gebhart/patrepeval huggingface dataset:
Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS (2018)

Infectious diseases are characterized by a complex interplay between host and pathogen, but how these interactions impact the host proteome is unclear. Here we applied a combined mass spectrometry-based proteomics strategy to investigate how the human proteome is transiently modified by the pathogen <i>Streptococcus pyogenes</i>, with a particular focus on bacterial cleavage of IgG <i>in vivo</i> In invasive diseases, <i>S. pyogenes</i> evokes a massive host response in blood, whereas superficial diseases are characterized by a local leakage of several blood plasma proteins at the site of infection including IgG. <i>S. pyogenes</i> produces IdeS, a protease cleaving IgG in the lower hinge region and we find highly effective IdeS-cleavage of IgG in samples from local IgG poor microenvironments. The results show that IdeS contributes to the adaptation of <i>S. pyogenes</i> to its normal ecological niches. Additionally, the work identifies novel clinical opportunities for <i>in vivo</i> pathogen detection.
HVDC Ground Fault Detection Method Based on the Shield Leakage Current Measurement for Long Cable Energization (2020)

HVDC transmission lines have been taking more and more importance among electric technologies. The importance of these lines mainly becomes from their asynchronous behavior and loss reductions. However, when a fault occurs, the grid stability can be affected and it could cause serious damages, especially in power electronics. For this reason, a new method to detect and differentiate ground faults from a normal energization during HVDC long cables connections with high inrush currents is here presented. The method considers the grounding of the extremes of the conductor's shield and the current measurement in these connections. If a fault exists in the cable, the current measured during the energization presents certain characteristics that can be used to distinguish a ground faulty energization from a normal one, and also to detect if the fault has occurred in the first half of the conductor or the last of it. To corroborate this method, numerous simulations have been carried out obtaining positive results.
High Energy Density Materials (2003)

Abstract : Synthetic pathways to the nitroazoxyamine, pentazole-N-oxide, and triazanitrate anions have been explored at a fundamental level. The reaction of nitrene equivalents such as organic azides, N-haloamines, N-acyl hydroxylamines N,O-diacyl hydroxylamines, and amides in the presence of lead tetra-acetate or phenyliodine diacetate, acting on N,N dialkylnitrosoamines in an attempt to generate alkylazoxyamines have all been examined. Initial results were not encouraging; in response to this, the N,N-dialkylnitrosoamine was silylated, methylated, and acylated to give 1, 1-dialkyl-2silyloxy diazenium cation and its analogues. These cations were reacted with a wide array of nucleophillic nitrene equivalents such as fluoronitramide anion or monobromo-tert, butylamme; again, no azoxy amine was observed. Intramolecular versions of the above mentioned methodologies were contrived; the appropriate intermediates were synthesized, characterized, and subjected to a variety of conditions designed to effect the intramolecular synthesis of the alkylazoxyamine, a useful precursor to the heretofore unknown nitroazoxyamine (diazanitrate). Still, no obvious evolution of the desired azoxyamine was observed. Many variations remain to be explored. One clear success in this program was the invention of HYDROXYNITROUREA, a high density oxidizer with potential use as a replacement for perchiorate. Kilogram quantities were made and tested commercially; it tended to burn too fast at elevated pressures. The ammonium salt of HNU shows much promise as a bum rate attenuator, and this is presently being explored.
Supplementary Fig. S9 from <i>Salmonella</i>-Based Therapy Targeting Indoleamine 2,3-Dioxygenase Coupled with Enzymatic Depletion of Tumor Hyaluronan Induces Complete Regression of Aggressive Pancreatic Tumors (2023)

&lt;p&gt;Evaluation of inflammatory cytokines and ICAM-1 in tumors of mice treated with PEGPH20/shIDO-ST. Mice bearing 14 day orthotopic KPC tumors were treated with indicated regimens. Tumors were excised 96 hours post-treatment and used for RT-qPCR to detect cytokines or immunofluorescence to detect ICAM-1. Data are representative of multiple experiments. (A) Total mRNA was isolated (Qiagen) to generate cDNA libraries using a RevertAid First Strand DNA kit (Thermo Scientific) and analyzed for indicated cytokine mRNAs (Power Syber Green kit, 7300 RT-PCR cycler (Applied Biosystems)). Experimental Ct values were normalized to GAPDH. Relative expression levels were calculated using the equation 2-delta deltaCt and using the CT values of the PEGPH20 only treatment group as the comparator . *p{less than or equal to}0.05, **p{less than or equal to}0.01, ***p{less than or equal to}0.001 using 1-way ANOVA. (B) Tissue sections from indicated treatment groups were stained for ICAM-1 (green), PMN (red) and nuclei (DAPI, blue). Arrows represent leading edges of PMN infiltration associated with ICAM-1. Magnification, 10X.&lt;/p&gt;
Testing of Gas Condensate Reservoirs - Sampling, Test Design and Analysis (2001)

