gebhart/patrepeval huggingface dataset:
Electro-infiltration: A method to form nanocomposite soft magnetic cores for integrated magnetic devices (2014)

This article introduces a scalable, process-integrable manufacturing method for creating microstructured, nanocomposite soft magnetic cores on planar substrates such as silicon wafers or printed circuit boards. To demonstrate this electro-infiltration process, maghemite (γ-Fe2O3) nanoparticles less than 50 nm are first evaporatively consolidated from suspension into photoresist molds on a silicon substrate, forming dimensionally defined porous microstructures. Next, a high-saturation soft magnetic iron cobalt alloy (Fe–Co) is electroplated up from a conductive layer on the substrate to fill in the void spaces of the consolidated particles. The result is a dense, two-phase nanocomposite, where the maghemite nanoparticles form an inclusion phase in the electroplated metal matrix phase. Improved high-frequency permeability is observed in the 100 MHz–2 GHz range.
Joint multi-mode dispersion extraction in Fourier and space time domains (2013)

In this paper we present a novel broadband approach for the extraction of dispersion curves of multiple time frequency overlapped dispersive modes such as in borehole acoustic data. The new approach works jointly in the Fourier and space time domains and, in contrast to existing space time approaches that mainly work for time frequency separated signals, efficiently handles multiple signals with significant time frequency overlap. The proposed method begins by exploiting the slowness (phase and group) and time location estimates based on frequency-wavenumber (f-k) domain sparsity penalized broadband dispersion extraction method as presented in \cite{AeronTSP2011}. In this context we first present a Cramer Rao Bound (CRB) analysis for slowness estimation in the (f-k) domain and show that for the f-k domain broadband processing, group slowness estimates have more variance than the phase slowness estimates and time location estimates. In order to improve the group slowness estimates we exploit the time compactness property of the modes to effectively represent the data as a linear superposition of time compact space time propagators parameterized by the phase and group slowness. A linear least squares estimation algorithm in the space time domain is then used to obtain improved group slowness estimates. The performance of the method is demonstrated on real borehole acoustic data sets.
A walk through tau therapeutic strategies (2019)

Tau neuronal and glial pathologies drive the clinical presentation of Alzheimer's disease and related human tauopathies. There is a growing body of evidence indicating that pathological tau species can travel from cell to cell and spread the pathology through the brain. Throughout the last decade, physiological and pathological tau have become attractive targets for AD therapies. Several therapeutic approaches have been proposed, including the inhibition of protein kinases or protein-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine/threonine Nacetylglucosaminyl hydrolase, the inhibition of tau aggregation, active and passive immunotherapies, and tau silencing by antisense oligonucleotides. New tau therapeutics, across the board, have demonstrated the ability to prevent or reduce tau lesions and improve either cognitive or motor impairment in a variety of animal models developing neurofibrillary pathology. The most advanced strategy for the treatment of human tauopathies remains immunotherapy, which has already reached the clinical stage of drug development. Tau vaccines or humanised antibodies target a variety of tau species either in the intracellular or extracellular spaces. Some of them recognise the amino-terminus or carboxy-terminus, while others display binding abilities to the proline-rich area or microtubule binding domains. The main therapeutic foci in existing clinical trials are on Alzheimer's disease, progressive supranuclear palsy and non-fluent primary progressive aphasia. Tau therapy offers a new hope for the treatment of many fatal brain disorders. First efficacy data from clinical trials will be available by the end of this decade.
A Rateless Coded Protocol for Half-Duplex Wireless Relay Channels (2010)

We propose a rateless coded protocol for a half-duplex wireless relay channel where all links experience independent quasi-static Rayleigh fading and the instantaneous channel realizations are unavailable at the transmitters. We assume that the network does not have a stringent delay constraint-thus the source and/or the relay continue transmitting until the destination acknowledges successful decoding. We identify rateless coded relaying as the natural choice, where each transmission from the source and/or the relay adds incremental redundancy to help the destination recover the original message. Our proposed protocol utilizes, in conjunction with rateless coding, a combination of the two popular relay cooperation schemes, namely decode-forward and compress-forward. Assuming very limited feedback from the destination, we derive the theoretical performance bounds specifically with binary phase-shift keying. We then implement the rateless coded relaying protocol using Raptor codes. The degree profiles for the Raptor codes are designed to maximize the average throughput-with the design formulated as a convex optimization problem. Using discretized density evolution for asymptotically large block lengths, the optimized codes lose approximately 5% in performance from the theoretical limit, whereas with practical finite block lengths, the performance loss is approximately 9%.
Data from Tumor-Infiltrating Merkel Cell Polyomavirus-Specific T Cells Are Diverse and Associated with Improved Patient Survival (2023)

