gebhart/patrepeval huggingface dataset:
Molecular Basis of Far-red Sensing in Cyanobacteriochrome (2020)

Abstract Cyanobacteriochromes are small, panchromatic photoreceptors in the phytochrome superfamily that regulate diverse light-mediated adaptive processes in cyanobacteria. The molecular basis of far-red (FR) light perception by cyanobacteriochromes is currently unknown. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome from Anabaena cylindrica PCC 7122, which exhibits a reversible far-red/orange photocycle. The 2.7 Å structure of its FR-absorbing dark state, determined by room temperature serial crystallography and cryo-crystallography, reveals an all-Z,syn configuration of its bound linear tetrapyrrole (bilin) chromophore that is less extended than the bilin chromophores of all known phytochromes. Based on structural comparisons with other bilin-binding proteins and extensive spectral analyses on mutants, we identify key protein-chromophore interactions that enable far-red sensing in bilin-binding proteins. We propose that FR-CBCRs employ two distinct tuning mechanisms, which work together to produce a large batho-chromatic shift. Findings of this work have important implications for development and improvement of photoproteins with far-red absorption and fluorescence. Significance Statement Phytochromes are well known far-red-light sensors found in plants that trigger adaptive responses to facilitate competition for light capture with neighboring plants. Red- and far-red-sensing are critical to cyanobacteria living in the far-red-enriched shade of plants. Here we report the crystal structure of a far-red-sensing cyanobacteriochrome, a distant cyanobacterial relative of phytochrome. These studies shed insight into the poorly understood molecular basis of far-red-sensing by phytobilin-based photoreceptors. Owing to the deep tissue penetration of far-red light, far-red-sensing photoreceptors offer promising protein scaffolds for developing gene-based photoswitches, optoacoustic contrast agents and fluorescent probes for in situ imaging and optogenetic applications.
Incorporating discourse context in spoken language translation through dialog acts (2008)

Current statistical speech translation approaches predominantly rely on just text transcripts and are limited in their use of rich contextual information such as prosody and discourse function. In this paper, we explore the role of discourse context characterized through dialog acts (DAs) in statistical translation. We present a bag-of-words (BOW) model that exploits DA tags in translation and contrast it with a phrase table interpolation approach presented in previous work. In addition to producing interpretable DA-annotated target language translations through our framework, we also obtain consistent improvements in terms of automatic evaluation metrics such as lexical selection accuracy and BLEU score using both the models. We also analyze the performance improvements per DA tag. Our experiments indicate that questions, acknowledgments, agreements and appreciations contribute to more improvement in comparison to statements.
FRET‐based Assay Measures the Organization of LDL‐LDL‐R Complexes During LDL Trafficking (2007)

Low Density Lipoprotein (LDL) is the primary mode of cholesterol transport in the bloodstream. Blood LDL enters liver cells via LDL‐receptor (LDL‐R)‐mediated endocytosis and is delivered to late endosomes/lysosomes, where low pH induces the release of LDL. Upon LDL degradation, cholesterol is released for cellular uptake. Here we study the sub‐cellular organization of LDL during LDL‐R‐mediated trafficking. We have developed a novel Fluorescence Resonance Energy Transfer (FRET)‐based assay that investigates the organization of fluorescently labeled LDL during internalization, release and breakdown. MDCK epithelial cells are loaded with LDL conjugated to donor or acceptor fluorophores at 37oC and confocal microscopy is used to collect multi‐channel FRET images. Custom software was developed to automatically process FRET images and reduce image reading bias. The automated ROI selection developed in this project is capable of accurately identifying fluorescent ROIs. Results show correlation between the energy transfer (E%) and acceptor levels; a direct relationship detected 30 minutes post internalization indicates a LDL random organization in late endosomes. Agents that slow LDL release generate a clustered LDL organization. As an in vivo assay for LDL release from LDL‐R, the package developed holds potential in screening agents that modify LDL and cholesterol trafficking.
Counting Grid Aggregation for Event Retrieval and Recognition (2016)

