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PubMed1998

Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model.

In this paper, a maximum likelihood estimator of population divergence time based on the infinite sites model is developed. It is demonstrated how this estimator may be applied to obtain maximum likelihood estimates of the topology of population phylogenies. This approach addresses several classical problems occurring in the inference of the phylogenetic relationship of populations, most notably the problem of shared ancestral polymorphisms. The method is applied to previously published data sets of human African populations and of Caribbean hawksbill turtles.

Animals↗
PubMed1992

Predicting all causes mortality in the general population as a function of blood pressure and smoking habits measured in population samples: a pilot study. Research Group ATS-RF2.

Nine population samples of mean aged 40-59, for a total of 1777 individuals drawn from nine health units, were examined in 1978-79 for the measurement of some risk factors possibly related to total mortality. The analysis evaluated the possible relationship between blood pressure levels and smoking habits measured in the population samples and the official death rates covering the period 1980-82 in the health units from which the samples were drawn. The analysis was conducted in a direct way but also by the help of a risk function linking blood pressure and smoking habits as obtained from another Italian population sample. The cograduation test between mean blood pressure in the nine areas and total mortality was 0.58 (linear correlation 0.57); the cograduation test was -0.70 for non-smokers, 0.62 for ex-smokers, 0.50 for present smokers (linear correlation of -0.27, 0.29 and 0.14 respectively). The death rates estimated by the risk function (Cox model) tended to overestimate the death rates from 5 to 64% (average 36.3%). The cograduation test between expected and observed death rates was 0.56 (linear correlation coefficient 0.66). Some limitations of this pilot study are largely explained by the small size of the sample and by the need to use a risk function provided by another population sample.

Adult↗
PubMed1983

Detection of surface differences between two closely related cell populations by partitioning isotopically labeled mixed cell populations in two-polymer aqueous phases. II. A correction.

The partition behavior of cells in dextran-poly(ethylene glycol) aqueous phases (i.e., the cells' relative affinity for the top or bottom phase or their adsorption at the interface) is greatly dependent on the polymer concentrations and ionic composition and concentration. Appropriate selection of phase system composition permits detection of differences in either charge-associated or lipid-related surface properties. We have now developed a method that can reveal differences by partitioning that fall within experimental error if one were to compare countercurrent distribution (CCD) curves of two closely related cell populations run separately. One cell population is isotopically labeled in vitro (e.g., with 51Cr-chromate) and is mixed with an excess of the unlabeled cell population with which it is to be compared. The mixture is subjected to CCD and the relative specific radio-activities are determined through the distribution. As control we also examine a mixture of labeled cells and unlabeled cells of the same population. The feasibility of this method was established by use of cell mixtures the relative partition coefficients of which were known. The procedure was then used to test for human erythrocyte subpopulations. 51Cr-chromate-labeled human young or old red blood cells were mixed with unfractionated erythrocytes and subjected to CCD in a phase system reflecting charge-associated properties. It was found that older cells had a high, young cells (probably only reticulocytes) a low partition coefficient. Because of the small differences involved these results were not previously obtained.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations.

To understand the types of gene action controlling seven quantitative traits in rice, we carried out quantitative trait locus (QTL) mapping in order to distinguish between the main-effect QTLs (M-QTLs) and digenic epistatic QTLs (E-QTLs) responsible for the trait performance of 254 recombinant inbred lines (RILs) from rice varieties Lemont/Teqing and two backcross hybrid (BCF1) populations derived from these RILs. We identified 44 M-QTL and 95 E-QTL pairs in the RI and BCF1 populations as having significant effects on the mean values and mid-parental heterosis of heading date, plant height, flag leaf length, flag leaf width, panicle length, spikelet number and spikelet fertility. The E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both the RI and BCF1 populations. In both BCF1 populations, over-dominant (or under-dominant) loci were more important than additive and complete or partially dominant loci for M-QTLs and E-QTL pairs, thereby supporting prior findings that overdominance resulting from epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice.

Chromosome Mapping↗
PubMed1999

Use of 16S-rRNA Based Techniques to Investigate the Ecological Succession of Microbial Populations in the Immature Lamb Rumen: Tracking of a Specific Strain of Inoculated Ruminococcus and Interactions with Other Microbial Populations in Vivo.

