Miracle-dz/UniFAR-FTUs huggingface dataset:
Fire and invasive exotic plant species in eastern oak communities: an assessment of current knowledge.

Successful regeneration of oak-dominated communities in the Eastern United States historically requires disturbance such as fire, making them vulnerable to invasion by exotic plants. Little is currently known about the effects of fire on invasive plant species and the effects of invasive plant species on fire regimes of this region. Seventeen common eastern invaders were evaluated for their response to fire and potential to change current fire regimes. Twelve species are potentially controllable with repeated growingseason burns (decreasers); five may increase in abundance in response to fire (increasers). Most of the woody decreasers are also potential resisters of fire at maturity. The presence of a seedbank or an outside seed source (evaders) for all but one species and a positive germination response to post-fire conditions (e.g., higher soil temperature, nitrogen availability, and light) make it less likely that most eastern plant invaders can be controlled by fire alone. Shifts in fire regime in eastern oak communities are undocumented but may occur due to changes in community flammability after an invasion. Current fire models are inadequate for predicting fire behavior in these oak communities due to a lack of information on eastern native and exotic plant species fuels. Consequently, fire behavior predictions are best made on a site-by-site basis, especially for sites with multiple invaders composed of increasers and decreasers as well as fire promoters and inhibitors.
DIVERSITY AND ABUNDANCE OF LEPIDOPTERAN POPULATIONS FROM SELECTED CROPS OF DISTRICT FAISALABAD, PAKISTAN

Perfor. of Summer forage legumes in Pothowar Lepidopterans are represented by one of the most diverse group of insects. They are phytophagous as well as pollinators at the same time. During present study four crops i.e Wheat, Fodder, Brassica and Vegetables were sampled to assess the diversity and abundance of Lepidopteran populations. A total of 2811 specimens belonging to 14 species and 6 families were recorded. Pieris brassicae (29.46%) was the dominant species followed by Trichoplusia ni (19.28%), Helicoverpa Zea (11.78%), Helicoverpa armigera (11.60%), Spodoptera exigua (6.65%), Psedoplusia includes (5.09%), Spodoptera litura (3.81%), Agrotis ipsilon (4.87%), Plutella xylostella (2.92%), Lymatria dispar (2.24%), Pieris rapae (0.92%), Galleria mellonella (0.71%), Evergestris rimosalis (0.53%) and Menduca sexta (0.14%). Significant differences were observed among different crops by applying Shannon Diversity Index and T - test. CA (Cluster analysis) represented the species association with different crops. Majority of the species showed association with Vegetables and Fodder and least association was observed with Wheat. Such types of studies are necessary to design integrated pest management programs to control these pests.
Morphological and molecular identification of a strain of the unicellular green alga Dunaliella sp. isolated from Tarquinia Salterns

1 - Algae of the genus Dunaliella are among the most studied micro-algae. They are used for the production of feed, for nutritional reinforcement as a vitamin A precursor and for pharmaceuticals and fine chemicals. 2 - The current taxonomy of the genus is based on morphological and physiological attributes including the ability of some species to grow over wide salinity ranges and at extreme salinities, as well as the accumulation of high levels of â-carotene. The taxonomic status of the genus Dunaliella involves some uncertainty, moreover it is very difficult to compare results from different authors, owing to uncertainty on names and species. 3 - In this work, we compare morphological and molecular analysis to characterize a strain of Dunaliella isolated from Tarquinia salt ponds. Samples of natural populations of the unicellular green alga, were collected at various times during the study period to detail the vegetative motile cells and the different stages of its life cycle microscopically. The ITS1 and ITS2 regions were used for the molecular identification analysis. Conserved oligonucleotides of 18S rDNAs (MA3) and speciesspecific primers (DSs), designed from variable sequences, were used to corroborate the identification. 4 - Blast results indicated that our sequences matched at the 100% level with Dunaliella salina Teod reported in Gen Bank. Consequently, based on comparative cell morphology and molecular analysis, the new Dunaliella isolate from Tarquinia salt ponds was classified as D. salina.
Ecological niche of weeds in spring cereals cultivars grown after winter oilseed rape

Summary The environmental conditions and ecological niches for weed survival and development in cereals crops are diversified. They are conditioned by biotic and abiotic factors of the environment and natural factors including quantitative rations between species of agrophytocenosis. The object of the studies carried out in 2009–2012 was to determine the weed species composition and infestation in crops of spring cereal species. Two cultivars were taken into consideration for each cereal species. The observations were done on the control (untreated) plots of a field experiment on evaluation of herbicide biological efficacy. The obtained results revealed that regardless of cereal species and cultivar, the weed species composition was similar, however the number of weeds and their biomass were different. The smaller weed biomass and their number were correlated with a higher competitiveness of cultivated cereal plants in relation to weeds. The rye cultivar Bojko showed the highest competitivenes, while the wheat cultivar Tybalt was the least competitive. The highest weed infestation was recorder for wheat in contrast to the lowest one in barley and rye crops. A proper selection of cereal species and cultivars with high competitive abilities should be taken into consideration by organic farms.
Observations on the Natural History of Sphodros abboti and Sphodros rufipes (Araneae, Atypidae), with Evidence for a Contact Sex Pheromone

