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PubMed2005

UniFrac: a new phylogenetic method for comparing microbial communities.

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.

Bacteria↗
PubMed2001

Ethics and geographical equity in health care.

Important variations in access to health care and health outcomes are associated with geography, giving rise to profound ethical concerns. This paper discusses the consequences of such concerns for the allocation of health care finance to geographical regions. Specifically, it examines the ethical drivers underlying capitation systems, which have become the principal method of allocating health care finance to regions in most countries. Although most capitation systems are based on empirical models of health care expenditure, there is much debate about which needs factors to include in (or exclude from) such models. This concern with legitimate and illegitimate drivers of health care expenditure reflects the ethical concerns underlying the geographical distribution of health care finance.

Delivery of Health Care↗
PubMed2002

Environmental analysis: insights from sociological and geographical perspectives.

Recent conceptual models, such as the Canadian Model of Occupational Performance, emphasize the transactional relationships between individuals, their occupations, and the environments in which they live. Nevertheless, further theoretical development is necessary in order to gain a comprehensive understanding of the nature of interconnections between the environment, occupation, and disability. This paper draws on concepts from sociology and geography that can broaden our understanding of the environment and the manner in which its different dimensions may influence individuals' experiences of disability. The paper demonstrates how theoretical ideas from these disciplines can be used to inform our understanding of the daily lives of three different individuals: a senior with Bipolar Affective Disorder, a man with HIV/AIDS, and a parent of a child with a severe disability. The paper concludes with a discussion of the implications of the analysis for occupational therapy theory and practice.

Acquired Immunodeficiency Syndrome↗
PubMed1989

Teaching social studies to high school students with academic handicaps in a mainstreamed setting: effects of a computerized study guide.

This research investigated the effectiveness of a computerized study guide, in comparison to a notetaking condition, as a method to increase textbook comprehension among students with learning disabilities and remedial education pupils enrolled in a ninth-grade world geography class. Results indicated that the computerized study guide produced significantly higher performance than notetaking for both groups of students. There was no significant difference in the performance of the two groups within treatments. Several practical issues concerning the implementation of computerized study guides in secondary programs serving students with academic handicaps are discussed.

Adolescent↗
PubMed1983

Urbanization and cancer: changing mortality patterns?

"Analysis of the relationship between cancer rates and urbanization for United States counties for the period 1950-54 reveals the expected urban/rural differences for many digestive, urinary and respiratory organ cancers and for female breast cancer. Similar urban/rural differences existed in many other Western countries. By 1970-75, however, urban/rural differences in the United States had substantially narrowed." It is noted that "available data do not allow formal tests of the relationship between these changes and specific etiological factors, but the data suggest that the spatial convergence is related to the changing geography of such risk factors as smoking, alcohol consumption, manufacturing, and socioeconomic status and to the diminished size and role of the white foreign-born population, as well as to such confounding factors as medical practices and population migration."

Alcohol Drinking↗
PubMedDate not supplied

Geographical knowledge in patients with Alzheimer's disease.

Geographical knowledge, a measure of remote memory for visuospatial information, was studied in mildly and moderately demented patients who met NINCDS-Alzheimer's Disease and Related Disorders Association criteria for Alzheimer's disease. Alzheimer's disease patients were moderately impaired on a test that emphasizes locating gross features of US geography and profoundly impaired in locating cities on a map of the region of the United States in which they resided. The possibility that performance on tests of geographical knowledge can be used to predict impending difficulties of demented patients in wayfinding is discussed.

Aged↗
PubMed1999

City and country in German psychiatry in the nineteenth and twentieth centuries - the example of Freiburg.

The situation (geography, topography) of asylums played an important role in German psychiatry during the last two centuries. In the first half of the nineteenth century asylums were built in the countryside. Although their establishment was partly driven by a bourgeois effort towards reform it was also still underpinned by the old autocratic ideas in respect to social ranking and by patriarchal medical concepts. Yet university psychiatry along the lines of Wilhelm Griesinger (1817-1868) was city-oriented. University psychiatry seemed to satisfy the needs of a modern industrialized state more effectively, but asylum psychiatry in Bismarckian and Wilhelmine times on the other hand corresponded strongly to the needs of the hierachical state. The history of the psychiatric hospital of the University of Freiburg illustrates how critical the dualism of country-oriented versus city-oriented psychiatry was for twentieth-century German psychiatry.

