gebhart/patrepeval huggingface dataset:
Linear stability analysis of capillary instabilities for concentric cylindrical shells (2010)

Motivated by complex multi-fluid geometries currently being explored in fibre-device manufacturing, we study capillary instabilities in concentric cylindrical flows of $N$ fluids with arbitrary viscosities, thicknesses, densities, and surface tensions in both the Stokes regime and for the full Navier--Stokes problem. Generalizing previous work by Tomotika (N=2), Stone &amp; Brenner (N=3, equal viscosities) and others, we present a full linear stability analysis of the growth modes and rates, reducing the system to a linear generalized eigenproblem in the Stokes case. Furthermore, we demonstrate by Plateau-style geometrical arguments that only axisymmetric instabilities need be considered. We show that the N=3 case is already sufficient to obtain several interesting phenomena: limiting cases of thin shells or low shell viscosity that reduce to N=2 problems, and a system with competing breakup processes at very different length scales. The latter is demonstrated with full 3-dimensional Stokes-flow simulations. Many $N &gt; 3$ cases remain to be explored, and as a first step we discuss two illustrative $N \to \infty$ cases, an alternating-layer structure and a geometry with a continuously varying viscosity.
Figure S3 from Neuregulin 1 Allosterically Enhances the Antitumor Effects of the Noncompeting Anti-HER3 Antibody 9F7-F11 by Increasing Its Binding to HER3 (2023)

&lt;p&gt;Supplemental Fig.S3. In pancreatic cancer cells, ch9F7-F11-Emb is a negative allosteric modulator of NRG1-mediated signaling. The low-fucose non-NRG1 competing allosteric anti-HER3 antibody ch9F7-F11-Emb inhibits in a dose-dependent manner NRG1-mediated cell signaling more efficiently than the ligand-competing H4B-121-Emb antibody. BxPC3 cells were pre-stimulated with 1nM NRG1 for 5min, before adding antibodies at various concentrations for another 25min. After cell lysis, the expression levels of total and phosphorylated HER3 (Tyr1289, Tyr1197 and Tyr1222), and total and phosphorylated AKT (Ser473) were measured by western blotting (A) using the appropriate antibodies. Phosphorylation was then pixel-quantified with Image J (B) and shown relative to the maximal phosphorylation (100%) evaluated in NRG1-stimulated cells without antibody treatment (M). Results are the mean {plus minus} SD of three independent experiments&lt;/p&gt;
Importance of the β12-β13 Loop in Protein Phosphatase-1 Catalytic Subunit for Inhibition by Toxins and Mammalian Protein Inhibitors (1999)

Type-1 protein serine/threonine phosphatases (PP1) are uniquely inhibited by the mammalian proteins, inhibitor-1 (I-1), inhibitor-2 (I-2), and nuclear inhibitor of PP1 (NIPP-1). In addition, several natural compounds inhibit both PP1 and the type-2 phosphatase, PP2A. Deletion of C-terminal sequences that included the beta12-beta13 loop attenuated the inhibition of the resulting PP1alpha catalytic core by I-1, I-2, NIPP-1, and several toxins, including tautomycin, microcystin-LR, calyculin A, and okadaic acid. Substitution of C-terminal sequences from the PP2A catalytic subunit produced a chimeric enzyme, CRHM2, that was inhibited by toxins with dose-response characteristics of PP1 and not PP2A. However, CRHM2 was insensitive to the PP1-specific inhibitors, I-1, I-2, and NIPP-1. The anticancer compound, fostriecin, differed from other phosphatase inhibitors in that it inhibited wild-type PP1alpha, the PP1alpha catalytic core, and CRHM2 with identical IC(50). Binding of wild-type and mutant phosphatases to immobilized microcystin-LR, NIPP-1, and I-2 established that the beta12-beta13 loop was essential for the association of PP1 with toxins and the protein inhibitors. These studies point to the importance of the beta12-beta13 loop structure and conformation for the control of PP1 functions by toxins and endogenous proteins.
Nanogranular TiN-ZrO2 intermediate layer induced improvement of isolation and grain size of FePt thin films (2014)

