gebhart/patrepeval huggingface dataset:
Probing the Active Site of Human Manganese Superoxide Dismutase:  The Role of Glutamine 143<sup>,</sup> (1998)

Structural and biochemical characterization of the nonliganding residue glutamine 143 near the manganese of human Mn superoxide dismutase (hMnSOD), a homotetramer of 22 kDa, reveals a functional role for this residue. In the wild-type protein, the side-chain amide group of Gln 143 is about 5 A from the metal and is hydrogen-bonded to Tyr 34, which is a second prominent side chain adjacent to the metal. We have prepared the site-specific mutant of hMnSOD with the conservative replacement of Gln 143 --> Asn (Q143N). The crystal structure of Q143N shows that the side-chain amide nitrogen of residue 143 is 1.7 A more distant from the manganese than in the wild-type enzyme. The Tyr 34 side-chain hydroxyl in Q143N is also moved to become 0.6 A more distant from the metal due to an additional water molecule. Differential scanning calorimetry showed that Q143N is slightly more stable than the wild-type enzyme with Tm for the main unfolding transition increased by 2 degrees C to 90.7 degrees C. Pulse radiolysis and stopped-flow spectrophotometry reveal that unlike wild-type hMnSOD, which is strongly inhibited by peroxide, Q143N MnSOD exhibits no product inhibition even at concentrations of O2. - in the millimolar range, and its catalysis follows Michaelis kinetics with no evidence of cooperativity. However, the overall catalytic activity of this mutant was decreased 2-3 orders of magnitude compared with the wild-type MnSOD, which can account for its lack of product inhibition. Q143N MnSOD lacked the visible absorption spectrum typical of wild-type Mn(III)SOD. Also, unlike the wild-type Mn(III)SOD, which is electron paramagnetic resonance (EPR) silent, Q143N MnSOD has a complex EPR spectrum with many resonances in the region below 2250 G. We conclude that the Gln 143 --> Asn mutation has increased the reduction potential of manganese to stabilize Mn(II), indicating that Gln 143 has a substantial role in maintaining a reduction potential favorable for the oxidation and reduction cycles in the catalytic disproportionation of superoxide. A solvent hydrogen isotope effect near 2 for kcat in catalysis by Q143N hMnSOD indicates rate-contributing proton transfers to form product hydroperoxide anion or hydrogen peroxide. The data demonstrate a prominent role for Gln 143 in maintaining the microenvironment of the manganese and in efficient catalysis of superoxide dismutation to oxygen and hydrogen peroxide.
P41 * IDENTIFICATION OF GLIOMA SPECIFIC APTAMER TARGETS (2014)

INTRODUCTION: Aptamers are in vitro generated DNA and RNA sequences which are randomly created as a library, with multiple permutations and combinations. These are then exposed to the target structure against which we want an aptamer ‘selected’ using Sequential Enumeration of Ligands by Exponential enrichment (SELEX). METHOD: Commercially available glioma and glial cell lines and in-house generated primary glioma cultures were used. Modified aptamers based on published sequences against glioma cell lines and newly generated sequences were used in the project to identify their binding targets. Cy3 or biotin- conjugated aptamers were incubated with live glioma cell cultures and imaged using confocal or light microscopy.To determine the target ligand, aptamers were then reacted with glial cell lysate and subjected to precipitation using streptavidin agarose beads and SDS polyacrylamide electrophoresis. Proteins were analysed by mass spectroscopy. RESULTS: Known and unknown aptamer protein ligands were co-precipitated. Ku70, Ku80 were precipitated along with nucleolin and related proteins. CONCLUSION: The aptamer has shown preferential binding to glioma cells and could act as a delivery system for therapeutic payloads. The aptamer targets Ku70 and Ku80, which are known to be over expressed in other forms of cancer but their role in gliomagenesis has not been fully elucidated. Other novel proteins have also been identified. Thus the aptamer co-precipitation technique has identified potential glioma biomarkers that may be of clinical significance.
Protein adsorption and smooth muscle cell adhesion on biodegradable agmatine‐modified poly(propylene fumarate‐<i>co</i>‐ethylene glycol) hydrogels (2003)

