the distribution of presynaptic sites, the distribution of postsynaptic sites over the surfaces of the dendrites of the target cells is not even. Although not studied in detail, the corresponding nearest-neighbour distances are much smaller, as little as 0.1 micron. Thus the wider spacing seen between sites over the receptor terminals is a function of the presynaptic cells, and not of their postsynaptic partners, and implies the existence of interactions between synaptic sites.

Animals↗