gebhart/patrepeval huggingface dataset:
USCT Image Reconstruction: Acceleration using Gauss-Newton Preconditioned Conjugate Gradient (2017)

Ultrasound transmission tomography offers quantitative characterization of the tissue or materials by their speed of sound and attenuation. Reconstruction of such images is an inverse problem which is solved iteratively based on a forward model of the Helmholtz equation by paraxial approximation and thus is time-consuming. Hence, developing optimizers that decrease this time, in particular reducing the number of forward propagations is of high relevance in order to bring this technology into clinical practice. In this paper, we solve the inverse problem of reconstruction in a two-level strategy, by an outer and an inner loop. At each iteration of the outer loop, the system is linearized and this linear subproblem is solved in the inner loop with a preconditioned conjugate gradient (CG). A standard Cholesky preconditioning method based on the system matrix is compared with a matrix-free Quasi-Newton update approach, where a preconditioned matrix-vector product is computed at the beginning of every CG iteration. We also use a multigrid scheme with multi-frequency reconstruction to get a convergent rough reconstruction at a lower frequency and then refine it on a higher-resolution grid. The Cholesky preconditioning reduces the number of CG iterations by approx. 70%~85%; but the computation time for determining the system matrix for the Cholesky preconditioner is dominating, offsetting the gains of the reduction of iterations. The matrix-free preconditioning method saves approx. 30% of the computation time on average for single-frequency and multi-frequency reconstruction. For the robust multifrequency reconstruction, we test three breast-like numerical phantoms resulting in a deviation of 0.13 m/s on average in speed of sound reconstruction and a deviation of 5.4% on average in attenuation reconstruction, from the ground truth simulation.
A Direct-Reticle-Referenced Alignment System (1985)

A direct-reticle-referenced die-by-die alignment system operating at the actinic wavelength has certain unique advantages and some advantages in common with other systems. The unique advantages are the elimination of baseline and baseline associated problems and the minimization of optical aberrations of the alignment signal. The other advantages are the capability of video collection, digitization and manipulation of large data bases, the opportunity to chose and vary algorithms to accommodate processed wafers and the minimal demands imposed upon processing. The cost of using the actinic wavelength is the limitation in the number of photons available for alignment and the resultant reduction of the signal-to-noise ratio. There are certain problems generic to most other die-by-die alignment systems. Both optical and mechanical complexity is added to the lithographic system. Thin-film structures must be tailored to accommodate the demands of contrast, and photoresist modulation effects can introduce uncertainties in alignment. We shall briefly describe these effects in the context of the Field Alignment System, describe some of our measurements on this system, particularly those pertaining to the efficacy of the algorithm and comment upon the alignment capability of this system.
Feature filling modeling for step and flash imprint lithography (2009)

The authors analyze the feature filling phenomena for step and flash imprint lithography (SFIL) via diffusion of a gas, entrapped in the features, through liquid imprint resist. The model and simulation for the dynamics of feature filling including gas dissolution during the SFIL imprint step is presented. Several factors including the gas concentration profile across the liquid resist drop, the filling progression, and the total filling time for different pattern configurations are investigated to quantify feature filling. Simulation results show that initial filling is pressure controlled and very rapid [∼O(1ms)]. The rest of the feature filling is diffusion controlled, but fast enough [∼O(1s)] to conclude that diffusion of entrapped gas is not a cause for nonfilling of features. Also, the result that the smaller size features fill faster than the larger ones (with the same depth) makes SFIL the prime contender for high resolution and high throughput next generation lithography.
Supplementary Figures S1 - S6 from Inhibition of Melanoma Growth by Small Molecules That Promote the Mitochondrial Localization of ATF2 (2023)

&lt;p&gt;Supplementary Figures S1 - S6 - PDF file 945K, Supplementary Figure S1. Effect of select compounds on ATF2 nuclear-mitochondrial Translocation; Supplementary Figure S2. SBI-0089410 or SBI-0087702 do not affect the subcellular localization of Stat3 or beta-catenin. Supplementary Figure S3. The expression of ATF252E attenuates apoptosis induced by SBI-0089410 or SBI-0087702; Supplementary Figure S4. SBI-0089410 or SBI-0087702-induced inhibition of cell motility and cell death are reversed by the stable expression of ATF252E; Supplementary Figure S5. itochondrial potential changes induced by SBI-0089410 or SBI-0087702 in melanoma cells; Supplementary Figure S6. The effect of SBI-0089410 or SBI-0087702 on ATF2 phosphorylation, PKC translocation and activation, and the viability of PLX4032-resistant melanoma cell lines.&lt;/p&gt;
Workload characterization of selected JEE-based Web 2.0 applications (2008)

