Miracle-dz/UniFAR-FTUs huggingface dataset:
Early development and the honesty of aposematic signals in a poison frog

The causes and consequences of variation in aposematic signals during immature stages are not clearly understood. This thesis explores the effects of early environment on the expression of aposematic signals in the green and black poison frog (Dendrobates auratus), and the consequences of variation in such components in the wild. It also explores how aposematic expression relates to levels of chemical defences in immature froglets. Embryos and larvae of poison frogs in the genus Dendrobates are known to be darkly pigmented. This thesis reports for the first time polymorphism in egg pigmentation in D. auratus and ontogenetic colour change through development reverting to a normally pigmented phenotype; however whether this pigmentation results from constraints or has adaptive consequences remains unclear. Evidence on how immature individuals allocate resources to growth and warning signalling is scarce. Experimental results in this thesis show that food supply during early environment affected body size and signal luminance in post-metamorphic froglets. Therefore the relative importance of these traits in relation to predation risk was further tested, using artificial prey in a field experiment. The results indicated that rates of attack by birds correlated negatively with body size, and on the contrary survival of artificial prey was independent of signal luminance. I therefore tested the hypothesis that in the wild larger, relatively well-nourished juvenile frogs are chemically better defended. I found that in fact larger juveniles are at a selective advantage conferred by their greater foraging efficiency and their superior levels of chemical defences. Overall, these results shows plasticity in aposematic traits in relation to early environmental nutrition in D. auratus; and suggests that acquiring large body size and similar integument colour as to adults are key determinants for survival during the early stages of their terrestrial life.
The mass-loss characteristics of AGB stars An observational view

Abstract The massive outflows of gas and dust which characterize giant stars on the Asymptotic Giant Branch (AGB), build cool circumstellar envelopes readily observed at infrared (IR) and sub-millimeter wavelengths. The observations will give the amount of matter lost by the star, the wind velocity (in the case of spectral line observations), and, when the spatial resolution is sufficient, the wind evolution over time. To gain detailed insight into the mass-loss process, we study the nearby (closer than 1 kpc) stars. Through these investigations we aim to determine the best constrained wind properties available. By combining this with theoretical results, mass-loss estimates for more distant sources can also be significantly improved. ALMA has opened up new opportunities to study the winds of AGB stars. The DEATHSTAR project (www.astro.uu.se/deathstar) has mapped the circumstellar CO emission from so far ∼50 nearby M- and C-type AGB stars. The data will initially be used to give a definitive mass-loss prescription for the sample sources, but the large-bandwidth observations opens for many different legacy projects. The current status and results are presented.
A Successful Language Teaching Model: Switzerland Case

Switzerland is like a language and culture pot with its four official languages and habitants from all over the world. The purpose of this study was to inspect this country’s special language education model. The study was designed as a case study and data were gathered with document analysis. Curriculums and other publications were analyzed with context analysis technique. The findings showed that the Swiss language teaching model aims to raise plurilingual children who are open to other cultures. Also, common points of languages and cultures are always stressed. Not having a single official language, Switzerland has citizens who can speak more than one language with each other. New methods like Communicative, content and task-based techniques are used in language teaching.
Optical interferometry of High-Mass X-ray Binaries: Resolving wind, disk and jet outflows at sub-milliarcsecond scale

Abstract Because of their small angular size < 1 mas, spatial information on High-mass X-ray binaries (HMXB) has typically been inferred from photometry or spectroscopy. Optical interferometry offers the possibility to spatially resolve such systems, but has been traditionally limited to bright targets or low spectral resolution. The VLTI instrument GRAVITY, working in the near-infrared K band, achieves unprecedented precision in differential interferometric quantities at high spectral resolution, allowing to study HMXBs through the lens of optical interferometry for the first time. We present GRAVITY observations on two X-ray binaries: the microquasar SS 433 and the supergiant HMXB BP Cru. The former is the only known steady super-Eddington accretor in the Galaxy and is in a unique stage of binary evolution, with probable ties to at least part of the ULX population. With GRAVITY, we resolve its massive winds and optical baryonic jets for the first time, finding evidence for powerful equatorial outflows and photoionization as the main heating process along the jets. BP Cru harbors an X-ray pulsar accreting from the wind of its early-blue hypergiant companion Wray 977. The GRAVITY observations resolve the inner parts of the stellar wind and allow probing the influence of the orbiting pulsar on the circumstellar environment.
Adaptation d'Alternaria brassicicola à son hôte : étude de composantes moléculaires impliquées dans la protection du champignon pathogène vis-à-vis des phytoalexines indoliques des Brassicaceae

