gebhart/patrepeval huggingface dataset:
Generalization of the Ensemble Kalman Filter Using Kernels for Non-gaussian Random Fields (2009)

Abstract Efficient history matching (model updating) of geologically complex reservoirs is important in many applications, but it is central in closed-loop reservoir modeling, in which real-time model updating is required. Within the context of closed-loop modeling, one history matching approach receiving the most attention to date is the ensemble Kalman filter (EnKF). Although the EnKF has many advantages such as ease of implementation and efficient uncertainty quantification, it is technically appropriate only for random fields (e.g., permeability) characterized by two-point geostatistics (multi-Gaussian random fields). Realistic systems however are much better described by multi-point geostatistics, which is capable of representing key geological structures such as channels. History matching algorithms that are able to reproduce realistic geology provide enhanced predictive capacity and can therefore lead to better reservoir management and optimization. In this work, we propose and formulate a generalized EnKF using kernels, capable of representing non-Gaussian random fields characterized by multi-point geostatistics. The main drawback of the standard EnKF is that the Kalman update essentially results in a linear combination of the forecasted ensemble, and the EnKF only uses the covariance and cross-covariance between the random fields (to be updated) and observations, thereby only preserving two-point statistics. Kernel methods allow the creation of nonlinear generalizations of linear algorithms that can be exclusively written in terms of dot products. By deriving the EnKF in a high-dimensional feature space implicitly defined using kernels, both the Kalman gain and update equations are nonlinearized, thus providing a completely general nonlinear set of EnKF equations, the nonlinearity being controlled by the kernel. By choosing high order polynomial kernels, multi-point statistics and therefore geological realism of the updated random fields can be preserved. The procedure is applied to two example cases where permeability is updated using production data as obserations, and is shown to better reproduce complex geology compared to the standard EnKF, while providing reasonable match to the production data.
High density fabrication process for single flux quantum circuits (2023)

We implemented, optimized, and fully tested a superconducting Josephson junction fabrication process over multiple runs tailored for integrated digital circuits that are used for control and readout of superconducting qubits operating at millikelvin temperatures. This process was optimized for highly energy efficient rapid single flux quantum (ERSFQ) circuits with critical currents reduced by a factor of ∼10 as compared to those operated at 4.2 K. Specifically, it implemented Josephson junctions with 10 μA unit critical current fabricated with 10 μA/μm2 critical current density. In order to circumvent the substantial size increase in the SFQ circuit inductors, we employed an NbN high kinetic inductance layer with 8.5 pH/sq sheet inductance. Similarly, to maintain the small size of junction resistive shunts, we used a non-superconducting PdAu alloy with 4.0 Ω/sq sheet resistance. For integration with quantum circuits in a multi-chip module, 5 and 10 μm height bump processes were also optimized. To keep the fabrication process in check, we developed and thoroughly tested a comprehensive process control monitor chip set.
A photonic integrated resonant accelerometer (2016)

We demonstrate a novel photonic integrated accelerometer having 6 μg/√Hz sensitivity. The device was realized by integrating millimeter-scale mechanical structures with sub-micron silicon photonics using a 200-mm silicon toolset. We review our initial results and discuss the potential realization of nano-g level performance in a chip-scale device.
Finding concurrency bugs with context-aware communication graphs (2009)

Incorrect thread synchronization often leads to concurrency bugs that manifest nondeterministically and are difficult to detect and fix. Past work on detecting concurrency bugs has addressed the general problem in an ad-hoc fashion, focusing mostly on data races and atomicity violations.
Human papillomavirus 16-specific T cell responses in classic HPV-related vulvar intra-epithelial neoplasia. Determination of strongly immunogenic regions from E6 and E7 proteins (2009)

