Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Studies on the Molecular Functions of Pax7 in Adult Muscle Satellite Cells

Pax3 and Pax7 belong to a family of conserved transcription factors that play important and diverse roles in development. In the embryo, they carry out similar roles in neural and somite development, but Pax7 fails to compensate for critical functions of Pax3 in the development of limb musculature. Conversely, in the adult, Pax7 is necessary for the maintenance and survival of muscle satellite cells, whereas Pax3 cannot effectively fulfill these roles in the absence of Pax7. To identify the unique roles of Pax7 in adult muscle cells, we have analyzed global binding of Pax3 and Pax7 by ChIP-Seq. Here, we show that despite highly homologous DNA-binding domains, the majority of binding sites are uniquely recognized by Pax7 and are enriched for homeobox motifs. Genes proximal to conserved, unique Pax7 binding sites cluster into specific functional groups which may reflect the unique biological roles of Pax7. Combining Pax7 binding sites with gene expression data, we describe the regulatory networks directed by Pax7 and show that Pax7 binding is associated with positive gene regulation. Moreover, we show Myf5 is a direct target of Pax7 and identify a novel binding site in the satellite cell control region upstream of Myf5.
Isolation of Growth Cones from Mouse Brain

[Abstract] Growth cones are motile structures at the tips of growing neurites, which play an essential role in regulation of growth and navigation of growing axons and dendrites of neurons in the developing nervous system. This protocol describes isolation of growth cones from the brain tissue from young mice. Growth cones isolated using this protocol have been extensively characterized using electron microscopy (Pfenninger et al., 1983) and may be used for any kind of subsequent biochemical and/or functional analyses, including Western blot analysis of protein expression (Westphal et al., 2010), analysis of the activity of growth cone-accumulated enzymes (Leshchyns’ka et al., 2003; Li et al., 2013), and analysis of the endocytosis and exocytosis rates (Chernyshova et al., 2011).
The effect of supplementing sow and piglet diets with different forms of iron

The objective of this study was to evaluate the effect of chelated iron supplementation on gestating and lactating sows and on their suckling and weaned piglets. Reproductive traits, piglet performance, hematological parameters, and the iron concentrations in colostrum, milk, and stillborn livers were measured. Ninety-six sows were subjected to one of three treatment groups. Group T1 comprised pregnant and lactating sows treated with diets supplemented with inorganic iron (551 mg Fe/kg) and suckling piglets administered 200 mg of injectable iron dextran. Group T2 was the same as T1, except that sows after 84 days of gestation, lactating sows, and suckling piglets were fed a diet supplemented with 150 mg Fe/kg of chelated iron, and suckling piglets were administered injectable iron dextran. Group T3 was the same as T2 but without injectable iron dextran for suckling piglets. During the nursery phase, all of the weaned piglets were penned with their original groups or treatments and received isonutritive and isocaloric feeds. Piglets from the T2 and T3 groups also received an additional 150 mg Fe/kg of chelated iron via their feed. There were no differences among the treatments for reproductive traits or the iron concentrations in the colostrum, milk, or liver. The piglets that did not receive the injectable iron dextran showed the poorest performance during the pre-and post-weaning phases and showed the poorest hematological parameters of the suckling piglets. The chelated iron supplementation is insufficient to meet piglet demand. The iron dextran supply is necessary for suckling and weaned piglets.
Aging: A Little (Oxidative) Stress is May be Good for You

Heightened interest in the aging process by the public and scientific community has occurred due to the increase in percentage of elderly in the population and the increase in health care expenditures committed to the elderly [1]. Due to this increased interest, current research into aging demonstrates it as a complex process that is the result of interplay between naturally occurring processes, such as changes in hormonal levels and gene transcription that occur during the biological timeline of human development, and the exposure of our body’s systems to environmental damage [2]. At a physiological level, aging is the functional decay overtime of cells, organs and tissues, specifically through chemical damage of the cellular components proteins, DNA and lipids. The problems of aging include issues such as declining muscle tone and mass, wrinkled skin and mutant mitochondria. What is noteworthy with studies done on laboratory animals is that it is not necessary to combat individually all the problems of aging, since through modifying a regulatory gene or signaling network is sufficient to induce longevity along with the postponement of age related diseases [3].
A Cytomorphometric Analysis of Cervical Diseases And Neutrophilic Morphology With Special Reference to West Bengal

