Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the fish assemblages in tidal salt marsh creeks and in adjoining mudflat areas in the Tejo estuary (Portugal)

Comparaison des assemblages ichtyques entre les chenaux de maree des marais sales et les vasieres contigues dans l'estuaire du Tage (Portugal). Une analyse comparative des communautes de poissons dans deux chenaux de maree de marais sales sous l'influence de la maree, ainsi que dans leurs secteurs contigus de bancs de vase, a ete realisee a partir de deux ans d'echantillonnages effectues au cours d'annees differentes en utilisant, respectivement, un verveux et un chalut a perche. La richesse specifique des poissons est plus elevee sur les vasieres (27 especes) que dans les chenaux de maree (14 especes). Liza ramada et Pomatoschistus microps sont plus abondantes dans les chenaux de maree, alors que P. microps et Pomatoschistus minutus le sont dans les secteurs contigus. Le modele de variation saisonniere est different entre les deux types d'habitat. Les principales differences sont observees lors de l'abondance maximale des especes residentes et pendant les periodes de colonisation de l'estuaire par les juveniles des especes marines qui l'utilisent comme nourricerie. Les resultats obtenus soulignent l'importance des chenaux de maree de marais dans l'estuaire pour certaines especes de poissons, en particulier pour leurs juveniles. Cet habitat est essentiellement utilise par ces especes en relation avec l'alimentation, ainsi que l'evitement de la predation.
Two-Stage Boosted Regression Tree Model to Characterize Southern Flounder Distribution in Texas Estuaries at Varying Population Sizes

Abstract Linking trends in fish population abundance to environmental characteristics is often difficult because fish use avariety of habitats throughout their ontogeny and may exhibit large interannual fluctuations in abundance. Wedeveloped a two-stage boosted regression tree model to investigate spatiotemporal patterns of Southern Flounder Paralichthys lethostigma abundance and distribution in Texas estuaries. We used a 36-year fishery-independent data set (1977–2012) to correlate distribution with environmental conditions and seasonal or long-term changes in abundance. Adult Southern Flounder were sampled with gill nets using a random-stratified design. Predictions of abundance were made to grids of environmental data to identify “hot spots” as well as seasonal or decadal shifts in distribution. Models were fit using cross validation, and variance was estimated using nonparametric bootstrapping. Depth, temperature, distance to a tidal inlet, and salinity were the primary environmental determinants of Southern Flounder distribution and abundance. Because distribution and response to environmental conditions can depend on population abundance, we also developed a standardized index of annual abundance using the same two-stage boosted regression tree model. The index identifies a long-term decline in abundance punctuated by recent recovery (possibly in response to management actions). Mapped results identify a coastwide decline in abundance between 1980–1984 and 2005–2009 but the magnitude varied substantially, suggesting disproportionate changes in abundance across the study area.
Biophysical modulation of peptide–membrane interactions

This chapter highlights current progress made in the elucidation of peptide–membrane interactions using model phospholipid membranes. The chapter covers specialist research findings published over the last few years to the time of its submission. It reviews literature sourced from different databases including Web of Science, RCSB Protein Data Bank and PubMed. A necessary reference to background information covers an unlimited timeframe. Naturally occuring and de novo peptide sequences with biologically relevant and membrane-mediated functions provide a primary focus of this discussion. Individual sections are arranged according to peptide–membrane models and measurement methods used for their characterisation, with a particular emphasis on spectroscopy measurements performed in solution. A number of mechanistic case studies are discussed in a separate section to give an overview of applied peptide–membrane systems.
Role of Xenobiotics and its Biodegradation

A xenobiotic is a synthetic foreign substance present in a living being which is not ordinarily normally created or exhibit inside the life form. Chemicals that are foreign to the biosphere are known as xenobiotic compounds. In particular, medications, for example, antibiotics are xenobiotics in humans because the human body does not deliver them itself, nor they part of a normal food. Natural compounds can likewise get to be xenobiotics on the off chance that they are taken up by another life form, for example, the uptake of normal human hormones by fish discovered downstream of sewage treatment plant outfalls, chemical defenses produced by some organisms as protection against predators. The body evacuates xenobiotics by xenobiotic metabolism. Xenobiotic organs would be created in a manner that they would not be rejected by the resistant framework. Any xenobiotics produce an assortment of natural impacts, which is utilized when they are portrayed utilizing bioassay. The term xenobiotic is likewise used to organs transplanted starting with one animal type to another.
BIOLOGY OF DISEASE - MACROPHAGES AND RENAL-DISEASE

