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PubMed2002

Groundwater vulnerability: interactions of chemical and site properties.

This study brings together extensive, multi-annual groundwater monitoring datasets from the UK and Midwestern US to test the relative importance of site (e.g. land use, soil and aquifer type) and chemical factors (e.g. solubility in water) and between and within year variations in controlling groundwater contamination by pesticides. ANOVA (general linear modelling) was used to test the significance and proportion of variation explained by each factor and their interactions. Results from both the UK and US datasets show that: (i) Chemical and site factors both have a statistically significant influence on groundwater pollution; (ii) Site factors on their own explain a greater proportion of data variance than chemical factors on their own; (iii) Interaction between site and chemical factors represents the most important control on the occurrence of pesticides in groundwater; (iv) Variation within the year was slight but still significant while there was no significant difference between data from consecutive years. The combination of factors analysed in this study were sufficient to explain the majority of the variation in the data save for that ascribable to the analytical detection limit. The results provide statistical evidence that it is viable to develop both molecular methods and groundwater vulnerability as tools to understanding pollution, but that a greater emphasis should be placed on their interaction to fully understand pesticide contamination.

Databases, Factual↗
PubMed2003

An illustration of variable precision rough set theory: the gender classification of the European barn swallow (Hirundo rustica).

This paper introduces a new technique in the investigation of object classification and illustrates the potential use of this technique for the analysis of a range of biological data, using avian morphometric data as an example. The nascent variable precision rough sets (VPRS) model is introduced and compared with the decision tree method ID3 (through a 'leave n out' approach), using the same dataset of morphometric measures of European barn swallows (Hirundo rustica) and assessing the accuracy of gender classification based on these measures. The results demonstrate that the VPRS model, allied with the use of a modern method of discretization of data, is comparable with the more traditional non-parametric ID3 decision tree method. We show that, particularly in small samples, the VPRS model can improve classification and to a lesser extent prediction aspects over ID3. Furthermore, through the 'leave n out' approach, some indication can be produced of the relative importance of the different morphometric measures used in this problem. In this case we suggest that VPRS has advantages over ID3, as it intelligently uses more of the morphometric data available for the data classification, whilst placing less emphasis on variables with low reliability. In biological terms, the results suggest that the gender of swallows can be determined with reasonable accuracy from morphometric data and highlight the most important variables in this process. We suggest that both analysis techniques are potentially useful for the analysis of a range of different types of biological datasets, and that VPRS in particular has potential for application to a range of biological circumstances.

Animals↗
PubMed2002

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations.

In the framework of genome annotation, scientific literature is obviously the major source of biological knowledge. The aim of the work described in this paper is to exploit this source of data for the model plant Arabidopsis thaliana. The first step has consisted in constituting a relevant bibliographic references dataset for plant genomic research. Genes co-citations have then been systematically annotated in this reference dataset, starting from the simple idea that if genes are cited in the same publication, they must probably share some related functional properties. In order to deal with the synonymous gene name problem, a gene name reference list has been constituted starting from A. thaliana SwissProt entries. This list was used to build clusters of co-cited genes by a single linkage procedure such that any gene in a given cluster possesses at least one co-cited partner in the same cluster. Analysis of the clusters demonstrate the biological consistency of this approach, with only very few fortuitous links. As an example, a cluster including genes related to flowering time is more deeply described in the paper. Finally, a graphical representation of each cluster was performed, which provides a convenient way to retrieve the genes (the nodes of the graphs) and the references in which they were co-cited (the edges of the graphs). All the results can be accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/.

Arabidopsis↗
PubMed1996

Are the marginal returns of coronary artery surgery smaller in high-rate areas? The Steering Committee of the Provincial Adult Cardiac Care Network of Ontario.