The effects of TiN-ZrO₂ intermediate layer on the microstructures and magnetic properties of FePt films were investigated. The TiN-ZrO2 intermediate layer was granular consisting of grains of solid solution of Ti(Zr)ON segregated by amorphous ZrO₂. By doping ZrO₂ into TiN intermediate layer, the FePt grains became better isolated from each other and the FePt grain size was reduced. For 20 vol. % ZrO₂ doping into TiN, the grain size decreased dramatically from 11. 2 nm to 6. 4 nm, and good perpendicular anisotropy was achieved simultaneously. For the FePt 4nm-SiO₂ 35 vol. % -C 20 vol. % films grown on top of the TiN-ZrO₂ 20 vol. % intermediate layer, well isolated FePt (001) granular films with coercivity higher than 18. 1 kOe and an average size as small as 6. 4 nm were achieved.
STRONG LENS TIME DELAY CHALLENGE. II. RESULTS OF TDC1 (2015)

We present the results of the first strong lens time delay challenge. The motivation, experimental design, and entry level challenge are described in a companion paper. This paper presents the main challenge, TDC1, which consisted of analyzing thousands of simulated light curves blindly. The observational properties of the light curves cover the range in quality obtained for current targeted efforts (e.g., COSMOGRAIL) and expected from future synoptic surveys (e.g., LSST), and include simulated systematic errors. Seven teams participated in TDC1, submitting results from 78 different method variants. After describing each method, we compute and analyze basic statisticsmeasuring accuracy (or bias) A, goodness of fit chi(2), precision P, and success rate f. For some methods we identify outliers as an important issue. Other methods show that outliers can be controlled via visual inspection or conservative quality control. Several methods are competitive, i.e., give vertical bar A vertical bar &lt; 0.03, P &lt; 0.03, and chi(2) &lt; 1.5, with some of the methods already reaching sub-percent accuracy. The fraction of light curves yielding a time delay measurement is typically in the range f = 20%-40%. It depends strongly on the quality of the data: COSMOGRAIL-quality cadence and light curve lengths yield significantly higher f than does sparser sampling. Taking the results of TDC1 at face value, we estimate that LSST should provide around 400 robust time-delay measurements, each with P &lt; 0.03 and vertical bar A vertical bar &lt; 0.01, comparable to current lens modeling uncertainties. In terms of observing strategies, we find that A and f depend mostly on season length, while P depends mostly on cadence and campaign duration.
Abstract 1158: Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC. (2013)

Abstract Hepatocellular carcinoma (HCC), the 5th most frequent cancer worldwide, has a 5-year survival rate of 14% because it is difficult to diagnose at its curative stages. The goal of this project is to determine if the detection of clonally expanded HBV DNA integration sites can be used as a marker for early detection of HBV related HCC (HBV-HCC) in order to improve its prognosis Hepatitis B virus (HBV) infections are associated with over 80% of HCC cases worldwide. Upon infection, the HBV genome integrates into the host chromosome at a random site, thus creating a unique genetic signature for each HBV infected cell. Certain HBV infected cells undergo progressive “uncontrolled clonal expansion” leading to the development of tumors, resulting in an over expansion of the unique HBV integration sites making them the predominant or “major HBV integration sites” (MIS). Cell-free circulating DNA from cancer patients reflects the characteristics of the tumor DNA. We and others have shown that urine contains DNA from the circulation and can be used as a source for cell-free circulating DNA. Successful detection of HBV integration sites in the circulation of HBV-HCC patients has not been demonstrated. In order to detect cell free circulating HBV DNA integration sites, a targeted enriched Next Generation Sequencing (NGS) assay was developed. Targeted enrichment was performed using an in-solution hybridization platform with biotinylated HBV RNA baits surrounding the HBV DNA nucleotide positions 1571 to 1960, the most frequent HBV breakpoint region. The assay was tested using library constructed DNA controls: Hep3B, which contains integrated DNA, and HepG2, which contains no HBV DNA. To determine the amount of captured DNA containing HBV DNA, the captured DNA was quantified for HBV containing DNA and total captured DNA. Almost all captured DNA contained HBV DNA. To confirm targeted capture of integrated HBV DNA, the captured DNA was cloned followed by sequencing. 3 out of 3 clones that were sequenced contain integrated HBV DNA. This assay demonstrated targeted capture and enrichment of HBV integration sites. This assay will be tested for sensitivity in detecting HBV integration sites and used to establish the criteria for the appearance of MIS as a biomarker for HBV-HCC. Overall, if successful, this cancer related HBV DNA marker would offer a high specificity and sensitivity in screening for HBV-HCC. Citation Format: Selena Lin, Surbhi Jain, Timothy Block, Frank Song, Ying Hsiu Su. Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1158. doi:10.1158/1538-7445.AM2013-1158
Exploring Empathy with Digital Humans (2022)

