gebhart/patrepeval huggingface dataset:
Data from An Integrative Approach to Inform Optimal Administration of OX40 Agonist Antibodies in Patients with Advanced Solid Tumors (2023)

<div>AbstractPurpose:<p>The success of checkpoint blockade has led to a significant increase in the development of a broad range of immunomodulatory molecules for the treatment of cancer, including agonists against T-cell costimulatory receptors, such as OX40. Unlike checkpoint blockade, where complete and sustained receptor saturation may be required for maximal activity, the optimal dosing regimen and receptor occupancy for agonist agents is less well understood and requires further study.</p>Experimental Design:<p>We integrated both preclinical and clinical biomarker data sets centered on dose, exposure, receptor occupancy, receptor engagement, and downstream pharmacodynamic changes to model the optimal dose and schedule for the OX40 agonist antibody BMS-986178 alone and in combination with checkpoint blockade.</p>Results:<p>Administration of the ligand-blocking anti-mouse surrogate antibody OX40.23 or BMS-986178 as monotherapy or in combination with checkpoint blockade led to increased peripheral CD4<sup>+</sup> and CD8<sup>+</sup> T-cell activation in tumor-bearing mice and patients with solid tumors, respectively. OX40 receptor occupancy between 20% and 50% both <i>in vitro</i> and <i>in vivo</i> was associated with maximal enhancement of T-cell effector function by anti-OX40 treatment, whereas a receptor occupancy > 40% led to a profound loss in OX40 receptor expression, with clear implications for availability for repeat dosing.</p>Conclusions:<p>Our results highlight the value of an integrated translational approach applied during early clinical development to aggregate preclinical and clinical data in an effort to define the optimal dose and schedule for T-cell agonists in the clinic.</p></div>
Isocitrate Dehydrogenase 1 Is a Novel Plasma Biomarker for the Diagnosis of Non–Small Cell Lung Cancer (2013)

IDH1 can be used as a plasma biomarker for the diagnosis of NSCLCs, particularly lung adenocarcinoma, with relatively high sensitivity and specificity.
Data-centric security: Integrating data privacy and data security (2009)

Classifying data according to its permissible use, appropriate handling, and business value is critical for data privacy and security protection. This is essential for compliance with the constantly evolving regulatory landscape concerning protected data. Problems arise when users compromise data privacy and security by overlooking the critical need to manage data according to these requirements. This paper considers the creation and application of data classification systems for security and privacy purposes. It focuses primarily on classifying information in a meaningful way through the use of a partially automated methodology that normalizes and classifies structured data throughout an enterprise. We introduce the three pillars of the data-centric security model, which are based on the data-centric security classification offering by IBM Global Business Services (GBS) and the IBM Research Division. In particular, we describe the data classification pillar of the data-centric security architecture, which provides the framework and method for partially automated classification of data to meet the demands of compliance standards.
Gain reductions due to scatter on wireless paths with directional antennas (1999)

The use of a directional terminal antenna on a wireless link can enhance received power by as much as the antenna gain. In local scattering, however, the enhancement will be smaller. We call this decrement the gain reduction factor, /spl Delta/. We present a statistical model of /spl Delta/ for fixed suburban paths at 1.9 GHz, based on angle-of-arrival measurements in New Jersey. Our results address the influences of antenna height, antenna beamwidth, distance and season.
Sphingosine 1-Phosphate-Metabolizing Enzymes Control Influenza Virus Propagation and Viral Cytopathogenicity (2010)