Web 2.0 represents the evolution of the web from a source of information to a platform. Network advances have permitted users to migrate from desktop applications to so-called Rich Internet Applications (RIAs) characterized by thin clients, which are browser-based and store their state on managed servers. Other Web 2.0 technologies have enabled users to more easily participate, collaborate, and share in web-based communities. With the emergence of wikis, blogs, and social networking, users are no longer only consumers, they become contributors to the collective knowledge accessible on the web. In another Web 2.0 development, content aggregation is moving from portal-based technologies to more sophisticated so-called mashups where aggregation capabilities are greatly expanded. While Web 2.0 has generated a great deal of interest and discussion, there has not been much work on analyzing these emerging workloads. This paper presents a detailed characterization of several applications that exploit Web 2.0 technologies, running on an IBM Power5 system, with the goal of establishing, whether the server-side workloads generated by Web 2.0 applications are significantly different from traditional web workloads, and whether they present new challenges to underlying systems. In this paper, we present a detailed characterization of three Web 2.0 workloads, and a synthetic benchmark representing commercial workloads that do not exploit Web 2.0, for comparison.
Author response: mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status (2021)

Vaccination is one of the best ways to prevent severe COVID-19. Two doses of mRNA vaccine protect against serious illness caused by the coronavirus SARS-CoV-2. They do this, in part, by encouraging the immune system to make specialised proteins known as antibodies that recognise the virus. Most of the vaccine research so far has focussed on these antibodies, but they are only one part of the immune response. Vaccines also activate immune cells called T cells. These cells have two main roles, coordinating the immune response and killing cells infected with viruses. It is likely that they play a key role in preventing severe COVID-19. There are many kinds of T cells, each with a different role. Currently, the identity and characteristics of the T cells that protect against COVID-19 is unclear. Different types of T cells have unique proteins on their surface. Examining these proteins can reveal details about how the T cells work, which part of the virus they recognise, and which part of the body they protect. A tool called cytometry by time of flight allows researchers to measure these proteins, one cell at a time. Using this technique, Neidleman, Luo et al. investigated T cells from 11 people before vaccination and after their first and second doses. Five people had never had COVID-19 before, and six had already recovered from COVID-19. Neidleman, Luo et al. found that the T cells recognizing SARS-CoV-2 in the two groups differed. In people who had never had COVID-19 before, the second dose of vaccine improved the quality and quantity of the T cells. The same was not true for people who had already recovered from COVID-19. However, although their T cells did not improve further after a second vaccine dose, they did show signs that they might offer more protection overall. The proteins on the cells suggest that they might last longer, and that they might specifically protect the nose, throat and lungs. Neidleman, Luo et al. also found that, for both groups, T cells activated by vaccination responded in the same way to different variants of the virus. This work highlights the importance of getting both vaccine doses for people who have never had COVID-19. It also suggests that vaccination in people who have had COVID-19 may generate better T cells. Larger studies could show whether these patterns remain true across the wider population. If so, it is possible that delivering vaccines to the nose or throat could boost immunity by mimicking natural infection. This might encourage T cells to make the surface proteins that allow them to home to these areas.
Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors (2019)

Abstract Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for synergistic interactions among stressors and the genetic variance and covariance among fitness-related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora , a reef-building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses ( e.g ., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were tradeoffs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive co-variances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health ( e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals’ adaptive capacity when predicting the future of coral reefs.
On-line testing of calibration of pressure transmitters in nuclear power plants (2003)

The author presents the preliminary results of an experimental research project recently initiated to validate the new techniques that have been developed for instrument calibration reduction in nuclear power plants. These techniques will permit online testing of calibration of pressure transmitters as installed in an operating nuclear power plant. In addition to the transmitter itself, the techniques will provide calibration testing of the signal conditioning equipment and other components of the instrument channel and thereby eliminate the need for much of the calibration effort currently carried out in nuclear power plants. The results of laboratory and in-plant research completed to date have shown that online drift monitoring should be successful for separating transmitters that must be calibrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reconfigurable beam steering metasurface absorbers (2014)

An ultra-thin reconfigurable metasurface absorber consisting of a mushroom type artificial magnetic conductor (AMC) is proposed. By capacitively loading the unit cells the reflection phase can be shifted, allowing the metasurface to steer the incoming wave to the desired direction, behaving as a phase gradient absorber. A formula based on antenna array theory was used to determine the required phase shift needed to steer the main beam. A reduction of 30dBm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> compare to a PEC ground plane was achieved for the design that steers the main beam to Φ=0° and θ= 15°, from the specular direction. Also, it was further shown that by incorporating resistors into the loaded structure the main beam width can be increased.
Compact UWB MIMO antenna with pattern diversity and band rejection characteristics (2017)

