gebhart/patrepeval huggingface dataset:
Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution (2012)

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550 – 1720 cm-1). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library. 1.
High performance quantum cascade lasers with superlattice active regions (1999)

Quantum cascade (QC) lasers based on optical transitions between mimbands in superlattices (SL)1 are an interesting alternative to standard QC laser designs featuring a vertical intersubband transition in double quantum well active regions.2
Near infrared bioluminescence resonance energy transfer from firefly luciferase—quantum dot bionanoconjugates (2014)

The bioluminescence resonance energy transfer (BRET) between firefly luciferase enzymes and semiconductive quantum dots (QDs) with near infrared emission is described. The QD were phase transferred to aqueous buffers using a histidine mediated phase transfer route, and incubated with a hexahistidine tagged, green emitting variant of firefly luciferase from Photinus pyralis (PPyGRTS). The PPyGRTS were bound to the QD interface via the hexahistidine tag, which effectively displaces the histidine layer and binds directly to the QD interfaces, allowing for short donor-acceptor distances (∼5.5 nm). Due to this, high BRET efficiency ratios of ∼5 were obtained. These PPyGRTS-QD bio-nano conjugates were characterized by transmission electron microscopy, thermal gravimetric analysis, Fourier transform infrared spectroscopy and BRET emission studies. The final optimized conjugate was easily observable by night vision imaging, demonstrating the potential of these materials in imaging and signaling/sensing applications.
STAR (2002)

With increasing demand for multimedia applications, local area network (LAN) technologies are rapidly being upgraded to provide support for quality of service (QoS). In a network that consists of an interconnection of multiple LANs via bridges, the QoS of a flow depends on the length of an end-to-end forwarding path. In the IEEE 802.1D standard for bridges, a spanning tree is built among the bridges for loop-free frame forwarding. Albeit simple, this approach does not support all-pair shortest paths. In this paper, we present a novel bridge protocol, the Spanning Tree Alternate Routing (STAR) Bridge Protocol, that attempts to find and forward frames over alternate paths that are provably shorter than their corresponding tree paths. Being backward compatible to IEEE 802.1D, our bridge protocol allows cost-effective performance enhancement of an existing extended LAN by incrementally replacing a few bridges in the extended LAN by the new STAR bridges. We develop a strategy to ascertain bridge locations for maximum performance gain. Our study shows that we can significantly improve the end-to-end performance when deploying our bridge protocol.
A One‐Step Staining Probe for Phosphatidylethanolamine (2015)

Phosphatidylethanolamine (PE) is an abundant phospholipid in cellular membranes, but relatively little is known about the kinetics of PE in biological membrane systems. Characterizing PE on a cellular level has been challenging owing to a lack of proper molecular tools. The lantibiotic duramycin and its structural analogue, cinnamycin, are currently the only known polypeptides that have an established stereospecific structure for binding membrane PE with high affinity and high specificity. These lantibiotics are recognized for their potential as molecular probes for studying PE kinetics in various membranes. However, owing to their antibiotic nature, duramycin and cinnamycin exhibit appreciable levels of cytotoxicity at low micromolar concentrations in cultured mammalian cells by inducing membrane distortion and possible PE redistribution. These issues can potentially complicate study design and data interpretation. Here, we report the construction of a molecular probe consisting of duramycin attached to the C terminus of green fluorescent protein (GFP) by a PEG linker at a stoichiometry of 1. The construct retained specific binding toward PE and essentially no cytotoxicity compared to native duramycin. The biological utilities of this probe were demonstrated in a number of cellular staining studies involving PE dynamics. The availability of a one-step, nontoxic molecular probe for PE will enable characterization of the biology of this important phospholipid.
A novel adaptive synthetic aperture radar ship detection system (2011)

The detection and characterization of vessels from space-based synthetic aperture radar (SAR) imagery has many applications, from monitoring fisheries to port security. Ideally, the detection and characterization of ships in SAR imagery should occur in a reliable and automated fashion. Additionally, given the wide variability in SAR imaging systems and imaging modes, it is desirable to have a SAR ship detection system capable of detecting ships independent of the system or mode. There are currently a wide range of SAR ship detection systems, for which many review papers have been written [3-7]. However, most operational SAR ship detection systems to date have been tailored to specific sensors or imaging modes. In addition, most produce significant false alarms, and often operate ideally in a semi-automated fashion.
An outbreak of virulent systemic feline calicivirus disease (2004)