Abstract Testing of gas condensate reservoirs requires careful coordination of all parameters in the analytical process. Therefore, the sampling procedure, the laboratory analysis of the collected samples, the design of the testing equipment, and the design and analysis of the test itself are all critical to the accuracy of the analysis. This paper will outline the methodology and procedures used in testing gas condensate reservoirs. Obtaining a representative formation fluid sample that may be used for compositional and pressure-volume-temperature (PVT) analysis is crucial in testing gas condensate reservoirs. In most cases, this means maintaining a monophasic sample as close as possible to actual reservoir conditions. New sampling technologies have been introduced that improve the quality of the initial sample and can maintain the sample integrity. Additionally, new downhole sensor technologies show promise of improving sample contamination estimates and making in-situ fluid property measurements. The various sampling techniques are discussed, and comparisons of processes that include wireline formation testing and bottomhole sampling, isokinetic sampling used in drillstem and production testing, and surface sampling are made. Laboratory testing procedures including sample quality validation, error propagation, and sample contamination are also discussed. The flow of gas condensate in a reservoir is a complicated mathematical problem involving phase changes, condensate loss into the small pores of the rock, multi-phase-flow of the wet gas oil and possibly water, phase redistribution in and around the wellbore, and finally, liquid vaporization back into the condensate gas. A well test can provide identification of the absolute reservoir and relative permeabilities, the source of declining gas permeability, near wellbore damage, and the reservoir pressure. It can also distinguish the extent of the liquid-condensate bank that forms a composite reservoir, as well as the location of the nearby boundaries. The analysis procedure and techniques will be illustrated through presentation of two field cases. In the first case, the flowing pressure is above the dewpoint pressure. Thus, the fluid inside the reservoir is a single-phase gas, and liquid dropout causes phase segregation in the wellbore. In the second case, the well is producing below the dewpoint pressure while the original reservoir pressure is above the dewpoint pressure. This caused the well test to resemble that of a composite reservoir with earlier phase-segregation effects.
Protection of entomopathogenic conidia against chemical fungicides afforded by an oil-based formulation (2010)

Abstract We evaluated the protection afforded by an oil formulation against non-compatible fungicides in mixtures with conidia of the entomopathogenic fungi Metarhizium anisopliae (Ma) and Beauveria bassiana (Bb). Under laboratory conditions, viability of unformulated (aqueous suspensions) Ma conidia was harmed by recommended label doses of carbendazim (not tested for Bb), and both Ma and Bb conidia were affected by triadimefon. On the other hand, effect of fungicides was usually nil or minimal on conidia formulated as oil-containing suspensions (emulsifiable oil + water). Germination rates for unformulated and oil-formulated Ma conidia subjected to carbendazim were reduced by 77.3 and 12.1%, respectively, compared to their fungicide-free counterparts. Germination rates at 16 h post-inoculation for unformulated and oil-formulated Bb conidia subjected to triadimefon were reduced by 20.5 and 5.5%, respectively, compared to their fungicide-free counterparts. No differences were observed at 20 h post inoculation, indicating a fungistatic action of this compound on Bb conidia. Virulence of unformulated conidia amended with fungicides against third instar Diatraea saccharalis larvae was negatively affected compared to their formulated counterparts. These results suggest that oil-formulated conidia can be effectively protected from damage caused by chemicals, which could have applications in tank mixing or alternate applications with shared spraying equipment, being especially relevant for IPM programs in which mycopesticides and chemicals are simultaneously sprayed. Keywords: biological controlmicrobial controlmycoinsecticide Metarhizium anisopliae Beauveria bassiana emulsifiable oil
Antisense Strategies to Specifically Deplete Levels of Factors II, VII and IX in Mice To Assess Their Potential as Targets for Anticoagulation. (2007)

