gebhart/patrepeval huggingface dataset:
The Novel Synthesis of a Pyrrolo(3,2-D)Pyrimidine C-Nucleoside Via a Pyrimidine Homo-C-Nucleoside. (1982)

The strategies used in the synthesis of 2,4-dimethoxy-7-C-(1-(beta)-D-ribofuranosyl)pyrrolo{3,2-d}pyrimidine (1b) and the (alpha) anomer (1a) are presented in this dissertation. Compounds 1a and 1b were made from the pyrimidine homo-C-nucleoside, 2-(2,4-dimethoxy-5-nitropyrimidin-6-yl)-2-C-(2,3-O-isopropylidene-5-O-trityl-1-(alpha)-D-ribofuranosyl)acetonitrile (2) which was prepared by the condensation under basic conditions of 6-cyanomethyl-2,4-dimethoxy-5-nitropyrimidine (3) and 2,3-O-isopropylidene-5-O-trityl-D-ribofuranosyl chloride (4). The synthesis of various other homo-C-nucleosides are also discussed in this work. It was found that 1,2,3,5-tetra-O-acyl-D-ribofuranose condensed with 1-hexene in the presence of stannic chloride to afford a complex mixture of olefinic and chloro-substituted products, whereas the reaction of allyl TMS with the same sugar in the presence of TMS triflate yielded the anomeric mixture 3-C-(2,3,5-tri-O-benzoyl-1-D-ribofuranosyl)-1-propene (5). Compound 5 was oxidized to the carboxylic acid 6 which was converted to ethyl 4-(2,3,5-tri-O-benzoyl-1-(alpha)((beta))-D-ribofuranosyl)acetoacetate (7) or to the corresponding anomeric ribofuranosylacetoacetonitrile (8). Treatment of 7 with guanidine afforded 2-amino-6-C-(1-D-ribofuranosyl)methylpyrimidin-4-one (9). Compounds 7 and 8 were reacted with diazonium salts to form the corresponding 2-phenyldiazo- and 2-(p-chlorophenyldiazo)- derivatives. Another homo-C-nucleoside procedure produced 2,4-dimethoxy-6-C-(2,3-O-isopropylidene-5-O-trityl-1-(beta)((alpha))-D-ribofuranosyl)methyl-5-nitropyrimidine (10) from the Wittig condensation involving 11 (the furanose analog of 4) and the corresponding pyrimidin-6-ylmethylenetriphenylphosphorane. Finally, two methods for the general synthesis of 2,4-dimethoxypyrrolo{3,2-d}pyrimidine from substituted pyrimidines such as 2 are presented.
Reliability Study of 14 nm Scan Chains and Its Application to Hardware Security (2022)

This paper studies the impact of accelerated aging of a circuit containing a large variety of 14 nm scan chains using elevated voltage stress. Both IDDQ and timing performance changes are monitored to observe the aging of the circuit. Particular attention is dedicated to discussing the impact of the test pattern selection for both stress and sensing. The scan chain results are compared against previous results from 14 nm ring oscillators, confirming a good agreement. Simplified models are developed to explain the results and help understand the impact of aging on the circuit. In addition, the application to the hardware security is suggested given the measured aging signature.
Mechanism of Electron Transfer from eaq− to Acceptors in Micelles (1975)

Abstract Pulse radiolysis experiments were carried out to investigate reactions A + e aq − → A − of hydrated electrons with acceptors A incorporated in the lipoidic part of micellar 10 −3 M sodium‐lauryl‐sulfate (SLS) and cetyl‐trimethyl‐ammonium‐bromide (CTAB). The acceptors were 9‐nitro‐anthracene and pyrene, the latter in both the singlet and triplet state (the triplet was produced by UV‐light irradiation shortly before the high energy electron pulse was applied). 9‐Nitro‐anthracene reacts with k = 9 · 10 10 M −1 s −1 in the cationic CTAB micelles and with k = 1.5 · 10 9 M −1 s −1 in the anionic SLS‐micelles. In the presence of 0.2 M sodium sulfate, k = 4 · 10 9 M −1 s −1 (SLS‐micelles). The singlet ground state of pyrene reacts with k = 10 11 M −1 s −1 in CTAB and with 4.8 · 10 8 M −1 s −1 in SLS‐micelles in the presence of 0.2 M sodium sulfate. The triplet state of pyrene reacts in CTAB‐micelles with a rate constant smaller by at least a factor of two than the singlet ground state. These reactions of the hydrated electron with acceptors in micelles are regarded as tunneling processes. The results can be understood in terms of the estimated distributions of occupied and unoccupied electronic redox levels in the redox systems aq/e aq − and A/A − involved. Electron transfer in heterogeneous biochemical systems may occur via a similar mechanism.
Molecular dynamics simulations of shallow nitrogen and silicon implantation into diamond (2016)

