Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of proteins involved in CRISPR-mediated antiviral defence in Sulfolobus solfataricus

One of the most surprising realisations to emerge from metagenomics studies in the early ‘00s was that the population of viruses and phages in nature is about 10 times larger than the population of prokaryotic organisms. Thus, bacteria and archaea are under constant pressure to develop resistance methods against a population of viruses with extremely high turnover and evolution rates, in what has been described as an evolutionary “arms race”. A novel, adaptive and heritable immune system encoded by prokaryotic genomes is the CRISPR/Cas system. Arrays of clustered regularly interspersed short palindromic repeats (CRISPR) are able to incorporate viral or plasmid sequences which are then used to inactivate the corresponding invader element via an RNA interference mechanism. A number of CRISPR-associated (Cas) protein families are responsible for the maintenance, expansion and function of the CRISPR loci. This system can be classified in a number of types and subtypes that differ widely in their gene composition and mode of action. This thesis describes the biochemical characteristics of CRISPR-mediated defense in the crenarchaeon Sulfolobus solfataricus. The process of CRISPR loci transcription and their subsequent maturation into small guide crRNA units by the processing endonuclease of the system (Cas6) is investigated. After this step, different pathways and effector proteins are involved in the recognition and silencing of DNA or RNA exogenous nucleic acids. This thesis reports the identification and purification of a native multiprotein complex from S. solfataricus P2, the Cmr complex, a homologue of which has been found to recognise and cleave RNA targets in P. furiosus. The recognition and silencing of DNA targets in E. coli has been shown to involve a multiprotein complex termed CASCADE as well as Cas3, a putative helicase-HD nuclease. S. solfataricus encodes orthologues for the core proteins of this complex, and the formation and function of an archaeal CASCADE is investigated in this thesis. Abstract
Protecting one, protecting both? Scale‐dependent ecological differences in two species using dead trees, the rosalia longicorn beetle and the barbastelle bat

Organisms sharing the same habitats may differ in small-scale microhabitat requirements or benefit from different management. In this study, set in Italy, we focused on two species of high conservation value, the cerambycid beetle Rosalia alpina and the bat Barbastella barbastellus, which often share the same forest areas and in several cases the same individual trees. We compared the potential distribution and, at two spatial scales, the niches between such species. The predicted distributions largely overlapped between the beetle and the bat. The niches proved to be similar on a broad scale, yet not on the plot one. Compared with B. barbastellus, R. alpina tends to occur at lower altitude in more irradiated sites with lower canopy closure and uses shorter trees with wider diameters. B. barbastellus occurred more often in trees within forest or along its edges, whereas R. alpina lays eggs in trees found in clearings. B. barbastellus plots were more frequent in forest, R. alpina plots in forested pasture and open-shredded forest. Overall, exposure to sun influenced more critically site and tree selection by R. alpina, as a warm microclimate is essential for larval development. Although B. barbastellus reproduction may be favored by warmer roosting conditions, bats may also find such conditions in dense forest and in strongly irradiated cavities high up in tall trees that project above the canopy. We emphasize that subtle differences in the ecological requirements of syntopic taxa could be missed at broad scales, so multiple-scale assessment is always advisable.
Role of IRF4 in the Regulation of Cellular Interferon Stimulated Genes and KSHV Lytic Gene Expression in Primary Effusion Lymphoma

The interferon regulatory factors (IRF) are a family of transcription factors that control intrinsic cellular responses to viral infections. The regulation of target gene expression by IRF proteins is mediated by binding to interferon-stimulated response elements (ISRE) DNA motifs located in the 5’ regulatory region of Interferon-stimulated genes (ISGs). Interferon regulatory factor 4 (IRF4), a hematopoietic-specific transcription factor, is a potential dual regulator of ISRE-mediated gene expression although its transcriptional signature is still poorly understood. Primary effusion lymphoma (PEL), a rare B-cell malignancy is characterized by the expression of high level of cellular IRF4, a disrupted B-cell transcriptional program, and latent infection with Kaposi’s sarcoma-associated herpesvirus (KSHV). The goal of this study is to elucidate the ability of IRF4 to alter the transcriptional expression of ISRE and ISRE-like sequence regulated genes in the absence of B-cell specific binding partners. Small-scale gene expression assays showed that IRF4 is capable of differentially regulating the expression of ISRE-responsive genes. The positive regulation of IRF4 target genes (ISG60 and Cig5) was shown to be in response to direct binding of IRF4 to chromatin regions corresponding to ISRE-motifs located at the 5’ promoter regulator regions of ISG60 and Cig5. To understand the role of IRF4 beyond cellular gene expression, we tested KSHV-encoded latency associated genes that modulated IRF4-mediated gene expression. We identified the viral FLICE inhibitory protein (vFLIP) as an enhancer of IRF4-mediated ISG induction and showed that this function is dependent on the activation of NF-kB. Finally, we examined the role of IRF4 in the regulation of lytic gene expression. The replicator and transcription activator (RTA) protein, is a sequence specific transcription factor that regulates the expression of a subset of early genes through binding ISRE-like motifs on their promoters. Studies aimed at understanding the consequences of IRF4 expression in PEL cells showed that IRF4 acts as a negative regulator of lytic gene expression by inhibiting RTA expression and RTA-mediated gene transactivation. These data support a model in which IRF4 mediates an antiviral cellular response, inhibiting lytic replication of KSHV while contributing to the transformative effects of KSHV by promoting viral latency.
Effect of factors affecting growth performance of sangamneri strain of deccani sheep

