gebhart/patrepeval huggingface dataset:
A GMCSF & IL15 Fusokine Leads to Paradoxical Immunosuppression In Vivo Via Asymmetrical JAK/STAT Signalling through the IL15 Receptor Complex. (2006)

Abstract Immune stimulatory cytokines can be exploited to treat human ailments including cancer. Amongst cytokines identified for such use, granulocyte-macrophage colony stimulating factor (GMCSF) has been under much scrutiny since it acts directly on the adaptive immune system by enhancing antigen presentation as well as costimulation. Furthermore, interleukin (IL)15 possesses overlapping activities with IL2 such as the activation of T-cells and the stimulation of natural killing as well as additive stimulatory effects on the immune system distinct from IL2. These features make IL15 an attractive companion to GMCSF as part of an immunotherapeutic fusokine. Therefore, we hypothesized that a GMCSF and IL15 fusion protein (GIFT15) would possess greater immune stimulatory properties than their combined use. Unexpectedly, tumor cells engineered to secrete GIFT15 protein led to enhanced tumor growth and suppression of natural killer (NK) and NKT-cell recruitment in vivo, suggesting an unheralded immune suppressive effect. We found that GIFT15 has pleiotropic effects on an array of immune competent cells. More specifically, peritoneal macrophages treatment with GIFT15 secrete de novo the tissue inhibitor of metalloproteinase-2 (TIMP-2); activated matrix metalloproteinase-2 (MMP-2); transforming growth factor-β (TGF-β) as well as vascular endothelial growth factor (VEGF). In terms of ligand-receptor interactions, we show by BIAcore analysis that the GIFT15 fusokine has increased affinity for the αchain component of the trimeric IL15R, which contributes to aberrant signalling through the β chain manifested by the hyperphosphorylation of STAT3 both in macrophages and splenocytes. In addition, GIFT15 and IL15R virtual interaction studies suggests that the GMCSF domain component of the GIFT15 fusokine may hinder the interaction of the IL15 domain component with the IL15Rγ chain, and thus leading to a downregulation of the JAK3/STAT5 pathway. We also show that GIFT15 leads to suppression of common γ chain-mediated STAT5 phosphorylation and blockade of the IL15-dependent IFN-γ response in mouse splenocytes We tested the utlity of GIFT15 as an immunosuppressor directly in vivo and demonstrated that it allowed engraftment of allogeneic B16F0 and human xenograft U87MG glioma cells in immunocompetent mice in a CD4-dependent maner. Thus, GIFT15 defines a new class of fusokine which mediates pro-angiogenic and potent immunosuppressive effects via aberrant signalling by the IL15R in lymphomyeloid cells. We propose that GIFT15 may serve as a novel pharmaceutical for tolerance induction of somatic allo or xenografts in mammals without requirement of toxic conditioning regimens.
Antibody of predetermined specificity to a carboxy-terminal region of H-ras gene products inhibits their guanine nucleotide-binding function. (1985)

The high prevalence of ras oncogenes in human tumors has given increasing impetus to efforts aimed at elucidating the structure and function of their p21 products. To identify functionally important domains of the p21 protein, antibodies were generated against synthetic peptides corresponding to various regions of the protein. Antibodies directed against a synthetic peptide fragment corresponding to amino acid residues 161 to 176 in the carboxy-terminal region of the H-ras-encoded p21 molecule specifically recognized H-ras-encoded p21 proteins. This antibody was also shown to strikingly and specifically inhibit the guanine nucleotide-binding function of the p21 protein. The inability of p21 protein to bind guanine nucleotides was associated with a lack of autophosphorylation or GTPase activities. These studies suggest that a region toward its carboxy terminus is directly or indirectly involved in the guanine nucleotide-binding function of the p21 molecule.
Chikungunya virus: epidemiology, replication, disease mechanisms, and prospective intervention strategies (2017)

