Miracle-dz/UniFAR-FTUs huggingface dataset:
Autonomic management of J2EE edge servers

Nowadays, one of the biggest challenges for companies is to cope with the high cost of their information technologies infrastructure. Edge computing is a new computing paradigm designed to allocate on-demand computing and storage resources. Those resources are web cache servers scattered over the ISP backbones. We argue that this paradigm could be applied for on-demand full application hosting, helping reduce cost. In this paper, we present a J2EE dynamic server able to deploy/host J2EE applications on demand and its autonomic manager. For that, we reengineer and experiment JOnAS, an open-source J2EE static server. Two management policies of the autonomic manager were stressed by a simulation of a worldwide ISP network.
NEW ALTERNATIVE METHOD OF DRUMSTICK TREE (Moringa oleifera Lam.) MICROPROPAGATION.

Tissue culture protocol reported in this study is an alternative method suggested to produce plantlets of drumstick tree (Moringa oleifera Lam.) with uniform genotypes for breeding, in vitro and in vivo production. The highest rate of micropropagtion will often depend not only on the selection of the most suitable explants, but also on sterilization agent and the best basal medium for that tissue. Sterilizing shoot tip explants of drumstick, using 15 % of clorex for 15 minutes showed the highest survival percentage and lowest contamination as well as sufficient browning percentage. For multiple shoot induction, the shoot tip explants of drumstick were cultured on Murashige and Skoog (MS) agar medium supplemented with different concentrations of 2-isopentinyl adenine (2iP) at (0.0,0.5,1.0 and 2.0 mg/L) alone or in combination with indol butyric acid (IBA) at ( 0.0,0.1,0.5and 1.0 mg/ L). The highest shoot multiplication rate was found in the 3 rd subculture. Moreover, the highest shoot number/explant (8.8) was obtained with the medium contained 0.5mg/l 2iP with 0.1mg/ L IBA and maintained at 25±2C compared to all other treatments. The control treatment alone significantly showed the highest shoot length compared to all other treatments Low concentrations (0.5mg/L ) with (0.1ml/L IBA) were more effective in increasing the number of leaves. Plantlets grown on the control medium produced the maximum number of healthy roots. The rooted plantlets were hardened and successfully established in the soil.
Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

One of the important questions in protein synthesis on the ribosome is how the nascent polypeptide chains fold during translation. Addressing this question has strong implications to health and disease. Ribosomes play an essential role in maintaining a healthy cellular proteome by modulating co-translational folding. And folding of the nascent chain (NC) is likely to be initiated within the ribosomal exit tunnel. Here, we report high-resolution cryo-EM structures of stalled ribosome nascent-chain complexes (RNCs) at two biosynthetic translation time-points that examine the role of the ribosome during co-translational folding. Structures of the RNCs reveal that NC is highly dynamic and adopts a range of trajectories within the vestibule of the exit tunnel, affecting positions of the folded immunoglobulin domain outside the ribosome. Local rearrangements of several ribosomal components suggest key sensor checkpoints that monitor co-translational protein folding.
Uncovering the environmental drivers of short-term temporal dynamics in an epibenthic community from the Western English Channel

Abstract Benthic communities, critical to the health and function of marine ecosystems, are under increasing pressure from anthropogenic impacts such as pollution, eutrophication and climate change. In order to refine predictions of likely future changes in benthic communities resulting from these impacts, we must first better constrain their responses to natural seasonality in environmental conditions. Epibenthic time series data (July 2008–May 2014) have been collected from Station L4, situated 7.25 nautical miles south of Plymouth in the Western English Channel. These data were analysed to establish patterns in community abundance, wet biomass and composition, and to link any observed patterns to environmental variables. A clear response to the input of organic material from phytoplankton blooms was detected, with sediment surface living deposit feeders showing an immediate increase in abundance, while predators and scavengers responded later, with an increase in biomass. We suggest that this response is a result of two factors. The low organic content of the L4 sediment results in food limitation of the community, and the mild winter/early spring bottom water temperatures allow the benthos to take immediate advantage of bloom sedimentation. An inter-annual change in community composition was also detected, as the community shifted from one dominated by the anomuran Anapagurus laevis to one dominated by the gastropod Turitella communis. This appeared to be related to a period of high larval recruitment for T. communis in 2013/2014, suggesting that changes in the recruitment success of one species can affect the structure of an entire community.
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug Repurposing Opportunities in Rare Diseases

