gebhart/patrepeval huggingface dataset:
Fundamental Properties of Routing Matrices and Their Implications for Network Tomography (2009)

Network performance tomography establishes linear relationships of the form Y = R Â· X between the characteristics of individual links (X) and those of end-to-end paths (Y) through a routing matrix R. A fundamental question is whether these relationships are sufficient for inferring the characteristics of links from end-to-end path measurements; there has been evidence, though not proof, that this is not the case due to Râs structure. In this paper, we formally prove that the routing matrix R is always rank deficient, in particular, Rank(R) â¤ |E| â |V|, where |E| is the number of links (also columns in R) and |V| the number of routers in the network. We identify a class of networks for which this upper bound is provably attainable. We also identify a (wider) class, which includes all real topologies we were able to collect using PlanetLab, for which we prove a lower bound on Râs rank. Using insights from our analysis, we develop an accurate algorithm that infers the loss rates of individual links from end-to-end path measurements. Unlike other work, we do not make any assumptions regarding the temporal correlation between measurement probes or the distribution of link loss rates. Using our algorithm, we built a PlanetLab-based network tomographer, which we use to experimentally validate the correctness of the routing-matrix rank bounds and demonstrate the accuracy of our link-loss inference.
Identification of a tomato UDP-arabinosyltransferase for airborne volatile reception (2023)

Volatiles from herbivore-infested plants function as a chemical warning of future herbivory for neighboring plants. (Z)-3-Hexenol emitted from tomato plants infested by common cutworms is taken up by uninfested plants and converted to (Z)-3-hexenyl β-vicianoside (HexVic). Here we show that a wild tomato species (Solanum pennellii) shows limited HexVic accumulation compared to a domesticated tomato species (Solanum lycopersicum) after (Z)-3-hexenol exposure. Common cutworms grow better on an introgression line containing an S. pennellii chromosome 11 segment that impairs HexVic accumulation, suggesting that (Z)-3-hexenol diglycosylation is involved in the defense of tomato against herbivory. We finally reveal that HexVic accumulation is genetically associated with a uridine diphosphate-glycosyltransferase (UGT) gene cluster that harbors UGT91R1 on chromosome 11. Biochemical and transgenic analyses of UGT91R1 show that it preferentially catalyzes (Z)-3-hexenyl β-D-glucopyranoside arabinosylation to produce HexVic in planta.
The Unified Policy Framework (UPF) (2014)

Archive of Formal Proofs (AFP),https://www.isa-afp.org/entries/UPF.shtml
Effects of metformin on BRIN‐BD11 beta‐cell insulin secretory desensitization induced by prolonged exposure to sulphonylureas (2010)

The results suggest that metformin can prevent the aspects of sulphonylurea-induced beta-cell desensitization.
Surface recombination measurements on III–V candidate materials for nanostructure light-emitting diodes (2000)

Surface recombination is an important characteristic of an optoelectronic material. Although surface recombination is a limiting factor for very small devices it has not been studied intensively. We have investigated surface recombination velocity on the exposed surfaces of the AlGaN, InGaAs, and InGaAlP material systems by using absolute photoluminescence quantum efficiency measurements. Two of these three material systems have low enough surface recombination velocity to be usable in nanoscale photonic crystal light-emitting diodes.
Equalization of Multichannel Acoustic Systems in Oversampled Subbands (2009)

Equalization of room transfer functions (RTFs) is an important topic with several applications in acoustic signal processing. RTFs are often modeled as finite-impulse response filters, characterized by orders of thousands of taps and non-minimum phase. In practice, only approximate estimates of the actual RTFs are available due to measurement noise, limited estimation accuracy, and temporal variation of source-receiver position. These issues make equalization a difficult problem. In this paper, we discuss multichannel equalization with focus on inexact RTF estimates. We present a multichannel method for the equalization filter design utilizing decimated and oversampled subbands, where the full-band acoustic impulse response is decomposed into equivalent subband filters prior to equalization. This technique is not only more computationally efficient but also more robust to impulse response inaccuracies compared with the full-band counterpart.
Highly sensitive grating coupler-based surface plasmon-coupled emission (SPCE) biosensor for immunoassay (2013)

