Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical composition, toxicity and antioxidant activities of essential oils of stem bark of Nigerian species of guava (Psidium guajava Linn.)

Essential oil from the stem bark of Nigerian species of Psidium guajava of the family Myrtaceae was obtained by hydro-distillation using an all-glass Clavenger apparatus. GC and GC/MS analysis were carried out on the essential oil and was found to contain 62 compounds constituting 99.98 % of the total oil composition. The principal constituents are hydrocarbons, amines, amides and esters with 3,6-dioxa-2,4,5,7-tetraoctane,2,2,4,4,5,5,7,7-octamethyl (11.67 %) and cyclononane (10.66 %) dominating the total essential oil. Brine shrimp lethality test was carried out to determine the toxicity of the oils to living organisms (shrimps). LC50 value (µg/ml) of 1.0009 obtained showed that the essential oil of P. guajava stem bark was toxic. The antioxidant property of essential oil was investigated by measuring the decrease in absorption at 517 nm of 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) in a UV/visible spectrophotometer. The oil showed better activity as a radical scavenger than α-tocopherol. The oil activity was 71.83 % at 0.2 mg/ml and the absorption is stoichiometric with respect to the number of electron taken up. Thus, the results of this study showed that the essential oil from P. guajava was not only toxic; it possessed antioxidant activity, which could exert beneficial actions against pathological alterations caused by the presence of highly reactive free radicals. The toxicity of the oil can be taken advantage of in the therapy of diseases involving cell or tumor growth.
The Java Starter: an Ontology-Based Tutoring System for Java Beginners

This paper presents the design and development of the Java Starter, an ontology-based tutoring system meant to support the teaching of the Java programming language to beginners. The developed prototype is capturing the domain knowledge in the form of an ontology, developed using the Protégé ontology editor. The reasoner used for inference tasks is HermiT 1.4. 3.456. The system has been tested at every level of implementation, using JUnit for the Java component, Selenium for the user interface, and the HermiT reasoner for the ontology.
Simulation of Influenza Virus Aerosol Transmission in Communities Based on the FLUENT

The fourth order accuracy Rungekutta and the method of large eddy simulation (LES) based on FLUENT were used to solve the differential equations of equine influenza, and its diffusion law was obtained. After verifying the reliability of the numerical model through indoor experiments, the unsteady movement of viruses outside buildings was simulated. Under the influence of the average wind field, virus particles spread faster in the building cluster. It can be seen that the location of the virus outbreak and the downwind direction were the most dangerous, the upstream buildings were the safest. Numerical models have certain accuracy in predicting the temporal and spatial distribution of epidemic transmission.
Coded Slotted ALOHA over Rayleigh Block Fading Channels: BP Threshold and Converse Bound

An asymptotic analysis method is proposed for the coded slotted ALOHA protocol over Rayleigh block fading channels. Here, maximum distance separable (MDS) codes are employed to recover erasure errors due to collisions and a channel code is used to mitigate multi-device interference. With the erasure probability of an MDS code and the average error probability of channel decoding in the presence of both fading and collisions, density evolution equations are formulated. On the basis of these equations, both a belief propagation (BP) decoding threshold and a converse bound of the offered traffic are derived. The numerical results show that MDS coding provides more flexible values of energy efficiency and higher BP thresholds than those of the conventional irregular repetition slotted ALOHA (IR-SA). The converse bound is tight in the sense that the BP threshold of a spatially coupled scheme is close to it.
Vroom: Accelerating the Mobile Web with Server-Aided Dependency Resolution

The existing slowness of the web on mobile devices frustrates users and hurts the revenue of website providers. Prior studies have attributed high page load times to dependencies within the page load process: network latency in fetching a resource delays its processing, which in turn delays when dependent resources can be discovered and fetched. To securely address the impact that these dependencies have on page load times, we present Vroom, a rethink of how clients and servers interact to facilitate web page loads. Unlike existing solutions, which require clients to either trust proxy servers or discover all the resources on any page themselves, Vroom's key characteristics are that clients fetch every resource directly from the domain that hosts it but web servers aid clients in discovering resources. Input from web servers decouples a client's processing of resources from its fetching of resources, thereby enabling independent use of both the CPU and the network. As a result, Vroom reduces the median page load time by more than 5 seconds across popular News and Sports sites. To enable these benefits, our contributions lie in making web servers capable of accurately aiding clients in resource discovery and judiciously scheduling a client's receipt of resources.
Effects of Footwear on Impact Forces and Soft Tissue Vibrations during Drop Jumps and Unanticipated Drop Landings

