gebhart/patrepeval huggingface dataset:
A novel approach for introducing the electron-electron and electron-impurity interactions in particle-based simulations (1999)

A new method for employed electron-electron (e-e) and electron-ion (e-i) interactions in Monte Carlo particle based simulators is presented. By using a corrected Coulomb force in conjunction with a proper cutoff range, the "double" counting of the long range interaction is eliminated while reducing the simulation time for molecular dynamics by a factor of 1000. The proposed method naturally incorporated the multi-ion contributions, local distortions in the scattering potential due to the movement of the free charges, and carrier-density fluctuations. The doping dependence of the low-field mobility obtained from three-dimensional (3-D) resistor simulation closely follows experimental results, thus proving the correctness of the proposed approach.
Audio Chord Recognition With A Hybrid Recurrent Neural Network. (2015)

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Synthesis of novel type pyrazolyl and tetrazolyl isoquinolinium zwitterions (2001)

Abstract New type pyrazol‐3‐yl‐isoquinolinium hydrochloride ( 8a ) and tetrazol‐5‐yl‐isoquinolinium ( 8b ) zwitterions were synthesised. Their structures were proved by ir, pmr, cmr, ms spectra as well as X‐ray diffraction analysis of model compounds.
Oxidative-addition processes in the reactions of (OC)4Fe.cntdot. with XCY3 molecules (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleOxidative-addition processes in the reactions of (OC)4Fe.cntdot. with XCY3 moleculesRichard N. McDonald, Philip L. Schell, and William D. McGheeCite this: Organometallics 1984, 3, 1, 182–184Publication Date (Print):January 1, 1984Publication History Published online1 May 2002Published inissue 1 January 1984https://pubs.acs.org/doi/10.1021/om00079a034https://doi.org/10.1021/om00079a034research-articleACS PublicationsRequest reuse permissionsArticle Views102Altmetric-Citations11LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Isolation of Caldorazole, a Thiazole-Containing Polyketide with Selective Cytotoxicity under Glucose-Restricted Conditions (2022)

Caldorazole (<b>1</b>) was isolated from the marine cyanobacterium <i>Caldora</i> sp. collected on Ishigaki Island, Okinawa, Japan. Its structure was determined to be a new polyketide that contained two thiazole rings and an <i>O</i>-methylenolpyruvamide moiety. Caldorazole (<b>1</b>) showed strong cytotoxicity toward tumor cells that had been seeded at a high density. Cell death induced by <b>1</b> in HeLa and A431 cells was also observed only in the presence of the glycolysis blocker 2-deoxy-d-glucose (2DG). Co-treatment with <b>1</b> and 2DG remarkably decreased ATP levels in these cells. Furthermore, <b>1</b> selectively inhibited complex I in the mitochondrial respiratory chain. Thus, <b>1</b> was demonstrated to exert cytotoxicity toward human tumor cells by blocking mitochondrial respiration.
Polysubstituted derivatives of triphenylene as high resolution electron beam resists for nanolithography (2000)

We have explored the application of polysubstituted derivatives of triphenylene as high resolution, high etch durability electron beam resists. Room temperature spin coating was used to produce films of the derivatives on silicon substrates. Exposure to a 20 keV electron beam was found to alter the dissolution rate of these derivatives in various organic solvents. Doses of between ∼3×10−4 and ∼2.5×10−3 C/cm2 substantially increased the solubility of the derivative hexapentyloxytriphenylene in polar solvents (positive tone behavior). Doses greater than ∼2.5×10−3 C/cm2 led to a decrease in solubility in both polar and nonpolar solvents (negative tone behavior). Other derivatives also demonstrated a reduction in their dissolution rate for doses between ∼1.5×10−3 and ∼6.5×10−3 C/cm2. The etch durabilities of the positive and negative tone patterns were found to be, respectively, ∼25% less and ∼70% greater than that of a conventional novolac based negative tone resist. Line and space patterns were defined in one of the resists with a resolution of ∼14 nm and structures with an aspect ratio of ∼50–1 were etched into silicon.
A Performance-Flexible Energy-Optimized Automotive-Grade Cortex-R4F SoC through Combined AVS/ABB/Bias-in-Memory-Array Closed-Loop Regulation in 28nm FD-SOI (2020)

We propose an automotive-grade ARM̅ Cortex̅-R4F core SoC in 28nm FD-SOI that optimizes its energy across 11X frequency-wide Operational Performance Points (OPPs) by combining Adaptive Voltage Scaling (AVS), Adaptive Body-Biasing (ABB) and Bias-in-Memory-Array (BiMA); with a 3mV/bit Tunable Replica Circuit (TRC) for safety, embedded power regulation and compensation. The reported techniques respectively improve by, 21X performance, 120mV lower V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MIN</sub> , and 8X lifetime, the Low-Power, Mid-, and High-Performance OPPs. Results have been measured at extreme conditions, covering SS/TT/FF process, 0.5/1.2V, -40/150°C, and EOL aging.
<title>Dielectric optical waveguide sensors integrated with GaAs active devices</title> (1993)

