Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of taurine related compounds in deep- and shallow-water mussel species

Densely packed invertebrate communities have been observed around deep-sea hydrothermal vents and cold seeps, despite the high concentrations of hydrogen sulfide present in these environments. The species that inhabit these environments have been reported to accumulate the sulfur-containing amino acid, thiotaurine. This non-toxic amino acid is synthesized from its precursor, hypotaurine and ambient hydrogen sulfide. In this study, we compared the levels of thiotaurine and hypotaurine in the gills and mantles of two deep-sea mussels (Bathymodiolus septemdierum and B. platifrons) and a shallow-water mussel (Mytilus galloprovincialis) to investigate their degree of dependence on the thiotaurine/hypotaurine system. The levels of thiotaurine and hypotaurine in the gill were higher than those present in the mantle in the two deep-sea species but lower or similar in M. galloprovincialis. The levels of thiotaurine and hypotaurine were the highest in the gill of B. septemdierum, estimated at 6.56 and 13.50 μmol/g wet weights, respectively. Moreover, B. septemdierum exhibited a higher thiotaurine/(hypotaurine+thiotaurine) ratio in the gill, B. septemdierum than that did B. platifrons and M. galloprovincialis. These results suggest that the levels of thiotaurine and hypotaurine in Bathymodiolus may be related to the ambient sulfide levels in their habitats.
Moose directly slow plant regeneration but have limited indirect effects on soil stoichiometry and litter decomposition rates in disturbed maritime boreal forests

Summary Foraging decisions by herbivores are modulated by physiological demands for nutrients and these decisions can influence the biomass, abundance and dynamics of plant species with consequences on key ecosystem processes, such as nutrient cycling and decomposition. Some studies have found that large browser populations can reduce the abundance of nutrient-rich preferred species, promoting the dominance of nutrient-poor non-preferred species. This can have indirect effects on soil nutrient concentrations, soil microbe community composition and above-ground invertebrates and birds that depend on nutrient-rich plant species. However, very little research has compared the impact of biotic and abiotic features on nutrient cycling and decomposition in areas of high moose density. We performed a field study to test the generality of moose effects on forest ecosystems observed in iconic study systems such as Isle Royale. Specifically, we used 10 paired moose exclosure and control plots to test the effects of moose on plant community characteristics, litter fall quantity, soil properties and litter decomposition rates in regenerating disturbed forests in Newfoundland, Canada. We found evidence that moose reduce plant height and plant litter biomass, thereby affecting the quantity of carbon, nitrogen and phosphorus available in litter fall with potential indirect effects on soil pH and soil depth. However, we found no evidence that the direct effects of moose lead to indirect effects on soil quality, soil moisture and litter decomposition rates. Disturbance regime and site explained a large portion of the variance in plant community characteristics, litter fall quantity, soil properties and litter decomposition. Our results suggest that while introduced moose in Newfoundland have measurable direct influence on plant regeneration and litter fall biomass, other factors such as disturbance history and climate may be more important predictors of landscape-scale variation in soil quality and litter decomposition rates. Our study suggests a need for further development of theory to predict the relative contribution of biotic vs. abiotic effects on nutrient cycling in forest ecosystems. A lay summary is available for this article.
Carbon-13 solid-state nuclear magnetic resonance of sporopollenins from modern and fossil plants

13 C solid-state nuclear magnetic resonance (NMR) has been applied to modern pollen and spore exines (Betula, Pinus and Lycopadium) and those of two fossil spores (Lagenicula and Parka) in order to assess the composition of their constituent sporopollenin. While they prove to have broadly similar structural characteristics, there are some significant differences between all types and particularly between the fossil and living material
Mechanistic understanding of ocean acidification impacts on larval feeding physiology and energy budgets of the mussel Mytilus californianus