We have evaluated the performance of a novel high-content gold grating coupler-based surface plasmon-coupled emission (SPCE) biosensor system. The polyelectrolyte (PEL) layer on the system's biosensor chip surface was formed on the gold surface using a layer-by-layer (LbL) deposition technique to spatially separate fluorophores from the gold surface and as a linker layer for protein immobilization. The characteristics of the PEL spacer layers were determined by surface plasmon resonance (SPR) analysis and by ellipsometry. The SPCE response decreased as the spacer layer thickness increased above a dominant quenching range (10 nm). Two PEL layers of poly(diallyldimethylammonium chloride) and poly(acrylic acid) were found to be an effective spacer that minimized the quenching effect while maximizing SPCE responses for both direct and sandwich immunoassay formats. A mouse IgG sandwich immunoassay using this optimized spacer layer configuration showed a dose-dependent response with a 1 pg ml(-1) limit of detection by the 3σ rule. A nine log dynamic range of human IgG concentrations in unfractionated human serum could be analyzed using this approach. These results show the potential of the grating coupler-based SPCE biosensor as a sensitive platform for high-content analysis.
Determining colour gamuts of digital cameras and scanners (2002)

Abstract The determination of the colour gamuts of colour reproduction media is an important aspect of both understanding them in isolation and using them in the context of a colour reproduction system. Although this is well understood for output colour reproduction media, a solution for input media is not to be had in a simple way. To this end, in this article, we propose a method based on simulating the responses of an input medium to given spectral power distributions. We then determine the gamut of an input medium on the basis of having a set of spectra that covers the majority of all possible spectra, knowing a medium's quantized responses to them, and then determining a boundary beyond which the medium does not produce variation in its responses. © 2002 Wiley Periodicals, Inc. Col Res Appl, 28, 59–68, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.
Direct observation of efficient heat dissipation in close-packed nanoheaters using coherent EUV beams (2016)

We use coherent EUV beams to probe transport away from nanoheater arrays of varying width, spacing and substrate. We validate new collectively-diffusive transport predictions, where nanowires cool faster when closely spaced than when widely separated.
Superluminal Raman laser with enhanced cavity length sensitivity (2019)

We demonstrate experimentally a superluminal ring laser based on optically pumped Raman gain, and a self-pumped Raman depletion for producing anomalous dispersion, employing two isotopes of rubidium. By fitting the experiment data with the theoretical model, we infer that the spectral sensitivity of the superluminal Raman laser to cavity length change is enhanced by a factor of more than a thousand, compared to a conventional laser.
Hypoxia-Inducible Factor-1α Promotes Nonhypoxia-Mediated Proliferation in Colon Cancer Cells and Xenografts (2006)

Hypoxia-inducible factor-1alpha (HIF-1alpha) is a transcription factor that directly transactivates genes important for the growth and metabolism of solid tumors. HIF-1alpha is overexpressed in cancer, and its level of expression is correlated with patient mortality. Increased synthesis or stability of HIF-1alpha can be induced by hypoxia-dependent or hypoxia-independent factors. Thus, HIF-1alpha is expressed in both nonhypoxic and hypoxic cancer cells. The role of HIF-1alpha in nonhypoxia-mediated cancer cell proliferation remains speculative. We have disrupted HIF-1alpha by targeted homologous recombination in HCT116 and RKO human colon cancer cells. Loss of HIF-1alpha significantly reduced nonhypoxia-mediated cell proliferation in vitro and in vivo. Paradoxically, loss of HIF-1alpha expression did not grossly affect the hypoxic compartments within tumor xenografts in vivo, although HIF-1alpha promoted cell proliferation and survival under hypoxia in vitro. To further test the role of HIF-1alpha within tumor compartments, we generated cells with combined disruptions of both HIF-1alpha and vascular endothelial growth factor (VEGF). In all xenografts, disruption of VEGF led to marked expansion of the hypoxic compartments and growth delay. Nonetheless, the presence or absence of HIF-1alpha did not grossly affect these expanded hypoxic compartments. These data provide compelling evidence that, in a subset of colon cancers, (a) HIF-1alpha is a positive factor for nonhypoxia-mediated cell proliferation in vitro and in vivo and (b) HIF-1alpha is a positive factor for cell proliferation and survival under hypoxic conditions in vitro, but does not grossly contribute to the tumor hypoxic compartments in vivo.
Coherent Lattice Vibrations in Single-Walled Carbon Nanotubes (2006)

