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Biomedical subjects

R Perkins

Publications and source records attributed to R Perkins.

At least 19 recordsLinked to original sources
PubMed2005

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.

BACKGROUND: The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer. RESULTS: In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism. CONCLUSION: The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Animals↗
PubMed2005

An in silico ensemble method for lead discovery: decision forest.

Recent progress in combinatorial chemistry and parallel synthesis has radically changed the approach to drug discovery in the pharmaceutical industry. At present, thousands of compounds can be made in a short period, creating a need for fast and effective in silico methods to select the most promising lead candidates. Decision forest is a novel pattern recognition method, which combines the results of multiple distinct but comparable decision tree models to reach a consensus prediction. In this article, a decision forest model was developed using a structurally diverse training data set containing 232 compounds whose estrogen receptor binding activity was tested at the U.S. Food and Drug Administration (FDA)'s National Center for Toxicological Research (NCTR). The model was subsequently validated using a test data set of 463 compounds selected from the literature, and then applied to a large data set with 57,145 compounds as a screening example. The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery.

Decision Trees↗
PubMed2004

Kv1.3 channel gene-targeted deletion produces "Super-Smeller Mice" with altered glomeruli, interacting scaffolding proteins, and biophysics.

Mice with gene-targeted deletion of the Kv1.3 channel were generated to study its role in olfactory function. Potassium currents in olfactory bulb mitral cells from Kv1.3 null mice have slow inactivation kinetics, a modified voltage dependence, and a dampened C-type inactivation and fail to be modulated by activators of receptor tyrosine signaling cascades. Kv1.3 deletion increases expression of scaffolding proteins that normally regulate the channel through protein-protein interactions. Kv1.3-/- mice have a 1,000- to 10,000-fold lower threshold for detection of odors and an increased ability to discriminate between odorants. In accordance with this heightened sense of smell, Kv1.3-/- mice have glomeruli or olfactory coding units that are smaller and more numerous than those of wild-type mice. These data suggest that Kv1.3 plays a far more reaching role in signal transduction, development, and olfactory coding than that of the classically defined role of a potassium channel-to shape excitability by influencing membrane potential.

14-3-3 Proteins↗
PubMed2002

An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity.

Recent legislation mandates the US Environmental Protection Agency (EPA) to develop a screening and testing program for potential endocrine disrupting chemicals (EDCs), of which xenoestrogens figure prominently. Under the legislation, a large number of chemicals will undergo various in vitro and in vivo assays for their potential estrogenicity, as well as other hormonal activities. There is a crucial need for priority setting before this strategy can be effectively implemented. Here we report an integrated computational approach to priority setting using estrogen receptor (ER) binding as an example. This approach rationally integrates different predictive computational models into a "Four-Phase" scheme so that it can effectively identify potential estrogenic EDCs based on their predicted ER relative binding affinity (RBA). The system has been validated using an in-house ER binding assay dataset for 232 chemicals that was designed to have both broad structural diversity and a wide range of binding affinities. When applied to 58,000 chemicals identified by Walker et al. as candidates for endocrine disruption screening, some 9100 chemicals were predicted to bind to ER. Of these, only 3600 were expected to bind to ER at RBA values up to 100,000-fold less than that of 17beta-estradiol. The method ruled out 83% of the chemicals as non-binders with a very low rate of false negatives. We believe that the same integrated scheme will be equally applicable to endpoints of other endocrine disrupting mechanisms, e.g. androgen receptor binding.

Biological Assay↗
PubMed2001

Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens.

Understanding structural requirements for a chemical to exhibit estrogen receptor (ER) binding has been important in various fields. This knowledge has been directly and indirectly applied to design drugs for human estrogen replacement therapy, and to identify estrogenic endocrine disruptors. This paper reports structure-activity relationships (SARs) based on a total of 230 chemicals, including both natural and xenoestrogens. Activities were generated using a validated ER competitive binding assay, which covers a 10(6)-fold range. This study is focused on identification of structural commonalities among diverse ER ligands. It provides an overall picture of how xenoestrogens structurally resemble endogenous 17beta-estradiol (E(2)) and the synthetic estrogen diethylstilbestrol (DES). On the basis of SAR analysis, five distinguishing criteria were found to be essential for xenoestrogen activity, using E(2) as a template: (1) H-bonding ability of the phenolic ring mimicking the 3-OH, (2) H-bond donor mimicking the17beta-OH and O-O distance between 3- and 17beta-OH, (3) precise steric hydrophobic centers mimicking steric 7alpha- and 11beta-substituents, (4) hydrophobicity, and (5) a ring structure. The 3-position H-bonding ability of phenols is a significant requirement for ER binding. This contributes as both a H-bond donor and acceptor, although predominantly as a donor. However, the 17beta-OH contributes as a H-bond donor only. The precise space (the size and orientation) of steric hydrophobic bulk groups is as important as a 17beta-OH. Where a direct comparison can be made, strong estrogens tend to be more hydrophobic. A rigid ring structure favors ER binding. The knowledge derived from this study is rationalized into a set of hierarchical rules that will be useful in guidance for identification of potential estrogens.

