gebhart/patrepeval huggingface dataset:
Abstract 2929: Comparative analysis of circulating human tumor DNA and bioluminescent imaging in monitoring tumor burden and therapeutic response of ionizing radiation in intratibial human prostate tumor xenografts (2021)

Abstract Purpose/Objective: Pre-clinical models of prostate cancer (PCa) metastases provide critical insight into tumor biology and therapeutic response. Current models require sophisticated reporter transgene models and/or expensive tools to noninvasively monitor tumors in metastatic sites, such as bone. Recent developments in the measurement of circulating tumor DNA (ctDNA) provide an alternative method to noninvasively assess tumor burden at a low cost. Here we present a comparative analysis of human PCa xenograft tumor growth and therapeutic response by simultaneous measurement of ctDNA and bioluminescence. Materials and methods: Male athymic nude mice were used for intra-tibial (n=10) modeling. LNCaP-CMV-Luc cells were implanted in the tibial medullary canal. Tumor burden was evaluated at pre and post-IR (focal exposure 6 Gy on day 28 post-implantation) time-points by in vivo bioluminescent imaging and quantitative real-time polymerase chain reaction (qPCR) for human LINE1/Alu DNA. qPCR was performed on plasma-derived DNA consecutively on the same day as bioluminescence. Results: Human genomic DNA quantification was sensitive to 0.1 pg and linear by hAlu (R2=0.98, for 0.1pg-150ng) and LINE DNA (R2=0.99, for 0.1pg-150ng) qPCR. hAlu DNA qPCR produces a much lower Ct value when compared to LINE1; possibly due to its higher copies in the human genome (Ct value 28 versus 22/0.1 pg). Following tumor inoculation, ctDNA level and tumor bioluminescence were strongly and significantly correlated over time (LINE1, r=0.65 and Alu, r=0.59, p&amp;lt;0.002). Following radiation, we observed an immediate (day 32) but transient decrease in the levels of ctDNA and bioluminescence, followed by a gradual increase due to tumor relapse. The correlation between ctDNA level and bioluminescence was not maintained, but responses followed a similar trend. Conclusions: In the present study, we report that the volume of human PCa xenografts can be accurately measured in the intra-tibial compartments of athymic nude mice by qPCR of circulating human Alu and LINE1 elements. Plasma-derived ctDNA levels highly correlated with tumor bioluminescence over time. Tumor directed radiation therapy exhibited slightly differential responses in ctDNA level and tumor bioluminescence, but overall both measurements followed a similar trend. Citation Format: Alok Mishra, Kenji Zennami, Esteban Velarde, Jonathan B. Coulter, Srinivasan Yegnasubramanian, Shawn E. Lupold, Theodore L. DeWeese. Comparative analysis of circulating human tumor DNA and bioluminescent imaging in monitoring tumor burden and therapeutic response of ionizing radiation in intratibial human prostate tumor xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2929.
P2‐468: In vivo follow‐up of cerebral aging and side effects of anti‐amyloid immunotherapies in the mouse lemur primate (2011)

