Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of the mechanisms of transgenerational inheritance of behavioural alterations induced by early stress in mice

The epigenome is the overall epigenetic state of a cell, and represents the ensemble of chromatin modifications. It is an essential mechanism for the regulation of the genome that depends on modifications of DNA and histones, but does not involve any change of the DNA sequence. It was previously assumed that in order for appropriate cellular development and differentiation to occur in mammals, the epigenome was fully erased and reestablished between generations. However, several examples of incomplete erasure at specific genes have been reported, and this is suggested to be associated with the epigenetic inheritance of gene profiles. Although the existence of such a mode of inheritance has been controversial, there is increasing evidence that it does occur in rodents and humans. In this review, we discuss the evidence that adverse environmental factors can affect not only the individuals directly exposed to these factors, but also their offspring. Because the epigenome is sensitive to environmental influence and, in some cases can, in part, be transmitted across generations, it provides a mechanism for the transgenerational transmission of the impact of environmental factors. Environmental factors examined include exposure to toxicants, diet, and postnatal care. DNA methylation is the main mechanism discussed in this review.
Recursive Model for Multiplying Multidimensional Matrices

Data parallelism is inherent to multidimensional matrices Algebra. Therefore, the operations of this algebra can be implemented in parallel using generalizations of parallel multiplication algorithms for ordinary matrices. The article discusses a recursive approach to multiplying multidimensional matrices for the operation of (2, 1)-contracted multiplication of four-dimensional matrices.
Circumtropical distribution of the epiphytic dinoflagellate Coolia malayensis (Dinophyceae): Morphology and molecular phylogeny from Puerto Rico and Brazil

The dinoflagellate genus Coolia, which contains potentially toxic species, is an important component of epiphytic assemblages in marine ecosystems. The morphology of C. malayensis has been illustrated from strains isolated in Asia and Oceania. In this study, strains of C. malayensis isolated from the Caribbean Sea in Puerto Rico, and for the first time from the South Atlantic Ocean in Brazil, were investigated by light, epifluorescence and scanning electron microscopies. No significant morphological differences between these new strains and other geographically distant strains of C. malayensis were observed. In the LSU rDNA phylogeny, the C. malayensis sequences from Brazil and Puerto Rico branched within the clade of strains from Oceania and Asia. The recently described species C. santacroce branched as a sister group of C. monotis, and C. palmyrensis was basal to the combined group of C. monotis/C. malayensis/C. santacroce. A tentative undescribed species from Florida and New Zealand branched as a sister group of C. malayensis. Our results confirm that C. malayensis showed a cosmopolitan distribution in tropical to subtropical waters, while the type species C. monotis remains endemic for the Mediterranean Sea and the temperate North Atlantic.
Observations on the microstructure and heat-induced changes in the viscoelasticity of commercial cheeses

Commercial samples of low-moisture mozzarella (LMMC), cheddar (CC) and analogue pizza cheese (APC) were evaluated for microstructure and heat-induced changes in viscoelasticity. Major inter-variety differences in microstructure were noted. The casein in the LMMC was in the form of longitudinally aligned fibres with entrapped fat columns, consisting of discrete and coalesced fat globules, of similar orientation. Less orientation of the casein and fat phases was evident in the CC. The microstructure of the APC was distinctly different from that of the LMMC and CC, having a more uniformly distributed paracasein matrix (with no orientation) and an emulsion of discrete, rounded fat droplets of varying size. Increasing the temperature resulted in a decrease in the elastic shear modulus, G', and an increase in the phase angle, δ, indicating a transition from an unmelted cheese, largely elastic in rheological response, to a melted cheese, which is more viscous in character. There was a distinct phase change from elastic to viscous nature in the LMMC and CC cheeses, as indicated by an abrupt increase in δ to ∼55-60° in the temperature range 60-82°C. In contrast, the increase in δ for the APC was more gradual and the maximum value attained was much lower, at ∼38°, There was good agreement between the viscoelastic parameters and functional attributes of the baked cheese, with low values of δ max and high values of G' mir (as in the APC samples) coinciding with relatively low flowability and high apparent viscosity.
Mechanisms of endoderm patterning and directed differentiation of human stem cells into foregut tissues

