Biomedical subjects

Rebecca Harris

Publications and source records attributed to Rebecca Harris.

14 recordsLinked to original sources

PubMed2006

Orbital energetics and molecular recognition.

We present preliminary data demonstrating that orbital eigenenergy fluctuation recorded in the course of ab initio molecular dynamics calculations may contain information relevant in determining molecular behavior and recognition. A simple scheme is presented that maps these data to molecular descriptors. Using computational drug design as the context, these descriptors are compared with previous electronic eigenvalue descriptor methods with encouraging results.

Journal Article↗

PubMed2005

Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.

A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Molecular Conformation↗

PubMed2004

Targacept active conformation search: a new method for predicting the conformation of a ligand bound to its protein target.

Targacept active conformation search (TACS) is a novel variation of well-established three-dimensional quantitative structure--activity relationship methodologies that seeks to determine probable conformation(s) of ligands bound to their protein targets. A combination of affinity or activity data and energetically accessible conformational ensembles, each conformer described by three-dimensional (3-D) sensitive descriptors, forms the basis of the TACS data model. Recursive pruning is used to reduce the size of both the conformational ensemble and the descriptor space until the TACS data model contains just enough information to determine probable conformation(s) of ligands bound to their protein targets. The TACS algorithm is comprised of five components: (1) conformational ensemble generation, (2) 3-D sensitive descriptor calculation, (3) ensemble descriptor preprocessing, (4) model generation, and (5) prediction of bound conformation(s). Significantly, this method precludes the need for subjective or objective molecular alignment. We report the application of this technique to five benchmark protein-ligand couples where the conformation of a bound ligand has been previously established using X-ray crystallography: 9-cis-retinoic (1) and 9-trans-retinoic acid (2), both agonists for the retinoic acid receptor gamma, compounds KH1060 (3) and MC1288 (4), which bind to the vitamin D3 receptor, and R04 (5), an inhibitor bound to human rhinovirus 14 thermolysin. The binding conformations predicted by TACS were compared to the crystallographic structures extracted from their respective binding sites using root-mean-squared deviation (rmsd) criteria. Three of the conformations found using TACS were within crystallographic error. 9-cis-Retinoic acid, 9-trans-retinoic acid, and MC1288, when superimposed on their crystallographic structures, gave rmsd values of 0.22, 0.17, and 0.34 A, respectively. The rmsd values for KH1060 (1.54 A) and R04 (1.01 A) were larger but still reasonable.

Binding Sites↗

PubMed2004

Fluorescence anisotropy microplate assay for analysis of steroid receptor-DNA interactions.

To analyze the interactions of steroid/nuclear hormone receptors with their DNA response elements, we used ultra low-volume microplates to develop a simple and rapid fluorescence anisotropy assay. The novel fluorescence anisotropy microplate assay (FAMA) was applied to the binding of estrogen and progesterone receptors (ER and PR, respectively) to their respective DNA response elements. The FAMA offers exceptional flexibility in its ability to test a variety of binding conditions and DNA response elements in real time. This assay can differentiate between, and quantitate, sequence-specific and nonspecific binding of receptors to DNA and offers the possibility of true solution analysis of the interaction of coregulators with the estrogen response element (ERE)-ER complex. To test suitability for screening large compound libraries, we demonstrated that the FAMA generates stable signals for more than 4 hours, is insensitive to inhibition by dimethyl sulfoxide (DMSO), and works well in 384-well plates. We analyzed inhibition of receptor-DNA interaction by several zinc chelators and demonstrated zinc dependence and a generally higher sensitivity to inhibition for PR-progesterone response element (PRE) interactions than for ER-ERE interactions. The FAMA is the first system suitable for screening large compound libraries to identify novel compounds that antagonize (or stimulate) binding of steroid receptors to their DNA response elements.

DNA↗

PubMed2004

Risk factors for dental caries in young children: a systematic review of the literature.

OBJECTIVE: To conduct a systematic review of the literature on risk factors for dental caries in deciduous teeth of children aged six years and under, to give a scientific framework for the international collaborative studies on inequalities in childhood caries. METHOD: Accepted guidelines were followed. Studies were identified by electronic searching and reviewed on the basis of key words, title and abstract by two reviewers to assess whether inclusion criteria were met. Copies of all articles were obtained and assessed for quality according to the study design. RESULTS: 1029 papers were identified from the electronic search, 260 met the prima facie inclusion criteria. 183 were excluded once full copies of these papers were obtained. Of the 77 studies included, 43 were cross sectional, 19 cohort studies, 8 case control studies and 7 interventional studies. Few obtained the highest quality scores. 106 risk factors were significantly related to the prevalence or incidence of caries. CONCLUSION: There is a shortage of high quality studies using the optimum study design, i.e. a longitudinal study. The evidence suggests that children are most likely to develop caries if Streptococcus Muttans is acquired at an early age, although this may be partly compensated by other factors such as good oral hygiene and a non-cariogenic diet. Diet and oral hygiene may interact so that if there is a balance of 'good' habits by way of maintaining good plaque control and 'bad' habits by way of having a cariogenic diet, the development of caries may be controlled.

