gebhart/patrepeval huggingface dataset:
Study Based on the AIAA Aerodynamic Design Optimization Discussion Group Test Cases (2015)

Three model problems associated with aerodynamic drag minimizations are studied. These test cases have been proposed by the aerodynamic design optimization discussion group, and they include an inviscid NACA0012 nonlifting airfoil, a viscous RAE2822 lifting airfoil, and a viscous lifting wing based on the NASA Common Research Model. Various optimization methods are used, including MDOPT, TRANAIR, SYN83, and SYN107. The resulting designed and associated baseline geometries are cross analyzed by several computational fluid dynamics codes, including OVERFLOW, TRANAIR, GGNS, and FLO82. Pathological issues are unveiled in both of the simple airfoil model problems. Designed geometries for the inviscid symmetric test case exhibit strong tendencies to permit nonsymmetric flow solutions. Designed airfoils for the viscous lifting case also support nonunique solutions and hysteresis loops at or near the design point in Reynolds-averaged Navier–Stokes and integral boundary-layer method simulations. These results provide further evidence that single-point aerodynamic optimization is often ill posed. In extreme cases, it can yield designs with very undesirable aerodynamic characteristics, at least as analyzed by Reynolds-averaged Navier–Stokes and integral boundary-layer methods occurring at offdesign, and even ondesign, conditions. These examples are used to further document the multiple-solution and pseudosolution phenomena for steady-state Reynolds-averaged Navier–Stokes. This provides evidence that, even in practical engineering settings, numerical methods to assess stability and uniqueness of steady-state solutions and/or predict the bifurcations of these solutions have value. The single-point wing design problem is likewise ill posed in the spanwise direction. A multipoint design with a potentially large number of points or the inclusion of inequality constraints can regularize the problem.
Electronically controlled metastable defect reaction in InP (1983)

We report the observation of a reversible charge-state---dependent defect reaction in 1- MeV-electron---irradiated $n$-type InP. The reaction, observed by capacitance transient spectroscopy and thermally stimulated capacitance, is characterized by metastable defect configurations at $T\ensuremath{\lesssim}160$ K. The electronic properties of the two configurations, together with the reaction kinetics, provide evidence regarding the nature of the defects involved. The phenomenon can be described by a model involving the interaction of a shallow donor with an intrinsic defect or defect complex. The defect charge state controls an electrostatically driven pairing-dissociation reaction which results in changes in the observed defect electronic properties.
Endogenous Gastrin Collaborates With Mutant KRAS in Pancreatic Carcinogenesis (2019)

This study supports the mitogenic role of gastrin in activation of KRAS during pancreatic carcinogenesis.
Environments and mechanistic roles of the tyrosine residues of .DELTA.5-3-ketosteroid isomerase (1993)

Delta 5-3-Ketosteroid isomerase (EC 5.3.3.1) from Pseudomonas testosteroni converts delta 5-3-ketosteroids to delta 4-3-ketosteroids by a stereoselective and conservative transfer of the 4 beta-proton to the 6 beta-position. The 10(9.5)-fold enzymatic rate acceleration can be attributed to a concerted rate-limiting enolization in which Tyr-14 and Asp-38, positioned orthogonally, act as general acid and base, respectively. The pKa value of the phenolic hydroxyl group of Tyr-14 of the Y55F/Y88F double mutant is 11.6 +/- 0.2 by UV titration. However, the fluorescence titration of Tyr-14 shows biphasic sigmoidal behavior with apparent pKa values of 9.5 and 11.5. This suggests the assistance of a basic residue at the active site, possibly a lysine or tyrosine residue. Mutation of each of the four lysine residues K119L, K108Q, K92Q, and K60Q lowered specific activities only slightly to between 43% and 98% of the wild-type enzyme. Similarly, mutations of Tyr-55, Tyr-88, or both to phenylalanine led to only 2-4-fold reductions in catalytic activity. These findings suggest that despite the enormous difference between the pKa value of Tyr-14 (11.6) and that of the 3-carbonyl group of the steroid (ca. pKa-7), the reaction may rely on the concerted participation of Tyr-14 and Asp-38 only. The apparent pKa value of 9.5 in the fluorescence titration of Tyr-14 and in kinetic measurements probably results from conformational changes of the enzyme. The unusually high pKa value of Tyr-14 of 11.6 +/- 0.2 was used to estimate a local dielectric constant of 18 +/- 2 near this residue.(ABSTRACT TRUNCATED AT 250 WORDS)
Flexible One Diode-One Phase Change Memory Array Enabled by Block Copolymer Self-Assembly (2015)