Alternaria brassicicola est un champignon necrotrophe responsable du « black spot » des Brassicaceae, causant d’importants degâts culturaux. Lors de l’infection, les Brassicaceae synthetisent divers composes de defense tels que les phytoalexines indoliques camalexine et brassinine. Une etude prealable avait suggere une action de ces molecules sur l’integrite de la membrane fongique et la mise en place chez le champignon d’un mecanisme adaptatif de type compensatoire visant a renforcer son integrite cellulaire. L’objectif de la these est d’identifier les composantes moleculaires regulant l’induction de ce mecanisme. Les travaux realises montrent que les voies de signalisation HOG, CWI, et UPR impliquees respectivement dans la regulation de l’osmose cellulaire, la biosynthese de la paroi et la reponse au stress de secretion sont activees chez A. brassicicola lors de l’exposition aux phytoalexines. Le phenotypage de mutants deficients pour des composantes cles de ces trois voies de signalisation montre qu’ils sont plus sensibles aux phytoalexines et presentent une baisse de leur agressivite in planta (AbSlt2Δ pour la voie CWI, AbHog1Δ pour la voie HOG) ou une perte de virulence (AbhacAΔ pour la voie UPR). Cette etude illustre le role crucial des voies de signalisation dans l’adaptation d’un champignon phytopathogene aux stress lies a la colonisation de son hote et donc dans la reussite du cycle infectieux. Ce role cle en fait de bons candidats comme cibles pour la definition de strategies de lutte contre l’alternariose.
Regulation of type III secretion system in Pseudomonas syringae

P. syringae is a group of bacterial phytopathogens that can infect a wide variety of plants. These bacteria rely on the type III secretion system (TTSS) to deliver effectors into plant cells for infection. The TTSS genes, that encode the TTSS apparatus and the effectors, are repressed when bacteria grow in nutrient rich media but are strongly induced in the plants and in minimal medium (MM). Plant cutin monomers appear to negatively regulate the P. syringae TTSS genes. It is poorly understood how bacteria sense the environmental signals to regulate the TTSS genes. By genetic screen, four sets of transposon insertion mutants displaying aberrant TTSS gene expression were isolated: KB and fin mutants derepress the TTSS genes in rich medium KB and in the presence of a cutin monomer precursor in MM, respectively; min and pin mutants are defective in induction of TTSS genes in MM and in plants, respectively. A putative two-component sensor histidine kinase, RohS, is identified to be required for the induction of avrPto-LUC in MM and in plants. The rohS gene is in an operon containing a two-component response regulator gene rohR. Mutation of rohS in P. s. phaseolicola and P. s. tomato reduced the bacterial pathogenicity on hosts and HR-inducing activity on non-hosts. Our results suggested that RohS acts upstream of HrpR/HrpS. The phosphorylated RohR represses TTSS genes. It is likely that RohS acts as phosphatase of RohR in the TTSS-inducing conditions, and subsequently derepresses TTSS genes. Simple sugars such as glucose, sucrose and fructose are known to be inducers of the TTSS genes. Isolation of four min mutants defective in fructose-uptake enabled us to study if sugars serve as extracellular signals or as essential nutrients. Our results suggest that fructose acts as an essential nutrient for the activation of type III genes. These mutants slightly compromised induction of avrPto promoter in Arabidopsis and pathogenicity on the host bean plant, but displayed normal HR elicitation on non-host plant tobacco. The reduced pathogenicity suggested that exploitation of fructose from the host tissue is an important means for pathogenesis of P. s. phaseolicola.
Evaluation of biochemical effects of diclofenac sodium in goats.

