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PubMed2003

[Spatial diversity index analysis on wildlife habitat pattern change in the Liaohe Delta].

Based on the study of land cover change in the Liaohe Delta with GIS and RS, the wildlife habitat pattern was described quantitatively, and the pattern change between 1988 and 1998 was analyzed with spatial diversity index. The results showed that the wildlife habitat pattern had an obvious change during the ten years caused by natural and human disturbance. The area of suitable habitat(Sd > or = 0.35) was becoming smaller and more fragmented, with a deteriorated quality. It was proved that spatial diversity index could reflect the habitat suitability of wildlife, and describe the habitat spatial pattern explicitly. This study would provide a scientific basis for protecting wild animals and their habitats.

Animals↗
PubMed2005

Managing molecular diversity.

The present work provides an overview of the different methods used in molecular diversity analysis. Issues like identifying voids in proprietary databases, reducing the number of redundancies present in databases, or designing focused libraries by grouping compounds similar to a template with the aim to fine tune its properties, are potent diversity analysis tools that may be used to optimize molecules based on their properties and specifically, to speed up the process of lead discovery and optimization. The present work describes first methods that are used to describe molecular systems. This is followed by a section devoted to describe different measures of similarity between molecules, to finish with a description of different methods used to select subsets molecules according to the constraints imposed. The final section deals with the validation of these methods, based on different studies available in the literature.

Cluster Analysis↗
PubMed1998

A picture of locational--occupational diversity: an analysis of the needs of rural and remote healthcare workers when writing RHSET applications. Rural Health Support Education and Training.

Methods for meeting the research needs of rural/remote health workers have been assessed on the assumption that these workers form a seemingly homogeneous group. This paper provides a picture of locational-occupational diversity not previously considered when addressing the needs of rural health workers writing research and project grant submissions. Rural/remote health workers and researchers were surveyed about their needs when seeking assistance with the development, implementation and evaluation of funded project/program proposals. New South Wales respondents were differentiated according to five geographical locations and 10 occupational categories. The results suggest that geographical location and occupational category are major factors in determining research requirements for rural/remote health workers and researchers, and should be considered when identifying barriers to the development and implementation of research projects in rural/remote health care issues. Those health workers most isolated required access to resource information and research and grant writing skills development, while researchers in metropolitan areas were more inclined to seek funding information and general assistance. Those in occupational categories who do not generally receive research and grant writing skills training are less likely to attract funding than their more 'academic' counterparts.

Attitude of Health Personnel↗
PubMed2026

No association between alcohol consumption and hip osteoarthritis: a diverse national analysis of 87,585 adults from the "All of Us" research program.

INTRODUCTION: Hip osteoarthritis (OA) is estimated to affect 62.6 million individuals by 2050. A probable link exists between alcohol use and hip OA. However, the results are inconsistent, and the relationship between alcohol and hip OA remains speculative. To address these gaps, this study aimed to utilize the diverse, nationally representative All of Us Research Program dataset to explore the association between alcohol consumption and hip OA. METHODS: This retrospective case-control study utilized data from the All of Us Research Program Controlled Tier Dataset v8. 17,517 hip OA cases and 70,068 controls were identified. A 1:4 case-to-control matching ratio was applied based on age and sex. Alcohol use frequency was categorized into five levels: Never, Monthly or Less, Two to Four Times per Month, Two to Three Times per Week, and Four or More Times per Week. Multivariable logistic regression models evaluated the association between alcohol use frequency and hip OA after adjusting for demographic and clinical variables. RESULTS: Multivariable analysis found that alcohol use frequency was not significantly associated with hip OA. Compared to never users, participants with low (OR 0.98, 95% CI 0.93-1.04, P = 0.583), moderate (OR 0.99-1.01, all P > 0.05), and high (OR 1.02, 95% CI 0.95-1.09, P = 0.599) levels of alcohol consumption had no statistically significant differences in odds of hip OA. Female sex, Asian race, diabetes, hypertension, hyperlipidemia, and nicotine dependence increased the odds of hip OA. CONCLUSION: Any level of alcohol consumption was not significantly associated with the odds of hip OA. This study adds valuable insight to the current body of conflicting evidence. Further prospective studies appear warranted to shed light on the long-term effects of different alcoholic beverages on different joints. Key Points • This study found no significant association between any degree of alcohol consumption and the odds of developing hip osteoarthritis. • Utilizing data from 87,585 adults in the NIH "All of Us" Research Program, this is the first study to analyze this relationship in a large, nationally representative population. • The research provides clarity to previously conflicting literature by demonstrating that alcohol lacks a clear harmful or protective effect on the clinical course of the disease. • The analysis highlights that independent risk factors such as Asian race, nicotine dependence, and components of metabolic syndrome increase the odds of hip osteoarthritis.