Sphingosine 1-phosphate (S1P)-metabolizing enzymes regulate the level of sphingolipids and have important biological functions. However, the effects of S1P-metabolizing enzymes on host defense against invading viruses remain unknown. In this study, we investigated the role of S1P-metabolizing enzymes in modulating cellular responses to influenza virus infection. Overexpression of S1P lyase (SPL), which induces the degradation of S1P, interfered with the amplification of infectious influenza virus. Accordingly, SPL-overexpressing cells were much more resistant than control cells to the cytopathic effects caused by influenza virus infection. SPL-mediated inhibition of virus-induced cell death was supported by impairment of the upregulation of the proapoptotic protein Bax, a critical factor for influenza virus cytopathogenicity. Importantly, influenza virus infection of SPL-overexpressing cells induced rapid activation of extracellular signal-regulated kinase (ERK) and STAT1 but not of p38 mitogen-activated protein kinase (MAPK), Akt, or c-Jun N-terminal kinase (JNK). Blockade of STAT1 expression or inhibition of Janus kinase (JAK) activity elevated the level of influenza virus replication in the cells, indicating that SPL protects cells from influenza virus via the activation of JAK/STAT signaling. In contrast to that of SPL, the overexpression of S1P-producing sphingosine kinase 1 heightened the cells' susceptibility to influenza virus infection, an effect that was reversed by the inhibition of its kinase activity, representing opposed enzymatic activity. These findings indicate that the modulation of S1P-metabolizing enzymes is crucial for controlling the host defense against infection with influenza virus. Thus, S1P-metabolizing enzymes are novel potential targets for the treatment of diseases caused by influenza virus infection.
Epileptic Seizure Prediction Using Big Data and Deep Learning: Toward a Mobile System (2017)

This study demonstrates that deep learning in combination with neuromorphic hardware can provide the basis for a wearable, real-time, always-on, patient-specific seizure warning system with low power consumption and reliable long-term performance.
Cholesterol Uptake Capacity: A New Measure of HDL Functionality for Coronary Risk Assessment (2017)

Cholesterol uptake capacity assay evaluates the functionality of HDL in a sensitive and high-throughput manner without using radioisotope label and cells. This assay system could be used for the assessment of CVD risk in the clinical settings.
Tunable poly(hydroxyl urethane) from CO<sub>2</sub>‐Based intermediates using thiol‐ene chemistry (2011)

Abstract CO 2 ‐based, crosslinked poly(hydroxyl urethane)s (PHUs) are accessed via a set of efficient reactions based on the addition chemistry of thiol‐ene and amines‐cyclic carbonates. This strategy to utilize 5‐membered cyclic carbonates produced from CO 2 is robust, facile, modular, and atomically efficient in nature. The thiol‐ene reaction was utilized to access bis(cyclic carbonate), tris(cyclic carbonate), and tetrakis(cyclic carbonate) in quantitative yield from 4‐vinyl‐1,3‐dioxolan‐2‐one and thiols. Multi‐functional cyclic carbonates were simply mixed with diethylenetriamine and/or 1,6‐diaminohexane to generate crosslinked PHUs from 25 to 80 °C. These materials are easy to scale‐up and are potential candidates in many applications such as coatings, binders, and resins. The resulting polymers have glass transition temperatures between −1 and 16 °C and thermal decomposition temperatures from 190 to 230 °C. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Supplementary Data from Overcoming Taxane Resistance: Preclinical and Phase 1 Studies of Relacorilant, a Selective Glucocorticoid Receptor Modulator, with Nab-Paclitaxel in Solid Tumors (2023)

Supplementary Data from Overcoming Taxane Resistance: Preclinical and Phase 1 Studies of Relacorilant, a Selective Glucocorticoid Receptor Modulator, with Nab-Paclitaxel in Solid Tumors
Abstract 3249: Design and synthesis of imidazopyridine derivatives as novel HSP90 inhibitors for the treatment of cancer (2011)

