gebhart/patrepeval huggingface dataset:
Crystal Structure of a Conserved Phosphatase Domain of Non-structural Protein-3 (nsp3) from the SARS Coronavirus (2006)

Severe Acute Respiratory Syndrome (SARS) is a debilitating pneumonia-like disease of the upper pulmonary tract in humans whose causative organism is a group II coronavirus (SARS-CoV). An early event in infected cells is the transcription of its genomic RNA into a large (~7000 residues) replicase polyprotein, which is then cleaved into 16 mature proteins known as non-structural proteins or nsps. Several groups have begun to characterize these proteins that form integral components of the SARS replicase/transcriptase complex. The third of these nsps, (nsp3) is a large 213kDa multidomain protein that arises due to cleavage of the polyprotein by the virally encoded papain-like protease or PLpro. It has at least six structural domains apart from a transmembrane domain. We have embarked on an NIAID funded program that aims to structur-ally and functionally characterize all the protein domains of the SARS pro-teome (sars.scripps.edu). The program
Grating-assisted superresolution of slow waves in Fourier space (2007)

We present a far-field optical technique allowing measurements of the dispersion relation of electromagnetic fields propagating under the light cone in photonic nanostructures. It relies on the use of a one-dimensional grating to probe the evanescent tail of the guided field in combination with a high-numerical-aperture Fourier-space imaging setup. A high-resolution spectroscopy of the far-field emission diagram allows us to accurately and efficiently determine the dispersion curve and the group-index dispersion of planar photonic crystal waveguides operating in the slow-light regime.
A PMOS mm-wave power amplifier at 77 GHz with 90 mW output power and 24% efficiency (2016)

In deeply scaled CMOS processes with gate lengths below 40 nm the analog performance of NMOS and PMOS FETs are comparable. At the same time PMOS FETs can typically operate under higher operating voltages than NMOS devices. In this paper, we present the first millimeter-wave power amplifier exclusively employing PMOS. The single stage, 3-stack power amplifier operates at 65 - 92 GHz with more than 35% fractional bandwidth and 12 dB gain. At 78 GHz, the PA achieves a maximum output power of 19.6 dBm and PAE of 18% with class-A bias, and 18.7 dBm and 24% PAE with class-AB bias. The PA has been fabricated in 32 nm CMOS SOI process and occupies 440 μm × 280 μm area (only 0.05 mm2 excluding pads). To the authors' knowledge this PA achieves the highest efficiency for any silicon PA in the 60-90 GHz frequency band. The output power is also the best reported in silicon for this frequency range, for amplifiers that do not use elaborate power-combining approaches.
Assessment of PFAS fate, transport, and treatment inhibition associated with a simulated AFFF release within a WASTEWATER treatment plant (2020)

Sequencing batch reactors (SBRs) were operated for 36 days to simulate the potential wastewater treatment impacts as well as fate and transport of per- and polyfluoroalkyl substances (PFAS) that could be associated with a release of alcohol resistant aqueous film forming foam (AR-AFFF) from on-site methanol fire suppression systems. The results of this study indicate that two days of exposure to AFFF were associated with small reductions in mixed liquor solids content and nitrification rates. No impacts on denitrification or biological phosphorus removal were observed. The addition of AFFF was associated with increases in 6:2 fluorotelomer sulfonate (6:2 FTS) in influent, effluent, and solids samples in the SBR. The following biotransformation pathway is proposed: an unidentified fluorotelomer precursor quickly degraded to 6:2 FTS, which then slowly degraded to several identified degradation intermediates and terminal, short-chain perfluorocarboxylic acid products. Data for 6:2 FTS, which was used as a proxy for AFFF-associated PFAS, were extrapolated to estimate that a removal of approximately 70% of AFFF via effluent and solids wasting would occur after 4 days at a full-scale treatment plant. This information can be used to better understand potential impacts on downstream processes, including potable reuse and biosolids production.
Asymmetric Hydrogenation of Aryl Ketones Mediated by a Copper Catalyst. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Characterization techniques (1993)

Doping and other materials parameters influence the properties of III–V devices in a profound manner. Examples of device parameters which are strongly influenced by the defect and doping concentration are the radiative efficiency of a laser, the minority carrier lifetime in the base of a bipolar transistor, the carrier mobility in the channel of a field-effect transistor, or the quantum efficiency of a pin photo-diode. In this chapter, characterization techniques are discussed that relate directly to shallow impurities as well as deep centers. The characterization techniques are categorized as (i) electronic (ii) optical, and (iii) chemical and structural techniques. Fundamental aspects of characterization techniques as well as practical ‘hints’ for the experimentalist are emphasized.
Membrane lipid order of human red blood cells is altered by physiological levels of hydrostatic pressure (1997)

