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PubMed2004

Microarrays in ecological research: a case study of a cDNA microarray for plant-herbivore interactions.

BACKGROUND: Microarray technology allows researchers to simultaneously monitor changes in the expression ratios (ERs) of hundreds of genes and has thereby revolutionized most of biology. Although this technique has the potential of elucidating early stages in an organism's phenotypic response to complex ecological interactions, to date, it has not been fully incorporated into ecological research. This is partially due to a lack of simple procedures of handling and analyzing the expression ratio (ER) data produced from microarrays. RESULTS: We describe an analysis of the sources of variation in ERs from 73 hybridized cDNA microarrays, each with 234 herbivory-elicited genes from the model ecological expression system, Nicotiana attenuata, using procedures that are commonly used in ecologic research. Each gene is represented by two independently labeled PCR products and each product was arrayed in quadruplicate. We present a robust method of normalizing and analyzing ERs based on arbitrary thresholds and statistical criteria, and characterize a "norm of reaction" of ERs for 6 genes (4 of known function, 2 of unknown) with different ERs as determined across all analyzed arrays to provide a biologically-informed alternative to the use of arbitrary expression ratios in determining significance of expression. These gene-specific ERs and their variance (gene CV) were used to calculate array-based variances (array CV), which, in turn, were used to study the effects of array age, probe cDNA quantity and quality, and quality of spotted PCR products as estimates of technical variation. Cluster analysis and a Principal Component Analysis (PCA) were used to reveal associations among the transcriptional "imprints" of arrays hybridized with cDNA probes derived from mRNA from N. attenuata plants variously elicited and attacked by different herbivore species and from three congeners: N. quadrivalis, N. longiflora and N. clevelandii. Additionally, the PCA revealed the contribution of individual gene ERs to the associations among arrays. CONCLUSIONS: While the costs of 'boutique' array fabrication are rapidly declining, familiar methods for the analysis of the data they create are still missing. The case history illustrated here demonstrates the ease with which this powerful technology can be adapted to ecological research.

Animals↗
PubMed1995

Technical note: perspex blocks for estimation of dose to a standard breast--effect of variation in block thickness.

Mean glandular dose in mammography may be deduced from measurements made using Perspex blocks. This method is almost universally used in the National Health Service Breast Screening Programme. The effect on the estimated mean glandular dose of variations in the measured thickness of Perspex from a nominal thickness of 40 mm was investigated. Results are presented from three UK Regions. Variations in measured Perspex thicknesses ranged from almost 8% below to about 2% above the 40 mm nominal, causing errors in dose estimation, if uncorrected, of about +20% to -6.5%. A means of correcting dose estimates for measured differences in block thickness is presented. An alternative method of ensuring consistent dosimetry would be to use accurately machined Perspex blocks.

Breast↗
PubMed2006

Evidence for diversity in transcriptional profiles of single hematopoietic stem cells.

Hematopoietic stem cells replenish all the cells of the blood throughout the lifetime of an animal. Although thousands of stem cells reside in the bone marrow, only a few contribute to blood production at any given time. Nothing is known about the differences between individual stem cells that dictate their particular state of activation readiness. To examine such differences between individual stem cells, we determined the global gene expression profile of 12 single stem cells using microarrays. We showed that at least half of the genetic expression variability between 12 single cells profiled was due to biological variation in 44% of the genes analyzed. We also identified specific genes with high biological variance that are candidates for influencing the state of readiness of individual hematopoietic stem cells, and confirmed the variability of a subset of these genes using single-cell real-time PCR. Because apparent variation of some genes is likely due to technical factors, we estimated the degree of biological versus technical variation for each gene using identical RNA samples containing an RNA amount equivalent to that of single cells. This enabled us to identify a large cohort of genes with low technical variability whose expression can be reliably measured on the arrays at the single-cell level. These data have established that gene expression of individual stem cells varies widely, despite extremely high phenotypic homogeneity. Some of this variation is in key regulators of stem cell activity, which could account for the differential responses of particular stem cells to exogenous stimuli. The capacity to accurately interrogate individual cells for global gene expression will facilitate a systems approach to biological processes at a single-cell level.

Animals↗
PubMed1986

Projection of death rates from ischemic heart disease in Japan, 1985-2000.

Death rates from all forms of ischemic heart disease and acute myocardial infarction were projected between 1985 and 2000 A.D., based on vital statistics from 1973 to 1982 and the estimated population by sex and age groups in Japan. It is predicted that the crude death rate from ischemic heart disease will increase (+1.4% per year for males and +1.8% for females), and that the age-adjusted death rate will decrease (-1.1% per year for males and -1.4% for females). The crude death rate from acute myocardial infarction is predicted to increase steadily (+2.4% per year for males and +2.2% for females), though the age-adjusted rate will decline slightly (-0.5% per year for males and -1.0% for females) throughout this period. The crude death rate from acute myocardial infarction is predicted to increase more than the rate from ischemic heart disease. It is estimated that the total number of deaths will increase from 48,000 (males and females combined) in 1982 to 72,000 in 2000 for ischemic heart disease, and from 29,600 in 1982 to 45,500 in 2000 for acute myocardial infarction.

Adult↗
PubMed1988

Estimates of pregnancies and pregnancy rates for the United States, 1976-85.

After increasing by 9 per cent in the period 1976-80 in the United States, pregnancy rates declined by 4 per cent between 1980 and 1984 (from 111.9 to 107.3 pregnancies per 1,000 women aged 15-44 years). Between 1984 and 1985, the rate rose by less than 1 per cent to 108.2. More detailed data by age and race, available only through 1983, indicate that the decline in the 1980-83 period was not shared by all age groups. For example, pregnancy rates continued to increase for women in their thirties, and teenage pregnancy remained substantially the same. In 1983, 61 per cent of all pregnancies ended in live birth, 26 per cent in induced abortion, and 13 per cent in fetal loss. Pregnancy rates in that year were two-thirds higher for women of races other than White than for White women, and pregnancies of other-than-White women were more likely to terminate as an induced abortion or fetal loss. However, White teenagers and teenagers of other races were about equally likely to have their pregnancy end in induced abortion or fetal loss.