Humans↗
PubMed2005

Putting microarrays in a context: integrated analysis of diverse biological data.

In recent years, multiple types of high-throughput functional genomic data that facilitate rapid functional annotation of sequenced genomes have become available. Gene expression microarrays are the most commonly available source of such data. However, genomic data often sacrifice specificity for scale, yielding very large quantities of relatively lower-quality data than traditional experimental methods. Thus sophisticated analysis methods are necessary to make accurate functional interpretation of these large-scale data sets. This review presents an overview of recently developed methods that integrate the analysis of microarray data with sequence, interaction, localisation and literature data, and further outlines current challenges in the field. The focus of this review is on the use of such methods for gene function prediction, understanding of protein regulation and modelling of biological networks.

Algorithms↗
PubMed2003

Characterization of biological diversity through analysis of discrete cranial traits.

In the present study, the frequency distributions of 20 discrete cranial traits in 70 major human populations from around the world were analyzed. The principal-coordinate and neighbor-joining analyses of Smith's mean measure of divergence (MMD), based on trait frequencies, indicate that 1). the clustering pattern is similar to those based on classic genetic markers, DNA polymorphisms, and craniometrics; 2). significant interregional separation and intraregional diversity are present in Subsaharan Africans; 3). clinal relationships exist among regional groups; 4). intraregional discontinuity exists in some populations inhabiting peripheral or isolated areas. For example, the Ainu are the most distinct outliers of the East Asian populations. These patterns suggest that founder effects, genetic drift, isolation, and population structure are the primary causes of regional variation in discrete cranial traits. Our results are compatible with a single origin for modern humans as well as the multiregional model, similar to the results of Relethford and Harpending ([1994] Am. J. Phys. Anthropol. 95:249-270). The results presented here provide additional measures of the morphological variation and diversification of modern human populations.

Anthropology, Physical↗
PubMed1982

A genetical analysis of diversity and asymmetry in finger ridge counts.

The genetics of asymmetry and diversity of finger ridge counts in man has been examined by jointly regressing the individual counts of each hand on to the mean values summed over left and right hands in a sample of twins. The resulting asymmetry terms are largely under environmental control but with a small significant genetic component. The diversity items show a larger degree of genetic control with a suggestion of dominance or additive X additive epistasis.

Dermatoglyphics↗
PubMed2002

The palaeoecology of the Upper Ndolanya Beds at Laetoli, Tanzania.

The palaeoecology of the fauna from the Ndolanya Beds, Laetoli, Tanzania, has been analysed to reconstruct the environment of this 2.6 Ma site. Community profiles have been constructed in relation to three variables that carry ecological meaning: body weight, locomotor adaptations and feeding preferences. Comparing the similarities and differences in the structure of the fossil faunas with those of modern environments allows us to draw inferences about palaeoenvironmental conditions, and this is based on a comparative dataset of 15 modern environments (44 localities) covering a wide range of climatic and ecological conditions across Asia, Africa and Central America. In addition, 16 fossil sites in East and South Africa have been analysed in the same way, and both sets of comparative data have been used as the basis for comparison with an ecological diversity analysis of the fauna from the Upper Ndolanya Beds. The Ndolanya fauna is characterized by a predominance of medium to large sized terrestrial and herbivorous species. There is evidence of taphonomic bias that eliminated many of the smaller species. A comparison of multivariate analyses of 23 selected modern localities conducted both with and without the small species included, indicates that the loss of these species does not adversely influence the results of an ecological diversity analysis. The evidence suggests that at the time of the deposition of the Ndolanya Beds the Laetoli region was a semi-arid bushland. This is considerably drier and more open than is suggested for the earlier Laetolil Beds.

Animals↗
PubMed2002

[Genetic analysis on diversity of reproductive modes of silver crucian carp inferred by transferrin and isozyme markers].

Silver crucian carp (Carassius auratus gibelio) has been known for its gynogenetic reproduction. In this paper, eggs from clone F of gynogenetic silver crucian carp were inseminated respectively by sperms of clone D, clone A and common carp, and polymorphic patterns of transferrin and isozymes of the produced three offspring FD, FA and FL were studied comparatively to explore the diversity in reproductive modes of silver crucian carp. As control, zymograms of FL progenies exhibited a maternally clonal inheritance, and gynogenesis was reconfirmed. However, differentiation of morphs and electrophoretic patterns was both observed among the FD progenies, and detection of bands specific for the clone F or clone D in some FD individuals urged the occurrence of recombination. Furthermore, extreme linkage disequilibrium for different protein loci suggested that linkage groups composed of different genes might function as the fundamental unit in the recombination. With respect to FA group, phenotypes of parental clones were both detected in the F2 generation (FA x FA progenies) while only maternal phenotypes were detected in the F1 generation. It appeared that both the parental chromosome sets could be transmitted to the offspring but expression of paternal genes were fundamentally upset in the F1 generation because of incompatibility of the parental genes. Generally, genetic analysis of FD and FA offspring primarily exhibited a particular syngamy for silver crucian carp. Besides the clonal reproduction of gynogenesis, syngamy could provide opportunities of recombination for silver crucian carp, which might remove some genetic loads from the genome and introduce new genotypes. Diversity in reproductive modes might play an important role in ecological adaptation of silver crucian carp.

