Miracle-dz/UniFAR-FTUs huggingface dataset:
GbWRKY1, a member of the WRKY transcription factor family identified from Gossypium barbadense, is involved in resistance to Verticillium wilt

Abstract WRKY transcription factors are involved in complex signalling processes that occur during stress responses. However, in contrast to the exploration of such mechanisms in model plants, far less research has focussed on the WRKY family in cotton. We previously identified GbWRKY1 in cotton (Gossypium barbadense), the expression of which is induced upon infection by Verticillium dahliae. Our current results indicate that this gene with three introns, has a group of cis-acting elements in its promoter that are associated with plant growth and development as well as responses to environmental stresses. Here, we used virus-induced gene silencing to characterize the role of GbWRKY1. Silencing in cotton simultaneously up-regulated salicylic acid (SA)-mediated responses and inhibited jasmonate (JA)-inducible and ethylene (ET)-inducible defences, resulting in an increased susceptibility to V. dahliae. However, when compared with wild-type Arabidopsis, transgenic plants exhibited more resistance to infection with V. dahliae. In the latter genotype, expression was increased for pathogen-related PR4 and ACS2, two genes involved in the JA pathway and ET biosynthesis, while expression of PR5, involved in the SA pathway, decreased after V. dahliae infection. Moreover, POD activity and lignin content related to ethylene synthesis in transgenic Arabidopsis were higher than those in wild-type Arabidopsis after V. dahliae infection. Collectively, these findings suggest that GbWRKY1 is regulated by signalling pathways for SA, JA and ET, and mainly involved in resistance to V. dahliae attack by ET signalling pathway the response. This highlights the importance of WRKYs in regulating pathogen-induced responses and plant development.
GENDERED SPACES: THE IMPACT OF THE CULTURAL ASPECTS ON THE SPATIAL ORGANISATION OF SPACES INSIDE THE HOUSES OF AMMAN DURING THE LAST CENTURY

The academic literature defines the concept of the house in numerous ways. Some scholars conceive a house as the rich psychological meaning it retains for its occupants (Stafford, 2011; Moore, 2000; Sixsmith, 1986). Other authors, such as Heathcote (2012); Lofgren (2010); and Rybczynski (1987), suggest that a house symbolises a typical social communication that describes the typical style, and represents the social network and social class of its owner. Likewise, Cambo (1991) examined Muslim houses as religious images, abstractions, shelters, and social communities. Accordingly, this research identifies the house as a symbolic place that offers notions of domesticity, comfort, and well-being through domestic intimacy and privacy; it integrates the spatial aspects with the social aspects in design. This interdisciplinary approach gives a comprehensive picture that helps when studying the transformation of the spatial organisation of houses in Amman and its relation to the cultural features.
Framework for Evaluating Credibility of External Links in Wikipedia

On the advent of Web 2.0, web users have graduated from mere information-consumers and have become information-producers. Wikipedia is one of the paramount examples of this phenomenon. Open collaborative editing model of Wikipedia allows anyone to contribute information, from anywhere. Hence, general public and particularly researchers are skeptical about the information available at Wikipedia. The whole data set of Wikipedia that ranges from Wikipedia content to editors’ communication is publically available and open to use. Using this information, it seems practical to design models and frameworks to measure authenticity of Wikipedia content. In order to measure authenticity of Wikipedia information, external links play an important role. The presence of external sources or links on a web page to other sites can increase credibility of information as it allows visitors to cross-check information at external sites. However, there should be some mechanism to validate these external sources. In this work, an External Link Verification framework has been proposed and evaluated on External Links of Wikipedia articles. The proposed framework could be used to compute credibility of an external link of any web page.
Portfolio Optimization by Fuzzy Interactive Genetic Algorithm