We synthesized positively charged biodegradable hydrogels from poly(propylene fumarate-co-ethylene glycol) block copolymer and agmatine-modified poly(ethylene glycol)-tethered fumarate by radical crosslinking, and investigated the effect of the guanidino group of agmatine on vascular smooth muscle cell adhesion and protein adsorption to the hydrogels. In the presence of serum, the number of adherent smooth muscle cells per unit surface area increased dose-dependently from 15 to 75% of the initial seeding density at 20 h as the initial agmatine-modified monomer content increased from 0 to 200 mg/g. Cell spreading also depended on the initial monomer content. In the absence of serum, the number of adherent cells per unit surface area increased slightly from 10 to 17% of the initial seeding density as the initial monomer content increased from 0 to 200 mg/g. Cell adhesion increased significantly by adding exogenous vitronectin to serum-free medium, whereas exogenous fibronectin addition did not enhance cell adhesion. The enzyme-linked immunosorbent assay of fibronectin and vitronectin adsorbed onto the hydrogels revealed that the incorporation of positive charges into the hydrogels enhanced vitronectin, but not fibronectin, adsorption significantly. These results suggest that the guanidino group of agmatine enhanced cell adhesion by promoting the adsorption of serum components, and vitronectin may be one of the components.
Development of a Novel Wireless Multi-Channel Stethograph System for Monitoring Cardiovascular and Cardiopulmonary Diseases (2021)

A multi-channel stethograph system was designed and developed as an electronic auscultation system for graphic recording of heart, lung, and trachea (HLT) sounds non-invasively through a set of 16 acoustic sensors. The multi-channel stethograph system was fabricated by placing 16 microphone based acoustic sensor in a CNC machined Delrin® housing cases that are covered using diaphragms. Among the 16 acoustic sensors, 14 were positioned in a memory foam pad, and two were placed directly on the heart and trachea to acquire sounds simultaneously from the lungs, heart, and trachea. The sounds acquired from the 16 acoustic sensors were processed through a custom designed and fabricated 16-channel PCB for signal conditioning. A National Instruments (NI) 9205 data acquisition device (DAQ) along with a NI 9191 wireless chassis was used to acquire and wirelessly transmit the data from the 16-channel PCB to a Wi-Fi enabled device such as a PC/tablet. A custom LabVIEW program was developed on a Wi-Fi enabled PC/tablet to record the data from the DAQ. In addition, a MATLAB program was developed to convert the recorded data from the acoustic sensors into 16 audio files (for audio playback) and plot the waveforms in time and frequency domain as well as spectrogram for visual examination of any abnormal patterns in inhalation and exhalation. This provides critical information on the presence of crackles, rhonchi and wheeze sounds as well as abnormal heartbeat and respiration rate which helps in analyzing the condition of heart and lungs. The graphically displayed HLT sounds will help physicians in the clinical diagnosis and monitoring of lung and heart disorders, particularly chronic obstructive pulmonary disease (COPD), asthma, pneumonia, and congestive heart failure by providing objective evidence.
A robust patch-based synthesis framework for combining inconsistent images (2013)

Current methods for combining different images produce visible artifacts when the sources have very different textures and structures, come from far view points, or capture dynamic scenes with motions. In this thesis, we propose a patch-based synthesis algorithm to plausibly combine different images that have color, texture, structural, and geometric inconsistencies. For some applications such as cloning and stitching where a gradual blend is required, we present a new method for synthesizing a transition region between two source images, such that inconsistent properties change gradually from one source to the other. We call this process image melding. For gradual blending, we generalized patch-based optimization foundation with three key generalizations: First, we enrich the patch search space with additional geometric and photometric transformations. Second, we integrate image gradients into the patch representation and replace the usual color averaging with a screened Poisson equation solver. Third, we propose a new energy based on mixed L2/L0 norms for colors and gradients that produces a gradual transition between sources without sacrificing texture sharpness. Together, all three generalizations enable patch-based solutions to a broad class of image melding problems involving inconsistent sources: object cloning, stitching challenging panoramas, hole filling from multiple photos, and image harmonization. We also demonstrate another application which requires us to address inconsistencies across the images: high dynamic range (HDR) reconstruction using sequential exposures. In this application, the results will suffer from objectionable artifacts for dynamic scenes if the inconsistencies caused by significant scene motions are not handled properly. In this thesis, we propose a new approach to HDR reconstruction that uses information in all exposures while being more robust to motion than previous techniques. Our algorithm is based on a novel patch-based energy-minimization formulation that integrates alignment and reconstruction in a joint optimization through an equation we call the HDR image synthesis equation. This allows us to produce an HDR result that is aligned to one of the exposures yet contains information from all of them. These two applications (image melding and high dynamic range reconstruction) show that patch based methods like the one proposed in this dissertation can address inconsistent images and could open the door to many new image editing applications in the future.
A 1.8 V 1.0 GS/s 10b Self-Calibrating Unified-Folding-Interpolating ADC With 9.1 ENOB at Nyquist Frequency (2009)