Outbreaks of highly virulent FCV disease are increasingly common. Strains causing such outbreaks have been genetically distinct from one another but caused similar disease signs and were resistant to vaccination. All cats with suspicious signs (including upper respiratory tract infection) should be handled with strict hygienic precautions. Sodium hypochlorite solution should be used for disinfection following suspected contamination. All exposed cats should be isolated until negative viral status is confirmed. Chronic viral shedding is possible but may not be clinically important. This and similar outbreaks have been described as being caused by hemorrhagic fever-like caliciviruses, but hemorrhage is uncommonly reported. Virulent systemic FCV infection is suggested as an alternative description.
Speed improvement of object recognition using Boundary-Bitmap of histogram of oriented Gradients (2016)

Commonly, HoG/SVM classifier uses rectangular images for HoG feature descriptor extraction and training. This means that significant additional work has to be done to process irrelevant pixels belonging to the background surrounding the object of interest. Moreover, some areas of the foreground also can be eliminated from the processing to improve the algorithm speed and memory wise. In Boundary-Bitmap HoG approach proposed in this paper, the boundary of irregular shape of the object is represented by a bitmap to avoid processing of extra background and (partially) foreground pixels. Bitmap, derived from the training dataset, encodes those portions of an image to be used to train a classifier. Experimental results show that not only the proposed algorithm decreases the workload associated with HoG/SVM classifiers by 92.5% compared to the state-of-the-art, but also it shows an average increase about 6% in recall and a decrease about 3% in precision in comparison with standard HoG.
Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 .ANG. resolution (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 .ANG. resolutionJohn R. Gunn, Alessandro Monge, Richard A. Friesner, and Christopher H. MarshallCite this: J. Phys. Chem. 1994, 98, 2, 702–711Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/j100053a053https://doi.org/10.1021/j100053a053research-articleACS PublicationsRequest reuse permissionsArticle Views53Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Design and Development of Aerogel-Based Antennas for Aerospace Applications: A Final Report to the NARI Seedling (2014)

As highly porous solids possessing low density and low dielectric permittivity combined with good mechanical properties, polyimide (PI) aerogels offer great promise as an enabling technology for lightweight aircraft antenna systems. While they have been aggressively explored for thermal insulation, barely any effort has been made to leverage these materials for antennas or other applications that take advantage of their aforementioned attributes. In Phase I of the NARI Seedling Project, we fabricated PI aerogels with properties tailored to enable new antenna concepts with performance characteristics (wide bandwidth and high gain) and material properties (low density, environmental stability, and robustness) superior to the state of practice (SOP). We characterized electromagnetic properties, including permittivity, reflectivity, and propagation losses for the aerogels. Simple, prototype planar printed circuit patch antennas from down-selected aerogel formulations were fabricated by molding the aerogels to net shapes and by gold-metalizing the pattern onto the templates via electron beam evaporation in a clean room environment. These aerogel based antennas were benchmarked against current antenna SOP, and exhibited both broader bandwidth and comparable or higher gain performance at appreciably lower mass. Phase II focused on the success of the Phase I results pushing the PI aerogel based antenna technology further by exploring alternative antenna design (i.e., slot coupled antennas) and by examining other techniques for fabricating the antennas including ink jet printing with the goal of optimizing antenna performance and simplifying production. We also examined new aerogel formulations with better moisture and solvent resistance to survive processing conditions. In addition, we investigated more complex antenna designs including passive phased arrays such as 2x4 and 4x8 element arrays to assess the scalability of the aerogel antenna concept. Furthermore, we explored the possibility of developing these arrays in thin, flexible form to make conformable antennas.
<title>Negative electron affinity photocathodes as high-performance electron sources. Part 1: achievement of ultrahigh brightness from an NEA photocathode</title> (1995)