BACKGROUND: Population-based rates of surgery vary within and between health-care systems, causing concern that case selection is less appropriate in high-rate areas. This inverse relationship has not been shown with appropriateness criteria generated by expert panels. We applied a trials-based measure of the potential survival benefit of coronary artery bypass graft surgery (CABG) to patients in a provincial registry, to determine the relationship between survival gains and rates of CABG. METHODS: We did a population-based retrospective review of linked registry and administrative datasets. 5058 patients in the linked datasets underwent isolated CABG in Ontario between April 1, 1992, and March 31, 1993. Potential survival benefit of surgery was scored with an algorithm derived from a published overview of trials comparing CABG to medical treatment, analysed by county and by referral regions. FINDINGS: Overall, case selection was appropriate whether assessed clinically (96.3% had either severe disease as judged on the coronary arteries affected or moderate to severe angina) or on the basis of survival benefit scores (94.0% predicted to obtain moderate or high benefit). There was significant variation in benefit scores across referral regions (p < 0.001). Benefit scores correlated inversely with county surgical rate (r = -0.49, p < 0.005) and the proportion of low-benefit cases increased with rates (r = 0.50, p < 0.005). Referral regions served by high-rate surgical centres had lower mean benefit scores. INTERPRETATION: Most patients undergoing CABG in Ontario are in the high-survival benefit category. Surgery is defensible for patients with low survival benefit on the grounds of symptom relief, but the proportion of cases with low benefit rises with higher local rates of surgery. The inverse relationship between surgery rates and appropriateness of case selection may be better understood as diminishing marginal returns for specific outcomes with rising local use of procedures.

Aged↗
PubMed1996

Preliminary evidence for genetic anticipation in Crohn's disease.

BACKGROUND: The term genetic anticipation is used to describe earlier onset of disease, increased severity, or both, in succeeding generations of families affected by a particular disease. This process has been linked with expanded genomic trinucleotide repeat regions in some neurological disorders. Crohn's disease, an inflammatory bowel disorder, has genetic influences, which remain undefined. We studied pairs of two-generation first-degree relatives with Crohn's disease to seek evidence for genetic anticipation in this disorder. METHODS: Through retrospective review of the records of 552 patients treated for Crohn's disease at Johns Hopkins Hospital, we identified 27 pairs of two-generation first-degree relatives. We also studied 32 such pairs identified through a multicentre survey. After exploratory analyses by t tests, a generalised estimating equations approach was used to fit a marginal regression model. FINDINGS: The age at diagnosis was earlier in the younger member of the pair both in the Johns Hopkins Hospital dataset (18.9 [SE 6.9] vs 31.4 [12.0] years) and in the multicentre survey dataset (16.9 [7.4] vs 33.1 [11.9] years). The regression model confirmed the findings: the best-fitting model for the Johns Hopkins Hospital data showed an average 10.8 (SE 4.2) year difference in age at diagnosis between parent and child; that for the multicentre data showed an average difference of 15.1 (1.5) years. There was evidence of a further difference between the second and third generations. Disease was more extensive in the offspring than in the parent for 15 of the 27 pairs at Johns Hopkins Hospital; in 13 of these pairs the affected parent was the father. INTERPRETATION: The evidence of a lower age at diagnosis and a greater extent of disease in the younger member of two-generation pairs affected by Crohn's disease, as well as the association with paternal transmission, suggest that genetic anticipation does occur in Crohn's disease. A search for triplet repeat regions is warranted.

Adolescent↗
PubMed2001

The North Cape oil spill: hydrocarbons in Rhode Island coastal waters and Point Judith Pond.

On 19 January 1996, the North Cape oil barge ran aground near Moonstone Beach, RI, and spilled over 2700 metric tons of No. 2 fuel oil during a severe winter storm. High winds and rough seas drove the oil into the water column, and the oil spread throughout Block Island Sound and into several coastal salt ponds. Over 50 water samples were collected from Point Judith Pond (PJP) and the southern coast of Rhode Island for four months after the spill and analyzed for polycyclic aromatic hydrocarbons (PAHs) and total petroleum hydrocarbons (TPHs). These analyses revealed that at least 60 km2 of coastal waters were impacted from the spill. Maximum concentrations of sigmaPAHs and TPHs were 115 and 3940 microg l(-1), respectively. The percentage of sigmaPAHs relative to the TPHs for all samples varied from 0.2 to 43%, showing that there was no clear relationship between sigmaPAHs and TPHs for the whole dataset and likely resulting from spatial and temporal partitioning over the course of the spill. However, within the dataset, there were stronger correlations for distinct samples collected at similar locations and times. In PJP, water column concentrations of individual PAHs decreased at rates of 0.08-0.24 day(-1) and lower-molecular weight PAHs were removed faster than higher-molecular weight PAHs.

