gebhart/patrepeval huggingface dataset:
Crystallization of a 45 kDa peroxygenase/peroxidase from the mushroomAgrocybe aegeritaand structure determination by SAD utilizing only the haem iron (2010)

Some litter-decaying fungi secrete haem-thiolate peroxygenases that oxidize numerous organic compounds and therefore have a high potential for applications such as the detoxification of recalcitrant organic waste and chemical synthesis. Like P450 enzymes, they transfer oxygen functionalities to aromatic and aliphatic substrates. However, in contrast to this class of enzymes, they only require H(2)O(2) for activity. Furthermore, they exhibit halogenation activity, as in the well characterized fungal chloroperoxidase, and display ether-cleavage activity. The major form of a highly glycosylated peroxygenase was produced from Agrocybe aegerita culture media, purified to apparent SDS homogeneity and crystallized under three different pH conditions. One crystal form containing two molecules per asymmetric unit was solved at 2.2 A resolution by SAD using the anomalous signal of the haem iron. Subsequently, two other crystal forms with four molecules per asymmetric unit were determined at 2.3 and 2.6 A resolution by molecular replacement.
Mono‐galloyl glucose derivatives are potent poly(ADP‐ribose) glycohydrolase (PARG) inhibitors and partially reduce PARP‐1‐dependent cell death (2008)

Taken together, our findings identify mono-galloyl glucose derivatives as potent PARG inhibitors, and emphasize the active function of this enzyme in cell death.
Tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis : Is it still a virus? (2020)

ABSTRACT Since the discovery of Acanthamoeba polyphaga Mimivirus, the first giant virus of amoeba, the historical hallmarks defining a virus have been challenged. Giant virion sizes can reach up to 2.3 µm, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production in Pandoravirus massiliensis , the largest of our giant virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins of P. massiliensis exhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; α-ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein of P. massiliensis , cloned and expressed in Escherichia coli , provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to α-ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in viruses, namely, pandoraviruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient in P. massiliensis coupled with the observation of genes of the tricarboxylic acid cycle make this virus a form a life for which it is legitimate to question ‘what is a virus?’.
SCN5A mutation type and topology are associated with the risk of ventricular arrhythmia by sodium channel blockers (2018)

SCN5A mutation is associated with an increased risk of drug-induced ventricular arrhythmia in patients without baseline type-1 ECG. In particular, S<sup>non-missense</sup> and S<sup>missense-TP</sup> are at high risk.
Kalman Filter Development for Real Time Proper Orthogonal Decomposition Disc Temperature Model (2016)

Extending disc life through online health monitoring has been a proven method of minimising engine downtime and maintenance costs. To properly monitor the disc requires a robust model of the disc’s non-linear thermal dynamics. A model can be improved by filtering the output using a measurement of the disc in real time. The damage models can then be computed with higher statistical confidence leading to increased safe life prediction. Recently, a model of disc temperature has been developed based on the proper orthogonal decomposition of simulated data. The model produced detailed thermal gradients for use in damage calculation and life assessment. This paper presents the development and implementation of a Kalman filter to augment that model. The location of the measurement has been assessed in order to select the most appropriate target for instrumentation. Points all around the front and back of the disc have been assessed, and the best practice result is found to be near the centre of the disc neck. Matching temperatures at this point represents a compromise between the fast dynamic response of the rim, with the slower response of the cob. The new model has been validated against an independent flight simulation that had previously been excluded from any training process. The addition of the Kalman filter allows the model to match aircraft dynamics outside the regular training trajectories. The accuracy is approximately ±30K, and there is a root-mean-square error of only 2K over the whole model at any one point in time.
Homomorphic Encryption-Based LSB Substitution for High Capacity Data Hiding in the Encrypted Domain (2020)

