Miracle-dz/UniFAR-FTUs huggingface dataset:
Life history traits of pumpkinseed (Lepomis gibbosus) populations introduced into warm thermal environments

Life history theory predicts that ectotherms living in warm thermal environments should mature early because of fast juvenile growth, but it is unclear whether such early maturity will occur in the absence of conditions that promote fast juvenile growth. To assess this possibility and to determine the effect of warm thermal regimes on body size at maturity, we compared the growth and life history patterns of three populations of pumpkinseed (Lepomis gibbosus) introduced into warm, Mediterranean waterbodies in southern France with native populations living in cool thermal regimes in Ontario, Canada. Growth and life history traits of the French populations were determined from monthly samples collected from May to September. Mean age at maturity in the French populations ranged from 1.3-2.3 years, and was significantly earlier than that of populations inhabiting Ontario lakes. Length at age 2, an indicator of the juvenile growth rate, was not significantly different between the French and Ontario populations, and the French populations matured significantly earlier than Ontario lake populations even when juvenile growth was taken into account. Length at maturity in the French populations was also significantly smaller, and although there was no significant difference between the French and Ontario populations in mean GSI, the results of a previous reproductive allocation experiment suggest that French populations have a longer breeding season, and greater reproductive effort than Ontario pumpkinseeds. The earlier maturity of French pumpkinseeds could be a direct physiological effect of the warm thermal environment, but factors other than thermal regime may he contributing to the difference in life history traits between the French and Ontario populations.
Pyrethroid resistance in the pod borer, Helicoverpa armigera, in southern India.

changes in the LD 50 of Helicoverpa armigera to cypermethrin at the International Crops Research Institute for the semi­ Arid Tropics (ICRISAT) and in the coastal cotton-growing region of Andhra pradesh state during the period 1986-92 are summarised and discussed. A provisional discriminating dose of lug cypermethrin was evaluated at ICRISAT and changes in resistance to cypermethrin monitored throughout 1991/92. Resistance was related to seasonal changes in insecticide use; it was lowest in August and increased with progression of the season. Prospects for insecticide resistance management of H. armigera in Andhra Pradesh are briefly discussed.
Color Homography: Theory and Applications

Images of co-planar points in 3-dimensional space taken from different camera positions are a homography apart. Homographies are at the heart of geometric methods in computer vision and are used in geometric camera calibration, 3D reconstruction, stereo vision and image mosaicking among other tasks. In this paper we show the surprising result that homographies are the apposite tool for relating image colors of the same scene when the capture conditions—illumination color, shading and device—change. Three applications of color homographies are investigated. First, we show that color calibration is correctly formulated as a homography problem. Second, we compare the chromaticity distributions of an image of colorful objects to a database of object chromaticity distributions using homography matching. In the color transfer problem, the colors in one image are mapped so that the resulting image color style matches that of a target image. We show that natural image color transfer can be re-interpreted as a color homography mapping. Experiments demonstrate that solving the color homography problem leads to more accurate calibration, improved color-based object recognition, and we present a new direction for developing natural color transfer algorithms.
Improvement of isolated microspore culture of ornamental kale (Brassica oleracea var. acephala): effects of sucrose concentration, medium replacement, and cold pre-treatment

Summary By evaluating the effects of the culture medium and cold pre-treatment on microspore embryogenesis, we have developed an efficient and reliable protocol for microspore culture and doubled-haploid plant regeneration of ornamental kale (Brassica oleracea var. acephala). Microspore embryogenesis at high frequency was obtained using a liquid NLN medium containing 16% (w/v) sucrose (NLN-16) without medium replacement. Of the genotypes tested, the cultivar ‘Peachy Dancing’ produced the highest yield of embryos (averaging 123.63 embryos per dish). Medium replacement was found to deplete embryo yield significantly in all three genotypes tested (namely, ‘Nagoya’, ‘Peachy Dancing’, and ‘P3’), when compared with continuous culture of microspores in the original incubation medium. A 48-h cold pre-treatment, delivered to the flower buds of ‘Nagoya’ and ‘P3’ before microspore isolation, significantly enhanced subsequent microspore embryogenesis; however, cold pre-treatment of flower buds had a negative effect on ‘Peachy Dancing’. Cotyledonary embryos were incubated on B5 basal medium and abnormal embryos on B5 medium containing 2% (w/v) sucrose, 1.5 mg l−1 6-benzylaminopurine, and 0.25 mg l−1 naphthaleneacetic acid. In each case, high quality embryos were regenerated that went on to produce healthy, vigorous plants. There were 38 – 50% spontaneous diploid, microspore-derived plants among the three genotypes tested.
Neurobiology of nematode muscle: ligand-gated ion-channels and anti-parasitic drugs.

