gebhart/patrepeval huggingface dataset:
Recursive prediction error identification of nonlinear state space models (2004)

A recursive prediction error algorithm for identification of systems described by nonlinear ordinary differential equation (ODE) models is presented. The model is a MIMO ODE model, parameterized with coefficients of a multi-variable polynomial that describes one component of the right hand side function of the ODE. It is explained why such a parameterization is a key to obtain a well defined algorithm, that does not suffer from singularities and over-parameterization problems. Furthermore, it is proved that the selected model can also handle systems with more complicated right hand side structure, by identification of an input-output equivalent system in the coordinate system of the selected states. The linear output measurements can be corrupted by zero mean disturbances that are correlated between measurements and over time. The disturbance correlation matrix is estimated online and need not be known beforehand. The algorithm is applied to live data from a system consisting of two cascaded tanks with free outlets. It is illustrated that the identification algorithm is capable of producing a highly accurate nonlinear model of the system, despite the fact that the right hand structure of the system has two nontrivial nonlinear components. A novel technique based on scaling of the sampling period that significantly improves the numerical properties of the algorithm is also disclosed.
Supplementary Figure 4 from Soluble CD200 Is Critical to Engraft Chronic Lymphocytic Leukemia Cells in Immunocompromised Mice (2023)

&lt;p&gt;PDF file - 66K, 6.Engraftment of CD19+CD5+ CLL cells in peritoneal cavity: Absolute count (x105 cells) of CD19+CD5+ CLL cells in the peritoneal cavity of animals receiving one of the three plasma infusions: sCD200hi CLL plasma, sCD200hi CLL plasma + anti-CD200 (Fab), or sCD200 absorbed CLL plasma&lt;/p&gt;
Comparative Evaluation of Profiles of Antibodies to Mycobacterial Capsular Polysaccharides in Tuberculosis Patients and Controls Stratified by HIV Status (2011)

Despite the complexity of tuberculosis (TB) serology, antibodies (Abs) remain attractive biomarkers for TB. Recent evidence of a mycobacterial capsule that consists mainly of the polysaccharides arabinomannan (AM) and glucan provides new options for serologic targets. For this study, Ab responses to AM and glucan for 47 U.S. TB patients (33 HIV negative [HIV(-)], 14 HIV positive [HIV(+)]), 42 healthy controls, and 38 asymptomatic HIV(+) controls were evaluated by enzyme-linked immunosorbent assays (ELISAs). The results were compared with Ab responses to the mycobacterial glycolipid cell wall antigen lipoarabinomannan (LAM) and to the proteins malate synthase (MS) and MPT51. We found that the main immunoglobulin (Ig) isotype response to polysaccharides was IgG, predominantly of subclass IgG2. IgG responses to AM were significantly higher for HIV(-) and HIV(+) TB cases than for controls (P, <0.0001 and <0.01, respectively); significantly higher for HIV(-) than for HIV(+) TB cases (P, <0.01); and significantly higher in sputum smear-positive than smear-negative patients in both HIV(-) and HIV(+) cases (P, 0.01 and 0.02, respectively). In both TB groups, titers of Ab to glucan were significantly lower than titers of Ab to AM (P, <0.0001). IgG responses to AM and MS or to AM and MPT51 did not correlate with each other in HIV(-) TB patients, while they correlated significantly in HIV(+) TB patients (P, 0.01 and 0.05, respectively). We conclude that Ab responses to AM could contribute to the serodiagnosis of TB, especially for HIV(-) TB patients. This study also provides new and important insights into the differences in the profiles of Abs to mycobacterial antigens between HIV(-) and HIV(+) TB patients.
STRUCTURES OF HYBRID SYNCHRONOUS MACHINES: PRINCIPLES AND COMPARISON (2000)

In this paper, we begin by discussing the main topologies of hybrid synchronous machines encountered in the literature. We then study an imbricated, hybrid excitation structure developed at LESiR laboratory. A finite element analysis is conducted and we conclude by presenting measurements that reveal the possibilities of flux-weakening.
Using Authenticated Encryption with Replay prOtection (AERO) in Datagram Transport Layer Security (DTLS) (2013)

