gebhart/patrepeval huggingface dataset:
Lookahead, Rollback and Lookback: Searching for Parallelism in Discrete Event Simulation (2002)

We discuss synchronization protocols for Parallel Discrete Event Simulations. We start with traditional conservative protocols based on lookahead and optimistic ones employing rollbacks. Next, we observe that a logical process may be able to change the simulation past locally (without involving other logical processes). This ability is named lookback, and is a basis for a new class of PDES synchronization protocols, named lookback-based protocols. Another notion, impact time, is introduced to identify the maximum amount of lookback. We also show that lookback is always larger than or equal to lookahead, and lookbackbased protocols can circumvent the execution time limit imposed by the cumulative execution time of events on the critical path on traditional conservative protocols and optimistic protocols with no optimization.
Converting Treebank Annotations to Language Neutral Syntax. (2004)

We describe the automatic conversion of English Penn Treebank (PTB) annotations into Language Neutral Syntax (LNS) (Campbell and Suzuki, 2002a,b). In this paper, we describe LNS and why it is useful, describe the conversion algorithm, present an evaluation of the conversion, and discuss some uses of the converted annotations and the potential for extending the coverage to other languages. The work described here is in the spirit of other automatic re-annotations of PTB trees (e.g. Frank, 2000 and Meyers, 2001), but differs in the nature of the output.
Joint Beam Management and User Scheduling for Massive MIMO with Hybrid Beamforming and Limited Feedback (2020)

In this paper, we consider the design of multiuser (MU) massive multiple-input and multiple-output (MIMO) employing hybrid beamforming, i.e., an analog radio frequency (RF) beamforming at the front end concatenated with a digital baseband precoding. We present several RF beam feedback protocols with small overhead, i.e. the RF beam indices with or without channel quality index (CQI). Based on the beam feedback schemes, we design novel algorithms to jointly select the transmit RF beams and schedule the users to improve the system throughput. Specifically, when the users feed back multiple candidate RF beams, the new algorithms resolve the conflicts when different users feedback some same RF beams. The simulation results demonstrate the efficacy of the proposed algorithms.
ChemInform Abstract: Synthesis and Luminescence Properties of Biphenyl‐Type Firefly Luciferin Analogues with a New, Near‐Infrared Light‐Emitting Bioluminophore. (2014)

Abstract The firefly luciferin analog (IIIa) shows high bioluminescence activity with a maximum at 675 nm.
Synthesis and evaluation of a novel bis-zinc(II)-dipicolylamine derivative for dual-modality PET/NIRF imaging of phosphatidylserine exposure (2013)

5 Objectives Anionic phosphatidylserine (PS) is highly exposed on the surfaces of cancer cells and tumor blood vessels. Synthetic bis-zinc(II)-dipicolylamine (Zn-DPA) derivatives have high selectivity for biological membranes enriched with PS. This study was designed to investigate the feasibility of a novel Zn-DPA containing probe for dual-modality PET/NIRF imaging of PS exposure. Methods Bis-dipicolylamine was conjugated with a NIRF dye using lysine as a linker. The precursor with a free epsilon amine group was radiolabeled with 4-nitrophenyl 2-[18F]fluoropropinate ([18F]NFP) to provide 18F-PS-TumorVue® which was then subjected to in vitro and in vivo evaluations, including U87MG cell uptake, PET/NIRF imaging, and direct tissue sampling biodistribution studies in a U87MG tumor xenografted mouse model. Results The synthesis of precursor was accomplished in five steps with >60% yield in each step. The F-18 radiolabeling was achieved with overall radiochemical yield of 60 ± 7% (decay corrected, n = 6) and radiochemical purity of >99%. The specific activity of 18F-PS-TumorVue® was 300-650 mCi/umol. The tumor-targeting efficacy and biodistribution pattern of 18F-PS-TumorVue® were evaluated in nude mice bearing U87MG xenografts (n = 5) at 1, 2, and 4 h with static microPET scans. The U87MG tumors were all clearly visible with good contrast to contralateral background at all measured time points. Ex vivo PET imaging of tumor and normal tissues of 18F-PS-TumorVue® confirmed the in vivo findings. NIRF imaging with 19F-PS-TumorVue® exhibited rapid U87MG tumor targeting at 0.5 h pi, and high tumor-to-background contrast at 4 h pi. Conclusions We have successfully developed a novel Zn-DPA derivative for dual-modality PET/NIRF imaging of PS exposure. The PET/NIRF probe offers synergistic advantages, not only allowing comprehensive collection of physiological information, but also facilitating clinical applications of image-guided surgery. Research Support This work was supported by the USC Department of Radiology.
Development of dental magnetic attachment with rare earth magnet. (1990)

