gebhart/patrepeval huggingface dataset:
Cognitive Database: A Step towards Endowing Relational Databases with Artificial Intelligence Capabilities (2017)

We propose Cognitive Databases, an approach for transparently enabling Artificial Intelligence (AI) capabilities in relational databases. A novel aspect of our design is to first view the structured data source as meaningful unstructured text, and then use the text to build an unsupervised neural network model using a Natural Language Processing (NLP) technique called word embedding. This model captures the hidden inter-/intra-column relationships between database tokens of different types. For each database token, the model includes a vector that encodes contextual semantic relationships. We seamlessly integrate the word embedding model into existing SQL query infrastructure and use it to enable a new class of SQL-based analytics queries called cognitive intelligence (CI) queries. CI queries use the model vectors to enable complex queries such as semantic matching, inductive reasoning queries such as analogies, predictive queries using entities not present in a database, and, more generally, using knowledge from external sources. We demonstrate unique capabilities of Cognitive Databases using an Apache Spark based prototype to execute inductive reasoning CI queries over a multi-modal database containing text and images. We believe our first-of-a-kind system exemplifies using AI functionality to endow relational databases with capabilities that were previously very hard to realize in practice.
Toward Variable-Rate Generative Compression by Reducing the Channel Redundancy (2020)

Compressing large images with a generative model goes beyond typical image encoding standards under a notably low bitrate. In this paper, we step toward practical generative compression systems based on recent advances. Specifically, we show that the channel redundancy of the latent representation produced by an autoencoder network can be effectively compressed via mask compression. The mask compression performs quantization on the channel variance of latent representation instead of original values. Instead of training multiple models, changing the mask leads to a simple and efficient variable rate compression scheme. Then, we estimate the relative bitrate by measuring the L1 norm of the channel variance and hence obtain the rate-distortion formulation. The L1 regularizer assumes a Laplacian prior on the channel variance, through which model we develop corresponding methods to produce approximate images at a target bitrate. This eliminates the need for manually searching hyperparameters for our variable-rate compression. We conduct exhaustive experiments to demonstrate the advanced performance of the proposed method in preserving image quality and semantics.
The Neurotrophic and Antiangiogenic Functions of PEDF: A Reflection of its Variable Phosphorylation States (2005)

The pigment epithelium-derived factor (PEDF) is a non-inhibitory serpin, which is expressed mainly in the eye, but was also reported to be present in the adult human brain, spinal cord and plasma. It is characterized as a neurotrophic/ neuroprotective factor and one of the most potent natural inhibitors of angiogenesis in the eye, where it plays a physiological regulatory role in retinal angiogenesis. In this review we describe the expression, structure-function relationships, biological activities and regulation of PEDF. In addition, we emphasize our recent findings on the role of extracellular phosphorylation in PEDF activity, and show that the neurotrophic and antiangiogenic functions of PEDF are highly influenced by its phosphorylation state. Hence, phosphorylation of PEDF may be one of the modes that determine its specific physiological outcome. Keywords: PEDF, antiangiogenesis, neurotrophic factor, extracellular phosphorylation, protein kinases
Screening for resistance against <i>Pseudomonas syringae</i> in rice‐FOX <i>Arabidopsis</i> lines identified a putative receptor‐like cytoplasmic kinase gene that confers resistance to major bacterial and fungal pathogens in <i>Arabidopsis</i> and rice (2010)

Approximately 20,000 of the rice-FOX Arabidopsis transgenic lines, which overexpress 13,000 rice full-length cDNAs at random in Arabidopsis, were screened for bacterial disease resistance by dip inoculation with Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The identities of the overexpressed genes were determined in 72 lines that showed consistent resistance after three independent screens. Pst DC3000 resistance was verified for 19 genes by characterizing other independent Arabidopsis lines for the same genes in the original rice-FOX hunting population or obtained by reintroducing the genes into ecotype Columbia by floral dip transformation. Thirteen lines of these 72 selections were also resistant to the fungal pathogen Colletotrichum higginsianum. Eight genes that conferred resistance to Pst DC3000 in Arabidopsis have been introduced into rice for overexpression, and transformants were evaluated for resistance to the rice bacterial pathogen, Xanthomonas oryzae pv. oryzae. One of the transgenic rice lines was highly resistant to Xanthomonas oryzae pv. oryzae. Interestingly, this line also showed remarkably high resistance to Magnaporthe grisea, the fungal pathogen causing rice blast, which is the most devastating rice disease in many countries. The causal rice gene, encoding a putative receptor-like cytoplasmic kinase, was therefore designated as BROAD-SPECTRUM RESISTANCE 1. Our results demonstrate the utility of the rice-FOX Arabidopsis lines as a tool for the identification of genes involved in plant defence and suggest the presence of a defence mechanism common between monocots and dicots.
Differentiation of Francisella tularensis Subspecies and Subtypes (2020)