In this multimodel overview, we have provided the seminal experimental evidence for the crucial contribution of macrophages in the progression of glomerular and interstitial fibrosis. Although all the experimental data provided in this review definitely increase our understanding of the progress of renal disease, we have been mindful to use caution in extrapolating data from animal experiments to the clinical setting (109). In addition, uncertainty still exists as to whether macrophages activation entails a generalized mechanism in which the cells release growth factors and other mediators such as bioactive lipids and nitric oxide simultaneously, or a selective mechanism in which the cells release some but not all macrophage products (110). However, we anticipate that further substantial clinical and experimental observations are on the horizon. Novel therapeutic strategies in these models must be concerned with the prevention of renal macrophage recruitment and/or the suppression of the fibrogenic ability of this pluripotential inflammatory cell.
Determination of SOD, POD, PPO and CAT Enzyme Activities in Rumex obtusifolius L.

Aims: The purpose of this study was to measure antioxidant enzyme (polyphenol oxidase, peroxidase, catalase and superoxide dismutase) activities of crude extract of Rumex obtusifolius L. in order to gain insight about this plant’s antioxidant potential. Study Design: The study was composed of the collection of plant material, extractions of the antioxidant enzymes, activity measurements of the enzymes and finally evaluation of the experimental results. Place and Duration of Study: Department of Chemistry (biochemistry laboratories), Faculty of Science and Arts of Sakarya University, between June 2015 and July 2015. Methodology: Enzymatic antioxidant activity of this plant was investigated by carrying out catalase, superoxide dismutase, peroxidase and polyphenol oxidase enzyme activity assays. Enzyme activities of the crude extract were measured by using spectrophotometric method. Optimum pH and temperature values of each enzyme were also determined for measurement of enzyme activities in ideal conditions. Results: Finally, our results showed that Rumex obtusifolius L. crude extract had good activity for all the enzymatic procedures tested. The activity levels of enzymatic antioxidants polyphenol oxidase, peroxidase, catalase and superoxide dismutase of the plant were found to be 12.8; 195.2; Original Research Article Alici and Arabaci; ARRB, 11(3): 1-7, 2016; Article no.ARRB. 29809 2 38.7; 11.6 EU/mL, respectively. Optimum pH and temperature values of all the enzymes (except PPO: optimum temperature 30°C) tested were also foun d to be 7.0 and 25°C, respectively. Conclusion: Our results demonstrate that this edible plant, Rumex obtusifolius L. , might be a potential source of natural antioxidants with good antioxidant enzyme capacity.
Effects of Food Processing on Mycotoxins.

Most data on mycotoxin contamination applies to agricultural products, such as grains, and could be used to assess human dietary intake of mycotoxins if the effects of food processing, storage and home cooking were known. Several factors - the nature of the process, the food matrix, moisture content of the foodstuff, additives, and mode and level of contamination - can affect experimental results on the decomposition or loss of mycotoxins during food processing. Additionally, the various mycotoxins that have been studied possess wide differences in stability. For example, during the making of bread from wheat flour, up to 100% of ergot alkaloids are destroyed, whereas vomitoxin is stable. Most research on processing of foods containing mycotoxins has been carried out with the aflatoxins, including studies on the sorting and roasting of peanuts, cleaning and milling of corn, the various stages in making vegetable oils, storage and cooking of meat, cooking of corn products, breadmaking, and (for aflatoxin M1) the processing of milk and cheese. In general, aflatoxins are moderately stable during roasting processes and persist into finished foods, such as peanut butter. Ochratoxin A, patulin, and vomitoxin and other trichothecenes have also received considerable attention. Little information is available on conversion products of mycotoxins during food processing.
Allelopathic activity of the picocyanobacterium Synechococcus sp. under varied light, temperature, and salinity conditions