A solid understanding of the implantation process of N and Si ions into diamond is needed for the controlled creation of shallow color centers for quantum computing, simulation, and sensing applications. Here, molecular dynamics simulations of the shallow implantation of N and Si ions into diamond is simulated at 100--5000 eV kinetic energies and different angles of incidence. We find that ion channeling is an important effect with an onset energy depending on the crystal orientation. Consequently, the molecular dynamics simulations produce improved predictions as compared to standard Monte Carlo simulations. When implanting in a channeling direction, the spatial distribution of the channeled ions becomes markedly narrow, allowing a higher degree of control over the location of the nitrogen vacancy (${\mathrm{NV}}^{\ensuremath{-}}$) centers. A contamination layer on the ion entry surface reduces the fraction of channeled ions. A comparison to an experimentally determined depth profile based on a NMR signal from protons yields a quantitative agreement, validating the simulation approach.
Adult Human Nasal Mesenchymal-Like Stem Cells Restore Cochlear Spiral Ganglion Neurons After Experimental Lesion (2013)

A loss of sensory hair cells or spiral ganglion neurons from the inner ear causes deafness, affecting millions of people. Currently, there is no effective therapy to repair the inner ear sensory structures in humans. Cochlear implantation can restore input, but only if auditory neurons remain intact. Efforts to develop stem cell-based treatments for deafness have demonstrated progress, most notably utilizing embryonic-derived cells. In an effort to bypass limitations of embryonic or induced pluripotent stem cells that may impede the translation to clinical applications, we sought to utilize an alternative cell source. Here, we show that adult human mesenchymal-like stem cells (MSCs) obtained from nasal tissue can repair spiral ganglion loss in experimentally lesioned cochlear cultures from neonatal rats. Stem cells engraft into gentamicin-lesioned organotypic cultures and orchestrate the restoration of the spiral ganglion neuronal population, involving both direct neuronal differentiation and secondary effects on endogenous cells. As a physiologic assay, nasal MSC-derived cells engrafted into lesioned spiral ganglia demonstrate responses to infrared laser stimulus that are consistent with those typical of excitable cells. The addition of a pharmacologic activator of the canonical Wnt/β-catenin pathway concurrent with stem cell treatment promoted robust neuronal differentiation. The availability of an effective adult autologous cell source for inner ear tissue repair should contribute to efforts to translate cell-based strategies to the clinic.
Hydrogen gas response of meta-materials made from the catalytic metal (2013)

The meta-materials with a catalytic metal are fabricated on Si substrate and the hydrogen gas reaction in the THz transmittance was measured. The results suggest that two different catalytic mechanisms contribute the change in transmittance in different frequency region.
Analyses of chamber wall coatings during the patterning of ultralow-k materials with a metal hard mask: Consequences on cleaning strategies (2007)

Changes in chamber wall conditions (e.g., chemical surface composition) are identified as one of the main causes of process drifts leading to changes in the process performance (etch rates, etch profiles, selectivity, uniformity, etc.). The impact of a metal hard mask on the coating formed on the chamber walls during the dielectric etching process and reactor dry cleaning procedure has been investigated. The authors have used a technique based on x-ray photoelectron spectroscopy to monitor the chemical composition of the layer deposited on an electrically floating sample placed on the top of a patterned wafer exposed to typical plasma processing conditions (coatings deposited on the floating sample are representative of those deposited on the chamber walls). They have patterned porous SiOCH damascene structures using a TiN hard mask. After hard mask opening in a silicon etcher using Cl2 based plasmas, they have shown that the chamber walls are coated by a thin SiOCl coating containing small concentrations of Ti. After photoresist ashing in the same etcher (with an O2 plasma), the chamber wall coating is oxidized leading to the formation of a mixed SiOx–TiOx deposit. The cleaning strategy to remove this coating from the chamber walls consists in using a two step cleaning procedure: (1) a Cl2 based plasma (Ti removal), followed by (2) a SF6∕O2 plasma (SiOCl species removal). During low-k etching in an oxide etcher with a fluorocarbon based chemistry, the chamber walls are coated by a fluorocarbon layer containing a significant concentration of Ti. They have developed a two step cleaning procedure: (1) a SF6 plasma to remove the fluorocarbon layer and Ti based species and (2) an O2 flash plasma (for a short time) to clean up the chamber walls from the remaining carbon.
Analysis and implementation of hybrid switching (1996)

