gebhart/patrepeval huggingface dataset:
Human pluripotent stem cell tools for cardiac optogenetics (2014)

It is likely that arrhythmias should be avoided for therapies based on human pluripotent stem cell (hPSC)-derived cardiomyocytes (CM) to be effective. Towards achieving this goal, we introduced light-activated channelrhodopsin-2 (ChR2), a cation channel activated with 480 nm light, into human embryonic stem cells (hESC). By using in vitro approaches, hESC-CM are able to be activated with light. ChR2 is stably transduced into undifferentiated hESC via a lentiviral vector. Via directed differentiation, hESC(ChR2)-CM are produced and subjected to optical stimulation. hESC(ChR2)-CM respond to traditional electrical stimulation and produce similar contractility features as their wild-type counterparts but only hESC(ChR2)-CM can be activated by optical stimulation. Here it is shown that a light sensitive protein can enable in vitro optical control of hESC-CM and that this activation occurs optimally above specific light stimulation intensity and pulse width thresholds. For future therapy, in vivo optical stimulation along with optical inhibition could allow for acute synchronization of implanted hPSC-CM with patient cardiac rhythms.
ChemInform Abstract: Bifunctional Building Blocks in the Ugi‐Azide Condensation Reaction: A General Strategy Toward Exploration of New Molecular Diversity. (2013)

Abstract Ugi‐azide reaction of tethered aldo/keto—acids/esters followed by a ring closing step opens access to a variety of complex lactam—tetrazoles.
Antibody Attributes that Predict the Neutralization and Effector Function of Polyclonal Responses to SARS-CoV-2 (2021)

While antibodies provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. In this study, we employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These predictive models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.
Improving Adversarial Robustness via Promoting Ensemble Diversity (2019)

Though deep neural networks have achieved significant progress on various tasks, often enhanced by model ensemble, existing high-performance models can be vulnerable to adversarial attacks. Many efforts have been devoted to enhancing the robustness of individual networks and then constructing a straightforward ensemble, e.g., by directly averaging the outputs, which ignores the interaction among networks. This paper presents a new method that explores the interaction among individual networks to improve robustness for ensemble models. Technically, we define a new notion of ensemble diversity in the adversarial setting as the diversity among non-maximal predictions of individual members, and present an adaptive diversity promoting (ADP) regularizer to encourage the diversity, which leads to globally better robustness for the ensemble by making adversarial examples difficult to transfer among individual members. Our method is computationally efficient and compatible with the defense methods acting on individual networks. Empirical results on various datasets verify that our method can improve adversarial robustness while maintaining state-of-the-art accuracy on normal examples.
Recognizing Arabic speakers with English phones. (2008)

We investigate the question of whether phone recognition models trained on large English databases can be used for speaker recognition in another language. Such a crosslanguage use of recognition models is an attractive option when a speaker recognition system is to be ported to a new language without the necessary data resources, while retaining some of the advantages of phone modeling and ASR-based feature extraction. We compare the performance of such systems to a baseline cepstral GMM system (which is inherently language independent), and to a phone-recognition-based system trained exclusively on Arabic data. Our results indicate that cross-language models are highly competitive, and, at least in our case, have a performance advantage over within-language training and the language-independent baseline. We also examine the effect of coverage of colloquial Arabic dialects in the training data. 1.
Multi-Drug Cocktail Therapy Improves Survival and Neurological Function after Asphyxial Cardiac Arrest in Rodents (2023)

Our findings demonstrate that, with its ability to target multiple damaging pathways, a multi-drug therapeutic cocktail offers promise both as a conceptual advance and as a specific multi-drug formulation capable of combatting neuronal degeneration and death following cardiac arrest. Clinical implementation of this therapy may improve neurologically favorable survival rates and neurological deficits in patients suffering from cardiac arrest.
Common variable immunodeficiency: long term clinical consequencies of splenectomy in a case of late-onset hypogammaglobulinaemia. (1978)

The following conversation took place in New York on May 19th 2018 with loose ends recently tied. The original transcript was much longer. We nerded over mathematics, technology and gay politics, scrambling about on fun tangents. One could define these tangents as frivolous and furthermore position &amp;#8220;frivolous&amp;#8221; as having a particular anglo gay tone. This tone carries into the varying roles Charles takes as an artist. One role he recently took was creating the exhibition design for the Robert Rauschenberg retrospective Among Friends, at MoMA New York. His practice refuses a stable single categorization drawing on community and collaboration while ...
Exploring demand flexibility in heterogeneous aggregators (2014)

