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PubMed2002

Sex-specific genetic differentiation and coalescence times: estimating sex-biased dispersal rates.

I derive the equilibrium values of sex-specific FST parameters, in an island model for a dioecious species with sex-biased dispersal and binomial distribution of family size before dispersal (as assumed in a Wright-Fisher population). I show that FST may take different values among males and among females whenever dispersal is a trait conditioned on gender. This has not always been recognized, because some models assumed that genes are sampled before dispersal. In particular, the ratios of sex-specific FST parameters evaluated after dispersal over FST evaluated before dispersal are simple functions of sex-specific dispersal rates. Therefore, a simple moment-based estimator of sex-specific dispersal rate is proposed. This method is based on the comparison of FST estimated before and after dispersal and assumes equilibrium between migration and drift. I evaluate this method through stochastic simulations for a range of sex-specific dispersal rates and sampling effort (sample size, number of loci scored).

Animals↗
PubMed2000

Cattle breed-variation in infestation by the horn fly Haematobia irritans.

A study was carried out to assess the resistance of pure and cross-bred groups of cattle to the horn fly Haematobia irritans (Linnaeus) (Diptera: Muscidae) in northern Argentina. Pure-bred cattle were Criolla, Iberian Bos taurus Linnaeus (Artiodactyla: Bovidae) and Nellore, Bos indicus Linnaeus (Artiodactyla: Bovidae). Cross-bred cattle were Hereford, British B. taurus (34%) X Nellore (66%) and Hereford (66%) X Nellore (34%). All were heifers and animals were maintained in two groups, each containing a mixture of pure and cross-breeds. The lowest fly numbers were found on Criolla heifers and the highest on Hereford X Nellore cross-breeds. However, it could not be determined from this study whether this was a consequence of breed and/or size, as Criolla heifers were lighter than the corresponding Hereford X Nellore heifers. Fly numbers on the heifers followed an approximately negative binomial distribution. However, the ranking of individual animals in their level of infestation within subgroups was not consistent. Hence, culling the most infested heifers on any given date would at best give only a small improvement in H. irritans control.

Animals↗
PubMed2003

An estimation of the entomological inoculation rate for Ifakara: a semi-urban area in a region of intense malaria transmission in Tanzania.

An entomological study on vectors of malaria and their relative contribution to Plasmodium falciparum transmission in the semi-urban area of Ifakara, south-eastern Tanzania, was conducted. A total of 32 houses were randomly sampled from the area and light trap catches (LTC) performed in one room in each house every 2 weeks for 1 year. A total of 147 448 mosquitoes were caught from 789 LTC; 26 134 Anopheles gambiae s.l., 615 A. funestus, 718 other anophelines and 119 981 culicines. More than 60% of the total A. gambiae s.l. were found in five (0.6%) LTCs, with a maximum of 5889 caught in a single trap. Of 505 A. gambiae s.l. speciated by polymerase chain reaction, 91.5% were found to be A. arabiensis. Plasmodium falciparum sporozoite enzyme-linked immunosorbent assay tests were performed on 10 108 anopheles mosquitoes and 39 (0.38%) were positive. Entomological inoculation rate (EIR) estimates were generated using a standard method and an alternative method that allows the calculation of confidence intervals based on a negative binomial distribution of sporozoite positive mosquitoes. Overall EIR estimates were similar; 31 vs. 29 [95% confidence interval (CI): 19, 44] infectious bites per annum, respectively. The EIR ranged from 4 (95% CI: 1, 17) in the cool season to 108 (95% CI: 69, 170) in the wet season and from 54 (95% CI: 30, 97) in the east of the town to 15 (95% CI: 8, 30) in the town centre. These estimates show large variations over short distances in time and space. They are all markedly lower than those reported from nearby rural areas and for other parts of Tanzania.

Animals↗
PubMed1986

Thersitina gasterostei (Pagenstecher, 1861) (Copepoda: Ergasilidae) infecting the stickleback Pungitius pungitius L. at Chalk Marshes, Gravesend, Kent.