The switching scheme of a point-to-point network determines how packets flow through each node, and is a primary element in determining the network's performance. In this paper, we present and evaluate a new switching scheme called hybrid switching. Hybrid switching dynamically combines both virtual cut-through and wormhole switching to provide higher achievable throughput than wormhole alone, while significantly reducing the buffer space required at intermediate nodes when compared to virtual cut-through. This scheme is motivated by a comparison of virtual cut-through and wormhole switching through cycle-level simulations, and then evaluated using the same methods. To show the feasibility of hybrid switching, as well as to provide a common base for simulating and implementing a variety of routing and switching schemes, we have designed SPIDER, a communication adapter built around a custom ASIC called the programmable routing controller (PRC).
Large-Scale Training Framework for Video Annotation (2019)

Video is one of the richest sources of information available online but extracting deep insights from video content at internet scale is still an open problem, both in terms of depth and breadth of understanding, as well as scale. Over the last few years, the field of video understanding has made great strides due to the availability of large-scale video datasets and core advances in image, audio, and video modeling architectures. However, the state-of-the-art architectures on small scale datasets are frequently impractical to deploy at internet scale, both in terms of the ability to train such deep networks on hundreds of millions of videos, and to deploy them for inference on billions of videos. In this paper, we present a MapReduce-based training framework, which exploits both data parallelism and model parallelism to scale training of complex video models. The proposed framework uses alternating optimization and full-batch fine-tuning, and supports large Mixture-of-Experts classifiers with hundreds of thousands of mixtures, which enables a trade-off between model depth and breadth, and the ability to shift model capacity between shared (generalization) layers and per-class (specialization) layers. We demonstrate that the proposed framework is able to reach state-of-the-art performance on the largest public video datasets, YouTube-8M and Sports-1M, and can scale to 100 times larger datasets.
Imaging of Calcium Wave Propagation in Guinea-Pig Ventricular Cell Pairs by Confocal Laser Scanning Microscopy. (1991)

We describe here the use of a confocal laser scanning microscope for imaging fast dynamic changes of the intracellular calcium ion concentration ([Ca2+]i) in isolated ventricular cell pairs. The scanning apparatus of our system, paired galvanometer mirrors, can perform narrow band scanning of an area of interest at a high temporal resolution of less than 70 msec per image. The actual [Ca2+]i is obtained directly through the fluorescence intensity of injected fluo-3, which responds to changes of [Ca2+]i in optically sectioned unit volumes of the cell. Images of the calcium wave obtained during propagation between paired cells revealed that the wavefront is constant in shape and propagates at constant velocity without any delay at the cell-to-cell junction. The confocal laser scanning microscope with depth-discriminating ability is a valuable tool for taking pictures of the sequence of biological events in living cells.
ChemInform Abstract: Reaction of Metal Fluorides with unsym‐Azetidinone Disulfides and 2β‐(Halomethyl)penams. The 3β‐Fluoro‐3α‐methylcephams. (1987)

Abstract The halomethylthiazoloazetidinones (I) react with metal fluorides, especially AgF, to yield the fluorocepham (IIa) as the main product.
Primocolonization is associated with colonic epithelial maturation during conventionalization (2012)