With the proposed penetration of electric vehicles and advanced metering technology, the demand side is foreseen to play a major role in flexible energy consumption scheduling. On the other hand, the past several years have witnessed utility companies' growing interests to integrate more renewable energy resources. These renewable resources, for example, wind or solar, due to their intermittent nature, brought great uncertainty to the power grid system. In this article, we propose a mechanism that attempts to mitigate the grid operational uncertainty induced by renewable energies by properly exploiting demand flexibility with the help of advanced smart-metering technology. To address the challenge, we develop a novel locational marginal price (LMP)-based pricing scheme that involves active demand-side participation by casting the network objective as a two-stage Stackelberg game between the local grid operator and several aggregators. In contrast to the conventional notion that generation follows load, our game formulation provides more flexibility for the operators and tries to provide adequate incentives for the loads to follow the (stochastic renewable) generation. We use the solution concept of subgame perfect equilibrium to analyze the resulting game. Subsequently, we discuss the optimal real-time conventional capacity planning for the local grid operator to achieve the minimal mismatch between supply and demand with the wind power integration. Finally, we assess our proposed scheme with field data. The simulation results show that our proposed scheme works reasonably well in the long term, even with simple heuristics.
Ultracompact bottom-up photonic crystal lasers on silicon-on-insulator (2017)

Compact on-chip light sources lie at the heart of practical nanophotonic devices since chip-scale photonic circuits have been regarded as the next generation computing tools. In this work, we demonstrate room-temperature lasing in 7 × 7 InGaAs/InGaP core-shell nanopillar array photonic crystals with an ultracompact footprint of 2300 × 2300 nm<sup>2</sup>, which are monolithically grown on silicon-on-insulator substrates. A strong lateral confinement is achieved by a photonic band-edge mode, which is leading to a strong light-matter interaction in the 7 × 7 nanopillar array, and by choosing an appropriate thickness of a silicon-on-insulator layer the band-edge mode can be trapped vertically in the nanopillars. The nanopillar array band-edge lasers exhibit single-mode operation, where the mode frequency is sensitive to the diameter of the nanopillars. Our demonstration represents an important first step towards developing practical and monolithic III-V photonic components on a silicon platform.
Computational modeling of continuum scale constitutive equations to improve biomass feedstock material handling and conveying systems (2019)

<b><sc>Abstract.</sc></b> Existing design practices for common feedstock handling equipment such as hoppers and screw feeders have not been successful in many situations. The lack of an appropriate toolset to characterize and model biomass flow behavior is deemed the root cause of plugging, stalls, and flow-related issues in biomass handling systems design and operations. New standardized characterization protocols in conjunction with appropriate constitutive models will lead to successful biomass handling system design and operations. This study investigates constitutive models for bulk solid flow based on the first principles to overcome issues in biomass handling. The focus is on two major issues in biomass handling, i.e., initiating and sustaining of flow in the hopper that is widely used in biomass conveying operation. Accordingly, this article focuses on analytical models of biomass hopper flow. Mohr-Coulomb, Drucker-Prager, and modified Cam-clay models are investigated as constitutive bulk solid flow models. Parameters of those models are determined using a set of triaxial tests. Triaxial tests are conducted using the cubical triaxial tester (CTT) in the Food and Biomaterials Lab of the Pennsylvania State University. Milled 1mm corn stover and 2mm wood chip biomass materials having different flow characteristics are examined, and their respective flow behavior out of a hopper are simulated using the Finite Element method implementing identified constitutive models and determined fundamental mechanical properties. It is found that, with the same hopper geometry, ground corn stover 1mm tends to exhibit funnel flow whereas ground Douglas fir 2 mm tends to exhibit mass flow. These simulation results are validated with hopper flow experiments. This study demonstrates how biomass flow problems can be predicted and mitigated by numerically modeled fundamental constitutive equations.
Interaction Mechanism between Hydrophobic and Hydrophilic Surfaces: Using Polystyrene and Mica as a Model System (2013)

The interactions between hydrophobic and hydrophilic molecules, particles, or surfaces occur in many biological phenomena and industrial processes. In this work, polystyrene (PS) and mica were chosen as a model system to investigate the interaction mechanism between hydrophilic and hydrophobic surfaces. Using a surface forces apparatus (SFA) coupled with a top-view optical microscope, interaction forces between PS and mica surfaces were directly probed in five different electrolyte solutions (i.e., NaCl, CaCl2, NaOH, HCl, and CH3COOH) of various concentrations. Long-range repulsion was observed in low electrolyte concentration (e.g., 0.001 M) which was mainly due to the presence of microscopic and submicroscopic bubbles on PS surface. A modified Derjaguin-Landau-Verwey-Overbeek (DLVO) theory well fits the interaction forces by taking into account the effect of bubbles on PS surface. The range of the repulsion was dramatically reduced in 1.0 M solutions of NaCl, CaCl2, and NaOH but did not significantly change in 1.0 M HCl and CH3COOH, which was due to ion specificity effect on the formation and stability of bubbles on PS surface. The range of repulsion was also significantly reduced to <20 nm in degassed electrolyte solutions. UV-ozone treatment changed the hydrophobic attraction of the untreated PS-PS system to pure repulsion between untreated PS and treated PS, demonstrating the important role of surface hydrophobicity on the formation and stability of bubbles on substrates. Our results indicate that DLVO forces dominate the interaction between hydrophilic surface (i.e., mica) and hydrophobic polymer (i.e., PS), while the types of electrolytes (ion specificity), electrolyte concentration, degassing, and surface hydrophobicity can significantly affect the formation and stability of bubbles on the interacting surfaces, thus affecting the range and magnitude of the interaction forces.
Search for top-squark pair production in final states with one lepton, jets, and missing transverse momentum using 36 fb−1 of $$ \sqrt{s}=13 $$ TeV pp collision data with the ATLAS detector (2018)