<div>Abstract<p>Tumor-infiltrating CD8<sup>+</sup> T cells are associated with improved survival of patients with Merkel cell carcinoma (MCC), an aggressive skin cancer causally linked to Merkel cell polyomavirus (MCPyV). However, CD8<sup>+</sup> T-cell infiltration is robust in only 4% to 18% of MCC tumors. We characterized the T-cell receptor (TCR) repertoire restricted to one prominent epitope of MCPyV (KLLEIAPNC, “KLL”) and assessed whether TCR diversity, tumor infiltration, or T-cell avidity correlated with clinical outcome. HLA-A*02:01/KLL tetramer<sup>+</sup> CD8<sup>+</sup> T cells from MCC patient peripheral blood mononuclear cells (PBMC) and tumor-infiltrating lymphocytes (TIL) were isolated via flow cytometry. TCRβ (<i>TRB</i>) sequencing was performed on tetramer<sup>+</sup> cells from PBMCs or TILs (<i>n</i> = 14) and matched tumors (<i>n</i> = 12). Functional avidity of T-cell clones was determined by IFNγ production. We identified KLL tetramer<sup>+</sup> T cells in 14% of PBMC and 21% of TIL from MCC patients. TRB repertoires were strikingly diverse (397 unique TRBs were identified from 12 patients) and mostly private (only one TCRb clonotype shared between two patients). An increased fraction of KLL-specific TIL (>1.9%) was associated with significantly increased MCC-specific survival <i>P</i> = 0.0009). T-cell cloning from four patients identified 42 distinct KLL-specific TCRa/b pairs. T-cell clones from patients with improved MCC-specific outcomes were more avid (<i>P</i> < 0.05) and recognized an HLA-appropriate MCC cell line. T cells specific for a single MCPyV epitope display marked TCR diversity within and between patients. Intratumoral infiltration by MCPyV-specific T cells was associated with significantly improved MCC-specific survival, suggesting that augmenting the number or avidity of virus-specific T cells may have therapeutic benefit. <i>Cancer Immunol Res; 5(2); 137–47. ©2017 AACR</i>.</p></div>
Antisense Oligodeoxynucleotides Targeting Internal Exon Sequences Efficiently Regulate TNF-α Expression (1999)

ABSTRACT Exon sequences upstream of splice sites play a critical role in mRNA processing, which is dependent on spliceosome interactions with these sites. Using antisense oligodeoxynucleotides (ODN), we targeted these and other sequences of the proinflammatory tumor necrosis factor-alpha (TNF-alpha) gene because it is multiply spliced and has been difficult to regulate with ODN in the past. ODN targeting exon sequences upstream of the donor splice sites of internal exons 2 (ORF4) and 3 (ORF6) significantly reduced TNF-alpha levels in stimulated U937 cells by 62%+/-7% and 51%+/-9%, respectively, in a dose-dependent manner but did not affect interleukin-6 (IL-6) levels. In contrast, ODN targeting the exon sequences downstream of the acceptor splice sites of exons 1, 2, and 3 failed to reduce TNF-alpha levels significantly under the same conditions. End-phosphorothioated ORF4 (ORF4-PE) significantly reduced TNF-alpha mRNA levels by greater than 80% (p < 0.001) and protein levels by 60% (p < 0.001) in U937 cells. ORF4-PE reduced newly synthesized TNF-alpha protein levels by >80% in lipopolysaccharide (LPS)-stimulated human macrophages, by greater than 60% in phorbol myristate acetate/phyto-hemagglutinin (PMA/PHA)-stimulated human peripheral blood mononuclear cells (PBMC), and by approximately 50% in LPS-stimulated murine monocytes. These results suggest that exon sequences flanking donor splice sites are highly susceptible target domains for antisense inhibition of TNF-alpha gene expression.
Using Bayesian Network to Model Drilling Fluids Practices in Saudi Arabia (2012)

