gebhart/patrepeval huggingface dataset:
Cross-Polarization-Extinction Enhancement and Spin-Orbit Coupling of Light for Quantum-Dot Cavity Quantum Electrodynamics Spectroscopy (2023)

Resonant laser spectroscopy is essential for the characterization, operation, and manipulation of single-quantum systems such as semiconductor quantum dots. The separation of the weak resonance fluorescence from the excitation laser is key for high-quality single- and entangled-photon sources. This is often achieved by cross-polarization laser extinction, which is limited by the quality of the optical elements. Recently, it was discovered that Fresnel-reflection birefringence in combination with single-mode filtering counteracting spin-orbit-coupling effects enables a three-order-of-magnitude improvement of polarization extinction [Benelajla et al., Phys. Rev. X 11, 021007 (2021)]. Here, we demonstrate this method for cross-polarization-extinction enhancement in cryogenic confocal microscopy of a resonantly excited semiconductor quantum dot in a birefringent optical microcavity, and observe a $10\ifmmode\times\else\texttimes\fi{}$ improvement of the single-photon contrast.
Plasma characteristics of a high power helicon discharge (2006)

A new high power helicon (HPH) plasma system has been designed to provide input powers of several tens of kilowatts to produce a large area (0.5 m2) of uniform high-density, of at least 5 × 1017 m−3, plasma downstream from the helicon coil. Axial and radial plasma characteristics show that the plasma is to a lesser extent created in and near the helicon coil and then is accelerated into the axial and equatorial regions. The bulk acceleration of the plasma is believed to be due to a coupling of the bulk of the electrons to the helicon field, which in turn transfers energy to the ions via ambipolar diffusion. The plasma beta is near unity a few centimetres away from the HPH system and Bdot measurements show ΔB perturbations in the order of the vacuum magnetic field magnitude. In the equatorial region, a magnetic separatrix is seen to develop roughly at the mid-point between the helicon and chamber wall. The magnetic perturbation develops on the time scale of the plasma flow speed and upon the plasma reaching the chamber wall decays to the vacuum magnetic field configuration within 200 µs.
Picomolar Inhibitors of HIV Reverse Transcriptase Featuring Bicyclic Replacement of a Cyanovinylphenyl Group (2013)

Members of the catechol diether class are highly potent non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). The most active compounds yield EC50 values below 0.5 nM in assays using human T-cells infected by wild-type HIV-1. However, these compounds such as rilpivirine, the most recently FDA-approved NNRTI, bear a cyanovinylphenyl (CVP) group. This is an uncommon substructure in drugs that gives reactivity concerns. In the present work, computer simulations were used to design bicyclic replacements for the CVP group. The predicted viability of a 2-cyanoindolizinyl alternative was confirmed experimentally and provided compounds with 0.4 nM activity against the wild-type virus. The compounds also performed well with EC50 values of 10 nM against the challenging HIV-1 variant that contains the Lys103Asn/Tyr181Cys double mutation in the RT enzyme. Indolyl and benzofuranyl analogues were also investigated; the most potent compounds in these cases have EC50 values toward wild-type HIV-1 near 10 nM and high-nanomolar activities toward the double-variant. The structural expectations from the modeling were much enhanced by obtaining an X-ray crystal structure at 2.88 Å resolution for the complex of the parent 2-cyanoindolizine 10b and HIV-1 RT. The aqueous solubilities of the most potent indolizine analogues were also measured to be ~40 μg/mL, which is similar to that for the approved drug efavirenz and ~1000-fold greater than for rilpivirine.
Electron Transfer in a Hg‐SAM//SAM‐Hg Junction Mediated by Redox Centers (2004)

Zwei selbstorganisierte redoxaktive Monoschichten aus [Ru(NH3)5(NC5H4-4-CH2NHCO(CH2)10SH](PF6)2 sind die Grundlage eines Metall-Molekül-Metall-Kontakts, dessen Elektronentransporteigenschaften beschrieben werden (siehe Bild). Der Kontakt wird leitend, wenn die Elektrodenpotentiale an das formale Potential der Redoxzentren angepasst werden, und zeigt Dioden- und Transistor-artige Charakteristika ähnlich denen von Festkörpersystemen.
Atomic Force Microscopy to Characterize Antimicrobial Peptide-Induced Defects in Model Supported Lipid Bilayers (2021)