The purpose of this study was to measure some cytomorphometric parameters in different female uterine cervical conditions to study the progression of pathology from normal to neoplastic conditions. Using a computerised cytomorphometry cell measurement pro- gram, the study was based on a cross sectional study of smear cases diagnosed with different uterine cervical conditions from 2014 to 2015.From different kinds of microscopic image (Differential Interference contrast, Phase contrast, bright field microscopy) 100 pictures of normal cells and 100 pictures of pathological cells are selected. Then some cytoplasmic and nuclear parameters(Area, Perimeter, Convex area, Eccentricity, Major axis length, Minor axis length, Equivalent diameter, Compactness, Mean RGB value, Minimum RGB value, Maximum RGB value, Standard deviation of RGB value, Entropy of RGB value, Cooc features (Stats, contrast, stats, correlation, stats, energy, stats, homogeneity) are assessed. Among the cytoplasmic features area is lowest in dysplasia and highest in neoplasia, major axis length is lowest in dysplasia and highest in hypertrophied cervix, minor axis length is lowest in dysplasia and highest in hypertrophied cervix, Equivalent diameter is lowest in cervicitis and highest in neoplasia. Among the nuclear features area is lowest in hypertrophied cervix and highest in neoplasia, major axis length is lowest in cervicitis and highest in neoplasia, minor axis length is lowest in cervicitis and highest in neoplasia, Equivalent diameter is lowest in cervicitis and highest in neoplasia. Areas,convex areas,minor axis lengths are lowest in normal conditions,highest in neoplasia.Perimeters,major axis lengths,equivalent diameters are lowest in nomal conditions,highest in cervicitis.It represents inflammatory reactions in neoplastic conditions.
Phylotranscriptomics resolves ancient divergences in the Lepidoptera

Classic morphological studies of the oldest, so‐called nonditrysian lineages of Lepidoptera yielded a well‐resolved phylogeny, supported by the stepwise origin of the traits characterizing the clade Ditrysia, which contains over 98% of extant lepidopterans. Subsequent polymerase chain reaction (PCR)‐based molecular studies have robustly supported many aspects of the morphological hypothesis and strongly contradicted others, while leaving some relationships unsettled. Here we bring the greatly expanded gene sampling of RNA‐Seq to bear on nonditrysian phylogeny, especially those aspects that were not conclusively resolved by the combination of morphology and previous PCR‐based multi‐gene studies. We analysed up to 2212 genes in each of 28 species representing all 12 superfamilies and 15 of 21 families of nonditrysians, plus trichopteran outgroups and representative Ditrysia. Our maximum likelihood phylogeny estimates used both nonsynonymous changes only (degen1 coding) and all nucleotides (nt123) partitioned by codon position, recovering a novel hypothesis for early glossatan relationships that is the most strongly supported to date. We find strong support for Micropterigidae alone as the sister group to all other Lepidoptera, in agreement with morphology and early molecular evidence, but in contrast to recent PCR‐based studies. Also very strongly supported are the previously recognized clades Angiospermivora, Heteroneura, Eulepidoptera and Euheteroneura. Finally, we find strong support for paraphyly of the southern hemisphere family Palaephatidae, with the South American genus Palaephatus Butler forming the previously undetermined sister group to Ditrysia. The remaining palaephatids, Australian and South American, form the sister group to Tischeriidae.
Cell Interactions as a Control Tool of Developmental Processes for Evolutionary Robotics

