Miracle-dz/UniFAR-FTUs huggingface dataset:
Inférence de réseaux causaux à partir de données interventionnelles

L'objet de cette these est l'utilisation de donnees transcriptomiques actuelles dans le but d'en inferer un reseau de regulation genique. Ces donnees sont souvent complexes, et en particulier des donnees d'interventions peuvent etre presente. L'utilisation de la theorie de la causalite permet d'utiliser ces interventions afin d'obtenir des reseaux causaux acycliques. Je questionne la notion d'acyclicite, puis en m'appuyant sur cette theorie, je propose plusieurs algorithmes et/ou ameliorations a des techniques actuelles permettant d'utiliser ce type de donnees particulieres.
Study on evaluation of training needs of goat farmers.

The study was conducted in five adopted villages viz., Pingari, Bhai, Gadaya, Jhandipur and Sanora of Block Farah, Distrct Mathura, U.P. Total 192 goat farmers were selected at random from Pingari (58), Bhai (50), Gadaya (35), Jhandipur (25), and Sanora (24) to identify the training needs of goat farmers. Training needs in 47 different topics under six main subject areas covering various aspects on goat rearing i.e. breeding management, nutrition, housing management, health management, products management and other management was covered. The results indicated that their preference for training on a threepoint continuum. The investigation revealed that health management was the first area of training followed by housing management, other management, nutritional management and products management. Breeding management appeared to be the last. The specific sub-areas viz. control of external and internal parasites, appropriate ventilation requirement, knowledge of different markets, importance of mineral mixture in feeds, sanitary milk production and care of a new born kid had top priority for training to the goat farmers.
Discovery of Novel Viruses From Animals, Plants, and Insect Vectors Using Viral Metagenomics

iv INTRODUCTION . 1 DISCUSSION . 10 REFERENCES . 22 APPENDIX 1: DISCOVERY OF A NOVEL SINGLE-STRANDED DNA VIRUS FROM A SEA TURTLE FIBROPAPILLOMA USING VIRAL METAGENOMICS . 29 APPENDIX 2: NOVEL ANELLOVIRUS DISCOVERED FROM A MORTALITY EVENT OF CAPTIVE CALIFORNIA SEA LIONS. 40 APPENDIX 3: VECTOR-ENABLED METAGENOMICS REVEALS HIGHLY DIVERSE AND UNCHARACTERIZED VERTEBRATE, PLANT, INSECT, AND BACTERIAL VIRUSES IN MOSQUITOES . 47 APPENDIX 4: EXPLORING THE DIVERSITY OF PLANT VIRUSES AND THEIR SATELLITES USING VECTOR-ENABLED METAGENOMICS ON WHITEFLIES . 82
ROLES FOR B-Raf KINASE IN THE SPECIFIC REGULATION OF α4β1 INTEGRIN IN T CELLS

iv Table of Figures . ix Chapter 1 . 1 General Background . 1 T Cells and the Adaptive Immune Response . 1 T Cell Migration . 2 T Cell Maturation . 2 T Cell Trafficking . 5 Integrin-­‐mediated Adhesion . 6 The Leukocyte Adhesion Cascade . 6 Integrins . 7 Inside-­‐out Integrin Activation . 15 Talin Structure . 15 Talin Activation . 19 Outside-­‐in Integrin Signaling . 20 Mitogen-­‐Activated Protein Kinase Pathway . 23 RAF kinases . 23 B-­‐Raf . 26 Non-­‐canonical MAPK . 29 Chapter 2 . 30 B-­‐Raf Regulation of Integrin-­‐mediated Resistance to Shear Stress . 30
Differences in reproductive strategies between two co-occurring mullets Mugil curema Valenciennes 1836 and Mugil liza Valenciennes 1836 (Mugilidae) in a tropical bay

