gebhart/patrepeval huggingface dataset:
Identification and validation of ecto-5' nucleotidase as an immunotherapeutic target in multiple myeloma (2022)

Interaction of plasmacytoid dendritic cells (pDCs) with multiple myeloma (MM) cells, T- or NK-effector cells in the bone marrow (BM) microenvironment induces tumor cell growth, as well as inhibits innate and adaptive immune responses. Defining pDC-MM interaction-triggered immunosuppressive mechanism(s) will enable design of interventional therapies to augment anti-MM immunity. In the present study, we show that pDC-MM interactions induce metabolic enzyme Ecto-5' Nucleotidase/CD73 in both pDCs and MM cells. Gene expression database from MM patients showed that CD73 levels inversely correlate with overall survival. Using our pDC-MM coculture models, we found that blockade of CD73 with anti-CD73 Abs: decreases adenosine levels; activates MM patient pDCs; triggers cytotoxic T lymphocytes (CTL) activity against autologous patient MM cells. Combination of anti-CD73 Abs and an immune-stimulating agent TLR-7 agonist enhances autologous MM-specific CD8<sup>+</sup> CTL activity. Taken together, our preclinical data suggest that the therapeutic targeting of CD73, alone or in combination with TLR-7 agonist, represents a promising novel strategy to restore host anti-MM immunity.
Synthesis of Multicyclic Pyridine and Quinoline Derivatives via Intramolecular C−H Bond Functionalization (2010)

An efficient method is reported for the preparation of multicyclic pyridines and quinolines by a rhodium-catalyzed intramolecular C-H bond functionalization process. The method shows good scope for branched and unbranched alkyl substituents on the pyridine ring and at the R position of the tethered alkene group. Starting materials capable of undergoing olefin isomerization to provide terminal 1,1-disubstituted alkenes also proved to be effective substrates.
Polyglutamine-related aggregates serve as a potent antigen source for cross presentation by dendritic cells (2019)

Abstract Protective MHC-I dependent immune responses require an overlap between repertoires of proteins directly presented on target cells and cross-presented by professional antigen presenting cells (APC), specifically dendritic cells (DCs). How stable proteins that rely on DRiPs for direct presentation are captured for cell-to-cell transfer remains enigmatic. Here we address this issue using a combination of in vitro and in vivo approaches involving stable and unstable versions of ovalbumin model antigens displaying DRiP-dependent and -independent antigen presentation, respectively. Apoptosis, but not necrosis of donor cells was found associated with robust p62-dependent global protein aggregate formation and captured stable proteins permissive for DC cross-presentation. Potency of aggregates to serve as antigen source was directly demonstrated using polyglutamine-equipped model substrates. Collectively, our data implicate global protein aggregation in apoptotic cells as a mechanism that ensures the overlap between MHC-I epitopes presented directly or cross-presented by APC and demonstrate the unusual ability of DC to process stable protein aggregates. Summary Protective T cell immunity relies on the overlap of the antigen repertoire expressed by cells and the repertoire presented by dendritic cells that are required to trigger naïve T cells. We suggest a mechanism that contributes to ensure this antigenic overlap. Our findings demonstrate that upon apoptosis stable proteins are aggregated in p62-dependent pathway and that dendritic cells are capable to efficiently process these aggregates to retrieve antigens for T cell stimulation.
Four-Stage Cascaded Predictive Control for Zero-Sequence Current Suppression of Open-End Winding Induction Motor (2020)

A four-stage cascaded predictive control method is proposed in this paper to suppress the zero-sequence current (ZSC) of the open-end winding induction motor (OEWIM). ZSC is generated when a single DC source feeds two inverters of an OEWIM. Circulation of ZSC in the motor windings increases the torque ripple and deteriorates the stator current waveform. The proposed method eliminates the ZSC by cascaded control of two inverters. By using voltage vectors of one inverter, the first and second stages control the torque and stator flux, respectively. Voltage vectors of the other inverter are used in third and fourth stages to eliminate ZSC beside the controlling stator flux and torque. In comparison to the conventional predictive control of OEWIM, this strategy won't impose an excessive burden on the control system. Moreover, the weighting factor of the stator flux is removed from the cost function. A comparison is made between the proposed strategy and the conventional method in simulations. Results show the superior performance of the proposed cascaded predictive control.
Decrypting Strong and Weak Single-Walled Carbon Nanotubes Interactions with Mitochondrial Voltage-Dependent Anion Channels Using Molecular Docking and Perturbation Theory (2017)

