Miracle-dz/UniFAR-FTUs huggingface dataset:
Cis and trans-acting factors that regulate hepatitis A virus translation;

Picornaviruses have been shown to translate their genomes by binding ribosomes to internal sequences within the 5'-noncoding region (5'NCR) of the viral RNA genome. The internal ribosome binding site (IRES) has been mapped to the 5'NCR of all picornaviruses studied so far. The experiments presented in this dissertation have been designed to identify the cisand transacting factors that effect hepatitis A virus (HA V) translation. Studies provided in chapter II describe the minimal sequence required for cap-independent translation of HA V monocistronic RNA in vitro. The region between nucleotides 347 and 734 is required for translation in this system. By utilizing bicistronic RNAs containing the HAV 5'NCR, Chapter III further defines those sequences by determining that HA V also translates by internal initiation and contains an IRES element that exists between nucleotides 45 and 734. Comparative analysis using capped and uncapped biand monocistronic RNAs showed that RNA synthesized with the 5'-terminal methylated cap group allows for more efficient translation than RNA containing only the HAVIRES. Studies in Chapter IV describe the existence of a trans-acting activity found in liver cells that stimulates HA V translation in vitro. This activity appears to be specific for HA V RNA and could not be found in other cells of tissue culture origin or kidney, heart and brain extracts derived from the mouse. In combination, the studies presented in this dissertation may help elucidate the possible causes for the slow-growth and pathogenicity exhibited by HA V.
Efficient sampling design for larvae of American lobster

For 13 years, lobster larvae were collected from the same 23 stations at approximately weekly intervals for the duration of the larval season (Scarratt, 1964). Using the most complete 8 years of collections, we produced several data subsets for each year by reducing the number of sampling dates and the number of stations per date. Our analyses were confined to the fourth and final larval stage, the most likely stage to be correlated with fishery yields. The means and confidence intervals for annual larval abundance were calculated on the data subsets and compared with the full dataset. We conclude that the usual lobster larval sampling frequency of weekly, or more often, was unnec- essary. Tows taken at 10 or 14 stations per week for 4 weeks of the 9 week larval season represented well the mean and confidence intervals on the full dataset. These choices remained the best after the costs of sampling were included. Further cost reduction could be achieved without loss of precision by removing collections from the net after every second, rather than after every tow. Mean annual density was found to be a good index of annual larval production. Thus, the collections during 4 weeks represented annual abundance and annual production.
Is the evaporative water loss of Knot Calidris canutus higher in tropical than in temperate climates

To test whether Knot Calidris canutus wintering in the tropics suffer higher rates of water loss through evaporation than do Knot wintering at temperate latitudes, we tried to develop a physically realistic model to predict evaporative heat loss from air temperature, wind and humidity. In separate experiments, involving respirometry and double-labelled water, we tried to estimate relevant parameters, In both sets of experiments, we were able to show significant effects of air temperature on evaporative water loss only, Knot which were able to eat and drink had an evaporative water loss three times that of postabsorptive Knot unable to drink when in a metabolic chamber. Water turnover rates of Knot feeding on bivalves under simulated field conditions were high and did not correlate with predicted evaporative water loss. Over 32 experimental bird-days, the average contribution of predicted evaporative water loss to daily water turnover was 20%. A comparison of predicted evaporative water loss in the north-temperate Dutch Wadden Sea and in the tropical Bane d'Arguin in Mauritania in midwinter showed that Knot wintering in the tropics may need only marginally more water for evaporative cooling than Knot wintering in the Dutch Wadden Sea. Knot foraging on intertidal invertebrates are able to maintain high water turnover rates with little need to drink seawater.
Lobster fishing in Ceylon

