Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth factors and kinases in glioblastoma growth

Glioblastoma multiforme (GBM) is the most aggressive type of brain cancer, having the highest invasion, migration, proliferation, and angiogenesis rates. Several signaling pathways are involved in the regulation of these processes including growth factors and their tyrosine kinase receptors, such as vascular endothelial growth factor (VEGF), transforming growth factor beta (TGFβ), fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), and insulin-like growth factor–I (IGF–I). Different kinases and regulators also participate in signaling pathways initiated by growth factors, such as mitogen-activated kinases (MAPK), protein kinases C (PKC), phosphatidylinositol-3 kinases (PI3K), protein kinase B (PKB or Akt), glycogen synthase kinase 3β (GSK3β), the mTOR complex, and Bcl-2. In this review, we will focus on the role of these proteins as possible therapeutic targets in GBM.
DNA demethylation through 5-methylcytosine excision. Molecular basis and potential applications

Active DNA demethylation is crucial for epigenetic control, but the underlying enzymatic mechanisms are incompletely understood. REPRESSOR OF SILENCING 1 (ROS1) is a 5-methylcytosine (5-meC) DNA glycosylase/lyase that initiates DNA demethylation in plants through a base excision repair process. The enzyme binds DNA nonspecifically and slides along the substrate in search of 5-meC. In this work, we have used homology modelling and biochemical analysis to gain insight into the mechanism of target location and recognition by ROS1. We have found that three putative helix-intercalating residues (Q607, R903 and M905) are required for processing of 5-meC:G pairs, but dispensable for excision of mismatched 5-meC. Mutant proteins Q607A, R903A and M905G retain the capacity to process an abasic site opposite G, thus suggesting that all three residues play a critical role in early steps of the base extrusion process and likely contribute to destabilization of 5meC:G pairs. While R903 and M905 are not essential for DNA binding, mutation of Q607 abrogates stable binding to both methylated and nonmethylated DNA. However, the mutant protein Q607A can form stable complexes with DNA substrates containing blocked ends, which suggests that Q607 intercalates into the helix and inhibits sliding. Altogether, our results suggest that ROS1 uses three predicted helixinvading residues to actively interrogate DNA in search for 5-meC.
False identification of other microorganisms as Staphylococcus aureus in Southern Nigeria

Purpose: Staphylococcus aureus is the causative agent of many infections and the advent MRSA has drawn much attention to it. However, some organisms have been noted to be wrongly identified as S. aureus through phenotypic identifications leading to wrong treatment of infections. This study is therefore undertaken to evaluate the rate of false identification of other organisms as S. aureus in Southern Nigeria. Methods: 507 microorganisms which have been previously identified as S. aureus in 8 States in Southern Nigeria through characteristic morphology on blood agar, Gram staining, growth and fermentation on Mannitol Salt Agar and coagulase formation were collected. All the isolates were identified in this study through sequencing of 16S rRNA and detection of spa gene. The percentages of true and false identities were determined. Results: Of the 507 isolates previously identified as S. aureus , only 54 (11 %) were confirmed as S. aureus while the rest were coagulase negative Staphylococci (85 % misidentification rate), Bacillus sp. (12 % misidentification rate), and Brevibacterium sp. (3 % misidentification rate). Conclusion: A high rate of false positive identification of S. aureus which could lead to the misuse of antibiotics in emergency situation has been identified in this study. The use of standard methods for the identification of S. aureus at all times is highly recommended. Keywords: Coagulase staphylococci differentiation, misidentification of S. aureus , phenotypic identifications, Southern Nigeria
Taste of Proline-containing Peptides

In order to investigate the role of the proline residue in the bitter taste of peptides, some oligopeptides containing proline were synthesized and their tastes were evaluated. Proline peptides exhibited bitterness, this aspect being different from hydrophobic amino acids. The most significant role of proline residue in peptide bitterness was dependent on the conformational alternation of the peptide molecule by folding the peptide skeleton due to the imino ring of the proline molecule. It was demonstrated that 2 bitter taste determinant sites were essential for peptide bitterness and that they should be adjacent in the steric conformation of the peptides.
The effect of extremely high bromide intake on the biologicalhalf-life of iodine in the rat

