gebhart/patrepeval huggingface dataset:
Differential Flatness and Absolute Equivalence of Nonlinear Control Systems (1998)

This paper presents a formulation of differential flatness---a concept originally introduced by Fliess, Levine, Martin, and Rouchon---in terms of absolute equivalence between exterior differential systems. Systems that are differentially flat have several useful properties that can be exploited to generate effective control strategies for nonlinear systems. The original definition of flatness was given in the context of differential algebra and required that all mappings be meromorphic functions. The formulation of flatness presented here does not require any algebraic structure and allows one to use tools from exterior differential systems to help characterize differentially flat systems. In particular, it is shown that, under regularity assumptions and in the case of single input control systems (i.e., codimension 2 Pfaffian systems), a system is differentially flat if and only if it is feedback linearizable via static state feedback. In higher codimensions our approach does not allow one to prove that feedback linearizability about an equilibrium point and flatness are equivalent: one must be careful with the role of time as well as the use of prolongations that may not be realizable as dynamic feedback in a control setting. Applications of differential flatness to nonlinear control systems and open questions are also discussed.
Fluorous Techniques for the Synthesis of Organic Molecules: A Unified Strategy for Reaction and Separation (2000)

Methods for workup and purification of organic reaction mixtures are beginning to change as synthesis and separation merge forces. Highly fluorinated, or fluorous, molecules offer a number of attractive features in both traditional and parallel synthesis venues.
Simulating execution time variations in Matlab/Simulink (2017)

Software-induced delays have a significant impact on real-time control system performance. While in extreme cases, jitter caused by execution time variations or start-time delays may compromise stability, such effects are often ignored in model-based approaches and simulations. We address this issue and discuss a Simulink block with a fundamentally new semantics that is used to encapsulate control functions as software tasks. It is particularly suited to model and observe software delays in complex control functions within software-in-the-loop (SIL) simulations. For this purpose, the controller source code is associated with platform-specific execution time information, which we assume to be available. We detail a synchronization mechanism between Simulink and such time-annotated task blocks implementing the control laws. It allows us to perform SIL simulations where controllers execute for a finite amount of simulation time and span multiple simulation steps at which they may interact with other controllers or the plant.
Requirements for energy based constitutive modeling in tire mechanics (1995)

The history, requirements, and theoretical basis of a new energy based constitutive model for (rubber) material elasticity, hysteresis, and failure are presented. Energy based elasticity is handled by many constitutive models, both in one dimension and in three dimensions. Conversion of mechanical energy to heat can be modeled with viscoelasticity or as structural hysteresis. We are seeking unification of elasticity, hysteresis, and failure mechanisms such as fatigue and wear. An energy state characterization for failure criteria of (rubber) materials may provide this unification and also help explain the interaction of temperature effects with failure mechanisms which are described as creation of growth of internal crack surface. Improved structural modeling of tires with FEM should result from such a unified constitutive theory. The theory will also guide experimental work and should enable better interpretation of the results of computational stress analyses.
Structure of the Complex of Bovine Pancreatic Phospholipase A2 with a Transition-State Analogue (1998)

The 1.89 A resolution structure of the complex of bovine pancreatic phospholipase A2 (PLA2) with the transition-state analogue L-1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine (TSA) has been determined. The crystal of the complex is trigonal, space group P3121, a = b = 46.58 and c = 102.91 A and isomorphous to the native recombinant wild type (WT). The structure was refined to a final crystallographic R value of 18.0% including 957 protein atoms, 88 water molecules, one calcium ion and all 31 non-H atoms of the inhibitor at 1.89 A resolution. In all, 7 726 reflections [F>2sigma(F)] were used between 8.0 and 1.89 A resolution. The inhibitor is deeply locked into the active-site cleft and coordinates to the calcium ion by displacing the two water molecules in the calcium pentagonal bipyramid by the anionic O atoms of the phosphate and phosphonate group. The hydroxyl group of Tyr69 hydrogen bonds to the second anionic O atom of the phosphate group while that of the phosphonate group replaces the third water, 'catalytic' water, which forms a hydrogen bond to Ndelta1 of His48. The fourth water which also shares Ndelta1 of His48 is displaced by the steric hinderance of the inhibitor. The fifth conserved structural water is still present in the active site and forms a network of hydrogen bonds with the surrounding residues. The structure is compared to the other known TSA-PLA2 complexes.
Low-complexity analytical approximations of switching frequency harmonics of 3-phase N-level voltage-source PWM converters (2014)

