Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutamine synthetase in broccoli (Brassica oleracea) is regulated in vivo by reciprocal cooperativity

Summary • Purified enzymes are known to exhibit either noncooperative or cooperative kinetics, with respect to their substrates. In all cases, enzyme activity increases with substrate concentration up to saturation. Here, we report a different kinetic pattern of a regulated enzyme: reciprocal cooperativity. • Broccoli plants (Brassica oleracea var. italica) were grown hydroponically in six nutrient solutions whose N concentrations ranged from deficient to toxic levels. Crude extracts, from leaves and roots of whole plants, were assayed for glutamine synthetase (GS) transferase activities at four developmental stages. • A negative exponential model was fitted to the mean effect of nitrogen availability on GS activity and a reciprocal activity coefficient (RAC) was defined as the reciprocal of the regulated GS activity when N was scarce. RACs were lowest in the presence of N at 25 mg l−1 and at the 30-d developmental stage. • These observations suggest that the RAC offers great potential as the basis for selection of isoenzymes or genotypes best adapted to low N environments. We have suggested an evolutionary and physiological basis for reciprocal cooperativity and have elaborated on three likely mechanisms for regulation of GS, based on substrate inhibition, feedback inhibitors and oxidative modification by endogenous oxidases.
Protection of chicks against environmental challenge with Salmonella enteritidis by ‘competitive exclusion’ and acid‐treated feed

‘Competitive exclusion’ treatment protected chicks against an environmental challenge with Salmonella enteritidis phage type 4, whether or not feed containing antimicrobial organic acids was also used. Treatment reduced the incidence of Salmonella‐positive caecal samples from 82 to 8%, with a corresponding reduction in liver infection from 52 to 13%. Although acid‐treated feed had no influence on an environmental challenge with salmonellas, its compatibility with ‘competitive exclusion’ suggests an advantage in their combined use to maximize protection of poultry against Salmonella infection.
Effect of mesoionic 4-phenyl-5-(cinnamoyl)-1,3,4-thiadiazolium-2-phenylamine chloride derivative salts on the activities of the nitric oxide synthase and arginase of Leishmania amazonensis

l-arginine is involved in the production of both nitric oxide (NO), mediated by nitric oxide synthase (NOS) and l-ornithine, by arginase activity. It is generally accepted that NO regulation occurs mainly at the transcriptional level of NOS. In a previous work we purported that there is evidence that Leishmania sp. can produce NO from l-arginine. An arginase activity in its gene sequence has also been reported in Leishmania parasites. In a search for intracellular targets as potential antileishmanicidal agents, such as the l-arginine metabolism, we used 1,3,4-thiadiazolium mesoionic compounds, that have been demonstrated to be cytotoxic to the Leishmania amazonensis, when compared to Pentamidine isethionate as a reference drug. Parasites were assayed in absence/presence of 4′- and 3′- methoxy mesoionic derivatives in order to verify the effect on NO production and arginase activity in L. amazonensis. The results indicated that the drugs reduce from 70 to 90% of the NO production by the parasite and act on a soluble nitric oxide synthase purified from L. amazonensis promastigotes and axenic amastigotes.
Identifying the Responses from the Estrogen Receptor-Expressed MCF7 Cells Treated in Anticancer Drugs of Different Modes of Action Using Live-Cell FTIR Spectroscopy

