Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Survivable Traffic Grooming with Path Protection at the Connection Level in WDM Mesh Networks

Survivable traffic grooming (STG) is a promising approach to provide reliable and resource-efficient multigranularity connection services in wavelength division multiplexing (WDM) optical networks. In this paper, we study the STG problem in WDM mesh optical networks employing path protection at the connection level. Both dedicated protection and shared protection schemes are considered. Given the network resources, the objective of the STG problem is to maximize network throughput. To enable survivability under various kinds of single failures such as fiber cut and duct cut, we consider the general shared risk link group (SRLG) diverse routing constraints. We first resort to the integer linear programming (ILP) approach to obtain optimal solutions. To address its high computational complexity, we then propose three efficient heuristics, namely separated survivable grooming algorithm (SSGA), integrated survivable grooming algorithm (ISGA) and tabu search survivable grooming algorithm (TSGA). While SSGA and ISGA correspond to an overlay network model and a peer network model respectively, TSGA further improves the grooming results from SSGA and ISGA by incorporating the effective tabu search method. Numerical results show that the heuristics achieve comparable solutions to the ILP approach, which uses significantly longer running times than the heuristics.

Screening bacterial metabolites for inhibitory effects against Batrachochytrium dendrobatidis using a spectrophotometric assay

Certain bacteria present on frog skin can prevent infection by the pathogenic fungus Batrachochytrium dendrobatidis (Bd), conferring disease resistance. Previous studies have used agar-based in vitro challenge assays to screen bacteria for Bd-inhibitory activity and to identify candidates for bacterial supplementation trials. However, agar-based assays can be difficult to set up and to replicate reliably. To overcome these difficulties, we developed a semi-quantitative spectrophotometric challenge assay technique. Cell-free supernatants were prepared from filtered bacterial cultures and added to 96-well plates in replicated wells containing Bd zoospores suspended in tryptone-gelatin hydrolysate-lactose (TGhL) broth medium. Plates were then read daily on a spectrophotometer until positive controls reached maximum growth in order to determine growth curves for Bd. We tested the technique by screening skin bacteria from the Australian green-eyed tree frog Litoria serrata. Of bacteria tested, 31% showed some degree of Bd inhibition, while some may have promoted Bd growth, a previously unknown effect. Our cell-free supernatant challenge assay technique is an effective in vitro method for screening bacterial isolates for strong Bd-inhibitory activity. It contributes to the expanding field of bioaugmentation research, which could play a significant role in mitigating the effects of chytridiomycosis on amphibians around the world.

Functional thin films fabricated by plasma polymerization and their biological applications

Plasma polymerization technique is widely accepted as an effective and simple method for the preparation of functional thin films. By careful choice of precursors and deposition parameters, plasma polymers bearing various functional groups could be easily obtained. In this work, I explored the deposition of four kinds of plasma polymerised functional thin films, including the protein-resistant coatings, the thermosensitive coatings, as well as, the coatings bearing amine or epoxide groups. The deposited plasma polymers were characterized by various techniques, such as X-ray photoelectron spectroscopy, atom force microscopy, Fourier transform infrared spectroscopy, surface plasmon resonance spectroscopy, optical waveguide spectroscopy, and so on. As expected, high retention of various functional groups could be achieved either at low plasma input power or at low duty cycle (duty cycle = Ton/(Ton+Toff)). The deposited functional thin films were found to contain some soluble materials, which could be removed simply by extraction treatment. Besides the thermosentive plasma polymer (see Chapter 9), other plasma polymers were used for developing DNA sensors. DNA sensing in this study was achieved using surface plasmon enhanced fluorescence spectroscopy. The nonfouling thin films (i.e., ppEO2, plasma polymerization of di(ethylene glycol) monovinyl ether) were used to make a multilayer protein-resistant DNA sensor (see Chapter 5). The resulted DNA sensors show good anti-fouling properties towards either BSA or fibrinogen. This sensor was successfully employed to discriminate different DNA sequences from protein-containing sample solutions. In Chapter 6, I investigated the immobilization of DNA probes onto the plasma polymerized epoxide surfaces (i.e., ppGMA, plasma polymerization of glycidyl methacrylate). The ppGMA prepared at a low duty cycle showed good reactivity with amine-modified DNA probes in a mild basic environment. A DNA sensor based on the ppGMA was successfully used to distinguish different DNA sequences. While most DNA detection systems rely on the immobilization of DNA probes onto sensor surfaces, a new homogeneous DNA detection method was demonstrated in Chapter 8. The labeled PNA serves not only as the DNA catcher recognizing a particular target DNA, but also as a fluorescent indicator. Plasma polymerized allylamine (ppAA) films were used here to provide a positively charged surface.

