gebhart/patrepeval huggingface dataset:
Sound speed and attenuation in the sea bottom from broadband sound propagation in the Yellow Sea. (2008)

A joint China-U.S. underwater acoustics experiment was conducted in August, 1996 in 75-m water in the Yellow Sea with a very flat bottom and a strong and sharp thermocline. Broadband explosive sources were detonated both above and below the thermocline along two radial lines and a quarter of circle. Two inversion schemes are used to obtain the sound speed in the bottom. The first scheme is based on extracting normal mode depth functions from the cross-spectral density matrix (CSDM). The CSDM is constructed from explosive signals measured using a 32-element vertical line array at a fixed long range. In the second scheme, the modal arrival times are extracted using an adaptive time-frequency analysis technique. The inverted bottom sound speed is used as a constraint on high-quality TL data to extract the bottom sound attenuation. The inverted bottom attenuation exhibits apparent nonlinear frequency dependence over a frequency range from 80 to 1260 Hz. A possible effect of mode-coupling on the inverted bottom attenuation is discussed. Measured TL as a function of frequency, range, and depth is in good agreement with the predictions based on the inverted bottom acoustic parameters. [Work supported by ONR.]
Feedback-based Digital Higher-order Terminal Sliding Mode for 6-DOF Industrial Manipulators (2021)

The precise motion control of a multi-degree of freedom (DOF) robot manipulator is always challenging due to its nonlinear dynamics, disturbances, and uncertainties. Because most manipulators are controlled by digital signals, a novel higher-order sliding mode controller in the discrete-time form with time delay estimation is proposed in this paper. The dynamic model of the manipulator used in the design allows proper handling of nonlinearities, uncertainties and disturbances involved in the problem. Specifically, parametric uncertainties and disturbances are handled by the time delay estimation and the nonlinearity of the manipulator is addressed by the feedback structure of the controller. The combination of terminal sliding mode surface and higher-order control scheme in the controller guarantees a fast response with a small chattering amplitude. Moreover, the controller is designed with a modified sliding mode surface and variable-gain structure, so that the performance of the controller is further enhanced. We also analyse the condition to guarantee the stability of the closed-loop system in this paper. Finally, the simulation and experimental results prove that the proposed control scheme has precise performance in a robot manipulator system.
Mutant lamin A links prophase to a p53 independent senescence program (2015)

Expression of oncogenes or short telomeres can trigger an anticancer response known as cellular senescence activating the p53 and RB tumor suppressor pathways. This mechanism is switched off in most tumor cells by mutations in p53 and RB signaling pathways. Surprisingly, p53 disabled tumor cells could be forced into senescence by expression of a mutant allele of the nuclear envelope protein lamin A. The pro-senescence lamin A mutant contains a deletion in the sequence required for processing by the protease ZMPSTE24 leading to accumulation of farnesylated lamin A in the nuclear envelope. In addition, the serine at position 22, a target for CDK1-dependent phosphorylation, was mutated to alanine, preventing CDK1-catalyzed nuclear envelope disassembly. The accumulation of this mutant lamin A compromised prophase to prometaphase transition leading to invaginations of the nuclear lamina, nuclear fragmentation and impaired chromosome condensation. Cells exited this impaired mitosis without cytokinesis and re-replicated their DNA ultimately arresting in interphase as polyploid cells with features of cellular senescence including increased expression of inflammatory gene products and a significant reduction of tumorigenicity in vivo.
Data from α<sub>v</sub>β<sub>3</sub>/α<sub>v</sub>β<sub>5</sub> Integrins-FAK-RhoB: A Novel Pathway for Hypoxia Regulation in Glioblastoma (2023)

