Transient dominance in a central African rain forest

The large-crowned emergent tree Microberlinia bisulcata dominates rain forest groves at Korup National Park, Cameroon, along with two codominants, Tetraberlinia bifoliolata and T. korupensis. M. bisulcata has a pronounced modal size frequency distribution around 110 cm stem diameter: its recruitment potential is very poor. It is a long-lived light-demanding species, one of many found in African forests. Tetraberlinia species lack modality, are more shade tolerant, and recruit better. All three species are ectomycorrhizal. M. bisulcata dominates grove basal area, even though it has similar numbers of trees (≥50 cm stem diameter) as each of the other two species. This situation presented a conundrum that prompted a long-term study of grove dynamics. Enumerations of two plots (82.5 and 56.25 ha) between 1990 and 2010 showed mortality and recruitment of M. bisulcata to be very low (both rates 0.2% per year) compared with Tetraberlinia (2.4% and 0.8% per year), and M. bisulcata grows twice as fast as the Tetraberlinia. Ordinations indicated that these three species determined community structure by their strong negative associations while other species showed almost none. Ranked species abundance curves fitted the Zipf-Mandelbrot model well and allowed “overdominance” of M. bisulcata to be estimated. Spatial analysis indicated strong repulsion by clusters of large (50 to <100 cm) and very large (≥100 cm) M. bisulcata of their own medium-sized (10 to <50 cm) trees and all sizes of Tetraberlinia. This was interpreted as competition by M. bisulcata increasing its dominance, but also inhibition of its own replacement potential. Stem coring showed a modal age of 200 years for M. bisulcata, but with large size variation (50–150 cm). Fifty-year model projections suggested little change in medium, decreases in large, and increases in very large trees of M. bisulcata, accompanied by overall decreases in medium and large trees of Tetraberlinia species. Realistically increasing very-large-tree mortality led to grove collapse without short-term replacement. M. bisulcata most likely depends on climatic events to rebuild its stands: the ratio of disturbance interval to median species' longevity is important. A new theory of transient dominance explains how M. bisulcata may be cycling in abundance over time and displaying nonequilibrium dynamics.

Time to renal disease and end-stage renal disease in PROFILE: a multiethnic lupus cohort.

BACKGROUND: Renal involvement is a serious manifestation of systemic lupus erythematosus (SLE); it may portend a poor prognosis as it may lead to end-stage renal disease (ESRD). The purpose of this study was to determine the factors predicting the development of renal involvement and its progression to ESRD in a multi-ethnic SLE cohort (PROFILE). METHODS AND FINDINGS: PROFILE includes SLE patients from five different United States institutions. We examined at baseline the socioeconomic-demographic, clinical, and genetic variables associated with the development of renal involvement and its progression to ESRD by univariable and multivariable Cox proportional hazards regression analyses. Analyses of onset of renal involvement included only patients with renal involvement after SLE diagnosis (n = 229). Analyses of ESRD included all patients, regardless of whether renal involvement occurred before, at, or after SLE diagnosis (34 of 438 patients). In addition, we performed a multivariable logistic regression analysis of the variables associated with the development of renal involvement at any time during the course of SLE.In the time-dependent multivariable analysis, patients developing renal involvement were more likely to have more American College of Rheumatology criteria for SLE, and to be younger, hypertensive, and of African-American or Hispanic (from Texas) ethnicity. Alternative regression models were consistent with these results. In addition to greater accrued disease damage (renal damage excluded), younger age, and Hispanic ethnicity (from Texas), homozygosity for the valine allele of FcgammaRIIIa (FCGR3A*GG) was a significant predictor of ESRD. Results from the multivariable logistic regression model that included all cases of renal involvement were consistent with those from the Cox model. CONCLUSIONS: Fcgamma receptor genotype is a risk factor for progression of renal disease to ESRD. Since the frequency distribution of FCGR3A alleles does not vary significantly among the ethnic groups studied, the additional factors underlying the ethnic disparities in renal disease progression remain to be elucidated.