Chikungunya virus (CHIKV), a reemerging arbovirus, causes a crippling musculoskeletal inflammatory disease in humans characterized by fever, polyarthralgia, myalgia, rash, and headache. CHIKV is transmitted by Aedes species of mosquitoes and is capable of an epidemic, urban transmission cycle with high rates of infection. Since 2004, CHIKV has spread to new areas, causing disease on a global scale, and the potential for CHIKV epidemics remains high. Although CHIKV has caused millions of cases of disease and significant economic burden in affected areas, no licensed vaccines or antiviral therapies are available. In this Review, we describe CHIKV epidemiology, replication cycle, pathogenesis and host immune responses, and prospects for effective vaccines and highlight important questions for future research.
Leveraging randomized compiling for the quantum imaginary-time-evolution algorithm (2022)

Recent progress in noisy intermediate-scale quantum (NISQ) hardware shows that quantum devices may be able to tackle complex problems even without error correction. However, coherent errors due to the increased complexity of these devices is an outstanding issue. They can accumulate through a circuit, making their impact on algorithms hard to predict and mitigate. Iterative algorithms like quantum imaginary time evolution are susceptible to these errors. This article presents the combination of both noise tailoring using randomized compiling and error mitigation with purification. We also show that cycle benchmarking gives an estimate of the reliability of the purification. We apply this method to the quantum imaginary time evolution of a transverse field Ising model and report an energy estimation error and a ground-state infidelity both below 1%. Our methodology is general and can be used for other algorithms and platforms. We show how combining noise tailoring and error mitigation will push forward the performance of NISQ devices.
A feasibility study of using gate-emitter voltage method to estimate IGBT online junction temperature in practical applications (2015)

The paper presents the feasibility of using gate-emitter voltage during IGBT turn-off in estimating the junction temperature of semiconductor chips in IGBT modules in real-time application. It is shown that the chosen parameter has negligible module and measurement circuit variation once calibrated and has been implemented successfully in a converter.
Antiresonant reflecting optical waveguides in SiO2-Si multilayer structures (1986)

A new type of optical waveguide utilizing an antiresonant reflector is described. Implementation in the SiO2-Si system gave losses as low as 0.4 dB/cm for the TE mode. The TM mode loss is &gt;60 dB/cm, making the device an excellent planar technology integrated optic polarizer.
Locality Filtering for Efficient Ride Sharing Platforms (2021)

Ride sharing has a tremendous potential to reduce the number of vehicles needed to serve a certain mobility demand. However, although ride sourcing services have flourished in recent years and are widely available worldwide (e.g. Uber, Didi, Lyft, Via), known ride sharing techniques still suffer severe scalability limitations, especially if the goal is combining multiple on-demand ride requests into a single trip within a large urban area. In the context of on-demand mobility systems, a complete enumeration of all candidate trip requests is unfortunately not a practical approach to find the optimal ride sharing solution. An efficient filtering approach is therefore needed in order to avoid both the storage of quadratic shortest-path lookup tables, as well as the exhaustive pairwise comparison of all mobility requests, with their GPS coordinates and time constraints. In this paper we present a ride sharing algorithm, which combined with the shareability networks method, is able to substantially speed up known approaches while only minimally impacting on the quality of the computed solution. The key building block is a novel <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">locality filter</i> , which allows to build a pruned version of the shareability network more efficiently in time and space than previous works. We corroborate this novel proposal with a large set of experiments executed over a dataset consisting of one month of trip requests (~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> ) performed in two different urban areas, namely Manhattan (NYC) and Singapore. Our experiments show that our approach achieves a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$5\times $ </tex-math></inline-formula> speed-up, or even more during so-called “rush times”, and it is robust under different traffic conditions.
Low Threshold Optical Oscillations in a Whispering Gallery Mode<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mrow><mml:mi mathvariant="normal">C</mml:mi><mml:mi mathvariant="normal">a</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:mrow><mml:mn>2</mml:mn></mml:msub></mml:math>Resonator (2004)