Dielectric optical waveguides exhibit properties that are well suited to sensor applications. They have low refractive index and are transparent to a wide range of wavelengths. They can react with the surrounding environment in a variety of controllable ways. In certain sensor applications, it is advantageous to integrate the dielectric waveguide on a semiconductor substrate with active devices. In this work, we demonstrate a tamper sensor based on dielectric waveguides that connect epitaxial GaAs-GaAlAs sources and detectors. The tamper sensing function is realized by attaching particles of absorbing material with high refractive index to the surface of the waveguides. These absorbers are then attached to a lid or cover, as in an integrated circuit package or multi-chip module. The absorbers attenuate the light in the waveguides as a function of absorber interaction. The absorbers are placed randomly on the waveguides, to form a unique attenuation pattern that is registered by the relative signal levels on the photodetectors. When the lid is moved, the pattern of absorbers changes, altering the photodetector signals. This dielectric waveguide arrangement is applicable to a variety of sensor functions, and can make use of resonant coupling properties between low refractive index dielectric waveguides and high-index absorbing materials.
Parallel Solver for Blood Flow in Human Vascular System (2000)

Abstract In order to simulate blood flow in human vascular system, the unsteady, three-dimensional, incompressible Navier-Stokes equations are solved numerically. The solver is capable of dealing with moving boundaries and moving grids. A second-order in time and third-order upwind finite volume method for solving time-accurate incompressible flows utilizing pseudo-compressibility technique is used. For parallel execution, the flow domain is partitioned. Communication between the subdomains of the flow on Riken’s VPP/700E supercomputer is implemented using MPI message-passing library. The code is capable of running on both shared and/or distributed memory architectures.
Deep Bleeder Acoustic Coagulation (DBAC)—part II: in vivo testing of a research prototype system (2015)

While not meeting all in vivo objectives, the overall performance of the DBAC applicator was positive. In particular, D&L automation workflow was verified during each of the tests, with processing times well under specified (10 min) limits, and all bleeder branches were detected and localized. Further, gross necropsy and tissue examination confirmed that the HIFU thermal lesions were coincident with the target vessel locations in over 90 % of the multi-array dosing treatments. The SFA/DFA bleeder models selected, and the protocols used, were the most suitable practical model options for the given DBAC anatomical and bleeder requirements. The animal models were imperfect in some challenging aspects, including requiring tissue-mimicking material (TMM) standoffs to achieve deep target depths, thereby introducing device-tissue motion, with resultant imaging artifacts. The model "bleeders" involved intact vessels, which are subject to less efficient heating and coagulation cascade behaviors than true puncture injuries.
Synthesis of pharmacologically active nitrogen analogs of the tetrahydrocannabinols (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of pharmacologically active nitrogen analogs of the tetrahydrocannabinolsMark Cushman and Neal Castagnoli Jr.Cite this: J. Org. Chem. 1974, 39, 11, 1546–1550Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://pubs.acs.org/doi/10.1021/jo00924a021https://doi.org/10.1021/jo00924a021research-articleACS PublicationsRequest reuse permissionsArticle Views203Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Clinical Validation of Discordant Trunk Driver Mutations in Paired Primary and Metastatic Lung Cancer Specimens (2019)

Trunk driver mutations are highly concordant in primary and metastatic tumors. Discordance of trunk drivers, once confirmed, may suggest a second primary cancer. Guidelines are recommended to establish standard operating procedures for validation of discordant trunk drivers.
Case-based repeatability and operating point variability of AI: breast lesion classification based on deep transfer learning (2022)

Characterization of case-based classification repeatability and variability of operating points can complement measures of classification performance in artificial intelligence/computer-aided diagnosis (AI/CADx). Building upon our previous work in this area using human-engineered radiomic features extracted from dynamic contrast-enhanced magnetic resonance (DCE-MR) images, we investigated the application of these methods to features extracted from pre-trained convolutional neural networks using deep transfer learning. The second post-contrast DCE-MR images for 601 unique breast lesions (194 benign, 407 malignant) were cropped and resized for input into a VGG-19 network, pretrained using ImageNet. Features were extracted and average pooled from the five max-pool layers, resulting in 1,472 features for each lesion. The assignment of cases to training and test sets was varied using a 1000-iteration 0.632 bootstrap. Overall classification performance for distinguishing between malignant and benign cases (using the area under the receiver operating characteristic curve (AUC) with 0.632+ bootstrap correction), case-based classification repeatability (using repeatability profiles which measure the 95% confidence interval (CI) of classifier output across its range), and attainment of a ‘preferred’ target (95%) or ‘optimal’ sensitivity and specificity were investigated using a random forest classifier. The AUC (median, [95% CI]) was 0.862 [0.806, 0.899]. The repeatability profile and attained sensitivity and specificity were similar to previous results for both the ‘preferred’ and ‘optimal’ targets when using human-engineered radiomic features. These results demonstrate the application of these methods to complement AI/CADx model assessment when using deep transfer learning features.
Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications (2022)

