The spatial movements of yellowfin tunas around the fish aggregating devices which were anchored below 40 meters water with a VEMCO VR2 receiver were investigated using ultrasonic telemetry tags V9P (VEMCO VP9-2H-S256). The experiment was conducted in the Shiao-Liu-Chiu Island of Taiwan from July to September, 2007. A pair of VEMCO VR2 receivers was separated by 400 meter distances in west of south sea ,Taiwan. A total of 9 tagged fishes with different sizes were monitored for maximum 19 days. Preliminary results showed that juvenile fish stayed longer and closer within FADs than the adult fish. Fish could move vertically to as low as 160 meters at daytime. They avoid the surface water where the temperature reach 30oC. In nighttime, juvenile fish that has fork length smaller than 55cm generally moves to the surface mixed layer. On the horizontal movement, there are three types. A) fish stays at FADs site. B) Fish move in and out FADs sites for a few hours period. C) fish moves away from FADs site for a long times (maybe 2~3 days). Sometimes juvenile fish would have B) or C) moved away from the FAD devices during dawn and dusk, and back at daytime. But this would not occurred with large fish. We estimated the attraction radius of FADs at least 1 km.

β-Glucosidase zymograms of certain maize genotypes (nulls) do not show any activity bands after electrophoresis. We have shown that a chimeric lectin called β-glucosidase aggregating factor (BGAF) is responsible for the absence of β-glucosidase activity bands on zymograms. BGAF specifically binds to maize β-glucosidase isozymes Glu1 and Glu2 and forms large, insoluble complexes. Furthermore, we have previously shown that the N-terminal (Glu⁵⁰-Val¹⁴⁵) and the C-terminal (Phe⁴⁶⁶-Ala⁵¹²) regions contain residues that make up the BGAF binding site on maize Glu1. However, sequence comparison between sorghum β-glucosidases (dhurrinases, Dhr1 and Dhr2), to which BGAF does not bind, and maize β-glucosidases, and an examination of the 3-D structure of Glu1 suggested that the BGAF binding site on Glu1 is much smaller than predicted previously. To define more precisely the BGAF binding site, we constructed additional chimeric β-glucosidases. The results showed that a region spanning 11 amino acids (Ile⁷²-Thr⁸²) on Glu1 is essential and sufficient for BGAF binding, whereas the extreme N-terminal region Ser¹-Thr²⁹, together with C-terminal region Phe⁴⁶⁶-Ala⁵¹², affects the size of Glu1-BGAF complexes. To determine the importance of each region for binding, we determined the dissociation constants (K_d) of chimeric β-glucosidase-BGAF interactions. The results demonstrated that the extreme N-terminal and C-terminal regions are important but not essential for binding. To confirm the importance of Ile⁷²-Thr⁸² on Glu1 for BGAF binding, we constructed chimeric Dhr2 (C-11, Dhr2 whose Val⁷²-Glu⁸² region was replaced with the Ile⁷²-Thr⁸² region of Glu1). C-11 binds to BGAF, indicating that the Ile⁷²-Thr⁸² region is indeed a major interaction site on Glu1 involved in BGAF binding. We also constructed mutant β-glucosidases to identify and define the contribution of individual amino acids in the above three regions to BGAF binding. In the N-terminal region (Ile⁷²-Thr⁸²), critical region for BGAF binding, Glu1 mutants K81E and T82Y failed to bind BGAF in the gel-shift assay and their frontal affinity chromatography (FAC) profiles were essentially similar to that of sorghum β-glucosidase (dhurrinase 2, Dhr2), a non-binder, indicating that these two amino acids within Ile⁷²-Thr⁸² region are essential for BGAF binding. In the extreme N-terminal (Ser¹-Thr²⁹) and C-terminal (Phe⁴⁶⁶-Ala⁵¹²) regions, N481E [substitution of asparagine-481 with glutamic acid (as in Dhr)] showed lower affinity for BGAF, whereas none of the single amino acid substitutions in the Ser¹-Thr²⁹ region showed any effect on BGAF binding indicating that these regions play a minor role. To further confirm the importance of lysine-81 and threonine-82 for BGAF binding, we produced a number of Dhr2 mutants, and the results showed that all four unique amino acids (isoleucine-72, asparagine-75, lysine-81, and threonine-82) of Glu1 in the peptide span Ile⁷²-Thr⁸² are required to impart BGAF binding ability to Dhr2. The sequence comparison among plant β-glucosidases supports the hypothesis that BGAF binding is specific to maize β-glucosidases because only maize β-glucosidases have threonine at position 82. / Ph. D.

