SEARCH · Search PubMed

Results for “Geography”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources

PubMed2025

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.

BACKGROUND: Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity. METHODS: In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from five hospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream S pyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity. FINDINGS: We identified 500 cases of invasive S pyogenes infection in patients in the Top End and 495 cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5·97 (95% CI 4·61-7·73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5·41, 4·28-6·89). The odds of in-hospital mortality (OR 0·43, 95% CI 0·26-0·70), 30-day mortality (0·38, 0·23-0·63), and ICU admission (0·42, 0·30-0·59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 S pyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hyperendemic Top End. Using a lower transmission rate, larger population size, and lower levels of migration similar to those of communities in urbanised southeast Australia, the transmission model qualitatively reproduced a pattern of dominant lineages that cycled in frequency. Despite distinct circulating lineages, the prevalence of accessory genes in the bacterial population was maintained across geographies and temporal periods. INTERPRETATION: In a hyperendemic setting, the replacement of distinct S pyogenes lineages occurred in waves, which could be linked to the disproportionate burden of disease and sparse human population in this setting. The maintenance of bacterial gene frequency could be consistent with multilocus selection. These findings suggest that lineage-specific interventions-such as vaccines under development-should consider disease setting and, without broad cross-protection, might lead to lineage replacement. FUNDING: National Health and Medical Research Council, and Leducq Foundation.

Humans↗

PubMed2025

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.

The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.

Humans↗

PubMed2005

Urban/rural inequalities in suicide in Scotland, 1981-1999.

Although suicide accounts for a small percentage of deaths in Scotland (1.4% in 1999), it has been steadily increasing over the last two decades. In the US, Australia, England and Wales the greatest rises in suicide for this time period, occurred in rural areas. This study describes the pattern and magnitude of urban/rural variation in suicide in Scotland, examines methods of suicide within differing geographies and looks at trends in suicides over time. Scotland is split into four rurality types. Suicide data for all areas of Scotland (apart from Grampian which underwent changes in postcode sector boundaries in 1996) are investigated using Standardised Mortality Ratios (SMRs) and multilevel Poisson modelling, adjusting for age, sex and deprivation. SMRs for 1981-85, 1989-93 and 1995-99 are created across the four geographies, using the populations of Scotland in 1983, 1991 and 1997 as the standard populations (SMR=100). The highest rates in 1995-99 are seen in "remote rural" areas, SMR=125 (95% confidence interval 107-146). Models adjusted for age and deprivation show significantly greater risk of male suicide in remote rural areas relative to urban areas and significantly lower risk of female suicide in accessible rural areas. The method of suicide varies across ruralities for both males and females. The study considers how the relationship between suicides and rurality varies over time and how methods of suicide vary across different ruralities. The steepest rises in suicide amongst men, adjusting for age and deprivation, were seen to occur in accessible rural areas, however highest rates remain in remote rural areas.

Adult↗

PubMed2006

Spaces of sobriety/sites of power: examining social model alcohol recovery programs as therapeutic landscapes.

While there has been interest in geographical variations in alcohol use and their implications for health, similar attention has not been given to geographies of alcohol treatment and recovery. This paper is concerned with exploring these geographies of alcohol recovery and treatment. Specifically, the paper uses the therapeutic landscape concept coupled with Foucault's concept of governmentality to frame a qualitative case study of a 'social model' recovery community in San Pedro, California. Analysis of the programs operating in San Pedro consisting of observation and interviews, demonstrates the complexity and contradictory character of such recovery landscapes. In particular, the governmentality perspective suggests that spaces created for alcohol recovery and support can be simultaneously understood as sites designed to govern the health-related conduct of individuals. Within programs, clients were provided with support and encouragement from staff and peers, but these same relations also made possible surveillance and the governing of daily routines. In the neighbourhood, program staff intervened to create 'healthy' spaces but these interventions also shaped the conduct of local residents and contributed to the spatial regulation of problem groups. While a focus on governmentality does not preclude recognition of the positive effects associated with therapeutic landscapes, it does provide an opportunity for further consideration of the complexities underlying such environments.

Alcoholics Anonymous↗

PubMed2004

Prognostic difference of surgical treatment of exophytic versus barrel-shaped bulky cervical cancer.

