Miracle-dz/UniFAR-FTUs huggingface dataset:
ヘドニック・アプローチを用いた津波災害リスクに対する住民意識の評価;ヘドニック・アプローチを用いた津波災害リスクに対する住民意識の評価;Evaluation of Residents Awareness Regarding Potential Risk of Tsunami due to Nankai Trough Earthquake by Hedonic Approach in Saiki, Oita

This study attempts to evaluate the potential risk of tsunami driven by Nankai trough earthquake with investigation of land price based on the hedonic approach in Saiki, Oita. Simulations have been conducted by the cabinet office, government of Japan and Oita local government, and results, e.g. the estimated inundation height and travelling time of tsunami, have been published. The land prices are assumed to be a good descriptor of the potential risk of tsunami as well as convenience and comfort of the life. The land prices were taken to be a function of accessibility to the Saiki train station, schools, and parks, and of risk factors, e.g. elevation, the predicted flood depth due to tsunami and so on. The multiple regression analyses show that the land prices decrease with increased distance from the Saiki station. The effect of the potential risk of tsunami is also described by the land prices, i.e. the land prices decrease as the estimated flood depth increases.
FUNCTIONAL CHARACTERIZATION OF HEME TRANSPORTERS IN ZEBRAFISH

Title of Dissertation: FUNCTIONAL CHARACTERIZATION OF HEME TRANSPORTERS IN ZEBRAFISH Jianbing Zhang, Doctor of Philosophy, 2017 Dissertation directed by: Professor Dr. Iqbal Hamza, Department of Animal and Avian Sciences Hrg1 and Mrp5 are identified as eukaryotic heme importer and exporter, respectively. Two Hrg1 paralogs have been annotated in zebrafish genome, Hrg1a (Slc48a1b) and Hrg1b (Slc48a1a) with 84% homology in protein sequences. Hrg1a and hrg1b are widely expressed in embryonic and adult zebrafish. Yeast growth assays reveal that zebrafish Hrg1a and Hrg1b are both capable of heme import. However, hrg1a and hrg1b double knockout (hrg1 DKO) zebrafish generated by CRISPR/Cas9 has no overt defects in differentiation and maturation of erythroid cells. Knockdown of hrg1a in hrg1b mutants or vice versa does not impair erythroid lineage in zebrafish embryos. These genetic results suggest that Hrg1 is not required for maturation and hemoglobinization of primitive erythroid cells. Hrg1a and hrg1b mRNA are upregulated in adult kidneys and spleens upon PHZ-induced hemolysis, together with hmox1, a downstream heme degrading enzyme, suggesting that Hrg1 is involved in adult heme-iron recycling during erythrophagcytosis in kidney and spleen of adult zebrafish. DAB-enhanced Perl’s iron staining reveals that iron is accumulated in macrophages in the kidney and spleen in adult wild-type zebrafish. However, macrophages with positive Perl’s staining are rarely found in the kidney of hrg1 DKO and instead large amount of iron is deposited in renal tubules, suggesting defects in heme-iron recycling by kidney macrophages in hrg1 DKO under PHZ-induced hemolysis. Whole transcriptome sequencing of mRNA extracted from spleens and kidneys reveals massive differentially expressed genes in hrg1 DKO involved in immune response, lipid transport, oxidation-reduction process and proteolysis. These indicate that hrg1 DKO are deficient in recycling heme-iron derived from damaged RBCs in the absence of functional Hrg1. Phylogenetic analysis reveals that Mrp5 and Mrp9 are closed homologs in the zebrafish genome. Yeast growth assays reveal that both zebrafish Mrp5 and Mrp9 are capable of heme export. Morpholino knockdown of mrp5 and mrp9 in zebrafish showed severe anemia in developing embryos indicating their involvements in erythropoietic development. Subsequent generation and characterization of mrp5 and mrp9 mutants by CRISPR/Cas9 will further define the function of Mrp5 and Mrp9 during zebrafish development. FUNCTIONAL CHARACTERIZATION OF HEME TRANSPORTERS IN ZEBRAFISH
Embryotoxicity of poorly soluble nanoparticles at various stages of Zebrafish development