Recently, we have shown that changes in Fourier transform infrared (FTIR) spectra of living MDA-MB-231 cells (a triple negative cell line) upon exposure to anticancer drugs reflect the changes in the cellular compositions which are correlated to the modes of action of drugs. In the present study, MCF7 cells (an estrogen receptor expressing breast cancer cell line) were exposed to three anticancer drugs belonging to two well-characterized anticancer classes: selective estrogen receptor modulators (SERMs) and DNA-intercalating agent. First, we evaluated if the changes in the spectrum of cells are according to the modes of action of drugs and the characteristics of the MCF7 cell line in the same way as the MDA-MB-231 cell. Living MCF7 cells were treated in the three drugs at half maximal inhibitory concentration (IC50), and the difference spectra were analyzed using principal component analysis (PCA). The results demonstrated clear separation between tamoxifen/toremifene (SERM)-treated cells from the doxorubicin (DNA-intercalator)-treated and untreated cells (control). Tamoxifen and toremifene induced similar spectral changes in the cellular compositions of MCF7 cells and lead to the clustering of these two drugs in the same quadrant of the principal component 1 (PC1) versus PC2 score plots. The separation is mostly attributed to their similar modes of actions. However, doxorubicin-treated MCF7 cells highlighted spectral changes that mainly occur in bands at 1085 and 1200–1240 cm–1, which could be associated with the DNA-intercalation effects of the drug. Second, the pairwise PCA at various individual time points was employed to investigate whether the spectral changes of MCF7 and MDA-MB-231 cells in response to the IC50 of tamoxifen/toremifene and doxorubicin are dependent on the characteristics of the cell lines. The estrogen-expressing MCF7 cells demonstrated significant differences in response to the SERMs in comparison to the triple negative MDA-MB-231 cells, suggesting that different modes of action have taken place in the two tested cell lines. In contrast, the doxorubicin-treated MDA-MB-231 and MCF7 cells show similar changes in 1150–950 cm–1, which indicates that the DNA intercalation effect of doxorubicin is found in both cell lines. The results have demonstrated that live-cell FTIR analysis is sensitive to the different modes of action from the same drugs on cells with different characteristics.
Automated brain segmentation methods for clinical quality MRI and CT images

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder associated with brain tissue loss. Accurate estimation of this loss is critical for the diagnosis, prognosis, and tracking the progression of AD. Structural magnetic resonance imaging (sMRI) and X-ray computed tomography (CT) are widely used imaging modalities that help to in vivo map brain tissue distributions. As manual image segmentations are tedious and time-consuming, automated segmentation methods are increasingly applied to head MRI and head CT images to estimate brain tissue volumes. However, existing automated methods can be applied only to images that have high spatial resolution and their accuracy on heterogeneous low-quality clinical images has not been tested. Further, automated brain tissue segmentation methods for CT are not available, although CT is more widely acquired than MRI in the clinical setting. For these reasons, large clinical imaging archives are unusable for research studies. In this work, we identify and develop
The Macroinvertebrates of Ruppia (Widgeon Grass) Beds in a Small Maine Estuary

Abstract Little information exists on macroinvertebrate community composition in small, micro-tidal, Ruppia maritima (widgeon grass)-dominated Maine estuaries. Qualitative and quantitative assessments of the macroinvertebrate fauna of widgeon grass beds in Northeast Creek estuary (Acadia National Park, ME) are presented here. The community was dominated by euryhaline freshwater invertebrates including midge larvae (Chironomidae: Dicrotendipes, Cricotopus, Chironomus), oligochaetes, damselfly larvae (Coenagrionidae: Enallagma), amphipods (Gammaridae: Gammarus), gastropods (Hydrobiidae: Hydrobia), ostracods (Cytheridae: Cyprideis), and water boatmen (Corixidae: Trichocorixa). Macroinvertebrate abundances at the sampled sites were 35,100 individuals/m2 in both August and September, and 22,200 individuals/m2 in October. This study provides baseline faunal-community data that can be used in future monitoring studies.
Effect of Phosphorylated Tau on Cortical Pyramidal Neuron Morphology during Hibernation

Abstract The dendritic spines of pyramidal cells are the main postsynaptic target of excitatory glutamatergic synapses. Morphological alterations have been described in hippocampal dendritic spines during hibernation—a state of inactivity and metabolic depression that occurs via a transient neuronal tau hyperphosphorylation. Here, we have used the hibernating Syrian hamster to investigate the effect of hyperphosphorylated tau regarding neocortical neuronal structure. In particular, we examined layer Va pyramidal neurons. Our results indicate that hibernation does not promote significant changes in dendritic spine density. However, tau hyperphosphorylated neurons show a decrease in complexity, an increase in the tortuosity of the apical dendrites, and an increase in the diameter of the basal dendrites. Tau protein hyperphosphorylation and aggregation have been associated with loss or alterations of dendritic spines in neurodegenerative diseases, such as Alzheimer’s disease (AD). Our results may shed light on the correlation between tau hyperphosphorylation and the neuropathological processes in AD. Moreover, we observed changes in the length and area of the apical and basal dendritic spines during hibernation regardless of tau hyperphosphorylation. The morphological changes observed here also suggest region specificity, opening up debate about a possible relationship with the differential brain activity registered in these regions in previous studies.
An assessment of Chironomidae as quantitative indicators of past climatic change