Abstract Texas A&M University recently has established a new method to develop a drilling expert system that can be used as a training tool for young engineers or as a consultation system in various drilling engineering concepts such as drilling and completion fluids, cementing, completion, and underbalanced drilling practices. To the best of the authors knowledge there is no standards developed to aid drilling engineers and scientists to formulate effective drilling fluids systems for the entire well sections. The objective of this paper is to set a module that should aid drilling engineers when designing drilling fluids. A module was created based on several inputs. To create this module, we interviewed experts to gather the information required to determine best practices as a function of different probabilities. Drilling fluids formulations were gathered from Saudi Arabia fields to build up this model. The Bayesian approach was found suitable for designing expert system. The model can work as a guide to aid drilling engineers and scientists to design and execute optimum drilling fluids. Using this approach to build up expert systems is more flexible than using flow charts. Updating flow charts is time consuming and require redesigning them again to be used by different experts or in different fields. Using Bayesian network allows us to update our industry practices by updating the probabilities states mentioned in this paper.
A Structure–Property Relationship Study of the Well-Defined Telodendrimers to Improve Hemocompatibility of Nanocarriers for Anticancer Drug Delivery (2014)

A series of telodendrimer (a linear polyethyelene glycol-block-dendritic oligo-cholic acid) have been synthesized via a bottom-up approach to optimize the hemocompatibility of the nanocarrier. Numbers of hydrophilic glycerol groups were introduced onto the polar surface of cholic acid to reduce the plasma membrane lytic activity of telodendrimers. An interesting result was observed: only an optimum number of glycerol introduced could reduce the hemolytic properties of the nanocarrier; on the contrary, more glycerols or the amino-glycerol substitution onto cholic acid significantly increased the hemolytic properties of the nanocarriers. To further elucidate the structure-property relationship, the molecular dynamic approach was used to simulate the conformation of the subunits of telodendrimers with different glycerol substitution, and the binding energies and the polar surface areas of the hairpin conformations were calculated to explain the membrane activities of nanocarriers. In addition, these telodendrimer subunits were synthesized and their membrane activities were tested directly, which validated the computational prediction and correlated with the observed hemolytic activity of nanocarriers. The glycerol substitution sustained the facial amphiphilicity of cholic acid, maintaining the superior drug loading capacity (paclitaxel and doxorubicin), stability, cell uptake, and anticancer efficacy of payloads. The in vivo optical imaging study indicated that the optimized nanocarriers can specifically deliver drug molecules to the tumor sites more efficiently than free drug administration, which is essential for the enhanced cancer treatment.
Non-Peptide Glycoprotein IIb/IIIa Inhibitors. 17. Design and Synthesis of Orally Active, Long-Acting Non-Peptide Fibrinogen Receptor Antagonists (1997)

The synthesis and pharmacological evaluation of 5 (L-738, 167), a potent, selective non-peptide fibrinogen receptor antagonist is reported. Compound 5 inhibited the aggregation of human gel-filtered platelets with an IC50 value of 8 nM and was found to be > 33000-fold less effective at inhibiting the attachment of human endothelial cells to fibrinogen, fibronectin, and vitronectin than it was at inhibiting platelet aggregation. Ex vivo platelet aggregation was inhibited by > 85% 24 h after the oral administration of 5 to dogs at 100 micrograms/kg. The extended pharmacodynamic profile exhibited by 5 appears to be a consequence of its high-affinity binding to GPIIb/IIIa on circulating platelets and suggests that 5 is suitable for once-a-day dosing.
Fiber-format Picosecond Source for Coherent Raman Microscopy (2012)

We present a fiber-based source for coherent Raman microscopy. Picosecond frequency conversion is achieved by normal dispersion four-wave mixing in photonic crystal fiber, yielding nanojoule pulses with 2800-3200 cm−1 frequency differences.
New digital acoustic signal processing for use in ultrasonic intrusion alarm systems (1979)

