Miracle-dz/UniFAR-FTUs huggingface dataset:
Cone normal stepping

This dissertation examines several methods of relief mapping, such as parallax mapping and cone step mapping, as well as methods for soft shadowing and ambient occlusion of relief maps. Ambient occlusion is an approximation of global illumination that only takes occlusion into account. New relief mapping methods are introduced to bridge the gap between distance fields and cone maps. The new methods allow calculating approximate distance fields from their cone map approximate ambient occlusion and soft shadows. The new methods are compared with linear, binary, and interval search as well as variants of cone mapping, such as relaxed cone mapping and quad cone mapping. These methods were evaluated with regards to performance and accuracy and were found to be similar in performance and accuracy than the existing methods. The new methods did not outperform existing methods on the tested scenes, but the new methods make use of approximate distance fields and remove the maximum cone angle limitation. It was also shown that in most cases linear search with interval mapping performed the best, given the error metric used.
Identification of Highly Informative Molecular Profile Components using Genetic Algorithms

Current techniques of DNA analysis enable the scoring of hundreds of electrophoretic bands using a small amount of DNA from an individual. The sample size in pilot experiments is typically orders of magnitude smaller then the number of bands contained in a molecular profile. Nevertheless, it is important to reduce the number of scored bands by identifying those subsets that contain useful information. The identified informative components can be further characterized using samples of larger size, so that experimental resources are not wasted. Highly informative profile components increase the ability to assign an individual whose membership is unknown to its actual group according to the scored band pattern. The features of this class of experiments make the use of standard statistical modelling involved. We propose the use of a Genetic Algorithm to obtain all the profile components that are highly informative given the available data. The theoretical justification of the objective function used by the Genetic Algorithm is based on Bayesian predictive arguments. Results from simulated datasets show that the implemented procedure is very promising for the identification of highly informative molecular profile components within the large set of observable bands produced in pilot experiments. Thus, Genetic Algorithms may be used to reduce the complexity of modern experiments in applied genetics.
Identification and Characterization of Differentially Expressed Genes in Ganoderma Boninense-Infected Oil Palms (Elaeis Guineensis)

Basal stem rot (BSR) caused by Ganoderma boninense is the most serious disease of oil palms in Malaysia. Thus, changes in the gene expression patterns of infected palms have gained interests among researchers as a tool to understand the disease. An indication that there are differences in susceptibility to BSR between germplasm materials from different genetic origins have provided hope in generating oil palm varieties with reduced levels of susceptibility by using existing genetic materials. The study of differentially expressed genes may also pave the way towards developing diagnostic tools for early disease detection in oil palms. A novel method combining elements of suppression subtractive hybridization (SSH) permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. This study used SSH and isolated 1,038 differentially expressed cDNAs from the G. boninense-inoculated oil palm seedlings (T1) when subtracted from its uninoculated counterpart (T2), using the basal stem and spear leaf tissues. Sequence data indicated that of the 1,038 clones obtained, 86% showed sequence similarity to proteins already registered in public databases, 10% showed similarity to putative protein sequences and 4% were unknown proteins with no records in public databases. Seven clones harboring genes encoding for defense mechanisms against fungal and insect pathogens in plants were identified. They were pathogenesis-related (PR)-genes and defense-related genes depending on their direct or indirect roles in plant defense against pathogens. Reverse northern analysis of these 7 clones demonstrated that 4 were differentially expressed in T1 but northern analysis showed that only 3 were differentially expressed. Further analysis via reverse transcription-PCR (RT-PCR) confirmed these 3 genes to be differentially expressed in G. boninense infected oil palms. They were MAG 43 that codes for serine palmitoyltransferase, MAG 59 for chitinase and MAG 225 for endochitinase.
Réponses de Streptococcus salivarius K12 à l'environnement et à la dynamique de la bouche simulés en bioréacteur