Muscle cell membranes of nematodes possess ion channel receptors that are opened by neurotransmitters and which are gated by selective therapeutic agents. This chapter is an introduction to the physiology and pharmacology of ligand-gated ion channels of nematode muscle. Nematode parasites present a serious problem for most animals and for humans in developing countries. These parasites produce various symptoms including ill thrift, poor growth, diarrhoea and, in around 1% of cases, loss of life. The economic forces are such that new drugs for the treatment of nematode parasites have been developed first for animal use and only later for human use. A recent example is the development of the antibiotic anthelmintic, ivermectin, which was introduced first for the treatment of cattle nematode parasites and has subsequently been used to control ‘river blindness’, an eye condition seen in west Africa caused by larvae of Onchocerca volvulus. There are two main mechanisms of action of important anti-nematode drugs.
Uncovering the functional effects of biomolecular mutations through computer simulations

VI LIST OF FIGURES . IX LIST OF TABLES . X CHAPTER 1: INTRODUCTION . 2 1.1 Overview . 2 1.2 Biological background of amino acid substitutions . 2 1.3 Predicting the effects of mutations in silico . 3 1.4 Molecular Simulations . 4 CHAPTER 2: FUNCTIONAL DETERMINANTS FOR DNA TARGETING BY ACTIVATION-­‐INDUCED CYTIDINE DEAMINASE . 10 2.1 Introduction . 10 2.1.1 Synopsis . 10 2.1.1 Background . 11 2.1.2 Experimental collaboration . 15 2.3 Methods . 23 2.3. 1 Molecular Modeling . 23 2.3. 2 System Preparation and MD Simulations . 25 2.3. 3 Analyses . 26 2.4 Results . 27 2.4. 1 AID-­‐WT interactions with hotspot and coldspot ssDNA . 27 Table 2.1. Solvent accessible surface area for side chain residues. 30
Analysis on electromechanical coupling vibration characteristics of in-wheel motor in electric vehicles considering air gap eccentricity

The distortion of air gap magnetic field caused by the rotor eccentricity contributes to the electromechanical coupling vibration of the brushless DC (BLDC) permanent magnet in-wheel motor (PMIWM) in electric vehicles (EV). The comfort of the BLDC in-wheel motor drive (IWMD) EV is seriously affected. To deeply investigate the electromechanical coupling vibration of the PMIWM under air gap eccentricity, the PMIWM, tyre and road excitation are analyzed first. The influence of air gap eccentricity on air gap magnetic density is investigated. The coupling law of the air gap and the unbalanced magnetic force (UMF) is studied. The coupling characteristics of eccentricity rate, air gap magnetic density, UMF, phase current and vibration acceleration are verified on the test bench in the laboratory. The mechanism of the electro-mechanical coupling vibration of the BLDC PMIWM under air gap static eccentricity (SE), dynamic eccentricity (DE) and hybrid eccentricity (HE) is revealed. DE and HE deteriorate the vibration acceleration amplitude, which contributes the electromechanical coupling vibration of the PMIWM. The research results provide a solid foundation for the vibration and noise suppression of the PMIWM in distributed drive EV.
New Zealand's extinct birds

The largest penguin ever known once roamed the shores of New Zealand, and there were many other strange bird species which soared the skies or stalked the land, false-toothed pelicans, eleven moa species including the tallest bird known, giant flightless geese and coots, the largest eagle known, adzebills, owlet-night jars and the world's only flightless perching bird. These weird and wonderful birds are now extinct. Some disappeared in the geologically distant past, but most were eliminated during the last 1000 years, unable to withstand the impact of humans on these lands.
The Western Australian HIV cohort study

