gebhart/patrepeval huggingface dataset:
Immune correlates of varlilumab (CDX-1127) treated cancer patients are consistent with CD27 costimulatory activity (2014)

Varlilumab is a human IgG1 agonist anti-CD27 antibody designed to activate T cells through CD27 costimulation. Preclinical studies have shown that Varlilumab efficiently activates human T cells when combined with T cell receptor stimulation, enhances antigen specific CD8 T cell responses in human CD27 transgenic mice when combined with vaccination, and mediates anti-tumor activity in these mice when challenged with syngeneic tumors. A multi-dose, dose-escalation/expansion trial of Varlilumab in patients with advanced solid tumors (n = 56) or lymphoma (n = 24) has demonstrated a good safety profile with no MTD reached through the 10 mg/kg dose level. Evidence of clinical activity includes a complete response in a treatment-refractory Stage IV Hodgkin’s patient (remains in remission at 12.9 months); a renal cell carcinoma (RCC) patient with a partial response (ongoing at 3.8 months); an additional RCC patient with extended stable disease (ongoing at 22.4+ months); and 12 additional patients with stable disease (range: 2.7+ to 14 months). We performed extensive correlative immune monitoring from serum and peripheral blood cells, particularly in melanoma and RCC patients. Differential gene expression analysis was assessed preand post-treatment by hybridizing RNA isolated from whole blood PAXgene RNA tubes onto Illumina HT-12 microarrays. Transcriptomic analysis showed significant impact of Varlilumab on immunological pathways, including T cell receptor signaling that was observed at early time points (day 2 and day 8 post treatment). Interestingly, these changes were most significant at low dose levels (0.1 and 0.3 mg/kg), however, a larger sample size would be required to confirm these results. Varlilumab administration was associated with enhanced T cell activity by evaluation of activation markers and functional analysis using IFN-g Elispot. In particular, evaluation of response to peptides derived from melanoma antigens in selected patients showed evidence that Varlilumab promoted CD8 T cell function against melanoma antigens. Specifically, expanded responses were detected to epitopes from gp100 and MART-1, while de novo responses to epitopes MAGE-A1, NY-ESO-1 and gp100 were evident. These responses were confirmed by MHC-multimer staining. These data, and our previous analyses demonstrating a transient increase in pro-inflammatory cytokines (IP-10, IL-6, MCP-1), up-regulation of HLA-DR expression on T cells, increase in NK cell numbers, and decrease in regulatory T cells in response to Varlilumab treatment, show a pattern consistent with CD27 costimulation. These results, together with our preclinical data, provide the rationale for initiating clinical studies of Varlilumab in combination with therapies such as vaccines, checkpoint inhibitors and targeted therapies.
Paleoproterozoic tectonics of the northern Colorado Rocky Mountains Front Range, USA (2022)

ABSTRACT Two models have been proposed to explain continental crust generation in accretionary orogens. One model suggests that accretionary orogens are formed by the successive collision of juvenile arcs. The second model invokes tectonic switching, which is the repeated cycles of slab rollback and extensional backarc basin formation followed by basin collapse caused by collision, shallow subduction, and/or increased convergence rate. The northern Colorado Front Range, specifically in and around the Big Thompson, Rist, and Poudre Canyons, offers excellent exposures of Paleoproterozoic rocks to test which accretionary model best explains crust generation for a portion of the Yavapai Province. In this contribution we have two goals: The first is to provide a field-trip guide that augments Mahan et al.’s (2013) field guide, which uses many stops that have become inaccessible or have changed because of catastrophic flooding that occurred in September 2013. This more current guide focuses on a variety of mostly Paleoproterozoic rocks within what some call the Poudre Basin. These rocks include clastic metasedimentary rocks, amphibolite, the Big Thompson Canyon tonalite suite, the northern Front Range granodiorite, granitic pegmatites, and Mesoproterozoic Silver Plume granite. The second goal is to present and synthesize new and existing geochemistry, geochronology, and isotopic data, and then discuss the origins, age, deformation, and metamorphism of these rocks in the context of the proposed tectonic models. These data were synthesized into the following tectonic model for the Poudre Basin. At ca. 1780 Ma, the juvenile Green Mountain arc, located today along the Colorado-Wyoming border, formed and extended shortly thereafter during slab rollback, resulting in the extensional backarc Poudre basin between the diverging arc fragments. Sedimentation within the basin began at inception and continued to ca. 1735 Ma when basin rocks were intruded by the Big Thompson Canyon tonalite suite and the northern Front Range granodiorite, all of which were subsequently metamorphosed and deformed at ca. 1725 Ma. Felsic magmatism and deformation within the basin were perhaps driven by the northward shallow subduction of an oceanic plateau or seamount. This suggests that following accretion of the Green Mountain Arc, tectonic switching explains formation and collapse of the Poudre Basin and creation of some of northern Colorado’s crust.
Recovery of volatile organics from small industrial sources (1988)

