Biomedical subjects

A Cooper

Publications and source records attributed to A Cooper.

At least 73 records · Page 4Linked to original sources

PubMed2000

An examination of the volume-mortality relationship for New York State trauma centers.

OBJECTIVES: New York State Trauma Registry data were analyzed to determine whether there is a significant relationship between the volume of trauma patients treated by a trauma center and its risk-adjusted inpatient mortality rate. METHODS: Stepwise logistic regression was used to identify significant independent predictors of mortality, their weights, and the probability of in-hospital mortality for each patient. These data were then used to calculate risk-adjusted mortality rates for various ranges of hospital volume. Ranges were identified on the basis of homogeneity of mortality rates, the number of hospitals in each range, and the number of patients in each range. Three volume measures were used: (1) total annual volume of trauma cases > or = 1200 and total annual volume > or = 240 for patients with Injury Severity Score (ISS) > or = 15 (equivalent to American College of Surgeons [ACS] criteria), (2) total annual volume of patients with ISS > or = 15, and (3) total annual volume of cases in the Registry (approximately, inpatients with ISS > or = 9). RESULTS: Results show that the 35 New York State trauma centers not meeting the ACS criteria had lower, but not significantly lower, observed and risk-adjusted mortality rates (7.62% and 8.25%, respectively) than the corresponding rates for the 8 New York State trauma centers that met the ACS criteria (9.36% and 8.83%, respectively). Regarding the other two criteria, hospital ranges representing lower annual volumes tended to have somewhat lower, although not significantly lower, observed and risk-adjusted mortality rates. For example, using a total annual volume for patients with ISS > or = 15, the risk-adjusted mortality rates for the volume ranges 1-150, 151-250, and 251+ were 7.78%, 9.23%, and 8.70%, respectively. CONCLUSIONS: We were unable to document an inverse relationship between hospital volume and inpatient mortality rate for trauma centers in New York State. Volume criteria should not be considered indicators of the quality of trauma care.

Age Distribution↗

PubMed2000

Accounting for intubation status in predicting mortality for victims of motor vehicle crashes.

BACKGROUND: Two of the important predictors of mortality for trauma patients are the Glasgow Coma Scale and the respiratory rate. However, for intubated patients, the verbal response component of the Glasgow Coma Scale and the respiratory rate cannot be accurately obtained. This study extends previous work that attempts to predict mortality accurately for intubated patients without using verbal response and respiratory rate. METHODS: The New York State Trauma Registry was used to identify 1994 and 1995 victims of motor vehicle crashes (MVCs). For the subset of patients who were not intubated, we developed two statistical models to predict mortality: one did not contain verbal response or respiratory rate, and the other contained a predicted verbal response. These were compared with a model that did include verbal response and respiratory rate. We also compared the predictive abilities of the first two models for all MVC patients (intubated and nonintubated) and determined the extent to which intubated patients were at increased risk of dying in the hospital after having adjusted for other predictors of mortality. RESULTS: For nonintubated patients, the statistical model without verbal response and the model with predicted verbal response had slightly better discrimination and worse calibration than the model that included verbal response and respiratory rate. Predicted verbal response did not improve the strength of the model without verbal response. For all MVC patients (intubated and nonintubated), predicted verbal response was not a significant predictor of mortality when used in combination with the other predictors. Intubation status was a significant predictor, with intubated patients having a higher probability of dying in the hospital than patients with otherwise identical risk factors. CONCLUSION: Inpatient mortality for intubated MVC patients can be accurately predicted without respiratory rate or verbal response. There appears to be no need for predicted verbal response to be part of the prediction formula, but intubation status is an important independent predictor of mortality and should be used in statistical models that predict mortality for MVC patients.

Accidents, Traffic↗

PubMed2000

Chest pain in the emergency department.

The assessment of patients with chest pain is challenging for any emergency physician because of the spectrum of illness covered by this symptom. Patients may have a serious life-threatening condition or a trivial self-limiting illness. This article presents an approach to the assessment and early management of patients presenting with acute non-traumatic chest pain in the emergency department.