A bstract The results of a search for the direct pair production of top squarks, the supersymmetric partner of the top quark, in final states with one isolated electron or muon, several energetic jets, and missing transverse momentum are reported. The analysis also targets spin-0 mediator models, where the mediator decays into a pair of dark-matter particles and is produced in association with a pair of top quarks. The search uses data from proton-proton collisions delivered by the Large Hadron Collider in 2015 and 2016 at a centre-of-mass energy of $$ \sqrt{s}=13 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> </mml:math> TeV and recorded by the ATLAS detector, corresponding to an integrated luminosity of 36 fb −1 . A wide range of signal scenarios with different mass-splittings between the top squark, the lightest neutralino and possible intermediate supersymmetric particles are considered, including cases where the W bosons or the top quarks produced in the decay chain are off-shell. No significant excess over the Standard Model prediction is observed. The null results are used to set exclusion limits at 95% confidence level in several supersymmetry benchmark models. For pair-produced top-squarks decaying into top quarks, top-squark masses up to 940 GeV are excluded. Stringent exclusion limits are also derived for all other considered top-squark decay scenarios. For the spin-0 mediator models, upper limits are set on the visible cross-section.
Cancellation of neutral current harmonics by using a four-branch star hybrid filter (2008)

This paper presents a new technique for filtering current harmonics in three-phase four-wire networks based on the usage of a four-branch star (FBS) filter topology. Based on single-phase inductors and capacitors, the specific layout of the FBS filter topology allows achieving a power filter with two independent and simultaneous resonance frequencies, i.e., one for positive-/negative-sequence and another one for zero-sequence components. The FBS filter topology can work either as a passive filter, when only passive components are employed, or as a hybrid filter, when its performance is improved by integrating a power converter into its structure. This paper analyzes the FBS topology and presents fundamental concepts regarding the control of a generic FBS hybrid power filter. A neutral current hybrid power filter and var compensator is presented as an illustrative example applying the FBS filtering topology to a three-phase four-wire system. An extensive evaluation using simulation and experimental results are conducted in this work to validate the good performance of the proposed solution for canceling current harmonics flowing through the neutral conductor.
基礎・ソート・データ構造・数学 (2012)

１ 基礎（計算におけるアルゴリズムの役割；さあ、始めよう；関数の増加；分割統治；確率的解析と乱択アルゴリズム） ２ ソートと順序統計量（ヒープソート；クイックソート；線形時間ソート；中央値と順序統計量） ３ データ構造（基本データ構造；ハッシュ表；２分探索木；２色木；データ構造の補強） 付録 数学的基礎（和；集合など；数え上げと確立；行列）
Supplementary Figures 1-6 from Multiple Injections of Electroporated Autologous T Cells Expressing a Chimeric Antigen Receptor Mediate Regression of Human Disseminated Tumor (2023)

Supplementary Figures 1-6 from Multiple Injections of Electroporated Autologous T Cells Expressing a Chimeric Antigen Receptor Mediate Regression of Human Disseminated Tumor
S-nitrosylation of Cdk5 (2012)

Aberrant activation of Cdk5 has been implicated in the process of neurodegenerative diseases such as Alzheimer's disease (AD). We recently reported that S-nitrosylation of Cdk5 (forming SNO-Cdk5) at specific cysteine residues results in excessive activation of Cdk5, contributing to mitochondrial dysfunction, synaptic damage, and neuronal cell death in models of AD. Furthermore, SNO-Cdk5 acts as a nascent S-nitrosylase, transnitrosylating the mitochondrial fission protein Drp1 and enhancing excessive mitochondrial fission in dendritic spines. However, a molecular mechanism that leads to the formation of SNO-Cdk5 in neuronal cells remained obscure. Here, we demonstrate that neuronal nitric oxide synthase (NOS1) interacts with Cdk5 and that the close proximity of the two proteins facilitates the formation of SNO-Cdk5. Interestingly, as a negative feedback mechanism, Cdk5 phosphorylates and suppresses NOS1 activity. Thus, together with our previous report, these findings delineate an S-nitrosylation pathway wherein Cdk5/NOS1 interaction enhances SNO-Cdk5 formation, mediating mitochondrial dysfunction and synaptic loss during the etiology of AD.
An investigation into the extent of occurrence of novel pathogenic Brachyspira species, including newly recognised agents of swine dysentery, in Australian pig herds. Report prepared for the Co-operative Research Centre for High Integrity Australian Pork (2015)

