Miracle-dz/UniFAR-FTUs huggingface dataset:
Approximate Bayesian inference methods for stochastic state space models

This thesis collects together research results obtained during my doctoral studies related to approximate Bayesian inference in stochastic state-space models. The published research spans a variety of topics including 1) application of Gaussian filtering in satellite orbit prediction, 2) outlier robust linear regression using variational Bayes (VB) approximation, 3) filtering and smoothing in continuous-discrete Gaussian models using VB approximation and 4) parameter estimation using twisted particle filters. The main goal of the introductory part of the thesis is to connect the results to the general framework of estimation of state and model parameters and present them in a unified manner. Bayesian inference for non-linear state space models generally requires use of approximations, since the exact posterior distribution is readily available only for a few special cases. The approximation methods can be roughly classified into to groups: deterministic methods, where the intractable posterior distribution is approximated from a family of more tractable distributions (e.g. Gaussian and VB approximations), and stochastic sampling based methods (e.g. particle filters). Gaussian approximation refers to directly approximating the posterior with a Gaussian distribution, and can be readily applied for models with Gaussian process and measurement noise. Well known examples are the extended Kalman filter and sigma-point based unscented Kalman filter. The VB method is based on minimizing the Kullback-Leibler divergence of the true posterior with respect to the approximate distribution, chosen from a family of more tractable simpler distributions. The first main contribution of the thesis is the development of a VB approximation for linear regression problems with outlier robust measurement distributions. A broad family of outlier robust distributions can be presented as an infinite mixture of Gaussians, called Gaussian scale mixture models, and include e.g. the t-distribution, the Laplace distribution and the contaminated normal distribution. The VB
Molecular Support for Species Status of the Nazca Booby (Sula granti)

Abstract Pitman and Jehl (1998) recently argued that Masked Boobies (formerly Sula dactylatra granti) breeding on the Nazca Plate in the eastern Pacific Ocean are morphologically and ecologically distinct from other Masked Boobies and may represent a full species. The American Ornithologists' Union subsequently elevated that subspecies to a full species: the Nazca Booby (S. granti). To evaluate that change in classification, we compared sequence variation in the mitochondrial cytochrome-b gene among 75 Nazca Boobies and 37 Masked Boobies representing three subspecies from the central and eastern Pacific and Atlantic oceans. Results indicated strong differentiation of cytochrome-b variation among taxa. Sequences constituted three distinct groups: Nazca Boobies, Masked Boobies from the central and eastern Pacific (S. d. personata and S. d. californica), and Masked Boobies (S. d. dactylatra) from the Caribbean and Atlantic. Those three groups probably diverged within a very short period, 400,000–500,000 years ago. Our results support the proposal that S. granti represents a distinct species.
Human lung fluke Paragonimus heterotremus : Differentiation of antigenic proteins of adult worms by enzyme-linkel immunoelectrotransfer blot technique

Delipidized protein prepared from lyophilized adult worms of Paragonimus heterotremus demonstrated about 40 stained bands with Coomassie brilliant blue after fractionating through 12% SDS-PAGE. Proteins (80 μg/serum sample) were run through SDS-PAGE and EITB with various human antisera from paragonimiasis, other helminthiases, and tuberculosis cases, as well as from normal controls. Results revealed immune complexes with serum IgG of 40 paragonimiasis presenting 9 major molecular weights of approximately 35, 33, 32.5, 31.5, 29, 28.5, 27, 26 and 16 kDa. Three polypeptide bands of 35, 33 and 32.5 kDa show no cross-reactivity with antibodies (IgGs) of other sera These components should be recognized as reacting antigens for the serodiagnosis of paragonimiasis.
INVESTIGATION ON PROMOTIONAL CRITERIA BASED ON HUMAN RESOURCE PRACTICES FOR BETTER ORGANIZATIONAL EFFECTIVENESS

Promotional decision is one of the important human resource practices that has been seen as a challenge for many organizations. Strong human capital is the successful factor for the development of an organization which can help the company to gain competitive advantage. Promotion criteria which based on seniority, competency, leadership and job attitude are going to discuss in this paper to test their relationship with company performance. 100 human resource executives from different companies will answer the self-directed questionnaire for data collection. Pearson correlation coefficient and multiple regressions will be used to analyse the relationship between independent variables and dependent variable. Results showed that all independent variables are positively related to dependent variable where competency is resulted in highest relationship. Managerial implications are provided to guide managers on the effective promotion criteria for better organizational effectiveness.
High mRNA expression of splice variant SYK short correlates with hepatic disease progression in chemonaive lymph node negative colon cancer patients