&lt;div&gt;Abstract&lt;p&gt;The presence of hypoxic areas in glioblastoma is an important determinant in tumor response to therapy and, in particular, to radiotherapy. Here we have explored the involvement of integrins, up to now known as regulators of angiogenesis and invasion, in the regulation of tumor hypoxia driven from the tumor cell. We first show that hypoxia induces the recruitment of α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3&lt;/sub&gt; and α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;5&lt;/sub&gt; integrins to the cellular membrane of U87 and SF763 glioblastoma cells, thereby activating the focal adhesion kinase (FAK). We then show that inhibiting α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3&lt;/sub&gt; or α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;5&lt;/sub&gt; integrins in hypoxic cells with a specific inhibitor or with siRNA decreases the hypoxia-inducible factor 1α (HIF-1α) intracellular level. This integrin-dependent regulation of HIF-1α is mediated through the regulation of FAK, which in turn activates the small GTPase RhoB, leading to the inhibition of GSK3-β. Furthermore, silencing this pathway in glioma cells of established xenografts dramatically reduces glioma hypoxia, associated with a significant decrease in vessel density. Our present results unravel a new mechanism of hypoxia regulation by establishing the existence of an α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3&lt;/sub&gt;/α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;5&lt;/sub&gt; integrin–dependent loop of hypoxia autoregulation in glioma. Targeting this hypoxia loop may be crucial to optimizing radiotherapy efficiency. [Cancer Res 2009;69(8):3308–16]&lt;/p&gt;&lt;/div&gt;
Control Architecture for a Switched Doubly Fed Machine Propulsion Drive (2014)

Doubly fed machines (DFMs) are well known for limited-speed-range applications such as in wind power generation due to their reduced requirement in power electronic rating. Switched DFM drives offer the same benefit on power electronic requirement but operate on a wide speed range. This makes them attractive for wide-speed-range high-power applications, e.g., in ship propulsion. A unique controller is needed to fit the different demands of a switched DFM drive, specifically where both ac and dc supplies are available. This paper presents a control architecture for a switched DFM drive intended for propulsion application. The proposed architecture adapts to the on-the-fly changes in DFM configuration and seamlessly controls the speed/torque during these variations.
Challenges Designing for FPGAs Using High-Level Synthesis (2022)

High-Level Synthesis (HLS) tools are aimed at enabling performant FPGA designs that are authored in a high-level language. While commercial HLS tools are available today, there is still a substantial performance gap between most designs developed via HLS relative to traditional, labor intensive approaches. We report on several cases where an anticipated performance improvement was either not realized or resulted in decreased performance. These include: programming paradigm choices between data parallel vs. pipelined designs; dataflow implementations; configuration parameter choices; and handling odd data set sizes. The results point to a number of improvements that are needed for HLS tool flows, including a strong need for performance modeling that can reliably guide the compilation optimization process.
Graphite Oxidation Simulation in HTR Accident Conditions (3<sup>rd</sup> Year and Final Technical Report) (2012)

Massive air and water ingress, following a pipe break or leak in steam-generator tubes, is a design-basis accident for high-temperature reactors (HTRs). Analysis of these accidents in both prismatic and pebble bed HTRs requires state-of-the-art capability for predictions of: 1) oxidation kinetics, 2) air helium gas mixture stratification and diffusion into the core following the depressurization, 3) transport of multi-species gas mixture, and 4) graphite corrosion. This project will develop a multi-dimensional, comprehensive oxidation kinetics model of graphite in HTRs, with diverse capabilities for handling different flow regimes. The chemical kinetics/multi-species transport model for graphite burning and oxidation will account for temperature-related changes in the properties of graphite, oxidants (O2, H2O, CO), reaction products (CO, CO2, H2, CH4) and other gases in the mixture (He and N2). The model will treat the oxidation and corrosion of graphite in geometries representative of HTR core component at temperatures of 900°C or higher. The developed chemical reaction kinetics model will be user-friendly for coupling to full core analysis codes such as MELCOR and RELAP, as well as computational fluid dynamics (CFD) codes such as CD-adapco. The research team will solve governing equations for the multi-dimensional flow and the chemical reactions and kinetics using Simulink, an extension of the MATLAB solver, and will validate and benchmark the model's predictions using reported experimental data. Researchers will develop an interface to couple the validated model to a commercially available CFD fluid flow and thermal-hydraulic model of the reactor , and will perform a simulation of a pipe break in a prismatic core HTR, with the potential for future application to a pebble-bed type HTR.
Correction: Discovery of 4,6-disubstituted pyrimidines as potent inhibitors of the heat shock factor 1 (HSF1) stress pathway and CDK9. See DOI: 10.1039/c6md00159a (2016)