A dental magnetic attachment is a denture retainer with a permanent magnet. It is suggested that it possesses many advantages compared with the conventional mechanical attachment which has often caused trouble in durability for retentive force as well as in esthetics. However it has not been put into practical use because of an attractive force shortage and corrosion of the magnet in the oral cavity. An advanced type of dental magnetic attachment has been developed with a sandwiched type of magnetic circuit in which a rare earth magnet is sandwiched by a pare of yokes. The attachment has a higher attractive force more than 4.9 N in spite of its small size. The magnet is sealed with a stainless steel cap laser-welded to the yoke so as to be perfectly protected against corrosion.
The Q121 PC-1 Variant and Obesity Have Additive and Independent Effects in Causing Insulin Resistance (2001)

PC-1 is a membrane glycoprotein that impairs insulin receptor function. Its K121Q polymorphism is a genetic determinant of insulin resistance. We investigated whether the PC-1 gene modulates insulin sensitivity independently of weight status (i.e. both in nonobese and obese individuals). Nondiabetic subjects [164 males, 267 females; age, 37 +/- 0.6 yr, mean +/- SEM; body mass index (BMI), 32.7 +/- 0.5 kg/m(2)], who were subdivided into 220 nonobese (BMI < or = 29.9) and 211 obese, were studied. Although subjects were nondiabetic by selection criteria, plasma insulin concentrations during oral glucose tolerance test were higher (P < 0.05) in Q allele-carrying subjects (K121Q or Q121Q genotypes), compared with K121K individuals, in both the nonobese and obese groups. Insulin sensitivity, measured by euglycemic clamp in a representative subgroup of 131 of 431 randomly selected subjects, progressively decreased (P < 0.001) from nonobese K121K [n = 61; glucose disposal (M) = 34.9 +/- 1.1 micromol/kg/min] to nonobese Q (n = 21; M = 29.9 +/- 2.0), obese K121K (n = 31, M = 18.5 +/- 1.2), and obese Q (n = 18, M = 15.5 +/- 1.2) carriers. The K121Q polymorphism was correlated with insulin sensitivity independently (P < 0.05) of BMI, gender, age, and waist circumference. In conclusion, the Q121 PC-1 variant and obesity have independent and additive effects in causing insulin resistance.
Molecular characterization of the human delta-aminolevulinate dehydratase 2 (ALAD2) allele: implications for molecular screening of individuals for genetic susceptibility to lead poisoning. (1991)

The second enzyme in the heme biosynthetic pathway, delta-aminolevulinate dehydratase (ALAD), is a homooctameric protein encoded by a gene localized to human chromosome 9q34. Expression of the two common alleles, ALAD1 (p = .9) and ALAD2 (q = .1), results in a polymorphic enzyme system with three distinct charge isozymes, designated 1-1, 1-2, and 2-2. Individuals heterozygous (2pq = .18) or homozygous (q2 = .01) for the ALAD2 allele have significantly higher blood lead levels than do ALAD1 homozygotes, when exposed to low or high levels of lead in the environment. To investigate the molecular nature of this common polymorphism, total RNA from an ALAD2 homozygote was oligo-dT primed and reverse transcribed, and then the ALAD2 cDNA was amplified, subcloned, and sequenced. Compared with the ALAD1 sequence, the only difference in the ALAD2 cDNA was a G-to-C transversion of nucleotide 177 in the coding region, which created an MspI restriction site. This base substitution predicted the replacement of a positively charged lysine by a neutral asparagine (K59N), an amino acid change consistent with the more electronegative charge of the ALAD-2 subunit. The ALAD1 and ALAD2 alleles were easily detected by amplification of a 916-bp region of genomic DNA and MspI digestion which results in 582- and 511-bp products, respectively. Molecular analysis of 85 ALAD1/ALAD2 heterozygotes and of eight ALAD2 homozygotes revealed no discrepancy between the predicted genotype and the erythrocyte isozyme phenotype, indicating that all the ALAD2 alleles analyzed had the G-to-C transversion.(ABSTRACT TRUNCATED AT 250 WORDS)
ZnO nanorods: synthesis, characterization and applications (2005)