Event retrieval and recognition in a large corpus of videos necessitates a holistic fixed-size visual representation at the video clip level that is comprehensive, compact, and yet discriminative. It shall comprehensively aggregate information across relevant video frames, while suppress redundant information, leading to a compact representation that can effectively differentiate among different visual events. In search for such a representation, we propose to build a spatially consistent counting grid model to aggregate together deep features extracted from different video frames. The spatial consistency of the counting grid model is achieved by introducing a prior model estimated from a large corpus of video data. The counting grid model produces an intermediate tensor representation for each video, which automatically identifies and removes the feature redundancy across the different frames. The tensor representation is subsequently reduced to a fixed-size vector representation by averaging over the counting grid. When compared to existing methods on both event retrieval and event classification benchmarks, we achieve significantly better accuracy with much more compact representation.
Optical triggering of a Q-switched Nd:YAG laser via transverse bleaching of a Cr:YAG saturable absorber (2009)

Optical triggering via direct bleaching of a Cr:YAG saturable absorber was applied to a monolithic Nd:YAG/Cr:YAG laser crystal. The method uses a single laser diode bar to bleach a thin sheet within the saturable absorber from a direction orthogonal to the lasing axis. By placing the Q-switch at the time corresponding to the steepest slope (dT/dt) for change in transmission during bleaching, the pulse-to-pulse timing jitter showed a 13.2x reduction in standard deviation, from 132 ns for free-running operation to 10 ns with optical triggering. We measured that a fluence of 60 kW/cm(2) was sufficient to enable optical triggering, where a diode appropriately sized for the length of the Cr:YAG (approximately 3 mm) would then require only approximately 150 W of optical power over a 1-2 micros duration to enable effective jitter reduction. Additionally, we measured an increase in optical-to-optical efficiency with optical triggering, where the efficiency improved from 12% to 13.5%.
Use of temperature-sensitive mutants of influenza A virus as live virus vaccine strains. Evaluation in laboratory animals, adults and children (1976)

Summary Temperature-sensitive (ts) recombinants of influenza A virus were evaluated for use in a live virus vaccine. Evidence from several sources suggested that the ts lesions were responsible for attenuation of these mutants. Specification of attenuation by defined genetic lesions which can be assayed for in the laboratory offers an advantage to the use of ts viruses for vaccination. This means that ts recombinants can be assessed for genetic stability during vaccine development, production and later during usage in man. One ts virus, influenza A/Hong Kong/68-ts-1[E], with a 38°C shut-off temperature, had the following properties desirable for a live virus vaccine: (1) satisfactory infectivity for seronegative (serum HI antibody titre ≤ 1:8) adults; (2) satisfactory attenuation for adults; (3) capacity to stimulate local and serum anti-haemagglutinin and anti-neuraminidase antibodies in seronegative volunteers; (4) stimulation of resistance to virulent, wild type virus; (5) relative genetic stability in vivo; (6) lack of communicability in man; (7) replication to high titre in avian leucosis virus-free eggs; and (8) localization of ts lesions to genes that do not code for the haemagglutinin and neuraminidase. The ts lesions of influenza A/Hong Kong/68-ts-1[E] virus were transferred to more current viruses within the H3N2 subtype (influenza A/Udorn/307/72 and influenza A/Georgia/101/74). These recombinant Udorn/72 and Georgia/74 ts viruses, which possessed the same shut-off temperature and the same ts lesions as the influenza A/Hong Kong/68-ts-1[E] parent virus, exhibited a pattern of infection and attenuation in hamsters and man similar to their ts parent. These data suggest that ts mutants which are sufficiently attenuated for man, could serve as donors of ts lesions for the rapid production of an attenuated vaccine when new antigenic variants arise. When the influenza A/Hong Kong/68-ts-1[E] virus was administered to children who lacked both anti-haemagglutinin and anti-neuraminidase antibody the virus replicated for a longer period than in adults and mild fever developed in some of the young vaccinees. A minority of children shed wild type revertant virus. The emergence of wild type virus in children, but not in adults, probably reflected the more extensive replication of the virus in the doubly seronegative children. The implications of these findings to the development and testing of live influenza A virus vaccines were discussed.
Generation of high frequency radiation by quasi-optical gyrotron at harmonics of the cyclotron frequency (1983)