Advanced Techniques for Face Recognition under Challenging Environments

Automatically recognizing faces captured under uncontrolled environments has always been a challenging topic in the past decades. In this work, we investigate cohort score normalization that has been widely used in biometric verification as means to improve the robustness of face recognition under challenging environments. In particular, we introduce cohort score normalization into undersampled face recognition problem. Further, we develop an effective cohort normalization method specifically for the unconstrained face pair matching problem. Extensive experiments conducted on several well known face databases demonstrate the effectiveness of cohort normalization on these challenging scenarios. In addition, to give a proper understanding of cohort behavior, we study the impact of the number and quality of cohort samples on the normalization performance. The experimental results show that bigger cohort set size gives more stable and often better results to a point before the performance saturates. And cohort samples with different quality indeed produce different cohort normalization performance. Recognizing faces gone after alterations is another challenging problem for current face recognition algorithms. Face image alterations can be roughly classified into two categories: unintentional (e.g., geometrics transformations introduced by the acquisition devide) and intentional alterations (e.g., plastic surgery). We study the impact of these alterations on face recognition accuracy. Our results show that state-of-the-art algorithms are able to overcome limited digital alterations but are sensitive to more relevant modifications. Further, we develop two useful descriptors for detecting those alterations which can significantly affect the recognition performance. In the end, we propose to use the Structural Similarity (SSIM) quality map to detect and model variations due to plastic surgeries. Extensive experiments conducted on a plastic surgery face database demonstrate the potential of SSIM map for matching face images after surgeries.

High-resolution summer temperature reconstruction from Lake Silvaplana based on in-situ reflectance spectroscopy

Annually laminated (varved) sediments of proglacial Lake Silvaplana (46 ̊27’N, 9 ̊48’E, 1791 m a.s.l., Engadine, eastern Swiss Alps) provide an excellent archive for quantitative high-resolution (seasonal – annual) reconstruction of high- and lowfrequency climate signals back to AD 1580. The chronology of the core is based on varve counting, Cs-137, Pb-210 and event stratigraphy. In this study we present a reconstruction based on in-situ reflectance spectroscopy. In situ reflectance spectroscopy is known as a cost- and time-effective non destructtive method for semi-quantitative analysis of pigments (e.g., chlorines and carotenoids) and of lithoclastic sediment fractions. Reflectance-dependent absorption (RDA) was measured with a Gretac Macbeth spectrolino at 2 mm resolution. The spectral coverage ranges from 380 nm to 730 nm at 10 nm band resolution. In proglacial Lake Silvaplana, 99% of the sediment is lithoclastic prior to AD 1950. Therefore, we concentrate on absorption features that are characteristic for lithoclastic sediment fractions. In Lake Silvaplana, two significant correlations that are stable in time were found between RDA typical for lithoclastics and meteorological data: (1) the time series R 570 /R 630 (ratio between RDA at 570 nm and 630 nm) of varves in Lake Silvaplana and May to October temperatures at nearby station of Sils correlate highly significantly (calibration period AD 1864 – 1951, r = 0.74, p < 0.01 for 5ptsmoothed series; RMSE is 0.28 ̊C, RE = 0.41 and CE = 0.38), and (2) the minimum reflectance within the 690nm band (min690) data correlate with May to October (calibration period AD 1864 – 1951, r = 0.68, p < 0.01 for 5pt-smoothed series; RMSE = 0.22 ̊C, RE = 0.5, CE = 0.31). Both proxy series (min690nm and R 570 /R 630 values) are internally highly consistent (r = 0.8, p < 0.001). In proglacial Lake Silvaplana the largest amount of sediment is transported by glacial meltwater. The melting season spans approximately from May to October, which gives us a good understanding of the geophysical processes explaining the correlations between lithoclastic proxies and the meteorological data. The reconstructions were extended back to AD 1580 and show a broad corresponddence with fully independent reconstructions from tree rings and documentary data.

