gebhart/patrepeval huggingface dataset:
Prevalence of and Risk Factors for Age-Related Macular Degeneration in a Multiethnic Asian Cohort (2011)

The prevalence of AMD was similar in the 3 major ethnic groups in Asia and comparable with white populations. Myopic refractive error was associated with reduced risk of AMD in Chinese men.
Speed-of-light effects in high-resolution long-cavity fiber Fabry–Perot scanning interferometers (1993)

High-resolution fiber Fabry–Perot scanning interferometers demonstrate bandwidths from 20 MHz to 4 kHz with corresponding cavity lengths from 26 mm to 500 m. Finite speed-of-light effects are observed for cavity lengths as short as 5 m. Analytical and experimental results show an inverse square-root dependence of bandwidth on cavity length in the speed-of-light-limited regime.
A Pliable Index Coding Approach to Data Shuffling (2017)

A promising research area that has recently emerged, is on how to use index coding to improve the communication efficiency in distributed computing systems, especially for data shuffling in iterative computations. In this paper, we posit that pliable index coding can offer a more efficient framework for data shuffling, as it can better leverage the many possible shuffling choices to reduce the number of transmissions. We theoretically analyze pliable index coding under data shuffling constraints, and design a hierarchical data-shuffling scheme that uses pliable coding as a component. We find benefits up to $O(ns/m)$ over index coding, where $ns/m$ is the average number of workers caching a message, and $m$, $n$, and $s$ are the numbers of messages, workers, and cache size, respectively.
1P264 Control of kinesin-microtubule motility by caged peptides derived from the kinesin C-terminus domain(9. Molecular motor (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006)

Kinesin is a motoT protcin LhaL meves along a microtubule (MT) tovvard thc p]us end. A number of kinesin molecules are involvcd in intracellular transportalions. In
MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins (2017)

Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3'UTR of either SOS1 or SOS2. Each of the 3'UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.
Membrane Association of Greasy Grouper Nervous Necrosis Virus Protein A and Characterization of Its Mitochondrial Localization Targeting Signal (2004)

Localization of RNA replication to intracellular membranes is a universal feature of positive-strand RNA viruses. The betanodavirus greasy grouper (Epinephelus tauvina) nervous necrosis virus (GGNNV) is a positive-RNA virus with one of the smallest genomes among RNA viruses replicating in fish cells. To understand the localization of GGNNV replication complexes, we generated polyclonal antisera against protein A, the GGNNV RNA-dependent RNA polymerase. Protein A was detected at 5 h postinfection in infected sea bass cells. Biochemical fractionation experiments revealed that GGNNV protein A sedimented with intracellular membranes upon treatment with an alkaline pH and a high salt concentration, indicating that GGNNV protein A is tightly associated with intracellular membranes in infected cells. Confocal immunofluorescence microscopy and bromo-UTP incorporation studies identified mitochondria as the intracellular site of protein A localization and viral RNA synthesis. In addition, protein A fused with green fluorescent protein (GFP) was detected in the mitochondria in transfected cells and was demonstrated to be tightly associated with intracellular membranes by biochemical fractionation analysis and membrane flotation assays, indicating that protein A alone was sufficient for mitochondrial localization in the absence of RNA replication, nonstructural protein B, or capsid proteins. Three sequence analysis programs showed two regions of hydrophobic amino acid residues, amino acids 153 to 173 and 229 to 249, to be transmembrane domains (TMD) that might contain a membrane association domain. Membrane fraction analysis showed that the major domain is N-terminal amino acids 215 to 255, containing the predicted TMD from amino acids 229 to 249. Using GFP as the reporter by systematically introducing deletions of these two regions in the constructs, we further confirmed that the N-terminal amino acids 215 to 255 of protein A function as a mitochondrial targeting signal.
Extracting Entities and Events from Cyber-Physical Security Incident Reports (2022)

Cyber- physical systems are an important part of many industries such as the chemical process industry, manufac- turing industry, automobiles, and even sophisticated weaponry. Given the economic importance and influence of these systems, they have increasingly faced the cybersecurity attacks. In this paper, we provide a dataset of real-life security incident reports on cyber-physical systems annotated with entities and events that are important for analysing such security incidents. We analyze and identify the limitations of the 'Domain Objects' in Structured Threat Information Expression (STIX) standard as well as recent research literature for the entity type clas- sification schemes in cybersecurity domain. We propose an updated classification scheme for entity types in the cybersecurity domain. The enhanced coverage provided by the entity scheme is important for automated information extraction and natural language understanding of textual reports containing details of the cybersecurity incident reports. We use deep-learning based sequence labelling techniques and cybersecurity domain specific word embed dings to set up a benchmark for entity and event extraction for cyber- physical security incident report analysis. The annotated dataset of real-life industrial security incidents will be made available for research purpose.
Fabrication of Silica Particles Functionalized with Chromophores and Amino Groups Using Synergism of Poly(vinylamine) Adsorption and Nucleophilic Aromatic Substitution with Fluoroaromatics (2006)