The efficacy of primary prophylactic treatment for opportunistic infections can be estimated in an observational cohort study by adjusting for clinical and laboratory markers of the immunodeficiency (e.g., oral candidiasis, CD4%, lymphocyte cell counts) as time-dependent co-variates (providing that the treatment does not directly alter the markers). However, the CD4 cell count provides an incomplete measure of the protective immune response, and the efficacy of treatment may be underestimated if there is inadequate adjustment for the severity of immunodeficiency. Unlike prophylactic therapies, the efficacy of which remains relatively constant over time, antiretroviral therapy may produce only transient or time-limited benefits. This problem can be minimized by allowing the effect of antiretroviral therapy to vary over time in Cox proportional hazards models (i.e., to allow the antiretroviral therapy coefficient to change over time). Another difficulty is that CD4 cell counts may underestimate the degree of immunodeficiency after prolonged zidovudine (AZT) monotherapy. If post-antiretroviral therapy CD4 cell counts are used to adjust for the stage of immunodeficiency, it may therefore be helpful to adjust for the duration of antiretroviral therapy with the CD4 cell count at the time of starting antiretroviral therapy. It is interesting to consider statistical models of progressive HIV-induced immunodeficiency in the context of the evolution of host immunity. HIV infection results in the loss of the relatively recently evolved adaptive CD4 T cell-mediated immunity to intracellular parasites. The infected host may compensate for this by making greater use of phylogenetically ancient, more innate protective responses. Because these compensatory responses are polymorphic, this results in the appearance of differences between individuals in the immune response to HIV as the disease progresses. Data from the Western Australia HIV Cohort Study support a two-stage model of immunopathology. The first stage of this model involves a loss of mucosal immunity and occurs at a variable CD4 cell count (of between 400 cells/mm3 and zero), and is marked by a loss of cutaneous delayed-type hypersensitivity responses and oral candidiasis, seborrheic dermatitis, and Pneumocystis carinii pneumonia. The second stage of the model involves a loss of systemic immunity and requires profound CD4 T-cell lymphopenia (CD4 cell count <50 cells/mm3), and is marked by infections such as cytomegalovirus and disseminated Mycobacterium avium infection. The influence of HLA type on the risk for such opportunistic infections becomes apparent during this late phase.
The Suspension World of the China A-Shares Market

This paper aims to study the suspension features of the China A-shares market and the results will be useful for market participants who carry out China A-shares investment and portfolio management. A comprehensive review is first carried out to study the properties of different types of suspension events with a focus on their occurrence frequency and duration. The empirical findings illustrate that the suspension length has been increasing in general and prolonged suspension is still an issue in the China A-shares market. Next we investigate how suspension occurrence is related to stock fundamental attributes and the results are useful for estimating the suspension probability of individual stocks. It is demonstrated that stocks with smaller size, less attractive valuation, higher volatility and past history of more frequent suspensions are more likely to experience future suspension. Another focus of this research is to evaluate the effectiveness of the stock trading suspension system in the China A-shares market by studying the volatility, return and trading pattern around the suspension window. The empirical results suggest that the stock suspension system is a semi-effective process.
Molecular Analysis of Arabidopsis thaliana Genes Involved in Stress Response

Arabidopsis thaliana is an excellent model plant to study various plant processes, including plant’s response to environment, its interactions with other organisms, etc. In this study I characterized eight Arabidopsis genes that are likely to regulate plant’s responses to biotic and abiotic stresses. Microarray analysis was done previously in our lab to identify Arabidopsis genes that are differentially expressed in response to various biotic and abiotic stresses and several plant hormones. The biotic stresses include bacterial, fungal and viral pathogens (both virulent and avirulent strains), sucking and chewing insects. The abiotic stresses include chemicals that induce variety of oxidative stresses (paraquat, 3AT, mixture of glucose/glucose oxidase, and mixture of xanthine/xantine), wounding, heat, cold, freezing, senescence, drought, flooding and salt. The plant hormones include IAA (auxin), 2,4-D (synthetic auxin), BA (cytokinin), GA (gibberellic acid) , ABA (abscisic acid) , ACC (ethylene precursor), JA (jasmonic acid), BR (brassinosteroid), and SA (salicylic acid). The results of these experiments were used to construct Arabidopsis Stress Microarray Database (ASMD). From this database, eight genes that were considerably up regulated in a number of different stress treatments were identified. To determine the role of these genes in regulating stresses, I constructed transgenic plants that overor under-express the target genes.
Biotic or abiotic factors: which has greater influence in determining the structure of rotifers in semi-arid reservoirs?