Cell-mediated immunity directed against human papillomavirus 16 (HPV-16) antigens was studied in 16 patients affected with classic vulvar intra-epithelial neoplasia (VIN), also known as bowenoid papulosis (BP). Ten patients had blood lymphocyte proliferative T cell responses directed against E6/2 (14-34) and/or E6/4 (45-68) peptides, which were identified in the present study as immunodominant among HPV-16 E6 and E7 large peptides. Ex vivo enzyme-linked immunospot-interferon (IFN)-gamma assay was positive in three patients who had proliferative responses. Twelve months later, proliferative T cell responses remained detectable in only six women and the immunodominant antigens remained the E6/2 (14-34) and E6/4 (45-68) peptides. The latter large fragments of peptides contained many epitopes able to bind to at least seven human leucocyte antigen (HLA) class I molecules and were strong binders to seven HLA-DR class II molecules. In order to build a therapeutic anti-HPV-16 vaccine, E6/2 (14-34) and E6/4 (45-68) fragments thus appear to be good candidates to increase HPV-specific effector T lymphocyte responses and clear classic VIN (BP) disease lesions.
Efficient generation (1.6%) of highly nondegenerate four-wave mixing signal in a semiconductor microcavity using oblique incidence configuration (1998)

Summary form only given. Highly nondegenerate four-wave mixing (NDFWM) is an important optical parametric process attracting increased current interest for applications in all-optical wavelength conversion in wavelength-division-multiplexed systems We report on ND-FWM in a semiconductor quantum well (QW) microcavity and its potential as a wavelength converter.
Melanocortin Receptors: Identification and Characterization by Melanotropic Peptide Agonists and Antagonists (1996)

Hormones are chemical messengers released from cells to act on and control the activity of other cells. Hormonal ligands initiate their actions by interacting with receptive substances (Langley, 1906) of the target cells. These receptors are proteins that are either integral components of the cell membrane or are localized cytoplasmically within cells. Ligand-receptor interaction results in either the stimulation or inhibition of cellular activity. Since most hormones bind rather specifically to receptors possessed by their target cells, labeling of hormonal ligands can be utilized to identify and localize cells within an animal. In this report we discuss what is presently known about melanocortin receptors (MCRs) as studied by the use of labeled melanotropic peptide ligands.
A simple method of microneedle array fabrication for transdermal drug delivery (2012)

The outermost layer of skin, stratum corneum, being lipophilic limits the passive transport of hydrophilic and large molecular weight drugs. Microfabrication technology has been adapted to fabricate micron scale needles, which are minimally invasive, yet able to deliver the drugs across this barrier layer. In this study, we fabricated microneedles from a biocompatible polymer, namely, poly (ethylene glycol) diacrylate. A simple lithographical approach was developed for microneedle array fabrication. Several factors including polymerization time, ultraviolet light intensity and distance from light source were studied for their effects on microneedle formation. The microneedle length and tip diameter can be controlled by varying these factors. The microneedles were shown to be able to penetrate cadaver pig skin. Model drug rhodamine B was encapsulated in the range of 50 µg to 450 µg per microneedle array. The fabricated microneedles containing rhodamine B increased the permeability by four times than the control. Altogether, we demonstrated that the microneedle arrays can be fabricated through a simple single-step process and needles were mechanically strong to penetrate skin, increasing the permeability of encapsulated drug through skin.
Identification of Ecdysis-Triggering Hormone from an Epitracheal Endocrine System (1996)

Developing insects repeatedly shed their cuticle by means of a stereotyped behavior called ecdysis, thought to be initiated by the brain peptide eclosion hormone. Here an ecdysis-triggering hormone, Mas-ETH, is described from the tobacco hornworm Manduca sexta. Mas-ETH contains 26 amino acids and is produced by a segmentally distributed endocrine system of epitracheal glands (EGs). The EGs undergo a marked reduction in volume, appearance, and immunohistochemical staining during ecdysis, at which time Mas-ETH is found in the hemolymph. Injection of EGs extract or synthetic Mas-ETH into pharate larvae, pupae, or adults initiates preecdysis within 2 to 10 minutes, followed by ecdysis. Sensitivity to injected Mas-ETH appears much earlier before ecdysis and occurs with shorter latency than that reported for eclosion hormone. The isolated central nervous system responds to Mas-ETH, but not to eclosion hormone, with patterned motor bursting corresponding to in vivo preecdysis and ecdysis. Mas-ETH may be an immediate blood-borne trigger for ecdysis through a direct action on the nervous system.
Intrinsic Physical-Layer Authentication of Integrated Circuits (2011)