One in ten people are affected by rare diseases, and three out of ten children with rare diseases will not live past age five. However, the small market size of individual rare diseases, combined with the time and capital requirements of pharmaceutical R&D, have hindered the development of new drugs for these cases. A promising alternative is drug repurposing, whereby existing FDA-approved drugs might be used to treat diseases different from their original indications. In order to generate drug repurposing hypotheses in a systematic and comprehensive fashion, it is essential to integrate information from across the literature of pharmacology, genetics, and pathology. To this end, we leverage a newly developed knowledge graph, the Global Network of Biomedical Relationships (GNBR). GNBR is a large, heterogeneous knowledge graph comprising drug, disease, and gene (or protein) entities linked by a small set of semantic themes derived from the abstracts of biomedical literature. We apply a knowledge graph embedding method that explicitly models the uncertainty associated with literature-derived relationships and uses link prediction to generate drug repurposing hypotheses. This approach achieves high performance on a gold-standard test set of known drug indications (AUROC = 0.89) and is capable of generating novel repurposing hypotheses, which we independently validate using external literature sources and protein interaction networks. Finally, we demonstrate the ability of our model to produce explanations of its predictions.
Adverse Outcome Pathway on inhibition of Na+/I- symporter (NIS) leads to learning and memory impairment

The thyroid hormones (TH) are essential for brain development, maturation, and function as they regulate the early key developmental processes. Normal human brain development and cognitive function relays on sufficient production of TH during the perinatal period. The function of Na+/I- symporter (NIS) is critical for the physiological production of TH levels in the serum. The present AOP describes causative links between inhibition of NIS function leading to the decreased levels of TH in the blood and consequently in the brain, causing learning and memory deficit in children. Learning and memory depend upon the coordinated action of different brain regions and neurotransmitter systems creating functionally integrated neural networks. Hippocampus and cortex are the most critical brain structures involved in the process of cognitive functions. The function of NIS and its essentiality for TH synthesis is well known across species, however, quantitative information of KERs is limited.
Low Tunnel Covering and Microclimate, Fruit Yield, and Quality in an Organic Strawberry Production System

Consumer demand for local and organic strawberries (Fragaria ×ananassa) is increasing. Growers who can meet this demand have a competitive edge in the direct-to-consumer market. Innovations in strawberry production for northern climates offer new opportunities for growers to meet the demand for local organic strawberries. Typically adopted for season extension, the use of poly-covered tunnels for crop protection provides other benefits including protection from adverse weather. Low tunnels are easy to install, low cost, temporary protective structures that are well-adapted for annual day-neutral strawberry production, and they are more space efficient than high tunnels for these low-stature crops. A range of specialty tunnel plastics that modify and diffuse light are available, but there is little information on how these influence strawberry plant growth and performance in the field. Our objectives were to determine the effects of experimental ultraviolet blocking and transmitting plastics on light and microclimate in low tunnel environments and assess differences in fruit yield and quality in the day-neutral strawberry cultivar Albion in an organic production system. This research was conducted on U.S. Department of Agriculture-certified organic land over 2 years, in 2016 and 2017. We found that ultraviolet intensity and daily light integral (DLI) were lower in covered plots than in the open field. Maximum daily temperatures were slightly higher in covered plots. Both ultraviolet-blocking and ultraviolet-transmitting plastics improved marketable fruit yield compared with the open-field control. Strawberries grown in the open-field treatment were lower in chroma than covered plots in 2017, and there was no difference in total soluble solids between treatments in either year. Low tunnel systems allow for increased environmental control and improved fruit quality and are well-adapted for day-neutral organic strawberry production systems.
The complete mitochondrial genome of Sarcophaga caudagalli (Diptera: Sarcophagidae)

Abstract Sarcophaga caudagalli belonging to the Sarcophagidae is significant for medical and veterinary management. The complete mitochondrial genome (mitogenome) of S. caudagalli was first sequenced and annotated. The circular molecule was 15,029 bp in length, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and an A + T-rich region). Phylogenetic analysis showed that the clade of S. caudagalli was clustered separately.
Quantitative phase microscopy using deep neural networks