abstract: Functional regression models are widely considered in practice. To precisely understand an underlying functional mechanism, a good sampling schedule for collecting informative functional data is necessary, especially when data collection is limited. However, scarce research has been conducted on the optimal sampling schedule design for the functional regression model so far. To address this design issue, efficient approaches are proposed for generating the best sampling plan in the functional regression setting. First, three optimal experimental designs are considered under a function-on-function linear model: the schedule that maximizes the relative efficiency for recovering the predictor function, the schedule that maximizes the relative efficiency for predicting the response function, and the schedule that maximizes the mixture of the relative efficiencies of both the predictor and response functions. The obtained sampling plan allows a precise recovery of the predictor function and a precise prediction of the response function. The proposed approach can also be reduced to identify the optimal sampling plan for the problem with a scalar-on-function linear regression model. In addition, the optimality criterion on predicting a scalar response using a functional predictor is derived when the quadratic relationship between these two variables is present, and proofs of important properties of the derived optimality criterion are also provided. To find such designs, an algorithm that is comparably fast, and can generate nearly optimal designs is proposed. As the optimality criterion includes quantities that must be estimated from prior knowledge (e.g., a pilot study), the effectiveness of the suggested optimal design highly depends on the quality of the estimates. However, in many situations, the estimates are unreliable; thus, a bootstrap aggregating (bagging) approach is employed for enhancing the quality of estimates and for finding sampling schedules stable to the misspecification of estimates. Through case studies, it is demonstrated that the proposed designs outperform other designs in terms of accurately predicting the response and recovering the predictor. It is also proposed that bagging-enhanced design generates a more robust sampling design under the misspecification of estimated quantities. / Dissertation/Thesis / Doctoral Dissertation Statistics 2020

No description available.

β-Glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) catalyzes the hydrolysis of aryl and alkyl β-D-glucosides as well as glucosides with a carbohydrate moiety such as cellobiose and other beta-linked oligosaccharides. In maize (Zea mays L.), β-glucosidase exists as 120 kD homodimers, but also forms high-molecular-weight (HMW) aggregates in certain maize inbreds (nulls). In this study we show that the null β-glucosidase phenotype is caused by the formation of HMW enzyme aggregates (>1.5 X 10⁶ Daltons), caused by a β-glucosidase aggregating factor (BGAF). BGAF is a 32 kD protein that binds specifically to β-glucosidase and renders it insoluble during extraction. The data unequivocally demonstrate that BGAF is solely responsible for β-glucosidase aggregation and insolubility, and thus, the apparent null phenotype. Additionally, I have isolated the cDNA encoding BGAF and have identified BGAF as a member of the small heat-shock protein (sHsp) family. Interestingly, BGAF binds to both maize β-glucosidase isozymes (Glu1 and Glu2), but does not bind to their sorghum homolog Dhurrinase-1 (Dhr1; Sorghum beta-glucosidase), that shares 70% sequence identity with Glu1 and Glu2. Therefore, these proteins provide an excellent system to study functional differences at nonconserved residues and elucidate the mechanism of enzyme aggregation and insolubility. By examining the behavior of β-glucosidase chimeras in binding assays, I demonstrate that BGAF binding is conformation dependent, highly specific, and reminiscent of antigen-antibody interactions. Additionally, I have identified two disparate polypeptide segments in the primary structure of the maize beta-glucosidase isozyme Glu1 that form a BGAF binding site in the tertiary structure of the enzyme. / Master of Science

No description available.