Environmental Monitoring↗
PubMed1999

The prevalence and circumstances of child sexual abuse: changes across a decade.

OBJECTIVE: This study reports the prevalence of child sexual abuse of African American and European American women and compares the circumstances of these incidents to data collected a decade ago. METHOD: Stratified probability sampling was used to recruit comparable samples of African American and European American women in Los Angeles County for a larger study of women's sexual decision making. Incidents of contact abuse were obtained from women 18 to 36 years old in 1994 and compared to women with those demographic characteristics from a comparable 1984 dataset. The prevalence of abuse, characteristics of the victim, assault, alleged perpetrator, disclosure, and long-term effects by ethnic group affiliation were assessed. RESULTS: Of the total sample, 34% reported at least one incident prior to age 18. Ethnic differences were found with respect to prevalence, location of abuse, and number of incidents of rape. While comparisons made with the 1984 dataset revealed no significant difference in prevalence rates over the 10 year period, changes in circumstances were noted. CONCLUSIONS: Although the prevalence of child sexual abuse in Los Angeles County remained fairly stable, several circumstances of abuse underwent change. These characteristics are discussed in relation to how sexual abuse among ethnically diverse samples in Los Angeles County has changed over a decade and how these differences can help better tailor prevention messages to different communities.

Black or African American↗
PubMed1999

Precision and accuracy of an electrogoniometer.

BACKGROUND: Spinal range of motion has been studied by use of a variety of different methods. One electrogoniometer has been used as a noninvasive, reliable, and accurate method. The accuracy and precision of this device has not been sufficiently documented. OBJECTIVE: To evaluate the precision and accuracy of an electrogoniometer in comparison with two manual protractors. STUDY DESIGN: This study investigated the precision and accuracy of an electrogoniometer (OSI CA 6000). METHODS: The precision and accuracy of the electrogoniometer were determined by a series of tests against two manual protractors. Six different movement directions were tested and 4 or 5 different angles for a given movement direction were evaluated. RESULTS: The precision of the electrogoniometer was found to be +/- 0.1 degree for 4 different angles (10 degrees, 20 degrees, 40 degrees, and 60 degrees) in 6 different movement directions (flexion, extension, left lateral flexion, right lateral flexion, left rotation, and right rotation). The accuracy was tested by comparing both manual protractors with the electrogoniometer. Substantial disagreement for 27 of 28 datasets was found. In only one dataset was there agreement between the two manual protractors and the electrogoniometer. The mean differences were in the interval 2.0% to 11.5% between the electrogoniometer and the protractors. CONCLUSION: The electrogoniometer evaluated has a very high precision when range of motion measurements are made. However, the accuracy of the device is less than acceptable.

Electrodiagnosis↗
PubMed2002

An efficient method for studying short-term plasticity with random impulse train stimuli.

In this article, we introduce an efficient method that models quantitatively nonlinear dynamics associated with short-term plasticity (STP) in biological neural systems. It is based on the Voterra-Wiener modeling approach adapted for special stimulus/response datasets. The stimuli are random impulse trains (RITs) of fixed amplitude and Poisson distributed, variable interimpulse intervals. The class of stimuli, we use can be viewed as a hybrid between the paired impulse approach (variable interimpulse interval between two input impulses) and the fixed frequency approach (impulses repeated at fixed intervals, varying in frequency from one stimulus dataset to the next). The responses are sequences of population spike amplitudes of variable size and are assumed to be contemporaneous with the corresponding impulses in the RITs they are evoked by. The nonlinear dynamics of the mechanisms underlying STP are captured by kernels used to create compact STP models with predictive capabilities. Compared to similar methods in the literature, the method presented in this article provides a comprehensive model of STP with considerable improvement in prediction accuracy and requires shorter experimental data collection time.

Action Potentials↗
PubMed2001

An epidemiological analysis of a canine-biopsies database compiled by a diagnostic histopathology service.