10-spined sticklebacks, Pungitius pungitius, taken from a drainage dyke at Chalk Marshes, Kent, between October 1979 and July 1980 were infested with adult females of the parasitic copepod Thersitina gasterostei. Relative density of the overwintering parasite population fell during the winter months to a minimum in April; however during this winter period the proportion of ovigerous females rose, reaching 100% in April. Young infective adults were first seen in May, and the peak of infection by the first summer generation occurred in June. The parasite was found to be overdispersed within the host population: in 8 of 10 monthly samples the negative binomial distribution was a good model for the observed data. Relative density was related to host length in only 3 of the 10 samples. Evidence is presented to suggest that infected fish are more likely than non-infected fish to recruit young parasite.

Animals↗
PubMed1993

Proliferation of follicular cells and the effect of FSH on the onset of follicular growth in the ovary of 30-day old rabbits studied by continuous labelling with 3H-thymidine.

The ovary of the 30-d-old rabbit contains only small follicles with, at most, 3 or 4 layers of cells. We have estimated the labelling index of the follicular cells only from follicles having at least one labelled cell and using a zero truncated binomial distribution. The labelling index of the follicular cells of such follicles was weak and enlarged with the number of cells. It never exceeded 20%. Repeated injections of tritiated thymidine up to 8 times entailed a significant increase of the labelling index even for the smallest follicles. The labelling index of follicles was significantly increased 30 h after 1 injection of FSH (2 mg P-FSH). These results confirmed that the fraction of follicular cells that proliferate was low in the young rabbit ovary and the doubling time of the cells was large and that at this age, FSH increased the proliferation of cells.

Animals↗
PubMed1976

Risk of congenital abnormality after inadvertent rubella vaccination of pregnant women.

The risk to a fetus after rubella vaccination of its mother is unknown. The Center for Disease Control has compiled information from the pregnancies of 343 women inadvertently given rubella vaccine shortly before or after conception. The pregnancies of 145 women were terminated by therapeutic abortion, and rubella vaccine virus was recovered from the products of conception of nine women, including six of the 28 known to be seronegative to rubella at the time of vaccination. None of the 172 infants carried to term had either clinical or serologic evidence of rubella infection, including 38 infants of women known to be susceptible and 12 additional women estimated to be susceptible at the time of rubella vaccination. On the basis of the binomial distribution, the maximum risk of fetal infection after maternal rubella vaccination is between 5 and 10 per cent. The actual risk is probably less.

Abortion, Therapeutic↗
PubMed2004

Intermolecular energy transfer involving an iridium complex studied by a combinatorial method.

A recently developed combinatorial method utilizing angular dependence of evaporation rate was used to create compositional spread thin film libraries of Tris(2-pyridin-2-yl-indolizino[3,4,5-ab] isoindole-C(1), N('))iridium(III) [Ir(pin)(3)] and 4,4(')-N,N(')-dicarbazol-biphenyl (CBP) composite, with the molar fraction of Ir(pin)(3) complex varying in the 0.0003 Ir(pin)(3) energy transfer proceeds by the Forster mechanism with the Forster radius of 30 A. The CBPxIr(pin)(3) composite has the highest photoluminescence quantum efficiency approximately 0.95, for chi(Ir(pin)(3) )=0.03 and is characterized by a structured green emission (lambda(max)=538 nm) originating from the ligand-centered (pi-pi(*))(3) state of the Ir(pin)(3) complex. On the contrary, the PL spectra of Ir(pin)(3) bulk are characterized by a weak red emission (lambda(max)=673 nm) attributed to the lowest metal-to-ligand charge transfer state. A statistical analysis based on a binomial distribution indicates that the emission from the (pi-pi(*))(3) state is quenched in Ir(pin)(3) molecules that are in a direct contact with each other.

Journal Article↗
PubMed2006

R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.

A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

Journal Article↗
PubMed2001

Teaching an abbreviated impression technique for complete dentures in an undergraduate dental curriculum.

STATEMENT OF PROBLEM: Traditional methods for teaching complete denture fabrication are time-consuming, difficult to master, and not used by many general practitioners. PURPOSE: This study compared the efficacy of traditional denture fabrication techniques with a more abbreviated method in a dental school setting. MATERIAL AND METHODS: A retrospective record review of 80 completely edentulous patients treated by predoctoral dental students was completed. Forty patients were treated with traditional denture techniques; the other 40 patients were treated with an abbreviated method. The data abstracted included the number of visits to completion and the number of postinsertion visits and relines required within the first 3 months after delivery. A Wilcoxon rank sum test was performed to determine statistical significance between the groups with regard to number of visits for fabrication and postinsertion adjustments. A test for a difference in proportions by using the normal approximation to the binomial distribution was performed for statistical analysis of the incidence of relines. RESULTS: The abbreviated denture technique resulted in a statistically significant difference in the number of visits for fabrication (P<.01) and postinsertion adjustments (P<.05.) There was no difference (P=.39) in the number of relines between the 2 groups. CONCLUSION: Teaching the abbreviated complete denture technique in an undergraduate dental clinic decreased the number of appointments necessary to complete denture therapy without increasing the number of adjustments or reline procedures.

