gebhart/patrepeval huggingface dataset:
Reduced Hardware NOrec (2015)

Because of hardware TM limitations, software fallbacks are the only way to make TM algorithms guarantee progress. Nevertheless, all known software fallbacks to date, from simple locks to sophisticated versions of the NOrec Hybrid TM algorithm, have either limited scalability or weakened semantics. We propose a novel reduced-hardware (RH) version of the NOrec HyTM algorithm. Instead of an all-software slow path, in our RH NOrec the slow-path is a "mix" of hardware and software: one short hardware transaction executes a maximal amount of initial reads in the hardware, and the second executes all of the writes. This novel combination of the RH approach and the NOrec algorithm delivers the first Hybrid TM that scales while fully preserving the hardware's original semantics of opacity and privatization.
Modulation of tumor eIF4E by antisense inhibition: A phase I/II translational clinical trial of ISIS 183750—an antisense oligonucleotide against eIF4E—in combination with irinotecan in solid tumors and irinotecan‐refractory colorectal cancer (2016)

The eukaryotic translation initiation factor 4E (eIF4E) is a potent oncogene that is found to be dysregulated in 30% of human cancer, including colorectal carcinogenesis (CRC). ISIS 183750 is a second-generation antisense oligonucleotide (ASO) designed to inhibit the production of the eIF4E protein. In preclinical studies we found that EIF4e ASOs reduced expression of EIF4e mRNA and inhibited proliferation of colorectal carcinoma cells. An additive antiproliferative effect was observed in combination with irinotecan. We then performed a clinical trial evaluating this combination in patients with refractory cancer. No dose-limiting toxicities were seen but based on pharmacokinetic data and tolerability the dose of irinotecan was reduced to 160 mg/m(2) biweekly. Efficacy was evaluated in 15 patients with irinotecan-refractory colorectal cancer. The median time of disease control was 22.1 weeks. After ISIS 183750 treatment, peripheral blood levels of eIF4E mRNA were decreased in 13 of 19 patients. Matched pre- and posttreatment tumor biopsies showed decreased eIF4E mRNA levels in five of nine patients. In tumor tissue, the intracellular and stromal presence of ISIS 183750 was detected by IHC in all biopsied patients. Although there were no objective responses stable disease was seen in seven of 15 (47%) patients who were progressing before study entry, six of whom were stable at the time of the week 16 CT scan. We were also able to confirm through mandatory pre- and posttherapy tumor biopsies penetration of the ASO into the site of metastasis.
Temperature dependant domain structures of lithium niobate single crystals (2003)

The domain structure of lithium niobate single crystals is studied from the corresponding crystallographic characteristics at different temperatures (ranging from room temperature to the Curie temperature). The temperature dependent nature of the domain reversal and domain structures of such ferroelectric crystals have been quantitatively analyzed. Various constituent chemical bonds and oxygen octahedra (formed by these bonds) of ferroelectric lithium niobate crystals are utilized as the starting point of this work. At low temperatures, the domain structure is simplex and regular owing to the regular occupancy of constituent ions at the corresponding lattice sites (of the space group R3c). With temperature increasing, the domain structure of the ferroelectric lithium niobate crystal becomes complex, due to the complicated site occupancies of constituent ions. At high temperatures, the multi-domain is formed owing to the fact that vacant sites are energetically available for Li/sup +/ cations (i.e., the random location of Li/sup +/ cations in the crystallographic frame).
Anterior encephalocele presenting as nasolacrimal obstruction. (1986)

A case of congenital anterior encephalocele presented originally with nasolacrimal obstruction. Associated paranasal masses and hypertelorism suggested the diagnosis, which was confirmed and delineated by computed tomography. Anterior encephalocele has various clinical presentations, but the diagnosis should be suspected in a child with nasolacrimal obstruction and associated congenital anomalies, particularly paranasal masses. Early recognition is essential to prevent trauma to CNS tissue, to prompt evaluation for other congenital anomalies, and to facilitate appropriate neurosurgical repair.
Endocrine consequences of immune checkpoint inhibitors (2019)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Direct measurement of Zernike aberration modes with a modal wavefront sensor (2003)

It is often convenient to represent a wavefront aberration by the superposition of several aberration modes, for example, using the set of Zernike polynomials. In many practical situations the total aberration can be accurately represented by a small number of such modes. It is therefore desirable to be able to measure directly the modal content of the wavefront. The modal wavefront sensor allows us to do just this. This sensor can be applied to closed-loop aberration correction in adaptive systems and to direct absolute measurement of modal aberration coefficients. One implementation offers the possibility of an adaptive optics system where we have disposed altogether of a separate wavefront sensor. We present here extension of the modal wavefront sensing theory and explore the options for optimization of the design. We investigate the linear measurement range of the sensor and the performance in closed-loop systems.
Engineering and implementing software architectural patterns based on feedback loops (2015)

