gebhart/patrepeval huggingface dataset:
The Singular Value Decomposition: Anatomy of Optimizing an Algorithm for Extreme Scale (2018)

The computation of the singular value decomposition, or SVD, has a long history with many improvements over the years, both in its implementations and algorithmically. Here, we survey the evolution of SVD algorithms for dense matrices, discussing the motivation and performance impacts of changes. There are two main branches of dense SVD methods: bidiagonalization and Jacobi. Bidiagonalization methods started with the implementation by Golub and Reinsch in Algol60, which was subsequently ported to Fortran in the EISPACK library, and was later more efficiently implemented in the LINPACK library, targeting contemporary vector machines. To address cache-based memory hierarchies, the SVD algorithm was reformulated to use Level 3 BLAS in the LAPACK library. To address new architectures, ScaLAPACK was introduced to take advantage of distributed computing, and MAGMA was developed for accelerators such as GPUs. Algorithmically, the divide and conquer and MRRR algorithms were developed to reduce the number of operations. Still, these methods remained memory bound, so two-stage algorithms were developed to reduce memory operations and increase the computational intensity, with efficient implementations in PLASMA, DPLASMA, and MAGMA. Jacobi methods started with the two-sided method of Kogbetliantz and the one-sided method of Hestenes. They have likewise had many developments, including parallel and block versions and preconditioning to improve convergence. In this paper, we investigate the impact of these changes by testing various historical and current implementations on a common, modern multicore machine and a distributed computing platform. We show that algorithmic and implementation improvements have increased the speed of the SVD by several orders of magnitude, while using up to 40 times less energy.
Tunable broadband mode power dividers based on a wavelength-insensitive coupler using the thermo-optic effect for flexible modal power adjustment in a mode-division multiplexing network (2021)

We demonstrate tunable broadband two-mode power dividers based on a wavelength-insensitive coupler for a mode-division multiplexing system. Ultra-small <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>0</mml:mn> </mml:msub> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>−</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>1</mml:mn> </mml:msub> </mml:mrow> </mml:math> and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>0</mml:mn> </mml:msub> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>−</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>2</mml:mn> </mml:msub> </mml:mrow> </mml:math> mode dividers based on Si-wire waveguides are designed based on the coupled-mode theory. Tunability is achieved by using the thermo-optic effect. In both dividers, arbitrary branching ratios can be realized over a wide wavelength range. We experimentally demonstrated for the first time, to the best of our knowledge, a tunable <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>0</mml:mn> </mml:msub> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>−</mml:mo> </mml:mrow> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msub> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">T</mml:mi> <mml:mi mathvariant="normal">E</mml:mi> </mml:mrow> </mml:mrow> <mml:mn>1</mml:mn> </mml:msub> </mml:mrow> </mml:math> mode divider based on Si-wire waveguides. From the experimental results, an arbitrary branching ratio can be achieved by adjusting the injection current to a TiN heater placed on top of one of the delay lines.
Comparison of Supersaturation Outputs from Different Programs and Their Application in Testing Correspondence with Kidney Stone Composition (2020)

<b><i>Introduction:</i></b> Relative supersaturation (SS) for calcium oxalate (CaOx), calcium phosphate (CaP), and uric acid (UA) has been used for assessing urinary crystallization and estimated by programs, including EQUIL, Joint Expert Speciation System (JESS), and Lithorisk. We compared outputs from these programs and their correspondence with stone composition. <b><i>Materials and Methods:</i></b> SS of CaOx, CaP, and UA, using EQUIL, JESS, and Lithorisk were calculated from stone-forming patients. Pearson correlation coefficients were used to ascertain the correspondence between the outputs. Fractional regression models evaluated the relationship between SS and the percentage of each compound in the stones. <b><i>Results:</i></b> Two hundred eleven patients were included. Pearson correlation coefficients for CaOx (<i>r</i> ≥ 0.96), CaP (<i>r</i> ≥ 0.99), and UA SS (<i>r</i> ≥ 0.99) showed a high correspondence between all programs. We observed a significant correspondence between CaOx SS and the percentage of CaOx dihydrate in the stone (<i>p</i> < 0.001), as well as between the percentage of brushite and apatite and CaP SS. UA SS showed the strongest correspondence with the percentage of UA in the stones (<i>p</i> < 0.001). <b><i>Conclusions:</i></b> Good correlation between EQUIL, JESS, and Lithorisk was observed and good correspondence with stone composition. The magnitude of the association demonstrated by fractional regression models supports evidence for applying SS in clinical practice.
Paraneoplastic syndromes in urologic malignancy: the many faces of renal cell carcinoma. (2002)

