Miracle-dz/UniFAR-FTUs huggingface dataset:
MetaSim—A Sequencing Simulator for Genomics and Metagenomics

Background The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. Methodology/Principal Findings To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. Conclusions/Significance MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.
Structural and biological properties of human recombinant myeloperoxidase produced by Chinese hamster ovary cell lines.

The cDNA encoding human myeloperoxidase carries three ATG codons in frame; 144, 111 and 66 bp upstream from the proprotein DNA sequence. In order to determine the most efficient signal sequence, three cDNA modules starting at each of the ATG were cloned into an eucaryotic expression vector and stably expressed in Chinese hamster ovary cell lines. In all three cases, recombinant human myeloperoxidase (recMPO) was secreted into the culture medium of transfected cells, indicating that each of the signal peptides functions efficiently. One of the recombinant cell lines, which was amplified using methotrexate, overexpresses enzymatically active recMPO up to 6 micrograms.ml-1.day-1. The recombinant product was purified by a combination of ion-exchange and metal-chelate chromatography, and characterized in terms of molecular mass, amino-terminal amino acid analysis, glycosylation, physicochemical properties and biological activity. The data show that recMPO is secreted essentially as a monomeric, heme-containing, single-chain precursor of 84 kDa which exhibits peroxidase activity. Amino-terminal analysis indicated that cleavage of the signal peptide occurs between amino acids 48 and 49. In addition, recMPO appeared to be glycosylated up to the last stage of sialylation, to an extent similar to that of the natural enzyme. Specific activity measurements as well as stability data, in various pH, temperature, ionic strength and reducing conditions, indicated that the recombinant single-chain enzyme behaves essentially in the same way as the natural two-chain molecule. Finally, recMPO was shown to exert potent cytotoxicity towards Escherichia coli when provided with its physiological substrates, i.e. hydrogen peroxide and chloride ions.
Shape Analysis of Three-Dimensional Curve Surface for Flexible Rolling Metal Plate

A method to analyze the shape of three-dimensional curve surface for flexible rolling forming metal plate is proposed based on the traditional rolling and multi-point adjustment technology. It has smaller rebound and better forming in comparison with the traditional method which is using the surface deformation. The simulation experiments are implemented using the developed experimental device to demonstrate the feasibility and practicality of the flexible rolling forming. The proposal could be used in the various industries.
Effects of the Selective α5-GABAAR Antagonist S44819 on Excitability in the Human Brain: A TMS–EMG and TMS–EEG Phase I Study

Alpha-5 gamma-aminobutyric acid type A receptors (α5-GABAARs) are located extrasynaptically, regulate neuronal excitability through tonic inhibition, and are fundamentally important for processes such as plasticity and learning. For example, pharmacological blockade of α5-GABAAR in mice with ischemic stroke improved recovery of function by normalizing exaggerated perilesional α5-GABAAR-dependent tonic inhibition. S44819 is a novel competitive selective antagonist of the α5-GABAAR at the GABA-binding site. Pharmacological modulation of α5-GABAAR-mediated tonic inhibition has never been investigated in the human brain. Here, we used transcranial magnetic stimulation (TMS) to test the effects of a single oral dose of 50 and 100 mg of S44819 on electromyographic (EMG) and electroencephalographic (EEG) measures of cortical excitability in 18 healthy young adults in a randomized, double-blinded, placebo-controlled, crossover phase I study. A dose of 100 mg, but not 50 mg, of S44819 decreased active motor threshold, the intensity needed to produce a motor evoked potential of 0.5 mV, and the amplitude of the N45, a GABAAergic component of the TMS-evoked EEG response. The peak serum concentration of 100 mg S44819 correlated directly with the decrease in N45 amplitude. Short-interval intracortical inhibition, a TMS–EMG measure of synaptic GABAAergic inhibition, and other components of the TMS-evoked EEG response remained unaffected. These findings provide first time evidence that the specific α5-GABAAR antagonist S44819 reached human cortex to impose an increase in cortical excitability. These data warrant further development of S44819 in a human clinical trial to test its efficacy in enhancing recovery of function after ischemic stroke. SIGNIFICANCE STATEMENT The extrasynaptic α-5 gamma-aminobutyric acid type A receptor (α5-GABAAR) regulates neuronal excitability through tonic inhibition in the mammalian brain. Tonic inhibition is important for many fundamental processes such as plasticity and learning. Pharmacological modulation of α5-GABAAR-mediated tonic inhibition has never been investigated in the human brain. This study demonstrates that S44819, a selective α5-GABAAR antagonist, increases cortical excitability in healthy human subjects, as indicated by specific markers of transcranial magnetic stimulation-induced muscle and brain responses measured by electromyography and electroencephalography. Our findings imply that tonic inhibition in human cortex can be modified effectively and that this modification can be quantified with noninvasive brain stimulation methods. The actions of S44819 may be suitable to improve plasticity and learning.
PCL assay application in superoxide anion-radical scavenging capacity of tea Camellia sinensis extracts.