The female reproductive strategies of Mugil curema Valenciennes 1836 and Mugil liza Valenciennes 1836 occurring in a tropical bay in southeastern Brazil were found to differ. Gonadosomatic index values and macroscopic staging of gonads showed that M. curema spawning took place between August and January, while M. liza spawning occurred between May and August. M. curema spawning began just before the rainy season, whereas M. liza spawned during the dry season. Estimates of absolute fecundity (F) and relative fecundity (RF) were significantly greater ( P < 0.01) for M. liza (mean F = 308 × 104 ± 10 4 × 10 3 ; mean RF = 1396.42 ± 67.02) than for M. curema (mean F = 415 × 10 3 ± 32 × 10 3 ; mean RF = 750.54 ± 40.52). Oocyte diameters were slightly greater in M. liza (0.55 to 0.82 mm) than in M. curema (0.49 to 0.71 mm). Temporal segregation of the spawning season between M. curema and M. liza may avoid interspecific competition between offspring that recruit in inner bay areas. Additionally, greater fecundity and oocyte size in M. liza increase the chance of reproductive success during the dry season when there is less food resources for early juveniles.
Influence of sediment organic enrichment and water alkalinity on growth of aquatic isoetid and elodeid plants

Summary 1. Lake eutrophication has increased phytoplankton blooms and sediment organic matter. Among higher plants, small, oligotrophic rosette species (isoetids) have disappeared, while a few tall, eutrophic species (elodeids) may have persisted. Despite recent reduction of nutrient loading in restored lakes, the vegetation has rarely regained its former composition and coverage. Patterns of recovery may depend on local alkalinity because HCO3− stimulates photosynthesis of elodeids and not of isoetids. In laboratory growth experiments with two isoetids (Lobelia dortmanna and Littorella uniflora) and two elodeids (Potamogeton crispus and P. perfoliatus), we test whether organic enrichment of lake sediments has a long-lasting influence by: (i) reducing plant growth because of oxygen stress on plant roots and (ii) inhibiting growth more for isoetids than elodeids. We also test whether (iii) increasing alkalinity (from 0.17 to 3.20 meq. L−1) enhances growth and reduces inhibition of organic sediment enrichment for elodeids but not for isoetids. 2. In low organic sediments, higher oxygen release from roots of isoetids than elodeids generated oxic conditions to greater sediment depth for Lobelia (4.3 cm) and Littorella (3.0 cm) than for Potamogeton species (1.6–2.2 cm). Sediment oxygen penetration depth fell rapidly to 0.4–1.0 cm for all four species at even modest organic enrichment and oxygen consumption in the sediments. Roots became shorter and isoetid roots became thicker to better supply oxygen to apical meristems. 3. Growth of elodeids was strongly inhibited across all levels of organic enrichment of sediments being eight-fold lower at the highest enrichment compared to the unenriched control. Leaf biomass of isoetids increased three-fold by moderate organic enrichment presumably because of greater CO2 supply from sediments being their main CO2 source. At higher organic enrichment, isoetid biomass was reduced, leaf chlorophyll declined up to 10-fold, root length declined from 7 to <2 cm and mortality rose (up to 50%) signalling high plant stress. 4. Lobelia was not affected by HCO3− addition in accordance with its use of sediment CO2. Biomass of elodeids increased severalfold by rising alkalinity from 0.17 to 3.20 meq. L−1 in accordance with their use of HCO3− for photosynthesis, while the negative impact of organically enriched sediments remained. 5. Overall, root development of all four species was so strongly restricted in sediments enriched with labile organic matter that plants if growing in situ may lose root anchorage. Other experiments demonstrate that this risk is enhanced by greater water content and reduced consolidation in organically rich sediments. Therefore, formation of more muddy and oxygen-demanding sediments during eutrophication will impede plant recovery in restored lakes while high local alkalinity will help elodeid recovery.
The importance of monitoring the Ceutorhynchus pallidactylus female flight activity for the timing of insecticidal treatment.

Seidenglanz M. , Poslusna J. Hrudova E. (2009): The importance of monitoring the Ceutorhynchus pallidactylus female flight activity for the timing of insecticidal treatment. Plant Protect. Sci., 45: 103–112. The effects of two pyrethroids and one combination of organophosphate and pyrethroid (alpha-cypermethrin, etofenprox, chlorpyrifos + cypermethrin) on Ceutorhynchus pallidactylus (Marsham, 1802) (Coleoptera: Curculionidae) were tested under field conditions in the Czech Republic in 2006–2008. Significant differences in the effects of the compared insecticides on C. pallidactylus were recorded in the particular years (2006, 2007, 2008). It was less important and somewhat less complicated to establish the most suitable time for spraying in the case of the chlorpyrifos + cypermethrin combination in comparison with the pyrethroids applied separately. The effectiveness of the tested insecticides was markedly influenced by the time of spraying. The effects of the pyrethroids applied singly achieved results comparable to those of the chlorpyrifos + cypermethrin combination only at the optimal spraying time. The most suitable time for spraying varied from the point when the first females appeared in yellow water traps in somewhat higher quantities to the time when a substantial proportion of caught females was able to lay eggs.
Transient and Selective NF-κB p65 Serine 536 Phosphorylation Induced by T Cell Costimulation Is Mediated by IκB Kinase β and Controls the Kinetics of p65 Nuclear Import 1