A quasi-optical cavity is designed for harmonic operation of gyrotrons. Lower harmonics are suppressed by exploiting their larger diffraction losses, and the field amplitude is kept below the breakdown value by taking advantage of the focusing properties of the radiation in the resonator.
Compressive Radar Imaging (2007)

We introduce a new approach to radar imaging based on the concept of compressive sensing (CS). In CS, a low-dimensional, nonadaptive, linear projection is used to acquire an efficient representation of a compressible signal directly using just a few measurements. The signal is then reconstructed by solving an inverse problem either through a linear program or a greedy pursuit. We demonstrate that CS has the potential to make two significant improvements to radar systems: (i) eliminating the need for the pulse compression matched filter at the receiver, and (ii) reducing the required receiver analog-to-digital conversion bandwidth so that it need operate only at the radar reflectivity's potentially low "information rate" rather than at its potentially high Nyquist rate. These ideas could enable the design of new, simplified radar systems, shifting the emphasis from expensive receiver hardware to smart signal recovery algorithms.
Osteopontin inhibits induction of nitric oxide synthase gene expression by inflammatory mediators in mouse kidney epithelial cells. (1994)

We report that osteopontin (OPN), a secreted, Arg-Gly-Asp-containing phosphoprotein expressed at high levels in the kidney, suppresses nitric oxide (NO) synthesis induced by the inflammatory mediators gamma-interferon and lipopolysaccharide in primary mouse kidney proximal tubule epithelial cells. Northern blot and immunofluorescence analyses of inducible nitric oxide synthase (iNOS) expression revealed that the inflammatory mediators increased iNOS mRNA and protein levels. Recombinant human OPN (purified from both mammalian cells and from Escherichia coli) inhibited this response by a process that was blocked by anti-OPN antiserum and by the peptide GRGDS, but not GRGES. The data suggest that inhibition of NO synthesis by OPN in these kidney cells is mediated by an integrin, possibly the alpha v beta 3 integrin, which is known to be an OPN receptor. NO is believed to control blood flow through the glomerulus, regulating salt and water balance, and to be important as a defense against tumor cells and infecting microorganisms. The ability of OPN to inhibit the induction of iNOS suggests that OPN may be an important regulator of the NO signaling pathway and NO-mediated cytotoxic processes.
Control of Neutron Albedo in Toroidal Fusion Reactors (1983)

The MCNP and ANISN codes have been used to obtain basic neutron albedo data for materials of interest for fusion applications. Simple physical models are presented which explain albedo dependence on pre- and post-reflection variables. The angular distribution of reflected neutrons is found to be roughly cose for all materials and all incident energies and angles. The energy spectra of reflected neutrons are presented, and it is shown that substantial variations in the total current at the outboard wall of a torus can be effected by changing materials behind the inboard wall. Analyses show that a maximum of four isolated incident current environments may be established simultaneously on the outboard side of a torus. With suitable inboard reflectors, global tritium breeding ratios significantly larger than unity can be produced in limited-coverage breeding blankets.
A Self-Stabilizing Synchronization Protocol for Arbitrary Digraphs (2011)