Child↗

PubMed2004

Developing explanatory models of health inequalities in childhood dental caries.

OBJECTIVE: Long-term aim is to determine optimum interventions to reduce dental caries in children in disadvantaged communities and minimise the effects of exclusion from health care systems, of ethnic diversity, and health inequalities. DESIGN: Generation of initial explanatory models, study protocol and development of two standardised measures. First, to investigate how parental attitudes may impact on their children's oral health-related behaviours and second, to assess how dentists' attitudes may impact on the provision of dental care. SUBJECTS: Core research team, lead methodologists, 44 consortium members from 18 countries. To complete the development of the questionnaire, the initial set of items was administered to parents (n = 23) with children in nursery schools in Dundee, Scotland and sent to the same parents one week later. A standardised measure examining barriers to providing dental care for children aged 3 to 6 years was developed. 20 dentists working in primary dental care in Scotland completed the measure on two different occasions separated by one week. RESULTS: Explanatory models were developed. Family questionnaire: test-retest reliability excellent (r = 0.93 p < or = 0.001) with very good internal reliability (alpha = 0.89). Dentists questionnaire: excellent test-re-test reliability r = 0.88, (alpha = 0.90). CONCLUSIONS: Interaction between consortium members enhanced the validity of the questionnaires and protocols for different cultural locations. There were challenges in developing and delivering this multi-centre study. Experience gained will support the development of substantive trials and longitudinal studies to address the considerable international health disparity of childhood dental caries.

Attitude of Health Personnel↗

PubMed2004

A multi-country comparison of caries-associated microflora in demographically diverse children.

OBJECTIVE: The aim of this formative international collaborative research on childhood dental caries was to undertake an initial investigation comparing the dental plaque of young children from diverse ethnic and socioeconomic backgrounds with and without dental caries. BASIC RESEARCH DESIGN: The following four null hypotheses were investigated. There were no differences in numbers of individual taxa when comparing plaque samples from: 1) caries-free children from deprived and non-deprived backgrounds; 2) children from deprived and non-deprived backgrounds with at least 3 decayed teeth; 3) children from non-deprived backgrounds who are caries free with those from similar backgrounds with at least 3 decayed teeth; and, 4) children from deprived backgrounds who are caries free with those from similar backgrounds with at least 3 decayed teeth. PARTICIPANTS: 277 children aged 3-4 years from 5 countries. MAIN OUTCOME MEASURES: A sample of interproximal plaque from anterior teeth was collected using sterile dental floss, and cultured according to accepted international standards. RESULTS: Analysis of the data found that the first null hypothesis was accepted and that the fourth was rejected. Unexpectedly, the second null hypothesis was rejected as the children with caries from deprived and non-deprived backgrounds had a different caries-associated flora. In particular, children living in deprivation harbored more caries-associated bacteria [mutans streptococci and lactobacilli]. This greater microbial challenge was associated with a higher level of cavitated carious lesions and with more frequent consumption of confectionery. Conclusions Children from deprived backgrounds with caries may be further disadvantaged by having higher levels of caries-associated microflora.

Candy↗

PubMed2004

International comparisons of health inequalities in childhood dental caries.

OBJECTIVE: To undertake formative studies investigating how the experience of dental caries in young children living in diverse settings relates to familial and cultural perceptions and beliefs, oral health-related behaviour and oral microflora. PARTICIPANTS: The scientific consortium came from 27 sites in 17 countries, each site followed a common protocol. Each aimed to recruit 100 families with children aged 3 or 4 years, half from deprived backgrounds, and within deprived and non-deprived groups, half to be "caries-free" and half to have at least 3 decayed teeth. OUTCOME MEASURES: Parents completed a questionnaire, developed using psychological models, on their beliefs, attitudes and behaviours related to their child's oral health. 10% of children had plaque sampled. RESULTS: 2,822 children and families were recruited. In multivariate analyses, reported toothbrushing behaviours that doubled the odds of being caries-free were a combination of brushing before age 1, brushing twice a day and adult involvement in brushing. Analyses combining beliefs, attitudes and behaviours found that parents' perceived ability to implement regular toothbrushing into their child's daily routine was the most important predictor of whether children had caries and this factor persisted in children from disadvantaged communities. 90% of children with lactobacillus had caries. CONCLUSIONS: Parental beliefs and attitudes play a key role in moderating oral health related behaviour in young children and in determining whether they develop caries. Further research is indicated to determine whether supporting the development of parenting skills would reduce dental caries in children from disadvantaged communities independent of ethnic origin.