In this paper, analytical calculations of the switching frequency harmonics of PWM-controlled 3-phase voltage-source DC/AC power converters are presented. Detailed knowledge of the modulation-dependent spectra of such systems is highly valuable for the EMI filter design and the estimation of the high-frequency losses in the filter components and the load. The paper presents a formula for the calculation of the switching frequency harmonics which is simple and highly versatile. It can be applied to converters with arbitrary numbers of voltage levels N and in combination with a broad variety of modulation signals. All calculations are verified by means of simulations and show a high accuracy over a wide range of input parameters. Finally, an EMI filter design example demonstrates the practical application and benefits of the derived formula. The MATLAB code used for the calculations is provided at the end of the paper.
MON-019 BETA-3-INTEGRIN STAINING IN KIDNEY BIOPSY AND CORRELATION WITH RESPONSE TO CALCINEURIN INHIBITORS IN STEROID RESISTANT NEPHROTIC SYNDROME (2019)

Steroid-resistant nephrotic syndrome (SRNS) is difficult to treat and carries a high risk of progression to chronic kidney disease (CKD). Calcineurin inhibitors (CNIs) are preferentially used in the treatment of SRNS. Variable response to treatment, the risk of nephrotoxicity and high rates of relapse on stopping treatment are major concerns with CNIs. Urokinase-type Plasminogen Activator Receptor (uPAR) – β3 integrin signaling is involved in the calcineurin-nuclear factor of activated T cells (NFAT) induced podocyte injury and hence the antiproteinuric effect of CNIs may be partially attributed to its inhibition of uPAR-β3 integrin signaling axis in podocytes.
Optimum schemes for wavefront sensorless adaptive optics in microscopy (2009)

In adaptive microscope systems, it is often desirable to dispense with the wavefront sensor and perform aberration correction through optimisation an appropriate quality metric, such as image brightness or sharpness. A sequence of trial aberrations is applied to the adaptive element and the metric values are calculated. The optimum aberration correction is derived from these measurements. An important choice in the design of these correction schemes is the modal aberration expansion. This choice may depend upon several factors, such as the deformable mirror, the optimisation metric, the aberration statistics or the image properties. We discuss these factors with particular reference to microscope imaging.
Superresolution Effects in Broadband Antenna Arrays (1990)

The problem of finding the angular 3-dB beamwidth for a wideband Griffiths-Jim adaptive beamformer is discussed. Approximate analytic expressions are presented and their relation to the Cramer-Rao bound (CRB) is considered. Results on the CRB in DOA (director of arrival) estimation for a sinusoidal signal are extended to narrowband and broadband signals, together with simple interpretations of their behavior. Superresolution results with five-element array for three target signal bandwidths (400-2000, 800-1600, and 1120-1280 Hz) are presented.
Deep Natural Language Processing for LinkedIn Search Systems (2021)

Many search systems work with large amounts of natural language data, e.g., search queries, user profiles and documents, where deep learning based natural language processing techniques (deep NLP) can be of great help. In this paper, we introduce a comprehensive study of applying deep NLP techniques to five representative tasks in search engines. Through the model design and experiments of the five tasks, readers can find answers to three important questions: (1) When is deep NLP helpful/not helpful in search systems? (2) How to address latency challenges? (3) How to ensure model robustness? This work builds on existing efforts of LinkedIn search, and is tested at scale on a commercial search engine. We believe our experiences can provide useful insights for the industry and research communities.
Supplementary Figure 2 from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers (2023)

