gebhart/patrepeval huggingface dataset:
BBK07 Immunodominant Peptides as Serodiagnostic Markers of Lyme Disease (2010)

Lyme disease (LD) is a tick-borne infection caused by the bacterial pathogen Borrelia burgdorferi. Current diagnostic tests mostly use borrelial lysates or select antigens to detect serum antibodies against B. burgdorferi. These immunoassays are not entirely effective, especially for detection of early infection. We have recently characterized an in vivo-induced antigen, BBK07, as a serodiagnostic marker for LD. We now report that in a line blot assay, recombinant BBK07 protein-based detection is 90% sensitive and nearly 100% specific against B. burgdorferi infection in humans. Using an overlapping peptide library of 23 peptides encompassing full-length BBK07, we identified the immunodominant epitopes of BBK07 during human infection. We show that a select combination of amino-terminal peptides significantly enhanced BBK07-based diagnostic accuracy compared to that with the full-length protein. Although in enzyme-linked immunosorbent assay (ELISA) studies BBK07 peptides had overall lower sensitivity than established serodiagnostic peptides, such as the VlsE peptide C6 and OspC peptide pepC10, for the detection of early human LD, a subset of serum samples that failed to recognize either VlsE or OspC peptides were preferentially reactive to BBK07 peptides. These results highlight the fact that BBK07 peptides could be useful to complement the efficacy of VlsE and OspC peptide-based serodiagnostic assays. Finally, using a panel of canine sera, we show that BBK07 peptide is also effective for LD diagnosis in infected dogs. Together, our data show that peptides from the B. burgdorferi surface protein BBK07 are highly specific and sensitive serodiagnostic markers, and we suggest their future use in LD diagnostic assays.
Rio Mamore Virus: Genetic Characterization of a Newly Recognized Hantavirus of the Pygmy Rice Rat, Oligoryzomys microtis, from Bolivia (1997)

"Rio Mamore Virus: Genetic Characterization of a Newly Recognized Hantavirus of the Pygmy Rice Rat, Oligoryzomys microtis, from Bolivia" published on Sep 1997 by The American Society of Tropical Medicine and Hygiene.
TTK Inhibitors as a Targeted Therapy for <i>CTNNB1</i> ( <b>β</b> -catenin) Mutant Cancers (2017)

The spindle assembly checkpoint kinase TTK (Mps1) is a key regulator of chromosome segregation and is the subject of novel targeted therapy approaches by small-molecule inhibitors. Although the first TTK inhibitors have entered phase I dose escalating studies in combination with taxane chemotherapy, a patient stratification strategy is still missing. With the aim to identify a genomic biomarker to predict the response of tumor cells to TTK inhibitor therapy, we profiled a set of preclinical and clinical TTK inhibitors from different chemical series on a panel of 66 genetically characterized cell lines derived from different tumors (Oncolines). Cell lines harboring activating mutations in the <i>CTNNB1</i> gene, encoding the Wnt pathway signaling regulator β-catenin, were on average up to five times more sensitive to TTK inhibitors than cell lines wild-type for <i>CTNNB1</i> The association of <i>CTNNB1</i>-mutant status and increased cancer cell line sensitivity to TTK inhibition was confirmed with isogenic cell line pairs harboring either mutant or wild-type <i>CTNNB1</i> Treatment of a xenograft model of a <i>CTNNB1</i>-mutant cell line with the TTK inhibitor NTRC 0066-0 resulted in complete inhibition of tumor growth. Mutations in <i>CTNNB1</i> occur at relatively high frequency in endometrial cancer and hepatocellular carcinoma, which are known to express high <i>TTK</i> levels. We propose mutant <i>CTNNB1</i> as a prognostic drug response biomarker, enabling the selection of patients most likely to respond to TTK inhibitor therapy in proof-of-concept clinical trials. <i>Mol Cancer Ther; 16(11); 2609-17. ©2017 AACR</i>.
Advanced Risk Analysis Approach for Optimization of a Water Injection Program -Illustration on a Brazilian Field Case (2005)