This data set could identify an improved specific, sensitive set of criteria for diagnosing clinical pneumonia and help identify sick children in need of referral to a higher level of care or a change of therapy. Field studies could be designed based on insights from PREPARE analyses to validate a potential revised pneumonia algorithm. The PREPARE methodology can also act as a model for disease database assembly.
Csurf (2007)

Web sites are designed for graphical mode of interaction. Sighted users can "cut to the chase" and quickly identify relevant information in Web pages. On the contrary, individuals with visual disabilities have to use screen-readers tobrowse the Web. As screen-readers process pages sequentially and read through everything, Web browsing can become strenuous and time-consuming. Although, the use ofshortcuts and searching offers some improvements, the problem still remains. In this paper, we address the problemof information overload in non-visual Web access using thenotion of context. Our prototype system, CSurf, embodyingour approach, provides the usual features of a screen-reader.However, when a user follows a link, CSurf captures thecontext of the link using a simple topic-boundary detectiontechnique, and uses it to identify relevant information onthe next page with the help of a Support Vector Machine, astatistical machine-learning model. Then, CSurf reads the Web page starting from the most relevant section, identifiedby the model. We conducted a series experiments to evaluate the performance of CSurf against the state-of-the-artscreen-reader, JAWS. Our results show that the use of context can potentially save browsing time and substantiallyimprove browsing experience of visually disabled people.
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression (2022)

Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
Functionalization of Carbon Nano-onions by Direct Fluorination (2007)

Carbon nano-onions (CNO) are made of concentric fullerene-like shells and range from double- and triple- to multilayered structures. They remain the least studied allotrope of carbon yet. In the present study, a one-step process for functionalization of CNO (50−100 nm diameter) by addition of fluorine through direct fluorination at variable temperatures is reported. The reactions of CNO at three different temperatures, 350, 410, and 480 °C, yield fluorinated nano-onions (F-NO) of approximately C10.1F, C3.3F, and C2.3F stoichiometry, respectively, representing a new family of nanoscale fluorocarbon materials. The F-NO were characterized by a set of materials characterization methods including FTIR, Raman, UV−vis, and X-ray photoelectron spectroscopy, scanning (SEM) and transmission electron microscopy (TEM), X-ray diffraction, and thermal gravimetric analysis. SEM and TEM images show that even after breaking of the graphene layers in CNO by fluorine, the F-NO products retain the spherical onion-shaped morphology. The subsequent defluorination of F-NO by hydrazine treatment results in remarkable “healing” of broken graphene layers which rejoin within the sphere to substantially restore the CNO microstructure. In comparison with pristine CNO, fluorinated nano-onions show dramatically improved solubility in organic solvents, e.g., alcohols and DMF, enabling their processing for lubricating coatings, paints, nanocomposites, and biomedical applications.
Distinct microglial response against Alzheimer's amyloid and tau pathologies characterized by P2Y12 receptor (2021)

Microglia are the resident phagocytes of the central nervous system, and microglial activation is considered to play an important role in the pathogenesis of neurodegenerative diseases. Recent studies with single-cell RNA analysis of CNS cells in Alzheimer's disease and diverse other neurodegenerative conditions revealed that the transition from homeostatic microglia to disease-associated microglia was defined by changes of gene expression levels, including down-regulation of the P2Y12 receptor gene (<i>P2Y12R</i>). However, it is yet to be clarified in Alzheimer's disease brains whether and when this down-regulation occurs in response to amyloid-β and tau depositions, which are core pathological processes in the disease etiology. To further evaluate the significance of P2Y12 receptor alterations in the neurodegenerative pathway of Alzheimer's disease and allied disorders, we generated an anti-P2Y12 receptor antibody and examined P2Y12 receptor expressions in the brains of humans and model mice bearing amyloid-β and tau pathologies. We observed that the brains of both Alzheimer's disease and non-Alzheimer's disease tauopathy patients and tauopathy model mice (rTg4510 and PS19 mouse lines) displayed declined microglial P2Y12 receptor levels in regions enriched with tau inclusions, despite an increase in the total microglial population. Notably, diminution of microglial immunoreactivity with P2Y12 receptor was noticeable prior to massive accumulations of phosphorylated tau aggregates and neurodegeneration in rTg4510 mouse brains, despite a progressive increase of total microglial population. On the other hand, Iba1-positive microglia encompassing compact and dense-cored amyloid-β plaques expressed P2Y12 receptor at varying levels in amyloid precursor protein (APP) mouse models (APP23 and <i>App<sup>NL-F/NL-F</sup></i> mice). By contrast, neuritic plaques in Alzheimer's disease brains were associated with P2Y12 receptor-negative microglia. These data suggest that the down-regulation of microglia P2Y12 receptor, which is characteristic of disease-associated microglia, is intimately associated with tau rather than amyloid-β pathologies from an early stage and could be a sensitive index for neuroinflammatory responses to Alzheimer's disease-related neurodegenerative processes.
Giant tunnel magnetoresistance in polycrystalline magnetic tunnel junctions with highly textured MgAl2O4(001) based barriers (2018)