Animals↗
PubMed1985

Clonal analysis of diversity in the BSp73 rat tumor.

By implantation of BSp73 ascites cells in a subcutaneous site and subsequent subcutaneous passage of either the local tumor node or metastatic lung tissue, variants were obtained which differed with respect to morphology and to metastatic capacity. The highly metastasizing variant ASML showed spherical morphology in culture, while the nonmetastatic variant AS showed adhesion and spreading. Upon cloning it was observed that colonies with fully expressed morphotypes were readily obtained from solid tissue of both variants. Parental ascites as well as the tumor line derived from the primary solid tumor gave rise to stable expression of either morphotype only after prolonged culturing. Mixing of established clones did not result in an interclonal adaptation of growth rates in vivo. Further characterization of variants AS and ASML revealed marked differences in the outer cell surface. Adhesion of AS cells onto plastic was found to be mediated by fibronectin, laminin and 4 out of 5 collagen types. ASML cells showed adhesion only with collagen type III at higher concentrations. Cytogenetic analysis revealed that the adaptation of BSp73 cells to ascitic growth ultimately led to an increase in chromosome numbers, and this was conserved in ASML cells (modal number 63, range 49-74). AS cells on the other hand showed a modal number of 47 (range 45-49). The chromosome count distribution was rather narrow in ascites cells in vivo, but it was very broad in clones derived thereof, indicating that diversity was obtained in culture rather than in vivo. The data are compatible with the assumption that the nonmetastatic variant was not preexisting in BSp73 ascites but represents a stable phenotype which infrequently arises in a particular microenvironment by chromosome loss from a hyperdiploid parental population.

Animals↗
PubMed2001

Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms.

We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations.

Africa↗
PubMed2004

Analysis of diversity among 3-chlorobenzoate-degrading strains of Rhodopseudomonas palustris.

The phenotypic and genetic characteristics of 14 strains of the purple nonsulfur bacterium Rhodopseudomonas palustris were studied to assess diversity within this species. While all strains had certain phenotypic characteristics in common, including the ability to metabolize benzoate and degrade 2- and 3-chlorobenzoate, there were also significant differences among the strains such as the rate of growth in media containing benzoate as a carbon source. Genetic characterization of the strains revealed there were three divergent lineages in the species. Based on 16S rRNA gene sequences, the 14 strains could be grouped into three distinct clusters (A, B, and C), and this clustering was congruent with that based on gene sequences of form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Although BOX-PCR genomic DNA fingerprints of all 14 strains exhibited differences, analysis of the fingerprint images and UPGMA/product-moment analysis of similarities showed there were three groupings that were entirely consistent with clusters based on other characteristics of the strains. Thus, regardless of the method of analysis used, strains in groups A and B consistently clustered together and were separate from those of group C. These results suggest that strains in groups A-B and C represent phylogenetically related clones that have diverged from one another. This indicates that at least three lineages of Rhodopseudomonas palustris exist among the strains included in this study, and that each may be particularly well adapted to a distinct ecological niche.

Base Sequence↗
PubMed2001

[Analysis of diversity of autosomal-recessive diseases in Russian populations].

The diversity of autosomal recessive (AR) diseases was studied in six Russian regions: the Kirov, Kostroma, and Bryansk oblasts; Adygea Republic; Krasnodar krai, and Marii El Republic (in the latter region, the Mari and Russian ethnic groups were studied separately). In total, more than 1.5 million people were studied. The spectrum of the AR diseases included 101 nosological forms; the total number of the affected subjects was 942. For all diseases, the prevalence rate in the region where they were found and the mean prevalence rate in the total population studied were calculated. Only seven AR diseases had prevalence rates of 1:50,000 or higher; however, this group contained about 50% of the patients. About half of the AR diseases (66) had an extremely low prevalence rate (1:877,483). Eleven diseases exhibit local accumulation. Accumulation of some or other diseases was only observed in four out of seven populations studied (Marii El, Adygea, and the Kirov and Bryansk oblasts). To determine the cause of the local accumulation of some diseases in populations, correlation analysis of the dependence of accumulation of hereditary diseases on the genetic structure of the populations studied was performed. The accumulation coefficients for AR and autosomal dominant (AD) diseases and the mean values of random inbreeding (Fst) in individual districts were calculated for all populations studied. The coefficients of the Spearman rank correlation between the accumulation coefficient and random inbreeding (Fst) were 0.68 and 0.86 for the AD and AR diseases, respectively. The correlation between the accumulation of AD and AR diseases was 0.86. The relationships found indicate that the diversity of AD and AR diseases, as well as the genetic load, distinctly depended on the population genetic structure and were largely determined by genetic drift.