—In this paper, we present a Portfolio optimization method based on Interactive Genetic Algorithm and a Fuzzy satisfaction function. Portfolio optimization is a formal mathematical approach to making investment decisions across a collection of financial instruments or assets. We will be using the classical approach, known as modern portfolio theory (MPT), that involves categorizing the investment universe based on risk (standard deviation) and return, and then choosing the mix of investments that achieve a desired risk versus return tradeoff. Genetic algorithms are stochastic search algorithms inspired by biological phenomena of genetic recombination and natural selection. They simulate the evolution of string individuals encoding candidate solutions to a given problem. Genetic algorithms proved robust and efficient in finding near-optimal solutions in complex problem spaces. They are usually exploited as an optimization method, suitable for both continuous and discrete optimization tasks. We present in our proposed method an Interactive Genetic Algorithm, since it is difficult to introduce a fitness function for this kind of problem, and we will exploit instead the user/expert knowledge by interacting with our method. Finally, we will discuss and evaluate the proposed solutions by using a Fuzzy satisfaction function that takes into account the investor’s subjective preference toward risk and/or return. 
Floral nectar of wild mānuka (Leptospermum scoparium) varies more among plants than among sites

ABSTRACT Understanding of the genetic and environmental controls of floral nectar production by mānuka (Leptospermum scoparium J.R.Forst. et G.Forst.) and other species is limited by high levels of variation. This study partitioned variation in mānuka floral nectar traits between sites, plants, and branches, and tested plant and environmental variables that might contribute to variation. Wild mānuka plants were sampled at five sites across the North Island of New Zealand at the time of flowering for each site. Nectar traits differed significantly between sites, but for most traits plant-to-plant variation within sites was the largest source of variation (40%–70%) identified by linear mixed-effect modelling. Nectar total sugar, dihydroxyacetone (DHA) and hexose and sucrose ratios varied more between plants within sites, than they did between sites or branches within plants. Radiation and night-time temperature accounted for approximately 80% of between-site variation in mean total sugar per flower, and DHA/total sugar, respectively. Nectar total sugar and DHA were correlated across years when nectar was sampled again from the same plants two years later at one site, confirming stable variation between plants over time. Variation in nectar traits between adjacent wild plants suggests interactions between genotype, environment and flowering phenology among plants.
The complete mitogenome of Caulerpa lentillifera and its phylogenetic analysis

Abstract Caulerpa lentillifera is a marine nutrient-rich edible green algae, with its external shape similar to ‘sea grape’, it has functions of purifying blood, anti-oxidation, anti-cancer, and anti-tumor. The mitogenome sequence of C. lentillifera is 209,894 bp long. A total of 67 genes were determined, including 17 protein-encoding genes, 3 rRNA genes, 27 tRNA genes, and 20 unidentified open reading frame (ORF). Phylogenetic analysis showed that C. lentillifera clustered together into a single branch. The mitogenome analysis will help the understanding of Ulvophyceae evolution.
Manganese-Doped Cerium Oxide Nanocomposite Induced Photodynamic Therapy in MCF-7 Cancer Cells and Antibacterial Activity

In this experimental approach, we explored the structures, morphologies, phototoxicities, and antibacterial activities of undoped and Mn-doped ceria nanocomposite materials, MnxCe1−xO2. The MnxCe1−xO2 nanocomposites were synthesized by employing a soft chemical route. Our prime focus was on the influence of different factors, both physical and chemical, i.e., the concentration of manganese in the product, size of the nanocomposite, drug dose, and incubation time, on the bacterial strains. Different bacterial strains were selected as experimental biological models of the antibacterial activity of the manganese-doped cerium oxide nanocomposite. In addition to the photodynamic response, the adenocarcinoma cell line (MCF-7) was also studied. Based on cell viability losses and bacterial inhibition analyses, the precise mechanisms of apoptosis or necrosis of 5-ALA/PpIX-exposed MCF-7 cells under 630 nm red lights and under dark conditions were elucidated. It was observed that the undoped nanocomposites had lower cytotoxicities and inhibitions compared with those of the doped nanocomposites towards pathogens. The antibacterial activity and effectiveness for photodynamic therapy were enhanced in the presence of the manganese-doped ceria nanocomposite, which could be attributed to the correlation of the maximum reactive oxygen species generation for targeted toxicity and maximum antioxidant property in bacteria growth inhibition. The optimized cell viability dose and doping concentration will be beneficial for treating cancer and bacterial infections in the future.
Seasonal alterations in the expression of inflammatory cytokines and cortisol concentrations in periparturient Sahiwal cows