The fundus (or corpus) of the stomach is required for normal digestive, metabolic, and immunologic functions, and it plays a key role in most human stomach diseases including peptic ulcer disease and gastric cancer. The global prevalence of gastric disease and the paucity of adequate animal models highlight the critical need for new methods to study human-specific fundus biology. Recently we developed a novel strategy for the de novo generation of human gastric tissue from pluripotent stem cells (PSCs), but this approach was only sufficient to promote the differentiation of the distal portion of the stomach, the antrum. The fundus and antrum are distinct regions of the stomach that derive from adjacent domains of the posterior foregut; however the molecular mechanisms that specify these lineages are largely unknown. Here we have used an innovative in vitro model of human stomach development to identify that early activation of Wnt/β-catenin is sufficient to specify fundus and repress an antral fate. Furthermore, precise temporal manipulation of Wnt/β-catenin signaling can be used to direct the differentiation of hPSCs into three-dimensional fundic gastric organoids expressing markers for all the cell types of the fundus, including parietal cells and chief cells. This is the first example of differentiation of fundic epithelium from PSCs, and the first established in vitro model of the human fundus. Human fundic organoids present a unique opportunity to identify new mechanisms of human fundic development and disease.
RELATIVE IMPORTANCE OF MANGROVES AS FEEDING HABITATS FOR FISHES: A COMPARISON BETWEEN MANGROVE HABITATS WITH DIFFERENT SETTINGS

The importance of mangroves as feeding grounds for fish and other macrozoob enthos in the Indian Ocean and elsewhere has been a subject of debate. This could partly be due to the fact that studies describing this role have been conducted in mangrove systems that differed in their settings. By using stable isotope analysis of carbon and nitrogen, w e investigated two different settings of mangroves along the Tanzanian coast, to establish if mangrove setting influences the extent to which this habitat is utilized as a potential feeding ground by fish. The two mangrove settings were: mangrove-lined creeks which retain water during low tides and fringing man groves that drain completely during low tides. The δ 13 C signatures of most fishes from the mangrove-lined creeks were similar to those of food items from the manmangrove-lined creeks were similar to those of food items from the manwere similar to those of food items from the man grove habitat, which suggests that these fishes feed from the mangrove habitats. In contrast, the overlap in δ 13 C of some food items from the fringing mangroves with those from adjacent habitats, and the more enriched δ 13 C signatures of fishes from the fringing mangroves with respect to most typical food items from the mangrove habitat could be an indication that these fishes feed from both habitats but to a lower extent from the fringing mangroves. The results suggest that fishes feed more from the mangrove-lined creeks as compared to fringing mangroves which is probably related to differences in the degree of mangrove inundation. Th e more or less conThe more or less con tinuous access provided more time for fishes to stay and feed in the mangrove-lined creeks compared to fishes from the fringing mangroves, which have access to these mangroves only during high tide and have to migrate to adjacent habitats with the ebbing tide. Mangrove ecosystems are widely recognized as potential nursery grounds for juve
Modeling of Aggregate Stiffness and Its Effect on Shrinkage of Concrete

This paper is aimed to propose a model for simulating aggregate phase stiffness and its effect on concrete shrinkage based on the concept of concrete as a two-phase material (paste phase and aggregate phase). Regarding the effect of aggregate phase, concrete shrinkage is found to be affected by the aggregate content, strain of the aggregate phase and the proportion between coarse aggregates and fine aggregates. The aggregate particles are considered to be uniformly distributed in the concrete and in contact with one another at various contact angles. As a result, the stress of the aggregate phase can be obtained from the summation of stresses of all contact angles. A two-dimensional constitutive model is used for computing the stiffness of the aggregate phase of concrete. The stiffness of the aggregate particle system is then derived from the ratio between stress and strain. Because of concrete shrinkage is restrained by aggregates, the effect of aggregate stiffness on concrete shrinkage is proposed based on the concrete shrinkage model by Tangtermsirikul and Nimityongskul. Verification tests on fine aggregates are conducted on mortar specimens while coarse aggregates and binary mixture of aggregates are conducted on concrete specimens. The verification indicated that the model is effective for deriving the stiffness of aggregate phase and predicting the shrinkage of concrete as well. From the test and analysis results, high aggregate contents induce great stiffness. As a result, it will have effect on small shrinkage.
Atmospheric Pressure DBD Low-Temperature Plasma Reactor for the Treatment of Sugarcane Bagasse