Acute Disease↗

PubMed2000

Cloning and characterization of the murine coagulation factor X gene.

The gene encoding murine coagulation factor X (fX) was isolated and characterized from a lamdaFIX II library generated from murine genomic DNA. The 20130 bp sequence contains 18049 nucleotides that extend from the initiating methionine to the polyadenylation site. 1056 nucleotides 5' of the start codon were determined and contain putative start sites for the FX mRNA as well as sites for binding of putative transcription factors. The sequence extends 1024 3' of the polyadenylation site. The gene contains 8 exons and 7 introns which were determined by comparing the mouse FX cDNA and gene sequences. The exonic structure of the gene is similar to that of the other mammalian vitamin K-dependent serine proteases of the coagulation system. These include an exon encoding the prepropepetide, the gla-domain, a short helical stack, two exons for the two EGF domains, the activation pepetide, and two exons encoding the serine protease domain. The 5' sequence of the mouse FX gene overlaps with the 3' region of the FVII gene indicating that the murine FVII and FX gene are arranged in a head to tail arrangement as they are in humans.

Animals↗

PubMed2000

Are women discriminated against for lipid lowering therapy? Results from a prospective cohort of women with coronary artery disease.

The objective of the study was to compare the lipid management of men and women with documented coronary artery disease in 587 patients (433 men and 154 women) undergoing coronary angiography between 1991 and 1995. A fasting total cholesterol (TC) was measured in all patients on the morning of angiography. A postal/telephone follow-up was carried out one year after angiography in a subpopulation of 278 patients (194 men and 84 women) who were not taking lipid-lowering therapy (LLT) or whose TC was > 5.2 mmol/l at the time of angiography. At baseline, mean TC was 5.89 mmol/l (SE 0.06) in the men and 6.47 mmol/l (SE 0.09) in the women (p = < 0.0001). Action or recommendation to institute LLT was taken in 141 (32.7%) men and 62 (40.3%) women (p = 0.09). In the follow-up population, comparing men with women, 74 (38.3%) vs 39 (46.4%) were taking LLT (p = 0.21); 56 (28.9%) vs 26 (31.0%) had not undergone repeat TC testing (p = 0.73); when performed, repeat TC was 5.75 (0.09) mmol/l vs 5.64 (0.16) mmol/l (p = 0.53); mean decrease in TC between baseline and follow-up was 0.86 (0.10) mmol/l vs 1.01 (0.21) mmol/l (p = 0.51). There was no significant gender difference in lipid management either at the time of coronary angiography or subsequent follow-up, although the level of lipid-lowering drug use remained inadequate in both sexes.

Cholesterol↗

PubMed1999

Quantitation of metal ion and DNA junction binding to the Holliday junction endonuclease Cce1.

Cce1 is a magnesium-dependent Holliday junction endonuclease involved in the resolution of recombining mitochondrial DNA in Saccharomyces cerevisiae. Cce1 binds four-way DNA junctions as a dimer, opening the junction into an extended, 4-fold symmetric structure, and resolves junctions by the introduction of paired nicks in opposing strands at the point of strand exchange. In the present study, we have examined the interactions of wild-type Cce1 with a noncleavable four-way DNA junction and metal ions (Mg(2+) and Mn(2+)) using isothermal titration calorimetry, EPR, and gel electrophoresis techniques. Mg(2+) or Mn(2+) ions bind to Cce1 in the absence of DNA junctions with a stoichiometry of two metal ions per Cce1 monomer. Cce1 binds to four-way junctions with a stoichiometry of two Cce1 dimers per junction molecule in the presence of EDTA, and one dimer of Cce1 per junction in 15 mM magnesium. The presence of 15 mM Mg(2+) dramatically reduces the affinity of Cce1 for four-way DNA junctions, by about 900-fold. This allows an estimation of DeltaG degrees for stacking of four-way DNA junction 7 of -4.1 kcal/mol, consistent with the estimate of -3.3 to -4.5 kcal/mol calculated from branch migration and NMR experiments [Overmars and Altona (1997) J. Mol. Biol. 273, 519-524; Panyutin et al. (1995) EMBO J. 14, 1819-1826]. The striking effect of magnesium ions on the affinity of Cce1 binding to the four-way junction is predicted to be a general one for proteins that unfold the stacked X-structure of the Holliday junction on binding.

