Miracle-dz/UniFAR-FTUs huggingface dataset:
Vote électronique : définitions et techniques d'analyse

Cette these porte sur l'etude de differents aspects de la securite des protocoles de vote electronique a distance. Ces protocoles decrivent comment organiser des elections par Internet de maniere securisee. Ils ont notamment pour but d'apporter des garanties de secret du vote, et de verifiabilite - ie, il doit etre possible de s'assurer que les votes sont correctement comptabilises. Nos contributions portent sur deux aspects principaux. Premierement, nous proposons une nouvelle technique d'analyse automatique de proprietes d'equivalence, dans le modele symbolique. De nombreuses proprietes en lien avec la vie privee s'expriment comme des proprietes d'equivalence, telles que le secret du vote en particulier, mais aussi l'anonymat ou la non-tracabilite. Notre approche repose sur le typage: nous mettons au point un systeme de typage qui permet d'analyser deux protocoles pour prouver leur equivalence. Nous montrons que notre systeme de typage est correct, c'est-a-dire qu'il implique effectivement l'equivalence de traces, a la fois pour des nombres bornes et non bornes de sessions. Nous comparons l'implementation d'un prototype de notre systeme avec les autres outils existants pour l'equivalence symbolique, sur divers protocoles de la litterature. Cette etude de cas montre que notre procedure est bien plus efficace que la plupart des autres outils - au prix d'une perte de precision (notre outil peut parfois echouer a prouver certaines equivalences). Notre seconde contribution est une etude des definitions du secret du vote et de la verifiabilite - ou, plus precisement, la verifiabilite individuelle, une propriete qui requiert que chaque votant soit en mesure de verifier que son propre vote a bien ete pris en compte. Nous prouvons, aussi bien dans les modeles symboliques que calculatoire, que le secret du vote implique la verifiabilite individuelle, alors meme que l'intuition et des resultats voisins deja etablis semblaient indiquer que ces deux proprietes s'opposent. Notre etude met egalement en evidence une limitation des definitions existantes du secret du vote par jeux cryptographiques : elles supposent une urne honnete, et par consequent expriment des garanties significativement plus faibles que celles que les protocoles visent a assurer. Nous proposons donc une nouvelle definition (par jeu) du secret du vote, contre une urne malhonnete. Nous relions notre definition a une notion de secret du vote par simulation, pour montrer qu'elle apporte des garanties fortes. Enfin, nous menons une etude de cas sur plusieurs systemes de vote existants.
Burkholderia thailandensis methylated hydroxy-alkylquinolines: biosynthesis and antimicrobial activity in co-culture experiments

The bacterium Burkholderia thailandensis produces an arsenal of secondary metabolites that have diverse structures and roles in the ecology of this soil-dwelling bacterium. In liquid co-culture experiments, B. thailandensis secretes a previously unstudied antimicrobial that nearly eliminates another soil bacterium, Bacillus subtilis. To identify the antimicrobial, we used a transposon mutagenesis approach. This screen identified antimicrobial-defective mutants with insertions in the hmqA, C and F genes involved in biosynthesis of a family of quinolones called 3-methyl-4-hydroxy-2-alkenylquinolines (HMAQs), which are related to the Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs). Insertions also occurred in a previously uncharacterized gene BTH_II1576. We confirm that BTH_II1576 is involved in generating N-oxide HMAQ (HMAQ-NO) in B. thailandensis and that HMAQ-NOs are sufficient to eliminate B. subtilis in co-cultures. Moreover, synthetic HMAQ-NO is ~50-fold more active than HMAQ. Both the methyl group and the length of the carbon side chain account for high activity of HMAQ-NO against B. subtilis. The results provide new information on the biosynthesis and activities of HMAQs and reveal new insight into how these molecules might be important for the ecology of B. thailandensis. IMPORTANCE The soil bacterium Burkholderia thailandensis produces methylated alkylquinolones, which are a family of relatively unstudied molecules related to the alkylquinolones of Pseudomonas aeruginosa. Several of the methylated alkylquinolones have antimicrobial activity against other species. We show N-oxidated methyl-alkenylquinolone is particularly antimicrobial and is sufficient to kill Bacillus subtilis in co-cultures, and requires a previously unstudied protein HmqL for biosynthesis. These results also provide new information about the biology of alkyl-quinolones, particularly the methylated alkylquinolones, which are unique to B. thailandensis. This study also has importance for understanding B. thailandensis secondary metabolites and has implications for potential therapeutic development.
SCREENING OF VEGETABLES FOR PHYTOEXTRACTION OF HEAVY METALS