OBJECTIVE: The aim of the study was to evaluate the prognostic significance of tumor geography, defined as exophytic or barrel-shaped growth, in bulky (>4 cm) cervical cancer. METHODS: Four hundred women with cervical cancer, treated by primary radical hysterectomy between January 1984 and November 2000, were followed in a prospective cohort study. Clinical and pathology data were stored in a databank and the clinical protocol was unchanged during the study except for the amendment of additional indications of postoperative radiation in 1997. The assessment of tumor geography was based on pelvic examination at the time of tumor staging or radical hysterectomy or from the pathology report. Survival probabilities were calculated by the Kaplan-Meier method and compared with the log-rank test. RESULTS: The mean age of the patients was 45 years and the mean follow-up duration 48 months. Tumors were of squamous cell type in 291 patients (73%). Lymph node metastases were present in 91 patients (24%) and postoperative radiation was given in 179 patients (45%). In 291 patients, tumor diameter was <4 cm; in 58 patients, the tumor was defined as bulky exophytic and in 51 patients as bulky barrel shaped. There were no differences among these three groups in terms of operating time, blood loss during surgery or complications at 3 or 6 months postoperatively. Bulky exophytic tumors had an identical overall survival as compared to small-diameter (<4 cm) tumors. The overall survival (OS) of bulky barrel-shaped tumors was significantly worse (P < 10(-4)). The same was found for disease-free survival (DFS). CONCLUSION: Bulky exophytic cervical cancer has an identical surgical morbidity, overall and disease-free survival as compared to nonbulky (<4 cm) cervical cancer. In view of these identical characteristics, primary surgical treatment should be considered for patients with bulky exophytic cervical cancer.

Adult↗

PubMed2026

Genome-wide SNP data support species boundaries in sympatric Polylepis Ruiz & Pav. (Rosaceae) species from Bolivia and Ecuador.

Species delimitation in the South American genus Polylepis is notoriously challenging due to high morphological similarity and phenotypic plasticity, likely driven by hybridization and gene flow. Previous phylogenetic studies suggested that genetic structure aligns more strongly with geography than with taxonomy, questioning existing species concepts and hampering conservation efforts. We used double-digest RAD sequencing (ddRADseq) to generate genome-wide SNP data for 11 Polylepis species sampled across multiple localities in Bolivia and Ecuador. Population genetic analyses, phylogenetic inference, and network approaches were combined to assess whether genetic structure aligns more closely with taxonomy or geography. Morphologically defined species formed largely cohesive genetic lineages across regions, with species identity explaining substantially more genetic variation than locality. While localized admixture and reticulation were detected among closely related taxa, widespread species showed strong genetic cohesion and clear separation from congeners. Our results indicate that the sampled Polylepis species from Bolivia and Ecuador maintain distinct genetic identities despite localized signals consistent with gene flow. This genome-wide support for current taxonomy highlights Polylepis as a valuable model for studying speciation under gene flow and indicates that multiple geographic sampling will be essential in reconstructing a robust phylogeny of the genus, with important implications for conservation planning in Andean montane forests.

Bolivia↗

PubMed1998

The refugee crisis in Africa and implications for health and disease: a political ecology approach.

Political violence in civil war and ethnic conflicts has generated millions of refugees across the African continent with unbelievable pictures of suffering and unnecessary death. Using a political ecology framework, this paper examines the geographies of exile and refugee movements and the associated implications for re-emerging and newly emerging infectious diseases in great detail. It examines how the political ecologic circumstances underlying the refugee crisis influences health services delivery and the problems of disease and health in refugee camps. It has four main themes, namely, an examination of the geography of the refugee crisis: the disruption of health services due to political ecologic forces that produce refugees; the breeding of disease in refugee camps due to the prevailing desperation and destitution; and the creation of an optimal environment for emergence and spread of disease due to the chaotic nature of war and violence that produces refugees. We argue in this paper that there is great potential of something more virulent than cholera and Ebola emerging and taking a big toll before being identified and controlled. We conclude by noting that once such a disease is out in the public rapid diffusion despite political boundaries is likely, a fact that has a direct bearing on global health. The extensive evidence presented in this paper of the overriding role of political factors in the refugee health problem calls for political reform and peace accords, engagement and empowerment of Pan-African organizations, foreign policy changes by Western governments and greater vigilance of non-governmental organizations (NGOs) in the allocation and distribution of relief aid.