BACKGROUND Plant polyphenols are known for their limiting of adverse effects on reactive oxygen species (ROS) in biological systems. The photochemiluminescence (PCL) assay allows to evaluate the antiradical activity of a compound in the presence of a superoxide anion-radical (O •-), which is one of the ROS directly associated with the human body. In this work, determination of the superoxide anion radical scavenging activity of different tea extracts using the PCL assay was performed. MATERIAL AND METHODS Investigations were conducted on different tea leaves extracts. The study included five kinds of tea leaves subjected to aqueous and ethanol extraction procedure. Catechins content was evaluated using HPLC. Antiradical activity of the samples was conducted with use of Photochem assay. RESULTS Analysis of total catechins content in tea aqueous extracts enabled them to be arranged as follows: yellow > green > white > red > black, while for ethanol extracts it was: yellow = green > white > red > black. The examined tea extracts were ranked from highest to lowest water-soluble antioxidative capacity (ACW) values as follows: yellow > green > white > red > black. The results of lipid-soluble antioxidative capacity (ACL) values for aqueous extracts were similar; however, were approximately 50% lower than those presented as ACW. The second examined group were ethanol extracts, which ranked for ACW values: yellow > green = red = white > black, while ACL values ranked as follows: yellow > white = black = red > green. PCL assay results were correlated with total catechin content in aqueous extracts. CONCLUSIONS Antiradical activity of different tea leaves extracts in PCL assay, showed that the highest activity was found in extracts of yellow tea; the lowest, however, was identified in black tea extracts.
Wind Farm SCADA System's Web Implementation Based on the Comet Technology

To improve the strong real-time performance and high reliability of wind farm SCADA system, this paper proposes a Comet-based strategy with HTTP long polling to achieve the web implementation of SCADA system. Compared to the asynchronous communication mechanism based on Ajax engine, Comet, using the server push technology as the core, can further enhance the information exchange's real-time performance effectively. It can also avoid a frequent exchange between client and server. Thus we can reduce the information congestion and transmission delay in network.
Application of the Boundary‐Element Method to Offshore Cathodic Protection Modeling

This paper deals with the main aspects of the calculation of current and potential distributions and summarizes some results obtained on different systems using a computer program based on the boundary-element method. Model results are compared to literature data for well-known geometries, and to experimental data obtained both in laboratory testing with a suitable cell and infield testing on offshore structures (in particular platform nodes). The good predictive capability of computer modeling is shown.
Efficient Level of Service Classification for Traffic Monitoring in the Compressed Video Domain

