gebhart/patrepeval huggingface dataset:
3G wireless capacity optimization for widely spaced antenna arrays (2000)

Adaptive arrays can significantly increase cell capacity, improve signal quality, and reduce transmitter power requirements. In this article we establish a relationship between the information theoretic capacity of a mobile radio system and the beam pattern of a multisensor array. We investigate the capacity improvement potentially achieved via an optimized design strategy for an unequally spaced array; that is, the positions and the weighting coefficients of the array elements are selected to improve the average system capacity subject to various constraints like minimizing the maximum sidelobe level or keeping the beamwidth of the main lobe to a minimum. Next, we investigate the effect of fading correlation on the performance of an unequally spaced adaptive array. Results are presented for optimum combining with flat fading as well as for frequency-selective fading using a two-path delay spread model. Computer simulations show that it is possible to achieve a gain of 1.5 dB for moderate to high signal-to-noise ratios when compared to the equally spaced array. Finally, it is shown that a base station with wide antenna element spacing has improved bit error rate performance over one with narrow element spacing under cochannel interference and multipath fading. In particular, we improve the performance for both uplink and downlink transmissions in a slow fading channel with cochannel interference. Promising results are presented for a 4 channel carrier time division duplexing system.
Enantioselective synthesis of β2-amino acids using rhodium-catalyzed hydrogenation (2006)

A series of protected beta2-dehydroamino acids has been prepared in three steps from commercially available starting materials in good yields. These were used as substrates in rhodium-catalyzed asymmetric hydrogenation applying a mixed ligand system of monodentate phosphoramidites and phosphines. Optimization of the catalyst structure was achieved by high throughput experimentation. High enantioselectivities were obtained (up to 91%) with full conversion for a number of beta-amino acids.
Kinetics versus Thermodynamics in Protein Folding (1994)

Until quite recently it has been generally believed that the observed tertiary structure of a protein is controlled by thermodynamic and not kinetic processes. In this essay we review several recent results which call into question the universality of the thermodynamic hypothesis and discuss their implications for the understanding of protein folding.
Physics-based machine learning for subcellular segmentation in living cells (2021)

Abstract Segmenting subcellular structures in living cells from fluorescence microscope images is a ground truth (GT)-deficient problem. The microscopes’ three-dimensional blurring function, finite optical resolution due to light diffraction, finite pixel resolution and the complex morphological manifestations of the structures all contribute to GT-hardness. Unsupervised segmentation approaches are quite inaccurate. Therefore, manual segmentation relying on heuristics and experience remains the preferred approach. However, this process is tedious, given the countless structures present inside a single cell, and generating analytics across a large population of cells or performing advanced artificial intelligence tasks such as tracking are greatly limited. Here we bring modelling and deep learning to a nexus for solving this GT-hard problem, improving both the accuracy and speed of subcellular segmentation. We introduce a simulation-supervision approach empowered by physics-based GT, which presents two advantages. First, the physics-based GT resolves the GT-hardness. Second, computational modelling of all the relevant physical aspects assists the deep learning models in learning to compensate, to a great extent, for the limitations of physics and the instrument. We show extensive results on the segmentation of small vesicles and mitochondria in diverse and independent living- and fixed-cell datasets. We demonstrate the adaptability of the approach across diverse microscopes through transfer learning, and illustrate biologically relevant applications of automated analytics and motion analysis.
A real-time machine-learning-driven control system of a deformable mirror for achieving aberration-free hard X-ray wavefronts (2023)

A neural-network machine learning model is developed to control a bimorph adaptive mirror to achieve and preserve aberration-free coherent X-ray wavefronts at synchrotron radiation and free electron laser beamlines. The controller is trained on a mirror actuator response directly measured at a beamline with a real-time single-shot wavefront sensor, which uses a coded mask and wavelet-transform analysis. The system has been successfully tested on a bimorph deformable mirror at the 28-ID IDEA beamline of the Advanced Photon Source at Argonne National Laboratory. It achieved a response time of a few seconds and maintained desired wavefront shapes (e.g., a spherical wavefront) with sub-wavelength accuracy at 20 keV of X-ray energy. This result is significantly better than what can be obtained using a linear model of the mirror’s response. The developed system has not been tailored to a specific mirror and can be applied, in principle, to different kinds of bending mechanisms and actuators.
Interferometric measurements of the solar line Fe I λ 5576.1 Å and its centre-to-limb variation (1991)