It has been the accepted belief that air turbulence in an ultrasonic alarm system produces a Doppler shift similar to that produced by a moving target, resulting in false alarms. A mathematical analysis of the entire acoustic system shows that this assumption is not true. It is shown that the received ultrasonic signal can be represented by a rotating phasor whose head exhibits circular motion when a moving target is present. The circular motion is virtually non-existent when a moving target is absent regardless of the presence of environmental disturbances, such as air turbulence and noise transients. The mathematical findings have been confirmed experimentally. An electronic circle detector incorporating a microprocessor was developed for recognizing the presence of circular motion in the head of a rotating phasor when it occurs in the received signal. This permits the system to absolutely detect a moving target while remaining immune to false alarms due to air turbulence and other environmental disturbances. This microprocessor-based digital signal processing also totally eliminates the need for any sensitivity controls as are required by all prior art systems.
A Small Molecule That Targets r(CGG)<sup>exp</sup> and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome (2012)

The development of small molecule chemical probes or therapeutics that target RNA remains a significant challenge despite the great interest in such compounds. The most significant barrier to compound development is defining which chemical and RNA motif spaces interact specifically. Herein, we describe a bioactive small molecule probe that targets expanded r(CGG) repeats, or r(CGG)(exp), that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS). The compound was identified by using information on the chemotypes and RNA motifs that interact. Specifically, 9-hydroxy-5,11-dimethyl-2-(2-(piperidin-1-yl)ethyl)-6H-pyrido[4,3-b]carbazol-2-ium binds the 5'CGG/3'GGC motifs in r(CGG)(exp) and disrupts a toxic r(CGG)(exp)-protein complex in vitro. Structure-activity relationship studies determined that the alkylated pyridyl and phenolic side chains are important chemotypes that drive molecular recognition of r(CGG)(exp). Importantly, the compound is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTAS-associated pre-mRNA splicing defects and to reduce the size and number of r(CGG)(exp)-containing nuclear foci. This approach may establish a general strategy to identify lead ligands that target RNA while also providing a chemical probe to dissect the varied mechanisms by which r(CGG)(exp) promotes toxicity.
Rapid Characterization of Magnetic Moment of Cells for Magnetic Separation (2013)

NCI-H1650 lung cancer cell lines labeled with magnetic nanoparticles via the Epithelial Cell Adhesion Molecule (EpCAM) antigen were previously shown to be captured at high efficiencies by a microfabricated magnetic sifter. If fine control and optimization of the magnetic separation process is to be achieved, it is vital to be able to characterize the labeled cells' magnetic moment rapidly. We have thus adapted a rapid prototyping method to obtain the saturation magnetic moment of these cells. This method utilizes a cross-correlation algorithm to analyze the cells' motion in a simple fluidic channel to obtain their magnetophoretic velocity, and is effective even when the magnetic moments of cells are small. This rapid characterization is proven useful in optimizing our microfabricated magnetic sifter procedures for magnetic cell capture.
Low-cross-talk 2 × 2optical switch (1981)

An electro-optical 2 x 2 switch for fiber-optic applications has been developed. Optical cross talk is reduced significantly by inserting two 2 x 1 switches in each optical path. A compact structure is used to contain the four 2 x 1's that are required. We observed -27-dB cross talk and 2.5-dB insertion loss in both switching states. The device is controlled by a 5-V twisted-nematic liquid-crystal cell. Multimode, unpolarized light is switched.
Studies on the Syntheses of 2 (1H)-Pyridone Derivatives. IV. Synthesis of Condensed Heterocyclic 2 (1H)-Pyridones (1979)

Condensation of 4-cyano-3-butenoates (IV) with 1, 2-diamine or 1, 2-aminothiol was carried out. Imidazopyridones were obtained by the reaction of IV with aliphatic 1, 2-diamine. The reaction of IV with o-phenylenediamine resulted in the formation of imino-pyridobenzimidazole (VII), which was converted to the corresponding pyridone derivative (IX) on hydrolysis. The predominant tautomeric forms of VII and IX are discussed on the basis of nuclear magnetic resonance and ultraviolet spectra. In the reaction of IV with 2-aminoethanethiol or o-aminothiophenol, the thiazoline ring was formed by condensation between the cyano group of IV and the amino and thiol groups of the 1, 2-aminothiol, and the resulting thiazoline compound was further converted into thiazolopyridone or oxo-pyridobenzothiazole, respectively, by cyclization with an acid catalyst. Some of these pyridone derivatives showed strong anti-inflammatory activity.
Dispersion-compensating fiber: is there merit in the figure of merit? (1996)