During the last few decades, multimedia security over the cloud has become a major issue. Public-key homomorphism is an efficient approach for data hiding in encrypted images (DHEI). An original image is encrypted using a public key and sent across a network and then processed to embed a secret message directly in the encrypted domain. During the decoding step, a private key is used to obtain a marked reconstructed image, where the secret message can be extracted. In this paper, we propose an efficient method of DHEI based on the Paillier cryptosystem. Using its homomorphic properties, pixel blocks and bits of the message are multiplied in the encrypted domain resulting in an addition in the clear domain. By applying a pre-processing step on the original image before encryption, this addition becomes a least significant bits (LSB) substitution. Experimental results show that using our proposed scheme, we obtain a high payload value (1 bpp) without expanding a lot the original image size contrary to current state-of-the-art methods. Indeed, whatever the key size, the expansion rate is always equal to 2. In addition, the original image and the marked reconstructed image are very similar.
Effect of a Moderately Energy‐ and Salt‐reduced Diet on Body Compartments and Blood Pressure Control in Obese Men with Mild Hypertension (1984)

Ten middle-aged moderately obese men with untreated mild hypertension were studied during a 6-week weight maintenance period and a 9-week period on a diet containing 5 MJ when body mass decreased by 8.4 kg (SE 1.4). According to urinary sodium excretion there was a mean reduction of 89 mmol/day (SE 16) in sodium intake. Mean arterial pressure fell by 2.5 to 14.1 mmHg (95% confidence interval) which was correlated to the reduction of body mass. The sympathetic nervous activity diminished with decreasing noradrenaline excretion and heart rate. There were no changes in the renin-aldosterone system. Estimation of the body composition with a four-compartment model utilizing determinations of body mass, total body potassium and total body water (TBW) showed reductions of body fat (8.4 kg (SE 1.4] and body cell mass (BCM) (2.4 kg (SE 0.6], but not of TBW. Extracellular water (ECW) increased significantly as judged from ECW/BCM calculations. Plasma volume was determined by Evan's blue and did not change significantly. We suggest that the observed changes in body composition represent one aspect of the adjustment to a weight reducing diet, while blood pressure is lowered by another mechanism in the adaptive response to dieting, i.e. reduction in sympathetic nervous activity.
ISPRS BENCHMARK ON MULTISENSORY INDOOR MAPPING AND POSITIONING (2020)

Abstract. In this paper, we present a publicly available benchmark dataset on multisensorial indoor mapping and positioning (MiMAP), which is sponsored by ISPRS scientific initiatives. The benchmark dataset includes point clouds captured by an indoor mobile laser scanning system in indoor environments of various complexity. The benchmark aims to stimulate and promote research in the following three fields: (1) LiDAR-based Simultaneous Localization and Mapping (SLAM); (2) automated Building Information Model (BIM) feature extraction; and (3) multisensory indoor positioning. The MiMAP project provides a common framework for the evaluation and comparison of LiDAR-based SLAM, BIM feature extraction, and smartphone-based indoor positioning methods. This paper describes the multisensory setup, data acquisition process, data description, challenges, and evaluation metrics included in the MiMAP project.
Serial-Robot Wrist-Singularity Mitigation Along Alternative Optimally Adjusted Paths (2021)

Abstract Adjusting the displacement path of a serial robot encountering the wrist singularity to pass either through the singularity or around it mitigates its adverse effects. Both such path adjustments are commonly called singularity avoidance and are applied here to either a spherical or an offset wrist. These adjustments avoid high joint rates that can occur at singularity encounter. A recent through-the singularity method limits joint rates and accelerations in the robot with either a spherical or offset wrist when conducting a constant rate of traversal of the tool manipulated by the robot. A kinematic model adding multiple virtual joints allows a modified high-order path-following algorithm to maintain accurate tool position while achieving an optimal level of tool deviation in orientation. Whereas a path reversal resulting from a turning-point type singularity had been revealed for an offset wrist over a finite range of close-approach, these conditions are met when connecting the isolated path segments. Procedures are developed here with this capability for an around-the-singularity path. Choosing between the through and around-singularity alternatives offers the overall optimum.
Phase estimation for grid synchronization using CORDIC algorithm with SRF-PLL (2012)