Interferometric absolute wavelength measurements of the solar line Fe I λ 5576.1 A at the solar disc centre and along the solar meridian are reported. The measurements have been performed in 1985 using a LASER-controlled Fabry-Perot interferometer with multilayer coatings, placed in front of the Littrow spectrograph of the Schauinsland Observatory near Freiburg. The resulting channeled spectra were recorded on film and digitized. The data reduction includes a correction for the phase dispersion on the Fabry Perot multilayer coatings
Fluorescent Trimeric Hemagglutinins Reveal Multivalent Receptor Binding Properties (2018)

Influenza A virus carries hundreds of trimeric hemagglutinin (HA) proteins on its viral envelope that interact with various sialylated glycans on a host cell. This interaction represents a multivalent binding event that is present in all the current receptor binding assays, including those employing viruses or precomplexed HA trimers. To study the nature of such multivalent binding events, we fused a superfolder green fluorescent protein (sfGFP) to the C-terminus of trimeric HA to allow for direct visualization of HA-receptor interactions without the need for additional fluorescent antibodies. The multivalent binding of the HA-sfGFP proteins was studied using glycan arrays and tissue staining. The HA-sfGFP with human-type receptor specificity was able to bind to a glycan array as the free trimer. In contrast, the HA-sfGFP with avian-type receptor specificity required multimerization by antibodies before binding to glycans on the glycan array could be observed. Interestingly, multimerization was not required for binding to tissues. The array data may be explained by the possible bivalent binding mode of a single human-specific HA trimer to complex branched N-glycans, which is not possible for the avian-specific HA due to geometrical constrains of the binding sites. The fact that this specificity pattern changes upon interaction with a cell surface probably represents the enhanced amount of glycan orientations and variable densities versus those on the glycan array.
Highly Efficient and Versatile Phosphine‐Phosphoramidite Ligands for Asymmetric Hydrogenation (2009)

Abstract magnified image A set of novel phosphine‐phosphoramidite ligands possessing two elements of chirality have been prepared through a modular synthetic approach. The ligands (11b S )‐ N ‐[2‐(diphenylphosphino)phenyl]‐ N ‐[( S )‐1‐phenylethyl]dinaphtho[2,1‐ d :1′,2′‐ f ][1,3,2]dioxaphosphepin‐4‐amine [( S a , S c )‐ 1a ] and (11b R )‐ N ‐[2‐(diphenylphosphino)phenyl]‐ N ‐[( S )‐1‐(1‐naphthyl)ethyl]dinaphtho[2,1‐ d :1′,2′‐ f ][1,3,2]dioxaphosphepin‐4‐amine [( S a , S c )‐ 1b ] are unique in providing enantioselectivities ≥96% ee and ≥94% ee , respectively, in mechanistically distinct hydrogenations of CC, CN and CO double bonds in combination with three different transition metals (rhodium, iridium, and ruthenium, respectively). Particularly remarkable are the enantiomeric excesses up to 97% achieved in the iridium‐catalyzed hydrogenation of 2‐substituted quinolines, where (11b S )‐ N ‐[2‐(diphenylphosphino)phenyl]‐ N ‐[( S )‐1‐(naphthalen‐1‐yl)ethyl]‐8,9,10,11, 12,13,14,15‐octahydrodinaphtho[2,1‐ d :1′,2′‐ f ][1,3,2]dioxaphosphepin‐4‐amine [( S a , S c )‐ 2 ] proved to be the most selective ligand. Substantially lower ee s were obtained with the mismatched diastereomer ( R a , S c )‐ 1b and with the N ‐phenyl‐substituted ligand 1c , missing a second element of chirality.
Inaccuracies of Giant Magneto-Resistive Angle Sensors Due to Assembly Tolerances (2009)

For automotive applications like steering wheel position, sensing the angular position of a mechanical axel is detected in a contactless way: a small permanent magnet at the end of the shaft is magnetized perpendicularly to the axis of rotation, and a magnetic field sensor is placed ahead. Even though the magnetic field sensor may be calibrated to have virtually no errors, assembly tolerances of the magnet and the sensor lead to errors in the estimated angular position of the shaft. A Taylor series expansion of the magnetic field up to second order is used to approximate these angle errors. Results of Monte-Carlo simulations show that worst case angle errors may be up to 10 times the average angle error due to error propagation in the nonlinear goniometric relationships. Various shapes of magnets are discussed and criteria for optimization are given. The strong effects of magnet size and distance between sensor and magnet are explained and the limit of infinite homogeneous magnetic field is derived. The results can be used to anticipate production spread of angle sensor systems.
Activités enzymatiques dans les genresHelvella, RussulaetCortinarius (1978)