Thesis (MSc)--Stellenbosch University, 2004. / ENGLISH ABSTRACT: It is possible to improve on the accuracy of a single neural network by using an ensemble of diverse and accurate networks. This thesis explores diversity in ensembles and looks at the underlying theory and mechanisms employed to generate and combine ensemble members. Bagging and boosting are studied in detail and I explain their success in terms of well-known theoretical instruments. An empirical evaluation of their performance is conducted and I compare them to a single classifier and to each other in terms of accuracy and diversity. / AFRIKAANSE OPSOMMING: Dit is moontlik om op die akkuraatheid van 'n enkele neurale netwerk te verbeter deur 'n ensemble van diverse en akkurate netwerke te gebruik. Hierdie tesis ondersoek diversiteit in ensembles, asook die meganismes waardeur lede van 'n ensemble geskep en gekombineer kan word. Die algoritmes "bagging" en "boosting" word in diepte bestudeer en hulle sukses word aan die hand van bekende teoretiese instrumente verduidelik. Die prestasie van hierdie twee algoritmes word eksperimenteel gemeet en hulle akkuraatheid en diversiteit word met 'n enkele netwerk vergelyk.

Le comportement des thons tropicaux autour des objets flottants : De l'étude des comportements individuels et collectifs à l'étude du piège écologiqueLes recherches en halieutique ont pour objectif d'améliorer les connaissances sur le fonctionnement des populations de poissons afin de transférer celle-ci vers des outils de gestion. Ce travail de thèse repose sur un ensemble d'expériences et de modélisations destinées à approfondir notre compréhension générale du comportement associatif de poissons grands pélagiques avec des objets flottantes à la surface de l'océan. Notre objectif est de tester si les milliers d'objets flottants artificiels déployés par les pêcheurs (DCP - Dispositifs de Concentration de Poissons) constituent des pièges écologiques pour les thons tropicaux. Pour mener à bien ce travail, nous avons dans le premier chapitre caractérisé le comportement individuel de thons dans un réseau de DCP ancrés. L'analyse de données de marquage acoustique de 96 thons albacores (Thunnus albacares) (30-96 cm) à Hawaii montre que les thons présentent une plasticité comportementale forte face aux DCP qu'ils rencontrent mais également que le temps de résidence sous les DCP diminue avec la taille des individus. Afin de quantifier l'impact de l'augmentation de la densité de DCP il est essentiel de comprendre les mécanismes et les facteurs qui influencent les temps de résidences sous les DCP. Dans le second chapitre, des expériences de choix binaires suggèrent un rôle de la biomasse agrégée dans la formation, la maintenance et la dispersion des agrégations que forment les thons sous les objets flottants. La quantification de la dynamique des arrivées et des départs des poissons aux DCP permettra de valider les hypothèses que nous proposons concernant les mécanismes sociaux sous-jacents d'une part et d'autre part de tester l'influence de la qualité de l'environnement et de la densité de DCP sur les temps de résidences individuels et la distribution spatiale des populations. Dans le troisième chapitre, la comparaison de facteurs de condition de listaos (Katsuwonus pelamis) matures capturés en bancs libres et sous objets flottants dans une zone naturellement riche en objets flottants, et relativement peu impactée par le déploiement de DCP (Le Canal du Mozambique), nous a permis d'établir un point de référence essentiel pour estimer les effets