Geography↗
PubMed1997

A place in the sun: international retirement migration from northern to southern Europe.

"This article considers four aspects of IRM [international retirement migration]. The first considers the limited literature on this... topic and identifies the distinctiveness of both its international and European features. The second reviews the existing statistical data for north-south IRM in Europe, particularly from the UK to Italy, Malta, Portugal and Spain; it establishes both the scale and the geography of these migrations. In the third section we investigate some of the major influences on both the volume and the spatial pattern of IRM. Finally, in the fourth section, a brief review is presented of the economic, social and cultural implications of IRM for both the emigrants and their host communities."

Data Collection↗
PubMed2005

MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation.

BACKGROUND: The picture of dog mtDNA diversity, as obtained from geographically wide samplings but from a small number of individuals per region or breed, has revealed weak geographic correlation and high degree of haplotype sharing between very distant breeds. We aimed at a more detailed picture through extensive sampling (n = 143) of four Portuguese autochthonous breeds - Castro Laboreiro Dog, Serra da Estrela Mountain Dog, Portuguese Sheepdog and Azores Cattle Dog-and comparatively reanalysing published worldwide data. RESULTS: Fifteen haplotypes belonging to four major haplogroups were found in these breeds, of which five are newly reported. The Castro Laboreiro Dog presented a 95% frequency of a new A haplotype, while all other breeds contained a diverse pool of existing lineages. The Serra da Estrela Mountain Dog, the most heterogeneous of the four Portuguese breeds, shared haplotypes with the other mainland breeds, while Azores Cattle Dog shared no haplotypes with the other Portuguese breeds.A review of mtDNA haplotypes in dogs across the world revealed that: (a) breeds tend to display haplotypes belonging to different haplogroups; (b) haplogroup A is present in all breeds, and even uncommon haplogroups are highly dispersed among breeds and continental areas; (c) haplotype sharing between breeds of the same region is lower than between breeds of different regions and (d) genetic distances between breeds do not correlate with geography. CONCLUSION: MtDNA haplotype sharing occurred between Serra da Estrela Mountain dogs (with putative origin in the centre of Portugal) and two breeds in the north and south of the country-with the Castro Laboreiro Dog (which behaves, at the mtDNA level, as a sub-sample of the Serra da Estrela Mountain Dog) and the southern Portuguese Sheepdog. In contrast, the Azores Cattle Dog did not share any haplotypes with the other Portuguese breeds, but with dogs sampled in Northern Europe. This suggested that the Azores Cattle Dog descended maternally from Northern European dogs rather than Portuguese mainland dogs. A review of published mtDNA haplotypes identified thirteen non-Portuguese breeds with sufficient data for comparison. Comparisons between these thirteen breeds, and the four Portuguese breeds, demonstrated widespread haplotype sharing, with the greatest diversity among Asian dogs, in accordance with the central role of Asia in canine domestication.

Animals↗
PubMed2001

Richness of Colchic vegetation: comparison between refugia of south-western and East Asia.

BACKGROUND: The Colchis is one of the species-rich refugia and a centre of biological diversity in western Eurasia. We analysed patterns of richness, endemism and invasions in relation to taxonomy (family membership), life form, certain habitats in the Colchis, and compared them to patterns found for Japan. RESULTS: We found that in the Colchis perennials are significantly over-represented in endemic species, and that they typically occur on limestone soils and in alpine tall herbaceous vegetation. The Asteraceae produce significantly large number of both endemic and alien species, whereas the Poaceae are over-represented in alien species but under-represented in endemics. Likewise, the Apiaceae are over-represented in endemics, whereas the Euphorbiaceae are over-represented in alien species. Similar patterns have been found in Yakushima, Japan. The Morisita-Horn index of similarity between these two sites was 0.83 (based on family size). Although the flora of Adjara comprised of fewer families than the flora of Yakushima, the largest families are richer in species in the flora of Adjara than in the flora of Yakushima. CONCLUSIONS: Floristic analysis of refugia of western Eurasia and their comparison with geographically distant areas can provide useful data for plant ecological and evolutionary studies. Potentially, such studies can produce testable hypotheses on plant migrations and on their historical geography. For example, the data presented in this study indicate that more severe conditions in the Pleistocene and geographical isolation of the Colchis may be responsible for the higher relative importance of adaptive radiation in the shaping of its modern flora.

Biodiversity↗
PubMed2006

The foci of scrub typhus and strategies of prevention in the Spring in Pingtan Island, Fujian Province.