In Sangamneri strain of Deccani sheep, the overall least squares means for body weights at birth 3, 6, 9 and 12 months of age were 2.87±0.01, 13.86±0.10, 8.02±0.12, 21.17±0.15 and 23.94±0.18 kg, respectively. The effect of year, season and sex were significant (P<0.01) on body weights at all the ages.
The sponge association of the abyssal Norwegian-Greenland Sea: species composition, substrate relationships and distribution

Abstract During the ‘Meteor’ Expedition 13 in July and August 1990 to the northern part of the Norwegian Sea off west Spitsbergen, 7 stations with a depth of 2000 m or more were sampled with Agassiz trawl or hyperbenthos sledge, 14 more with a large box corer. Sponges were found at 6 of the trawl stations and in 2 box cores. A total of 19 species occurred, most of which were new to the area. Eight of the species were encountered more often than the other 11. Literature review and check of unpublished samples showed that by distribution, frequency of occurrence or abundance these species can be defined as the typical sponge association of the Norwegian and Greenland abyssal sea. This sponge association has a wide occurrence over the deep Norwegian-Greenland seas and parts of the Arctic basins. The analysis of substrate utilization of the 8 core species shows that all of them are able to colonize soft bottom, even some that previously had been considered to be dependent on hard substrate exclusively. Altern.
Effect of fungicides, seaweed extracts, tea tree oil, and fungal agents on fruit rot and yield in strawberry.

Seven fungicides, 2 seaweed extracts (Maxicrop and Seasol), tea tree oil (Multicrop), and fungal agents including yeasts and an isolate of a Trichoderma sp. , were compared for the control of fruit rots in strawberries in 5 field trials in Victoria, Australia. The fungicides tested were thiram, iprodione, dichlofluanid, chlorothalonil, fluazinam, phosphorous acid and fosetyl-aluminium. All treatments were applied as foliar sprays (at recommended rates) at weekly intervals, except for one of the Trichoderma treatments in which Trichoderma was cultured on rice and applied around plants at 1 and 5 weeks after the start of the trial. Rots were assessed after harvest by incubating fruit for 3 days at room temperature (15–25˚C). Between 55 and 71% of fruit developed rot in the unsprayed plots and consisted mainly of grey mould (Botrytis cinerea), leak (Rhizopus and Mucor spp.), anthracnose (Colletotrichum acutatum), leather rot (Phytophthora cactorum), and stem end rot (Gnomonia comari). All fungicides except fosetyl-aluminium and phosphorous acid significantly (P<0.05) reduced the total incidence of fruit rots by 27–72%. Thiram, dichlofluanid and chlorothalonil reduced grey mould by 61–94%, anthracnose by 63–100% and leather rot by 65–100%; iprodione reduced grey mould by 60–94% and leak by 74–96%. In one experiment each, fluazinam reduced grey mould by 85% and leather rot by 100%, and phosphorous acid reduced leather rot by 100%. Thiram, iprodione and phosphorous acid also reduced stem end rot by 55–100%. Of the biocontrols, seaweed extracts and oil, only tea tree oil in 1 trial of 3 reduced the total incidence of fruit rots significantly (by 31%), and in 2 trials significantly reduced anthracnose, and leather rot by 60–88% and 71–72% respectively. In 2 out of 3 trials, Trichoderma sp. reduced (P<0.05) grey mould by 29–63%. In one trial each, seaweed extract 1, and a yeast treatment amended with malt extract, both reduced grey mould by 40 or 54% respectively. The addition of sucrose to the yeast treatments significantly increased the incidence of anthracnose infection. Chlorothalonil, dichlofluanid, thiram and iprodione sprays increased the yield (weight) of healthy fruit significantly (P<0.05) compared with that from untreated plants by 43–114%. By contrast, none of the biocontrol treatments, the seaweed extracts or tea tree oil increased fruit yields.
Implicitly constituted fluids and their flows in complicated geometries