Adult↗

PubMed2003

Development of in vitro matured, in vitro fertilized domestic cat embryos following cryopreservation, culture and transfer.

The ability of embryos to successfully survive cryopreservation is dependent on both morphological and developmental characteristics. Domestic cat oocytes matured in vitro exhibit alterations in nuclear and cytoplasmic maturation that may affect developmental competence, particularly after cryopreservation. In Experiment 1, we evaluated the developmental competence of in vitro produced (IVM/IVF) cat embryos after cryopreservation on Days 2, 4 or 5 of IVC. In Experiment 2, in vivo viability was examined by transfer of cryopreserved embryos into recipient queens. Oocytes recovered from minced ovaries were cultured in TCM-199 with hCG/eCG and EGF at 38 degrees C in 5% O(2), 5% CO(2), 90% N(2) for 24h. In Experiment 1, after IVM/IVF, on Day 2 (n=56), Day 4 (n=48) and Day 5 (n=42) of IVC, embryos were equilibrated for 10 min at 22 degrees C in HEPES (15m M) Tyrode's (HeTy) with 1.4M propylene glycol (PG), 0.125 M sucrose (S), 10% dextran and 10% FBS, loaded into 0.25 ml straws, cooled at 2.0 degrees C/min to -6.0 degrees C and held for 10 min. After seeding, cooling resumed at 0.3 degrees C/min to -30 degrees C and after a 10 min hold, straws were plunged into liquid nitrogen (LN(2)). Straws were thawed in air for 2 min and cryoprotectant was removed by a five-step rinse consisting of 3 min each in HeTY with 0.95 M PG/0.25 M S; 0.95 M PG/0.125 M S; 0.45 M PG/0.125 M S; 0 PG/0.125 M S; 0 PG/0.0625 M S. Contemporary IVM/IVF embryos were used as nonfrozen controls (Day 2, n=14; Day 4, n=26; Day 5, n=35). After 8 days of IVC, the number of embryos developing to blastocysts was recorded and blastocyst cell numbers were counted after staining with Hoechst 33342. In Experiment 1, developmental stage did not affect the survival rate after thawing (Day 2=79%, Day 4=90%, Day 5=98%) and was not different from that of controls (Day 2=89%, Day 4=88%, Day 5=96%). Blastocyst development was similar among days both after cryopreservation (Day 2=59%, Day 4=54%, Day 5=63%) and in controls (Day 2=55%, Day 4=54%, Day 5=58%). Mean (+/-S.D.) cell number of blastocysts was slightly lower (NS) in cryopreserved embryos (Day 2=152+/-19, Day 4=124+/-20, Day 5=121+/-24) than in controls (Day 2=141+/-25, Day 4=169+/-21, Day 5=172+/-19). In Experiment 2, embryos frozen on Day 2 (n=68), Day 4 (n=49) or Day 5 (n=73) were thawed and cultured for 3, 1, or 0 days before transfer by laparotomy to 5 (mean=12.6+/-2.4), 4 (mean=12.2+/-3.7) and 6 (mean=12.0+/-1.6) recipients, respectively. Four recipients were pregnant on Day 21; two from embryos frozen on Day 4 and two from Day 5. Two live kittens were born at 66 days, a third kitten died during parturition at 64 days and a fourth pregnancy aborted by Day 45. In summary, we have shown that a controlled rate cryopreservation technique can be successfully applied to cat embryos produced by IVM/IVF. In vitro development to the blastocyst stage was not affected by the age of embryos at cryopreservation. The births of live kittens after ET of cryopreserved embryos is additional validation of progress toward applying assisted reproductive technology to preservation of endangered felids.

Animals↗

PubMedDate not supplied

Genetic algorithms and self-organizing maps: a powerful combination for modeling complex QSAR and QSPR problems.

Modeling non-linear descriptor-target activity/property relationships with many dependent descriptors has been a long-standing challenge in the design of biologically active molecules. In an effort to address this problem, we couple the supervised self-organizing map with the genetic algorithm. Although self-organizing maps are non-linear and topology-preserving techniques that hold great potential for modeling and decoding relationships, the large number of descriptors in typical quantitative structure-activity relationship or quantitative structure-property relationship analysis may lead to spurious correlation(s) and/or difficulty in the interpretation of resulting models. To reduce the number of descriptors to a manageable size, we chose the genetic algorithm for descriptor selection because of its flexibility and efficiency in solving complex problems. Feasibility studies were conducted using six different datasets, of moderate-to-large size and moderate-to-great diversity; each with a different biological endpoint. Since favorable training set statistics do not necessarily indicate a highly predictive model, the quality of all models was confirmed by withholding a portion of each dataset for external validation. We also address the variability introduced onto modeling through dataset partitioning and through the stochastic nature of the combined genetic algorithm supervised self-organizing map method using the z-score and other tests. Experiments show that the combined method provides comparable accuracy to the supervised self-organizing map alone, but using significantly fewer descriptors in the models generated. We observed consistently better results than partial least squares models. We conclude that the combination of genetic algorithms with the supervised self-organizing map shows great potential as a quantitative structure-activity/property relationship modeling tool.