Antimicrobial peptides (AMPs) interact with bacterial cell membranes through a variety of mechanisms, causing changes extending from nanopore formation to microscale membrane lysis, eventually leading to cell death. Several AMPs also disrupt mammalian cell membranes, despite their significantly different lipid composition and such collateral hemolytic damage hinders the potential therapeutic applicability of the AMP as an anti-microbial. Elucidating the mechanisms underlying the AMP-membrane interactions is challenging due to the variations in the chemical and structural features of the AMPs, the complex compositional variations of cell membranes and the inadequacy of any single experimental technique to comprehensively probe them. (1) Background: Atomic Force Microscopy (AFM) imaging can be used in combination with other techniques to help understand how AMPs alter the orientation and structural organization of the molecules within cell membranes exposed to AMPs. The structure, size, net charge, hydrophobicity and amphipathicity of the AMPs affect how they interact with cell membranes of differing lipid compositions. (2) Methods: Our study examined two different types of AMPs, a 20-amino acid, neutral, α-helical (amphipathic) peptide, alamethicin, and a 13-amino acid, non-α-helical cationic peptide, indolicidin (which intramolecularly folds, creating a hydrophobic core), for their interactions with supported lipid bilayers (SLBs). Robust SLB model membranes on quartz supports, incorporating predominantly anionic lipids representative of bacterial cells, are currently not available and remain to be developed. Therefore, the SLBs of zwitterionic egg phosphatidylcholine (PC), which represents the composition of a mammalian cell membrane, was utilized as the model membrane. This also allows for a comparison with the results obtained from the Quartz Crystal Microbalance with Dissipation (QCM-D) experiments conducted for these peptides interacting with the same zwitterionic SLBs. Further, in the case of alamethicin, because of its neutrality, the lipid charge may be less relevant for understanding its membrane interactions. (3) Results: Using AFM imaging and roughness analysis, we found that alamethicin produced large, unstable defects in the membrane at 5 µM concentrations, and completely removed the bilayer at 10 µM. Indolicidin produced smaller holes in the bilayer at 5 and 10 µM, although they were able to fill in over time. The root-mean-square (RMS) roughness values for the images showed that the surface roughness caused by visible defects peaked after peptide injection and gradually decreased over time. (4) Conclusions: AFM is useful for helping to uncover the dynamic interactions between different AMPs and cell membranes, which can facilitate the selection and design of more efficient AMPs for use in therapeutics and antimicrobial applications.
A 65nm CMOS, ring-oscillator based, high accuracy Digital Phase Lock Loop for USB2.0 (2009)

A high accuracy, ring-oscillator based Digital Phase Lock Loop (DPLL), suitable for USB2.0 application, is presented here. The Digitally Controlled Oscillator (DCO) of the DPLL consists of a current mode Digital to Analog Converter (DAC) combined with a Current Controlled Oscillator (ICO). Sigma-Delta (SigmaDelta) dithering is used on the DAC for improved frequency accuracy. To reduce noise due to SigmaDelta dithering and to allow for passive filtering of this noise, the SigmaDelta section of the DAC is limited to a small range. This range, however, is not sufficient to account for frequency drifts due to temperature: a novel temperature compensation scheme is used for this purpose. The DPLL is built in 65 nm technology, and provides a 480 MHz output, with a phase noise of -103.5 dBc/Hz at 1 MHz offset, and a frequency accuracy of +/-100 ppm. It supports a list of input frequencies: 13 MHz, 12 MHz, 19.2 MHz, 24 MHz and 48 MHz, occupies a die area of 0.21 sq mm, and does not require external components.
농약·환경 ( PESTICIDE·ENVIRONMENT CHEMISTRY ) : 새로운 2-이미노티아졸린 유도체의 합성과 항균 활성 (1) (1997)

This research aims at developing a new pesticide by means of synthesizing new 2-iminothiazoline derivatives and testing their bilolgical activity. In an effort to prepare 2-iminothiazolines, primary amines were treated to have reaction with isothiocyanate, followed by a treatment of a-halo ketone derivatives. Their antifungal activity was tested against six different plant diseases. A compound that has a phenylimino group at C-2, methyl at C-3, phenylcarbamoylmethyl at C-4, and hydrogen at C-5 on the thiazoline skeleton was found to be most active.
Microrelay packaging technology using flip-chip assembly (2002)