Full transcriptional activity of the nuclear, DNA-bound form of NF-κB requires additional posttranslational modifications. In this study, we systematically mapped the T cell costimulation-induced phosphorylation sites within the C-terminal half of the strongly trans-activating NF-κB p65 subunit and identified serine 536 as the main phosphorylation site. The transient kinetics of serine 536 phosphorylation paralleled the kinetics of IκBα and IκB kinase (IKK) phosphorylation and also mirrored the principle of T cell costimulation. The TCR-induced pathway leading to serine 536 phosphorylation is regulated by the kinases Cot (Tpl2), receptor interacting protein, protein kinase Cθ, and NF-κB-inducing kinase, but is independent from the phosphatidylinositol 3-kinase/Akt signaling pathway. Loss-of-function and gain-of-function experiments showed phosphorylation of p65 serine 536 by IKKβ, but not by IKKα. Phosphorylation occurs within the cytoplasmic and intact NF-κB/IκBα complex and requires prior phosphorylation of IκBα at serines 32 and 36. Reconstitution of p65−/− cells either with wild-type p65 or a p65 mutant containing a serine to alanine mutation revealed the importance of this phosphorylation site for cytosolic IκBα localization and the kinetics of p65 nuclear import.
Animal Welfare Science: Recent Publication Trends and Future Research Priorities

Animal welfare science is a young and thriving field. Over the last two decades, the output of scientific publications on welfare has increased by c. 10-15% annually (tripling as a proportion of all science papers logged by ISI’s Web of Science), with just under half the c. 8500 total being published in the last 4 years. These papers span an incredible 500+ journals, but around three quarters have been in 80 animal science, veterinary, ethology, conservation and specialized welfare publications, and nearly 25% are published in just two: Animal Welfare and Applied Animal Behaviour Science. Farmed animals – especially mammals – have attracted by far the most research. This broadly reflects the vastness of their populations and the degree of public concern they elicit; poultry, however, are under-studied, and farmed fish ever more so: fish have only recently attracted welfare research, and are by far the least studied of all agricultural species, perhaps because of ongoing doubts about their sentience. We predict this farm animal focus will continue in the future, but embracing more farmed fish, reptiles and invertebrates, and placing its findings within broader international contexts such as environmental and food security concerns. Laboratory animals have been consistently well studied, with a shift in recent years away from primates and towards rodents. Pets, the second largest animal sector after farmed animals, have in contrast been little studied considering their huge populations (cats being especially overlooked): we anticipate research on them increasing in the future. Captive wild animals, especially mammals, have attracted a consistent level of welfare research over the last two decades. Given the many thousands of diverse species kept by zoos, this must, and we predict will, increase. Future challenges and opportunities including refining the use of preference tests, stereotypic behaviour, corticosteroid outputs and putative indicators of positive affect, to enable more valid conclusions about welfare; investigating the evolution and functions of affective states; and last but not least, identifying which taxonomic groups and stages of development are actually sentient and so worthy of welfare concern.
Wildlife of the Tibetan Steppes