Animals↗
PubMed2001

Home treatment.

BACKGROUND: Deinstitutionalisation has stressed where care is no longer taking place. Home treatment in rehabilitation reflects the steady increase in emphasis on support and treatment for individuals with long-term disorders where it matters for them--in their own homes. MATERIALS AND DISCUSSION: Whether dealing with individuals discharged after long periods in hospital or with the increasing number who have experienced repeated short-term admissions, most modern day rehabilitation takes place in the patients' homes and neighbourhoods. We are increasingly convinced that this decentralisation is a positive strength, not a problem. Its advantages include improving social inclusion and the ability to conduct more accurate, personalised assessments of disabilities and strengths. Skills training is more focused and we discuss the components of home treatment and assertive community treatment as they are relevant to rehabilitation. This involves both medication and practical help, brokerage and involvement with the voluntary sector. CONCLUSIONS: Rehabilitation remains, at its core, a set of relationships between whole individuals (not just skills and needs). A home-based approach is proposed as the norm, not the exception. It is based on a rounded understanding of the patient as a unique person and emphasises the importance of a strong working alliance.

Community Mental Health Services↗
PubMed2000

Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene.

Exon skipping that accompanies exonic mutation might be caused by an effect of the mutation on pre-mRNA secondary structure. Previous attempts to associate predicted secondary structure of pre-mRNA with exon skipping have been hindered by either a small number of available mutations, sub-optimal structures, or weak effects on exon skipping. This report identifies more extensive sets of mutations from the human and hamster Hprt gene whose association with exon skipping is clear. Optimal secondary structures of the wild-type and mutant pre-mRNA surrounding each exon were predicted by energy minimization and were compared by energy dot plots. A significant association was found between the occurrence of exon skipping and the disruption of a stem containing the acceptor site consensus sequences of exon 8 of the human Hprt gene. However, no change in secondary structure was associated with skipping of exon 4 of the hamster Hprt gene. Using updated energy parameters we found a different structure than that previously reported for exon 2 of the hamster Hprt gene. In contrast to the previously reported structure, no significant association was found between predicted structural changes and skipping of exon 2. For all three Hprt exons studied, there was a significantly greater number of deoxythymidine substitutions among mutations accompanied by exon skipping than among mutations without exon skipping. For exon 8, deoxythymidine substitution was also associated with structural changes in the stem containing the acceptor site consensus sequences. For exon 51 of the human fibrillin gene, structural differences from wild type were predicted for all four mutations accompanied by exon skipping that were not were predicted for a single mutation without exon skipping. Our results suggest that both primary and secondary pre-mRNA structure contribute to definition of Hprt exons, which may involve exonic splicing enhancers.

Animals↗
PubMed2000

Corporate governance of public health services: lessons from New Zealand for the state sector.

New Zealand public hospitals and related services were grouped into 23 Crown Health Enterprises and registered as companies in 1993. Integral to this change was the introduction of corporate governance. New directors, largely from the business sector, were appointed to govern these organisations as efficient and effective businesses. This article presents the results of a survey of directors of New Zealand publicly-owned health provider organisations. Although directors thought they performed well in business systems development, they acknowledged their shortcomings in meeting government expectations in respect to financial performance and social responsibility. Changes in public health sector provider performance indicators have resulted in a mixed report card for the sector six years after corporate governance was instituted.

Delivery of Health Care↗
PubMed2000

The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands.

We have utilized a validated (standardized) estrogen receptor (ER) competitive-binding assay to determine the ER affinity for a large, structurally diverse group of chemicals. Uteri from ovariectomized Sprague-Dawley rats were the ER source for the competitive-binding assay. Initially, test chemicals were screened at high concentrations to determine whether a chemical competed with [3H]-estradiol for the ER. Test chemicals that exhibited affinity for the ER in the first tier were subsequently assayed using a wide range of concentrations to characterize the binding curve and to determine each chemical's IC50 and relative binding affinity (RBA) values. Overall, we assayed 188 chemicals, covering a 1 x 10(6)-fold range of RBAs from several different chemical or use categories, including steroidal estrogens, synthetic estrogens, antiestrogens, other miscellaneous steroids, alkylphenols, diphenyl derivatives, organochlorines, pesticides, alkylhydroxybenzoate preservatives (parabens), phthalates, benzophenone compounds, and a number of other miscellaneous chemicals. Of the 188 chemicals tested, 100 bound to the ER while 88 were non-binders. Included in the 100 chemicals that bound to the ER were 4-benzyloxyphenol, 2,4-dihydroxybenzophenone, and 2,2'-methylenebis(4-chlorophenol), compounds that have not been shown previously to bind the ER. It was also evident that certain structural features, such as an overall ring structure, were important for ER binding. The current study provides the most structurally diverse ER RBA data set with the widest range of RBA values published to date.

