gebhart/patrepeval huggingface dataset:
An efficient scheme for providing high availability (1992)

Replication at the partition level is a promising approach for increasing availability in a Shared Nothing architecture. We propose an algorithm for maintaining replicas with little overhead during normal failure-free processing. Our mechanism updates the secondary replica in an asynchronous manner: entire dirty pages are sent to the secondary at some time before they are discarded from primary's buffer. A log server node (hardened against failures) maintains the log for each node. If a primary node fails, the secondary fetches the log from the log server, applied it to its replica, and brings itself to the primary's last transaction-consistent state. We study the performance of various policies for sending pages to secondary and the corresponding trade-offs between recovery time and overhead during failure-free processing.
High-throughput pairing of T cell receptor alpha and beta sequences (TECH2P.930) (2015)

Abstract Conventional high-throughput immunosequencing methods profile TCR alpha (TRA) and/or TCR beta (TRB) repertoires, but do not enable pairing of the cognate subunits comprising functional TCRs. We developed a method called pairSEQ that can pair hundreds of thousands of TRA and TRB sequences in a single experiment. Our approach works by allocating random samples of T cells to a micro-titer plate, sequencing amplified cDNA from TRA and TRB genes, and DNA bar-coding the wells. Most TCR sequences uniquely identify clonal cell populations, so pairs can be assigned based on TRA and TRB sequences that occupy the same wells. To validate our method we identified cognate pairs from a sample of cells mixed from two people. The cross-sample pairs directly measure false pairing rates, which closely matched predictions from our statistical model. To show our method can be targeted to any clonal frequency range of interest, we designed a 3-plate experiment to capture pairs with repertoire frequencies from 0.5% to less than 1 in 10 million. These experiments yielded over 300,000 confident TCR pairs with one 96-well plate alone providing over 200,000 pairs. This technology is not restricted by material; in a single experiment we used this method to identify 6,349 TCR pairs from tumor infiltrating lymphocytes in 9 tumor samples. Our TCR pairing method is highly scalable, and should be broadly applicable to all somatically rearranged immune receptor loci, including immunoglobulins.
<title>Digital video blue-screen editing in compressed domain</title> (1997)

Chroma-keying or blue screen matting is an important video editing operational. In blue screen matting, everything in the image that has the 'user specified level for the blue channel' is 'keyed' out and replaced by either another image or a color from a color generator. We develop a technique for blue screen matting that manipulates the image when the information for the image is available only in compressed form such as a JPEG or MPEG bitstream. Specifically, for the compressed domain approach, we show that the matting process is a convolution operation; hence, we develop a DCT convolution theorem. The DCT convolution theorem can be used to show that the compressed domain approach proposed in this paper provides a significant reduction in computation complexity compared to previously developed approaches which were mostly adhoc techniques. The convolution theorem exploits the sparseness as well as the orthogonality of the data available in the DCT domain and thus yields an efficient algorithm for he chroma-keying or blue screen matting. The algorithm extends to the DCT domain concepts such as alpha channel and premultiplied alpha. The method is also extended to MPEG video domain wherein we explore the efficiency of the matting process when interframe coding is used.
Iterative Nonproteinogenic Residue Incorporation Yields α/β‐Peptides with a Helix–Loop–Helix Tertiary Structure and High Affinity for VEGF (2016)

Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (α/β-peptides) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix "mini-Z-domain" can be modified to contain β and other nonproteinogenic residues while retaining the target-binding epitope by using iterative unnatural residue incorporation. The resulting α/β-peptides are less susceptible to proteolysis than is their parent α-peptide, and some of these α/β-peptides match the full-length Z-domain in terms of affinity for receptor-recognition surfaces on the VEGF homodimer.
Spectral Digitization of Color Photographic Paper Through Dye Density Estimation (1995)

A methodology has been developed to digitize images from photographic color paper (reflection prints) and store the spectral information as a function of the three dye density basis functions inherent to the paper film type. The result is a highly accurate digitization of the spectral information at each spatial pixel that can be digitally stored with very little additional storage space over conventional RGB-type methodologies.
Surface loss calculations and design of a superconducting transmon qubit with tapered wiring (2022)

Abstract Analytical formulas are presented for simplified but useful qubit geometries that predict surface dielectric loss when its thickness is much less than the metal thickness, the limiting case needed for real devices. These formulas can thus be used to precisely predict loss and optimize the qubit layout. Surprisingly, a significant fraction of surface loss comes from the small wire that connects the Josephson junction to the qubit capacitor. Tapering this wire is shown to significantly lower its loss. Also predicted are the size and density of the two-level state (TLS) spectrum from individual surface dissipation sites.
Abstract 5780: Development of potent inhibitors of the DNA-dependent protein kinase (DNA-PK) (2010)