Origins and evolution of VNTR loci: The apolipoprotein B 3$\sp\prime$ VNTR

I studied the apolipoprotein (apo) B 3$\sp\prime$ variable number tandem repeat (VNTR) and did computer simulations of the stepwise mutation model to address four questions: (1) How did the apo B VNTR originate? (2) What is the mutational mechanism of repeat number change at the apo B VNTR? (3) To what extent are population and molecular level events responsible for the determination of the contemporary apo B allele frequency distribution? (4) Can VNTR allele frequency distributions be explained by a simple and conservative mutation-drift model? I used three general approaches to address these questions: (1) I characterized the apo B VNTR region in non-human primate species; (2) I constructed haplotypes of polymorphic markers flanking the apo B VNTR in a sample of individuals from Lorrain, France and studied the associations between the flanking-marker haplotypes and apo B VNTR size; (3) I did computer simulations of the one-step stepwise mutation model and compared the results to real data in terms of four allele frequency distribution characteristics.^ The results of this work have allowed me to conclude that the apo B VNTR originated after an initial duplication of a sequence which is still present as a single copy sequence in New World monkey species. I conclude that this locus did not originate by the transposition of an array of repeats from somewhere else in the genome. It is unlikely that recombination is the primary mutational mechanism. Furthermore, the clustered nature of these associations implicates a stepwise mutational mechanism. From the high frequencies of certain haplotype-allele size combinations, it is evident that population level events have also been important in the determination of the apo B VNTR allele frequency distribution. Results from computer simulations of the one-step stepwise mutation model have allowed me to conclude that bimodal and multimodal allele frequency distributions are not unexpected at loci evolving via stepwise mutation mechanisms. Short tandem repeat loci fit the stepwise mutation model best, followed by microsatellite loci. I therefore conclude that there are differences in the mutational mechanisms of VNTR loci as classed by repeat unit size. (Abstract shortened by UMI.) ^

Population genetics of VNTR loci and their applications in evolutionary studies

Variable number of tandem repeats (VNTR) are genetic loci at which short sequence motifs are found repeated different numbers of times among chromosomes. To explore the potential utility of VNTR loci in evolutionary studies, I have conducted a series of studies to address the following questions: (1) What are the population genetic properties of these loci? (2) What are the mutational mechanisms of repeat number change at these loci? (3) Can DNA profiles be used to measure the relatedness between a pair of individuals? (4) Can DNA fingerprint be used to measure the relatedness between populations in evolutionary studies? (5) Can microsatellite and short tandem repeat (STR) loci which mutate stepwisely be used in evolutionary analyses?^ A large number of VNTR loci typed in many populations were studied by means of statistical methods developed recently. The results of this work indicate that there is no significant departure from Hardy-Weinberg expectation (HWE) at VNTR loci in most of the human populations examined, and the departure from HWE in some VNTR loci are not solely caused by the presence of population sub-structure.^ A statistical procedure is developed to investigate the mutational mechanisms of VNTR loci by studying the allele frequency distributions of these loci. Comparisons of frequency distribution data on several hundreds VNTR loci with the predictions of two mutation models demonstrated that there are differences among VNTR loci grouped by repeat unit sizes.^ By extending the ITO method, I derived the distribution of the number of shared bands between individuals with any kinship relationship. A maximum likelihood estimation procedure is proposed to estimate the relatedness between individuals from the observed number of shared bands between them.^ It was believed that classical measures of genetic distance are not applicable to analysis of DNA fingerprints which reveal many minisatellite loci simultaneously in the genome, because the information regarding underlying alleles and loci is not available. I proposed a new measure of genetic distance based on band sharing between individuals that is applicable to DNA fingerprint data.^ To address the concern that microsatellite and STR loci may not be useful for evolutionary studies because of the convergent nature of their mutation mechanisms, by a theoretical study as well as by computer simulation, I conclude that the possible bias caused by the convergent mutations can be corrected, and a novel measure of genetic distance that makes the correction is suggested. In summary, I conclude that hypervariable VNTR loci are useful in evolutionary studies of closely related populations or species, especially in the study of human evolution and the history of geographic dispersal of Homo sapiens. (Abstract shortened by UMI.) ^

Evaluating gillnetting protocols to characterize lacustrine fish communities

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70 m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.

