gebhart/patrepeval huggingface dataset:
Using Dynamics Measurements While Drilling to Detect Lithology Changes and to Model Drilling Dynamics (2007)

As a result of bit-rock interaction, downhole weight-on-bit, downhole torque, instantaneous downhole rotational speed and bit motion (acceleration and rate of penetration) are directly affected by the formations being drilled. Since these measurements react differently to different lithologies, and assuming that drilling problems do not effect these measurements, any changes in the measurements in some way will reflect changes in the properties of the lithology. If, based on these measurements, the lithology is assumed to have certain properties, then it is possible to derive models for the interaction between bit, formation and drillstring. With these models it is possible to simulate the dynamic behavior of the system including phenomena like stick-slip. Rate of penetration has long been used as a lithology indicator, and drilling models have been developed using surface measured drilling parameters to infer changes in lithology. With the advent of MWD measurements, significant improvements were made in the mathematical models by involving downhole torque. The model derived parameters were shown to be related to rock strength (drilling and shear strength) and proved to be good indicators of formation changes. Similar expressions in the form of simple bit models can be used in combination with a finite element model of the drillstring to simulate the dynamic behavior of the complete system. A significant improvement in this analysis can be affected by introducing measurements from the dynamics tool, such as instantaneous torque, weight and rotation rate, as well as the bit acceleration. These measurements provide not only static but also dynamic data which can be used to validate simulations and the underlying models. The present analysis explores the use of the dynamic measurements and the application of some drilling models in analyzing formation changes while drilling, and the use of these data and models in simulating drilling dynamics.
Corrigendum: Novel Non-Histocompatibility Antigen Mismatched Variants Improve the Ability to Predict Antibody-Mediated Rejection Risk in Kidney Transplant (2018)

CORRECTION article Front. Immunol., 31 January 2018Sec. Alloimmunity and Transplantation Volume 9 - 2018 | https://doi.org/10.3389/fimmu.2018.00107
Neuroprotective and neurorestorative effects of thymosin β4 treatment following experimental traumatic brain injury (2012)

Traumatic brain injury (TBI) remains a leading cause of mortality and morbidity worldwide. No effective pharmacological treatments are available for TBI because all phase II/III TBI clinical trials have failed. This highlights a compelling need to develop effective treatments for TBI. Endogenous neurorestoration occurs in the brain after TBI, including angiogenesis, neurogenesis, synaptogenesis, oligodendrogenesis, and axonal remodeling, which may be associated with spontaneous functional recovery after TBI. However, the endogenous neurorestoration following TBI is limited. Treatments amplifying these neurorestorative processes may promote functional recovery after TBI. Thymosin beta 4 (Tβ4) is the major G-actin-sequestering molecule in eukaryotic cells. In addition, Tβ4 has other properties including antiapoptosis and anti-inflammation, promotion of angiogenesis, wound healing, stem/progenitor cell differentiation, and cell migration and survival, which provide the scientific foundation for the corneal, dermal, and cardiac wound repair multicenter clinical trials. Here, we describe Tβ4 as a neuroprotective and neurorestorative candidate for treatment of TBI.
Anticancer activity of silver(I) cyclohexyldiphenylphosphine complexes toward SNO cancer cells (2017)

Silver and its derivatives have been and are currently used as antimicrobial and antibacterial agents. However, their use is rather limited to date as anticancer agents. Thus, this study focuses on the synthesis and characterization of three silver(I) complexes which have the ability to adopt different geometries, and to induce cancer cell death in SNO esophageal cancer cells. Silver thiocyanate was reacted in different ratios with cyclohexyldiphenylphosphine to obtain 1:1 (complex 1), 1:2 (complex 2), and 1:3 (complex 3) molar ratios of silver(I):cyclohexyldiphenylphosphine complexes. These complexes were characterized using conventional spectroscopic techniques, which included 1H, 13C, and 31P NMR, FTIR, and microanalysis (%C, H, N, S). In addition, the single-crystal X-ray structures of complexes 1 and 2 were determined. Moreover, all three complexes displayed toxic activity toward the malignant SNO cells with IC50 concentrations below 5 μM as determined with an alamarBlue® viability assay. Morphological and flow cytometric analyses were included to identify the possible mode of cancer cell death. These biochemical assays revealed that all three treatments induced apoptosis due to the presence of specific apoptotic markers.
Convolutional Recurrent Neural Networks for Small-Footprint Keyword Spotting (2017)