Algorithms↗

PubMedDate not supplied

Supervised self-organizing maps in drug discovery. 1. Robust behavior with overdetermined data sets.

The utility of the supervised Kohonen self-organizing map was assessed and compared to several statistical methods used in QSAR analysis. The self-organizing map (SOM) describes a family of nonlinear, topology preserving mapping methods with attributes of both vector quantization and clustering that provides visualization options unavailable with other nonlinear methods. In contrast to most chemometric methods, the supervised SOM (sSOM) is shown to be relatively insensitive to noise and feature redundancy. Additionally, sSOMs can make use of descriptors having only nominal linear correlation with the target property. Results herein are contrasted to partial least squares, stepwise multiple linear regression, the genetic functional algorithm, and genetic partial least squares, collectively referred to throughout as the "standard methods". The k-nearest neighbor (kNN) classification method was also performed to provide a direct comparison with a different classification method. The widely studied dihydrofolate reductase (DHFR) inhibition data set of Hansch and Silipo is used to evaluate the ability of sSOMs to classify unknowns as a function of increasing class resolution. The contribution of the sSOM neighborhood kernel to its predictive ability is assessed in two experiments: (1) training with the k-means clustering limit, where the neighborhood radius is zero throughout the training regimen, and (2) training the sSOM until the neighborhood radius is reduced to zero. Results demonstrate that sSOMs provide more accurate predictions than standard linear QSAR methods.

Algorithms↗

PubMedDate not supplied

Supervised self-organizing maps in drug discovery. 2. Improvements in descriptor selection and model validation.

The modeling of nonlinear descriptor-target relationships is a topic of considerable interest in drug discovery. We, herein, continue reporting the use of the self-organizing map-a nonlinear, topology-preserving pattern recognition technique that exhibits considerable promise in modeling and decoding these relationships. Since simulated annealing is an efficient tool for solving optimization problems, we combined the supervised self-organizing map with simulated annealing to build high-quality, highly predictive quantitative structure-activity/property relationship models. This technique was applied to six data sets representing a variety of biological endpoints. Since a high statistical correlation in the training set does not indicate a highly predictive model, the quality of all the models was confirmed by withholding a portion of each data set for external validation. Finally, we introduce new cross-validation and dynamic partitioning techniques to address model overfitting and assessment.

Algorithms↗

PubMedDate not supplied

Angel Flight story.

Explore the source record for details and available documents.

Aircraft↗

PubMedDate not supplied

Clinical evaluation and symptoms of chemosensory impairment: one thousand consecutive cases from the Nasal Dysfunction Clinic in San Diego.

BACKGROUND: The aim of this study was to measure olfactory impairment in patients with various etiologies using symptom ratings and psychophysical measures of olfactory function. METHODS: We performed a cross-sectional, population-based study at the Nasal Dysfunction Clinic of the University of California, San Diego (UCSD), Medical Center. One thousand consecutive patients presented to the UCSD Nasal Dysfunction Clinic for evaluation of chemosensory dysfunction. Olfactory impairment was assessed by odor threshold and odor identification and symptom scores were assessed by self-report. RESULTS: The degree of olfactory impairment was driven by diagnostic category, age, and gender. Postviral disturbance was more prevalent in women and among elderly people. Elderly people and patients under 20 years of age showed the highest incidence of head trauma. Overall, older patients had poorer thresholds. Men showed higher prevalence of olfactory loss secondary to inflammation and toxin exposure. Patients with inflammation scored better than patients with other diagnoses (i.e., congenital, head trauma, postviral, toxin exposure, and miscellaneous causes). Patients with congenital etiologies and head trauma had the poorest scores. Symptom ratings were significantly different depending on diagnostic category, age, and gender. Patients with inflammation rated the majority of symptoms as most bothersome. Patients with postviral diagnoses were most likely to report parosmias. Patients with head trauma rated taste and smell loss as significantly more severe than other patients. CONCLUSION: Evaluation of 1000 patients at the UCSD Nasal Dysfunction Clinic in San Diego revealed differential olfactory impairment and differential symptom complaints based on diagnostic category, age, and gender.

Adolescent↗