The establishment of microorganisms in the rumen is a critical step if rumen manipulation is to be accomplished by use of microbial inoculants. Microbial populations in the maturing rumen undergo successional changes and, while in a state of flux, provide a possible opportunity for the introduction of specific strains of bacteria. While the rumen of the young lamb was maturing, we measured changes in several microbial populations with 16S-rRNA specific oligonucleotides: Rumincoccus, Fibrobacter, eukaryotes, Gram-positive bacteria, the Bacteroides-Porphromonas-Prevotella group, and anaerobic rumen fungi. In this study we repeatedly dosed 15 lambs with approximately 3.4 x 10(8) to 0.8 x 10(9) Ruminococcus cells dose(-1), twice a week, for 7 wk from 23 d to 63 d of age. Of the five Ruminococcus strains dosed (R. albus SY3 and AR67, and R. flavefaciens Y1, LP9155, and AR72) the most specific primers (based on 16S rDNA) were obtained for strain SY3. There was an increase in the eukaryotic population during dosing, and it was hypothesized that protozoal predation contributed to the disappearance of strain SY3. At the end of dosing PCR amplification showed that SY3 were approximately 10(9) cells ml(-1), but decreased to below the detection limit of the PCR system (8.6 x 10(4) ml(-1)) within 28 d postdosing. These experiments showed that fibrolytic populations increased significantly (P < 0.1) above the controls during the dosing period and were elevated for several days postdosing. This suggests that dosing of highly fibrolytic bacteria makes more of the fiber available to other organisms able to degrade fiber, and in so doing increases the overall fibrolytic activity of the rumen. Examination of the succession of gram-positive bacteria and the Bacteroides-Porphromonas-Prevotella group showed a decline in relative abundance as the lambs matured.

Journal Article↗
PubMed1992

Analyses of affinity distributions within polyclonal populations of antigen-specific antibodies. Evaluation of their accuracy in population detection using monoclonal antibodies.

The potential of an ELISA based detection of affinity distributions within polyclonal populations of antigen-specific serum antibodies was assessed by analyzing defined probes composed of monoclonal antibodies (MAb). In a competitive binding ELISA in which the concentration of antigen in the liquid phase and the solid phase was varied, we analyzed mixtures containing defined percentage compositions of MAb exhibiting apparent affinity constants (aK) between 3 x 10(6) and 2 x 10(9) M-1 for Pseudomonas aeruginosa exotoxin A. Our results indicate that the detectability of antibody populations depends on the antigen concentrations in the solid phase and on the affinity distribution of the probe to be analyzed. In wells coated with high antigen concentrations, antibody titers reflected antibody concentrations, whereas at low antigen concentrations antibody titers primarily reflect antibody affinities. Independent of their affinities, subpopulations less than 10% could not be detected. Low affinity antibodies were preferentially underestimated. The degree of distortion depended on the composition of the probe to be analyzed. In general, the higher the absolute and the relative affinity of a population, the stronger was its capacity to interfere with the detection of other populations. As a consequence, the heterogeneity of affinity distributions in polyclonal samples may be substantially underestimated. The experiments reported provide guidelines for an optimal design and an adequate interpretation of ELISA based qualitative analyses of polyclonal antibody samples.

ADP Ribose Transferases↗
PubMed1989

The thymus has two functionally distinct populations of immature alpha beta + T cells: one population is deleted by ligation of alpha beta TCR.

During T cell development, the processes of selection and tolerance act on the universe of expressed T cell receptors in the thymic cortex to form the repertoire of mature T cells that will respond to foreign antigen in the context of self-MHC in that animal. We have subdivided the cortical thymocytes into three functionally distinct populations: one population which is antigen-receptor negative, a second population which is antigen-receptor positive and is resistant to deletion by signaling through the antigen receptor, and a third population which is also antigen-receptor positive but is sensitive to deletion. These results have implications for the cellular compartments in which positive and negative selection occur and for the biochemical mechanisms that mediate selection and tolerance.

Animals↗
PubMed1993

Behavioral parameters of the spatial memory correlate with the potentiation of the population spike, but not with the population excitatory postsynaptic potential, of the CA1 region in rat hippocampal slices.

Rats were tested for spatial performance in a water maze with further in vitro investigation of short-term and long-term potentiation (STP and LTP) in the CA1 region of the hippocampus. Recordings of the population spike in stratum pyramidale and population excitatory postsynaptic potential (EPSP) in stratum radiatum were made with extracellular electrodes after stimulation of the radiatum and oriens inputs in the region. It was found that for both inputs, STP and LTP of the population spike amplitude correlated with behavioral parameters of memory: latency of reaching the hidden platform (escape latency) and percent of time which the animal spent inside the quadrant with the platform. Potentiation of the initial slope of EPSP, in contrast, did not correlate with these parameters. These data support the hypothesis that hippocampal LTP may underlie spatial performance and show that potentiation of the output characteristic of the hippocampus (population spike), but not of the EPSP, is a physiological correlate for spatial memory.