Correction for ‘Discovery of 4,6-disubstituted pyrimidines as potent inhibitors of the heat shock factor 1 (HSF1) stress pathway and CDK9’ by Carl S. Rye <italic>et al.</italic>, <italic>Med. Chem. Commun.</italic>, 2016, <bold>7</bold>, 1580–1586.
Subjective and objective evaluation of localisation accuracy in wave field sysnthesis (2008)

cote interne IRCAM: Sanson08b
Identification of end stage renal disease metabolic signatures from human perspiration (2022)

End stage renal disease (ESRD), characterized by cessation in kidney function, has been linked to severe metabolic disturbances, caused by buildup of toxic solutes in blood. To remove these solutes, ESRD patients undergo dialysis. As a proof of concept, we tested whether ESRD-related metabolic signatures can be detected in perspiration samples using a combined methodology. Our rapid methodology involves swabbing a glass slide across the patient’s forehead, detecting the metabolites in the imprint using desorption electrospray ionization mass spectrometry, and identifying the key differences using machine learning methods. Based on collecting 42 healthy and 27 ESRD samples, we find saturated fatty acids are consistently suppressed in ESRD patients, with little change after dialysis. Also, our method enables the detection of uremic solutes, where we find elevated levels of uric acid (6.7 fold higher on average) that sharply decrease after dialysis. Beyond the study of individual metabolites, we find that a lasso model, which selects for 8 m/z fragments from 24,602 detected analytes, achieves area under the curve performance of 0.85 and 0.87 on training (n=52) and validation sets (n=17) respectively. Together, these results suggest that this methodology is promising for detecting signatures relevant for Precision Health.
Syk and Yea Shall Find (2015)

The article by Ghosh and Ghealen in the current issue of EBioMedicine provides new insights into the pathophysiology of the inflammatory system in Alzheimer's disease (AD). The story describing the accumulation of aggregated proteins in the AD brain, including β-amyloid and tau protein, has been developing since Alois Alzheimer first identified neurofibrillary tangles with a silver stain more than 100years ago. Classically, neuritic plaques composed of aggregated Aβ peptides accumulate in the neuropil, outside neurons and glia, while neurofibrillary tangles composed of aggregated tau accumulate within neurons.
N-alkyl-3-decarboxy-3-hydroxymethylsiastatin B, a New Family of Glycosidase Inhibitors ofgem-diamine 1-n-iminosugars (2001)

N-Alkyl-3-decarboxy-3-hydroxymethylsiastatin B, N-alkyl analogues of gem-diamine 1-N-iminosugars, is a new family of glycosidase inhibitors that have been synthesized from siastatin B isolated from Streptomyces culture. These compounds were evaluated as glycosidase inhibitors.
Translational potential of JAX humanized APOE mice: Peripheral interferon gamma induces systemic immuno‐metabolic dysfunction (2022)

Abstract Background Inflammation is a well‐documented feature of Alzheimer’s disease (AD) in human brain. Previous findings from our group demonstrated upregulated immune transcripts in the AD brain as well as sex differences in immune transcript levels during pre‐clinical midlife aging. Using our humanized APOE mouse model, we identified elevated immune transcripts in the female brain including interferon signaling genes, CD3, CD4, and MHCII. We hypothesized that activation via increased interferon gamma (IFN‐γ) during endocrine aging may disrupt the immune‐metabolic balance in the brain and therefore advance changes in grey and white matter. With this study, we test the hypothesis that increased levels of peripheral IFN‐γ induces genotype dependent immuno‐metabolic changes in the JAX humanized APOE (hAPOE) mouse model. Method To determine the role of IFN‐γ in female midlife aging and AD risk, pre‐menopausal and peri‐menopausal hAPOE mice were intraperitoneally treated with recombinant IFN‐γ for 9 days. Immunophenotyping using multi‐color flow cytometry was conducted microglial reactivity, phagocytosis, neutral lipid content, oxidative stress, and the presence of lymphocytes were determined. Structural and diffusion weighted analysis using MRI was conducted to evaluate grey and white matter structural integrity in the brain. ELISA assays were conducted to assess the presence of beta amyloid 40 and 42 and levels of pro‐inflammatory cytokines. Result IFN‐γ treated animals exhibited upregulation of markers that perpetuate neuroinflammation and white matter catabolism including MHCII, CD8, pHrodo, and BODIPY. Peripheral immune effects were genotype dependent while immune signaling in brain largely exhibited treatment‐dependent effects. Fasting blood glucose levels were significantly increased by IFN‐γ consistent with an accelerated aging profile. Diffusion metrics including mean and radial kurtosis in addition to mean, axial, and radial diffusivity were greater in IFN‐treated animals. Conclusion Peripheral increase of interferon gamma signaling during female endocrine aging in hAPOE mice induced 1) dysfunction of metabolic systems and neuroinflammatory response and 2) decreases in white and grey matter microstructural integrity throughout the brain. These outcomes support the investigation of therapeutic strategies targeting interferon signaling pathways at the earliest stages of midlife aging to reduce risk of AD or delay AD onset.
On the High-Speed Turn-Off of a Power Transistor by a Small Saturable Core (1986)