Abstract The recovery of volatile organic compounds (VOCs) from contaminated air generated by small industrial operations such as coating operations and spray painting is an important alternative to other air cleaning techniques such as thermal or catalytic incineration. Three technologies—adsorption, absorption, and condensation—are discussed herein. The focus of this article, and by far the most widely applied technique, is activated carbon adsorption. Commercial systems are generally designed for gas streams containing roughly 300 to 5,000 ppm VOC at flow rates from 200 to 100,000 ft 3 (STP)/min (5.7 to 2,830 m 3 (STP)/min). General design parameters and costs, along with their application to example cases, are given for VOC recovery by activated carbon adsorption and condensation. No commercial systems specifically for VOC recovery by absorption have yet been reported, though this technology is extremely important for other air pollution control needs.
Incorporation of aptamers in the terminal loop of shRNAs yields an effective and novel combinatorial targeting strategy (2017)

Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme and RNA decoy. To further improve this therapeutic vector against viral escape, we sought an additional reagent to target HIV integrase. Here, we report the development of a new strategy for selection and expression of aptamer for gene therapy. We developed a SELEX protocol (multi-tag SELEX) for selecting RNA aptamers against proteins with low solubility or stability, such as integrase. More importantly, we expressed these aptamers in vivo by incorporating them in the terminal loop of shRNAs. This novel strategy allowed efficient expression of the shRNA-aptamer fusions that targeted RNAs and proteins simultaneously. Expressed shRNA-aptamer fusions targeting HIV integrase or reverse transcriptase inhibited HIV replication in cell cultures. Viral inhibition was further enhanced by combining an anti-integrase aptamer with an anti-HIV Tat-Rev shRNA. This construct exhibited efficacy comparable to that of integrase inhibitor Raltegravir. Our strategy for the selection and expression of RNA aptamers can potentially extend to other gene therapy applications.
Investigation of (110) SnO2 growth mechanisms on TiO2 substrates by plasma-assisted molecular beam epitaxy (2009)

We investigated the growth mechanisms of (110) SnO2 on (110) TiO2 by varying tin fluxes under a fixed oxygen pressure by plasma-assisted molecular beam epitaxy. A growth diagram was constructed that consists of two distinct growth regimes: an increase in growth rates in an oxygen-rich environment and a decrease in growth rates in a tin-rich environment. The excess tin played an important role for the unexpected decreasing growth rate in a tin-rich regime. Without a buildup of the tin adlayer coverage, the accumulation of macroscopic tin droplets on the SnO2 film surface was confirmed by the spotty high energy electron diffraction pattern and the absence of intensity oscillations. No SnO2 growth was observed when the impinging tin flux was larger than twice the stoichiometric tin flux, suggesting that all active oxygen atoms were consumed by evaporated tin atoms to form volatile tin suboxide (SnO). The formation of volatile SnO, causing the decreasing growth rate in a tin-rich condition, was monitored by in situ quadrupole mass spectrometry.
Synchronous Deletion of Mtv-Superantigen-Reactive Thymocytes in the CD3medium/high CD4+CD8+ Subset (2000)