The three populations of S. abboti studied exhibit much higher densities than the two of S. rufipes. In S. abboti mating occurs in July, egg laying in August, hatching in September, and the fully equipped and self-sufficient third instar spiderlings develop by November. The tubes of S. abboti are proportionately longer and have a greater aerial length to underground length ratio than do those of S. rufipes. Other differences in tube architecture exist. Both species capture and feed upon a wide variety of ground arthropods and discard prey remains through the upper end of the tube. S. abboti males search for mates in day light and appear to be generalized wasp-ant mimics. Our observations of S. abboti male behavior suggests that adult female tubes are marked by a contact sex pheromone.
Improvement of Callogenesis Ability by Selecting a Better Hormonal Balance in Potato (Solanum tuberosum L).

Response in tissue culture is highly genotype dependent, significant genotypic diferences in callus initiation response were observed among both potato genotype investigated. The Spunta variety devleops the best calogenesis in all media compared to Kondor variety depending on hormones concentration,there is a range of variations in days needed for callus initiation,percentage of explant that developed callus, its texture, color and the degre of its formation.Our resutls chow that the callus depends on explant type.Sprout explant respond best to callus formation. the amount of callus ranges from 60% to 90 % for Spunta . Callus color after eight weekwas light green or green yelow for both varieties.The higest amount of callus 100% was obtained with the combination (NAAxBAP)(0.5/1, medium M2) and (2/2 ,medium M3) with Kondor bud explant . In media M1(1/0.5 mg/l),M2 (0.5/1 mg/l) and M3 (2/2 mg/l) with sprout explant of Spunta the amount of 80 %was noted,callus in media M1 and M2 produced microtubers,shoots and roots.
Die deutsche Version des Big Five Inventory 2 (BFI-2)

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Investigating mechanisms of Hepatitis C virus endocytosis

Many viruses exploit and, in some cases, promote host cell endocytic pathways for infection. These pathways include caveolar and clathrin-mediated endocytosis, as well as macropinocytosis. The entry mechanisms of many viruses are not clear cut, with more than one pathway implicated in some cases. Hepatitis C virus (HCV) is a hepatotropic virus associated with liver disease, fibrosis, cirrhosis and hepatocellular carcinoma. There are four co-receptors or “entry factors” for HCV: the tetraspanin CD81, scavenger receptor BI (SR-BI and the tight junction proteins Claudin 1 (CLDN1) and Occludin (OCLN). Clathrin-dependent endocytosis of HCV has been demonstrated in hepatoma cell lines and has also been shown to be the route of entry for co-receptor CD81; however, other endocytic pathways have not been considered. This thesis investigates a role for caveolae in HCV entry. In addition, it has recently become apparent that the epidermal growth factor receptor (EGFR) is required for viral entry into hepatoma cells and that stimulation with EGF results in increased entry and infection. This thesis investigates the role of EGFR in the endocytosis and trafficking of HCV receptors/entry factors, with a particular focus on CD81, using live-cell and super-resolution imaging techniques.
Incidental learning of new meanings for familiar words

3 Impact statement . 4 Statement of contributions . 5 Acknowledgements . 5 List of figures. 10 List of tables . 14 Chapter 1: General introduction. 16 1.
Fecundity and spawning frequency of Rasbora tawarensis (Pisces: Cyprinidae) an endemic species from Lake Laut Tawar, Aceh, Indonesia.

This paper is contributing the additional importance information on the reproductive biology of Rasbora tawarensis in relation to provide comprehensive our understanding on the reproductive biology of this species. Monthly sampling was conducted from April 2008 to July 2009. The highest absolute fecundity was observed in December, but it was not significantly different (p>0.05) from January, May, July, August, October and November. The highest relative fecundity was observed in July but it was not different significantly (p>0.05) from January, May, June, August, September, November and December. The average absolute fecundity was 3715.4±893.6 eggs, while the average relative fecundity was 518±95.64 eggs.g body weight. The spawning frequency of the female was 2 to 11 days and fish was frequent spawned during the reproductive seasons in March, September and December.
Genetic Diversity of Medaka ( Oryzias latipes ) in Paddy Field Water Channels:- A case study using microsatellite markers in Wanouchi Town, Gifu Prefecture -