This paper presents a self-stabilizing distributed clock synchronization protocol in the absence of faults in the system. It is focused on the distributed clock synchronization of an arbitrary, non-partitioned digraph ranging from fully connected to 1-connected networks of nodes while allowing for differences in the network elements. This protocol does not rely on assumptions about the initial state of the system, other than the presence of at least one node, and no central clock or a centrally generated signal, pulse, or message is used. Nodes are anonymous, i.e., they do not have unique identities. There is no theoretical limit on the maximum number of participating nodes. The only constraint on the behavior of the node is that the interactions with other nodes are restricted to defined links and interfaces. This protocol deterministically converges within a time bound that is a linear function of the self-stabilization period. We present an outline of a deductive proof of the correctness of the protocol. A bounded model of the protocol was mechanically verified for a variety of topologies. Results of the mechanical proof of the correctness of the protocol are provided. The model checking results have verified the correctness of the protocol as they apply to the networks with unidirectional and bidirectional links. In addition, the results confirm the claims of determinism and linear convergence. As a result, we conjecture that the protocol solves the general case of this problem. We also present several variations of the protocol and discuss that this synchronization protocol is indeed an emergent system.
Design and discovery of 3-aryl-5-substituted-isoquinolin-1-ones as potent tankyrase inhibitors (2015)

The tankyrase proteins (TNKS, TNKS2) are attractive anti-cancer drug targets, particularly as inhibition of their catalytic activity has been shown to antagonise oncogenic WNT signalling.
Machine Learning-based Laundry Weight Estimation for Vertical Axis Washing Machines (2018)

In laundry treatment appliances, the weight of the laundry loaded by the user inside the drum dramatically affects the operating behavior. Therefore, it is important to obtain a good estimate of the said quantity in order to correctly configure the machine before the washing/drying starts. In Vertical Axis Washing Machines the laundry weight is computed by exploiting the quantity of water absorbed by the clothes. However, such approach does not grant accurate results because the water absorption depends on the clothes fabric. For this reason, we propose a Soft Sensing approach for weight estimation that exploits the information obtained from physical sensors available on board without added costs. Data-driven Soft Sensors are developed, where, using Machine Learning techniques, a statistical model of the phenomenon of interest is created from a set of sample data.
Hiding in the Crowd: Privacy Preservation on Evolving Streams through Correlation Tracking (2007)

We address the problem of preserving privacy in streams, which has received surprisingly limited attention. For static data, a well-studied and widely used approach is based on random perturbation of the data values. However, streams pose additional challenges. First, analysis of the data has to be performed incrementally, using limited processing time and buffer space, making batch approaches unsuitable. Second, the characteristics of streams evolve over time. Consequently, approaches based on global analysis of the data are not adequate. We show that it is possible to efficiently and effectively track the correlation and autocorrelation structure of multivariate streams and leverage it to add noise which maximally preserves privacy, in the sense that it is very hard to remove. Our techniques achieve much better results than previous static, global approaches, while requiring limited processing time and memory. We provide both a mathematical analysis and experimental evaluation on real data to validate the correctness, efficiency, and effectiveness of our algorithms.
Double-Blind, Placebo-Controlled, Crossover Trial of Glycine Adjuvant Therapy for Treatment-Resistant Schizophrenia (1996)

These results extend previous findings and suggest an additional approach to the pharmacotherapy of negative symptoms and cognitive deficits in schizophrenia.
Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen‐specific modulation of immune reactivity (2015)

Magnitude and functionality of T helper cell responses differ substantially in season vs. out of season in allergic and non-allergic subjects. The results indicate the specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programmes associated with health and allergic disease.
Pulse generation without gain-bandwidth limitation in a laser with self-similar evolution (2012)

With existing techniques for mode-locking, the bandwidth of ultrashort pulses from a laser is determined primarily by the spectrum of the gain medium. Lasers with self-similar evolution of the pulse in the gain medium can tolerate strong spectral breathing, which is stabilized by nonlinear attraction to the parabolic self-similar pulse. Here we show that this property can be exploited in a fiber laser to eliminate the gain-bandwidth limitation to the pulse duration. Broad (∼200 nm) spectra are generated through passive nonlinear propagation in a normal-dispersion laser, and these can be dechirped to ∼20-fs duration.
Review of sputter deposited mid- to high- temperature solar selective coatings for flat plate/evacuated tube collectors and solar thermal power generation applications (2010)