Using flip-chip assembly, micromachined connectors can be used to create a high density, actuatable electronics packaging technology. Internal residual stress is used to press bimorph beam connectors upwards against a device chip. Deformation can be increased by introducing stress through a heat treating process. The effects of heat treatment are more prominent on larger devices and are long lasting in nature. The connectors' actuation behavior is described, including appropriate mathematical models. The electrostatically actuated beams will disconnect when driven by a 53 volt signal and will reconnect when voltage falls below 43 volts. When switching signals, reconnection occurs in as little as 5.8 /spl mu/s, disconnection occurs in as little as 4.0 /spl mu/s. A microconnector's current carrying capability can be as high as 285.3 mA and its maximum power dissipation as high as 1.47 W.
Value of Information in Feedback Control (2018)

In this article, we investigate the impact of information on networked control systems, and illustrate how to quantify a fundamental property of stochastic processes that can enrich our understanding about such systems. To that end, we develop a theoretical framework for the joint design of an event trigger and a controller in optimal event-triggered control. We cover two distinct information patterns: perfect information and imperfect information. In both cases, observations are available at the event trigger instantly, but are transmitted to the controller sporadically with one-step delay. For each information pattern, we characterize the optimal triggering policy and optimal control policy such that the corresponding policy profile represents a Nash equilibrium. Accordingly, we quantify the value of information $\operatorname{VoI}_k$ as the variation in the cost-to-go of the system given an observation at time $k$. Finally, we provide an algorithm for approximation of the value of information, and synthesize a closed-form suboptimal triggering policy with a performance guarantee that can readily be implemented.
Overexpression of mitochondrial manganese superoxide dismutase promotes the survival of tumor cells exposed to interleukin‐1, tumor necrosis factor, selected anticancer drugs, and ionizing radiation (1993)

Interleukin-1 (IL-1) and tumor necrosis factor (TNF) selectively induce mitochondrial manganese superoxide dismutase (MnSOD) production in various cell types. We have evaluated the capacity of tumor cells that overexpress MnSOD to recover from the cytostatic and cytotoxic effects of cytokines (IL-1 and TNF), chemotherapeutic agents, and ionizing irradiation. Clones of human melanoma cell line, A375, which overexpressed MnSOD after sense MnSOD cDNA transfection, showed increased recovery from treatment with cytostatic and cytotoxic doses of IL-1 alpha and TNF alpha, whereas clones of A375 cells that were transfected with anti-sense MnSOD cDNA recovered less well than normal cells from IL-1 alpha and TNF alpha. In addition, Chinese hamster ovary (CHO) cells transfected with sense MnSOD cDNA showed increased survival after treatment with doxorubicin, mitomycin C, and gamma (gamma) radiation in vitro. It is hypothesized that mitochondrial MnSOD, by scavenging oxygen radicals induced by cytokines, some cytotoxic drugs, and ionizing radiation, is protective and promotes the survival of cells from the lethal effects of these treatments.
Polymer Informatics: Opportunities and Challenges (2017)

We are entering an era where large volumes of scientific data, coupled with algorithmic and computational advances, can reduce both the time and cost of developing new materials. This emerging field known as materials informatics has gained acceptance for a number of classes of materials, including metals and oxides. In the particular case of polymer science, however, there are important challenges that must be addressed before one can start to deploy advanced machine learning approaches for designing new materials. These challenges are primarily related to the manner in which polymeric systems and their properties are reported. In this viewpoint, we discuss the opportunities and challenges for making materials informatics as applied to polymers, or equivalently polymer informatics, a reality.
Abstract 120: Methamphetamine-induced Cardiomyopathy Associated With Mitochondrial Dysfunction, Cardiac Fibrosis and Hypertrophy (2019)