The proper operation of grid connected inverter system is determined by grid voltage conditions such as phase, amplitude and frequency. In such applications, an accurate and fast detection of the phase angle, amplitude and frequency of the grid voltage is essential for reference current generation. Phase angle plays an important role in control being used to transform the feedback variables to a suitable reference frame in which the control structure is implemented. Hence grid synchronization has a significant role in the control of grid connected inverter system. However, accurate on-line tracking of phase angle of the grid voltages under distorted grid condition is critical especially; during line notching, voltage unbalance, voltage dips, frequency variations etc. This paper presents phase estimation technique for grid synchronization using CORDIC algorithm with Synchronous Reference Frame-Phase Locked Loop (SRF-PLL) during unbalanced three-phase grid voltage conditions. By proposing CORDIC algorithm with SRF PLL, we can largely reduce the computational time while it will be implemented in real time platform using FPGA or DSP. Computer simulations have been carried out using MATLAB-Simulink package for feasibility of the study.
Measurement of sticking probability and sputtering yield of Au by low-energy mass selected ion beams with a quartz crystal microbalance (2008)

A measurement system of sticking probability and sputtering yield in the energy range of 0–500 eV has been established with a low-energy mass selected ion beam system. The small change in mass of the substrate material by injected ions can be evaluated with the quartz crystal microbalance (QCM). In this study, sticking probabilities and self-sputtering yields of Au were measured as functions of the injection energy of Au ions.
Purification and characterization of thermostable aspartate aminotransferase from a thermophilic Bacillus species (1990)

Aspartate aminotransferase (EC 2.6.1.1) was purified to homogeneity from cell extracts of a newly isolated thermophilic bacterium, Bacillus sp. strain YM-2. The enzyme consisted of two subunits identical in molecular weight (Mr, 42,000) and showed microheterogeneity, giving two bands with pIs of 4.1 and 4.5 upon isoelectric focusing. The enzyme contained 1 mol of pyridoxal 5'-phosphate per mol of subunit and exhibited maxima at about 360 and 415 nm in absorption and circular dichroism spectra. The intensities of the two bands were dependent on the buffer pH; at neutral or slightly alkaline pH, where the enzyme showed its maximum activity, the absorption peak at 360 nm was prominent. The enzyme was specific for L-aspartate and L-cysteine sulfinate as amino donors and alpha-ketoglutarate as an amino acceptor; the KmS were determined to be 3.0 mM for L-aspartate and 2.6 mM for alpha-ketoglutarate. The enzyme was most active at 70 degrees C and had a higher thermostability than the enzyme from Escherichia coli. The N-terminal amino acid sequence (24 residues) did not show any similarity with the sequences of mammalian and E. coli enzymes, but several residues were identical with those of the thermoacidophilic archaebacterial enzyme recently reported.
Preparation of linear low‐density polyethylene by the in situ copolymerization of ethylene with an iron oligomerization catalyst and rac‐ethylene bis(indenyl) zirconium (IV) dichloride (2005)

Abstract An iron oligomerization catalyst, [(2‐ArNC(Me)) 2 C 5 H 3 N]FeCl 2 [Ar = 2,6‐C 6 H 3 (F) 2 ], was combined with rac ‐ethylene bis(indenyl)zirconium (IV) dichloride [ rac ‐Et(Ind) 2 ZrCl 2 ] to prepare linear low‐density polyethylene (LLDPE) by the in situ copolymerization of ethylene. A series of LLDPEs with different properties were prepared by the alteration of the reaction temperature, Fe/Zr molar ratio, Al/(Fe + Zr) molar ratio, and reaction time. The structures of the polymers were characterized with differential scanning calorimetry, 13 C NMR, gel permeation chromatography (GPC), and so forth. The melting points, crystallizations, and densities of the resulting products increased, and the average branching degree decreased, as the reaction temperature, Al/(Fe + Zr) ratio, and reaction time increased. The melting points, crystallizations, and densities of the polymers decreased, and the average branching degree increased, when the Fe/Zr ratio increased. The 13 C NMR and GPC results showed that there were no unreacted α‐olefins remaining in the resulting polymers because the percentage of low‐molar‐mass sections (C 4 –C 10 ) of the oligomers obtained with this catalyst was very high (&gt;70%). In addition, the formation of polymers with two melting points under different reaction conditions was examined in detail, and the results indicated that the two melting points of the polymers could be attributed to polyethylene with different branches. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 984–993, 2005
Operating Characteristics of Acoustically Driven Filtration Processes for Particulate Suspensions (2000)

