gebhart/patrepeval huggingface dataset:
Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD (2015)

Chronic Obstructive Pulmonary Disease (COPD) is a complex disease. Genetic, epigenetic, and environmental factors are known to contribute to COPD risk and disease progression. Therefore we developed a systematic approach to identify key regulators of COPD that integrates genome-wide DNA methylation, gene expression, and phenotype data in lung tissue from COPD and control samples. Our integrative analysis identified 126 key regulators of COPD. We identified EPAS1 as the only key regulator whose downstream genes significantly overlapped with multiple genes sets associated with COPD disease severity. EPAS1 is distinct in comparison with other key regulators in terms of methylation profile and downstream target genes. Genes predicted to be regulated by EPAS1 were enriched for biological processes including signaling, cell communications, and system development. We confirmed that EPAS1 protein levels are lower in human COPD lung tissue compared to non-disease controls and that Epas1 gene expression is reduced in mice chronically exposed to cigarette smoke. As EPAS1 downstream genes were significantly enriched for hypoxia responsive genes in endothelial cells, we tested EPAS1 function in human endothelial cells. EPAS1 knockdown by siRNA in endothelial cells impacted genes that significantly overlapped with EPAS1 downstream genes in lung tissue including hypoxia responsive genes, and genes associated with emphysema severity. Our first integrative analysis of genome-wide DNA methylation and gene expression profiles illustrates that not only does DNA methylation play a 'causal' role in the molecular pathophysiology of COPD, but it can be leveraged to directly identify novel key mediators of this pathophysiology.
Long-range surface plasmon polariton waveguides with TE and TM guiding (2006)

Long-range surface plasmon polariton (LRSPP) waveguides supporting both TE and TM polarized light are demonstrated experimentally. The waveguides consist of metallic nanowires with approximately 150-nm square cross sections embedded in a polymer matrix. The wavelength dependence of propagation loss and coupling loss to single mode fibers is presented. At wavelengths around 1550 nm, the nanowires exhibit a propagation loss around 4.0 dB/cm for the TM mode and 4.5 dB/cm for the TE mode. The mode field is close to symmetric and suitable for coupling to and from optical fibers. A small increase in the waveguide width, resulting in a deviation from a square cross section, is sufficient to extinguish the TE mode, making asymmetric nanowire waveguides similar to the more conventional LRSPP thin stripe waveguides. Finally, we demonstrate a compact thermo-optical variable optical attenuator based on a LRSPP nanowire waveguide.
Aberration estimation using EUV mask roughness (2015)

We present a method to extract aberrations from through-focus aerial images of mask roughness on an Extreme Ultraviolet (EUV) lithography mask. The algorithm uses a phase recovery algorithm based on the Weak Object Transfer Function to recover the phase and amplitude of the roughness, while considering aberrations and partially coherent illumination. Using the self-consistency of the recovered object, aberrations, and measured images as a metric, we optimize over the space of aberrations to estimate aberrations. Partially coherent illumination is needed to allow the effects of the object field and aberrations to be separated. We apply the algorithm to the EUV aerial image microscope, SHARP, using a parameterized ray tracing model to calculate the aberrations from a lower dimensional parameter space.
Direct exoplanet imaging with small-angle Vortex coronagraphs (2015)

Vortex coronagraphs are among the most promising solutions to perform high contrast imaging at small angular separations from bright stars. They enhance the dynamic range at very small inner working angle (down to the diffraction limit of the telescope) and provide a clear 360 degree discovery space for high-contrast direct imaging of exoplanets. In this talk, we will report on the first scientific results obtained with Vortex coronagraphs installed on 10-m class telescopes (i.e., the VLT and the LBT) and on the recent installation of one Vortex at Keck. We will describe the in-lab and on-sky performance of the Vortex, and describe the lessons learned after a few years of operation. Finally, we will discuss the prospects of our vortices for future extremely large telescopes and space missions.
Poly(ADP-ribose) has a branched structure in vivo. (1982)

We have searched for the presence of branching in the chromosomal polymer poly(ADP-ribose) as it occurs in vivo. Treatment of the polymer with phosphodiesterase asnd phosphomonoesterase results in the conversion of internal residues to the nucleoside ribosyladenosine and the conversion of points of branching to diribosyladenosine. We have detected diribosyladenosine in digests of the polymer derived from carcinogen-treated SV40 virus-formed 3T3 cells and in normal rat liver, kidney, and spleen. The frequency of residues involved in branching varied from 0.8 to 1.6 mole % over a 50-fold range of total levels of poly(ADP-ribose). Thus, branching seems to be a general feature of poly(ADP-ribose) as it occurs in vivo.
Balancing Physicochemical Properties of Phenylthiazole Compounds with Antibacterial Potency by Modifying the Lipophilic Side Chain (2019)