Datagram Transport Layer Security (DTLS) is a communication security
protocol that is attractive for use in constrained environments, in
which it is important to minimize the data expansion added by the
security protocol, and to support multicast security . Authenticated
Encryption with Replay prOtection (AERO) is a cryptographic technique
that is well suited for use in DTLS, especially in these scenarios: it
has minimal data expansion, avoids the need to manage implicit state,
works well with multiple receivers and multiple senders, and provides
strong misuse resistance. This document describes how AERO can be used
in DTLS.
Applications of a Synthetic Neuraminidase Substrate (1973)

A rapid and precise assay for neuraminidase using 2-(3'-methoxyphenyl)-N-acetyl-alpha-neuraminic acid (MPN) is described. It is proposed that this substrate be used for the standardization of activity of neuraminidases from viral, bacterial, and mammalian sources. MPN is also used as a chromogenic substrate to localize influenza and parainfluenza virus foci in tissue culture. This technique permits the recovery of infective virus from these stained "plaques." It has also been demonstrated that immunoprecipitin lines containing neuraminidase complexes with antibody in the Ouchterlony test can be observed by a similar staining procedure. No enzyme inhibition occurs in the presence of anti-neuraminidase antibodies or concanavalin A when MPN is used as a substrate in contrast to the results with high-molecular-weight substrates such as fetuin.
MHC Class I Family Proteins Retard Systemic Lupus Erythematosus Autoimmunity and B Cell Lymphomagenesis (2011)

Dysregulation of the T cell-dependent Ab response can lead to numerous immunological disorders, ranging from systemic lupus erythematosus to B cell lymphomas. Cellular processes governed by MHC class II proteins play a major role in this response and its dysregulation. The extent to which processes controlled by the diverse family of MHC class I proteins impact such autoimmune and neoplastic disorders, however, is less clear. In this study, we genetically dissect the contributions of individual MHC class I family members and the pathological processes under their control in the systemic lupus erythematosus-like disease of BXSB.Yaa mice and B cell lymphomagenesis of SJL mice. This study reveals a powerful repressive regulatory axis comprised of MHC class I-dependent CD8(+) T cells and NK cells. These results indicate that the predominant role of the MHC class I protein family in such immunological disorders is to protect from more aggressive diseases.
Emerging effects of oxygen accumulation on orbital torque (2023)

Abstract The orbital angular momentum is an electron’s essential degree of freedom and provides an alternative opportunity for the further development of spintronics. Recent studies suggest orbital transport as a potential tool to realize practical and highly-efficient spin manipulation with diverse material classes. Nevertheless, utilization of the orbital transport remains a challenging issue considering that the orbital transport often bares distinctive properties to the spin transport. Here we study the role of oxygen atom accumulation on the orbital transport in CoFe/Cu/Al2O3 ultrathin structures. By varying the type of oxygen accumulation, we revealed that the gradient of the oxygen accumulation nearby the CoFe/Cu interface can be a crucial factor of the orbital transport, modulating the orbital torque by a factor of about ~3. Our finding will encourage to realize efficient and versatile utilization of orbital transport for nano-spintronic devices.
The Rab5 activator RME-6 is required for amyloid precursor protein endocytosis depending on the YTSI motif (2020)

Endocytosis of the amyloid precursor protein (APP) is critical for generation of β-amyloid, aggregating in Alzheimer's disease. APP endocytosis depending on the intracellular NPTY motif is well investigated, whereas involvement of the YTSI (also termed BaSS) motif remains controversial. Here, we show that APP lacking the YTSI motif (ΔYTSI) displays reduced localization to early endosomes and decreased internalization rates, similar to APP ΔNPTY. Additionally, we show that the YTSI-binding protein, PAT1a interacts with the Rab5 activator RME-6, as shown by several independent assays. Interestingly, knockdown of RME-6 decreased APP endocytosis, whereas overexpression increased the same. Similarly, APP ΔNPTY endocytosis was affected by PAT1a and RME-6 overexpression, whereas APP ΔYTSI internalization remained unchanged. Moreover, we could show that RME-6 mediated increase of APP endocytosis can be diminished upon knocking down PAT1a. Together, our data identify RME-6 as a novel player in APP endocytosis, involving the YTSI-binding protein PAT1a.
Phosphine‐Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation (2019)