An advance in folding-interpolating analog-to-digital converters (ADCs) is demonstrated which simplifies their extension to higher resolution by building the converter out of identical but scaled pipelined cascaded folding stages. In this unified folding architecture the parallel coarse channel has been eliminated by recursively using the previous folding stage as the coarse channel for each following cascaded stage. This new architecture is demonstrated in a 10-bit ADC using six cascaded folding-by-3 stages with a total folding order of 729. At 1.0 GS/s, this interleave-by-2 ADC achieves <±0.2 LSB DNL, ¿ ±0.5 LSB INL, 9.2 ENOB at 100 MHz input, 9.1 ENOB at Nyquist, and 8.8 ENOB at 1 GHz input. The value at F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">IN</sub> = 1 GHz is 1 ENOB higher than any value published to date. The power consumption from a single 1.8 V supply is 1.2 W/channel which includes the LVDS drivers for this dual-channel (I and Q each running at 1 GS/s) ADC.
Optical Spectroscopic Method for <i>in vivo</i> Measurement of Cardiac Myoglobin Oxygen Saturation (1999)

A fiber-optic-based spectrophotometer was developed to acquire optical reflectance spectra from a living dog heart. A bullseye concentric optical probe with a 3 mm source-to-detector fiber separation was designed to obtain a 1.5 mm average tissue depth of light penetration. Spectra were analyzed in the near-infrared region from 660 to 840 nm. Myoglobin oxygen saturation was determined by partial least-squares analysis using a calibration spectral data set developed in vitro. Comparison of in vivo and in vitro spectra by Mahalanobis distance and residual ratio tests demonstrated good similarity, justifying use of partial least-squares analysis. Coronary perfusion with an oxygenated blood substitute, Fluosol®, was used to demonstrate that hemoglobin had little effect on the analysis. An increase in myoglobin saturation of 5% was noted when the animals were changed from inspired room air to 100% oxygen. Occlusion of the coronary artery resulted in prompt decrease in myoglobin saturation, and release of the occlusion was followed by rapid increase in saturation to a value above baseline. These experiments demonstrate that it is feasible to use partial least-squares analysis of near-infrared reflectance spectra to determine myoglobin saturation in the blood-perfused, beating heart.
A Novel Pathway for Regulation of Insulin Secretion by Fractalkine and CX3CR1 System (LB772) (2014)

Fractalkine (FKN) (CX3CL1) and its receptor CX3CR1 mediate cell‐to‐cell interactions in different tissues. Here, we demonstrate that the FKN/CX3CR1 system represents a novel regulatory mechanism for pancreatic islet beta cell function and insulin secretion. CX3CR1 KO mice exhibit glucose intolerance with normal insulin sensitivity, due to a marked beta cell defect in glucose and GLP1‐stimulated insulin secretion. The defect in insulin secretion was also observed in vitro in isolated islets from CX3CR1 KO mice. In vivo administration of FKN improved glucose tolerance with an increase in insulin secretion. In vitro treatment of islets with FKN increased intracellular Ca2+ level and potentiated insulin secretion. The KO islets exhibited reduced expression of a set of genes which are necessary for the fully functional, differentiated beta cell state, whereas, treatment of WT islets with FKN leads to increased expression of these genes. Lastly, expression of FKN in islets was decreased by aging and HFD/obesity, suggesting that decreased fractalkine/CX3CR1 signaling could be a mechanism underlying beta cell dysfunction in type 2 diabetes.
Less Corrosive, Non-Damaging Iron Sulfide Scale Remover (2016)