Active anti-amyloid immunotherapy is a strategy developed against Alzheimer's disease. Approaches with Aß1-42 or K6Aß1-30 immunogens in an adjuvant decrease amyloid-ß burden and prevent cognitive decline in transgenic mice (Asuni et al, 2006). However, clinical trials of Aß1-42 immunotherapy have induced side effects like encephalitis and possibly microhemorrhages (Orgogozo et al, 2003; Ferrer et al, 2004). Mouse lemurs can develop Aß plaques with age (Mestre-Francès et al, 2000). Such a primate model may be more predictive than rodents of human side effects. We studied, by magnetic resonance imaging (MRI), immunotherapies in these primates. A first cohort was used to compare K6Aß1-30 (n = 4; 5.8 ± 0.2years) and Aß1-42 (n = 4; 5.9 ± 0.2years) immunogens in alum adjuvant. A second cohort was used to evaluate K6Aß1-30 (n = 6; 4.6 ± 0.2years) compared to adjuvant alone (n = 6; 4.7 ± 0.3years). All the animals were followed-up by MRI (7T PharmaScan-Bruker) to evaluate neuroinflammation, microhemorrhages and other forms of iron deposition, with T2-weighted and T2*-weighted sequences (resolution = (234x234x234)Âμm3). The hypointense regions from T2*-weighted images were quantified and evaluate by histology. A complementary study of age effect was performed with twenty other naive animals (1.5 to 4.9years). TheT2-weighted images did not show any neuroinflammation during immunization, irrespective of the immunogen. Microhemorrhages were detected in the cerebral parenchyma at the histological analysis of the first cohort. The animals treated with K6Aß1-30 presented less microhemorrhages compared to those treated with Aß1-42 vaccine (Mann-Whitney, p < 0.05). These small microhemorrhages were not detected on the T2*-weighted images. However hypointense signal was detected on MRI and corresponded to iron deposits in the choroid plexus. Its volume increased with natural aging (r = 0.60; p < 0.001) and with Aß1-42 compared to K6Aß1-30 treatment (ANOVA, p < 0.05). No difference was detected between K6Aß1-30 and adjuvant alone. The immunotherapies studied in the mouse lemur primate did not lead to any MRI sign of neuroinflammation. The K6Aß1-30 strategy appears to be safer than the Aß1-42 strategy as it provokes less microhemorrhages in the cerebral parenchyma and less iron deposits in the choroid plexus.
Plasmonics for ultrasensitive biomolecular nanospectroscopy (2010)

Plasmonics, by localizing light to the sub-wavelength volumes and dramatically enhancing local fields, is enabling myriad of exciting possibilities in bio-detection field [1]. In this talk, first I will demonstrate an ultra-sensitive surface-enhanced infrared spectroscopy enabling direct detection of molecular specific signatures of proteins from monolayer thick films. Our method exploits engineering of diffractive couplings among plasmonic nano-antenna arrays. I will then present a low-cost fabrication method for high-throughput fabrication of these engineered antenna arrays. Finally, I will show an integrated nanoplasmonic-nanofluidic sensor platform leading to targeted analyte delivery and dramatically improved sensor response time.
Single phase liquid cooling of hotspots in a heterogeneous pin-fin-enhanced microgap with non-uniform fin array (2017)

Single-phase liquid cooling in microchannels and microgaps has been successfully demonstrated for heat fluxes of ~1 kW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in Si components. Surface area enhancements such as uniformly distributed pin-fin arrays can provide further improvements in cooling performance. However, effectively managing localized hot spots in heterogeneous integration (HI), which refers to the integration of various components that achieves complex functionalities, entails a thermal challenge. Here we address this thermal challenge of HI by using nonuniform pin-fin array-enhanced microgap liquid-cooling. This paper tests the liquid-cooling performance of four test device vehicles (TDVs), each with a pin-fin-enhanced microgap with non-uniform fin arrays. Multiple combinations of hot spot and background heat fluxes are evaluated. Nonuniform heating conditions were created using four background heaters located from the upstream to the downstream, and one additional hotspot heater located in the center. Thermal performance of cylindrical fin-enhanced TDVs and hydrofoil fin-enhanced TDVs are examined. Both have two designs: one with increased fin density around the hotspot only, and another with increased fin density along the spanwise direction. Deionized (DI) water is the coolant for all test cases, with heat flux varying from 125 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> to 625 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the hotspot, and 125 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> to 250 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for background heaters. The resulting heat flux ratio of the localized hotspot to background heaters varies from 1 to 5. The TDVs of the spanwise-increased hydrofoil fins exhibited the best thermal performance-6% to 14% lower hotspot temperature than others. The TDVs of the spanwise-increased cylindrical fins maintain a balance between hotspot cooling performance and pressure drop. In general, as the temperature of hotspot remains around 70°C with a heat flux of 625 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , the non-uniform fin-enhanced microchannel-cooling technology appears to be a promising hotspot thermal management approach under moderate background heat flux.
Microfluidic Bead Suspension Hopper (2014)

