Biomedical subjects

L Hunter

Publications and source records attributed to L Hunter.

At least 19 recordsLinked to original sources

PubMed2005

Adipokine gene expression in dog adipose tissues and dog white adipocytes differentiated in primary culture.

Obesity and its associated disorders are increasing in companion animals, particularly in dogs. We have investigated whether genes encoding key adipokines, some of which are implicated in the pathologies linked to obesity, are expressed in canine adipose tissues. Using RT-PCR, mRNAs encoding the following adipokines were detected in dog white adipose tissue: adiponectin, leptin, angiotensinogen, plasminogen activator inhibitor-1, IL-6, haptoglobin, metallothionein-1 and 2, and nerve growth factor. The adipokine mRNAs were present in all fat depots examined. Fractionation of adipose tissue by collagenase digestion showed that each gene was expressed in mature adipocytes. The mRNA for TNFalpha was not evident in adipose tissue, but was detected in isolated adipocytes. Fibroblastic preadipocytes from gonadal white fat were differentiated into adipocytes in primary culture and adipokine expression examined before and after differentiation (days 0 and 11, respectively). Each adipokine gene expressed in dog white adipocytes was also expressed in the differentiated cells. These results demonstrate that dog white adipose tissue expresses major adipokine genes, expression being in the adipocytes. Investigation of adipokine production and function will provide insight into the mechanisms involved in obesity-related pathologies in dogs and serve as a model for the related human diseases.

Adipocytes↗

PubMed2005

The investigation of the changing facial appearance of identical twins employing a three-dimensional laser imaging system.

OBJECTIVE: An investigation to determine the changing facial appearance of identical twins. DESIGN: Clinical study. MATERIALS AND METHODS: Two Minolta Vivid 900 3D optical laser scanners were placed as a stereo pair to capture the soft tissues of a pair of identical twins. Each scan took approximately 2.5 s. The scanned whole faces were superimposed to determine changes in facial morphologies at different time intervals. OUTCOME MEASURES: The shell deviations between left and right scans of each patient were recorded and analysed for differences. Furthermore, final merged faces were overlaid to determine the changes in facial morphology over time. RESULTS: The results showed that changes in height and weight correlated with changes in facial morphology. CONCLUSION: The 3D laser scanning device is a clinically useful tool in the study of facial growth and facial morphology in a pair of twins.

Body Height↗

PubMed2005

Go molecular function terms are predictive of subcellular localization.

A protein's function is closely linked to its subcellular localization. Use of Gene Ontology (GO) molecular function terms to extend sequence-based subcellular localization prediction has been previously shown to improve predictive performance. Here, we explore directly the relationship between GO function annotations and localization information, identifying both highly predictive single terms, and terms with large information gain with respect to location. The results identify a number of predictive and informative GO terms with respect to subcellular location, particularly nucleus, extracellular space, membrane, mitochondrion, endoplasmic reticulum and Golgi. There are several clear examples illustrating why the addition of function information provides additional predictive power over sequence alone. Other interesting phenomena can also be seen in the results. Most predictive or informative terms are imperfect, and incorrect prediction may often call out significant biological phenomena. Finally, these results may be useful in the GO annotation process.

Amino Acid Sequence↗

PubMed2004

The compositional structure of Gene Ontology terms.

An analysis of the term names in the Gene Ontology reveals the prevalence of substring relations between terms: 65.3% of all GO terms contain another GO term as a proper substring. This substring relation often coincides with a derivational relationship between the terms. For example, the term regulation of cell proliferation (GO:0042127) is derived from the term cell proliferation (GO:0008283) by addition of the phrase regulation of. Further, we note that particular substrings which are not themselves GO terms (e.g. regulation of in the preceding example) recur frequently and in consistent subtrees of the ontology, and that these frequently occurring substrings often indicate interesting semantic relationships between the related terms. We describe the extent of these phenomena--substring relations between terms, and the recurrence of derivational phrases such as regulation of--and propose that these phenomena can be exploited in various ways to make the information in GO more computationally accessible, to construct a conceptually richer representation of the data encoded in the ontology, and to assist in the analysis of natural language texts.

Computational Biology↗

PubMed2004

Regulation of adipose tissue leptin secretion by alpha-melanocyte-stimulating hormone and agouti-related protein: further evidence of an interaction between leptin and the melanocortin signalling system.