Keyword spotting (KWS) constitutes a major component of human-technology interfaces.Maximizing the detection accuracy at a low false alarm (FA) rate, while minimizing the footprint size, latency and complexity are the goals for KWS.Towards achieving them, we study Convolutional Recurrent Neural Networks (CRNNs).Inspired by large-scale state-ofthe-art speech recognition systems, we combine the strengths of convolutional layers and recurrent layers to exploit local structure and long-range context.We analyze the effect of architecture parameters, and propose training strategies to improve performance.With only ~230k parameters, our CRNN model yields acceptably low latency, and achieves 97.71% accuracy at 0.5 FA/hour for 5 dB signal-to-noise ratio.
Blind pattern matching attack on watermarking systems (2003)

Billions of dollars allegedly lost to piracy of multimedia content have triggered the industry to rethink the way music and films are distributed on the Internet. As encryption is vulnerable to digital or analog re-recording, currently almost all copyright protection mechanisms rely to a certain extent on watermarking. A watermark is an imperceptive secret hidden into a host signal. We analyze the security of multimedia copyright protection systems that use watermarks by proposing a new breed of attacks on generic watermarking systems. A typical blind pattern matching attack relies on the observation that multimedia content is often highly repetitive. Thus, the attack procedure identifies subsets of signal blocks that are similar and permutes these blocks. Assuming the permuted blocks are marked with distinct secrets, it can be shown that any watermark detector is facing a task of exponential complexity to reverse the permutations as a preprocessing step for watermark detection. We describe the logistics of the attack and an implementation against a spread-spectrum and a quantization index modulation data hiding technology for audio signals.
Purification and biochemical characterization of pyruvate oxidase from Lactobacillus plantarum (1984)

Pyruvate oxidase (EC 1.2.3.3) was isolated and characterized from Lactobacillus plantarum. The enzyme catalyzes the oxidative decarboxylation of pyruvate in the presence of phosphate and oxygen, yielding acetyl phosphate, carbon dioxide, and hydrogen peroxide. This pyruvate oxidase is a flavoprotein, with the relatively tightly bound cofactors flavin adenine dinucleotide, thiamine pyrophosphate, and a divalent metal ion, with Mn2+ being the most effective. The enzyme is only slightly inhibited by EDTA, implying that the enzyme-bound metal ion is poorly accessible to EDTA. Only under relatively drastic conditions, such as acid ammonium sulfate precipitation, could a colorless and entirely inactive apoenzyme be obtained. A partial reactivation of the enzyme was only possible by the combined addition of flavin adenine dinucleotide, thiamine pyrophosphate, and MnSO4. The enzyme has a molecular weight of ca. 260,000 and consists of four subunits with apparently identical molecular weights of 68,000. For catalytic activity the optimum pH is 5.7, and the optimum temperature is 30 degrees C. The Km values for pyruvate, phosphate, and arsenate are 0.4, 2.3, and 1.2 mM, respectively. The substrate specificity revealed that the enzyme reacts also with certain aldehydes and that phosphate can be replaced by arsenate. In addition to oxygen, several artificial compounds can function as electron acceptors.
PRIORI-T: A tool for rare disease gene prioritization using MEDLINE (2020)

PRIORI-T exhibited improved gene prioritization performance without requiring high quality curated data. Thus, it holds great promise in phenotype-driven gene prioritization for rare disease studies.
Fabrication and Testing of Photonic Thermometers (2018)

In recent years, a push for developing novel silicon photonic devices for telecommunications has generated a vast knowledge base that is now being leveraged for developing sophisticated photonic sensors. Silicon photonic sensors seek to exploit the strong confinement of light in nano-waveguides to transduce changes in physical state to changes in resonance frequency. In the case of thermometry, the thermo-optic coefficient, i.e., changes in refractive index due to temperature, causes the resonant frequency of the photonic device such as a Bragg grating to drift with temperature. We are developing a suite of photonic devices that leverage recent advances in telecom compatible light sources to fabricate cost-effective photonic temperature sensors, which can be deployed in a wide variety of settings ranging from controlled laboratory conditions, to the noisy environment of a factory floor or a residence. In this manuscript, we detail our protocol for the fabrication and testing of photonic thermometers.
<title>Easily aligned deformable-helix ferroelectric liquid crystal mixture and its use in devices</title> (1992)