The biological effects of the poorly soluble nanoparticles (NPs) of different chemical nature and structural characteristics were evaluated. It was established that the Zebrafish test response to contamination of aqueous medium with nickel NPs (nNi), platinum (nPt), zinc oxide (nZnO) and cerium oxide (nCeO2) depends on the physicochemical properties of the NPs and embryo development stage. The concentrations of NPs not causing disruptions in embryonic development of Zebrafish were determined. The smallest impact on embryogenesis was exerted by nCeO2: coagulation of a small number of embryos was observed only at C = 20.0 mg/L. The same effect was observed when exposed to lower concentrations of nPt (C = 5.0 mg/L) and nNi (C = 0.1 mg/L). The greatest number of coagulated embryos was observed when grown in the DS nZnO: 37.5% of embryos died at the DS concentration of C = 0.1 mg/L. Zebrafish cultivation in the DS with low concentrations (C ≤ LC10) of nNi and nZnO caused distortions in the development of embry.
Age and Sex-Specific Effect of Caloric Restriction on Circadian Clock and Longevity-Associated Gene Expression

The rhythms in the expression of circadian clock genes are affected by calorie restriction (CR), a dietary paradigm known to increase lifespan. In our current study, we show that circadian rhythms are influenced by sex and the effects of CR are different between males and females. In particular, we found a group of clock genes which showed a sex-dependent difference in expression, as well as in response to CR (Rev-Erb , Ror  and both Cryptochromes: Cry1 and Cry2 genes). Two clock genes showed no difference in expression but their response to CR showed sexual dimorphism (Ror  and Rev-Erb ). Finally, we found some of the clock genes to be expressed in a sex-independent manner (Bmal1, Per1, Per2 and Per3). The response to CR for these genes did not show sexual dimorphism as well. Several genes were also previously reported to be regulated by CR. These genes showed a sex-dependent difference in expression as well as the sexual dimorphism in the response to CR in mouse liver (Fmo3, Mup4, Serpina12, Cyp4a12b and Cyp4a14a). IGF signaling plays an important role in aging and CR effects. Igf-1 expression is regulated by CR and by the circadian clock, we found that rhythms in Igf-1 expression have sexual dimorphism. We also investigated the differences in expression levels in young versus old mice to see if the effect of short-term CR differs from the effect of long-term CR. In all of the 4 analyzed genes, the expression does not
Craniodental morphology and diet of Leptarctus oregonensis (Mammalia, Carnivora, Mustelidae) from the Mascall Formation (Miocene) of central Oregon

Abstract. The Leptarctinae are an enigmatic subfamily of mustelids present in North America and Eurasia during the Miocene (Arikareean to Hemphillian North American Land Mammal Ages). Their diet and ecology have been particularly controversial. Some workers have suggested they were similar to koalas, whereas others suggested they were crushing omnivores analogous to raccoons. Leptarctus oregonensis Stock, 1930, a poorly known leptarctine from the early Barstovian, is represented by fragmented cranial elements and isolated teeth from the Mascall Formation of Oregon, and some fairly complete but undescribed material from the Olcott Formation of western Nebraska. Herein, we describe the first well-preserved skull of L. oregonensis from the type formation. Based on this new specimen, we confirm that L. oregonensis is a distinct species from L. primus Leidy, 1856 and L. ancipidens White, 1941 that is characterized by a distinct morphology of its tympanic projections and first upper molars. We are also able to describe intraspecific variation within L. oregonensis coinciding with the geographic distribution of the specimens (Oregon and Nebraska). The most variable characters are concentrated in the morphology of the frontals and the upper fourth premolar. Additional specimens will be needed to settle the debate over sexual dimorphism in this species, but this new specimen suggests that Leptarctus oregonensis, despite being one of the smallest members of the Leptarctinae, was an animal-dominated omnivore with considerable crushing ability.
Genetic variation, Heritability estimates and GXE effects on yield traits of Mesoamerican common bean (Phaseolus vulgaris L) germplasm in Uganda

