gebhart/patrepeval huggingface dataset:
Abstract 233: Bispecific HER2 ADC: Making more potent HER2 ADC by improving target internalization (2019)

Abstract Trastuzumab-emtansine (T-DM1) targets the well-characterized breast cancer oncogene HER2, and has shown success in the clinic, but tumors expressing intermediate levels of HER2 remain resistant to T-DM1 therapy, apparently due to insufficient lysosomal trafficking of T-DM1. Here, we engineered bispecific HER2-DM1 conjugates that bridge HER2 with the rapidly internalizing receptor APLP2. The high affinity arm of HER2xAPLP2 bispecific antibodies mediates surface binding to HER2+ tumor cells (but not to HER2- normal cells). After binding to HER2, the low affinity APLP2 arm promotes antibody internalization and lysosomal degradation. The strength of the APLP2 arm allows for modulation of the degree of internalization, degradation and killing. In in vitro killing assays, HER2xAPLP2-DM1 were significantly more potent than T-DM1 in cell lines expressing high (IHC3+) and intermediate (IHC 2+) levels of HER2, albeit induced little or no killing in cell lines expressing low HER2 levels (IHC 1+). Monovalent APLP2-ADCs induced little or no killing in all cell lines tested. Selected HER2xAPLP2-DM1 conjugates had acceptable PK profile in APLP2 humanized mice while significantly outperforming T-DM1 in inhibiting growth of IHC2+ tumor xenografts. These data pave the way to generate clinical candidate ADCs that will improve on T-DM1. In addition, our study opens up a possibility to exploit internalizing proteins such as APLP2 in combination with bispecific antibodies to enhance efficacy of ADCs. Citation Format: Andres Perez Bay, Anuj Kalsy, Shiwani Tiwari, Bo Luan, Art Kunz, Zhaoyuan Chen, Li Zhang, Terra Potocky, Thomas Nittoli, Gavin Thurston, Christopher Daly, Julian Andreev. Bispecific HER2 ADC: Making more potent HER2 ADC by improving target internalization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 233.
Clinical Use of Serum c-erbB-2 in Patients with Ovarian Masses (1999)

The c-erbB-2 (Her-2/neu) gene product has a large extracellular domain (ECD) and part of which could be identified in the serum. We measured the serum level of c-erbB-2 ECD in 93 patients, who presented with ovarian masses, with an enzyme immunoassay test and an elevated level was found in 5.5, 16.7 and 38% of patients with benign, borderline and malignant ovarian neoplasms, respectively. This serum marker may reflect the overexpression of c-erbB-2 gene in tumor tissues, which is associated with poor prognosis. However, measurement of c-erbB-2 ECD when used alone or in combination with CA 125 is not useful in differentiating benign from malignant ovarian tumors.
The plasmonic Kapitza-Dirac effect and electron shaping with plasmonic fields (2023)

We present a novel method to shape single-electron wavepackets via their interaction with tunable plasmonic fields. We further demonstrate the first instance of electron diffraction from a standing electromagnetic surface wave - a plasmonic Kapitza-Dirac effect.
Kinesin Spindel Protein (KSP) Inhibitors. Part 3. Synthesis and Evaluation of Phenolic 2,4‐Diaryl‐2,5‐dihydropyrroles with Reduced hERG Binding and Employment of a Phosphate Prodrug Strategy for Aqueous Solubility. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Substrate Nitridation Effects on GaN Grown on GaAs Substrates by Molecular Beam Epitaxy Using RF-Radical Nitrogen Source (1993)

The initial substrate nitridation effects on the crystal structure of GaN epitaxial layers grown on GaAs substrates by gas source molecular beam epitaxy using RF-radical N2 as a nitrogen source were investigated. The crystal structure of GaN grown on (100) GaAs substrates was critically influenced by substrate nitridation time, that is, zincblende GaN was grown on the substrate without nitridation, and wurtzite GaN was grown on the nitrided substrate (longer than 120 s). The substrate misorientation effects on surface morphology and X-ray full width at half-maximum of zincblende GaN layers were also studied. A featureless smooth surface was obtained for a layer grown under the high V/III beam flux ratio condition.
Spinodal Decomposition in Lead-free Piezoelectric BaTiO3–CaTiO3–BaZrO3 Crystals (2018)