Animals↗
PubMed2000

A dose-ranging study of rapacuronium in pediatric patients.

BACKGROUND: The aim of this study was to determine the dose or doses of the new rapid-onset, short-acting, neuromuscular blocking drug rapacuronium that would provide satisfactory conditions for tracheal intubation at 60 s in infants and children. METHODS: Sixty-five infants (< 1 yr), 51 younger children (1-6 yr), and 49 older children (7-12 yr) were studied. Anesthesia was induced with thiopental-nitrous oxide-oxygen. Tracheal intubation was attempted 60 s after administration of one of five doses of rapacuronium (0.5, 1.0, 1.5, 2.0, or 2.5 mg/kg) and intubating conditions were assessed using a four-point scale. Following tracheal intubation, anesthesia was maintained with nitrous oxide-oxygen and alfentanil (12.5-50 microg/kg) as necessary. Neuromuscular transmission was monitored in an uncalibrated fashion using an acceleromyograph. RESULTS: Intubating conditions were good or excellent at 60 s in all infants after doses of 1.5 mg/kg or more and in all younger and older children after doses of 2.0 mg/kg or more. The duration of action of rapacuronium was dose- and age-dependent. Mean times to reappearance of the third twitch of the train-of-four (TOF; T3) were less than 10 min in infants at doses of 1.5 mg/kg or less and in younger and older children at doses of 2.0 mg/kg or less. Recovery of T3 after 1.0-2.0 mg/kg rapacuronium was significantly slower in infants compared with younger (P = 0.001) and older (P = 0.02) children. Five adverse experiences were related to rapacuronium administration: Bronchospasm (two instances), tachycardia (one instance), and increased salivation (two instances). None were serious. CONCLUSIONS: Doses of 1.5 and 2.0 mg/kg rapacuronium can produce satisfactory intubating conditions at 60 s in anesthetized infants and children, respectively, and are associated with a short duration of action.

Age Factors↗
PubMed2000

Ionization and photoelectric smoke alarms in rural Alaskan homes.

OBJECTIVE: To compare rates of nuisance alarms and disconnection between ionization and photoelectric smoke alarms. DESIGN: A prospective cohort study. SETTING: Four Inupiat Eskimo villages in the Northwest Arctic Borough region of Alaska, 48 km (30 mi) above the Arctic Circle. SUBJECTS: Households in 4 communities with similar populations, number of homes, mean income, size of household, and square footage per home. INTERVENTION: Two villages had photoelectric alarms installed (58 homes), and 2 other villages had ionization alarms installed (65 homes) in standard locations. Follow-up household surveys were conducted after 6 months to determine rates of false alarms and detector disconnection. All of the households that could be contacted 104/123 agreed to participate in the follow-up surveys. Main outcome measures The proportion of households experiencing false alarms and the proportion of disabled alarms in households in each of the test communities. RESULTS: Homes with ionization alarms had more than 8 times the rate of false alarms as those with photoelectric alarms. Eleven of the ionization alarms (19%) were disconnected compared with 2 of the photoelectric devices (4%). CONCLUSIONS: In small rural residences, photoelectric smoke alarms have lower rates of false alarms and disconnection. Photoelectric alarms may be the preferred choice for dwellings with limited living space or frequent false alarms.

Alaska↗
PubMed2000

Quantitative comparisons of in vitro assays for estrogenic activities.

Substances that may act as estrogens show a broad chemical structural diversity. To thoroughly address the question of possible adverse estrogenic effects, reliable methods are needed to detect and identify the chemicals of these diverse structural classes. We compared three assays--in vitro estrogen receptor competitive binding assays (ER binding assays), yeast-based reporter gene assays (yeast assays), and the MCF-7 cell proliferation assay (E-SCREEN assay)--to determine their quantitative agreement in identifying structurally diverse estrogens. We examined assay performance for relative sensitivity, detection of active/inactive chemicals, and estrogen/antiestrogen activities. In this examination, we combined individual data sets in a specific, quantitative data mining exercise. Data sets for at least 29 chemicals from five laboratories were analyzed pair-wise by X-Y plots. The ER binding assay was a good predictor for the other two assay results when the antiestrogens were excluded (r(2) is 0.78 for the yeast assays and 0.85 for the E-SCREEN assays). Additionally, the examination strongly suggests that biologic information that is not apparent from any of the individual assays can be discovered by quantitative pair-wise comparisons among assays. Antiestrogens are identified as outliers in the ER binding/yeast assay, while complete antagonists are identified in the ER binding and E-SCREEN assays. Furthermore, the presence of outliers may be explained by different mechanisms that induce an endocrine response, different impurities in different batches of chemicals, different species sensitivity, or limitations of the assay techniques. Although these assays involve different levels of biologic complexity, the major conclusion is that they generally provided consistent information in quantitatively determining estrogenic activity for the five data sets examined. The results should provide guidance for expanded data mining examinations and the selection of appropriate assays to screen estrogenic endocrine disruptors.

Binding, Competitive↗