Ferroelectric smectic C* liquid crystals have been shown to exhibit high speed, multistate electro-optic and display device applications, particularly when incorporated into the surface stabilized ferroelectric liquid crystal (SSFLC) light valve. The SSFLC geometry results in two distinct stable states. Unfortunately, the lack of intermediate electrically addressed states precludes a natural gray-scale effect. The recently discovered Deformed Helix Ferroelectric liquid crystal (DHFLC) effect opens the door to linear gray scale or linear phase modulation in a ferroelectric liquid crystal device on a microsecond time-scale. One drawback of currently available DHFLC materials is that their alignment quality is limited due to the lack of a nematic phase above their smectic A phase. While alignment can be improved by the use of shear techniques, this represents an undesirable option for a manufacturing process. We show that DHFLC mixtures can possess a nematic phase with a long N* pitch and tight C* pitch in the C* phase. These new easily aligned DHFLC mixtures are discussed as well as their use in beam-steering devices that can benefit from analog optical response.
The Effect of Eculizumab Therapy on Red Cell Response Kinetics in Patients with Paroxysmal Nocturnal Hemoglobinuria. (2005)

Abstract Paroxysmal nocturnal hemoglobinuria (PNH) is characterized by clonal expansion of PNH red cells that are highly sensitive to lysis by terminal complement. The primary lesion in PNH is bone marrow failure in the form of immune-mediated aplastic anemia and peripheral blood cytopenias of varying severity. We have previously reported the successful control of hemolysis and transfusion in 11 patients with the terminal complement inhibitor eculizumab. Ten of these 11 patients remain on eculizumab therapy after approximately 3 years with maintained reductions in intravascular hemolysis and transfusion. The effectiveness of eculizumab therapy in these patients is through the protection of the PNH red cell from complement-mediated lysis and the expansion of this cell population. Flow cytometry studies have shown that the percentage of PNH red cells increased significantly from a mean of 36.7% before treatment to 58.4% at week 64 of therapy. Importantly, granulocyte, monocyte and platelet PNH clone sizes were &gt;90% before treatment and remained stable for all patients throughout the trial suggesting that the majority of hematopoiesis is derived from PNH stem cells. We hypothesize that the PNH red cell clone should approach the clone size of other myeloid hematopoietic cells in a given patient when hemolysis is prevented by eculizumab therapy as this more accurately depicts PNH stem cell activity. Furthermore, the magnitude and rapidity of response in terms of absolute red cell counts is unknown and could potentially provide important insights into the pathophysiology of PNH. In all patients hemolysis was substantially reduced by 21 days. In 9/11 patients, there was a rapid rise in PNH red cell count with the mean absolute number of PNH red cells increasing from 1.37 x 1012/L before treatment to 1.50 x 1012/L at 2 weeks (P=0.21), 1.74 x 1012/L at 4 weeks (P=0.002), and 2.11 x 1012/L at 12 weeks (P=0.001) of eculizumab treatment. The maximum theoretical red cell response was achieved in a mean of 178 days (range 49 – 419 days). The mean absolute number of PNH red cells increased to 2.37 x 1012/L at maximum response (P=0.001), an increase of 73% (range 36% – 207%). All patients achieved a maximum response prior to 18 months of treatment and clone size was subsequently stable. In 2 patients, despite the effectiveness of eculizumab in resolving hemolysis, there was no change in absolute numbers of PNH red cells pre and post-treatment. This is likely due to a combination of a lower degree of hemolysis and more profound bone marrow insufficiency in these patients. The determination of absolute PNH red cell counts during the first 12 months of eculizumab therapy may identify which patients will become transfusion independent and which patients may benefit from additional growth factor support to boost erythropoiesis. Furthermore, long-term eculizumab therapy appeared to be associated with a stable PNH red cell clone size in this initial clinical study.
Rapid Optical Cavity PCR (2015)