A case-control study was carried out on data from 21,371 canine tissue biopsies submitted to the external histopathology diagnostic service at the University of Glasgow Veterinary School (GUVS) over a 12.5-year period. Biopsies were received from 545 privately owned and charity veterinary practices located throughout the UK. The overall prevalence of neoplasia in samples with a confirmed diagnosis was 58.7%. A total of 156 pure breeds were represented in the dataset, with 22.2% of samples originating from mixed-breed dogs. Univariable and multivariable analyses assessed the effects of sex, breed, age and site on the likelihood of a diagnosis of neoplasia. Logistic regression showed that the highest odds ratio was associated with the mammary gland (OR=6.53;skin=the referent category). Using the Labrador retriever as the referent breed, Boxers had increased odds of neoplasia; the German shepherd dog and Doberman were among breeds with decreased odds ratios. Intact females and dogs over the age of 10 years were (unsurprisingly) also high-risk groups. Potential sources of bias influencing the dataset include the relative ease with which clinical abnormalities of the skin and mammary gland initially are detected by sight and/or palpation, compared with other organs. The high prevalence of biopsies originating from the skin and mammary gland is also likely to reflect the readiness of the veterinarian to biopsy lesions in these sites, compared with sites within the body cavities. The findings confirm many of the perceived risks for neoplasia based on previous clinical descriptive and univariable investigations. The results might also assist the pathologist in prioritisation of biopsy examination in busy histopathology laboratories.

Animals↗
PubMed1997

An overview of techniques for dealing with large numbers of independent variables in epidemiologic studies.

Many studies of health and production problems in livestock involve the simultaneous evaluation of large numbers of risk factors. These analyses may be complicated by a number of problems including: multicollinearity (which arises because many of the risk factors may be related (correlated) to each other), confounding, interaction, problems related to sample size (and hence the power of the study), and the fact that many associations are evaluated from a single dataset. This paper focuses primarily on the problem of multicollinearity and discusses a number of techniques for dealing with this problem. However, some of the techniques discussed may also help to deal with the other problems identified above. The first general approach to dealing with multicollinearity involves reducing the number of independent variables prior to investigating associations with the disease. Techniques to accomplish this include: (1) excluding variables after screening for associations among independent variables; (2) creating indices or scores which combine data from multiple factors into a single variable; (3) creating a smaller set of independent variables through the use of multivariable techniques such as principal components analysis or factor analysis. The second general approach is to use appropriate steps and statistical techniques to investigate associations between the independent variables and the dependent variable. A preliminary screening of these associations may be performed using simple statistical tests. Subsequently, multivariable techniques such as linear or logistic regression or correspondence analysis can be used to identify important associations. The strengths and limitations of these techniques are discussed and the techniques are demonstrated using a dataset from a recent study of risk factors for pneumonia in swine. Emphasis is placed on comparing correspondence analysis with other techniques as it has been used less in the epidemiology literature.

Animal Diseases↗
PubMed1997

Associations between farm management practices, productivity, and bovine leukemia virus infection in Ontario dairy herds.

The objective of this study was to investigate the associations between herd-level bovine leukemia virus (BLV) status and herd-level management and production variables. The study population consisted of 1330 cows sampled from 102 Ontario dairy herds. The individual-cow prevalence of BLV infection in the population (based on AGID testing) was 23%, with 69.6% of herds having one or more positive animals. The herd-level explanatory variables were divided into two datasets containing winter housing variables and all non-seasonal variables, and summer housing variables and all non-seasonal variables. In both datasets, multivariable analyses found a negative association between herd-level milk production and BLV status, and positive associations between weaning age and purchasing animals from outside sources, and BLV status. Housing pre-weaned calves in hutches or separate calf buildings in either season was associated with an increased risk of BLV. The model containing winter housing variables also included positive associations between contact with older animals and BLV status, and between BLV status and the facilities used to house dry cows in the winter.

Aging↗
PubMed2003

Application of a disposable transparent filtration membrane to the infrared spectroscopic discrimination among bacterial species.

This study describes the application of filtration, infrared spectroscopy, and multivariate analysis to the identification of 10 foodborne bacterial species. The bacteria were applied by filtration to a disposable optical membrane that is transparent to infrared radiation. The filtration step was rapid (2 min). Observed cellular infrared spectra were unique and were used to discriminate among the different species. A dataset for the 10 bacterial species investigated was successfully used to correctly identify unknowns included in the dataset.

Bacteria↗
PubMed2003

Molecular features of non-B, non-C hepatocellular carcinoma: a PCR-array gene expression profiling study.