Objective Overall and splice specific expression of Spleen Tyrosine Kinase (SYK) has been posed as a marker predicting both poor and favorable outcome in various epithelial malignancies. However, its role in colorectal cancer is largely unknown. The aim of this study was to explore the prognostic role of SYK in three cohorts of colon cancer patients. Methods Total messenger RNA (mRNA) expression of SYK, SYK(T), and mRNA expression of its two splice variants SYK short (S) and SYK long (L) were measured using quantitative reverse transcriptase (RT-qPCR) in 240 primary colon cancer patients (n = 160 patients with chemonaive lymph node negative [LNN] and n = 80 patients with adjuvant treated lymph node positive [LNP] colon cancer) and related to microsatellite instability (MSI), known colorectal cancer mutations, and disease-free (DFS), hepatic metastasis-free (HFS) and overall survival (OS). Two independent cohorts of patients with respectively 48 and 118 chemonaive LNN colon cancer were used for validation. Results Expression of SYK and its splice variants was significantly lower in tumors with MSI, and in KRAS wild type, BRAF mutant and PTEN mutant tumors. In a multivariate Cox regression analysis, as a continuous variable, increasing SYK(S) mRNA expression was associated with worse HFS (Hazard Ratio[HR] = 1.83; 95% Confidence Interval[CI] = 1.08–3.12; p = 0.026) in the LNN group, indicating a prognostic role for SYK(S) mRNA in patients with chemonaive LNN colon cancer. However, only a non-significant trend between SYK(S) and HFS in one of the two validation cohorts was observed (HR = 4.68; 95%CI = 0.75–29.15; p = 0.098). Conclusion In our cohort, we discovered SYK(S) as a significant prognostic marker for HFS for patients with untreated LNN colon cancer. This association could however not be confirmed in two independent smaller cohorts, suggesting that further extensive validation is needed to confirm the prognostic value of SYK(S) expression in chemonaive LNN colon cancer.
Degradabilidad ruminal in situ e in vitro de la metionina protegida

Rumen microbes rapidly degrade amino acids in ruminant diets, and in response DL-methionine has been rumen-protected (RPMet) to increase duodenal digestible methionine. Two experiments were conducted to estimate rumen degradability of a commercial rumen-protected methionine (Mepron.M85, Degussa-Hulls). In the first experiment, in situ degradability of RPMet was determined at 12, 18 and 24 h using two cows fitted with rumen cannula. In the second experiment, in vitro degradability of RPMet at 12 and 18 h were replicated for four consecutive incubations using a mixture of rumen liquid from two cannulated cows as inoculum. Differences were recorded depending on incubation time (P<0.01) in both experiments. in situ degradability of RPMet dry matter was 25.1 % at 12 h incubation, 40.7 % at 18 h and 55.5 % at 24 h, while for RPMet crude protein it was 26.5 % at 12 h, 43.0 % at 18 h and 58.2 % at 24 h. in vitro degradability of RPMet dry matter was 24.7 % at 12 h incubation and 36.5 % at 18 h, while for RPMet crude protein it was 26.7 % at 12 h and 35.1 % 18 h. RPMet digestion rate at 24 h was 3.3 % h-1 for dry matter and 3.6 % h-1 for crude protein. Results indicate that rumen-protected methionine experiences moderate degradation at 12 h, though it can increase to more than 35 % after 18 h in the rumen.
Taxonomic and evolutionary implications of spore ornamentation in Davalliaceae