Many high-throughput analytical platforms, from next-generation DNA sequencing to drug discovery, rely on beads as carriers of molecular diversity. Microfluidic systems are ideally suited to handle and analyze such bead libraries with high precision and at minute volume scales; however, the challenge of introducing bead suspensions into devices before they sediment usually confounds microfluidic handling and analysis. We developed a bead suspension hopper that exploits sedimentation to load beads into a microfluidic droplet generator. A suspension hopper continuously delivered synthesis resin beads (17 μm diameter, 112,000 over 2.67 h) functionalized with a photolabile linker and pepstatin A into picoliter-scale droplets of an HIV-1 protease activity assay to model ultraminiaturized compound screening. Likewise, trypsinogen template DNA-coated magnetic beads (2.8 μm diameter, 176,000 over 5.5 h) were loaded into droplets of an in vitro transcription/translation system to model a protein evolution experiment. The suspension hopper should effectively remove any barriers to using suspensions as sample inputs, paving the way for microfluidic automation to replace robotic library distribution.
Dixon Sequence with Superimposed Model-Based Bone Compartment Provides Highly Accurate PET/MR Attenuation Correction of the Brain (2016)

Bone compartment and linear AC modifications result in a highly accurate MR AC method in subjects with suspected neurodegeneration. This prototype MR AC solution appears equivalent to other recently proposed solutions and does not require additional MR sequences and scanning time. These data also suggest that exclusively model-based MR AC approaches may be adversely affected by common individual variations in skull anatomy.
Data from CHFR Protein Expression Predicts Outcomes to Taxane-Based First Line Therapy in Metastatic NSCLC (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Currently, there is no clinically validated test for the prediction of response to tubulin-targeting agents in non–small cell lung cancer (NSCLC). Here, we investigated the significance of nuclear expression of the mitotic checkpoint gene &lt;i&gt;checkpoint with forkhead and ringfinger domains&lt;/i&gt; (CHFR) as predictor of response and overall survival with taxane-based first-line chemotherapy in advanced stage NSCLC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We studied a cohort of 41 patients (median age 63 years) with advanced NSCLC treated at the Atlanta VAMC between 1999 and 2010. CHFR expression by immunohistochemistry (score 0–4) was correlated with clinical outcome using chi-square test and Cox proportional models. A cutoff score of “3” was determined by receiver operator characteristics analysis for “low” CHFR expression. Results were validated in an additional 20 patients who received taxane-based chemotherapy at Emory University Hospital and the Atlanta VAMC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; High expression (score = 4) of CHFR is strongly associated with adverse outcomes: the risk for progressive disease after first-line chemotherapy with carboplatin–paclitaxel was 52% in patients with CHFR-high versus only 19% in those with CHFR-low tumors (&lt;i&gt;P&lt;/i&gt; = 0.033). Median overall survival was strongly correlated with CHFR expression status (CHFR low: 9.9 months; CHFR high: 6.2 months; &lt;i&gt;P&lt;/i&gt; = 0.002). After multivariate adjustment, reduced CHFR expression remained a powerful predictor of improved overall survival (HR = 0.24; 95% CI, 0.1–0.58%; &lt;i&gt;P&lt;/i&gt; = 0.002). In the validation set, low CHFR expression was associated with higher likelihood of clinical benefit (&lt;i&gt;P&lt;/i&gt; = 0.03) and improved overall survival (&lt;i&gt;P&lt;/i&gt; = 0.038).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; CHFR expression is a novel predictive marker of response and overall survival in NSCLC patients treated with taxane-containing chemotherapy. &lt;i&gt;Clin Cancer Res; 19(6); 1603–11. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Optimal catalyst temperature management of Plug-in Hybrid Electric Vehicles (2011)