A highly decentralized system of autonomous service components consists of multiple and interacting feedback loops which can be organized into a variety of architectural patterns. The highly complex nature of these loops make engineering and implementation of these patterns a very challenging task. In this paper, we present SimSOTA - an integrated Eclipse plug-in to architect, engineer and implement self-adaptive systems based on our feedback loop-based approach. SimSOTA adopts model-driven development to model and simulate complex self-adaptive architectural patterns, and to automate the generation of Java-based implementation code. The approach is validated using a case study in cooperative electric vehicles.
La conoscopie: un concept original pour la vision tridimentionnelle (1994)

peer reviewed
The classification of power system disturbance waveforms using a neural network approach (2002)

Owing to the rise in power quality problems, the use of transient recorders to monitor power systems has increased steadily. The triggering strategies used by these transient recorders to capture disturbance waveforms are usually based on the violation of a set of predetermined measurement thresholds. Unfortunately, threshold based triggering strategies are difficult to apply in situations when only waveforms corresponding to a given class of disturbances need to be recorded. This inability of the reader to automatically discriminate between waveform types tends to burden the user with the task of manually sifting and sorting through a large number of captured waveforms. This paper describes an artificial neural network methodology for the classification of waveforms that are captured, as part of a larger scheme to automate the data collection process of recorders. Two different neural network paradigms are investigated: the more common feedforward network; and a modification of that, the time-delay network, which has the ability to encode temporal relationships found in the input data and exhibits a translation shift invariance property. Comparisons of both network paradigms, based on a typical distribution circuit configuration, are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gate sizing in the presence of gate switching activity and input vector control (2013)

We introduce a novel gate sizing approach that considers both the gate switching activity (SA) and gate input vector control leakage (IVC). We first extract SA using simulation and find promising input vectors. Next, in an iterative framework, we interchangeably conduct gate sizing and refining the IVC. As dictated by the new objective function, our algorithm conducts iterative gate freezing and unlocking with cut-based search for the most beneficial gate sizes under delay constraints. We evaluate our approach on standard benchmarks in 45 nm technology, showing promising improvement, achieving up to 62% (29% avg.) energy savings compared to the traditional objective function.
Interferometric measurements of the position of a macroscopic body: Towards observation of quantum limits (1999)

An optomechanical sensor suitable for the study of quantum effects has been developed and characterized. The sensor reads out the vibrations of a microfabricated miniature silicon mechanical oscillator which forms one end mirror of a high finesse Fabry-P\'erot cavity. The mechanical quality factor is up to $Q=300000$ at 300 K and rises up to $Q=4\ifmmode\times\else\texttimes\fi{}{10}^{6}$ at 4 K. The thermal noise of the oscillator has been measured in the time and frequency domains at room temperature and at 4.5 K. The prospects for observing the standard quantum limit are discussed.
RF-powered cognitive radio networks: technical challenges and limitations (2015)

The increasing demand for spectral- and energy-efficient communication networks has spurred great interest in energy harvesting cognitive radio networks. Such a revolutionary technology represents a paradigm shift in the development of wireless networks, as it can simultaneously enable the efficient use of the available spectrum and the exploitation of RF energy in order to reduce reliance on traditional energy sources. This is mainly triggered by the recent advancements in microelectronics that puts forward RF energy harvesting as a plausible technique in the near future. On the other hand, it has been suggested that the operation of a network relying on harvested energy needs to be redesigned to allow the network to reliably function in the long term. To this end, the aim of this survey article is to provide a comprehensive overview of recent development and the challenges regarding the operation of CRNs powered by RF energy. In addition, the potential open issues that might be considered for future research are also discussed in this article.
A computational tool to accurately and quickly predict 19 F NMR chemical shifts of molecules with fluorine–carbon and fluorine–boron bonds (2022)

We report the evaluation of density-functional-theory (DFT) based procedures for predicting <sup>19</sup>F NMR chemical shifts at modest computational cost for a range of molecules with fluorine bonds, to be used as a tool for assisting the characterisation of reaction intermediates and products and as an aid to identifying mechanistic pathways. The results for a balanced learning set of molecules were then checked using two further testing sets, resulting in the recommendation of the ωB97XD/aug-cc-pvdz DFT method and basis set as having the best combination of accuracy and computational time, with a RMS error of 3.57 ppm. Cationic molecules calculated without counter-anion showed normal errors, whilst anionic molecules showed somewhat larger errors. The method was applied to the prediction of the conformationally averaged <sup>19</sup>F chemical shifts of 2,2,3,3,4,4,5,5-octafluoropentan-1-ol, in which gauche stereoelectronic effects involving fluorine dominate and to determining the position of coordination equilibria of fluorinated boranes as an aid to verifying the relative energies of intermediate species involved in catalytic amidation reactions involving boron catalysts.
Leveraging amino acid sensors as therapeutic targets for tauopathies and related dementias (2020)

