Uncertainty About the Incubation Period of AIDS and its Impact on Backcalculation

We analyze three sets of doubly-censored cohort data on incubation times, estimating incubation distributions using semi-parametric methods and assessing the comparability of the estimates. Weibull models appear to be inappropriate for at least one of the cohorts, and the estimates for the different cohorts are substantially different. We use these estimates as inputs for backcalculation, using a nonparametric method based on maximum penalized likelihood. The different incubations all produce fits to the reported AIDS counts that are as good as the fit from a nonstationary incubation distribution that models treatment effects, but the estimated infection curves are very different. We also develop a method for estimating nonstationarity as part of the backcalculation procedure and find that such estimates also depend very heavily on the assumed incubation distribution. We conclude that incubation distributions are so uncertain that meaningful error bounds are difficult to place on backcalculated estimates and that backcalculation may be too unreliable to be used without being supplemented by other sources of information in HIV prevalence and incidence.

Integrating methods for determining length-at-age to improve growth estimates for two large scombrids

Fish growth is commonly estimated from length-at-age data obtained from otoliths. There are several techniques for estimating length-at-age from otoliths including 1) direct observed counts of annual increments; 2) age adjustment based on a categorization of otolith margins; 3) age adjustment based on known periods of spawning and annuli formation; 4) back-calculation to all annuli, and 5) back-calculation to the last annulus only. In this study we compared growth estimates (von Bertalanffy growth functions) obtained from the above five methods for estimating length-at-age from otoliths for two large scombrids: narrow-barred Spanish mackerel (Scomberomorus commerson) and broad-barred king mackerel (Scomberomorus semifasciatus). Likelihood ratio tests revealed that the largest differences in growth occurred between the back-calculation methods and the observed and adjusted methods for both species of mackerel. The pattern, however, was more pronounced for S. commerson than for S. semifasciatus, because of the pronounced effect of gear selectivity demonstrated for S. commerson. We propose a method of substituting length-at-age data from observed or adjusted methods with back-calculated length-at-age data to provide more appropriate estimates of population growth than those obtained with the individual methods alone, particularly when faster growing young fish are disproportionately selected for. Substitution of observed or adjusted length-at-age data with back-calculated length-at-age data provided more realistic estimates of length for younger ages than observed or adjusted methods as well as more realistic estimates of mean maximum length than those derived from backcalculation methods alone.

Determinação da idade e crescimento da piramutaba Brachyplatystoma vaillantii (Valenciennes, 1840) (Siluriformes : Pimelodidae) capturada no estuário amazônico

Neste trabalho foram analisados exemplares de piramutaba (Brachyplalystoma vaillantii) provenientes de pescarias experimentais no estuário amazônico. Para o estudo de determinação da idade foram analisados acúleos das nadadeiras peitorais e dorsal, opérculos, otólitos (lapillus) e vértebras. Da análise destas estruturas rígidas foi concluído que a vértebra é a estrutura mais adequada para determinar a idade da piramutaba, pois esta estrutura apresentou 59% de anéis nítidos e uma boa correlação entre o seu raio e o comprimento furcal do peixe (r² = 0,9889 e p<0,05). Os anéis etários das vértebras foram validados pelo método da distribuição de freqüências por classes de comprimento. A piramutaba forma dois anéis etários por ano em suas vértebras. A relação entre o peso total e o comprimento furcal da piramutaba descreve seu crescimento como alométrico e a equação que descreve este crescimento é Wt = 6,1 * 10^-6 * Lf^3,1129. A proporção sexual de piramutaba verificada não foi de 1:1, onde o número de fêmeas foi superior ao de machos. Foi observado um número máximo de dez anéis nítidos nas vértebras de piramutaba. O modelo de crescimento utilizado neste trabalho foi o de von Bertalanffy para as estimativas das equações de crescimento em comprimento e em peso. Os parâmetros de crescimento (k, t₀ e L∞) foram estimados através de quatro diferentes métodos: contagem de anéis nas vértebras, retrocálculo, decomposição dos raios e distribuição de freqüências por classes de comprimento. Os parâmetros de crescimento foram: k = 0,138 ano^-1, t₀ = -0,239 e L∞ = 110,5 cm (contagem de anéis); k = 0,119 ano^-1, t₀ = -0,202 e L∞ = 110,5 cm (retrocálculo); k = 0,096 ano^-1, t₀ = -0,146 e L∞ = 110,5 cm (decomposição dos raios) e k = 0,127 ano^-1, t₀ = -0,236 e L∞ = 110,5 cm (distribuição de freqüências).