For driving cycles that require use of the engine (i.e. the trip distance exceeds the All Electric Range (AER) of a Plug-in Hybrid Electric Vehicle (PHEV) or a driving cycle demands power exceeding the battery peak power), the catalyst temperature management for reduced tailpipe emissions is a challenging control problem due to the frequent and extended engine shut-down and catalyst cool-down. In this paper, we develop a method to synthesize a supervisory powertrain controller (SPC) that achieves near-optimal fuel economy and tailpipe emissions under known travel distances. We first find the globally optimal solution using dynamic programming (DP), which provides an optimal control policy and state trajectories. Based on the analysis of the optimal state trajectories, a variable Energy-to-Distance Ratio (EDR) is introduced to quantify the level of battery state-of-charge (SOC) relative to the remaining distance. A novel two-dimensional extraction method is developed to extract engine on/off, gear-shift, and power-split control strategies as functions of both EDR and the catalyst temperature from the DP control policy. Based on the extracted results, an adaptive SPC that optimally adjusts the engine on/off, gear-shift, and power-split strategies under various EDR and catalyst temperature conditions was developed to achieve near-optimal fuel economy and emission performance.
Cytokine Convection Affects Cancer Metastasis by a Shear Rate Dependent Mechanism (2008)

Malignant melanoma is the most deadly form of skin cancer due to its propensity to spread, or metastasize. No current treatment exists that is effective against melanoma metastasis [1,2].
A Boundary-Constrained Swarm Robot with Granular Jamming (2020)

This paper describes a new type of compliant and configurable soft robot, a boundary-constrained swarm. The robot consists of a sealed flexible membrane that constrains both a number of mobile robotic subunits and passive granular material. The robot can change the volume fraction of the sealed membrane by applying a vacuum, which gives the robot the ability to operate in two distinct states: compliant and jammed. The compliant state allows the robot to surround and conform to objects or pass through narrow corridors. Jamming allows the robot to form a desired shape; grasp, (a) manipulate, and exert relatively high forces on external objects; and achieve relatively higher locomotion speeds. Locomotion is achieved with a combination of whegs (wheeled legs) and vibration motors that are located on the robotic subunits. The paper describes the mechanical design of the robot, the control methodology, and its object handling capability.
Knowledge-Enhanced Causal Reinforcement Learning Model for Interactive Recommendation (2023)

Owing to its inherently dynamic nature and economical training cost, offline reinforcement learning (RL) is typically employed to implement an interactive recommender system (IRS). A crucial challenge in offline RL-based IRSs is the data sparsity issue, i.e., it is hard to mine user preferences well from the limited number of user-item interactions. In this article, we propose a knowledge-enhanced causal reinforcement learning model (KCRL) to mitigate data sparsity in IRSs. We make technical extensions to the offline RL framework in terms of the reward function and state representation. Specifically, we first propose a group preference-injected causal user model (GCUM) to learn user satisfaction (i.e., reward) estimation. We introduce beneficial group preference information, namely, the group effect, via causal inference to compensate for incomplete user interests extracted from sparse data. Then, we learn the RL recommendation policy with the reward given by the GCUM. We propose a knowledge-enhanced state encoder (KSE) to generate knowledge-enriched user state representations at each time step, which is assisted by a self-constructed user-item knowledge graph. Extensive experimental results on real-world datasets demonstrate that our model significantly outperforms the baselines.
Spinal Compared with General Anesthesia in Contemporary Primary Total Hip Arthroplasties (2022)

Therapeutic Level III . See Instructions for Authors for a complete description of levels of evidence.
Breaking RSA May Be As Difficult As Factoring. (2005)

If factoring is hard, then straight line programs cannot efficiently solve the low public exponent RSA problem. More precisely, no efficient algorithm can take an RSA public key as input and then output a straight line program that efficiently solves the low public exponent RSA problem for the given public key — unless factoring is easy. More generally, it suffices that the public exponent has a small factor. Of course, other kinds of algorithms may well be able to solve the RSA problem. 1
Switching Speed Analysis and Controlled Oscillatory Behavior of a Cr-Doped V2O3 Threshold Switching Device for Memory Selector and Neuromorphic Computing Application (2019)