Renal cell carcinoma is unique among the genitourinary malignancies in that close to one third of affected patients show signs and symptoms of a paraneoplastic syndrome. The paraneoplastic syndromes associated with renal cell carcinoma range from those manifesting in constitutional symptoms (ie, fever, cachexia, and weight loss) to those that result in specific metabolic and biochemical abnormalities (ie, hypercalcemia, nonmetastatic hepatic dysfunction, amyloidosis, etc). The presence of a paraneoplastic syndrome in a patient with renal cell carcinoma is neither a marker of metastatic disease nor necessarily indicative of a poor prognosis. The importance of understanding the pathophysiology and biology behind the many paraneoplastic syndromes associated with renal cell carcinoma lies in the fact that the presence of these protean symptoms may be the initial presentation of either primary or recurrent disease. In this review, we will describe the proposed mechanisms of action of the many paraneoplastic syndromes associated with renal cell carcinoma as well as outline the clinical evaluation and treatment options currently available for these noteworthy disorders.
Impaired mucus detachment disrupts mucociliary transport in a piglet model of cystic fibrosis (2014)

Lung disease in people with cystic fibrosis (CF) is initiated by defective host defense that predisposes airways to bacterial infection. Advanced CF is characterized by a deficit in mucociliary transport (MCT), a process that traps and propels bacteria out of the lungs, but whether this deficit occurs first or is secondary to airway remodeling has been unclear. To assess MCT, we tracked movement of radiodense microdisks in airways of newborn piglets with CF. Cholinergic stimulation, which elicits mucus secretion, substantially reduced microdisk movement. Impaired MCT was not due to periciliary liquid depletion; rather, CF submucosal glands secreted mucus strands that remained tethered to gland ducts. Inhibiting anion secretion in non-CF airways replicated CF abnormalities. Thus, impaired MCT is a primary defect in CF, suggesting that submucosal glands and tethered mucus may be targets for early CF treatment.
Bone Regeneration Mediated by BMP4-Expressing Muscle-Derived Stem Cells Is Affected by Delivery System (2008)

This study investigated the delivery of bone morphogenetic protein (BMP)4-secreting muscle-derived stem cells (MDSC-B4) capable of inducing bone formation in mice using collagen gel (CG), fibrin sealant (FS), and gelatin sponge carriers. After implanting these various cell-loaded scaffolds intramuscularly or into critical-size skull defects, we measured the extent of heterotopic ossification and calvarial defect healing over a 6-week period via radiographic, radiomorphometric, histological, and micro-computed tomography analyses. As expected, in the absence of MDSC-B4, there was no ectopic ossification and only minimal calvarial regeneration using each type of scaffold. Although CG and gelatin sponges loaded with BMP4-secreting cells produced the most ectopic bone, FS constructs produced bone with comparably less mineralization. In the mouse calvaria, we observed MDSC-B4-loaded scaffolds able to promote bone defect healing to a variable degree, but there were differences between these implants in the volume, shape, and morphology of regenerated bone. MDSC-B4 delivery in a gelatin sponge produced hypertrophic bone, whereas delivery in a CG and FS healed the defect with bone that closely resembled the quantity and configuration of native calvarium. In summary, hydrogels are suitable carriers for osteocompetent MDSCs in promoting bone regeneration, especially at craniofacial injury sites.
Comparative IR Study of Ethylene Adsorption on a PtRh Alloy and Monometallic Pt and Rh Catalysts Supported on Al2O3. Identification of Alloy-Specific Binding Sites (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparative IR Study of Ethylene Adsorption on a PtRh Alloy and Monometallic Pt and Rh Catalysts Supported on Al2O3. Identification of Alloy-Specific Binding SitesHugo Celio, Michael Trenary, and Heinz J. RobotaCite this: J. Phys. Chem. 1995, 99, 16, 6024–6028Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/j100016a044https://doi.org/10.1021/j100016a044research-articleACS PublicationsRequest reuse permissionsArticle Views137Altmetric-Citations9LEARN 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 options Get e-Alerts
Leakage and breakdown mechanisms of GaN vertical power FinFETs (2019)