Africa↗

PubMed1999

Disease and immunity in the pre-Spanish Philippines.

It is generally asserted that Filipino populations did not suffer the same demographic collapse that followed Spanish conquest in the Americas because they had previously acquired immunity to Old World diseases through trading contacts with Asia. This assertion is examined by trying to establish which diseases were present in the islands in pre-Spanish times and whether populations there could have acquired immunity to them. This is done through an analysis of the evidence for the presence of infections in China and Japan in particular and the existence of trading contacts with and between the Philippine islands. The likelihood of immunity being acquired is addressed first through a discussion of the physical and human geography of the islands and what is known of the epidemiology of individual diseases from modern scientific research. Second, it reviews evidence from early colonial documents and Filipino dictionaries for the presence and impact of Old World diseases in the early colonial period. The study suggests that Filipino populations had not acquired significant immunities to acute infections in pre-Spanish times, and that their limited demographic impact in the colonial period derived more from the particular geography of the islands. It suggests that in terms of its disease history, the Philippines had more in common with the Pacific islands than mainland Asia, and that the microbiological boundary between the Old World and the New is better conceived of as a broad zone.

China↗

PubMed1998

Therapeutic landscapes of the Jola, The Gambia, West Africa.

This paper contributes to the 'new' medical geography through its analysis of the therapeutic landscapes of the Jola of The Gambia. The paper advances the debate surrounding the conceptualization of medicine and health through a review of literature on African medicinal systems; it examines in detail the health care system of the Jola of The Gambia, documenting indigenous human and ethnoveterinary medical beliefs and practices and focusing in particular on the role of herbal medicine; and it discusses the interactions and links between indigenous medicine and biomedicine, thus demonstrating the importance of placing an understanding of health care systems in different places within an awareness of global power relations. The paper therefore links cultural perspectives with a political economy analysis, to highlight the importance of place and specificity of cultural context when investigating health care beliefs and practices. The intention of the paper is to present a theoretically informed empirical case study which reinforces the practical value of a 'new' medical geography.

Animals↗

PubMed2001

[Application behavior and disability in ambulatory care according to SGB XI. A structural regional approach].

A REGIONAL ANALYSIS: The target of this task undertaken by a geographer was an analysis according to limited regional areas, of application for and demands on benefits granted by the statutory social long-term care insurance body, and hence an interdisciplinary estimate. Definite differences between individual areas in Schleswig-Holstein were seen, and it was partly possible to explain why such differences exist. The infrastructure, the housing space ownership conditions and individual self-assessment are essential factors when applying for benefits. Identification of the geography of the relevant residential location was effected by the individual zip code. In 79.8% of the cases included in a random test the locations were clearly defined. The combination of geography and epidemiology enables a clear allocation of medical phenomena also for further research concerning differences between well-defined areas.

Activities of Daily Living↗

PubMed2006

Early maize (Zea mays L.) cultivation in Mexico: dating sedimentary pollen records and its implications.

A sedimentary pollen sequence from the coastal plain of Veracruz, Mexico, demonstrates maize cultivation by 5,000 years ago, refining understanding of the geography of early maize cultivation. Methodological issues related to bioturbation involved in dating that record combine with its similarity to a pollen sequence from the coastal plain of Tabasco, Mexico, to suggest that the inception of maize cultivation in that record occurred as much as 1,000-2,000 years more recently than the previously accepted 7,000 years ago. Our analysis thereby has substantive, theoretical, and methodological implications for understanding the complex process of maize domestication. Substantively, it demonstrates that the earliest securely dated evidence of maize comes from macrofossils excavated near Oaxaca and Tehuacán, Mexico, and not from the coastal plain along the southern Gulf of Mexico. Theoretically, that evidence best supports the hypothesis that people in the Southern Highlands domesticated this important crop plant. Methodologically, sedimentary pollen and other microfossil sequences can make valuable contributions to reconstructing the geography of early maize cultivation, but we must acknowledge the limits to precision that bioturbation in coastal lagoons imposes on the dating of such records.