Abstract This paper presents an advanced risk analysis approach that has been applied on a Brazilian field case to manage and quantify the reservoir uncertainties during production forecasting and production scheme optimization. The oil field (named PBR) is located offshore Brazil. The PBR reservoir consists of a complex lithology, including mainly turbiditic sandstones interbedded by shales and marls. The workflow of the PBR reservoir modeling from the geostatistical lithofacies model, built using the non-stationary truncated gaussian method, to the flow model (about 24000 active cells) has been implemented in a fully integrated chain. The field was considered in this hypothetical study at its appraisal stage. Main challenge consisted in selecting an optimal water injection scheme to maximize oil production while minimizing water production and maintaining pressure over the 15 years of production, taking into account the overall major sources of uncertainties in the reservoir. Advanced risk analysis methods were used with the following objectives: – Determine the impact of the main uncertainties on the field production forecasts versus time and versus geographical locations of production and injection wells – Optimize the water injection phase to maintain pressure over time, while producing maximum oil and minimum water in a 15-years period. – Quantify the impact of main uncontrollable reservoir uncertainties on production forecasts and fluid distribution maps versus time for the optimal water injection program selected in order to identify potential risks with non-drained zones and pressure drops. At each step, either classical or optimal experimental designs were used to be able to perform an accurate analysis at a minimum cost in terms of reservoir simulation and interpretation. Results show that this innovative methodology can be successfully applied on complex real cases to quantify the risk associated with the main reservoir uncertainties during production forecasts and to optimize the water injection. In particular, this example illustrates how some innovative interpretation tools can be combined with experimental design methodology to perform advanced risk analysis for reservoir management.
Amplitude Control Using Variable Feedback Gain in Self-Excited Driving Vibratory Machine. (1996)

The driving system of a vibratory machine with self-excited vibration follows the resonance frequency change automatically, and reduces electric power consumption. Self-excited vibration is generated by the positive feedback of vibration velocity or the phase delay control of vibration displacement deviation on a mechanical resonance system. The self-excited vibration whose amplitude is limited by saturation of a power amplifier output contains many higher-harmonic components. On the other hand, the self-excited vibration whose amplitude is limited by variable feedback gain becomes a pure sine wave. The feedback gain is controlled by amplitude deviation. The controller consists of a constant term, which is equal to the critical gain on the stability of the feedback system, a linear term and a third-power term of amplitude deviation. The constant term and the linear term influence the steady-state vibration, and the third-power term influences the rising characteristics of vibration.
Statistical identification of encrypted Web browsing traffic (2005)

Encryption is often proposed as a tool for protecting the privacy of World Wide Web browsing. However, encryption-particularly as typically implemented in, or in concert with popular Web browsers-does not hide all information about the encrypted plaintext. Specifically, HTTP object count and sizes are often revealed (or at least incompletely concealed). We investigate the identifiability of World Wide Web traffic based on this unconcealed information in a large sample of Web pages, and show that it suffices to identify a significant fraction of them quite reliably. We also suggest some possible countermeasures against the exposure of this kind of information and experimentally evaluate their effectiveness.
A Quantum-Limited Highly Linear Monolithic CMOS Detector for Computed Tomography (2011)

Computed tomography (CT) detector requires quantizing the wide dynamic range (WDR) photocurrent with high speed. Existing CMOS CT detectors are limited by their low linearity. They also need high-resolution external analog-to-digital converters (ADC) to quantize the WDR. In this work, a novel synchronous partial quantization technique is developed to enable monolithic CMOS CT pixel detector. Improved from previous current quantization designs, the new pixel detector quantizes the photocurrent in the charge domain with constant charge packet size. As the result, the pixel detector can quantize the WDR photocurrent with improved linearity. The two-step charge-domain ADC scheme also allows low resolution single-slope ADCs for residual voltage quantization, which enables in-pixel integration. A prototype pixel detector is fabricated in a 0.35 μm CMOS process. Silicon measurements show the detector can quantize signal currents from 6 pA to 63.4 nA with relative gain deviation lower than 0.06% at 1.1 kHz frame rate, which does not generate detector-induced artifact after the image reconstruction. The detector noise is smaller than the X-ray Poisson noise in the whole signal range. The minimum detector noise is 0.8 pA <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> . Hence, the detector achieves 16.6 bits dynamic range. The geometrical detective efficiency (GDE) of the detector is 75.5% including the band-gap voltage reference and ADC. The digital pixel detector can be easily tiled into a 2-D CT detection panel.
Thromboxane synthetase inhibitors and antihypertensive agents. 3. N-[(1H-imidazol-1-yl)alkyl]heteroaryl amides as potent enzyme inhibitors (1987)