ABSTRACT Heat stress during the transition period of dairy cows disturbs the homeostasis of their physiology and ultimately their health and production. Our objective was to study the seasonal variations of plasma cortisol levels and the expression of inflammatory cytokines in the peripheral blood mononuclear cells (PBMC) of 12 periparturient Sahiwal cows. Blood samples were obtained at weekly intervals from three weeks prepartum to three weeks postpartum during the winter (Temperature–humidity index, THI = 59.7) and summer (THI = 81.5) seasons. Gene expression study of pro-inflammatory (IL-1β, IL-6, and TNF-α) and anti-inflammatory (IL-10) cytokines was done by RT-PCR and plasma cortisol by sandwich ELISA. The plasma concentration of cortisol and the relative mRNA expression of various inflammatory cytokines in PBMC were higher (p< 0.01) in the summer compared to winter season irrespective of the days of the transition period. Highest levels of cortisol and greater expression of pro-inflammatory cytokines were recorded on the day of calving in both seasons. Our study showed a higher inflammatory response, immune disturbance and greater levels of the stress hormone (cortisol) during the summer season, particularly on the day of calving.
Donor monocyte-derived macrophages promote human acute graft versus host disease

Myelopoiesis is invariably present, and contributes to pathology, in animal models of graft versus host disease (GVHD). In humans, a rich inflammatory infiltrate bearing macrophage markers has also been described in histological studies. In order to determine the origin, functional properties and role in pathogenesis of these cells, we isolated single cell suspensions from acute cutaneous GVHD and subjected them to genotype, transcriptome and in vitro functional analysis. A donor-derived population of CD11c+CD14+ cells was the dominant population of all leukocytes in GVHD. Surface phenotype and nanostring gene expression profiling indicated the closest steady-state counterpart of these cells to be monocyte-derived macrophages. In GVHD, however, there was upregulation of monocyte antigens SIRPα and S100A8/9, and transcripts associated with leukocyte trafficking, pattern recognition, antigen presentation, and co-stimulation. Isolated GVHD macrophages stimulated greater proliferation and activation of allogeneic T cells, and secreted higher levels of inflammatory cytokines than their steady-state counterparts. In HLA-matched mixed leukocyte reactions, we also observed differentiation of activated macrophages with a similar phenotype. These exhibited cytopathicity to a cell line and mediated pathological damage to skin explants, independently of T cells. Together, these results define the origin, functional properties and potential pathogenic roles of human GVHD macrophages.
11C-MCG: Synthesis, Uptake Selectivity, and Primate PET of a Probe for Glutamate Carboxypeptidase II (NAALADase)

Imaging of glutamate carboxypeptidase II (GCP II), also known as N-acetylated α-linked l-amino dipeptidase (NAALADase), may enable study of glutamatergic transmission, prostate cancer, and tumor neovasculature in vivo. Our goal was to develop a probe for GCP II for use with positron emission tomography (PET). Radiosynthesis of 11C–MeCys–C(O)–Glu or 11C-(S)-2-[3-((R)-1-carboxy-2-methylsulfanyl-ethyl)-ureido]-pentanedioic acid (11C-MCG), an asymmetric urea and potent (Ki = 1.9 nM) inhibitor of GCP II, was performed by C-11 methylation of the free thiol. Biodistribution of 11C-MCG was assayed in mice, and quantitative PET was performed in a baboon. 11C-MCG was obtained in 16% radiochemical yield at the end of synthesis with specific radioactivities over 167 GBq/mmol (4000 Ci/mmol) within 30 min after the end of bombardment. At 30 min postinjection, 11C-MCG showed 33.0 ± 5.1%, 0.4 ± 0.1%, and 1.1 ± 0.2% ID/g in mouse kidney (target tissue), muscle, and blood, respectively. Little radioactivity gained access to the brain. Blockade with unlabeled MCG or 2-(phosphonomethyl)pentanedioic acid (PMPA), another potent inhibitor of GCP II, provided sevenfold and threefold reductions, respectively, in binding to target tissue. For PET, distribution volumes (DVs) were 1.38 then 0.87 pre- and postblocker (PMPA). Little metabolism of 11C-MCG occurred in the mouse or baboon. These results suggest that 11C-MCG may be useful for imaging GCP II in the periphery.
Optimal Dietary Levels of 1α-Hydroxycholecalciferol in Broiler Chickens from 1 to 42 Days of Age