This article presents a compact size asymmetric CPW strip-fed UWB two-element MIMO antenna, with notched-band behavior. The single-antenna element of the MIMO configuration is composed of a semi-elliptical patch radiator with asymmetric ground plane. The notched-band behavior of the proposed antenna is achieved by inserting a simple folded stub to the patch radiator. This stub achieves the desired single stop-band from 3.3 to 3.9 GHz for WIMAX. The two-antenna elements are placed orthogonally to achieve pattern diversity which leads to an improved MIMO system performance and enhances the isolation between elements without using any decoupling structures. The antenna has dimensions of 50 × 28 mm2. The edge-to-edge distance between antenna elements is 0.15λ0 at 3 GHz. The proposed antenna is designed, simulated, fabricated, and tested. Results show that the two-antenna elements operate at frequencies ranging from 2.8 to 11.5 GHz with return loss lower than −10 dB and insertion loss lower than −18 dB. The performance of the MIMO antenna diversity characteristics were verified through the calculation of the standard parameters and show the antenna suitability for MIMO systems. © 2017 Wiley Periodicals, Inc. Microwave Opt Technol Lett 59:1460–1464, 2017
Adversarial Attack on Graph Structured Data (2018)

Deep learning on graph structures has shown exciting results in various applications. However, few attentions have been paid to the robustness of such models, in contrast to numerous research work for image or text adversarial attack and defense. In this paper, we focus on the adversarial attacks that fool the model by modifying the combinatorial structure of data. We first propose a reinforcement learning based attack method that learns the generalizable attack policy, while only requiring prediction labels from the target classifier. Also, variants of genetic algorithms and gradient methods are presented in the scenario where prediction confidence or gradients are available. We use both synthetic and real-world data to show that, a family of Graph Neural Network models are vulnerable to these attacks, in both graph-level and node-level classification tasks. We also show such attacks can be used to diagnose the learned classifiers.
Extra‐Large Mechanical Anisotropy of a Hydrogel with Maximized Electrostatic Repulsion between Cofacially Aligned 2D Electrolytes (2018)

Abstract In our previous work, we have shown that “electrostatic forces”, when generated anisotropically in aqueous media by 2D electrolytes upon cofacial orientation, enable the formation of a hydrogel with an anisotropic parameter, as defined by the ratio of elastic moduli E ⊥ / E ∥ , of 3.0. Herein, we successfully developed the design strategy for a hydrogel with an anisotropic parameter of no less than 85. This value is not only 28 times greater than that of our previous anisotropic hydrogel but also 6 times larger than the current champion record in synthetic hydrogels ( E ⊥ / E ∥ ∼15). Firstly, we simply lowered ionic contaminants in the hydrogel and were able to enhance the anisotropic parameter from 3.0 to 18. Then, we chose a supporting polymer network allowing the hydrogel to carry a higher interior permittivity. Consequently, the anisotropic parameter was further enhanced from 18 to 85. Owing to the enhanced mechanical anisotropy, our new hydrogel displayed a superb ability of seismic isolation.
Standard perturbative analysis of zero-average dispersion management (1999)

One of the noteworthy features of the dispersion-managed (DM) soliton is the feet that, in contrast with the conventional NLS soliton, it can sustain stable propagation not only in the anomalous average dispersion regime but also at zero or normal average dispersion [1].
Efficiency of static core turn-off in a system-on-a-chip with variation (2023)

A processor-implemented method for improving efficiency of a static core turn-off in a multi-core processor with variation, the method comprising: conducting via a simulation a turn-off analysis of the multi-core processor at the multi-core processor&#x27;s design stage, wherein the turn-off analysis of the multi-core processor at the multi-core processor&#x27;s design stage includes a first output corresponding to a first multi-core processor core to turn off; conducting a turn-off analysis of the multi-core processor at the multi-core processor&#x27;s testing stage, wherein the turn-off analysis of the multi-core processor at the multi-core processor&#x27;s testing stage includes a second output corresponding to a second multi-core processor core to turn off; comparing the first output and the second output to determine if the first output is referring to the same core to turn off as the second output; outputting a third output corresponding to the first multi-core processor core if the first output and the second output are both referring to the same core to turn off.
VEGFR1 signaling in retinal angiogenesis and microinflammation (2021)