Abstract The molecular chaperone heat shock protein 90 (HSP90) is involved in folding and stabilization of a wide range of client proteins, including key proteins involved in cancer. Through structure-based design, we synthesized a novel imidazopyridine class of potent HSP90 inhibitors. The synthesis and SAR surrounding this class of compounds will be discussed. The extensive SAR study and lead optimization resulted in the identification of the development candidate CUDC-305, later renamed Debio 0932. Debio 0932 displays high oral bioavailability (96% in mouse), high drug concentrations and a prolonged half-life (20 hr) in tumor tissues. In vitro, Debio 0932 displays potent HSP90 inhibitory activity (IC50, 100 nM) as well as anti-proliferation and apoptosis-inducing activities against a broad range of cancer cell lines (IC50, 40 – 900 nM). In vivo, Debio 0932 is highly effective against various cancer models including NSCLC, AML, breast and colorectal cancers, as well as brain cancers, benefited by its ability to cross the blood-brain barrier to reach therapeutic levels in brain tissue. Debio 0932 also exhibits high selectivity and a favorable safety profile. It was therefore selected as a drug candidate and is currently in Phase 1 clinical trials. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3249. doi:10.1158/1538-7445.AM2011-3249
RAPID SOLIDIFICATION OF OXIDE SUPERCONDUCTORS IN THE Y-Ba-Cu-O SYSTEM (1987)

Three compositions which lie along the YBa{sub 2}Cu{sub 3}O{sub 9-x}-BaCuO{sub 2} tie-line were melted and solidified with different cooling rates. Rapid solidification of all three compositions results in new, previously unreported phases. Slower solidification rates yield multi-phase materials. Annealing all three compositions in O{sub 2} transforms them to the YBa{sub 2}Cu{sub 3}O{sub 9-x} orthorhombic phase plus varying amounts of BaCuO{sub 2}. The annealed materials all show superconductivity with an average T{sub c} = 88.5 K as measured through the resistivity, which is in good agreement with measurements on a SQUID magnetometer.
Twelve pseudo-differential transmission schemes (2011)

By combining 4 pseudo-differential architectures with compatible types of termination circuit, we identify 12 multichannel pseudo-differential transmission schemes. Each provides a reduced external crosstalk compared to multiple single-ended links, using fewer conductors than multiple differential links.
Asymptotically optimal scalable coding for minimum weighted mean square error (2002)

We derive an asymptotically optimal multi-layer coding scheme for entropy-coded scalar quantizers (SQ) that minimizes the weighted mean-squared error (WMSE). The optimal entropy-coded SQ is non-uniform in the case of WMSE. The conventional multi-layer coder quantizes the base-layer reconstruction error at the enhancement-layer, and is sub-optimal for the WMSE criterion. We consider the compander representation of the quantizer, and propose to implement scalability in the compressed domain. We show that such a multi-layer coding system achieves the operational rate-distortion bound given by the non-scalable entropy-coded SQ, at the limit of high resolution. Simulation results for a synthetic memoryless Laplace source with /spl mu/-law companding are presented for various values of layer rates. Substantial gains are also achieved on the "real-world" sources of audio signals, when the optimal multi-layer approach is applied to a two-layer scalable MPEG-4 Advanced Audio Coder.
Impact of Type 1 Diabetes and Insulin Treatment on Plasma Levels and Fractional Synthesis Rate of Retinol-Binding Protein 4 (2009)

Insulin treatment that achieved normoglycemia but relative hyperinsulinemia was associated with lower RBP4 synthesis and levels in T1D. Short-term insulin deprivation and hyperglycemia had no effect on RBP4 levels and synthesis rates in T1D.
Acoustic measurements of gas density (1990)

Density measurements can be made in a gas contained in an enclosure by measuring the sound pressure level at a receiver located near a dipole source driven at constant velocity amplitude at low frequencies. Analytical results are given in terms of geometrical parameters, wave numbers, and source type for simple model problems and compared with data available in a paper by Haran [Tech. Mess. 50, 43 (1983)].
Local Tomography and the Motion Estimation Problem (2011)