1α-Hydroxycholecalciferol (1α-OH-D3) is an active vitamin D derivative. In this study, three experiments were conducted to evaluate the optimal dietary levels of 1α-OH-D3 in broiler chickens from 1 to 42 days of age. 1α-OH-D3 levels used were 0, 1.25, 2.5, 5, and 10 µg/kg in experiment 1, 0.625, 1.25, 2.5, 5, 7.5, and 10 µg/kg in experiment 2, and 2, 2.5, 3, 3.5, 4, 4.5, and 5 µg/kg in experiment 3. In experiment 1, the addition of 0 to 10 µg/kg of 1α-OH-D3 quadratically improved growth performance, tibia development, and mRNA expression levels of nuclear vitamin D receptor (nVDR), membrane vitamin D receptor (mVDR), and type IIb sodium-phosphate cotransporter (NaPi-IIb) in the duodenum of broiler chickens from 1 to 12 days of age. Body weight gain (BWG), the weight and ash weight of the tibia, and mRNA expression levels of mVDR and NaPi-IIb of broilers fed with 0 and 10 µg/kg of 1α-OH-D3 were lower than those of birds fed with 2.5 µg/kg of 1α-OH-D3. In experiment 2, 1α-OH-D3 levels were quadratically related to BWG and to weight and ash weight of the femur and the tibia of broiler chickens at 42 days of age. The highest values of growth performance and bone mineralization were recorded in broilers fed with 2.5 to 5 µg/kg of 1α-OH-D3. In experiment 3, there was no difference observed in BWG and the weight and ash weight of the femur and the tibia of the 42-day-old broilers fed with 2 to 5 µg/kg of 1α-OH-D3. These data suggest that the optimal dietary levels of 1α-OH-D3 were 2 to 5 µg/kg for broiler chickens from 1 to 42 days of age.
Eukaryotic Molecular Biology Databases: An Overview

A biological database is a big, structured body of continuous information, generally connected with computerized software intended to update, query, and recover information elements deposited within the framework. A straightforward database could be a single folder comprising several data, each carrying the same number of data. Such famous databases are GenBank from the National Center for Biotechnology Information, SwissProt from the Swiss Institute of Bioinformatics and PIR from the Protein Information Resource. Biological databases are bibliotheques of life science data, gathered from science studies, published literature, high-performance experimental technology, and computational analysis. Here we brefly described some recently published molecular databases.
3D Modeling of Patrimonium Objectives Using Laser Technology

This paper aims to present the advantages of using the terrestrial laser scanning technology (TLS) as a method of creating a 3D database and 3D documentation. This state-of-the-art technology is an innovation that has the advantage of acquiring a large amount of data in a short time. This technology together with UAV equipment has the advantage of obtaining a digital terrain model. The creation of 3D patrimony models, archaeological objects and sites in their current state requires specialized equipment, knowledge, and have a powerful methodology capable of digitally capturing and shaping geometric details and fine layout of these sites. Digital recording, documentation and preservation are required because our patrimony (natural, cultural or mixed) suffers from various anthropogenic and/or natural actions (natural disasters, climate change and forgetfulness of human neglect).
Dynamic Reconfiguration, Fragmentation, and Integration of Whole-Brain Modular Structure across Depths of Unconsciousness