Binding Sites↗

PubMed1999

Relationships of the extinct moa-nalos, flightless Hawaiian waterfowl, based on ancient DNA.

The extinct moa-nalos were very large, flightless waterfowl from the Hawaiian islands. We extracted, amplified and sequenced mitochondrial DNA from fossil moa-nalo bones to determine their systematic relationships and lend insight into their biogeographical history. The closest living relatives of these massive, goose-like birds are the familiar dabbling ducks (tribe Anatini). Moa-nalos, however, are not closely related to any one extant species, but represent an ancient lineage that colonized the Hawaiian islands and evolved flightlessness long before the emergence of the youngest island, Hawaii, from which they are absent. Ancient DNA yields a novel hypothesis for the relationships of these bizarre birds, whereas the evidence of phylogeny in morphological characters was obscured by the evolutionary transformation of a small, volant duck into a giant, terrestrial herbivore.

Animals↗

PubMed1999

Homing in on the role of transition metals in the HNH motif of colicin endonucleases.

The cytotoxic domain of the bacteriocin colicin E9 (the E9 DNase) is a nonspecific endonuclease that must traverse two membranes to reach its cellular target, bacterial DNA. Recent structural studies revealed that the active site of colicin DNases encompasses the HNH motif found in homing endonucleases, and bound within this motif a single transition metal ion (either Zn(2+) or Ni(2+)) the role of which is unknown. In the present work we find that neither Zn(2+) nor Ni(2+) is required for DNase activity, which instead requires Mg(2+) ions, but binding transition metals to the E9 DNase causes subtle changes to both secondary and tertiary structure. Spectroscopic, proteolytic, and calorimetric data show that, accompanying the binding of 1 eq of Zn(2+), Ni(2+), or Co(2+), the thermodynamic stability of the domain increased substantially, and that the equilibrium dissociation constant for Zn(2+) was less than or equal to nanomolar, while that for Co(2+) and Ni (2+) was micromolar. Our data demonstrate that the transition metal is not essential for colicin DNase activity but rather serves a structural role. We speculate that the HNH motif has been adapted for use by endonuclease colicins because of its involvement in DNA recognition and because removal of the bound metal ion destabilizes the DNase domain, a likely prerequisite for its translocation across bacterial membranes.

Bacterial Proteins↗

PubMed1999

Formation and biochemical characterization of tube/pelle death domain complexes: critical regulators of postreceptor signaling by the Drosophila toll receptor.

In Drosophila, the Toll receptor signaling pathway is required for embryonic dorso-ventral patterning and at later developmental stages for innate immune responses. It is thought that dimerization of the receptor by binding of the ligand spätzle causes the formation of a postreceptor activation complex at the cytoplasmic surface of the membrane. Two components of this complex are the adaptor tube and protein kinase pelle. These proteins both have "death domains", protein interaction motifs found in a number of signaling pathways, particularly those involved in apoptotic cell death. It is thought that pelle is bound by tube during formation of the activation complexes, and that this interaction is mediated by the death domains. In this paper, we show using the yeast two-hybrid system that the wild-type tube and pelle death domains bind together. Mutant tube proteins which do not support signaling in the embryo are also unable to bind pelle in the 2-hybrid assay. We have purified proteins corresponding to the death domains of tube and pelle and show that these form corresponding heterodimeric complexes in vitro. Partial proteolysis reveals a smaller core consisting of the minimal death domain sequences. We have studied the tube/pelle interaction with the techniques of surface plasmon resonance, analytical ultracentrifugation and isothermal titration calorimetry. These measurements produce a value of K(d) for the complex of about 0.5 microM.