Ce travail de these vise a mieux comprendre l'effet de l'environnement buccal sur le comportement d'une bacterie orale probiotique, Streptococcus salivarius K12. La croissance et la maintenance de S. salivarius K12 ont tout d'abord ete caracterisees dans une salive artificielle complementee (CAS) concue pour l'etude. Dans ce milieu, cette bacterie demontre un taux de croissance eleve et un temps de latence court, mais elle ne produit pas de bacteriocines actives. La survie de S. salivarius K12 en phase stationnaire est, en revanche, affectee dans le milieu CAS. Ce phenomene est explique par une synthese moindre des proteines impliquees dans le metabolisme energetique, dont celui du glycogene. Toutefois, malgre une sensibilite accrue en phase stationnaire, le milieu CAS permet la croissance et la maintenance de S. salivarius K12. Les effets de plusieurs facteurs environnementaux specifiques de la bouche, sur S. salivarius K12, ont ete determines en milieu CAS. Ainsi, l'apport de saccharose, conduit a une degradation de la viabilite. Des enzymes, ajoutees a leur concentration physiologique, affectent egalement les cellules bacteriennes. Le lysozyme accroit la mortalite de S. salivarius par son action sur la paroi bacterienne. La peroxidase ameliore sa viabilite en diminuant le potentiel redox du milieu. Le role cle du potentiel redox sur S. salivarius K12 est confirme par l'impact negatif de l'injection d'air enrichi a 5% de CO2, qui accroit le potentiel redox. Enfin, l'amylase a demontre un role a la fois positif (augmentation de la biomasse) et negatif (diminution du taux de croissance). En consequence, les etudes impliquant des bacteries orales se doivent de prendre en compte ces facteurs environnementaux influant sur les l'etat physiologique bacterien. La mise en place de cultures continues respectant les variations de flux salivaire et permettant l'apport periodique de nutriments, tout en combinant l'ensemble des conditions environnementales identifiees precedemment, a permis de simuler la dynamique des conditions buccales. Les resultats demontrent que S. salivarius K12 est bien adapte a ces conditions de culture. Les cellules sont capables de se maintenir a un niveau de cultivabilite constant, malgre la carence nutritionnelle et le lessivage auxquels elles sont soumises. Certains mecanismes moleculaires expliquant cette adaptation ont ete caracterises : activation des voies d'utilisation de sources de carbone alternatives, stockage de l'energie, augmentation de la competence genetique naturelle. Finalement, ces travaux ont permis d'identifier certains mecanismes permettant a Streptococcus salivarius K12 de s'adapter a l'environnement buccal, grâce a la mise en place de methodes d'etude in vitro du comportement des bacteries orales.
Aislamiento y cultivo de protoplastos en Maracuyá

In this research we adjust the protoplasts culture and regeneration conditions, necessary to advance into somatic hybrids obtention. Isolation of Passiflora edulis var. flavicarpa protoplasts from in vitro seedlings cotyledons and leaves was carried out. These tissues were plasmolysed in a CPW13M solution, then exposed to enzymatic solutions. The better yields were 6,48 x 106 and 4,60 x 106 protoplasts/500 mg of tissue, reached with the mixture Cellulase R-10 1% and Pectolyase Y-23 0,05% from leaves, and the enzymatic solution Cellulase 2% and Macerozyme 0,4% from cotyledons tissue, respectively. The best densities for protoplasts culture were 5 x 104 protoplasts/ml obtained from cotyledons and 1,5 x 105 protoplast/ml from leaves, employing agarose droplets system, bathing by KM8p liquid media with glucose 100g/l and cefotaxime 300μg/ml. When first cell divisions occurred, the osmotic concentration was reduced by removing the liquid media and adding equal volume of fresh mix media KM8p:KM8 in a ratio of 3:1. Every seven days, this action was repited using mix media in ratios of 2:1, 1:1, and 1:3, until colonies and callus formation was achieved. Then, the call were transferred into MS media with BAP 2 mg/l and IBA 1 mg/l for plant regeneration on light conditions. After six weeks shoot differentiation was promoved, finally those shoots were subcultured to free regulators media for rooting.
Phylogeographic analysis and environmental niche modeling of widespread shrub Rhododendron simsii in China reveals multiple glacial refugia during the last glacial maximum