&lt;p&gt;PDF file - 358K&lt;/p&gt;
Abstract 468: Smooth Muscle Cells Accelerate Endothelial Regeneration Through a Protein Kinase C-delta-Dependent Secretion of CXCR2 Ligands (2017)

Background: Efficient regeneration of denuded endothelial cells (ECs) is an important process that counteracts the pro-stenotic activities. Unfortunately, this natural healing process is frequently compromised by disease conditions such as diabetes. Protein kinase C-delta (PKCδ) plays a complex role in the arterial injury response by regulating apoptosis of vascular smooth muscle cells (SMCs) as well as production of chemokines capable of attracting resident and circulating cells. In this study, we explored whether SMCs participate in endothelial repair through a PKCδ-dependent paracrine mechanism. Methods and Results: Following balloon injury to the rat carotid, SMC-specific gene transfer of Prkcd accelerated reendothelialization compared to the empty vector, reflected by a larger area excluded from Evans blue measured 14 days post injury (59.60±5.01% vs 25.38±7.52%). In contrast, SMC-specific knockdown of endogenous Prkcd delayed reendothelialization compared to the non-targeting shRNA control (41.31±6.54% vs 70.31±5.97%). In vitro , media conditioned by AdPKCδ-infected SMCs increased endothelial wound healing without affecting their proliferation and viability. In addition, SMCs in a PKCδ-dependent fashion attracted circulating angiogenic cells (CACs), a cell population that promotes neovascularization via production of angiogenic factors. A PCR-based array analysis identified Cxcl1 and Cxcl7 among others as PKCδ-mediated chemokines produced by SMCs. Blocking CXCL7 or CXCR2 significantly inhibited endothelial wound healing and CAC migration in response to AdPKCδ-infected SMC conditioned media. In vivo , PKCδ overexpression in SMCs following balloon injury increased CXCL7 production and stimulated CACs recruitment to injured arteries. Furthermore, insertion of a Cxcl7 cDNA in the lentiviral vector that carries a Prkcd shRNA overcame the negative effects of Prkcd knockdown on reendothelialization. Conclusions: Regeneration of denuded endothelium involves multiple cell types from the vascular wall as well as circulation. SMCs stimulate reendothelialization in a PKCδ-dependent paracrine mechanism, likely through CXCL7-mediated recruitment of ECs from uninjured endothelium and CACs from circulation.
Optimization for dynamic inverted index maintenance (1989)

For free-text search over rapidly evolving corpora, dynamic update of inverted indices is a basic requirement. B-trees are an effective tool in implementing such indices. The Zipfian distribution of postings suggests space and time optimizations unique to this task. In particular, we present two novel optimizations, merge update, which performs better than straight forward block update, and pulsing which significantly reduces space requirements without sacrificing performance.
Observation of efficient transfer from Mott–Wannier to Frenkel excitons in a hybrid semiconductor quantum dot/polymer composite at room temperature (2010)

Efficient conversion from Mott–Wannier to Frenkel excitons is observed at room temperature. The time-resolved photoluminescence shows that the energy transfer rate and efficiency reach 0.262 ns−1 and 80.9%, respectively. The energy transfer is enabled by strong dipole-dipole coupling in a hybrid inorganic/organic system of CdSe/ZnS core/shell heteronanocrystal and poly[2-methoxy-5-(3,7-dimethyl-octyloxy)-1,4-phenylenevinylene] homopolymer composite, and the measured energy transfer efficiencies are consistent with the analytical model.
Vehicle Behavior Learning via Sparse Reconstruction with $\ell_{2}-\ell_{p}$ Minimization and Trajectory Similarity (2016)