In this paper we study local tomography (LT) in the motion contaminated case. It is shown that microlocally, away from some critical directions, LT is equivalent to a pseudodifferential operator of order one. LT also produces nonlocal artifacts that are of the same strength as useful singularities. If motion is not accurately known, singularities inside the object f being scanned spread in different directions. A single edge can become a double edge. In such a case the image of f looks cluttered. Based on this observation we propose an algorithm for motion estimation. We propose an empiric measure of image clutter, which we call edge entropy. By minimizing edge entropy we find the motion model. The algorithm is quite flexible and is also used for solving the misalignment correction problem. The results of numerical experiments on motion estimation and misalignment correction are very encouraging.
An Integrated IR4.0 Software Enables Autonomous Casing Crossflow Rate Calculation (2021)

Abstract This paper will present an alternative calculation technique to predict wellbore crossflow rate in a water injection well resulting from a casing leak. The method provides a self-governing process for wellbore related calculations inspired by the fourth industrial revolution technologies. In an earlier work, calculations techniques were presented which do not require the conventional use of downhole flowmeter (spinner) to obtain the flow rate. Rather, continuous surface injection data prior to crossflow development and shut-in well are used to estimate the rate. In this alternative methodology, surface injection data post crossflow development are factored in to calculate the rate with the same accuracy. To illustrate the process an example water injector well is used. To quantify the casing leak crossflow rate, the following calculation methodology was applied:Generate a well performance model using pre-crossflow injection data. Normal modeling techniques are applied in this step to obtain an accurate model for the injection well as a baseline case.Generate an imaginary injection well model: An injection well mimicking the flow characteristics and properties of the water injector is envisioned to simulate crossflow at flowing (injecting) conditions. In this step, we simulate an injector that has total depth up to the crossflow location only and not the total depth of the example water well.Generate the performance model for the secondary formation using post crossflow data: The total injection rate measured at surface has two portions: one portion goes into the shallower secondary formation and another goes into the deeper (primary) formation. The modeling inputs from the first two steps will be used here to obtain the rate for the downhole formation at crossflow conditions.Generate an imaginary production well model: The normal model for the water injector will be inversed to obtain a production model instead. The inputs from previous steps will be incorporated in the inverse modeling.Obtaining the crossflow rate at shut-in conditions: Performance curves generated from step 3 & 4 will be plotted together to obtain an intersection that corresponds to the crossflow rate at shut-in conditions. This numerical methodology was analytically derived and the prediction results were verified on syntactic field data with very high accuracy. The application of this model will benefit oil operators by avoiding wireline logging costs and associated safety risks with mechanical intervention.
Supporting dual-mode forwarding in content-centric network (2012)

Information-centric networking (ICN) aims to replace current host-centric IP architecture with one based on efficient, secure, and reliable dissemination of information. This paper extends content-centric networking (CCN), one of the ICN architectures, for dual-mode forwarding, wherein, the forwarding plane distinguishes sharable traffic from non-sharable traffic characterized by its global shareability. The proposed extensions allow sharable traffic to be forwarded in a non-expedite mode following the packet processing of CCN, while non-sharable traffic is forwarded in the proposed expedite mode subjected to fast-path forwarding only involving the FIB. We enable this dual-mode forwarding using a new header which optionally includes a source-object name. We support our proposal with simulation results where the benefit of separating these two types of traffic in the forwarding plane results in better utilization of content store, pending interest table, and improved user QoE for sharable applications in terms of content delivery latency.
Research on Ambiguity Solution Integrity Monitoring for Moving Base RTK (2020)