Abstract The phylogeography of common and widespread species can help us to understand the history of local flora and vegetation. Here, we study the semi‐evergreen shrub Rhododendron simsii Planch. , which is found in most areas of current evergreen broad leaved forest in China. Two noncoding chloroplast DNA (cpDNA) regions (rpl20‐rps12 and trnL‐F) and three amplified fragment length polymorphism (AFLP) primer sets (E‐AAC/M‐CTA, E‐AGC/M‐CTA and E‐AGG/M‐CAT) were used to examine the phylogeographic pattern in relation to past (last glacial maximum) and present distributions based on ecological niche modeling. The cpDNA data revealed four phylogeographic groups (East, South, West, and North groups) corresponding to geographic regions. Molecular dating suggests that lineage diversification within species likely occurred during the mid‐to‐late Pleistocene. In contrast, the four main cpDNA phylogeographic groups were not supported by the AFLP dataset. The highest likelihood of the AFLP data was obtained when samples were clustered into three groups (K= 3). However, these groupings did not correspond to separate geographic regions supported by cpDNA data. Both mismatch distribution analysis and environmental niche modeling (ENM) indicated that multiple glacial refugia were maintained across the range of Rhododendron simsii during the last glacial maximum, contrary to the previous hypothesis that subtropical broad leaved evergreen forests were forced to retreat southward as far as 25° N. The discordance between the patterns revealed by cpDNA and AFLP data indicate that localized postglacial range expansions may facilitate extensive gene flow between the major glacial refugia.
Distribution of Freshwater Turtles in Punjab, Pakistan

A total of 3528 specimens of freshwater turtles belonging to two families viz., Geoemydidae (Brown River Turtle, Kachuga smithi; Indian Saw-backed turtle, K. tecta; Brahminy Rrive Turtle, Hardella thurgi; Spotted Pond Turtle, Geoclemys hamiltonii) and Trionychidae (Indian Soft-shell Turtle, Aspederates gangeticus; Peacock Soft-shell Turtle, A.hurum; Narrow-headed Soft-shell Turtle, Chitra indica; Indian Flap-shell Turtle, Lissemys punciata) were identified. Kachuga smithi (43.62%) and K.tecta (42.06%) had abundant population status, whereas, Hardella thurgi (0.88%) and Chitra indica (0.54%) were rare. Capturing of turtles for supply to foreigners and export is a major threat to these animals. Fishermen also kill them during fishing. Canal closure and de-silting is also harmful to turtles. It is concluded that it is necessary to provide immediate legal protection/coverage to all turtle species under the Punjab Wildlife Act, 1974, Pakistan; otherwise turtle species will become extinct.
Ecology and distribution of Armillaria species in Norway

Summary The occurence of Armillaria species was assessed in Norway, enabling the northern-most distribution of this genus to be determined in Europe. Four Armillaria species were found in Norway. Armillaria borealis was the most common species occurring on woody vegetation to the permafrost zone (ca. 69� N). Armillaria cepistipes was present in southern and central Norway, but was not found further than 66� N. Armillaria solidipes and Armillaria gallica were rare, found at only one locality each; 59� 40¢ and 59� 32¢, respectively. Armillaria species were found on 14 hosts, but there was no significant difference between occurrence of A. borealis and A. cepistipes on declining and dead trees. Phylogenetic analyses separated each species into separate clades. All isolates of A. borealis, except one, and most isolates of A. solidipes were in separate clades. However, a subclade within the A. borealis clade was formed of two A. ostoyae and one A. borealis isolates. Two small A. cepistipes genets were found in a declining oak stand.
Incongruence between Morphological and Molecular Traits in Populations of J'7ola violacea (Violaceaej in Yamagata Prefecture, Northern Honshu, Japan

Yamagata Prefecture, Tohoku district by comparing leaf morphology, nuclear ribo-sornal DNA (nrDNA) ITS, and the trnL-trnF intergenic region ofthe chloroplast DNA (cpDNA). The leafmorphology ef M vioiacea var, violacea-like plants in Yamagata was identical to lf vioiacea var. violacea elsewhere, but the nrDNA ITS sequences ofthe Yamagata plants were more simiLar to M viotacea var. makinoi, This cLear difference was not found in the cpDNA trnL-trnF region. The incongruity between Ieaf morphology and molecular traits may be due to Z violacea var. viotacea populations that are more closely related to K violacea var. makinoi or to intraspecific hybridization. To confirm these hypotheses, more extensive study is needed. morphology undertook molecular phylogenetic anaiyses populations varieties. Previous morphological comparisons of P': vioiacea starting that
Early eusuchia crocodylomorpha from the vertebrate‐rich Plattenkalk of Pietraroia (Lower Albian, southern Apennines, Italy)