The current molecular docking study provided the Free Energy of Binding (FEB) for the interaction (nanotoxicity) between VDAC mitochondrial channels of three species (VDAC1-Mus musculus, VDAC1-Homo sapiens, VDAC2-Danio rerio) with SWCNT-H, SWCNT-OH, SWCNT-COOH carbon nanotubes. The general results showed that the FEB values were statistically more negative (p < 0.05) in the following order: (SWCNT-VDAC2-Danio rerio) > (SWCNT-VDAC1-Mus musculus) > (SWCNT-VDAC1-Homo sapiens) > (ATP-VDAC). More negative FEB values for SWCNT-COOH and OH were found in VDAC2-Danio rerio when compared with VDAC1-Mus musculus and VDAC1-Homo sapiens (p < 0.05). In addition, a significant correlation (0.66 > r<sup>2</sup> > 0.97) was observed between n-Hamada index and VDAC nanotoxicity (or FEB) for the zigzag topologies of SWCNT-COOH and SWCNT-OH. Predictive Nanoparticles-Quantitative-Structure Binding-Relationship models (nano-QSBR) for strong and weak SWCNT-VDAC docking interactions were performed using Perturbation Theory, regression and classification models. Thus, 405 SWCNT-VDAC interactions were predicted using a nano-PT-QSBR classifications model with high accuracy, specificity, and sensitivity (73-98%) in training and validation series, and a maximum AUROC value of 0.978. In addition, the best regression model was obtained with Random Forest (R<sup>2</sup> of 0.833, RMSE of 0.0844), suggesting an excellent potential to predict SWCNT-VDAC channel nanotoxicity. All study data are available at https://doi.org/10.6084/m9.figshare.4802320.v2 .
Omega-bianisotropic Wire-Loop Huygens’ Metasurface for Wide-Angle Refraction (2019)

Huygens' metasurfaces allow the arbitrary control of electromagnetic waves by utilizing both electric and magnetic currents. These electrically thin structures interact with incident electromagnetic waves on a sub-wavelength scale to produce desired wave effects. To realize Huygens' metasurfaces, different unit cell topologies such as the wire-loop or the stacked-layer configurations can be utilized. In recent years, Omega-bianisotropic Huygens' metasurfaces have been demonstrated utilizing asymmetric stacked-layer unit cells, allowing the realization of reflectionless transformations. However, an Omega-bianisotropic version of the wire-loop unit cell has yet to be demonstrated for modulated Huygens' metasurfaces. In this paper, the design and fullwave simulation results of Omega-bianisotropic Huygens' wire-loop metasurfaces for reflectionless wide-angle refraction from normal incidence to 71.8° for both transverse-electric and transverse-magnetic polarizations centered at 20GHz are presented.
Perturbational Analysis of the Generation of Ghost Pulses in 40 Gbit/s Fibre-Optic Communication Systems (2001)

The nonlinear generation and the dynamics of ghost pulses in communication systems using dispersion management are investigated. A perturbational approach is used to analyse the limits set by ghost pulses in realistic systems.
MP26-12 TRIFECTA OUTCOMES OF PARTIAL NEPHRECTOMY IN PATIENTS OVER 75 YEARS OLD: A MULTI-INSTITUTIONAL STUDY: ANALYSIS OF THE RENAL SURGERY IN ELDERLY (RESURGE) GROUP (2018)