Digital humans are autonomously-animated virtual people whose social interactions are driven by artificial intelligence. They are increasingly being deployed in applications such as healthcare, customer service, and education, and they may have a place in the metaverse. For digital humans to have effective social relationships with users, it is important that they are capable of empathetic interactions. This research aims to evaluate and build upon the autonomous empathy system of a digital human through five experimental studies. Psychological and physiological data will be collected, and the effects will be compared in an Augmented Reality environment and cross-culturally. This paper presents the research agenda, and discusses considerations and challenges for empathetic interactions with digital humans.
Preparation of Ultra thin SrBi2Ta2O9 Films Using Metalorganic Chemical Vapor Deposition Combined with a Modified Annealing Method (2001)

We report a capacitor-preparation method using an ultra thin SrBi 2 Ta 2 O 9 (SBT) film for application to low-voltage-operated ferroelectric random-access memories (FeRAMs). As the film thickness was reduced below 100 nm, the SBT capacitor reached dielectric breakdown at a much lower electric field. Atomic force microscopy (AFM) analysis revealed that the crystallization annealing roughened the interface between the electrode and SBT. We attributed the electrical breakdown to the localized electric field at the roughened interface. By modifying the annealing method for crystallization of SBT, the interface was maintained smooth and flat even after the crystallization annealing, resulting in good performance in terms of the leakage current vs. appled voltage ( I – V ) characteristics. Employing a 50 nm thick SBT film, by the modified annealing method, a low-voltage operation as well as highly insulating properties was realized; the remanent polarization (2 P r ), coercive field ( V c ) and leakage current density ( J ) at 1.5 V were 12.2 µC/cm 2 , 0.36 V and approximately 5×10 -9 A/cm 2 , respectively.
An 8Gb/s 1.5mW/Gb/s 8-tap 6b NRZ/PAM-4 Tomlinson-Harashima precoding transmitter for future memory-link applications in 22nm CMOS (2013)

Memory links use variable-impedance drivers, feed-forward equalization (FFE) [1], on-die termination (ODT) and slew-rate control to optimize the signal integrity (SI). An asymmetric DRAM link configuration exploits the availability of a fast CMOS technology on the memory controller side to implement powerful equalization, while keeping the circuit complexity on the DRAM side relatively simple. This paper proposes the use of Tomlinson Harashima precoding (THP) [2-4] in a memory controller as replacement of the afore-mentioned SI optimization techniques. THP is a transmitter equalization technique in which post-cursor inter-symbol interference (ISI) is cancelled by means of an infinite impulse response (IIR) filter with modulo-based amplitude limitation; similar to a decision feedback equalizer (DFE) on the receive side. However, in contrast to a DFE, THP does not suffer from error propagation.
Control of variable geometry turbocharged diesel engines for reduced emissions (1998)

A multivariable control scheme is designed to minimize emission of nitrogen oxides (NO/sub x/) and generation of smoke in a diesel engine equipped with a variable geometry turbocharger (VGT) and an external exhaust gas recirculation system (EGR). Steady-state optimization results in operating points where NO/sub x/ emissions and smoke generation are highly coupled and require joint management by VGT and EGR actuators.
Interference Effects in Femtosecond Sum Frequency Spectra of Model Cellulose Films (2016)

Application of sum frequency spectroscopy (SFS) to thin film structures results in complex spectra, which require theoretical deconvolution. In the present work, a new copropagating model for SF emission from model cellulose surfaces has been developed, thereby enabling the study of cellulose surface characteristics and various aspects of wood utilization. Immobilized model cellulose films have been prepared on gold-coated silicon wafers for characterization by SFS. Before quantitatively analyzing SF spectra derived from cellulose, the thickness-dependent interference effect between multiple SF sources in the cellulose/gold system was investigated theoretically. Comparisons between experimental and simulated SF spectra enable an accurate understanding of thickness/phase and thickness/intensity interference effects, which are essential to the application of SFS to cellulose and other thin films on gold. It was shown that the resonant SF signal generated at the cellulose/gold interface is small, is constant with film thickness, and that the cellulose orientation is opposite that at the cellulose/air interface. As such, resonant SF signals generated at the air/cellulose interface dominate the SF spectra, although a minor contribution from the cellulose/gold interface does exist.
Abstract PR02: Integrated metabolic and epigenomic reprograming by H3K27M mutations in diffuse intrinsic pontine gliomas (2020)