BACKGROUND/AIMS: Hepatocellular carcinoma (HCC) usually develops following chronic liver inflammation caused by hepatitis C or B virus. Through expression profiling in a rare type of HCC, for which the causes are unknown, we sought to find key genes responsible for each step of hepatocarcinogenesis in the absence of viral influence. METHODS: We used 68 non-B, non-C liver tissues (20 HCC, 17 non-tumor, 31 normal liver) for expression profiling with PCR-array carrying 3072 genes known to be expressed in liver tissues. To select the differentially expressed genes, we performed random permutation testing. A weighted voting classification algorithm was used to confirm the reliability of gene selection. We then compared these genes with the results of previous expression profiling studies. RESULTS: A total of 220 differentially expressed genes were selected by random permutation tests. The classification accuracies using these genes were 91.8, 92.0 and 100.0% by a leave-one-out cross-validation, an additional PCR-array dataset and a Stanford DNA microarray dataset, respectively. By comparing our results with previous reports on virus-infected HCC, four genes (ALB, A2M, ECHS1 and IGFBP3) were commonly selected in some studies. CONCLUSIONS: The 220 differentially expressed genes selected by PCR-array are potentially responsible for hepatocarcinogenesis in the absence of viral influence.

Aged↗
PubMed2003

An automated method to position prosthetic components within multiple anatomical spaces.

The level of fit and fill of a stem in the host femur is the most critical factor for the mechanical stability and success of the prosthesis. It would be useful to have a simulation tool able to investigate the anatomical compatibility of a new implant in a large library of femoral anatomies in the early phases of the design process. In order to realise this tool, it is necessary to develop an automatic method for the positioning of the stem in a database of anatomies. The aim of this study was to develop and evaluate a method for the automatic positioning of the stem geometry in the anatomical CT dataset. Two different strategies were considered: a completely automatic registration technique and a semi-automatic method based on an anatomical referencing. The two procedures were compared to the manual positioning obtained by an expert surgeon in a set of nine CT datasets. For both methods in each femur the positioning and the orientation of the stem were good. The results showed a better level of fitting for the automatic method, while the shift of the hip joint centre was lower for the anatomical referencing technique. However, the anatomical referencing method requires a higher computational effort without being significantly better than the automatic method. For this reason, the automatic method should be chosen to develop the automatic positioning of a stem in a database of anatomies.

Arthroplasty, Replacement, Hip↗
PubMed2003

Model validation software for classification models using repeated partitioning: MVREP.

The process of assessing the prediction ability of a computational model is called model validation. For models predicting a categorical response, the prediction ability is usually quantified by prediction measures such as sensitivity, specificity, and accuracy. This paper presents a software Model Validation using Repeated Partitioning (MVREP) that implements a computer-intensive, nonparametric approach to model validation, which we call the re-partitioning method. MVREP, developed using the SAS Macro language, repeats the process of randomly partitioning a dataset and subsequently performing standard model validation procedures, such as cross-validation, a large number of times and generates the empirical sampling distributions of prediction measures. The means of the sampling distributions serve as the point estimates of prediction measures of the model. The variances of the sampling distributions provide a direct assessment of variability for the point estimates of prediction measures. An example is presented using a mouse developmental toxicity chemical dataset to illustrate how the software can be used for the assessment of structure-activity relationships models.

Animals↗
PubMed1999

Climate change and trophic interactions.

With confirmation of anthropogenically induced climate change, the spotlight is on biologists to predict and detect effects on populations. The complexity of interactions within and between the biotic and abiotic components involved makes this a tough challenge, and most studies have consequently considered effects of only single climate variables on single species. However, some have gone further, and recently published long-term datasets now offer opportunities that complement new experimental approaches that span trophic levels. With these datasets, predicting relative shifts in temporal and spatial associations could be among the most tractable problems.

Journal Article↗
PubMed2002

Support vector machines for predicting the specificity of GalNAc-transferase.

Support Vector Machines (SVMs) which is one kind of learning machines, was applied to predict the specificity of GalNAc-transferase. The examination for the self-consistency and the jackknife test of the SVMs method were tested for the training dataset (305 oligopeptides), the correct rate of self-consistency and jackknife test reaches 100% and 84.9%, respectively. Furthermore, the prediction of the independent testing dataset (30 oligopeptides) was tested, the rate reaches 76.67%.

Algorithms↗