Polycrystals and centimeter-sized BaTiO3-based single crystals were grown by top seeded solution growth from the BaTiO3–CaTiO3–BaZrO3 system. High effective partition coefficients of Zr ranging from 15 to 6 with small Zr content have been calculated from Castaing microprobe measurements, whereas those of Ca increase slightly from 0.45 to 0.7. A spinodal decomposition mechanism is emphasized during the growth leading to the emergence of two phases with close compositions. Chemical analysis displayed periodical Zr and Ca content fluctuations within the whole boules, and Rietveld measurements highlighted two phases belonging to perovskite structures with tetragonal P4mm and orthorhombic Amm2 space groups. Samples with various calcium and zirconium contents were characterized by means of dielectric and piezoelectric measurements. Most efficient samples are indistinctly polycrystals or oriented single crystals where electromechanical performances are compositional-dependent. Polycrystalline samples and single crystals oriented along (001)pc and (110)pc displayed Curie temperatures ranging from 50 to 111 °C. Electromechanical coupling factor up to 58% and piezoelectric charge coefficient d33 = 496 pC·N–1 were obtained at room temperature. The miscibility gap between the two perovskite solid solutions as well as Ca and Zr element content variation in single crystals lower crystal piezoelectric response that remains nonetheless of the same efficiency compared to that of ceramics of the same composition.
Targeted deletion of p53 prevents cardiac rupture after myocardial infarction in mice (2006)

p53 is involved in cardiac rupture after MI, probably via the induction of a proapoptotic pathway. The inhibition of p53 may be a potentially useful therapeutic strategy to manage post-MI patients.
Des limites à la réduction d'échelle en réacteur de test catalytique en lit fixe? (2014)

In order to lower costs, testing of catalytic pellets (spheres or extrudates) is performed in ever smaller fixed bed reactors whereas catalytic pellet size is unchanged. The object of this thesis is to explore domains where downsizing leads to new questions in terms of physics, repeatability and modeling. The thesis is built in 5 chapters, 1) a detailed introduction of the context and a review of the literature on small fixed bed reactors, 2) a discussion about flow patterns in fixed beds filled with fine powder where capilary effects are not negligible, 3) a presentation of a methodology to assess the impact of sampling small number of pellets out of a non uniform set and results for internally mass transfer limited reactions, 4) a study of the effect of randomness in fixed beds first through a pore network model with a good ability to predict trends but lacking accuracy, then using direct numerical simulation of a reactive flow in fixed beds made of 8 cylinders arranged in several configuration showing that packing effects occur, concurrently with external mass transfer limitations, when cross flow diffusion is not fast enough to level out convection and reaction induced gradients, 5) a conclusion that summarizes design criteria and offers a few perspectives for R&D in downsizing
A sub-picojoule-per-bit CMOS photonic receiver for densely integrated systems (2009)

We report ultra-low-power (690fJ/bit) operation of an optical receiver consisting of a germanium-silicon waveguide detector intimately integrated with a receiver circuit and embedded in a clocked digital receiver. We show a wall-plug power efficiency of 690microW/Gbps for the photonic receiver made of a 130nm SOI CMOS Ge waveguide detector integrated to a 90nm Si CMOS receiver circuit. The hybrid CMOS photonic receiver achieved a sensitivity of -18.9dBm at 5Gbps for BER of 10(-12). Enabled by a unique low-overhead bias refresh scheme, the receiver operates without the need for DC balanced transmission. Small signal measurements of the CMOS Ge waveguide detector showed a 3dB bandwidth of 10GHz at 1V of reverse bias, indicating that further increases in transmission rate and reductions of energy-per-bit will be possible.
Enhanced spot preparation for liquid extractive sampling and analysis (2023)

A method for performing surface sampling of an analyte, includes the step of placing the analyte on a stage with a material in molar excess to the analyte, such that analyte-analyte interactions are prevented and the analyte can be solubilized for further analysis. The material can be a matrix material that is mixed with the analyte. The material can be provided on a sample support. The analyte can then be contacted with a solvent to extract the analyte for further processing, such as by electrospray mass spectrometry.
Supplemental Figure S1. MV score ROC cutoffs and Kaplan-Meier survival curves for distant metastasis-free survival, split by treatment subgroups from An Endothelial Gene Signature Score Predicts Poor Outcome in Patients with Endocrine-Treated, Low Genomic Grade Breast Tumors (2023)

&lt;p&gt;(A) ROC and (B) Kaplan-Meier analysis of our training dataset in patient subgroups (i) All, (ii) Untreated, (iii) Untreated ER positive and (iv) Endocrine treated patients.&lt;/p&gt;
On dielectric data analysis. Using the Monte Carlo method to obtain relaxation time distribution and comparing non-linear spectral function fits (2001)