Abstract Germplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop's improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype × environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.
Onboard rearing attempts for the Japanese eel leptocephali using POM-enriched water collected in the Western North Pacific

Hatchery produced leptocephalus larvae of the Japanese eel (Anguilla japonica ) were reared on a research vessel and fed natural particulate organic matter (POM) collected in the Western North Pacific. A small net (36 cm diameter, 60 µm mesh) was vertically towed from 200 m depth to surface in 2013, and POM-enriched water (POMEW) filtered through 350 µm mesh was fed to the leptocephali for 11 days. Although the swollen gut corroborated the active ingestion of POM by the leptocephali, low survival rate and heavily melanized gut followed by necrosis in the mid-hindgut region of the leptocephali were observed. A large net (1.14 m diameter, 30 µm mesh) was used in 2014 and 2015, which was horizontally drifted subsurface (100–175 m). POMEWs filtered through 53 or 25 µm meshes were fed to the leptocephali for 5–18 days. Neither melanized gut nor necrosis occurred, but considerably low survival rate and little growth comparable with that in a starved condition were observed. No apparent shift in stable carbon and nitrogen isotope ratios was observed in the reared leptocephali. These indicated that the ingested POMs were not assimilated by the leptocephali and suggested that smaller particles may be important for the leptocephali.
Elucidating matrix protein import and beta-oxidation pathways in plant peroxisomes

Plant peroxisomes function in fatty acid β-oxidation, jasmonic acid (JA) synthesis, and conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid (IAA). Peroxisomes lack genetic material; proteins required for peroxisomal processes are imported posttranslationally. The PEX5 and PEX7 receptors import proteins containing one of two peroxisomal targeting signals (PTS1 or PTS2). I took a genetic approach to better understand protein import and to elucidate the role of Acyl-CoA Oxidase (ACX) enzymes in the model plant Arabidopsis thaliana. ACX enzymes catalyze the first step in β-oxidation. There are six ACX genes in Arabidopsis and each ACX enzyme acts on specific chain-length targets, but in a partially overlapping manner. To elucidate the substrate specificity of ACX enzymes and examine their roles in planta, I generated higher order acx mutants. ACX gene expression studies show distinct patterns between Col-0 and Ws and the enzymes showed altered activity during development. acx triple mutants showed reduced seed-storage mobilization and resistance to IBA. Several mutants specifically showed reduced fertility and the acx1acx3acx5 defect was rescued with JA. Analysis of the higher order acx mutants has allowed me to determine which ACXs act in specific peroxisomal β-oxidation pathways. To elucidate the mechanism of peroxisome matrix protein import, I studied an insertion mutant in the PEX5 receptor. This mutant, designated pex5-10, makes a truncated pex5 protein, has germination defects and is dependent on sucrose for establishment. PTS1 and PTS2 protein import and enzymatic processes are also disrupted. To specifically study PTS1 protein import, I created a pex5 mutant lacking the PTS1 binding region. This mutant rescued the PTS2 import defects in pex5-10. The pex5-10 and PTS2 rescued lines allowed me to separate specific processes affected by import of PTS1 or PTS2 proteins. This study has contributed to our understanding of the differences in the ACX genes and proteins in different Arabidopsis accessions and the role each protein plays in peroxisomal processes. The study also provides a better understanding of PTS1 and PTS2 proteins in specific peroxisomal pathways. Together these studies will contribute to elucidating the mechanism for the requirement for peroxisomal processes in plant growth
Modelo de Tratamiento para Tumores en Presencia de Radiaci\'on

In this work, we combine a new form of the cell survival fraction developed in [29] with the Gompertz cell growth model. The result is an equation that models the cell growth/death under a radiation dose and can be applied in a conventional radiation treatment (we chose conventional fractionation and hypofractionation). Later we optimize this equation in order to obtain the optimal doses that reduce the tumor's size or the number of cancer cells. We applied our results to breast cancer data: invasive ductal carcinoma (IDC) and ductal carcinoma in situ (DCIS)
Modèles intégrés de mécanistique et de résistance en oncopharmacologie-sénescence : Caenorhabditis elegans et Hypsibius dujardini