Although single-crystalline spinel (MgAl2O4)-based magnetic tunnel junctions (MTJs) are known to show a good bias voltage dependence of a tunnel magnetoresistance (TMR) ratio over MgO-based MTJs, no polycrystalline MgAl2O4-based MTJs exhibiting large TMR ratios have been grown previously due to the lack of crystallinity of the MgAl2O4 barrier. In this work, we demonstrate the growth of polycrystalline-based MTJs with large TMR ratios exceeding 240% and an improved bias voltage dependence compared to that of MgO-based MTJs. An ultra-thin CoFe/MgO seed layer on the amorphous CoFeB layer induced the growth of a highly (001)-textured MgAl2O4 barrier, which worked as a template layer for the solid epitaxy of CoFe grains during the crystallization of the CoFeB layers. High resolution scanning transmission electron microscopy shows lattice-matched epitaxy between the (001)-textured MgAl2O4 barrier and CoFe grains. This study demonstrates the industrial viability of MgAl2O4-based polycrystalline MTJs with an improved bias voltage dependence.
Crank it up or dial it down (2013)

Dynamic power management features are now an integral part of processor chip and system design. Dynamic voltage and frequency scaling (DVFS), core folding and per-core power gating (PCPG) are power control actuators (or "knobs") that are available in modern multi-core systems. However, figuring out the actuation protocol for such knobs in order to achieve maximum efficiency has so far remained an open research problem. In the context of specific system utilization dynamics, the desirable order of applying these knobs is not easy to determine.
The Role of Three‐Dimensional Magnetic Resonance Elastography in the Diagnosis of Nonalcoholic Steatohepatitis in Obese Patients Undergoing Bariatric Surgery (2018)

The lack of reliable, noninvasive methods to diagnose early nonalcoholic steatohepatitis (NASH) is a major unmet need. We aimed to determine the diagnostic accuracy of three-dimensional magnetic resonance elastography (3D-MRE), with shear stiffness measured at 60 Hz, damping ratio at 40 Hz, and magnetic resonance imaging proton density fat fraction (MRI-PDFF) in the detection of NASH in individuals undergoing bariatric surgery. Obese adults at risk for NASH were enrolled between 2015 and 2017 (prospective cohort, n = 88) and 2010 and 2013 (retrospective cohort, n = 87). The imaging protocol consisted of multifrequency 3D-MRE (mf3D-MRE) with shear waves delivered at different frequencies to explore parameters that best correlated with histologic NASH, and MRI-PDFF to estimate steatosis. The prospective cohort was used to establish the optimal mf3D-MRE technical parameters for NASH detection. The two cohorts were then combined to derive predictive models of NASH and disease activity by nonalcoholic fatty liver disease activity score (NAS) using the three imaging parameters that correlated with NASH. A total of 175 patients (median age 45, 81% women, and 81 [46%] with histologic NASH) were used for model derivation. From the complex shear modulus output generated by mf3D-MRE, the damping ratio at 40 Hz and shear stiffness at 60 Hz best correlated with NASH. The fat fraction obtained from MRI-PDFF correlated with steatosis (P < 0.05 for all). These three parameters were fit into a logistic regression model that predicted NASH with cross-validated area under the receiver operating characteristic curve (AUROC) = 0.73, sensitivity = 0.67, specificity = 0.80, positive predictive value = 0.73 and negative predictive value = 0.74, and disease activity by NAS with cross-validated AUROC = 0.82. Conclusion: The mf3D-MRE allows identification of imaging parameters that predict early NASH and disease activity. This imaging biomarker represents a promising alternative to liver biopsy for NASH diagnosis and monitoring. The results provide motivation for further studies in nonbariatric cohorts.