This paper presents a review of current research activities on ZnO nanorods (or nanowires). We begin this paper with a variety of physical and chemical methods that have been used to synthesize ZnO nanorods (or nanowires). There follows a discussion of techniques for fabricating aligned arrays, heterostructures and doping of ZnO nanorods. At the end of this paper, we discuss a wide range of interesting properties such as luminescence, field emission, gas sensing and electron transport, associated with ZnO nanorods, as well as various intriguing applications. We conclude with personal remarks on the outlook for research on ZnO nanorods.
New concept for optical residue processors (1982)

A new principle for the conversion of residue numbers into binary representation and vice versa by optical means is proposed. It utilizes the similarity of the periodic nature of interference patterns and residue numbers. The optical arrangement, an interferometric converter, consists of lasers, phase-modulators, and photodiodes. Some electronic circuitry is needed for evaluation of the results. A mathematical analysis demonstrates its feasibility. It is also shown that this new device can be used as an adder for residue numbers.
Structure–Activity Relationships of Nickel–Hexaaluminates in Reforming Reactions Part II: Activity and Stability of Nanostructured Nickel–Hexaaluminate‐Based Catalysts in the Dry Reforming of Methane (2014)

Abstract Ni–hexaaluminates exhibiting a high magnetoplumbite or β“‐alumina phase content (>80 wt %) and high specific surface areas (10–30 m 2 g −1 ) were investigated under dry reforming conditions. Ni content and choice of mirror plane cation are the key factors controlling the structure–property relationship in the dry reforming reaction of CH 4 . The Ni content is favorably kept below a threshold of y =0.25 in ANi y Al 12‐ y O 19− δ , (A=Ba, La, Sr) to ensure controlled nanoparticle formation and to avoid uncontrolled Ni 0 nanoparticle growth apart from the support. Sr,Ni and Ba,Ni–hexaaluminates promote high activity of the catalyst in the dry reforming reaction of CH 4 , but show fast deactivation if the Ni content is maladjusted in the hexaaluminate framework ( y ≥0.5). La,Ni–magnetoplumbites display much lower activity accompanied by fast deactivation. The use of very high calcination temperatures (1600 °C) resulting in low specific surface area is detrimental to the activity in the dry reforming of CH 4 , simultaneously higher hexaaluminate phase content obtained undoes catalytic stability, reasoned by Ni 0 nanoparticles produced after reduction cannot be stabilized over surface defects typically found on hexaaluminate platelets calcined at moderated temperatures (<1300 °C). As a result, larger metallic Ni ensembles are built up, selectivity to coke is increased and catalytic stability is compromised.
Dual Adeno-Associated Virus Vectors Result in Efficient <i>In Vitro</i> and <i>In Vivo</i> Expression of an Oversized Gene, <i>MYO7A</i> (2014)

Usher syndrome 1B (USH1B) is a severe, autosomal recessive, deaf-blind disorder caused by mutations in myosin 7A (MYO7A). Patients are born profoundly deaf and exhibit progressive loss of vision starting in their first decade. MYO7A is expressed in human photoreceptors and retinal pigment epithelium, but disease pathology begins in photoreceptors, highlighting the need to develop a gene replacement strategy that effectively targets this cell type. For its safety and efficacy in clinical trials and ability to transduce postmitotic photoreceptors, we have focused on developing a clinically applicable adeno-associated virus (AAV) platform for delivering full-length MYO7A cDNA (∼6.7 kb). Packaging of full-length MYO7A cDNA in AAV produces vectors with heterogeneous, fragmented genomes ("fAAV") capable of reconstituting full-length cDNA postinfection. We previously showed that fAAV vectors effectively delivered full-length MYO7A in vitro and in vivo. However, fAAV vectors are relatively inefficient and their heterogeneous genomes preclude definitive characterization, a drawback for clinical translatability. The aim of this study was to overcome these limitations by creating dual-AAV-vector platforms for USH1B with defined genomes. Human MYO7A was cloned in AAV vector pairs, each containing genomes <5 kb and intact inverted terminal repeats. One vector contained a promoter and 5' portion of the cDNA and the partner vector contained a 3' portion and polyadenylation signal. "Simple overlap" vectors share a central part of the MYO7A cDNA sequence. "Trans-splicing" and "hybrid" vectors utilize splice donor and acceptor sites with and without an additional central recombinogenic sequence, respectively. Vector pairs expressed full-length MYO7A in vitro and in vivo with equal or higher efficiency than fAAV, with a hybrid platform being most efficient. Importantly, analysis of MYO7A mRNA derived from each dual-vector platform revealed 100% fidelity to the predicted sequence. Our results suggest that dual AAV vectors with defined genetic payloads are a potential treatment option for USH1B.
Viscosity-compensated shear speed imaging with acoustic radiation force (2015)