Bacterial resistance to antibiotics is presently one of the most pressing healthcare challenges and necessitates the discovery of new antibacterials with unique chemical scaffolds. However, the determination of the optimal balance between structural requirements for pharmacological action and pharmacokinetic properties of novel antibacterial compounds is a significant challenge in drug development. The incorporation of lipophilic moieties within a compound's core structure can enhance biological activity but have a deleterious effect on drug-like properties. In this Article, the lipophilicity of alkynylphenylthiazoles, previously identified as novel antibacterial agents, was reduced by introducing cyclic amines to the lipophilic side chain. In this regard, substitution with methylpiperidine (compounds <b>14</b>-<b>16</b>) and thiomorpholine (compound <b>19</b>) substituents significantly enhanced the aqueous solubility profile of the new compounds more than 150-fold compared to the first-generation lead compound <b>1b</b>. Consequently, the pharmacokinetic profile of compound <b>15</b> was significantly enhanced with a notable improvement in both half-life and the time the compound's plasma concentration remained above its minimum inhibitory concentration (MIC) against methicillin-resistant <i>Staphylococcus aureus</i> (MRSA). In addition, compounds <b>14</b>-<b>16</b> and <b>19</b> were found to exert a bactericidal mode of action against MRSA and were not susceptible to resistance formation after 14 serial passages. Moreover, these compounds (at 2× MIC) were superior to the antibiotic vancomycin in the disruption of the mature MRSA biofilm. The modifications to the alkynylphenylthiazoles reported herein successfully improved the pharmacokinetic profile of this new series while maintaining the compounds' biological activity against MRSA.
Curriculum Innovation For Simulation And Design Of Wireless Communications Systems (2020)

The U. S. telecommunications industry is experiencing an unprecedented demand for trained electrical engineers with the expertise to design and deploy new wireless communications services, encompassing the high growth areas of cellular telephone, personal communications, paging services, and wireless local area networks. The project described in this paper teams electrical engineering faculty from Virginia Tech's Mobile and Portable Radio Research Group (MPRG) and from the University of Missouri-Rolla to develop an innovative communications curriculum which draws from current research on radio signal propagation modeling, computer-aided design and simulation of wireless communication systems, and digital signal processing techniques to improve the performance and spectral efficiency of wireless modems. * Creation of a signal modulator using direct digital synthesis * Design and implementation of a coherent demodulator * Design and creation of a non-coherent demodulator * Design and implementation of a symbol timing recovery system * Design and implementation of a spread spectrum direct sequence synchronizer * Implementation of an adaptive filter for equalization and interference rejection * A voice coder and decoder.
Hollow Fiber Adsorbents for CO2 Removal from Flue Gas (2009)

The nation’s pulverized coal infrastructure is aging, and implementation of current retrofit postcombustion capture methods is extremely expensive. This paper describes a technology based on hollow polymeric fibers with sorbent particles embedded in the porous fiber wall to enable postcombustion CO2 capture via a rapid temperature swing adsorption (RTSA) system. The system takes advantage of the hollow fiber morphology by passing cooling water through the bores during sorption to maximize sorption capacities and steam through the bores during desorption to desorb CO2 efficiently. The thin-walled hollow fibers offer the advantage of rapid heat and mass transport. To avoid mass transfer between the core and the fiber sheath, a dense lumen layer is used on the interior of the fiber wall. This system has advantages over competing technologies. Specifically, the fiber sorbent contactor minimizes flue gas pressure drop across the bed, while maximizing sorption efficiencies via rapid thermal cycles and low regenerative thermal requirements.
Hypoallergenic allergen derivatives of Pru p 3 for immunotherapy of IgE-mediated peach allergy (2013)

The major peach allergen Pru p 3 is responsible for allergies occurring mainly in the Mediterranean area. Hypoallergenic derivatives of Pru p 3 are disclosed which can be used as a vaccine in the treatment of allergic patients.
TinyMBERT: Multi-Stage Distillation Framework for Massive Multi-lingual NER. (2020)

Deep and large pre-trained language models are the state-of-the-art for various natural language processing tasks. However, the huge size of these models could be a deterrent to use them in practice. Some recent and concurrent works use knowledge distillation to compress these huge models into shallow ones. In this work we study knowledge distillation with a focus on multi-lingual Named Entity Recognition (NER). In particular, we study several distillation strategies and propose a stage-wise optimization scheme leveraging teacher internal representations that is agnostic of teacher architecture and show that it outperforms strategies employed in prior works. Additionally, we investigate the role of several factors like the amount of unlabeled data, annotation resources, model architecture and inference latency to name a few. We show that our approach leads to massive compression of MBERT-like teacher models by upto 35x in terms of parameters and 51x in terms of latency for batch inference while retaining 95% of its F1-score for NER over 41 languages.
Low-Cost 3-D Integration of RF and Micro-Cooling Systems (2008)

