gebhart/patrepeval huggingface dataset:
Expression Changes and Novel Interaction Partners of Talin 1 in Effector Cells of Autoimmune Uveitis (2013)

Autoimmune uveitis is characterized by crossing of blood-retinal barrier (BRB) by autoaggressive immune cells. Equine recurrent uveitis (ERU) is a valuable spontaneous model for autoimmune uveitis and analyses of differentially expressed proteins in ERU unraveled changed protein clusters in target tissues and immune system. Healthy eyes are devoid of leukocytes. In ERU, however, leukocytes enter the inner eye and subsequently destroy it. Molecular mechanisms enabling cell migration through BRB still remain elusive. Previously, we detected decreased talin 1 expression in blood-derived granulocytes of ERU cases, linking the innate immune system to ERU. Because changes in leukocyte protein expression pattern may play a role in pathological abnormalities leading to migration ability, we aimed at identifying interactors of talin 1 in leukocytes with immunoprecipitation, followed by LC-MS/MS for candidate identification. This enabled us to identify CD90 (Thy1) as novel interactor of talin 1 besides several other interactors. In blood-derived granulocytes from healthy individuals, CD90 was highly abundant and significantly reduced in ERU, especially in effector cells. Connection between talin 1 and CD90 and their expression differences in inflammation is an interesting novel finding allowing deeper insight into immune response of innate immune system and granulocyte migration ability in this organ-specific autoimmune disease.
Supplementary Table S2 from Oral Iloprost Improves Endobronchial Dysplasia in Former Smokers (2023)

Supplementary Table S2 from Oral Iloprost Improves Endobronchial Dysplasia in Former Smokers
A CTL epitope on the circumsporozoite protein of P. yoelii. (1990)

Humans are infected with malaria by the bite of anophelene mosquitos carrying plasmodia sporozoites. These sporozoites pass quickly from the blood into hepatocytes, where they develop into mature liver-stage parasites over several days. The clinical stage of the illness begins only when the liver-stage parasites rupture into the bloodstream and erythrocytes are invaded. The pre-erythrocytic stages of malaria are inviting targets for vaccine development, because an effective immune response to these early stages would prevent symptomatic infections.
Analysis of the Torque Production Mechanism for Flux-Switching Permanent-Magnet Machines (2015)

This paper investigates the principles underlying torque production in a flux-switching permanent-magnet (FSPM) machine. Because the phase windings and permanent magnets (PMs) in FSPM machines are both located on the stator, the torque production mechanism is not the same as for a conventional PM synchronous machine. Spatial harmonic analysis is applied to examine the frequency components present in the electric and magnetic loading of the machine. Since torque is proportional to the product of the electric and magnetic loading, understanding the source of the principal harmonics in these waveforms yields powerful insights into the components that result in torque production. The analysis is first presented for a specific FSPM machine (12-slot/10-pole) and then extended to a general FSPM machine. The primary torque-producing harmonics in the air-gap flux density waveform are found to be the heterodyned harmonics of the magnetomotive force produced by the stator magnets and the air-gap permeance seen by the stator looking into the rotor. Analytical results are compared to results from finite-element analysis and exhibit good agreement.
Interlaboratory evaluation of methods to quantify skin sensitizing hydroperoxides potentially formed from linalool and limonene in perfumes (2017)