This paper describes new genetic and developmental principles for an artificial evolutionary system (AES) and reports the first simulation results. Emphasis is placed on those developmental processes which reduce the length of the genome to code for a given problem. We exemplify the usefulness of developmental processes with cell growth, cell differentiation and the creation of neural control structures which we used to control a real world autonomous agent. The importance of including developmental processes relies much on the fact that a neural network can be specified implicitly by using cell-to-cell communication.
SITEMATE RECOGNITION : THE CASE OF ANOCHETUS TRAEGORDHI (HYMENOPTERA; FORMICIDAE) PREYING ON NASUTITERMES (ISOPTERA : TERMITIDAE)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Sitemate Recognition: the Case of Anochetus traegordhi (Hymenoptera; Formicidae) Preying on Nasutitermes (Isoptera: Termitidae) Bertrand Schatz, Orivel Jérôme, Jean-Paul Lachaud, Guy Beugnon, Alain Dejean
The co-pigmentation of anthocyanin isolated from mangosteen pericarp (Garcinia Mangostana L.) as Natural Dye for Dye- Sensitized Solar Cells (DSSC)

Study of color stability of anthocyanin from extract mangosteen pericarp (Garcinia mangostana L.) with co-pigmentation method has been conducted. Malic acid and ascorbic acid used as a co-pigment to stabilize the anthocyanin structure through formation of new binding between anthocyanin. Anthocyanin from mangosteen pericarp were isolated by several steps, including maceration, extraction, and Thin Layer Chromatography (TLC). The anthocyanin separation was conducted by TLC, while the identification of functional groups of those compound, were used FTIR (Fourier Transform Infrared Spectroscopy) for spectra analysis. Ultraviolet- visible absorption spectra have represented differences absorbance and color intensity in various pH. Copigmentation with malic acid and ascorbic acid in many composition and temperature were also well described. Meanwhile, anthocyanin-malic acid and anthocyanin-ascorbic acid have color retention higher than that of pure anthocyanin. Maximum color retention has been achieved at a ratio of 1:3 and 1:5 for ascorbic acid and malic acid, respectively. Therefore, the addition of ascorbic acid and malic acid as a copigment shows the ability to protect color retention of anthocyanin (mangosteen pericarp) from degradation process. The better efficiency of DSSC (η) have been achieved, whereas n of controlled anthocyanin, anthocyanin-ascorbic acid, and anthocyanin-malic acid were 0,1996%, 0,2922%, 0,3029%, respectively.
RECUPERACIÓN ECOLÓGICA DE ÁREAS AFECTADAS POR UN INCENDIO FORESTAL EN LA MICROCUENCA TINTALES (BOYACÁ, COLOMBIA)

The tintales watershed, located in the Santuario de Flora y Fauna (SFF) of Iguaque, Boyaca, was affected by a wildfire. In that area, the natural regeneration was evaluated in 29 permanent plots. Two phyto-physiognomies, a rocky outcrop and oak were evaluated to compare their richness, diversity and dominance, with rocky outcrop yielding a greater richness and diversity. The Asteraceae family was the one that obtained greater representation, with a dominance of species such as Hypoxis decumbens, Pteridium aquilinum and Andropogon bicornis. The diversity in the whole sampling was low and uniform due to the repeated incidence of forest fires that have caused changes in the structure and composition of vegetation. The vegetation found did not differ substantially from other studies reported for this life zone and the region, where the dynamics of land use are similar, with high deforestation and fires. The vegetation established after the fire is dominated by colonizing and pioneering species. In the two phyto physiognomies studied after a year of the fire, two plant communities with statistically significant differences in wealth and homogeneity could be stablished. To start the restoration process, it is recommended to use as one of the inputs, the taxonomic differences found between oak and rocky outcrop.
Regulation Of Lipid Metabolism By SREBPs