des perturbations actuelles. Plus généralement, les résultats obtenus dans les différents chapitres tendent à conforter l'hypothèse d'un rôle social et non trophique des objets flottants dans l'écologie de thonidés. Les résultats obtenus durant cette thèse amènent à poser un regard nouveau sur l'hypothèse du piège écologique. Notre travail s'est principalement intéressé à un modèle biologique de choix, les thons tropicaux. Cependant le cadre théorique des questions abordées, les outils d'observations et les méthodes d'analyses développées sont assez génériques pour être appliqués aux autres espèces rencontrées sous les objets flottants. Cette recherche s'intègre plus généralement dans les problématiques visant à mieux comprendre les stratégies comportementales et la distribution des populations dans des environnements multi-sites. / Research in fisheries science aims at investigating the functioning of fish population with the objective of using this knowledge to propose sustainable management measures. This PhD thesis relies on a collection of experiments and modelling designed to further our knowledge on the aggregative behaviour of large pelagic fish with floating structures at the surface of the ocean. The overall objective is to test whether the thousands of man-made floating structures deployed by fishermen (also referred as Fish Aggregating Device –FAD) act as ecological traps for tropical tunas. To archive this main objective, it was first necessary to characterize the individual behaviour of tuna in a network of FAD. In the first chapter, the analysis of 96 acoustically tagged yellowfin tuna (Thunnus albacares) between 30-96 cm FL in the array of anchored FADs around Oahu (Hawaii, US) shows that individuals tuna exhibited behavioural plasticity while in the array and that behaviour around FAD is size dependent. In order to assess the impact of the increasing density of FAD, the major habitat modification, it is essential to understand the factors that influence the residence time at FADs. In the second chapter, binary choice experiments suggest that the aggregated biomass under the FAD play a role in the aggregative process. Nonetheless, quantification of arrival and departure dynamics of fish to FAD are required to validate the assumptions we proposed on the underlying social mechanism. Such model would, then, allow testing the effect of FAD density and environmental conditions on individual residence time and spatial distribution of population. In the third chapter, the comparison of skipjack tuna (Katsuwonus pelamis) condition between individual associated with logs and in free swimming schools in the Mozambique Channel, an area known to be naturally enriched with logs with few FADs, highlights the need for estimating reference points prior to assessing the impacts of anthropogenic modifications to habitats on animals.Combining the different chapters, our results tend to favour a social rather than a trophic role of floating objects in the ecology of tunas. More generally, we discuss what novel insight our results bring up on the ecological trap hypothesis. Tropical tunas represent an interesting model species on which we focused. However, the theoretical framework of the questions we addressed, the observation and analytical tools we developed are generic enough to be applied to the others species that are encountered around floating structures. In a broader extent, this work meets the general topic of studying behavioural strategies and distribution of population in multi-patch environment.