Comprendre les mecanismes de senescence ou developper de nouveaux anti-cancereux impose d’utiliser des modeles biologiques divers et complementaires. De par sa facilite de mise en œuvre, la culture cellulaire est une des methodes les plus employees. Cependant, travailler sur des cellules isolees ne permet pas toujours d’extrapoler les resultats a des conditions plus complexes comme un organisme entier. Les biologistes disposent alors de modeles integres plus ou moins evolues : levures, poissons (zebrafish …), grenouille (xenope …), insectes (drosophile …), rongeurs (souris, rats …), chien, primates, etc. Cependant leur mise en œuvre est souvent difficile, tant d’un point de vue administratif que technologique.L’objectif de notre travail a ete d’initier le developpement de deux nouveaux modeles biologiques integres (Caenorhabditis elegans et Hypsibius dujardini), beaucoup plus facilement manipulables, pour des etudes en oncopharmacologie et senescence.Le potentiel de Caenorhabditis elegans a ete evalue au travers de deux axes : (i) nous avons utilise le nematode pour determiner les potentiels toxiques, mutagenes et cancerogenes de gaz candidats au remplacement du gaz SF6 (ii) a l’aide du Seahorse XF24 Analyzer, nous avons mis au point un test fonctionnel original : la mesure de la respiration mitochondriale du nematode entier.Nous avons choisi de developper comme second modele, Hypsibius dujardini, beaucoup moins travaille que C. elegans. C’est un tardigrade connu pour sa resistance aux conditions extremes, notamment a la dessication. Afin de mieux comprendre cette resistance, nous avons choisi d’analyser le fonctionnement mitochondrial de cet organisme en sortie d’anhydrobiose, en utilisant des marquages mitochondriaux et en mesurant sa respiration a l’aide du Seahorse XF24 Analyzer.
Mechanism of Fenoxaprop-P-ethyl Resistance in Italian Ryegrass (Lolium perenne ssp. multiflorum) from China

Italian ryegrass has invaded wheat fields in China and is becoming a predominant, troublesome weed. Fenoxaprop-P-ethyl has been widely used for weed control on Chinese farms since the 1990s. However, overuse has led to fenoxaprop-P-ethyl resistance in Italian ryegrass in Chinese wheat fields. In this study, we identified a putative fenoxaprop-P-ethyl—resistant population of Italian ryegrass, HZYC-6, from Henan province, China. Mutations involving Asp-2078-Gly and Ile-1781-Leu substitutions were identified in the carboxyl-transferase domain of acetyl-coenzyme A carboxylase in this population, and these mutations are the likely cause of the target site—based resistance to fenoxaprop-P-ethyl. In addition, we identified cytochrome P450—mediated metabolism of herbicides (non—target site based resistance) in the HZYC-6 population, indicating that multiple mechanisms of resistance may be segregating in this population. Furthermore, HZYC-6 was also highly resistant to haloxyfop-P-methyl and quizalofop-P-ethyl, moderately resistant to clodinafop-propargyl and sethoxydim, and had low resistance to clethodim and pinoxaden. Nomenclature: Clethodim; clodinafop-propargyl; fenoxaprop-P-ethyl; haloxyfop-P-methyl; pinoxaden; quizalofop-P-ethyl; sethoxydim; Italian ryegrass, Lolium perenne ssp. multiflorum (Lam.) Husnot; wheat, Triticum aestivum L.
ZmCOL3, a CCT-domain containing gene affects maize adaptation as a repressor and upstream of ZmCCT