RésuméLes auteurs ont montré la présence de protéases très actives dans les carpophores de tout le genre Helvella. La laccase est largement répandue chez les Russules mais de fortes teneurs ont été trouvées presque exclusivement chez les Compactae, les Piperinae et les Foetentinae. Le genre Cortinarius est caractérisé par la présence d'hémicellulase, de catalase, de laccase et de Peroxydase. Les activités peroxydasiques s'avèrent particulièrement élevées uniquement dans ce genre de macromycètes.
A WIRNA receiver architecture based 16 GHz optical analog heterodyne FM link (2005)

We demonstrate a 16 GHz analog heterodyne FM link with pre-emphasis operating at 1540 nm wavelength, with a NF (noise figure) of (40/spl plusmn/1) dB and SFDR (spurious-free dynamic range) of (108/spl plusmn/2) dB-Hz/sup 2/3/, employing a WIRNA (wide-band rectifier narrow-band amplifier) receiver to reduce phase noise.
A methodology for performance driven data-path compilation (2002)

In this paper, a methodology is described for performance driven compilation of data-paths suited for high throughput real time DSP applications. The emphasis lies on the designers point of view, i.e. on the effect of the different performance optimizations, and the sequence in which to apply them. The resulting methodology has been implemented in a tool called Chopin.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Salvage radiation therapy for prostate cancer patients after prostatectomy (2018)

While SRT is the most important secondary treatment option for patients with BCR after RP, the effectiveness of SRT may not be uniform. The combination of risk factors such as microvascular invasion in RP specimens and pre-SRT PSA may provide a better way to stratify the risk of BCR after SRT.
A three dimensional analysis of slotted tube resonator for MRI (1994)

A three dimensional model of a slotted tube resonator (STR) used as a probe in the magnetic resonance imaging (MRI), which is loaded by a dielectric body and surrounded by a conducting shield, is analyzed by using the variational method and the dyadic Green's function of a circular waveguide having a dielectric core. Three surface current modes are properly assumed to expand the currents on the STR. The characteristics such as the input impedance, the resonance frequency, the Q value, and the magnetic field distribution are obtained to show the effects of the dielectric body and the conducting shield. Some theoretical results are compared with the measured data to confirm the validity of the present analysis.
Single photon avalanche diodes (SPADs) for 1.5 μm photon counting applications (2007)

The paper reports on the design and characterization of InGaAs/InP single photon avalanche diodes (SPADs) for photon counting applications at wavelengths near 1.5 µm. It is shown how lower internal electric field amplitudes can lead to reduced dark count rates, but at the expense of degraded afterpulsing behaviour and larger timing jitter. Dark count rate behaviour provides evidence of thermally assisted tunnelling with an average thermal activation energy of ∼0.14 eV between 150 K and 220 K. Afterpulsing behaviour exhibits a structure-dependent afterpulsing activation energy, which quantifies how carrier de-trapping varies with temperature. SPAD performance simultaneously exhibits a dark count rate of 10 kHz at a detection efficiency of 20% with timing jitter of 100 ps at 200 K, and with appropriate performance tradeoffs, we demonstrate a 200 K dark count rate as low as 3 kHz, a detection efficiency as high as 45%, and a timing jitter as low as 30 ps.
ALL-1/MLL1, a homologue of Drosophila TRITHORAX, modifies chromatin and is directly involved in infant acute leukaemia (2004)

Rearrangements of the ALL-1/MLL1 gene underlie the majority of infant acute leukaemias, as well as of therapy-related leukaemias developing in cancer patients treated with inhibitors of topoisomerase II, such as VP16 and doxorubicin. The rearrangements fuse ALL-1 to any of >50 partner genes or to itself. Here, we describe the unique features of ALL-1-associated leukaemias, and recent progress in understanding molecular mechanisms involved in the activity of the ALL-1 protein and of its Drosophila homologue TRITHORAX.
Mathematics of Deep Learning (2017)