Flexible memory is the fundamental component for data processing, storage, and radio frequency communication in flexible electronic systems. Among several emerging memory technologies, phase-change random-access memory (PRAM) is one of the strongest candidate for next-generation nonvolatile memories due to its remarkable merits of large cycling endurance, high speed, and excellent scalability. Although there are a few approaches for flexible phase-change memory (PCM), high reset current is the biggest obstacle for the practical operation of flexible PCM devices. In this paper, we report a flexible PCM realized by incorporating nanoinsulators derived from a Si-containing block copolymer (BCP) to significantly lower the operating current of the flexible memory formed on plastic substrate. The reduction of thermal stress by BCP nanostructures enables the reliable operation of flexible PCM devices integrated with ultrathin flexible diodes during more than 100 switching cycles and 1000 bending cycles.
From TagME to WAT (2014)

In this paper we propose a novel entity annotator for texts which hinges on TagME's algorithmic technology, currently the best one available. The novelty is twofold: from the one hand, we have engineered the software in order to be modular and more efficient; from the other hand, we have improved the annotation pipeline by re-designing all of its three main modules: spotting, disambiguation and pruning. In particular, the re-design has involved the detailed inspection of the performance of these modules by developing new algorithms which have been in turn tested over all publicly available datasets (i.e. AIDA, IITB, MSN, AQUAINT, and the one of the ERD Challenge). This extensive experimentation allowed us to derive the best combination which achieved on the ERD development dataset an F1 score of 74.8%, which turned to be 67.2% F1 for the test dataset. This final result was due to an impressive precision equal to 87.6%, but very low recall 54.5%. With respect to classic TagME on the development dataset the improvement ranged from 1% to 9% on the D2W benchmark, depending on the disambiguation algorithm being used. As a side result, the final software can be interpreted as a flexible library of several parsing/disambiguation and pruning modules that can be used to build up new and more sophisticated entity annotators. We plan to release our library to the public as an open-source project.
Heterogeneity of Inflammatory Bowel Diseases (2010)

This chapter contains sections titled: Introduction Classical clinical heterogeneity Laboratory heterogeneity Genetic heterogeneity Biomarkers of disease Heterogeneity of treatment responses Evidence of IBD heterogeneity from animal models Harnessing heterogeneity – the future of IBD research Conclusion References
<title>Applications of Raman spectroscopy to industrial processes</title> (1992)

The role of on-line chemical analyzers is vital to process monitoring and control and product quality. Although traditional optical filter methods such as UV-VIS, NIR, and IR have enjoyed considerable success when applied on-line, they often require inconvenient and complex sampling schemes. These restrictions can be largely eliminated by fiber optic probes as evidenced by their growing popularity. Fiber optic technology also allows remote location of full spectrum analyzers which in turn facilitates multicomponent analysis. Recently, we have developed a Raman spectrograph which utilizes fiber optic probes and a CCD detector. We have been most successful with this system when it is applied to processes in a short term, investigative role. Examples of reaction intermediates and products, contaminant identification, and process optimization will be given.
In situ growth of epitaxial yttrium aluminum oxide (YAlO3) thin films by metalorganic chemical vapor deposition (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIn situ growth of epitaxial yttrium aluminum oxide (YAlO3) thin films by metalorganic chemical vapor depositionBin Han, Deborah A. Neumayer, Douglas L. Schulz, Bruce J. Hinds, Tobin J. Marks, Hong Zhang, and Vinayak P. DravidCite this: Chem. Mater. 1993, 5, 1, 14–16Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/cm00025a006https://doi.org/10.1021/cm00025a006research-articleACS PublicationsRequest reuse permissionsArticle Views211Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Comparative Metabolomic Evaluation of Behcet’s Disease with Arthritis and Seronegative Arthritis Using Synovial Fluid (2015)