The title compounds were prepared as the heterocyclic analogues of thromboxane (TX) synthetase inhibitors and antihypertensive agents previously reported from our laboratories. These compounds were at least as active TX synthetase inhibitors as their benzene isosteres with the indole derivatives 50-55 having the most potent enzyme inhibiting activity measured to date in our laboratories. The best compound, 54, is more than 200-fold more potent than the standard, dazoxiben. In contrast, the antihypertensive activity of these series of compounds was no better than their benzene counterparts and is far lower than the isoindoledione derivatives prepared in a related series. The structure-activity relationship results from this study were similar to our previous observations and include the fact that the amide moiety effectively replaces a carboxylic acid for potent TX synthetase inhibition and that a four to six methylene unit separation (approximately 8.5 A) between amide and imidazole moieties achieves maximal activity.
Stable ruthenium indenylidene complexes with a sterically reduced NHC ligand (2013)

Stable and active Ru olefin metathesis catalyst 7 bearing a sterically reduced NHC ligand was synthesized. Upon action of pyridine, 7 forms complex 24, the first example of an Ru–indenylidene catalyst bearing a labile pyridine ligand and a sterically less demanding NHC ligand.
Identification of Continuous B-Cell Epitopes on the Protein Moiety of the 58-Kilodalton Cell Wall Mannoprotein of<i>Candida albicans</i>Belonging to a Family of Immunodominant Fungal Antigens (2001)

The 58-kiloDalton mannoprotein (mp58) on the surface of Candida albicans is highly immunogenic, is expressed by all C. albicans isolates tested, and elicits strong antibody responses during candidiasis. It belongs to a family of immunodominant fungal antigens with representatives also in different species of Aspergillus. The amino acid sequence of the protein portion of mp58 as deduced from the DNA sequence of its encoding gene (FBP1/PRA1) was used to synthesize a complete set of overlapping dodecapeptides (overlap, 7; offset, 5) covalently attached to the surface of derivatized polyethylene pins. The pin-coupled peptides were used in a modified enzyme-linked immunosorbent assay (ELISA) to identify continuous epitopes recognized by a number of antiserum preparations containing anti-mp58 antibodies. This comprehensive epitope-scanning study revealed the presence of multiple immunoreactive continuous B-cell epitopes within the protein sequence. Regions of increased reactivity included both the amino and carboxy termini of the mature protein (encompassing amino acid residues 16 to 50 and 286 to 299, respectively) and four internal regions spanning amino acids at positions 66 to 92, 121 to 142, 148 to 192, and 211 to 232. Further delineation of epitopic regions and identification of the boundaries of the antigenic sites was performed upon ELISA testing with a second Pepset consisting of completely overlapping 8-mer peptides spanning these reactive regions in the protein moiety of mp58. The highly reactive epitopic region at the C terminus of the protein was further evaluated using both window net and replacement net analyses. A synthetic peptide corresponding to the last 10 amino acid residues at the C terminus of the protein was immunogenic when injected into mice after being coupled to a carrier protein. Moreover, antibodies in the resulting sera specifically recognized the homologous mp58 in ELISAs and immunoblot assays. Delineation of the antibody responses to mp58 could provide the basis for the development of novel immunity-based prophylactic, therapeutic, and diagnostic techniques for the management of candidiasis.
Reduced ATP release from erythrocytes of humans with type 2 diabetes is increased by the phosphodiesterase 3 inhibitor cilostazol (2006)

