gebhart/patrepeval huggingface dataset:
Advances in the development of a High Order, Viscous-Inviscid Interaction Solver (2013)

We present a high order viscous-inviscid interaction solver for aerodynamic flows. Our approach is based on a split formulation where the viscous and inviscid effects are solved in two different domains that overlap near solid walls or the wake centerline and are coupled using the equivalent mass transpiration proposed by Lighthill. Both the viscous and inviscid solvers are based on a high order Hybridized Discontinuous Galerkin scheme (HDG). In the case of the viscous solver, the mesh is extruded on the fly from the surface mesh using a normal scaling indicator δ, based on integrated boundary layer quantities, that is computed as part of the solution. Results will be presented to validate the coupled viscous-inviscid solver in a variety of cases using the Euler equations as well as the full potential equation as inviscid models.
Development of a RNA-Seq Based Prognostic Signature in Lung Adenocarcinoma (2016)

Here, we present the first RNA-seq prognostic signature for lung adenocarcinoma that can provide a powerful prognostic tool for precision oncology as part of an integrated RNA-seq clinical sequencing program.
Adaptive temporal smoothing of sinogram data using Karhunen-Loeve (KL) transform for myocardial blood flow estimation from dose-reduced dynamic CT (2014)

There is a strong need for an accurate and easily available technique for myocardial blood flow (MBF) estimation to aid in the diagnosis and treatment of coronary artery disease (CAD). Dynamic CT would provide a quick and widely available technique to do so. However, its biggest limitation is the dose imparted to the patient. We are exploring techniques to reduce the patient dose by either reducing the tube current or by reducing the number of temporal frames in the dynamic CT sequence. Both of these dose reduction techniques result in very noisy data. In order to extract the myocardial blood flow information from the noisy sinograms, we have been looking at several data-domain smoothing techniques. In our previous work,<sup>1</sup> we explored the sinogram restoration technique in both the spatial and temporal domain. In this work, we explore the use of Karhunen-Loeve (KL) transform to provide temporal smoothing in the sinogram domain. This technique has been applied previously to dynamic image sequences in PET.<sup>2, 3</sup> We find that the cluster-based KL transform method yields noticeable improvement in the smoothness of time attenuation curves (TAC). We make use of a quantitative blood flow model to estimate MBF from these TACs and determine which smoothing method provides the most accurate MBF estimates.
The total synthesis of (±)-indolizidines 235B and 235B′ (1991)

The total synthesis of racemic indolizidines 235B 1 and 235B′2 is described, in which the key step is the intramolecular thermal cycloaddition of the (Z)-N-alkenylnitrones 10b and 10a, respectively. Cyclisation of the isoxazolidines 12, followed by reductive N–O bond cleavage, epimerisation of the resulting axial hydroxymethyl side chain to the equatorial configuration, and further reduction to a methyl group gave the target molecules. Intramolecular cyclisation of the related nitrone 18, a potential precursor to the solenopsins, was less regioselective, affording a 6:1 mixture of the adducts 19 and 20, which indicates a dependence on the nature of the substituent α to nitrogen.
Optically Concatenated 4-Fold 40-Gbit/s Multicasting, 4-Fold 40-to-160-Gbit/s Multiplexing, and 160-to-40-Gbit/s Demultiplexing Using Highly Nonlinear Fibers (2009)

We experimentally demonstrate concatenated 4-fold 40-Gbit/s signal multicasting, 4-fold 40-to-160-Gbit/s multiplexing and subsequent 160-to-40-Gbit/s demultiplexing based on supercontinuum generation and cross-phase modulation in highly nonlinear fibers. 5–9 dB penalty at 10−9 BER was observed after the nonlinear processes.
Point Processes of Segments and Rectangles for Building Extraction from Digital Elevation Models (2006)

In this work, we propose a new model based on stochastic geometry for extracting features from images. This type of model allows the incorporation of a prior knowledge on the interactions between features within the extraction process. We focus on the specific problem of automatic building extraction from digital elevation models (DEMs). The model we propose is based on two interacting spatial point processes, the former being a process of rectangles, the latter a process of segments. An energy associated with the resulting process is defined. This energy consists in five main parts. We first define two energy data terms to make the rectangles fit the homogeneous areas and the segments fit meaningful discontinuities. Two prior terms favoring respectively the alignment of rectangles and the connection of segments are incorporated. The last part of the energy is an interaction term that makes the two types of objects cooperate. We present results on real data provided by the IGN (French Geographic Institute)
Missing pixel correction algorithm for image sensors (1998)

