gebhart/patrepeval huggingface dataset:
Translational research to identify clinical applications of hepatocyte growth factor (2009)

Hepatocyte growth factor (HGF), originally purified from the plasma of patients with fulminant hepatic failure, has been shown to carry out various physiological functions. HGF not only stimulates liver regeneration, but also acts as an antiapoptotic factor in in vivo experimental models. Therefore, HGF is a promising therapeutic agent for the treatment of fatal liver diseases, including fulminant hepatic failure. After performing a number of preclinical tests, our group began an investigator-initiated registered phase I/II clinical trial of patients with fulminant hepatic failure to examine the safety and clinical efficacy of recombinant human HGF. In this article, we will discuss the basic research results as well as the translational research that underpins current attempts to use HGF in various clinical settings.
Recombinant PSP94 (prostate secretory protein of 94 amino acids) demonstrates similar linear epitope structure as natural PSP94 protein (1996)

PSP94 has the potential to be a useful diagnostic marker and therapeutic agent in prostate cancer. Recently, different immunoassay systems for quantitative analysis of PSP94 in clinical samples have been developed, but the epitope structure of PSP94 protein has not been elucidated. In this study, we report an Escherichia coli expression system for recombinant GST-PSP94 fusion protein. GST-PSP94 contains antigenic determinants similar to natural PSP94 protein (determined both by Western blotting experiments and by ELISA) and can be used to study the structure of natural PSP94 antigen. Since GST-PSP94 was expressed in E. coli and purification involved a denaturing process, we propose that the epitope structure of PSP94 is linear and largely dependent on the primary amino acid sequence, rather than conformational structure. This hypothesis was supported by reciprocal competition in ELISA among natural, GST-PSP94 fusion protein, and purified recombinant PSP94 protein. The results demonstrate that the various forms of PSP94 can compete with each other in binding to rabbit PSP94 polyclonal antibody, although the natural PSP94 has a slightly higher affinity. When natural and recombinant PSP94 protein were denatured in vitro with urea and alkali, no effect on the binding to antibody was found. The epitope activity of natural PSP94 was also shown to be resistant to the treatment of detergent and reducing agent. The location of one of the linear epitopes recognized by the PSP94 antibody was determined to be in the N-terminus by using two synthetic peptides representing N- and C-terminal sequences. Competitive ELISA between the N-terminal peptide and PSP94 protein indicate that both natural and GST-PSP94 have similar immunoactive N-termini.
System to measure the chromatic dispersion of optical fibers (1994)

Abstract Because of the progress in optical communication technology, understanding the propagation characteristic of optical fibers has become very important. In particular, since optical networks have been used widely, the evaluation of optical fibers in the field is essential. This paper describes the measurement of the chromatic dispersion of optical fibers and a system suitable for the measurement in the field. The approach is based on the baseband phase‐comparison method. First, the conditions required for this measurement system will be clarified. Then the measurement of wavelengths and wavelength separation satisfying the requirements will be obtained by simulation. The source of each wavelength must be modulated. However, to increase the fiber length and to improve measurement precision, a modulation method based on multiple sinusoidal waves will be proposed, and the upper and lower limit of the optimum modulation frequency will be clarified. The measurement system will be constructed from these results. The technical problems in realizing the system will be shown. Finally, an example of data measured by the constructed system will be shown, and it will be demonstrated that a resolution of 0.01 ps/nm/km and measurement precision of ± 0.3 ps/nm/km can be achieved at wavelengths of 1.3 and 1.55 μm.
PrivateEye: Scalable and Privacy-Preserving Compromise Detection in the Cloud (2020)

Today, it is difficult for operators to detect compromised VMs in their data centers (DCs). Despite their benefits, the compromise detection systems operators offer are mostly unused. Operators are faced with a dilemma: allow VMs to remain unprotected, or mandate all customers use the compromise detection systems they provide. Neither is appealing: unprotected VMs can be used to attack other VMs. Many customers would view a mandate to use these detection systems as unacceptable due to privacy and performance concerns. Data from a production cloud show their compromise detection systems protect less than 5% of VMs. PrivateEye is a scalable and privacy-preserving solution. It uses sanitized summaries of network traffic patterns obtained from the vSwitch, rather than installing binaries in customer VMs, introspection at the hypervisor, or packet captures. The challenge it addresses is protecting all VMs at DC-scale while preserving customer privacy using low-signal data. We developed PrivateEye to meet the needs of production DCs, and our data collection agent is deployed across all DCs of a large cloud. Evaluation on VMs of both internal and customer VM’s shows it has an area under the ROC curve — the curve showing the model’s true positive rate vs its false-positive rate — of 0.96.
28GHz Dual Polarized Beam Steering Antenna with Substrate Integrated Frequency Selective Structure (2019)

