gebhart/patrepeval huggingface dataset:
Discovery and Characterization of an Isopeptidase That Linearizes Lasso Peptides (2013)

Lasso peptides are a class of ribosomally derived natural products with diverse bioactivities. The characteristic threaded lasso structure in these peptides derives from an isopeptide bond attaching the N-terminus of the peptide to an acidic side chain. Here we describe the heterologous expression of a lasso peptide gene cluster encoding two lasso peptides, astexin-2 and astexin-3, and solve the solution structure of astexin-3. This cluster also encodes an enzyme annotated as a protease. We show that this enzyme, AtxE2, is a lasso peptide isopeptidase that specifically hydrolyzes astexins-2 and -3, converting them to linear peptides. Astexin-3 is highly thermostable and resists unthreading after extensive heat treatment. In contrast, astexin-2 unthreads upon heat treatment. AtxE2 has no activity toward unthreaded astexin-2, demonstrating that this isopeptidase must recognize a knotted structure in order to function. We also use this isopeptidase as a tool to study evolutionary relationships between lasso peptide gene clusters.
Fusion Proteins Containing Family 1 and Family 2 PspA Fragments Elicit Protection against <i>Streptococcus pneumoniae</i> That Correlates with Antibody-Mediated Enhancement of Complement Deposition (2007)

PspA is an important pneumococcal vaccine candidate that is capable of inducing protection in different animal models. Because of its structural diversity, a PspA-based vaccine should contain at least one fragment from each of the two major families (1 and 2) in order to elicit broader protection. In the present work, we have tested the potential of PspA hybrids containing fused portions of family 1 and 2 (PspA1ABC-4B and PspA1ABC-3AB) PspA fragments to induce protection against pneumococci bearing distinct PspA fragments. Sera from mice immunized with these hybrid PspA fragments were able to increase C3 deposition on pneumococci bearing PspA fragments from both families, in contrast with sera made against the PspA family 1 (PspA1ABC) and PspA family 2 (PspA3ABC) fragments, which were effective only within the same family. Although PspA hybrids were able to extend protection against pneumococcal infection with strains bearing diverse PspA fragments, the immunity elicited by family 2 was clade dependent, suggesting that PspA fragments from family 2 clades 3 and 4 should both be included in a comprehensive PspA vaccine. These results indicate that PspA fusion proteins constitute an efficient immunization strategy for future PspA-based antipneumococcal vaccines since they are able to extend protection provided by a protein derived from a single transcript.
Adaptive optics compensation of multiple orbital angular momentum beams propagating through emulated atmospheric turbulence (2014)

We propose an adaptive optics compensation scheme to simultaneously compensate multiple orbital angular momentum (OAM) beams propagating through atmospheric turbulence. A Gaussian beam on one polarization is used to probe the turbulence-induced wavefront distortions and derive the correction pattern for compensating the OAM beams on the orthogonal polarization. By using this scheme, we experimentally demonstrate simultaneous compensation of multiple OAM beams, each carrying a 100 Gbit/s data channel through emulated atmospheric turbulence. The experimental results indicate that the correction pattern obtained from the Gaussian probe beam could be used to simultaneously compensate multiple turbulence-distorted OAM beams with different orders. It is found that the turbulence-induced crosstalk effects on neighboring modes are efficiently reduced by 12.5 dB, and the system power penalty is improved by 11 dB after compensation.
Logistic regression over encrypted data from fully homomorphic encryption. (2018)

One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was for the data holder to encrypt the records using homomorphic encryption, and send them to an untrusted cloud for storage. The cloud could then homomorphically apply a training algorithm on the encrypted data to obtain an encrypted logistic regression model, which can be sent to the data holder for decryption. In this way, the data holder could successfully outsource the training process without revealing either her sensitive data, or the trained model, to the cloud. Our solution to this problem has several novelties: we use a multi-bit plaintext space in fully homomorphic encryption together with fixed point number encoding; we combine bootstrapping in fully homomorphic encryption with a scaling operation in fixed point arithmetic; we use a minimax polynomial approximation to the sigmoid function and the 1-bit gradient descent method to reduce the plaintext growth in the training process. Our algorithm for training over encrypted data takes 0.4–3.2 hours per iteration of gradient descent. We demonstrate the feasibility but high computational cost of training over encrypted data. On the other hand, our method can guarantee the highest level of data privacy in critical applications.
Object tracking using adaptive block matching (2003)

We propose an object-tracking algorithm that predicts the object contour using motion vector information. Tracking is achieved by predicting the object boundary using motion vectors, followed by contour update, using occlusions/disocclusion detection. An adaptive block-based approach has been used for estimating motion between frames. An efficient modulation scheme is used to control the gap between frames used for object tracking. The algorithm for detecting occlusions proceeds in two steps. First, covered regions are estimated from the displaced frame difference. These covered regions are classified into actual occlusions and false alarms using motion characteristics. Disocclusion detection is also performed in a similar manner. The immediate applications of the proposed tracking algorithm are video compression using MPEG-4 and content retrieval based on standards like H.26L. Preliminary simulation results demonstrate the performance of the proposed algorithm.
Reflective Bistable Twisted Nematic Liquid Crystal Display (1998)

