Miracle-dz/UniFAR-FTUs huggingface dataset:
Développement de biomarqueur Sentinelle en réponse à la pollution aquatique à partir de l'expression de protéines de phénotype "Multidrug Resistance" dans les érythrocytes de la truite Salmo trutta fario

La pollution croissante des milieux aquatiques necessite la mise au point de nouvelles technologies permettant d’optimiser la surveillance de la qualite de l’eau. Dans ce contexte, nous avons developpe un biomarqueur de susceptibilite du degre de la pollution globale des milieux aquatiques intitule « Sentinelle ». Le principe du biomarqueur Sentinelle est base sur le niveau de coexpression de deux proteines « Multidrug Resistance » (MDR), la proteine ABCG2-like et la P-gp, dans les erythrocytes de la truite Salmo trutta fario. Le biomarqueur sentinelle a ete valide en conditions in vitro grâce au developpement des cultures primaires d’erythrocytes de truite. Apres l’exposition des globules rouges de truites a des concentrations croissantes d’un polluant modele, le Benzo-a-pyrene, l’expression de la proteine ABCG2-like et de la P-gp augmente d’une maniere dose dependante. Le biomarqueur Sentinelle a ensuite ete valide en milieu naturel sur des truites fario en provenance de differents cours d’eau d’Auvergne. En milieu naturel, les deux proteines MDR sont exprimees differemment dans les erythrocytes de truites fario selon le degre de contamination du cours d’eau. En effet, dans une riviere ou la pollution est faible voire nulle, seule la proteine ABCG2-like est exprimee, alors que dans une riviere presentant une contamination plus importante, la P-gp et l’ABCG2-like sont toutes les deux coexprimees par une reponse de type relais. Les experiences menees en conditions in vitro et en milieu naturel, laissent supposer que la proteine ABCG2-like assure une fonction de garde alors que la P-gp assurerait une fonction de protection defensive. En consequence, selon le niveau d’expression de la proteine de garde et de la proteine de defense, le degre de contamination de la riviere pourrait etre evalue. L’interet de l’utilisation du biomarqueur Sentinelle a aussi ete valide sur des Salmonides en provenance de pisciculture. Ce nouvel outil biologique apporte des informations plus integratives et plus precoces sur la qualite des milieux aquatiques, informations essentielles pour une meilleure gestion des ressources en eau.
Growth-retarding Effects of Paclobutrazol on Weeping Fig

Paclobutrazol was found to be an effective growth retardant for weeping fig (Ficus benjamina L.). Plants treated with a soil drench at rates of application from 0.125 mg a.i. to 8.0 mg a.i. per 10-cm pot exhibited retardation in plant height, leaf production, internode length, and leaf size. All measured responses were retarded linearly with increasing concentration, to the point of saturation at 0.5 mg a.i. per 10cm pot. Leaves developing under the influence of paclobutrazol also appeared darker green than in untreated plants. The growth retarding influence of a single application of PP333 persisted after transplanting. Chemical names used: (2RS,3RS)-l-(4-chlorophenyl)-4,4-dimethyl-2(l,2,4-triazole-l-yl)pentan-3-ol (paclobutrazol; ICI-PP333).
Divergência genética entre cultivares de caupi

This work aimed to determine the genetic divergence among cowpea cultivars [Vigna unguiculata (L.) Walp. ] when grouped in a multivariate analysis concerning to select superior parents. So 16 cowpea cultivars were used from the germplasm bank of the Centro de Ciencias Agrarias of the Universidade Federal do Ceara, in Brazil. The data were accomplished in complete randomized blocks, with six blocks, 16 treatments and three cultivar checks. The total area of experimental plots was 24 m2 and the net area was 16 m2, displayed in four rows, plants were spaced about 1.0 x 0.5 m with two plants in each plot. The phenotypic data were estimated from five competitive plants as casual samples on two central rows of each replicate. Breeding among the groups I [TVx-337-3F and Vita-4 (TVu 1977-OD)] and II (Bengala and V-4 Alagoas) may be the direct way to obtain new more productive cultivars because these groups are the most geneticaly divergent. The characters that contributed most to genetic divergence were the medium length of the plants (36.80%) and weight of 100 seeds (19.21%).
GENETIC VARIABILITY FOR YIELD COMPONENTS AND FIBRE CHARACTERS IN COTTON (GOSSYPIUM ARBOREUM L.)