Appointments and Schedules↗
PubMed1989

The risk of stroke with occlusion of the internal carotid artery.

Reports of all cervicocephalic arteriograms (n = 1836) performed at one institution during a 10-year period were reviewed and the patients were classified into three groups according to the indication for arteriography. Group I included all patients with symptoms or findings compatible with occlusive disease of the carotid or vertebral artery (n = 806). Group II included patients with cerebrovascular symptoms unrelated to carotid or vertebral disease (e.g., patients with subarachnoid hemorrhage) (n = 367). Group III consisted of patients with no evidence of cerebrovascular disease (e.g., patients with primary and metastatic brain tumors) (n = 663). One hundred ten atherosclerotic occlusions of the internal carotid artery (ICA) were found in 106 patients in group I. Fifty-one percent of these patients had a history of stroke before arteriography, 24% had transient ischemic attacks (TIAs) or amaurosis fugax (AF), and 12% had nonhemispheric symptoms. Only 13% (1.7% of group I patients) were without symptoms. Ninety-one percent of the strokes and 75% of the TIAs or AF were ipsilateral to the ICA occlusion. Seventy-six percent of patients with stroke and 80% with ipsilateral TIAs or AF vs only 29% of patients without symptoms had contralateral stenosis of 60% diameter reduction or greater (p less than 0.003). No occlusions of the ICA occurred in groups II or III. Three hundred forty-six patients in groups II and III were more than 60 years of age. Assuming either Poisson or binomial distributions, the incidence of silent ICA occlusion in the population at large older than 60 years was estimated at less than 1% (p less than 0.03).

Adult↗
PubMed1995

min K channels form by assembly of at least 14 subunits.

Injection of min K mRNA into Xenopus oocytes results in expression of slowly activating voltage-dependent potassium channels, distinct from those induced by expression of other cloned potassium channels. The min K protein also differs in structure, containing only a single predicted transmembrane domain. While it has been demonstrated that all other cloned potassium channels form by association of four independent subunits, the number of min K monomers which constitute a functional channel is unknown. In rat min K, replacement of Ser-69 by Ala (S69A) causes a shift in the current-voltage (I-V) relationship to more depolarized potentials; currents are not observed at potentials negative to 0 mV. To determine the subunit stoichiometry of min K channels, wild-type and S69A subunits were coexpressed. Injections of a constant amount of wild-type mRNA with increasing amounts of S69A mRNA led to potassium currents of decreasing amplitude upon voltage commands to -20 mV. Applying a binomial distribution to the reduction of current amplitudes as a function of the different coinjection mixtures yielded a subunit stoichiometry of at least 14 monomers for each functional min K channel. A model is presented for how min K subunits may form a channel.

Animals↗
PubMed2000

The dominant negative LQT2 mutation A561V reduces wild-type HERG expression.

HERG(1) K(+) channel mutations are responsible for one form of dominantly inherited long QT syndrome (LQT). Some LQT mutations exert a dominant negative effect on wild-type current expression. To investigate mechanisms of dominant-negative behavior, we co-expressed wild-type HERG with the A561V mutant in mammalian cells. Transfection with various cDNA ratios produced HERG K(+) current densities that approached a predicted binomial distribution where mutant and wild-type subunits co-assemble in a tetramer with nearly complete dominance. Using C terminus myc-tagged wild-type HERG we specifically followed the mutant's effect on full-length wild-type HERG protein expression. Co-expression with A561V reduced the abundance of full-length wild-type HERG protein comparable to the current reduction. Reduction of wild-type protein was due to decreased synthesis and increased turnover. Conditions facilitating protein folding (growth at 30 degrees C, or in 10% glycerol) resulted in partial rescue from the dominant effect, as did the 26 S proteosome inhibitor ALLN. Thus, for A561V, dominant negative effects result from assembly of wild-type subunits with mutant very early in production leading to rapid recognition of mutant channels and targeting for proteolysis. These results establish protein misfolding, cellular proofreading, and bystander involvement as contributing mechanisms for dominant effects in LQT2.