A reflective bistable twisted nematic (BTN) liquid crystal display has been developed. It combines the advantages of a truly reflective display without the rear polarizer, and the bistable nature of the zero voltage state. It was found experimentally that switching between the two bistable twist states could be achieved by adjusting the magnitude of the selection voltage pulse, just like the case in transmittive BTNs. In demonstrating the reflective BTN, we also show for the first time bistability between the -36° and 324° twist states.
Permeability prediction from thin sections using the Lattice‐Boltzmann flow simulation (2003)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2003Permeability prediction from thin sections using the Lattice‐Boltzmann flow simulationAuthors: Youngseuk KeehmTapan MukerjiManika PrasadAmos NurYoungseuk KeehmRock Physics Laboratory, Geophysics Department, Stanford University, CA 94305, Tapan MukerjiRock Physics Laboratory, Geophysics Department, Stanford University, CA 94305, Manika PrasadRock Physics Laboratory, Geophysics Department, Stanford University, CA 94305, and Amos NurRock Physics Laboratory, Geophysics Department, Stanford University, CA 94305https://doi.org/10.1190/1.1817626 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1817626FiguresReferencesRelatedDetailsCited byPermeability and relative permeability from digital rocks: Issues on grid resolution and representative elementary volumeYoungseuk Keehm and Tapan Mukerji3 January 2005 SEG Technical Program Expanded Abstracts 2003ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2003 Pages: 2452 publication data© 2003 Copyright © 2003 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 03 Jan 2005 CITATION INFORMATION Youngseuk Keehm, Tapan Mukerji, Manika Prasad, and Amos Nur, (2003), "Permeability prediction from thin sections using the Lattice‐Boltzmann flow simulation," SEG Technical Program Expanded Abstracts : 1668-1671. https://doi.org/10.1190/1.1817626 Plain-Language Summary PDF DownloadLoading ...
Instrumented Measurement of Patellar Mobility (1995)

To provide an objective analysis of medial and lateral patellofemoral laxity, we examined 94 uninjured athletic subjects and 22 patients with unilateral lateral patellar dislocation. We developed an instrument to measure the compliance of the medial and lateral patellar restraints. The instrument recorded the force-displacement relationship as the patella was pushed medially and laterally. Subtracting the medial displacement from the lateral displacement at a given force level allowed the tester to assess the peripatellar soft tissue "balance." The results for both the 2.5- and the 5-pound tests were significant. Paired comparisons differentiated the three groups, with significant differences between control and affected (P = 0.0001), control and contralateral (P = 0.0036), and affected and contralateral (P = 0.0157) knees. The mean result of the lateral minus medial displacement test for our sample population of control subjects was -2.1 mm for the 5-pound test. A negative value in this test indicates that medial displacement exceeds lateral displacement. This finding was present in 81% of control subjects. In contrast, the mean result for the patients' affected knees was +3.2 mm for the 5-pound test. Using the value of 0.0 mm as the diagnostic determinant for peripatellar imbalance, we found a test sensitivity of 91% and a specificity of 81%.
A fiber-optic connector (1994)

Abstract : There is presented a fiber-optic connector and a method of making same. The connector comprises a plurality of ferrules, each of the ferrules having extending centrally therethrough a single optical fiber. The connector further includes structure abutting at least a portion of the ferrules for exercising a radially compressive force on the ferrules for urging the ferrules into a configuration in which said bodies are co-parallel and nested so as to form a stable bundle which in transverse section is substantially axisymmetrical, and retaining the ferrules in the configuration. The connector still further includes alignment structure for angular positioning of said bodies in said connector in said transverse section about a nominal longitudinal axis of said bundle for registry of the connector with a second connector of complementary configuration.
Experiments with soft-x-ray Fourier-transform holography (1990)

We report tests of a holographic microscope with submicrometer resolution. We used the microscope to record Fourier-transform holograms of gold test patterns (50 nm finest dimension) with 3.4 nm wavelength radiation from the soft-x-ray undulator at the National Synchrotron Light Source. The high-brightness undulator source enabled us to generate holograms of sufficient contrast to be numerically reconstructed from exposures of 10-30 min obtained with a chargecoupled-device (CCD) detector. The coherent x-ray flux through the 100 µ 2 test objects was 9 × 10 5 photons/s and was 2 × 10 6 photons/s in the reference source. The microscope used a 90 µ m diameter zone plate as a beam splitter (50 nm finest zone width) both to illuminate the object and to form a focused reference spot. A low-noise integrating CCD camera recorded the interference between the reference and object wavefields, which had a mean spatial period of ~200 µ m. After making background corrections, we performed discrete Fourier-transform reconstructions of 512 × 512 pixel arrays of the hologram data, which yielded images of the test patterns having features resolved to better than 1 µ m. This approach to Fourier-transform holography demonstrates high-resolution x-ray microscopy by using a relatively coarse-grained detector; this permits fast turnaround from hologram acquisition to wave-front reconstruction.
<title>Optoelectronic multichip modules based on imaging fiber bundle structures</title> (2000)