Vehicle behavior learning can be used in video surveillance systems to identify normal and abnormal vehicle motion patterns for the management of traffic operations, public services, and law enforcement. The purpose of this paper is to develop a novel adaptive sparse reconstruction method for vehicle behavior learning based on video surveillance systems. First, the ℓ0 minimization problem of sparse reconstruction is relaxed to the ℓp minimization problem (0 <; p <; 1). A hybrid algorithm orthogonal matching pursuit-quasi-Newton is proposed to effectively find the sparse solutions. Then, a sparse reconstruction and similarity-based trajectory classifier is developed to learn vehicle behavior based on the sparse solutions and the trajectory similarity. In order to validate the performance and the effectiveness of the proposed method, four datasets, including CROSS, i-LIDA, Stop Sign, and I5 are used in the experiments. The results show that the classification and the anomaly detection accuracies of the proposed method are superior to the representative methods, including the Naïve Bayes classifier, k nearest neighbor, support vector machine, and traditional sparse reconstruction-based trajectory learning methods.
Apoptosis in hematopoietic cells is associated with an extensive decrease in cellular phosphotyrosine content that can be inhibited by the tyrosine phosphatase antagonist pervanadate (1996)

In the present study, we investigated whether apoptosis in hematopoietic cells is associated with changes in cellular phosphotyrosine content. Murine thymocytes and B cells, human leukemia cells, and normal peripheral blood leukocytes were induced to undergo apoptosis by treatment with specific stimuli or by incubation in growth factor-deprived medium. Multiparameter flow cytometry was used to measure changes in phosphotyrosine content that correlated with the appearance of features of programmed cell death, such as cell shrinkage, DNA fragmentation, and loss of membrane integrity. The results show that conditions that induced apoptosis also induced a dramatic decrease in cellular phosphotyrosine levels. Tyrosine dephosphorylation preceded the loss of plasma membrane integrity and, in most cases, was temporally correlated with the onset of DNA fragmentation. The protein tyrosine phosphatase antagonist pervanadate had a dose-dependent inhibitory effect on both dephosphorylation and apoptosis in murine thymocytes, which were treated with dexamethasone or with the topoisomerase II inhibitor etoposide. The results suggest that extensive tyrosine dephosphorylation is an intrinsic part of the apoptotic process of hematopoietic cells and may be involved mechanistically in the apoptosis induced by certain stimuli.
Observation of Associated Near-Side and Away-Side Long-Range Correlations insNN=5.02  TeVProton-Lead Collisions with the ATLAS Detector (2013)

Two-particle correlations in relative azimuthal angle (Δø) and pseudorapidity (Δη) are measured in sqrt[s(NN)] = 5.02 TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 μb(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (ΣE(T)(Pb)) summed over 3.1 < η < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < |Δ η | < 5) "near-side" (Δø ~ 0) correlation that grows rapidly with increasing ΣE(T)(Pb). A long-range "away-side" (Δø ~ π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE(T)(Pb), is found to match the near-side correlation in magnitude, shape (in Δη and Δø) and ΣE(T)(Pb) dependence. The resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).
Raman modes of metallic carbon nanotubes (1998)

The anomalous resonant behavior of the tangential Raman modes of carbon nanotubes has been studied in the critical region of laser energies 1.7--2.2 eV. The special enhancement of the Raman modes is explained by a model that takes into account the transition between the singularities in the one-dimensional density of electronic states for the metallic nanotubes and the distribution of diameters in the sample. The results agree with direct measurements of the electronic density of states for the metallic nanotubes and establish their association with the specially enhanced high frequency, first-order Raman modes.
“ERS/ATS Task Force onUndifferentiated Forms of CTD-ILD”. An official European RespiratorySociety/American Thoracic Society research statement: interstitial pneumonia withautoimmunefeatures (2015)

Many patients with an idiopathic interstitial pneumonia (IIP) have clinical features that suggest an underlying autoimmune process but do not meet established criteria for a connective tissue disease (CTD). Researchers have proposed differing criteria and terms to describe these patients, and lack of consensus over nomenclature and classification limits the ability to conduct prospective studies of a uniform cohort.The "European Respiratory Society/American Thoracic Society Task Force on Undifferentiated Forms of Connective Tissue Disease-associated Interstitial Lung Disease" was formed to create consensus regarding the nomenclature and classification criteria for patients with IIP and features of autoimmunity.The task force proposes the term "interstitial pneumonia with autoimmune features" (IPAF) and offers classification criteria organised around the presence of a combination of features from three domains: a clinical domain consisting of specific extra-thoracic features, a serologic domain consisting of specific autoantibodies, and a morphologic domain consisting of specific chest imaging, histopathologic or pulmonary physiologic features.A designation of IPAF should be used to identify individuals with IIP and features suggestive of, but not definitive for, a CTD. With IPAF, a sound platform has been provided from which to launch the requisite future research investigations of a more uniform cohort.
Preparative isolation of six major saponins from Platycodi Radix by high‐speed counter‐current chromatography (2009)