We describe a compact algorithm that can on the fly detect and correct isolated missing pixels in the output stream of an image sensor, without significantly degrading the image quality. The algorithm is in essence a small kernel non- linear filter. It is based on the prediction of the allowed range of gray values for a pixel, for the gray values of the neighborhood of that pixel. A few examples will illustrate the effect of the algorithm on realistic images.
NEt3-Triggered Synthesis of UHMWPE Using Chromium Complexes Bearing Non-innocent Iminopyridine Ligands (2021)

Chromium complexes bearing non-innocent iminopyridine ligands were investigated as precatalysts for the polymerization of ethylene using different aluminum cocatalysts and Lewis base NEt3 as additive. Beyond confirming the key role of the chromium to ligand synergy in accessing the active complex, other factors that play a crucial role are (i) the nature of the aluminum activator that influences the ion pair generated, (ii) the presence of the additive that boosts the synthesis of UHMWPE with narrow and unimodal molecular weight distribution even at 40 °C, and (iii) the polymerization temperature that affects the polymerization catalysis and the polymer molecular weight. UV–vis–NIR and Fourier transform infrared (FT-IR) spectroscopic techniques have been applied to inspect the activation process and to understand the mode of action by which NEt3 affects the catalytic conversion of ethylene. NEt3 interacts with the aluminum cocatalyst (rather than with the chromium complex) to form an Et3N*AlRx adduct, thus affecting the catalytic ion pair.
Overexpression of HSP72 after Induction of Experimental Stroke Protects Neurons from Ischemic Damage (2001)

The 72-kD inducible heat shock protein (HSP72) can attenuate cerebral ischemic injury when overexpressed before ischemia onset. Whether HSP72 overexpression is protective when applied after ischemia onset is not known, but would have important clinical implications. Fifty-seven rats underwent middle cerebral artery occlusion for 1 hour. Defective herpes simplex viral (HSV) vectors expressing hsp72 with lacZ as a reporter were delivered 0.5, 2, and 5 hours after ischemia onset into each striatum. Control animals received an identical vector containing only lacZ. Striatal neuron survival at 2 days was improved by 23% and 15% when HSP72 vectors were delayed 0.5 and 2 hours after ischemic onset, respectively ( P < 0.05). However, when delayed by 5 hours, HSP72 overexpression was no longer protective. This is the first demonstration that HSP72 gene transfer even after ischemia onset is neuroprotective. Because expression from these HSV vectors begins 4 to 6 hours after injection, this suggests that the temporal therapeutic window for HSP72 is at least 6 hours after ischemia onset. Future strategies aimed at enhancing HSP72 expression after clinical stroke may be worth pursuing. The authors suggest that in the future HSP72 may be an effective treatment for stroke.
DQPSK Receiver tolerance to transmitter frequency stability (2006)

In case of Differential Quadrature Phase Shift Keying transmission, the diode laser frequency instability affects the quality of the received signal. Free-running transmitters are employed to experimentally evaluate the tolerance of the interferometric DQPSK receiver to this instability. Heterodyne measure of the frequency offset is discussed for different transmitters. Experimental data are related both with BER performance and power penalty. Polarization-dependent delay impairment is isolated as well.
Radio Frequency Thermal Plasma Treatment for Size Reduction and Spheroidization of Glass Powders Used in Ceramic Electronic Devices (2007)