Abstract The purpose of this study was to explore the footwear effects on impact forces and soft-tissue vibrations during landing. 12 male basketball players were instructed to perform drop jumps and unanticipated drop landings from 30 cm, 45 cm, and 60 cm heights in basketball shoes (BS) and control shoes (CS). 3D kinematics, ground reaction force (GRF), and soft-tissue vibrations of the leg, and acceleration of the shoe heel counter were measured simultaneously. The results showed no significant shoe effect on the characteristics of the impact force nor on the resonance frequency and peak transmissibility of soft-tissue vibrations during the impact phase of the drop jump. For the unanticipated drop landings, however, the magnitude of both peak GRF and peak loading rate were significantly lower with BS compared to CS across all 3 heights (p<0.05); meanwhile BS showed a significant decrease in GRF frequency compared to CS at 45 cm (p<0.05) and 60 cm (p<0.01) heights. Furthermore, the peak transmissibility in BS was significantly lower than that in CS for both the quadriceps and hamstrings during the 60 cm unanticipated drop landing (p<0.05). These findings provide preliminary evidence suggesting that if the neuromuscular system fails to prepare properly for an impact during landing, a shoe intervention may be an effective method for minimizing impact force and reducing soft tissue resonance.
Breaking and Fixing Destructive Code Read Defenses

Just-in-time return-oriented programming (JIT-ROP) is a powerful memory corruption attack that bypasses various forms of code randomization. Execute-only memory (XOM) can potentially prevent these attacks, but requires source code. In contrast, destructive code reads (DCR) provide a trade-off between security and legacy compatibility. The common belief is that DCR provides strong protection if combined with a high-entropy code randomization. The contribution of this paper is twofold: first, we demonstrate that DCR can be bypassed regardless of the underlying code randomization scheme. To this end, we show novel, generic attacks that infer the code layout for highly randomized program code. Second, we present the design and implementation of BGDX (Byte-Granular DCR and XOM), a novel mitigation technique that protects legacy binaries against code inference attacks. BGDX enforces memory permissions on a byte-granular level allowing us to combine DCR and XOM for legacy, off-the-shelf binaries. Our evaluation shows that BGDX is not only effective, but highly efficient, imposing only a geometric mean performance overhead of 3.95 % on SPEC.
Dok-4 Is a Novel Negative Regulator of T Cell Activation1

Dok-4 (downstream of tyrosine kinase-4) is a recently identified member of the Dok family of adaptor proteins, which are characterized by an amino-terminal pleckstrin homology domain, a phosphotyrosine-binding domain, and a carboxyl-terminal region containing several tyrosines and poly-proline-rich motifs. Two members of the Dok family, Dok-1 and Dok-2, have already been described as negative regulators in T cells. However, the function of Dok-4, which is also expressed in T cells, remains unknown. In this study, we report that Dok-4 is phosphorylated after TCR engagement and shuttled within the cytoplasm of T cells before being recruited to the polarized microtubule organizing center after the formation of the immunological synapse. Loss-of-function experiments using RNA interference constructs show that Dok-4 is a negative regulator of ERK phosphorylation, IL-2 promoter activity, and T cell proliferation. Exogenous expression of wild-type Dok-4 induces a significant activation of Rap1, which is involved in the regulation of ERK. The pleckstrin homology domain of Dok-4 is required both for its cytoplasmic shuttling and relocalization as well as for its inhibitory properties on T cell activation. Thus, Dok-4 represents a novel negative regulator of T cells.
Pro-inflammatory Macrophages Sustain Pyruvate Oxidation through Pyruvate Dehydrogenase for the Synthesis of Itaconate and to Enable Cytokine Expression*

Upon stimulation with Th1 cytokines or bacterial lipopolysaccharides, resting macrophages shift their phenotype toward a pro-inflammatory state as part of the innate immune response. LPS-activated macrophages undergo profound metabolic changes to adapt to these new physiological requirements. One key step to mediate this metabolic adaptation is the stabilization of HIF1α, which leads to increased glycolysis and lactate release, as well as decreased oxygen consumption. HIF1 abundance can result in the induction of the gene encoding pyruvate dehydrogenase kinase 1 (PDK1), which inhibits pyruvate dehydrogenase (PDH) via phosphorylation. Therefore, it has been speculated that pyruvate oxidation through PDH is decreased in pro-inflammatory macrophages. However, to answer this open question, an in-depth analysis of this metabolic branching point was so far lacking. In this work, we applied stable isotope-assisted metabolomics techniques and demonstrate that pyruvate oxidation is maintained in mature pro-inflammatory macrophages. Glucose-derived pyruvate is oxidized via PDH to generate citrate in the mitochondria. Citrate is used for the synthesis of the antimicrobial metabolite itaconate and for lipogenesis. An increased demand for these metabolites decreases citrate oxidation through the tricarboxylic acid cycle, whereas increased glutamine uptake serves to replenish the TCA cycle. Furthermore, we found that the PDH flux is maintained by unchanged PDK1 abundance, despite the presence of HIF1. By pharmacological intervention, we demonstrate that the PDH flux is an important node for M(LPS) macrophage activation. Therefore, PDH represents a metabolic intervention point that might become a research target for translational medicine to treat chronic inflammatory diseases.
Independent stimulation of glucose metabolism and Na+-K+ exchange by insulin in the human forearm.