To understand the phytoextraction of heavy metals from contaminated soil, eighteen seasonalvegetable crops were investigated. The soil was artificially contaminated each with 300 mg kg-1CuCl2, 500 mg kg-1 Pb (NO3)2, 800 mg kg-1 ZnCl2 or their mixed metal (1600 mg kg-1). Lowestcopper (Cu) accumulation was recorded in Brassica juncea and highest in Vicia faba, while lowestlead (Pb) accumulation in Solanum tuberosum, and highest in Allium fistulossum; and lowest zinc(Zn) accumulation in both Allium fistulossum and Solanum tuberosum, and highest was in Vicia fabafrom the single metal contamination. Similarly, lowest Cu, Pb and Zn was recorded in Brassicajuncea, Brassica caulorapa and Allium fistulossum, respectively; and highest accumulation of Cu andPb was in Spinacea oleracea and Zn in Spinacea oleracea from their mixed metal treatments. DOI: http://dx.doi. org/10.3126/eco.v20i0. 11469 ECOPRINT An International Journal of Ecology Vol. 20, 2013 page: 81-88
High-resolution yeast quiescence profiling in human-like media reveals interacting influences of auxotrophy and nutrient availability

Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence, and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, Target of Rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.
The effect of dispersal and preferential mating on the genetic control of mosquitoes

Mosquito-borne diseases cause significant social and economic damage across much of the globe. New biotechnologies that utilise manipulations of the mosquito genome have been developed to combat disease. The successful implementation of genetic mosquito control technologies may depend upon ecological, evolutionary and environmental factors, as well as the specifications of the chosen technology. Understanding the influence of these external factors will help inform how best to deploy a chosen technology to control vectors of infectious diseases. We use a continuous-time stochastic spatial network model of a mosquito life-cycle coupled to population genetics models to investigate the impact of releasing seven types of genetic control technology: a self-limiting lethal gene, two underdominance threshold gene drives, two homing gene drives and two Wolbachia systems. We apply the mathematical framework to understand control interventions of two archetypes of mosquito species: a short-range dispersing Aedes aegypti and comparatively longer-range dispersing Anopheles gambiae. We show that mosquito dispersal behaviour is an extremely important factor in determining the outcome of a release programme. Assortative mating – where the mating success of genetically modified males is lower than their wild counterparts – can facilitate the spatial containment of gene drives. The rapid evolution of strong mating preference can damage the efficacy of control efforts for all control technologies. We suggest that there cannot be a one-size-fits-all approach to regulation and implementation of vector control; there must be application-specific control plans that take account of understudied ecological, evolutionary and environmental factors.
Genetic structure of French populations of the mountain butterfly Parnassius mnemosyne L. (Lepidoptera: Papilionidae)

Geographical variation in allozyme frequencies among 24 populations of the butterfly Parnassius mnemosyne in southern France was studied by enzyme electrophoresis. Clustering procedures were used to define the geographical organization of genetic variation and an analysis of genetic differentiation was performed to test the degree of potential gene flow between the colonies using the methodologies derived from F-statistics and the private alleles model. Further, an approach using reduced space ordinations (factorial analysis of correspondences and discriminant analysis), was used to allow the visualization of genetically intermediate populations and to determine the roles of individual alleles at various levels of geographical structure. In P. mnemosyne, the effect of both isolation by distance and geographical barriers upon gene flow is complex. Some barriers appear to be very efficient, but others, at least as strong geographically, do not act in such a way. Multivariate analyses underlined the progressive transition between some groups while in other instances, a sharp cut was observed without obvious topographical barriers. Ecogeographical data and historical events (such as colonization processes) should probably be taken into account in order to explain the geographical variation of genetic structure.
Content-Based Similarity Search in Large-Scale DNA Data Storage Systems

Synthetic DNA has the potential to store the world’s continuously growing amount of data in an extremely dense and durable medium. Current proposals for DNA-based digital storage systems include the ability to retrieve individual files by their unique identifier, but not by their content. Here, we demonstrate content-based retrieval from a DNA database by learning a mapping from images to DNA sequences such that an encoded query image will retrieve visually similar images from the database via DNA hybridization. We encoded and synthesized a database of 1.6 million images and queried it with a variety of images, showing that each query retrieves a sample of the database containing visually similar images are retrieved at a rate much greater than chance. We compare our results with several algorithms for similarity search in electronic systems, and demonstrate that our molecular approach is competitive with state-of-the-art electronics. One Sentence Summary Learned encodings enable content-based image similarity search from a database of 1.6 million images encoded in synthetic DNA.
A study on the effect of frequency of urea ingestion on the utilization of low quality roughage by steers