Diclofenac sodium is one of the most commonly using Non steroidal anti – inflammatory drugs (NSAID) worldwide in medical as well as veterinary practices. Use of anti-inflammatory drugs may affect liver function which may or may not be reversible in various livestock breeds. In this study effect of diclofenac sodium on Alanin transaminase (ALT), Aspartate transaminase (AST), Alkaline phosphatase (ALK), serum creatinine, serum uric acid, blood urea and total protein of liver and kidney of local dairy goats has been evaluated at Sindh Agriculture University, Tandojam since 2007. The drug was administered in six goats in two phases with adequate wash out period of 21 days between each phase. Dose rates, 2.5mg/kg (b.w) and 1 mg/kg (b.w), of diclofenac was administered in Phase-1 and Phase-2 respectively. For biochemical analysis the blood samples were collected at different intervals up to 96 hrs post drug administration. Significant change (p<0.05) with high dose was documented at 2, 3, 6, 12, 24 48 hrs in blood serum level of ALT, AST, ALK.PO4, creatinine, uric acid, and blood urea respectively. Where as highly significant change (p<0.01) was monitored at 6, 12, 24, 48 hrs in ALT and AST, ALK.PO4, and blood urea respectively. Significant increase in serum level of Alanin transaminase, Aspartate transaminase and Alkaline phosphatase was noticed at 12 and 24 hrs with low dose of diclofenac respectively. No significant change in serum creatinine and uric acid was observed but blood urea significantly increased at 48 hrs with low dose. No change was examined in total serum protein with both the doses. The effect of diclofenac was short-lived and most of the parameters went back to normal after 72hrs of drug administration.
Stability analysis and synthesis for linear impulsive stochastic systems

This paper presents a general framework for analyzing stability of linear impulsive stochastic systems (LISSs). Some simple mean square stability criteria for the three types of LISSs are firstly derived by analyzing an equivalent system. By exploring the hybrid characteristics of impulsive systems, the novel quasi‐periodic composite polynomial Lyapunov function and the time‐varying discretized Lyapunov function are developed, which leads to unified dwell‐time–based criteria for mean square stability and almost sure stability of LISSs without imposing the stability condition on continuous‐ and discrete‐time dynamics. Next, based on the established stability criteria, the synthesis problem of state‐feedback controller is solved. The computational complexity and the comparison with existing results on the deterministic systems are discussed. Finally, numerical examples are provided to illustrate the usefulness of the proposed results.
Characterization of Subcellular Localization Signals Using HYPOTHESISCREATOR

Proteins are first synthesized in the cytosol and then carried to specified locations of the cell. The information which determines where the proteins are carried is believed to be encoded in the amino acid sequence. Mitochondrial targeting peptides (mTP), chloroplast targeting peptides (cTP), signal peptide, are some of the known targeting signals. Our approach differs from previous methods [5, 1, 2] which try to characterize these signals in that we try to extract a simple rule or knowledge which may be easily understood. In our experiments, we use an alphabet indexing combined with string pattern matching, similar to [6]. Concerning mitochondrial targeting peptides, we have succeeded in discovering a simple rule which seems to capture important biological knowledge about the signals.
Micropatterned co-cultures of hepatocytes and nonparenchymal cells : mechanisms of differentiation, dynamics and applications

Engineered liver tissue has the potential to support patients with hepatic dysfunction as well as provide an in vitro model of the liver for pharmaceutical drug development. Such applications mandate the use of primary hepatocytes- the parenchymal cell of the liver; however, hepatocytes rapidly lose viability and phenotypic functions in vitro. Co-cultivation of hepatocytes with nonparenchymal cells (NPC) has been reported to prevent this deterioration. Several aspects of this so-called 'co- culture effect' remain incompletely understood: the molecular mechanisms by which NPC stabilize liver-specific functions, dynamics of interaction (i.e. whether continuous NPC support is required to maintain hepatic functions), and whether this model system can provide a useful tool for drug development. In this dissertation, gene expression profiling, electroactive surface chemistry, and microfabrication tools are used to answer these questions. First, a functional genomic approach utilizing gene expression profiling was developed to identify and validate molecular mediators that modulate liver-specific functions in co-cultures. Second, the role of one candidate, T-cadherin, was characterized in detail. T- cadherin was found to upregulate hepatocyte functions in vitro upon presentation in both cellular (CHO cells) and acellular (immobilized protein) contexts. Third, micropatterned electroactive substrates were used to selectively release fibroblasts at various time points from co-culture to probe the dynamics of cell-cell interaction. Results indicated that continuous fibroblast stimulation was required to maintain hepatic functions. Finally, soft lithography tools were utilized to develop miniaturized, multi-well co-culture models of the human and rat liver that were stable for several weeks. Utility of microscale tissues for evaluating species-specific drug metabolism, drug-drug interactions, and susceptibility to a panel of hepatotoxins was demonstrated. These studies will have an impact on developing functional models of liver tissue for use in fundamental hepatology, cell-based therapies for liver disease and pharmaceutical drug development. Furthermore, the methods developed here can be generalized to other tissues where cell-cell interactions modulate cellular fates
Bioactive proanthocyanidins from the root bark of Cassia abbreviata