General anesthetics are routinely used to induce unconsciousness, and much is known about their effects on receptor function and single neuron activity. Much less is known about how these local effects are manifest at the whole-brain level, nor how they influence network dynamics, especially past the point of induced unconsciousness. Using resting-state functional magnetic resonance imaging (fMRI) with nonhuman primates, we investigated the dose-dependent effects of anesthesia on whole-brain temporal modular structure, following loss of consciousness. We found that higher isoflurane dose was associated with an increase in both the number and isolation of whole-brain modules, as well as an increase in the uncoordinated movement of brain regions between those modules. Conversely, we found that higher dose was associated with a decrease in the cohesive movement of brain regions between modules, as well as a decrease in the proportion of modules in which brain regions participated. Moreover, higher dose was associated with a decrease in the overall integrity of networks derived from the temporal modules, with the exception of a single, sensory-motor network. Together, these findings suggest that anaesthesia-induced unconsciousness results from the hierarchical fragmentation of dynamic whole-brain network structure, leading to the discoordination of temporal interactions between cortical modules.
Wavelet-based approach for the fusion of low-light image pairs

When taking pictures in low-light scene, due to the insufficient light, we are often posed to the following problem: Using short exposure setting, image tends to be dim and noise, but with a sharp outline. While using longer exposure setting, image captures more color and detail information, but with partly blurred areas. A very common situation, none of those images is good enough. Good brightness and color information are retained in long-exposure images, while sharp outlines are retained in shorter ones. In this paper, we propose a fusion method based on wavelet decomposition for such low-light image pair. In this work, we firstly decompose the original image pair into different frequency subbands. After that, we compute the importance weight maps according to the difference value between corresponding subbands. In order to refuse artifacts and ghost, we compute weight maps in Gauss model. Finally, the coefficients of subbands are blended into a high-quality fusion image. Experimental results show that the proposed method effectively preserves sharp edges of the short-exposure image, and maintains the color, brightness, and details of the long-exposure image.
User-guided Graph Exploration: A Framework for Algorithmic Complexity Reduction in Large Data Sets

Human exploration of large data sets becomes increasingly difficult with growing amounts of data. For this purpose, such data sets are often visualized as large graphs, depicting information and interrelations as interconnected vertices. A visual representation of such large graphs (for example, social networks, collaboration analyses or biological data sets) has to find a trade-off between showing details in a magnified—or zoomed-in—view and the overall graph structure. Showing these two aspects at the same time results in a visual overload that is largely inaccessible to human users. In this article, we augment previous work and present a new approach to address this overload by combining and extending graph-theoretic properties with community detection algorithms. Our non-destructive approach to reducing visual complexity while retaining core properties of the given graph is user-guided and semi-automated. The results yielded by applying our approach to large real-world network data sets reveal a massive reduction of displayed vertices and connections while keeping essential graph structures intact.
Expression changes in the TaNAC2 and TaNAC69-1 transcription factors in drought stress tolerant and susceptible accessions of Triticum boeoticum

Abstract Triticum boeoticum is a valuable gene source for tolerance to drought stress. In order to study the effect of drought stress on this plant, and to understand its adaptive mechanisms at the molecular level, 10 accessions of T. boeoticum were evaluated under non- and drought stress conditions. Evaluation of 31 different phenological, morpho-physiological and root-related traits showed that there were significant differences between accessions. Using the bi-plot resulting from the PCA, the studied traits and accessions were separated in different groups. The most tolerant (B5) and susceptible (B6) accessions to drought stress were identified, so these accessions were used for assessment of changes in the TaNAC2 and TaNAC69-1 transcription factors (TFs) expression. The results showed that in the most tolerant and susceptible accessions, TaNAC2 and TaNAC69-1 expression levels increased between non-stress and stress conditions significantly, but the increased level of these two genes expression in the most tolerant accession was much higher than the most susceptible accession. According to the obtained results, T. boeoticum can be a suitable and promising gene source for improving modern wheat. In addition, the results of TFs expression could improve our understanding about the complex mechanisms associated with drought tolerance in wheat, especially wild wheat.