We propose a new type of mm wave beam steering antennas that permits larger steering angular range and almost no gain dispersion versus steering angle. Indeed, the limited angular range and the gain decrease when the steering angle increases are the main drawbacks of conventional planar phased arrays. The proposed design method starts with a substrate integrated waveguide which has a switchable frequency selective structure. The next design steps consist on a dual polarized conformal arrays, the feeding port structure of a power divider in a radial waveguide, the transitions to the radiating elements, the substrate integrated circular frequency selective structure and finally the full antenna. Based on this design methodology, a dual polarized beam steering antenna operating at 28 GHz is presented.
The Reverse Cholesterol Transport Pathway Improves Understanding of Genetic Networks for Fat Deposition and Muscle Growth in Beef Cattle (2010)

In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F(1) bulls, 113 F(1) dams, and 246 F(2) progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F(1) bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F(2) progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production.
Analysis of Handoff Interference and Outage along Arbitrary Trajectories in Cellular Networks (2008)

We introduce a new system performance measure due to handoff called handoff interference, which characterizes the additional interference noise induced by the handoff process. The handoff interference experienced by a mobile unit is determined by the parameters of the handoff algorithm. We present an exact analysis of the handoff interference and the outage probability and develop a discrete-time method to efficiently and accurately compute these performance metrics along arbitrary trajectories in a cellular network. Our numerical results reveal critical tradeoffs among the critical handoff performance metrics, which should be taken into account in dimensioning the handoff parameters to optimize system performance. We discuss an example handoff design problem, which illustrates how to dimension the handoff parameters to optimize this tradeoff using the proposed handoff analysis.
A verifiable SSA program representation for aggressive compiler optimization (2006)

We present a verifiable low-level program representation to embed, propagate, and preserve safety information in high perfor-mance compilers for safe languages such as Java and C#. Our representation precisely encodes safety information via static single-assignment (SSA) [11, 3] proof variables that are first-class constructs in the program.We argue that our representation allows a compiler to both (1) express aggressively optimized machine-independent code and (2) leverage existing compiler infrastructure to preserve safety information during optimization. We demonstrate that this approach supports standard compiler optimizations, requires minimal changes to the implementation of those optimizations, and does not artificially impede those optimizations to preserve safety. We also describe a simple type system that formalizes type safety in an SSA-style control-flow graph program representation. Through the types of proof variables, our system enables compositional verification of memory safety in optimized code. Finally, we discuss experiences integrating this representation into the machine-independent global optimizer of STARJIT, a high-performance just-in-time compiler that performs aggressive control-flow, data-flow, and algebraic optimizations and is competitive with top production systems.
Improved Time Series Reconstruction for Dynamic Magnetic Resonance Imaging (2009)

Time series of in vivo magnetic resonance images exhibit high levels of temporal correlation. Higher temporal resolution reconstructions are obtained by acquiring data at a fraction of the Nyquist rate and resolving the resulting aliasing using the correlation information. The dynamic imaging experiment is modeled as a linear dynamical system. A Kalman filter based unaliasing reconstruction is described for accelerated dynamic magnetic resonance imaging (MRI). The algorithm handles arbitrary readout trajectories naturally. The reconstruction is causal and very fast, making it applicable to real-time imaging. In vivo results are presented for cardiac MRI of healthy volunteers.
New multiple specimen potentiostatic system (1993)

A new potentiostatic system has been designed which is capable of controlling and monitoring for large periods of time a large number of specimen electrodes at many different set potentials, all within a single test tank or process stream. The advantages of the new system are illustrated by comparing block diagrams of a version which contains two potentiostats with those of the system which would have to be used to achieve the same results with the standard potentiostat configuration. In order to assess the performance of the new system, a prototype was built with two potentiostats that were independent except for their sharing of a common auxiliary electrode within a single test cell. An experiment was conducted in which one working electrode made from AISI430 stainless steel was subjected to the potentiostatic anodic polarisation scan outlined in ASTM G5–82 while the other identical working electrode was held at a constant potential that was 200 mV more negative than its corrosion potential. The current density at each potential for the electrode subjected to the anodic polarisation scan fell within the range of acceptable values presented in ASTM G5–82. The gradual decrease of current density observed at the electrode held at constant potential was not affected by interrupting the current flowing through the other electrode at the end of its scan. These observations indicate that there was no measurable interaction between the two working electrodes. Thus, the validity of the concept leading to the design of the new system has been demonstrated.
Variable density acoustic tomography (1985)