ObjectiveThe objective of this study is to evaluate whether the distribution of structural attributes of rotifers in reservoirs in the semiarid region is more strongly influenced by abiotic or biotic environmental factors (density of cyanobacteria). MethodSampling occurred in two reservoirs in the Paraiba Basin, northeastern Brazil (Pocoes and Camalau) during April and June 2012. Eight sampling points were distributed at two stations in each reservoir: the region near the entrance of the main tributary and region of the dam and collections were made in the limnetic and littoral zone in every season. To assess the abiotic influence and density of cyanobacteria in the distribution of the structural attributes of rotifers, environmental variables bivariate correlation was conducted in series.ResultsIn Pocoes reservoir, the distribution of rotifer biomass was negatively related to the density of cyanobacteria; among the environmental variables, chlorophyll-a and total nitrogen were negatively related to all of the tested structural attributes, while the concentrations of total phosphorus were strongly related to the abundance of rotifers. In the Camalau reservoir, the biomass was a structural attribute with a stronger correlation to the density of cyanobacteria; between the environmental variables and Egeria densa, nitrate was negatively related to all of the attributes tested, while transparency was moderately related to the abundance, biomass and richness as well as Chara sp. with abundance.ConclusionsAssemblages of rotifers are more clearly related to environmental conditions, especially those indicative of trophic conditions, despite the density of cyanobacteria having been a factor that was positively related to the structural characteristics of rotifers and thus indicative of such structural assemblies. This can be used for analysis of local environmental condition factors.
Kelkit Vadisi (Türkiye) Alydidae, Rhopalidae ve Stenocephalidae (Heteroptera: Coreoidea) türleri üzerine araştırmalar

Alydidae, Rhopalidae ve Stenocephalidae familyaları Coreoidea (Heteroptera) üstfamilyası içinde yer almaktadırlar. Palearktik Bölgede; Alydidae familyasına ait 26 cinse bağlı 69 tür, Rhopalidae familyasına ait 14 cinse bağlı 68 tür ve Stenocephalidae familyasına ait bir cinse bağlı 18 tür bulunmaktadır (Dolling, 2006). Türkiye’de ise Alydidae familyasına ait iki cinse bağlı beş tür, Rhopalidae familyasına ait 12 cinse bağlı 30 tür ve Stenocephalidae familyasından Dicranocephalus cinsine bağlı altı türün bulunduğu bilinmektedir (Pehlivan, 1981; Dolling, 2006; Önder et al., 2006).
The prevalence of antimicrobial resistant Salmonella spp. and the risk factors associated with their occurrence in finisher pigs in Seberang Perai, Malaysia.

Across sectional study to determine the occurrence and antimicrobial resistance pattern of Salmonella spp. in finishing pigs was carried out at 12 selected pig farms. The farm characteristics and certain management practices associated with the occurrence of Salmonella spp. were also evaluated. Rectal swabs were collected aseptically from 210 randomly selected finishing pigs. Suspect Salmonella colonies isolated were identified using a set of conventional biochemical tests and these isolates were sent to the Veterinary Research Institute (VRI) for serotyping. The antimicrobial sensitivity test was conducted on the isolates against a panel of selected antimicrobials that are commonly used in local pig production using disc diffusion method. In addition, a questionnaire on the management of farms, herd health programme,and common antimicrobial usage was collected from farm representative, resulting in variables that could be analyzed to identify factors associated with the occurrence of Salmonella. The results showed that 32 out of 210 finishing pigs (15.2%)tested were positive for Salmonella typhimurium and the isolates were detected from 9 out of 12 farms sampled (75.0%). Most of the isolates showed a relatively high level of antimicrobial resistance. The occurrence of Salmonella in pigs were significantly associated with (1) farms which were not equipped with footbath or vehicle wheels dip; (2) farms with vermins/birds in the surrounding; (3) farms with less frequent pen cleaning and (4) farms which are located adjacent to the neighbouring farms.
Investigation into the role of La/SS-B in Interferon regulation and its relevance in health and human disease