: Ocean acidification (OA) — a process describing the ocean’s increase in dissolved carbon dioxide (p CO 2 ) and a reduction in pH and aragonite saturation state ( Ω ar ) due to higher concentrations of atmospheric CO 2 — is considered a threat to bivalve mollusks and other marine calcifiers. While many studies have focused on the effects of OA on shell formation and growth, we present findings on the separate effects of p CO 2 , Ω ar , and pH on larval feeding physiology (ini-tiation of feeding, gut fullness, and ingestion rates) of the California mussel Mytilus californianus . We found that elevated p CO 2 delays initiation of feeding, while gut fullness and ingestion rates were best predicted by Ω ar ; however, pH was not found to have a significant effect on these feeding processes under the range of OA conditions tested. We also modeled how OA impacts on initial shell development and how feeding physiology might subsequently affect larval energy budget components (e.g. scope for growth) and developmental rate to 260 μm shell length, a size at which larvae typically become pediveligers. Our model predicted that Ω ar impacts on larval shell size and ingestion rates over the initial 48 h period of development would result in a developmental delay to the pediveliger stage of >4 d, compared with larvae initially developing in supersaturated conditions ( Ω ar > 1). Collectively, these results suggest that predicted increases in p CO 2 and reduced Ω ar values may negatively impact feeding activity and energy balances of bivalve larvae, reducing their overall fitness and recruitment success.
Estimating Occurrence and Detection Probabilities for Stream-Breeding Salamanders in the Gulf Coastal Plain

Abstract Large gaps exist in our knowledge of the ecology of stream-breeding plethodontid salamanders in the Gulf Coastal Plain. Data describing where these salamanders are likely to occur along environmental gradients, as well as their likelihood of detection, are important for the prevention and management of amphibian declines. We used presence/absence data from leaf litter bag surveys and a hierarchical Bayesian multispecies single-season occupancy model to estimate the occurrence of five species of plethodontids across reaches in headwater streams in the Gulf Coastal Plain. Average detection probabilities were high (range = 0.432–0.942) and unaffected by sampling covariates specific to the use of litter bags (i.e., bag submergence, sampling season, in-stream cover). Estimates of occurrence probabilities differed substantially between species (range = 0.092–0.703) and were influenced by the size of the upstream drainage area and by the maximum proportion of the reach that dried. The effects of these two factors were not equivalent across species. Our results demonstrate that hierarchical multispecies models successfully estimate occurrence parameters for both rare and common stream-breeding plethodontids. The resulting models clarify how species are distributed within stream networks, and they provide baseline values that will be useful in evaluating the conservation statuses of plethodontid species within lotic systems in the Gulf Coastal Plain.
Potassium Intake of the U.S. Population, What We Eat In America, NHANES 2009–2010

Potassium is identified in the 2010 Dietary Guidelines for Americans as a nutrient to be increased in the diet, and the Institute of Medicine's Adequate Intake (AI) recommendation is set at 4,700 mg per day for adults. To describe the potassium intake of the U.S. population, data were analyzed from 1‐day food intakes of individuals 2+ years, excluding breastfed infants (N=9042) in What We Eat In America, NHANES, 2009–2010, and the contribution of different foods to population total potassium intake was determined. On the reporting day, the mean (SE) intake was 2640 (18) mg; adult males 20+ years (N=2789) consumed 3172 (44) mg and adult females 20+ years (N=2973) consumed 2408 (22) mg. Potassium density (mg/1000 kcal) was higher in the diets of females compared to males (p<0.0001). Compared to whites and Hispanics, blacks consumed less potassium (−338 mg, p<0.0001); there was no difference between intakes of whites and Hispanics. The top foods contributing to potassium intake were fruits and vegetables (20%), milk and milk drinks (11%), meats and poultry (10%), grain‐based mixed dishes (10%), coffee and tea (7%). By age, the highest contributors to potassium intake were milk and milk drinks for children 2–5 years (27%) and 6–11 years (22%), mixed dishes for adolescents 12–19 years (20%), and fruits and vegetables for adults 20+ years (21%). These data can inform monitoring of population dietary intake and dietary guidance.
ALLELOPATHIC ACTIVITY OF RYE (SECALECEREALE) AND COMMON VETCH (VICIAVILLOSA) ON CORN AND SOME WEED SPECIES