Agriculture↗

PubMed1992

Origins of the Indo-Europeans: genetic evidence.

Two theories of the origins of the Indo-Europeans currently compete. M. Gimbutas believes that early Indo-Europeans entered southeastern Europe from the Pontic Steppes starting ca. 4500 B.C. and spread from there. C. Renfrew equates early Indo-Europeans with early farmers who entered southeastern Europe from Asia Minor ca. 7000 BC and spread through the continent. We tested genetic distance matrices for each of 25 systems in numerous Indo-European-speaking samples from Europe. To match each of these matrices, we created other distance matrices representing geography, language, time since origin of agriculture, Gimbutas' model, and Renfrew's model. The correlation between genetics and language is significant. Geography, when held constant, produces a markedly lower, yet still highly significant partial correlation between genetics and language, showing that more remains to be explained. However, none of the remaining three distances--time since origin of agriculture, Gimbutas' model, or Renfrew's model--reduces the partial correlation further. Thus, neither of the two theories appears able to explain the origin of the Indo-Europeans as gauged by the genetics-language correlation.

Blood Group Antigens↗

PubMedDate not supplied

Population structure and anthropometric variation in rural western Ireland: migration and biological differentiation.

Models of population structure can be investigated using data on anthropometric variation among local populations. Anthropometric data collected by Dupertuis and Dawson during the 1930s were analysed from 347 males and 261 females in 12 towns in three counties of western Ireland. We hypothesized that recent migration would decrease the degree of among-group variation. To test this hypothesis, two additional samples were created by excluding known inter-county migrants from both male and female samples. Based on ethnographic data, a fifth sample was created using unmarried females only, in order to control partially for local migration upon marriage. Univariate and multivariate measures of relative differentiation were developed to compare different levels of migration and differences among the sexes. We found that the degree of among-group variation decreased as the amount of migration increased, in accordance with spatial models of population structure. Using non-parametric correlations of geographic and anthropometric distance, the observed patterns of differentiation were closely related to geography, suggesting a spatial model of gene flow to be appropriate in interpreting among-group variation. The female samples showed greater differentiation and higher correlations with geography than the males. It seems that this results from the sensitivity of males to developmental and local environmental influences, causing an increase in the relative amount of within-group variation.

Age Factors↗

PubMed2000

Detecting the Geographical Pattern of Speciation from Species-Level Phylogenies.

We introduce a general approach for investigating the role of geography in speciation, based on analyzing the geography of sister clades across all nodes in a species-level phylogeny. We examine the predictions of allopatric, sympatric, and peripatric models of speciation in several animal groups, using patterns of range overlap and range size symmetry between sister clades. A simple model of cladogenesis incorporating random movements of species' ranges is used to illustrate the effects of range changes on expected patterns. We find evidence for a predominantly allopatric mode of speciation in our study groups, with sympatry arising through postspeciational range changes. In addition, we find that relatively recent speciation events are characterized by greater asymmetry in range size between sister clades than expected under our null models, providing potential support for the peripatric model of speciation. We discuss the possible confounding effects of postspeciational range changes on our conclusions.

biogeography↗

PubMed1986

The genetic structure of a tribal population, the Yanomama Indians. XV. Patterns inferred by autocorrelation analysis.

Fifteen allele frequencies have previously been determined for 50 villages of the Yanomama, an Amerindian tribe from southern Venezuela and northern Brazil. These frequencies were subjected to spatial autocorrelation analysis to investigate their population structure. There are significant spatial patterns for most allele frequencies. Clinical patterns, investigated by one-dimensional and directional spatial correlograms, were relatively few in number and were moderate in strength. Overall, however, there is a marked decline in genetic similarity with geographic distance. The results are compatible with a hierarchic population structure superimposed on the geography, and generated by a stochastic fission-fusion model of village propagation, followed by localized gene flow. Strong temporal autocorrelations of allele frequencies based on linguistic-historical distances representing time since divergence were also found. There appears to be a stronger relation between geography and linguistic-historical hierarchic subdivisions than between either feature and genetic distances. These findings confirm by different approaches the results of earlier analyses concerning the important roles of both stochastic and social factors in determining village allele frequencies and the occurrence within this tribe of some allele frequency clines most likely due to the operation of chance historical processes.