Animals↗
PubMed2006

Stable isotope tagging of epitopes: a highly selective strategy for the identification of major histocompatibility complex class I-associated peptides induced upon viral infection.

Identification of peptides presented in major histocompatibility complex (MHC) class I molecules after viral infection is of strategic importance for vaccine development. Until recently, mass spectrometric identification of virus-induced peptides was based on comparative analysis of peptide pools isolated from uninfected and virus-infected cells. Here we report on a powerful strategy aiming at the rapid, unambiguous identification of naturally processed MHC class I-associated peptides, which are induced by viral infection. The methodology, stable isotope tagging of epitopes (SITE), is based on metabolic labeling of endogenously synthesized proteins during infection. This is accomplished by culturing virus-infected cells with stable isotope-labeled amino acids that are expected to be anchor residues (i.e. residues of the peptide that have amino acid side chains that bind into pockets lining the peptide-binding groove of the MHC class I molecule) for the human leukocyte antigen allele of interest. Subsequently these cells are mixed with an equal number of non-infected cells, which are cultured in normal medium. Finally peptides are acid-eluted from immunoprecipitated MHC molecules and subjected to two-dimensional nanoscale LC-MS analysis. Virus-induced peptides are identified through computer-assisted detection of characteristic, binomially distributed ratios of labeled and unlabeled molecules. Using this approach we identified novel measles virus and respiratory syncytial virus epitopes as well as infection-induced self-peptides in several cell types, showing that SITE is a unique and versatile method for unequivocal identification of disease-related MHC class I epitopes.

Amino Acid Sequence↗
PubMed2006

Occupancy-abundance models for predicting densities of three leaf beetles damaging the multipurpose tree Sesbania sesban in eastern and southern Africa.

Mesoplatys ochroptera Stål, Exosoma and Ootheca spp. seriously damage sesbania, Sesbania sesban (L.) Merril, a multipurpose leguminous tree widely used in tropical agroforestry. This is discouraging farmers from expanding the planting of sesbania in various agroforestry systems in eastern and south-central Africa. Rapid methods are needed for estimation of population densities of these beetles for decision making in pest management. A study was conducted with the objectives of determining the existence of any positive relationship between the occupancy and abundance of Mesoplatys, Exosoma and Ootheca and determining the model that best predicts abundance from occupancy for rapid estimation of population densities. The Poisson model assuming spatial randomness, the negative binomial distribution (NBD) model assuming spatial aggregation, the Nachman model without any distribution assumption, and a General model incorporating spatial variance-abundance and occupancy-abundance relationships were fitted to data on adult M. ochroptera, Exosoma and Ootheca from western Kenya, southern Malawi and eastern Zambia. Very strong variance to abundance relationships were observed in the spatial pattern of all three beetles. The occupancy-abundance relationships were also positive and strong in all beetles. The occupancy and abundance predicted by the four models were closest to the observed at lower densities compared with higher beetle densities. At higher population densities, the NBD and the General model gave better fit for M. ochroptera and Exosoma. For Ootheca populations, the Poisson and NBD models gave better fit at higher population densities. The relationships established here can be used as guide to estimate beetle densities for decision-making in pest management.

Africa↗
PubMed1996

Patterns of health-care utilization and morbidity in a rural community near Lahore, Pakistan.

Patterns of health-care utilization and of morbidity were investigated in a demographically defined community: the 1400 inhabitants of a rural village near Lahore, Pakistan. The data collected, by semi-monthly clinic surveys from February 1982 to January 1983, showed that 42% of the study population sought health care during the year-long study period, between one and 10 (mean 2.1) times each. Females attended the clinics twice as often as males. The 1193 person-visits that were recorded at the field clinics yielded a total of 1354 cases of various diseases. The cumulative number of clinic-visits per person fitted a negative binomial distribution, indicating that health problems were concentrated in a small portion of the population. When the patients were classified according to the International Classification of Diseases, the most common disease category was that of the respiratory system (27.6%), followed by infectious and parasitic diseases (18.7%), diseases of the skin (13.7%) and those of the nervous system and sense organs (10.9%). Classification of the cases by single disease condition indicated that diarrhoea, helminthiasis, malaria, anaemia, conjunctivitis, bronchitis, coryza, pharyngitis, tonsillitis, dyspepsia and pyoderma were the most common diseases. In view of the fact that infectious diseases continue to be a major public health problem in rural Pakistan, the need for a sound health policy that is primarily focused on preventive medicine, especially health education, is apparent.