Five vascular endothelial growth factor receptor (VEGFR) ligands (VEGF-A, -B, -C, -D, and placental growth factor [PlGF]) constitute the VEGF family. VEGF-A binds VEGF receptors 1 and 2 (VEGFR1/2), whereas VEGF-B and PlGF only bind VEGFR1. Although much research has been conducted on VEGFR2 to elucidate its key role in retinal diseases, recent efforts have shown the importance and involvement of VEGFR1 and its family of ligands in angiogenesis, vascular permeability, and microinflammatory cascades within the retina. Expression of VEGFR1 depends on the microenvironment, is differentially regulated under hypoxic and inflammatory conditions, and it has been detected in retinal and choroidal endothelial cells, pericytes, retinal and choroidal mononuclear phagocytes (including microglia), Müller cells, photoreceptor cells, and the retinal pigment epithelium. Whilst the VEGF-A decoy function of VEGFR1 is well established, consequences of its direct signaling are less clear. VEGFR1 activation can affect vascular permeability and induce macrophage and microglia production of proinflammatory and proangiogenic mediators. However the ability of the VEGFR1 ligands (VEGF-A, PlGF, and VEGF-B) to compete against each other for receptor binding and to heterodimerize complicates our understanding of the relative contribution of VEGFR1 signaling alone toward the pathologic processes seen in diabetic retinopathy, retinal vascular occlusions, retinopathy of prematurity, and age-related macular degeneration. Clinically, anti-VEGF drugs have proven transformational in these pathologies and their impact on modulation of VEGFR1 signaling is still an opportunity-rich field for further research.
Correction: Synthesis, spectroscopic characterization, X-ray structure and electrochemistry of new bis(1,2-diaminocyclohexane)gold(iii) chloride compounds and their anticancer activities against PC3 and SGC7901 cancer cell lines (2020)

Correction for ‘Synthesis, spectroscopic characterization, X-ray structure and electrochemistry of new bis(1,2-diaminocyclohexane)gold(<sc>iii</sc>) chloride compounds and their anticancer activities against PC3 and SGC7901 cancer cell lines’ by Said S. Al-Jaroudi <italic>et al.</italic>, <italic>New J. Chem.</italic>, 2014, <bold>38</bold>, 3199–3211, DOI: 10.1039/C3NJ01624B.
Fabrication of 3D Printed Thermoelectric Devices for Integration Into Liquid Crystal Elastomer Actuators (2022)

Abstract Shape memory materials such as liquid crystal elastomers (LCE) have been explored as soft robotic actuators due to their high mechanical robustness and muscle-like work densities. The main drawback of LCEs is slow response times and low energy efficiencies stemming from poor thermal management. Thermoelectric devices (TED), which generate temperatures differentials across semiconductors through the Peltier effect when current is applied, have the potential to address these long response times. By introducing additive manufacturing along with conductive liquid metal (LM) traces, we introduce TED for soft robotic applications. In this study, we build on recent work in soft thermoelectric generators to create high density arrays of thermoelectric semiconductors to actively heat and cool LCEs. We describe advancements in the manufacturing of a soft TED in which we achieve a 28% fill factor of semiconductors through the use of 3D printing. We report maximum power densities of 236 μWcm−2 at ΔT = 60 °C. By coating LCE on each side of the TED we create single input multidirectional liquid crystal elastomer thermoelectric device (LCE-TED) actuators. Thermal management design challenges are discussed along with the introduction of liquid metal embedded elastomer composites (LMEE) into TED design. Lastly, we introduce an inchworm inspired soft robot walker based on these LCE-TED actuators. We highlight gait mechanics for three cycles of actuation for this soft robotic system.
A comparison study of two indirect methods for measuring the systolic pulmonary arterial pressure (2011)

This paper presents a comparison study between two non invasive approaches for the estimation of Pulmonary Artery Pressure (PAP). The first method relies on the Pulsed Doppler echocardiography which has been used in this case for the measurement of maximum tricuspid transvalvular pressure gradient. The second method is based on the elaboration of heart acoustic sounds and particularly of the second heart sound. In the present works results relevant to the first experimental campaign are reported and relevant to PAP measurements on 40 athletes of different kinds of sport. Results show encouraging matching between two methods.
Research Data Supporting Order Enables Efficient Electron-hole Separation at an Organic Heterojunction with a Small Energy Loss (2017)

Pump Push Probe Transient Absorption Images for PIPCP and PIPCP:PCBM Films. Images were acquired as described in the associated manuscript. Images were acquired as a function of Pump Probe delay time at a variety of Pump Push delays, Push energies, Push fluences, and Pump fluences. Also included are the Pump Probe and Push Probe images that are acquired simultaneously