Nucleophilic aromatic substitution reactions of fluoronitro-substituted aromatic compounds with poly(vinylamine) (PVAm)/silica adsorbates were studied to equip silica particles with primary amino as well as several chromophoric groups. 4-Fluoronitrobenzene (1, 4-FNB), 2-fluoronitrobenzene (2, 2-FNB), 4-fluoro-3-nitroaniline (3, 4-FNA), N,N-dimethyl-4-fluoro-3-nitroaniline (4, 4-DMFNA), 1-fluoro-2,4-dinitrobenzene (5, Sangers reagent, FDNB), 1,5-difluoro-2,4-dinitrobenzene (6, DFDNB), 4-fluoro-3-nitroazobenzene (7, FNAzoB), N-(2‘,4‘-dinitrophenyl)-4-fluoro-3-nitroaniline (8, N-DNP-FNA), and 4-fluoro-3,4‘-dinitrostilbene (9, FDNstilbene) have been used as functionalization reagents. Various chromophoric functionalities could be readily synthesized on the silica surface by this elegant method. The degree of PVAm functionalization with chromophores was determined from the redissolved fraction of the functionalized polymer by means of UV/vis spectroscopy using model compounds as references. The surface structures of the chromophores fixed on polymer-modified silica particles were studied using X-ray photoelectron spectroscopy (XPS) and UV/vis spectroscopy. Brunauer−Emmett−Teller (BET) measurements and XPS studies suggest that the chromophores introduced in the PVAm layer on silica are differently distributed in the adsorbed PVAm layers. The vertical distribution of the chromophore in the PVAm layer depends on the reactivity of the fluoroaromatic. The more reactive the fluoroaromatic, the more unaffected remains the former pore-size distribution of silica. Changes of the surface charge were investigated by means of electrokinetic measurements.
Consequences of resistance: in vitro fitness, in vivo infectivity, and transmissibility of oseltamivir‐resistant influenza A viruses (2012)

The development of drug resistance is a major drawback to any antiviral therapy, and the specific anti-influenza drugs, the neuraminidase (NA) inhibitors (NAIs), are not excluded from this rule. The impact of drug resistance depends on the degree of reduction in fitness of the particular drug-resistant virus. If the resistance mutations lead to only a modest biological fitness cost and the virus remains highly transmissible, the effectiveness of antiviral use is likely to be reduced. This review focuses on the fitness of oseltamivir-resistant seasonal H1N1 and H3N2, 2009 pandemic H1N1 (H1N1pdm09), and highly pathogenic H5N1 influenza A viruses carrying clinically derived NAI resistance-associated NA mutations.
Design rules for quantum imaging devices: experimental progress using CMOS single-photon detectors (2006)

We continue our previous program<sup>1</sup> where we introduced a set of quantum-based design rules directed at quantum engineers who design single-photon quantum communications and quantum imaging devices. Here, we report on experimental progress using SPAD (single photon avalanche diode) arrays of our design and fabricated in CMOS (complementary metal oxide semiconductor) technology. Emerging high-resolution imaging techniques based on SPAD arrays have proven useful in a variety of disciplines including bio-fluorescence microscopy and 3D vision systems. They have also been particularly successful for intra-chip optical communications implemented entirely in CMOS technology. More importantly for our purposes, a very low dark count allows SPADs to detect rare photon events with a high dynamic range and high signal-to-noise ratio. Our CMOS SPADs support multi-channel detection of photon arrivals with picosecond accuracy, several million times per second, due to a very short detection cycle. The tiny chip area means they are suitable for highly miniaturized quantum imaging devices and that is how we employ them in this paper. Our quantum path integral analysis of the Young-Afshar-Wheeler interferometer showed that Bohr's complementarity principle was not violated due the previously overlooked effect of photon bifurcation within the lens--a phenomenon consistent with our quantum design rules--which accounts for the loss of which-path information in the presence of interference. In this paper, we report on our progress toward the construction of quantitative design rules as well as some proposed tests for quantum imaging devices using entangled photon sources with our SPAD imager.
Anxiolytic- and antidepressant-like profiles of the galanin-3 receptor (Gal 3 ) antagonists SNAP 37889 and SNAP 398299 (2005)