Ambiguity integrity monitoring is very important for some navigation applications that utilize highprecision carrier-phase differential positioning technology, which can greatly improve the safety of navigation applications. At present, the methods of solving the ambiguity problem are relatively mature. However, in different relative positioning scenarios, the ambiguity solution varies due to the existence of different relative positioning modes, which can lead to difficulty fixing the ambiguity. Therefore, it is necessary to analyze the difference in position domain integrity risk considering the cycle resolution in the carrier phase under different relative positioning modes and improve the integrity risk calculation algorithm. This paper utilized the actual Beidou Navigation Satellite System (BDS) positioning data collected from Dongying Airport to simulate different relative positioning modes by using two different vehicles, and the influence of different relative positioning modes on ambiguity fixing was analyzed. Furthermore, we develop an improved algorithm framework for position-domain integrity risk-based ambiguity considering the cycle resolution in carrier-phase navigation systems. The improvements are as follows: (1) LAMBDA is used to analyze the ambiguity in different relative positioning modes; (2) Two vehicles are used to build a test environment and simulate relative positioning scenarios in different modes; (3) The ambiguity fixing process is investigated, the probability of correctly fixing the ambiguity is calculated, and the effects of incorrectly fixed ambiguity solutions on the position-domain integrity risk are compared; (4) An integrity algorithm framework is proposed to establish an integrity monitoring scheme suitable for the moving-base RTK relative positioning mode. The results provide a reference for more complex and high-precision positioning technology in navigation applications.
Elastic breakdown via multi-core high frequency discharge for lean-burn ignition (2021)

An advanced ignition technique is developed to achieve multi-event breakdown and multi-site ignition using a single coil for ignition quality improvements. The igniter enables a unique elastic breakdown process embracing a series of high-frequency discharge events at the spark gap. The equivalent electric circuits and current/voltage equations are identified and verified for the first time to explain the working principle that governs such an elastic breakdown process. Benchmarking tests are first performed to compare the elastic breakdown ignition with the conventional and advanced multi-electrode ignition systems. The elastic breakdown and spark events are thereafter analyzed through current and voltage measurements and high-speed imaging techniques. Finally, ignition tests in combustion chambers are performed to examine the effects on the ignition process in comparison with conventional coil-based ignition systems. The experiments show that, the elastic breakdown ignition can distribute multiple high-frequency breakdown events at all electrode pairs of a multi-electrode sparkplug while using only one ignition coil, thereby offering significant cost saving advantage and packaging practicability.
Mining mammalian genomes for folding competent proteins using Tat‐dependent genetic selection in <i>Escherichia coli</i> (2009)

Recombinant expression of eukaryotic proteins in Escherichia coli is often limited by poor folding and solubility. To address this problem, we employed a recently developed genetic selection for protein folding and solubility based on the bacterial twin-arginine translocation (Tat) pathway to rapidly identify properly folded recombinant proteins or soluble protein domains of mammalian origin. The coding sequences for 29 different mammalian polypeptides were cloned as sandwich fusions between an N-terminal Tat export signal and a C-terminal selectable marker, namely beta-lactamase. Hence, expression of the selectable marker and survival on selective media was linked to Tat export of the target mammalian protein. Since the folding quality control feature of the Tat pathway prevents export of misfolded proteins, only correctly folded fusion proteins reached the periplasm and conferred cell survival. In general, the ability to confer growth was found to relate closely to the solubility profile and molecular weight of the protein, although other features such as number of contiguous hydrophobic amino acids and cysteine content may also be important. These results highlight the capacity of Tat selection to reveal the folding potential of mammalian proteins and protein domains without the need for structural or functional information about the target protein.
Amino acid excretion enhances virulence of bioherbicides. (2000)

Numerous host-specific plant pathogens suppress weed species, but do not provide control comparable to chemical herbicides. We have developed a novel method to increase the virulence of these plant pathogens. Certain amino acids, such as valine, are inhibitory to plants. Spontaneous Fusarium oxysporum Sclecht. mutants that are resistant to toxic analogs of the amino acid valine excrete high levels of valine. Growth chamber pathogenicity studies of these mutants showed increased pathogenicity to the target weed. Target plants inoculated with these mutants demonstrated symptoms similar to frenching disease of tobacco, a disease caused by an amino acid-excreting root saprophyte. The host range of these mutants was not altered. In addition, resistance of the mutant strains to the toxic analog marks the strains for field release. Thus, we propose this method as a means to enhance the virulence of all mycoherbicides.