Cassia abbreviata is an important medicinal plant used in the treatment of various infectious diseases. The ethnomedical efficacy of extracts of this plant species is attributed to its phytochemical constituents most of which are phenolics and anthraquinones. The aim of this study was to isolate and elucidate bioactive phenolic compounds from the root bark of this species. Consequently, two novel trimmeric proanthocyanidins; 3,7,4'-trihydroxyflavan-(4β→8)-3,5,7,4'-tetrahydroxyflavan-(3'→6)-3,5,7,2',4'- pentahydroxyflavan (cassinidin A) and 3,7,2',4'-tetrahydroxyflavan-(4α→8)-3,5,7,4'-tetrahydroxyflavan-(4α→6)-3,5,7,2',4'-pentahydroxyflavan (cassinidin B) were isolated from the root bark of Cassia abbreviata . The chemical structures were determined using NMR, MS and HRMS spectroscopic data. The cassinidin A and B showed higher to moderate antimicrobial activity against Escherichia coli, Bacillus subtilis, Staphylococcus aureus and Candida mycoderma . Keywords : Medicinal plant, Cassia abbreviata , Caesalpinioideae, root bark, Cassinidin A, Cassinidin B, antimicrobial
RNA : protein interactions : a practical approach

Applications of chemically-synthesized RNA preparation of RNA-protein complexes for x-ray crystallography and NMR uses of site-specifically modified RNAs constructed by RNA ligation the electrophoretic mobility shift assay for RNA binding proteins affinity methods for isolating RNA-binding proteins synthetic lethal/enhancer screening to identify snRNA-protein and protein-protein interactions in yeast pre-mRNA splicing detecting RNA-protein interactions and isolating cDNA clones by northwestern screening a three-hybrid system to detect and analyze RNA-protein interactions in vivo in-vivo selection of specific RNA-binding polypeptides using a transcription anti-termination reporter assay foot-printing and modification-interference analysis of binding sites on RNA analysis of RNA-protein and RNA-RNA contacts between ribosomes and functional ligands using site-directed cross-linking techniques in-vitro selection of nucleic acid ligands.
INFLUENCE OF SPAN LENGTH AND CROSSBEAM ON LOAD DISTRIBUTION FACTOR FOR GIRDER BRIDGES

Load distribution factor at concrete girder bridges and steel girder bridges are analyzed with finite element method to see effect of span length and cross beam to load distribution factor. Span lengths of analyzed bridge models are 30m, 40m, 50m and 60m. The number of intermediate cross beam is increased from one to until distance between cross beams becomes 5m. The finite element analysis results show that concrete girder and steel girder can use same load distribution factor and span length doesn’t affect to load distribution factor. Even though load distribution factor in interior girders is not influenced by cross beam, in exterior girders it is influenced by cross beam. Effect of cross beam in exterior girder is influenced by the number of lanes and distance from exterior girder to curb. Since design code introduces conservative load distribution factor, economically improved load distribution factor is proposed. The proposed load distribution factor includes cross beam effect with the number of lanes and distance from exterior girder to curb. The proposed equation is compared with AASHTO code and grillage method which is well-known method to calculate load distribution. The comparison results showed that the proposed equation is more efficient and useful than AASHTO and safer than the grillage method.
Flavonols and flavones in foods and their relation with cancer and coronary heart disease risk