CONCLUSIONS: Nanoparticle directed MR/US fusion-guided transperineal focal photothermal ablation for PCa is a safe and feasible treatment modality. Further studies evaluating oncologic efficacy and functional outcomes are ongoing.
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence (2017)

It has recently been shown that the organization of genes in eukaryotic genomes, and specifically in 3D, is strongly related to gene expression and function and partially conserved between organisms. However, previous studies of 3D genomic organization analyzed each organism independently from others. Here, we propose an approach for unified inter-organismal analysis of gene organization based on a network representation of Hi-C data. We define and detect four classes of spatially co-evolving orthologous modules (SCOMs), i.e. gene families that co-evolve in their 3D organization, based on patterns of divergence and conservation of distances. We demonstrate our methodology on Hi-C data from Saccharomyces cerevisiae and Schizosaccharomyces pombe, and identify, among others, modules relating to RNA splicing machinery and chromatin silencing by small RNA which are central to S. pombe's lifestyle. Our results emphasize the importance of 3D genomic organization in eukaryotes and suggest that the evolutionary mechanisms that shape gene organization affect the organism fitness and phenotypes. The proposed algorithms can be utilized in future studies of genome evolution and comparative analysis of spatial genomic organization in different tissues, conditions and single cells.
Assessment of Polishing-Related Surface Damage in Silicon Carbide (2002)

The subsurface damage generated by the polishing of silicon carbide crystals was investigated by measuring dislocation densities in sublimation grown SiC layers and through the use of high-resolution X-ray diffraction. Physical vapor transport growth on silicon carbide seeds, with a typical polishing finish using 1 μm diamond paste, leads to the nucleation of threading edge dislocations of density on the order of and threading screw dislocations of density on the order of Chemical mechanical polishing lowered the dislocation density by four orders of magnitude for threading screw dislocations and two orders of magnitude for threading edge dislocations. Controlled high temperature hydrogen etching was used to determine the depth of damage produced by mechanical polishing and it was found to be Diffuse scattering from mechanically polished, chemical mechanically polished, and hydrogen etched SiC crystals were quantified by triple axis high-resolution X-ray diffraction. A consistent trend of decreasing diffuse scattering intensity was observed in mechanically polished, chemical mechanically polished, and hydrogen etched surfaces. Root mean squared (rms) roughness measurements of the surface finishes, obtained with atomic force microscopy, were in agreement with the high-resolution X-ray diffraction results. The mechanically polished surfaces had an rms roughness that was two to three times larger than the chemical mechanically polished surfaces. © 2002 The Electrochemical Society. All rights reserved.
Meldrum's acid derivatives and chiral ammonium phenoxides : a useful combination for asymmetric synthesis (2016)

International audience
Finding Fallen Objects Via Asynchronous Audio-Visual Integration (2022)

The way an object looks and sounds provide complementary reflections of its physical properties. In many settings cues from vision and audition arrive asynchronously but must be integrated, as when we hear an object dropped on the floor and then must find it. In this paper, we introduce a setting in which to study multi-modal object localization in 3D virtual environments. An object is dropped somewhere in a room. An embodied robot agent, equipped with a camera and microphone, must determine what object has been dropped -- and where -- by combining audio and visual signals with knowledge of the underlying physics. To study this problem, we have generated a large-scale dataset -- the Fallen Objects dataset -- that includes 8000 instances of 30 physical object categories in 64 rooms. The dataset uses the ThreeDWorld platform which can simulate physics-based impact sounds and complex physical interactions between objects in a photorealistic setting. As a first step toward addressing this challenge, we develop a set of embodied agent baselines, based on imitation learning, reinforcement learning, and modular planning, and perform an in-depth analysis of the challenge of this new task.
Multiple peptide synthesis using a single support (MPS3) (1990)

