Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor*

The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
Biochemical effect of l-Carnitine in Valporate induced hyperammonemia in rabbits

The present study was undertaken to elucidate the harmful effects of hyperammonemia induced by valporate (VPA) in white male New-Zealand rabbits; Morever, evaluation the potential protective and the therapeutic effect of L-carnitine (L-C). Fifty one white male New-Zealand rabbits were divided into five groups. Group I: (control group): comprised 12 white male New-Zealand rabbits, received no drugs. Group II: (L-C group): comprised 9 white male New-Zealand rabbits, received oral L-C (95 mg/kg body weight/day) daily for 30 days. Group III: (VPA group): comprised 12 white male New-Zealand rabbits, received a single intravenous dose of (130 mg/kg body weight) of VPA for induction of hyperammonemia. Group IV: (protective group): comprised 9 white male New-Zealand rabbits, received L-carnitine as in group II prior VPA administration. Group V: (therapeutic group): comprised 9 white male New-Zealand rabbits, received VPA as in group III prior L-C administration and the treatment was continued for 30 days later. Blood samples as well as liver and brain tissues were collected at 10th, 20th, 30th days from the onset of L-carnitine administration, and after 1 hour and at 10th, 20th, 30th days from the onset of VPA administration for determination of serum (Ammonia (NH3), Nitric oxide (NO), Gama-aminobutyric acid (GABA), Mono-amine oxidase (MAO)), liver and brain tissue (Catalase (CAT), Super oxide dismutase (SOD), Glutathion reductase (GR), and Malondialdehyde (L-MDA)) activities. The obtained results showed that, VPAinduced hyperammonemia caused a significant increase in serum NH3, NO, GABA, MAO, and liver and brain tissue MDA concentration. However, liver and brain tissue CAT, SOD, and GR activities were significantly decreased. Administration of LC was able to mitigate hyperammonemia induced by VPA through decreasing of NH3, NO, GABA, MAO, as well as liver and brain tissue MDA concentration in addition CAT, SOD, and GR activities in liver and brain tissues were significantly increased. These results suggest that, L-C may be successful in therapeutic of hyperammonemia, hyperammonaemic encephalopathy (HE) and hepatotoxicity (HT).
The conserved kinase NHK-1 is essential for mitotic progression and unifying acentrosomal meiotic spindles in Drosophila melanogaster

Conventional centrosomes are absent from the spindle in female meiosis in many species, but it is not clear how multiple chromosomes form one shared bipolar spindle without centrosomes. We identified a female sterile mutant in which each bivalent chromosome often forms a separate bipolar metaphase I spindle. Unlike wild type, prophase I chromosomes fail to form a single compact structure within the oocyte nucleus, although the integrity of metaphase I chromosomes appears to be normal. Molecular analysis indicates that the mutant is defective in the conserved kinase nucleosomal histone kinase-1 (NHK-1). Isolation of further alleles and RNA interference in S2 cells demonstrated that NHK-1 is also required for mitotic progression. NHK-1 itself is phosphorylated in mitosis and female meiosis, suggesting that this kinase is part of the regulatory system coordinating progression of mitosis and meiosis.
Comparative analysis of antioxidant and phenolic content of chloroform extract/fraction of Terminalia chebula

In the present study, two chloroform extracts of fruits of Terminalia chebula viz. “CHL1” and “CHL 2” prepared by maceration and sequential method respectively was compared for their antioxidant efficacy and phenolic content. The extraction procedure of plant material plays an important role in the activity of phytochemicals. Also, the assessment of antioxidant capacity of phytochemicals cannot be executed precisely by any single method due to complex nature of phytochemicals as multiple reaction characteristics and mechanisms can be involved. So, no single assay could accurately reflect comparison in a mixed or complex system. Therefore in the present study the comparison of extracts was done by using most widely used assays viz. DPPH, deoxyribose, reducing power, chelating power and lipid peroxidation assay. Furthermore, the UV-Vis spectrum of both extracts and the correlation between total phenolic content was examined in order to give an orientation to the search of phytochemicals responsible for their activity. From the results, it was concluded that antioxidant activity and phenolic compounds were predominant in the ‘CHL 2’ prepared by sequential method. The present study enlightening the useful extraction procedure of plant material
Effectively Integrating Technology in the Audit Course: An Application of the Technology Acceptance Model