This work studies the leakage and breakdown mechanisms of 1.2 kV GaN vertical power FinFETs with edge termination. Two competing leakage and breakdown mechanisms have been identified. The first mechanism is dominated by the electric field, with the leakage current dominated by the electric field in the drift region and destructive breakdown voltage by the peak electric field at the edge termination. The second leakage and breakdown mechanism is controlled by an energy (or potential) barrier in the fin channel. This energy barrier suffers from the drain-induced barrier lowering (DIBL) effect and is highly dependent on gate/drain biases, fin geometries, and GaN/oxide interface charges. The electrons injected into the drift region due to the DIBL effect further lead to trap-assisted space-charge-limited conduction, which results in a nondestructive early breakdown. The barrier height in the fin channel determines which mechanism is dominant; the same device could show either destructive or nondestructive breakdown at different gate biases. To enable the normally off power switching, it is important to suppress the leakage from the second mechanism and maintain a sufficiently high energy barrier in the fin channel up to high drain voltages. Finally, the key device parameters determining the energy barrier in the fin channel have been identified. The findings in this work provide critical device understanding and design guidelines for GaN vertical power FinFETs and other "junctionless" vertical high-voltage power transistors.
Robustness of Distributed Multi-User Beamforming: An Experimental Evaluation (2022)

In this paper, we study the robustness of distributed beamforming in the presence of hardware imperfections. In particular, we characterize the impact of carrier frequency offset (CFO) between distributed antennas on multi-user receive beamforming. We characterize the performance of distributed beamforming in the presence of CFO using a massive MIMO platform. Using datasets collected from the platform, we measure and compare the beamforming performance in the presence and absence of CFO. Further, we study the effect of variation in CFO among beamforming antennas on the performance through simulations. Interestingly, we observe that this drop in performance is higher as more distributed antennas are included in beamforming. Our results can be used to determine the optimal number of antennas in distributed beamforming systems.
An inception network for positron emission tomography based dose estimation in carbon ion therapy (2022)

<i>Objective</i>. We aim to evaluate a method for estimating 1D physical dose deposition profiles in carbon ion therapy via analysis of dynamic PET images using a deep residual learning convolutional neural network (CNN). The method is validated using Monte Carlo simulations of<sup>12</sup>C ion spread-out Bragg peak (SOBP) profiles, and demonstrated with an experimental PET image.<i>Approach</i>. A set of dose deposition and positron annihilation profiles for monoenergetic<sup>12</sup>C ion pencil beams in PMMA are first generated using Monte Carlo simulations. From these, a set of random polyenergetic dose and positron annihilation profiles are synthesised and used to train the CNN. Performance is evaluated by generating a second set of simulated<sup>12</sup>C ion SOBP profiles (one 116 mm SOBP profile and ten 60 mm SOBP profiles), and using the trained neural network to estimate the dose profile deposited by each beam and the position of the distal edge of the SOBP. Next, the same methods are used to evaluate the network using an experimental PET image, obtained after irradiating a PMMA phantom with a<sup>12</sup>C ion beam at QST's Heavy Ion Medical Accelerator in Chiba facility in Chiba, Japan. The performance of the CNN is compared to that of a recently published iterative technique using the same simulated and experimental<sup>12</sup>C SOBP profiles.<i>Main results</i>. The CNN estimated the simulated dose profiles with a mean relative error (MRE) of 0.7% ± 1.0% and the distal edge position with an accuracy of 0.1 mm ± 0.2 mm, and estimate the dose delivered by the experimental<sup>12</sup>C ion beam with a MRE of 3.7%, and the distal edge with an accuracy of 1.7 mm.<i>Significance</i>. The CNN was able to produce estimates of the dose distribution with comparable or improved accuracy and computational efficiency compared to the iterative method and other similar PET-based direct dose quantification techniques.
Glutamate metabolism in malnutrition and sepsis in man (1981)

The metabolism of intravenous glutamate has been studied for its usefulness as a nutrient in intravenous feeding regimens. Intravenously infused monosodium L-glutamate was rapidly removed from the blood with a half-life of 10.7 and 9.1 min in healthy control and malnourished septic patients, respectively. Under the same conditions, alanine was metabolized much more slowly, with a half-life of 35 min (1). After the infusion of glutamate, blood lactate fell and glucose was increased in the control patients but not in the sick patients. Blood pyruvate, ketone bodies, glutamine, aspartate and alanine levels did not change after the infusion of glutamate in either group of patients. Increased urinary excretion of aspartate was observed in the control patients following the infusion of glutamate, but in the sick patients there was an increased excretion of glutamine. Insulin concentration in the blood rose after the infusion of glutamate in the control patients but not in the sick patients. Although the glutamate half-life life was similar in the two groups of patients, glutamate was metabolized differently in the sick. Deamination predominates over transamination. We conclude that glutamate, in the amounts provided in intravenous feeding, is safe, although its effectiveness may be less than previously thought.
A superconducting bandpass delta-sigma modulator for direct analog-to-digital conversion of microwave radio (2003)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.
Sialylation of MUC4β N-glycans by ST6GAL1 orchestrates human airway epithelial cell differentiation associated with type-2 inflammation (2019)