This paper presents a new method for estimating the level of service (LOS) on motorways in the compressed video domain. The method performs statistical computations on motion vectors of MPEG4 encoded video streams within a predefined region of interest to determine a set of four motion features describing the speed and density of the traffic stream. These features are fed into a Gaussian radial basis function network to classify the corresponding LOS. To improve the classification results, vectors of moving objects are clustered and outliers are eliminated. The proposed method is designed to be executed on a server system, where a large number of camera live streams can be analyzed in parallel in real-time. Evaluations with a comprehensive set of real-world training and test data from an Austrian motorway have shown an average accuracy of 86.7% on the test data set for classifying all four LOS levels. With a mean execution time of 48 microseconds per frame on a common server, hundreds of video streams can be analyzed in real-time.
SoK: Secure Messaging

Motivated by recent revelations of widespread state surveillance of personal communication, many solutions now claim to offer secure and private messaging. This includes both a large number of new projects and many widely adopted tools that have added security features. The intense pressure in the past two years to deliver solutions quickly has resulted in varying threat models, incomplete objectives, dubious security claims, and a lack of broad perspective on the existing cryptographic literature on secure communication. In this paper, we evaluate and systematize current secure messaging solutions and propose an evaluation framework for their security, usability, and ease-of-adoption properties. We consider solutions from academia, but also identify innovative and promising approaches used "in-the-wild" that are not considered by the academic literature. We identify three key challenges and map the design landscape for each: trust establishment, conversation security, and transport privacy. Trust establishment approaches offering strong security and privacy features perform poorly from a usability and adoption perspective, whereas some hybrid approaches that have not been well studied in the academic literature might provide better trade-offs in practice. In contrast, once trust is established, conversation security can be achieved without any user involvement in most two-party conversations, though conversations between larger groups still lack a good solution. Finally, transport privacy appears to be the most difficult problem to solve without paying significant performance penalties.
Electrophysiological Characterization of the Rat Epithelial Na+ Channel (rENaC) Expressed in MDCK Cells

The epithelial Na+ channel (ENaC), composed of three subunits (α, β, and γ), is expressed in several epithelia and plays a critical role in salt and water balance and in the regulation of blood pressure. Little is known, however, about the electrophysiological properties of this cloned channel when expressed in epithelial cells. Using whole-cell and single channel current recording techniques, we have now characterized the rat αβγENaC (rENaC) stably transfected and expressed in Madin-Darby canine kidney (MDCK) cells. Under whole-cell patch-clamp configuration, the αβγrENaC-expressing MDCK cells exhibited greater whole cell Na+ current at −143 mV (−1,466.2 ± 297.5 pA) than did untransfected cells (−47.6 ± 10.7 pA). This conductance was completely and reversibly inhibited by 10 μM amiloride, with a Ki of 20 nM at a membrane potential of −103 mV; the amiloride inhibition was slightly voltage dependent. Amiloride-sensitive whole-cell current of MDCK cells expressing αβ or αγ subunits alone was −115.2 ± 41.4 pA and −52.1 ± 24.5 pA at −143 mV, respectively, similar to the whole-cell Na+ current of untransfected cells. Relaxation analysis of the amiloride-sensitive current after voltage steps suggested that the channels were activated by membrane hyperpolarization. Ion selectivity sequence of the Na+ conductance was Li+ > Na+ >> K+ = N-methyl-d-glucamine+ (NMDG+). Using excised outside-out patches, amiloride-sensitive single channel conductance, likely responsible for the macroscopic Na+ channel current, was found to be ∼5 and 8 pS when Na+ and Li+ were used as a charge carrier, respectively. K+ conductance through the channel was undetectable. The channel activity, defined as a product of the number of active channel (n) and open probability (P o), was increased by membrane hyperpolarization. Both whole-cell Na+ current and conductance were saturated with increased extracellular Na+ concentrations, which likely resulted from saturation of the single channel conductance. The channel activity (nP o) was significantly decreased when cytosolic Na+ concentration was increased from 0 to 50 mM in inside-out patches. Whole-cell Na+ conductance (with Li+ as a charge carrier) was inhibited by the addition of ionomycin (1 μM) and Ca2+ (1 mM) to the bath. Dialysis of the cells with a pipette solution containing 1 μM Ca2+ caused a biphasic inhibition, with time constants of 1.7 ± 0.3 min (n = 3) and 128.4 ± 33.4 min (n = 3). An increase in cytosolic Ca2+ concentration from <1 nM to 1 μM was accompanied by a decrease in channel activity. Increasing cytosolic Ca2+ to 10 μM exhibited a pronounced inhibitory effect. Single channel conductance, however, was unchanged by increasing free Ca2+ concentrations from <1 nM to 10 μM. Collectively, these results provide the first characterization of rENaC heterologously expressed in a mammalian epithelial cell line, and provide evidence for channel regulation by cytosolic Na+ and Ca2+.
A model of nonlinear motor cortical integration and its relation to movement speed profile control