We have generated and detected coherent lattice vibrations in single-walled carbon nanotubes corresponding to the radial breathing mode (RBM) using ultrashort laser pulses. Because the band gap is a function of diameter, these RBM-induced diameter oscillations cause ultrafast band gap oscillations, thereby modulating the interband excitonic resonances at the phonon frequencies (3-9 THz). Excitation spectra show a large number of pronounced peaks, allowing the determination of the chiralities present in particular samples and relative population differences of particular chiralities between samples.
Single Molecules, Cells, and Super‐Resolution Optics (Nobel Lecture) (2015)

The resolution of a microscope is determined by the diffraction limit in classical microscopy, whereby objects that are separated by half a wavelength can no longer be visually separated. To go below the diffraction limit required several tricks and discoveries. In his Nobel Lecture, E. Betzig describes the developments that have led to modern super high-resolution microscopy.
NIMG-03. PREDICTING IDH MUTATION STATUS ON ROUTINE TREATMENT-NAÏVE MRI USING RADIOGENOMIC FEATURES FROM PERITUMORAL BRAIN PARENCHYMA (2016)

Mutations in isocitrate dehydrogenase (IDH-mut) are considered one of the strongest independent prognostic markers of survival in glioma. Currently, IDH-mut is determined through DNA sequencing of biopsied tissue. In IDH-mut gliomas, vascular endothelial growth factor (VEGF) expression is antagonized which reduces edema due to its dependence on hypoxia-inducible factors (HIFα). Similarly, IDH wild-type (WT, unmutated) gliomas upregulate VEGF, which induces more edema by high vascular permeability. We hypothesized that the tissue-level morphologic heterogeneity caused due to IDH-mut is reflected in the peritumoral brain parenchyma at the imaging (MRI) scale, and can possibly be captured via directional gradients (Gabor) and local intensity statistics (Haralick, Laws) texture operators. A cohort consisting of 78 studies (glioblastomas =32, low-grade gliomas =46) with T1w, T2w, FLAIR protocols was obtained from the TCIA database. 46 cases were IDH-mut and 32 were IDH-WT. Every lesion was delineated into four possible compartments: enhancing, non-enhancing, necrosis, and edema on each of the 3 protocols by an expert. Four first order statistics (mean, standard deviation, skewness, kurtosis) were derived from the various texture operators (eg., Haralick, Law, Gabor) resulting in 540 features for every sequence. Using t-test (p<0.01) and principal component analysis, a reduced set of orthogonal features were identified, to categorize every study as belonging to IDH/ IDH-WT. Gabor (captures directional gradients) and Laws (captures spotty, and wave-like patterns) features from the peritumoral edema region on T2w MRI were the most significant (p<0.01) predictors of IDH mutation, as compared to the other compartments and protocols. PCA based clustering of T2w features from edema region resulted in a sensitivity of 88.2% (PPV = 0.83, NPV = 0.90). Our results suggest that gradient and intensity statistics texture features within edema enable discrimination of IDH1 mutation vs wild type and warrants further validation on an independent dataset.
Optimizing the association between disability and biological markers in MS (2001)

Brain volume measurements are correlated with disability as assessed by the MSFC. Although in the early phase of the disease the amount of focal demyelination is important, the residual brain volume seems to be more relevant in determining disability in later phases of the disease.
P2X7 Antagonists for CNS Indications: Recent Patent Disclosures (2017)

P2X7, a ligand-gated purinergic ion channel, has been at the center of intense efforts in the pharmaceutical industry in the last 15 years due to the growing appreciation of its role in inflammation. Since 2008-2009, increased focus on CNS available compounds has led to the publication of various patents on behalf of several pharmaceutical companies. This patent review aims at analyzing the recent patent literature (2008-2016) with a particular emphasis on those patents that are thought to deal with CNS penetrant compounds on the basis of their physicochemical features, the assays described in the patents and the uses these compounds are claimed for.
Exergoeconomic and Normalized Sensitivity Analysis of Plate Heat Exchangers: A Theoretical Framework with Application (2021)