Recently there has been a dramatic increase in the performance of recognition systems due to the introduction of deep architectures for representation learning and classification. However, the mathematical reasons for this success remain elusive. This tutorial will review recent work that aims to provide a mathematical justification for several properties of deep networks, such as global optimality, geometric stability, and invariance of the learned representations.
Fluoride Chemistry in Tin Halide Perovskites (2021)

Tin is the frontrunner for substituting toxic lead in perovskite solar cells. However, tin suffers the detrimental oxidation of Sn<sup>II</sup> to Sn<sup>IV</sup> . Most of reported strategies employ SnF<sub>2</sub> in the perovskite precursor solution to prevent Sn<sup>IV</sup> formation. Nevertheless, the working mechanism of this additive remains debated. To further elucidate it, we investigate the fluoride chemistry in tin halide perovskites by complementary analytical tools. NMR analysis of the precursor solution discloses a strong preferential affinity of fluoride anions for Sn<sup>IV</sup> over Sn<sup>II</sup> , selectively complexing it as SnF<sub>4</sub> . Hard X-ray photoelectron spectroscopy on films shows the lower tendency of SnF<sub>4</sub> than SnI<sub>4</sub> to get included in the perovskite structure, hence preventing the inclusion of Sn<sup>IV</sup> in the film. Finally, small-angle X-ray scattering reveals the strong influence of fluoride on the colloidal chemistry of precursor dispersions, directly affecting perovskite crystallization.
The Prophylactic and Therapeutic Efficacy of the Broadly Active Antiviral Ribonucleoside N 4 -Hydroxycytidine (EIDD-1931) in a Mouse Model of Lethal Ebola Virus Infection (2022)

ABSTRACT The unprecedented magnitude of the 2013-2016 Ebola virus (EBOV) epidemic in West Africa resulted in over 11,000 deaths and spurred an international public health emergency. A second outbreak in 2018-2020 in DRC resulted in an additional &gt;3400 cases and nearly 2300 deaths (WHO Disease Outbreak News: Update 26 June, 2020). These large outbreaks across geographically diverse regions highlight the need for the development of effective oral therapeutic agents that can be easily distributed for self-administration to populations with active disease or at risk of infection. Herein, we report the in vivo efficacy of N 4 -hydroxycytidine (EIDD-1931), a broadly active ribonucleoside analog and the active metabolite of the prodrug EIDD-2801 (molnupiravir), in murine models of lethal EBOV infection. Twice daily oral dosing with EIDD-1931 at 200 mg/kg for 7 days, initiated either with a prophylactic dose 2 hours before infection, or as therapeutic treatment starting 6 hours post-infection, resulted in 92-100% survival of mice challenged with lethal doses of EBOV, reduced clinical signs of Ebola virus disease (EVD), reduced serum virus titers, and facilitated weight loss recovery. These results support further investigation of molnupiravir as a potential therapeutic or prophylactic treatment for EVD.
Oxidative Stress in Heart Failure: Impact on Cardiac Function and Ventricular Remodeling (2005)

Despite several decades of advances in heart failure (HF) therapeutics resulting in substantial reductions in morbidity and mortality, symptomatic HF continues to be a major cause of mortality and hospitalization in the United States. Because of this, improved understanding of HF pathophysiology is crucial in developing novel and effective treatments for this syndrome. Oxidative stress is defined as an imbalance between the production and degradation of endogenously produced, highly reactive free radicals, also known as reactive oxygen species (ROS). Free radicals are atoms or molecules with an unpaired electron. In this regard, superoxide and nitric oxide represent primary examples of endogenously produced free radicals. One of the most convincing pieces of evidence that free radicals are implicated in the disruption of cardiac function is myocardial stunning—the phenomenon of prolonged cardiac dysfunction after brief periods of ischemia in the absence of irreversible injury. There is strong evidence suggesting that such stunning is associated with generation of ROS.
Fourier Transform Infrared Reflectance Microspectroscopy Study of Bacillus Subtilis Engineered without Dipicolinic Acid: The Contribution of Calcium Dipicolinate to the Mid-Infrared Absorbance of Bacillus Subtilis Endospores (2005)