cDNA Library Generation for the Analysis of Small RNAs by High-Throughput Sequencing

The RNome of a cell is highly diverse and consists besides messenger RNAs (mRNAs), transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) also of other small and long transcript entities without apparent coding potential. This class of molecules, commonly referred to as non-protein-coding RNAs (ncRNAs), is involved in regulating numerous biological processes and thought to contribute to cellular complexity. Therefore, much effort is put into their identification and further functional characterization. Here we provide a cost-effective and reliable method for cDNA library construction of small RNAs in the size range of 20-500 residues. The effectiveness of the described method is demonstrated by the analysis of ribosome-associated small RNAs in the eukaryotic model organism Trypanosoma brucei.

Fruit and vegetable dietary patterns and weight loss in Mexican-American women

Although dietary patterns and their association with health outcomes is not a new topic, they have not been widely studied in Mexican-American populations. There are no studies of fruit and vegetable dietary patterns related to weight loss in Mexican-American women. This study aims to examine whether a change in proportion of fruit and vegetable consumption results in a change in weight. A secondary data analysis of 208 overweight or obese Mexican-American women from the Unidos en Salud weight loss intervention study was performed to investigate this relationship. Through regression analysis, the change in weight for every unit change in proportion of fruits and vegetables was tested with appropriate adjustment for age. The results showed a significant inverse association between fruit and vegetable intake densities and weight change. These results support previous studies and provide a possible effective and efficient method to reduce body mass index (BMI) among overweight or obese Mexican-American women. ^

Physical properties of sediments at DSDP Holes 78-541 and 78-543

Sediment cored within the Barbados subduction complex at Sites 541 and 542 are underconsolidated. Underconsolidation and changes in physical properties of the cored section can be related to excess pore water pressure that equals the lithostatic load at Site 542 and to major thrust faulting observed at Site 541. Apparently, the pore fluids within the subduction complex are absorbing the tectonic shock of underthrusting. Sediment sampled from the reference Site 543 on the adjacent Atlantic Plate are also underconsolidated. However, underconsolidation in Hole 543 is apparently due to the movement of excess nitrogen gas observed deeper in the hole. Excess gas was not observed at Sites 541 and 542.

Porosity and density of the AND-1B sediment core

A study of density and porosity is presented for the 1285-m-long AND-1B core recovered from a flexural moat in the McMurdo Sound (Antarctica) in order to interpret sediment consolidation in an ice-proximal location on the Antarctic shelf. Various lithologies imply environmental changes from open marine to subglacial, and are numerically expressed in high-resolution whole-core wet-bulk density (WBD). Grain density data interpolated from discrete samples range from 2.14 to 3.85 g/cm3 and are used to calculate porosity from WBD in order to avoid the 5%-15% overestimation and underestimation of porosities obtained by standard methods. The trend of porosity extends from 0.5 near the top (Pleistocene) to 0.2 at the bottom (Miocene). Porosity fluctuations in different lithologies are superimposed with 0.2-0.3 in sequences younger than ca. 1 Ma and 0.5-0.8 in Pliocene diatomites. The AND-1B porosities and void ratios of Pliocene diatomites and Pleistocene mudstones exhibit a large negative offset compared to modern lithological analogs and their consolidation trends. This offset cannot be explained in terms of the effective stress at the AND-1B site. The effective stress ranges from 0 to 4000 kPa in the upper 600 m, and reaches 13,000 kPa at the base of the AND-1B hole. We suggest an excess of effective overburden stress of ~1700 and ~6000 kPa to explain porosities in Pliocene diatomites and Pleistocene mudstones, respectively. This is interpreted as glacial preconsolidation by subsequently grounded ice sheets under subpolar to polar, followed by colder polar types of glaciations. Information on Miocene consolidation is sparse due to alteration by diagenesis.