The effect of hydrostatic pressure at levels applied in diving or hyperbaric treatment (thus considered "physiological") on the order of lipid domains in human red blood cell (RBC) membrane was studied. Membrane order was determined by measuring 1) the fluorescence anisotropy (FAn) of lipid probes, 2) the resonance energy transfer from tryptophan to lipid probes, and 3) spectral shifts in Laurdan fluorescence emission. It was found that the application of mild pressure (< 15 atm) 1) increased, selectively, the FAn of lipid probes that monitor the membrane lipid core, 2) increased the tryptophan FAn, 3) increased the resonance energy transfer from tryptophan to lipid probes residing in the lipid core, and 4) induced changes in the Laurdan fluorescence spectrum, which corresponded to reduced membrane hydration. It is proposed that the application of pressure of several atmospheres increases the phase order of membrane lipid domains, particularly in the proximity of proteins. Because the membrane lipid order ("fluidity") of RBCs plays an important role in their cellular and rheological functions, the pressure-induced alterations of the RBC membrane might be pertinent to microcirculatory disorders observed in humans subjected to elevated pressure.
Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis (2015)

The nonhuman primate model has been widely used in the preclinical assessment of human vaccines. Next-generation sequencing of B-cell repertoires provides a quantitative tool to analyze B-cell responses to a vaccine. In this study, the longitudinal B-cell repertoire analysis of a rhesus macaque immunized with an HIV-1 trimer vaccine revealed complex B-cell lineage patterns and showed the potential to facilitate the evaluation of future HIV-1 vaccines. The repertoire sequencing technologies and antibodyomics methods reported here can be extended to vaccine development for other human pathogens utilizing the nonhuman primate model.
Discovering Human and Machine Readable Descriptions of Malware Families. (2016)

While an immense amount of work has gone into novel clustering algorithms, little work has focused on developing compact, domain-specific explanations for the results of the clustering algorithms. Attaching semantic meaning to a cluster has numerous benefits, including the ability for such a description to be both human and machine readable. In this paper, we assume that the clusters are given to us, and find the minimal set of features that can differentiate one cluster from the remaining set of samples. We formulate this problem as an integer linear program. By using samples not belonging to the cluster in the optimization formulation, the resulting description will be minimal and contain no false positives. The efficacy of this method is demonstrated on simulation data and real-world malware data run in a sandbox that collects behavioral characteristics. In the case of malware, once it has been clustered, it would have been sent to a reverse engineer who would have been tasked with creating the actual meaning of the clustering results and disseminating this information through signatures or indicators of compromise. This is a time-consuming process that can take hours to weeks depending on the complexity of the malware family. The methods presented in this paper automatically generate optimal signatures, which can then be quickly propagated to help contain the spread of a malware family.
Collagen VI myopathies: pathogenic mechanism and therapeutic strategies (2011)

Collagen (Col) VI is a major component of the extracellular matrix which, in skeletal muscle, is localized just outside the basement membrane. Deficiency of ColVI in humans due to mutations of <em>COL6</em> genes gives rise to Bethlem Myopathy (BM), Ullrich Congenital Muscular Dystrophy (UCMD), and Myosclerosis Myopathy. About 70 different <em>COL6</em> gene mutations have been associated to ColVI myopathies which, although present a wide range of clinical features, share a common pathogenesis. This mechanism, initially identified in the <em>Col6a1</em>-/- model (Irwin et al., 2003), and then in cultures from BM and UCMD patients (Angelin et al., 2007), involves a mitochondrial dysfunction due to deregulation of the permeability transition pore (PTP). The pat hogenic role of PTP opening, causing the release of proapoptotic factors, has been confirmed by the normalizing effect of cyclosporine A (CsA) on the mitochondrial defect and on the increased apoptotic rate in both the mouse model and in a selected group of patients (Merlini et al., 2008). We have recently demonstrated that the persistence of abnormal mitochondria and apoptosis are amplified by defective autophagy (Grumati et al., 2010). In fact, forced activation of autophagy by genetic, dietary and pharmacological approaches restore myofiber survival and ameliorate the dystrophic phenotype in mice. Since also muscle cells of BM and UCMD patients present a defective activation of the autophagic machinery, it will be possible to restore this activity by using a low protein diet or drugs capable to reactivate autophagy. To monitor the effects of therapies on ColVI-related myopathies highly invasive muscle/skin biopsies have been so far utilized. We have recently obtained evidence that ColVI expression in blood macrophages from BM and UCMD patients can be detected at levels comparable to those observed in muscle biopsies and cultured skin fibroblasts (Gualandi et al., 2011). These data support the suitability of peripheral blood macrophages as a reliable, minimally invasive tool for supplementing or replacing highly invasive biopsies in the diagnosis and monitoring of ColVI myopathies. 1. Irwin WA et al., Nat Genet 2003;35:267-71 2. Angelin A et al., PNAS USA 2007;104:991-6 3. Merlini L et al., PNAS USA 2008;105:5225-9 4. Gualandi F et al., Muscle Nerve 2011;44:80-4
Platys Social: Relating Shared Places and Private Social Circles (2011)