Among thirteen varieties of cotton maximum variability was observed for seed cotton yield per hectare followed by bolls per plant and boll weight during the seasons studied. High heritability coupled with high genetic advance was also observed for seed cotton yield per hectare, bolls per plant, ginning percentage, halo length and fibre strength which indicates additive gene action in these characters.
Direct and Maternal Additive Effects on Rabbit Growth and Linear Body Measurements

Growth and linear body measurements of rabbits which consisted of 17 ew Zealand White (ZW), 19 Chinchilla (CH), 29 ZW x CH and 33 CH x ZW kittens were compared. The aim of the experiment was to evaluate the crossbreeding effects (i.e direct and maternal additive effect) for growth (individual body weight, IBW) and linear body traits (nose to shoulder, TS; shoulder to tail length, STL; heart girth, HG; trunk length, TL; length of ear, LE). Results revealed that significant (P 0.01) for all the traits except IBW. It could be recommended that CH sires be used to mate ZW dams to improve body weight and linear body traits. ZW does could be favoured to give the best IBW based on their superior maternal ability. Crossing between ZW and CH could be advantageous in increasing IBW and linear body measurements. Keywords: Growth, linear body measurements, heterosis, maternal, additive effect
Improving water productivity in the Australian Grains industry—a nationally coordinated approach

Abstract. Improving the water-limited yield of dryland crops and farming systems has been an underpinning objective of research within the Australian grains industry since the concept was defined in the 1970s. Recent slowing in productivity growth has stimulated a search for new sources of improvement, but few previous research investments have been targeted on a national scale. In 2008, the Australian grains industry established the 5-year, AU$17.6 million, Water Use Efficiency (WUE) Initiative, which challenged growers and researchers to lift WUE of grain-based production systems by 10%. Sixteen regional grower research teams distributed across southern Australia (300–700 mm annual rainfall) proposed a range of agronomic management strategies to improve water-limited productivity. A coordinating project involving a team of agronomists, plant physiologists, soil scientists and system modellers was funded to provide consistent understanding and benchmarking of water-limited yield, experimental advice and assistance, integrating system science and modelling, and to play an integration and communication role. The 16 diverse regional project activities were organised into four themes related to the type of innovation pursued (integrating break-crops, managing summer fallows, managing in-season water-use, managing variable and constraining soils), and the important interactions between these at the farm-scale were explored and emphasised. At annual meetings, the teams compared the impacts of various management strategies across different regions, and the interactions from management combinations. Simulation studies provided predictions of both a priori outcomes that were tested experimentally and extrapolation of results across sites, seasons and up to the whole-farm scale. We demonstrated experimentally that potential exists to improve water productivity at paddock scale by levels well above the 10% target by better summer weed control (37–140%), inclusion of break crops (16–83%), earlier sowing of appropriate varieties (21–33%) and matching N supply to soil type (91% on deep sands). Capturing synergies from combinations of pre- and in-crop management could increase wheat yield at farm scale by 11–47%, and significant on-farm validation and adoption of some innovations has occurred during the Initiative. An ex post economic analysis of the Initiative estimated a benefit : cost ratio of 3.7 : 1, and an internal return on investment of 18.5%. We briefly review the structure and operation of the initiative and summarise some of the key strategies that emerged to improve WUE at paddock and farm-scale.
Survival comparison between thymic carcinoma and thymic carcinoid: does it matter in clinical practice?

Thymic carcinoma (TC), a cancer derived from thymic epithelial cells, was first recognized by Shimosato and associates in 1977 in a study of 8 squamous cell carcinomas of the thymus (1). Thymic carcinoid was initially described by Rosai and Higa in 1972 as a “mediastinal endocrine neoplasm”, a separate entity from thymoma (2). Both TC and thymic carcinoid were previously categorized as Type C thymoma.
Small mammals of a bitterbrush-cheatgrass community

Small mammals were live-trapped in burned and unburned segments of a bitterbrush-cheatgrass community during the years 1974-1979. Results indicate that the shrub-dominated unburned area supports about three times as many small mammals as the cheatgrass-dominated burned area. Species composition was similar in both areas with the exception of one ground squirrel (Spermophilus townsendii) captured on the unburned area. Other species caught were the Great Basin pocket mouse (Perognathus parvus), deer mouse (Peromyscus maniculatus), northern grasshopper mouse (Onychomys leucogaster), and the western harvest mouse (Reithrodontomys megalotis).
Microscopic swimming in biological fluids