Heat exchangers are the mainstay of thermal systems and have been extensively used in desalination systems, heating, cooling units, power plants, and energy recovery systems. This chapter demonstrates a robust theoretical framework for heat exchangers investigation based on two advanced tools, i.e., exergoeconomic analysis and Normalized Sensitivity Analysis. The former is applied as a mutual application of economic and thermodynamic analyses, which is much more impactful than the conventional thermodynamic and economic analyses. This is because it allows the investigation of combinatory effects of thermodynamic and fiscal parameters which are not achieved with the conventional methods. Similarly, the Normalized Sensitivity Analysis allows a one-on-one comparison of the sensitivity of output parameters to the input parameters with entirely different magnitudes on a common platform. This rationale comparison is obtained by normalizing the sensitivity coefficients by their nominal values, which is not possible with the conventional sensitivity analyses. An experimentally validated example of a plate heat exchanger is used to demonstrate the application of the proposed framework from a desalination system.
A Novel Phase Rotation Scheme on the Constellations for the E-UTRA Uplink ACK/NACK Signals (2009)

Hybrid automatic repeat request (HARQ) is employed for the Evolved Universal Terrestrial Radio Access (E-UTRA) downlink. The ACK/NACK signals from each user equipment (UE) are multiplexed by code division multiple access (CDMA) and transmitted via a physical uplink control channel (PUCCH). The ACK/NACK signals are code spread by the cyclic shift (CS) sequences made from zero auto-correlation (ZAC) sequences; however, the orthogonality of these sequences is not guaranteed depending on the propagation channels; moreover, the amount of inter-code interference (ICI) depends on the delay spread of the channel and the transmitting timing control error of each UE. In the conventional PUCCH structure, ICI between two ACK signals does not degrade their detection performance, whereas ICI between an ACK signal and a NACK signal degrades the detection performance. This causes a serious gap between the detection performances of ACK and NACK signals, because generally in a PUCCH, there are more ACK signals than NACK signals. In this paper, we propose a novel phase rotation scheme on the constellations of ACK/NACK signals that can resolve this issue, and the simulation evaluation results confirm the benefits of the proposed phase rotation scheme.
5,6-Diaminocytidine, a Versatile Synthon for Pyrimidine-Based Bicyclic Nucleosides (2000)

This communication describes a convenient, facile, and high-yield synthesis of 3-(beta-D-ribofuranosyl)isoguanine and its 8-methyl derivative, as well as nucleoside analogues of pteridines, from a common precursor, 5,6-diaminocytidine. 5,6-Diamino-2',3', 5'-tri-O-benzoylcytidine was synthesized from 4, 6-diamino-2-oxopyrimidine in three steps.
Minority electron transport anisotropy in p-type Al/sub x/Ga/sub 1-x/N/GaN superlattices (2001)

The minority electron diffusion length, L, in Mg-doped molecular beam epitaxy (MBE) grown p-type Al/sub x/Ga/sub 1-x/N/GaN superlattices with aluminum content x=0.1 and 0.2 was measured perpendicular and parallel to the superlattice planes by the electron beam induced current technique. A large anisotropy in the transport properties was observed with the effect varying from 1:3 to 1:6. We attribute an experimentally observed diffusion length anisotropy to minority electron scattering during transport across the potential barriers of the superlattice. Reference p-GaN samples were also investigated, and the diffusion length was observed to be isotropic in both MOCVD (L=0.5 /spl mu/m) and MBE (L=0.27 /spl mu/m) grown samples.
Thetrans-10,cis-12 conjugated linoleic acid increases triacylglycerol hydrolysis in yeastSaccharomyces cerevisiae (2017)

This study revealed new aspects of the functionality of CLA in eukaryotic lipid metabolism. Yeast was proven to be an applicable model to study further the mechanism of trans-10,cis-12 CLA functionality on lipid metabolism.
Aromatic nucleophilic substitution of Cr(CO)3-complexed halogenoarenes: a new entry to dibenzo crown ethers (1985)

A new entry to dibenzo crown ethers via nucleophilic substitution of Cr(CO)3-complexed o-dichlorobenzene with the appropriate ethers is reported.
Peripheral Nerve Stimulation in MRI: Insights from a three level analysis and coupled EM-electrophysiological simulations in neuro-functionalized human models (2017)