Radio frequency (RF) thermal plasma treatment is studied for the size reduction and the spheroidization of coarse glass particles to change them into submicrometer‐sized powders of spherical shape. Such ultra‐fine spherical powders are the key ingredients of a sintering aid to achieve efficient package and high performance in ceramic electronic applications. The coarse glass powders injected into the high‐temperature RF thermal plasma undergo rapid heating, melting, and evaporation, followed by quenching, and then condense to very fine spherical powders. In the thermal plasma treatment with high RF powers of 18–23 kW at a powder feeding rate of 3 g/min, the scanning electron microscopy images and the particle size distribution graphs obtained from the treated glass powders indicate that most glass powders with initial average diameters of around 2 μm are reformed into spherical ones with sizes of below 500 nm. It is also observed in a 4 MHz RF thermal plasma reactor that the maximum size of particles decreases down to 200 nm when the reactor is operated under conditions of reduced pressure, low powder feeding rate, and high RF power. The compositions of glass powders before and after the plasma treatment are compared by using the wet and the inductively coupled plasma‐optical emission spectroscopy analyses. Negligible composition changes appear within a range of &lt;2 wt% during the RF thermal plasma process, which demonstrates the successful preparation of submicrometer‐sized glass powders in spherical shape applicable to the advanced ceramic electronic devices.
Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation (2023)

&lt;p&gt;Complete supplementary figures containing: Suppl. Fig. 1: HLA-coverage (Caucasian); Suppl. Fig. 2: Maximum attainable quantities of source proteins; Suppl. Fig. 3: Comparsion with complete benign dataset; Suppl. Fig. 4: Legend PANTHER analysis; Suppl. Fig. 5: Legend KEGG analysis; Suppl. Fig. 6: Representation analysis HLA class II&lt;/p&gt;
Secrecy sum-rates with regularized channel inversion precoding under imperfect CSI at the transmitter (2013)

In this paper, we study the performance of regularized channel inversion precoding in MISO broadcast channels with confidential messages under imperfect channel state information at the transmitter (CSIT). We obtain an approximation for the achievable secrecy sum-rate which is almost surely exact as the number of transmit antennas and the number of users grow to infinity in a fixed ratio. Simulations prove this anaylsis accurate even for finite-size systems. For FDD systems, we determine how the CSIT error must scale with the SNR, and we derive the number of feedback bits required to ensure a constant high-SNR rate gap to the case with perfect CSIT. For TDD systems, we study the optimum amount of channel training that maximizes the high-SNR secrecy sum-rate.
Ex vivo response to RMD in multiple longitudinal samples from the same donors. (2015)

&lt;p&gt;Resting CD4 T cells isolated from 2 cART-suppressed HIV-infected patients were treated continuously with RMD or with anti-CD3/CD28 antibodies (AC, activation control) for 7 days. HIV RNA in cell culture supernatants was quantified by COBAS on day 7. Data for a high-responding (&lt;b&gt;A&lt;/b&gt;) and a low-responding donor (&lt;b&gt;B&lt;/b&gt;) to RMD is shown; each donor was tested at 3 different time points separated by at least 2 weeks (Exp 1–3). VC/NDC, vehicle control/no-drug control. Asterisk (*) indicates no value due to COBAS analysis failure. Dashed lines indicate the limit of HIV quantification by COBAS (20 copies/ml). Data for each individual donor and condition including results of the statistical analysis are summarized in Supplementary &lt;a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004071#ppat.1004071.s008" target="_blank"&gt;Table S4&lt;/a&gt;.&lt;/p&gt;
The Role of Nucleation Inhibition in Optical Resolutions with Families of Resolving Agents (2002)

Not double Dutch! The resolution of racemates with families of structurally related resolving agents (see examples depicted) is termed Dutch Resolution. Certain family members are regularly not incorporated; these turn out to be nucleation inhibitors. This leads to a simplified, two-component resolution procedure with a high chance of initial success.
Neuropsychological Change After a Single Season of Head Impact Exposure in Youth Football (2020)

These findings suggest that in the 9-10 age cluster, the average seasonal level of HIE had inverse, negative relationships with cognitive change over one season that was not found in the older group. The mediation effects of age and weight have not been explored previously and appear to contribute to the effects of HIE on cognition in youth football players.
Adapting a medical speech to speech translation system (MedSLT) to Arabic (2007)

We describe the adaptation for Arabic of the grammar-based MedSLT medical speech system. The system supports simple medical diagnosis questions about headaches using vocabulary of 322 words. We show that the MedSLT architecture based on motivated general grammars produces very good results, with a limited effort. Based on the grammars for other languages covered by the system, it is in fact very easy to develop an Arabic grammar and to specialize it efficiently for the different system tasks. In this paper, we focus on generation.
Potentially reactive cyclic carbamate metabolite of the antiepileptic drug felbamate produced by human liver tissue in vitro. (1998)