Fluid interactions are ubiquitous in the natural world; all organisms must find strategies to generate, utilise or resist flow in order to be successful. A process fundamental to all life on earth is reproduction, which in many cases entails the swimming of sperm cells. Cell swimming arises from coupled interactions between physical and biological processes. We will focus on the effects of changing fluid rheology on microscopic swimmers, with a particular application to the study of internal mammalian fertilisation. To reach the egg, mammalian sperm must navigate the convoluted geometry of the female reproductive tract, actively bending their flagella in order to propel themselves through cervical mucus: a suspension of polymer chains that twist, tangle and align with flow, giving it complex properties. Whilst recent work has examined the effects of fluid viscoelasticity on sperm-like swimmers, relatively less attention has been given to the shear-thinning property. We develop a new finite element technique to simulate free swimmers with prescribed beat kinematics in shear-thinning fluids with nonlinear governing equations. This technique is then applied to three qualitatively different viscous swimmers in order to examine the different phenomena that arise from swimmer interactions with of shear-thinning fluid.
THE ROLE OF CYTOPLASMIC CHAPERONES IN THE BIOGENESIS, MATURATION, AND DEGRADATION OF CYTOPLASMIC AND INTEGRAL MEMBRANE PROTEINS

I have characterized chaperone requirements for the biogenesis, maturation, and degradation of a cytosolic substrate, firefly luciferase (FFLux), in yeast, and of an integral membrane protein, cystic fibrosis transmembrane conductance regulator (CFTR), in yeast and in mammals. It was previously demonstrated that the cytoplasmic Hsp40, Ydj1p, is required for efficient expression of FFLux in yeast. This raised the question whether two Ydj1p-interacting molecular chaperones, the yeast Hsp70, Ssa1p, and the yeast Hsp90, Hsp82, also impact FFLux expression. The possible influence of a nucleotide exchange factor for Ssa1p, Fes1p, was also investigated. I found that the chaperone requirements for FFLux biogenesis are distinct but overlapping. Whereas Ssa1p and Fes1p likely collaborate to fold FFLux, Ssa1p, independent of its nucleotide exchange factor, was necessary for stabilizing FFLux protein and message, and for efficient induction of FFLux mRNA. Therefore, Fes1p impacts only a subset of Ssa1pi¦s actions. Although FFLux folding progresses independent of Hsp82, efficient expression of FFLux depends on Hsp82, mainly due to Hsp82i¦s contribution to FFLux translation. To identify the complete spectrum of chaperones that affect ER associated degradation (ERAD) of CFTR, I took a genomic approach in yeast. Transcriptional profiles between yeast expressing CFTR and control strains were examined by microarray analysis. Among the genes up-regulated in strains expressing CFTR was one encoding a small heat shock protein (sHsp), HSP26. Therefore, I investigated CFTR degradation in yeast strains lacking HSP26 and found that the protein was stabilized; stabilization was enhanced in a strain lacking both HSP26 and another sHsp-encoding gene, HSP42. In contrast, degradation of a soluble ERAD substrate and of another transmembrane protein proceeded with equal efficiency in wild type and in hsp26hsp42 mutant yeast. Next, I examined whether sHsps regulate CFTR biogenesis in mammalian cells. I found that ƒ´F508-CFTR degradation was enhanced when ƒNA-crystallin was over-expressed in HEK293 cells, although wild type CFTR biogenesis was unaffected. To examine why this sHsp accelerated degradation of ƒ´F508-CFTR, ƒNA-crystallin was purified and I found that it was able to suppress aggregation of CFTRi¦s first nucleotide binding domain. Together, these results suggest that sHsps increase ƒ´F508-CFTRi¦s accessibility during proteasome-mediated degradation.
2 Progress toward Understanding the Origin of the RNA World