Summary form only given. This paper investigates how dispersion, loss, and effective area of a dispersion compensating fiber (DCF) interplay to determine the performance of a system, and introduces the new figure of merit F/sub nl/, which describes the quality of a DCF from a system performance point of view. This is accomplished by evaluating the performance degradation that a DCF with given values of dispersion, loss and effective area introduces compared with a system with an ideal dispersion compensator.
Oblique surface reconstruction to approximate cone-beam helical data in multislice CT (2000)

Multi-slice helical beam scanning involves cone-beam geometry. The primary advantages for use of divergent cone- beams include reduced data acquisition, improved image resolution and optimized photon utilization. Due to the complexity of 3D cone-beam reconstruction, approximate algorithms have been sought to handle the cone-beam reconstruction. This paper presents a new approximate algorithm termed as oblique surface reconstruction (OSR). Theoretical considerations as well as the reconstruction of simulated phantom data in comparison to the current standard 180 degree(s) LI are presented. OSR is shown to be effective and practical to generate images with diagnostic quality.
Algorithms for efficient transaction management and consistent queries in client-server semantic object-oriented parallel databases (1998)

Large read-only or read-write transactions with a large read set and a small write set constitute an important class of transactions used in such applications as data mining, data warehousing, statistical applications, and report generators. Such transactions are best supported with optimistic concurrency, because locking of large amounts of data for extended periods of time is not an acceptable solution. The abort rate in regular optimistic concurrency algorithms increases exponentially with the size of the transaction. The algorithm proposed in this dissertation solves this problem by using a new transaction scheduling technique that allows a large transaction to commit safely with significantly greater probability that can exceed several orders of magnitude versus regular optimistic concurrency algorithms. A performance simulation study and a formal proof of serializability and external consistency of the proposed algorithm are also presented. This dissertation also proposes a new query optimization technique (lazy queries). Lazy Queries is an adaptive query execution scheme which optimizes itself as the query runs. Lazy queries can be used to find an intersection of sub-queries in a very efficient way, which does not require full execution of large sub-queries nor does it require any statistical knowledge about the data. An efficient optimistic concurrency control algorithm used in a massively parallel B-tree with variable-length keys is introduced. B-trees with variable-length keys can be effectively used in a variety of database types. In particular, we show how such a B-tree was used in our implementation of a semantic object-oriented DBMS. The concurrency control algorithm uses semantically safe optimistic virtual "locks" that achieve very fine granularity in conflict detection. This algorithm ensures serializability and external consistency by using logical clocks and backward validation of transactional queries. A formal proof of correctness of the proposed algorithm is also presented.
Validation of an Affordable Handheld Wavefront Autorefractor (2019)

This study found excellent agreement between the measurements obtained with the portable autorefractor and the prescriptions based on SR and only small differences between the VA achieved by either method.
Anti-RNA polymerase I antibodies in the urine of patients with systemic lupus erythematosus. (1990)

Urine samples from patients with systemic lupus erythematosus (SLE) (n = 80), patients with rheumatoid arthritis (RA) (n = 21), and healthy controls (n = 36) were analyzed by radio-immunoassay (RIA) for anti-RNA polymerase I (RPI) antibodies. Significant levels of anti-RPI antibodies were detected in the urine of 46% of the patients with SLE but in only 19% of the patients with RA and in no sample from healthy individuals. The presence of anti-RPI antibodies in the urine was confirmed by demonstrating that IgG purified from the urine of patients with SLE was capable of inhibiting the transcriptional activity of RPI in vitro. If the quantity of anti-RPI antibodies excreted is related to disease activity, analysis of urine for these antibodies may be a useful alternative for the purpose of monitoring the progression of disease in individuals with SLE because of the ease by which the sample can be collected.