Davalliaceae is a small family of derived ferns that grow epiphytic or occasionally epilithic in the tropics and subtropics of the Old World. Despite recent taxonomic and phylogenetic achievements, some aspects of its classification remain controversial. In this study, we provided new spore observations on Davalliaceae by using scanning electron microscopy. The newly generated data were integrated together with previously reported spore evidence of this group. The evolution of spore ornamentation and taxonomic implications of spore characters was optimized onto a phylogenetic tree based on plastid sequences. Verrucate colliculate spore ornamentation was identified as plesiomorphic character state within Davalliaceae. The Humata clade was characterized by the transition from verrucate colliculate to fused verrucate ornamentation. Several species complexes subject to taxonomic controversy were found to show informative variation in the spore ornamentation. In conclusion, our observations support the utility of spores as a morphological taxonomic trait in ferns, as long as the evolution of spore morphology is considered.
Characteristics and Spatial Segregation of Sympatric Saugers and Walleyes in the Ottawa River, Canada

AbstractFew comparative studies exist on the sympatric populations of Saugers Sander canadensis and Walleyes S. vitreus, especially in northern rivers. Depth-stratified, standardized index netting surveys were conducted in the Ottawa River, Canada—a large, fragmented northern river. The objectives of this study were to (1) determine whether Saugers and Walleyes were spatially segregated within river reaches; (2) assess whether relative abundances of the two species were correlated within river reaches and ascertain factors affecting their relative abundances; (3) determine whether life history characteristics in this northern river were within the variation reported for each species; and (4) evaluate whether there was synchrony in year-class strength between the two species and identify the factors affecting year-class strength. Saugers and Walleyes were spatially segregated, specifically by depth. Probability of capture was greatest in the 20–35-m depth stratum for Saugers and in the 6–12-m depth stratum.
Sesotho names for exotic and indigenous edible plants in southern Africa

A comprehensive checklist of Sesotho names of both indigenous and exotic food plants is presented, based on a literature survey and the first author's experience. The list includes the scientific names. English common names and parts of the plant that are used. Where possible, the origin or meaning of the Sesotho names is given. Exotic edible plants for which the English common names are in general use have been excluded. The list includes 164 indigenous and 39 names of exotic species.
Human‐mediated introductions of Australian acacias – a global experiment in biogeography

Aim Australian acacias (1012 recognized species native to Australia, which were previously grouped in Acacia subgenus Phyllodineae) have been moved extensively around the world by humans over the past 250 years. This has created the opportunity to explore how evolutionary, ecological, historical and sociological factors interact to affect the distribution, usage, invasiveness and perceptions of a globally important group of plants. This editorial provides the background for the 20 papers in this special issue of Diversity and Distributions that focusses on the global cross‐disciplinary experiment of introduced Australian acacias.
Haematology of Australian Mammals

Haematology of Australian Mammals is a valuable guide to collecting and analysing the blood of Australian mammals for haematological studies and diagnosis and monitoring of disease. It outlines general principles for selecting sites for blood collection and for handling and analysing samples to achieve quality results. Chapters then describe the morphology and function of haematological cells, with reference to the known characteristics of Australian mammals in health and the changes that may be encountered in response to common diseases. Haemoparasites that have been encountered in Australian mammals are discussed next, along with comments on their pathogenicity. Lastly, haematological values from previously published studies are compiled into species-specific tables, providing a convenient reference to compare to the results of clinical cases. Written descriptions and colour photomicrographs of haematological cells from more than 100 species aid the identification of cells and the detection of abnormalities. Information is provided throughout for representative species from all the major groups of native Australian mammals including monotremes, polyprotodont marsupials, diprotodont marsupials, rats and mice, bats and marine mammals.
Effect of a Silicate Fertilizer Supplemented to a Medium on the Growth and Development of Potted Plants

This experiment was carried out to examine the effect of a silicate fertilizer on the growth and development of potted plants. Cutting of Kalanchoe blossfeldiana ‘Kaluna’ and ‘Taos’, and Dianthus caryophyllus L. ‘Kazan’ and ‘Tula’ were grown in 50 and 128-cell plug trays, respectively. Rooted cuttings transplanted to the mixture of a commercial medium and perlite (5:1, v/v) supplemented with a silicate fertilizer at 0, 40, 80, 120 or 160 gㆍL? ¹ medium was evaluated. A silicate fertilizer supplementation at 40 gㆍL? ¹ medium resulted in the greatest plant height, leaf thickness, and root fresh and dry weights in both kalanchoe and carnation. However, plant height was suppressed in the treatment of a silicate fertilizer supplementation at higher concentrations in both kalanchoe and carnation. According to the scanning electron microscope images of transversal sections of tissues of roots and leaves in kalanchoe and carnation, the treatment of a silicate fertilizer supplementation at 40 gㆍL? ¹ medium resulted in plants with more compact tissue than the control.
The rms1 Mutant of Pea Has Elevated Indole-3-Acetic Acid Levels and Reduced Root-Sap Zeatin Riboside Content but Increased Branching Controlled by Graft-Transmissible Signal(s)

