Miracle-dz/UniFAR-FTUs huggingface dataset:
Etudes par cryo-microscopie électronique de la structure de virus : application aux bactériophages Gifsy-2 de Salmonella Typhimirium et T5 d'Escherichia Coli

Les genomes de bacteriophages sont connus pour etre mosaiques. Avec l'augmentation des structures disponibles sur ces virus, leur morphologie aussi apparait de plus en plus comme telle. Les structures de 4 differents intermediaires dans l'assemblage de la capside icosaedrique du bacteriophage Gifsy-2, infectant les bacteries Salmonella ont ete resolues par cryo-microscopie electronique jusqu'a une resolution de 12A. Au niveau genetique, un long gene code en partie Cterminale pour la proteine de capside majeure alors que sa partie Nterminale est fortement similaire du point de vue de sa sequence primaire aux proteases de la famille Clp. Ces resultats et ceux obtenus sur d'autres phages suggerent que les 200 residus en partie centrale regroupent les fonctions restantes, necessaire a l'assemblage de la capside. Cette organisation en un gene unique est une nouvelle variante des strategies developpees par les phages pour modifier la voie d'assemblage de leur capside. Nous avons aussi determine les structures de la capside et de la queue du phage T5 , infectant la bacterie E.Coli a des resolutions de 19 et 30 A respectivement confirmant l'inhabituelle symetrie d'ordre 3 de sa queue. Sa capside icosaedrique est composee par des pentameres et hexameres de pb8 et par pb10 s'attachant au centre de ces derniers, le tout etant decrit par une geometrie T=13. La comparaison des sequences primaires de pb8 et gp5 d'HK97 et la modelisation du modele atomique de gp5 dans la capside de T5 montrent que ces 2 proteines adoptent surement le meme repliement 3D. Nous proposons aussi que le domaine Nterminal de la proteine pb8 soit implique dans l'assemblage initial de la capside d'une maniere similaire a HK97.
Ecology and control of Fusarium species and mycotoxins in wheat grain

This study investigated the effect of interacting environmental factors on the ecophysiology of Fusarium culmorum and F. graminearum and mycotoxin production, and potential for controlling growth and deoxynivalenol (DON) and nivalenol (NIV) production using antioxidants and essential oils on wheat grain. Twodimensional temporal profiles of growth and DON/NIV production for F. culmorum and F. graminearum were constructed for the first time and showed that the water activity (aw, ) ranges required for growth and DON/NIV production were different in vitro and on wheat grain. Growth occurred over a wider aW range (0.9-0.99) while DON/NIV production occurred over a significantly narrower range (0.95 0.99 a,,, ) at both 15 and 25°C over a 40 day incubation period. Interactions between aW, temperature, and sub-optimal concentrations of fungicides had a significant impact on growth and competitiveness of F. culmorum in interspecific interactions with 5-6 other wheat grain fungi. This had an impact on both colonisation capacity in vitro and in situ and affected DON/NIV production. Interactions were complex changing with environmental or fungicide stress resulting in significant stimulation or reduction of both fungal growth and mycotoxin production. An Index of Dominance was developed to compare interspecific interactions between F. culmorum and other wheat spoilage fungi and showed that competitiveness of F. culmorum increased as temperature and a,, level approached the optimum conditions for growth and DON/NIV production. Niche overlap indices (NOI) and niche maps were developed for the first time and showed that interspecific competitiveness was closely related to the number of nutritional carbon sources shared between spoilage fungi. Hydrolytic enzyme profiles for seven different enzymes by F. culmorum, other Fusaria and spoilage fungi showed that the most competitive species produced the highest specific activity of N-acetyl-ß-D-glucosaminidase. Potential for control of Fusarium species post-harvest using 23 essential oils and 8 antioxidants was investigated. Cinnamon, clove, bay, butylated hydroxyanisole and propyl paraben (500 μg g"1) were able to significantly reduce (>90%) the colonisation of wheat grain by three Fusarium species and DON/NIV production. Bay essential oil was the most effective at controlling total fungal populations and DONNIV in naturally contaminated wheat grain.
Induction of Perfect Flowers on Gynoecious Muskmelon by Silver Nitrate and Aminoethoxyvinylglycine1

Silver nitrate at 100, 200 and 400 ppm and aminoethoxyvinylglycine (AVG) at 50, 100 and 200 ppm induced perfect flowers on gynoecious muskmelon (Cucumis melo L. cv. MSU-1G) in the greenhouse. Some phytotoxicity was observed in plants treated with AgNO3 and AVG at the higher concentrations.
INVESTIGATION OF POXVIRUS HOST-RANGE AND GENE EXPRESSION IN MAMMALIAN CELLS.