Abstract The fragrant terpenes limonene and linalool can form skin sensitizing hydroperoxides upon prolonged exposure to air. Recently, high frequencies of positive patch tests to oxidized linalool and limonene were reported from multiple dermatological centres. However, there is a lack of data indicating potential sources of consumer exposure to sensitizing doses of terpene hydroperoxides which explains this frequent contact allergy. Within the IDEA project (International Dialogue for the Evaluation of Allergens; http://ideaproject.info /), a taskforce was formed to drive analytical method development and evaluation. In an inter‐laboratory study in five laboratories, a method based on hydroperoxide reduction combined with GC–MS was tested for reproducibility. Blinded samples of commercial fine fragrances were spiked with four different hydroperoxides. In samples spiked with 100–200 μg/ml, an average recovery of 86–105% with a relative standard deviation between laboratories of 7.4–22% was found. In samples spiked with 20–50 μg/ml, the recovery was 85–91%. The reduction approach offers a transferable and reproducible method to indirectly detect low levels of hydroperoxides, at least in fine fragrances. Ideally, one would prefer to directly detect the parent hydroperoxide. Therefore the same samples were further tested with three LC‐based methods directly detecting the parent hydroperoxide. LC coupled to chemiluminescence, LC‐Q‐TOF‐MS or LC‐orbitrap‐MS were used. Results indicate that with specific gradients a separation of the four analytes and quantification in the fragrance matrix can be achieved. Results of this method evaluation study present a toolbox of methods to detect terpene hydroperoxides to further investigate consumer exposure.
Spatial Representations From Perception and Cognitive Mediation: The Case of Ultrasound. (2018)

Spatial representations can be derived not only by direct perception, but also through cognitive mediation. Conventional or ex-situ ultrasound displays, which displace imaged data to a remote screen, require both types of process. To determine the depth of a target hidden beneath a surface, ultrasound users must both perceive how deeply the ultrasound transducer indents the surface and interpret the on-screen image to visualize how deeply the target lies below the transducer. Combining these perceptual and cognitive depth components requires a spatial representation that has been called amodal. We report experiments measuring errors in perceptual and cognitively mediated depth estimates and show that these estimates can be concatenated (linked) without further error, providing evidence for an amodal representation. We further contrast conventional ultrasound with an in-situ display whereby an ultrasound image appears to float at the precise location being imaged, enabling the depth of a target to be directly perceived. The research has the potential to enhance ultrasound-guided surgical intervention.
Polyphenols from Korean prostrate spurge Euphorbia supina induce apoptosis through the Fas-associated extrinsic pathway and activation of ERK in human leukemic U937 cells (2016)

The Korean prostrate spurge Euphorbia supina (Euphorbiaceae family) has been used as a folk medicine in Korea against a variety of ailments such as bronchitis, hemorrhage, jaundice and multiple gastrointestinal diseases. Polyphenols from Korean E. supina (PES) which include quercetin and kaempferol derivatives have anticancer properties. Hence, we investigated the anticancer effects of PES on U937 human leukemic cells. Firstly, PES significantly inhibited the proliferation of U937 cells in a dose-dependent manner. PES induced accumulation of the sub-G1 DNA content (apoptotic cell population), apoptotic bodies and chromatin condensation and DNA fragmentation in the U937 cells. PES also induced activation of caspase-3, -8 and -9, subsequent cleavage of PARP, and significantly suppressed XIAP, cIAP-1 and cIAP-2 in a dose-dependent manner. Furthermore, PES activated Bid, and induced the loss of mitochondrial membrane potential (MMP, ΔΨm) along with upregulation of pro-apoptotic proteins (Bax and Bad), and downregulation of anti-apoptotic proteins (Bcl-2 and Bcl-xL) and cytochrome c release. The Fas receptor was upregulated by PES in a dose-dependent manner, suggesting that the extrinsic pathway was also involved in the PES-induced apoptosis. Moreover, the PES-induced apoptosis was at least in part associated with extracellular signal-regulated kinase (ERK) activation in the U937 human leukemic cells. This study provides evidence that PES may be useful in the treatment of leukemia.
Characterization of novel myelin components 3‐O‐acetyl‐sphingosine galactosylceramides by electrospray ionization Q‐TOF MS and MS/CID‐MS of Li+ adducts (2007)