Solar energy is the most abundant source of renewable energy. Solar radiation is converted into thermal energy and subsequently to electrical energy by solar thermal concentrating systems. Concentrated solar power systems use solar absorbers to convert sunlight to thermal electric power. Solar absorbers are coated with solar selective coatings with high solar absorptance and low thermal emittance. Spectrally selective coatings which are stable up to temperatures  400C (in air and vacuum) have been developed in the past. However, in order to increase the efficiency of solar thermal power plants, solar selective coatings with high thermal stability are required. In recent years, great advances have been made in the field of solar selective coatings with high solar absorptance and low thermal emittance at higher temperatures (T > 450C). Transition metal based solar selective coatings in particular, have emerged as novel high temperature solar selective coatings which can be used for solar thermal power plants for electricity generation. Further research is currently underway in order to increase the thermal stability of the coatings and subsequently improve the efficiency of solar thermal power plants. We present a comprehensive review of sputter deposited mid- to high-temperature solar selective coatings used for solar thermal applications. This report also describes in detail about the commercially available sputter deposited solar selective coatings for flat-plate/evacuated tube collector and solar thermal power generation applications. The worldwide scenario of parabolic trough power plants which are in operation and, under development is discussed in brief.
Design, Fabrication, Characterization, and Evaluation of X-ray Detectors Based on n-type 4H-SiC Epitaxial Layer (2012)

The Schottky barrier diode (SBD) radiation detectors on n-type 4H-SiC epitaxial layer have been designed, fabricated, and evaluated for low energy x-rays detection. The detectors were found to be highly sensitive to x-ray flux in the 50 eV to few keV range and showed significantly improved response compared to the commercial of-the-shelf (COTS) SiC UV photodiodes. Thermally stimulated current (TSC) measurements performed in wide temperature range (94 - 550 K) revealed low density of deep level centers in the epitaxial layer. The high quality of the epitaxial layer was confirmed by XRD rocking curve measurements and defect delineating chemical etching. The detectors fabricated on 4H-SiC epitaxial layers exhibited low leakage current at 475 K (< 1 nA at 200 V) revealing great possibility of high temperature operation.
Process for CO<sub>2</sub> Capture from High-Pressure and Moderate-Temperature Gas Streams (2012)

A novel CO2 capture process was developed using a Mg(OH)2-based sorbent suitable for warm gas CO2 removal from high-pressure coal gasification gas streams. The purpose of this study is to perform a preliminary energy study and develop a method to implement this sorbent in a power plant. The proposed CO2 removal process involves sorption of CO2 at 200–300 °C and regeneration at 385 °C. The operational temperature is ideal for CO2 capture downstream to the water–gas shift reactor in an integrated gasification combined cycle (IGCC) power plant but is applicable to other warm gas cleanup processes as well. This technology offers the ability to fully utilize the potential efficiency increases associated with warm gas clean up. Additionally, the sorbent is able to operate in the presence of steam, which distinguishes it from other technologies that require an energy-intensive drying step prior to CO2 separation. Regeneration is carried out at 280 psi and 400 °C, resulting in a high-pressure CO2 product stream, which significantly reduces the auxiliary load normally associated with CO2 compression for sequestration. The chemistry of the sorption process also reduces the amount of steam traditionally required for the water–gas shift reactor by 50%, increasing the overall efficiency of the plant. The incorporation of the sorbent and the described methods resulted in an overall IGCC power plant efficiency greater than that of the competing Selexol technology.
Plasmonic color printing (2015)

In this paper we present our recent work on plasmonic color printing using metallic nanostructures. This is a new form of structural color where colors arise due to the local resonances of metallic nanostructures instead of diffractive effects. These metal nanostructures combined with a backreflector support plasmon resonances that can span the entire visible range by varying the dimensions of the structures. As the structures are in the ~100 nm length scale are based on metals, plasmonic color printing enables high resolution and fade-free prints. We show experimental results and compare calculated reflectance spectra from metals such as gold, silver and aluminum used in creating miniaturized color images on Si substrates.