Multiple model systems have demonstrated that negatively selected thymocytes can be deleted during the immature CD4(+)CD8(+) CD3(low) stage after high affinity interaction of T-cell receptors (TCRs) with antigen:major histocompatibility complex (MHC) complexes. Superantigens (SAGs) derived from endogenous mammary tumour viruses (Mtv) induce negative selection of Mtv-SAG-reactive thymocytes regardless of which peptide antigen is presented by MHC molecules. In this study, the timing of deletion of multiple subsets of Mtv-SAG-reactive CD4(+)CD8(+) thymocytes was investigated by a 4 colour flow cytometry in SJL x CBA/J cross-bred mice. Deletion of V beta 3(+), V beta 5(+), V beta 11(+), and V beta 17(+) Mtv-SAG-reactive thymocytes was found to occur synchronously in the most mature CD3(medium) and early CD3(high) subsets of CD4(+)CD8(+) thymocytes, in contrast with reports showing that the deletion of Mtv-SAG-reactive thymocytes can occur at different stages in particular model systems.
A TDD/FDD SAW-less superheterodyne receiver with blocker-resilient band-pass filter and multi-stage HR in 28nm CMOS (2015)

A SAW-less discrete-time superheterodyne receiver (RX) with multi-stage harmonic rejection in 28nm CMOS, featuring highly linear LNTA, employs a novel blocker-resilient octal charge-sharing band-pass filter to achieve low power consumption. The RX features NF of 2.1 to 2.6 dB, and IIP3 of 8 to 14 dBm, while drawing only 24 to 37 mW in different operating modes.
The Neural Mechanisms of Associative Memory Revisited: fMRI Evidence from Implicit Contingency Learning (2020)

The literature describes a basic neurofunctional antagonism between episodic memory encoding and retrieval with opposed patterns of neural activation and deactivation, particularly in posterior midline regions. This has been coined the encoding/retrieval (E/R) flip. The present fMRI study uses an innovative task paradigm to further elucidate neurofunctional relations of encoding and retrieval in associative memory. Thereby, memory encoding is implemented as implicit (non-deliberate) cognitive process, whereas the prior literature focused mainly on explicit encoding. Moreover, instead of defining brain activations related to successful (vs. unsuccessful) memory performance, the task paradigm provides proper no-memory baseline conditions. More specifically, the encoding task includes trials with non-contingent (not learnable) stimulus combinations, while the retrieval task uses trials with a simple matching exercise with no mnemonic requirements. The analyses revealed circumscribed activation in the posterior middle cingulate cortex (pMCC) together with prominent deactivation in the anterior insula cortex (aIC) as core neural substrate of implicit memory encoding. Thereby, the pMCC exhibited positive functional connectivity to the hippocampus. Memory retrieval was related to an activation pattern exactly opposed to memory encoding with deactivation in the pMCC and activation in the aIC, while the aIC additionally exhibited a negative (i.e., arguably inhibitive) functional connectivity to the pMCC. Important to note, the observed pattern of activations/de-activations in the pMCC appears to conflict with prevalent E/R flip findings. The outlined results and their (alleged) discrepancies with prior study reports are discussed primarily in the context of the default mode network's functioning and its context-sensitive regulation. Finally, we point out the relevance of the present work for the understanding and further investigation of the neurofunctional aberrations occurring during normal and pathological aging.
Relevance of Nanotechnology in Modulating Oxidative Stress: An Overview (2013)

The emergence of nanotechnology has already had a groundbreaking impact in biomedical research. In recent years, there has been significant interest by researchers to use nanotechnology to treat various oxidative stress-related ailments. We have seen a paradigm change in delivery methods of natural antioxidants for the treatment and prevention of various diseases. The use of nanotechnology to deliver natural antioxidants is highlighted, and current and future prospects of nanotechnology are briefly discussed.
A Fast GRB Source Localization Pipeline for the Advanced Particle-astrophysics Telescope (2021)

We present a pipeline for fast GRB source localization for the Advanced Particle-astrophysics Telescope. APT records multiple Compton scatterings of incoming photons across 20 CsI detector layers, from which we infer the incident angle of each photon's first scattering to localize its source direction to a circle centered on the vector formed by its first two scatterings. Circles from multiple photons are then intersected to identify their common source direction. Our pipeline, which runs in real time on low-power hardware, uses an efficient tree search to determine the most likely ordering of scatterings for each photon (which cannot be measured due to the coarse time-scale of detection), followed by likelihood-weighted averaging and iterative least-squares refinement to combine all circles into an estimated source direction. Uncertainties in the scattering locations and energy deposits require that our pipeline be robust to high levels of noise. To test our methods, we reconstructed GRB events produced by a Geant4 simulation of APT's detectors paired with a second simulator that models measurement noise induced by the detector hardware. Our methods proved robust against noise and the effects of pair production, producing sub-degree localization for GRBs with fluence 0.3 MeV/cm^2. GRBs with fluence 0.03 MeV/cm^2 provided fewer photons for analysis but could still be localized within 2.5 degrees 68% of the time. Localization time for a 1-second 1.0 MeV/cm^2 GRB, measured on a quad-core, 1.4 GHz ARMv8 processor (Raspberry Pi 3B+), was consistently under 0.2 seconds — fast enough to permit real-time redirection of other instruments for follow-up observations.
Buckling of ZnO nanowires under uniaxial compression (2008)