Marked effects of high bromide levels in the organism on iodine metabolism in the thyroid of rats were observed. High bromide intake decreased the amount of iodide accumulated in the thyroid; changed the proportion between the amount of iodine retained in the thyroid and the total amount of absorbed iodine; significantly shortened the biological half-life of iodine in the thyroid; changed the time course (added a further phase) of iodine elimination from the body.
Bumble Bee Colonization, Extinction, and Reproduction in Subalpine Meadows in Northeastern Utah

The distributional patterns of six bumble bee (Bombus) species in discrete subalpine meadows in Utah were studied over the course of a summer. Data on the movements of individuals were obtained through mark—recapture studies of queens during nest initiation and of workers later in the summer. Censuses of the species and abundance of bumble bees and flowers in sample quadrats of 20 meadows revealed patterns of diversity, colony extinction (inferred from the absence of a species after it had been previously recorded in the meadow), and production of new reproductives. The results suggest that the number and diversity of queens that colonize a meadow in early summer is a function of meadow area. In mid to late season, after nest sites have been chosen and colonies established, meadow floristics (flower composition) governs within—meadow Bombus species composition and the persistence, ontogeny, and reproduction of bumble bee colonies. Workers appear not to utilize flowers outside the meadow where their colony is located. Specific results were that (1) mid— to late—summer bumble bee diversity was best correlated with meadow floristics, (2) flower compositions in meadows where local extinctions of Bombus occurred differed markedly from those where all species persisted, (3) the distribution of new reproductives among the meadows was independent of bombus species composition, and (4) late—season reproductive timing of Bombus flavifrons appeared to be a function of floristic composition and, particularly, nectar availability. These results underscore the importance of flower resources while downplaying the role of interactions among Bombus colonies and species in accounting for patterns of species persistence and colony reproduction.
Reproductive biology, seasonality and distribution of Tenagomysis macropsis W. Tattersall, 1923 ( Crustacea, Mysidacea) in a New Zealand estuary

Size at maturity averaged 6.4-8.7 mm (TL) for males, 6.6-8.8 mm (TL) for females, and varied seasonally showing strong inverse correlation with temperature. Mean number of stage I young per brood was 11 (max. 25), the number and size of these being correlated with female body-size and therefore varying seasonally also. During winter the population contained a maximum percentage of large females producing maximum numbers of large embryos. Brood mortality approximates 20%. The sampled population was found in salinities averaging 4-30per mille with maximum numbers (64/m) in waters of 19per mille. Tolerance tests confirmed a salinity optimum in the vicinity of 20per mille but demonstrated broad euryhalinity. Population numbers were lowest during summer and early autumn, highest during late winter/spring. Data did not demonstrate a consistent seasonal population cycle, and it is suggested this was related to differing salinity regimes, recruitment rates, breeding aggregation and migration. There was a relatively up-estuary shift in distribution in spring, especially of adult females and to a less extent of juveniles. This may be part of a broader inshore- offshore migration pattern. Large sexually differentiated individuals dominated (90%) the winter population, the first sexually mature individuals having appeared in late autumn. Reproductive activity resulted in new recruitment by late winter which continued through summer and autumn. The population was dominated by juveniles during summer, by which time the overwintering adult cohort was lost. Females dominated the population, probably producing >1 brood per year, and having a longevity of one year. Early post-mating mortality of males is indicated. -from Authors
Assessment of ideal dietary amino acid ratios between branched-chain amino acids for growing chicken