This paper embodies the results of experimental studies of a dielectric barrier discharge low-temperature nonequilibrium plasma reactor that runs in air and nitrogen at atmospheric-pressure conceived for surface treatment applications. A homemade reactor, of typical plane-to-plane geometry with the dielectric covering the upper electrode which is stressed by a high voltage (40 kV, 3–20 kHz) is used. Electrical signals (current and voltage), optical emission spectroscopy records, and total light emission measured by photomultiplier have been analyzed and used to distinguish different plasma regimes which are studied for the treatment of a lignocellulosic material (sugarcane bagasse). In the filamentary discharge regime, the gas temperature of few tens of degree Celsius above the ambient one was determined, the electronic temperature of some electronvolts and electron density in the range of 1012–1013 cm−3 were estimated. Plasma treated pellets of sugarcane bagasse were analyzed by diffuse reflectance infrared Fourier transform spectrometry and the relative results obtained under filamentary discharge regime have shown significant degradation of the lignin macromolecule. It has been shown important modifications on the lignocellulosic material, namely, the plasma attacks drastically the lignin bonds. Strong modification of lignin was observed near wavenumber of 3400 cm−1, due to stretching vibrations of OH, and for the band 1114 cm−1 which is related to C=C and C=O stretching. Severe decrease of the band intensity 1596 cm−1, which due to C=C stretching and C=O, is also a result of the treatments done in this paper.
Analysis of Developing Pollen Grains within Intact Arabidopsis thaliana Anthers by Olympus Two-Photon Laser Scanning Microscopy

[Abstract] The method consists of imaging developing pollen grains as they form within intact, immature Arabidopsis thaliana anthers. Using two-photon excitation in the infrared wavelength range, the intrinsic fluorescence (autofluorescence) of developing pollen grains and surrounding sporophytic tissues of the anther wall, including the tapetum, middle layer, endothecium and epidermis, can be visualized in the three-dimensional space of an intact anther. In contrast to conventional confocal microscopy, the application of red-shifted light by two-photon microscopy improves depth penetration into specimens, while the scattering of light and subsequent phototoxicity is minimized, making this a superior method for imaging the developing pollen grains and tapetal cells enclosed within anthers. The technique described was optimized for the detection of autofluorescent components of the pollen wall, including sporopollenin and the pollen coat, and provided spatial and developmental data on the autofluorescent metabolites in anthers of wild-type and pollen wall mutant plants (Quilichini et al., 2014). The use of two-photon imaging of live, intact anthers holds potential for future studies aimed at understanding the spatial relationship between gametophytic and sporophytic tissues during pollen development and the distribution of metabolites or fluorescently-tagged proteins within developing anthers.
Regulation of vitamin E and the tocopherol transfer protein

Vitamin E (tocopherol) is the major lipid soluble antioxidant. Consequently, maintaining adequate vitamin E levels is critical for the prevention of oxidative stress-related diseases. The tocopherol transfer protein (TTP), which is highly expressed in the liver and to a lesser extent in the brain, functions as the major regulator of vitamin E status. Mutations in TTP result in a heritable disease that is characterized by very low vitamin E levels and neurological consequences that manifest as spinocerebellar ataxia. Despite the importance of vitamin E in maintaining neurological function, the majority of our knowledge regarding vitamin E transport is limited to in the liver. Using primary dissociated cells and organotypic slice cultures, we established that TTP is preferentially expressed in astrocytes. In accordance with the function of liver TTP, we find an increase in efflux of tocopherol from TTP-expressing astrocyte cells. Finally, we report that TtpA expression increases in conditions of oxidative stress in the astrocyte cells. Taken together, our data suggests that TTP-expressing astrocytes distribute tocopherol to protect neurons from oxidative-stress induced damage. This astrocyte-neuron transport interaction is similar for other lipids, including
Kentlerde Yapısal ve Yeşil Alanlardaki Hava ve Yüzey Sıcaklıklarının İrdelenmesi: Ankara Örneği