The Kosice meteorite fall: Recovery and strewn field

We provide the circumstances and details of the fireball observation, search expeditions, recovery, strewn field, and physical characteristics of the Kosice meteorite that fell in Slovakia on February 28, 2010. The meteorite was only the 15th case of an observed bolide with a recovered mass and subsequent orbit determination. Despite multiple eyewitness reports of the bolide, only three videos from security cameras in Hungary were used for the strewn field determination and orbit computation. Multiple expeditions of professionals and individual searchers found 218 fragments with total weight of 11.3 kg. The strewn field with the size of 593 km is characterized with respect to the space distribution of the fragments, their mass and size-frequency distribution. This work describes a catalog of 78 fragments, mass, size, volume, fusion crust, names of discoverers, geographic location, and time of discovery, which represents the most complex study of a fresh meteorite fall. From the analytical results, we classified the Kosice meteorite as an ordinary H5 chondrite.

Theoretical and experimental studies of linkage disequilibrium in human populations

Linkage disequilibrium (LD) is defined as the nonrandom association of alleles at two or more loci in a population and may be a useful tool in a diverse array of applications including disease gene mapping, elucidating the demographic history of populations, and testing hypotheses of human evolution. However, the successful application of LD-based approaches to pertinent genetic questions is hampered by a lack of understanding about the forces that mediate the genome-wide distribution of LD within and between human populations. Delineating the genomic patterns of LD is a complex task that will require interdisciplinary research that transcends traditional scientific boundaries. The research presented in this dissertation is predicated upon the need for interdisciplinary studies and both theoretical and experimental projects were pursued. In the theoretical studies, I have investigated the effect of genotyping errors and SNP identification strategies on estimates of LD. The primary importance of these two chapters is that they provide important insights and guidance for the design of future empirical LD studies. Furthermore, I analyzed the allele frequency distribution of 26,530 single nucleotide polymorphisms (SNPs) in three populations and generated the first-generation natural selection map of the human genome, which will be an important resource for explaining and understanding genomic patterns of LD. Finally, in the experimental study, I describe a novel and simple, low-cost, and high-throughput SNP genotyping method. The theoretical analyses and experimental tools developed in this dissertation will facilitate a more complete understanding of patterns of LD in human populations. ^

The identification of child abuse in Harris County in 1998

Characteristics of child abuse cases are not well known. In this study I collected data on 70 child abuse cases that were reported to Children's Protective Services in Harris County in 1998. The purpose of this study was to determine the factors in Harris County that lead to the identification of physical and sexual abuse. In order to answer the questions of who, what, where and when relative to the discovery of abuse I applied the same questionnaire (see Appendix) to each of 35 Sexual Abuse case reports and to each of 35 Physical Abuse/Neglect case reports. Answers to the first four questions were arranged by frequency distribution to show the predominant reporter, the 10 most common indicators, the most common locale, and the most frequent timing. Tables of the age, sex, and ethnicity of the children indicate the identity of those whose victimization was most reported. In addition the relationship between the form questions and the characteristics of the children was explored. A comparison of Sexual Abuse cases with Physical Abuse/Neglect cases was conducted and the results were analyzed and recorded in the Tables. ^ Child maltreatment often has negative short and long term effects on children's mental health and development. Suicide, violence, delinquency, drug and alcohol abuse and other forms of criminality are frequently child abuse related. Early detection and treatment helps to alleviate the myriad mental and physical ailments that untreated victims present as adults. This translates into medical dollar savings. ^ The long term objectives of my research were to reduce the number of undetected and unreported child abuse cases in Harris County by formulating better educational programs and literature for medical professionals and other personnel who are in contact with children. ^

Bayesian models for the analysis of genetic structure when populations are correlated

Motivation: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. Results: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to over-estimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework.