Abstract The cellular response to DNA double-strand break (DSB) formation is an essential component of normal cell survival, following exposure to DNA-damaging chemicals and ionising radiation. The serine/threonine kinase DNA-dependent protein kinase (DNA-PK) is a member of the phosphatidylinositol (PI) 3-kinase related kinase (PIKK) family of enzymes, and plays an important role in DNA DSB repair via the non-homologous end-joining (NHEJ) pathway. DNA-PK inhibitors may, therefore, be useful as agents to improve the activity of radio- and chemo-therapy in the treatment of cancer. Identification of the lead benzo[h]chromen-4-one DNA-PK inhibitor NU7026 (IC50 = 0.23 uM) guided the development of the potent and selective ATP-competitive chromenone NU7441 (DNA-PK IC50 = 30 nM). Structure-activity relationship studies for DNA-PK inhibition by chromenone-derivatives were conducted in conjunction with homology modelling. Library synthesis was undertaken employing a solution multiple-parallel approach, by O-alkylation or N-acylation of the appropriately substituted NU7441 derivatives, respectively, followed by reaction with a range of amines to afford the target compounds. These studies resulted in the identification of the highly potent inhibitor KU-0060648 (IC50 = 8.6 nM). The further development of KU-0060648 and analogues will be described. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5780.
Modelling, analysis, and implementation of a switched‐inductor based DC/DC converter with reduced switch current stress (2021)

Abstract This paper proposes a technique for switch current stress reduction in a Switched Inductor DC‐DC Boost Converter (SIBC). The proposed technique comes up with a low‐cost design, high voltage conversion ratio with a less duty cycle value, and lower current stress without increasing the component count. This topology is basically a transformer‐less design where one diode of the traditional switched inductor configuration has been replaced with a switch, which is in parallel with the existing switch, resulting in a design that can incorporate active switches with a low current rating, since the total input current is equally shared by them. The detailed modes of operation in both continuous conduction mode (CCM) and discontinuous conduction mode (DCM) and steady‐state analysis, the non‐idealities’ effect on voltage gain, design approach, and a comparative study with other DC‐DC converters for some significant performance characteristics are provided. The experimental validations for the performance and working of the 500 W designed prototype are presented.
Noncontact video-based eye-gaze detection method allowing large head displacements (2002)

The noncontact video-based eye-gaze detection method which allows large head displacements was developed. The eye was tracked by a two-dimensional camera rotation system. The distance between the camera rotation center and the eye was measured by an ultrasonic distance meter. A theory using trigonometry was proposed to determine the pupil center position in three-dimensional space. At this time, the displacements of the pupil from the camera frame center were considered to precisely determine the coordinates of the eye-gaze point on a computer display. The angle of eye's line of sight against the camera axis was determined from the relative positions of the centers of the feature points in the eye image, i.e., the glint (corneal reflection) and the pupil. The eye-gaze points while a subject fixated visual targets presented on the display were measured at video rate using custom-made image processors. Under the small head-movement condition and under the large head-displacements condition, the results showed almost no distortion between the target and eye-gaze positions. This indicated that the theory is adequate and the system worked well. The average error was approximately 0.7 deg in visual angle.
Thermoset/Thermoplastic Aromatic Polyamides for Composites (1983)

Aromatic polyamides are processed at relatively low temperature, then heat-treated to attain high softening temperature required when polyamides are used as matrix resins in structural composites. New polyamides are compatable with organic fibers often used as reinforcing agents in such composites Pendent propargyl groups serve as latent cross-linking agents in new series of polyamide resins.
Similarity of binaries through re-optimization (2017)

We present a scalable approach for establishing similarity between stripped binaries (with no debug information). The main challenge in binary similarity, is to establish similarity even when the code has been compiled using different compilers, with different optimization levels, or targeting different architectures. Overcoming this challenge, while avoiding false positives, is invaluable to the process of reverse engineering and the process of locating vulnerable code.
Spray-Formed Hybrid-Field Electric Motor (2016)

A new class of electric motors with hybrid-field topology is introduced. Departing from conventional radial- or axial-field designs, the motors feature three-dimensional magnetic flux paths, which are enabled by an advanced isotropic soft magnetic material produced by a unique additive-manufacturing process based on spray forming. The motors provide considerably higher power output (40% higher power density) and improved energy efficiency (up to 15% lower losses) compared to the state of the art. A prototype spray-formed hybrid-field motor has been designed and constructed, and the size, power and efficiency benefits have been demonstrated.
TrustRank: Inducing Trust in Automatic Translations via Ranking (2010)