In this paper, we present a new packaging architecture for chip-level optical interconnections based on imaging fiber bundles. Imaging fiber bundles consist of densely packed arrays of small core fibers such that an object imaged at one end of the bundle is correspondingly imaged on the opposite end. In optical communication applications fiber bundles can be directly coupled to an array of optical sources. Each spot is carried by multiple fibers that in turn can directly illuminate each element in a detector array. Neither end requires any additional optical elements. Thus, imaging fiber bundles are capable of supporting the spatial parallelism of free space interconnects with relaxed alignment and geometry constraints. This paper is focused specifically on multi-chip system designs.
Error-correction of binary masks using hidden Markov models (2010)

Binary masking is a simple and efficient method for source separation, and a high increase in intelligibility can be obtained by applying the target binary mask to noisy speech. The target binary mask can only be calculated under ideal conditions and will contain errors when estimated in real-life applications. This paper proposes a method for correcting these errors. The error-correction is based on a hidden Markov model and uses the Viterbi algorithm to calculate the most probable error-free target binary mask from a target binary mask containing errors. The results demonstrate that it is possible to correct errors in the target binary mask and reduce the noise energy. However, speech energy is also reduced by the error-correction, but the impact on speech intelligibility and speech quality are not established or evaluated in the present study.
Practical Total Synthesis of Ciguatoxin CTX3C by Improved Protective Group Strategy (2002)

[structure: see text] Ciguatoxin CTX3C is a representative congener of ciguatoxins, which are known to be the principal causative agents of ciguatera seafood poisoning. The structure of CTX3C spans more than 3 nm and is characterized by 13 ether rings. In this paper, an improved total synthesis of CTX3C is reported. Alteration of the protective group from benzyl ether to 2-naphthylmethyl (NAP) ether drastically increases the yield for final global deprotection and has provided a sufficient amount of sample for further biological studies.
Upgrading Calcium Bentonite to Sodium Bentonite Using Seawater and Soda Ash (2019)

In this paper, a new method is introduced to produce sodium bentonite by treating calcium bentonite using seawater to eliminate the use of freshwater and reduces the amount of soda ash required for the treatment, which significantly minimizes the cost of bentonite production. In this study, calcium bentonite was collected as rocks from local resources, ground, purified, characterized, and the physical properties were measured. Then, bentonite was treated using seawater under heating and stirring for different time periods to optimize the treatment conditions. Soda ash was also added with different concentrations, and the produced bentonite samples were characterized, evaluated, and compared to the standard sodium bentonite used in drilling fluid formulation. The results of this study showed that the treatment with soda ash under heating and stirring in seawater environment converts calcium bentonite into sodium bentonite by sodium and calcium cations exchange between soda ash and calcium bentonite. This exchange will improve the rheological and swelling properties of bentonite that can efficiently be used as a drilling fluid and cement additive.
Fabrication of a miniature all-glass fibre optic pressure and temperature sensor (2011)

In this paper the fabrication of a miniature all-glass fibre optic pressure and temperature sensor is presented. The sensor combines the functionality of a miniature all-silica diaphragm based Extrinsic Fabry Perot Interferometric (EFPI) Fibre Optic Pressure Sensor (FOPS) and an in-Fibre Bragg Grating (FBG) sensor. The reported fibre optic sensor has several advantages such as being cost-effective, simple to fabricate, miniature in size, mechanically robust and can be designed to withstand high temperatures or/and pressures.
Strategic Overview of High-Voltage SiC Power Device Development Aiming at Global Energy Savings (2014)

Advanced high-voltage (≥10 kV) silicon carbide (SiC) devices described in this paper have the potential to significantly impact the system size, weight, high-temperature reliability, and cost of modern variable-speed medium-voltage (MV) systems such as variable speed (VSD) drives for electric motors, integration of renewable energy including energy storage, micro-grids, traction control, and compact pulsed power systems. In this paper, we review the current status of the development of 10 kV-20 kV class power devices in SiC, including MOSFETs, JBS diodes, IGBTs, GTO thyristors, and PiN diodes at Cree. Advantages and weakness of each device are discussed and compared. A strategy for high-voltage SiC power device development is proposed.
Two-Dimensional Active Learning for image classification (2008)