School screening for tuberculosis in high risk areas of Texas

Screening for latent tuberculosis infection (LTBI) is an integral component of an effective tuberculosis control strategy, but one that is often relegated to the lowest priority. In a state with higher than national average rates of tuberculosis, due consideration should be given to LTBI screening. Recent large scale contact investigations in the middle school of Del Rio, Texas, raised questions about the status of school screening for LTBI. An evidence based approach was used to evaluate school screening in high risk areas of Texas. A review of the literature revealed that the current recommendations for LTBI screening in children is based on administration of a risk factor questionnaire that should be based on the four main risk factors for LTBI in children that have been identified. Six representative areas in Texas were identified for evaluation of the occurrence of contact investigations in schools for the period of 2006 to 2009 and any use of school screening programs. Of the five reporting areas that responded, only one utilized a school screening program; this reporting area had the lowest percentage of contact investigations occurring in schools. Contact investigations were most common in middle schools and least common in elementary schools. In metropolitan areas, colleges represented up to 42.9% of contact investigations. The number of contact investigations has increased from 2006 to 2008. This report represents a small sample, and further research into the frequency, distribution and risk for contact investigations in schools and the efficacy of screening programs should be done. ^

Benthic foraminifers from the Japan Sea

Five holes were drilled at two sites in the Sea of Japan during Ocean Drilling Program (ODP) Leg 128. Site 798 is located on Oki Ridge at a depth of about 900 m. Sediment age at Site 798 ranges from Pliocene to Holocene. Site 799 is located in the Kita-Yamato Trough at depth of 2000 m and below the present calcite compensation depth (CCD); the sediment ranges from Miocene to Holocene in age. Samples from all holes contain benthic foraminifers. Faunal evidence of downslope displacement is frequent in Holes 799A and 799B. The vertical frequency distribution of some dominant species shows that significant faunal changes occur in Holes 798A-C on Oki Ridge. Based on the faunal change and the thickness of sediments, it appears that the Oki Ridge was uplifted more than 1,000 m during last 4 m.y. Benthic foraminifers also demonstrate that the water depth of Site 799 rapidly changed from upper bathyal to lower bathyal during middle Miocene time. The appearance of benthic foraminifer species common to anaerobic environments suggests that the dysaerobic to anaerobic bottom conditions existed during the evolution of the Sea of Japan. Faunal distributions also suggest that the 'Tertiary-type' species recognized in the Neogene strata of the Japan Sea coastal regions disappeared sequentially from the Sea of Japan during Pliocene to late Pleistocene.

Características palinológicas de mieles de eucalipto (Eucalyptus sp.) y tréboles (Trifolium sp.) provenientes de la Provincia Fitogeográfica Pampeana Argentina

El objetivo de este trabajo fue estudiar el perfil polínico de mieles de tréboles y de eucalipto de la Provincia Fitogeográfica Pampeana Argentina, con el fin de contribuir a su caracterización palinológica. Se realizó un análisis polínico cualitativo y se aplicaron técnicas estadísticas descriptivas y multivariadas, para conocer la distribución de frecuencia de los pólenes y caracterizar cada origen floral, según los pólenes acompañantes y los años de cosecha. Se analizaron 81 muestras de miel, de cuatro cosechas diferentes. Se encontraron 41 tipos morfológicos de polen, cuya variación por muestra osciló entre dos y ocho. El taxón presente en más del 80% de las mieles fue Eucalyptus sp. Los principales pólenes acompañantes encontrados pertenecieron a los tipos Helianthus annuus y Carduus sp., para ambos orígenes florales estudiados, y a la familia de las Brassicaceae, para las mieles de tréboles. Los años de cosecha estudiados mostraron diferentes espectros polínicos.

Programas preventivos basados en fluoruros en preescolares de riesgo social con altos índices de caries