It is recognized that natural point-to-point movements are characterized by bell-shaped speed profiles. However, the neural basis of this smooth, substantially symmetric time course is unknown. Here it is demonstrated via a simplified compartmental model of tufted layer V (TL5) pyramidal neurons, the principal output units of the motor cortex, that nonlinear integration may underlie the bell-shaped profile. Specifically, it is shown that TL5 neuronal output depends upon an approximately multiplicative relationship between inputs to its apical or basal regions (zones A and B, respectively) and those to its central zone (C). This is because the latter facilitate Ca2+ dependent bursting that enhances responsiveness to other inputs. As a result, when part of TL5 output returns to zones A and C via thalamocortical and cerebrocerebellar feedback, TL5 neuronal firing rate initially increases before decreasing, rather than progressively decrease as would the output of a linear integrator. This yields a sigmoidal position vs. time response in the musculoskeletal plant and therefore a bell-shaped speed curve. Because of this mechanism, smooth movements may be triggered and modulated by step-like and tonic inputs to zone C as might be received from SMA or basal ganglia. The model thus gives possible insight into the basis of certain features of motor dysfunction in Parkinson's and cerebellar disease
Construction and Characterization of Murine Cytomegaloviruses That Contain Transposon Insertions at Open Reading Frames m09 and M83

ABSTRACT A transposon derived from Escherichia coliTn3 was introduced into the genome of murine cytomegalovirus (MCMV) to generate a pool of viral mutants, including two recombinant viruses that contained the transposon sequence within open reading frames m09 and M83. Our studies provide the first direct evidence to suggest that m09 is not essential for viral replication in mouse NIH 3T3 cells. Studies in cultured cells and in both BALB/c-Byj and CB17 severe combined immunodeficient (SCID) mice indicated that the transposon insertion is stable during viral propagation both in vitro and in vivo. Moreover, the virus that contained the insertion mutation in m09 exhibited a titer similar to that of the wild-type virus in the salivary glands, lungs, livers, spleens, and kidneys of both the BALB/c and SCID mice and was as virulent as the wild-type virus in killing the SCID mice when these animals were intraperitoneally infected with these viruses. These results suggest that m09 is dispensable for viral growth in these organs and that the presence of the transposon sequence in the viral genome does not significantly affect viral replication in vivo. In contrast, the virus that contained the insertion mutation in M83 exhibited a titer of at least 60-fold lower than that of the wild-type virus in the organs of the SCID mice and was attenuated in killing the SCID mice. These results demonstrate the utility of using the Tn3-based system as a mutagenesis approach for studying the function of MCMV genes in both immunocompetent and immunodeficient animals.
Hemorrhage in the Atherosclerotic Carotid Plaque: A High-Resolution MRI Study