Six of the main bioactive platycosides in Platycodi Radix could be isolated and purified systematically by HSCCC.
Through-Silicon Via Design for a 3-D Solid-State Drive System With Boost Converter in a Package (2011)

A 3-D solid-state drive system with through-silicon via (TSV) technology and boost converter is presented in this paper. The proposed boost converter enables the supply voltage reduction to 1.8 V and smaller NAND Flash memory chips. From the simulation results, the conventional bonding-wire technology can achieve only eight NAND chip integrations not only due to their structural problem but also due to the performance degradation. On the other hand, 128 NAND Flash memory chips can be integrated into a package with full-copper TSVs and the proposed system has about 1.70 μs of rise time for 20 V, 74.2 nJ of the energy dissipation, and 225 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of additional Si area consumption for a NAND chip. Even if poly-Si TSVs are used, because of the process restriction, 64 NAND chips can be stacked with about 34% longer rise time and 22% degradation of energy dissipation compared to a full-copper TSV by grinding the Si-substrate to 10 μm .
‘ONCOSENSOR’ for Noninvasive High-Specificity Breast Cancer Diagnosis by Carbogen-Enhanced Neutron Femto-Oximetry (2010)

Based on the first experiment on Differential Femto Oximetry (Paper 13270), we conducted a computer simulated study of the feasibility of conceptual design for our noninvasive malignancy probe, Oncosensor, to diagnose hypoxia of malignancy M = −0.90, measured by pO2 — which correspond to volume averaged hypoxia M′ = −0.09 — in 1cm, 3 cm and 5 cm DIA tumors embedded in the middle of a 10 cm DIA breast. M′ is further masked by background γ’s from the in vivo tissue by factor x = 4.4–7 for subcutaneous and central tumor, respectively, to apparent M″ = M′/X which, in turn, renders hypoxia non-diagnosable for 1 cm tumors; marginally so for 3 cm ones with specificity S = 75%, and fully diagnosable with S = 95% in 5 cm ones. To diagnose 1–3 cm and smaller tumors, we propose to enhance M″ by a factor of ≈ 3 by replacing air breathing with that of Carbogen (O2 95%, CO2 5%). With carbogen breathing, simulations predict hypoxia detection in 1 cm subcutaneous tumor with S = 68%, and in 3 cm ones with S = 95–99.9%. Carbogen renders possible 2 additional diagnostic tests for redundancy. Significant improvements of the above measurement accuracies are projected. Oncosensor will be tested in vivo with R3230 tumors in Fischer rats at UCI’s Center for Functional Onco-Imaging. Oncosensor requires imaging guidance.
Identification of 8‐Hydroxyquinoline Derivatives Active Against Somatic V658F Mutant JAK1‐Dependent Cells (2016)

Janus kinases (JAKs) and their gain-of-function mutants have been implicated in a range of oncological, inflammatory, and autoimmune conditions, which has sparked great research interest in the discovery and development of small-molecule JAK inhibitors. Two molecules are currently marketed as JAK inhibitors, but due to the displayed side effects (owing to their suboptimal selectivities among the various JAK subtypes) new JAK inhibitors are still sought after. We present the results of an extensive virtual screening campaign based on a multi-step screening protocol involving ligand docking. The screening yielded five new, experimentally validated inhibitors of JAK1 with 8-hydroxyquinoline as a novel hinge-binding scaffold. The compounds did not only display favorable potencies in a JAK1<sup>V658F</sup> -driven cell-based assay but were also shown to be non-cytotoxic on rat liver cells.