Lipid synthesis requires molecular oxygen. Consequently, maintenance of cell growth under hypoxic conditions requires adaptive mechanisms that control lipid homeostasis. In mammalian cells, sterol regulatory element‐binding protein (SREBP) transcription factors are central regulators of cellular lipid homeostasis. Our studies in fungi demonstrate that SREBPs are oxygen‐responsive transcription factors required for adaptation to low oxygen and for host infection by pathogenic fungi. In fission yeast, proteolytic release of SREBP in response to low oxygen requires the Golgi membrane‐anchored Dsc E3 ligase complex, but no SREBP protease has yet been identified. Recently, we identified an uncharacterized protease required for SREBP proteolytic processing, and we will present our results on how this protease functions in SREBP activation. In addition, fission yeast SREBP does not activate all lipid synthesis genes under low oxygen, for example, those required for unsaturated fatty acid synthesis. We will present data demonstrating that the transcription factor Mga2 is also oxygen‐responsive and functions as an SREBP‐like transcription factor during hypoxic adaptation. Collectively, these two pathways control lipid homeostasis in response to low oxygen in fission yeast.
Leaf margin analysis of Chinese woody plants and the constraints on its application to palaeoclimatic reconstruction

Aim Leaf margin states have been found to be strongly related to temperature, and hence have been used to reconstruct palaeotemperatures. Here, we aimed to explore the uncertainties and conditions of use of this technique in China by testing the influences of plant life-form, precipitation and evolutionary history on the relationship between percentage of untoothed species and temperature. Location China. Methods Using distribution maps and leaf margin states (untoothed versus toothed) of 10,480 Chinese woody dicots and dated family-level phylogenies, we evaluated the phylogenetic signal of leaf margin state, and demonstrated the variation in the patterns of leaf margin percentage and the relationship with temperature across different life-forms (evergreen and deciduous; trees, shrubs and lianas), regions with different precipitation and species quartiles with different family ages. Results Significant phylogenetic signals were found for the percentage of untoothed species within families. Relationships between leaf margin percentage and temperature were: (1) weak or insignificant for all woody dicots, shrubs, evergreen and deciduous dicots, but strong for trees and lianas; (2) significantly enhanced with increasing precipitation, and (3) significantly weakened for trees belonging to old families. Main conclusions Our results showed the complete leaf margin spectrum found in China and revealed great uncertainties in its relationship with temperature induced by life-form, precipitation and evolutionary history. These findings suggest that analysis of leaf margins for palaeotemperature reconstruction should be done cautiously: (1) only dicot trees with a relatively young family age can be used and their leaf margin states are more strongly affected by winter cold than by mean annual temperature; (2) the transfer function between leaf margin percentage and temperature is only reliable in humid and semi-humid regions of China.
Scedosporium species: emerging agents of systemic disease

Recently, fundamental taxonomic changes have been proposed in Scedosporium and its sexual phase Pseudallescheria. The most common currently accepted taxa, P apiosperma and P boydii, are molecular siblings distinguished by tubulin and calmodulin genes, but with limited morphological and physiological discriminative parameters. In regions with temperate climates, these two species represent, together with S prolificans, the most prevalent agents in human infections. Therefore, validated molecular tools for routine identification are urgently needed for clinical diagnostics, as well as for epidemiology and studies on antifungal susceptibility patterns. This review provides an overview of state-of-the-art taxonomy; isolation and molecular identification; predisposing factors and risk assessment; pathogenicity, with a focus on systemic and disseminated infections; and in vitro susceptibility.
Transferability of habitat suitability models for nesting woodpeckers associated with wildfire

ABSTRACT Following wildfire, forest managers are challenged with meeting both socioeconomic demands (e.g., salvage logging) and mandates requiring habitat conservation for disturbance-associated wildlife (e.g., woodpeckers). Habitat suitability models for nesting woodpeckers can be informative, but tests of model transferability are needed to understand how broadly models developed at one location can be applied to inform post-fire forest management at other locations. We developed habitat suitability models and tested their transferability for 2 disturbance-associated woodpecker species, Black-backed (Picoides arcticus) and Lewis's (Melanerpes lewis) woodpecker. Habitat suitability models consisted of weighted logistic regression models comparing environmental conditions at nest versus non-nest sites. We developed models at each of 3 wildfire locations in Washington, Oregon, and Idaho, and then examined predictive performance for each model at alternate (“application”) locations. Models generally discriminated nest from non-nest sites well at locations where they were developed but performance was variable at application locations, indicating limited transferability. Models for Black-backed Woodpecker and those that included field-collected environmental covariates exhibited greater transferability than models for Lewis's Woodpecker and those that only included remotely sensed covariates. Transferability was also generally poor between Oregon and the other 2 locations. Limitations to model transferability observed in this study suggest models developed at any one wildfire location are unlikely to be generally applicable across the entire range of Black-backed and Lewis's woodpeckers. Generally applicable models to inform post-fire forest management will therefore likely require integration of data from multiple wildfire locations.
Functions of phytoliths in vascular plants: an evolutionary perspective