Analise do fator dinâmico nas fórmulas de Janbu e Hiley com base em resultados de CAPWAPC

This study aimed to evaluate the dynamic factor applied to the results obtained by dynamic resistance formulas Janbu and Hiley, would lead to the results obtained by static strength analysis CAPWAPC ®. The evaluation was done by backcalculation dynamic loading tests (ECD), taking into consideration the type of soil in which the cutting base precast concrete were settled, and using the information on the effective energy transmitted to the stakes by hammers, obtained by CAPWAPC ®. The results are shown in tables and graphs, and showed that the use of these formulations and their dynamic factors can become an efficient and economical field, assisting the engineer in making decisions regarding the staking of the work

Analisi dell'accrescimento giornaliero della Sardina pilchardus nel Canale di Sicilia

Lo studio effettuato riguarda l’accrescimento giornaliero della Sardina pilchardus, (Walbaum, 1792) tramite la lettura degli anelli di crescita giornaliera negli otoliti. Nel Mediterraneo centrale il lavoro svolto è il primo di questo tipo su S. pilchardus. Il campionamento è avvenuto durante la campagna oceanografica "Anchevatir 2012", 69 otoliti sono stati estratti da esemplari con lunghezza totale compresa tra 7 ed 12.5 cm e successivamente sottoposti ad inclusione, sezionamento e levigatura per la realizzazione di sezioni sottili. Sull’intero campione è stata stimata l’età con due metodi: lettura degli anelli giornalieri sotto microscopio e conteggio dei microincrementi tramite analisi d’immagine. L’età stimata è compresa tra i 90 e 230 giorni, tuttavia la maggior parte degli individui presenta un’età tra i 120 e 150 giorni. Inoltre è stata determinata la data di nascita degli esemplari, avvenuta tra Dicembre 2011 e Febbraio 2012. In seguito è stata condotta un’analisi della media dell’ampiezza degli incrementi per descrivere i pattern di crescita giornaliera: l’andamento risultante è crescente con il procedere dell’età fino a circa il 50° giorno, poi si stabilizza fino al 150°, infine i valori medi decrescono. La backcalculation ha permesso di stimare il tasso di accrescimento giornaliero della lunghezza del corpo. Sono state analizzate tre serie distinte per data di nascita (Dicembre 2011, Gennaio 2012 e Febbraio 2012); queste hanno mostrato pattern di accrescimento analogo. La crescita iniziale stimata è di 0.2 mm/d, raggiunge 0.6 mm/d intorno al 40° giorno, ed oltre il 100° si è osservato un decremento nell’accrescimento giornaliero, soprattutto nella serie di Dicembre. Le differenze più rilevanti nei pattern delle tre serie mensili sono state riscontrate nei valori medi fra Dicembre e Febbraio. L’analisi della temperatura media superficiale ha permesso di ipotizzare che questa crescita maggiore degli individui nati in Febbraio sia collegata all’aumento di temperatura registrato da Marzo in poi. Tale risultato suggerisce che le condizioni ambientali e quindi i ritmi metabolici e d’accrescimento nei mesi successivi a Febbraio sono più favorevoli rispetto ai mesi invernali.

The Impact of Uncertainty in the AIDS Incubation Period on Reconstructions of the HIV Epidemic

Backcalculation is the primary method used to reconstruct past human immunodeficiency virus (HIV) infection rates, to estimate current prevalence of HIV infection, and to project future incidence of acquired immunodeficiency syndrome (AIDS). The method is very sensitive to uncertainty about the incubation period. We estimate incubation distributions from three sets of cohort data and find that the estimates for the cohorts are substantially different. Backcalculations employing the different estimates produce equally good fits to reported AIDS counts but quite different estimates of cumulative infections. These results suggest that the incubation distribution is likely to differ for different populations and that the differences are large enough to have a big impact on the resulting estimates of HIV infection rates. This seriously limits the usefulness of backcalculation for populations (such as intravenous drug users, heterosexuals, and women) that lack precise information on incubation times.

