gebhart/patrepeval huggingface dataset:
Synthesis of synchronous elastic architectures (2006)

A simple protocol for latency-insensitive design is presented. The main features of the protocol are the efficient implementation of elastic communication channels and the automatable design methodology. With this approach, fine-granularity elasticity can be introduced at the level of functional units (e.g. ALUs, memories). A formal specification of the protocol is defined and an efficient scheme for the implementation of elasticity that involves no datapath overhead is presented. The opportunities this protocol opens for microarchitectural design are discussed.
High frequency Differential MIMO: Basic theory and transceiver architectures (2015)

We propose a new multiple input multiple output (MIMO) transceiver architecture- Differential MIMO (D-MIMO) - that enables linear interference suppression between multiple spatially multiplexed and differentially encoded data streams. The D-MIMO transceiver architecture is particularly attractive in emerging high-frequency systems, such as millimeter-wave systems, in which the requirement of a phase-coherent local oscillator at the receiver can be challenging. A direct application of conventional linear interference suppression techniques is not possible with differential communication. Thus, we first develop a general model for D-MIMO systems, with a corresponding D-MIMO channel matrix, that forms the basis of the development in this paper. A surprising result is that a quasi-coherent version of the underlying channel matrix can also be estimated from the D-MIMO matrix, making conventional linear interference suppression possible as well. This leads to two D-MIMO transceiver architectures that are developed. Numerical results illustrate the promising and nearly identical performance of the proposed transceivers and the communication breakdown that can occur without interference suppression.
Targeting the DNM3OS / miR-199a~214 cluster for the treatment of fibroproliferative diseases (2018)

Abstract Given the paucity of effective treatments for fibrotic disorders, new insights into the deleterious mechanisms controlling fibroblast activation, the key cell type driving the fibrogenic process, are essential to develop new therapeutic strategies. Here, we identified the long non-coding RNA DNM3OS as a critical downstream effector of TGF-β-induced myofibroblast activation. Mechanistically, DNM3OS regulates this process in trans by giving rise to 3 distinct profibrotic mature miRNAs (i.e. miR-199a-5p/3p and miR-214-3p), which influence both SMAD and non-SMAD components of TGF-β signaling in a multifaceted way, through two modes of action consisting of either signal amplification or mediation. Finally, we provide preclinical evidence that interfering with DNM3OS function using distinct strategies not only prevents lung and kidney fibrosis but also improves established lung fibrosis, providing thus a novel paradigm for the treatment of refractory fibrotic diseases such as idiopathic pulmonary fibrosis. One Sentence Summary The DNM3OS lncRNA is a reservoir of fibromiRs with major functions in fibroblast response to TGF-β and represents a valuable therapeutic target for refractory fibrotic diseases such as idiopathic pulmonary fibrosis (IPF).
Sodium Hydroxide Catalyzed Dehydrocoupling of Alcohols with Hydrosilanes (2016)

An O-Si bond construction protocol employing abundantly available and inexpensive NaOH as the catalyst is described. The method enables the cross-dehydrogenative coupling of an alcohol and hydrosilane to directly generate the corresponding silyl ether under mild conditions and without the production of stoichiometric salt byproducts. The scope of both coupling partners is excellent, positioning the method for use in complex molecule and materials science applications. A novel Si-based cross-coupling reagent is also reported.
Differential Regulation of VEGF Signaling by PKC-α and PKC-ε in Endothelial Cells (2008)

By regulating VEGFR2 expression and activation, PKC-epsilon expression is critical for activation of Akt and eNOS by VEGF and contributes to VEGF-stimulated Erk activation, whereas PKC-alpha has opposite effects.
Novel biosensors from photonic crystals (2008)