Amino Acid Sequence↗

PubMed1999

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.

BACKGROUND: Many enzymes that digest polysaccharides contain separate polysaccharide-binding domains. Structures have been previously determined for a number of cellulose-binding domains (CBDs) from cellulases. RESULTS: The family IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan but not cellulose. Its structure is similar to that of the homologous family IIa CBD from C. fimi Cex, consisting of two four-stranded beta sheets that form a twisted 'beta sandwich'. The xylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar residues. CONCLUSIONS: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplanar, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary structures of the ligands cellulose and xylan. XBD1 and CexCBD represent a striking example of two proteins that have high sequence similarity but a different function.

Amino Acid Sequence↗

PubMed1999

Independently melting modules and highly structured intermodular junctions within complement receptor type 1.

A segment of complement receptor type 1 (CR1) corresponding to modules 15-17 was overexpressed as a functionally active recombinant protein with N-glycosylation sites ablated by mutagenesis (referred to as CR1 approximately 15-17(-)). A protein consisting of modules 15 and 16 and another corresponding to module 16 were also overexpressed. Comparison of heteronuclear nuclear magnetic resonance (NMR) spectra for the single, double, and triple module fragments indicated that module 16 makes more extensive contacts with module 15 than with module 17. A combination of NMR, differential scanning calorimetry, circular dichroism, and tryptophan-derived fluorescence indicated a complex unfolding pathway for CR1 approximately 15-17(-). As temperature or denaturant concentration was increased, the 16-17 junction appeared to melt first, followed by the 15-16 junction, and module 17 itself; finally, modules 15 and 16 became denatured. Modules 15 and 16 adopted an intermediate state prior to total denaturation. These results are compared with a previously published study [Clark, N. S., Dodd, I, Mossakowska, D. E., Smith, R. A. G., and Gore, M. G. (1996) Protein Eng. 9, 877-884] on a fragment consisting of the N-terminal three CR1 modules which appeared to melt as a single unit.

Amino Acid Sequence↗

PubMed1999

Sequence-divergent units of the ABA-1 polyprotein array of the nematode Ascaris suum have similar fatty-acid- and retinol-binding properties but different binding-site environments.

Polyproteins comprise long polypeptides that are post-translationally cleaved into proteins of different function, or tandemly repetitive polypeptides which are processed into multiple versions of proteins which are presumed to have the same function. In the latter case the individual units of the polyprotein can differ substantially in sequence. Identity of function between the different units therefore cannot be assumed. Here we have examined the ABA-1 polyprotein allergen of the parasitic nematode Ascaris suum and found it to contain units which show a 50% difference in amino acid sequence. The parasite therefore produces at least two radically different forms of the allergen encoded within the polyprotein array. In fluorescence-based ligand-binding assays, recombinant polypeptides representing the two forms (designated ABA-1A1 and ABA-1B1) showed similar binding affinities for a range of fluorescent active-site probes [retinol, dansylundecanoic acid, dansyl-DL-alpha-amino-octanoic acid, cis-parinaric acid (cPnA)] and for the non-specific hydrophobic surface probe 8-anilinonaphthalene-1-sulphonic acid. However, the molecular environments in the active sites are markedly different, as indicated by disparate fluorescence emission peaks and intensities of bound probes. CD showed that the proteins have similar secondary structures but differ in susceptibility to chemical denaturation/unfolding by guanidinium chloride. Both retain a single conserved tryptophan residue in a characteristic non-polar environment, as revealed by extreme fluorescence blue shift. Thus the gross differences in sequence of the two proteins are not reflected in their ligand-binding specificities but in their binding-site environments.

Allergens↗

PubMed1999

Predictors of local recurrence following excision alone for ductal carcinoma in situ.