Operating characteristics for an ultrasonically assisted filtration technique applicable to micron to millimeter-sized particles suspended in liquid have been studied. The technique uses a highly porous filtration medium having pores up to two orders of magnitude larger than the particles being collected. When a resonant ultrasonic standing wave field is applied to the medium, the particles become trapped on the elements comprising the porous medium or within its pores. The test suspension consisted of 325-mesh polystyrene particles in water. The porous medium was a polyester mesh containing 30 pores per inch (the nominal pore size is 847 μm). Filtration efficiencies ranging from 60 to 85% have been observed. The effect of flow configuration on filtration efficiency and two approaches for cleaning of the mesh have been examined.
Ultra-broadband support determination for extreme ultraviolet coherent diffractive imaging from a high harmonic source (2013)

Conventional coherent diffractive imaging (CDI) techniques rely on inversion of the two-dimensional phase problem in the fully coherent limit. Current work using synchrotrons has shown that by introducing a flexible parameter in a technique known as polyCDI, some reduced temporal coherence with relative bandwidth ~3% can be tolerated for simple non-dispersive objects. We demonstrate that using a high harmonic source with modulated spectral characteristics, although the excellent temporal coherence properties are lost in detection, it is possible to increase the tolerable relative bandwidth to ~20% by using the shrinkwrap technique and treating the data as if they were fully coherent but noisy. This reduces the integration time by a factor of ~5. This result is critical for the future use of lab-based sources of extreme ultraviolet and soft x-rays for CDI of non-dispersive objects, and we anticipate that it will improve results at synchrotron sources also.
Peri-intraventricular hemorrhage and arterial blood pressure fluctuation in the critically ill preterm infant (2002)

Arterial blood pressure (ABP) fluctuations and peri-intraventricular hemorrhage (PIVH) were studied in 44 premature infants. Twenty-two infants were treated with pancuronium. ABP waveforms were continuously monitored at 100 Hz, the coefficient of variation of systolic pressure (CVS) was measured by every 50 waveforms, and the percentage of recording time during which CVS was above 5% or above 10% was calculated in each patient. Results indicate that (1) pancuronium administration does not reduce the PIVH incidence, (2) that ABP fluctuation is similar whether PIVH is present or not, and (3) that pancuronium is highly efficient in maintaining a stable ABP pattern.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A virtualized testbed with physical outlets for hands-on computer networking education (2014)

Many computer science curricula include practical courses to undergraduate and graduate students to offer them hands-on networking experience by connecting PCs, switches, and routers in a testbed. Such testbeds are expensive, bulky, energy-intensive, and cause heat problems. Virtualization of PCs and routers on commodity hardware is a solution to those problems. A challenge is to provide physical interfaces for the virtualized components so that students still have the hands-on experience including cabling. In this work, we propose a solution based on inexpensive hardware that can be mounted in a standard 19-inch cabinet. As WiFi adapters, headsets, or additional serial interfaces are needed for advanced experiments, we provide means to connect them as USB devices to virtualized PCs and routers. The system is configured so that students have only access to the virtual machines and their physical interfaces.
Magnetization reversal and magnetic anisotropies in epitaxial Fe/MgO and Fe/MgO/Fe heterostructures grown on Si(001) (2003)