Screening the biochemical interaction of potential pharmaceutical compounds against a wide array of proteins and cells is a critical early step in drug discovery. In this way, costly failures can be avoided before the drug is introduced to animals and humans. Similarly, testing patients’ blood or tissue samples for expression of a gene profile will become common practice in decisions regarding the most promising course of treatment. Reliable assays are also essential to applications such as environmental monitoring, crop protection, and the detection of biological warfare agents. Biological substances may be most simply sensed directly through their dielectric permittivity, a measure of how they affect electric fields, in so-called label-free detection. Even greater sensitivity may be obtained by attaching a fluorescent compound to the substance of interest, and then exciting the florescent molecule. We have developed a new class of biosensors based on optical devices known as photonic crystals (PCs) that can be used for both label-free and fluorescence-based detection.1–6 The key attributes for acceptance of new technology in these fields are sensitivity (how low a concentration of a chemical, protein, or gene may be detected), cost per test, and throughput (the number of tests that can be performed at once). PCs represent a unique and versatile class of optical devices for manipulating the electromagnetic fields associated with light. Through the proper application of PC design and fabrication, electromagnetic fields may be confined and concentrated to enhance the interaction between light and biological material in contact with the PC. We have developed methods that enable PC biosensors to be inexpensively produced in plastic, as well as associated instrumentation.7 Combined, the biosensors and detection instruments enable high-throughput detection of biochemical binding kinetics, imaging large arrays of biochemical tests,8–11 and imaging detection of cells.12–14 Figure 1. Device structure for the PC surface. (A) Schematic crosssection of the device structure. (B) Scanning electron microscope photo of top view and cross-section of a replica-molded 2D grating comprising an array of bumps coated with titanium dioxide (TiO2) highrefractive-index dielectric material. (C) Photo of the fabricated device attached to an ordinary glass microscope slide, where the entire surface of the slide is populated by the PC sensor.
Audio hot spotting and retrieval using multiple features (2004)

This paper reports our on-going efforts to exploit multiple features derived from an audio stream using source material such as broadcast news, teleconferences, and meetings. These features are derived from algorithms including automatic speech recognition, automatic speech indexing, speaker identification, prosodic and audio feature extraction. We describe our research prototype -the Audio Hot Spotting Systemthat allows users to query and retrieve data from multimedia sources utilizing these multiple features.
Isolation of the Tomato <i>Cf-9</i> Gene for Resistance to <i>Cladosporium fulvum</i> by Transposon Tagging (1994)

The tomato Cf-9 gene confers resistance to infection by races of the fungus Cladosporium fulvum that carry the avirulence gene Avr9. The Cf-9 gene was isolated by transposon tagging with the maize transposable element Dissociation. The DNA sequence of Cf-9 encodes a putative membrane-anchored extracytoplasmic glycoprotein. The predicted protein shows homology to the receptor domain of several receptor-like protein kinases in Arabidopsis, to antifungal polygalacturonase-inhibiting proteins in plants, and to other members of the leucine-rich repeat family of proteins. This structure is consistent with that of a receptor that could bind Avr9 peptide and activate plant defense.
Characterization of the Interaction Between the <i>Staphylococcus Aureus</i> Clumping Factor (ClfA) and Fibrinogen (1997)

The ability of Staphylococcus aureus to adhere to adsorbed fibrinogen and fibrin is believed to be an important step in the initiation of biomaterial and wound-associated infections. In this study, we show that the binding site in fibrinogen for the recently identified S. aureus fibrinogen-binding protein clumping factor (ClfA) is within the C-terminus of the fibrinogen gamma chain. S. aureus Newman cells expressing ClfA adhered to microtitre wells coated with recombinant fibrinogen purified from BHK cells, but did not adhere to wells coated with a purified recombinant fibrinogen variant where the 4 C-terminal residues of the gamma chain were replaced by 20 unrelated residues. In addition, a synthetic peptide corresponding to the 17 C-terminal amino acids of the fibrinogen gamma chain effectively inhibited adherence of ClfA-expressing cells to fibrinogen. In western ligand blots, a recombinant truncated ClfA protein called Clf33 (residues 221-550) recognized intact recombinant fibrinogen gamma chains, but failed to recognize recombinant fibrinogen gamma chains where the 4 C-terminal amino acids were altered by deletion or substitution. Previous studies have shown that the C-terminal domain of fibrinogen gamma chains contains a binding site for the integrin alphaIIb beta3 (glycoprotein gpIIb/IIIa) receptor on platelets [Kloczewiak, M., Timmons, S., Bednarek, M. A., Sakon, M. & Hawiger, J. (1989) Biochemistry 28, 2915-1919; Farrell, D. H., Thiagarajan, P., Chung, D. W. & Davie, E. W. (1992) Proc. Natl. Acad. Sci. USA 89, 10729-10732; Hettasch, J. M., Bolyard, M. G. & Lord, S. T. (1992) Thromb. Haemostasis 68, 701-706]. We now show that Clf33 inhibits ADP-induced, fibrinogen-dependent platelet aggregation in a concentration-dependent manner and inhibits adhesion of platelets to immobilized fibrinogen under fluid shear stress, indicating that the binding sites for the platelet integrin and the staphylococcal adhesin overlap. The interaction between Clf33 and fibrinogen was further characterized using the BIAcore biosensor. When soluble Clf33 was allowed to bind to immobilized fibrinogen, a Kd of 0.51 +/- 0.19 microM was experimentally determined using equilibrium binding data. It was also shown that the synthetic C-terminal gamma-chain peptide effectively inhibited this interaction.
Mobile Microscopy and Machine Learning Provide Accurate and High-throughput Monitoring of Air Quality (2017)