Deep learning has been proven to achieve ground-breaking accuracy in various tasks. In this paper, we implemented a deep neural network (DNN) to achieve phase retrieval in a wide-field microscope. Our DNN utilized the residual neural network (ResNet) architecture and was trained using the data generated by a phase SLM. The results showed that our DNN was able to reconstruct the profile of the phase target qualitatively. In the meantime, large error still existed, which indicated that our approach still need to be improved.
Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana

Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and positional variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting conserved and variable CNS roles in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.
Effects of rice gluten meal inclusion on productive
and economic performance in broilers

We show valid non-traditional feedstuffs in broiler diets. Arbor Acres plus unsexed one-day old broiler chicks (n = 250) were used to study the effect of rice gluten meal (RGM) on growth performance, carcass characteristics, some serum biochemical parameters and economic efficiency as an alternative to soybean meal and corn gluten meal. They were randomly assigned to five treatments with five replicates per treatment (fifty chicks/ treatment; ten chicks/replicate). The experimental chicks were fed with isoenergetic and isonitrogenous diets supplemented with 0 (control), 3, 6, 9 and 12% RGM for 6 weeks. Growth performance parameters were monitored weekly. Five broilers from each treatment were slaughtered on day 42, for measuring the weight percentages of carcass dressing and internal organs. At 42 days of age, blood samples were collected and serum was separated for determination of serum lipid profile, glucose, total protein, albumin, and globulin. Results showed that broilers fed RGM (up to 12%) had the same performance parameters like the control diet and there was no significant alter among the different groups. RGM had no effect on dressing percentage and internal organs among treatments. Also, no significant change in the serum glucose, total cholesterol, triglycerides, HDL, LDL, total protein, albumin, globulin, ALT, AST, creatinine, uric acid and urea in dietary groups fed on diets contained RGM. The total returns (TR) and net profit revealed no significant (P>0.05) variation was recorded between the dietary groups. In conclusion, broilers fed the RGM diets compared well with those fed the control for growth performance, carcass dressing and blood metabolites and can be included in the broiler diet up to 12% without any deleterious impacts.
Gamma oscillations during episodic memory processing reveal reversal of information flow between the hippocampus and prefrontal cortex

A critical and emerging question in human episodic memory is how the hippocampus interacts with the prefrontal cortex during the encoding and retrieval of items and their contexts. In the present study, participants performed an episodic memory task (free recall) while intracranial electrodes were simultaneously inserted into the hippocampus and multiple prefrontal locations, allowing the quantification of relative onset times of gamma band activity in the cortex and the hippocampus in the same individual. We observed that in left anterior ventrolateral prefrontal cortex (aVLPFC) gamma band activity onset was significantly later than in the hippocampus during memory encoding, whereas its activity significantly preceded that in the hippocampus during memory retrieval. These findings provide direct evidence to support models of prefrontal-hippocampal interactions derived from studies of rodents, but suggest that in humans, it is the aVLPFC rather than medial prefrontal cortex that demonstrate these reciprocal interactions.
Determination of Some Flavonoid Derivatives Inhibitory Effect on Bovine Milk Lactoperoxidase Enzyme

Peroxidases (PODs) are a group of enzymes that are commonly found in bacteria, fungi, plants and animals and have important uses in the food, pharmaceutical industry and clinical diagnostics. Lactoperoxidase (LPO) enzyme, which is included in peroxidase enzyme class, is found milk, saliva and tears in mammals. With thiocyanate and hydrogen peroxide, it forms one of the body's defense systems against infections. Flavonoid derivatives are abundant in plants and constitute an important part of the diet. These derivatives, which are produced synthetically or naturally, have many pharmacological activities. In this study, the effect of some flavonoid derivatives (5,7-Dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-4H-chromen-4-one (a) , 3,5,7-Trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one (b) , 7-Hydroxy-4'-nitroisoflavone (c) , 6-Fluoroflavone (d) , 7-Hydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one (e) , 7-Methoxy-2-phenyl-4H-chromen-4-one (f) ) on the lactoperoxidase enzyme was investigated. Firstly, by using Sepharose-4B-L-tyrosine-sulfanilamide affinity chromatography, the LPO enzyme was purified 65 fold (with a yield of 23%) from bovine milk and kinetic studies were carried out with flavonoid derivatives using this enzyme . The K i values of six molecules were found in ranging from 7.85 µM to 0.023 μM. 6-Fluoroflavone was the most effective inhibitor with K i value of 0.023 μM.
Investigations of Processing–Induced Structural Changes in Horse Type-I Collagen at Sub and Supramolecular Levels