Steers were fed a low quality roughage supplemented with 50 g urea day-1 administered at different frequencies. The effect of the different treatments was measured in terms of intake, digestibility, nitrogen balance and changes of some rumen fermentation measures in two different but complementary experiments. Utilization of the roughage was enhanced as the frequency of ingestion of urea increased. Organic matter digestibility was unaffected but voluntary intake was stimulated by all urea treatments. There was negative nitrogen balance in control animals but all treated were in positive nitrogen balance. However, the greatest retention was produced when urea was sprayed onto the ration. Possible reasons for the better utilization of urea as the frequency of ingestion spreads over the day are suggested by the results observed in the fermentation measures considered.
Reference genome and demographic history of the most endangered marine mammal, the vaquita

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.
IMiDs induce FAM83F degradation via an interaction with CK1α to attenuate Wnt signalling

IMiDs induce the degradation of the FAM83F–CK1α complex but no other FAM83–CK1α complexes, resulting in attenuation of Wnt signalling. Immunomodulatory imide drugs (IMiDs) bind CRBN, a substrate receptor of the Cul4A E3 ligase complex, enabling the recruitment of neo-substrates, such as CK1α, and their degradation via the ubiquitinproteasome system. Here, we report FAM83F as such a neo-substrate. The eight FAM83 proteins (A-H) interact with and regulate the subcellular distribution of CK1α. We demonstrate that IMiD-induced FAM83F degradation requires its association with CK1α. However, no other FAM83 protein is degraded by IMiDs. We have recently identified FAM83F as a mediator of the canonical Wnt signalling pathway. The IMiD-induced degradation of FAM83F attenuated Wnt signalling in colorectal cancer cells and removed CK1α from the plasma membrane, mirroring the phenotypes observed with genetic ablation of FAM83F. Intriguingly, the expression of FAM83G, which also binds to CK1α, appears to attenuate the IMiD-induced degradation of CK1α, suggesting a protective role for FAM83G on CK1α. Our findings reveal that the efficiency and extent of target protein degradation by IMiDs depends on the nature of inherent multiprotein complex in which the target protein is part of.
Atoh7-independent specification of retinal ganglion cell identity

Atoh7 promotes retinal ganglion survival and is not required for specification of most retinal ganglion cells. Retinal ganglion cells (RGCs) relay visual information from the eye to the brain. RGCs are the first cell type generated during retinal neurogenesis. Loss of function of the transcription factor Atoh7, expressed in multipotent early neurogenic retinal progenitors leads to a selective and essentially complete loss of RGCs. Therefore, Atoh7 is considered essential for conferring competence on progenitors to generate RGCs. Despite the importance of Atoh7 in RGC specification, we find that inhibiting apoptosis in Atoh7-deficient mice by loss of function of Bax only modestly reduces RGC numbers. Single-cell RNA sequencing of Atoh7;Bax-deficient retinas shows that RGC differentiation is delayed but that the gene expression profile of RGC precursors is grossly normal. Atoh7;Bax-deficient RGCs eventually mature, fire action potentials, and incorporate into retinal circuitry but exhibit severe axonal guidance defects. This study reveals an essential role for Atoh7 in RGC survival and demonstrates Atoh7-dependent and Atoh7-independent mechanisms for RGC specification.
Variations in benthic fauna between differing lake outlet types in New Zealand

Physico-chemical conditions and macroinvertebrate faunas of 20 South Island lake outlets were investigated in summer-early autumn of 1990-94. Four outlet types were recognised: unregulated alpine, unregulated mid/low elevation, regulated hypolimnetic and regulated epilimnetic outlets. Alpine outlet waters had significantly lower (P < 0.05) alkalinities and conductivities (6-12mg I"1 CaCO3 and 13^5 /uS cm"1) than all other outlets (1 l-36mg I"1 CaCO, and 36-93 /vS cm"1), whereas pH values were similar among outlet types. Substrate size was significantly greater in modified epilimnetic than natural mid/low elevation outlets (P < 0.01). Total number of taxa and invertebrate densities were significantly lower in alpine and hypolimnetic outlets than natural mid/low elevation outlets (P < 0.05, and P < 0.01 respectively), and distinct differences were observed in the relative abundances of major taxonomic groups. Alpine streams were dominated by the mayflies Deleatidium (Leptophlebiidae), and Nesameletus (Siphlonuridae), the gripopterygid stonefly Zelandoperla decorata and predatory hydrobiosid caddisflies; molluscs were absent, and filter-feeding hydropsychid caddisflies rare. In contrast, the hypolimnetic outlets were dominated by filter- feeding hydropsychids (87-93% of the fauna), and no stoneflies were found. Epilimnetic and unregulated mid/low elevation outlets had similar communities, however invertebrate densities were significantly lower in regulated surface release outlets. Altitude, outlet width, velocity, con-
Economics of Irrigated Continuous Corn under Conventional‐Till and No‐Till in Northern Colorado