Improvement of amino acid (AA) recommendations are a precondition for sustainable conversion of feed to food proteins and have to be based on physiological acceptable and validated procedures to derive both quantitative daily AA requirements and optimal dietary AA ratios. According to earlier applications of an exponential nitrogen (N)-utilization model (Samadi and Liebert, 2006, 2008; Liebert, 2008), two experiments were conducted to obtain new data about ideal amino acid ratio (IAAR) between branched-chain amino acids (BCAA) leucine (Leu), isoleucine (Ile), valine (Val) and lysine (Lys) in meat type chicken diets.
Loudly heard, little seen, and rarely understood: Spatiotemporal variation and environmental drivers of sound production by snapping shrimp

Snapping shrimp are abundant soniferous crustaceans that form large aggregations, creating a pervasive crackling in many coastal environments worldwide. The short-duration broadband “snap” generated by their specialized claw is among the loudest bioacoustic sound in the marine environment. Variation in snapping shrimp acoustic activity can substantially alter ambient soundscape characteristics, yet relatively little is known about snapping shrimp sound production patterns, the underlying behavioral ecology or role of environmental factors. Our analyses of acoustic data from tropical and sub-tropical reefs show that snap rates exhibit diurnal rhythms, but that these rhythms vary over small spatial scales (e.g., opposite diurnal patterns between adjacent reefs) and shift over time (e.g., daytime versus nighttime dominance in different seasons). Snapping patterns correlate to abiotic variables such as temperature and light, but the underlying causal mechanisms remain unclear. Ongoing lab experiments to inves.
Bio-efficacy of phytoextracts and oil cakes on Macrophomina phaseolina (Tassi) causing stem rot disease of jute, Corchorus spp.

In the present study efforts were made to explore the efficacy of various plant extracts and oil cakes against Macrophomina phaseolina . The efficacy of eight different plant species, Zingiber officianale , Aloe indica , Lawsonia inermis , Chenopodium album , Allium cepa , Piper betel , Murraya koenigii , Parthenium hysterophorus aqueous extracts including oil cakes of mustard and neem were evaluated by using of poisoned food technique in vitro for their inhibitory effect on mycelial growth of M. phaseolina causing stem rot of jute ( Corchorus olitorius and C. capsularis ). The rhizome extract of Z. officinale produced maximum growth inhibition (74.59%) of the pathogen followed by leaf extracts of A. indica (63.57%), and leaf extract of L. inermis (60.17%) at the concentration of 10%. The maximum mycelial growth inhibition (52.40%) was recorded with neem cake ( Azadirachta indica ) at the concentrations of 20% followed by 42.61% and 29.60% with concentration of 15% and 10%, respectively. However, maximum mycelial growth inhibition (19.42%) was recorded with mustard cake ( Brassica juncea ) at the concentration of 20% followed by 16.64% and 12.20% at the concentration of 15% and 10% respectively. In general mycelial growth inhibition was dose dependent and it was maximum in case of neem cake than mustard cake. The present study revealed that, these plant extracts and oilcake extracts could be exploited for the possible control of deadly pathogen M. phaseolina . Accordingly, this is an important proactive measure in preventing the spread of the stem rot disease through a more ecofriendly approach.
Limitation of the recruitment of Pinus nigra in a gradient of post-fire environmental conditions1

Abstract: Pinus nigra subsp. salzmannii is a pine species that regenerates quite well under its own canopy but has difficulty regenerating after fire. This study analyzes, by means of greenhouse and field experiments, the pattern of seed germination and seedling establishment of P. nigra in a gradient of post-fire environmental conditions. The results obtained in the controlled conditions experiment of cover effects in the absence of vegetation interference indicate that seed germination and seedling survival and growth of P. nigra attained their maximum values under high cover levels. In the field, seed germination and seedling survival of P. nigra were considerably lower than in the experiment outdoors but also followed to a large extent the cover gradient. However, there were differences among microhabitats depending on the type of vegetation present. In general, the behaviour of P. nigra is more similar to that of shade-tolerant species, such as oaks, than to low-altitude Mediterranean pines, because the establishment of P. nigra seedlings is improved under high cover conditions. As these conditions are usually lacking in recently burned areas, the regeneration of this species is strongly limited after fire. The difficulty in recovering after fire of P. nigra forests confirms that they require specific conservation measures to prevent their disappearance in the short term.
Modelling responses of western Amazonian palms to soil nutrients