In this paper, we propose a two-dimensional active learning scheme and show its application in image classification. Traditional active learning methods select samples only along the sample dimension. While this is the right strategy in binary classification, it is sub-optimal for multi-label classification. In multi-label classification, we argue that, for each selected sample, only a part of more effective labels are necessary to be annotated while others can be inferred by exploring the correlations among the labels. The reason is that the contributions of different labels to minimizing the classification error are different due to the inherent label correlations. To this end, we propose to select sample-label pairs, rather than only samples, to minimize a multi-label Bayesian classification error bound. This new active learning strategy not only considers the sample dimension but also the label dimension, and we call it Two-Dimensional Active Learning (2DAL). We also show that the traditional active learning formulation is a special case of 2DAL when there is only one label. Extensive experiments conducted on two real-world applications show that the 2DAL significantly outperforms the best existing approaches which did not take label correlation into account.
Quantitative evaluation of <i>k</i>‐space reordering schemes for compatible dual‐echo arteriovenography (CODEA) (2010)

Compatible dual-echo arteriovenography (CODEA) is a recently developed technique for simultaneous acquisition of time-of-flight MR angiogram (MRA) and blood oxygenation level-dependent MR venogram (MRV) using an echo-specific k-space reordering scheme. In this study, we evaluated and compared the image quality of CODEA MRA/MRV implemented with two different schemes of echo-specific k-space reordering: one along the 1st phase-encode direction (one-dimensional) only and the other along both phase-encode directions (two-dimensional). Our results showed that use of the two-dimensional reordering scheme improved contrast-to-noise ratio of small arteries by approximately 8%, although not statistically significant (P > 0.1). Contrast-to-noise ratio of the CODEA MRAs was better than that for the non-CODEA dual-echo MRA without k-space reordering (contrast-to-noise ratio increased in large arteries by approximately 10% and small arteries by approximately 45%; P < 0.1). Contrast-to-noise ratio of the CODEA MRAs was comparable with that of the conventional single-echo MRA for large arteries but reduced by approximately 20% for small arteries. Contrast-to-noise ratio of veins on the CODEA MRVs was equivalent to that of the conventional single-echo and the non-CODEA dual-echo MRVs. However, some veins in the CODEA MRVs showed stronger contrast than those in the single-echo MRV in relation to the contrast of neighboring arterial signals.
Rapid Induction of Therapeutic Hypothermia Using Transnasal High Flow Dry Air (2016)

Early induction of therapeutic hypothermia (TH) is recommended in out-of-hospital cardiac arrest (CA); however, currently no reliable methods exist to initiate cooling. We investigated the effect of high flow transnasal dry air on brain and body temperatures in adult porcine animals. Adult porcine animals (n = 23) under general anesthesia were subject to high flow of transnasal dry air. Mouth was kept open to create a unidirectional airflow, in through the nostrils and out through the mouth. Brain, internal jugular, and aortic temperatures were recorded. The effect of varying airflow rate and the air humidity (0% or 100%) on the temperature profiles were recorded. The degree of brain cooling was measured as the differential temperature from baseline. A 10-minute exposure of high flow dry air caused rapid cooling of brain and gradual cooling of the jugular and the aortic temperatures in all animals. The degree of brain cooling was flow dependent and significantly higher at higher airflow rates (0.8°C ± 0.3°C, 1.03°C ± 0.6°C, and 1.3°C ± 0.7°C for 20, 40, and 80 L, respectively, p < 0.05 for all comparisons). Air temperature had minimal effect on the brain cooling over 10 minutes with similar decrease in temperature at 4°C and 30°C. At a constant flow rate (40 LPM) and temperature, the degree of cooling over 10 minutes during dry air exposure was significantly higher compared to humid air (100% saturation) (1.22°C ± 0.35°C vs. 0.21°C ± 0.12°C, p < 0.001). High flow transnasal dry air causes flow dependent cooling of the brain and the core temperatures in intubated porcine animals. The mechanism of cooling appears to be evaporation of nasal mucus as cooling is mitigated by humidifying the air. This mechanism may be exploited to initiate TH in CA.
Motion control of a hydraulic free-piston engine (2012)

Free-piston engine (FPE), as an alternative of the conventional internal combustion engine, has a high potential in terms of energy saving given its wide range of potential applications and high efficiency. One of the technical barriers that prevents the wide spread of this technology is the lack of precise piston motion control. This paper presents a novel strategy on the motion control of a hydraulic FPE. A robust repetitive controller is designed and implemented to form a virtual crankshaft that would provide a precise and stable engine operation. Based on the controller, a hardware-in-the-loop (HIL) environment that integrates the combustion chamber dynamics with the hydraulic system is developed to further validate the proposed control design. The experimental data of engine motoring tests with virtual crankshaft control demonstrates the effectiveness of the proposed approach.