Title: INVESTIGATION OF POXVIRUS HOST-RANGE AND GENE EXPRESSION IN MAMMALIAN CELLS. Jorge David Méndez Ríos, Doctor of Philosophy, 2014. Directed By: Dr. Bernard Moss, Chief, Laboratory of Viral Diseases, NIAID, NIH; Adjunct Professor Department of Cell Biology and Molecular Genetics, University of Maryland; Members of the Poxviridae family have been known as human pathogens for centuries. Their impact in society included several epidemics that decimated the population. In the last few centuries, Smallpox was of great concern that led to the development of our modern vaccines. The systematic study of Poxvirus host-range and immunogenicity provided the knowledge to translate those observations into practice. After the global vaccination campaign by the World Health Organization, Smallpox was the first infectious disease to be eradicated. Nevertheless, diseases such as Monkeypox, Molluscum contagiosum, new bioterrorist threads, and the use of poxviruses as vaccines or vectors provided the necessity to further understand the host-range from a molecular level. Here, we take advantage of the newly developed technologies such as 454 pyrosequencing and RNA-Seq to address previously unresolved questions for the field. First, we were able to identify the Erytrhomelagia-related poxvirus (ERPV) 25 years after its isolation in Hubei, China. Whole-genome sequencing and bioinformatics identified ERPV as an Ectromelia strain closely related to the Ectromelia Naval strain. Second, by using RNA-Seq, the first MOCV in vivo and in vitro transcriptome was generated. New tools have been developed to support future research and for this human pathogen. Finally, deep-sequencing and comparative genomes of several recombinant MVAs (rMVAs) in conjunction with classical virology allowed us to confirm several genes (O1, F5, C17, F11) association to plaque formation in mammalian cell lines. We also provided additional evidence that plaque formation and virus replication can be independent. More importantly, we identified vgf as the first gene outside MVA’s deletion that explains its host-restriction. Replacement of this region with a vgf cassette derived from a replication-competent virus demonstrated to be sufficient to increase viral yield in all mammalian cell lines tested. Several research and clinical applications can be envisioned derived from this work. INVESTIGATION OF POXVIRUS HOST-RANGE AND GENE EXPRESSION IN MAMMALIAN CELLS. By Jorge David Méndez Ríos Dissertation submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2014 Advisory Committee: Dr. Jeffrey DeStefano, Chair Dr. Bernard Moss, Vice-chair Dr. James Culver, Dean’s Representative Dr. Kim Green Dr. Alison McBride Dr. Donald Nuss © Copyright by Jorge David Mendez Rios 2014
The role of brain endothelial MAP kinases in ICAM-1-mediated lymphocyte transmigration

Leukocyte migration from the blood vessel, across the vascular wall and into the tissue underneath occurs in both an inflammatory response as well as immunosurveillance. During this process multiple adhesive interactions occur between leukocytes and vascular endothelial cells (ECs). The EC itself is rendered compliant to transmigration following inside-out signalling in response to leukocyte adhesion altering the activity of a number of different cellular components including the actin cytoskeleton, Rho GTPases and various protein kinases. For this, adhesion to endothelial intercellular adhesion molecule-1 (ICAM-1/CD54) is particularly important and the focus of this study. Indeed, previous work in our lab has shown that endothelial ICAM-1 signalling controls lymphocyte diapedesis by modulating interendothelial VE-cadherin (VEC) junction phosphorylation via a pathway involving calcium, AMP kinase and nitric oxide synthase (eNOS). In this study, I have investigated if ICAM-1-mediated endothelial mitogen-activated protein (MAP) kinases activation played a role during lymphocyte transmigration across brain microvascular ECs. All three MAP kinases, namely ERK, JNK and p38, were found to be activated in response to ICAM-1 engagement, however only JNK was important for lymphocyte transmigration. Significantly, specific neutralisation experiments using small-molecule inhibitors or dominant-negative plasmids inhibiting JNK resulted in inhibition of transmigration. Activation of JNK required Src, Rho GTPase, MKK7 and protein kinase C (PKC), with all these components also found to be important for lymphocyte transmigration. I further demonstrate that this novel pathway led to the phosphorylation of the actin-associated protein paxillin and its association with VEC. Ultimately this triggered VEC internalisation, suggesting that adherens junction modulation is an important element during transendothelial leukocyte migration. Furthermore, this also suggests that at least two endothelial signalling pathways (JNK-paxillin and eNOS-VEC) converge and cooperate to regulate ICAM-1-mediated lymphocyte transmigration.
Machine learning for public policy making : how to use data-driven predictive modeling for the social good