Abstract Iron sulfide scale is a common scale in sour oil and gas wells. It can form in wells producing oil and gas, as well as water injection wells. Iron sulfide scale has different forms based on the iron-to-sulfur ratio. Iron sulfide scale can form in soft forms that are removed easily by acids such as phyrrotite. The scale can also form in hard forms such as pyrite that is difficult to remove by acids. Several attempts have been made to investigate the removal of different forms of iron sulfide. Scale can reduce production and injection rates. At the end, it may completely plug the tubing and the only remedy will be to change the tubing. In the previous work either low pH corrosive fluids were used or high pH fluids with low solubility. In this study, we introduced a new formulation to remove the iron sulfide scale (especially the hard scale) pyrite form of the iron sulfide. The new formulation has a pH value greater than six with low corrosion rate. Solubility, stability, as well as corrosion experiments, were performed to assess the new formulation. The new formulation is based on a chelating agent and a low pH fluid mixture. Also coreflooding experiments were performed on carbonate cores to assess the performance of the new formulation if it invaded the near-wellbore during scale removal operations. The XRD of actual scale sample from a gas producer well showed that the scale sample contains 43 % pyrite, 35% mackinawite, and 22% iron silicon compounds. The scale solubility reached 81.6% using the new formulation. The new formulation remained stable for more than 48 hours at a high temperature. The corrosion rate of actual tubing coupons was 0.03 lb/ft2 without using corrosion inhibitors at 125°C/257°F. This corrosion rate within the allowable limit for the industry standards (should be less than (0.05 lb/ft2). Coreflooding experiments showed permeability enhancement using the new formulation which eliminates the risk of using this chemical in scale removal because it will not cause formation damage to the near-wellbore if it invades the formation.
Multiple Instrument Distributed Aperture Sensor (MIDAS) for planetary remote sensing (2004)

An innovative approach that enables greatly increased return from planetary science remote sensing missions is described. Our concept, called Multiple Instrument Distributed Aperture Sensor (MIDAS), provides a large-aperture, wide-field telescope at a fraction of the cost, mass and volume of conventional space telescopes, by integrating advanced optical interferometry technologies. All optical assemblies are integrated into MIDAS as the primary remote sensing science payload, thereby reducing the cost, resources, complexity, integration and risks of a set of back-end science instruments (SI’s) tailored to a specific mission, such as advanced SI’s now in development for future planetary remote sensing missions. MIDAS interfaces to multiple SI’s for redundancy and to enable synchronized concurrent science investigations, such as with multiple highly sensitive spectrometers. Passive imaging modes with MIDAS enable high resolution remote sensing at the diffraction limit of the overall synthetic aperture, sequentially by each science instrument as well as in somewhat lower resolution by multiple science instruments acting concurrently on the image, such as in different wavebands. Our MIDAS concept inherently provides nanometer-resolution hyperspectral passive imaging without the need for any moving parts in the science instruments. In its active remote sensing modes using an integrated laser subsystem, MIDAS enables LIDAR, vibrometry, illumination, various active laser spectroscopies such as ablative, breakdown, fluorescence, Raman and time-resolved spectroscopy. The MIDAS optical design also provides high-resolution imaging for long dwell times at high altitudes, thereby enabling real-time, wide-area remote sensing of dynamic changes in planet surface processes. These remote sensing capabilities significantly enhance astrobiologic, geologic, atmospheric, and similar scientific objectives for planetary exploration missions.
SOMA: Security Evaluation of Obfuscation Methods via Attack Sequencing (2021)