The impact of environmental factors and mode of action of allelopathic compounds produced by picocyanobacteria on microalgae remains unknown. Therefore, it is essential to characterize allelopathic interactions under different experimental conditions. In this study, the influence of allelopathic activity on the diatom Navicula perminuta was investigated by the addition of cell-free filtrate of picocyanobacterium Synechococcus sp. cultures grown under different light, temperature, and salinity conditions. Temperature affected the most the donor cyanobacterium by increasing its allelopathic activity. The highest decline in growth, fluorescence parameter Fv/Fm and maximal photosynthesis Pm were observed after the addition of cell-free filtrate obtained from Synechococcus sp. grown at 190 μmol photons · m−2 · s−1, 25°C and 8 PSU. These studies indicate for the first time that the picocyanobacterium Synechococcus sp. affect coexisting diatom N. perminuta negatively. It was examined that the Synechococcus sp. reveals allelopathic activity on the photosynthesis and chlorophyll fluorescence, which results in the inhibition of growth of analyzed microalgae. These findings indicate that the production of allelopathic substances by picocyanobacterium is regulated by the availability of environmental factors such as light, temperature, and salinity. Moreover, these results demonstrated that variation in light intensity, water temperature, and salinity should be considered when estimating the potential effects of cyanobacterial allelopathy in aquatic environments.
Molecular interactions of zinc with the glycine receptor

The ionotropic receptors including nicotinic acetylcholine (nAChR), y-aminobutyric acid type A and C (GABAa/c), serotonin (5HT-3) and glycine receptors (GlyR) all comprise the cys-loop receptor family. A pentameric configuration is adopted by these receptors featuring a large extra cellular domain, four transmembrane (M) spanning domains and an intracellular compartment primarily contributed from the M3-4 loop. The recent advent of an X-ray crystal structure of the related ACh binding protein from snail, Lymnaea stagnalis, and an electron micrograph nearing atomic resolution of the transmembrane domains for the Torpedo nAChR provide the opportunity to homology model the structures of all cys-loop ligand-gated receptors and investigate critical elements of receptor function with unprecedented accuracy. By using homology modelling to guide site-directed mutagenesis in combination with whole-cell patch clamp electrophysiology, molecular elements that mediate the biphasic modulation of glycine receptors by Zn2+ were investigated. The structure of a previously identified low sensitivity inhibitory Zn2+ site was clarified revealing critical determinants of GlyR subtype selectivity for Zn2+ mediated inhibition. Intriguingly these experiments also revealed a novel functional asymmetry at this site suggesting that one specific side of the site directs downstream transduction of the inhibitory Zn2 effect. This enabled the elucidation of a hydrophobic pathway leading directly through the core of the GlyR from the inhibitory Zn2+ site to the agonist binding site suggesting a mechanism for Zn2+ mediated inhibition. This study also investigated the structural basis for Zn2* enhancement of GlyR function. A comparative study of GlyR al and a2 followed by a directed mutagenesis regional scan led to the identification of a complete and novel site for Zn2+ potentiation. Further studies also elucidated a potential mechanism of action for this site by identifying an important gating component of the GlyR, which exhibited a strong interaction with this novel potentiation site for Zn2+. These studies demonstrate the power of a homology modelling strategy to resolve key elements of cys-loop ligand-gated receptor function. Identifying and understanding receptor modulation by allosteric effectors is a key requisite to understanding receptor function. This work describes the key structural determinants involved in the biphasic Zn2+ modulation of GlyRs both in terms of actual binding sites and downstream effector mechanisms.
An Induced Mutant Line Lacking the α-subunit of β-conglycinin in Soybean [Glycihe max (L.) Merrill]

We identified a novel mutant line lacking an α-subunit. The line was obtained by subjecting to gamma-ray irradiation Kari-kei 434, a genetically fixed line with a low level of β-conglycinin which is characterized by the absence of the α '-subunit and low levels of both the α -and β-subunits of β -conglycinin, one of the major soybean storage pro-teins. The mutant line which lacks both the α - and α '-subunits went through two generations without displaying any physiological abnormalities. We concluded that the induced trait characterized by the lack of the α -subunit is truly inherited.
Winter Cover Crops and Nitrogen Management in Sweet Corn and Broccoli Rotations