Flowering time is a vital trait to control the adaptation of flowering plants to different environments. CCT-domain containing genes are considered to play an important role in plants flowering. Among 53 maize CCT family genes, 28 of them were located in the flowering time QTL regions and 16 genes were significant associated with flowering time based on candidate gene-based association mapping analysis. Furthermore, a CCT gene named as ZmCOL3 was validated to be a flowering repressor upstream of ZmCCT which is one of the key genes regulating maize flowering. The overexpressed ZmCOL3 could delay flowering time about 4 days whether in long day or short day conditions. The absent of one cytosine in 3’UTR and the present of 551bp fragment in promoter regions are likely the causal polymorphisms which may contribute to the maize adaptation from tropical to temperate regions. ZmCOL3 could transactivate ZmCCT transcription or interfere circadian clock to inhibit flowering which was integrated in the modified model of maize photoperiod pathway. Highlight Maize CCT genes influence flowering time in different latitude environments and one of them named ZmCOL3 is a flowering time repressor which could transactivate ZmCCT transcription to delay flowering.
Giant nevus unius lateralis: Two cases

Verrucous epidermal nevus is a common type of keratinocyte hamartoma present at birth or occurring later in life. Widespread multiple epidermal nevi (EN) may reflect genetic or chromosomal mosaicism. Blaschko has documented characteristic linear, zosteriform, unilateral or systematized patterns with streaks and swirls. They are resistant to treatment with the risk of recurrence. Giant congenital nevus unius lateralis (NUL) is known for its benign course with good supportive treatment however one particular case had a fatal neonatal outcome due to associated complications. Two interesting rare cases will be reviewed here.
From birth to birth A cell cycle control network of S. cerevisiae

The survival of a species depends on the correct transmission of an intact genome from one generation to the next. The cell cycle regulates this process and its correct execution is vital for survival of a species. The cell cycle underlies a strict control mechanism ensuring accurate cell cycle progression, as aberrations in cell cycle progression are often linked to serious defects and diseases such as cancer. Understanding this regulatory machinery of the cell cycle offers insights into how life functions on a molecular level and also provides for a better understanding of diseases and possible approaches to control them. Cell cycle control is furthermore a complex mechanism and studying it holistically provides for understanding its collective properties. Computational approaches facilitate holistic cell cycle control studies. However, the properties of the cell cycle control network challenge large-scale in silico studies with respect to scalability, model execution and parameter estimation. This thesis presents a mechanistically detailed and executable large-scale reconstruction of the Saccharomyces cerevisiae cell cycle control network based on reactioncontingency language. The reconstruction accounts for 229 proteins and consists of three individual cycles corresponding to the macroscopic events of DNA replication, spindle pole body duplication, and bud emergence and growth. The reconstruction translated into a bipartite Boolean model has, using an initial state determined with a priori knowledge, a cyclic attractor which reproduces the cyclic behavior of a wildtype yeast cell. The bipartite Boolean model has 2506 nodes and correctly responds to four cell cycle arrest chemicals. Furthermore, the bipartite Boolean model was used in a mutational study where 37 mutants were tested and 32 mutants found to reproduce known phenotypes. The reconstruction of the cell cycle control network of S. cerevisiae demonstrates the power of the reaction-contingency based approach, and paves the way for network extension with regard to the cell cycle machinery itself, and several signal transduction pathways interfering with the cell cycle.
Factors responsible for the continuous persistence and evolution of low pathogenic avian influenza virus (H9N2)

Avian influenza virus (AIV) type A subtype H9N2 usually causes mild asymptomatic infections, and is mostly undetected and is, therefore, under-reported. This has allowed the virus to rapidly evolve via mutations and reassortments in its genome with other avian influenza subtypes especially H1N1, H5N1 and H7N3 thereby introducing new variant strains and producing severe disease. It has been reported that the AIV H9N2 donated its internal genes for the devastating 1997 Hong Kong outbreak and furthermore, it may be the cause of the next influenza pandemic. There are many factors such as its wide host range, ability to cross the species barrier, ecological diversity, antiviral resistance and zoonotic importance that make it an excellent candidate for the next influenza pandemic. These and other factors like ineffective vaccination, negative immunological pressures, lack of surveillance, which contribute to its continuous persistence and evolutionary dynamics are discussed in this paper. It is important to take the necessary measures to control and prevent its unchecked circulation to prevent the future outbreaks.