Long-term success in their careers requires that accounting students are knowledgeable in the theory of accounting as well as the impact that information technology will have on the application of that theory. There is currently little guidance, however, for faculty to achieve effective integration of accounting and information technology in the classroom. One measure of effectiveness would be the students’ acceptance of the technology integration. To measure the success of a technology implementation in a business setting, many researchers have applied the Technology Acceptance Model (TAM), developed by Davis (Davis, Bagozzi, and Warshaw, 1989). This paper applies the TAM to a curriculum context where computer assisted auditing techniques (CAATs) were integrated into a financial statement auditing class and provides evidence supporting the application.
Derivatives of Mutual Information in Gaussian Vector Channels with Applications

In this paper, derivatives of mutual information for a general linear Gaussian vector channel are considered. We consider two applications. First, it is shown how the corresponding gradient relates to the minimum mean squared error (MMSE) estimator and its error matrix. Secondly, we determine the directional derivative of mutual information and use this geometrically intuitive concept to characterize the capacity-achieving input distribution of the above channel subject to certain power constraints. The well-known water-filling solution is revisited and obtained as a special case. Also for shaping constraints on the maximum and the Euclidean norm of mean powers explicit solutions are derived. Moreover, uncorrected sum power constraints are considered. The optimum input can here always be achieved by linear precoding.
A Black-Box Approach in Modeling Valve

Several valve stiction models have been proposed in the literature to help understand and study the behavior of sticky valves. In this paper, an alternative black-box modeling approach based on Neural Network (NN) is presented. It is shown that with proper network type and optimum model structures, the performance of the developed NN stiction model is comparable to other established method. The resulting NN model is also tested for its robustness against the uncertainty in the stiction parameter values. Predictive mode operation also shows excellent performance of the proposed model for multi-steps ahead prediction. Keywords—Control valve stiction, neural network, modeling.
BISD: Scan-based Built-In self-diagnosis

Built-In Self-Test (BIST) is less often applied to random logic than to embedded memories due to the following reasons: Firstly, for a satisfiable fault coverage it may be necessary to apply additional deterministic patterns, which cause additional hardware costs. Secondly, the BIST-signature reveals only poor diagnostic information. Recently, the first issue has been addressed successfully. The paper at hand proposes a viable, effective and cost efficient solution for the second problem.
Mining NANOG Mailing List

It had been shown that the misbehaviors by few malicious, compromised or misconfigured BGP routers could lead to serious outages in Internet. This failing becomes progressively crucial as the recent prosper of outage-sensitive applications such as Voice over IP, streaming media, and video conferencing. To address these misbehaviors, previous work mainly focus on distributedly detect or prevent outages using limited state of Internet. In this paper, we present a first step towards efficient troubleshooting by mining network operators mailing lists. Using Natural Language Processing (NLP) and Machine Learning, we develop a new approach to extract useful information from the mailing forum on North American Network Operators Group (NANOG). Our experimental results show that the proposed approach detects 94 out of 105 outages from NANOG with a false positive rate of only 7.3%. We validate the extracted outage using real network logs collected by Route Views project. While our approach is not perfectly accurate, we envision it to be a useful information to existing anomaly detection/prevension mechanisms.
Toll receptors and sepsis

Toll-like receptors are a family of receptors that recognize components of bacteria and induce a proinflammatory response by cells, including macrophages and endothelial cells. Ten human Toll receptors differing in their specificity for microbial components have been cloned. They respond to various components, including lipopolysaccharide of Gram-negative bacteria, lipopeptides of Gram-positive cell walls, bacterial DNA, and flagella. Some Toll-like receptors require the cooperation of an adapter protein. Toll-like receptor 4 function requires the presence of the protein MD2. Recently, it has been shown that Toll-like receptors function cooperatively to increase the specificity of response to a given microbe. Human polymorphisms of Toll-like receptor genes have been discovered and are associated with hyporesponsiveness to bacterial components.
Twitter Paraphrase Identification with Simple Overlap Features and SVMs

We present an approach to identifying Twitter paraphrases using simple lexical over-lap features. The work is part of ongoing re-search into the applicability of knowledge-lean techniques to paraphrase identification. We utilize features based on overlap of word and character n-grams and train support vector machine (SVM). Our results demonstrate that character and word level overlap features in combination can give performance comparable to methods employing more sophisticated NLP processing tools and external resources. We achieve the highest F-score for identifying paraphrases on the Twitter Paraphrase Corpus as part of the SemEval-2015 Task1.
Damage Monitoring of Dry and Saturated Rocks Using Piezo Transducers