The mechanisms of peripheral nerve stimulation (PNS) induced by the fast switching of MRI gradient coils are only partially understood, stimulation sites and E-field (or dB/dt) thresholds show large inter-subject variability and neurostimulation models based on the amphibian SENN axon model are not ideal. We propose a 3 level computational investigation that combines analysis of E-field exposure, of activation functions, and of multi-parametric EM-electrophysiological simulations in neuro-functionalized human models for different axon models and gradient waveforms. Results concerning E-field/dB/dt thresholds values and sites of neurostimulation are compared with published experimental data. A functional uncertainty analysis is also provided.
Channel Properties of SiC Trench-Etched Double-Implanted MOS (TED MOS) (2016)

We comprehensively studied the channel properties of a silicon carbide trench-etched double-implanted MOS (SiC TED MOS). The TED MOS structure provides three types of channels: trench-side-wall (TSW); top; and bottom. The mobility of the TSW channels is about three times higher than that of the top channel. In contrast, the mobility of the bottom channel is negligibly small. We argue that the difference is due to the interface trap density by using the amplitude-sweep charge pumping method. In the TSW channels, the interface trap density is much lower than in the top and bottom channels.
Death of the Safety Guidewire (2016)

The safety guidewire has been an integral tool in endourologic percutaneous and ureteroscopic procedures for the last three decades, providing access to the collecting system or ureter in the event of loss of renal contact or ureteral perforation, respectively. However, recent advances in endourologic techniques and instrumentation have obviated the need of routine safety guidewire placement. Today the establishment of a "through-and-through" flank to urethral meatus guidewire eliminates the need of an additional guidewire during percutaneous procedures. Likewise, the availability of smaller flexible ureteroscopes, as well as modern ureteral access sheaths, has reduced the necessity of safety guidewire placement in ureteroscopic procedures. Herein, we trace the historical development of the safety guidewire concept, review recent advances in technologies that have obsoleted the safety guidewire, and evaluate recent data suggesting that continued use of a safety guidewire during ureteroscopic procedures may indeed be counterproductive.
Image enhancement and denoising by complex diffusion processes (2004)

The linear and nonlinear scale spaces, generated by the inherently real-valued diffusion equation, are generalized to complex diffusion processes, by incorporating the free Schrödinger equation. A fundamental solution for the linear case of the complex diffusion equation is developed. Analysis of its behavior shows that the generalized diffusion process combines properties of both forward and inverse diffusion. We prove that the imaginary part is a smoothed second derivative, scaled by time, when the complex diffusion coefficient approaches the real axis. Based on this observation, we develop two examples of nonlinear complex processes, useful in image processing: a regularized shock filter for image enhancement and a ramp preserving denoising process.
Initiation and maturation of cilia-generated flow in newborn and postnatal mouse airway (2009)

Mucociliary clearance in the adult trachea is well characterized, but there are limited data in newborns. Cilia-generated flow was quantified across longitudinal sections of mouse trachea from birth through postnatal day (PND) 28 by tracking fluorescent microsphere speed and directionality. The percentage of ciliated tracheal epithelial cells, as determined by immunohistochemistry, was shown to increase linearly between PND 0 and PND 21 (R(2) = 0.94). While directionality measurements detected patches of flow starting at PND 3, uniform flow across the epithelia was not observed until PND 7 at a approximately 35% ciliated cell density. Flow became established at a maximal rate at PND 9 and beyond. A linear correlation was observed between the percentage of ciliated cells versus flow speed (R(2) = 0.495) and directionality (R(2) = 0.975) between PND 0 and PND 9. Cilia beat frequency (CBF) was higher at PND 0 than at all subsequent time points, but cilia beat waveform was not noticeably different. Tracheal epithelia from a mouse model of primary ciliary dyskinesia (PCD) harboring a Mdnah5 mutation showed that ciliated cell density was unaffected, but no cilia-generated flow was detected. Cilia in mutant airways were either immotile or with slow dyssynchronous beat and abnormal ciliary waveform. Overall, our studies showed that the initiation of cilia-generated flow is directly correlated with an increase in epithelial ciliation, with the measurement of directionality being more sensitive than speed for detecting flow. The higher CBF observed in newborn epithelia suggests unique physiology in the newborn trachea, indicating possible clinical relevance to the pathophysiology of respiratory distress seen in newborn PCD patients.