In this paper, we present a technique for analyzing dielectric response data in the frequency domain, /spl chi/(/spl omega/)=/spl epsiv/(/spl omega/)-/spl epsiv//sub /spl infin//=/spl epsiv/'(/spl omega/)-/spl epsiv//sub /spl infin//-i/spl epsiv/(/spl omega/). We use a predistribution of relaxation times and reconstruct the original data by single Debye relaxations using a box constraint, least squares algorithm. The resulting relaxation times /spl tau/(D/sub i/) and their amplitudes /spl Delta//spl epsiv//sub i/,, yield the relaxation time spectrum, where i is equal or less than the number of data points. Two different predistributions of relaxation times are considered, log-uniform and adaptive. The adaptive predistribution is determined by the real part of the dielectric susceptibility /spl chi//spl xi/', and it allows for the increase of the number of effective relaxation times used in the fitting procedure. Furthermore, since the number of unknowns is limited to the number of data points, the Monte Carlo technique is introduced. In this way, the fitting procedure is repeated many times with randomly selected relaxation times, and the number of relaxation times treated in the procedure becomes continuous. The proposed method is tested for 'ideal' and measured data. Finally, the method is compared with a nonlinear curve fitting by a spectral function which consists of three contributions, i.e. the Havriliak-Negami relaxation polarization, low frequency dispersion and de conductivity. It has been found that more information can be obtained from a particular data set if it is compared with a nonlinear curve fitting procedure. The method also can be used instead of the Kramers-Kronig transformation.
Inverse design and demonstration of on-chip laser-driven particle accelerators (Conference Presentation) (2020)

We present the first demonstration of a waveguide-integrated dielectric laser accelerator. This structure and associated grating coupler are designed using a gradient-based inverse design approach. A waveguide is directly interfaced with an accelerator structure which is patterned with sub-wavelength features to produce near-fields phase-matched to electrons travelling through a 250 nm gap in the structure. We have experimentally demonstrated these waveguide-integrated accelerators by showing acceleration of subrelativistic electrons of initial energy 83.5 keV. We observe a maximum energy modulation of 1.19 keV over 30 μm. These results represent a significant step toward scalable and integrable on-chip dielectric laser accelerators for applications in ultrafast, medical, and high-energy technologies.
Data-driven Operation-based Aircraft Design Optimization (2020)

In this work, we integrate a mission analysis algorithm into the Multidisciplinary Airplane Research Integrated Library (MARILib), which is a multidisciplinary optimization tool for aircraft sizing. The main purpose of such an integration is to include aircraft operational data from the initial design process, to develop a more realistic aircraft design framework. With this approach, the design and mission requirements that reflect how aircraft actually operate are considered in the design process. Mission analysis tools are developed to model realistic aircraft operations. Data analytics, including clustering algorithms, is performed to extract information from flight data, which then becomes input to MARILib. The aim of the framework is to reduce operational costs of aircraft starting from the initial design itself, by incorporating air transportation data into the conceptual design stages.
Comb-assisted ultrastable laser system for quantum technologies (2021)

Quantum technologies are nowadays emerging as enabling tools for practical applications, such as quantum sensing, quantum computing and quantum metrology. Lasers play a central role in many of these technological platforms, e.g. for atomic clocks, ion-based or neutral atom-based quantum computers or atom interferometers. Here we present a complete laser system to cool, trap and control strontium atoms in an optical lattice or in tweezer arrays. A sub-Hz linewidth master laser, locked to a high-finesse optical cavity provides the frequency reference for an ultra-low noise comb. The rack-mounted laser system consists of all cooling, repumping, and clock lasers stabilized to the optical frequency comb. Each of the involved laser frequencies can therefore be tuned and mapped in the frequency domain with a high degree of stability. The system is controlled via a software interface, allowing to operate the cold-atom-based physics package autonomously. The system is tailored for the operation of 88Sr or 87Sr optical lattice clocks, or for quantum computing applications, but other sub-Hz lasers could be obtained by phase locking additional clock laser frequencies to the ultra-stable comb, enabling convenient and accurate optical frequency ratio measurements. The laser system architecture and the relevant characterization measurements will be presented, proposing some user-cases such as quantum computing and atom interferometry on strontium atoms. This represents a technological leap for quantum optics, allowing to explore further applications of quantum sensors outside a traditional lab.
Research in Medical Informatics at Georgia Tech : An Overview (2005)

The overall objective of this paper is to describe ongoing research programs in the Medical Informatics Laboratory in the Bioengineering Center of the Georgia Institute of Technology. Current research projects are highly interdisciplinary, spanning such areas as computer vision and image processing, artificial intelligence, and computer graphics and visualization. In general, the emphasis of the research programs is placed on the processing, interpretation, and display of biomedical imagery. These investigations, supported by an expanding academic program in bioengineering and performed in collaboration with medical researchers, are aimed at exploring basic issues in science and engineering while at the same time contributing practical solutions to a variety of problems in health care.
Fixed Feed Temperature-Programmed Modulation—A Quantitative Method To Obtain Thermophysical Parameters: Application to Chemical Warfare Agent Adsorbents (2019)