Flavonoids are polyphenolic antioxidants occurring ubiquitously in vegetable foods. Flavonols and flavones inhibit chemically induced tumors in rodents. The flavonol quercetin also inhibits LDL oxidation and platelet aggregation in vitro . We therefore decided to investigate the relation between flavonoid intake and cancer and coronary heart disease risk in humans. The three flavonols quercetin, kaempferol, myricetin, and the two flavones luteolin and apigenin were selected because of their anticarcinogenic and antioxidant activities and because of their ubiquitous occurrence in foods. We first developed and validated a HPLC method for the quantitative determination of these flavonoids in foods. We then determined the flavonol and flavone content of 28 types of vegetables, 12 types of fruits and 9 types of beverages commonly consumed in The Netherlands. Quercetin was the main flavonoid and occurred in most fruits, beverages and in some vegetables. Mean intake of flavonols and flavones combined among Dutch adults was 23 mg/day, and main dietary sources of these flavonoids were tea (48 %), onions (38%), and apples (8 %). Mean flavonol and flavone intake of 805 men aged 65-84 years participating in the Zutphen Elderly Study 1985 was 26 mg/day. During five year followup period 75 men had a first diagnosis of cancer, of which 28 men had lung cancer. Thirty-four men died from all-cause cancer. Intake of flavonols and flavones in 1985 was not related to subsequent (lung) cancer morbidity ( P trend 0.54) and mortality ( P trend 0.51). Between 1985 and 1990 43 men died from coronary heart disease and 38 men had a first myocardial infarction. Intake of flavonols and flavones, expressed as tertiles of intake, was, independently from known risk- and confounding factors, inversely associated with mortality from coronary heart disease ( P trend 0.015) and incidence of a first myocardial infarction ( P trend 0.08). Average intake of flavonols and flavones in 16 cohorts participating in the Seven Countries Study around 1960 was also inversely related to mortality from coronary heart disease after 25 years of follow-up, but it was not related to cancer mortality. In multivariate regression analysis including saturated fat intake, flavonoid intake, and percentage of smokers as independent variables about 90 % of the total variance in coronary heart mortality was explained. Flavonol and flavone intake contributed about 9 % to the explained variance. We conclude that intake of flavonols and flavones may protect against coronary heart disease in humans, but that it does not seem to be an important determinant of cancer risk. However, more experimental, clinical, and epidemiological evidence is needed before firm conclusions on the health effects of these flavonoids can be drawn.
The proteomic approach to investigate Parkinson's desease: pathogenetic mechanisms and biomarkers discovery.

4 1.INTRODUCTION 6 1.1 The proteomic approach to investigate pathogenethic mechanisms and to find biomarkers for Parkinson‟s disease 7 1.2 Parkinson‟s disease 8 1.2. 1. Epidemiology and Genetics 11 1.3 Alteration of dopamine homeostasis and oxidative stress 13 1.4 α-Synuclein 14 1.5 DJ-1 19 1.6 Cellular models to investigate dopamine and α-synuclein toxicity 20 1.7 Parkinson‟s disease as a mitochondrial disease 22 1.8 Biomarkers for Parkinson‟s disease 27 1.8. 1 Rationale for peripheral PD biomarkers 29 1.8. 2 Potential source for peripheral biomarkers of PD: Peripheral blood lymphocytes 30 2.AIM OF THE PROJECT 34 3.MATERIALS AND METHODS 36 3.1 A SH-SY5Y MODEL TO INVESTIGATE PD PATHOGENETIC MECHANISMS . 37 3.1.1 Cell cultures and transfection 37 3.1.2 Cell viability 37 3.1.3 2-DE electrophoresis and statistical analysis 38 3.1.4 LC-MS-MS analysis for protein identification 39 3.1.5 Bioinformatics enrichment and network clustering 40 3.1.6 Apoptosis analysis 40 3.1.7 Transient transfection and luciferase gene reporter assay 41 3.1.8 Western blotting of α-synuclein, HSP70 and 14-3-3 41 3.1. 9 Cell cycle analysis 42 3.1.10 Western blotting of Voltage Dependent Anion Channels (VDACs) 43 MONODIMENSIONAL WESTERN BLOTTING (TIME COURSE) 43 VDAC2 TWO-DIMENSIONAL WESTERN BLOTTING 44 3.1.11 Tetramethylrhodamine methyl ester (TMRM) staining 44 3.1.12 Measurement of Ca2+ flux to mitochondria using Aequorin 45 CELL PREPARATION, CALCIUM-PHOSPHATE TRANSFECTION PROCEDURE AND RECONSTITUTION OF FUNCTIONAL AEQUORIN 45