The central role of the melanocortin system in the regulation of energy balance has been studied in great detail. However, the functions of circulating melanocortins and the roles of their peripheral receptors remain to be elucidated. There is increasing evidence of a peripheral action of melanocortins in the regulation of leptin production by adipocytes. Here we investigate the interaction of alpha-melanocyte stimulating hormone (alpha-MSH) and agouti-related protein (AgRP) in the regulation of leptin secretion from cultured rat adipocytes and examine the changes in circulating alpha-MSH and AgRP in lean and obese rodents after hormonal and energetic challenge. Leptin secretion (measured by ELISA) and gene expression (by real-time quantitative PCR) of differentiated rat adipocytes cultured in vitro were inhibited by the administration of alpha-MSH (EC50=0.24 nM), and this effect was antagonised by antagonists of the melanocortin receptors MC4R and MC3R (AgRP and SHU9119). The presence of MC4R in rat adipocytes (RT-PCR and restriction digest) supports the involvement of this receptor subtype in this interaction. Leptin administered to ob/ob mice in turn increases the release of alpha-MSH into the circulation, suggesting a possible feedback loop between the site of alpha-MSH release and the release of leptin from the adipose tissue. However, the physiological significance of this putative feedback probably depends upon the underlying state of energy balance, since in the fasting state low plasma alpha-MSH is paralleled by low plasma leptin.

Adipocytes↗

PubMed2003

Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development.

Trajectory clustering is a novel and statistically well-founded method for clustering time series data from gene expression arrays. Trajectory clustering uses non-parametric statistics and is hence not sensitive to the particular distributions underlying gene expression data. Each cluster is clearly defined in terms of direction of change of expression for successive time points (its 'trajectory'), and therefore has easily appreciated biological meaning. Applying the method to a dataset from mouse mammary gland development, we demonstrate that it produces different clusters than Hierarchical, K-means, and Jackknife clustering methods, even when those methods are applied to differences between successive time points. Compared to all of the other methods, trajectory clustering was better able to match a manual clustering by a domain expert, and was better able to cluster groups of genes with known related functions.

Algorithms↗

PubMed2002

The pre-operative identification of low-risk endometrialcancer: an audit of women treated in the South Island of New Zealand 1998-2000.

OBJECTIVE: To determine whether pre-operative investigations identify a group of patients with low-risk endometrial cancer, who do not require tertiary referral for surgical staging or pelvic radiotherapy. DESIGN: Retrospective chart review. SETTING: South Island of New Zealand gynaecological oncology services. SAMPLE: One hundred and forty consecutive patients with newly diagnosed endometrial cancer from 1988 to 2000. METHODS: The results of preoperative investigations were compared with the final pathology. MAIN OUTCOME MEASURES: Correlation of preoperative investigations with low risk disease. For the purpose of the study, women with grade 1 or 2 endometrioid tumours confined to the uterine body and less than 50% myometrial invasion were considered to have low risk disease. RESULTS: In total, 50 women had low risk disease. Only 53% of patients with grade 1 tumours on initial biopsy had low risk disease. Women who had a grade 1 tumour at biopsy and, an ultrasound report with an endometrial thickness of less than 20 mm, and no evidence of myometrial invasion, cervical involvement or adnexal metastasis had a 76% chance of having low risk disease. CONCLUSION: We were unable to accurately define the low risk group from pre-operative assessment.

Curettage↗

PubMed2001

GEST: a gene expression search tool based on a novel Bayesian similarity metric.

Gene expression array technology has made possible the assay of expression levels of tens of thousands of genes at a time; large databases of such measurements are currently under construction. One important use of such databases is the ability to search for experiments that have similar gene expression levels as a query, potentially identifying previously unsuspected relationships among cellular states. Such searches depend crucially on the metric used to assess the similarity between pairs of experiments. The complex joint distribution of gene expression levels, particularly their correlational structure and non-normality, make simple similarity metrics such as Euclidean distance or correlational similarity scores suboptimal for use in this application. We present a similarity metric for gene expression array experiments that takes into account the complex joint distribution of expression values. We provide a computationally tractable approximation to this measure, and have implemented a database search tool based on it. We discuss implementation issues and efficiency, and we compare our new metric to other standard metrics.

Bayes Theorem↗

PubMed2001

Identifying indicators of laboratory management performance: a multiple constituency approach.