Hardware intellectual properties (IPs) used in diverse electronic systems face several critical security issues during their life cycle, including piracy, reverse engineering, and extraction of design secrets. To combat these issues, pre-silicon hardware obfuscation or logic locking has emerged as a promising solution and has been an active research topic over the past decade. However, in parallel, a number of functional and structural attacks on obfuscation have been discovered by the research community to break the protection provided by the existing obfuscation schemes. These attacks have played a major role in enhancing the security of hardware obfuscation schemes. In this paper, we introduce a novel combined attack modality, referred to as SOMA, which relies on judiciously combining the existing attacks to produce a significantly more powerful one. We demonstrate that such an attack can expose hidden exploits and measure the level of security offered by a given obfuscation technique. SOMA creates a sequence of attacks, where the outcome of each attack is used to guide the next and concludes with a key-refinement measure to restore the functionality of a locked IP. We demonstrate that SOMA can easily break major existing locking schemes that are believed to be secure with an attack accuracy average of 94.88%.
A transparent WDM network featuring shared virtual rings (2000)

We propose and demonstrate a transparent wavelength division multiplexing (WDM) metro ring architecture in which optics enables simultaneous provisioning of dedicated wavelengths for high-end users, while low-end users share wavelengths on "virtual rings". All wavelengths are sourced by the network and remotely modulated at customer end stations (ES) by low-cost semiconductor optical amplifiers (SOAs), which also serve as transmission amplifiers. Measured bit error rate (BER) data for three different ring configurations show negligible power penalties associated with upstream transmission around a 120-km 3-mode ring through as many as four cascaded SOA/modulators. Preliminary tests indicate that the SOAs are suitable modulators for packet transmission over the network.
Lidar system with nonmechanical electrowetting-based wide-angle beam steering (2019)

A light detection and ranging (lidar) system with ±90° of steering based on an adaptive electrowetting-based prism for nonmechanical beam steering has been demonstrated. Electrowetting-based prisms provide a transmissive, low power, and compact alternative to conventional adaptive optics as a nonmechanical beam scanner. The electrowetting prism has a steering range of ±7.8°. We demonstrate a method to amplify the scan angle to ±90° and perform a one-dimensional scan in a lidar system.
A New Consistency Method for Tomato Products: The Precipitate Weight Ratio (1983)

ABSTRACT The precipitate weight ratio (PPT) which refers to the weight ratio of precipitate to the initial sample weight after centrifugation was found to be highly correlated with the Bostwick consistency and the efflux viscosity of tomato products. Lower correlation coefficients were found for products containing added ingredients. However, the PPT may be a unique and reliable parameter to evaluate the consistency of tomato products before formulation.
Campylobacter hyointestinalis Isolated from Pigs Produces Multiple Variants of Biologically Active Cytolethal Distending Toxin (2015)

Campylobacter hyointestinalis isolated from swine with proliferative enteritis often is considered to be pathogenic. While the precise virulence mechanisms of this species remain unclear, we have recently identified a cytolethal distending toxin (cdt) gene cluster in C. hyointestinalis isolated from a patient with diarrhea (W. Samosornsuk et al., J Med Microbiol, 27 July 2015, http://dx.doi.org/10.1099/jmm.0.000145). However, the sequences of the cdt genes in C. hyointestinalis were found to be significantly different and the gene products are immunologically distinct from those of other Campylobacter species. In this study, we demonstrate the presence of a second variant of the cdt gene cluster in C. hyointestinalis, designated cdt-II, while the former is named cdt-I. Sequencing of the cdt-II gene cluster and deduced amino acid sequences revealed that homologies between the subunits CdtA, CdtB, and CdtC of ChCDT-I and ChCDT-II are 25.0, 56.0, and 24.8%, respectively. Furthermore, the CdtB subunit of ChCDT-II was found to be immunologically unrelated to that of ChCDT-I by Ouchterlony double gel diffusion test. Recombinant ChCDT-II also induced cell distention and death of HeLa cells by blocking the cell cycle at G2/M phase. Interestingly, the cdt-II genes were detected in all 23 animal isolates and in 1 human isolate of C. hyointestinalis, and 21 of these strains carried both cdt-I and cdt-II gene clusters. Altogether, our results indicate that ChCDT-II is an important virulence factor of C. hyointestinalis in animals.