Behcet's disease (BD) with arthritis is often confused with seronegative arthritis (SNA) because of shared clinical symptoms and the lack of definitive biomarkers for BD. To investigate possible metabolic patterns and potential biomarkers of BD with arthritis, metabolomic profiling of synovial fluid (SF) from 6 patients with BD with arthritis and 18 patients with SNA was performed using gas chromatography/time-of-flight mass spectrometry in conjunction with univariate and multivariate statistical analyses. A total of 123 metabolites were identified from samples. Orthogonal partial least square-discriminant analysis showed clear discrimination between BD with arthritis and SNA. A set of 11 metabolites were identified as potential biomarkers for BD using variable importance for projection values and the Wilcoxon-Mann-Whitney test. Compared with SNA, BD with arthritis exhibited relatively high levels of glutamate, valine, citramalate, leucine, methionine sulfoxide, glycerate, phosphate, lysine, isoleucine, urea, and citrulline. There were two markers identified, elevated methionine sulfoxide and citrulline, that were associated with increased oxidative stress, providing a potential link to BD-associated neutrophil hyperactivity. Glutamate, citramalate, and valine were selected and validated as putative biomarkers for BD with arthritis (sensitivity, 100%; specificity, 61.1%). This is the first report to present potential biomarkers from SF for discriminating BD with arthritis from SNA. The metabolomics of SF may be helpful in searching for potential biomarkers and elucidating the clinicopathogenesis of BD with arthritis.
Role of Symmetry Breaking on the Optical Transitions in Lead-Salt Quantum Dots (2010)

The influence of quantum confinement on the one- and two-photon absorption spectra (1PA and 2PA) of PbS and PbSe semiconductor quantum dots (QDs) is investigated. The results show 2PA peaks at energies where only 1PA transitions are predicted and 1PA peaks where only 2PA transitions are predicted by the often used isotropic k x p four-band envelope function formalism. The first experimentally identified two-photon absorption peak coincides with the energy of the first one photon allowed transition. This first two-photon peak cannot be explained by band anisotropy, verifying that the inversion symmetry of the wave functions is broken and relaxation of the parity selection rules has to be taken into account to explain optical transitions in lead-salt QDs. Thus, while the band anisotropy of the bulk semiconductor plays a role in the absorption spectra, especially for the more anisotropic PbSe QDs, a complete model of the absorption spectra, for both 1PA and 2PA, must also include symmetry breaking of the quantum confined wave functions. These studies clarify the controversy of the origin of spectral features in lead-salt QDs.
ChemInform Abstract: A NEW APPROACH TO THE SYNTHESIS OF PRIMARY AMINES, ISOTHIOCYANATES, AND 1‐AMINOALKANEPHOSPHONATES VIA N‐PHOSPHINYL ALDOXIMES AND KETOXIMES (1978)

Abstract Oxime (I) werden mit Chlordiphenylphosphin (II) in Gegenwart von Triethylamin in Petrolether/ Methylenchlorid zu Diphenylphosphinamiden (III) umgesetzt, die mit Natriumborhydrid zu (IV) reduziert werden.
Vertical Cavity Laser High Speed Dynamics and Modeling (1993)

Vertical cavity lasers have been demonstrated with low thresholds and high efficiency. Wafer level testing is possible and packaging is simpler with excellent coupling to optical fibers. Two dimensional arrays of these lasers offer a new set of applications for semiconductor lasers. The design and properties of vertical cavity lasers are significantly different from in-plane lasers and present difficult theoretical design and analysis problems. Three important examples will be discussed here: Coupling between waveguides and DBR reflectors, relaxation oscillation dynamics, and chirping of vertical cavity laser output.
Clinical Utility of a Novel Ultrafast T2-Weighted Sequence for Spine Imaging (2018)