Abstract Background Tauopathies including Alzheimer’s disease (AD) comprise of over 27 neurodegenerative diseases. Our group has uncovered a unique interaction between uncoupling of amino acid sensors and tauopathies. L‐Arginine metabolism impacts multiple processes that seemingly show considerable influence upon tau biology. Several protein sensors have been identified that sense arginine within the lysosomal lumen, cytoplasm and signal to the mechanistic target of rapamycin complex 1 (mTORC1). GPRC6a, g‐protein coupled receptor also senses arginine levels but also signals to mTORC1. We posit that GPRC6a remains tonically active through extracellular arginine. GPRC6a signaling increases during tauopathies and thereby promotes hyper‐mTORC1 activation and impairs autophagy flux. Method We performed PCR‐array analysis, biochemical analysis for gene transcripts and protein expression for Alzheimer’s disease brain tissue and aged matched controls. We performed a series of mechanistic studies on GPRC6a and tau biology using siRNA, shRNA, drug pharmacology in cell culture models and (PS19 tau mice) or wild‐type littermates. RNA seq was performed on GPRC6a knockout mice crossed with PS19 mice. Result Our work indicates dysregulation of gene transcripts for arginine sensors, components of mTORC1 signaling in Alzheimer’s disease (AD) brains and mice with tauopathy. AD brains and tau PS19 mice showed increased GPRC6a, CASTOR1 and SLC38A9 signifying dysfunction in arginine sensing. Tau PS19 mice showed increased total and extracellular arginine in the brain, which further increased with neuronal activity. GPRC6a gene repression or novel allosteric antagonists decreased mTORC1 activation and reduced tau burden. Conversely, GPRC6a overexpression increased mTORC1 and tau accumulation. Knockout mice for GPRC6a crossed with PS19 tau transgenic mice reversed tau‐induced mRNA signatures in the brain via RNA seq. Microglia and neurometabolism were most affected in GPRC6a knockout mice signifying a critical role for arginine sensors in microglia during tau deposition. Importantly, novel allosteric antagonists to GPRC6a increased microglia phagocytosis and index. Conclusion Our work identifies a new pathway activated in AD and models of tauopathy yet provides the discovery of a new class of agents that govern microglia function, autophagy and neurometabolism. These data provide new therapeutic strategies for proteinopathies that exploit nutrient sensing dysfunction in AD.
A (−)-Sparteine-Directed Highly Enantioselective Synthesis of Boroproline. Solid- and Solution-State Structure and Properties (2007)

A two-step, direct asymmetric synthesis of the trifluoroacetate ammonium salt of boroproline is reported. (-)-Sparteine-mediated lithiation of N-Boc-pyrrolidine afforded N-Boc-aminoboronic acid in good yield and enantioselectivity as determined by HPLC (pinanediol ester). Deprotection using TFA yielded the ammonium salt; full characterization data are presented, and the structure in aqueous solution and the occurrence of a B-N species are discussed.
CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging (2022)

<b>Rationale:</b> A prevailing paradigm recognizes idiopathic pulmonary fibrosis (IPF) originating from various alveolar epithelial cell (AEC) injuries, and there is a growing appreciation of AEC aging as a key driver of the pathogenesis. Despite this progress, it is incompletely understood what main factor(s) contribute to the worsened alveolar epithelial aging in lung fibrosis. It remains a challenge how to dampen AEC aging and thereby mitigate the disease progression. <b>Objectives:</b> To determine the role of AEC CD38 (cluster of differentiation 38) in promoting cellular aging and lung fibrosis. <b>Methods:</b> We used single-cell RNA sequencing, real-time PCR, flow cytometry, and Western blotting. <b>Measurements and Main Results:</b> We discovered a pivotal role of CD38, a cardinal nicotinamide adenine dinucleotide (NAD) hydrolase, in AEC aging and its promotion of lung fibrosis. We found increased CD38 expression in IPF lungs that inversely correlated with the lung functions of patients. CD38 was primarily located in the AECs of human lung parenchyma and was markedly induced in IPF AECs. Similarly, CD38 expression was elevated in the AECs of fibrotic lungs of young mice and further augmented in those of old mice, which was in accordance with a worsened AEC aging phenotype and an aggravated lung fibrosis in the old animals. Mechanistically, we found that CD38 elevation downregulated intracellular NAD, which likely led to the aging promoting impairment of the NAD-dependent cellular and molecular activities. Furthermore, we demonstrated that genetic and pharmacological inactivation of CD38 improved these NAD dependent events and ameliorated bleomycin-induced lung fibrosis. <b>Conclusions:</b> Our study suggests targeting alveolar CD38 as a novel and effective therapeutic strategy to treat this pathology.
Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device (2017)