The highly infectious and zoonotic pathogen <i>Francisella tularensis</i> is the etiologic agent of tularemia, a potentially fatal disease if untreated. Despite the high average nucleotide identity, which is >99.2% for the virulent subspecies and >98% for all four subspecies, including the opportunistic microbe <i>Francisella tularensis</i> subsp. <i>novicida</i>, there are considerable differences in genetic organization. These chromosomal disparities contribute to the substantial differences in virulence observed between the various <i>F. tularensis</i> subspecies and subtypes. The methods currently available to genotype <i>F. tularensis</i> cannot conclusively identify the associated subpopulation without using time-consuming testing or complex scoring matrices. To address this need, we developed both single and multiplex quantitative real-time PCR (qPCR) assays that can accurately detect and identify the hypervirulent <i>F. tularensis</i> subsp. <i>tularensis</i> subtype A.I, the virulent <i>F. tularensis</i> subsp. <i>tularensis</i> subtype A.II, <i>F. tularensis</i> subsp. <i>holarctica</i> (also referred to as type B), and <i>F. tularensis</i> subsp. <i>mediasiatica</i>, as well as opportunistic <i>F. tularensis</i> subsp. <i>novicida</i> from each other and near neighbors, such as <i>Francisella philomiragia</i>, <i>Francisella persica</i>, and <i>Francisella</i>-like endosymbionts found in ticks. These fluorescence-based singleplex and non-matrix scoring multiplex qPCR assays utilize a hydrolysis probe, providing sensitive and specific <i>F. tularensis</i> subspecies and subtype identification in a rapid manner. Furthermore, sequencing of the amplified <i>F. tularensis</i> targets provides clade confirmation and informative strain-specific details. Application of these qPCR- and sequencing-based detection assays will provide an improved capability for molecular typing and clinical diagnostics, as well as facilitate the accurate identification and differentiation of <i>F. tularensis</i> subpopulations during epidemiological investigations of tularemia source outbreaks.
A Modular All-Digital PLL Architecture Enabling Both 1-to-2GHz and 24-to-32GHz Operation in 65nm CMOS (2008)

We report two DPLLs fabricated in a standard 65 nm bulk CMOS process. One PLL, targeting 1-to-2 GHz clock generation for the ASIC consumer market, is realized using a 5-stage static CMOS-ring digitally-controlled oscillator (ring-DCO). The second PLL, an exploratory design for 20-to-30 GHz applications, is realized using an LC-tank DCO. Both PLLs use the same proportional-integral (PI) loop filter, DeltaSigma modulator (DeltaSigmaM), multi-modulus feedback divider and bang-bang phase and frequency detector (BB-PFD).
Structure-Based Optimization of Protein Tyrosine Phosphatase 1B Inhibitors:  From the Active Site to the Second Phosphotyrosine Binding Site (2007)

Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin receptor pathways and thus an attractive therapeutic target for diabetes and obesity. Starting with a high micromolar lead compound, structure-based optimization of novel PTP1B inhibitors by extension of the molecule from the enzyme active site into the second phosphotyrosine binding site is described. Medicinal chemistry, guided by X-ray complex structure and molecular modeling, has yielded low nanomolar PTP1B inhibitors in an efficient manner. Compounds from this chemical series were found to be actively transported into hepatocytes. This active uptake into target tissues could be one of the possible avenues to overcome the poor membrane permeability of PTP1B inhibitors.
Power system effects and mitigation recommendations for DER cyberattacks (2019)

Extensive deployment of interoperable distributed energy resources (DER) is increasing the power system cyber security attack surface. National and jurisdictional interconnection standards require DER to include a range of autonomous and commanded grid‐support functions, which can drastically influence power quality, voltage, and bulk system frequency. Here, the authors investigate the impact to the cyber‐physical power system in scenarios where communications and operations of DER are controlled by an adversary. The findings show that each grid‐support function exposes the power system to distinct types and magnitudes of risk. The physical impact from cyber actions was analysed in cases of DER providing distribution system voltage regulation and transmission system support. Finally, recommendations are presented for minimising the risk using engineered parameter limits and segmenting the control network to minimise common‐mode vulnerabilities.
Hyaluronic acid‐based nanocomposite hydrogels for ocular drug delivery applications (2013)