Lensfree computational microscopy and machine learning enable a field-portable and cost-effective platform for high-throughput and accurate quantification of particulate matter (PM). Spatio-temporal mapping using this device reveals increased PM concentrations >7km away from LAX airport.
Registration of ‘CL261’ Rice (2014)

‘CL261’ (Reg. No. CV-143; PI 658539), a Clearfield (BASF, Ludwigshafen, Germany) medium-grain rice (Oryza sativa L.) cultivar, was developed by the Louisiana State University Agricultural Center at the Rice Research Station (RRS) near Crowley, LA, and approved for release by the director of the Louisiana Agricultural Experiment Station in 2011. CL261 was derived from the cross ‘Bengal’/‘CL161’ that was made in 2002 at the RRS and advanced in 2006 as an F2:5–bulked selection based on agronomic characteristics. Testing in the Clearfield preliminary yield trials in 2007 indicated high yield potential and favorable agronomic characteristics. In 2010 and 2011, CL261 was evaluated in 44 statewide yield performance trials, along with two high-yielding Clearfield check cultivars, ‘CL111’ and ‘CL151’. Grain yield of CL261 was 8.6 Mg ha−1 compared with 8.7 and 9.3 Mg ha−1 for CL111 and CL151, respectively. Plant height for CL261 was 97 cm compared with 99 cm for both CL111 and CL151. CL261 reached 50% heading in 79 d while CL111 reached 50% heading in 76 d and CL151 in 80 d. CL261 has a semi-erect flag leaf, and the leaves are dark green and display an intermediate leaf angle. The lemma and palea are straw-colored and glabrous, and the apiculus, light purple at heading, is colorless as the grain approaches harvest maturity. CL261 is susceptible to sheath blight (Rhizoctonia solani) and blast disease (Magnaporthe grisea) and moderately susceptible to straighthead disorder.
COVIRDS: Shape Modeling in a Virtual Reality Environment (1997)

Abstract Rapid shape creation and visualization of solid models remains a tedious task despite advances in the field of Computer Aided Design (CAD)/Solid Modeling. CAD systems require a significant level of detail, such as vertices, edges, and faces to be specified by the user, even before the simplest of shapes can be created and viewed. In addition, most CAD systems have an essentially 2D interface for designing artifacts. This makes artifact visualization, for example by interactive rotation, difficult since all manipulations have be achieved by 2D translation of the mouse or by typing in the required angles of rotation. The limited visualization capability and the requirement to create shapes through the specification of low level entities is especially cumbersome in the concept shape design stage. This paper describes the Conceptual Virtual Design System, COVIRDS, a tool for product concept design. COVIRDS provides an intuitive voice and hand input-based interface for modeling of products using a ‘construction’ approach. Product shape models are created by ‘attaching’ simpler parametrically defined ‘Shape Elements’ to other elements to create more complex models. Voice commands are used to instantiate shape elements and change their parameters, for example, the width, length and height of a block element. 3D hand input is used for positioning shape elements during element attachment. The voice and hand input-based interface together with a stereoscopic visual display facilitates rapid creation and visualization of concept shape models.
A non-enumerative path delay fault simulator for sequential circuits (2002)