The distribution among Labrador (Canada) lakes of remains from 21 chironomid taxa was analysed by means of canonical correspondence analysis (CCA). Tests with partial CCA of three hypotheses revealed that the distributions of chironomid taxa were significantly correlated with summer surface-water temperature and maximum lake depth, but not sediment organic content. In addition, an exploratory CCA revealed possible relationships of chironomid fauna with residual longitude and Fe concentration. A weighted-averaging-regression/calibration model of the chironomid–temperature relationship (derived from a temperature-constrained CCA) allowed the summer surface-water temperature of lakes to be inferred from chironomid remains. Accurate quantitative reconstructions of late glacial and Holocene temperature variations should be possible from fossil Chironomidae.
Membrane lipid dynamics and lipid peroxidation in the early stages of low-temperature sweetening in tubers of Solanum tuberosum

Sugar accumulation and membrane lipid parameters associated with membrane permeability in chilling injury and senescence were followed in the early stages of low-temperature sweetening in Solanum tuberosum tubers to monitor their dynamics. Norchip, a low-temperature sweetening-susceptible potato cultivar, and North Dakota 860-2, a low-temperature sweetening-tolerant selection, were stored for 55 days at 4 and 12°C. Sugar accumulations were not linear and were characterized by fluctuations or cycles over storage time. Sucrose cycling and accumulation were greatest for Norchip tubers stored at 4°C as compared to the other treatments. Increases in membrane permeability were not detected by increases in electrolyte leakage. No significant changes in the phospholipid, galactolipid, free sterol levels or phospholipid to free sterol ratio were observed. The double bond index obtained from the fatty acid profiles of the total lipid fraction decreased significantly (decreased unsaturation) for Norchip tubers at 4°C over time. Free fatty acid and diene conjugation values fluctuated and increased over time for all treatments with greater amplitude of fluctuations observed for Norchip tubers stored at 4°C. These latter effects may be due to the high levels of lipid acyl hydrolase and lipoxygenase found in potato tubers. When free fatty acid and diene conjugation values were plotted with glucose accumulation over time, a possible relationship among the variables was revealed. The observed peroxidation products could relate low-temperature stress and the resultant low-temperature sweetening to chilling injury and drought stress. The anti-oxidative potential of potato tubers should be considered for future cultivar development as a mechanism to lessen the severity or rate of low-temperature sweetening development.
The Contribution of Stressful Marital Interactions to Loneliness and Health across Mid-life and Later Adulthood

Although past research has noted longitudinal, and sometimes bi-directional, associations between marital interactions, loneliness, and physical health, previous work has not identified long-term associations and differential associations over life-course stages (i.e., mid-life and later adulthood). Utilizing a life-course stress process perspective and a sample of 250 couples in enduring marriages over 17 years (2001–2017), a structural equation model within a dyadic framework assessed the unique influences of stressful marital interactions on loneliness and physical health and the variation in bi-directional influences of loneliness and physical health over time. Marital interactions were relatively stable across life stages, yet marital interactions appear to influence loneliness and physical health. Notable distinctions were evident across life stages (from mid-life to later adulthood and then within later adulthood). Findings are discussed with an emphasis on the implications for health promotion and prevention programs targeting couples’ quality of life in later years.
Perceived predation risk, parasitism, and the foraging behavior of a freshwater snail (Potamopyrgus antipodarum)