An automated multiple peptide synthesis method to synthesize, cleave, and purify several peptides simultaneously in a single batch has been developed. The technique is based on the synthesis of multiple peptides on a single solid phase support and is easily adapted to manual or to automated methods. The approach relies on coupling of amino acid mixtures to the resin and it has been found that DCC/HOBt gives the best coupling performance. Fast Atom Bombardment Mass Spectrometry (FAB-MS) was used to rapidly and efficiently identify the peptides in each synthetic mixture which significantly assisted the purification process by HPLC. The method has been successfully applied to the synthesis of magainin 2 and angiotensinogen peptides.
Sediment Production and Evolution of Proterozoic Carbonate Platforms: ABSTRACT (1987)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Investigations on the structural, optical and electronic properties of Nd doped ZnO thin films (2009)

We report the synthesis and characterization of Nd doped ZnO thin films grown on Si (1 0 0) substrates by the spray pyrolysis method. The surface morphology of these thin films was investigated by scanning electron microscopy and shows the presence of randomly distributed structures of nanorods. Grazing angle x-ray diffraction studies confirm that the doped Nd ions occupied Zn sites and these samples exhibited a wurtzite hexagonal-like crystal structure similar to that of the parent compound, ZnO. The micro-photoluminescence measurement shows a decrease in the near band edge position with Nd doping in the ZnO matrix due to the impurity levels. The near-edge x-ray absorption fine structure (NEXAFS) measurements at the O K edge clearly exhibit a pre-edge spectral feature which evolves with Nd doping, suggesting incorporation of more charge carriers in the ZnO system and the presence of strong hybridization between O 2p‐Nd 5d orbitals. The Nd M5 edge NEXAFS spectra reveal that the Nd ions are in the trivalent state. (Some figures in this article are in colour only in the electronic version)
H/sup infinity /-optimal control for singularly perturbed systems. II. Imperfect state measurements (2005)

The authors study H/sup infinity /-optimal control of singularly perturbed linear systems under general imperfect state measurements using infinite-horizon formulations. Using a differential game theoretic approach, they first show that, as the singular perturbation parameter in approaches zero, the optimal disturbance attenuation level for the full-order system under a quadratic performance index converges to the maximum of the optimal disturbance attenuation levels for the slow and fast subsystems under appropriate slow and fast quadratic cost functions. Then, they construct a controller based on the slow subsystem only, and obtain conditions under which it delivers a desired performance level even though the fast dynamics have been completely neglected. The ultimate performance level achieved by this slow controller can be uniformly improved by a composite controller that uses some feedback from the output of the fast subsystem. The authors construct one such controller, using a two-step sequential procedure, which uses static feedback from the fast output and dynamic feedback from an appropriate slow output, each obtained by solving appropriate in -independent lower-dimensional H/sup infinity /-optimal control problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Constraining Attacker Capabilities Through Actuator Saturation (2018)

For LTI control systems, we provide mathematical tools - in terms of Linear Matrix Inequalities - for computing outer ellipsoidal bounds on the reachable sets that attacks can induce in the system when they are subject to the physical limits of the actuators. Next, for a given set of dangerous states, states that (if reached) compromise the integrity or safe operation of the system, we provide tools for designing new artificial limits on the actuators (smaller than their physical bounds) such that the new ellipsoidal bounds (and thus the new reachable sets) are as large as possible (in terms of volume) while guaranteeing that the dangerous states are not reachable. This guarantees that the new bounds cut as little as possible from the original reachable set to minimize the loss of system performance. Computer simulations using a platoon of vehicles are presented to illustrate the performance of our tools.
Universal scattering with general dispersion relations (2022)