The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small-molecule triggers that turn on proteins through a Staudinger reduction/self-immolation cascade with substantially improved kinetics and yields. We achieved this through site-specific incorporation of a new set of azidobenzyloxycarbonyl lysine derivatives in mammalian cells. This approach allowed us to activate proteins by adding a nontoxic, bioorthogonal phosphine trigger. We applied this methodology to control a post-translational modification (SUMOylation) in live cells, using native modification machinery. This work significantly improves the rate, yield, and tunability of the Staudinger reduction-based activation, paving the way for its application in other proteins and organisms.
GaN Substrate Technologies for Optical Devices (2013)

Large GaN single-crystal substrates with low dislocation density are the key materials for the commercial production of GaN-based laser diodes. We developed a new method to reduce the dislocations, named dislocation elimination by the epitaxial-growth with inverse-pyramidal pits (DEEP). A thick GaN film is epitaxially grown on a GaAs substrate with hydride vapor-phase epitaxy and then is separated from the GaAs substrate. The thick GaN layer grows with numerous large inverse-pyramidal pits. As the growth proceeds, dislocations in the GaN film are concentrated to the center of the pit and a wide area with low dislocation density is formed within the pit except the center area. To control the dislocation artificially, the position of the pits is fixed at a predetermined position by means of the selective growth of different polarity GaN film. This process was named as advanced DEEP (A-DEEP). GaN substrates with the A-DEEP method satisfied all the requirements for the violet laser diodes. We continued to develop new GaN substrates such as large-diameter c-plane substrates as well as nonpolar/semipolar GaN substrates. In particular, we overcame the green gap problem and developed the world's first true green laser diodes by selecting an optimal crystal plane.
Long-range third-harmonic generation in air using ultrashort intense laser pulses (2005)

The generation of a powerful third-harmonic pulse in atmospheric air has been controlled over long-distance propagation using divergent and negatively chirped fundamental pulses. The cofilamentation of the high-intensity fundamental and third-harmonic pulses was observed over long propagation distance using the Lidar technique. The high peak intensity and the extremely broad spectral content generated by both fundamental and third-harmonic pulses imply promising applications for atmospheric remote sensing of pollutants and bioaerosols.
Absence of MCP-induced Protein 1 Enhances Blood–Brain Barrier Breakdown after Experimental Stroke in Mice (2019)

Focal cerebral ischemia can cause blood-brain barrier (BBB) breakdown, which is implicated in neuroinflammation and progression of brain damage. Monocyte chemotactic protein 1-induced protein 1 (MCPIP1) is a newly identified zinc-finger protein that negatively regulates inflammatory signaling pathways. We aimed to evaluate the impact of genetic MCPIP1 deletion on BBB breakdown and expression of BBB-related matrix metalloproteinases (MMPs) and tight junction proteins after cerebral ischemia/reperfusion (I/R) using MCPIP1-deficient (MCPIP1<sup>-/-</sup>) mice. Transient middle cerebral artery occlusion was induced in the MCPIP1<sup>-/-</sup> mice and their wild-type littermates for 2 h followed by reperfusion for 24 h. The degree of BBB breakdown was evaluated by injection of fluorescein isothiocyanate (FITC)-dextran. Quantitative real-time polymerase chain reaction, western blot, and immunohistochemistry were performed to compare the expression of MMPs and claudin-5 and zonula occludens-1 (ZO-1). MCPIP1 deficiency in mice resulted in enhanced leakage of FITC-dextran, increased expression of MMP-9/3, and reduced expression of claudin-5 and ZO-1 in the brain compared to that seen in their wild-type littermates subjected to cerebral I/R. These results demonstrate that absence of MCPIP1 exacerbates cerebral I/R-induced BBB disruption by enhancing the expression of MMP-9/3 and the degradation of claudin-5 and ZO-1, providing novel insights into the mechanisms underlying BBB breakdown after cerebral ischemia/reperfusion.
Molecular Dynamics Study of the Nanoscale Proton Density Distribution at the Ionomer-Catalyst Interface (2020)