The locality of Pietraroia (Lower Albian, southern Apennines, Italy) has provided two fully articulated crocodylomorphs, exposed in ventral and in dorsal aspect, which are described here as representing a new species of a new genus, Pietraroiasuchus ormezzanoi gen. nov, sp. nov. The new taxon is found to be the sister taxon of Pachycheilosuchus trinquei from the Albian of the Glen Rose Formation, Texas. Pietraroiasuchus ormezzanoi resolves the phylogenetic position of the controversial P. trinquei, and is crucial in enabling an extensive understanding of the family Hylaeochampsidae. Phylogenetic analysis places Hylaeochampsa vectiana as a sister group of Iharkutosuchus makadii plus Pachycheilosuchus and Pietraroiasuchus. The phylogenetic result reveals the presence of an evolutionary mosaicism within non-crocodylian eusuchians. Mosaic features in Pietraroiasuchus are denoted by the combination of primitive character states, such as the position of the choana with its anterior margin formed by an inverted V-shaped palatine processeses, and the presumed presence of a tiny antorbital fossa, in conjunction with derived states involving the slight vertebral procoelia, the presence of tetraserial segmented dermal armour with an accessory lateral row, and isolated nuchal osteoderms. The disjoint occurrence between Pachycheilosuchus and Pietraroiasuchus species suggests that Pietraroia was a refuge island inhabited by endemic forms. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, S199–S227.
EVALUATION OF THE ANTIOXIDANT ACTIVITY OF ESSENTIAL OILS FROM CAPER (CAPPARIS SPINOSA) AND SEA FENNEL (CRITHMUM MARITIMUM) BY DIFFERENT METHODS

In this study, essential oils from wild-grown caper (Capparis spinosa L.) and sea fennel (Crithmum maritimum L.) from Dalmatia (Croatia) were iso- lated by hydrodistillation and analyzed by gas chromatography with mass spectrometry. Methyl isothiocyanate (92.06%) was detected as major compo- nent of essential oil from caper leaves and flower buds, while limonene (58.37%), sabinene (26.46%), terpinene-4-ol (5.59%) and g-terpinene (2.81%) were identified as dominant compounds in sea fennel essential oil. Tested essential oils did not exhibit radical-scavenging activity by 1,1- diphenyl-2-picrylhydrazyl hydrate method, while they showed the antioxidant activity by b-carotene bleaching method and thiobarbituric acid reactive species assay. In addition, sea fennel essential oil exhibited very high inhibi- tory effect on the oxidation of human low-density lipoprotein.
IFN-γ and STAT1 Arrest Monocyte Migration and Modulate RAC/CDC42 Pathways1

Positive regulation of cell migration by chemotactic factors and downstream signaling pathways has been extensively investigated. In contrast, little is known about factors and mechanisms that induce migration arrest, a process important for retention of cells at inflammatory sites and homeostatic regulation of cell trafficking. In this study, we found that IFN-γ directly inhibited monocyte migration by suppressing remodeling of the actin cytoskeleton and cell polarization in response to the chemokine CCL2. Inhibition was dependent on STAT1 and downstream genes, whereas STAT3 promoted migration. IFN-γ altered monocyte responses to CCL2 by modulating the activity of Pyk2, JNK, and the GTPases Rac and Cdc42, and inhibiting CCL2-induced activation of the downstream p21-activated kinase that regulates the cytoskeleton and cell polarization. These results identify a new role for IFN-γ in arresting monocyte chemotaxis by a mechanism that involves modulation of cytoskeleton remodeling. Crosstalk between Jak-STAT and Rac/Cdc42 GTPase-mediated signaling pathways provides a molecular mechanism by which cytokines can regulate cell migration.
Comparative Population Structure Of The Caribbean Sea Fan Coral Gorgonia Ventalina, And Its Dinoflagellate Endosymbiont, Symbiodinium Sp.