Abstract Numerous potential intervention points exist within coagulation pathways for development of novel anticoagulant agents. To help determine the most suitable target for the discovery of novel antithrombotic agents, we have implemented an antisense strategy to specifically deplete levels of various coagulation factors in mice. Here we report the effects of antisense oligonucleotides (ASOs) targeting factors II, VII, and IX on target RNA and protein levels in mice, as well as PT/aPTT. ISIS 401025 targeting factor II, ISIS 403102 targeting factor VII, and ISIS 402618 targeting factor IX dose-dependently suppressed their respective target transcript levels in a specific manner in primary mouse hepatocytes. Following subcutaneous administration to mice, each ASO reduced target RNA levels in liver and target protein levels in plasma in a specific and dose-dependent fashion (ED95 of approximate 25 mg/kg for each ASO). In conjunction with these effects, clotting times were also prolonged in a similar dose responsive fashion. Both PT and aPTT were increased following factor II inhibition and a PT-INR of 2.5 was achieved at 25 mg/kg, corresponding to a reduction in prothrombin transcript of 95%. As expected following factor VII ASO treatment, PT was significantly increased, while aPTT was unchanged. Conversely, following factor IX ASO treatment, aPTT was marginally but significantly prolonged, while PT was unchanged. These results demonstrate the capability of ASOs to dose-dependently and specifically modulate coagulation factor activity depletion and support the ASO approach as a novel strategy for the discovery of novel anticoagulation agents. Studies are in progress to assess relative safety and to expand the anticoagulation profile in mice for each of the factors under study.
The Equilibrium Dynamics of Thermostatic End-use Load Diversity as a Function of Demand (2004)

A recently developed state-of-the-art agent-based simulation of power distribution systems is capable of modeling the thermal and demand response behavior of many thousands of thermostatic end-use loads. It computes the total power consumed by electric power customers when responding to real-time prices. Investigation of the initialization transients has led to a more precise understanding of the relationship between the end-use state probability of thermostatic loads, end-use demand, and load diversity.
Targeting alpha fetoprotein with TCR engineered T cells in HCC. (2016)

3051 Background: Alpha fetoprotein (AFP), an oncofetal protein, is transcriptionally repressed after birth. Reappearance of AFP in adult circulation indicates liver regeneration, hepatitis, chronic liver diseases, or malignant growth. When AFP positive, expression in HCC tends to be very high and homogeneous, making it an attractive immunotherapy target. Methods: A TCR specific for the HLA-A2-resricted peptide AFP158-165 (FMNKFIYEI) was identified and engineered to generate a panel of 12 affinity-enhanced TCRs (KD: 79.5-0.31mM). One clone (10mM KD), demonstrating enhanced potency against AFP-expressing liver tumor cell lines and no response to normal hepatocytes, was selected. Molecular mapping of each position of the target peptide was performed; the generated binding motif was searched against the human genome, identifying 165 potentially reactive peptides, which were synthesized, loaded onto T2 cells, and tested for reactivity by AFP TCR engineered T cells (AFP-T). Results: No safety concerns were identified. 126 normal cells and 42 tumor cell lines from various organ systems were screened for AFP-T reactivity; AFP-T showed cytokine secretion and cytotoxic activity against HCC cell lines in 2D culture and 3D microtissues, but no relevant response to any other HLA-A*0201-expressing cells. Alloreactivity was detected against a subset of HLA-A*0202 primary cells. A full alloreactivity screen performed using a panel of 51 EBV- transformed B cell lines covering 38 HLA-A, 63 HLA-B and 28 HLA-C alleles, demonstrated enhanced responses against HLA-C*0404 and HLA-B*5103. AFP-T did not recognize the AFP peptide in the context of HLA-A*0203. Patients with HLA-C*0404 and -B*5103 and -A*0202 will be excluded. Conclusions: A Phase I study will evaluate preconditioning- and cell- dose escalation to investigate the safety and anti-tumor activity of AFP-T in HLA-A*0201+ patients with AFP+ HCC and good residual liver function. Clinical safety measures for mitigating treatment-related hepatotoxicity include pre-treatment biopsy evidence of low AFP expression in non-cancerous liver, and monitoring/management strategies within the protocol. Three cell-dose cohorts at 1x108, 1x109, 5x109 total transduced cells will be investigated.
Organic Synthesis (2002)