The neuropeptide galanin mediates its effects through the receptor subtypes Gal(1), Gal(2), and Gal(3) and has been implicated in anxiety- and depression-related behaviors. Nevertheless, the receptor subtypes relevant to these behaviors are not known because of the lack of available galanin-selective ligands. In this article, we use behavioral, neurochemical, and electrophysiological approaches to investigate the anxiolytic- and antidepressant-like effects of two potent small-molecule, Gal(3)-selective antagonists, SNAP 37889 and the more soluble analog SNAP 398299. Acute administration of SNAP 37889 or SNAP 398299 enhanced rat social interaction. Furthermore, acute SNAP 37889 was also shown to reduce guinea pig vocalizations after maternal separation, to attenuate stress-induced hyperthermia in mice, to increase punished drinking in rats, and to decrease immobility and increase swimming time during forced swim tests with rats. Moreover, SNAP 37889 increased the social interaction time after 14 days of treatment and maintained its antidepressant effects during forced swim tests with rats after 21 days of treatment. In microdialysis studies, SNAP 37889 partially antagonized the galanin-evoked reduction in hippocampal serotonin (5-hydroxytryptamine, 5-HT), as did the 5-HT(1A) receptor antagonist WAY100635. Their combination produced a complete reversal of the effect of galanin. SNAP 398299 partially reversed the galanin-evoked inhibition of dorsal raphe cell firing and galanin-evoked hyperpolarizing currents. These results indicate that Gal(3)-selective antagonists produce anxiolytic- and antidepressant-like effects, possibly by attenuating the inhibitory influence of galanin on 5-HT transmission at the level of the dorsal raphe nucleus.
Multiparty Key Exchange, Efficient Traitor Tracing, and More from Indistinguishability Obfuscation. (2013)

In this work, we show how to use indistinguishability obfuscation (iO) to build multiparty key exchange, efficient broadcast encryption, and efficient traitor tracing. Our schemes enjoy several interesting properties that have not been achievable before: • Our multiparty non-interactive key exchange protocol does not require a trusted setup. Moreover, the size of the published value from each user is independent of the total number of users. • Our broadcast encryption schemes support distributed setup, where users choose their own secret keys rather than be given secret keys by a trusted entity. The broadcast ciphertext size is independent of the number of users. • Our traitor tracing system is fully collusion resistant with short ciphertexts, secret keys, and public key. Ciphertext size is logarithmic in the number of users and secret-key size is independent of the number of users. Our public key size is polylogarithmic in the number of users. The recent functional encryption system of Garg, Gentry, Halevi, Raykova, Sahai, and Waters also leads to a traitor tracing with similar ciphertext and secret key size, but the construction in this paper is simpler and more direct. These constructions resolve an open problem relating to differential privacy. • Generalizing our traitor tracing system gives a private broadcast encryption scheme (where broadcast ciphertexts reveal minimal information about the recipient set) with optimal size ciphertext. Our proof of security for private broadcast encryption and traitor tracing introduces a new tool for iO proofs: the construction makes use of a key-homomorphic symmetric cipher which plays a crucial role in the proof of security.
Assessment of the Technologies for Molecular Biodosimetry for Human Low-Dose Radiation Exposure Symposium (2009)

Exposure to ionizing radiation produces few immediate outwardly-visible clinical signs, yet, depending on dose, can severely damage vital physiological functions within days to weeks and produce long-lasting health consequences among survivors. In the event of a radiological accident, the rapid evaluation of the individual absorbed dose is paramount to discriminate the worried but unharmed from those individuals who must receive medical attention. Physical, clinical and biological dosimetry are usually combined for the best dose assessment. However, because of the practical limits of physical and clinical dosimetry, many attempts have been made to develop a dosimetry system based on changes in biological parameters, including techniques for hematology, biochemistry, immunology, cytogenetics, etc. Lymphocyte counts and chromosome aberrations analyses are among the methods that have been routinely used for estimating radiation dose. However, these assays require several days to a week to be completed and therefore cannot be used to obtain a fast estimate of the dose during the first few days after exposure when the information would be most critical for identifying victims of radiation accidents who could benefit the most by medical intervention. The steadily increasing sophistication in our understanding of the early biochemical responses of irradiated cells and tissues provides the opportunity for developing mechanism-based biosignatures of exposure. Compelling breakthroughs have been made in the technologies for genome-scale analysis of cellular transcriptional and proteomic profiles. There have also been major strides in the mechanistic understanding of the early events in DNA damage and radiation damage products, as well as in the cellular pathways that lead to radiation injury. New research with genomic- and proteomic-wide tools is showing that within minutes to hours after exposure to ionizing radiation protein machines are modified and activated, and large-scale changes occur in the gene expression profile involving a broad variety of cell-process pathways after a wide range of both low (<10 cGy) and high dose (>10 cGy) exposures. Evaluation of these potential gene and protein biomarkers for early and late diagnostic information will be critical for determining the efficacy of the signatures to both low and high dose IR exposures. Also needed are approaches that enable rapid handling and processing for mass-casualty and population triage scenarios. Development of in vivo model system will be crucial for validating both the biological and the instrumentation for biodosimetry. Such studies will also help further understanding of the molecular mechanisms of the biological effects of radiation and the differences of responses due to individual genetic variation.
Efficient production of free fatty acids from soybean meal carbohydrates (2015)