Summary Solid biosilica (phytoliths) deposited in plant tissues is thought to function as structural support, as a cost-effective alternative to lignin, and in herbivore defence, by limiting nutrient access/extraction and abrading herbivore mouthparts. It has been assumed that active phytolith accumulation evolved for these purposes, but these hypotheses remain untested. For example, an influential idea holds that grasses became so silica-rich through antagonistic co-evolution with mammalian grazers during the Cenozoic. We examine whether phytoliths fulfil criteria established for adaptations, focusing on three aspects. First, we evaluate the recent debate concerning whether plant silica wears herbivore mouthparts/teeth. Secondly, we test whether the evolutionary pattern of phytolith accumulation is consistent with adaptive hypotheses by mapping silica content onto time-calibrated land plant and grass phylogenies. Thirdly, we compare with palaeontological evidence for the timing of the ‘demand’ for the hypothesized function (structural support, herbivore defence). Our survey demonstrates that phytoliths meet several criteria for adaptations, but key aspects require further study. For example, phytoliths wear teeth but are likely less important than dietary grit, suggesting that silica deterrence is ineffective against large mammalian grazers. Mapping analysis indicates that active silica accumulation evolved numerous times, rather than being ancestral in land plants. However, a clear temporal link between these events and hypothesized functional ‘demands’ is still missing. For example, we find no convincing evidence for Cenozoic grass-grazer co-evolution. Synthesis. Phytoliths help support and defend plants today, but the adaptive origin of this trait requires further testing. Such tests should integrate the phylogenetic distributions of phytoliths with ecology and biomechanics and use fossil evidence to evaluate the correlation between functional ‘demand’ and plant evolution.
PREDICTIVE ANALYTICS OF CIGS SOLAR CELL USING A COMBINATIONAL GRA-MLR-GA MODEL

Thin-film Copper Indium Gallium Selenide (CIGS) solar cell is identified to be one of the promising structures to replace conventional silicon-based solar cell due to its lower cost and reduced thickness. Nevertheless, the impact of layer thickness and doping concentration of a window layer Zinc oxide (ZnO), a buffer layer Cadmium sulfide (Cds) and an absorber layer (CIGS) needs to be intelligently controlled for more balanced CIGS solar cell performances. Thus, this paper proposes a newly predictive analytics using a combination of Grey relational analysis (GRA), multiple linear regressions (MLR) and genetic algorithm (GA) to optimize the CIGS solar cell parameters for better device performances. The CIGS solar cell model is developed and simulated using solar cell capacitance simulator (SCAPS). The final results prove that the proposed combinational GRA-MLR-GA model has successfully optimized the CIGS solar cell parameters in which ZnO thickness (TZnO), Cds thickness (TCds), CIGS thickness (TCIGS) and CIGS doping concentration (NaCIGS) are predictively optimized to be 0.03 μm, 0.03μm, 2.86 μm and 9.937x1017 cm-3 respectively. The most optimum magnitudes for open circuit voltage (Voc), short circuit current density (Jsc), fill factor (FF), and power conversion efficiency (η) after the predictive analytics are measured at 0.8206 V, 32.419 mA/cm2, 83.23% and 22.14% reciprocally.
Title: Biodiversity is a cauliflower under the sunlight

For long time ecologists questioned on the variations of biodiversity across the latitudinal gradient. Recently emerged that the changes in β-diversity is caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rise up to three moving towards the equator. It follows that the best figure that graphically synthesize the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.