In contemporary metropolitan cities, as a result of lessening green areas and evaporation surfaces, and increasing asphalted surfaces and built areas with materials which have more heat conveying and storing properties meteorological parameters change and cause local and regional climate changes which makes the cities unhealthy places that have their own climatic properties. Although it is known that in Ankara, the temperature is changing as a result of rapid and dense urbanization. With this study, first the surface temperatures utilizing Landsat satelite image at regional scale in Ankara metropolitan area caused by the changes in land use and land coverage is determined. In three case areas (Migros, Bahcelievler and Anýtkabir) having different densities of built up areas and various sizes of green areas determined in the light of the former study, air temperature measurements between 11 July-11 September 2005 has done. At the end of the study it's determined that surface temperature is higher in areas covered with asphalt-concrete, while it's lower in gren areas. Relatedly air temperature is higher in areas covered with asphalt-concrete, while it's lower in gren areas. The simultaneous air temperature difference in conifer and decidious tree groups, and concrete covered surfaces may rise up to 15°C
MUTAGENESIS OF RIBOSOMAL RNA: ANALYSING DRUG-TARGET INTERACTION OF ANTIBIOTIC COMPOUNDS TARGETING THE RIBOSOMAL DECODING SITE

Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the nonWatson-Crick U1406·U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6’ (either hydroxyl or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409–G1491 to A1409–U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6’-NH3 aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406·U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406·U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies. ChemBioChem 2003, 4, 1078 1088
Screening of Egyptian Apricot Seedlings for Response to Salinity

Individual Egyptian apricot (Prunus armeniaca L.) seedlings differed considerably in their response to 87 and 174 mm NaCl in nutrient solution supplied to roots. Wilting and/or necrosis of leaves were indices of sensitivity and survival. Damage occurred sooner, and more plants were affected at 174 mm salt. Some seedlings survived longer than others at both levels of NaCl. Root systems were reduced with prolonged treatment and some root death appeared to occur. Root damage occurred in some plants before toxicity symptoms appeared on leaves. Attempts to identify further apricot germplasm with improved tolerance to salinity appear warranted.
The effect of anthropogenic disturbance on non-native plant species in Madagascar

Abstract: Non-native species impact tropical ecosystems, but the role of different anthropogenic disturbances on the success of non-natives remains unclear, especially in island tropical forests. We sought to understand the influence of anthropogenic habitat degradation and disturbance on non-native plant species in Madagascar. Specifically, we evaluated how densities of non-native species of woody shrub (Lantana camara), climber (Mucuna pruriens) and tree (Mangifera indica, Albizia lebbeck, Tamarindus indica) varied with forest habitat degradation and by disturbance type. We surveyed 60400 m2, recording 482 instances of disturbance and 903 non-native plants in and around the Ankarana National Park. Non-native plant densities were higher in degraded than primary forest. Within degraded forest, densities of non-native trees increased with disturbance. Tree densities correlated with extent of tree damage only in Tamarindus indica, never correlated with extent of tree removal, and always correlated with proximity to roads and trails. Our results suggest roads and trails have relatively greater importance in facilitating the success of non-native tree species than structural changes to habitat. In contrast, densities of Lantana camara and Tamarindus indica did not correlate with any measured type of disturbance; other unmeasured or historical factors may be more important drivers of these smaller, faster-reproducing species.
DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis

ABSTRACT Skeletal muscle wasting in facioscapulohumeral muscular dystrophy (FSHD) results in substantial morbidity. On a disease-permissive chromosome 4qA haplotype, genomic and/or epigenetic changes at the D4Z4 macrosatellite repeat allows transcription of the DUX4 retrogene. Analysing transgenic mice carrying a human D4Z4 genomic locus from an FSHD-affected individual showed that DUX4 was transiently induced in myoblasts during skeletal muscle regeneration. Centromeric to the D4Z4 repeats is an inverted D4Z4 unit encoding DUX4c. Expression of DUX4, DUX4c and DUX4 constructs, including constitutively active, dominant-negative and truncated versions, revealed that DUX4 activates target genes to inhibit proliferation and differentiation of satellite cells, but that it also downregulates target genes to suppress myogenic differentiation. These transcriptional changes elicited by DUX4 in mouse have significant overlap with genes regulated by DUX4 in man. Comparison of DUX4 and DUX4c transcriptional perturbations revealed that DUX4 regulates genes involved in cell proliferation, whereas DUX4c regulates genes engaged in angiogenesis and muscle development, with both DUX4 and DUX4c modifing genes involved in urogenital development. Transcriptomic analysis showed that DUX4 operates through both target gene activation and repression to orchestrate a transcriptome characteristic of a less-differentiated cell state. Summary: DUX4 underlies pathogenesis in facioscapulohumeral muscular dystrophy. DUX4 acts mainly as a transcriptional activator that inhibits myogenesis by orchestrating a gene expression profile representative of a more stem-cell-like state.