This study investigates the foci of tsutsugamushi disease on Pingtan Island, China, with emphasis on cases of illness that occur in the spring. The investigation of the physical and medical geography in the endemic area and detection of 141 sera samples in the population of Pingtan Island is described. The serum samples were taken from 102 soldiers and 39 residents and were tested by the indirect immunofluorescence assay. An island resident's history of illness inquiry was also conducted, and the results are discussed. We were able to determine the most prevalent types of rats and mites from the rat bodies. We isolated the DNA from the spleen of 40 rats and from five groups of mites by polymerase chain reaction. Orientia tsutsugamushi was isolated by perctoneally injecting KM mice with the patient's untreated blood along with ground rat viscera (R. losea) and ground mites (L. deliense), respectively. The isolates were typed at the molecular level. This study will then present direct prevention strategies that emphasize personal hygiene, methods of personal protection, keeping living environments clean, and it will provide strategies to eliminate rats and mites. As a result of adopting these strategies, no case of scrub typhus occurred in this region in approximately 2003-2004.

Animals↗
PubMed2005

Use of graph theory to identify patterns of deprivation and high morbidity and mortality in public health data sets.

OBJECTIVE: An important part of public health is identifying patterns of poor health and deprivation. Specific patterns of poor health may be associated with features of the geographic environment where contamination or pollution may be occurring. For example, there may be clusters of poor health surrounding nuclear power stations, whereas major roads or rivers may be associated with areas of poor health alongside the feature in chains. Current methods are limited in their capacity to search for complex patterns in geographic data sets. The objective of this study was to determine whether graph theory could be used to identify patterns of geographic areas that have high levels of deprivation, morbidity, and mortality in a public health database. The geographic areas used in the study were enumeration districts (EDs), which are the lowest level of census geography in England and Wales, representing on average 200 households in the 1991 census. More specifically, the study aimed to identify chains of EDs with high deprivation, morbidity, and mortality that might be adjacent to specific types of geographic features, i.e., rivers or major roads. DESIGN: The maximum common subgraph (MCS) algorithm was used to search for seven query patterns of deprivation and poor health within the Trent region. Query pattern 1 represented a linear chain of five EDs and query patterns 2 to 7 represented the possible clusters of the five EDs. To identify chains of EDs with high deprivation, morbidity, and mortality, the results from the query patterns 2 to 7 were used to remove patterns (option 1) and EDs (option 2) from the results of query pattern 1. MEASUREMENTS: Data on the Townsend Material Deprivation Index, standardized long-term limiting illness and standardized all-cause mortality rates were used for the 10,665 EDs within the Trent region. RESULTS: The MCS algorithm retrieved a range of patterns and EDs from the database for the queries. Query pattern 1 identified 3,838 patterns containing a total of 195 EDs. When the patterns retrieved using query patterns 2 to 7 were removed from the 3,838 patterns using option 1, 1,704 patterns remained containing 161 EDs. When the EDs retrieved using query patterns 2 to 7 were removed from the 195 EDs identified by query pattern 1 using option 2, 12 EDs remained. The MCS algorithm was therefore able to reduce the numbers of patterns and EDs to allow manual examination for chains of EDs and for that which might be associated with them. CONCLUSION: The study demonstrates the potential of the MCS algorithm for searching for specific patterns of need. This method has potential for identifying such patterns in relation to local geographic features for public health.

Algorithms↗
PubMed2006

Effect of patient socioeconomic status and body mass index on the quality of breast cancer adjuvant chemotherapy.

PURPOSE: The purpose of this study was to investigate the relationship between socioeconomic status (SES) and the use of intentionally reduced doses of chemotherapy in the adjuvant treatment of breast cancer. PATIENTS AND METHODS: Patients with breast cancer treated with a standard chemotherapy regimen (n = 764) were enrolled in a prospective registry after signing informed consent. Detailed information was collected on patient, disease, and treatment, including chemotherapy doses. Zip code level data on median household income, proportion of people living below the poverty level, and educational attainment were obtained from the US Census. Doses for the first cycle of chemotherapy lower than 85% of standard were considered to be reduced. Univariate analyses and multivariate logistic regression were performed to identify factors associated with the use of reduced first cycle doses. RESULTS: In univariate analysis, individual education attainment, zip code SES measures, body mass index, and geographic region were all significantly associated with receipt of intentionally reduced doses of chemotherapy. In multivariate analysis, controlling for geography, factors independently associated with reduced doses were obesity (odds ratio [OR], 2.47; 95% CI, 1.36 to 4.51), severe obesity (OR, 4.04; 95% CI, 1.46 to 11.19), and education less than high school (OR, 3.07; 95% CI, 1.57 to 5.99). CONCLUSION: Social disparities in breast cancer outcomes may be in part the result of lower quality chemotherapy doses in the adjuvant treatment of breast cancer. Efforts to address such prescribing patterns may help reduce SES disparities in breast cancer survival.