Insulin promotes potassium uptake into skeletal muscle by stimulating the activity of the Na+-K+ pump. To test whether insulin-induced glucose and potassium uptake are linked processes in vivo, we used the perfused forearm technique in healthy volunteers. Local hyperinsulinemia (125 +/- 11 microU/ml for 100 min) induced a net uptake of glucose and potassium (4.79 +/- 0.61 and 0.76 +/- 0.22 mumol.min-1.100 ml-1 of forearm volume, respectively). When an intra-arterial ouabain infusion (0.72 microgram.min-1.100 ml-1, producing local levels of approximately 0.5 mM) was superimposed on the insulin infusion, potassium uptake was blocked (0.026 +/- 0.190 ml.min-1.100 ml-1, P less than 0.02), and glucose uptake was decreased (to 3.31 +/- 0.34 mumol.min-1.100 ml-1, P less than 0.03). The latter change was explained by a 30% fall in forearm blood flow (from 2.95 +/- 0.10 to 2.01 +/- 0.18 ml.min-1.100 ml-1, P less than 0.001). To separate out the effect of blood flow, in another series of studies forearm blood flow was clamped by co-infusing propranolol and phentolamine (7 and 8 micrograms.min-1.100 ml-1, respectively). Under these conditions of fixed flow (7.0 +/- 0.8 ml.min-1.100 ml-1), ouabain still abolished the stimulatory effect of insulin on potassium uptake but had only a small (and statistically insignificant) effect on forearm glucose extraction (from 20 +/- 2 to 16 +/- 2%, P = N>). We conclude that in human forearm muscle ouabain inhibits Na+-K+ exchange and depresses insulin-induced glucose uptake via an adrenergic-mediated limitation of blood flow. (ABSTRACT TRUNCATED AT 250 WORDS)
Growth windows of epitaxial NbN x ﬁlms on c -plane sapphire and their structural and superconducting properties

NbN ﬁlms are grown on c -plane sapphire substrates by molecular beam epitaxy. The structural and super-conducting properties of the ﬁlms are characterized to demonstrate that growth parameters such as substrate temperature and active nitrogen ﬂux affect the structural phase of ﬁlms, and thereby the superconducting critical temperature. Four phases of NbN are identiﬁed for ﬁlms grown in different conditions. We demonstrate that atomically ﬂat and highly crystalline β -Nb 2 N ﬁlms can be grown at substrate temperatures of 1100 ◦ C or higher, and that the superconducting critical temperature of phase-pure β -Nb 2 N ﬁlms is 0 . 35 < T c < 0 . 6 K for ﬁlms grown at different substrate temperatures.
Underdetermined AOA Estimation of Correlated Sources Using Hybrid Beamforming Based on NSC Structure

Inheriting the enhanced degree of freedom (DOF) from nonuniform array processing, the hybrid beamforming (HBF) structure based on interleaved nonuniform subarray connection has been shown to perform well when the number of signal sources to be estimated is larger than the number of radio frequency (RF) chains. However, the angle-of-arrival (AOA) estimation may fail if the signal sources are correlated (e.g., when there are multiple arriving paths belonging to the same signal source). In this paper, we intend to exploit the enhanced DOF of the HBF with nonuniform subarray connection (NSC) in the presence of correlated signals. We investigate the effect of correlated signals on the difference co-array and propose two-dimensional (2D) indexing for AOA estimation. By adopting the compressed sensing (CS) framework to identify the 2D indices corresponding to possible signal sources, the underde-termined AOA estimation is achieved. In addition, correlation (e.g., multipath) association can be conducted using the index information. Simulation results show that the proposed method can effectively achieve underdetermined AOA estimation when there is a mixture of correlated and uncorrelated signals. This is the first such result for the NSC- HBF system.
Thermal interface conductance in Si/Ge superlattices by equilibrium molecular dynamics

Gesuperlattices.Thermalconductancecalculationsofsuperlatticeswithperiodthicknessesrangingfrom0. 5to60nmarepresentedaswellasthetemperaturedependence.ResultshavebeencomparedtocomplementaryGreen-Kubothermalconductivitycalculationsdemonstratingthatthermalconductivityofperfectsuperlatticescanbedirectlydeduced from interfacial conductance in the investigated period range. This conﬁrms the predominant role ofinterfaces in materials with large phonon mean free paths.DOI: 10.1103/PhysRevB.85. 195302 PACS number(s): 65
Anti‐oxidative and cholesterol efflux capacities of high‐density lipoprotein are reduced in ischaemic cardiomyopathy