Conversion of biomass feedstock to chemicals and fuels has attracted increasing attention recently. Soybean meal, containing significant quantities of carbohydrates, is an inexpensive renewable feedstock. Glucose, galactose, and fructose can be obtained by enzymatic hydrolysis of soluble carbohydrates of soybean meal. Free fatty acids (FFAs) are valuable molecules that can be used as precursors for the production of fuels and other value-added chemicals. In this study, free fatty acids were produced by mutant Escherichia coli strains with plasmid pXZ18Z (carrying acyl-ACP thioesterase (TE) and (3R)-hydroxyacyl-ACP dehydratase) using individual sugars, sugar mixtures, and enzymatic hydrolyzed soybean meal extract. For individual sugar fermentations, strain ML211 (MG1655 fadD(-) fabR(-) )/pXZ18Z showed the best performance, which produced 4.22, 3.79, 3.49 g/L free fatty acids on glucose, fructose, and galactose, respectively. While the strain ML211/pXZ18Z performed the best with individual sugars, however, for sugar mixture fermentation, the triple mutant strain XZK211 (MG1655 fadD(-) fabR(-) ptsG(-) )/pXZ18Z with an additional deletion of ptsG encoding the glucose-specific transporter, functioned the best due to relieved catabolite repression. This strain produced approximately 3.18 g/L of fatty acids with a yield of 0.22 g fatty acids/g total sugar. Maximum free fatty acids production of 2.78 g/L with a high yield of 0.21 g/g was achieved using soybean meal extract hydrolysate. The results suggested that soybean meal carbohydrates after enzymatic treatment could serve as an inexpensive feedstock for the efficient production of free fatty acids.
Evaluation of bonding between oxygen plasma treated polydimethyl siloxane and passivated silicon (2006)

Oxygen plasma treatment has been used extensively to bond polydimethyl siloxane to polydimethyl siloxane or glass in the rapid prototyping of microfluidic devices. This study aimed to improve the bonding quality of polydimethyl siloxane to passivated silicon using oxygen plasma treatment, and also to evaluate the bonding quality. Four types of passivated silicon were used: phosphosilicate glass, undoped silicate glass, silicon nitride and thermally grown silicon dioxide. Bonding strength was evaluated qualitatively and quantitatively using manual peel and mechanical shear tests respectively. Through peel tests we found that the lowering of plasma pressure from 500 to 30 mTorr and using a plasma power between 20 to 60 W helped to improve the bond quality for the first three types of passivation. Detailed analysis and discussion were conducted to explain the discrepancy between the bonding strength results and peeling results. Our results suggested that polydimethyl siloxane can be effectively bonded to passivated silicon, just as to polydimethyl siloxane or glass.
Novel LDPE/halloysite nanotube films with sustained carvacrol release for broad-spectrum antimicrobial activity (2015)

Halloysite nanotubes are employed as nanocarriers of carvacrol, allowing for its high-temperature melt compounding with polyethylene, and resulting in highly potent antimicrobial films.
Effect of TCP on UMTS-HSDPA system performance and capacity (2005)

An analytical model to evaluate the impact of TCP on the UMTS-HSDPA capacity is presented. A method to minimize the effect of TCP on wireless networks using shared channels is also proposed. HSDPA (high speed downlink packet access) achieves higher aggregate bit rates through the introduction of adaptive modulation and coding, hybrid ARQ, fast scheduling, fast cell selection and MIMO (space time coding and BLAST) techniques. The proposed model is used to evaluate the effect of the TCP protocol on the bit rate of various data services (at 64 and 128 Kbps). As expected, the bit rate per flow decreases strongly if congestion in the wired network increases. However, the capacity achieved by HSDPA is not as affected by TCP. Using this result, a method to maintain the bit rate per TCP flow at a given value without losing much cell capacity is proposed. The findings are supported by simulation results.
Expanding the Functional Group Compatibility of Small‐Molecule Microarrays: Discovery of Novel Calmodulin Ligands (2003)

The importance of the pKa value: Phenols, carboxylic acids, and compounds containing comparably acidic functional groups are covalently captured on a diazobenzylidene-functionalized glass surface. This new covalent slide-capture method has been used to print 6336 diversity-oriented synthesis-derived phenol-containing fused bicycles and tetracycles, from which new calmodulin ligands were identified (see schematic representation). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51043_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.