Understanding the responses of individual plant species along different edaphic gradients is a key question in ecology, with implications to community assembly, functioning of forest ecosystems, niche theory and conservation planning. In tropical rain forests, responses to soil nutrients have been described only for a handful of species. Even abundant and conspicuous components of the forest, such as the palms (Arecaceae), remain largely unknown in this respect. We inventoried all palm species and analysed soil chemistry in 96 sites across western Amazonia to (i) assess the relative importance of some micronutrients vs. macronutrients as drivers of patterns in palm species composition, (ii) model the response shapes of 61 palm taxa and of canopy vs. understorey palms along gradients of selected soil nutrients, (iii) determine if the response shapes of conspecific palm varieties differ in relation to the most important observed soil nutrient and (iv) assess if the rank order of the most abundant canopy species changes along edaphic gradients. Patterns in palm species composition were best explained by Mehlich‐III extractable exchangeable bases (Ca, K, Mg) and phosphorus (P), with the different palm species clearly separating along the soil cation concentration gradient. All 61 palm taxa exhibited statistical responses along soil nutrient gradients. Response shapes in relation to exchangeable bases varied among bimodal skewed (51% of species), unimodal skewed (47%) and monotonic (2%). There were no significant differences between canopy vs. understorey species in their mean response shapes to the exchangeable bases, but canopy species had significantly higher mean optimum value for soil P and greater mean niche width along the Ca, K, Mg, P and boron (B) gradients. Varieties of the same species of Bactris, Desmoncus and Geonoma generally had different response shapes and different optima for the exchangeable bases. Synthesis. Among the soil variables we studied, macronutrients (especially exchangeable bases and P) emerged as more important than micronutrients in predicting species abundances in palm communities of western Amazonian non‐inundated forests. Non‐Gaussian responses were predominant, conspecific palm varieties exhibited different response types, and the rank order of dominance of canopy palms varied along the gradients of exchangeable bases and P. Together, these findings advance niche theory about palms and may be used for generating better predictive models of palm species distributions and for experimental studies that search for the physiological mechanisms underlying inter‐ and infra‐specific trade‐offs along edaphic gradients.
Procrustean co-inertia analysis for the linking of multivariate datasets

Abstract Procrustes analysis is a method for fitting a set of points to another. These two sets of points are often defined by the measurements of two sets of variables for the same individuals (e.g., measurements of species abundances and environmental variables at the same sites). We present a solution for graphical representation of the results of procrustes analysis when the number of variables in each of the two datasets exceeds two. This method is named procrustean co-inertia analysis because it is based on the joint use of procrustes analysis and co-inertia analysis, which is a coupling method for finding linear combinations of two sets of variables of maximal covariance. It provides better graphical representation of the concordance between the two datasets than classical co-inertia analysis. Moreover, distance matrices can be introduced in the analysis to improve its ecological meaning. Lastly, a randomization test equivalent to PROTEST is proposed as an alternative to the Mantel test. An ecological example is presented to illustrate the method.
Colistin susceptibility of gram-negative clinical isolates from Tamil Nadu, India