The aim of this work is to evaluate the effects of different extraction and material processing protocols on the collagen structure and hierarchical organization of equine tendons. Wide and Small Angle X-ray Scattering investigations on raw powders and thin films revealed that not only the extraction and purification treatments, but also the processing conditions may affect the extent of the protein crystalline domain and induce a nanoscale “shield effect. ” This is due to the supramolecular fiber organization, which protects the atomic scale structure from the modifications that occur during fabrication protocols. Moreover, X-ray analyses and Fourier Transform Infrared spectroscopy performed on the biomaterial sheds light on the relationship between processing conditions, triple helical content and the organization in atomic and nanoscale domains. It was found that the mechanical homogenization of the slurry in acidic solution is a treatment that ensures a high content of super-organization of collagen into triple helices and a lower crystalline domain in the material. Finally, mechanical tensile tests were carried out, proving that the acidic solution is the condition which most enhances both mechanical stiffness and supramolecular fiber organization of the films.
Status, conservation and ecology of Pallavicinia lyellii (Hook.) Carruth. in a key region of England

ABSTRACT Introduction. Pallavicinia lyellii is recognised as being of principal importance for conservation in England and is threatened with extinction in Europe. The aims of this study were to investigate the current status, conservation and ecology of the species in S Hampshire, a key region for the plant. Methods. All recent and historic locations for Pallavicinia lyellii in S Hampshire were searched and information collected on distribution, abundance and ecology. Results. Pallavicinia lyellii was re-found at three sites. It is almost certainly extinct at two sites and may have been lost from a third. Whilst few colonies were sterile, most comprised a single sex. Colonies with both male and female plants were confined to Cadnam Bog, which supported 49 (91%) of the colonies found. Overall, female shoots occurred at 41 (76%) colonies and males at 26 (48%), producing a female sex bias (1.6:1). All colonies occur in boggy woodland, mostly on the sides of low mounds of damp, acidic, peaty soil developed, due to poaching by ponies and cattle, at the base of trees, usually I. aquifolium. The community mainly comprises a species-poor mix of acidophilous mosses and liverworts, most frequently Mnium hornum, Pseudotaxiphyllum elegans and Leucobryum juniperoideum. Conclusions. Cadnam Bog appears to support the largest sexually reproducing population of Pallavicinia lyellii in England. The site is specially protected, actively managed with consideration to P. lyellii and seemingly in favourable condition for the plant. Research is needed to quantify canopy shade favoured by the plant and assess implications for woodland management. Future monitoring should include re-survey of populations every 3 yr.
Accumulation of Anthocyanins: An Adaptation Strategy of Mikania micrantha to Low Temperature in Winter

The accumulation of anthocyanins in leaves and stems of Mikania micrantha improves its adaptability to low-temperature environments during winter in areas where this species is invasive. The accumulation of anthocyanins in M. micrantha causes the plants to exhibit red coloration when encountering low-temperature environments during winter. Many studies have reported that the accumulation of anthocyanins near the plant surface filters light and improves photoprotection. However, the results of this study showed that the main role of anthocyanins accumulation in M. micrantha during winter was to increase both antioxidant capability and tolerance to low temperature. The results showed that the anthocyanin contents were significantly higher in red leaves and stems than in green leaves and stems, with more than 60-fold greater content in red leaves than in green leaves. In addition, the total antioxidant capability was significantly greater in red leaves and stems than in green leaves and stems. After 4°C treatment for 12 h, a large amount of reactive oxygen species accumulated in green leaves and stems, and the maximum photochemical efficiency decreased significantly. Compared with that of the green leaves, the net photosynthetic rate of red leaves was significantly higher. The biomass statistics revealed that the dry matter accumulation of M. micrantha plants with relatively large amounts of anthocyanins was significantly greater than that of plants with relatively low anthocyanin levels during the same period. Our results suggest that the accumulation of anthocyanins during winter is an adaptation strategy of M. micrantha to low winter temperatures.
Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.