Glycosphingolipids with R(f) values higher than those of monoglycosylceramides (MGCs) in normal phase HPTLC appear to be normal components of myelin. A series of such low polarity components, referred to as 'fast moving cerebrosides' (FMCs), have been isolated from rat brain, and two of these fractions (FMC-1 and FMC-2) were found to be novel derivatives of galactosylceramide (GalCer) exhibiting O-acetylation at the 3-hydroxy group of the sphingoid moiety, and incorporating either non-hydroxy or 2-hydroxy fatty-N-acylation (Dasgupta S, Levery SB, Hogan EL. J. Lipid Res. 2002; 43: 751-761). Similar to the parent compounds, the 3-O-acetyl-sphingoid derivatives exhibit considerable diversity with respect to fatty-N-acyl chain length, manifested by heterogeneous molecular ion (Li(+) adduct) profiles. However, a detailed analysis of the individual molecular variants ('lipoforms'), e.g. by tandem MS/CID-MS analysis, was not carried out. In addition, several other FMCs distinguished by even lower polarity (higher HPTLC R(f) values) were isolated but have remained uncharacterized. For this study, analysis of both the known and unknown FMC components was carried out by positive ion ESI-MS and MS/CID-MS of their Li(+) adducts on a Q-TOF mass spectrometer. Since a Q-TOF instrument has not yet been applied to MS of lithiated cerebrosides and FMCs, MS/CID-MS spectra of bovine brain GalCer (both types) and the previously characterized rat brain FMCs (FMC-1 and FMC-2), having 3-O-acetylation of the sphingoid, were systematically acquired and their fragmentation behavior compared. This was followed by systematic analysis of previously uncharacterized FMC fractions (FMC-3 through FMC-5/6/7). The GalCer and FMC components proved to be amenable to analysis by this technique, and the data confirm that the latter are all related 3-O-acetyl-sphingoid derivatives, with the higher R(f) components carrying additional O-acetyl modifications on the galactosyl residue, which further reduce their polarity. The utility of the technique, the structures of unknown FMCs, and their characteristic fragmentation patterns are described.
Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism (2018)

The Embden-Meyerhoff-Parnas (EMP) pathway, commonly known as glycolysis, represents the fundamental biochemical infrastructure for sugar catabolism in almost all organisms, as it provides key components for biosynthesis, energy metabolism, and global regulation. EMP-based metabolism synthesizes three-carbon (C3) metabolites before two-carbon (C2) metabolites and must emit one CO<sub>2</sub> in the synthesis of the C2 building block, acetyl-CoA, a precursor for many industrially important products. Using rational design, genome editing, and evolution, here we replaced the native glycolytic pathways in <i>Escherichia coli</i> with the previously designed nonoxidative glycolysis (NOG), which bypasses initial C3 formation and directly generates stoichiometric amounts of C2 metabolites. The resulting strain, which contains 11 gene overexpressions, 10 gene deletions by design, and more than 50 genomic mutations (including 3 global regulators) through evolution, grows aerobically in glucose minimal medium but can ferment anaerobically to products with nearly complete carbon conservation. We confirmed that the strain metabolizes glucose through NOG by <sup>13</sup>C tracer experiments. This redesigned <i>E. coli</i> strain represents a different approach for carbon catabolism and may serve as a useful platform for bioproduction.
Demonstration of Advanced EMI Models for Live-Site UXO Discrimination at Waikoloa, Hawaii (2015)

Abstract : This report describes in detail the procedures and approaches WRT Inc. team took to complete an Environmental Security Technology Certification Program (ESTCP)-funded live-site UXO demonstration study at the former Waikoloa Maneuver Area (WMA) in Waikoloa, Hawaii, under ESTCP Munitions Response Project MR-201227.
Metal–semiconductor junctions on p-type strained Si1−xGex layers (1996)

The electrical properties of Schottky junctions on high-quality p-type strained Si1−xGex layers have been studied for Ge fractions 0≤x≤0.24. A multicrystal high-resolution x-ray diffractometer was used to investigate the sample’s quality and the strain state and to accurately determine the Ge fraction in the fabricated devices. Several different metals, having a wide range of barrier heights, were used to reach conclusions on the variation of barrier height with the Ge content in the grown strained Si1−xGex layers. It has been found that the Schottky barrier height decreases with increasing Ge fraction in the Si1−xGex layer for the different metals investigated. The change in the barrier height with x has been found to be directly correlated to the valence band discontinuity in the Si/Si1−xGex heterojunction.
Numerical and experimental analysis of trench-assisted bend-insensitive multimode fibers (2013)