The proton density in the cathode catalyst layer is a crucial variable to define the local reaction conditions in and thereby determine the performance and lifetime of polymer electrolyte fuel cells. We present a molecular modeling study to examine the proton density distribution in a water-filled, slab-like pore. The slab is confined by two distinct boundaries, the first consisting of a platinum single-crystalline surface and the second being a thin and dense skin layer of proton-conducting ionomer. Classical molecular dynamics simulations serve as a valuable tool to rationalize the impact of the molecular structure and properties of the ionomer film as well as the adsorption and charging state of the metal surface on structure and properties of interfacial water and the spatial distribution of protons. Boundary conditions at the metal surface are obtained from explicit quantum mechanical simulations at the DFT level. The oxide coverage at the metal surface and the water layer thickness are considered as crucial parameters. Results of detailed structural analyses elucidate the impact of a structured layer of near-surface water molecules at the platinum surface on accumulating protons at the interface.
Methods for Systematic Identification of Membrane Proteins for Specific Capture of Cancer-Derived Extracellular Vesicles (2019)

Analysis of cancer-derived extracellular vesicles (EVs) in biofluids potentially provides a source of disease biomarkers. At present there is no procedure to systematically identify which antigens should be targeted to differentiate cancer-derived from normal host cell-derived EVs. Here, we propose a computational framework that integrates information about membrane proteins in tumors and normal tissues from databases: UniProt, The Cancer Genome Atlas, the Genotype-Tissue Expression Project, and the Human Protein Atlas. We developed two methods to assess capture of EVs from specific cell types. (1) We used palmitoylated fluorescent protein (palmtdTomato) to label tumor-derived EVs. Beads displaying antibodies of interest were incubated with conditioned medium from palmtdTomato-expressing cells. Bound EVs were quantified using flow cytometry. (2) We also showed that membrane-bound Gaussia luciferase allows the detection of cancer-derived EVs in blood of tumor-bearing animals. Our analytical and validation platform should be applicable to identify antigens on EVs from any tumor type.
Novel Ceramic/Camphene‐Based Co‐Extrusion for Highly Aligned Porous Alumina Ceramic Tubes (2012)

We herein propose a novel way of producing highly aligned porous alumina tubes by co‐extruding an initial feed rod, which comprised of a pure camphene core and a frozen alumina/camphene shell. This new and simple technique produced alumina tubes (~4.4 ± 0.1 mm in outer diameter) having uniform alumina walls (~1.1 ± 0.12 mm in thickness) with highly aligned pores, which were created by removing the extensively elongated camphene dendrites in the extruded alumina/camphene shell. Furthermore, the heat treatment of the extruded bodies at 33°C, which is close to the freezing point of the alumina/camphene slurry, led to a considerable increase in the size of the aligned pores formed in the alumina walls, from ~&lt;5 to ~54 μm with increasing heat‐treatment time from 0 to 6 h. The compressive strength also increased significantly from 21 ± 1.6 to 61 ± 11.6 MPa, which was attributed mainly to the achievement of well densified alumina walls.
The design of a contact-less energy transfer system for a people mover system (2002)

This paper describes a contactless power transfer system to provide intervention free battery charging to a specially designed low weight electric vehicle for use in an historic New Zealand national park. The noncontact feature of the ICPT (inductively coupled power transfer) system is significant in that the charging is transparent to the driver. When the driver stops at the loading platform, the charging unit automatically senses the vehicle and begins charging if required. Four charging bays (buried under the ground) are provided allowing opportunity charging throughout the day. This minimises the necessary on-board batteries, and therefore the vehicle weight, while still allowing the vehicles to be operated continuously.
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation (2015)

Single-cell RNA-sequencing data provide a unique view of transcriptome function; however, careful analysis is required in order to use single-cell RNA-sequencing measurements for this purpose. Technical variation must be considered in single-cell RNA-sequencing studies of expression variation. For a subset of genes, biological variability within each cell type appears to be regulated in order to perform dynamic functions, rather than solely molecular noise.
T-Cell Activation by Antigen-Loaded pH-Sensitive Hydrogel Particles in Vivo: The Effect of Particle Size (2008)