Abstract Background Colistin is one of the oldest antibiotics in the polymyxin group, and is used mostly against gramnegative bacteria. Because of developing resistance among clinical isolates colistin has become an alternative drug for multidrug resistant bacteria. Objectives To determine colistin resistance among isolates from Tamil Nadu, India. Methods We included 94 gram-negative isolates from two centers in Tamil Nadu in the present study. Isolates were identified by 16S rRNA sequencing. Minimal inhibitory concentrations (MICs) were determined by agar dilution. Results The isolates identified at species level included 48 Escherichia coli, 9 Klebsiella pneumoniae, 10 Pseudomonas aeruginosa, 5 Proteus mirabilis, 4 Salmonella enterica, 3 Enterobacter hormaechei, 3 Enterobacter cloacae, 2 Achromobacter xylosoxidans, 2 Acinetobacter baumannii, 1 Providencia vermicola, 1 Acinetobacter towneri, 1 Enterobacter gergoviae, 2 Providencia rettgeri, 1 Enterobacter asburiae, 1 Pseudomonas stutzeri, and 1 Salmonella typhi. The MIC of colistin ranged from 0.12 μg/ml to 128 μg/ml. The MIC50 was 1 μg/mL and MIC90 was >128 μg/ml. The MIC ≥ 8 μg/mL was resistant breakpoint for all the species. A total of 27 isolates were resistant to colistin. Colistin resistant isolates included E. coli (9/48), K. pneumoniae (6/9), P. aeruginosa (3/10), A. baumannii (1/2), P. mirabilis (4/5), E. cloacae (1/3), P. rettgeri (2/2), and S. enterica (1/4). Carbapenem susceptibility of colistin resistant isolates was tested and 14 were found to be resistant to meropenem. Conclusions Our study indicates the emergence of colistin resistant isolates from clinical samples among different groups of gram-negative organisms. Resistance to both carbapenem and colistin occurs. Developing new antibiotics and programs to reduce nosocomial infections is necessary especially for multidrug resistant isolates.
Social discount rates and welfare weights for public investment decisions in Turkey

This study is concerned with the measurement of the social discount rate (SDR) to be used in the evaluation of public sector projects and the application of regional welfare weights (RWW) to facilitate the implementation of regional development policy in Turkey. The issue of an appropriate SDR and a set of RWW is particularly important for Turkey since the country has acquired candidate status for membership of the EU and therefore is eligible for EU funds such as the instrument for Pre-Accession Assistance. However, the EU regulations stipulate that all major investment projects to be considered for a share of the EU funds must be supported by a cost benefit analysis which requires the application of a discount rate. Moreover, Chapter 21 of the acquis communautaire sets out regional development as one of the most important policy concerns for the EU. Thus, it is crucially important for Turkey to develop coherent and viable regional policies in the context of its negotiations for full membership of the EU. However, Turkey currently has neither a consistent and explicit policy regarding the application of a social discount rate in the appraisal of its public projects, nor a set of coherent and viable policies with respect to regional development. There is also a gap in the literature regarding these issues. Therefore, the twin objectives of this study are the estimation of an SDR for Turkey and the calculation and application of welfare weights in regional policy.
Effect of leaf chemistry of Vitis vinifera L. on the performance and development of Epiphyas postvittana (Lepidoptera: Tortricidae)

Background and Aims In the context of life-history performance, better fitness is evident in insect populations when they correlate positively with the nutritional quality of their host-plants. We determined the chemical differences in the leaves of five cultivars of Vitis vinifera in relation to feeding by Epiphyas postvittana and evaluated larval and adult reproductive performance on the selected cultivars. Methods and Results We determined total nitrogen, carbohydrates, phenolic substances and potassium, iron, sodium and zinc in V. vinifera cv. Chardonnay, Sauvignon Blanc, Merlot, Semillon and Marsanne. The life-history performance of E. postvittana was evaluated by raising it from eggs on leaves of the cultivars. Nitrogen content of Chardonnay was significantly greater than that of the other cultivars. Different cultivars of V. vinifera influenced growth parameters such as larval-developmental time and female-pupal mass. Reproductive-performance, measured as fecundity and fertility rates and adult-male longevity, varied when reared on leaves of the cultivars of V. vinifera. Conclusion Leaves of Chardonnay have the highest nitrogen concentration and enhanced larval performance of E. postvittana. A fitness-index study shows that female-reproductive performance was significantly enhanced when reared on Chardonnay, whereas it declined when reared on Marsanne. Significance of the Study Differences among cultivars of V. vinifera in terms of leaf chemistry are critical for larval performance and adult-reproductive potential. The poor response of E. postvittana on Marsanne could be useful in integrated pest management via push—pull strategy by planting Marsanne either near or among the susceptible cultivars of V. vinifera.