We numerically analyze the guided modes and leaky modes of bend-insensitive multimode fibers assisted with a deep refractive-index trench. The impact of the leaky modes on the transmission characteristics is clarified numerically and experimentally.
In situ tracking of defect healing and purification of single-wall carbon nanotubes with laser radiation by time-resolved Raman spectroscopy (2015)

Fine-tuned localised laser heating of pristine or mechanically dispersed (for composite processing) SWCNTs resulting in precision healing and purification.
Advancing proton minibeam radiation therapy: magnetically focussed proton minibeams at a clinical centre (2020)

Proton minibeam radiation therapy (pMBRT) is a novel therapeutic strategy that has proven to significantly increase dose tolerances and sparing of normal tissue. It uses very narrow proton beams (diameter ≤1 mm), roughly one order of magnitude smaller than state-of-the-art pencil beams. The current implementation of pMBRT with mechanical collimators is suboptimal as it is inflexible, decreases efficiency and produces additional secondary neutrons. As a potential solution, we explore in this article minibeam generation through magnetic focussing and investigate possibilities for the integration of such a technique at existing clinical centres. For this, a model of the pencil beam scanning (PBS) nozzle and beam at the Orsay Proton Therapy Centre was established and Monte Carlo simulations were performed to determine its focussing capabilities. Moreover, various modifications of the nozzle geometry were considered. It was found that the PBS nozzle in its current state is not suitable for magnetic minibeam generation. Instead, a new, optimised nozzle design has been proposed and conditions necessary for minibeam generation were benchmarked. In addition, dose simulations in a water phantom were performed which showed improved dose distributions compared to those obtained with mechanical collimators.
ChemInform Abstract: HINDERED ROTATION OF THE ISOPROPENYL GROUP IN SUBSTITUTED ISOPROPENYLCYCLOHEXANES AND IDENTIFICATION OF PREFERRED ROTAMERS BY NUCLEAR MAGNETIC RESONANCE. BENT BONDS MAY BE BETTER BONDS (1983)

Abstract Die sterische Hinderung der Rotation bei Isopropenyl‐cyclohexanen mit benachbarter Permethylierung, z.B. in (I)‐(III), wird untersucht, und Kotamere werden NMR‐spektroskopisch nachgewiesen.
MedLDA (2009)

Supervised topic models utilize document's side information for discovering predictive low dimensional representations of documents; and existing models apply likelihood-based estimation. In this paper, we present a max-margin supervised topic model for both continuous and categorical response variables. Our approach, the maximum entropy discrimination latent Dirichlet allocation (MedLDA), utilizes the max-margin principle to train supervised topic models and estimate predictive topic representations that are arguably more suitable for prediction. We develop efficient variational methods for posterior inference and demonstrate qualitatively and quantitatively the advantages of MedLDA over likelihood-based topic models on movie review and 20 Newsgroups data sets.
First demonstration of nanosecond photon timing in the near-infrared with InGaAs/InP detectors (1993)

We show that SAGM InGaAs/InP Avalanche Photodiodes, cooled at 200K, detect the arrival time of single photons with nanosecond resolution. Hole trapping at the heterointerface impairs the performance of presently available devices. However, a proper design of the structure for low temperature operation is expected to improve their timing performance well below the nanosecond limit.
Real-time kinematic positioning with GPS and GLONASS (2016)

Recently, low-cost dual constellation receivers with simultaneous tracking of GPS and GLONASS satellites and raw carrier phase output have become available. This enables a faster and more reliable ambiguity fixing especially in areas with limited satellite visibility, e.g. street canyons. In this paper, we present a combined GPS/GLONASS RTK positioning with code multipath estimation for low-cost receivers. We use double difference measurements and take the integer property of both the GPS and GLONASS ambiguities into account. For GLONASS, this requires a reparametrization of the double difference ambiguities and a subsequent parameter mapping. The re-parameterized measurement models are used for ambiguity fixing with real measurements from two low-cost dual constellation GNSS receivers. We obtain residuals of a few centimeters for both GPS and GLONASS fixed carrier phases.
KeyPose: Multi-View 3D Labeling and Keypoint Estimation for Transparent Objects (2019)