Assessing the interaction between an adsorbate and a surface is essential for optimal engineering and design of adsorbents. For low-vapor-pressure adsorbates, which also exhibit relatively weak adsorption behavior (physisorption), both the sample and the system (manifolding, reactor, etc.) demonstrate similar affinities for the probe molecule. To minimize errors, researchers often use large sample masses, which are not often convenient to obtain, particularly for new lab-generated materials. To circumvent this issue, we demonstrate an approach where we fix the thermodynamic state of the system, and then thermally perturb a small sample under fixed feed conditions, thus eliminating the impact of the system response. By varying the thermal modulation rate, various regimes for analyzing adsorption, desorption, and reactions are possible, which enables the extraction of thermophyiscal parameters. In this paper, we first validate the fixed feed temperature-programmed modulation (FFTPM) method against a common adsorbate/adsorbent (methanol/BPL carbon) and then extend the technique to dimethyl methyl phosphonate (DMMP)/carbon systems. We demonstrate the utility of such an approach for quantitatively assessing adsorption capacities, differential heats of adsorption, isosteric heats of adsorption, and adsorption kinetics parameter estimation for DMMP on carbon adsorbents. The FFTPM method is well-suited for rapidly screening and characterizing adsorbents, reactive sorbents, and other systems which exhibit physisorption phenomena.
Reactive animation: From piecemeal experimentation to reactive biological systems (2011)

Over the past decade, multi-level complex behavior and reactive nature of biological systems, has been a focus point for the biomedical community. We have developed a computational approach, termed Reactive Animation (RA) for simulating such complex biological systems. RA is an approach for describing the dynamic characteristics of biological systems based on facts collected from experiments. These data are integrated bottom-up by computational tools and methods for reactive systems development and are simulated concomitantly to a front-end user friendly visualization and reporting systems. Using RA, the experimenter may intervene mid-simulation, suggest new hypotheses for cellular and molecular interactions, apply them to the simulation and observe their resulting outcomes "on-line". Several RA models have been developed including models of T cell activation, thymocyte development and pancreatic organogenesis, which are describe in the in this review.
Cross-Layer Routing and Dynamic Spectrum Allocation in Cognitive Radio Ad Hoc Networks (2010)

Throughput maximization is one of the main challenges in cognitive radio <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ad hoc</i> networks, where the availability of local spectrum resources may change from time to time and hop by hop. For this reason, a cross-layer opportunistic spectrum access and dynamic routing algorithm for cognitive radio networks is proposed, which is called the routing and dynamic spectrum-allocation (ROSA) algorithm. Through local control actions, ROSA aims to maximize the network throughput by performing joint routing, dynamic spectrum allocation, scheduling, and transmit power control. Specifically, the algorithm dynamically allocates spectrum resources to maximize the capacity of links without generating harmful interference to other users while guaranteeing a bounded bit error rate (BER) for the receiver. In addition, the algorithm aims to maximize the weighted sum of differential backlogs to stabilize the system by giving priority to higher capacity links with a high differential backlog. The proposed algorithm is distributed, computationally efficient, and has bounded BER guarantees. ROSA is shown through numerical model-based evaluation and discrete-event packet-level simulations to outperform baseline solutions, leading to a high throughput, low delay, and fair bandwidth allocation.
Deformable 3D-2D registration for guiding K-wire placement in pelvic trauma surgery (2017)

Pelvic Kirschner wire (K-wire) insertion is a challenging surgical task requiring interpretation of complex 3D anatomical shape from 2D projections (fluoroscopy) and delivery of device trajectories within fairly narrow bone corridors in proximity to adjacent nerves and vessels. Over long trajectories (~10-25 cm), K-wires tend to curve (deform), making conventional rigid navigation inaccurate at the tip location. A system is presented that provides accurate 3D localization and guidance of rigid or deformable surgical devices ("components" - e.g., K-wires) based on 3D-2D registration. The patient is registered to a preoperative CT image by virtually projecting digitally reconstructed radiographs (DRRs) and matching to two or more intraoperative x-ray projections. The K-wire is localized using an analogous procedure matching DRRs of a deformably parametrized model for the device component (deformable known-component registration, or dKC-Reg). A cadaver study was performed in which a K-wire trajectory was delivered in the pelvis. The system demonstrated target registration error (TRE) of 2.1 ± 0.3 mm in location of the K-wire tip (median ± interquartile range, IQR) and 0.8 ± 1.4° in orientation at the tip (median ± IQR), providing functionality analogous to surgical tracking/navigation using imaging systems already in the surgical arsenal without reliance on a surgical tracker. The method offers quantitative 3D guidance using images (e.g., inlet/outlet views) already acquired in the standard of care, potentially extending the advantages of navigation to broader utilization in trauma surgery to improve surgical precision and safety.