Biological management of weeds has become an interesting priority for many farmers and researchers across the globe. In order to determine germination and early growth response of some weed species and corn to presence of rye and common vetch residues in soil, an outdoor pot study was conducted at Faculty of Agriculture and Natural Resources, Razi University, Kermanshah, Iran in 2013. Treatments were included of addition of ground residues of rye and common vetch and a mixture of them to pots containing seeds of Echinochloacrus-galli, Setariaviridis, Chenopodium album, Amaranthusretroflexus, Xanthium strumarium, and Zeamays. According to the results addition of rye and common vetch residues resulted in reducing the shoot and root dry weight of all tested weeds while corn was not affected. Mixing residue of rye and common vetch resulted in the highest reduction of weight of shoot and root of all treated weed species. It can be suggested that incorporating of rye and common vetch residues into the soil can reduce the population and competition of weeds in corn. Both rye and common vetch selectively reduced weeds seed germination of weed species while corn was not significantly influenced
Towards a Customizable Framework for Evaluating Visualization Recommendations

—Visualization recommendation systems such as Voyager [40], VizDeck [20], SeeDB [37], and Foresight [11] have become popular in recent years. These systems use a variety of metrics to recommended visualizations to end users (e.g., data scientists and analysts). However, due to high variability in the design of recommendation algorithms, evaluations of these systems are often done in isolation, and lack standardization, potentially leading to biased outcomes. In this paper, we present a new framework to evaluate the recommendations these systems produce in a standardized, usable and unbiased manner. Our framework produces a score from 0 - 100, thereby allowing the user to make a determination as to which system they believe provides results most relevant to their work. Our framework incorporates a range of metrics derived directly from the visualization literature. Every component of the framework can be conﬁgured to better match different analysis scenarios and user goals. We present results from evaluating our framework through both individual case studies and surveying visualization experts, demonstrating the efﬁcacy of our framework in practice in ﬁve different visualization cases. We highlight lessons learned through the development and evaluation of our framework, and propose future research directions to further our goal of designing a robust, customizable, and easy-to-use metric for evaluating visualization recommendation systems.
Chalcones to control Alternaria alternata in murcott tangor fruits = Chalconas no controle de Alternaria alternata em frutos de tangor murcote

Alternaria brown spot (ABS), caused by the fungus Alternaria alternata pathotype tangerine, is one of the main phytosanitary problems for mandarin growers. About 15 applications per year of harmful fungicides are required for controlling ABS disease in citrus orchards. As chalcones seem to be less toxic to humans and environment than the commercial fungicides in use, this study initially aimed at synthesizing 137 chalcones through aldolic condensations between benzaldehydes and acetophenones. The resulting chalcones were screened for activity against A. altern ata through a fungal growth assay that was carried out in 96-cell polypropylene plates, using the same concentration to all studied substances. The four active chalcones underwent conidia germination and mycelial growth, which confirmed the antifungal activity of the compounds. These chalcones were then poured onto Murcott tangor fruit that had been inoculated with conidia of the fungus. All four chalcones reduced the ABS progress to values significantly smaller (P≤0.05) than that observed for the control. Statistical calculations showed that the best results were afforded by two compounds, bearing a 2,4,5-trimethoxyphenyl group at position 3 of prop-2-enal and a 3-nitro- or 3-hydroxyphenyl group at position 1 of the aldehyde. Such compounds reduced the incidence of the disease in Murcott tangor fruit to values that did not differ statistically from those obtained with a commercial fungicide.
GENE DUPLICATION ASSESSMENT AND SEQUENCE ANALYSIS OF CHALCONE SYNTHASE GENE IN PLANTS