Introduction: Methamphetamine (METH) is one of the most commonly abused illicit drugs in the United States, exerting a range of adverse effects upon multiple organ systems. Cardiovascular complications are among the major causes of death in METH users. METH-induced cardiomyopathy is a poorly characterized disease entity as METH-induced molecular perturbations, and histopathological changes in the heart remain under-explored. Objectives: We studied histopathology in the hearts of human METH users. We also observed the histological alteration and changes in mitochondrial function in mice that received ‘binge’ administration of METH. Methods and Results: We obtained 32 autopsy heart samples from humans with positive toxicology for chronic METH use and performed Sirius Red and Masson’s Trichrome (MT) staining on left ventricular (LV) sections. Notably, chronic METH user hearts showed intense perivascular and interstitial fibrosis in LVs. ‘Binge’ METH administration in mice for 4 weeks showed an increase in heart weight-to-tibia length and increase in myocyte cross-sectional area in WGA stained LVs compared to saline-treated mice. Sirius red and MT staining also showed an increase in perivascular and interstitial fibrosis in METH mice heart. Isolated mitochondria from METH-treated mice heart showed suppressed mitochondrial bioenergetics measured by Seahorse Analyzer. Immunoblotting in heart lysates and mitochondrial fractions showed altered mitochondrial dynamics regulatory proteins expression in METH mice compared to control saline group. METH-treated cultured neonatal rat ventricular cardiomyocytes also showed suppression of mitochondrial respiration and mitochondrial network disorganization indicating a direct effect of METH on cardiomyocytes. Conclusions: We report that maladaptive cardiac fibrotic remodeling is typical in a human and pre-clinical mouse model of METH abuse. ‘Binge’ METH exposure in mice induces cardiac hypertrophy, cardiac fibrosis, and suppression of mitochondrial respiration. Thus, chronic METH use induces maladaptive cardiac remodeling associated with mitochondrial dysfunction.
Outlier Detection with Autoencoder Ensembles (2017)

In this paper, we introduce autoencoder ensembles for unsupervised outlier detection. One problem with neural networks is that they are sensitive to noise and often require large data sets to work robustly, while increasing data size makes them slow. As a result, there are only a few existing works in the literature on the use of neural networks in outlier detection. This paper shows that neural networks can be a very competitive technique to other existing methods. The basic idea is to randomly vary on the connectivity architecture of the autoencoder to obtain significantly better performance. Furthermore, we combine this technique with an adaptive sampling method to make our approach more efficient and effective. Experimental results comparing the proposed approach with state-of-the-art detectors are presented on several benchmark data sets showing the accuracy of our approach.
Acylnitrene Route to Vicinal Amino Alcohols. Application to the Synthesis of (−)-Bestatin and Analogues (1999)

Bestatin, valinoctin A, and microginin are naturally occurring small peptides containing a nonproteinogenic alpha-hydroxy-beta-amino acid at the N-terminus of the peptide chain. We report here our development of a general method for the synthesis of alpha-hydroxy-beta-amino acids and exemplify this with a synthesis of (-)-bestatin and analogues. Our synthesis utilizes an intramolecular acylnitrene-mediated aziridination to generate a key bicyclic aziridine in excellent yield and stereoselectivity. This bicyclic aziridine can be opened with a number of organometallic reagents to provide a series of substituted oxazolidinones. The oxazolidinones are readily converted to bestatin and a series of bestatin analogues. As part of this approach, we have developed a new method for the synthesis of azidoformates. We have also demonstrated that oxazolidinones can be selectively hydrolyzed in the presence of peptide bonds. This acylnitrene route to bestatin should prove useful for the synthesis of a variety of analogues of bestatin as well as other alpha-hydroxy-beta-amino acids and their corresponding peptides.
Fabrication of Foldable Metal Interconnections by Hybridizing with Amorphous Carbon Ultrathin Anisotropic Conductive Film (2019)

With the advent of foldable electronics, it is necessary to develop a technology ensuring foldability when the circuit lines are placed on the topmost substrate rather than in the neutral plane used in the present industry. Considering the potential technological impacts, conversion of the conventional printed circuit boards to foldable ones is most desirable to achieve the topmost circuitry. This study realizes this unconventional conversion concept by coating an ultrathin anisotropic conductive film (UACF) on a printed metal circuit board. This study presents rapid large-area synthesis of hydrogenated amorphous carbon (a-C:H) thin films and their use as the UACF. Since the synthesized a-C:H thin film has electrical transparency, the metal/a-C:H hybrid board reflects the complexity of the underlying metal circuit board. The a-C:H thin film electrically connects the cracked area of the metal line; thus, the hybrid circuit board is foldable without resistance change during repeated folding cycles. The metal/UACF hybrid circuit board can be applied to the fabrication of various foldable electronic devices.
Tapered optical fiber tip probes based on focused ion beam-milled Fabry-Perot microcavities (2016)