ABSTRACT Advances in 3 rd generation sequencing have opened new possibilities for ‘benchtop’ whole genome sequencing. The MinION is a portable device that uses nanopore technology and can sequence long DNA molecules. MinION long reads are well suited for sequencing and de novo assembly of complex genomes with large repetitive elements. Long reads also facilitate the identification of complex genomic rearrangements such as those observed in tumor genomes. To assess the feasibility of the de novo assembly of large complex genomes using both MinION and Illumina platforms, we sequenced the genome of a Caenorhabditis elegans strain that contains a complex acetaldehyde-induced rearrangement and a biolistic bombardment-mediated insertion of a GFP containing plasmid. Using ∼5.8 gigabases of MinION sequence data, we were able to assemble a C. elegans genome containing 145 contigs (N50 contig length = 1.22 Mb) that covered &gt;99% of the 100,286,401 bp reference genome. In contrast, using ∼8.04 gigabases of Illumina sequence data, we were able to assemble a C. elegans genome in 38,645 contigs (N50 contig length = ∼26 kb) containing 117 Mb. From the MinION genome assembly we identified the complex structures of both the acetaldehyde-induced mutation and the biolistic-mediated insertion. To date, this is the largest genome to be assembled exclusively from MinION data and is the first demonstration that the long reads of MinION sequencing can be used for whole genome assembly of large (100 Mb) genomes and the elucidation of complex genomic rearrangements.
Definition of effective area shape and guide for superdirective antenna design using poynting streamlines analysis (2016)

A receiving antenna can be considered as a electromagnetic energy concentration device that the field around the antenna either terminated by the antenna load or pass by the antenna. In this paper, streamlines of the Poynting density vector are used to understand the field energy flow near the linear antenna, aperture antenna and superdirective antenna. Poynting streamline method gives a way to intuitively describe the physical nature of receiving antennas. By calculating the locus of streamlines terminated on the antenna load, the geometrical shape of effective area for any type antennas is achieved, which can be consider a supplementary to the IEEE standard definition of the effective area based on the mathematical results. The streamline method is used to guide the design of a superdirective horn antenna with almost 200% aperture efficiency.
3D gradient echo snapshot CEST MRI with low power saturation for human studies at 3T (2018)

A sophisticated CEST tool ready for clinical application was developed and tested for feasibility.
AS LITERATURAS ORAIS E MARGINALIZADAS (2007)

Oral / popular / traditional literatures show specific ways of adaptation to new contexts andstimulus. This text is about their capacity of reinvention and of use of new media (from the book to theCD-ROM), where they prove to be alive under new forms, in a constant process of dynamictransformation.
Real World Issues in Deploying a Wireless Sensor Network for Oceanography. (2005)

In this paper we describe some of the practical issues involved in designing, building and deploying a sensor network for oceanographic monitoring. The paper explains some of the design decisions and their consequences, and some of the lessons learned from a first sensor network trial at sea.
Iterative learning control for variable setpoints, applied to a motion system (2003)

Iterative Learning Control (ILC) is a known technique for improving the performance of systems or processes that operate repetitively over a fixed time interval. ILC generates a feedforward signal effective for providing good tracking control. However, there still exist a number of problems which hinder extensions of ILC schemes. The major obstacle is perhaps the requirement that the trajectory (or repetitive disturbance) must be strictly repeatable over operations. ILC has also liability to deal with stochastic effects. This paper presents the design and the implementation of a time-frequency adaptive ILC that is applicable for motion systems which execute the same kind of repetitive tasks. For the motion system, we show that the adaptive algorithm we propose leads to design one (learned) feed-forward signal suitable for different setpoints. We demonstrate that, when implementing time-frequency adaptive ILC, very good time performance (tracking errors) is obtained. The proposed algorithm converges faster than standard ILC. With time-frequency adaptive ILC noise amplification is reduced.
Adjustable virtual pore-size filter for automated sample preparation using acoustic radiation force (2008)

We present a rapid and robust size-based separation method for high throughput microfluidic devices using acoustic radiation force. We developed a finite element modeling tool to predict the two-dimensional acoustic radiation force field perpendicular to the flow direction in microfluidic devices. Here we compare the results from this model with experimental parametric studies including variations of the PZT driving frequencies and voltages as well as various particle sizes and compressidensities. These experimental parametric studies also provide insight into the development of an adjustable 'virtual' pore-size filter as well as optimal operating conditions for various microparticle sizes. We demonstrated the separation of Saccharomyces cerevisiae and MS2 bacteriophage using acoustic focusing. The acoustic radiation force did not affect the MS2 viruses, and their concentration profile remained unchanged. With optimized design of our microfluidic flow system we were able to achieve yields of &gt; 90% for the MS2 with &gt; 80% of the S. cerevisiae being removed in this continuous-flow sample preparation device.