Many synthetic quantum systems allow particles to have dispersion relations that are neither linear nor quadratic functions. Here, we explore single-particle scattering in general spatial dimension $D\ensuremath{\ge}1$ when the density of states diverges at a specific energy. To illustrate the underlying principles in an experimentally relevant setting, we focus on waveguide quantum electrodynamics (QED) problems (i.e., $D=1$) with dispersion relation $\ensuremath{\epsilon}(k)=\ifmmode\pm\else\textpm\fi{}|d|{k}^{m}$, where $m\ensuremath{\ge}2$ is an integer. For a large class of these problems for any positive integer $m$, we rigorously prove that when there are no bright zero-energy eigenstates, the $S$ matrix evaluated at an energy $E\ensuremath{\rightarrow}0$ converges to a universal limit that is only dependent on $m$. We also give a generalization of a key index theorem in quantum scattering theory known as Levinson's theorem---which relates the scattering phases to the number of bound states---to waveguide QED scattering for these more general dispersion relations. We then extend these results to general integer dimensions $D\ensuremath{\ge}1$, dispersion relations $\ensuremath{\epsilon}(\mathbit{k})={|\mathbit{k}|}^{a}$ for a $D$-dimensional momentum vector $\mathbit{k}$ with any real positive $a$, and separable potential scattering.
How interesting images are: An atypicality approach for social networks (2016)

With the exponential growth in information, “Big Data,” a key question is what to do with this information. A classic possibility is to characterize it through statistics. The perspective in this paper is the opposite, namely that most of the value in the information is in the parts that deviates from the average, that are unusual, atypical. Think of art: The valuable paintings or writings are those that deviate from the norms, that are atypical. With the same perspective think of social networks: Flickr is an example that has a rating for images based on how interesting they are. In previous works, researchers introduced algorithms to find the interesting images based on human psychological taste; but in this paper, we are proposing a new method to rate an image based on their level of interestingness using atypicality, in which interestingness is equivalent to having atypical structure. The paper first discusses what exactly should be understood by “atypical.” It has to be a well defined theoretical concept corresponding to some intuitive idea of atypicality, which when applied gives useful results. This is followed by applying the notion of atypicality to the general discrete scenario with finite alphabet and then putting it in to the framework of the quantized wavelet image coding. Finally our proposed algorithm is applied on Labeled Faces in the Wild (LFW) database with 13,233 images in order to find the interesting ones.
Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm (2009)

This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes.
Risk Aversion as Attitude towards Probabilities: A Paradox (2011)

Theories of decision under risk that challenge expected utility theory model risk attitudes at least partly with transformation of probabilities. We explain how attributing risk aversion (partly or wholly) to attitude towards probabilities, can produce extreme probability distortions that imply paradoxical risk aversion.
Physics based modeling for time-frequency damage classification (2008)

We have recently proposed a method for classifying waveforms from healthy and damaged structures in a structural health monitoring framework. This method is based on the use of hidden Markov models with preselected feature vectors obtained from the time-frequency based matching pursuit decomposition. In order to investigate the performance of the classifier for different signal-to-noise ratios (SNR), we simulate the response of a lug joint sample with different crack lengths using finite element modeling (FEM). Unlike experimental noisy data, the modeled data is noise free. As a result, different levels of noise can be added to the modeled data in order to obtain the true performance of the classifier under additive white Gaussian noise. We use the finite element package ABAQUS to simulate a lug joint sample with different crack lengths and piezoelectric sensor signals. A mesoscale internal state variable damage model defines the progressive damage and is incorporated in the macroscale model. We furthermore use a hybrid method (boundary element-finite element method) to model wave reflection as well as mode conversion of the Lamb waves from the free edges and scattering of the waves from the internal defects. The hybrid method simplifies the modeling problem and provides better performance in the analysis of high stress gradient problems.
Transient collateral augmentation during coronary arterial spasm associated with ST-segment depression. (1983)

To examine the possible existence of collateral circulation during coronary artery spasm, we attempted to visualize the transient appearance of collateral vessels that could serve to salvage otherwise jeopardized ischemic areas. In three patients with vasospastic angina, total spastic obstruction of a major coronary artery was associated with transient collateral augmentation, which was supplied by the nonspastic artery during anginal period associated with ST-segment depression. These collateral vessels disappeared when the angina and ST changes resolved after nitroglycerin administration. These findings suggest that the collateral blood supply could transiently occur through preexisting vessels to perfuse the ischemic area during coronary artery spasm and that such collateral flow could have a role in preventing transmural myocardial ischemia, resulting in a lesser degree of ischemia associated with ST-segment depression.