Interaction between the gut microbiota and the host starts immediately after birth with the progressive colonization of the sterile intestine. Our aim was to investigate the interactions taking place in the colonic epithelium after the first exposure to gut microbiota. Germ-free (GF) rats were inoculated with two different microbiotas: the first, obtained from suckling rats, was rich in primocolonizing bacteria and the second, obtained from adult rats, was representative of a mature microbiota. Once transferred into GF rats, these two microbiotas evolved such that they converged, and recapitulated the primocolonization pattern, mimicking the chronological scheme of implantation following birth. The two microbiotas induced common responses in the colonic epithelium: a transitory proliferative phase followed by a compensatory phase characterized by increases in the abundance of p21(Cip1) and p27(Kip1) and in the number of goblet cells. The effects of the two microbiotas diverged only through their effects on colonic transporters. Analyses of solute carriers and aquaporins revealed that functional maturation was more pronounced following exposure to adult microbiota than suckling microbiota. The colon matured in parallel with the evolution of the microbiota composition, and we therefore suggest a link between intestinal events regulating homeostasis of the colon and modulation of microbial composition.
Correction: Corrigendum: Word pair classification during imagined speech using direct brain recordings (2017)

Scientific Reports 6: Article number: 25803; published online: 11 May 2016; updated: 23 March 2017 This Article contains errors in the order of Figures 1, 2 and 3. Figure 1 was published as Figure 2, Figure 2 was published as Figure 3 and Figure 3 was published as Figure 1. The correct Figures appear below.
Role of apoptosis and CD95‐receptor/ligand system in aspirin‐ and Helicobacter pylori‐induced cell death (2004)

These data suggest that although aspirin-mediated CD95 up-regulation is not relevant for its direct apoptotic effect it may sensitize gastric epithelial cells for H. pylori-induced apoptosis. Collectively our data demonstrate the relation of aspirin- and H. pylori-induced apoptosis from a new perspective.
Input and Structure Choices of Neural Networks on the Fuel Flow Rate Prediction in the Transient Operation Condition (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Measurement accuracy and repeatability for fuel rate is the key to successfully improve fuel economy of diesel engines as fuel economy could only be achieve by precisely controlling air/fuel ratio and monitor real-time fuel consumption. The volumetric and gravimetric measurement principles are well-known methods to measure the fuel consumption of internal combustion engines. However, the fuel flow rate measured by these methods is not suitable for either real-time control or real-time measurement purposes. The problem concerning discontinuous data of fuel flow rate measured by using an AVL 733s fuel meter was solved for the steady state scenario by using neural networks. It is easier to choose inputs of the neural networks for the steady state scenario because the inputs could be chosen as the particular inputs which excited the system in the application. But for transient scenario, such as the NRTC cycle, it will be difficult to choose inputs as there are no excited inputs that could be chosen. This paper attempts to solve the problem of the input choice for the transient state.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This paper illustrates input choices to catch fast and slow dynamics using both phenomenon models and principal component analysis (PCA) and demonstrates a comprehensive and detailed black-box modelling technique for engine applications in the transient condition. A non road transient cycle (NRTC) is used for system identification. Different neural network structures are compared among feed-forward NN, feed-forward NN with delays and non-linear autoregressive model with exogenous inputs (NLARX). The NLARX is the best structure for fuel flow rate prediction in the transient operation of the engine. It is shown that the input choice is reasonable and could be proved by both theory and simulation results. This paper shows that using chosen the inputs, NLARX could predict fuel flow rate accurately with R-square above 0.99.&lt;/div&gt;&lt;/div&gt;
A source impedance compensated artificial voice for mask speech intelligibility testing: Thevenin model (1996)

This paper describes the development of a Thevenin model of the human voice for mask speech intelligibility testing. The following steps were used to develop the Thevenin model: (1) the long-term average speech spectrum of ten male speakers was measured; (2) the corresponding average vocal tract shape was estimated using linear prediction; (3) a Thevenin model of the voice was determined based on the vocal tract shape. Electroacoustic analogs are used to predict the mask speech spectra produced by the Thevenin model and a mouth simulator consisting of a loudspeaker equalized for free-air speech. Comparing the two spectra allows us to examine how the interaction between the driving point impedance of the voice and the load impedance of a mask affects objective speech intelligibility measurements. The Thevenin model is used in a voice simulator that is described in a future paper.
Interocular contrast gain control plus monocular luminance gain control can explain binocular luminance summation (2015)