Rms1 is one of the series of five ramosus loci in pea (Pisum sativum L.) in which recessive mutant alleles confer increased branching at basal and aerial vegetative nodes. Shoots of the nonallelic rms1 and rms2 mutants are phenotypically similar in most respects. However, we found an up to 40-fold difference in root-sap zeatin riboside ([9R]Z) concentration between rms1 and rms2 plants. Compared with wild-type (WT) plants, the concentration of [9R]Z in rms1 root sap was very low and the concentration in rms2 root sap was slightly elevated. To our knowledge, the rms1 mutant is therefore the second ramosus mutant (rms4 being the first) to be characterized with low root-sap [9R]Z content. Like rms2, the apical bud and upper nodes of rms1 plants contain elevated indole-3-acetic acid levels compared with WT shoots. Therefore, the rms1 mutant demonstrates that high shoot auxin levels and low root-sap cytokinin levels are not necessarily correlated with increased apical dominance in pea. A graft-transmissible basis of action has been demonstrated for both mutants from reciprocal grafts between mutant and WT plants. Branching was also largely inhibited in rms1 shoots when grafted to rms2 rootstocks, but was not inhibited in rms2 shoots grafted to rms1 rootstocks. These grafting results are discussed, along with the conclusion that hormone-like signals other than auxin and cytokinin are also involved.
Quantum Chemical Estimation of Environmental and Metabolic Fates of Pesticides

Recent progress in computer hardware and programs of molecular orbital (MO) calculations provides an opportunity for us to examine electronic properties of chemicals and reaction mechanisms at a molecular level. The semiempirical and ab initio MO methods have been applied to theoretically estimate the various transformation processes of pesticides in the environment. The electron distribution in the frontier MO's was used as the most convenient index to explain a reactivity of pesticides together with its regioselectivity. Mulliken charge at an individual atom and electrostatic interaction with a hydroxide ion were used as an index to explain the relative ease of hydrolysis for organophosphorus pesticides and hydrolysis pathways of carbamates. The reaction coordinate technique was further applied to seek out transition states and hydrolysis pathways could be estimated together with a substituent effect. Electronic properties in the excited states were useful to estimate photooxidation and photosensitization of pesticides. The photoinduced decarboxylation and isomerization of pyrethroids were successfully explained by the new photolysis index d M which was defined as a change of electron population at each bond via molecular excitation. In the case of metabolic oxidation catalyzed by cytochrome P-450, the detailed analysis using reaction indices suggested the triplet mechanism for aliphatic hydroxylation. The relative ease of aromatic hydroxylation at an individual carbon atom was qualitatively estimated by the electron distribution of the highest occupied MO, but the steric constraint at an enzyme active site was found to be an important factor to determine its regioselectivity.
Association of Major Depression with Serum Prolidase Activity and Oxidative Stress

Aim: Stress is a major causative factor for the progression of major depressive disorder (MDD). The present study aimed to know the association of serum prolidase activity (SPA) and oxidative stress with the progression of MDD. Methodology: 80 patients with MDD and 80 healthy controls of matched age and genders were selected. Serums SPA, total oxidant status (TOS), oxidative stress index (OSI) and total antioxidant status (TAS) were measured spectrophotometrically. Results: Increased SPA, TOS, and OSI were observed in patients with MDD than healthy controls (all P < 0.001). However, TAS was significantly decreased (P < 0.001). SPA, TOS and OSI were also increased in patients with > 1 years of MDD than patients with ≤ 1 years of MDD. Positive, linear and significant correlations were observed between duration of MDD and SPA, and TOS, and OSI (all P < 0.001). However, negative, linear and significant correlation was observed between duration of MDD and TAS (P < 0.001). Conclusions: The study concluded that SPA and oxidative stress have been significantly increased in the patients with MDD than healthy individuals. Increased SPA and oxidative stress might be significantly correlated to progression of MDD and may be responsible for its pathogenesis.
Correlation of electrical conductivity and other vigor tests with field emergence of soybean seedlings