We have observed low-threshold optical hyperparametric oscillations in a high-Q fluorite whispering gallery mode resonator. The oscillations result from the resonantly enhanced four-wave mixing occurring due to Kerr nonlinearity of the material. We demonstrate that, because of the narrow bandwidth of the resonator modes as well as the high efficiency of the resonant frequency conversion, the oscillations produce stable narrow-band beat-note of the pump, signal, and idler waves. A theoretical model for this process is described.
Structural, Dielectric, and Piezoelectric Properties of Mn-Doped BaTiO<sub>3</sub>–Bi(Mg<sub>1/2</sub>Ti<sub>1/2</sub>)O<sub>3</sub>–BiFeO<sub>3</sub>Ceramics (2011)

Mn-doped (0.9-x)BaTiO3–0.1Bi(Mg1/2Ti1/2)O3–xBiFeO3 (x = 0.6, 0.7, and 0.8) ceramics were studied as candidate lead-free piezoelectric materials. The crystal structures were a pseudo-cubic perovskite at x = 0.6, a rhombohedral perovskite at x = 0.8, and a mixture of the pseudo-cubic and rhombohedral perovskite at x = 0.7. The Curie temperature was found to be 470 °C at x = 0.6 and more than 600 °C at x = 0.7 and 0.8. A strong pinning of domain walls was observed for high-field responses at x = 0.7 and 0.8, which was relaxed by high-temperature annealing and subsequent quenching. Piezoelectric properties increased with decreasing x, and the small-field piezoelectric constants d33 and d31 were 94 and 31 pC/N at x = 0.6, respectively.
Target detection under influence of sound wave scatterers using time reversal. (2009)

In general, it is difficult to detect the forward scattering wave from the target located between the sound source and the array. In a word, because the sound wave from the sound source is strong, the forward scattering wave from the target cannot be isolated. Moreover, when the sound wave scatterers except the target exist, the scattered sound wave acts mutually, and the target cannot be isolated. Therefore, the propagation environment is divided into the reference sound field without the target and the target sound field including the target. Next, the forward scattering wave from the target is extracted by using the signal obtained in each sound field. The time-reversal processing was performed to the extracted scattered wave, and the target position was obtained. As a result, the forward scattering wave was extracted by selecting the referring sound field and the target sound field, and the position of the target could be obtained in the environment that scatterers except target influenced. To establish this method, it is necessary to confirm that the propagation environment retains the phase conjugate.
Approximate-min* constraint node updating for ldpc code decoding (2004)

This work introduces a technique for updating messages that originate at the constraint nodes of bi-partite graphs in low-density parity-check codes. The technique computes only two outgoing magnitudes at each constraint node and exhibits no measurable performance loss as compared to exact belief propagation which computes a unique magnitude for each departing edge from a given constraint node. The technique eliminates the need for memory based table look-up in the constraint node processing and has been implemented using only shift, add, and comparison operations. Finite wordlength results for a 'worst-case' code indicate that 6 bit quantization yields performance that is similar to that provided by full floating point computation.
Inhibition of ghrelin <i>O</i> -acyltransferase (GOAT) by octanoylated pentapeptides (2008)

The discovery of ghrelin O-acyltransferase (GOAT) opens the way to the design of drugs that block the attachment of an octanoyl group to the appetite-stimulating peptide hormone ghrelin, potentially preventing obesity. Here, we develop a biochemical assay that uses membranes from insect cells infected with baculovirus encoding mouse GOAT. The GOAT-containing membranes transferred the [(3)H]octanoyl group from [(3)H]octanoyl CoA to recombinant proghrelin in vitro. Transfer depended on the serine at residue 3 of proghrelin, which is the known site of acylation. GOAT also transferred [(3)H]octanoyl to a pentapeptide containing only the N-terminal five amino acids of proghrelin. GOAT activity could be inhibited by an octanoylated ghrelin pentapeptide, and its potency was enhanced 45-fold when the octanoylated serine-3 was replaced by octanoylated diaminopropionic acid. The data suggest that GOAT is subjected to end-product inhibition and this inhibition is better achieved with substrates having the octanoyl group attached through an amide linkage rather than the corresponding ester. These insights may facilitate the future design of useful inhibitors of GOAT.
Improving performance of coherent coded OFDM systemsusing space time transmit diversity (2001)