Foraging behavior can be influenced by such factors as predation risk, individual size, and parasite infection. Snails (Potamopyrgus antipodarum) placed in tanks with large rocks were exposed to four types of water: (1) water with crushed snails, (2) water from a tank in which fish (Gobiomorphus cotidianus) were fed only trout chow, (3) water from a tank where the fish were also fed snails, and (4) plain water. Snails could respond by moving to the top of rocks (where algal food was present) or to the bottom of rocks (where the predation risk was lower). The snails responded to fish chemicals by moving to the bottom of rocks. The response was dependent on snail size and fish diet. Smaller snails moved to the bottom of rocks more than larger snails did. Trematode-infected snails were found on top of the rocks more than other classes of snails, but infected snails still moved to the bottom of rocks in response to the fish predator. Snails eaten by fish in the field tend to be smaller than snails in the over.
Effects of nitrogen fertiliser on tree/pasture competition during the establishment phase of a silvopastoral system

Summary The establishment phase of an upland silvopastoral system was studied to examine the growth and nutrition of wild cherry (Prunus avium L.) trees under different nitrogen fertiliser treatments. High rates of nitrogen fertiliser exacerbated competition between trees and pasture in a dry year when low fertiliser treatments produced faster tree height growth. When herbicides were not used to control grass growth after the third growing season, tree growth was significantly reduced showing that below-ground competition may be a significant factor on stony upland soils. Tree growth was correlated with foliar nitrogen concentrations and not soil water, suggesting competition for soil nitrogen reduced tree growth. The importance of the interaction of fertiliser use with competition is considered in relation to successful establishment.
Sweet on biomineralization : effects of carbohydrates on the early stages of calcium carbonate crystallization

The present study aims to elucidate the effects of different carbohydrates on the early stages of calcium carbonate mineralization by following a systematic potentiometric titration-based approach. Distinct mono-, oligo- and polysaccharides were evaluated with respect to their influence on the formation of solute pre-nucleation clusters, the nucleation process itself, and the solubility of the initially precipitated phase. By assaying 29 carbohydrates, we show that sugar stereochemistry, polarity, presence of Ca 2+ binding sites, as well as the nature of glycosidic linkages can play an important role in the interactions between the additives and the mineral species occurring in the course of CaCO 3 crystallization from solution.
Overview of H-Formulation: A Versatile Tool for Modeling Electromagnetics in High-Temperature Superconductor Applications

This paper reviews the modeling of high-temperature superconductors (HTS) using the finite-element method (FEM) based on the <inline-formula> <tex-math notation="LaTeX">$\boldsymbol {H}$ </tex-math></inline-formula>-formulation of Maxwell’s equations. This formulation has become the most popular numerical modeling method for simulating the electromagnetic behavior of HTS, especially thanks to the easiness of implementation in the commercial finite-element program COMSOL Multiphysics. Numerous studies prove that the <inline-formula> <tex-math notation="LaTeX">$\boldsymbol {H}$ </tex-math></inline-formula>-formulation is able to simulate a wide scope of HTS topologies, from simple geometries such as HTS tapes and coils, to more complex HTS devices, up to large superconducting magnets. In this paper, we review the basics of the <inline-formula> <tex-math notation="LaTeX">$\boldsymbol {H}$ </tex-math></inline-formula>-formulation, its evolution from 2D to 3D, its application for calculating critical currents and AC losses as well as magnetization of HTS bulks and tape stacks. We also review the use of the <inline-formula> <tex-math notation="LaTeX">$\boldsymbol {H}$ </tex-math></inline-formula>-formulation for large-scale HTS applications, its use to solve multi-physics problems involving electromagnetic-thermal and electromagnetic-mechanical couplings, and its application to study the dynamic resistance of superconductors and flux pumps.
National Set of MAES Indicators in Greece: Ecosystem Services and Management Implications