Swine dysentery (SD) is a bacterial disease of grower and finisher pigs, causing colitis and bloody mucoid diarrhoea. In infected herds it can have a major economic impact through reduced growth rates, poor food conversion, mortalities and costs of control.&#13;\n&#13;\nThe classical agent of SD is an anaerobic spirochaete called Brachyspira hyodysenteriae, although in the last decade two other species named “Brachyspira hampsonii” and “Brachyspira suanatina” have been identified as also causing SD in North America and Europe. As these species may have a different epidemiology to B. hyodysenteriae, the main aim of the current study was to determine whether they occurred in Australia. A subsidiary linked aim was to provide updated information on the occurrence, distribution and characteristics of B. hyodysenteriae strains that are currently present in Australia.
New garnet structure phosphors, Lu3−xYxMgAl3SiO12:Ce3+ (x = 0–3), developed by solid solution design (2016)

(Lu,Y)MgAl<sub>3</sub>SiO<sub>12</sub>:Ce<sup>3+</sup> yellow light emitting phosphors are developed by solid solution design and their crystal structures and photoluminescence properties are identified.
Update of the development progress of the high power LPP-EUV light source using a magnetic field (2019)

Gigaphoton Inc. has been developing a CO<sub>2</sub>-Sn-LPP (LPP: Laser Produced Plasma) extreme ultraviolet (EUV) light source system for high-volume manufacturing (HVM) semiconductor lithography. Key components of the source include a high-power CO<sub>2</sub> laser with 15 ns pulse duration and 100 kHz repetition frequency, a solid-state pre-pulse laser with 10 ps pulse duration and a magnetic field debris mitigation system. To achieve 330 W with long collector mirror lifetime and stable output, we improved the performance of key system components; especially, the laser beam quality at 26 kW CO<sub>2</sub> laser output power by upgrading the CO<sub>2</sub> laser beam transfer system, the conversion efficiency (CE) by the optimization of plasma-related parameters to now 6 %, the dose stability and suppression of small Tin (Sn) debris by upgrading the shooting control system, the collector mirror degradation rate by the optimization of H<sub>2</sub> flow condition and changes in the EUV chamber structure. This paper presents the key technology update of our EUV light source.
A compiler for universal photonic quantum computers (2022)

Photons are a natural resource in quantum information, and the last decade showed significant progress in high-quality single photon generation and detection. Furthermore, photonic qubits are easy to manipulate and do not require particularly strongly sealed environments, making them an appealing platform for quantum computing. With the one-way model, the vision of a universal and large-scale quantum computer based on photonics becomes feasible. In one-way computing, the input state is not an initial product state, but a so-called cluster state. A series of measurements on the cluster state's individual qubits and their temporal order, together with a feed-forward procedure, determine the quantum circuit to be executed. We propose a pipeline to convert a QASM circuit into a graph representation named measurement-graph (m-graph), that can be directly translated to hardware instructions on an optical one-way quantum computer. In addition, we optimize the graph using ZX-Calculus before evaluating the execution on an experimental discrete variable photonic platform.
Immersion defectivity study with volume production immersion lithography tool for 45 nm node and below (2008)

Volume production of 45nm node devices utilizing Nikon's S610C immersion lithography tool has started. Important to the success in achieving high-yields in volume production with immersion lithography has been defectivity reduction. In this study we evaluate several methods of defectivity reduction. The tools used in our defectivity analysis included a dedicated immersion cluster tools consisting of a Nikon S610C, a volume production immersion exposure tool with NA of 1.3, and a resist coater-developer LITHIUS i+ from TEL. In our initial procedure we evaluated defectivity behavior by comparing on a topcoat-less resist process to a conventional topcoat process. Because of its simplicity the topcoatless resist shows lower defect levels than the topcoat process. In a second study we evaluated the defect reduction by introducing the TEL bevel rinse and pre-immersion bevel cleaning techniques. This technique was shown to successfully reduce the defect levels by reducing the particles at the wafer bevel region. For the third defect reduction method, two types of tool cleaning processes are shown. Finally, we discuss the overall defectivity behavior at the 45nm node. To facilitate an understanding of the root cause of the defects, defect source analysis (DSA) was applied to separate the defects into three classes according to the source of defects. DSA analysis revealed that more than 99% of defects relate to material and process, and less than 1% of the defects relate to the exposure tool. Material and process optimization by collaborative work between exposure tool vendors, track vendors and material vendors is a key for success of 45nm node device manufacturing.