The challenges for laboratory management posed by cost control, managed care, organizational restructuring, information networking and health system integration call for new measures to evaluate how effectively laboratories manage emerging performance expectations. This study identifies the Delphi panel method in achieving consensus on measures of effectiveness and considers a specific application, the identification of indicators of laboratory performance, from the perspective of key constituencies.

Attitude of Health Personnel↗

PubMed2000

Ontogeny of the expression of leptin and its receptor in the murine fetus and placenta.

Leptin is a 167-amino acid protein that is secreted from adipose cells and expressed in placental tissues. It is important nutritionally in the regulation of energy balance, but also has other functions such as a role in reproduction. To investigate the function of the leptin system in fetal development we examined, primarily by in-situ hybridization and immunohistochemistry, the expression (both mRNA and protein) of leptin and its receptor (including the signalling splice variant) in tissues from 11.5, 13.5, 16.5 and 18.5 d postcoitus murine fetuses and associated placentas. We detected leptin mRNA (at low levels) and protein predominantly in the cytotrophoblasts of the labyrinth part of the placenta, an area of nutrient exchange between the developing fetus and the placenta, and in the trophoblast giant cells situated in the junctional zone at the maternal interface. In addition, leptin was strongly expressed in the fetal cartilage-bone and at a lower level in the hair follicles, heart, and liver of the murine fetus at differing stages of development. The leptin receptor, including the signalling splice variant, was also identified in specific fetal tissues. The physiological importance of expression of both leptin and the leptin receptor (OB-R and OB-Rb) in the placenta remains to be determined. In addition, the high levels of expression of leptin and its receptor in discrete areas of the murine fetus suggest that leptin has a critical role in fetal development.

Animals↗

PubMed2000

Placental leptin in normal, diabetic and fetal growth-retarded pregnancies.

Leptin expression in third trimester placenta (p) and leptin concentrations in umbilical cord blood (cb) were investigated in normal pregnancies [n = 10 (p), 31 (cb)] and abnormal pregnancies complicated with (i) maternal insulin-dependent diabetes [IDDM: n = 3 (p), 13 (cb)], (ii) gestational diabetes [GD: n = 2 (p), 10 (cb)] and (iii) fetal growth retardation [FGR: n = 5 (p), 5 (cb)]. By in-situ hybridization and immunohistochemistry, placental leptin mRNA and protein were co-localized to the syncytiotrophoblast and villous vascular endothelial cells. Leptin receptor was immunolocalized to the syncytiotrophoblast. Relative to controls, the FGR group was characterized by low concentrations of placental and cord blood leptin. In a twin pregnancy, the normal-sized infant exhibited more placental and cord blood leptin than its growth-retarded twin. In contrast, both diabetic groups exhibited high concentrations of placental leptin mRNA and protein. The IDDM group exhibited the highest concentrations of leptin in cord blood. No change was observed in the expression of the leptin receptor in either the growth-retarded or diabetic pregnancies. In conclusion, the localization of placental leptin suggests that it may be released into both maternal and fetal blood. Furthermore, in fetal growth-retarded and diabetic pregnancies, the changes in leptin expression in the placenta and in leptin concentrations in umbilical cord blood appear to be related.

Carrier Proteins↗

PubMed2000

Development of a local advanced practice nurse coalition.

PURPOSE: To describe the experiences of a group of advanced practice nurses (APNs) in a rural area in developing an APN Coalition. DATA SOURCES: Selective review of literature and documents from the newly developed organizational framework for the coalition. CONCLUSION: Professional connections can begin at the local level through the development of local APN coalitions and then expand to involvement in state and national organizations. IMPLICATIONS FOR PRACTICE: Guidelines for establishing the coalition organizational structure are included and can be used as a template by similar evolving APN coalitions.

Group Practice↗

PubMed2000

Visual management of large scale data mining projects.