Genes, Recessive↗
PubMed2006

Layered expression scanning: multiplex molecular analysis of diverse life science platforms.

With the advent of the genomic era, there is an increasing use of high-throughput techniques to generate transcriptome- and proteome-based profiles of biological specimens. Each of these methodologies offers a unique window into the inner workings of cell and tissue samples. Often, these studies generate large data sets and provide investigators with a substantial number of candidate dysregulated genes and pathways. Follow-up studies are then undertaken to independently validate the original findings and to extend the study to additional samples or more quantitative measurements. Although there are several methods available for these validation efforts, they are often tedious and laborious to perform; thus, additional tools that enable this task are needed. One such approach is layered expression scanning (LES), a new technique developed via a cooperative research and development agreement (CRADA) between the National Cancer Institute and 20/20 GeneSystems, Inc. The technique is based on the movement of biomolecules from a two-dimensional life science platform (histological tissue section, electrophoresis gel, multi-well plate, etc.) through a set of analysis membranes while maintaining the original distribution pattern of the molecules. Each membrane measures one analyte and the data are then mapped back to the original specimen, permitting each component of the life science platform to be studied in detail. LES can be configured in several different ways depending on the goals of the study. In this review, we summarize the use of the LES technique for a variety of biological applications.

Membranes, Artificial↗
PubMed1993

Genome macrorestriction analysis of diversity and variability of Pseudomonas aeruginosa strains infecting cystic fibrosis patients.

Genome macrorestriction fingerprinting with XbaI and DraI was used to analyze the relatedness of 166 Pseudomonas aeruginosa isolates collected from 31 cystic fibrosis patients over a 1- to 20-month period and to correlate their genotype with patterns of resistance to 14 antimicrobial agents. Quantitative comparison of intra- and interpatient similarities of P. aeruginosa macrorestriction patterns disclosed two discrete ranges that clearly discriminated subclonal variation (> 80% relatedness) and clonal diversity (10 to 70% relatedness). Cloning-derived mutants exhibited up to 20% divergence of genomic macrorestriction patterns during the course of chronic colonization of individual patients. Change of susceptibility to multiple antimicrobial agents developed in 50% of sequential pairs of isolates from individual patients. Only 19% of these susceptibility changes were attributable to strain substitution, while the majority (56%) of resistance changes were associated with minor genomic variations of a persistent strain. Sixty-six percent of patients harbored one strain, and 33% carried two strains. Three common strains colonized 5 (28%) of 18 patients attending a cystic fibrosis clinic, and another two strains colonized two patient pairs (31%) of 13 patients staying at a rehabilitation center, suggesting potential cross-infection in these settings. By indexing regional polymorphisms throughout the chromosome structure, macrorestriction analysis can monitor subclonal evolution of P. aeruginosa and identify isogenic resistance mutants. Quantitative macrorestriction fingerprinting enables discrimination between clonal variants and clones of distinct origins and should therefore provide a reliable tool for investigating the mode of acquisition of P. aeruginosa in cystic fibrosis patients.

Cross Infection↗
PubMed1994

Analysis of diversity of T cell antigen receptor genes using polymerase chain reaction and sequencing gel electrophoresis.

A sensitive, highly resolvable, and quantitative method was designed to analyse the diversity of polymerase chain reaction (PCR)-amplified transcripts which possess length polymorphism. A reverse transcriptase-PCR technique was used to amplify rearranged T cell antigen receptor (TCR) transcripts isolated from human blood. Oligonucleotide primers specific for conserved TCR V and C region sequences were used in PCR, with one of the primers end-labeled with 32P. Amplified cDNA products were analysed by polyacrylamide sequencing gel electrophoresis with an M13mp18 sequencing ladder as a size marker. 32P-labeled products were detected by either autoradiography or PhosphorImager. The method allowed determination of the sizes of PCR products with the precision of one nucleotide. The resolution using this technique was much higher than by electrophoresis in agarose gel with ethidium bromide staining. The sizes of PCR products determined by sequencing gel electrophoresis were consistent with the lengths of nucleotide sequences obtained after subcloning PCR products in competent bacterial cells. Analysis of PCR products by sequencing gel electrophoresis was more rapid and as accurate as nucleotide sequence analysis in determining the relative ratios of TCR mRNA in mixtures of T cell clones. The method is applicable for analysis of both rearranged TCR and immunoglobulin genes.

Base Sequence↗