Recent outbreaks of deadly infectious diseases, such as Ebola and Middle East respiratory syndrome coronavirus, have motivated the research for accurate, rapid diagnostics that can be administered at the point of care. Nucleic acid biomarkers for these diseases can be amplified and quantified via polymerase chain reaction (PCR). In order to solve the problems of conventional PCR--speed, uniform heating and cooling, and massive metal heating blocks--an innovative optofluidic cavity PCR method using light-emitting diodes (LEDs) is accomplished. Using this device, 30 thermal cycles between 94 °C and 68 °C can be accomplished in 4 min for 1.3 μL (10 min for 10 μL). Simulation results show that temperature differences across the 750 μm thick cavity are less than 2 °C and 0.2 °C, respectively, at 94 °C and 68 °C. Nucleic acid concentrations as low as 10(-8) ng μL(-1) (2 DNA copies per μL) can be amplified with 40 PCR thermal cycles. This simple, ultrafast, precise, robust, and low-cost optofluidic cavity PCR is favorable for advanced molecular diagnostics and precision medicine. It is especially important for the development of lightweight, point-of-care devices for use in both developing and developed countries.
Investigation of delay path modifications of Surface Acoustic Wave sensors (2013)

Surface Acoustic Wave (SAW) sensors monitor the interaction between a receptor and its target in real time through changes in the properties of the traveling wave (i.e. frequency or phase, and amplitude). A key sensing parameter is power consumption. To increase power transfer we have developed a SAW sensor with microcavities in the delay path on 36° YX LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and 90° ST-X Quartz. Three parameters were identified that determine the effectiveness of microcavities: 1) IDT offset, 2) microcavity depth, and 3) microcavity cross-sectional area. Finite element (FE) simulations were performed using ANSYS to determine the optimum value of each parameter to decrease insertion loss (I.L.). Our results show that the best parameter values are; IDT offset = 10 μm, microcavity depth = 2.5 μm and microcavity cross-sectional area = 10 μm × 10 μm, for a device with center frequency of about 100 MHz.
Magnetic arrays and their resonant frequencies for the production of binary codes (1998)

An array of cantilevers of varying lengths containing at least a layer of magnetic material has been fabricated to produce oscillations at the resonant frequencies of the cantilevers via magneto-mechanical coupling. The acoustic or magnetic fields resulting from the oscillations were detected using microphones or detection coils. The presence or absence of an oscillation at a given frequency of a preselected set of frequencies was used to represent a "1" or a "0", respectively, to create a binary code. The array can be designed and assembled to serve as a multibit magnetic tag.
Content-weighted video quality assessment using a three-component image model (2010)

Objective image and video quality measures play important roles in numerous image and video processing applications. In this work, we propose a new content-weighted method for full-reference (FR) video quality assessment using a three-component image model. Using the idea that different image regions have different perceptual significance relative to quality, we deploy a model that classifies image local regions according to their image gradient properties, then apply variable weights to structural similarity image index (SSIM) [and peak signal-to-noise ratio (PSNR)] scores according to region. A frame-based video quality assessment algorithm is thereby derived. Experimental results on the Video Quality Experts Group (VQEG) FR-TV Phase 1 test dataset show that the proposed algorithm outperforms existing video quality assessment methods.
Abstract 4751: Structure and inhibition of mitogen-activated protein kinase kinase 4 (MEK4): A prostate cancer pro-invasion protein (2012)