We extend the path status graph (PSG) method of delay fault simulation to sequential circuits. By devising a layered PSG and restricting the number of time-frames over which a fault must be detected, we preserve the non-enumerative nature of the simulation algorithm. The program is capable of simulating a wide variety of circuits (synchronous, asynchronous, multiple-clock and tri-state logic.) Both rated and variable clock modes, as well as robust, non-robust or functional sensitization detection options, are available. The simulation can be stopped and restarted through a check pointing facility. The program can target any given list of paths. This path list can also be generated by the program based on user-selectable criteria (all paths, longest paths, paths between certain I/O pairs, etc.) User reports include a histogram of path coverage versus path length. Detected and undetected path data remain implicit in the PSG and can be retrieved through post-processing commands. Due to its non-enumerative stature, the program can process most production level digital logic circuits.
Role of the constant region domain in the structural diversity of human antibody light chains (2017)

Issues regarding the structural diversity (heterogeneity) of an antibody molecule have been the subject of discussion along with the development of antibody drugs. Research on heterogeneity has been extensive in recent years, but no clear solution has been reached. Heterogeneity is also observed in catalytic antibody κ light chains (CLs). In this study, we investigated how the constant region domain of CLs concerns structural diversity because it is a simple and good example for elucidating heterogeneity. By means of cation-exchange chromatography, SDS-PAGE, and 2-dimensional electrophoresis for the CL, multimolecular forms consisting of different electrical charges and molecular sizes coexisted in the solution, resulting in the similar heterogeneity of the full length of CLs. The addition of copper ion could cause the multimolecular forms to change to monomolecular forms. Copper ion contributed greatly to the enrichment of the dimer form of CL and the homogenization of the differently charged CLs. Two molecules of the CL protein bound one copper ion. The binding affinity of the ion was 48.0 μM<sup>-1</sup> Several divalent metal ions were examined, but only zinc showed a similar effect.-Hifumi, E., Taguchi, H., Kato, R., Uda, T. Role of the constant region domain in the structural diversity of human antibody light chains.
An integrated ADAS for assessing risky situations in urban driving (2013)

Advanced Driver Assistance Systems (ADAS) are becoming more and more popular. Many of these systems though are limited to specific scenes and often detect risky situations very late so they can only mitigate accidents. These effects are mainly caused by the use of simple physical prediction methods, e.g. to estimate the time-to-contact with another vehicle. In this paper we show an ADAS that extends the functionality of physical collision warnings by additionally estimating potential risks based on implicit predictions. As an example we demonstrate the use of vehicle orientation information for classifying situations. Through this, we can in particular assess the risk of static cars, for which physical prediction does not apply, but which can nevertheless easily cause an accident if they start moving into our driving corridor. The proposed system is evaluated online in a test car and is shown to reliably detect classical risky situations as well as those involving static cars.
Adenovirus adenine nucleotide translocator-2 shRNA effectively induces apoptosis and enhances chemosensitivity by the down-regulation of ABCG2 in breast cancer stem-like cells (2012)

Cancer stem cells (CSCs) are resistant to chemo- and radio-therapy, and can survive to regenerate new tumors. This is an important reason why various anti- cancer therapies often fail to completely control tumors, although they kill and eliminate the bulk of cancer cells. In this study, we determined whether or not adenine nucleotide translocator-2 (ANT2) suppression could also be effective in inducing cell death of breast cancer stem-like cells. A sub-population (SP; CD44+/ CD24-) of breast cancer cells has been reported to have stem/progenitor cell properties. We utilized the adeno- ANT2 shRNA virus to inhibit ANT2 expression and then observed the treatment effect in a SP of breast cancer cell line. In this study, MCF7, MDA-MB-231 cells, and breast epithelial cells (MCF10A) mesenchymally-transdifferentiated through E-cadherin knockdown were used. ANT2 expression was high in both stem-like cells and non-stem-like cells of MCF7 and MDA-MB-231 cells, and was induced and up-regulated by mesenchymal transdifferentiation in MCF10A cells (MCF10A(EMT)). Knockdown of ANT2 by adeno-shRNA virus efficiently induced apoptotic cell death in the stem-like cells of MCF7 and MDA-MB-231 cells, and MCF10A(EMT). Stem-like cells of MCF7 and MDA-MB-231, and MCF10A(EMT) cells exhibited increased drug (doxorubicin) resistance, and expressed a multi-drug resistant related molecule, ABCG2, at a high level. Adeno-ANT2 shRNA virus markedly sensitized the stem-like cells of MCF7 and MDA-MB-231, and the MCF10A(EMT) cells to doxorubicin, which was accompanied by down-regulation of ABCG2. Our results suggest that ANT2 suppression by adeno-shRNA virus is an effective strategy to induce cell death and increase the chemosensitivity of stem-like cells in breast cancer.
Huge magnetoresistance in graphene-based magnetic tunnel junctions with superlattice barriers (2015)