Abstract H3K27M-midline gliomas are fatal tumors that mainly harbor H3.3K27M mutations resulting in global H3K27me3 reduction that impacts neuroglial-differentiation. However, the exact mechanisms by which H3.3K27M mutations promote cancer are poorly understood. Metabolic reprogramming is a hallmark of cancer and we hypothesized that H3.3K27M mutations can reprogram metabolism to support uncontrolled growth. We demonstrate that H3.3K27M-mutant cells show elevated levels of critical enzymes related to glycolysis and TCA cycle metabolism including hexokinase-2, isocitrate dehydrogenase (IDH)-1 and glutamate dehydrogenase. H3.3K27M cells also demonstrated enhanced glycolysis, glutamine and TCA-cycle metabolism accompanied by increased alpha-ketoglutarate (α-KG) production. Mutant IDH (mIDH)1/2 converts α-KG to D-2-hydroxyglutarate (D-2HG). D-2HG increases H3K27me3 by inhibiting α-KG’s function to drive H3K27-demethylases. We discovered that H3.3K27M cells use α-KG in an opposing manner to maintain low H3K27me3. Inhibiting enzymes related to α-KG generation including hexokinase-2, glutamate-dehydrogenase and wild type-IDH1 increased global H3K27me3, altered chromatin accessibility at neuroglial-differentiation factors, lowered tumor cell proliferation, and increased overall survival in vivo in two independent H3.3K27M animal models (p&amp;lt; 0.0001). H3K27M and mIDH1 were mutually exclusive in-patient tumor samples and D-2HG treatment or forced-mIDH1 expression in H3.3K27M cells increased global H3K27me3 and cell death. Finally, H3.3K27M and mIDH1 were synthetic lethal in vitro. Our data suggest that H3.3K27M and mIDH1 hijack a critical and conserved metabolic pathway in opposing manners to regulate global H3K27me3. These results have implications for understanding the pathogenesis of fatal H3K27M-gliomas and for developing therapeutic strategies by disruption of an integrated metabolic/epigenetic-axis. Citation Format: Chan Chung, Stefan Sweha, Drew Pratt, Benita Tamrazi, Pooja Panwalkar, Adam Banda, Jill Bayliss, Debra Hawes, Fusheng Yang, Ho-Joon Lee, Mengrou Shan, Marcin Cieslik, Tingting Qin, Christian Werner, Daniel Wahl, Costas Lyssiotis, Viveka Nand Yadav, Carl Koschmann, Arul Chinnaiyan, Stefan Blüml, Alexander Judkins, Sriram Venneti. Integrated metabolic and epigenomic reprograming by H3K27M mutations in diffuse intrinsic pontine gliomas [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR02.
An evaluation of multiplex bead-based analysis of cytokines and soluble proteins in archived lithium heparin plasma, EDTA plasma and serum samples (2016)

Stored serum, LH plasma, and EDTA plasma from clinical trials can be used for analysis of circulating cytokines and proteins. Variations in measurements occur, but are within reasonable ranges. The optimal type of media depends on the analytes, as different analytes have low number of measurements below the lower limit of quantification and higher dynamic ranges in different media.
Addressing the problem of plastic waste: Development of an enzymatic process for PET recycling (2019)

International audience
Axial nonuniformity of geometric and mechanical properties of mouse aorta is increased during postnatal growth (2005)