T. A. Vaughan, J. M. Ryan, N. J. Czaplewski. 2000. Mammalogy. 4th ed. Saunders College Publishing, Fort Worth, Texas, 565 pp. ISBN 0-03-025034-X, price (hardcover), $86.50. This edition of a popular mammalogy textbook is attractive, the scientific illustrations are magnificent, and the print is readable with important words set in boldface type. Web sites listed at the end of each chapter suggest additional information. A mammalogy textbook is a treatise on one hand and a learning device for a student on the other. Years ago, this reviewer's class was mostly graduate students in vertebrate zoology, some had courses in paleontology, and all had comparative anatomy. In my teaching (63 semesters with 2–3 classes each), students were mostly undergraduates. I love this book, but for many students today it extends well beyond their available time and earlier coursework. Even for less-advanced mammalogy classes, certainly to be considered important, instructors will find this comprehensive work helpful. In “Classification,” within the Introduction (Chapter 1), one appreciates the quote from George Gaylord Simpson (1945) about putting all things into formal arrangement. Simpson continued further that modern taxonomy includes other sciences, and that studies on phylogeny will extend mammalian taxonomy a couple of centuries. To him, and to us, taxonomy (or what our authors call “systematics”) becomes mammalogy. This text introduces students to powerful, modern phyletics. The authors introduce early in the book terms as synapomorphies and outgroups, all part of the powerful, modern way of making phylogenetic dendrograms. This is painful initiation for field-oriented students of general biology and wildlife management. However, terms such as phylogeny, homology, and analogy ought to be introduced. Analogy and homology are not confined to interspecific comparisons (e.g., serial homology is the basis of the dental formula). The text has a drawback in hardly emphasizing the Linnaean system, and not naming Carolus Linnaeus as the starting point of our taxonomy. Nomenclature is never defined; such a technological text should mention its basic rules: priority, synonymy, …
INFLUENCE OF METHIONINE AND LYSINE SUPPLEMENTATION ON NUTRIENT DIGESTIBILITY IN WEANED RABBITS FED GRADED LEVELS OF SWEET POTATO VINES

This experiment was conducted to evaluate the effect of feeding sweet potato vines on the digestibility in seventy-two weaned rabbits comprising males and females between six and weeks old, with initial liveweight ranging from 600 1130 g. They were allocated to twelve treatment diets in a 3 x 2 x 2 factorial experiment in a completely randomized design. The factors were sweet potato vines (0, 15 and 30 %), methionine (0.07 and 0.1 kg supplemental levels) and lysine (0.12 and 0.15 kg supplemental levels). the study lasted ten days with three days adjustment to crates and seven days of fecal and urine collection. Dry matter, crude fibre, ether extract, ash, acid detergent fibre and neutral detergent fibre digestibility decreased significantly as level of sweet potato vine increased. Interaction between sweet potato vines and lysine showed significant difference in acid detergent fibre and neutral detergent fibre. High level of methionine and lysine supplementation resulted in higher nutrients digestibility. It was concluded that supplementation of higher levels of methionine and lysine (0.1 and 0.15 kg) respectively in the diets of rabbits improved nutrient digestibility.
Protozoan parasites and pathogens of forest pest arthropods.

Study of protozoan parasites and pathogens of forest pest insects is a perspective concerning the biological control. The subject of our investigations in this respect were 2 arthropod species which are serious pests in the forests, nurseries, greenhouses, etc.: Lymantria dispar and Oxidus gracillis. Our research on the pathogens of L. dispar started since 1995 in cooperation with European and USA investigators. As a result of our study three protozoan parasites – Vairimorpha disparis, Nosema lymantriae and Endoreticulatus schubergi (Microsporidia) were observed on this pest. In 2000 experimental studies on the introduction of an entomopathogenic fungus Entomophaga maimaiga into L. dispar populations in Bulgaria have started. The results obtained showed that the fungus has been successfully introduced in Bulgaria and practical results are expected in the next years. O. gracilis is a new invasive species for Bulgarian fauna from Far East which lives so far in greenhouses, nurseries, etc. Its wider distribution in the country is expected at our climatic conditions. Three protozoan parasites were recorded in this millipede – Stenophora nematoides, Stenophora robusta and Fonsecaia polymorpha (Apicomplexa: Sporozoa). While S. nematoides and S. robusta showed a high prevalence, F. polymorpha was detected in a few individuals only.
Contribuição das concentrações de nitrogênio em bulbilhos de alho tratados com doses de N em cobertura