Although type-2-induced (T2-induced) epithelial dysfunction is likely to profoundly alter epithelial differentiation and repair in asthma, the mechanisms for these effects are poorly understood. A role for specific mucins, heavily N-glycosylated epithelial glycoproteins, in orchestrating epithelial cell fate in response to T2 stimuli has not previously been investigated. Levels of a sialylated MUC4β isoform were found to be increased in airway specimens from asthmatic patients in association with T2 inflammation. We hypothesized that IL-13 would increase sialylation of MUC4β, thereby altering its function and that the β-galactoside α-2,6-sialyltransferase 1 (ST6GAL1) would regulate the sialylation. Using human biologic specimens and cultured primary human airway epithelial cells (HAECs),we demonstrated that IL-13 increases ST6GAL1-mediated sialylation of MUC4β and that both were increased in asthma, particularly in sputum supernatant and/or fresh isolated HAECs with elevated T2 biomarkers. ST6GAL1-induced sialylation of MUC4β altered its lectin binding and secretion. Both ST6GAL1 and MUC4β inhibited epithelial cell proliferation while promoting goblet cell differentiation. These in vivo and in vitro data provide strong evidence for a critical role for ST6GAL1-induced sialylation of MUC4β in epithelial dysfunction associated with T2-high asthma, thereby identifying specific sialylation pathways as potential targets in asthma.
Automatic and scalable fault detection for mobile applications (2014)

This paper describes the design, implementation, and evaluation of VanarSena, an automated fault finder for mobile applications (``apps''). The techniques in VanarSena are driven by a study of 25 million real-world crash reports of Windows Phone apps reported in 2012. Our analysis indicates that a modest number of root causes are responsible for many observed failures, but that they occur in a wide range of places in an app, requiring a wide coverage of possible execution paths. VanarSena adopts a ``greybox'' testing method, instrumenting the app binary to achieve both coverage and speed. VanarSena runs on cloud servers: the developer uploads the app binary; VanarSena then runs several app ``monkeys'' in parallel to emulate user, network, and sensor data behavior, returning a detailed report of crashes and failures. We have tested VanarSena with 3000 apps from the Windows Phone store, finding that 1108 of them had failures; VanarSena uncovered 2969 distinct bugs in existing apps, including 1227 that were not previously reported. Because we anticipate VanarSena being used in regular regression tests, testing speed is important. VanarSena uses two techniques to improve speed. First, it uses a ``hit testing'' method to quickly emulate an app by identifying which user interface controls map to the same execution handlers in the code. Second, it generates a ProcessingCompleted event to accurately determine when to start the next interaction. These features are key benefits of VanarSena's greybox philosophy.
Crystal and magnetic structures of the superconductor CeNi0.8Bi2 (2011)

We have performed powder neutron diffraction on the new superconductor, CeNi${}_{0.8}$Bi${}_{2}$ with a superconducting transtion temperature ${T}_{\mathrm{c}}~$ 4.2 K. The structural parameters of this compound at room temperature are determined by Rietveld analysis. Below about 5 K, the clear magnetic Bragg peaks with propagation vector $q$ $=$ (0 0 0) are observed. The observed intensities of magnetic Bragg peaks can be explained by the magnetic structure that the two Ce moments in the unit cell are antiparallel along the $c$ axis. The magnetic Bragg peaks are observed in the superconducting state, indicating the coexistence of the antiferromagnetic ordering and the superconductivity in this compound. The intensity of magnetic Bragg peak monotonously increases with decreasing temperature below ${T}_{\mathrm{N}}$ and does not exhibit apparent anomaly at ${T}_{\mathrm{c}}$, obviously different from cases of heavy fermion superconductors in which the magnetic ordering and the superconductivity coexist, for example, Cd-doped CeCoIn${}_{5}$. These results suggest that the 4$f$ electron of the Ce atom is not coupled with the superconducting carrier, and the magnetic ordering is almost independent of the superconductivity in CeNi${}_{0.8}$Bi${}_{2}$.
W18 - PDMST '07 & GRep '07: 4th international workshop on P2P Data Management, Security, and Trust: 3rd international workshop on Data management in Global data Repositories (2014)

10.1109/DEXA.2007.4312999
Unsupervised Neural Hidden Markov Models (2016)

In this work, we present the first results for neuralizing an Unsupervised Hidden Markov Model. We evaluate our approach on tag in- duction. Our approach outperforms existing generative models and is competitive with the state-of-the-art though with a simpler model easily extended to include additional context.