The performance gain of space time transmit diversity (STTD) for coded OFDM systems using space time block coding (STBC) is investigated. In particular, it is proposed to use pilot patterns, which are orthogonal in both the frequency and time directions. Therefore, to obtain channel estimates from the separate transmit antennas the receiver can use either adjacent pilots in the frequency direction or adjacent pilots in the time direction.
An automatic procedure to detect microseismic events embedded in high noise (2009)

Automatic detection of the presence of microseismic events in noisy recorded hydraulic fracture montoring (HFM) data is not an easy task. The main reasons are first that most of the processing has to be done in an unsupervised manner and next that the signal to noise ratio can vary enormously from one experiment to another and indeed can be quite low; making it difficult to detect the signal embedded in the noise. Moreover the noise often includes spatially correlated components such as borehole modes from pump noise which could look like propagating events making it difficult to identify which are the true desired events. Therefore, in order to solve this detection problem, a statistical procedure combining both the signal and noise information is developed to properly and automatically detect weak events embedded in high noise. This approach based on a new statistical test is applied to detect which time windows contain coherent arrivals across components and sensors in the multi‐component array and to indicate the confidence in this detection. Examples on real field data are presented indicating the effectiveness of this method.
Image simulation for automatic license plate recognition (2012)

Automatic license plate recognition (ALPR) is an important capability for traffic surveillance applications, including toll monitoring and detection of different types of traffic violations. ALPR is a multi-stage process comprising plate localization, character segmentation, optical character recognition (OCR), and identification of originating jurisdiction (i.e. state or province). Training of an ALPR system for a new jurisdiction typically involves gathering vast amounts of license plate images and associated ground truth data, followed by iterative tuning and optimization of the ALPR algorithms. The substantial time and effort required to train and optimize the ALPR system can result in excessive operational cost and overhead. In this paper we propose a framework to create an artificial set of license plate images for accelerated training and optimization of ALPR algorithms. The framework comprises two steps: the synthesis of license plate images according to the design and layout for a jurisdiction of interest; and the modeling of imaging transformations and distortions typically encountered in the image capture process. Distortion parameters are estimated by measurements of real plate images. The simulation methodology is successfully demonstrated for training of OCR.
A Lentiviral Vector Expressing Japanese Encephalitis Virus-like Particles Elicits Broad Neutralizing Antibody Response in Pigs (2015)

Immunization of pigs with the lentiviral vector expressing JEV virus-like particles is particularly efficient to prime antigen-specific humoral immunity and trigger neutralizing antibody responses against JEV genotypes 1, 3, and 5. The titers of neutralizing antibodies elicited by the TRIP/JEV vector are sufficient to confer protection in domestic pigs against different genotypes of JEV and this could be of a great utility in endemic regions where more than one genotype is circulating.
High‐throughput screening for inhibitors of iron transport in E. coli (LB238) (2014)

Iron acquisition is a component of the pathogenesis of Gram‐negative bacteria, therefore as a form of 'nutritional immunity' host organisms sequester iron. To obtain iron bacteria secrete siderophores that scavenge iron. The E. coli outer membrane protein FepA actively transports the siderophore ferric enterobactin (FeEnt) into the periplasm. We observe this uptake reaction by fluorescently labeling FepA in live bacteria, monitoring quenching that occurs upon binding of FeEnt, and then fluorescence recovery during transport. We developed methods to screen for iron transport inhibitors using a cell‐based high‐throughput screening platform (HTS). This novel assay measures the fluorescence of bacterial cells before and after addition of FeEnt, and monitors its transport. Using this microtiter assay we differentiate between three possible events: no binding of FeEnt to FepA, binding without transport, and binding with transport into the periplasm. After optimizing the assay parameters (cell density, FeEnt concentration, and measurement timing) we found a Z' factor of ~0.7. This test allows for evaluation of libraries of compounds in 96‐well or 384‐well formats using live bacteria, in less than 1 hour. Grant Funding Source : Supported by: NIH GM53836
Design of Superhydrophobic Porous Coordination Polymers through the Introduction of External Surface Corrugation by the Use of an Aromatic Hydrocarbon Building Unit (2014)