The presence of spiny lobsters in the reefs lying off the coasts of Ceylon is known to local fishermen and skin divers. However, a well-established fishery for these lobsters does not exist as fishermen engaged occasionally in this activity catch only a few lobsters during the course of a day's fishing. Considering the present state of development of lobster fishing in Ceylon, it is not possible to state whether lobsters are found in sufficient numbers in the seas off Ceylon. This knowledge is very important before the introduction of new methods of fishing can be made. Experiments were therefore conducted to determine the most efficient type of trap that could be used to appraise the resources present in the coral reefs and other rocky areas. Designs of traps, similar to those used in Scotland, England, Wales and Canada, were made locally. These were tested for efficiency in areas known to be inhabited by spiny lobsters.
Anurans of Turvo State Park: testing the validity of Seasonal Forest as a new biome in Brazil

The composition of the anuran community of Turvo State Park was compared with that of other localities of Mesophytic semideciduous Forest, aiming to test the hypothesis that localities situated nearest the Misiones nucleus support the new phytogeographic unit, known as Tropical Seasonal Forests Region. In total 32 amphibian species were recorded in the park area and surroundings: Anura, 30 native species and one exotic; Gymnophiona, one species. The ordination among the 20 localities of Seasonal Forest showed the formation of three groups with 45% similarity: group 1, composed of localities of south-eastern and central western regions; group 2, composed of the localities of the transitional portion with the Atlantic Forest sensu stricto and group 3, composed of the southern localities. The consolidation of the second group, which includes the occurrence of endemic species, supports the proposal of a new phytogeographic unit.
Polyphenols and antioxidant properties in forced and naturally aged Brazilian beer

Beer is a beverage obtained through alcoholic fermentation of malt wort, usually made of barley, which could be added of other cereals, such as corn, rice or wheat. Its alcoholic content is between 3 and 8%. It can be considered a good source of polyphenols derived both from malt and hop. Due to its antioxidant capacity and low alcoholic content, its able to improve plasma antioxidant activity, reducing the risk of cardiovascular diseases, without the negative effects of high doses of alcohol. Beer is an unstable product that is involved in a series of chemical, physical and sensorial transformations during its shelf life. This study evaluated the oxidative profile of two different types of Brazilian beer submitted to a forced aging process (6 days at 42°C) and natural aging (4 months at room temperature). The applied tests were: total polyphenol content, hydrogen-donating ability (DPPH), reducing power and copper reducing activity. Results showed no changes in total polyphenol content or antioxidant capacity during forced aging. Beers aged naturally showed a decrease in their polyphenol content and antioxidant capacity.
The Ovicidal and Larvicidal Capabilities of Recent Reduced Risk Insecticides on Codling Moth Cydia pomonella

I propose an analysis of two insecticides, Chlorantraniliprole and Methoxyfenozide on a major agricultural pest, Codling Moth, Cydia pomonella. Crop losses are derived from consumer expectancy of impeccable crops placing severe pressure upon farmers. Today the consumers expect perfect crops, including apples, resulting in severe financial losses for farmers. The continued application of insecticides including organophosphates has led to increased resistance and severe impacts upon non-target species. Reduced-risk insecticides limit impacts upon non-target species and the environment. Two more recent reduced-risk insecticides Chlorantraniliprole and Methoxyfenozide are promising ovicides (egg killers) or larvicides (larvae killers). I examined the application of each by dipping or spraying, prior to or after oviposition (egg deposition), with or without surfactants. After I dipped or sprayed each insecticide prior to or after oviposition, with or without surfactants, upon each individual apple, I then studied, analyzed and determined if efficacy of each improved. I discovered that both Chlorantraniliprole and Methoxyfenozide mortality rates averaged 50% or greater. I found Chlorantraniliprole was most effective when I dipped it prior to oviposition. Methoxyfenozide was most effective when I dipped or sprayed it after oviposition. Both insecticides targeted Codling Moth before damage occurred.
Sciurid Habitat Relationships in Forests Managed Under Selection and Shelterwood Silviculture in Ontario