Felbamate (FBM) is a novel antiepileptic drug that was approved in 1993 for treatment of several forms of epilepsy. After its introduction, toxic reactions (aplastic anemia and hepatotoxicity) associated with its use were reported. It is unknown whether FBM or one of its metabolites is responsible for these idiosyncratic adverse reactions. Although the metabolism of FBM has not been fully characterized, three primary metabolites of FBM have been identified, i.e. 2-hydroxy, p-hydroxy, and monocarbamate metabolites. In addition, the monocarbamate metabolite leads to a carboxylic acid, which is the major metabolite of FBM in humans. Formation of the hydroxylated products of FBM involves cytochrome P450 enzymes, but the enzymes involved in the formation and further metabolism of the monocarbamate have not yet been elucidated. Recently, mercapturate metabolites of FBM have been identified in human urine, and a metabolic scheme involving reactive aldehyde metabolite formation from the monocarbamate metabolite has been proposed. The present study confirmed the formation of the proposed metabolites using human liver tissue in vitro. The aldehyde intermediates were trapped as oxime derivatives, and the cyclic equilibrium product (proposed as a storage and transport form for the aldehydes) was monitored directly by HPLC or GC/MS. Formation of putative toxic aldehyde intermediates and the major carboxylic acid metabolite of FBM was differentially effected with the cofactors NADP+ and NAD+. It is possible that the cofactors may influence the relative metabolism via activation and inactivation pathways.
A type of shadowing and distributional chaos (2020)

For any continuous self-map of a compact metric space, we prove a saturation of distributionally scrambled Mycielski sets under a type of shadowing and the chain transitivity.
Molecular Orientation and Electrical Properties in <i>tert</i>-Butylated Phthalocyanine Thin Film Fabricated by Uniaxial Solution Coating (2020)

Molecular orientation, molecular packing structure, and electrical properties of thermally stable phthalocyanine, tert-butylated phthalocyanine (t-BuPcH2) in the thin film fabricated by bar-coating method were investigated. The XRD patterns indicated that the columns composed of t-BuPcH2 molecules formed hexagonal structure, the axis of which was parallel to the bar-sweep direction, and t-BuPcH2 molecules were vertically aligned to the bar-sweep direction. Uniaxially oriented thin films of t-BuPcH2 were successfully fabricated on Si substrate covered with polyimide by bar-coating method, and the field effect mobility of t-BuPcH2 was estimated to be 1.32×10-4 cm2 V-1 s-1 at maximum. The field effect mobility parallel to the bar-sweep direction was approximately three times higher than that perpendicular to the bar-sweep direction due to high electrical conduction along the column axis of t-BuPcH2.
Bis(Pentafluorophenyl)(2-perfluorobiphenylyl)borane. A New Perfluoroarylborane Cocatalyst for Single-Site Olefin Polymerization (2000)

Bis(pentafluorophenyl)(2-perfluorobiphenylyl)borane, (C6F5)2B(C12F9) (BPB), has been synthesized and characterized to serve as a new strong organo-Lewis acid cocatalyst for single-site olefin polymerization. BPB efficiently activates a variety of group 4 dimethyl complexes to form highly active homogeneous Ziegler−Natta olefin polymerization catalysts. Reaction of BPB with Cp2ZrMe2, rac-Me2Si(Ind)2ZrMe2, and (CGC)MMe2 (M = Zr, Ti; CGC = Me2Si(η5-Me4C5)(tBuN)) (1:1 molar ratio) rapidly and cleanly produces the base-free cationic complexes Cp2ZrMe+[MeB(C12F9)(C6F5)2]- (1), rac-Me2Si(Ind)2ZrMe+[MeB(C12F9)(C6F5)2]- (2), and (CGC)MMe+[MeB(C12F9)(C6F5)2]- (M = Zr, 3; M = Ti, 4), respectively. These complexes have been characterized by NMR and elemental analysis and are shown to be competent for ethylene and propylene polymerization. In general, BPB-derived catalysts exhibit polymerization activities comparable to or higher than those of the B(C6F5)3-derived analogues, with the products exhibiting higher molecular weights but comparable polydispersities, polypropylene isotacticities, and, for ethylene + 1-hexene, comonomer incorporation.
Lung-derived macrophage migration inhibitory factor in adult patients with septic shock, and its role in cardiocirculatory depression (2007)