Instability and buckling characterization of vertical well aligned single crystal of ZnO nanowires grown on SiC substrate was done quantitatively by nanoindentation technique. The critical load was found to be 477μN and the corresponding buckling energy was 3.46×10−11J. Based on the Euler model for long nanowire and Johnson model which is an extension of the Euler model for intermediate nanowire, the modulus of elasticity of single wire was calculated. Also, the critical buckling stress and strain were determined for the as grown single wire of ZnO. We found how the modulus of elasticity is dependent on the slenderness ratio.
RENAL Nephrometry Scoring System: The Radiologist’s Perspective (2012)

The scoring system has implications for surgical planning and has been widely adopted by urologists but is less familiar to radiologists.
Fractalkine receptor expression by T lymphocyte subpopulations and in vivo production of fractalkine in human (2000)

Expression and function of the fractalkine receptor CX3CR1 by T lymphocyte subpopulations was evaluated in healthy individuals.In CD8 + T lymphocytes, CX3CR1 was expressed by and functional in both CD45RO -and CD45RO + cells.In CD4 + T lymphocytes, CX3CR1 was expressed mainly by CD45RO + cells, and almost exclusively by activated HLA-DR + T lymphocytes.This receptor was functional in CD45RO + cells, but not in CD45RO -cells.Expression of fractalkine was detected by in situ hybridization and immunohistochemistry in endothelial cells of normal lung and thymus.In hyperplastic lymph nodes, fractalkine was expressed by endothelial cells of high endothelial venules and of subcapsular vessels, by follicular dendritic cells (FDC) and by some follicle lymphocytes.Fractalkine mRNA was constitutively present in the HK FDC-like cell line, and it was induced in vitro in B lymphocytes stimulated by an anti-?or by a CD40 mAb.These findings indicate that fractalkine may contribute to the recruitment of effector T helper lymphocytes, either in peripheral tissues or in lymphoid organs.In these tissues, fractalkine and its receptor may favor contact within follicles between activated T helper lymphocytes, activated B lymphocytes and FDC, thus contributing to the maturation of the B lymphocyte response.
The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum (2021)

These results indicate that common inherited risk variation (MAF ≥0.01) accounts for most of the heritable variation in OCD. SNPs with low MAF contribute meaningfully to the heritability of OCD, and the results are consistent with expectation under the "infinitesimal model" (also referred to as the "polygenic model"), where risk is influenced by a large number of loci across the genome and across MAF bins.
Long-term proliferation of immature hypoxia-dependent JMML cells supported by a 3D in vitro system (2022)

Juvenile myelomonocytic leukemia (JMML) is a rare clonal stem cell disorder that occurs in early childhood and is characterized by the hyperactivation of the RAS pathway in 95% of the patients. JMML is characterized by a hyperproliferation of granulocytes and monocytes, and little is known about the heterogeneous nature of leukemia-initiating cells, as well as of the cellular hierarchy of the JMML bone marrow. In this study, we report the generation and characterization of a novel patient-derived three-dimensional (3D) in vitro JMML model, called patient-derived JMML Atypical Organoid (pd-JAO), sustaining the long-term proliferation of JMML cells with stem cell features and patient-specific hallmarks. JMML cells brewed in a 3D model under different microenvironmental conditions acquired proliferative and survival advantages when placed under low oxygen tension. Transcriptomic and microscopic analyses revealed the activation of specific metabolic energy pathways and the inactivation of processes leading to cell death. Furthermore, we demonstrated the pd-JAO-derived cells' migratory, propagation, and self-renewal capacities. Our study contributes to the development of a robust JMML 3D in vitro model for studying and defining the impact of microenvironmental stimuli on JMML disease and the molecular mechanisms that regulate JMML initiating and propagating cells. Pd-JAO may become a promising model for compound tests focusing on new therapeutic interventions aimed at eradicating JMML progenitors and controlling JMML disease.
Abstract 15048: Outcomes Following Left Atrial Appendage Occlusion in Patients With Cerebral Amyloid Angiopathy and Prior Intracerebral Hemorrhage (2019)

