gebhart/patrepeval huggingface dataset:
Atomic force microscope tip deconvolution using calibration arrays (1995)

An algorithm for the deconvolution of the probe tips used with the atomic force microscope from the images of calibration grids made using very large scale integrated technology, which is useful in visualization of the tip before or after imaging for the elucidation of the condition of the stylus, is presented. This procedure described is of general applicability: it makes no assumptions about the tip geometry and requires no pretreatment of the data, such as filtering. Grids having circular depressions are shown to reproduce the geometries of circular and conical tips faithfully, but are limited when imaging those which are square pyramidal. Slight variations in the size and shapes of the depressions within a grid pattern limit the accuracy of the tip reconstruction.
Inhibition of Influenza A Virus Infection <i>in Vitro</i> by Saliphenylhalamide-Loaded Porous Silicon Nanoparticles (2013)

Influenza A viruses (IAVs) cause recurrent epidemics in humans, with serious threat of lethal worldwide pandemics. The occurrence of antiviral-resistant virus strains and the emergence of highly pathogenic influenza viruses have triggered an urgent need to develop new anti-IAV treatments. One compound found to inhibit IAV, and other virus infections, is saliphenylhalamide (SaliPhe). SaliPhe targets host vacuolar-ATPase and inhibits acidification of endosomes, a process needed for productive virus infection. The major obstacle for the further development of SaliPhe as antiviral drug has been its poor solubility. Here, we investigated the possibility to increase SaliPhe solubility by loading the compound in thermally hydrocarbonized porous silicon (THCPSi) nanoparticles. SaliPhe-loaded nanoparticles were further investigated for the ability to inhibit influenza A infection in human retinal pigment epithelium and Madin-Darby canine kidney cells, and we show that upon release from THCPSi, SaliPhe inhibited IAV infection in vitro and reduced the amount of progeny virus in IAV-infected cells. Overall, the PSi-based nanosystem exhibited increased dissolution of the investigated anti-IAV drug SaliPhe and displayed excellent in vitro stability, low cytotoxicity, and remarkable reduction of viral load in the absence of organic solvents. This proof-of-principle study indicates that PSi nanoparticles could be used for efficient delivery of antivirals to infected cells.
A Low Cost Angular Rate Sensor in Si-Surface Micromachining Technology for Automotive Application (1999)

<div class="htmlview paragraph">This paper reports on a new generation of silicon gyroscopes, which can be used as angular rate sensors for roll-over sensing or navigation control. The sensor is fabricated in standard Si-surface micromachining technology and encapsulated under vacuum conditions using an Si-micromachined cap wafer. The sensor consists of an electrostatically driven oscillating disk, which reacts with a tilt movement when an angular rate is applied due to the conservation law for angular momentums. The tilt movement is then detected capacitively by electrodes on the substrate underneath the oscillating disk. The sensor is packaged in a standard SMD housing (PLCC44).</div>
Memory‐Based Multiagent Coevolution Modeling for Robust Moving Object Tracking (2013)

The three-stage human brain memory model is incorporated into a multiagent coevolutionary process for finding the best match of the appearance of an object, and a memory-based multiagent coevolution algorithm for robust tracking the moving objects is presented in this paper. Each agent can remember, retrieve, or forget the appearance of the object through its own memory system by its own experience. A number of such memory-based agents are randomly distributed nearby the located object region and then mapped onto a 2D lattice-like environment for predicting the new location of the object by their coevolutionary behaviors, such as competition, recombination, and migration. Experimental results show that the proposed method can deal with large appearance changes and heavy occlusions when tracking a moving object. It can locate the correct object after the appearance changed or the occlusion recovered and outperforms the traditional particle filter-based tracking methods.
Real-time Deep Video Deinterlacing (2017)

Interlacing is a widely used technique, for television broadcast and video recording, to double the perceived frame rate without increasing the bandwidth. But it presents annoying visual artifacts, such as flickering and silhouette "serration," during the playback. Existing state-of-the-art deinterlacing methods either ignore the temporal information to provide real-time performance but lower visual quality, or estimate the motion for better deinterlacing but with a trade-off of higher computational cost. In this paper, we present the first and novel deep convolutional neural networks (DCNNs) based method to deinterlace with high visual quality and real-time performance. Unlike existing models for super-resolution problems which relies on the translation-invariant assumption, our proposed DCNN model utilizes the temporal information from both the odd and even half frames to reconstruct only the missing scanlines, and retains the given odd and even scanlines for producing the full deinterlaced frames. By further introducing a layer-sharable architecture, our system can achieve real-time performance on a single GPU. Experiments shows that our method outperforms all existing methods, in terms of reconstruction accuracy and computational performance.
miR-223 reverses experimental pulmonary arterial hypertension (2015)