The adoption of Machine Translation technology for commercial applications is hampered by the lack of trust associated with machine-translated output. In this paper, we describe TrustRank, an MT system enhanced with a capability to rank the quality of translation outputs from good to bad. This enables the user to set a quality threshold, granting the user control over the quality of the translations. We quantify the gains we obtain in translation quality, and show that our solution works on a wide variety of domains and language pairs. 1
Enhancing spectral efficiency in cooperative cognitive two-way amplify-and-forward relaying networks (2016)

In this work, a new cooperative cognitive two-way amplify-and-forward (AF) relaying scheme is proposed. In this model, a primary user (PU) network consisting of two PU sources communicate with each other via a single AF relay. In addition, a secondary user (SU) source transmits its data to a SU destination via the same PU relay node via decode-and-forward protocol. In order to mitigate SU interference caused to the PU network, the PU network considers the SU network pairs (i.e., source and destination) as two additional relay nodes helping the original PU relay node in improving the PU network performance. As a reward for its cooperation, the PU network allows the SU network to communicate simultaneously via the PU relay node using the decode-and-forward (DF) protocol. Two power allocation optimization problems are formulated; the first problem minimizes the weighted sum of the average symbol error probability (SEP) of both PU and SU systems, whereas the second problem maximizes the total achievable sum rate of the PU and SU networks. Results show that the error performance of the proposed model outperforms the conventional two-way relaying networks with amplify-and-forward protocol. Moreover, the total achievable sum rate of the proposed model is higher than the total achievable rate of the conventional ones.
Hybrid Intrusion Detection System Design for Distributed Energy Resource Systems (2019)

The integration of communication-enabled grid-support functions in distributed energy resources (DER) and other smart grid features will increase the U.S. power grid's exposure to cyber-physical attacks. Unwanted changes in DER system data and control signals can damage electrical infrastructure and lead to outages. To protect against these threats, intrusion detection systems (IDSs) can be deployed, but their implementation presents a unique set of challenges in industrial control systems (ICSs), New approaches need to be developed that not only sense cyber anomalies, but also detect undesired physical system behaviors. For DER systems, a combination of cyber security data and power system and control information should be collected by the IDS to provide insight into the nature of an anomalous event. This allows joint forensic analysis to be conducted to reveal any relationships between the observed cyber and physical events. In this paper, we propose a hybrid IDS approach that monitors and evaluates both physical and cyber network data in DER systems, and present a series of scenarios to demonstrate how our approach enables the cyber-physical IDS to achieve more robust identification and mitigation of malicious events on the DER system.
Combining Color Indices and Textures of UAV-Based Digital Imagery for Rice LAI Estimation (2019)

Leaf area index (LAI) is a fundamental indicator of plant growth status in agronomic and environmental studies. Due to rapid advances in unmanned aerial vehicle (UAV) and sensor technologies, UAV-based remote sensing is emerging as a promising solution for monitoring crop LAI with great flexibility and applicability. This study aimed to determine the feasibility of combining color and texture information derived from UAV-based digital images for estimating LAI of rice (Oryza sativa L.). Rice field trials were conducted at two sites using different nitrogen application rates, varieties, and transplanting methods during 2016 to 2017. Digital images were collected using a consumer-grade UAV after sampling at key growth stages of tillering, stem elongation, panicle initiation and booting. Vegetation color indices (CIs) and grey level co-occurrence matrix-based textures were extracted from mosaicked UAV ortho-images for each plot. As a solution of using indices composed by two different textures, normalized difference texture indices (NDTIs) were calculated by two randomly selected textures. The relationships between rice LAIs and each calculated index were then compared using simple linear regression. Multivariate regression models with different input sets were further used to test the potential of combining CIs with various textures for rice LAI estimation. The results revealed that the visible atmospherically resistant index (VARI) based on three visible bands and the NDTI based on the mean textures derived from the red and green bands were the best for LAI retrieval in the CI and NDTI groups, respectively. Independent accuracy assessment showed that random forest (RF) exhibited the best predictive performance when combining CI and texture inputs (R2 = 0.84, RMSE = 0.87, MAE = 0.69). This study introduces a promising solution of combining color indices and textures from UAV-based digital imagery for rice LAI estimation. Future studies are needed on finding the best operation mode, suitable ground resolution, and optimal predictive methods for practical applications.
Methodology for the optimization of an i-line lithographic process for defect reduction (1998)