Machine learning gives computers the ability to learn from data without being explicitly programmed. Due to its excellent prediction abilities, it has recently gained traction in economics, statistics and social sciences. Real-world problems machine learning has been applied to include predicting the probability that individuals commit crimes, targeting hygiene inspections by data-mining online restaurant reviews or estimating poverty levels based on satellite imagery. In this thesis I explore how machine learning can help to solve such and other prediction problems in public policy making and what challenges it faces. My goal is to bring the two fields closer together as most public policy makers likely do not even know that they face prediction problems that machine learning can help solving. After an introduction to prediction problems, I give an overview of how machine learning works and explain under what circumstances machine learning can be used for data-driven predictive modeling for the social good. A case study about predicting hygiene violations in restaurants illustrates the lessons learned and allows to get an idea of what applying machine learning looks like in practice. I then look into the challenges and limitations that machine predictions face in public policy making. Besides the fundamental limits of prediction, these range from technical and human challenges to ethical and legal issues due to biased predictions, black-box algorithms and questions of responsibility.
Cortical Circuits: Synaptic Organization of the Cerebral Cortex

I Anatomy. - 1 General Organization of the Cerebral Cortex. - Cortical Areas. - Summary. - Lamination. - Summary. - Vertical Arrangements. - Summary. - Neurotransmitters and Receptors in the Cerebral Cortex. - Summary. - Summary of Chapter 1. - 2 Cell Types. - Pyramidal Cells. - Dendrites and Their Relationships With Cortical Laminae. - Collateral Axonal Branches. - Laminar Relationships of Cortical Efferent Cells. - Neurotransmitters of Pyramidal Cells. - Summary. - Nonpyramidal Cells. - Chandelier Cells. - Basket Cells. - Vertically Oriented Neurons. - Spiny Stellate Cells. - Smooth and Sparsely Shiny Local Plexus Neurons. - Cross-Species Correlations of Nonpyramidal Neuronal Types. - Other Morphological Cell Types. - Summary. - Summary of Chapter 2. - 3 Synaptic Connections Between Identified Elements. - Intrinsic Connections of Pyramidal Neurons. - Local Projections of Superficial Pyramids. - Local Projections of Deep Pyramids. - Summary. - Intrinsic Connections of Nonpyramidal Neurons. - Summary. - Synapses of Extrinsic Afferents With Cortical Neurons. - Summary. - Quantitative Aspects of Circuitry Involving Extrinsic Cortical Afferents. - Summary. - Summary of Chapter 3. - General Aspects of Brain Circuitry. - References for Part I. - II Functional Aspects of Cortical Circuitry. - 4 Functional Properties of Cortical Neurons. - Functional Columns. - Physiological Identification of Functional Columns. - Anatomical Demonstration of Functional Columns. - Receptive Field Properties of Cortical Neurons. - Receptive Field Properties of Somatosensory Neurons. - Receptive Field Properties of Visual Neurons. - Laminar Distribution of Functionally Defined Neurons. - Functional Properties of Morphologically Identified Neurons. - Receptive Field Properties of Identified Neurons. - Pyramidal Neurons. - Nonpyramidal Neurons. - Shape of the Dendritic Tree. - Biophysical Properties of Identified Neurons. - Summary of Chapter 4. - 5 Synaptic Circuitry Revealed by Electrophysiology. - Extrinsic Afferents. - Intrinsic Pathways. - Excitatory Interactions. - Inhibitory Interactions. - Summary of Chapter 5. - 6 GABAergic Inhibition in the Cerebral Cortex. - GABA-Mediated Inhibition. - Anatomical Demonstration of GABAergic Neurons. - Physiological Basis of GABA-Mediated Inhibition. - GABAergic Inhibition and Receptive Fields. - Summary of Chapter 6. - General Aspects of Brain Circuitry (Continued). - References for Part II. - III Facts, Theories, and Models. - 7 An Integrative View of Cortical Circuitry. - Synaptic Triads. - Hierarchical Versus Parallel Processing. - Specificity of Synaptic Connections. - Nonselectivity of Synaptic Connections: The Basis for a Selection Process. - Epilogue. - References for Part III.
Ecological Aspects of Nitrogen Metabolism in Plants