Here we report primers for ten microsatellite loci from the Caribbean sea fan coral, Gorgonia ventalina. Primers were tested on 237 genomic DNA extracts taken directly from tissue samples of G. ventalina. All loci were polymorphic with allelic richness ranging from 4 to 52. Expected heterozygosity ranged from 0.14 to 0.96. Preliminary data suggest that these microsatellites will be useful tools for studies of the population genetics of this important Caribbean coral species. INTRODUCTION Gorgonian corals are conspicuous benthic inhabitants of most healthy Caribbean reefs (Opresko 1973, Yoshioka and Yoshioka 1989, Sanchez et al. 1997). Their high abundance and complex three-dimensional structure provide essential habitat for a diversity of reef fauna, making them important ecosystem structuring organisms. One of the most abundant Caribbean gorgonian species is the sea fan coral, Gorgonia ventalina (Ward et al. 2006). Over the past two decades, populations of G. ventalina have been heavily impacted by the fungal disease aspergillosis (Nagelkerken et al. 1997, Kim and Harvell 2004, Kim et al. 2006), and numerous studies have investigated the ecology, epidemiology, and immunology of this coral disease system. Yet most basic information regarding the life history and population biology of G. ventalina remains unknown. An understanding of the distribution and dynamics of population genetic diversity is essential for effective management and conservation, particularly for species such as G. ventalina that have been heavily
Comparative Biology of Three Species of Costa Rican Haeterini

Tropical forest insects are vertically stratified between the canopy and understorey. Using 60 traps set at two heights above the forest floor (30 at 15 cm and 30 at 1 m) we compared abundances in capture height, persistence in traps, and sex of three co-occurring understorey butterflies (Cithaerias pireta, Dulcedo polita, and Pierella helvina) in Costa Rica. We captured, marked and released 283 individual butterflies (65 C. pireta, 79 D. polita, 139 P. helvina) and showed all three species were captured more often in low traps, and P. helvina was captured only in low traps. The probability of remaining in traps for 24 h did not differ significantly for D. polita and P. helvina, but was significantly lower for C. pireta. The odds of trapping either sex did not differ significantly for P. helvina and C. pireta, but they were significantly lower for D. polita males. We experimentally demonstrate that these cooccurring species fly and feed just above the forest floor, but differ with respect to their persistence in traps and attraction to traps by sex. Our study implies that closely related species can exhibit behavioural differences that may influence population abundance estimates in multi-species studies.
Molecular Evolution of Vasopressin and Oxytocin Receptor Genes in Owl Monkeys (aotus Azarai) of Northern Argentina

The arginine vasopressin (AVP) and oxytocin (OT) hormone pathways are involved in a multitude of physiological processes, and their receptor genes (AVPR1A and OXTR) have been implicated in increased partner preference and pair bonding behavior in mammalian lineages. This observation is of considerable importance for understanding social monogamy in primates, which is present in only a small subset of primate taxa, including Azara's owl monkeys (Aotus azarai). Thus, it is the goal of this dissertation to examine the molecular evolution of AVPR1A and OXTR in owl monkeys to better understand how the pro-social behaviors related to those loci may have evolved. However, in order to properly contextualize functional neurogenetic variation related to such sociobehavioral pattterns, it is necessary to first establish the range of molecular variation occurring at non-related genetic loci. To address this issue, we sequenced the entire mitochondrial genome of two species of Aotus (A. azarai and A. nancymaae), and analyzed 39 haplotypes of the mitochondrial COII gene from ten different owl monkey taxa. Next, to understand the recent evolutionary history and genetic structure of our focal owl monkey population, we assessed variation of the mtDNA control region (D-loop) in 118 wild individuals. Furthermore, to establish our knowledge of genetic kinship and individual identity within the wild population, we investigated autosomal variation in the form of 24 short tandem repeat (STR) microsatellite loci. In concert with these analyses, we characterized the molecular features of AVPR1A and OXTR in A. azarai and other platyrrhines through direct sequencing, and demonstrated that there are substantial sequence differences at both loci across primate species. These data provide new clues on the possible basis of pair bonding in New World species, and may help to explain the sporadic appearance of monogamy in this infraorder. Specifically, despite a common molecular origin, we argue that the AVP and OT pathways have evolved in markedly different ways, due in part to their chromosomal locations and their relative proximity to regions of molecular instability. This study reinforces the notion that neurogenetic loci in primates have undergone significant evolutionary changes, and suggests that monogamy has arisen multiple times in the primate order through different molecular mechanisms. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Anthropology First Advisor Theodore G. Schurr This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/489