Abstract Although partial forest harvesting is practiced over large areas, managers know little about its impacts on sciurid rodents, particularly on northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) in the northeastern United States and Canada. We examined habitat relationships of sciurid rodents (northern flying squirrels, southern flying squirrels, red squirrels [Tamiasciurus hudsonicus], and eastern chipmunks [Tamias striatus]) at 2 spatial scales in managed and unmanaged coniferous and hardwood forests of Algonquin Provincial Park, Ontario, Canada. We live-trapped rodents in 26 northern hardwood stands and in 16 white pine (Pinus strobus) stands from 2002 to 2004. Northern flying squirrel and red squirrel densities were significantly lower in recently harvested (3–10 yr since harvest) shelterwood stands than in unmanaged stands. In contrast, southern flying squirrel densities were higher in selection-harvested stands than in old-forest areas. The densities of northern flying squirrels and red squirrels had a strong relationship with the density of large spruce (Picea sp.) and hardwood trees and snags in conifer sites. Southern flying squirrel numbers had a positive association with the density of mast trees at the landscape level but not at the stand level in hardwood forests. Eastern chipmunk density had a positive correlation with the volume of old downed woody debris and the stems per hectare of declining trees. We recommend forest managers retain more large spruce and hardwood trees to mitigate the impacts of shelterwood harvesting on northern flying squirrels and red squirrels, and that they maintain high mast availability at the landscape level to ensure the persistence of southern flying squirrels.
Designing tools to evaluate fishery management strategies: can the scientific community deliver?

Techniques for quantitative fishery management have evolved rapidly during a period when computers, programming languages, and computational algorithms have also changed dramatically. Despite these advances, many stock assessment methods remain untested. A process of management strategy evaluation (MSE) could potentially rectify this problem, but it would require a framework in which to conduct systematic tests. We survey the tools currently used for stock assessments and discuss the development of new standards for testing management procedures. A successful project would depend on human skills scattered among various nations, organizations, and academic disciplines. Analogies from civil engineering illustrate the discipline and collaboration required for an effective outcome. If the world community of fishery scientists could design, build, and support such a project, it would revolutionize the theory, teaching, and practice of scientific fishery management.
Thermodynamic Analysis of the Interaction of Lipopolysaccharides with Cationic Compounds

Bacterial lipopolysaccharides (LPS) from Gram‐negative bacteria, located in the outer leaflet of their outer membrane, are called endotoxins due to their ability to induce a variety of biological effects in mammals. Their lipid moiety, lipid A, is called “the endotoxic principle” and is responsible for the toxic effects of LPS. As a result of the polyanionic character of LPS, the study of the interaction with divalent cations Mg2+ and Ca2+ and polycationic peptides such as polymyxin B (PMB) and its nonapeptide PMBN is of considerable interest, and therefore the authors have investigated the interaction of LPS/lipid A with cationic compounds by applying isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC). The data indicate a clear binding of the divalent cations with the anionic glycolipids, leading to calorimetric reactions, such as an increase in the phase transition temperature, Tm, of the gel to the liquid crystalline phase of LPS, indicating a stabilization of the gel phase. The peptides react quite differently as assessed by DSC. In contrast to the interaction of divalent cations with the glycolipids, a destabilization of the gel phase is observed, accompanied by a decrease in the gel to liquid crystalline phase transition enthalpy for the peptide‐glycolipid interaction. The extent of this effect is peptide‐concentration‐dependent. Using ITC for the analysis of the binding reaction of the cations and the peptides with the glycolipid in the liquid crystalline phase, strong exothermic effects are observed. These are indicative of the dominance of electrostatic attractions between the reaction partners. Interestingly, Ca2+ binding to LPS leads to a slightly exothermic reaction, whereas Mg2+ binding leads to an endothermic reaction (some kJ/mol). The observed highly endothermic binding reactions for the lipid‐peptide interaction in the gel phase are mainly driven by a gain in entropy. This is explained by the fact that during binding, water molecules from the hydration shells of the components are liberated. Although the electrostatic attraction is still the driving force of the interaction, it is quantitatively of minor importance for the interaction in the gel phase. The binding results are discussed in terms of competition between electrostatic interaction and hydration forces. These data are of importance for the understanding of the reaction mechanisms of cationic compounds with LPS under physiological conditions.
Habitat Choice of Palestine Saw-Scaled Viper (Echis coloratus) in an Extreme Environment