The hemodynamic conditions of aorta are relatively uniform prenatally and become more heterogeneous postnatally. Our objective was to quantify the heterogeneity of geometry and mechanical properties during growth and development. To accomplish this objective, we obtained a systematic set of data on the geometry and mechanical properties along the length of mouse aorta during postnatal development. C57BL/6 mice of ages 1-33 days were studied. The ascending aorta was cannulated in situ and preconditioned with several cyclic changes in pressure. We investigated the axial variations of geometry (diameter and length) and mechanical properties (stress-stain relation, elastic modulus and compliance) of the mouse aorta from the aortic valve to the common iliac. Our results show that the arterial blood pressure of mice increased from approximately 30 to 80 mmHg during the first 2 wk of life. The stretch ratio, diameter, wall (intima-media) thickness, and total lumen volume of mouse aorta increased with age. The aorta was transformed from a cylindrical tube at birth to a tapered structure during growth. Furthermore, we found the mechanical properties were fairly uniform along the length of the aorta at birth and become more nonuniform with age. We conclude that the rapid change of blood pressure and blood flow after birth alter the geometric and mechanical properties differentially along the length of the aorta. Hence, the axial nonuniformity of the aorta increases as the organ becomes more specialized during growth and development.
Shared Risk Link Group disjointness and geodiverse routing: A trade‐off between benefit and practical effort (2020)

Abstract The resilience to disasters is a very relevant problem in telecommunication networks. This work addresses the problem of 1 + 1 optical lightpath protection considering maximally shared risk link group (SRLG)‐disjoint geodiverse paths, applied in the context of an optical network. The resilience to geographically correlated disasters is accomplished by guaranteeing geodiversity of the paths. This work focuses on estimating the increase of the path lengths and the increase in cost of the required transponders, compared to simple link‐disjointness (i.e., when no constraints on SRLG‐disjointness or geodiversity are considered). Results in different networks allow to evaluate the effect of SRLG‐disjointness to ensure some geodiversity.
On directional modulation: An analysis of transmission scheme with multiple directions (2015)

Increasing the spectral efficiency was always the motivation behind the evolution of wireless communication systems. Also, due to the widespread usage of wireless systems, securing the transmitted data rises as a main concern nowadays. Hereby, we introduce a scheme that increases the capacity of wireless systems by transmitting multiple independent data streams, while using the space domain as a source of separation. The scheme also utilizes the space domain, in order to provide a secure communication link for each of the transmitted streams. The analysis is performed by using different orders of QAM constellations, and also baseband orthogonal-frequency-division-multiplexing signal structure. The scheme shows a high randomization for the received signal along the directions out of the desired transmission beams, and fits to the standard bit-error-rate curves for all desired transmission directions. Besides, the scheme can be easily synthesized, using low complexity algorithms.
Giant coupled, multiplicative enhancement of optical emissions from fractal aggregate/microcavity composites (2003)

Summary form only given. The giant enhancement of the optical response in metal nanocomposites and thin metallic films containing nanoscale surface features has been intensively studied in recent years. This enhancement is associated with the excitation of surface plasmons, collective electromagnetic modes whose characteristics are strongly dependent on the geometrical structure of the metallic component of the medium. In the present paper, we demonstrate that huge, multiplicative enhancement factors are obtained under the simultaneous, combined action of two resonant processes when the emitting species (dye) is adsorbed onto metal fractal aggregates contained within high-Q microcavities.
ChemInform Abstract: A Facile Synthesis of Novel Unsymmetrical N‐(4‐Oxo‐2‐phenyl‐3(4H)‐quinazolinoyl)‐N‐(aryl)acetamidines. (2010)

Abstract Ethanimidoate derivatives (I) react with electron‐rich aromatic amines to give the target compounds which are isolated as their HCl salts.
Differential Role of MyD88 in Macrophage-Mediated Responses to Opportunistic Fungal Pathogens (2003)

Toll-like receptors mediate macrophage recognition of microbial ligands, inducing expression of microbicidal molecules and cytokines via the adapter protein MyD88. We investigated the role of MyD88 in regulating murine macrophage responses to a pathogenic yeast (Candida albicans) and mold (Aspergillus fumigatus). Macrophages derived from bone marrow of MyD88-deficient mice (MyD88(-/-)) demonstrated impaired phagocytosis and intracellular killing of C. albicans compared to wild-type (MyD88(+/+)) macrophages. In contrast, ingestion and killing of A. fumigatus conidia was MyD88 independent. Cytokine production by MyD88(-/-) macrophages in response to C. albicans yeasts and hyphae was substantially decreased, but responses to A. fumigatus hyphae were preserved. These results provide evidence that MyD88 signaling is involved in phagocytosis and killing of live C. albicans, but not A. fumigatus. The differential role of MyD88 may represent one mechanism by which macrophages regulate innate responses specific to different pathogenic fungi.