Adult↗
PubMed2006

Geriatric education across 94 million acres: adapting conference programming in a rural state.

Montana, a predominantly rural state, with a unique blend of geography and history, low population density, and cultural diversity represents the challenges for program development and implementation across remote areas. The paper discusses two statewide multidisciplinary geriatric education programs for health professionals offered by the recently established Montana Geriatric Education Center (MTGEC); use of telecommunications technology; collaborations with Geriatric Education Centers (GECs) and the Montana Healthcare Telemedicine Alliance (MHTA); and training outcomes, insights, and implications for continuing education of health professionals who practice in hard-to-reach regions. In addition, data from a statewide needs assessment are presented specific to preferred format. The MTGEC training model that combined traditional classroom and videoconference increased attendance by twofold and may be adapted in other regions to train providers in remote areas of the U.S.

Adult↗
PubMed1998

Breaking down information barriers: a guide to international research of medical resources on the World Wide Web.

The purpose of this paper is to facilitate international research of medical resources on the World Wide Web. International research consists of overcoming a unique set of obstacles and challenges that are not involved when undertaking research tasks using only U.S.-based information. Utilizing the World Wide Web can help us to overcome most of the restraints we would have to face when we perform research outside of our local geography. Currently, there are a number of Internet Web sites that may assist us in breaking down the barriers to undertaking international research.

Directories as Topic↗
PubMed2001

Inbreeding in Gredos mountain range (Spain): contribution of multiple consanguinity and intervalley variation.

The present paper examines consanguineous marriages occurring between 1874 and 1975 in three valleys (Tormes, Alberche, and Tiétar) in the Sierra de Gredos mountain range, Avila province, Spain. Information was obtained from parish registers of 42 localities, corresponding to a total of 41,696 weddings. Consanguineous marriages were defined as those up to the third degree of consanguinity (second cousins). From 1874 to 1975 the percentage of related mates was 4.45% and the inbreeding coefficient was 0.0011868 (for 1874 to 1917 corresponding figures up to the fourth degree were 16.44% and 0.00 19085, respectively). In order to ascertain the characteristics and evolution of mating patterns in Gredos, the contribution of each degree of kinship was analyzed as a whole and then for each valley separately. Regarding total consanguineous marriages in Gredos, there is a low frequency of uncle-niece matings (0.21%) and a first-second cousin mating ratio (C22/C33) of 0.23 (up to the third degree of consanguinity). Before 1918 multiple matings (i.e., those involving more than a single relationship) accounted for 19.16% of consanguineous marriages (up to the fourth degree). The observed frequencies of multiple consanguineous marriages was, on average, about twice that expected at random, and the proportion of such marriages to total inbreeding was 34.65%. The temporal change of the Gredos inbreeding pattern was characterized by a recent decrease; the highest inbreeding levels correspond to the period from 1915 to 1944. Finally, intervalley differences (maximum inbreeding coefficient in the Tormes, minimum in the Tiétar) are interpreted considering the geography, population size, and population mobility for each valley

Consanguinity↗
PubMedDate not supplied

Overcoming disparities in U.S. health care.

Disparities in U.S. health care result from a complex mixture of systemic quality and access problems intertwined with historic injury. The many dimensions of health disparities include race, ethnicity, socioeconomic status, and geography. It is critically important for policymakers to define the problem correctly so that our solutions address their intended goal-health security for all regardless of socioeconomic characteristics. Further, U.S. efforts to eliminate disparities must also be part of a broader effort to transform health care and thus must focus, first and foremost, on improving the quality of care delivered to the individual patient.

Delivery of Health Care↗
PubMed2005

Nucleotide polymorphism and linkage disequilibrium in wild populations of the partial selfer Caenorhabditis elegans.

An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, extending even between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using "scattered" samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is shaped largely by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.

Animals↗