We demonstrate a new approach to superhydrophobic porous coordination polymers by incorporating an anisotropic crystal morphology featuring a predominant surface that is highly corrugated and terminated by aromatic hydrocarbon moieties. The resulting low-energy surface provides particularly promising hydrophobic properties without the need for postsynthetic modifications or surface processing that would block the porosity of the framework. Consequently, hydrophobic organic molecules and water vapor are able to penetrate the surface and be densely accommodated within the pores, whereas bulk water is repelled as a result of the exterior surface corrugation derived from the aromatic surface groups. This study provides a new strategy for the design and development of superhydrophobic porous materials.
Detection of BCR-ABL proteins in blood cells of benign phase chronic myelogenous leukemia patients. (1991)

More than 95% of patients with chronic myelogenous leukemia (CML) contain an abnormal chromosome termed the Philadelphia chromosome (Ph1). Ph1 and the resulting BCR-ABL fused genes are markers for this type of leukemia. The product of the fused BCR-ABL genes is a protein of about 2000 amino acids termed P210 BCR-ABL. Although the BCR-ABL protein can be routinely detected in blood cells from blast crisis CML patients by assaying for its activated tyrosine kinase activity, detection of P210 BCR-ABL in early stage CML patients (chronic phase) has not yet been possible (S. A. Maxwell et al., Cancer Res., 47: 1731, 1987). A procedure involving Western blotting with an anti-ABL monoclonal antibody was developed that allows detection of P210 BCR-ABL and P145 ABL in cells from chronic phase and blast crisis CML patients, but as expected only P145 ABL was found in normal white blood cells. Most chronic phase patients also contained one to two ABL proteins with a molecular weight of about 190,000. Interestingly, the ratio of BCR-ABL to ABL proteins increased in four blast crisis patients compared to 18 chronic phase patients. Also, one chronic phase patient analyzed on three separate occasions lacked P210 BCR-ABL and exhibited only the Mr 190,000 form. This assay should also be useful in other leukemias that express altered forms of the ABL protein.
Three-Degree-of-Freedom Parallel Robot Arm (2006)

This paper presents single- and dual-end-effector configurations of a planar three-degree of freedom parallel robot arm designed for automated pick-place operations in vacuum cluster tools for semiconductor and flat-panel-display manufacturing applications. The basic single end-effector configuration of the arm consists of a pivoting base platform, two elbow platforms and a wrist platform, which are connected through two symmetric pairs of parallelogram mechanisms. The wrist platform carries an end-effector, the position and angular orientation of which can be controlled independently by three motors located at the base of the robot. The joints and links of the mechanism are arranged in a unique geometric configuration which provides a sufficient range of motion for typical vacuum cluster tools. The geometric properties of the mechanism are further optimized for a given motion path of the robot. In addition to the basic symmetric single end-effector configuration, an asymmetric costeffective version of the mechanism is derived, and two dual-end-effector alternatives for improved throughput performance are described. In contrast to prior attempts to control angular orientation of the end-effector(s) of the conventional arms employed currently in vacuum cluster tools, all of the motors that drive the arm can be located at the stationary base of the robot with no need for joint actuators carried by the arm or complicated belt arrangements running through the arm. As a result, the motors do not contribute to the mass and inertia properties of the moving parts of the arm, no power and signal wires through the arm are necessary, the reliability and maintenance aspects of operation are improved, and the level of undesirable particle generation is reduced. This is particularly beneficial for high-throughput applications in vacuum and particlesensitive environments.