Various pathological changes lead to the development of heart failure (HF). HDL is dysfunctional in both acute coronary syndrome, as measured by the HDL inflammatory index (HII) assay, and stable coronary disease, as measured by cholesterol efflux capacity. We therefore hypothesized that these functions of HDL are also impaired in subjects with ischaemic cardiomyopathy.
Massive Expansion of Ubiquitination-Related Gene Families within the Chlamydiae

Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.
1 AN ALGORITHM BASED ON DIFFERENTIAL EVOLUTION FOR MULTIOBJECTIVE PROBLEMS

This paper presents a new multi-objective evolutionary algorithm based on differential evolution. The proposed approach adopts a secondary population in order to retain the non-dominated solutions found during the evolutionary process. Additionally, the approach also incorporates the concept of ε-dominance to get a good distribution of the solutions retained. The main goal of this work was to keep the fast convergence exhibited by Differential Evolution in global optimization when extending this heuristic to multiobjective optimization. We adopted standard test functions and performance measures reported in the specialized literature to validate our proposal. Our results are compared with respect to another multi-objective evolutionary algorithm based on differential evolution (Pareto Differential Evolution) and with respect to two approaches that are representative of the state-of-the-art in the area: the NSGA-II and ε-MOEA.
Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context

Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify putative T4Es from the complete genome of α- and γ-proteobacteria, we developed a Perl-based command line bioinformatics tool called S4TE (searching algorithm for type-IV secretion system effectors). The tool predicts and ranks T4E candidates by using a combination of 13 sequence characteristics, including homology to known effectors, homology to eukaryotic domains, presence of subcellular localization signals or secretion signals, etc. S4TE software is modular, and specific motif searches are run independently before ultimate combination of the outputs to generate a score and sort the strongest T4Es candidates. The user keeps the possibility to adjust various searching parameters such as the weight of each module, the selection threshold or the input databases. The algorithm also provides a GC% and local gene density analysis, which strengthen the selection of T4E candidates. S4TE is a unique predicting tool for T4Es, finding its utility upstream from experimental biology.
Tocotrienols prevent hydrogen peroxide-induced axon and dendrite degeneration in cerebellar granule cells

It is well known that reactive oxygen species (ROS) attack several living tissues and increase the risk of development and progression of serious diseases. In neuronal level, ROS induce cell death in concentration-dependent fashion. However, little is known about the mechanisms of neuronal changes by ROS prior to induction of cell death. Here we found that treatment of cerebellar granule neurons (CGCs) with 0.5 μM hydrogen peroxide induced axonal injury, but not cell death. The number of dendrites remarkably decreased in hydrogen peroxide-treated CGCs, and extensive beading was observed on survival dendrites. In addition, an abnormal band of the original collapsin response mediator protein (CRMP)-2 was detected by Western blotting in hydrogen peroxide-treated CGCs. Treatment with each tocotrienol isoform prevented axonal and dendrite degeneration and induction of the abnormal band of the original band of CRMP-2 in hydrogen peroxide-treated CGCs. These results indicate that treatment with tocotrienols may therefore be neuroprotective in the presence of hydrogen peroxide by preventing changes to the CRMP-2 that occur before neuron death.
Stenotrophomonas maltophilia Phenotypic and Genotypic Diversity during a 10-year Colonization in the Lungs of a Cystic Fibrosis Patient

The present study was carried out to understand the adaptive strategies developed by Stenotrophomonas maltophilia for chronic colonization of the cystic fibrosis (CF) lung. For this purpose, 13 temporally isolated strains from a single CF patient chronically infected over a 10-year period were systematically characterized for growth rate, biofilm formation, motility, mutation frequencies, antibiotic resistance, and pathogenicity. Pulsed-field gel electrophoresis (PFGE) showed over time the presence of two distinct groups, each consisting of two different pulsotypes. The pattern of evolution followed by S. maltophilia was dependent on pulsotype considered, with strains belonging to pulsotype 1.1 resulting to be the most adapted, being significantly changed in all traits considered. Generally, S. maltophilia adaptation to CF lung leads to increased growth rate and antibiotic resistance, whereas both in vivo and in vitro pathogenicity as well as biofilm formation were decreased. Overall, our results show for the first time that S. maltophilia can successfully adapt to a highly stressful environment such as CF lung by paying a “biological cost,” as suggested by the presence of relevant genotypic and phenotypic heterogeneity within bacterial population. S. maltophilia populations are, therefore, significantly complex and dynamic being able to fluctuate rapidly under changing selective pressures.