Pulmonary arterial hypertension (PAH) is a devastating disease affecting lung vasculature. The pulmonary arteries become occluded due to increased proliferation and suppressed apoptosis of the pulmonary artery smooth muscle cells (PASMCs) within the vascular wall. It was recently shown that DNA damage could trigger this phenotype by upregulating poly(ADP-ribose)polymerase 1 (PARP-1) expression, although the exact mechanism remains unclear. In silico analyses and studies in cancer demonstrated that microRNA miR-223 targets PARP-1. We thus hypothesized that miR-223 downregulation triggers PARP-1 overexpression, as well as the proliferation/apoptosis imbalance observed in PAH. We provide evidence that miR-223 is downregulated in human PAH lungs, distal PAs, and isolated PASMCs. Furthermore, using a gain and loss of function approach, we showed that increased hypoxia-inducible factor 1α, which is observed in PAH, triggers this decrease in miR-223 expression and subsequent overexpression of PARP-1 allowing PAH-PASMC proliferation and resistance to apoptosis. Finally, we demonstrated that restoring the expression of miR-223 in lungs of rats with monocrotaline-induced PAH reversed established PAH and provided beneficial effects on vascular remodeling, pulmonary resistance, right ventricle hypertrophy, and survival. We provide evidence that miR-223 downregulation in PAH plays an important role in numerous pathways implicated in the disease and restoring its expression is able to reverse PAH.
The Initiator Element: A Paradigm for Core Promoter Heterogeneity within Metazoan Protein-coding Genes (1998)

In metazoans, an enormous number of protein-codinggenes must be differentially expressed in specific celltypes, during developmental processes, and in response toan array of extracellular signals. Combinatorial gene regulation strategies must be employed to generate these diverse expression patterns because only a limited number oftranscription factors can be encoded by a genome of limited size. Combinatorial regulation involves multiple layers of events: For a gene to be activated, higher-order chromatin structures must first be unpacked, individualnucleosomes must be remodeled, transcription factorsmust bind to promoters and enhancers, and the transcription factors must then communicate with the general transcription machinery in concert with appropriate coactivator proteins. Another fundamental feature of combinatorialregulation is the requirement for several distinct transcription factors to activate a gene. By combining each transcription factor encoded by the genome with various combinations of other factors, the number of gene expressionpatterns that can be achieved in an animal is greatly enhanced...
Micro Capsule Endoscope for Gastro Intestinal Tract (2007)

A novel capsule endoscope (CE) named "MiRo" was developed based on a completely new transmission technology known as "electric-field propagation." This technology marks the initial achievement of cooperative research between the Intelligent Microsystem Center of KIST, IntroMedic Co., Ltd, and Yonsei University College of Medicine under Korea's Frontier 21 project. The specifications of "MiRo" include real-time image receiving, 10.8 x 24 mm, 3.3 g, 320 x 320 pixel formats, 3 frame/sec, and over 11 hours of battery time.
Conserved Initiator Proteins in Eukaryotes (1995)

The origin recognition complex (ORC), a multisubunit protein identified in Saccharomyces cerevisiae, binds to chromosomal replicators and is required for the initiation of cellular DNA replication. Complementary DNAs (cDNAs) encoding proteins related to the two largest subunits of ORC were cloned from various eukaryotes. The cDNAs encoding proteins related to S. cerevisiae Orc1p were cloned from the budding yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and human cells. These proteins show similarity to regulators of the S and M phases of the cell cycle. Genetic analysis of orc1+ from S. pombe reveals that it is essential for cell viability. The cDNAs encoding proteins related to S. cerevisiae Orc2p were cloned from Arabidopsis thaliana, Caenorhabditis elegans, and human cells. The human ORC-related proteins interact in vivo to form a complex. These studies studies suggest that ORC subunits are conserved and that the role of ORC is a general feature of eukaryotic DNA replication.
Yarn‐Like Carbon Nanotube Fibers (2010)

A fiber made of carbon nanotubes is shown to resemble a conventional yarn in terms of its structure, composed of discrete fibrillar sub-units, and its properties, such as high flexibility in bending, cutting resistance and 100% knot efficiency. Its combination of yarn-like character and tensile properties in the high-performance range make this CNT fiber an exceptional new material. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Knowledge-Graph-Based Semantic Labeling of Tabular Data (2020)