Hyaluronic acid (HA) is a widely investigated biomaterial for many therapeutic applications owing to its unique properties of biocompatibility, biodegradation, and viscoelasticity. HA being a natural component of eye tissue with significant role in wound healing is a natural choice as a carrier for ocular drug delivery, provided the incorporated drugs are released in a sustained manner. However, localized sustained release of drugs inside eye has been difficult to achieve because of the inability to retain carriers for long periods in the eye. Using noncrosslinked (soluble) HA offers limited control over site retention of drugs. In order to obtain prolonged sustained delivery, two HA-based composite hydrogels incorporating nanocarriers, have been synthesized and characterized for swelling, rheology, degradation, and in vitro release of latanoprost, a drug used to reduce intraocular pressure. The HA is first chemically modified, mixed with drug-loaded liposomes, and then crosslinked to obtain nanocomposite hydrogels. In vitro release study shows longer sustained release of latanoprost from composite hydrogels as compared to liposomes or hydrogels alone indicating additional resistance to drug diffusion because of the incorporation of liposomes inside the hydrogels. It is believed that these nanocomposite hydrogels, with controlled degradation properties and sustained release, could serve as potential drug delivery systems for many ocular diseases.
Synthesis and Reactions of Hydrophilic Functional Microspheres for Immunological Studies (1979)

Abstract There is a need for hydrophilic polymeric microspheres with functional groups on their surface which can be reacted efficiently with proteins. These microspheres with antibodies (immunoglobulins) covalently bound to their surfaces constitute valuable immunoreagents capable of marking specific receptors (antigens) on cell surface membranes. The main requirements of the microspheres for the above applications are: insolubility in aqueous or organic media, absence of aggregation and of nonspecific interaction with cells and presence of suitable functional groups for covalent binding with antibodies. Hydrophobic polystyrene or poly(methyl methacrylate) latices do not meet these requirements. Copolymerization of hydrophilic monomers under suitable experimental conditions yielded microspheres with the required characteristics. Emulsion polymerization and ionizing radiation were found to constitute convenient techniques for the synthesis of hydrophilic and crosslinked (and therefore insoluble) functional microspheres ranging in diameter from 0.01 to 8 μm. By choosing suitable comonomers, it was possible to incorporate hydroxyl, carboxyl, amido, and dimethylamino functional groups into the particles. Copolymerization with isomeric vinylpyridines or dimethylamino methacrylate yielded weakly or strongly basic groups, respectively, capable of binding with acids. The experimental conditions suitable for obtaining desired particle sizes, in a relatively narrow distribution, were determined. It was found that the particle size depended to a large extent on the water solubility of the monomers, the presence or absence of stabilizer, the concentration of a surfactant, and the monomer concentration. The preferred technique to bind antibodies to the microsphere surface consisted of reacting amino groups with glutaraldehyde followed by the reaction with proteins. The use of polyglutaraldehyde instead of glutaraldehyde was also investigated. For this purpose the rate of polymerization of glutaraldehyde as a function of concentration and pH was first studied, followed by a study of the reactivity of polyglutaraldehyde micro-spheres with immunoglobulins. A recent new development of importance for cell separation is the synthesis of functional microspheres containing magnetic iron oxide. Preliminary investigations show that red blood cells and lymphocytes labeled with magnetic immunomicrospheres can be efficiently separated by means of permanent magnet. Separation of labeled from unlabeled human red blood cells was also achieved by means of a free-flow electrophoretic instrument.
Myocardial Contrast Echocardiography: A New Gold Standard for Perfusion Imaging? (2001)

Recent developments have permitted myocardial contrast echocardiography (MCE) to become a new method of noninvasively assessing myocardial perfusion in humans. Preliminary studies of myocardial perfusion imaging during adenosine, dipyridamole, and dobutamine stress echocardiography have shown excellent agreement with either radionuclide uptake or quantitative angiography. This article reviews the recent advances in microbubble technology, ultrasound imaging, and myocardial physiology that have made contrast echocardiography a potential new gold standard for perfusion imaging in the new millennium.
Development of a fluorescence polarization submersible instrument for the detection of submerged heavy oil spills (2012)

Spills of Group V heavy oils are a concern because once spilled heavy oils will immediately sink to the bottom and
can harm wetlands, beaches, and marine life. Recently, we developed a new tool-fluorescence polarization (FP)- for
locating heavy oil deposits. The method relies on the observation that heavy, viscous oil fractions exhibit polarized
fluorescence while the ubiquitous fluorescence background characteristic of chlorophyll and humic compounds do not. The basic FP measurement entails exciting the fluorophore with polarized light and observing the intensities of the emission polarized perpendicular and parallel to it. Heavy, tarry oils containing higher molecular weight polynuclear aromatic hydrocarbons fractions exhibit strong FP. The development of a remotely operated, submersible FP instrument will be presented, as well as testing results of the instrument in a simulated spill set up by the US Coast Guard at the National Oil Spill Response Research and Renewable Energy Test Facility (OHMSETT). The FP instrument utilizes a laser (532 nm) to excite the oil matrix. A small refracting telescope with variable focus is employed as the front optics and used to focus the laser beam and to collect the polarized fluorescence from the sample at a standoff distance. An embedded computer resides inside and controls the various operations such as autofocusing of the telescope and data acquisition. The embedded computer also allows autonomous or remotely controlled operation. FP along with phase sensitive detection combines to provide excellent sunlight rejection, thus allowing the use of the instrument during daylight hours.
Ultra-long range distributed fibre sensing using virtually transparent propagation (2011)