Abstract We hypothesized that Palestine Saw-Scaled Vipers (Echis coloratus) select ambush sites that allow them to remain in a relatively cooler microclimate. During spring 2010, we identified the locations of 27 vipers in the Eilat Bird Sanctuary, Israel. Twenty-six (96%) of Vipers were recorded in 15 Salvadora persica, one (4%) in Zygophyllum dumosum, and none in Ochradenus baccatus. The temperature at the base of the S. persica was on average 6°C lower that in O. baccatus. We also found that the greater the apron radius of S. persica, the lower the temperature in the bush, and that bushes of S. persica occupied by vipers, have greater apron radius that those without snakes. We found that each of the snakes remained in the bush in which it was found during the whole three months of the study. We conclude that the cues used by E. coloratus for predicting future prey availability seem to be the structure of the microhabitat rather than prey odor. Our study is of conservation importance and enhances our understanding of habitat choice in this little-studied snake.
EVALUATION OF ANTIOXIDANT POTENTIAL OF SOLVENT EXTRACTS OF FEMALE CONES AND LEAVES OF CYCAS REVOLUTA

In the ethno-pharmacological approach, local knowledge about the potential uses of the plants is very useful as compared to the random approach where indigenous knowledge is not taken into consideration. Phytochemicals produced in plants are secondary compounds responsible metabolic activities and defense in purpose. Phytochemicals are produced by specific biochemical pathways, which occur inside the plant cells. The gymnosperm, Cycas revoluta is a natural companion for palms, working well as under planting or in the foreground. In the present investigation, different solvent extracts viz. chloroformic and hydro-alcoholic extracts of Cycas female cone and leaves were prepared and in vitro antioxidant activity was determined as per the conventional procedures. The results showed that both the leaves and female cones of Cycas revoluta are potent antioxidant agents. It was observed that chloroformic extracts of female cones and leaves were more potent than hydroalcoholic extracts. The results showed that chloroformic extracts of the cones was having potent antioxidant activity followed by the chloroformic extracts of leaves.
Some important properties and classification of vertisols under Mediterranean climate.

Vertisols comprise some of the important arable land in northwestern Turkey. Five sites were selected to present Vertisols occurring in different parent materials of the study area. These soils occur on flat to gently sloping plains of the region. Clay content is high in the studied sites. The high cation exchange capacity and CEC/clay ratios suggest montmorillonitic and mixed mineralogy. Calcium was the most dominant extractable cation followed by magnesium. The similar patterns of distribution for the electrical conductivity values and soluble cations throughout the studied soil sites indicate the low leaching rate, eluviation and illuviation processes within these studied sites. All soils belong to the Haploxererts soil great group.
Pharmacology of α-Conotoxin MII-Sensitive Subtypes of Nicotinic Acetylcholine Receptors Isolated by Breeding of Null Mutant Mice