Polymeric carriers designed to encapsulate protein antigens have great potential for improving the efficacy of vaccines and immunotherapeutics for diseases such as cancer. We recently developed a carrier system based on polyacrylamide hydrogel microparticles cross-linked with acid-labile moieties. After being phagocytosed by antigen-presenting cells, the protein encapsulated within the carrier is released and processed for subsequent presentation of antigenic epitopes. To understand the impact of particle size on the activation of T-cells following uptake by antigen-presenting cells, particles with mean diameters of 3.5 microm and 35 nm encapsulating a model protein antigen were synthesized by emulsion and microemulsion based polymerization techniques, respectively. In vivo tests demonstrated that both sizes of particles were effective at stimulating the proliferation of T-cells and were capable of generating an antigen-specific cytotoxic T-cell response when coadministered with immunostimulatory DNA. Contrary to previous reports in the literature, our results suggest that there is no significant difference in the magnitude of T-cell activation for the two sizes of particles used in these experiments. This disparity in findings may be related to fundamental differences in material properties of the carriers used in these studies, such as the hydrophilicity of the polyacrylamide particles described here versus the hydrophobic nature of carriers investigated by other groups.
Quantitative Evaluation of Common Subexpression Elimination on Queue Machines (2008)

Queue computation model is a novel alternative for high performance architectures. Compiling for queue machines requires a different approach than compiling for traditional architectures. We have solved the problem of generating correct code with the queue compiler infrastructure. In this paper we introduce some problems encountered when optimizing code for queue machines. Common-subexpression elimination (CSE) is a widely used optimization to improve execution time. This paper makes a quantitative evaluation of how this optimization affects the characteristics of queue programs. We have found that in average, 28% of instructions are eliminated, and 15% of the critical path is reduced. We determine how enlarging the scope of compilation from expressions to basic blocks affects the distribution of offsetted instructions.
A Statistical Modeling based System for Blink Detection in Digital Cameras (2008)

In this paper we describe a system which uses statistical eye modeling to track the eyes and detect eyes blinking. The main challenge was to design an eye model robust to small variations of head pose and to extract the parameters of the model which encode the variation caused by blinking.
An English-Hindi Code-Mixed Corpus: Stance Annotation and Baseline System (2018)

Social media has become one of the main channels for peo- ple to communicate and share their views with the society. We can often detect from these views whether the person is in favor, against or neu- tral towards a given topic. These opinions from social media are very useful for various companies. We present a new dataset that consists of 3545 English-Hindi code-mixed tweets with opinion towards Demoneti- sation that was implemented in India in 2016 which was followed by a large countrywide debate. We present a baseline supervised classification system for stance detection developed using the same dataset that uses various machine learning techniques to achieve an accuracy of 58.7% on 10-fold cross validation.
Study of surface interactions for encapsulation of phase change memory materials (2022)

Switching of phase change memory (PCM) materials between crystalline and amorphous phase with electrical pulses and optical properties make it an important candidate for storage class memory and neuromorphic computing. However, PCM materials can be sensitive to air exposure during integration, therefore in-vacuo RIE and encapsulation is important to provide the required oxygen diffusion barrier. Low temperature SiN deposition can be used for low thermal budget integration schemes provided a good film conformality is achieved and damage or etching to the PCM elements is mitigated. In this work, ammonia- (NH3-) free, plasma enhanced chemical vapor deposition (PECVD) SiN films deposited at 40°C (microwave plasma) and 200°C (inductively coupled plasma), are compared and wet etch rates and optical properties are evaluated. NH3-free SiN films were deposited using SiH4, N2, H2, and Ar as source gases. Tuning the plasma parameters during encapsulation we observed simultaneous selective etching of GST and controlled SiN film deposition. Hydrogen and argon addition to the plasma mixture provided the main control knob for in-situ GST trimming during deposition, avoiding any type of elemental or structural damage to the GST films.