A lot of data are published on the Web using tabular data formats (e.g., spreadsheets). This is especially the case for the data made available in open data portals by public and private institutions. However, one of the main challenges for their effective (re)use is their generalized lack of semantics: column names are not usually standardized, and their meaning and content are not always clear. In parallel, knowledge graphs have started to be widely adopted by some data providers as a means to publish large amounts of structured data. They commonly use graph-based formats (e.g., RDF) and make references to lightweight ontologies. It is well understood that the reuse of such tabular data may be improved by annotating them with the classes and properties used by the data available in knowledge graphs. Several challenges exist in performing semantic labeling, such as the commonality or duplication of entity names, the difference in measurements and rounding errors of numeric values, and the noise in published tabular data and knowledge graphs. In this work, we present a novel approach to automatically label columns in tabular data with ontology classes and properties referred to by existing knowledge graphs. We evaluated the performance of our approach on entity columns and numeric columns separately. For the entity columns, we applied our approach to annotated tables from the T2D gold standard. For the numeric columns, we manually annotated numeric columns in the T2D gold standard and then applied our technique to this data. We report the performance of our approach using precision, recall, and F1 scores, which is the conventional way to report the performance of semantic labeling in the literature. The experiments showed that our proposed approach successfully labeled the majority of the entity and numeric columns in the used dataset. In contrast with other existing proposals in the state-of-the-art, our approach does not require the use of external linguistic resources, other sources of information, or human in the loop.
Logic computation using coupled neural oscillators (2004)

This work presents our recent work in using neural oscillators inspired by olfactory cortex models for Boolean logic computation. Two such coupled oscillators are sufficient to implement all the Boolean primitives (including AND, OR and XOR). Although the same computational model is being studied as a content addressable memory, these results indicate that additional computational power exists in this class of oscillatory neural networks. Detailed configuration of the proposed structure, experimental results and potential applications are presented.
Synthesis and Characterization of 4- and 4,4′-Phosphorylated2,2′-Bis(diphenylphosphanyl)-1,1′-binaphthyls (2001)

A convenient reaction sequence has been established to obtain selectively the mono- or bisphosphorylated BINAP derivatives 6−9. The structure of the new compounds was confirmed by NMR spectroscopy. The sodium salts of the phosphonic acid derivatives 8 and 9 can be used in aqueous biphasic catalysis.
8-VSB channel coding analysis for DTV broadcast (2000)

This article analyzes channel coding and equalization stages in the 8-level vestigial sideband transmission for the digital television broadcast system developed by ATSC, the Advanced Television Systems Committee. We present bit error rate versus C/N performance for a simulator developed by the authors for the purpose of assessing the robustness of the ATSC 8-VSB coding and equalization stages in the presence of multipath propagation, additive Gaussian noise and of channel impulsive noise surges. Implementation aspects for the developed simulator are discussed.
Energy metabolism in heart failure (2003)

Heart failure (HF) is a syndrome resulting from the inability of the cardiac pump to meet the energy requirements of the body. Despite intensive work, the pathogenesis of the cardiac intracellular abnormalities that result from HF remains incompletely understood. Factors that lead to abnormal contraction and relaxation in the failing heart include metabolic pathway abnormalities that result in decreased energy production, energy transfer and energy utilization. Heart failure also affects the periphery. Patients suffering from heart failure always complain of early muscular fatigue and exercise intolerance. This is linked in part to intrinsic alterations of skeletal muscle, among which decreases in the mitochondrial ATP production and in the transfer of energy through the phosphotransfer kinases play an important role. Alterations in energy metabolism that affect both cardiac and skeletal muscles argue for a generalized metabolic myopathy in heart failure. Recent evidence shows that decreased expression of mitochondrial transcription factors and mitochondrial proteins are involved in mechanisms causing the energy starvation in heart failure. This review will focus on energy metabolism alterations in long-term chronic heart failure with only a few references to compensated hypertrophy when necessary. It will briefly describe the energy metabolism of normal heart and skeletal muscles and their alterations in chronic heart failure. It is beyond the scope of this review to address the metabolic switches occurring in compensated hypertrophy; readers could refer to well-documented reviews on this subject.
The reliability of curvature estimates from linear elastic tactile sensors (2002)

This papers analyzes the reliability of radius of curvature estimates from tactile sensor data. A linear elastic model is used to fit the indenter parameters, load, location, and curvature, to the sensor output. It was found that both contact models and calibration techniques could dramatically effect the bias and variance of the estimated indenter parameters. The Fourier series is found to be an appropriate basis in which to analyze both the calibration of tactile sensors and the problem of band limited shape interpretation.
An Efficient Flame Ionization Detection System for Liquid Chromatography (1972)

A system has been developed for increasing the productivity of quantitative liquid chromatography analyses that use hydrogen flame ionization detection. Several separations are carried out simultaneously, and the column effluents are deposited on a slowly moving wire helix from which the volatile solvents are evaporated. A 35 cm long helix containing the effluent eluted from a column over a thirty-minute period could be passed through the flame in three minutes, thus offering at least a ten-fold increase in productivity without loss of resolution. Quantitative accuracy was good to within ±10%.
Survey of Polygonal Surface Simplification Algorithms (1997)