Focused ion beam technology is combined with dynamic chemical etching to create microcavities in tapered optical fiber tips, resulting in fiber probes for temperature and refractive index sensing. Dynamic chemical etching uses hydrofluoric acid and a syringe pump to etch standard optical fibers into cone structures called tapered fiber tips where the length, shape, and cone angle can be precisely controlled. On these tips, focused ion beam is used to mill several different types of Fabry-Perot microcavities. Two main cavity types are initially compared and then combined to form a third, complex cavity structure. In the first case, a gap is milled on the tapered fiber tip which allows the external medium to penetrate the light guiding region and thus presents sensitivity to external refractive index changes. In the second, two slots that function as mirrors are milled on the tip creating a silica cavity that is only sensitive to temperature changes. Finally, both cavities are combined on a single tapered fiber tip, resulting in a multi-cavity structure capable of discriminating between temperature and refractive index variations. This dual characterization is performed with the aid of a fast Fourier transform method to separate the contributions of each cavity and thus of temperature and refractive index. Ultimately, a tapered optical fiber tip probe with sub-standard dimensions containing a multi-cavity structure is projected, fabricated, characterized and applied as a sensing element for simultaneous temperature and refractive index discrimination.
Supplementary Figure Legends and Supplementary Table 1 from Preclinical Pharmacology, Antitumor Activity, and Development of Pharmacodynamic Markers for the Novel, Potent AKT Inhibitor CCT128930 (2023)

Supplementary Figure Legends and Supplementary Table 1 from Preclinical Pharmacology, Antitumor Activity, and Development of Pharmacodynamic Markers for the Novel, Potent AKT Inhibitor CCT128930
Modeling of Nucleic Acid Complexes with Cationic Ligands: A Specialized Molecular Mechanics Force Field and Its Application (1991)

A potential energy force field designed for modeling nucleic acids and particularly their complexes with cationic ligands is presented. The force field is a modified version of that developed by Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A.,J. Comp. Chem. 7,230-252 (1986) and is based upon the use of a distance dependent dielectric constant, epsilon = 4rij, and partially neutralized phosphates to represent solvent and counterion. Changes from the Weiner et al. force field include additional atom types and modifications to van der Waals, electrostatic, hydrogen bonding and torsional parameters. Molecular modeling test cases of the force field are presented for a number of simple small molecules, as well as uracil and benzene dimerization, thymine-adenine and cytosine-guanine base pair formation, and adenosine/deoxyadenosine pseudorotation. Several DNA and RNA oligomers and DNA/RNA intercalation complexes with ethidium are also modeled with the force field. In all cases, the modeling results compare favorably with available experimental results. Additionally, conformational trends observed experimentally for nucleic acids by NMR and X-ray crystallographic techniques are reproduced. The modeling results for ethidium intercalation indicate a complex in which the favorable interactions are primarily van der Waals contacts, and in which electrostatic interactions are a relatively minor component. We feel the force field is particularly useful for molecular mechanics aided drug design, and an analysis of modeling results with respect to design of drugs which bind selectively to RNA is presented.
Magnetic Resonance Imaging of Asymptomatic Knees in Collegiate Basketball Players (2016)

A high prevalence of abnormal knee MRI findings was observed in a population of asymptomatic young elite athletes. These preliminary data suggest that high-intensity basketball may have potentially deleterious effects on articular cartilage.
Greedy Algorithms for Distributed Compressed Sensing (2014)

A fibular flap has great versatility in reconstructive procedures. Osteomies and ostectomies enable the flap to be used for variable defects. We used combined horizontal/vertical osteotomy and ostectomy for reconstruction of complex craniofacial defects with one flap in two patients. Vertical osteotomy transforms the tubular structure of a fibula into a flat bone that can be used for reconstruction of wider defects with less vertical height. Neither vertical osteotomy nor ostectomy had negative effects on viability and bony healing of the segments in our patients. We think that the fibular flap, thanks to its versatility, can be used for reconstruction of complex orbito-zygomatic and orbito-cranial defects successfully.