We present a fast T2-weighted spine protocol using variable refocusing flip angles, including a single-shot variant. The sequences have better point spread function behavior than their constant flip angle counterparts and, being faster, should be less sensitive to patient motion, often seen in the longer TSE scans.
In Vivo PET Imaging of Histone Deacetylases by 18F-Suberoylanilide Hydroxamic Acid (18F-SAHA) (2011)

Histone deacetylases (HDACs) are a group of enzymes that modulate gene expression and cell state by deacetylation of both histone and non-histone proteins. A variety of HDAC inhibitors (HDACi) have already undergone clinical testing in cancer. Real-time in vivo imaging of HDACs and their inhibition would be invaluable; however, the development of appropriate imaging agents has remained a major challenge. Here, we describe the development and evaluation of (18)F-suberoylanilide hydroxamic acid ((18)F-SAHA 1a), a close analogue of the most clinically relevant HDAC inhibitor suberoylanilide hydroxamic acid (SAHA). We demonstrate that 1a has near identical biochemical activity profiles to that of SAHA and report findings from pharmacokinetic studies. Using a murine ovarian cancer model, we likewise show that HDAC inhibitor target binding efficacy can be quantitated within 24 h of administration. 1a thus represents the first (18)F-positron emission tomography (PET) HDAC imaging agent, which also exhibits low nanomolar potency and is pharmacologically analogous to a clinically relevant HDAC inhibitor.
Recognition of PF4-VWF complexes by heparin-induced thrombocytopenia antibodies contributes to thrombus propagation (2020)

Heparin-induced thrombocytopenia (HIT) is a prothrombotic disorder mediated by complexes between platelet factor 4 (PF4) and heparin or other polyanions, but the risk of thrombosis extends beyond exposure to heparin implicating other PF4 partners. We recently reported that peri-thrombus endothelium is targeted by HIT antibodies, but the binding site(s) has not been identified. We now show that PF4 binds at multiple discrete sites along the surface of extended strings of von Willebrand factor (VWF) released from the endothelium following photochemical injury in an endothelialized microfluidic system under flow. The HIT-like monoclonal antibody KKO and HIT patient antibodies recognize PF4-VWF complexes, promoting platelet adhesion and enlargement of thrombi within the microfluidic channels. Platelet adhesion to the PF4-VWF-HIT antibody complexes is inhibited by antibodies that block FcγRIIA or the glycoprotein Ib-IX complex on platelets. Disruption of PF4-VWF-HIT antibody complexes by drugs that prevent or block VWF oligomerization attenuate thrombus formation in a murine model of HIT. Together, these studies demonstrate assembly of HIT immune complexes along VWF strings released by injured endothelium that might propagate the risk of thrombosis in HIT. Disruption of PF4-VWF complex formation may provide a new therapeutic approach to HIT.
Solution‐Processed Nickel Oxide Hole Transport Layers in High Efficiency Polymer Photovoltaic Cells (2013)

Abstract The detailed characterization of solution‐derived nickel (II) oxide (NiO) hole‐transporting layer (HTL) films and their application in high efficiency organic photovoltaic (OPV) cells is reported. The NiO precursor solution is examined in situ to determine the chemical species present. Coordination complexes of monoethanolamine (MEA) with Ni in ethanol thermally decompose to form non‐stoichiometric NiO. Specifically, the [Ni(MEA) 2 (OAc)] + ion is found to be the most prevalent species in the precursor solution. The defect‐induced Ni 3+ ion, which is present in non‐stoichiometric NiO and signifies the p‐type conduction of NiO, as well as the dipolar nickel oxyhydroxide (NiOOH) species are confirmed using X‐ray photoelectron spectroscopy. Bulk heterojunction (BHJ) solar cells with a polymer/fullerene photoactive layer blend composed of poly‐dithienogermole‐thienopyrrolodione (pDTG‐TPD) and [6,6]‐phenyl‐C71‐butyric acid methyl ester (PC 71 BM) are fabricated using these solution‐processed NiO films. The resulting devices show an average power conversion efficiency (PCE) of 7.8%, which is a 15% improvement over devices utilizing a poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) HTL. The enhancement is due to the optical resonance in the solar cell and the hydrophobicity of NiO, which promotes a more homogeneous donor/acceptor morphology in the active layer at the NiO/BHJ interface. Finally, devices incorporating NiO as a HTL are more stable in air than devices using PEDOT:PSS.
Toward image-based facial hair modeling (2010)