Brightness, energy spread and emission area are key parameters of electron sources for instruments such as electron microscopes and electron beam lithography tools. In developing transmission-mode NEA photocathodes as sources for these applications, these characteristics have been measured in specialized sealed tubes. Average lateral energies were measured at 63 meV for 1.5 micron thick photocathode, and 83 meV for a 0.5 micron thick photocathode, which was known to be emitting `hot' electrons. A current density of 841 A/cm<SUP>2</SUP> was obtained from a 1.7 micron diameter emission area. This high current density can be explained in terms of lateral drift and diffusion of surface trapped electrons. Combined angular and current density data indicate a brightness of approximately 10<SUP>8</SUP> A/cm<SUP>2</SUP>-sr at 3 kV.
Identity of a peptide domain of human C9 that is bound by the cell-surface complement inhibitor, CD59 (1994)

The CD59 antigen is a plasma membrane glycoprotein that serves as an inhibitor of the C5b-9 complex of complement. This inhibitory activity appears related to the capacity of CD59 to bind with high affinity to sites that are nascently exposed in the alpha-chain subunit of human C8, as well as within the C9b domain (amino acid residues 245-538) of human C9, during assembly of the C5b-9 complex on the target membrane (Ninomiya, H., and Sims, P. J. (1992) J. Biol. Chem. 267, 13675-13680). The CD59 binding site in C9 was first investigated by N-terminal sequencing of CD59-binding peptides generated by limited digest of the isolated C9b domain. These experiments revealed a 17-kDa fragment (starting at C9 residue Thr-320) that retained affinity for CD59, suggesting the possibility for localizing the CD59 binding site by mapping with small C9-derived peptides. Peptides spanning the entire C9b sequence were expressed in Escherichia coli and then probed with CD59. CD59 bound specifically to all peptides starting N-terminal to C9 residue 359 with C termini extending beyond residue 411. Little to no CD59 binding was observed for various C9-derived peptides that started C-terminal to residue 359 or that were truncated N-terminal to residue 411. Affinity-purified antibody against C9 residues 320-411 inhibited CD59 binding to C9 by > 50% and completely inhibited its binding to the isolated C9b domain. Little to no specific binding of CD59 was detected for peptides restricted to the putative hinge domain within C9b (residues 245-271). These results indicate that a CD59 binding site is located between residues 320 and 411 of the C9 polypeptide and suggest that the affinity of this site is principally determined by residues 359-411.
Modeling Acoustic Correlations by Factor Analysis (1997)

Hidden Markov models (HMMs) for automatic speech recognition rely on high dimensional feature vectors to summarize the short-time properties of speech. Correlations between features can arise when the speech signal is non-stationary or corrupted by noise. We investigate how to model these correlations using factor analysis, a statistical method for dimensionality reduction. Factor analysis uses a small number of parameters to model the covariance struc-ture of high dimensional data. These parameters are estimated by an Expectation-Maximization (EM) algorithm that can be em-bedded in the training procedures for HMMs. We evaluate the combined use of mixture densities and factor analysis in HMMs that recognize alphanumeric strings. Holding the total number of parameters fixed, we find that these methods, properly combined, yield better models than either method on its own. 1
Polyketide Biosynthesis beyond the Type I, II, and III Polyketide Synthase Paradigms: A Progress Report (2007)

The archetypical polyketide synthases (PKSs), known as type I, II, and III PKSs, have accounted for the vast structural diversities embodied by polyketide natural products, but recent progress in polyketide biosynthesis clearly suggests much greater diversity for PKS mechanism and structure. We have previously argued the emergence of novel PKSs and cautioned the oversimplification of polyketide biosynthesis according to the type I, II, and III PKS paradigms on the basis of our studies on the biosynthesis of the enediynes, the macrotetrolides, and leinamycin. We present here a brief progress report on our current effort to mechanistically characterize these novel PKSs.
Robotically-aligned optical coherence tomography with 5-degree of freedom eye tracking for subject motion and gaze compensation (Conference Presentation) (2020)

Optical coherence tomography (OCT) has revolutionized diagnostics in ophthalmology. However, OCT traditionally requires an operator and patient cooperation to align a scanner with the subject’s eye and image a specific location of the retina. We have developed a robot-mounted OCT scanner that automatically aligns with the subjects’ eye by compensating motion and gaze. In addition to using face and pupil tracking feedback to align the scanner, the system uses gaze feedback to track a retinal region of interest, such as the fovea. We demonstrate our system by tracking the fovea of human eyes subject to physiological motion and gaze change.
New approach to cross-polarized optical coherence tomography based on orthogonal arbitrarily polarized modes (2007)