We study behavior of incompressible non-Newtonian fluids with a relation between the shear stress and the shear rate given by a non-monotone S-shaped curve. These fluids are described with a special class of implicit constitutive relations that may be derived in a thermodynamically consistent manner using the entropy production maximization principle or gradient dynamics. In the latter approach, the constitutive relation is given as the derivative of a non-convex dissipation potential. The concept of dissipation potential allows us to discuss stability of the constitutive relation and explain the experimentally observed response discontinuities. We are also concerned with hydrodynamic stability of flows of implicitly constituted fluids. Finally, we propose a numerical scheme for simulation of transient flows of fluids with a specific non-monotone constitutive relation. We employ the numerical scheme in a simulation of two-dimensional Taylor–Couette flow and the numerical results confirm our theoretical observations concerning the admissible flow states.
The Structure of Evolutionary Theory

* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index
EFFECT OF ACETIC ACID AND DATE RESIDUES ON SOME PHYSIOLOGICAL CHARACTERISTICS, PRODUCTIVE AND REPRODUCTIVE PARAMETERS OF QUAIL DURING SUMMER SEASON

One hundred and eight 8 wk-old Japanese quail were distributed randomly into six different dietary treatments in a 2 x 3 factorial with three replicates, each containing 6 birds (2 males and 4 females), assigning experimental unit to investigate the effect of vinegar (acetic acid) and date residues (date’s by-product) on egg production, fertility and hatchability percentages, some physiological characteristics, blood parameters, hormones, antioxidant indices and immunity parameter. Average temperature ranged between 40°C and 43°C with 50 % relative humidity from 8 to 14 weeks of age. Dietary treatments were date residues levels (0 and 10%) supplemented into diets with three levels of acetic acid (0.0, 0.5 and 1ml /liter water) in drinking water. Results showed that dates residues and vinegar (acetic acid) and interactions between them had significant effect on all the productive performance (egg weight, egg production, egg mass/hen/day, feed conversion as (g feed/g egg)) and improved significantly (P<0.05) fertility and hatchability percentages while decreased significantly (P<0.05) non pipping embryos (%) and embryonic mortality (%). All treatments and interactions between them increased significantly some blood hematological, blood biochemical parameters, antioxidant indices and immunity parameter and hormones of quail, i.e., total protein, albumin, total lipids, HDL, GPX ,GSH, SOD, IgG, progesterone and T3, T4 hormones, but WBCs count in all treatments were slightly increased in number, while serum cholesterol, glucose concentrations, AST and ALT were decreased significantly (P<0.05) birds' in compared with control group. The nutrients digestibility were improved by treatment groups and interactions between them. The counts of total aerobic and anaerobic bacteria and total coliform of chick intestinal were decreased due to add different treatments compared with the control. In conclusion, It may be the application of date residues 10% (in feed) with vinegar (acetic acid) in drinking water (0.5 or 1ml/liter) improved the productive performance such as egg production, fertility, hatchability percentages, some physiological parameters and nutrients digestibility of laying Japanese quail during summer season.
Deep Unordered Composition Rivals Syntactic Methods for Text Classification

Many existing deep learning models for natural language processing tasks focus on learning the compositionality of their inputs, which requires many expensive computations. We present a simple deep neural network that competes with and, in some cases, outperforms such models on sentiment analysis and factoid question answering tasks while taking only a fraction of the training time. While our model is syntactically-ignorant, we show significant improvements over previous bag-of-words models by deepening our network and applying a novel variant of dropout. Moreover, our model performs better than syntactic models on datasets with high syntactic variance. We show that our model makes similar errors to syntactically-aware models, indicating that for the tasks we consider, nonlinearly transforming the input is more important than tailoring a network to incorporate word order and syntax.
Removing the Training Wheels: A Coreference Dataset that Entertains Humans and Challenges Computers

Coreference is a core nlp problem. However, newswire data, the primary source of existing coreference data, lack the richness necessary to truly solve coreference. We present a new domain with denser references—quiz bowl questions—that is challenging and enjoyable to humans, and we use the quiz bowl community to develop a new coreference dataset, together with an annotation framework that can tag any text data with coreferences and named entities. We also successfully integrate active learning into this annotation pipeline to collect documents maximally useful to coreference models. State-of-the-art coreference systems underperform a simple classifier on our new dataset, motivating non-newswire data for future coreference research.
Mixing broccoli cuItivars reduces cabbage aphid numbers