Background and Purpose— High-resolution, multicontrast magnetic resonance imaging (MRI) has developed into an effective tool for the identification of carotid atherosclerotic plaque components, such as necrotic core, fibrous matrix, and hemorrhage/thrombus. Factors that may lead to plaque instability are lipid content, thin fibrous cap, and intraplaque hemorrhage. Determining the age of intraplaque hemorrhage can give insight to the history and current condition of the biologically active plaque. The aim of this study was to develop criteria for the identification of the stages of intraplaque hemorrhage using high-resolution MRI. Methods— Twenty-seven patients, scheduled for carotid endarterectomy (CEA), were imaged on a 1.5-T GE SIGNA scanner (sequences: 3-dimensional time of flight, double-inversion recovery, T1-weighted (T1W), PDW and T2W). Two readers, blinded to histology, reviewed MR images and grouped hemorrhage into fresh, recent, and old categories using a modified cerebral hemorrhage criteria. The CEA specimens were serially sectioned and graded as to presence and stage of hemorrhage. Results— Hemorrhage was histologically identified and staged in 145/189 (77%) of carotid artery plaque locations. MRI detected intraplaque hemorrhage with high sensitivity (90%) but moderate specificity (74%). Moderate agreement in classifying stages occurred between MRI and histology (Cohen κ = 0.7, 95% CI: 0.5 to 0.8 for reviewer 1 and 0.4, 95% CI: 0.2 to 0.6 for reviewer 2), with moderate agreement between the 2 MRI readers (κ = 0.4, 95% CI: 0.3 to 0.6). Conclusion— Multicontrast MRI can detect and classify carotid intraplaque hemorrhage with high sensitivity and moderate specificity.
Indebted Households Profiling: A Knowledge Discovery from Database Approach

A major challenge in consumer credit risk portfolio management is to classify households according to their risk profile. In order to build such risk profiles it is necessary to employ an approach that analyses data systematically in order to detect important relationships, interactions, dependencies and associations amongst the available continuous and categorical variables altogether and accurately generate profiles of most interesting household segments according to their credit risk. The objective of this work is to employ a knowledge discovery from database process to identify groups of indebted households and describe their profiles using a database collected by the Consumer Credit Counselling Service (CCCS) in the UK. Employing a framework that allows the usage of both categorical and continuous data altogether to find hidden structures in unlabelled data it was established the ideal number of clusters and such clusters were described in order to identify the households who exhibit a high propensity of excessive debt levels.
Integrated mechatronic system for reformer tube internal geometric distortion inspection

Reformer tube is a kind of pressure vessel working under high temperature. It is a major and expensive component in chemical process industry especially in oil and gas industry. Each reformer tube costs over thousands of dollars. A reformer furnace could contain hundreds of over 15-meter long vertically installed reformer tubes working under pressure up to 15 to 20 bar and temperature reaching 700 to 800°C. Any tube failure during production time means a catastrophic production failure and million-dollar lost. Periodic tube inspections are mandatory. Such inspections can call for significant manpower, time, and financial investment in order to meet the national and international legislations and standards for health and safety. This paper presents an approach moving towards automated reformer tube inspection. The approach presents an integrated mechatronic system that consists of five major units: reformer tube sensing, reducer (pigtail) checking, data acquisition, communication, and real time control. Such an integrated tube inspection system has the advantages of measuring both tube body and pigtail using one integrated device, obtaining distortion data in real time and processing data analysis on site to support tube replacement decision making. With the available sensing, communication, and control methodologies and technologies, the proposed integrated reformer tube inspection system could be a feasible and economical solution for plant maintenance in oil and gas industry.
The Liquidity Effects of Official Bond Market Intervention

To "ensure depth and liquidity," the European Central Bank intervened in sovereign debt markets through its Securities Markets Programme (SMP), providing a unique opportunity to estimate the effects of large-scale asset purchases on sovereign bond liquidity premia. From reduced-form estimates, we find robust, economically significant impact and lasting reductions in sovereign bonds' liquidity premia in response to official purchases. We develop a search-based asset-pricing model to understand our empirical results. The theory implies that bond liquidity premia fall in response to both official purchases and rising sovereign default probabilities, as seen in the data.