FundaÃÃo de Amparo à Pesquisa do Estado do Cearà / O presente trabalho tem por objetivo a caracterizaÃÃo dos aspectos tecnolÃgicos e da composiÃÃo das capturas, complementados com estudos sobre o crescimento e a alimentaÃÃo das principais espÃcies na pesca de atuns e afins em cardumes associados no AtlÃntico Oeste Equatorial. Para tanto, foram acompanhados 109 desembarques em Areia Branca, RN, no perÃodo entre jun/2010 e mai/2013, assim como o embarque em nove cruzeiros de pesca no perÃodo entre fev/2011 e dez/2012. O estudo de idade e crescimento, foi realizado com base nas leituras de anÃis etÃrios nos espinhos dorsais e microincrementos diÃrios de otÃlitos de Thunnus albacares ajustados aos modelos de crescimento de von Bertalanffy, Gompertz e LogÃstico, os quais foram selecionados a partir dos valores de AIC (Akaikeâs Criterion Information). O estudo de alimentaÃÃo foi desenvolvido por meio da identificaÃÃo e avaliaÃÃo dos itens alimentares presentes no conteÃdo estomacal de T. obesus e T. albacares. Foram observadas 9 embarcaÃÃes, com comprimento total mÃdio de 13,4 m, as quais utilizam diversas tÃcnicas de captura como a linha de mÃo, vara e linha, corrico e corso, com o uso de iscas artificiais e naturais. Os desembarques totalizaram 691.533 kg de pescado, dentre os quais, as espÃcies alvo foram a albacora bandolim e a albacora laje, sendo retidas tambem espÃcies como o dourado, agulhÃo negro, bonito-listrado, cavala empinge, peixe rei e ainda, ocasionalmente, espÃcies como espadarte e cangulo. Os valores de L ̅_∞ foram estimados em 175,13 e 171,6 cm para os dados observados e retrocalculados a partir dos espinhos dorsais e em 166,6; 171,14; e 155,38 cm respectivamente para os dados agrupados, para machos e fÃmeas a partir dos microincrementos diÃrios de otÃlitos. Os principais itens alimentares observados na dieta de ambos os predadores foram os peixes das famÃlias Myctophidae, Exocoetidae, Bramidae e Nomeidae, sendo observadas com menor frequÃncia os cefalÃpodes e os crustÃceos. Podemos concluir que os resultados obtidos fornecem informaÃÃes essÃnciais que ajudarÃo a compreender as atividades de pesca, bem como ampliarÃo os conhecimentos sobre a biologia das principais espÃcies capturadas. / The present study aims to characterize the technolo gical features and the catch composition, complemented with studies on the age a nd growth and feeding of the target species in the fishery for tunas in associated schools in the western equatorial Atlantic. For this purpose, a total of 109 landings by the fleet based on Areia Branca, RN, were observed in the period from June 2010 to M ay 2013, as well as on board in nine fishing cruises in the period from February 2011 to December 2012. The age and growth study was performed based on readings of age rings of the dorsal spines and daily microincrements present in the otolith of Thunnus albacares, adjusted to von Bertalanffy , Gompertz and Logistic growth models, which were selected based on their AIC (Akaike 's Information Criterion) valu es. The feeding study was developed through the identification and assessment of food items present in the stomach contents from T. obesus and T. albacares . The fleet consisted of 9 boats, with an average length overall of 13.4 m, which use various fishing techniques such as handline, rod and line and trolling, combined with natural baits or lures. Landings amounted 691,533 kg, from which, the target species were bigeye and yellowfin tunas, as well as bycatch, species such as dolphinfish, blue marlin, skipjack, wahoo, rainbow runner and, even occasionally, species such as swordfish and triggerfish. The values of L were estimated at 175.13 and 171.6 cm for the obser ved and backcalculated data from the dorsal spines and 166.6, 171.14 and 155.38 cm, respectively for the pooled data, males and females based on otolith daily microstructure. The main food items observed in the diet of both predators were the following fish families: Myctophidae, Exocoetidae, Bramidae and Nomeidae. Cephalopods and crustaceans were occasionally observed. We can conclude that results provide essential information that will ass ist in the understanding of fishing activities as well as expand the knowledge on the biology of the target species.

Classification of data from repeated measurements is useful in various disciplines, for example that of medicine. This thesis explores how classification trees (CART) can be used for classifying repeated measures data. The reader is introduced to variations of the CART algorithm which can be used for classifying the data set and tests the performance of these algorithms on a data set that can be modelled using bilinear regression. The performance is compared with that of a classification rule based on linear discriminant analysis. It is found that while the performance of the CART algorithm can be satisfactory, using linear discriminant analysis is more reliable for achieving good results. / Klassificering av data från upprepade mätningar är användbart inom olika discipliner, till exempel medicin. Denna uppsats undersöker hur klassificeringsträd (CART) kan användas för att klassificera upprepade mätningar. Läsaren introduceras till varianter av CART-algoritmen som kan användas för att klassificera datamängden och testar prestandan för dessa algoritmer på en datamängd som kan modelleras med hjälp av bilinjär regression. Prestandan jämförs med en klassificeringsregel baserad på linjär diskriminantanalys. Det har visar sig att även om prestandan för CART-algoritmen kan vara tillfredsställande, är användning av linjär diskriminantanalys mer tillförlitlig för att uppnå goda resultat.