Introduction: Left atrial appendage occlusion (LAAO) is a method of preventing embolic strokes in patients with atrial fibrillation (AF), as an alternative to oral anticoagulation. This is an attra...
High-Q Optical Nanocavities in Bulk Single-crystal Diamond (2014)

Optical nanocavities (racetrack resonators and photonic crystal cavities) are fabricated in bulk single-crystal diamond via angled-etching. Devices operating in the telecom band exhibited Q-factors exceeding 105, while devices in the visible yielded Q-factors approaching 104.
Message from the workshop chairs (2011)

As the organizing committee, it is our pleasure to present the proceedings of the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> IEEE International Workshop on Data Security and PrivAcy in wireless Networks (D-SPAN), held on June 20, 2011, in Lucca, Italy. The goal of this one-day workshop, organized in conjunction with the 12 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> IEEE WoWMoM 2011, is to exchange cutting-edge ideas for securing the next-generation wireless networks, systems and applications. The scope of D-SPAN includes a wide variety of topics, including security and privacy of data collection, transmission, storage, publishing, and sharing in wireless networks broadly defined - such as cellular and mobile ad hoc networks (MANET), vehicular ad hoc networks (VANET), cognitive and sensor networks - to applying data analytics techniques to address security and privacy challenges in these networks. D-SPAN provides a forum for academic and industry researchers to present research ideas that build bridges across three communities: wireless networks and databases, and security.
Pure balanced steady‐state free precession imaging (pure bSSFP) (2021)

In the limit of short enough TR, tissues become apparently pure for bSSFP. This limit can be reached for brain tissue at 1.5 T with TR <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>∼</mml:mo></mml:math> 1-2 ms at clinically relevant resolutions.
Generalization performance of a deep learning based engine-out emissions model (2021)

In our previous work [1], an ensemble of Convolutional Neural Network (CNN) models was used to predict engine-out emissions of Carbon Monoxide (CO), Unburned Hydrocarbons (HC) and Smoke directly from in-cylinder contours of multiple scalar fields - Equivalence Ratio, Temperature, Velocity and Turbulent Kinetic Energy (TKE) at Exhaust Valve Opening (EVO) generated by physics based Computational Fluid Dynamics (CFD) simulations and experimentally measured emissions data. A dataset of 600 CFD generated images, one for each engine operating condition, from a 1.6L light-duty diesel engine was used for training, validation and testing of the CNN ensemble model. In this short communication, several modifications were made to the image data generation and training procedure. The ensemble of CNN models was re-trained per the new procedure on the modified image dataset from the 1.6L engine. The generalization capability of this re-trained deep learning model was investigated by evaluating its prediction performance on a test dataset from a 3.0L diesel engine that was not used previously for training, validation or testing. The CNN ensemble model re-trained on the 1.6L engine dataset captured the qualitative trends for all three emissions species on the 3.0L engine test dataset, however, quantitatively its prediction performance was not as good. Future work with additional engines and input features is planned to improve the generalization performance of the CNN based emissions prediction model.
Shared Genetic Predisposition in Peripartum and Dilated Cardiomyopathies (2016)

( N Engl J Med . 2016;374:233–241) It is possible that peripartum cardiomyopathy is influenced by genetic factors, though this remains unclear. Similar to idiopathic dilated cardiomyopathy, this disease is associated with decreased systolic function, enlarged cardiac dimensions, and nonspecific histologic findings. These similarities are significant in that idiopathic dilated cardiomyopathy has been shown to be caused by a number of gene mutations. The authors of this study sequenced the DNA of 172 women suffering from peripartum cardiomyopathy to investigate whether there was a contribution from variants in the 43 genes known to be associated with dilated cardiomyopathy.