Contributors. Preface. Section 1 The Nitrogen Cycle. 1 The New Global Nitrogen Cycle (Jan Willem Erisman). Section 2 Plant-Soil Microbe Interactions. 2 Plant Associations with Mycorrhizae and Rhizobium Evolutionary Origins and Divergence of Strategies in Recruiting Soil Microbes (Gerben Bijl, Stephane De Mita, and Rene Geurts). 3 Arbuscular Mycorrhizas and N Acquisition by Plants (Luisa Lanfranco, Mike Guether, and Paola Bonfante). 4 Ectomycorrhiza and Nitrogen Provision to the Host Tree (Michel Chalot and Claude Plassard). 5 Proteins in the Rhizosphere: Another Example of Plant-Microbe Exchange (Clelia De-la-Pena and Jorge M. Vivanco). 6 Actinorhizal Symbioses (Katharina Pawlowski). 7 Two in the Far North: The Alder-Frankia Symbiosis, with an Alaskan Case Study (Mike Anderson). 8 The Path of Rhizobia: From a Free-Living Soil Bacterium to Root Nodulation (Pedro F. Mateos, Raul Rivas, Marta Robledo, Encarna Velazquez, Eustoquio Martinez-Molina, and David W. Emerich). 9 Exploiting Mycorrhizae and Rhizobium Symbioses to Recover Seriously Degraded Soils (Sergio Miana de Faria, Alexander S. Resende, Orivaldo J. Saggin Junior, and Robert M. Boddey). Section 3 Epi- and Endo-Phytic Microbes. 10 Nitrogen: Give and Take from Phylloplane Microbes (Mark A. Holland). 11 N2-Fixing Endophytes of Grasses and Cereals (Veronica Massena Reis, Jos Vanderleyden, and Stijn Spaepen). Section 4 Arthropods. 12 Effects of Insect Herbivores on the Nitrogen Economy of Plants (Leiling Tao and Mark D. Hunter). 13 Plant Defense Proteins That Inhibit Insect Peptidases (Carlos Peres Silva and Richard Ian Samuels). 14 Nutrient Acquisition and Concentration by Ant Symbionts: The Incidence and Importance of Biological Interactions to Plant Nutrition (Cynthia L. Sagers). Section 5 Environmental Signalling in N Acquisition. 15 The Functions of Flavonoids in Legume-Rhizobia Interactions (Oliver Yu and Yechun Wang). 16 Plant Hormones and Initiation of Legume Nodulation and Arbuscular Mycorrhization (Arijit Mukherjee and Jean-Michel Ane). 17 Nitric Oxide as a Signal Molecule in Intracellular and Extracellular Bacteria-plant Interactions (Andres Arruebarrena Di Palma, Lorenzo Lamattina, and Cecilia M. Creus). Index.
COST Action 863 "Euroberry research: from genomics to sustainable production, quality and health".