Social circles can be valuable in online applications, but existing approaches don't readily support such grouping: they either require a user to manually tag connections or offer no more than broad-brush acquaintanceship between connections. Platys Social is a novel approach that learns users' social circles and prioritizes their connections by bringing together contextual information and user interactions. Platys Social runs incrementally, can execute on a resource-limited mobile device, and can potentially avoid storing users' private information on a remote site.
Reliability and Life Study of Hydraulic Solenoid Valve - Part 2 - Experimental Study (2009)

&lt;div class="htmlview paragraph"&gt;The current work studies the reliability of a solenoid valve (SV) used in automobile transmissions through a joint theoretical and experimental approach. The goal of this work is to use accelerated tests to characterize SV failure and correlate the results to new comprehensive finite element models (Part 1).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A custom test apparatus has been designed and built to simultaneously monitor and actuate up to four SVs. The test apparatus is capable of applying a controlled duty cycle, current and actuation frequency. The SVs are also placed in a thermal chamber so that the ambient temperature can be controlled precisely. The apparatus measures in real-time the temperature, current, and voltage of each SV. A series of tests have been conducted to produce repeated failures of the SV. The failure of the SV appears to be caused by overheating and failure of the insulation used in the solenoid coil. The current tests are run at a 100°C ambient temperature, 16.8V of average peak voltage, 50% duty cycle, and 60 Hertz actuation frequency. Upon failure, the solenoid electrical resistance drops to a significantly lower value due to shorting of the solenoid coil. This drop in resistance causes a measurable and noticeable increase in the average current. The insulation also melts and exits the SV. Hence, increasing ambient temperature and current is believed to cause a decrease in SV reliability.&lt;/div&gt;
Reduction of mortality by sulphinpyrazone after experimental myocardial infarction in the rat (1980)

Journal Article Reduction of mortality by sulphinpyrazone after experimental myocardial infarction in the rat Get access L Brunner, L Brunner Biological Research Laboratories, Pharmaceuticals Division, CIBA-GEIGY Limited, Basle, Switzerland Correspondence: Biological Research Laboratories, Pharmaceuticals Division, CIBA-GEIGY Limited, Basle, Switzerland Search for other works by this author on: Oxford Academic Google Scholar J Stepanek, J Stepanek Biological Research Laboratories, Pharmaceuticals Division, CIBA-GEIGY Limited, Basle, Switzerland Search for other works by this author on: Oxford Academic Google Scholar H Brunner H Brunner Biological Research Laboratories, Pharmaceuticals Division, CIBA-GEIGY Limited, Basle, Switzerland Search for other works by this author on: Oxford Academic Google Scholar Journal of Pharmacy and Pharmacology, Volume 32, Issue 1, September 1980, Pages 714–715, https://doi.org/10.1111/j.2042-7158.1980.tb13047.x Published: 12 April 2011 Article history Received: 15 February 1980 Published: 12 April 2011
On the Trail of Xanthates: Some New Chemistry from an Old Functional Group (1997)

Abstract The use of free radical reactions in organic synthesis has witnessed an extraordinary development in recent years. When properly conceived, radical processes often exhibit many of the properties desired by synthetic organic chemists, such as flexibility, mildness, and selectivity. Unfortunately, the number of synthetically useful radical‐generating systems is still limited, and most applications have relied on tin hydride chemistry. Secondary O ‐alkyl‐ S ‐methyl xanthates, for example, eact with tributyltin hydride to give the corresponding alkane (the Barton‐McCombie reaction). It was, however, found that the isomeric O ‐methyl‐ S ‐alkyl xanthates undergo cleavage of the weaker carbon–sulfur bond and that a chain reaction can be sustained without tin or other heavy metals. A variety of synthetically interesting free radicals can thus be produced and captured, the last propagating step being a reversible transfer of the xanthate group. S ‐Propargyl xanthates represent a special class. Their radical chemistry can be easily overshadowed by hitherto unknown but equally interesting nonradical behavior. Upon heating, a thermal [3,3] sigmatropic rearrangement occurs to give the allenyl isomer, which is in equilibrium with a novel betaine structure. This species is at the heart of a number of new transformations, including formal [3+2] cycloadditions, formation of esters with inversion in the case of secondary alcohols, conversion into 1,3‐dithiol‐2‐ones, generation of cisoid dienes, carbon, carbon‐carbon bond formation through reaction with acid chlorides etc. This account provides a brief description of this original radical and nonradical chemistry of xanthates, an old family of compounds that still harbors many mysteries.
UV-Curable Liquid Crystal for a Retarder (2010)