Alleles↗

PubMed1990

Geographic variation in human mitochondrial DNA from Papua New Guinea.

High resolution mitochondrial DNA (mtDNA) restriction maps, consisting of an average of 370 sites per mtDNA map, were constructed for 119 people from 25 localities in Papua New Guinea (PNG). Comparison of these PNG restriction maps to published maps from Australian, Caucasian, Asian and African mtDNAs reveals that PNG has the lowest amount of mtDNA variation, and that PNG mtDNA lineages originated from Southeast Asia. The statistical significance of geographic structuring of populations with respect to mtDNA was assessed by comparing observed GST values to a distribution of GST values generated by random resampling of the data. These analyses show that there is significant structuring of mtDNA variation among worldwide populations, between highland and coastal PNG populations, and even between two highland PNG populations located approximately 200 km apart. However, coastal PNG populations are essentially panmictic, despite being spread over several hundred kilometers. Highland PNG populations also have more mtDNA variability and more mtDNA types represented per founding lineage than coastal PNG populations. All of these observations are consistent with a more ancient, restricted origin of highland PNG populations, internal isolation of highland PNG populations from one another and from coastal populations, and more recent and extensive population movements through coastal PNG. An apparent linguistic effect on PNG mtDNA variation disappeared when geography was taken into account. The high resolution technique for examining mtDNA variation, coupled with extensive geographic sampling within a single defined area, leads to an enhanced understanding of the influence of geography on mtDNA variation in human populations.

Australia↗

PubMed2025

Isolation by distance promotes strain diversification in the wild mouse gut microbiota.

Bacterial species within the mammalian gut microbiota exhibit considerable strain diversity associated with both geography and host genetic ancestry. However, because geography and host ancestry are typically confounded, disentangling their contributions to the diversification of gut bacterial strains has remained challenging. Here, we show through joint profiling of gut bacterial and mitochondrial genomes from wild-living populations of deer mice (Peromyscus maniculatus) sampled across the United States that isolation by distance (IBD) drives gut bacterial strain diversification independently of the effects of host ancestry. Analyses revealed significant IBD in 27 predominant gut bacterial species, including members of the Muribaculaceae and Lachnospiraceae, but limited evidence for co-inheritance of gut bacterial genomes with mitochondria during the diversification of extant mouse populations. Gut bacterial species capable of forming spores exhibited reduced IBD independently of phylogenetic history, indicating that adaptations facilitating bacterial dispersal can mitigate the geographic structuring of strain diversity. These results show that the diversification of gut bacterial strains within rodent species has been mediated by geographic separation of host populations rather than host genealogical divergence.

biogeography↗

PubMed2000

Trapped rossby waves

The possibility of tidal dynamics at strictly imaginary Lamb parameters has been known for more than three decades. The present paper explores the prevailing physics in this parameter regime. To this end, basic features of the global circulation such as baroclinicity and geostrophy have to be incorporated into tidal dynamics. The tidal equations of the thermal wind are readily obtained in the framework of spherical bishallow water theory. Density surfaces of a circulation with available potential energy alter the spatial inhomogenities of the generic tidal problem. Wave dynamics in an inhomogeneous medium are characterized not only by a dispersion relation but also by a wave guide geography: significant wave amplitudes are trapped in specific regions of frequency-dependent width. As an inherently global issue, evaluation of the Rossby wave guide geography for a given circulation cannot rely on the familiar regional filters of tidal theory. On the global domain, the Rossby wave specification is given by the Margules filter. A thermal wind is stable against nondivergent Rossby wave disturbances. Rossby waves propagating with a geostrophic wind are governed by prolate dynamics (real Lamb parameters) while imaginary Lamb parameters emerge for the oblate dynamics of Rossby waves running against a geostrophic wind. Oblate Rossby wave dynamics include pole-centered wave guides and very low-frequency disturbances propagating eastward against a westward wind.

Journal Article↗