En Mendoza se realizó un estudio clínico de intervención, prospectivo de dos años, dirigido a preescolares en riesgo social con alto índice de caries con el objetivo de evaluar la eficacia y efectividad de un programa preventivo basado en fluoruros. El programa preventivo se basó en acciones de educación para la salud, enseñanza de técnicas de higiene bucal y aplicación tópica de flúor fosfato acidulado realizadas dos veces durante el ciclo escolar. La muestra intencionada sumó 96 niños de sala de 4 años (2009) que fueron evaluados en su cursado posterior en sala de 5 años (2010) y en 1er año de EGB durante 2011. Niños asistentes a sala de 5 años y primer año EGB al momento del examen basal (2009) conformaron el grupo control. Se les aplicó el mismo programa por razones éticas. A 12 y 24 meses de aplicado el programa se evaluó: porcentaje de libres de caries, ceod+CPOD, cpos+CPOS y sus valores discriminados, medias de categorías ICDAS II, índice de Placa Bacteriana de Löe y Silness e índice de necesidad de tratamiento de caries de Bordoni. Se determinó la distribución de frecuencias e intervalos de confianza para cada variable; medidas de tendencia central y dispersión y se realizaron comparaciones entre grupos mediante la prueba T de Student y chi cuadrado con un nivel de p=0.05. Resultados: Comparando sala 5 años 2010 / sala de 5 años 2009: disminuyeron significativamente las medias de ceod +CPOD, ICDAS 6, Índice Placa Löe e índice de necesidad de tratamiento. Comparando 1er año 2011 / 1er año 2009: disminuyeron significativamente las medias de cs+CS, ceos+CPOS e ICDAS 4. El resto de los valores no mostró diferencias significativas. Conclusión: Un programa preventivo basado en fluoruros es efectivo y tiene efectos positivos sobre la prevalencia de caries en preescolares de Mendoza.

Estudio de distribución y frecuencia de caries en preescolares de alto riesgo social

Objetivos: El presente trabajo establece en el escenario local, un patrón de distribución y severidad de caries en una población de riesgo social de niños preescolares, datos necesarios para la programación de recursos en programas de salud bucal Método: estudio descriptivo, correlacional y transversal sobre muestra intencionada de 150 niños preescolares de 4 y 5 años de edad, de ambos sexos, con actividad de caries, pertenecientes a escuelas públicas, del ámbito urbano-marginal-Distrito Pedro Molina-Mendoza. Rep. Argentina, cuyos padres hubieron firmado el consentimiento informado. Se registraron las lesiones de caries según diente y sitio, y la severidad según ICDAS II (Pitts, 2004). Se establecieron distribución de frecuencias para las variables diente, sitio y categoría de ICDAS II. Para establecer asociaciones entre variables se aplicó prueba de chi cuadrado, con un nivel de significación de 0.05. Resultados: 1º y 2º molares temporarios son los más afectados, principalmente 75 y 85. El valor 6 de ICDAS II es el más frecuente, seguido por valores 3 y 5. El 84 presenta mayor frecuencia de valores grado 6. La superficie oclusal es la más afectada (42.6%). Existe asociación entre diente y categoría de ICDAS II y entre diente y sitio de la lesión para 55, 52, 51, 61, 62, 63 y 64, 84 y 75. Conclusiones: la distribución y severidad de caries en denticióntemporaria de los niños estudiados evidencia una alta frecuencia de lesiones de caries en molares, y una necesidad de tratamiento complejo involucrando para su resolución niveles de atención sanitaria II y III que deberá encontrar como contraparte un sistema sanitario preparado para su resolución.

Occurence of flood laminae in sediments of Ammersee

A 450 year spring-summer flood layer time series at seasonal resolution has been established from the varved sediment record of Lake Ammersee (southern Germany), applying a novel methodological approach. The main results are (1) the attainment of a precise chronology by microscopic varve counting, (2) the identification of detrital layers representing flood-triggered fluxes of catchment material into the lake, and (3) the recognition of the seasonality of these flood layers from their microstratigraphic position within a varve. Tracing flood layers in a proximal and a distal core and correlating them by application of the precise chronology provided information on the depositional processes. Comparing the seasonal flood layer record with daily runoff data of the inflowing River Ammer for the period from 1926 to 1999 allowed the definition of an approximate threshold in flood magnitude above which the formation of flood layers becomes very likely. Moreover, it was possible for the first time to estimate the "completeness" of the flood layer time series and to recognize that mainly floods in spring and summer, representing the main flood seasons in this region, are well preserved in the sediment archive. Their frequency distribution over the entire 450 year time series is not stationary but reveals maxima for colder periods of the Little Ice Age when solar activity was reduced. The observed spring-summer flood layer frequency further shows trends similar to those of the occurrence of flood-prone weather regimes since A.D. 1881, probably suggesting a causal link between solar variability and changes in midlatitude atmospheric circulation patterns.