A heterogeneous 3-D integration scheme of low cost Liquid Crystal Polymer (LCP) and silicon substrates with microfluidic channels and circulating water is demonstrated. Theoretical and experimental data show the applicability of this technique as a means to introduce effective active cooling in high-frequency electronics without adversely impacting their RF performance. An LCP coplanar waveguide fabricated on top of a silicon-etched microchannel with circulating water under a shielding ground plane is the vehicle to demonstrate the integration technology of this paper. The measured RF results are nearly identical with and without water in the microchannel. A water flow rate of ~12 ml/min is measured with a micropump that occupies less than 9.5 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> and consumes less than 1.2 W.
Active noise control: Open problems and challenges (2010)

This paper introduces active noise control (ANC) techniques focusing on challenges in developing practical applications and open problems for research from the signal processing perspective. We propose advanced strategies to further improve ANC performance that include virtual sensing, residual noise masking, and active sound quality control. We also present several challenges for real-world applications such as canceling high-frequency and impulse-like noises, and reducing noises generated from moving sources. Finally, ANC applications in consumer products and healthcare devices are used to demonstrate some potential add-on functions for promoting cost-effective ANC products.
Recall of pre-existing cross-reactive B cell memory following Omicron breakthrough infection (2022)

Abstract Understanding immune responses following SARS-CoV-2 breakthrough infection will facilitate the development of next-generation vaccines. Here, we profiled spike (S)-specific B cell responses following Omicron/BA.1 infection in mRNA-vaccinated donors. The acute antibody response was characterized by high levels of somatic hypermutation (SHM) and a bias toward recognition of ancestral SARS-CoV-2 strains, suggesting the early activation of vaccine-induced memory B cells (MBCs). BA.1 breakthrough infection induced a shift in B cell immunodominance hierarchy from the S2 subunit toward the receptor binding domain (RBD). A large proportion of RBD-directed neutralizing antibodies isolated from BA.1 breakthrough infection donors displayed convergent sequence features and broadly recognized SARS-CoV-2 variants of concern (VOCs). Together, these findings provide fundamental insights into the role of pre-existing immunity in shaping the B cell response to heterologous SARS-CoV-2 variant exposure. One sentence summary BA.1 breakthrough infection activates pre-existing memory B cells with broad activity against SARS-CoV-2 variants.
Extraction error analysis, diagnosis and correction in custom-made high-performance designs (2004)

Test model generation is crucial in the test generation process of a high-performance design. A key process in test model generation extracts a gate-level (logic) model from the transistor level representation of the circuit under test. Due to the limitation of the extraction tools and human interference, logic extraction may introduce errors. Such errors require a resource intensive and time consuming manual process to debug. We present a set of extraction errors typical in an industrial environment. It also proposes an automated solution to extraction error diagnosis and correction. Experiments on circuits with architecture similar to high speed custom-made industrial blocks confirm the fitness of the approach.
Investigation of expression and activity levels of primary rat hepatocyte detoxication genes under various flow rates and cell densities in microfluidic biochips (2013)

We investigated the behavior of primary rat hepatocytes in biochips using a microfluidic platform (the integrated dynamic cell culture microchip). We studied the effects of cell inoculation densities (0.2-0.5 × 10(6) cells/biochip) and perfusion flow rates (10, 25, and 40 µL/min) during 72 h of perfusion. No effects were observed on hepatocyte morphology, but the levels of mRNA and CYP1A2 activity were found to be dependent on the initial cell densities and flow rates. The dataset made it possible to extract a best estimated range of parameters in which the rat hepatocytes appeared the most functional in the biochips. Namely, at 0.25 × 10(6) inoculated cells cultivated at 25 µL/min for 72 h, we demonstrated better induction of the expression of all the genes analyzed in comparison with other cell densities and flow rates. More precisely, when primary rat hepatocytes were cultivated at these conditions, the time-lapse analysis demonstrated an over expression of CYP3A1, CYP2B1, ABCC1b and ABCC2 in the biochips when compared to the postextraction levels. Furthermore, the AHR, CYP1A2, GSTA2, SULT1A1, and UGT1A6 levels remained higher than 50% of the postextraction values whereas values of HNF4α, CEBP, and PXR remained higher than 20% during the duration of the culture process. Nevertheless, an important reduction in mRNA levels was found for the xenosensors CAR and FXR, and the related CYP (CYP2E1, CYP7A1, CYP3A2, and CYP2D2). CYP1A2 functionality was illustrated by 700 ± 100 pmol/h/10(6) cells resorufin production. This study highlighted the functionality in optimized conditions of primary rat hepatocytes in parallelized microfluidic cultures and their potential for drug screening applications.
Microstructure Informed Tractography: Pitfalls and Open Challenges (2016)