BACKGROUND: The treatment of ductal carcinoma in situ (DCIS) remains controversial, particularly in regard to the selection of patients who may be appropriately treated with wide excision alone. To help identify such patients, the authors assessed prognostic factors for local recurrence in patients with DCIS treated with excision alone. METHODS: The study population consisted of 59 patients diagnosed with DCIS between 1985 and 1990. All had been treated with excision alone, had their histologic slides available for re-review by a study pathologist, and had negative margins of excision on review. The median age at diagnosis was 54 years, and the median follow-up time was 95.5 months. Ninety-six percent presented with mammographic findings only; all patients had a reexcision. The size of the DCIS was assessed by the total number of low-power fields (LPF) in which DCIS was present (median LPF = 5). RESULTS: Ten patients experienced a local recurrence (LR) at 5-132 months (median, 37 months) after excision. The actuarial 5-year LR rate was 10%. Four of the recurrences were invasive carcinomas, and 6 were DCIS. No patients have developed metastatic disease or have died of disease. Lesion size >5 LPF was the only significant prognostic factor for local recurrence on univariate analysis (3% vs. 17% for < or = 5 vs. > or = 5 LPF, P = 0.02) and in proportional hazards models. Although patients with nuclear Grade 3 lesions had a higher LR rate than those with nuclear Grade 1 and 2 lesions (18% vs. 6% and 5%, respectively) and patients with close margins (< or = 1 mm) had a higher LR rate than patients with negative margins (>1 mm) (25% vs. 8%), these differences did not reach statistical significance. Among the 19 cases with margins negative by more than 1 mm, lesion size < or = 5 LPF, and nuclear Grade 1 or 2, there were no LRs; by contrast, the remaining 40 patients had a 5-year actuarial LR rate of 15% (P = 0.08). CONCLUSIONS: Lesion size was the only statistically significant prognostic factor for local recurrence in this series of patients with DCIS treated with excision alone. Other factors, such as margin status and nuclear grade, may also be useful in the identification of patients with DCIS who can be managed with excision alone. However, the most reliable and reproducible method of assessing these factors and the best way to combine them have not been determined.

Adult↗

PubMed1999

Cryopreservation of bovine ovarian tissue: structural normality of follicles after thawing and culture in vitro.

The recovery of viable follicles from cryopreserved ovarian tissue would be of benefit in many areas of assisted reproduction. Structural integrity needs to be maintained following cryopreservation of ovarian tissue in order to retrieve healthy follicles which can then be cultured in vitro to produce viable oocytes. We have assessed the effect of in vitro culture of bovine tissue for 0, 1, 4, 24, or 48 h after exposure to, or cryopreservation in, dimethylsulphoxide. Immediately after freezing, normality of primary and preantral follicles within the tissue was significantly lower than for tissue exposed to the cryoprotectant without freezing or for control tissue. After 4 h in culture, cryopreserved tissue appeared to have recovered from damage caused by freezing, although the percentage of tissue with normal morphology declined after 24 and 48 h of culture. There was no significant difference between percentage normality in control tissue and tissue exposed to the cryoprotectant without freezing for any of the culture times studied. These data indicate that it is possible to freeze/thaw bovine ovarian tissue while retaining a reasonable yield of morphologically intact follicles and that a short period of post-thaw culture may enhance follicle recovery.

Animals↗

PubMed1999

Ligand binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations.

Antibody IgE Lb4 interacts favorably with a large number of different compounds. To improve the current understanding of the structural basis of this vast cross-reactivity, the binding of three dinitrophenyl (DNP) amino acids (DNP-alanine, DNP-glycine, and DNP-serine) is investigated in detail by means of docking and molecular dynamics free energy simulations. Experimental binding energies obtained by isothermal titration microcalorimetry are used to judge the results of the computational studies. For all three ligands, the docking procedure proposes two plausible subsites within the binding region formed by the antibody CDR loops. By subsequent molecular dynamics simulations and calculations of relative free energies of binding, one of these subsites, a tyrosine-surrounded pocket, is revealed as the preferred point of complexation. For this subsite, results consistent with experimental observations are obtained; DNP-glycine is found to bind better than DNP-serine, and this, in turn, is found to bind better than DNP-alanine. The suggested binding mode makes it possible to explain both the moderate binding affinity and the differences in binding energy among the three ligands.