xxi Chapter 1: General Introduction. 1 1.1 The immune system. 2 1.2 Autoimmunity. 4 1.3 Systemic Lupus Erythematosus. 5 1.3. 1 Autoantibodies. 6 1.3. 2 Pathogenesis. 7 1.3. 3 Viral infection and SLE. 9 1.3. 4 Interferons (IFNs) in SLE. 11 1.4 Pathogen Recognition Receptors (PRRs). 13 1.4.1 Toll-like receptors (TLRs). 14 1.4.1.1 MyD88-dependent signalling. 16 1.4.1.2. TRIF-dependent signalling. 17 1.4.1.3 Anti-viral TLRs in SLE. 18 1.4.2 NOD-like receptors (NLRs). 21 1.4.3 DNA receptors. 24 1.4.4 RIG-I-like receptors (RLRs). 28 1.4.4.1 Structure. 29 1.4.4.2 LGP-2. 30 1.4.4.3 Ligand and strain specificity. 31 1.4.4. 4 Signal transduction. 32 1.4.4.5 A role for RLRs in SLE? 35 1.5 Regulation of anti-viral signalling. 35 1.5.1 Autoantigens in IFN regulation. 37 1.6 La autoantigen. 38 1.7 Hypothesis & Aims. 44 Chapter 2: Materials and Methods. 45 2.1 Materials. 46 2.1.1 General Chemicals and Conditions. 46 2.1.2 Antibody conditions. 52 2.1.3 Plasmid constructs. 53 2.1.4 Cells. 54 2.1.5 Ligand information. 54 2.1.6 List of Suppliers. 54 2.2 Methods. 57 2.2.1 Cell Culture. 57 2.2.1.1 Growth and maintenance of HEK-293T and HeLa cell line. 57 2.2.1.2 Cell counting and viability. 57 2.2.2 Isolation of Peripheral Blood Mononuclear Cells. 59 2.2. 3 Cell Proliferation (MTT) Assay. 60 2.2. 4 Plasmid Purification. 62 2.2. 4.1 Transformation of Ultra Competent Cells. 62 2.2. 4.2 Maxi-scale preparation of plasmid from Escherichia coli. 62 2.2. 5 Transient transfection. 63 2.2. 5.1 Reporter gene assays. 65 2.2. 6 SDS PAGE and Western Blot Analysis. 66 2.2. 6.1 Preparation of Whole Cell Lysates. 66 2.2. 6.2 Bicinchoninic Acid (BCA) Protein Assay. 67 2.2. 6.3 Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDSPAGE). 68 2.2. 6.4 Transfer of Proteins to Membrane. 69 2.2. 6.5 Antibody Blotting. 70 2.2. 6.6 Densitometric analysis. 71 2.2. 7 Immunoprecipitation. 71 2.2. 7.1 Antibody Pre-Coupling. 72 2.2. 7.2 Buffer Optimisation. 72 2.2. 7.3 Immunoprecipitation. 73 2.2. 8 RNA Immunoprecipitation. 74 2.2. 9 Recombinant Protein Pull-downs. 74 2.2. 9.1 Preparation of recombinant protein and cell lysis. 74 2.2. 9.2 Purification of recombinant protein using Nickel Agarose. 75 2.2. 9.3 Recombinant Pull-down experiments. 76 2.2.10 Nuclear & cytoplasmic fractionation. 76 2.2.11 Polymerase Chain Reaction (PCR) Analysis. 77 2.2.11.1 Extracting RNA using the Trizol Method. 78 2.2.11.2 Reverse Transcription. 78 2.2.11.3 PCR. 79 2.2.11.4 Gel Electrophoresis of PCR products. 81 2.2.11.5 Real-Time PCR. 81 2.2.12 Immunofluorescence. 82 2.2.13 Analysis of Cytokine Production. 83 2.2.13.1 Enzyme-linked Immunosorbence Assay (ELISA). 84 2.2.13.2 Multiplex 7-spot cytokine analysis. 85 2.2.14 Viral Infection. 86 2.2.15 Patient Recruitment. 87 2.2.16 Statistical Analysis. 87 Chapter 3: La inhibits RLR-mediated IFN-β induction. 88 3.
Dispersal in a haplo-diploid red algal species: genetic structure and gene flow in Gracilaria gracilis

Nous avons etudie la structure genetique de dix populations de Gracilaria gracilis reparties le long des cotes francaises. La structuration genetique intra-population d'une part, et la variation de la differenciation genetique entre populations en relation avec la distance geographique d'autre part, ont ete analysees grâce a l'utilisation de deux marqueurs microsatellites. Nos resultats montrent que les populations sont faiblement structurees et que cette espece, contrairement a nos predictions, est caracterisee par un regime de reproduction faiblement consanguin. Quoiqu'il en soit, les flux geniques se produisent essentiellement entre populations proches geographiquement ce qui demontre qu'il existe un phenomene d'isolement par la distance. Neanmoins, sur une echelle locale (inferieure au kilometre), la differenciation entre populations ne depend pas seulement de la distance et il est probable que la maree puisse jouer un role dans l'orientation des flux geniques a cette echelle.