Shear wave elastography imaging (SWEI) with ultrasound uses an applied acoustic radiation force to obtain quantitative images of liver, breast, prostate, and other soft tissues. In SWEI, shear velocity waveforms are collected along a line, and then, the shear speed is estimated either with a k-space or a correlation-based method. Although these yield effective estimates in elastic media, both methods consistently overestimate the shear speed in viscoelastic soft tissue because neither considers the shear viscosity. To address this problem, we have created a new shear speed estimation approach that also accounts for the effect of shear viscosity. The new approach is evaluated in a computational model that calculates the three-dimensional (3D) intensity field generated by a linear array transducer in FOCUS (http://www.egr.msu.edu/~fultras-web) and then simulates the shear wave velocities in a viscoelastic medium with a 3D finite difference model. In the viscoelastic shear wave simulation model, the shear speed constant is 1.5 m/s, and the shear viscosity is 1 Pa·s. Correlation-based shear speed estimates are compared to the viscosity-compensated estimates, and the results show that the viscosity-compensated approach consistently achieves improved shear speed estimates relative to the correlation-based method. [Work supported in part by NIH Grant Nos. R01EB012079 and R01DK092255.]
Roadmap on deep learning for microscopy (2025)

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients (2015)

Pancreatic adenocarcinoma has the worst mortality of any solid cancer. In this study, to evaluate the clinical implications of genomic alterations in this tumour type, we perform whole-exome analyses of 24 tumours, targeted genomic analyses of 77 tumours, and use non-invasive approaches to examine tumour-specific mutations in the circulation of these patients. These analyses reveal somatic mutations in chromatin-regulating genes MLL, MLL2, MLL3 and ARID1A in 20% of patients that are associated with improved survival. We observe alterations in genes with potential therapeutic utility in over a third of cases. Liquid biopsy analyses demonstrate that 43% of patients with localized disease have detectable circulating tumour DNA (ctDNA) at diagnosis. Detection of ctDNA after resection predicts clinical relapse and poor outcome, with recurrence by ctDNA detected 6.5 months earlier than with CT imaging. These observations provide genetic predictors of outcome in pancreatic cancer and have implications for new avenues of therapeutic intervention.
Achieving Gaussian outputs from large-mode-area higher-order-mode fibers (2007)

We describe an alternative to fiber-gratings for converting higher-order LP(0m) (m>1) fiber modes into a nearly fundamental Gaussian shape at the output of a fiber. This schematic enables the use of light propagation in higher-order modes of a fiber, a fiber-platform that has recently shown great promise for achieving very large mode areas needed for future high-power lasers and amplifiers. The conversion will be done by using a binary phase plate in the near field of the fiber, which emits the LP(0m) mode. Since the binary phase plate alone cannot increase the quality factor M(2) of the laser beam because of some broad sidebands, a filtering of the sidebands is done in the Fourier plane of a telescope. Of course, this will cost some of the total light power, but on the other side the M(2) factor can be reduced to nearly the ideal value near 1.0, and it is shown that approximately 76% of the total light power can be conserved for all investigated modes (2<or=m<or=8). A tolerance analysis for the phase plate and its adjustment is made, and different optical imaging systems to form a magnified image of the fiber mode on the phase plate are discussed in order to have more tolerance for the adjustment of the phase plate.
Alkylsilyl Compounds of Selenium and Tellurium: New Precursors for ALD (2009)