This paper explores the possibility of using the electro-mechanical impedance (EMI) technique for structural health monitoring (SHM) of underground rock structures. The underground structures are complex in design and require continuous inspection for their maintenance. However, some of the underground areas are inaccessible for the inspection team or might warrant a special clearing arrangement, leaving the structure out of service. The complexity in their design, their construction, and the conditions encountered during service life necessitate the deployment of a dedicated SHM system. Sometimes the stress ratio in rock because of overburden stress and tectonic activities may reach a high value exceeding threshold, which may lead to rock bursts and subsequent failure of the structure. The SHM technique becomes important for underground infrastructure to enable timely detection of the damage caused by any anticipated or unanticipated loads. In the present study, rock specimens have been tested in a laboratory environment under saturated, as well as dry, conditions, under pre-loaded stress conditions by applying continuous quasi-static loading, so as to simulate the near-real-life underground conditions. The EMI technique is used for damage monitoring. The vibrations generated by the actuation of lead zirconate titanate (PZT) patch are sensed by the same PZT patch and recorded in the form of conductance and susceptance signatures. The signatures have been quantified using root-mean-square-deviation (RMSD) method. The test results clearly establish the potential of the EMI technique in detecting and quantifying load-induced damage in dry, as well as saturated, conditions in the underground structures, opening avenues for applications in real-life situations.
Phase retrieval in 3D X-ray magnified phase nano CT: Imaging bone tissue at the nanoscale

X-ray phase computed tomography (CT) offers higher sensitivity than conventional X-ray CT. A new phase-CT instrument producing a nano-focused beam has been developed at the ESRF (European Synchrotron Radiation Facility) for nano-imaging. In order to obtain final images, a suited phase retrieval algorithm is necessary, which is attracting broader interest recently. In this paper, we explicit the 3D phase CT image reconstruction problem, including the stage of phase retrieval prior to 3D CT reconstruction. The phase retrieval problem is solved by extending the single distance Paganin method to multi-distance acquisitions, followed by an iterative non-linear conjugate gradient descent optimization method. The method is evaluated on bone tissue samples imaged at voxel sizes of 120 nm. The results obtained from acquisition at 1 and 4 distances, with and without the iterative refinement are compared. The results show that this method yields improved images compared to other methods.
Text Classification Using Graph-Encoded Linguistic Elements

Inspired by the goal to more accurately classify text, we describe an effort to map tokens and their characteristic linguistic elements into a graph and use that expressive representation to classify text phrases. We outperform the bag-of-words approach by exploiting word order and the semantic and syntactic characteristics within the phases. In this study, we map tagged corpora into a placeholder graph structure and classify the phrases within, using the crossdimensional linguistic characteristics of each token. Finally, we present heuristics for use in applying this method to other corpora.
Influences of ambient temperature, surface fluctuation and charge density on wettability properties of graphene film

Some molecular dynamics simulations focusing on the interactions between graphene films and water droplets are carried out in this article to investigate the fluid–solid interfacial behavior of surface wettability. The wettability of an ideal graphene film is investigated at room temperature at the beginning of the simulations, then the influences of ambient temperature, surface fluctuation and charge density of the graphene film on the wetting behaviors of water droplets on the film are also discussed from three points of view, namely the interaction energy of the graphene and the water droplet, the mass density of water and the water contact angle on the graphene film. The simulation results indicate that the ideal graphene film is slightly hydrophobic and that both the ambient temperature and the fluctuation of the graphene film play a negative role during the wetting processes. The observations also show that, once charged, the wetting property of graphene changes massively, from slightly hydrophobic to super-hydrophilic.
Mapping of O-GlcNAc Sites of 20 S Proteasome Subunits and Hsp90 by a Novel Biotin-Cystamine Tag

The post-translational modification of proteins with O-GlcNAc is involved in various cellular processes including signal transduction, transcription, translation, and nuclear transport. This transient protein modification enables cells or tissues to adapt to nutrient conditions or stress. O-Glycosylation of the 26 S proteasome ATPase subunit Rpt2 is known to influence the stability of proteins by reducing their proteasome-dependent degradation. In contrast, knowledge of the sites of O-GlcNAcylation on the subunits of the catalytic core of the 26 S proteasome, the 20 S proteasome, and the impact on proteasome activity is very limited. This is predominantly because O-GlcNAc modifications are often substoichiometric and because 20 S proteasomes represent a complex protein mixture of different subtypes. Therefore, identification of O-GlcNAcylation sites on proteasome subunits essentially requires effective enrichment strategies. Here we describe an adapted β-elimination-based derivatization method of O-GlcNAc peptides using a novel biotin-cystamine tag. The specificity of the reaction was increased by differential isotopic labeling with either “light” biotin-cystamine or deuterated “heavy” biotin-cystamine. The enriched peptides were analyzed by LC-MALDI-TOF/TOF-MS and relatively quantified. The method was optimized using bovine α-crystallin and then applied to murine 20 S proteasomes isolated from spleen and brain and murine Hsp90 isolated from liver. Using this approach, we identified five novel and one known O-GlcNAc sites within the murine 20 S proteasome core complex that are located on five different subunits and in addition two novel O-GlcNAc sites on murine Hsp90β, of which one corresponds to a previously described phosphorylation site.
Role of Automation in Computer-based Systems