Radio-frequency distinct native attribute (RF-DNA) fingerprinting is adapted as a physical-layer technique to improve the security of integrated circuit (IC)-based multifactor authentication systems. Device recognition tasks (both identification and verification) are accomplished by passively monitoring and exploiting the intrinsic features of an IC's unintentional RF emissions without requiring any modification to the device being analyzed. Device discrimination is achieved using RF-DNA fingerprints comprised of higher order statistical features based on instantaneous amplitude, phase, and frequency responses as a device executes a sequence of operations. The recognition system is trained using multiple discriminant analysis to reduce data dimensionality while retaining class separability, and the resultant fingerprints are classified using a linear Bayesian classifier. Demonstrated identification and verification performance includes average identification accuracy of greater than 99.5% and equal error rates of less than 0.05% for 40 near-identical devices. Depending on the level of required classification accuracy, RF-DNA fingerprint-based authentication is well-suited for implementation as a countermeasure to device cloning, and is promising for use in a wide variety of related security problems.
Expanding the structure–activity relationship of sulfoxaflor: the synthesis and biological activity of <i>N</i>‐heterocyclic sulfoximines (2014)

The novel series of N-heterocyclic sulfoximines helped to advance the current knowledge of the sulfoxaflor SAR, and demonstrated that the structural requirement for the sulfoximine nitrogen position was not limited to small, electron-deficient moeities, but rather was tolerant of larger functionality.
An Integrated Simulation Environment Combining Process-Driven and Event-Driven Models (2009)

Colorectal cancer (CRC) is a significant health burden especially among African Americans (AA). Epidemiological studies have correlated low serum vitamin D with CRC risk, and, while hypovitaminosis D is more common and more severe in AA, the mechanisms by which vitamin D modulates CRC risk and how these differ by race are not well understood. Active vitamin D (1α,25(OH)<sub>2</sub>D<sub>3</sub>) has chemoprotective effects primarily through transcriptional regulation of target genes in the colon. We hypothesized that transcriptional response to 1α,25(OH)<sub>2</sub>D<sub>3</sub> differs between AA and European Americans (EA) irrespective of serum vitamin D and that regulatory variants could impact transcriptional response. We treated ex vivo colon cultures from 34 healthy subjects (16 AA and 18 EA) with 0.1μM 1α,25(OH)<sub>2</sub>D<sub>3</sub> or vehicle control for 6h and performed genome-wide transcriptional profiling. We found 8 genes with significant differences in transcriptional response to 1α,25(OH)<sub>2</sub>D<sub>3</sub> between AA and EA with definitive replication of inter-ethnic differences for uridine phosphorylase 1 (UPP1) and zinc finger-SWIM containing 4 (ZSWIM4). We performed expression quantitative trait loci (eQTL) mapping and identified response cis-eQTLs for ZSWIM4 as well as for histone deacetylase 3 (HDAC3), the latter of which showed a trend toward significant inter-ethnic differences in transcriptional response. Allele frequency differences of eQTLs for ZSWIM4 and HDAC3 accounted for observed transcriptional differences between populations. Taken together, our results demonstrate that transcriptional response to 1α,25(OH)<sub>2</sub>D<sub>3</sub> differs between AA and EA independent of serum 25(OH)D levels. We provide evidence in support of a genetic regulatory mechanism underlying transcriptional differences between populations for ZSWIM4 and HDAC3. Further work is needed to elucidate how response eQTLs modify vitamin D response and whether genotype and/or transcriptional response correlate with chemopreventive effects. Relevant biomarkers, such as tissue-specific 1α,25(OH)<sub>2</sub>D<sub>3</sub> transcriptional response, could identify individuals likely to benefit from vitamin D for CRC prevention as well as elucidate basic mechanisms underlying CRC disparities.
Altering the fatty acid composition of Corn Belt corn through Tripsacum introgression (2006)