Chalcone synthase gene is a key enzyme in the biosynthesis of flavonoids and isoflavonoids. This gene assumes several functions in plants such as protection against UV ray and defense against pathogenic factors. In this study, chalcone synthase gene was studied and evaluated in terms of evolutionary rate in 119 species of creatures such as agricultural plants as eukaryote creatures and bacteria as prokaryotes. The evolutionary analyses were performed using bioinformatics tools. After preparing the phylogenic tree, the evolutionary study and comparison were performed. Also divergent time of chalcone synthase gene was investigated in the agricultural plants and bacteria. This study led to obtaining two general conclusions: First, the evolutionary rate between two prokaryote and eukaryote groups is different over time, and second, considering the calculation of divergent time for the genome of prokaryotes from eukaryotes in the previous works, it is recommended to consider the Chalcone synthase gene duplication time as about 410 million years.
Effects of Site, Year, and Estimator Choice on Home Ranges of Bog Turtles (Glyptemys muhlenbergii) in Maryland

Abstract Bog Turtles (Glyptemys muhlenbergii) are some of the most imperiled turtles in North America, and because of threats posed by habitat loss and collection for the pet trade, the species currently is listed as threatened under the U.S. Endangered Species Act. Numerous studies have investigated home ranges and movements of this species, and reported home-range sizes have varied widely. Typically, these studies were conducted at different sites and used different home-range estimators, and these factors may influence home ranges. Few studies have assessed the impact of estimator choice on home-range size for Bog Turtles or how habitat changes have affected their movements. Our study investigated home-range sizes of female Bog Turtles at two sites in Maryland, using multiple home-range estimators. Female turtles were tracked using radiotelemetry between April and August in 2013 and 2014. Home-range sizes differed significantly between study sites but did not differ significantly between years. Choice of estimator had a significant effect on home-range size; 50% kernel and 95% minimum convex polygons were similar, but 95% kernels were significantly larger than 50% kernels or 95% polygons. A study conducted at one of our two study sites over 15 years ago reported smaller home-range sizes than were found in our study, perhaps indicating that habitat has deteriorated at that site.
Liver X receptors in cardiac hypertrophy

The heart responds to pathological stress by shifting myocardial substrate metabolism toward a greater reliance on glucose. Liver X receptors (LXRs) are nuclear receptors that play a central role in lipid and glucose metabolism. Although it has been suggested that pharmacological LXR activation may protect the heart, lipogenic side effects of current LXR agonists preclude their clinical applicability, while the heart-specific effects of LXRs in cardiac pathophysiology and metabolism remain unknown. For this, we created transgenic mice with cardiac-specific LXRα overexpression, and demonstrate that the cardioprotective effects of LXRα are indeed heart-specific in the attenuation of cardiac hypertrophy, myocardial fibrosis, and dysfunction. This was also confirmed in pharmacological studies using a novel high affinity LXR agonist, AZ876. LXRα transgenic mice were protected from diverse hypertrophic perturbations, such as chronic pressure overload, angiotensin II stimulation, and obesity-induced diabetes. Gene profiling analyses uncovered novel roles for LXRα in the regulation of several metabolic pathways. In response to hypertrophic stress, LXRα overexpression markedly enhanced the capacity for glucose uptake, whereas this adaptation was impaired in LXRα-deficient mice. Further, we identified increased glucose-O-GlcNAc-dependent signalling and regulation of natriuretic peptide expression to be a major protective mechanism in this respect. Overall, we believe these findings advance our current understanding of myocardial glucose metabolism and its role in cardiac protection, and highlight the potential therapeutic value of LXRs as a target for metabolic intervention in cardiac hypertrophy and heart failure.
Genetics and ecosystem effects of the invasive mussel Semimytilus algosus, on the West Coast of South Africa