An effective method for reducing the size and weight of the switching dc-dc converter is to increase the switching frequency. To accomplish this with no deterioration in efficiency, it is necessary to suppress the switching loss per cycle by shortening the switching time. An efficient dc-dc converter operating at the megahertz region is presented. The turn-off time is shortened by using the current feedback and the core saturation. The turn-off mechanism is analyzed with the equivalent circuits. As a result, it is found that the excess carrier in the base region is discharged quickly by the large reverse base current, which flows when the energy stored in the base-emitter capacitance of the power transistor is transferred to the saturated inductance of the core with high frequency oscillation.
Mechanochemically tuned structural annealing: a new pathway to enhancing Li-ion intercalation activity in nanosized βII Li2FeSiO4 (2019)

Controlled mechano-activation of ortho-LFS nanocrystals induces structural annealing that leads to enhanced Li-ion intercalation.
Supplementary Figure 8 from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 8 from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Partial Liquid Ventilation in Critically Ill Infants Receiving Extracorporeal Life Support (1997)

The study suggests that perflubron PLV is safe, improves lung function, and recruits lung volume in critically ill infants receiving ECLS. PLV therapy for infants with ARDS seems to have a great deal of promise. Based on this and other phase I and II trials, studies of PLV on selected full-term infants before ECLS have been initiated.
MAFTIA: Reference Model and Use Cases (2000)

This document constitutes the first deliverable of MAFTIA work package. The objective of this work package is to define a consistent framework for ensuring the dependability of distributed applications in the face of a wide class of threats. In particular, the aim is to develop a coherent set of concepts for an architecture that can tolerate deliberately malicious faults, such as intrusions, in applications distributed over the Internet. The intrusions of concern include not only those perpetrated by external penetrators, but also those carried out by corrupt insiders, i.e., users who are authorized to access the system but not authorized for the accessed data, program or resource, and administrators who misuse their rights. Although intrusions are the primary class of targeted faults, the architecture should also be adequately robust towards accidental physical faults and accidental design faults.
Towards an Oligosaccharide-BasedGlycoconjugate Vaccine AgainstShigelladysenteriaeType 1 (2003)

This review summarizes the authors’ studies in the past decade aimed at developing a synthetic oligosaccharide-based glycoconjugate vaccine to prevent a serious human disease caused by the Gram negative bacterium Shigella dysenteriae type 1. Starting from simple monosaccharides, oligosaccharides as large as a 24 monosaccharide-containing linear polymer, were assembled. Under suitable conditions, oligosaccharides containing 4 to 16 hexopyranose residues were covalently attached to an immunogenic protein. The serum response to the synthetic glycoconjugates depends, both on the size of the oligosaccharides, and on the molar ratio of the oligosaccharides to the carrier protein. Also reviewed are studies of the fine specificities of the interaction between oligosaccharides and anti-polysaccharide monoclonal antibodies as well as conformational studies of the synthetic oligosaccharides.
Model Based Iterative Reconstruction With Spatially Adaptive Sinogram Weights for Wide-Cone Cardiac CT (2018)