Epitaxial Fe/MgO heterostructures have been grown on Si(001) by a combination of sputtering and laser ablation deposition techniques. The growth of MgO on Si(001) is mainly determined by the nature of the interface, with large lattice mismatch and the presence of an amorphous layer of unclear origin. Reflection high energy electron diffraction patterns of this MgO buffer layer are characteristic of an epitaxial, but disordered, structure. The structural quality of subsequent Fe and MgO layers continuously improves due to the better lattice match and the burial of defects. A weak uniaxial in-plane magnetic anisotropy is found superimposed on the expected cubic biaxial anisotropy. This additional anisotropy, of interfacial nature and often found in Fe/MgO and Fe/MgO/GaAs(001) systems, is less intense here due to the poorer MgO/Si interface quality compared with that of other systems. From the evolution of the anisotropy field with film thickness, magnetic anisotropy is also found to depend on the crystal quality. Kerr measurements of a Fe/MgO multilayered structure grown on Si show two different switching fields, suggesting magnetic coupling of two of the three Fe layers. Nevertheless, due to the little sensitivity to the bottom Fe film, independent switching of the three layers cannot be ruled out.
Fixed percentage of wavelet coefficients to be zeroed for ECG compression (2003)

A new method for ECG compression is presented. After the pyramidal wavelet decomposition, the resultant coefficients are subjected to an iterative threshold until a fixed percentage target of wavelet coefficients to be zeroed is reached. Next, the lossless Huffman's coding is used to increase the compression ratio. Quality preservation for good compression ratios is reported.
DEVELOPMENT OF AN INFOSHOP SERVICE SYSTEM (2005)

In this paper, we describe the Information Communication Processing Systern(ICPS) developed to support the Infoshop service and discuss the Advanced Communication Processing System(ACPS) for an improved version that can support a global, flexible, eflcient, and fair provision of value-added services.
Aberrant Methylation of RASGRF1 Is Associated with an Epigenetic Field Defect and Increased Risk of Gastric Cancer (2012)

Aberrant DNA methylation is implicated in the epigenetic field defect seen in gastric cancer. Our aim in this study was to identify predictive biomarkers by screening for DNA methylation in noncancerous background gastric mucosa from patients with gastric cancer. Using methylated-CpG island amplification coupled with CpG island microarray (MCAM) analysis, we identified 224 genes that were methylated in the noncancerous gastric mucosa of patients with gastric cancer. Among them, RASGRF1 methylation was significantly elevated in gastric mucosa from patients with either intestinal or diffuse type gastric cancer, as compared with mucosa from healthy individuals (8.3% vs. 22.4%, P < 0.001; 8.3% vs. 19.4%, P < 0.001). RASGRF1 methylation was independent of mucosal atrophy and could be used to distinguish both serum pepsinogen test-positive [sensitivity, 70.0%; specificity, 86.7%; area under the receiver operator characteristic (ROC) curve, AUC, 0.763] and -negative patients with gastric cancer (sensitivity, 72.2%; specificity, 87.0%; AUC, 0.844) from healthy individuals. Ectopic expression of RASGRF1 suppressed colony formation and Matrigel invasion by gastric cancer cells, suggesting it may be involved in gastric tumorigenesis. Collectively, our data suggest that RASGRF1 methylation is significantly involved in an epigenetic field defect in the stomach, and that it could be a useful biomarker to identify individuals at high risk for gastric cancer.
CAD Applications for Material Handling in the Construction Environment (1993)

Research at Va. Tech in the area of dynamic behavior modeling and crane damping have been undertaken. The dynamic behavior modeling capability has been designed to us 3-D CAD models and to realistically model multiple cranes or other material handling tools. The crane damping work has been conceived to provide for a novel approach to the issue of crane payload motion control. The dynamic behavior modeler will also be used to model control theory behavior as the research progresses to replicate experimental results.