Distributed fibre sensors provide unique capabilities for monitoring large infrastructures with high resolution. Distributed amplification allows having a more homogeneous signal power along the sensing fibre, which also enables reducing the signal power at the input and therefore avoiding nonlinearities. However, in long structures (>; 50 km), plain distributed amplification does not perfectly compensate the losses and significant power variations along the fibre are to be expected, leading to inevitable limitations in the measurements. From this perspective, it is simple to understand intuitively that the best possible solution for distributed sensors would be offered by a virtually transparent fibre, i.e. a fibre exhibiting effectively zero attenuation in the spectral region of the pulse. In addition, it can be shown that lossless transmission is the working point that allows the minimization of the amplified spontaneous emission (ASE) noise build-up.
Photo-Cross-Linked Biodegradable Poly(Ester Anhydride) Networks Prepared from Alkenylsuccinic Anhydride Functionalized Poly(ε-caprolactone) Precursors (2011)

Biodegradable poly(ester anhydride) networks based on linear and star-shaped poly(ε-caprolactone)-based precursors were synthesized with the aim of obtaining matrixes suitable for release of macromolecular active agents. The ring-opening polymerization yielded hydroxyl telechelic oligomers, which were end-functionalized with succinic anhydride or with alkenylsuccinic anhydrides containing 8, 12, or 18 carbons in their alkenyl chains. Before cross-linking, the acid-terminated oligomers were reacted with methacrylic anhydride to obtain methacrylated precursors containing labile anhydride bonds. The degrees of substitution for the acid functionalization and methacrylation were >93%. Cross-linking of the precursors was carried out with visible light at room temperature. Gel contents and cross-linking densities were higher for networks cross-linked from the star-shaped precursors than for networks prepared from the linear precursors. In in vitro erosion tests, the presence of the alkenyl chain slowed down the erosion rate. The networks exhibited characteristic surface erosion: the mass loss was linear, whereas the dimensions of the specimens decreased steadily. A macromolecular release study showed the release of the model compound to be linear and in proportion to the mass loss.
Mesoporous MoO<sub>3–</sub><i><sub>x</sub></i> Material as an Efficient Electrocatalyst for Hydrogen Evolution Reactions (2016)

A unique approach for the synthesis of nonstoichiometric, mesoporous molybdenum oxide (MoO 3– x ) with nanosized crystalline walls by using a soft template (PEO‐ b ‐PS) synthesis method is introduced. The as‐synthesized mesoporous MoO 3– x is very active and stable (durability > 12 h) for the electrochemical hydrogen evolution reaction (HER) under both acidic and alkaline conditions. The intrinsic MoO 3 serves as an HER electrocatalyst without the assistance of carbon materials, noble metals, or MoS 2 materials. The results from transmission electron microscopy and N 2 sorption techniques show that the as‐synthesized mesoporous MoO 3– x has large accessible pores (20–40 nm), which are able to facilitate mass transport and charge transfer during HER. In terms of X‐ray diffraction, X‐ray photoelectron spectroscopy, temperature‐programmed oxidation, and diffusive reflectance UV–vis spectroscopy, the mesoporous MoO 3– x exhibits mixed oxidation states (Mo 5+ , Mo 6+ ) and an oxygen‐deficient structure. The as‐synthesized MoO 3– x only requires a low overpotential (≈0.14 V) to achieve a 10 mA cm −2 current density in 0.1 m KOH and the Tafel slope is as low as 56 mV dec −1 . Density functional theory calculations demonstrate a change of electronic structure and the possible reaction pathway of HER. Oxygen vacancies and mesoporosity serve as key factors for excellent performance.
Multi-Material Topology Optimization for Additive Manufacturing (2015)

Additive manufacturing (AM) and topology optimization strongly complement each other in that the complex and optimal designs created through the latter can directly be fabricated through AM, leading to reduced design and fabrication time. As AM expands into multi-material fabrication, there is a natural need for efficient multi-material topology optimization methods, where one must simultaneously optimize the topology, and the distribution of various materials within the topology. In this paper we generalize the single-material Pareto tracing method of topology optimization to multiple materials, and discuss its implementation using assembly-free finite element analysis, and first-order element-sensitivity. The effectiveness of the algorithm is demonstrated through illustrative examples.
Diagnosis of fatty liver disease by a multiphoton-active and lipid-droplet-specific AIEgen with nonaromatic rotors (2020)

We present a two-photon AIEgen, ABCXF with nonaromatic rotors (–CF <sub>3</sub> ), a high two-photon absorption cross-section, bright red emission in the solid-state, and remarkably high photostability for fatty liver disease diagnosis.