Breeders need sources of genes for altering the fatty acid content of oil in maize (Zea maize L.) that are not available in Corn Belt germplasm. Previously we determined lines developed from maize introgressed with genes from Tripsacum dactyloides had useful variation for fatty acid composition. We conducted this study to validate the variation, thereby showing that the trait could be transferred to Corn Belt inbreds using traditional plant breeding methods to create maize lines with altered fatty acid composition useful for an oil quality breeding program. Based on their fatty acid profiles, maize lines were selected from an open pollinated population that was introgressed with genes from Tripsacum dactyloides. These introgressed lines were both self-pollinated and backcrossed to Corn Belt lines while undergoing selection for various fatty acid compositions. The parental lines and S1 and S3 progeny from the backcrosses were compared to commercial Corn Belt hybrids and inbreds in an experiment using a randomized complete block design with two replications at two locations near Ames, Iowa. The plants were hand pollinated and hand harvested. The fatty acid compositions were analyzed by using Gas Chromatography to characterize the fatty acid methyl esters made from the oil of five individual kernels from each ear. The relative amounts of the two types of fatty acids of interest, a monounsaturated fatty acid, (oleic acid) and saturated fatty acids (palmitic and stearic acids), were greatly increased by selection breeding within the Tripsacum introgressed germplasm. New oil products with more healthful fatty acid compositions and products with reduced trans fats can be developed from these new lines.
Stable, Efficient, High-resolution Radon Transforms (2002)

F-34 STABLE EFFICIENT HIGH-RESOLUTION RADON TRANSFORMS Summary 1 Conventional Radon transforms are limited in their ability to resolve events and to handle aliased data. High-resolution transforms address both these issues but can be expensive or susceptible to noise. This paper reviews existing schemes for performing high-resolution transforms in an efficient manner and suggests a new scheme that retains the efficiency but is more stable and can potentially provide improved resolution at low frequencies. Introduction Conventional Radon transforms (Beylkin 1987; Hampson 1986) are exactly invertible for discretely sampled finite-aperture data. However sufficient resolution and proper sampling of the data in the
Quantum resource estimates for computing elliptic curve discrete\n logarithms (2017)

We give precise quantum resource estimates for Shor's algorithm to compute\ndiscrete logarithms on elliptic curves over prime fields. The estimates are\nderived from a simulation of a Toffoli gate network for controlled elliptic\ncurve point addition, implemented within the framework of the quantum computing\nsoftware tool suite LIQ$Ui|\\rangle$. We determine circuit implementations for\nreversible modular arithmetic, including modular addition, multiplication and\ninversion, as well as reversible elliptic curve point addition. We conclude\nthat elliptic curve discrete logarithms on an elliptic curve defined over an\n$n$-bit prime field can be computed on a quantum computer with at most $9n +\n2\\lceil\\log_2(n)\\rceil+10$ qubits using a quantum circuit of at most $448 n^3\n\\log_2(n) + 4090 n^3$ Toffoli gates. We are able to classically simulate the\nToffoli networks corresponding to the controlled elliptic curve point addition\nas the core piece of Shor's algorithm for the NIST standard curves P-192,\nP-224, P-256, P-384 and P-521. Our approach allows gate-level comparisons to\nrecent resource estimates for Shor's factoring algorithm. The results also\nsupport estimates given earlier by Proos and Zalka and indicate that, for\ncurrent parameters at comparable classical security levels, the number of\nqubits required to tackle elliptic curves is less than for attacking RSA,\nsuggesting that indeed ECC is an easier target than RSA.\n
Ultrasonic Phased Array Inspection of Turbine Components (2006)

The advent and proliferation of Ultrasonic Phased Arrays as a method of choice for the advanced inspection of industrial components has brought many of the benefits of this technology into the mainstream. Some of the benefits have been the reduction in inspection time resulting in cost savings as well as reduction in the logistics that the conventional method required. While using Phased Arrays offers a variety of benefits to suit the needs of different applications, in certain types of complex exams it is imperative that proper methods of examination and validation be developed. This paper addresses the development of Ultrasonic Phased Array methods for inspection of turbine rotor discs and turbine blade attachments and the validation of such methods. It also discusses issues as they pertain to probe positioning, ultrasound behavior, and component geometry.
Efficacy and safety of a new selective laser device to create anterior capsulotomies in cataract patients (2019)