In this paper we present a novel efficient and fully automated technique to synthesize realistic facial hair---such as beards and eyebrows---on 3D head models. The method requires registered texture images of a target model on which hair needs to be generated. In a first stage of our two-step approach a statistical measure for hair density is computed for each pixel of the texture. In addition, other geometric features such as 2D pixel orientations are extracted, which are subsequently used to generate a 3D model of the individual hair strands. Missing or incomplete information is estimated based on statistical models derived from a database of texture images of over 70 individuals. Using the new approach, characteristics of the hair extracted from a given head may be also transferred to another target.
Temperature tracking: An innovative run-time approach for hardware Trojan detection (2013)

The hardware Trojan threat has motivated development of Trojan detection schemes at all stages of the integrated circuit (IC) lifecycle. While the majority of existing schemes focus on ICs at test-time, there are many unique advantages offered by post-deployment/run-time Trojan detection. However, run-time approaches have been underutilized with prior work highlighting the challenges of implementing them with limited hardware resources. In this paper, we propose innovative low-overhead approaches for run-time Trojan detection which exploit the thermal sensors already available in many modern systems to detect deviations in power/thermal profiles caused by Trojan activation. Simulation results using state-of-the-art tools on publicly available Trojan benchmarks verify that our approaches can detect active Trojans quickly and with few false positives.
Faculty Opinions recommendation of Negative regulation of Toll-like receptor 4 signaling by the Toll-like receptor homolog RP105. (2005)

Activation of Toll-like receptor (TLR) signaling by microbial signatures is critical to the induction of immune responses. Such responses demand tight regulation. RP105 is a TLR homolog, thought to be largely B cell-specific, which lacks a signaling domain. We report that RP105 expression is wide, directly mirroring that of TLR4 on antigen presenting cells. We further show that RP105 is a specific inhibitor of TLR4 signaling in HEK293 cells, a function conferred by its extracellular domain. Notably, RP105 and its helper molecule, MD-1, interacted directly with the TLR4 signaling complex, inhibiting its ability to bind microbial ligand. Finally, we demonstrate that RP105 regulates TLR4 signaling in dendritic cells, as well as endotoxin responses in vivo. Thus, these results identify RP105 as a physiological negative regulator of TLR4 responses.
Flexibility (2018)

Deep learning inference has become the key workload to accelerate in our AI-powered world. FPGAs are an ideal platform for the acceleration of deep learning inference by combining low-latency performance, power-efficiency, and flexibility. This paper examines the flexibility aspect, and its impact on FPGA design methodology, physical design tools and CAD. We describe the degrees of flexibility required for creating efficient deep learning accelerators. We quantify the varying effects of precision, vectorization, and buffering on both performance and accuracy, and show how the FPGA can yield superior performance through architecture customization tuned for a specific neural network. We describe the need for abstraction and propose solutions in modern FPGA design flows to enable the rapid creation of these customized accelerator architectures for deep learning inference acceleration. Finally, we examine the implications on physical design tools and CAD.
Noisy Blackbox Optimization using Multi-fidelity Queries: A Tree Search Approach (2019)

We study the problem of black-box optimization of a noisy function in the presence of low-cost approximations or fidelities, which is motivated by problems like hyper-parameter tuning. In hyper-parameter tuning evaluating the black-box function at a point involves training a learning algorithm on a large data-set at a particular hyper-parameter and evaluating the validation error. Even a single such evaluation can be prohibitively expensive. Therefore, it is beneficial to use low-cost approximations, like training the learning algorithm on a sub-sampled version of the whole data-set. These low-cost approximations/fidelities can however provide a biased and noisy estimate of the function value. In this work, we combine structured state-space exploration through hierarchical partitioning with querying these partitions at multiple fidelities, and develop a multi-fidelity bandit based tree-search algorithm for noisy black-box optimization. We derive simple regret guarantees for our algorithm and validate its performance on real and synthetic datasets.