Flexible pavement layer moduli determination : an adaptive artificial neural network approach

The estimation of pavement layer moduli through the use of an artificial neural network is a new concept which provides a less strenuous strategy for backcalculation procedures. Artificial Neural Networks are biologically inspired models of the human nervous system. They are specifically designed to carry out a mapping characteristic. This study demonstrates how an artificial neural network uses non-destructive pavement test data in determining flexible pavement layer moduli. The input parameters include plate loadings, corresponding sensor deflections, temperature of pavement surface, pavement layer thicknesses and independently deduced pavement layer moduli.

Soft computing based parameter identification in pavements and geomechanical systems

Accurate estimation of road pavement geometry and layer material properties through the use of proper nondestructive testing and sensor technologies is essential for evaluating pavement’s structural condition and determining options for maintenance and rehabilitation. For these purposes, pavement deflection basins produced by the nondestructive Falling Weight Deflectometer (FWD) test data are commonly used. The nondestructive FWD test drops weights on the pavement to simulate traffic loads and measures the created pavement deflection basins. Backcalculation of pavement geometry and layer properties using FWD deflections is a difficult inverse problem, and the solution with conventional mathematical methods is often challenging due to the ill-posed nature of the problem. In this dissertation, a hybrid algorithm was developed to seek robust and fast solutions to this inverse problem. The algorithm is based on soft computing techniques, mainly Artificial Neural Networks (ANNs) and Genetic Algorithms (GAs) as well as the use of numerical analysis techniques to properly simulate the geomechanical system. A widely used pavement layered analysis program ILLI-PAVE was employed in the analyses of flexible pavements of various pavement types; including full-depth asphalt and conventional flexible pavements, were built on either lime stabilized soils or untreated subgrade. Nonlinear properties of the subgrade soil and the base course aggregate as transportation geomaterials were also considered. A computer program, Soft Computing Based System Identifier or SOFTSYS, was developed. In SOFTSYS, ANNs were used as surrogate models to provide faster solutions of the nonlinear finite element program ILLI-PAVE. The deflections obtained from FWD tests in the field were matched with the predictions obtained from the numerical simulations to develop SOFTSYS models. The solution to the inverse problem for multi-layered pavements is computationally hard to achieve and is often not feasible due to field variability and quality of the collected data. The primary difficulty in the analysis arises from the substantial increase in the degree of non-uniqueness of the mapping from the pavement layer parameters to the FWD deflections. The insensitivity of some layer properties lowered SOFTSYS model performances. Still, SOFTSYS models were shown to work effectively with the synthetic data obtained from ILLI-PAVE finite element solutions. In general, SOFTSYS solutions very closely matched the ILLI-PAVE mechanistic pavement analysis results. For SOFTSYS validation, field collected FWD data were successfully used to predict pavement layer thicknesses and layer moduli of in-service flexible pavements. Some of the very promising SOFTSYS results indicated average absolute errors on the order of 2%, 7%, and 4% for the Hot Mix Asphalt (HMA) thickness estimation of full-depth asphalt pavements, full-depth pavements on lime stabilized soils and conventional flexible pavements, respectively. The field validations of SOFTSYS data also produced meaningful results. The thickness data obtained from Ground Penetrating Radar testing matched reasonably well with predictions from SOFTSYS models. The differences observed in the HMA and lime stabilized soil layer thicknesses observed were attributed to deflection data variability from FWD tests. The backcalculated asphalt concrete layer thickness results matched better in the case of full-depth asphalt flexible pavements built on lime stabilized soils compared to conventional flexible pavements. Overall, SOFTSYS was capable of producing reliable thickness estimates despite the variability of field constructed asphalt layer thicknesses.

Recruitment patterns and processes of coastal fish species in a temperate rocky reef

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências do Mar, Especialização em Ecologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016