The theory and algorithms of diffraction tomography are generalized to the case of acoustic objects whose density and compressibility vary as a function of position. A generalized projection-slice theorem is presented for objects of this class and filtered backpropagation algorithms are derived that allow separate reconstructions of the objects’ density and compressibility using measurements of the transmitted acoustic field performed at two distinct frequencies. Computer simulations are presented testing the algorithms in the noise-free case.
Powder-Bed Stabilization for Powder-Based Additive Manufacturing (2014)

The most successful additive manufacturing (AM) technologies are based on thelayer-by-layer depositionof a flowable powder. Although considered as the third industrial revolution, one factor still limiting these processes to become completely autonomous is the often necessary build-up of support structures. Besides the prevention of lateral shifts of the part during the deposition of layers, the support assures quality and stability to the built process. The loose powder itself surrounding the built object, or so-called powder-bed, does not provide this sustenance in most existent technology available. Here we present a simple but effective and economical method for stabilizing the powder-bed, preventing distortions in the geometry with no need for support structures. This effect, achieved by applying an air flow through the powder-bed, is enabling an entirely autonomous generation of parts and is a major contribution to all powder-based additive manufacturing technologies. Moreover, it makes powder-based AM independent of gravitational forces, which will facilitate crafting items in space from a variety of powdery materials.
Designing color filter arrays for the joint capture of visible and near-infrared images (2009)

Digital camera sensors are inherently sensitive to the near-infrared (NIR) part of the light spectrum. In this paper, we propose a general design for color filter arrays that allow the joint capture of visible/NIR images using a single sensor. We pose the CFA design as a novel spatial domain optimization problem, and provide an efficient iterative procedure that finds (locally) optimal solutions. Numerical experiments confirm the effectiveness of the proposed CFA design, which can simultaneously capture high quality visible and NIR image pairs.
An adaptive, on-line, statistical method for detection of broken bars in motors using stator current and torque estimation (2002)

In this paper, we propose an adaptive statistical time-frequency method to detect broken bars using digital torque estimation. The key idea in the proposed method is to transform motor current into a time-frequency spectrum to capture the time variation of the frequency components and to analyze the spectrum statistically to distinguish fault conditions from the normal operating conditions of the motor. Since each motor has a distinct geometry, we adapt a supervised approach in which the algorithm is trained to recognize the normal operating conditions of the motor prior to actual fault detection. To estimate the broken bar frequencies, we utilize the digital torque estimator.
Back‐Side Electrical Contacts for Patterned Electrochromic Devices on Porous Substrates (2005)

Patterned electrodes on porous substrates, where the contacts to address these electrodes are hidden on the back of the substrates are described. To demonstrate the applicability of this method in fabricating organic electronic devices, a reflective-type polymer electrochromic device is constructed. A 7-pixel numerical-display device, showing the number “6” in the Figure, benefits from the color contrast between gold and a poly(3,4-propylenedioxythiophene) derivative.
High-throughput screening identifies small molecules that enhance the pharmacological effects of oligonucleotides (2015)

The therapeutic use of antisense and siRNA oligonucleotides has been constrained by the limited ability of these membrane-impermeable molecules to reach their intracellular sites of action. We sought to address this problem using small organic molecules to enhance the effects of oligonucleotides by modulating their intracellular trafficking and release from endosomes. A high-throughput screen of multiple small molecule libraries yielded several hits that markedly potentiated the actions of splice switching oligonucleotides in cell culture. These compounds also enhanced the effects of antisense and siRNA oligonucleotides. The hit compounds preferentially caused release of fluorescent oligonucleotides from late endosomes rather than other intracellular compartments. Studies in a transgenic mouse model indicated that these compounds could enhance the in vivo effects of a splice-switching oligonucleotide without causing significant toxicity. These observations suggest that selected small molecule enhancers may eventually be of value in oligonucleotide-based therapeutics.
Robust production of infectious viral particles in Huh-7 cells by introducing mutations in hepatitis C virus structural proteins (2007)