11 Chapter 1 General introduction, aims and overview . 12 Chapter 2 Molecular identification of Semimytilus algosus, Aulacomya atra and an unknown invasive mussel from Lüderitz in comparisons of southern African and Chilean populations. 19 Chapter 3 Field surveys of Semimytilus algosus in South Africa: abundance, zonation and tolerance to wave exposure. 37 Chapter 4 Comparisons of life-history strategies of S. algosus and three other mussel species on the West Coast of South Africa . 55 Chapter 5 Field experiments assessing survival, growth, condition, recruitment and interactions between Semimytilus algosus and Mytilus galloprovincialis at different shore heights. 84 Chapter 6 Phylogeography of the invasive mussel Semimytilus algosus in South Africa relative to natural populations in Chile and Namibia. 126 Chapter 7 Synthesis and conclusions . 145
Weevil-fungus interaction on Amaranthus hybridus (Amaranthaceae) in South Africa : short communication

Amaranth (Amaranthus spp., Amaranthaceae) is a potentially valuable food crop, with both seed (Early 1985) and vegetable (Stallknecht & Schultz-Schaeffer 1991) varieties offering excellent possibilities for improving human nutrition, especially in impoverished semi-arid regions. Increasing interest in amaranth is ascribed to its high protein and mineral content, C4 photosynthetic pathway, high genetic diversity and phenotypic plasticity, and high degree of drought tolerance (Dowton 1972; Hauptli 1977; Jain et al. 1979; Kaufmann & Haas 1983). Studies to elucidate the biotic and abiotic factors that could affect successful cultivation of amaranth as a crop in South Africa were initiated during 1995.
Evaluation of the Effects of BT-Maize on Non-Target Insects Using a Demographic Approach

An experiment on life-table of the aphid on Bt-maize and isoline was performed. No significant differences were found between treatments. Differences in aphid performance were the lower adult and total longevity on the second generation, and the opposite trend of the pre-reproductive time that increased from the first to the second generation on isoline and decreased on Bt-maize. None of the demographic parameters analyzed showed significant differences. LTREs showed that this trend could be ascribed to a higher fecundity of young adult aphids of the second generation, probably connected to the lower pre-reproductive time. These differences could be the result of differences in chemical constituents. Analyses of secondary metabolites showed significant reduction of free polyphenols in Bt-maize. The experiment with the coccinellid H. variegata were performed evaluating the effects due to eating Cry1Ab toxin in maize pollen. No significant differences were found between GM and near-isogenic maize in all the parameter studied. Even if no significant, the reduced λ of H. variegata feeding on Bt-maize pollen, caused a population delay of 28 days. LTRE decomposition showed a lower egg and larval survival in the offspring of Bt pollen fed H. variegata, all contributing most on λ reduction. A bioassays were carried out in the greenhouse to assess the population-level responses of the coccinellid H. variegata, feeding on aphids reared on Bt-Maize and near-isogenic plants in a more realistic condition respect to laboratory trials. No differences in the mean number of eggs, larvae, pupae, and adults of H. variegata between Bt-maize and near-isogenic line. A higher number of pupae was found a week early in Bt-maize. No differences observed in H. variegata population growth rates between treatments. Using LTRE decomposition, the effect of Bt-maize exposition on λ have been decomposed into contributions arising from the effect on each stage-specific parameter.
The Domestication of Humans

The domestication of humans is not an issue of domesticity but of the effects of the domestication syndrome on a hominin species and its genome. These effects are well expressed in the ‘anatomically modern humans’, in their physiology, behavior, genetic defects, neuropathology, and distinctive neoteny. The physiological differences between modern (gracile) humans and their ancestors, robust Homo sapiens types, are all accounted for by the domestication syndrome. From deductions we can draw about early human behavior, it appears that modifications are attributable to the same cause. The domestication hypothesis ascribes the initiation of the changes to selective breeding introduced by the consistent selection of neotenous features. That would trigger genetic pleiotropy, causing the changes that are observed.