Subtypes of nicotinic acetylcholine receptors (nAChR) containing α6 subunits comprise 25 to 30% of the presynaptic nAChRs expressed in striatal dopaminergic terminals in rodents and 70% in monkeys. This class of receptors, potentially important in nicotine addiction, binds α-conotoxin MII (α-CtxMII) with high affinity and is heterogeneous, consisting of several subtypes in mice, possibly an important consideration for the design of compounds that selectively activate or antagonize the α6 subclass of nAChRs. Selected-null mutant mice were bred to generate isolated subtypes of α6β2* nAChRs expressed in vivo for assessing pharmacology of α6β2* nAChRs. Binding to striatal membranes and function in synaptosomes from (α4–/–)(β3+/+) and (α4–/–)(β3–/–) mice were measured and compared with wild-type (α4+/+)(β3+/+) mice. Gene deletions (α4 and β3) decreased binding of 125I-α-CtxMII without affecting affinity for α-CtxMII or inhibition of α-CtxMII binding by epibatidine or nicotine. Deletion of the α4 subunit substantially increased EC50 values for both nicotine- and cytisine-stimulated α-CtxMII-sensitive dopamine release from striatal synaptosomes. A further increase in EC50 values was seen upon the additional deletion of the β3 subunit. The data indicate that one α-CtxMII-sensitive nAChR subtype, prevalent on wild-type dopaminergic terminals, has the lowest EC50 for a nicotine-mediated function so far measured in mice. In conclusion, the gene deletion strategy enabled isolation of α6* subtypes, and these nAChR subtypes exhibited differential activation by nicotine and cytisine.
Calculating dry matter consumption of dairy herds in Australia: the need to fully account for energy requirements and issues with estimating energy supply

Feed costs are the major component of the variable costs and a significant component of the total costs of milk production on Australian dairy farms. To improve farm productivity, farmers need to understand how much feed is being consumed and the nutritive characteristics of the diet. This paper reviews an existing simple approach, the ‘Target 10’ approach, which is commonly used by the dairy industry in Victoria to estimate annual forage consumption. An alternative approach – the ‘Feeding Systems’ approach – is then introduced. The ‘Feeding Systems’ approach is compared with estimated forage consumption measured under experimental conditions. An analysis of the sensitivity of both approaches to incremental changes in key variables is presented. The ‘Feeding Standards’ approach was concordant with estimated forage consumption measured under experimental conditions. Sensitivity analysis has highlighted key variables which may have considerable influence over simulated forage consumption using this approach. Given that none of the key variables tested in this analysis can be varied in the ‘Target 10’ approach, we feel confident that the ‘Feeding Standards’ approach provides an improved method of back-calculating annual on-farm forage consumption. Using a robust approach to calculate forage consumption which fully accounts for metabolisable energy requirements is important where farmers are using home-grown forage consumption as an indicator of farm feeding system performance. It is also important to understand the assumptions involved in estimating metabolisable energy supply from either supplements or forage.
Restoring Lepidopteran Communities to Oak Savannas: Contrasting Influences of Habitat Quantity and Quality

Ecological restoration is deemed important for the long‐term conservation of biodiversity, but ecologists still lack an understanding of how habitat availability and habitat quality in a restored system interact to determine species diversity. This problem seems particularly apparent in Tallgrass Prairie and savanna ecoregions, where restored management units represent the majority of extant habitat. In this study, we tested three principal hypotheses, each stating that the diversity of Lepidoptera would be greater in (1) patches of savanna habitat that were larger; (2) patches that were of higher habitat quality; and (3) patches that had greater connectivity to management units of similar physiognomy. Lepidoptera were sampled in 2003 from 13 unmanaged woodland remnants within Neal Smith National Wildlife Refuge, a 2,292‐ha prairie and savanna reconstruction project. We also measured 11 environmental variables within each site to assess variation in habitat quantity and quality. Principal components analysis (PCA) was used to identify major gradients of environmental variation among the 13 sites. Our PCA differentiated among woodlands along three environmental gradients, defined by (1) stand size, shape, topography, and oak dominance; (2) degree of disturbance; and (3) isolation. Total lepidopteran species richness, however, was only predicted by variation in the first principal component. Species richness of Lepidoptera known to be oak specialists was significantly affected by variation along all three PCA gradients. Surprisingly, more isolated woodland remnants contained a greater richness of oak feeders. Our results suggest that approaches to restoring oak savannas should emphasize aspects of both habitat quantity and quality. Beyond making individual management units larger, priority sites for restoration should possess a low importance of trees that are indicative of past habitat disturbance (e.g., Honey locust, White mulberry) even if canopy closure is substantial. Connectivity among restored habitats may benefit savanna moth communities only when habitat linkages contain a flora similar in composition to focal patches.