To analyze genetic diversity of endangered medaka ( Oryzias latipes ), primers for PCR (polymerase chain reaction) were constructed that could amplify ten microsatellite loci of medaka genome based on the contig/scaffold sequences published. DNA was extracted from the caudal fin of medaka collected at six different sampling points in Wanouchi Town, Gifu Prefecture. Genetic diversity within each sampling point was relatively high, whereas genetic differentiation between sampling points was small (pairwise F ST = 0.023-0.086) but significant for all except three pairs of the sampling points. The genetic difference between the populations of the sampling points could be explained not only by the geographical distances but by the waterway connectivity between the points. These results indicated the importance of planning agricultural channel corrections considering migration of medaka between populations, to conserve genetic features of medaka in this study site where within-population genetic diversity is not much deteriorated yet.
DEVELOPMENT OF GLOMERELLA LEAF SPOT IS ENHANCED IN VIRUS-INFECTED MAXI GALA APPLES

Apples are commercially grown in Brazil in a subtropical environment that favors the development of fungal diseases such as Glomerella leaf spot (GLS) caused mainly by Glomerella cingulata (anamorph Colletotrichum gloeosporioides). The main objective of this work was to evaluate the effect of mixed infections by Apple stem grooving virus (ASGV) and Apple stem pitting virus (ASPV) on the infection and the colonization processes of C. gloeosporiodes in cv. Maxi Gala plants. Leaves of 16-month-old potted plants were spray-inoculated and both the disease incidence and lesion count were monitored over time and leaf severity was assessed in the final evaluation using an image analysis tool. Results showed that initial infection estimated from a monomolecular model fitted to progress of lesion count was higher and the incubation period (time to reach 50% incidence) was on average 10 h shorter in virus-infected plants compared to non-infected plants. It is hypothesized that initial events such as conidial germination and fungal penetration into plant cells were facilitated by the presence of viral infection. Also, final GLS severity was significantly higher in the virus-infected plants. Mixed infections by ASGV/ASPV seemed to make apple leaves more susceptible to the initial infection and colonization by C. gloeosporioides.
Shifts in depth of water extraction and photosynthetic capacity inferred from stable isotope proxies across an ecotone of Juniperus osteosperma (Utah juniper) and Artemisia tridentata (big sagebrush)

1 In western North America, juniper trees (Juniperus spp.) are apparently encroaching into numerous communities including sagebrush‐dominated (Artemisia tridentata) valleys, where, as density of juniper increases, the density and condition of sagebrush decline but juniper condition appears unaffected. 2 We examined stable isotope proxies of plant gas exchange and relative depth of soil water extraction of Juniperus osteosperma and Artemisia tridentata as their relative densities changed across a transition zone in northern Utah, USA. Measurement of 13C and 18O of foliage allowed separation of the contributions of stomatal and biochemical factors to differences in mean intercellular CO2 concentration, while deuterium composition of stem water served as an indicator of the relative depth of water extraction. 3 Leaf δ13C of juniper and, to a lesser extent, of sagebrush increased with decreasing density of juniper. Foliage 18O did not vary significantly with juniper density, indicating that this was primarily caused by an increase in photosynthetic capacity rather than decreased supply of CO2. Increased foliage nitrogen concentration of both species with decreasing juniper density is also consistent with increased photosynthetic capacity. 4 The much greater mean age of juniper trees in the high juniper density plots may explain their lower photosynthetic capacity. 5 Averaged across densities, juniper always extracted water deeper in the profile than did sagebrush, but in June and August, only the high juniper density plots showed an effect. Sagebrush is either restricted from using water at greater depth in the presence of juniper at high density or was in such poor condition that deep‐water sources were not necessary to maintain their reduced function. 6 Ecotones can serve as useful, spatially constrained stages for examining resource partitioning and relationships among plant species. We observed spatial and temporal variation in resource use and partitioning of limited resources that will enable better design of manipulative experiments to explicitly examine competition.
Engineering bacteria for the degradation of halopropanes

Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, prohibiting the development of a biological process for groundwater treatment. The critical step in the aerobic degradation of TCP is the initial dehalogenation to 2,3-dichloro-1-propanol. We used random mutagenesis and screening on eosine-methylene blue agar plates to improve the activity on TCP of the haloalkane dehalogenase from Rhodococcus sp. m15-3 (DhaA). A second-generation mutant containing two amino acid substitutions, Cys176Tyr and Tyr273Phe, was nearly eight times more efficient in dehalogenating TCP than wild type dehalogenase. Molecular modelling of the mutant dehalogenase indicated that the Cys176Tyr mutation has a global effect on the active-site structure allowing a more productive binding of TCP within the active site, which was further fine-tuned by Tyr273Phe. The evolved haloalkane dehalogenase was expressed under control of a constitutive promoter in the 2,3-dichloro-1-propanol utilizing bacterium Agrobacterium radiobacter AD1 and the resulting strain was able to utilize TCP as the sole carbon-and energy source. These results demonstrated that directed evolution of a key catabolic enzyme and its subsequent recruitment by a suitable host organism can be used for the construction of bacteria for the degradation of a toxic and environmentally recalcitrant chemical.
Microtechnologies Enable Cytogenetics