Animals↗

PubMed1999

Priorities for research in Emergency Medical Services for Children: results of a consensus conference. EMSC Research Agenda Consensus Committee, National EMSC Resource Alliance.

STUDY OBJECTIVE: The study objective was to arrive at a consensus on the priorities for future research in Emergency Medical Services for Children (EMSC). METHODS: A consensus group was convened using the Rand'-UCLA Consensus Process. The group took part in a 3-phase process. Phase I involved reviewing a compendium of relevant research articles and answering a mailed questionnaire. Panel members were asked to prioritize topics based on the 1993 Institute of Medicine Report on Emergency Medical Services for Children. Participants were asked to rate each topic based on the significance of the research and whether the topic would (1) improve general knowledge, (2) change behavior, (3) improve health, (4) decrease the cost of care, or (5) change public policy. A 4-point Likert scale was used. They were also asked in the research would require a multicenter study and if the research were feasible. Round II of the study involved a meeting of the panel, where the results of Round I were discussed and the topics reprioritized. The topics were given a rank order and a final ranking was done in Round III. RESULTS: The panel considered a list of 32 topics and these were combined and reworded to give them more precise meaning. Several new topics were also added. Fifteen topics were given a rank order and placed within the 7 broad categories of the Institute of Medicine report. Clinical aspects of emergency care systems organization, configuration and operation and injury prevention were given high priority rankings. The first 5 topics were very close in point-rank order. CONCLUSION: The panel was able to develop a list of important topics for future research in EMSC that can be used by foundations, governmental agencies, and others in setting a research agenda for EMSC.

Child↗

PubMed1999

Priorities for research in emergency medical services for children: results of a consensus conference.

STUDY OBJECTIVE: To arrive at a consensus on the priorities for future research in emergency medical services for children. METHODS: A consensus group was convened using the Rand-UCLA Consensus Process. The group took part in a 3-phase process. Round 1 involved reviewing a compendium of relevant research articles and answering a mailed questionnaire. Panel members were asked to prioritize topics on the basis of the 1993 Institute of Medicine Report on Emergency Medical Services for Children. Participants were asked to rate each topic based on the significance of the research, and whether the topic would (1) improve general knowledge, (2) change behavior, (3) improve health, (4) decrease the cost of care, or (5) change public policy. A 4-point Likert scale was used. Participants were also asked if the research would require a multicenter study and if the research were feasible. Round 2 of the study involved a meeting of the panel, where the results of Round 1 were discussed and the topics were reprioritized. The topics were given a rank order and a final ranking was done in Round 3. RESULTS: The panel considered a list of 32 topics; these were combined and reworded to give them more precise meaning. Several new topics were also added. Fifteen topics were given a rank order and placed within the 7 broad categories of the Institute of Medicine report. Clinical aspects of emergency care, systems organization, configuration, and operation and injury prevention were given high priority rankings. The first 5 topics were very close in point-rank order. CONCLUSION: The panel was able to develop a list of important topics for future research in emergency medical services for children that can be used by foundations, governmental agencies, and others in setting a research agenda for such services.

Child↗

PubMed1999

Thermodynamic analysis of biomolecular interactions.

Direct measurement of the thermodynamics of biomolecular interactions is now relatively easy. Interpretation of these thermodynamics in simple molecular terms is not. Recent work shows how the multiplicity of weak noncovalent interactions, and the inevitable enthalpy/entropy compensation that these interactions engender, lead to difficulties in teasing out the different components.

Animals↗