Seeds from six soybean cultivars (Cristalina, IAC 31-Foscarin, IAC-15, UFV-10, IAC-14 and IAS-5) and from five soybean cultivars (1AC 31-Foscarin, IAC-15, IAC-14, IAS-5 and Iguacu) were evaluated in 1993 and 1994, respectively, in terms of physiological seed quality by the mechanical damage (MD), standard germination (SG), accelerated aging (AA), electrical conductivity (EC), and seedling field emergence (FE) tests. Significant correlations were detected between SG, AA and EC and FE. However, in terms of the cultivar or the year, the degree of association among these parameters can change based on the environmental conditions of each year.
Dégradation des fibres pariétales et système xylanolytique de Bacteroides xylanisolvens XB1AT et Roseburia intestinalis XB6B4, espèces bactériennes du microbiote intestinal humain

Chez l'Homme, les parois vegetales contenues dans les fibres alimentaires sont degradees puis fermentees par les bacteries fibrolytiques du colon. Le xylane etant l'un des principaux polysaccharides constituant ces parois vegetales, deux bacteries possedant de fortes activites xylanolytiques, Bacteroides xylanisolvens XB1AT et Roseburia intestinalis XB6B4, ont ete caracterisees. Les activites xylanolytiques de ces especes vis-a-vis de differents substrats riches en xylanes ont ete analysees quantitativement et qualitativement. Ces deux especes degradent et fermentent tres efficacement ces substrats, mais les colonisent differemment. L'equipement enzymatique de ces souches, compare par zymogramme, revele un grand nombre de xylanases dont la masse molaire varie de 37 kDa a 170 kDa. Les activites specifiques des extraits proteiques des deux bacteries sont tres elevees et sont majoritairement associees aux cellules. Les genes codant pour les xylanases de ces deux especes bacteriennes et d'une troisieme bacterie xylanolytique du colon, Bacteroides sp. XB12B, ont ete identifies. Ils codent pour des xylanases appartenant aux familles 10 et 43 des glycosyl-hydrolases, et sont modulaires. Certaines xylanases ont aussi ete identifiees par proteomique. Les conditions d'expression de certains de ces genes ont ete etudiees par PCR quantitative, et montrent une regulation par le xylane. Des regroupements de genes pouvant etre impliques dans la degradation des hemicelluloses ont ete trouves dans le genome de B. xylanisolvens XB1A. Enfin, une xylanase de 38 kDa, de la famille 10 des glycosyl hydrolases, produite par B. xylanisolvens XB1AT, a ete caracterisee : le gene codant cette enzyme a ete clone et la xylanase, nommee Xyn10A, produite chez E. coli. Cette enzyme, qui pourrait etre periplasmique chez B. xylanisolvens XB1AT, degrade in vitro les xylanes et les xylooligosaccharides, mais aussi tres faiblement la CMC. Ces travaux permettent de mieux comprendre les mecanismes de degradation des xylanes par deux especes appartenant aux genres majeurs du colon humain Bacteroides et Roseburia, et representent une avancee significative dans la connaissance de leurs roles respectifs dans cet ecosysteme.
Analysis of expressed sequence tags from the chrysophycean alga Ochromonas danica (Heterokontophyta)

A cDNA library was constructed from the chrysophycean alga, Ochromonas danica E. G. Pringsheim. 5′-end sequencing of about 600 cDNA clones yielded 476 authentic expressed sequence tags (EST) of which 275 showed significant matches (E-value <10-4) to sequences in a public database. The annotation of these ESTs was carried out to assess subcellular localization of the putative proteins using several internetaccessible prediction programs for subcellular localization. These analyses revealed that putative plastid proteins in Ochromonas possess N-terminal bipartite presequences with a conserved phenylalanine at the N-terminus of the predicted transit peptide-like domains, similar to other ‘red-lineage’ secondary symbiotic organisms. The examination of sequences of 3′-UTR revealed that, similarly to chlorophyte algae, UGUAA may represent a putative polyadenylation signal in O. danica.