Recently, the characterization of a cell culture system allowing the amplification of an authentic virus, named hepatitis C virus cell culture (HCVcc), has been reported by several groups. To obtain higher HCV particle productions, we investigated the potential effect of some amino acid changes on the infectivity of the JFH-1 isolate. As a first approach, successive infections of naïve Huh-7 cells were performed until high viral titres were obtained, and mutations that appeared during this selection were identified by sequencing. Only one major modification, N534K, located in the E2 glycoprotein sequence was found. Interestingly, this mutation prevented core glycosylation of E2 site 6. In addition, JFH-1 generated with this modification facilitated the infection of Huh-7 cells. In a second approach to identify mutations favouring HCVcc infectivity, we exploited the observation that a chimeric virus containing the genotype 1a core protein in the context of JFH-1 background was more infectious than wild-type JFH-1 isolate. Sequence alignment between JFH-1 and our chimera, led us to identify two major positions, 172 and 173, which were not occupied by similar amino acids in these two viruses. Importantly, higher viral titres were obtained by introducing these residues in the context of wild-type JFH-1. Altogether, our data indicate that a more robust production of HCVcc particles can be obtained by introducing a few specific mutations in JFH-1 structural proteins.
Accelerated 4D flow imaging using randomly undersampled echo planer imaging with compressed-sensing reconstruction (2014)

Background 4D flow imaging using phase contrast CMR (PC CMR) allows visualization and quantification of blood flow. One of the major limitations of 4D flow imaging is its long scan time (in the order of 10-20 min). In this study, we sought to investigate an accelerate 4D flow imaging sequence that combines an efficient data sampling strategy using echo planar imaging (EPI) with randomly undersampled 3D k-space sampling pattern. The randomly undersampled k-space data are then reconstructed using compressed sensing (CS). Methods Figure 1 shows the k-space acquisition strategy. Similar to regular EPI acquisition, the k-space data are divided into multiple segments. For each segment, the profiles are undersampled with the CS rate such that all EPI segments have the same undersampling pattern. The proposed EPI random sampling strategy was implemented. Seven subjects were recruited (26 ± 12 years; 3 males) for 4D flow CMR on a 1.5T Philips Achieva magnet. Images were acquired axially using a GRE sequence (FOV =3 40 ×2 80 ×6 0 mm 3 ,r esolution =2× 2×3m m 3 ,T R/TE/a = 7.4/3.8 ms/20°, EPI factor = 3, Turbo Factor =2 , CS rate =3 ) in av olume covering the ascending and descending aorta, and the aortic bifurcation. Only foot-head flow encoding was used to provide an adequate temporal resolution of 30 ms for the measurements. A single beam navigator placed on the right hemi-diaphragm was used to gate the acquisition with the respiratory cycle. The nominal scan time for this scan was 3:30 minutes at 70 bpm assuming 100% gating efficiency (vs. 8:40 minutes if standard parallel imaging with rate 4 was used). For each subject, the 4D-PC scan was followed by a standard breath-hold 2D-PC scan with the same flow encoding direction (FOV = 340 × 280 mm2, resolution = 2 × 2 mm 2 , slice thickness = 5 mm 3 , SENSE rate = 2.5). The acquired 2D slice is selected from the previously obtained 4D scan and approximately at the aortic bifurcation. Data are then transferred to a separate station where the CS reconstruction was performed using a total variation minimization algorithm. Next, flow quantifications were performed on both the ascending and the descending aorta for all acquisitions and then compared between the 2D scans and the corresponding slices in the 4D scans.
Streak artifact reduction in helical cone beam CT with redundancy weighting (2011)

Redundant data weighting in helical CT affects reconstruction accuracy, susceptibility to motion artifacts and noise. Cone beam weighting (CBW) is used in helical CT with wide cone angle to reduce cone beam artifact and also improve detector utilization and reduce image noise. Earlier proposed approaches usually consider a case when reconstruction view range is less than one rotation (1-PI). However, most practical settings in clinical helical CT use between one and two rotations view range for each reconstructed slice. In this case CBW weighting can be extended to N-PI case. With N ≥ 2 streak artifacts are caused by singularity of the CBW function at Z-positions near the image plane. Note that in this case image plane projects to a small fraction of detector row; and the non-linear form of CBW weight cannot be accurately determined for all image pixels, which causes inaccuracies in CBW weighting that manifests itself in form of streak artifacts. We show that artifacts can be successfully removed by applying upsampling in the segment direction. By making the upsampling adaptive to the view Z-position, numerical performance of the proposed approach can be optimized. Evaluation shows that artifact is completely removed by the proposed approach.