Mid-infrared spectra of spores of two strains of Bacillus subtilis, PS832 (wild-type) and FB122 (sleB spoVF), that are isogenic except for the two mutations in FB122 were obtained by Fourier transform infrared (FT-IR) reflectance microspectroscopy. The mutations in FB122 cause the spores of this strain to be devoid of dipicolinic acid (pyridine-2,6-dicarboxylic acid; DPA), a biomarker characteristic of bacterial spores. Analysis of these two strains by difference spectroscopy revealed a spectrum similar to that of calcium dipicolinate (CaDPA), a chelate salt of DPA. This difference spectrum was compared to mid-infrared spectra of both DPA and CaDPA, and was attributed to CaDPA only. This is the first report known to the authors of a genetically engineered organism being used to identify the spectral contribution of a particular cellular component.
Long-term results after total condylar knee arthroplasty. Significance of radiolucent lines. (1987)

In a prospective study of 123 total condylar knee arthroplasties, radiolucent lines were noted at the bone-cement interface about the tibial component in 65% of the knees. In 36%, the line was thin (less than 2 mm) and under either the medial or lateral tibial plateau. In 22%, thin lines were seen under both the medial and lateral plateaus. There was no statistically significant correlation between the occurrence of thin radiolucent lines in any location and the eventual postoperative clinical result. In 7%, thick lines (greater than 2 mm) were noted about the central peg of the prosthesis as well as under both plateaus and were associated with poor results. A 1-mm radiolucent interface was attached to various tibial components, which were then cemented into cadaver knees. For the polyethylene total condylar component, flexion or rotation of the prosthesis more than 5 degrees, angulation of the roentgen beam more than 6 degrees, or offsetting the beam more than 2.5 cm prevented visualization of the radiolucent line. With metal-backed components, more than 4 degrees of flexion obscured the lines. Therefore, extremely careful positioning of postoperative radiographs is essential for evaluating radiolucent lines after total knee arthroplasty.
Approaching the Interconnection of Heterogeneous Knowledge Bases on a Knowledge Grid (2008)

This paper presents a method for the interconnection of heterogeneous knowledge bases on a knowledge grid for knowledge sharing and provision. Various knowledge bases have been created by using collaborative editing environments such as Wiki in each field. Each knowledge base exists independently. On the other hand, an event affects various aspects of an area, field or community. Therefore, in today's global environment, it is important to transmit significant knowledge related to accidental or irregular events to actual users from various knowledge bases. In this paper, we propose a method for the extraction of related items across heterogeneous fields by interconnecting each knowledge base arranged on a knowledge grid.
A Direct Capture Method for Purification and Detection of Viral Nucleic Acid Enables Epidemiological Surveillance of SARS-CoV-2 (2021)

Abstract Studies have demonstrated that SARS-CoV-2 RNA can be detected in the feces of infected individuals. This finding spurred investigation into using wastewater-based epidemiology (WBE) to monitor SARS-CoV-2 RNA and track the appearance and spread of COVID-19 in communities. SARS-CoV-2 is present at low levels in wastewater, making sample concentration a prerequisite for sensitive detection and utility in WBE. Whereas common methods for isolating viral genetic material are biased toward intact virus isolation, it is likely that a relatively low percentage of the total SARS-CoV-2 RNA genome in wastewater is contained within intact virions. Therefore, we hypothesized that a direct unbiased total nucleic acid extraction method could overcome the cumbersome protocols, variability and low recovery rates associated with the former methods. This led to development of a simple, rapid, and modular alternative to existing purification methods. In an initial concentration step, chaotropic agents are added to raw sewage allowing binding of nucleic acid from free nucleoprotein complexes, partially intact, and intact virions to a silica matrix. The eluted nucleic acid is then purified using manual or semi-automated methods. RT-qPCR enzyme mixes were formulated that demonstrate substantial inhibitor resistance. In addition, multiplexed probe-based RT-qPCR assays detecting the N1, N2 (nucleocapsid) and E (envelope) gene fragments of SARS-CoV-2 were developed. The RT-qPCR assays also contain primers and probes to detect Pepper Mild Mottle Virus (PMMoV), a fecal indicator RNA virus present in wastewater, and an exogenous control RNA to measure effects of RT-qPCR inhibitors. Using this workflow, we monitored wastewater samples from three wastewater treatment plants (WWTP) in Dane County, Wisconsin. We also successfully sequenced a subset of samples to ensure compatibility with a SARS-CoV-2 amplicon panel and demonstrated the potential for SARS-CoV-2 variant detection. Data obtained here underscore the potential for wastewater surveillance of SARS-CoV-2 and other infectious agents in communities.