Consolidation and permeability characteristics at DSDP Sites 87-582, 87-583, and 87-584

The results of nine consolidation and permeability tests are presented for sediment samples from the Japan Trench and Nankai Trough sites of Leg 87. Coring and degassing disturbance results in an underconsolidated state for most Site 582 samples; however, the compressional effects of the subduction zone and high sediment accumulation rates may also play a role in causing underconsolidation. Samples collected at Site 583 exhibit similar evidence of disturbance but are slightly overconsolidated, confirming the possibility of sediment erosion at this site. The highly diatomaceous sediments at Site 584 are all overconsolidated, but the trend of overconsolidation decreases with depth. Disturbances of the diatom clay structure may increase the sediment compressibility and create this apparent overconsolidation

Shear experiments from IODP Expedition 322 and 333 samples

The mechanical behavior of the plate boundary fault zone is of paramount importance in subduction zones, because it controls megathrust earthquake nucleation and propagation as well as the structural style of the forearc. In the Nankai area along the NanTroSEIZE (Kumano) drilling transect offshore SW Japan, a heterogeneous sedimentary sequence overlying the oceanic crust enters the subduction zone. In order to predict how variations in lithology, and thus mechanical properties, affect the formation and evolution of the plate boundary fault, we conducted laboratory tests measuring the shear strengths of sediments approaching the trench covering each major lithological sedimentary unit. We observe that shear strength increases nonlinearly with depth, such that the (apparent) coefficient of friction decreases. In combination with a critical taper analysis, the results imply that the plate boundary position is located on the main frontal thrust. Further landward, the plate boundary is expected to step down into progressively lower stratigraphic units, assisted by moderately elevated pore pressures. As seismogenic depths are approached, the décollement may further step down to lower volcaniclastic or pelagic strata but this requires specific overpressure conditions. High-taper angle and elevated strengths in the toe region may be local features restricted to the Kumano transect.

Permeability measurements on sheared and unsheared samples from different IODP Holes of Leg 316 and from IODP Hole 315-C0001E and ODP Hole 190-1174B

At subduction zones, the permeability of major fault zones influences pore pressure generation, controls fluid flow pathways and rates, and affects fault slip behavior and mechanical strength by mediating effective normal stress. Therefore, there is a need for detailed and systematic permeability measurements of natural materials from fault systems, particularly measurements that allow direct comparison between the permeability of sheared and unsheared samples from the same host rock or sediment. We conducted laboratory experiments to compare the permeability of sheared and uniaxially consolidated (unsheared) marine sediments sampled during IODP Expedition 316 and ODP Leg 190 to the Nankai Trough offshore Japan. These samples were retrieved from: (1) The décollement zone and incoming trench fill offshore Shikoku Island (the Muroto transect); (2) Slope sediments sampled offshore SW Honshu (the Kumano transect) ~ 25 km landward of the trench, including material overriden by a major out-of-sequence thrust fault, termed the "megasplay"; and (3) A region of diffuse thrust faulting near the toe of the accretionary prism along the Kumano transect. Our results show that shearing reduces fault-normal permeability by up to 1 order of magnitude, and this reduction is largest for shallow (< 500 mbsf) samples. Shearing-induced permeability reduction is smaller in samples from greater depth, where pre-existing fabric from compaction and lithification may be better developed. Our results indicate that localized shearing in fault zones should result in heterogeneous permeability in the uppermost few kilometers in accretionary prisms, which favors both the trapping of fluids beneath and within major faults, and the channeling of flow parallel to fault structure. These low permeabilities promote the development of elevated pore fluid pressures during accretion and underthrusting, and will also facilitate dynamic hydrologic processes within shear zones including dilatancy hardening and thermal pressurization.