With the recent introduction of CT scanners with large cone angles, wide coverage detectors now provide a desirable scanning platform for cardiac CT that allows whole heart imaging in a single rotation. On these scanners, while half-scan data is strictly sufficient to produce images with the best temporal resolution, acquiring a full 360 degree rotation worth of data is beneficial for wide-cone image reconstruction at negligible additional radiation dose. Applying Model-Based Iterative Reconstruction (MBIR) algorithm to the heart has shown to yield significant enhancement in image quality for cardiac CT. But imaging the heart in large cone angle geometry leads to apparently conflicting data usage considerations. On the one hand, in addition to using the fastest available scanner rotation speed, a minimal complete data set of 180 degrees plus the fan angle is typically used to minimize both cardiac and respiratory motion. On the other hand, a full 360 degree acquisition helps better handle the challenges of missing frequencies and incomplete projections associated with wide-cone half-scan data acquisition. In this paper, we develop a Spatially Adaptive sinogram Weights MBIR algorithm (SAW-MBIR) that is designed to achieve the benefits of both half and full-scan reconstructions in order to maximize temporal resolution over the heart region while providing stable results over the whole volume covered with the wide-area detector. Spatially-adaptive sinogram weights applied to each projection measurement in SAW-MBIR are designed to selectively perform backprojection from the full and half-scan portion of the sinogram based on both projection angle and reconstructed voxel location. We demonstrate with experimental results of SAW-MBIR applied to whole-heart cardiac CT clinical data that overall temporal resolution matches half-scan while full volume image quality is on par with full-scan MBIR.
Grid integration and a power quality assessment of a wave‐energy park (2019)

This study presents a step toward the grid connection of a wave‐energy park through an electric power conversion system (EPCS) developed and installed for the wave‐energy harvesting in Lysekil, Sweden. The EPCS comprises a rectifier, a DC bus, and an inverter followed by a harmonic filter (HF). The higher‐ and lower‐order harmonics injected by the inverter in a power quality context are investigated. The lower‐order voltage harmonics partially distort the voltage‐source inverter output grid current. A phase‐locked loop‐based (PLL) grid‐phase tracking is used to attenuate the lower‐order harmonics by reflecting the grid harmonics in the inverter output. An expression for the grid‐current harmonics as a function of the grid‐voltage harmonics has been derived and implemented. A mathematical model is derived to obtain a transfer function for the PLL, and finally, proportional–integral gains are tuned for stable system operation. An HF for mitigating the higher‐order harmonics has been implemented. The total harmonic distortion is evaluated experimentally, and the results fulfil the grid‐code requirements at various frequencies and harmonic orders.
Optimized intensity modulation for a dynamic beam attenuator in x-ray computed tomography (2019)

In our previous study we successfully built a novel sheet-based dynamic beam attenuator (sbDBA) for fluence field modulation in X-ray computed tomography (CT) and performed a first-time experimental validation. In this work, we focus on the optimization of the DBA transmission properties for a given object. In clinical routine, CT scanners must cope with various attenuation properties differing from patient to patient. Typically, the attenuation of patients is high in the center of the fan beam, decreasing towards the periphery. The attenuation profiles of an object can also change for different X-ray tube positions. These variations cause unfavorable imbalances of image quality in the reconstructed object. Typically, the peripheral region, which is generally of minor diagnostically relevance, has relatively lower noise than the central region because the rays contributing to the peripheral region are less attenuated. This imbalance can be reduced by using beam-shaping prefilters, e.g. bowtie filters, attenuating the propagated intensity towards the periphery in a predefined, static profile. Bowtie filters, however, are not capable of dynamically adapting their attenuation to the attenuation profile of the patient. This can be accomplished by using dynamic beam attenuators (DBA) where the fan beam intensity can dynamically be modulated on a view-by-view basis, reducing noise inhomogeneities and enabling region-of-interest (ROI) imaging. Different scenarios (no attenuator, tube current modulation, conventional bowtie filter, the sbDBA and an ideal DBA) are compared in terms of image quality. The optimized sbDBA with tube current modulation (TCM) not only reduces the total radiation dose but also allows for spatial selection of intensity as required for ROI imaging.