Interocular contrast gain-control (interocular-CG) was first used to model binocular phase combination (Ding & Sperling 2006), and later modified to explain both phase and contrast combination in binocular vision (Huang et al 2010, Ding et al 2013). In the present study, we demonstrate that, by adding monocular luminance gain-control (monocular-LG), the interocular-CG model can also explain binocular luminance summation. Luminance disks were used as stimuli. The target luminance was either increased by 1, 2, 4, 8, 16 cd/m2 against a darker background (0, 2, 4, 8, 16 cd/m2) or decreased against a lighter background (4, 8, 16 cd/m2). Experimental trials consisted of two stimulus intervals, one with a standard luminance which was identical in the two eyes, and the other with a test luminance presented to both eyes. The interocular ratio of the test luminance varied from trial to trial. The observer’s task was to judge which interval had the higher luminance increment or decrement. Consistent with previous studies, we found that binocular luminance summation behaves very differently depending on the background luminance. Fechner’s paradox was observed on the equal-luminance-increment contour with the dark background (0 cd/m2), while an apparent winner-take-all phenomenon was observed on both increment- and decrement-contours with the light background (16 cd/m2). Using one set of model parameters, 3 parameters for monocular-LG and 3 parameters for interocular-CG, the combined model provides a unified explanation of binocular combination of both luminance increments and decrements over a large range of luminance input (reduced-chi-square = 2.35). Combined with previous studies on phase (Ding & Sperling 2006), contrast matching (Huang et al 2010, Ding et al 2013), contrast discrimination (Ding et al 2013), stereovision (Hou et al 2013), and second-order stimuli (Zhou et al 2014), we conclude that the interocular-CG can provide a unified explanation of binocular combination for multiple binocular tasks. Meeting abstract presented at VSS 2015
51 In vitro and in vivo activity of sacituzumab govitecan, in ovarian cancer (2019)

<h3>Objectives</h3> Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. Sacituzumab govitecan (SG) is a novel antibody-drug-conjugate (ADC) targeting trophoblast-antigen-2 (Trop-2), a cell surface glycoprotein highly expressed in many epithelial tumors, to deliver SN-38, the active metabolite of irinotecan. This study aimed to evaluate the efficacy of SG in primary EOC cell lines and xenografts. <h3>Methods</h3> Trop-2 expression was evaluated in 90 formalin-fixed-paraffin-embedded (FFPE) tumors and 9 primary tumor cell lines by immunohistochemistry and flow cytometry, respectively. Trop-2 expression and cell viability after exposure to SG in primary tumor cell lines, non-targeting control-ADC (h679-CL2A-SN-38), and SG-parental antibody hRS7 IgG wereevaluated using flow-cytometry-based-assays. Antibody-dependent-cell-cytotoxicity (ADCC) against Trop-2+ and Trop-2- EOC cell lines was evaluated <i>in vitro</i>using 4-h Chromium-release-assays. <i>In vivo</i>activity of SG was tested againstTrop-2+ EOC xenografts. <h3>Results</h3> Moderate-to-strong staining was seen in 47% (42/90) of ovarian tumors while 89% (8/9) of the primary EOC cell lines overexpressed Trop-2. EOC overexpressing Trop-2 were significantly more sensitive to SG compared to control ADC (p&lt;0.05). Both SG and hRS7 mediated high ADCC activity only against Trop2+ cell lines. SGalso induced bystander killing of Trop-2- tumor cells. <i>In vivo</i>experiments with SG in EOC xenografts demonstrated greater antitumor effects and increased survival compared to ADC controls (p&lt;0.05). SG was well tolerated by the animals. <h3>Conclusions</h3> SG has shown remarkable preclinical activity against biologically aggressive EOC and it is endowed with significant bystander effect against tumors with heterogenous TROP-2 expression. Clinical trials are warranted.
Computer simulation of single-ion trajectories in paul-type ion traps (1993)

The computer simulation of single-ion trajectories using a number of computer programs is described together with associated theory. The programs permit calculation of ion trajectories while the ion is subjected to collisions with buffer gas of variable pressure, resonance excitation in any of three modes, and static or ramped DC and radiofrequency levels. Initially, the programs were designed for the calculation of ion trajectories in a quadrupole ion trap. The programs now permit such calculations for ions confined in traps having electrodes shaped to include percentages of hexapole and octupole components in the electric field as well as electrode surface geometries for which there is no closed-form expression. The Langevin collision theory is reviewed and a theoretical treatment of the multipole trap is presented.