The G protein, Gi, and adenylyl cyclase (AC) are components of a pathway for ATP release from erythrocytes (RBCs), a stimulus for vascular NO synthesis. Exposure to reduced oxygen tension (PO2) or Gi activation with mastoparan 7 (MAS7) results in ATP release from healthy human (HH) RBCs. Here, we investigate the hypothesis that ATP release from and cAMP accumulation in RBCs of humans with diabetes type 2 (DM2) are decreased and that a phosphodiesterase 3 (PDE3) inhibitor, cilostazol (CZ), attenuates these defects. ATP values are normalized to 4x10 5 RBC/mm 3 and cAMP values to 5x10 8 RBC/mm 3 . In response to reduced PO2 (24±1 mm Hg), ATP release from DM2 RBCs (n=3) and HH RBCs (n=7) was 1±1 μM and 12±4 μM, respectively (P<0.01). MAS7‐induced ATP release from DM2 RBCs (10 μM, n=8) was 0.3±0.1 μM compared to 0.9±0.2 μM from HH RBCs (n=8) (P<0.01). Pretreatment of DM2 RBCs with CZ (10 μM) increased MAS7‐induced cAMP from 2.1 ±0.1 (n=9) to 2.9±0.9 pmole (n=7) (P<0.01) and ATP release from 0.3±1 to 0.5±1 μM (n=4) (P<0.05). Thus, both hypoxia‐ and MAS7‐induced increases in ATP release are reduced in DM2 RBCs. Importantly, MAS7‐induced ATP release and cAMP accumulation in DM2 RBCs were increased by CZ, a PDE3 inhibitor approved for human use in peripheral vascular disease. These findings are consistent with the hypothesis that decreased release of ATP from RBCs may contribute to reduced vascular reactivity in DM2 and that PDE3 inhibitors could improve this defect via a heretofore unrecognized effect on RBCs. Supported by NIH grants HL‐64180 and HL‐51298 and an ADA Innovation Award.
Fully Automated Parallel Oligonucleotide Synthesizer (2001)

Design and construction of automated synthesizers using the tilted plate centrifugation technology is described. Wash solutions and reagents common to all synthesized species are delivered automatically through a 96-channel distributor connected to a gear pump through two four-port selector valves. Building blocks and other specific reagents are delivered automatically through banks of solenoid valves, positioned over the individual wells of the microtiterplate. These instruments have the following capabilities: Parallel solid-phase oligonucleotide synthesis in the wells of polypropylene microtiter plates, which are slightly tilted down towards the center of rotation, thus generating a pocket in each well, in which the solid support is collected during centrifugation, while the liquid is expelled from the wells. Eight microtiterplates are processed simultaneously, providing thus a synthesizer with a capacity of 768 parallel syntheses. The instruments are capable of unattended continuous operation, providing thus a capacity of over two millions 20-mer oligonucleotides in a year.
High-sensitivity photoacoustic leak testing (2004)

The photoacoustic effect may be exploited for detection and localization of gas leaks on the surface of otherwise sealed components. The technique involves filling the test component with a photoactive tracer gas, and irradiating the component to produce photoacoustic sound from any leak site where a tracer gas cloud forms. This presentation describes demonstration experiments utilizing 10.6-μm radiation from a nominally 145-W carbon-dioxide laser with sulfur hexafluoride as a tracer gas. Here, photoacoustic sounds from six NIST-traceable calibrated leak sources with leak rates between 1 cc in 4.6 h, and 1 cc in 6.3 years were recorded with 12 microphones in a bandwidth from 3 to 80 kHz. Bartlett matched-field processing of the microphone array measurements both detect and localize these leaks when the leak and the array are separated by 152 mm. These experiments suggest that the sensitivity of photoacoustic leak testing may reach or even exceed the capabilities of the most sensitive commercial leak test systems using helium mass-spectrometers. Comparison of the measured results and an analytical scaling law suggests that tracer cloud geometry influences the photoacoustic signal amplitude. [Work supported by the U.S. Dept. of Energy.]
Multifunctional use of innovative chitin nanofibrils for skin care (2006)

Chitin nanofibrils occur in biological tissues, mainly crustacean and insect exoskeletons, according to structural hierarchies together with proteins and inorganic compounds. They have helped elucidate the chitin structure, considering their high degree of crystallization. Isolated nanofibrils are useful to impart strength to several materials such as soy proteins, natural rubber, poly(caprolactone) and poly(vinyl alcohol). They also find applications in the cosmetic and biomedical areas, particularly for the ordered regeneration of wound tissues and as dermal fillers. The main advantage over the usual chitin powders is their enormous surface area, that enables them to interact effectively with cells, factors, proteins and other compounds.
1Bounds on the Reconstruction of Sparse Signal Ensembles from Distributed Measurements (2016)