Abstract UV-curable liquid crystal is mesogenic monomer which can be aligned by usual method such as a rubbing technique. By UV-irradiation, it polymerizes to give a polymer in which the alignment of the liquid crystal is fixed. Applications and materials for the retarder are reviewed. Keywords: Mesogenic monomerretardation film Notes Δn was measured at λ = 589 nm.
Cosmological problems with multiple axion-like fields (2011)

Incorporating the QCD axion and simultaneously satisfying current constraints on the dark matter density and isocurvature fluctuations requires non-minimal fine-tuning of inflationary parameters or the axion misalignment angle (or both) for Peccei-Quinn symmetry-breaking scales $f_a > 10^{12}$ GeV. To gauge the degree of tuning in models with many axion-like fields at similar symmetry-breaking scales and masses, as may occur in string theoretic models that include a QCD axion, we introduce a figure of merit ${\cal F}$ that measures the fractional volume of allowed parameter space: the product of the slow roll parameter $\epsilon$ and each of the axion misalignment angles, $\theta_0$. For a single axion, $\mathcal{F} \lesssim 10^{-11}$ is needed to avoid conflict with observations. We show that the fine tuning of $\mathcal{F}$ becomes exponentially more extreme in the case of numerous axion-like fields. Anthropic arguments are insufficient to explain the fine tuning because the bulk of the anthropically allowed parameter space is observationally ruled out by limits on the cosmic microwave background isocurvature modes. Therefore, this tuning presents a challenge to the compatibility of string-theoretic models with light axions and inflationary cosmology.
Broadband frequency conversion and shaping of single photons emitted from a nonlinear cavity (2009)

Much recent effort has focused on coupling individual quantum emitters to optical microcavities in order to produce single photons on demand, enable single-photon optical switching, and implement functional nodes of a quantum network. Techniques to control the bandwidth and frequency of the outgoing single photons are of practical importance, allowing direct emission into telecommunications wavelengths and "hybrid" quantum networks incorporating different emitters. Here, we describe an integrated approach involving a quantum emitter coupled to a nonlinear optical resonator, in which the emission wavelength and pulse shape are controlled using the intra-cavity nonlinearity. Our scheme is general in nature, and demonstrates how the photonic environment of a quantum emitter can be tailored to determine the emission properties. As specific examples, we discuss a high Q-factor, TE-TM double-mode photonic crystal cavity design that allows for direct generation of single photons at telecom wavelengths (1425 nm) starting from an InAs/GaAs quantum dot with a 950 nm transition wavelength, and a scheme for direct optical coupling between such a quantum dot and a diamond nitrogen-vacancy center at 637 nm.
Annealed Langevin Dynamics for Massive MIMO Detection (2022)

Solving the optimal symbol detection problem in multiple-input multiple-output (MIMO) systems is known to be NP-hard. Hence, the objective of any detector of practical relevance is to get reasonably close to the optimal solution while keeping the computational complexity in check. In this work, we propose a MIMO detector based on an annealed version of Langevin (stochastic) dynamics. More precisely, we define a stochastic dynamical process whose stationary distribution coincides with the posterior distribution of the symbols given our observations. In essence, this allows us to approximate the maximum a posteriori estimator of the transmitted symbols by sampling from the proposed Langevin dynamic. Furthermore, we carefully craft this stochastic dynamic by gradually adding a sequence of noise with decreasing variance to the trajectories, which ensures that the estimated symbols belong to a pre-specified discrete constellation. Based on the proposed MIMO detector, we also design a robust version of the method by unfolding and parameterizing one term -- the score of the likelihood -- by a neural network. Through numerical experiments in both synthetic and real-world data, we show that our proposed detector yields state-of-the-art symbol error rate performance and the robust version becomes noise-variance agnostic.
The Asia-Australia Gravitational Wave Detector Concept (2017)

The discovery of gravitational waves enabled assessment of the science benefits of new improved gravitational wave detectors. This paper discusses the science benefits of an Asia-Australia Gravitational wave Observatory (AAGO) consisting of a pair of widely spaced gravitational wave detectors on a north-south axis. Initial sensitivity would be ∼4 times better than the projected sensitivity of Advanced LIGO, but designed for future upgrades to match proposed third generation detectors. AAGO would enable near optimum angular resolution of sources, and signal detections at a rate ∼1 per hour, sufficient to monitor a substantial fraction of all large mass black hole merger events in the universe. The proposed conceptual design and infrastructure, technical issues and challenges are discussed.
Prospero‐related homeobox 1 and liver receptor homolog 1 coordinately regulate long‐term proliferation of murine fetal hepatoblasts† (2008)

These results suggested that Prox1 and Lrh1 coordinately regulate development of hepatic stem/progenitor cells and that Prox1 induces fetal hepatocytic proliferation through the suppression of the promoter activity of p16(ink4a).