Abortion, Induced↗
PubMed1992

Implications of population growth on prevalence of diabetes. A look at the future.

The purpose of this study was to present projections of the future population of diabetes patients, to discuss policy implications of these projections, and to suggest ways that these projections might be made more useful to medical professionals. Under the assumption that the incidence of diabetes in four age-groups will remain constant in future years, previous estimates of the incidence of diabetes will be applied to Bureau of the Census population projections to project the number of new cases of diabetes that can be expected in future years in each of these age-groups. The prevalence of diabetes will remain relatively constant at approximately 1 million patients in younger populations (less than 45 yr old) through the middle of the next century. As the post-World War II baby boom ages, the number of older diabetes patients (45 and older) will almost double from 6.5 million in 1987 to an estimated 11.6 million in the year 2030. Although there is little doubt that the aging of the population will increase the number of diabetes patients, the assumption of constant incidence rates is a very limiting one. These projections would be more useful for the planning of research and training if the incidence of diabetes could be estimated for more refined categories of demographic and medical characteristics.

Adult↗
PubMed2006

Technical note: A model to estimate individual feed intake of swine in group feeding.

In most animal growth experiments, groups of animals are housed within a pen. Occasionally, an individual animal shows a very different growth rate than its pen mates or dies during the experiment. When this happens, if pen feed intake (PFI) cannot be reestimated for the calculation of ADFI and feed efficiency, an observation will be lost from the data set. Therefore, we propose a model to estimate individual feed intake (IFI) of pigs in group feeding, with subsequent validation of the model using group feeding simulation studies. In the proposed model, the feed intake (FI) of each affected pen is partitioned into FI for maintenance (FI(m)) and FI for growth (FI(g)) for each animal within that pen. First, individual pig FI(m) for the period is calculated using the 1998 National Research Council estimation of ME for maintenance. Then, FI(m) for all pigs in the pen is summed. The difference between the summed FI(m) and the total PFI is that which supported growth in the pen. Next, FI(g) is calculated by apportioning the remaining feed equally to each unit of gain within the pen. Finally, the estimated IFI for the pig being removed from the pen is the sum of FI(m) and FI(g) for that pig; this FI estimate is subtracted from the original PFI to leave the new PFI for the remaining pigs. The validity of the estimated IFI is dependent on the accuracy of the maintenance energy equation and the energy analysis of the feedstuffs. In simulation studies, we compared the accuracy of the proposed method with 2 other methods. In simulation study 1, the proposed model showed better accuracy than at least one of the other methods during all tested periods (P < 0.001). In simulation study 2, the greater accuracy of the proposed method compared with 2 other methods was demonstrated again. Because calculation of IFI is relatively cumbersome, we developed a feed intake correction spreadsheet (FICS), an Excel spreadsheet containing macros for FI correction. All of the calculation procedures in the proposed model are included within the feed intake correction spreadsheet. The Excel file and instructions are being made available via a Web site.

Animals↗
PubMed1984

Integrated population and employment projections for national-regional planning in the Federal Republic of Germany.

"The concepts, methodological approach, assumptions and results of a long-term forecast for 88 federal planning regions in West Germany are presented and discussed. It is emphasized that population and employment projections for policy consultation purposes must be of an intermediate complexity in order to remain transparent and reconstructable. To facilitate the interpretation of the forecasting results, a typology of the planning regions along the dimension of forecasted labour market developments is presented." It is found that "rural peripheral regions with employment problems stemming mainly from demographic factors and old industrial regions with severe labour market imbalances caused by structural change are...the actual and future problem regions in West Germany."

Demography↗
PubMed1991

A surface model approach to small area population estimation.

The author applies a surface model approach to the estimation of small-area population and household characteristics. "The representation of population-related information by means of surface concepts offers a way to overcome many of the limitations of traditional, 'fixed' zone-based methods. The approach has the potential to give planners and policy-makers greatly improved flexibility in handling and interpreting spatially referenced data. One practical area of application is the estimation of population at local levels for which the underlying concepts and methods are discussed in this article."

Demography↗
PubMed1997

Projecting rates of urbanisation in England, 1991-2016: method, policy application and results.

"The rate of conversion of land from rural to urban uses has been a central concern of the British planning system. Despite this interest, however, the factual basis of the debate on the pace of urban growth, its form and distribution has been extremely weak. The reason for this is lack of appropriate data. This paper reports research on two new data sources on land use--a digital database of the boundaries of tracts of urban land in 1981 and 1991 and the Land Use Change Statistics--to analyse recent urban growth in England and, in conjunction with current household projections, to estimate the likely extent of urbanisation in 2016. In addition to assessing the geographical distribution of this growth, the paper draws out some implications for policy analysis of the method of projecting the extent of land in urban use."

Agriculture↗
PubMed1996

Population and dwelling unit estimates from space.

"To increase the utility of satellite imagery as a source of cheap and current information for planning and managing cities some problems have to be resolved.... One answer is to adopt interpretation methods that use the increased information in a more detailed scene. This paper reports on attempts to measure the morphological patterns in an urban satellite scene and to use these for image interpretation. The interpretation task addressed is the estimation of residential dwelling units from the patterns discernible in high resolution satellite images of cities. The practical results include dwelling estimates that can be aggregated to any geographical unit of analysis, population estimates for cities and a dwelling density surface that can be categorised into any number of residential land-use classes."

Data Collection↗