The pathogenesis of endotoxemic tubular dysfunction with failure in urine concentration is poorly understood. Urea plays an important role in the urinary concentrating mechanism and expression of the urea transporters UT-A1, UT-A2, UT-A3, UT-A4 and UT-B is essential for tubular urea reabsorption. The present study attempts to assess the regulation of renal urea transporters during severe inflammation in vivo. Materials and methods By agreement of the animal protection committee C57BL/6J, mice were injected with lipopolysaccharides (LPS, 10 mg/kg) or proinflammatory cytokines. Hemodynamic, renal parameters and the expression of renal urea transporters were investigated. To clarify the role of cytokines and renal ischemia in the regulation of renal urea transporters, experiments were performed with cytokine knockout mice, mice treated with low-dose LPS (1, 5 mg/kg) as a sepsis model without induction of hypotension, glucocorticoid-treated mice, and mice with renal artery clipping serving as a model for renal ischemia. Results and discussion LPS-injected mice (10 mg/kg) presented with reduced glomerular filtration rate, fractional urea excretion and inner medulla osmolality associated with a marked decrease in expression of UT-A1, UT-A2, UT-A3, UT-A4 and UT-B (Figure Similar alterations were observed after application of TNF, IL-1, IFN or IL-6. LPS-induced downregulation of urea transporters was not affected in knockout mice with deficient TNF, IL-receptor-1, IFN or IL-6. Glucocorticoid treatment inhibited LPS-induced increases of tissue TNF, IL-1, IFN or IL-6 concentration, diminished LPS-induced renal dysfunction and attenuated the downregulation of renal urea transporters. Injection of low-dose LPS (1, 5 mg/kg) also led to renal dysfunction paralleled by a downregulation of renal urea transporters without alterations in blood pressure. Renal ischemia induced by renal artery clipping did not influence the expression of urea transporters. Conclusion Our findings demonstrate downregulation of renal urea transporters that probably accounts for tubular dysfunction during sepsis. Furthermore, they suggest that downregulation of Figure 1 (abstract P1) Effect of lipopolysaccharide (LPS) (10 mg/kg), dexamethasone (10 mg/kg) and the combination of both on UT-A1, UT-A2, UT-A3, UT-A4 and UT-B mRNA in the kidney 6, 12 and 24 hours after intraperitoneal injection. Values are related to signals obtained for -actin mRNA and presented as the percentage of vehicle control. Mean SEM of six animals per group. *P < 0.05 versus control, # P < 0.05 versus LPS treatment. S2
Genetic variability of hepatitis C virus in chronically infected patients with viral breakthrough during interferon–ribavirin therapy (2004)

Little is known about hepatitis C virus (HCV) breakthrough during antiviral therapy, although it would help in understanding HCV resistance to current antiviral treatments. To analyse the implication of virological factors and the vigour of humoral immune responses in this phenomenon, we studied nine chronic hepatitis C patients with a viral breakthrough during IFN/ribavirin combination therapy, as well as five responders and five non-responders. The IRES and regions coding for the capsid protein, the PePHD domain of envelope glycoprotein E2 and the NS5A and 5B proteins were amplified by RT-PCR before treatment, before and during breakthrough, and after treatment. The major variant sequence was obtained by direct sequencing. The heterogeneity of quasispecies was studied by SSCP in all patients and sequencing after cloning in seven genotype 1b-infected patients. Humoral responses against HCV epitopes were also analysed. The major sequences of IRES, PePHD, and NS5B remained stable during treatment, regardless of the treatment response. However, the capsid protein and the regions flanking PePHD showed sequence variations in breakthrough patients, although no specific mutation was identified. The variable V3 region of NS5A, but not the PKR-binding domain and the ISDR, seemed to be associated with differences in response to treatment. The analysis of HCV quasispecies revealed no characteristic pattern during treatment in breakthrough patients, whose HCV genome profiles looked most similar to that of non-responders. The humoral response was similar between groups. In conclusion, viral breakthrough does not seem to be due to selection of resistant strains with signature mutations.