Action Potentials↗
PubMed1995

D1S80 VNTR locus genotypes in population of south Poland; meta-analysis pointer to genetic disequilibrium of human populations.

A highly variable number of tandem repeats (VNTRs) in a human locus D1S80 can prove to be useful for forensic science purposes. As with other genetic polymorphisms, a database of a local population allelic frequencies is needed to ensure that no departure from genetic equilibrium exists. DNA from the locus D1S80 was amplified by polymerase chain reaction (PCR) and analyzed by horizontal PAGE followed by silver staining. Samples from 133 unrelated inhabitants of Southern Poland were examined. The amplified fragment length polymorphism (AMP-FLP) analysis of the D1S80 locus demonstrated 21 alleles and heterozygosity of 0.85%. Out of the 231 possible genotypes, 47 were observed. The results were compared to the published D1S80 population studies and a meta-analysis of the genotype frequencies was performed. The G statistics revealed a deviation from genetic equilibrium in the Spanish population. Replicated goodness of fit tests showed highly significant heterogeneity of genotype distribution between tested populations. Therefore, interpretation of the casework on the basis of D1S80 locus typing may be biased by interpopulation differences.

Adult↗
PubMed2004

Risk factors associated with habitual snoring and sleep-disordered breathing in a multi-ethnic Asian population: a population-based study.

INTRODUCTION: There is scant data on the risk factors of sleep-disordered breathing (SDB) in the general population in Asian countries. METHODS: Cross-sectional survey of a random population sample of 2298 adults aged 20-75 years, stratified by gender, ethnicity (Chinese, Malay and Indian) and age. An interviewer-administered questionnaire was used to elicit responses to questions on daytime somnolence and nocturnal events. Three categories of SDB were defined for analysis: habitual snoring; apnoeic snoring (SDB I); and apnoeic snoring or snoring with diurnal hypersomnia (SDB II). RESULTS: Snoring was reported by 201 persons (6.8%), SDB-I in 44 (1.9%) and SDB-II in 112 (4.9%) in the sample. The adjusted odds ratio (95% C.I.) of association with snoring were: male gender, 3.79 (2.69-5.33); older age (>60 years old), 2.15 (1.41-3.29); Indian versus Chinese, 1.54 (1.05-2.25); family history, 2.21 (1.56-3.12); obesity (BMI>30), 2.64 (1.62-4.30); neck circumference (>40 cm), 2.57 (1.59-4.11); and cigarette smoking, 2.05 (1.21-3.45). The risk factors for SDB were similar to that of snoring. CONCLUSION: Population risk factors associated with habitual snoring and SDB in Singapore are largely similar to those reported in other populations. Differential risks underscore the importance of ethnicity in determining the burden of SDB.

Adult↗
PubMed2004

A comparison of ovarian cancer treatments: analysis of utility assessments of ovarian cancer patients, at-risk population, general population, and physicians.

OBJECTIVES: Perceptions of the severity of chemotherapy-related toxicity differ among physicians, ovarian cancer patients, at-risk individuals, and persons in the general population. In this study, we elicited assessments of toxicity from women with ovarian cancer, women at increased risk of developing ovarian cancer, women in the general population, and gynecologic oncologists. METHODS: Thirty-nine ovarian cancer patients, fifteen women at increased risk, thirty-nine women at baseline risk, and eleven gynecologic oncologists completed utility assessment surveys. RESULTS: There was good face validity to the utility exercise as assessments of health states. Health states with toxicity were consistently associated with less favorable assessments than the health states with no toxicity. The ovarian cancer patients as a group and the women at risk for the development of ovarian cancer viewed health states with toxicity similarly and more favorably than women in the general population. However, patient assessments varied, with the most favorable assessment of life with toxicity being reported from individuals who had experienced such toxicity. Physician assessments of the impact of toxicity on overall health status were most similar to those obtained from patients who had experienced moderate to severe toxicity, and were more favorable than those elicited from patients who had not experienced any toxicity. CONCLUSIONS: Assessments of the impact of chemotherapy-related toxicity vary depending on the perspective of the individual responding to these questions. In discussing ovarian cancer treatments with at-risk women and the general population, concerns over treatment-related toxicity are likely to be greater than those expressed by persons who are more familiar with the actual occurrence of such events and therapeutic preferences may be affected as a result.

Adult↗
PubMed2006

Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus.