This paper surveys methods for simplifying and approximating polygonal surfaces. A polygonal surface is a piecewise-linear surface in 3-D defined by a set of polygons; typically a set of triangles. Methods from computer graphics, computer vision, cartography, computational geometry, and other fields are classified, summarized, and compared both practically and theoretically. The surface types range from height fields (bivariate functions), to manifolds, to non-manifold self-intersecting surfaces. Piecewise-linear curve simplification is also briefly surveyed.
Deletion Analysis of a Defective Interfering Semliki Forest Virus RNA Genome Defines a Region in the nsP2 Sequence That Is Required for Efficient Packaging of the Genome into Virus Particles (1998)

The 1,244-nucleotide genome of Semliki Forest virus (SFV) defective interfering (DI) RNA 19 (DI-19) is coterminal with the infectious genome and contains two major deletions. One deletion removes the end of the nsP1 gene and the beginning of the nsP2 gene, and the other removes the end of the nsP2 gene, the nsP3 and nsP4 genes, and all of the structural protein genes (M. Thomson and N. J. Dimmock, Virology 199:354-365, 1994). Like all DI SFV RNAs, DI-19 contains three regions that are conserved. Region a comprises the 5' terminus continuous with part of the nsP1 gene, region b comprises a central part of the nsP2 gene, and region c comprises the 3' terminus and the associated untranslated region. A deletion analysis of the 265-nucleotide b region (nucleotides 679 to 943, inclusive) was undertaken to determine its role in genome replication and packaging into DI virus particles. Deleted plasmids were constructed and transcribed, and the resulting DI RNAs were transfected into SFV-infected BHK cells. Putative progeny DI virus particles that had been released into the tissue culture fluid were then serially passaged in new monolayers together with added high-multiplicity SFV, and cells and tissue culture fluids were tested for the presence of DI RNA by reverse transcription-PCR. DI RNA that had all of the b region deleted was replicated well in BHK-21 cells, as shown by the presence of large amounts of negative-sense DI RNA and an increase in the amount of positive-sense RNA in the cytoplasm, but was packaged very inefficiently, as indicated by very low amounts of DI RNA in the tissue culture fluid. The genome of a deletion mutant that retained the 3' 224 nucleotides of region b was packaged successfully, but one that retained only the 5' 41 nucleotides was not detected in the tissue culture fluid. These and other data suggest that nucleotides 720 to 777 of region b are of particular importance in the packaging process. This finding agrees with data obtained with Ross River virus and contrasts with the well-studied Sindbis alphavirus major packaging signal that is located within the nsP1 gene.
Subchondral bone osteoclasts induce sensory innervation and osteoarthritis pain (2018)

Joint pain is the defining symptom of osteoarthritis (OA) but its origin and mechanisms remain unclear. Here, we investigated an unprecedented role of osteoclast-initiated subchondral bone remodeling in sensory innervation for OA pain. We show that osteoclasts secrete netrin-1 to induce sensory nerve axonal growth in subchondral bone. Reduction of osteoclast formation by knockout of receptor activator of nuclear factor kappa-B ligand (Rankl) in osteocytes inhibited the growth of sensory nerves into subchondral bone, dorsal root ganglion neuron hyperexcitability, and behavioral measures of pain hypersensitivity in OA mice. Moreover, we demonstrated a possible role for netrin-1 secreted by osteoclasts during aberrant subchondral bone remodeling in inducing sensory innervation and OA pain through its receptor DCC (deleted in colorectal cancer). Importantly, knockout of Netrin1 in tartrate-resistant acid phosphatase-positive (TRAP-positive) osteoclasts or knockdown of Dcc reduces OA pain behavior. In particular, inhibition of osteoclast activity by alendronate modifies aberrant subchondral bone remodeling and reduces innervation and pain behavior at the early stage of OA. These results suggest that intervention of the axonal guidance molecules (e.g., netrin-1) derived from aberrant subchondral bone remodeling may have therapeutic potential for OA pain.
Integrity Regions: Authentication through Presence in Wireless Networks (2010)

Despite years of intensive research, the main deterrents of widely deploying secure communication between wireless nodes remains the cumbersome key setup process. In this paper, we address this problem and we introduce Integrity (I) regions, a novel security primitive that enables message authentication in wireless networks without the use of preestablished or precertified keys. Integrity regions are based on the verification of entity proximity through time-of-arrival ranging techniques. IRegions can be efficiently implemented with ultrasonic ranging, in spite of the fact that ultrasound ranging techniques are vulnerable to distance enlargement and reduction attacks. We further show how IRegions can be used for key establishment in mobile peer-to-peer wireless networks and we propose a novel automatic key establishment approach, largely transparent to users, by leveraging on IRegions and nodes' mobility. We analyze our proposals against a multitude of security threats and we validate our findings via extensive simulations.