One of the major limitations of diffusion MRI tractography is that the fiber tracts recovered by existing algorithms are not truly quantitative. Local techniques for estimating more quantitative features of the tissue microstructure exist, but their combination with tractography has always been considered intractable. Recent advances in local and global modeling made it possible to fill this gap and a number of promising techniques for microstructure informed tractography have been suggested, opening new and exciting perspectives for the quantification of brain connectivity. The ease-of-use of the proposed solutions made it very attractive for researchers to include such advanced methods in their analyses; however, this apparent simplicity should not hide some critical open questions raised by the complexity of these very high-dimensional problems, otherwise some fundamental issues may be pushed into the background. The aim of this article is to raise awareness in the diffusion MRI community, notably researchers working on brain connectivity, about some potential pitfalls and modeling choices that make the interpretation of the outcomes from these novel techniques rather cumbersome. Through a series of experiments on synthetic and real data, we illustrate practical situations where erroneous and severely biased conclusions may be drawn about the connectivity if these pitfalls are overlooked, like the presence of partial/missing/duplicate fibers or the critical importance of the diffusion model adopted. Microstructure informed tractography is a young but very promising technology, and by acknowledging its current limitations as done in this paper, we hope our observations will trigger further research in this direction and new ideas for truly quantitative and biologically meaningful analyses of the connectivity.
Chiral-at-metal iridium complex for efficient enantioselective transfer hydrogenation of ketones (2016)

A bis-cyclometalated iridium(III) complex with metal-centered chirality catalyzes the enantioselective transfer hydrogenation of ketones with high enantioselectivities at low catalyst loadings down to 0.002 mol%. Importantly, the rate of catalysis and enantioselectivity are markedly improved in the presence of a pyrazole co-ligand. The reaction is proposed to proceed via an iridium-hydride intermediate exploiting metal-ligand cooperativity (bifunctional catalysis).
The Association for the Advancement of Artificial Intelligence 2020 Workshop Program (2020)

The Association for the Advancement of Artificial Intelligence 2020 Workshop Program included twenty‐three workshops covering a wide range of topics in artificial intelligence. This report contains the required reports, which were submitted by most, but not all, of the workshop chairs.
Fluorocarbons Dissolved in Supercritical Carbon Dioxide. NMR Evidence for Specific Solute−Solvent Interactions (1998)

The proton and fluorine chemical shifts of n-hexane, perfluoro-n-hexane, and 1,1-dihydroperfluorooctylpropionate dissolved in supercritical carbon dioxide have been studied using high-pressure, high-resolution nuclear magnetic resonance. The CO2 density differentially influences 1H and 19F chemical shifts, which, in turn, suggest specific solute−solvent interactions between CO2 and fluorinated compounds. The density-dependent proton chemical shifts are exclusively governed by changes in the bulk susceptibility of CO2; these shifts exhibit only a slight temperature dependence. By contrast, the 19F signals show that an additional mechanisma van der Waals termcontributes to the magnetic shielding, and this has to be taken into account to explain the experimental shifts as a function of CO2 density and temperature. Furthermore, the 19F NMR data also show a distinct site specificity which is qualitatively explained in terms of the surface accessibility of fluorine atoms in the various CF2(CF3) units in fluorocarbons.
Single elecronics: potentials and issues (2006)

Single electron devices have specific characteristics and properties, especially the existence of periodic Coulomb blockade oscillations, a high charge sensitivity and an operation based on charge quantization. Many investigations have been done to take advantage of them. However, there are several challenging issues to face before any concrete application. The paper presents an overview of the potential of these devices and discusses their merits and drawbacks. Although some niche applications exist, it is concluded that their future should be thought in hybrid association with CMOS
Optimal resource allocation for MIMO ad hoc cognitive radio networks (2008)

Maximization of the weighted sum-rate of secondary users (SUs) possibly equipped with multi-antenna transmitters and receivers is considered in the context of cognitive radio (CR) networks with coexisting primary user(s) (PU). Total interference power received at the primary receiver is constrained to maintain reliable communication for the PU. An interference channel configuration is considered for ad hoc networking, where the receivers treat the interference from undesired transmitters as noise. Without the CR constraint, a distributed algorithm is developed to obtain (at least) a locally optimal solution. With the CR constraint, a semi-distributed algorithm is also introduced along with an alternative centralized algorithm based on geometric programming and network duality.
Combinatorial Optimization of a Molecular Glass Photoresist System for Electron Beam Lithography (2011)

Electron beam lithography is a powerful technique for the production of nanostructures but pattern quality depends on numerous interacting process variables. Orthogonal gradients of resist composition, baking temperatures, and development time as well as dose variations inside writing fields are used to prepare ternary combinatorial libraries for an efficient stepwise optimization of a molecular glass negative tone resist system.