The switching speed of a threshold switching Cr-doped V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> device as function of voltage and resistive load is understood by means of a thermal device model. It is found that conditions that result in switching trajectories traveling further from equilibrium result in reduced switching time and energy, providing interesting guidelines for the optimization of the 1S1R memory cell. Secondly, the addition of capacitive loads is investigated. Voltage-controlled oscillatory behavior in the frequency range of 10-30 MHz has been obtained and also properly simulated by our device model. Such nanodevice oscillators are of high interest for new neuromorphic computing paradigms.
Vitamin E δ-tocotrienol sensitizes human pancreatic cancer cells to TRAIL-induced apoptosis through proteasome-mediated down-regulation of c-FLIPs (2019)

c-FLIP degradation is a key event for death receptor-induced apoptosis by anticancer bioactive vitamin E compounds in pancreatic cancer cells. Moreover, VEDT augmented TRAIL inhibition of pancreatic tumor growth and induction of apoptosis in vivo. Combination therapy with TRAIL agonists and bioactive vitamin E compounds may offer a novel strategy for pancreatic cancer intervention.
Influence of phase separation microstructure on the mechanical properties of transparent modifier-free glasses (2022)

In this work, we use heat treatment to vary the size of nanoscale droplets in a phase-separated B2O3-SiO2-Al2O3-P2O5 glass without traditional modifiers and explore the effect of phase separation on the mechanical properties. The melt-quenched version of this glass already exhibits phase separation with a droplet phase rich in B2O3. The glass transition temperature (Tg) of the droplet phase is lower than that of silica-rich glass matrix. Upon heat treatment at a temperature below the Tg of the droplet phase, the size of droplets decreases but the fraction of the droplet phase increases. Consequently, the crack initiation resistance more than doubles. Upon heat treatment at the Tg of the matrix phase, the fracture toughness increases from 0.61 to 0.73 MPa·m0.5, which is primarily due to the aggregation of individual droplets. Upon the different heat treatments, the phase-separated glasses retain their optical transparency, while the hardness increases slightly.
Spectral estimation of artist oil paints using multi-filter trichromatic imaging (2002)

A practical and easy way to capture images of oil-paintings and estimate their spectral reflectance as a function of position was tested. For the image acquisition, a trichromatic digital camera was used in conjunction with an absorption filter producing six channels. From an a priori statistical analysis of common artist oil paints, spectral reflectance was estimated. These experiments showed that it is possible to estimate the spectral reflectance with an accuracy of average &Delta;E*<SUB>94</SUB> of 1.7 and spectral reflectance rms error of 2.2%. Of particular interest is guidance towards the design of a universal calibration target for imaging paintings.
Regiospecific Synthesis of Bicyclo‐ and Heterobicyclo‐gem‐difluorocyclobutenes Using Functionalized Fluoroallenes and a Novel Mo‐Catalyzed Intramolecular [2 + 2] Cycloaddition Reaction. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Holistic power analysis of implementation alternatives for a very large scale synthesis array with phased array stations (2014)

The Square Kilometre Array (SKA) will be the largest radio telescope in the world, generating data at Pb/s rates. Real-time processing will require 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> compute operations per second and system operating costs will be dominated by energy consumption. In this paper we explore design options for the aperture array of the first SKA construction phase and provide lower bounds on their power consumption. We analyze the system's components from the antenna front-end to the central signal processor and identify the main power consumers. We compare ASIC-based and FPGA-based data processing pipelines and show that ASICs can lead to 1.6 to 4 times more power efficiency.
New color centers in diamond for long distance quantum communication (2017)

Color centers in diamond are a promising platform for quantum communication, as they can serve as solid state quantum memories with efficient optical transitions. Much recent attention has focused on the negatively charged NV center in diamond, which has a spin triplet ground state electronic configuration that can be measured and initialized optically, exhibits long spin coherence times at room temperature, and has narrow, spin-conserving optical transitions. However, the NV center exhibits a large static and dynamic inhomogeneous linewidth, and over 97% of its emission is in a broad, incoherent phonon side band, severely limiting scalability. Alternatively, the negatively charged SiV center exhibits excellent optical properties, with 70% of its emission in the zero phonon line and a narrow inhomogeneous linewidth. However, SiV− suffers from short electron spin coherence times, limited by an orbital relaxation rate (T1) of around 40 ns at 5 K.