Cytogenetic analysis is an important tool in preand postnatal diagnosis as well as cancer detection. In a traditional cytogenetic technique known as karyotyping the metaphase chromosome spreads are prepared on a glass slide and stained with a Giemsa stain. The stain reveals a specific banding pattern for each chromosome – a chromosome bar code. Karyotyping is often supplemented by the molecular cytogenetic technique Fluorescent In Situ hybridization (FISH), which requires the use of fluorescently labeled DNA probes to target a specific chromosome region. In FISH the chromosome preparations (metaphase spreads or interphase nuclei) are heat denatured, followed by application of the probe and hybridization at 37 °C. FISH can be performed on interphase nuclei on non-cultured cells in less than 24 hrs, but the chromosome structure cannot be visualized. On the other hand, metaphase FISH has the advantage of visualizing the entire karyotype at once and can detect potential abnormalities at a high resolution. But, the long analysis time and culturing required for metaphase FISH are important disadvantages.
Obinutuzumab (Gazyva®), a Novel Glycoengineered Type II CD20 Antibody for the Treatment of Chronic Lymphocytic Leukemia and Non‐Hodgkin's Lymphoma

CD20 is a transmembrane antigen expressed on the surface of malignant and non-malignant preand mature B-lymphocytes, but not on hematopoietic stem cells, pro-B cells, normal plasma cells, or other normal tissues [1, 2]. CD20 is believed to exist predominantly as a tetramer on cell surface and not to be subjected to shedding or internalization upon antibody binding. The physiological role of CD20 has not been clearly elucidated as yet, although it was suggested that it could be involved in calcium signaling following B-cell receptor activation [1, 2]. Rituximab (MabThera/Rituxan) was the first monoclonal antibody to be approved for the treatment of non-Hodgkin’s lymphoma (NHL) including indolent nonHodgkin’s lymphoma (iNHL), diffuse large B-cell lymphoma (DLBCL), and chronic lymphocytic leukemia (CLL) in combination with chemotherapy. Recently, the human CD20 antibody ofatumumab (Arzerra) was approved for a subpopulation of fludarabine-refractory CLL patients [3]. Although the exact mechanism of action of rituximab remains to be fully elucidated, it is thought that CD20 antibodies trigger at least three different mechanisms of action: (i) cell death induction (also described as direct cell death or apoptosis), (ii) antibody-dependent cellular cytotoxicity (ADCC) and/or antibody-dependent cellular phagocytosis (ADCP), and (iii) complement-dependent cytotoxicity (CDC). The relative contribution of these mechanisms to the overall efficacy of rituximab is not clear; however, ADCC/ADCP are considered as the most important mechanisms of action of rituximab in patients, with CDC and induction of cell death playing a less important role [4, 5]. In the clinical setting, CD20 antibodies have been shown to work synergistically in combination with chemotherapy [2, 6]. Furthermore, the induction of an adaptive immune response following therapy with rituximab, also termed vaccinal effect, is currently being discussed [2, 7]. Obinutuzumab (also known as GA101, RO5072759 or GAZYVA) is a humanized glycoengineered Type II CD20 monoclonal antibody of the immunoglobulin G1 (IgG1) isotype. Obinutuzumab was designed to mediate enhanced direct and immune effector-cell-mediated killing of tumor cells compared to the Type I CD20
NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

Cytotoxic T cells are of central importance in the immune system’s response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. Therefore, in the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has attracted widespread attention. In the past, predictors of peptide–MHC interactions have primarily been trained on binding affinity data. Recently, an increasing number of MHC-presented peptides identified by mass spectrometry have been reported containing information about peptide-processing steps in the presentation pathway and the length distribution of naturally presented peptides. In this article, we present NetMHCpan-4.0, a method trained on binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes.
Differences Between South American H Haplome Diploids and I Haplome Diploids from the Perspective of the 5S rDNA Gene in the Genus Hordeum

Twelve South American diploid Hordeum species belonging to the H genome and three diploid species belonging to the I genome (including cultivated barley) were investigated for their 5S rDNA sequence diversity. The 374 sequenced clones were assigned to classes called "unit classes" which were further assigned to haplomes. Two unit classes were found to be present in each haplome. These were labelled to reflect the haplomes, viz. the long H1 and short I1 unit classes for the I haplome diploids, and the long H2 and long Y2 unit classes for the South American H genome diploids. The aligned sequences were subjected to a series of Maximum Likelihood analyses and various tests, including molecular clock, which are presented and discussed. The divergences among the unit classes suggest that the genus Hordeum might be of paleopolyploid origin.