The general idea that, in the development of life on the earth, evolution based on RNA replication preceded the appearance of protein synthesis was first proposed almost 40 years ago (Woese 1967; Crick 1968; Orgel 1968). It was suggested that catalysts made entirely of RNA are likely to have been important at this early stage in the evolution of life, but the possibility that RNA catalysts might still be present in contemporary organisms was overlooked. The unanticipated discovery of ribozymes (Kruger et al. 1982; Guerrier-Takada et al. 1983) initiated extensive discussion of the role of RNA in the origins of life (Pace and Marsh 1985; Sharp 1985; Lewin 1986) and led to the coining of the phrase “the RNA World” (Gilbert 1986). “The RNA World” means different things to different investigators, so it would be futile to attempt a restrictive definition. All RNA World hypotheses include three basic assumptions: (1) At some time in the evolution of life, genetic continuity was assured by the replication of RNA; (2) Watson-Crick base-pairing was the key to replication; (3) genetically encoded proteins were not involved as catalysts. RNA World hypotheses differ in what they assume about life that may have preceded the RNA World, about the metabolic complexity of the RNA World, and about the role of low-molecular-weight cofactors, possibly including peptides, in the chemistry of the RNA World. There is now strong evidence indicating that an RNA World did indeed exist on the early earth. The smoking gun is seen in the.
Specificity and polyreactivity of the antibody response during natural HIV-1 infection

The specificity and polyreactivity of the antibody response in natural HIV1 infection were studied. First, to investigate the overall antibody response, overlapping linear peptides were used to screen sera taken from HIV1 -infected individuals. The polyclonal antibody response was relatively stable during long-term infection, compared with acute infection, and mostly directed against immunodominant regions. Low level, transient antibody responses were detected against membrane proximal external region of gp4 1. To test if these Abs are neutralizing, an affinity purification method was developed to isolate these serum antibodies. Second, in terms of polyreactivity of antibody response, we found that two broadly-neutralizing monoclonal antibodies bound only weakly to self antigen, cardiolipin. Moreover, sera were screened against cardiolipin; no significant reactivity
Case 3650 Tapirus pygmaeus Van Roosmalen & Van Hooft in Van Roosmalen, 2013 (Mammalia, Perissodactyla, tapiridae): proposed confirmation of availability of the specific name and of the book in which this nominal species was proposed

Abstract. The purpose of this application, under Articles 78.2. 3 and 80.2. 1 of the Code, is to confirm the availability of the nominal species Tapirus pygmaeus Van Roosmalen & Van Hooft in Van Roosmalen 2013 [22 April] for the black dwarf tapir, thus also confirming its priority over the subjective synonym Tapirus kabomani Cozzuol et al., 2013 [December], by ruling that Van Roosmalen's edited book Barefoot through the Amazon — On the path of evolution, in which T. pygmaeus was proposed, is not unavailable solely on account of its being advertised as a print-on-demand work, but is an original multiple-copy, simultaneously available edition. It is shown that Van Roosmalen & Van Hooft's publication contained information sufficient to satisfy the criteria of availability under Articles 10 to 20 of the Code.
Clinical and Genetic Characterization of Familial Adenomatous Polyposis: An Iranian Population Study

Background: Familial adenomatous polyposis (FAP) is an inherited autosomal dominant disorder, which can develop into cancer in early adulthood (100%) and is a result of germline mutations in the adenomatous polyposis coli (APC) genes. Objectives: Identify APC germline mutations and assessed relationships between genotypes and phenotypes. Methods: In a census-based cross-sectional study, FAP patients were selected from the referral medical centers of East Azarbaijan province between 2013 and 2016. Written informed consent was obtained from all patients for blood sampling and genetic testing. Patients undergo genetic counseling, and the pedigree was drawn. After peripheral blood sampling and DNA extraction, the potential mutation of the APC gene was detected by polymerase chain reaction (PCR), and DNA sequencing. Statistical tests were carried out using SPSS version 16.0. Categorical data between two groups were compared using the chi-square test. Independent sample ttest was used for comparison of continuous variables between two groups. The P-value < 0.05 was considered statistically significant. Results: We identified APC gene mutations in 18 of the 30 unrelated patients with FAP (60%), including one novel frame shiftmutation, three nonsense mutations, and 14 novel missense mutations (78%). The most frequent mutations were in codon 1308 and 1350. Meanwhile, we found a novel polymorphism. Conclusions: Our study results indicated that the APC gene has a high mutation detection rate (60%) between codons 999 and 1410, and codons 1308, and 1350 are two mutation hotspot regions.
Phylogenetics and diversification of Escallonia (Escalloniaceae)