As device geometries shrink into the sub-half micron regime, controlling and reducing defect levels becomes increasingly important in both R&D and Manufacturing environments. Any delay in addressing the causes and cures of these yield killers can prolong the development cycle and production release of new product technologies. However, defect evaluation for a new lithography process on product wafers is difficult due to metrology limitation, substrate noises and previous layer defects. This problem is particularly pronounced for backend layers where differences in the metal grain sizes and reflectivity can confound defect inspection tools and can be picked up as false defects. Often yield learning is long delayed awaiting sort data, before lithographers can determine the beneficial effects of proposed manufacturing improvements. In this paper, we will discuss a methodology for optimizing an I-line lithographic process with the aid of a photo defect monitor. Clean Silicon wafers were fully processed through a photocluster cell to simulate the actual processing conditions for the product, then inspected on a KLA 2132 for pattern defects. An in-line low voltage SEM system was used to review and to classify defect types. In a case study presented here, post develop residue was found to be the predominant defect for a new I-line resist used in the backend layers of the 0.25 micrometer process technology. The resolution of the resist residue deposition problem was commenced by evaluating different processes with multiple puddles/rinses for their defect densities. Based on this work, a low defect developer process was chosen for further study. Other process variables such as resist profile, CD uniformity and Etch bias as well as electrical defect parameters were compared between the old and the new processes. The goal is to demonstrate that given equal performance in all other respects, a quick implementation of this new low defect process, prior to the sort yield confirmation, would not have any detrimental effect on device yield. An example of a non- killer defect, water stain droplets, discovered during the defect review will be shown. Further refining of the dry cycle in the process eliminated this cosmetic defect. Finally, the KLA defect trend chart will show an improvement in defect density with the new develop process.
Shotgun Metabolomics Approach for the Analysis of Negatively Charged Water-Soluble Cellular Metabolites from Mouse Heart Tissue (2007)

A shotgun metabolomics approach using MALDI-TOF/TOF mass spectrometry was developed for the rapid analysis of negatively charged water-soluble cellular metabolites. Through the use of neutral organic solvents to inactivate endogenous enzyme activities (i.e., methanol/chloroform/H2O extraction), in conjunction with a matrix having minimal background noise (9-amnioacridine), a set of multiplexed conditions was developed that allowed identification of 285 peaks corresponding to negatively charged metabolites from mouse heart extracts. Identification of metabolite peaks was based on mass accuracy and was confirmed by tandem mass spectrometry for 90 of the identified metabolite peaks. Through multiplexing ionization conditions, new suites of metabolites could be ionized and "spectrometric isolation" of closely neighboring peaks for subsequent tandem mass spectrometric interrogation could be achieved. Moreover, assignments of ions from isomeric metabolites and quantitation of their relative abundance was achieved in many cases through tandem mass spectrometry by identification of diagnostic fragmentation ions (e.g., discrimination of ATP from dGTP). The high sensitivity of this approach facilitated the detection of extremely low abundance metabolites including important signaling metabolites such as IP3, cAMP, and cGMP. Collectively, these results identify a multiplexed MALDI-TOF/TOF MS approach for analysis of negatively charged metabolites in mammalian tissues.
High‐Resolution LC–MS‐Based Mass Defect Filter Approach: Basic Concept and Application in Metabolite Detection (2008)

This chapter contains sections titled: Introduction What is Mass Defect? Concept of MDF Implementation of MDF Applications of MDF in Metabolite Identification MDF in Conjunction with Control Sample Comparison Comparison of MDF with Precursor Ion Scan and Constant-Neutral-Loss Scan Applicability of MDF for Drugs in Different Biological Matrices Summary Acknowledgments References
Near-field scanning optical microscopy (1986)

In general, conventional methods of optical imaging are limited in spatial resolution by either the wavelength of the radiation used or by the aberrations of the optical elements. This is true whether one uses a scanning probe or a fixed beam method. The reason for the wavelength limit of resolution is due to the far field methods of producing or detecting the radiation. If one resorts to restricting our probes to the near field optical region, then the possibility exists of obtaining spatial resolutions more than an order of magnitude smaller than the optical wavelength of the radiation used. In this paper, we will describe the principles underlying such "near field" imaging and present some preliminary results from a near field scanning optical microscope (NS0M) that uses visible radiation and is capable of resolutions comparable to an SEM. The advantage of such a technique is the possibility of completely nondestructive imaging in air at spatial resolutions of about 50nm.