Estimating the 3D pose of desktop objects is crucial for applications such as robotic manipulation. Many existing approaches to this problem require a depth map of the object for both training and prediction, which restricts them to opaque, lambertian objects that produce good returns in an RGBD sensor. In this paper we forgo using a depth sensor in favor of raw stereo input. We address two problems: first, we establish an easy method for capturing and labeling 3D keypoints on desktop objects with an RGB camera; and second, we develop a deep neural network, called $KeyPose$, that learns to accurately predict object poses using 3D keypoints, from stereo input, and works even for transparent objects. To evaluate the performance of our method, we create a dataset of 15 clear objects in five classes, with 48K 3D-keypoint labeled images. We train both instance and category models, and show generalization to new textures, poses, and objects. KeyPose surpasses state-of-the-art performance in 3D pose estimation on this dataset by factors of 1.5 to 3.5, even in cases where the competing method is provided with ground-truth depth. Stereo input is essential for this performance as it improves results compared to using monocular input by a factor of 2. We will release a public version of the data capture and labeling pipeline, the transparent object database, and the KeyPose models and evaluation code. Project website: https://sites.google.com/corp/view/keypose.
The cyber-physical bike (2011)

To improve road cycling safety, we present an approach that augments bicycles with video processing and computational capabilities. This Cyber-Physical bicycle system continuously monitors the environment behind the biker, automatically detects rear-approaching vehicles, and alerts the biker prior to the approach. In this paper, we (i) identify biker safety as a problem that can be addressed using mobile video sensing and processing, (ii) present the design of a Cyber-Physical bicycle system, which applies video processing techniques to perform automated vehicle detection, and (iii) demonstrate the feasibility of this system through the evaluation of our prototype implementation. Early results show that our approach operates with good accuracy at normal frame rates, and can perform detection in real time with reduced frame rates.
Parameter identification of a semi-flexible kinematic model for serial manipulators (1996)

SUMMARY Structural and control flexibilities affect the absolute precision of serial manipulators. A semi-flexible kinematic model is developed, to improve the absolute static precision. It expands the solid body model by incorporating a spring effect for each joint and a beam effect for each link. The identifiability of the added parameters and the effect of measurement noise are explored on a R4 robot. It requires efforts and pose errors to be known in the tool frame only. Simulation results show that identification of some of the parameters is sensitive to measurement noise on forces and pose. In fact, joint flexibility displacement and beam flexion that occur in the same plane are difficult to dissociate in noisy condition. However, a subset of the original parameters can be defined leading to a model that can be more accurately identified when measurement noise is present. In simulation, precompensation is used in an inverse semi-flexible model that results in a 98% decrease of pose error compared to the rigid body inverse geometric model.
Roadmapping the Next Generation of Silicon Photonics (2023)

Silicon photonics has developed into a mainstream technology driven by advances in optical communications. The current generation has led to a proliferation of integrated photonic devices from thousands to millions - mainly in the form of communication transceivers for data centers. Products in many exciting applications, such as sensing and computing, are around the corner. What will it take to increase the proliferation of silicon photonics from millions to billions of units shipped? What will the next generation of silicon photonics look like? What are the common threads in the integration and fabrication bottlenecks that silicon photonic applications face, and which emerging technologies can solve them? This perspective article is an attempt to answer such questions. We chart the generational trends in silicon photonics technology, drawing parallels from the generational definitions of CMOS technology. We identify the crucial challenges that must be solved to make giant strides in CMOS-foundry-compatible devices, circuits, integration, and packaging. We identify challenges critical to the next generation of systems and applications - in communication, signal processing, and sensing. By identifying and summarizing such challenges and opportunities, we aim to stimulate further research on devices, circuits, and systems for the silicon photonics ecosystem.