Combining the features of graphene, spintronics and superlattices, this study reports huge tunnel magnetoresistance achieved using graphene-based magnetic tunnel junctions with superlattice barriers. Our calculation results show that the tunnel magnetoresistance of as much as 107% is obtained using a magnetic tunnel junction with a six-cell superlattice barrier. This magnetoresistance increases as the number of cells in the superlattice barrier increases. This remarkable value can be linked to the artificially tailored band structures of the superlattice barriers. This generic nature provides new opportunities for other spintronics applications, using graphene superlattices.
Artificial ligand binding within the HIF2α PAS-B domain of the HIF2 transcription factor (2009)

The hypoxia-inducible factor (HIF) basic helix-loop-helix Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim (bHLH-PAS) transcription factors are master regulators of the conserved molecular mechanism by which metazoans sense and respond to reductions in local oxygen concentrations. In humans, HIF is critically important for the sustained growth and metastasis of solid tumors. Here, we describe crystal structures of the heterodimer formed by the C-terminal PAS domains from the HIF2alpha and ARNT subunits of the HIF2 transcription factor, both in the absence and presence of an artificial ligand. Unexpectedly, the HIF2alpha PAS-B domain contains a large internal cavity that accommodates ligands identified from a small-molecule screen. Binding one of these ligands to HIF2alpha PAS-B modulates the affinity of the HIF2alpha:ARNT PAS-B heterodimer in vitro. Given the essential role of PAS domains in forming active HIF heterodimers, these results suggest a presently uncharacterized ligand-mediated mechanism for regulating HIF2 activity in endogenous and clinical settings.
XPEDIA (2009)

Data Integration engines increasingly need to provide sophisticated processing options for XML data. In the past, it was adequate for these engines to support basic shredding and XML generation capabilities. However, with the steady growth of XML in applications and databases, integration platforms need to provide more direct operations on XML as well as improve the scalability and efficiency of these operations. In this paper, we describe a robust and comprehensive framework for performing Extract-Transform-Load (ETL) of XML. This includes (i) full computational model and engine capabilities to perform these operations in an ETL flow, (ii) an approach to pushing down XML operations into a database engine capable of supporting XML processing, and (iii) methods to apply partitioning techniques to provide scalable, parallel processing for large XML documents. We describe experimental results showing the effectiveness of these techniques.
Isolation and characterization of NAD(P)-dependent L-sorbosone dehydrogenase from Gluconobacter melanogenus UV10. (1991)

NAD(P)-Dependent L-sorbosone dehydrogenase has been purified from the cytosol fraction of Gluconobacter melanogenus UV10. The enzyme was purified about 30-fold with an overall yield of 19% by column chromatographies on DEAE-Sepharose CL-6B, DEAE-Sephadex A-50, and Blue Sepharose CL-6B. The enzyme required NAD or NADP as a cofactor, and showed broad substrate specificity on various aldehyde compounds. Among them, L-sorbosone was the best substrate for the enzyme. In this respect, the enzyme is a kind of aldehyde dehydrogenase.
Improving Loading and Unloading Transient Response of a Voltage Regulator Module Using a Load-Side Auxiliary Gyrator Circuit (2016)

This paper introduces a new voltage regulator module (VRM) that merges a highly efficient switched-inductor converter as the main unit with a load-side switched-capacitor-based converter to assist during load transient events. The resulting hybrid-VRM exhibits improved dynamic performance for both loading and unloading transient events, while maintaining a compact design with reduced output capacitance and lower components stress. The hybrid controller that has been developed allows operation that is based on output voltage measurement alone, further reducing the circuit complexity. A power processing efficiency analysis that has been carried out shows efficiency improvement in favor of the hybrid-VRM when compared to time-optimal control under varying load conditions. The operation of the VRM is verified on a 20-W, 12V-to-1.5-V prototype with peak power conversion efficiency of 93%, demonstrating near-ideal transient recovery.