Conversion of irrigated cropland from conventional tillage (CT) to no-till (NT) could have several environmental benefi ts including reduced erosion potential, reduction of greenhouse gas emissions, and conservation of water. However NT must be economically viable if it is to be adopted. Costs of production and economic returns were evaluated for an irrigated, continuous corn (Zea mays L.) system under CT and NT over 6 yr on a clay loam soil in northern Colorado. Yield responses to N fertilization were included to determine economic optimum fertilization rates under each tillage system. Corn grain yields at economic optimum N fertilizer rates were 1.1 to 1.4 Mg ha –1 lower for NT than for CT. However, net returns were $46 to 74 ha –1 higher for NT than for CT due to reductions in operating costs of $57 to 114 ha –1 and reductions in machinery ownership costs of $87 to 90 ha –1 . Operating cost savings were realized largely due to fuel and labor reductions of 75% and 71 to 72%, respectively, and in spite of higher N fertilizer requirements of 16 to 55 kg ha –1 for NT compared to CT. No-till, irrigated, continuous corn appears to be an economically viable option for replacing CT production systems in the central Great Plains, especially when combined with the environmental benefi ts of the NT system.
Top-down cascade from a bitrophic predator in an old-field community

We tested the hypothesis that a bitrophic (third and fourth level) arthropod predator can exert a cascading, top—down influence on other arthropods and plants in an early successional old field. First—stadium mantids, Tenodera sinensis, were added to replicated open—field plots in numbers corresponding to naturally occurring egg hatch density and allowed to remain for $\approx 2$ mo. Sticky—trap dispersal barriers around both control and mantid—addition plots allowed us to monitor emigration of arthropods continuously during the experiment. Biomass of herbivores, carnivores, and plants, and abundances of arthropod taxa within plots were determined at the beginning, middle, and end of the experiment. The impact of mantids on the community was a top—down trophic cascade, beginning at the fourth trophic level and evident at each of the lower three levels. Mantids induced marked behavioral responses in other predators, but inteference among predators did not prevent the trophic cascade. The most common predators, cursorial spiders, emigrated from mantid addition plots in significantly greater numbers than from controls. This behavioral response may have resulted from avoidance of predation or competition. Mantids decreased biomass of herbivorous arthropods through predation, and this decrease in turn increased biomass of plants. Therefore, these generalist predators were able to decrease herbivory enough to affect plant growth. This and other recent studies indicate that top—down effects can be important in structuring terrestrial communities. Ours is the first example of a top—down cascade by a generalist arthropod predator in a nonagricultural ecosystem and illustrates the importance of detecting behavioral responses in studies of trophic interactions.
Construction of Antibodies for Detection and Diagnosis of Cucumber green mottle mosaic virus from Watermelon Plants

We immunized BALB/c mice with purified Cucumber green mottle mosaic virus isolate HY1 (CGMMV-HY1). Through the selection of positive clones that were grown on the HAT medium, four sensitive monoclonal clones (CG99-01, CG99-02, CG99-03, and CG99-04) were selected from 500 Hypoxanthine-guanine phosphoribosyltransferase positive hybridoma cells. Four sensitive clones of CGMMV-HYI were determined as IgM type of the subclass of mouse immunoglobulins Ig group. The titer of monoclonal antiserum against CGMMVHY1 was estimated 1:12,800 by the indirect ELISA. Although monoclonal antibodies (MAbs) from CG99-01 and from CG99-04 cross-reacted with Zucchini green mottle mosaic virus and Kyuri green mottle mosaic virus, MAb from the cell line CG99-03 was highly specific to CGMMV. No MAbs cross-reacted with Cucumber mosaic virus-Fny. Only CG99-04 reacted with Pepper mild mottle virus weakly and CG99-02 reacted with both CGMMV and KGMMV. CGMMV was detected from the rind of watermelon fruit by DAS-ELISA of CGMMV-HY1, but not from the flesh of watermelon. Average seed transmission rate of CGMMV in watermelon was from symptomatic watermelon collected from 5 regions of Gyeongnam province. CGMMV was detected by DAS-ELISA with specific MAb of CGMMVHY1 periodically from root stock, during the sequential process for nursery seedling in Haman. Necrotic spots on cotyledons of root stock seedling progressed to reveal the typical symptomatology on the primary leaves of scion upon grafting. Here, we have established MAb based ELISA system, which could accurately detect CGMMV from watermelon seeds, nursery seedlings, transplants and field samples from greenhouse or open out door field as well.