Research Highlights: The developed National Set of Indicators for the Mapping and Assessment of Ecosystems and their Services (MAES) implementation in Greece at the national level sets the official, national basis on which future studies will be conducted for MAES reporting for the achievement of targets within the National and the European Union (EU) biodiversity Strategy. Background and Objectives: Greece is currently developing and implementing a MAES nation-wide program based on the region’s unique characteristics following the proposed methodologies by the European Commission, in the frame of the LIFE-IP 4 NATURA project (Integrated actions for the conservation and management of Natura 2000 sites, species, habitats and ecosystems in Greece). In this paper, we present the steps followed to compile standardized MAES indicators for Greece that include: (a) collection and review of the available MAES-related datasets, (b) shortcomings and limitations encountered and overcome, (c) identification of data gaps and (d) assumptions and framework setting. Correspondence to EU and National Strategies and Policies are also examined to provide an initial guidance for detailed thematic studies. Materials and Methods: We followed the requirements of the EU MAES framework for ecosystem services and ecosystem condition indicator selection. Ecosystem services reported under the selected indicators were assigned following the Common International Classification of Ecosystem Services. Spatial analysis techniques were applied to create relevant thematic maps. Results: A set of 40 MAES indicators was drafted, distributed in six general indicator groups, i.e., Biodiversity, Environmental quality, Food, material and energy, Forestry, Recreation and Water resources. The protocols for the development and implementation of an indicator were also drafted and adopted for future MAES studies in Greece, providing guidance for adaptive development and adding extra indicators when and where needed. Thematic maps representing ecosystem services (ES) bundles and ES hotspots were also created to identify areas of ES importance and simultaneously communicate the results at the national and regional levels.
Do pre-visit preparation and post-visit activities improve student outcomes on field trips?

Abstract Studies of individual environmental education (EE) field trip programs have found that pre-visit preparation and post-visit follow-up activities can enhance desired student outcomes. We examined these relationships across a broad sample of single-day EE field trip programs for adolescent youth (grades 5-8) across the United States. We measured student outcomes, reflecting environmental literacy, 21st century skills, positive youth development, and student learning, through end-of-visit retrospective student surveys and follow-up surveys with visiting teachers two weeks after the field trip. Pre-visit logistical preparation as well as both pre-visit preparation and post-visit follow-up related to the subject matter were each associated with more positive student outcomes. The study provides further evidence across a large sample of programs that pre-visit preparation and post-visit follow-up can have meaningful impacts on student outcomes for EE field trips. We discuss the implications of the findings and provide examples and guidance for future programming efforts.
Bacteria, fungi and the breakdown of leaf litter in a large river

We examined the dynamics of leaf mass loss and microbial biomass associated with decomposing leaf litter in a seventh order river. This was in an attempt to test the hypothesis that fungal contribution to the breakdown process is less important in major rivers than was previously found for headwater streams. Bacterial biomass was estimated from direct cell counts coupled with determinations of bacterial biovolumes. Fungal biomass was estimated on the basis of ergosterol measurements, species-specific conversion factors, and the relative abundance of the dominant fungal species. Sporulation rates of aquatic hyphomycetes were determined by counting conidia released from leaf litter during brief laboratory incubations. Compared to low-order streams, the breakdown of willow, poplar and plane leaves was slow with exponential decay coefficients k ranging from 0.0045 to 0.0091 d-'. Numbers of bacteria first increased exponentially on all leaf species but reached a plateau of almost 108 cells per mg AFDM after 4-8 weeks of leaf submergence. This corresponds to a peak bacterial biomass of 0.3-0.5% of detrital carbon. Fungal biomass attained peaks of 5-10% of detrital carbon after 4-8 weeks and greatly exceeded bacterial biomass at any instance. On average, fungi accounted for 96% of the total microbial (fungal plus bacterial) biomass in leaf litter. Dynamics of sporulation rates of aquatic hyphomycetes were characterized by early peaks of 1.2-1.4 conidia µg-' AFDM d-', followed by sharp declines to about 0.2 µg-' d-'. Peaks occurred before the corresponding peaks in fungal biomass. Rough organic matter budgets suggest that fungi assimilated a minimum of 16-23% of the initial leaf carbon, and accounted for 42-65% of the overall carbon loss from leaves during periods of highest fungal activity. Taken together, these findings indicate that fungi play an eminently important role in the biological transformation of leaf litter even in major rivers. Bacterial contribution is likely to be small in spite of increases in biomass at advanced stages of breakdown. With regard to leaf decomposition, large fluvial systems would thus appear to behave like their headwater counterparts, suggesting that the present results can be generalized for lotic ecosystems.