This paper is dedicated to the memory of Hyeokho Choi, our colleague, mentor, and friend. In compressive sensing, a small collection of linear projections of a sparse signal contains enough information to permit signal recovery. Distributed compressive sensing (DCS) extends this framework, allowing a correlated ensemble of sparse signals to be jointly recovered from a collection of separately acquired compressive measurements. In this paper, we introduce an ensemble sparsity model for capturing the intra- and inter-signal correlations within a collection of sparse signals. For strictly sparse signals obeying an ensemble sparsity model, we characterize the fundamental number of noiseless measurements that each sensor must collect to ensure that the signals are jointly recoverable. Our analysis is based on a novel bipartite graph representation that links the sparse signal coefficients with the measurements obtained for each signal.
Low-cost digital radiographic imaging systems: the x-ray light valve (2006)

In recent years, new x-ray radiographic systems based on large area flat panel technology have revolutionized our capability to produce digital x-ray radiographic images. However, these active matrix flat panel imagers (AMFPI) are extraordinarily expensive compared to the systems they are replacing. Thus there is a clear need for a low cost digital imaging system for general applications in radiology. Different approaches have been considered to make lower cost xray imaging devices for digital radiography, including: reducing the cost of existing flat panel systems, scanned projection x-ray, an approach based on computed radiography (CR) technology, and optically demagnified x-ray screen/camera systems. All of these approaches are quite expensive and none have the image quality of AMFPIs. We have identified a new approach - the X-ray Light Valve (XLV). It combines three well-established technologies: an a- Se layer to convert x-rays to image charge, a liquid crystal (LC) cell, and a scanned digital readout. This device achieves our goal of immediate readout with image quality comparable to an AMFPI, while keeping costs low. The XLV system has been shown to have all the properties required for general radiography.
Identification of Immunogenic Salmonella enterica Serotype Typhi Antigens Expressed in Chronic Biliary Carriers of S. Typhi in Kathmandu, Nepal (2013)

Further evaluation of YncE and other antigens identified by IVIAT could lead to the development of improved diagnostic assays to identify asymptomatic S. Typhi carriers.
Mechatronic Design of a Novel Robotic Manta with Pectoral Fins (2019)

This paper proposes an innovative design scheme of a manta-inspired robot system for both fast swimming and high maneuverability. Based on some hydrodynamic and biological studies on manta rays, a new pectoral fin with two separate DOFs is designed, to mimic the compound motion of two vertical waves as well as the tip trajectory of the natural pectoral fin, which have important influence on the efficient swimming of manta rays. Besides, a special buoyance adjustment mechanism is incorporated to pursue gliding ability and three-dimensional maneuverability of robotic manta. With novel structural design and powerful servomotors, the robotic manta is expected to achieve high propulsion efficiency while maintaining good swimming speed. Specifically, the motion principles and geometrical parameters of the pectoral fin are discussed in detail. Moreover, the basic control method of robotic manta is given and simulation analyses are conducted to verify the presented new design.
Hg-201 (+) CO-Magnetometer for HG-199(+) Trapped Ion Space Atomic Clocks (2011)

Local magnetic field strength in a trapped ion atomic clock is measured in real time, with high accuracy and without degrading clock performance, and the measurement is used to compensate for ambient magnetic field perturbations. First and second isotopes of an element are co-located within the linear ion trap. The first isotope has a resonant microwave transition between two hyperfine energy states, and the second isotope has a resonant Zeeman transition. Optical sources emit ultraviolet light that optically pump both isotopes. A microwave radiation source simultaneously emits microwave fields resonant with the first isotope's clock transition and the second isotope's Zeeman transition, and an optical detector measures the fluorescence from optically pumping both isotopes. The second isotope's Zeeman transition provides the measure of magnetic field strength, and the measurement is used to compensate the first isotope's clock transition or to adjust the applied C-field to reduce the effects of ambient magnetic field perturbations.