Abstract Introduction: Metastasis of Prostate Cancer (PCa) represents the second highest cause of death due to cancer among men in the United States. If this unregulated movement of cells can be inhibited, mortality arising from PCa will be greatly reduced. Our group has shown that Mitogen-activated protein kinase kinase 4 (MAP2K4/MEK4), a 399 amino acid protein, activates pro-invasion signaling pathways in human PCa. Further, we have shown that 4,5,7-trihydroxyisoavone (genistein) inhibits MEK4 kinase activity, cell invasion and metastasis of human PCa cells in a murine model. While therapeutically effective, genistein represents a non-chemically optimized natural product with additional undesired effects such as estrogenic receptor stimulation. Recognizing that MEK4 represents a novel and important therapeutic target, we have sought to characterize its structure, biochemical function and have synthesized genistein analogs designed to target it. Summary of Results: Using X-ray crystallography we have obtained a 3.38Å resolution structure of the MEK4 catalytic domain. We are in the process of improving our resolution, and of deriving 3D structures with inhibitors bound to MEK4. We have evaluated biophysical interactions between MEK4 and ligands (i.e., genistein and its analogs). Ligand binding to a protein tends to increase its stability, thereby increasing the temperature of denaturation, or melting. Using a fluorescence thermal shift (FTS) assay, we demonstrated that genistein and 6 of 39 novel analogs thermally stabilized MEK4 in a concentration dependent manner, consistent with MEK4 binding. We identified a similar pattern in 5 compounds from a commercial library, one of which was staurosporine - a broad spectrum protein kinase inhibitor. We developed and characterized a novel in vitro MEK4 kinase assay, using kinase dead p38MAPK (K53A) as substrate. In human PCa cells, MEK4 activates the p38 MAPK pro-invasion pathway. To date, we have used this assay system to demonstrate that staurosporine inhibits MEK4 with nanomolar IC50 values. Conclusions and Future Directions: MEK4 is a novel target for therapeutic intervention in PCa. Our ultimate goal is to synergistically utilize structural and biochemical information to inform the synthesis of inhibitors that specifically and selectively act upon MEK4 to inhibit human PCa metastasis in man. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4751. doi:1538-7445.AM2012-4751
A Compact Optical Head using Holographic Optical Element for CD Players (1987)

An optical head for optical disk system has three optical functions, in addition to light beam focusing on a disk. These are splitting the reflected beam from the optical axis, focusing error detection optics, and tracking error detection optics. Conventional optical heads have employed several bulky optical elements to realize these three optical functions, for example, a half mirror, a cylindrical lens and a spherical lens pair, and a grating, respectively. This complicated optics set up has prevented realizing a small size and light weight optical head.
Dual-Fed Hollow Dielectric Antenna for Dual-Frequency Operation With Large Frequency Ratio (2017)

A new dual-fed dual-frequency antenna that integrates a microwave hollow dielectric resonator antenna (DRA) with a high-gain millimeter-wave dielectric Fabry-Perot resonator antenna (FPRA) is investigated. To obtain the dual-frequency operation, the dielectric and air regions of the hollow DRA are designed to satisfy the resonance condition of the FPRA. The DRA and FPRA are excited by a strip and a WR-34 waveguide, respectively. For demonstration, a prototype that covers both 2.4- and 24-GHz ISM bands was fabricated and tested. The S-parameters, radiation pattern, antenna gain, and antenna efficiency are studied, and reasonable agreement between the measured and simulated results is found.
Effect of Image Quality, Color, and Format on the Measurement of Retinal Vascular Fractal Dimension (2010)

Variations in image brightness, focus, and contrast can significantly affect the measurement of retinal vascular fractals. Standardization of image parameters and consistent use of either monochrome or color images would reduce measurement noise and enhance the comparability of the results.
A Quantum Key Distribution Network: Integrated Design and Prototypical Implementation (2007)

Quantum key distribution (QKD) is a cryptographic primitive, which offers an extremely high security standard known as unconditional or information-theoretic security, relying on intrinsically quantum properties of communication (light) signals. A general trusted relay technique was adopted and developed by the Integrated EU-project SECOQC. What makes the SECOQC approach unique is on the one hand the introduction of an integrated network design, specifically tailored for the distribution of secrets, which is logically completely independent from the communication network employed by the corresponding security application layer. On the other hand, from a structural design point of view, there is a clear system separation into two basic components: a quantum key generation one, realized by a QKD link, i.e. a pair of QKD devices connected by quantum channel, and a classical secret maintenance and distribution one, realized by a dedicated "node device" with a universal interface between these two components. The main deliverable of SECOQC is the implementation and operation of a test network in Vienna and lower Austria. The paper focuses on the design approach developed in SECOQC and the implementation status of the prototype.