This chapter contains sections titled: Stoichiometric Organic Reactions and Acid-Catalyzed Reactions in Ionic Liquids Stoichiometric Organic Reactions Acid-Catalyzed Reactions Transition Metal Catalysis in Ionic Liquids Why use Ionic Liquids as Solvents for Transition Metal Catalysis? The Role of the Ionic Liquid Methods of Analysis of Transition Metal Catalysts in Ionic Liquids Selected Examples of the Application of Ionic Liquids in Transition Metal Catalysis Concluding Remarks Ionic Liquids in Multiphasic Reactions Multiphasic Reactions: General Features, Scope, and Limitations Multiphasic Catalysis: Limitations and Challenges Why Ionic Liquids in Multiphasic Catalysis? Different Technical Solutions to Catalyst Separation through the Use of Ionic Liquids Immobilization of Catalysts in Ionic Liquids Scaling up Ionic Liquid Technology from Laboratory to Continuous Pilot Plant Operation Concluding Remarks and Outlook Multiphasic Catalysis with Ionic Liquids in Combination with Compressed CO2 Introduction Catalytic Reaction with Subsequent Product Extraction Catalytic Reaction with Simultaneous Product Extraction Catalytic Conversion of CO2 in an Ionic Liquid/scCO2 Biphasic Mixture Continuous Reactions in an Ionic Liquid/Compressed CO2 System Concluding Remarks and Outlook
Visualization of Concurrent Computations: Doctor of Science Dissertation Proposal (1989)

Visualization, defined as the graphical representation of symbolic objects and processes, is recognized as an important tool to aid human understanding. This is particularly true in the area of program visualization, which uses images to illustrate the execution of programs. This proposal describes research to investigate the visualization of concurrent computations. The research has two major goals: the development of a model of visualization suitable for concurrent computations, and the development of methodology for constructing visualizations. The proposed visualization model treats visualization as a function from the state of the computation to an image. This differs significantly from the approach used by existing (single-process) visualization systems, but seems highly suitable for concurrent computations. The proposed methodology uses the concepts of program correctness to identify the key properties of a computation and suggest methods of visualizing these properties.
Behavior of the regularized sampling inverse scattering method at internal resonance frequencies — Abstract (2003)

The original proof of the Colton‐Kirsch regularized sampling inverse scattering algorithm does not apply at frequencies which are eigenvalues of the interior Helmholtz problem. We explain numerical observations of the behavior of the method and show that useful information about scatterer shape can be obtained at internal resonance frequencies.
Plasma Levels of Soluble PD-L1 Correlate With Tumor Regression in Patients With Lung and Gastric Cancer Treated With Immune Checkpoint Inhibitors (2019)

sPD-L1 might be derived and secreted from tumors and might be useful to identify primary responders to ICIs at a relatively early treatment timepoint.
The Use of Nanoarrays for Highly Sensitive and Selective Detection of Human Immunodeficiency Virus Type 1 in Plasma (2004)

Arrays of antibodies with well-defined feature size and spacing are necessary for developing highly sensitive and selective immunoassays to detect macromolecules in complex solutions. Here we report the application of nanometer-scale antibody array-based analysis to determine the presence of the human immunodeficiency virus type 1 (HIV-1) in blood samples. Dip-pen nanolithography (DPN) was used to generate nanoscale patterns of antibodies against the HIV-1 p24 antigen on a gold surface. Feature sizes were less than 100-nanometers, and the activity of the antibody was preserved. HIV-1 p24 antigen in plasma obtained directly from HIV-1-infected patients was hybridized to the antibody array in situ, and the bound protein was hybridized to a gold antibody-functionalized nanoparticle probe for signal enhancement. The nanoarray features in the three-component sandwich assay were confirmed by atomic force microscopy (AFM). Demonstration of measurable amounts of HIV-1 p24 antigen in plasma obtained from men with less than 50 copies of RNA per ml of plasma (corresponding to 0.025 pg per ml) illustrates that the nanoarray-based assay can exceed the limit of detection of conventional enzyme-linked immunosorbent assay (ELISA)-based immunoassays (5 pg per ml of plasma) by more than 1000-fold.
Digestion Process Development for the Egg-Shaped Digesters Facility at DCWASA'S Blue Plains AWTP (2005)