Adaptação do ensaio SPT para determinação de parâmetros adicionais para o dimensionamento de fundações

A presente pesquisa foi desenvolvida com o intuito de agregar alguns procedimentos ao Ensaio SPT, para se obter um maior número de parâmetros para o dimensionamento de fundações, visto que este ensaio é o tipo de investigação de subsolo mais utilizado no Brasil para este fim. Os procedimentos adicionados foram: medida de eficiência do equipamento e ensaio de arrancamento do amostrador em cada camada distinta de solo atravessado. Foram realizados nove ensaios de arrancamento do amostrador, em três furos de sondagem, nas profundidades de dois, cinco e dez metros (três camadas de solos distintas). Em um quarto furo foram realizadas duas provas de carga à compressão no amostrador (nas profundidades de dois e cinco metros) para determinação da eficiência do equipamento. Por meio destes ensaios foi possível obter: a resistência de ponta do ensaio SPT, a resistência por atrito lateral na face externa do amostrador, e a razão de atrito do ensaio SPT, que pode ser usada para a classificação de solo de modo similar ao utilizado para o ensaio de cone. Além destes resultados, neste trabalho foi também analisada a relação entre a resistência por atrito interna e externa no amostrador durante o ensaio, conhecida por a. Esta relação mostrou-se maior para a camada de solo com grande porcentagem de pedregulho e menor para a camada que apresentava maior porcentagem de argila. Foi observado também que o valor de a cresce linearmente com a razão entre o valor de NSPT e a tensão vertical efetiva na profundidade do ensaio. Os resultados deste trabalho também mostraram que o valor da razão entre a resistência de ponta do ensaio SPT (qSPT) e o valor de NSPT é único para o mesmo tipo de solo. Além disso, os valores encontrados nesta pesquisa da razão qSPT/ NSPT são próximos aos valores da razão entre a resistência de ponta do ensaio de cone e o NSPT encontrados na literatura.

Modelo computacional para avaliação do desempenho hidrodinâmico de embarcações de planeio em águas calmas.

Em geral, uma embarcação de planeio é projetada para atingir elevados níveis de velocidade. Esse atributo de desempenho está diretamente relacionado ao porte da embarcação e à potência instalada em sua planta propulsiva. Tradicionalmente, durante o projeto de uma embarcação, as análises de desempenho são realizadas através de resultados de embarcações já existentes, retirados de séries sistemáticas ou de embarcações já desenvolvidas pelo estaleiro e/ou projetista. Além disso, a determinação dos atributos de desempenho pode ser feita através de métodos empíricos e/ou estatísticos, onde a embarcação é representada através de seus parâmetros geométricos principais; ou a partir de testes em modelos em escala reduzida ou protótipos. No caso específico de embarcações de planeio, o custo dos testes em escala reduzida é muito elevado em relação ao custo de projeto. Isso faz com que a maioria dos projetistas não opte por ensaios experimentais das novas embarcações em desenvolvimento. Ao longo dos últimos anos, o método de Savitsky foi largamente utilizado para se realizar estimativas de potência instalada de uma embarcação de planeio. Esse método utiliza um conjunto de equações semi-empíricas para determinar os esforços atuantes na embarcação, a partir dos quais é possível determinar a posição de equilíbrio de operação e a força propulsora necessária para navegar em uma dada velocidade. O método de Savitsky é muito utilizado nas fases iniciais de projeto, onde a geometria do casco ainda não foi totalmente definida, pois utiliza apenas as características geométricas principais da embarcação para realização das estimativas de esforços. À medida que se avança nas etapas de projeto, aumenta o detalhamento necessário das estimativas de desempenho. Para a realização, por exemplo, do projeto estrutural é necessária uma estimativa do campo de pressão atuante no fundo do casco, o qual não pode ser determinado pelo método de Savitsky. O método computacional implementado nesta dissertação, tem o objetivo de determinar as características do escoamento e o campo de pressão atuante no casco de uma embarcação de planeio navegando em águas calmas. O escoamento é determinado através de um problema de valor de contorno, no qual a superfície molhada no casco é considerada um corpo esbelto. Devido ao uso da teoria de corpo esbelto o problema pode ser tratado, separadamente, em cada seção, onde as condições de contorno são forçadamente respeitadas através de uma distribuição de vórtices.