Selective laser capsulotomy using a new proprietary trypan blue formulation was safe and effective in cataract surgery. The sizing, circularity, and centration of the laser capsulotomy were more accurate than those of the manual CCC, resulting in consistent 360-degree IOL coverage.
Absence of Replication-Competent Human-Tropic Porcine Endogenous Retroviruses in the Germ Line DNA of Inbred Miniature Swine (2004)

The potential transmission of porcine endogenous retroviruses (PERVs) has raised concern in the development of porcine xenotransplantation products. Our previous studies have resulted in the identification of animals within a research herd of inbred miniature swine that lack the capacity to transmit PERV to human cells in vitro. In contrast, other animals were capable of PERV transmission. The PERVs that were transmitted to human cells are recombinants between PERV-A and PERV-C in the post-VRA region of the envelope (B. A. Oldmixon, J. C. Wood, T. A. Ericsson, C. A. Wilson, M. E. White-Scharf, G. Andersson, J. L. Greenstein, H. J. Schuurman, and C. Patience, J. Virol. 76:3045-3048, 2002); these viruses we term PERV-A/C. This observation prompted us to determine whether these human-tropic replication-competent (HTRC) PERV-A/C recombinants were present in the genomic DNA of these miniature swine. Genomic DNA libraries were generated from one miniature swine that transmitted HTRC PERV as well as from one miniature swine that did not transmit HTRC PERV. HTRC PERV-A/C proviruses were not identified in the germ line DNAs of these pigs by using genomic mapping. Similarly, although PERV-A loci were identified in both libraries that possessed long env open reading frames, the Env proteins encoded by these loci were nonfunctional according to pseudotype assays. In the absence of a germ line source for HTRC PERV, further studies are warranted to assess the mechanisms by which HTRC PERV can be generated. Once identified, it may prove possible to generate animals with further reduced potential to produce HTRC PERV.
AMAD: Resource Consumption Profile-Aware Attack Detection in IaaS Cloud (2014)

Cloud infrastructures are prone to various anomalies due to their ever-growing complexity and dynamics. Monitoring behavior of dynamic resource management systems is necessary to guarantee cloud reliability. In this paper, we present AMAD, a system designed for detecting an abusive use of dynamic virtual machine migration, in the case of the abusive virtual machine migration attack. This attack is performed by malicious manipulation of the amounts of resources consumed by Virtual Machines (VMs). AMAD identifies the VMs possibly at the origin of the attack by analyzing resource consumption profiles of the VMs to detect the fluctuating and highly correlated ones. We have implemented AMAD on top of the VMware ESXi platform and evaluated it both on our lab platform and under real cloud configurations. Our results show that AMAD pinpoints the attacking VMs which were intentionally injected in our experimentations, with high accuracy.
Development of 2‘-<i>O</i>-Methoxyethyl Phosphorothioate Oligonucleotides as Antisense Drugs under Stereochemical Control (2002)

A systematic investigation of the stereoreproducibility of 2‘-O-methoxyethylribonucleoside phosphoramidite-based phosphorothioate oligonucleotide synthesis reveals that 1H-tetrazole-catalyzed phosphoramidite coupling followed by sulfurization with phenylacetyl disulfide (PADS) is under inherent stereochemical control. Analyses of single phosphorothioate linkages in oligonucleotides as well as in dimers by 31P NMR spectroscopy reveal reproducible stereochemical control in deoxy/2‘-O-methoxyethylribo- and 2‘-O-methoxyethylribo/deoxydinucleotide phosphorothioates and in 2‘-O-methoxyethylribo/2‘-O-methoxyethylribonucleotide phosphorothioate linkages. Particularly interesting is the fact that the R,S ratio of the phosphorothioate linkage is reproducible (within limits of experimental error) between syntheses and is independent of diastereomeric composition of phosphoramidites, synthesis scale, solid support, reactor, concentration during coupling or synthesis conditions. Activators, however, play a major role in determining the diastereomeric ratio of 2‘-O-methoxyethyl RNA phosphorothioate internucleotide linkages.