Cover crops hold potential to improve soil quality, to recover residual fertilizer N in the soil after a summer crop that otherwise might leach to the groundwater, and to be a source of N for subsequently planted vegetable crops. The objective of this 5-year study was to determine the N uptake by winter cover crops and its effect on summer vegetable productivity. Winter cover crops [red clover (Trifolium pratense L.), cereal rye (Secale cereale L. var. Wheeler), a cereal rye/Austrian winter pea (Pisum sativum L.) mix, or a winter fallow control] were in a rotation with alternate years of sweet corn (Zea mays L. cv. Jubilee) and broccoli (Brassica oleracea L. Botrytis Group cv. Gem). The subplots were N rate (zero, intermediate, and as recommended for vegetable crop). Summer relay plantings of red clover or cereal rye were also used to gain early establishment of the cover crop. Cereal rye cover crops recovered residual fertilizer N at an average of 40 kg.ha -1 following the recommended N rates, but after 5 years of cropping, there was no evidence that the N conserved by the cereal rye cover crop would permit a reduction in inorganic N inputs to maintain yields. Intermediate rates of N applied to summer crops in combination with winter cover crops containing legumes produced vegetable yields similar to those with recommended rates of N in combination with winter fallow or cereal rye cover crops. There was a consistent trend (P < 0.12) for cereal rye cover crops to cause a small decrease in broccoli yields as compared to winter fallow.
Transient facial sensory symptoms following exposure to synthetic pyrethroids: a clinical and electrophysiological assessment.

: Amongst twenty-three workers exposed to synthetic pyrethroids, ninteen had experienced one or more episodes of abnormal facial sensation, developing between thirty min and three hr after exposure and persisting for thirty min to eight hr. There were no abnormal neurological signs and electrophysiological studies were normal in the arms and legs. It is concluded that the symptoms are most likely to be due to transient lowering of the threshold of sensory nerve fibres or sensory nerve endings following exposure of the facial skin to pyrethroids, similar to the phenomena that have been described following exposure of animal nerves to pyrethroids.
Arsenic-induced metabolic disturbances and their mitigation mechanisms in crop plants: A review

Abstract Arsenic (As) is one of the highly toxic metalloids distributed ubiquitously in nature. Two inorganic forms of As are present abundantly: arsenite (AsIII) and arsenate (AsV), former being 100 times more toxic than latter. Arsenic is a well known inducer of reactive oxygen species (ROS) in crop plants either directly during conversion of AsV to AsIII or indirectly via inactivation of the antioxidants by binding to their thiol groups. Arsenic-mediated oxidative stress causes an array of metabolic dysfunctions in plants. Therefore, in recent years, demonstration of various mechanisms to improve crop productivity and/or alleviation of As toxicity has become a prime concern. Modulation of cellular thiol molecules for protection against ROS-induced damage has been used as a strategy against As. Accrual of proline, polyphenols and exogenous application of salicylic acid, nitric oxide, phosphate and potassium show protection against As-mediated injuries in crop plants. Proline, nitric oxide and salicylic acid display defensive functions by activating antioxidant machinery of crop plants whereas phosphate and potassium reduce As toxicity by controlling As-uptake or maintaining cellular protein and antioxidant enzymes in plants. Likewise, polyphenols serve as antioxidants and reduce activities of ROS synthesizing enzymes, thereby confering As-stress tolerance. In this review we have attempted to collate recent advances on 1) mechanism(s) of As uptake by plants, 2) toxicity responses [physiological, biochemical and molecular] exerted by As, and 3) roles of varied molecules in amelioration of As effects in crop plants. Gaps in the existing knowledge and future research prospects have also been highlighted in this review.
Evaluating confidence in climate‐based predictions of population change in a migratory species