0 pportunistic pathogens and insect pests with high adaptability and a wide genetic variability have become an increasing problem in modern, genetically uniform, agricultural systems. Some plant pathologists have recognized this situation and have suggested increasing genetic diversity in crop fields to reduce epidemic outbreaks. Among the available options, mixing cultivars of different resistances (variety mixtures or multilines) has been found to reduce disease levels (especially rusts) in several grain production systems. The use of this strategy in insect control has been virtually unexplored, although some entomologists have examined it as a way of deploying resistant germplasm to lower the rate at which insect pests adapt to a given resistant cultivar. Despite the biological differences between pathogens and insects, we believe some elements of the theory of pathogen epidemiology in variety mixtures could be used to explain insect responses in fields composed of mixed varieties. The presence of resistant plants impedes pathogen spread by increasing the separation between susceptible plants. It is possible that, depending on the degree to which insect pests discriminate between resistant and susceptible cultivars, the intensity of insect attack could be reduced in a field with a wide array of crop cultivars. We studied the effects of varietal diversity in the field on the population response of the cabbage aphid, Brevicoryne brussicue (LA Stands of broccoli, Brassica oleruceu botrytis (L.), composed of a single cultivar or mixed cultivars were used to determine how aphid population densities were affected by variety mixtures, variety proportions, planting arrangements, and planting times of different broccoli varieties. Our main objective was to test whether increased cultivar diversity in crops reduces pest populations. Methods
Exclusion of ground predators improves Northern Lapwing Vanellus vanellus chick survival

Many farmland-breeding wader species have declined across Europe, probably due to reductions in reproductive output caused by high nest losses as a result of agriculture or predation, or low chick survival between hatching and fledging. Most studies have focused on nest failures, and the factors affecting post-hatching survival of chicks are poorly known. In an experimental approach, we fenced parts of the arable foraging areas of Northern Lapwing Vanellus vanellus families to quantify chick survival simultaneously in the presence and absence of ground predators. Lapwing chicks were radiotagged to estimate survival probabilities by daily locations, applying multistate capture–recapture models. During the night, chick survival was considerably lower outside fenced plots than within. During the day, chick survival was higher than at night and did not differ between protected and unprotected plots. This suggests that nocturnal ground predators such as Red Foxes Vulpes vulpes were responsible for a significant proportion of chick mortality. Cumulative survival probability from hatching to fledging was 0.24 in chicks within fenced plots, but virtually zero in chicks outside fenced plots. In farmland, temporary electric fences can be effective in minimizing the impact of ground predators and offer a promising short-term method to increase fledging success of precocial birds.
Discipline-specific open access publishing practices and barriers to change: an evidence-based review

Background: Many of the discussions surrounding Open Access (OA) revolve around how it affects publishing practices across different academic disciplines. It was a long-held view that it would be only a matter of time before all disciplines fully and relatively homogeneously implemented OA. Recent large-scale bibliometric studies show, however, that the uptake of OA differs substantially across disciplines. We aimed to answer two questions: First, how do different disciplines adopt and shape OA publishing practices? Second, what discipline-specific barriers to and potentials for OA can be identified? Methods: In a first step, we identified and synthesized relevant bibliometric studies that assessed OA prevalence and publishing patterns across disciplines. In a second step, and adopting a social shaping of technology perspective, we studied evidence on the socio-technical forces that shape OA publishing practices. We examined a variety of data sources, including, but not limited to, publisher policies and guidelines, OA mandates and policies and author surveys. Results: Over the last three decades, scholarly publishing has experienced a shift from “closed” access to OA as the proportion of scholarly literature that is openly accessible has increased continuously. Estimated OA levels for publication years after 2010 varied between 29.4% and 66%. The shift towards OA is uneven across disciplines in two respects: first, the growth of OA has been uneven across disciplines, which manifests itself in varying OA prevalence levels. Second, disciplines use different OA publishing channels to make research outputs OA. Conclusions: We conclude that historically rooted publishing practices differ in terms of their compatibility with OA, which is the reason why OA can be assumed to be a natural continuation of publishing cultures in some disciplines, whereas in other disciplines, the implementation of OA faces major barriers and would require a change of research culture.
Divisional morphogenesis in the marine ciliate Anteholosticha manca (Kahl,1932) Berger,2003 (Ciliophora:Urostylida)

The cortical development and macronuclear evolution of the marine hypotrichous ciliate Anteholosticha manca, collected from the coastal waters near Qingdao, China, were investigated using the protargol impregnation method.The morphogenesis of A.manca is generally typical for the genus, and can be characterized as the following features: (1) in the proter, a new oral primordium is formed on the bottom (beneath the pellicle) of the buccal cavity, disorganization of the parental undulating membranes do not contribute to the formation of this primordium; (2) FVT-cirral anlagen in both dividers develop independently, and very likely only a few midventral cirri join in the formation of these primordia; (3) both marginal row and dorsal kinety anlagen develop intrakinetally within the parental structure; (4) at the middle stage, macronuclear segments fuse together to form a single mass as observed in most of its related forms.