Despite a large accumulation of evidence on the high richness of plant species in the mountains of South America, little is known about the historical underpinnings and the ecological processes that have shaped the extraordinarily distinctive, diverse, and endangered flora of these regions. In an effort to contribute to our understanding of the origin and diversification of plant species in these mountains, I analyzed geographic patterns of variation in molecular and phenotypic characters for the genus Escallonia L.f. (Escalloniaceae), a group of shrubs and small trees widespread in montane habitats in South America. Molecular phylogenetic analyses using chloroplast and nuclear loci and involving an exhaustive sampling at the species level revealed i) that Escallonia is monophyletic, ii) a remarkable level of geographical phylogenetic structure, and iii) a widespread absence of species-level monophyly. These results are consistent with the hypothesis that geography played an important role in the early history of Escallonia by separating populations, which later diversified rapidly and/or recently in isolation. To evaluate whether the lack of monophyly could reflect problems with species boundaries, I present a new statistical approach that uses morphological and geographical data to i) weigh the strength of the evidence to support the hypothesis that distinct species are separated by morphological gaps, and ii) examine if morphological gaps could be explained by an alternative hypothesis of geographic differentiation within a single species rather than by a hypothesis of a species boundary. Multivariate analyses of morphological data using this approach provided support to several of the current hypotheses of species boundaries within Escallonia, suggesting that neutral molecular Felipe Zapata, 2010, Ph.D. Dissertation, p. iv
Chorioretinal thinning in chronic kidney disease links to inflammation and endothelial dysfunction

BACKGROUND. Chronic kidney disease (CKD) is strongly associated with cardiovascular disease and there is an established association between vasculopathy affecting the kidney and eye. Optical coherence tomography (OCT) is a novel, rapid method for high-definition imaging of the retina and choroid. Its use in patients at high cardiovascular disease risk remains unexplored. METHODS. We used the new SPECTRALIS OCT machine to examine retinal and retinal nerve fiber layer (RNFL) thickness, macular volume, and choroidal thickness in a prospective cross-sectional study in 150 subjects: 50 patients with hypertension (defined as a documented clinic BP greater than or equal to 140/90 mmHg (prior to starting any treatment) with no underlying cause identified); 50 with CKD (estimated glomerular filtration rate (eGFR) 8–125 ml/min/1.73 m2); and 50 matched healthy controls. We excluded those with diabetes. The same, masked ophthalmologist carried out each study. Plasma IL-6, TNF-α , asymmetric dimethylarginine (ADMA), and endothelin-1 (ET-1), as measures of inflammation and endothelial function, were also assessed. RESULTS. Retinal thickness, macular volume, and choroidal thickness were all reduced in CKD compared with hypertensive and healthy subjects (for retinal thickness and macular volume P < 0.0001 for CKD vs. healthy and for CKD vs. hypertensive subjects; for choroidal thickness P < 0.001 for CKD vs. healthy and for CKD vs. hypertensive subjects). RNFL thickness did not differ between groups. Interestingly, a thinner choroid was associated with a lower eGFR (r = 0.35, P <0.0001) and, in CKD, with proteinuria (r = –0.58, P < 0.001) as well as increased circulating C-reactive protein (r = –0.57, P = 0.0002), IL-6 (r = –0.40, P < 0.01), ADMA (r = –0.37, P = 0.02), and ET-1 (r = –0.44, P < 0.01). Finally, choroidal thinning was associated with renal histological inflammation and arterial stiffness. In a model of hypertension, choroidal thinning was seen only in the presence of renal injury. CONCLUSIONS. Chorioretinal thinning in CKD is associated with lower eGFR and greater proteinuria, but not BP. Larger studies, in more targeted groups of patients, are now needed to clarify whether these eye changes reflect the natural history of CKD. Similarly, the associations with arterial stiffness, inflammation, and endothelial dysfunction warrant further examination. TRIAL REGISTRATION. Registration number at www.clinicalTrials. gov: NCT02132741. SOURCE OF FUNDING. TR was supported by a bursary from the Erasmus Medical Centre, Rotterdam. JJMHvB was supported by a bursary from the Utrecht University. JRC is supported by a Rowling Scholarship. SB was supported by a Wellcome Trust funded clinical research fellowship from the Scottish Translational Medicine and Therapeutics Initiative, and by a Rowling Scholarship, at the time of this work. ND is supported by a British Heart Foundation Intermediate Clinical Research Fellowship (FS/13/30/29994).