The Cape hake species, Merluccius capensis and Merluccius paradoxus are the most important resource of the South African and Namibian demersal fishery, but it is unclear whether there is a single population of each shared by both countries. We analysed the population structure and evolutionary history of these two species using the variable 5' region of the mtDNA control region for 311 specimens of M. capensis and 333 specimens of M. paradoxus sampled between Lüderitz (southern Namibia) to south of Cape Point (South Africa). 107 haplotypes for M. capensis and eight haplotypes for M. paradoxus were recovered. AMOVA and pairwise Phi(st) analyses revealed no structure in M. capensis, however significant genetic differentiation between Namibian and South African 'populations' was detected for M. paradoxus. This was only restricted to mature fish older than 3 and 4 years and not for juvenile fish younger than 3 years. Analyses reveal that M. capensis has undergone population expansion (Fu's Fs=-26.65, P<0.001), possibly within the last 4500-23,000 years, whereas M. paradoxus has not. Our study highlights the utility of genetic markers to unravel the evolutionary history of sympatric species, as well as addressing management issues within regions where commercially valuable fish stocks are shared between nations.

Animals↗
PubMed2001

Differential effects of pentylenetetrazol-kindling on long-term potentiation of population excitatory postsynaptic potentials and population spikes in the CA1 region of rat hippocampus.

The effects of pentylenetetrazol-kindling on synaptic transmission and the effectiveness of &theta; pattern primed-bursts (PBs) for the induction of long-term potentiation (LTP) of population excitatory postsynaptic potentials and population spikes were investigated in hippocampal CA1 of pentylenetetrazol-kindled rats. Experiments were carried out in the control and kindled animals at two post-kindling periods, i.e., 48-144 h (early phase) and 30-33 days (long lasting phase). Field potentials (population excitatory postsynaptic potentials, pEPSPs; and population spikes, PSs) were recorded at the stratum radiatum and the stratum pyramidale following stimulation of the stratum fibers, respectively. PBs were delivered to stratum fibers and PB potentiation was assessed. The results showed that 48-144 h after kindling there was no significant difference for pEPSP slope and PS amplitude between two groups. But at 30-33 days after kindling, the pEPSP slope in the stratum radiatum of kindled animals decreased, whereas the amplitude of PSs increased compared to those of controls. Shortly after kindling, control animals had normal LTP of pEPSP slope and PS amplitude in response to PBs, but kindled rats lack LTP of pEPSP slope and PBs induced LTP of PS amplitude in most of kindled animals. In 30-33 days after kindling, PB potentiation was not observed in the stratum radiatum of kindled animals but PBs induced LTP of PS amplitude, which was significantly greater than that of control animals. The effect is compatible with the hypothesis, which postulates kindling-associated functional deficit in hippocampus, especially CA1, as an explanation for the behavioral deficits seen with the kindling model of epilepsy.

Action Potentials↗
PubMed2003

Linking lysosomal biomarker and population responses in a field population of Aporrectodea caliginosa (Oligochaeta) exposed to the fungicide copper oxychloride.

The effects of the fungicide copper oxychloride on a field population of the earthworm Aporrectodea caliginosa were investigated. Changes were monitored in earthworm numbers and biomass, copper concentrations in soil and earthworms, and neutral red retention times (NRRTs) of coelomocytes. The aim was to establish whether the cellular responses could be linked to changes at the population level. Results indicated that there was a significant (P<0.05) impact on worm density and biomass on the treated plots 6 months after spraying with the fungicide stopped. NRRTs of treated earthworms were significantly lower after one spraying when earthworms had elevated concentrations of copper in their body tissues. Six months after spraying stopped, copper levels in both soil and earthworm tissues declined significantly, but the earthworm numbers and biomass were still significantly lower in the treated plots. This indicated that the effects of the copper oxychloride exposure manifested at a much later stage at the population level, than on NRRT. We conclude that the decrease in NRRTs, which preceded the decrease in both earthworm biomass and numbers, may have predictive value as a biomarker of impending population changes.

Animals↗
PubMed2000

Social determinants of health in Canada's immigrant population: results from the National Population Health Survey.