This paper describes a unified framework for visualizing the preparations for, and results of, hundreds of machine learning experiments. These experiments were designed to improve the accuracy of enzyme functional predictions from sequence, and in many cases were successful. Our system provides graphical user interfaces for defining and exploring training datasets and various representational alternatives, for inspecting the hypotheses induced by various types of learning algorithms, for visualizing the global results, and for inspecting in detail results for specific training sets (functions) and examples (proteins). The visualization tools serve as a navigational aid through a large amount of sequence data and induced knowledge. They provided significant help in understanding both the significance and the underlying biological explanations of our successes and failures. Using these visualizations it was possible to efficiently identify weaknesses of the modular sequence representations and induction algorithms which suggest better learning strategies. The context in which our data mining visualization toolkit was developed was the problem of accurately predicting enzyme function from protein sequence data. Previous work demonstrated that approximately 6% of enzyme protein sequences are likely to be assigned incorrect functions on the basis of sequence similarity alone. In order to test the hypothesis that more detailed sequence analysis using machine learning techniques and modular domain representations could address many of these failures, we designed a series of more than 250 experiments using information-theoretic decision tree induction and naive Bayesian learning on local sequence domain representations of problematic enzyme function classes. In more than half of these cases, our methods were able to perfectly discriminate among various possible functions of similar sequences. We developed and tested our visualization techniques on this application.

Alcohol Dehydrogenase↗

PubMed2000

EDGAR: extraction of drugs, genes and relations from the biomedical literature.

EDGAR (Extraction of Drugs, Genes and Relations) is a natural language processing system that extracts information about drugs and genes relevant to cancer from the biomedical literature. This automatically extracted information has remarkable potential to facilitate computational analysis in the molecular biology of cancer, and the technology is straightforwardly generalizable to many areas of biomedicine. This paper reports on the mechanisms for automatically generating such assertions and on a simple application, conceptual clustering of documents. The system uses a stochastic part of speech tagger, generates an underspecified syntactic parse and then uses semantic and pragmatic information to construct its assertions. The system builds on two important existing resources: the MEDLINE database of biomedical citations and abstracts and the Unified Medical Language System, which provides syntactic and semantic information about the terms found in biomedical abstracts.

Algorithms↗

PubMed1999

Sucking cup caries.

Explore the source record for details and available documents.

Child, Preschool↗

PubMed1999

Leptin receptor and neuropeptide Y gene expression in the sheep brain.

Leptin, a protein secretory product of adipocytes, is important in appetite control, energy balance and reproduction. In rodents, the physiological effects of leptin are centrally mediated, in part via the neuropeptide Y (NPY) system in the hypothalamus. The role of leptin in ruminants, where appropriate nutrition and reproductive status are of major economic concern, is largely unknown. To elucidate the function of leptin in sheep we have investigated putative sites of action for leptin in the brain and pituitary gland using both in-situ hybridization to detect expression of the signalling form of the leptin receptor (OB-Rb) and in-vitro autoradiography using (125I)leptin to detect sites of specific leptin binding. OB-Rb gene expression occurred in the hippocampus, cerebral cortex, preoptic area, stria terminalis and choroid plexus, and within the hypothalamus in the paraventricular (PVN), ventromedial (VHM) and arcuate (ARC) nuclei. OB-Rb gene expression in the ovine pituitary gland was not detected by in-situ hybridization. Sites of OB-Rb and NPY gene expression were compared using both in-situ hybridization on adjacent sections containing the arcuate and ventromedial nuclei, and dual in-situ hybridization on sections containing these areas. In serial sections, OB-Rb expression was found to correspond closely with that of NPY over the arcuate nuclei. Using dual in-situ hybridization, NPY expressing neurones in the arcuate nuclei were also positive for OB-Rb gene expression. Therefore, it appears that leptin may partly act via OB-Rb located on NPY neurones in the sheep hypothalamus as in the rodent.

Animals↗

PubMed1999

MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.

The trend toward high-throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available information. This problem is particularly severe in the rapidly expanding area of gene expression experiments, for example, those carried out with cDNA microarrays or oligonucleotide chips. We present an Internet-based hypertext program, MedMiner, which filters and organizes large amounts of textual and structured information returned from public search engines like GeneCards and PubMed. We demonstrate the value of the approach for the analysis of gene expression data, but MedMiner can also be extended to other areas involving molecular genetic or pharmacological information. More generally still, MedMiner can be used to organize the information returned from any arbitrary PubMed search.

Databases, Factual↗

PubMed1999

Mining molecular binding terminology from biomedical text.

Automatic access to information regarding macromolecular binding relationships would provide a valuable resource to the biomedical community. We report on a pilot project to mine such information from the molecular biology literature. The program being developed takes advantage of natural language processing techniques and is supported by two repositories of biomolecular knowledge. A formative evaluation has been conducted on a subset of MEDLINE abstracts.

Algorithms↗