A novel cross-polarized optical coherence tomography (CP-OCT) system based on standard isotropic single-mode fiber has been developed. We exploit the property of an arbitrary pair of orthogonal waves propagating in a single-mode fiber to maintain their orthogonality in the absence of anisotropy losses, regardless of the induced phase anisotropy. The well-known isotropic fiber based OCT scheme that commonly comprises an optical probe with a Fizeau interferometer and a compensating Michelson interferometer with Faraday mirrors is modified. We introduce an additional optical element to form the initial radiation as two mutually time-delayed and strictly orthogonal polarized waves. The suggested scheme allows reaching very low level of cross talk in co and cross-polarized images.
A Novel Estrogen Receptor Intramolecular Folding–based Titratable Transgene Expression System (2009)

The use of regulated gene expression systems is important for successful gene therapy applications. In this study, ligand-induced structural change in the estrogen receptor (ER) was used to develop a novel ER intramolecular folding-based transcriptional activation system. The system was studied using ER-variants of different lengths, flanked on either side by the GAL4-DNA-binding domain and the VP16-transactivation domain (GAL4(DBD)-ER-VP16). The ER ligands of different types showed efficient ligand-regulated transactivation. We also characterized a bidirectional transactivation system based on the ER and demonstrated its utility in titrating both reporter and therapeutic gene expression. The ligand-regulated transactivation system developed by using a mutant form of the ER (G521T, lacking affinity for the endogenous ligand 17beta-estradiol, whereas maintaining affinity for other ligands) showed efficient activation by the ligand raloxifene in living mice without significant interference from the circulating endogenous ligand. The ligand-regulated transactivation system was used to test the therapeutic efficiency of the tumor suppressor protein p53 in HepG2 (p53(+/+)) and SKBr3 (p53(-/-)/mutant-p53(+/+)) cells in culture and tumor xenografts in living mice. The multifunctional capabilities of this system should be useful for gene therapy applications, to study ER biology, to evaluate gene regulation, ER ligand screening, and ER ligand biocharacterization in cells and living animals.
Hybrid Window and Rate Based Congestion Control for Delay Sensitive Applications (2010)

There has been a dramatic increase in interactive cloud based software applications. Compared to classical real-time media applications (voice over IP (VoIP)/conferencing) and non real-time file delivery, these interactive software applications have unique characteristics: 1) they are delay sensitive yet demand in order and reliable data delivery, and 2) the traffic is usually bursty. Traditional window based congestion control does not work well for interactive applications because the bursty arrival of data leads to bursty network traffic, which causes additional queuing delay and packet loss in the network which reduces its delay performance. In this paper, we propose a new hybrid window plus rate based congestion control technique. This algorithm improves the delay performance of interactive applications by preventing congestion induced loss and minimizing queuing delay while still fully utilizing network capacity and maintaining fairness across multiple flows.
Modular and Processable Fluoropolymers Prepared via a Safe, Mild, Iodo–Ene Polymerization (2019)

Fluoropolymers have infiltrated society as coatings and insulators. However, low processability, few opportunities for polymer functionalization, and explosive monomers hampering academic investigation of these materials have precluded the extension of the unique properties of perfluorocarbons to the cutting edge of material science. Here, we present semifluorinated iodo-ene polymers as a scaffold to overcome fluoropolymer limitations. A sodium dithionate initiated polymerization of perfluorodiiodides and dienes allows for high-molecular-weight polymers (>100 kDa) to be prepared in the presence of oxygen and water with up to 59 wt % fluorine content. These conditions are sufficiently mild to enable the polymerization of functional dienes, leading to biodegradable fluoropolymers. The iodo-ene polymerization results in the addition of polarizable iodine atoms, which improve polymer processability; yet, these atoms can be removed after processing for enhanced stability. Displacement of the iodine atoms with thiols or azides facilitates covalent surface modification and cross-linking. Finally, the low bond dissociation energy of the C-I bond allows allyl group addition as well as photo-cross-linking. Collectively, the simple synthesis and modular nature of the semifluorinated iodo-ene polymers will enable the convergence of perfluorocarbons and advanced materials.