As part of the Metropolis project--a large-scale investigation of immigration and integration, including well-being of immigrants in a number of areas of social life--in this paper we investigate the social determinants of health in Canada's immigrant population using Canada's National Population Health Survey (NPHS). Specifically, we examine differences in health status and health care utilization between immigrants and non-immigrants, immigrants of European and non-European origin, and immigrants of < 10 years and > 10 years' residence in Canada. We also examine social determinants of health care utilization and health status in immigrants and non-immigrants, and evaluate the utility of large-scale, national databases for these purposes. Our conceptual approach draws upon a 'population health' perspective, which suggests that the most important antecedents of human health status are not medical care inputs and health behaviours (smoking, diet, exercise, etc.), but rather social and economic characteristics of individuals and populations. We find no obvious, consistent pattern of association between socio-economic characteristics and immigration characteristics on the one hand, and health status on the other, in the NPHS data. This does not mean that socio-economic factors in Canada are not influential in shaping immigrants' health status. In fact, the results of the logistic regression models calculated for immigrants and non-immigrants on four outcome variables in this study suggest that socio-economic factors are more important for immigrants than non-immigrants, although in ways that defy a simple explanation. The complexity of immigrants' experiences, combined with the inherent limitations of cross-sectional survey data are discussed as major limitations to this kind of research.

Adult↗
PubMed2001

Evaluating the impact of population changes in diet, physical activity, and weight status on population risk for colon cancer (United States).

OBJECTIVE: To estimate the effects of observed population-level changes in risk factors on population risk and incidence of disease. METHODS: Trends in a set of risk factors for colon cancer (vegetable intake, red meat intake, alcohol consumption, physical activity levels, and weight status) were modeled for the US adult population over the years 1975-1995 and combined with relative risk estimates from epidemiologic studies and a probability distribution for the induction period to estimate the percentage change in incidence rates from 1985 to 1995 due to the five risk factors. A sensitivity analysis was performed to account for imprecision related to estimates of trends in behavior and epidemiologic risk. RESULTS: Increased vegetable intake and decreased intakes of red meat and alcohol reduced risk, while reduced physical activity and increased body mass index increased risk for colon cancer. When all five factors were considered together, change in the average population relative risk was small and the risk factors accounted for little of the recently observed decline in incidence. CONCLUSIONS: Although these factors have the potential to greatly affect risk of colon cancer and incidence rates, little of that potential was realized since adverse trends neutralized what progress had been made in the areas of vegetables, red meat, and alcohol consumption.

Adult↗
PubMed1999

The use of population attributable risk to estimate the impact of prevention and early detection of type 2 diabetes on population-wide mortality risk in US males.

The Population Attributable Risk (PAR) represents the proportion of the deaths (in a specified time) in the whole population that may be preventable if a cause of mortality were totally eliminated. This population-based measure was used to assess the potential impact of three public health interventions for type 2 diabetes (early detection + standard therapy; early detection + intensive therapy; and primary prevention) on the mortality risk from all causes and from cardiovascular (CVD) diseases. Potential reduction in mortality risks for several levels of compliance or implementation (25%, 50%, 75%, 100%) for each intervention were also estimated. Results suggest that among males aged 45-74 years, the interventions may have greater population-wide impact on total deaths among black males, and greater impact on the CVD deaths among white males. Overall, primary prevention (reduction in all-cause mortality 6.2-10.0%, and CVD mortality 7.9-9.0%) may offer greater marginal benefit than screening and early treatment (reduction in all-cause mortality 3.5-8.3%, and CVD mortality 2.8-8.6%). Often the question facing policy makers is not simply whether to but how much of an intervention is worth implementing? Estimated benefits for various intensities of intervention (as provided) may be useful to assess the likely marginal benefits of each intervention, and can be especially useful if combined with estimated marginal costs.

Black or African American↗
PubMed1999

Mating systems of diploid and allotetraploid populations of tragopogon (Asteraceae). I. Natural populations

Although polyploidy is a significant force in the diversification of plants, the evolutionary consequences of polyploidization are not thoroughly understood. One possible consequence of polyploidy predicted by most population genetic theories is that the newly synthesized polyploid will self-fertilize at a greater rate than its diploid progenitors. To test for increased selfing rates in a polyploid, the mating systems of the allotetraploid Tragopogon mirus and one of its diploid progenitors, T. dubius, were compared. Tragopogon mirus is a recently derived species that arose sometime in the last 80 years and thus provides an opportunity to probe how quickly a shift in outcrossing rates might occur. Based on analyses of variation in maternal plants and their progeny arrays, the two tetraploid populations surveyed have higher outcrossing rates than the two diploid populations. This result is the opposite of that predicted by population genetic theory. This discrepancy between theoretical and empirical results may result from bias in the genetic sample, traits in the natural histories of the taxa involved or a lack of sufficient time since the formation of the polyploid (80 years or 40-80 generations) for a shift towards increased selfing to have occurred. Alternatively, the partial dominance model of inbreeding depression typically applied to polyploids may not be appropriate; the overdominance model predicts outcrossing rates in diploids and their tetraploid derivatives that are consistent with those observed in T. dubius and T. mirus.

Journal Article↗