Digestion Process Development for the Egg-Shaped Digesters Facility at DCWASA'S Blue Plains AWTPThe Washington DC Water and Sewer Authority (DCWASA) is developing its Egg-Shaped Digesters Facility at the 1400 megaliter/day-capacity Blue Plains Advanced Wastewater Treatment Plant. Preliminary Design evaluations included analysis of several anaerobic digestion process options, sludge heating (and cooling) options, and assessments of pre-digestion and post-digestion processes. The temperature...Author(s)Perry SchaferPaul SchlegelGary VolpeWalt BaileyChris PeotSudhir MurthyJohn CarrTom SadickTim SheaSteve KrugelHermann NiehoffSourceProceedings of the Water Environment FederationSubjectSession 1: Recent Advances in Anaerobic DigestionDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2005ISSN1938-6478SICI1938-6478(20050101)2005:2L.30;1-DOI10.2175/193864705783968132Volume / Issue2005 / 2Content sourceResiduals and Biosolids ConferenceFirst / last page(s)30 - 57Copyright2005Word count248
Spectrally sparse optical coherence tomography (2020)

Swept-source optical coherence tomography (OCT) typically relies on expensive and complex swept-source lasers, the cost of which currently limits the suitability of OCT for new applications. In this work, we demonstrate spectrally sparse OCT utilizing randomly spaced low-bandwidth optical chirps, suitable for low-cost implementation with telecommunications grade devices. Micron scale distance estimation accuracy with a resolution of 40 μm at a standoff imaging distance greater than 10 cm is demonstrated using a stepped chirp approach with approximately 23% occupancy of 4 THz bandwidth. For imaging of sparse scenes, comparable performance to full bandwidth occupancy is verified for metallic targets.
Data from Elimination of IL-10–Inducing T-Helper Epitopes from an IGFBP-2 Vaccine Ensures Potent Antitumor Activity (2023)

&lt;div&gt;Abstract&lt;p&gt;Immunization against self-tumor antigens can induce T-regulatory cells, which inhibit proliferation of type I CD4&lt;sup&gt;+&lt;/sup&gt; T-helper (T&lt;sub&gt;H&lt;/sub&gt;1) and CD8&lt;sup&gt;+&lt;/sup&gt; cytotoxic T cells. Type I T cells are required for potent antitumor immunity. We questioned whether immunosuppressive epitopes could be identified and deleted from a cancer vaccine targeting insulin-like growth factor–binding protein (IGFBP-2) and enhance vaccine efficacy. Screening breast cancer patient lymphocytes with IFN-γ and interleukin (IL)-10 ELISPOT, we found epitopes in the N-terminus of IGFBP-2 that elicited predominantly T&lt;sub&gt;H&lt;/sub&gt;1 whereas the C-terminus stimulated T&lt;sub&gt;H&lt;/sub&gt;2 and mixed T&lt;sub&gt;H&lt;/sub&gt;1/T&lt;sub&gt;H&lt;/sub&gt;2 responses. Epitope-specific T&lt;sub&gt;H&lt;/sub&gt;2 demonstrated a higher functional avidity for antigen than epitopes, which induced IFN-γ (&lt;i&gt;P&lt;/i&gt; = 0.014). We immunized TgMMTV-neu mice with DNA constructs encoding IGFBP-2 N-and C-termini. T cell lines expanded from the C-terminus vaccinated animals secreted significantly more type II cytokines than those vaccinated with the N-terminus and could not control tumor growth when infused into tumor-bearing animals. In contrast, N-terminus epitope–specific T cells secreted T&lt;sub&gt;H&lt;/sub&gt;1 cytokines and significantly inhibited tumor growth, as compared with naïve T cells, when adoptively transferred (&lt;i&gt;P&lt;/i&gt; = 0.005). To determine whether removal of T&lt;sub&gt;H&lt;/sub&gt;2-inducing epitopes had any effect on the vaccinated antitumor response, we immunized mice with the N-terminus, C-terminus, and a mix of equivalent concentrations of both vaccines. The N-terminus vaccine significantly inhibited tumor growth (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) as compared with the C-terminus vaccine, which had no antitumor effect. Mixing the C-terminus with the N-terminus vaccine abrogated the antitumor response of the N-terminus vaccine alone. The clinical efficacy of cancer vaccines targeting self-tumor antigens may be greatly improved by identification and removal of immunosuppressive epitopes. &lt;i&gt;Cancer Res; 74(10); 2710–8. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;