"Manual Vs Automatic" has been a controversial topic for ages in Social Sciences and recently (a couple of decades) in Computer Science. This paper argues that, where applicable, automation should be adopted as a prime strategy where human beings are likely to make more mistakes as compared to machines. Paper describes how most of the problems observed in computer-based systems are due to human mistakes at various stages of system development life cycle (analysis, design, implementation, testing, deployment and operations) and then describes the role of automation in reducing such problems, where applicable.
BlogScope: spatio-temporal analysis of the blogosphere

We present BlogScope (www.blogscope.net), a system for analyzing the Blogosphere. BlogScope is an information discovery and text analysis system that offers a set of unique features. Such features include, spatio-temporal analysis of blogs, flexible navigation of the Blogosphere through information bursts, keyword correlations and burst synopsis, as well as enhanced ranking functions for improved query answer relevance. We describe the system, its design and the features of the current version of BlogScope.
Nox-generated ROS modulate glucose uptake in a leukaemic cell line

The discovery of superoxide-generating enzymes homologues of phagocytic NAD(P)H oxidase, the Nox family, has led to the concept that reactive oxygen species (ROS) are ‘intentionally’ generated with biological functions in various cell types. In this study, by treating an acute leukaemic cell line with different antioxidants, ROS generation was shown to be crucially involved in the modulation of glucose transport (mediated by Glut1), which is frequently up-regulated in cancer cells. Then, this study tried to elucidate ROS source(s) and mechanisms by which ROS are involved in Glut1 activity regulation. Results prove that Nox2 and Nox4 are the candidates and that phosphorylation processes are important in the regulation of glucose uptake on which cancer cells rely. On the whole, data suggest that both Glut1 and Nox homologues may be considered new potential targets in the treatment of leukaemia.
A study on keyhole evolution and weld ripple formation in dissimilar welding under pulsed laser

A three-transient multiphase model is developed to study the dissimilar metal welding of pure niobium plate to titanium alloy Ti–6Al–4V sheet under pulsed laser. The physical process of dissimilar metal welding involves melting, resolidification, mass transfer, self-consistent keyhole, and weld bead formation. The major physical factors, such as recoil pressure induced by vapourisation, surface tension, heat transfer, fluid flow, Marangoni shear stress, buoyancy force, and their coupling are considered. The results show that the keyhole mainly occurs on the Ti–6Al–4V side due to the differences in physical properties of the materials. The effects of pulse overlapping factor on the weld bead are studied. It is found that the pulsed laser has a significant influence on the weld bead formation. The mixing of materials mostly occurred in the upper part of the molten pool. The simulated weld bead profile and the phase distribution agree well with the experimental results.
Combining X-ray and Electron Based in situ Characterization of Catalysts

To understand the function of catalysts for heterogeneous catalysis and improve catalytic properties, a fundamental insight into structure-functionality relationships is required. As catalysts may change their structure with respect to the environment, it is essential to investigate the catalysts under reaction conditions. Furthermore, structural and compositional information have to be acquired on different length scales [1] and such in situ studies require dedicated complementary techniques. In situ X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are eminent to follow the average catalyst’s structural (local and global) and electronic changes during synthesis and reaction conditions [2]. In order to follow the dynamics (stability, topography, etc.) of the surface and interfaces, imaging is often the solution [3]. Nanoscale imaging and spectroscopy of catalysts in a gaseous environment is traditionally performed in an environmental transmission electron microscope (ETEM). TEM gives insight in the atomic changes during reaction, however it is restricted to relatively low pressure (<~1 kPa) and a thin sample (<~100 nm) [4]. Spatially resolved information on the meso scale (50 nm–1 µm) can be obtained by X-ray microscopy, which enables in situ studies at both ambient and elevated pressure [5]. Furthermore, due to the much higher penetration depth of X-rays compared to electrons, X-ray based characterization techniques are more suited for realistic sample and conditions. This contribution illustrates how catalyst properties can be elucidated by the combination of X-ray and electron based methods in general. One example is the study of Ga-based (PdGa and NiGa) catalysts for methanol synthesis, where the average local structure and electronic structure obtained with XAS is combined with the average global structural information from XRD. Additionally, single nanoparticle (NP) compositional and structural studied by high-resolution ETEM The catalysts were investigated during formation and methanol