Adolescent↗
PubMed1993

Determination of cell dose-survival relationships from endpoint dilution assays.

Methods for fitting radiation survival curves to data obtained from endpoint-dilution assays are described. It is shown that for functional forms such as the linear-quadratic model the problem can be recast as a generalized linear model (GLM) and the data fitted using standard software. For functional forms which are not capable of being linearized, such as the multitarget model, the direct maximum likelihood (DML) techniques of Thames et al. (1986) can be used. Both these techniques produce exact maximum likelihood parameter estimates. Compared with the weighted least-squares (WLS) approach traditionally employed, these approaches avoid the need to approximate the binomial distribution of the number of negative wells by a normal distribution, and avoid the biases introduced by the need for arbitrary treatment of data points with 0 or 100% negative wells. The results of fittings using the novel GLM and DML approaches are compared with those obtained using the WLS method on a large series of datasets. For most datasets the WLS method performs well, compared with the exact method, but in a small number of cases the WLS predicted parameter estimates can be in error by as much as their estimated standard errors. A method for the use of a concurrent control to correct for interexperimental variation is outlined. The methods have been implemented in a Fortran computer program using the NAG subroutine library.

Cell Survival↗
PubMed2006

Air particulate pollution due to bushfires and respiratory hospital admissions in Brisbane, Australia.

To examine the impact of bushfire smoke on hospital admission rates for respiratory disease, a time series study was conducted in Brisbane, Australia. Data on particles of 10 microns or less in aerodynamic diameter (PM10) per cubic metre, bushfire events, meteorological conditions, and daily respiratory hospital admissions were obtained for the period of 1 July 1997 to 31 December 2000. A generalized linear model with the negative binomial distribution was used to estimate the effects of bushfire smoke on respiratory hospital admissions. The results of this study show that daily respiratory hospital admission rates consistently increased with increasing levels of PM10 for both bushfire and non-bushfire periods. This relationship appeared stronger during bushfire periods than non-bushfire periods, especially for the current day. The findings suggest that bushfire smoke was statistically significantly associated with an increased risk of respiratory hospital admissions in Brisbane (p < 0.05). The health impact assessment needs to be considered in the control and management of bushfires.

Air Pollutants↗
PubMed1999

Type I error and the power of the s-test: old lessons from a new, analytically justified statistical test for phylogenies.

We present a new procedure for assessing the statistical significance of the most likely unrooted dichotomous topology inferrable from four DNA sequences. The procedure calculates directly a P-value for the support given to this topology by the informative sites congruent with it, assuming the most likely star topology as the null hypothesis. Informative sites are crucial in the determination of the maximum likelihood dichotomous topology and are therefore an obvious target for a statistical test of phylogenies. Our P-value is the probability of producing through parallel substitutions on the branches of the star topology at least as much support as that given to the maximum likelihood dichotomous topology by the aforementioned informative sites, for any of the three possible dichotomous topologies. The degree of statistical significance is simply the complement of this P-value. Ours is therefore an a posteriori testing approach, in which no dichotomous topology is specified in advance. We implement the test for the case in which all sites behave identically and the substitution model has a single parameter. Under these conditions, the P-value can be easily calculated on the basis of the probabilities of change on the branches of the most likely star topology, because under these assumptions, each site can become informative independently from every other site; accordingly, the total number of informative sites of each kind is binomially distributed. We explore the test's type I error by applying it to data produced in star topologies having all branches equally long, or having two short and two long branches, and various degrees of homoplasy. The test is conservative but we demonstrate, by means of a discreteness correction and progressively assumption-free calculations of the P-values, that (1) the conservativeness is mostly due to the discrete nature of informative sites and (2) the P-values calculated empirically are moreover mostly quite accurate in absolute terms. Applying the test to data produced in dichotomous topologies with increasing internal branch length shows that, despite the test's "conservativeness," its power is much higher than that of the bootstrap, especially when the relevant informative sites are few.

Likelihood Functions↗