Aim Forecasting ecological responses to climate change is a common objective, but there are few methods for evaluating confidence in such predictions. For migratory species, in particular, it is also essential to consider the extent of spatial synchrony among separate breeding populations in range-wide predictions. We develop a quantitative method to evaluate the accuracy of climate-based ecological predictions and use this approach to assess the extent of spatio-temporal synchrony among distinct regions within the breeding range of a single migratory population. Location We model weekly site-specific summer abundances (1996–2011) of monarch butterflies (Danaus plexippus) in the Midwestern USA as a function of climate conditions experienced during a shared spring migration/breeding phase in Texas and separate summer recruitment periods in Ohio and Illinois. Methods Using negative binomial regression models, we evaluate spatio-temporal synchrony between monarchs in the two states and develop a novel quantitative assessment approach to determine the temporal predictive strength of our model with Bayesian P-values. Results Monarchs breeding in the Midwest exhibit spatio-temporal synchrony in Ohio and Illinois; cooler spring temperatures, average to above average precipitation in Texas and cooler than average summer temperatures are associated with higher population abundances in both states. At least 10 years of data are needed for adequate model predictability of average future counts. Because annual spring weather conditions in Texas primarily drive yearly abundances, as opposed to localized summer effects, year-specific counts are often difficult to predict reliably, specifically when predictive spring conditions are outside the range of typical regional conditions. Main conclusions Our assessment method can be used in similar analyses to more confidently interpret ecological responses to climate change. Our results demonstrate the relative importance of climatic drivers in predicting abundances of a migratory species and the difficulties in producing reliable predictions of animal populations in the face of climate change.
Charged hadron transverse momentum distributions in Au+Au collisions at $\sqrt{s_{_{NN}}} =$ 200 GeV

We present transverse momentum distributions of charged hadrons produced in Au+Au collisions at $\sqrt{s_{_{NN}}} =$ 200 GeV. The evolution of the spectra for transverse momenta $p_T$ from 0.25 to 5 GeV/C is studied as a function of collision centrality. We find a significant change of the spectral shape between proton-antiproton and peripheral Au+Au collisions. When comparing peripheral to central Au+Au collisions, we find that the yields at the highest $p_T$ exhibit approximate scaling with the number of participating nucleons, rather than scaling with the number of binary collisions.
Occurrence of some nematode parasites in the gastrointestinal tract of Ariidae (Teleostei: Siluriformes) catfish, Arius arius (Hamilton, 1822) from Karachi coast

Current study was carried out in December, 2014 to investigate the occurrence of helminth parasites in catfish species belonging to family Ariidae (Blecker, 1862). Four species of catfishes namely Arius arius (Hamilton, 1822), Arius caelatus (Valenciennes, 1840), Arius dussumieri (Valenciennes, 1840) and Arius sona (Hamilton, 1822) off the Karachi coast were screened for the occurrence of helminth parasites. Fish were examined after washing contents of gastrointestinal tract and observed under light microscope with the help of regular parasitological methods. The nematode parasites namely; Raphidascaris acus (Bloch, 1779) larvae, Metabronema magnum (Taylor, 1925), Haplonema immutatum (Ward et Magath, 1917) and Hedruris bryttosi (Yamaguti, 1935) were recorded from the gut of the catfish, Arius arius (Hamilton, 1822). These are new host records as these parasites have not been reported from Arius arius species in the region, off the Karachi coast
Effects of Nickel and Cadmium Contaminated Fish Meat on Chromosomal Aberrations and Sperm Morphology of Swiss Albino Mice

Two heavy metals Ni and Cd were determined in a freshwater fish, Barbus xanthopterus using 700-atomic absorption: the highest values were found to be (82.1 12 µg g-1), and (4.702 µg g-1), respectively. Flesh of this fish was fed to mice in two groups for each two periods (1 and 2 months) to monitor chromosomal aberrations and sperm morphology. In Group (1) first period: the ring chromosome (3.2 ± 0.200) and centromeric gap (2.9 ± 0.314) have the highest value of aberration type, while the lowest value was chromatid break (0.0 ± 0.000), in second period: the centromere gap (4 ± 0.333) and chromatid gap (3.4 ± 0.266) have the highest value of aberration type, while the lowest value was polyploidy (0.6 ± 0.266). In Group (2) first period: the highest value of abnormality type was sperm without tail (4.9 ± 0.276) swollen head sperm (4.1 ± 0.622) and sperm without hook (3.9 ±0.433), while the lowest value was blunt hook sperm (0.0 ±0.000). In second period: the highest value of abnormality type was defective head sperm (4.2± 0.416), sperm without tail (3.7 ± 0.488) and swollen head sperm (3.7 ±0.667), and the lowest value was blunt hook sperm (1.0 ±0.421).