Several alkylsilyl compounds of selenium and tellurium were synthesized and characterized. Crystal structures of (tBuMe2Si)2Se and (tBuMe2Si)2Te were solved. Thermal properties of the compounds were studied with TGA. It was found that these compounds are very volatile and thermally stable therefore suitable ALD precursors. Reactivity of the compounds was preliminarily studied by mixing the compounds with different metal precursors in solution. It was found that the compounds are highly reactive against many metal halides and other metal compounds. They have also been tested successfully in ALD. For Ge2Sb2Te5 low growth temperature (60-90 oC) was found the most suitable while ZnSe and ZnTe films were grown at 400 {degree sign}C.
Annoyance Model Driven Selective Active Noise Control (2018)

In this article, we present an annoyance model driven selective active noise control (ANC) system. Our approach uses Block Sparse Nonnegative Matrix Factorization (B-NMF) to identify the background noises that are present in the acoustic environment using any remote microphone recording, and assigns a soft membership score to each of the noises present. These scores have then been used along with an annoyance score computed for the noise types present in the environment, using a psycho acoustic annoyance model, to decide which are the most annoying sounds currently present in the environment. This information is further used in a Kalman Filter based noise canceler to just cancel the annoying sounds, but pass through everything else. This proposed selective ANC system delivers a pleasant yet acoustically aware listening experience to the user.
Controlled-Root Approach To Digital Phase-Locked Loops (1995)

Performance tailored more flexibly and directly to satisfy design requirements. Controlled-root approach improved method for analysis and design of digital phase-locked loops (DPLLs). Developed rigorously from first principles for fully digital loops, making DPLL theory and design simpler and more straightforward (particularly for third- or fourth-order DPLL) and controlling performance more accurately in case of high gain.
CYTOLETHAL DISTENDING TOXIN (CDT): GENETIC DIVERSITY, STRUCTURE AND ROLE IN DIARRHEAL DISEASE (2006)

In 1987, cytolethal distending toxin (CDT) was discovered by Johnson and Lior as a new type of protein toxin produced by certain strains of Escherichia coli, which is different from heat-labile enterotoxin (LT) produced by enterotoxigenic E. coli. Although LT causes only cell elongation, CDT causes cell elongation, cell distention, irreversible cell cycle arrest, and consequently, death of the cultured mammalian cells. Recently, CDT was recognized as a new family of bacterial toxin, as a genotoxin, produced by a diverse group of gram-negative bacteria, all of which are related to mucosal infection. Although tremendous efforts have been made to study the structure and mode of action of CDT, its role in bacterial pathogenesis still remains unclear. In this review, we focus mainly on CDT produced by enteric bacteria and describe the history of CDT, their gene and protein structure, structure-function relationship, and its mode of action particularly how CDT contributes to the gastrointestinal infections.
Improvement in catalytic activity and thermostability of a GH10 xylanase and its synergistic degradation of biomass with cellulase (2019)

This study provides a successful strategy to improve the catalytic properties and thermostability of enzymes. We identified several xylanase candidates for applications in bioenergy and biorefinery. Synergistic degradation experiments elucidated a possible mechanism of cellulase inhibition by xylan and xylo-oligomers.
Dynamic spiral MRI of pulmonary gas flow using hyperpolarized <sup>3</sup>He: Preliminary studies in healthy and diseased lungs (2001)

An optimized interleaved-spiral pulse sequence, providing high spatial and temporal resolution, was developed for dynamic imaging of pulmonary ventilation with hyperpolarized (3)He, and tested in healthy volunteers and patients with lung disease. Off-resonance artifacts were minimized by using a short data-sampling period per interleaf, and gradient-fidelity errors were compensated for by using measured k-space trajectories for image reconstruction. A nonsequential acquisition order was implemented to improve image quality during periods of rapid signal change, such as early inspiration. Using a sliding-window reconstruction, cine-movies with a frame rate of 100 images per second were generated. Dynamic images demonstrating minimal susceptibility- and motion-induced artifacts were obtained in sagittal, coronal, and axial orientations. The pulse sequence had the flexibility to image multiple slices almost simultaneously. Our initial experience in healthy volunteers and subjects with lung pathology demonstrated the potential of this new tool for capturing the features of lung gas-flow dynamics.