The main objective of the EUROBERRY COST 863 Action is to improve the quality and production of four berries (strawberry, raspberry, currant and blueberry) for the benefit of the consumers' health and to take action to maintain profitable European production using sustainable and innovative systems, based on 'omics' knowledge.
The Entrepreneurial Culture in Europe - New Challenges in the New Economy

There is nowadays a growing concern in Europe regarding its lagging behind other countries, especially the US, in the fierce competition to make the forth industrial revolution a reality. One of the most frequently mentioned obstacles to fill this gap is the lack of entrepreneurial culture in Europe. Some of the conclusions of recent studies or articles concerning this aspect are: â€žEurope lacks a solid entrepreneurial cultureâ€ , â€žMore than money, Europe needs entrepreneurial culture changeâ€ , â€žEurope needs more entrepreneursâ€ , â€žEurope has a chronic failure to encourage ambitious entrepreneursâ€ etc. The plenty of similar remarks illustrate not only the importance but also the great audience of the abovementioned subject; it also represent a strong incentive for politicians, academics, researchers, the civil society etc. to reflect, identify and analyse crucial aspects of Europeâ€™s vulnerability as regards its entrepreneurial spirit and culture. These are in short the objectives of the present paper.
Silicons Role in Improving Plant Salinity Tolerance

Salinization is a main abiotic stress that affects crop growth and productivity all over the world, thus how to improve the resistance levels of crops to salinity has attracted worldwide attention. Silicon (Si) is the second most prevalent element in the earth’s crust. When the solution pH is below 9, silicon is absorbed by higher plants in the form of silicic acid [Si(OH)4]. Although silicon has not been considered as essential element for higher plant, it is generally considered to be a ‘beneficial element’. A number of studies have shown that silicon can increase plant resistance to multiple abiotic and biotic stresses, including drought, salt stress, heavy metal toxicity, freezing, and plant diseases.
The Morphology of Male Gonads of the Neotenic Cave Salamander (Proteus anguinus)

Proteus anguinus is a cave‐dwelling urodele amphibian that is endemic to underground waters in Dinaric karst regions of Central Europe. It is an obligate neotene, with a very long life span and late sexual maturity. The reproductive period is a‐seasonal and lasts at least 30 years with each female laying eggs at intervals of 6 ‐ 12.5 years. The objective of this study was to describe the morphology of the testes of Proteus for better understanding of the reproductive strategy of this neotenic cave amphibian with the long‐term goal of establishing a facility for captive breeding. The testes used for this research were removed from our permanent collection of archived specimens. At least three morphological forms of testes are present independent of the size of the specimens, most likely representing phases of maturation of the gonads. The internal histological structure the testis is a simple cystic type of cyts enclosed in lobules with synchronous maturation of the germ cells within each cyst. The development of cysts inside a particular lobule is either synchronous or asynchronous. Spermatogenesis progresses in caudo‐cephalic direction of the testis as well as in proximal‐distal direction in relation to internal collecting ducts and appears to be independent of the seasons of the year. We can conclude that the reproductive peculiarities in Proteus probably reflect the fact that it lives in a relatively stable habitat with environmental conditions that are conducive to a‐seasonal reproductive cycles, similar to tropical salamanders. This research was supported by a grant from the Ministry of Higher Education, Science and Technology, Republic of Slovenia (P1–0184).
Association between DQA1 gene polymorphism and reproductive, immunity performance and heat tolerance in Holstein cattle.

This investigated was conducted in Al-Salam station for Dairy cattle /private sector, for the period from 1-11-2016 to 1-112017, to determine the association between DQA1 gene’s genotypes with some reproductive traits, immunity and heat tolerance coefficient in Holstein cows. The results DQA1 gene analysis showed a highly significant Different (P<0.01) between genotypes of DQA1 gene’s genotypes A, B& C, the percentage were 47.06, 5.88 and 47.06% respectively. The results of the current study showed that services per conception and days open was significantly affected (P<0.05) by different genotypes of the DQA1 gene for the cows with C genotype. There was also a significant difference (P<0.05) between the genotypes of DQA1 gene for IgG concentration in calves blood who belong to mother’s with A& C genotypes compared with B genotype. The concentration of IgG in this study 44.73 ± 2.68&43.55 ± 1.82 g/L. blood which belong to cows with A &C genotypes respectively and it was higher than claves which belong to cows with C genotype (37.09 ± 1.77 g / L. blood). For the heat tolerance coefficient it was found that there was a significant (P<0.05) difference between the genotypes of the DQA1 gene in this trait and for the cows with B &C genotype in the second and third months of the lactation season, while there was no effect of DQA1 gene genotypes of the heat tolerance coefficient during the first month of the lactation season. It was possible to conclude from this study the possibility of DQA1 gene’s genotypes in the development of genetic improvement strategies and in breeding programs in dairy cows.