Bulbs originated from different concentrations of nitrogen fertilization may differ on the N content of the cloves, which can influence the development of the next generation and in its response to nitrogen fertilization. The objective was the evaluation of the contribution of N present in cloves of garlic plants free of viruses, originated from garlic seed with different N concentrations, and response to increasing doses of N. The experimental design was a randomized block with split plot arrangement. The treatments were rates of N in side dressing (0, 150, 300 and 450 kg ha-1 of N) and rates of N in cloves (0, 80, 160 and 320 kg ha-1 of N) of an experiment in the previous year and 4 repetitions. We used cultivar Cacador L.V. (virus free). The N content in cloves influenced the values of Relative Index of Chlorophyll (IRC) until 30 days after emergence (DAE), not interfering, however, in the yield of the bulbs. The applied doses of N in side dressing provided an increase in the IRC value, in the yield and the average weight of bulbs. Total and marketable yield were 10 t ha-1, using 325 kg ha-1 of N. The highest bulb weight (35 g) was reached with 321 kg ha-1 of N. There was no incidence of plants with secondary growth.
Co-existence between Humans and Wolves – A New Challenge for the Old World

Author(s): Granlund, Kaj | Abstract: After centuries of persecution, European wolf populations are recovering across many areas due to favorable legislation and the rise of the “rewilding” movement over the past few decades. The central mechanism triggering the rewilding of Europe was the European Union Habitat Directive, approved in May of 1992. The directive classifies the wolf as a strictly protected species and all EU-countries have implemented the directive in their legislation. Since the 1990’s, the number of wolves in Europe has steadily increased and the total number of wolves, excluding Russia, Belarus and Ukraine, exceeds 12,000 wolves. At the same time conflicts between farmers, wolf protectors and authorities are becoming more frequent. Wolves living in Central Europe, Finland and Scandinavia must cope with the fact that there are human settlements throughout their habitat. This results in a strong habituation to humans and a growing number of attacks against cattle and sheep under the cover of darkness as well during dawn, dusk, and night. The appearance of wolves in settled areas in broad daylight seems to be more and more the rule rather than the exception. While authorities explain this as being a part of the wolf's normal behavior, human tolerance in areas where wolves return is rapidly lowering. Wolves’ depredation on livestock, and especially a behavior called surplus killing, has resulted in several clashes between farmers and authorities in France and Italy. Surplus killing is a behavior exhibited by wolves in which they kill more prey than they are able to consume and then abandon the remainder. Incidents from Southern Europe show that a single wolf pack may kill hundreds of sheep in one single attack. In this paper I will review the implications of human-wolf coexistence in settled areas in different parts of Europe. I will highlight a number of problems experienced as well as solutions and their outcome.
Vegetation Analysis Along Elevational and Topographical Gradients in Mt. Jumbong in Central Korea

Vegetational changes along elevational and topographical gradients were studied in Mt. Jumbong which is located at the core area of the Mt. Sorak Biosphere Reserve in Kangwon-do Province in central Korea. Two 500 m north-south transects crossing two valleys and a small ridge were laid out, and fifty-one 10 m10 m permanent quadrats were systematically set up. All trees bigger than 2.5 cm DBH were marked with numbered aluminum tags, and their DBH measured and the species identified. Coverage of plant species in the herb layer were determined in two 2 m 2 m subquadrats in each of the permanent quadrats. Thirty-two species of woody plants occurred in the tree layer in the permanent quadrats studied. Quercus mongolica was the dominant species across the study site, and Acer pseudosieboldianum and Carpinus cordata were also important. Quercus mongolica occurred on the ridges and south-facing slopes, and Acer pseudosieboldianum occurred extensively except for valleys. In contrast, Fraxinus mandshurica, Acer mono, Acer triflorum, and Ulmus laciniata were common in valleys. At the herbaceous layer, 112 species were identified. Dominant species were Ainsliaea acerifolia and Sasa borealis on the ridges, Meehania urticifolia on north-facing slopes, and Deutzia glabrata on valleys. Soil environmental factors were compared among the quadrats. pH was lower in the quadrats located on ridges and south-facing slopes, and organic matter was lowest on south-facing slopes. Quadrats located on valleys were generally higher in pH, organic matter, N, P, K, Ca and Mg. DCA ordinations for tree layer and herb layer were carried out in order to identify the dominant environmental factors affecting the distribution of plant species along the environmental gradients. Correlation analysis between ordination axis scores and environmental factors showed that axis one was negatively correlated with elevation and positively correlated with soil organic matter, pH, Ca, Mg, and P, but that axis two was positively correlated with elevation. These results indicate that vegetation responds very sensitively to elevational and topographical gradients although the study area is relatively small with about 100 m in elevational variation.