gebhart/patrepeval huggingface dataset:
Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4B (2019)

Development of antiviral drug resistance is a continuous concern for viruses with high mutation rates such as influenza. The use of antiviral drugs targeting host proteins required for viral replication is less likely to result in the selection of resistant viruses than treating with direct-acting antivirals. The iminosugar UV-4B is a host-targeted glucomimetic that inhibits endoplasmic reticulum α-glucosidase I and II enzymes resulting in improper glycosylation and misfolding of viral glycoproteins. UV-4B has broad-spectrum antiviral activity against diverse viruses including dengue and influenza. To examine the ability of influenza virus to develop resistance against UV-4B, mouse-adapted influenza virus was passaged in mice in the presence or absence of UV-4B and virus isolated from lungs was used to infect the next cohort of mice, for five successive passages. Deep sequencing was performed to identify changes in the viral genome during passaging in the presence or absence of UV-4B. Relatively few minor variants were identified within each virus and the ratio of nonsynonymous to synonymous (dN/dS) substitutions of minor variants confirmed no apparent positive selection following sustained exposure to UV-4B. Three substitutions (one synonymous in PB2, one nonsynonymous in M and PA each) were specifically enriched (>3%) in UV-4B-treated groups at passage five. Recombinant viruses containing each individual or combinations of these nonsynonymous mutations remained sensitive to UV-4B treatment in mice. Overall, these data provide evidence that there is a high genetic barrier to the generation and selection of escape mutants following exposure to host-targeted iminosugar antivirals.
A fusion system for real-time forward collision warning in automobiles (2004)

We describe a fusion system that combines vision-data from a single forward-looking camera with forward-looking radar data for real-time forward collision warning in automobiles. Our approach employs computer vision techniques to primarily perform the detection and tracking of vehicles and overhead structure. These detections are then fused using a probabilistic framework with co-registered radar data to reliably obtain vehicle azimuth and depth by minimizing false alarms. The resulting detections can then be used as input to any forward collision warning system. Experimental results are presented to illustrate the performance of the algorithm.
Activation of the Endothelial Nitric-oxide Synthase by Tumor Necrosis Factor-α (2001)

Cell death via apoptosis induced by tumor necrosis factor-alpha (TNF-alpha) plays an important role in many physiological and pathological conditions. The signal transduction pathway activated by this cytokine is known to be regulated by several intracellular messengers. In particular, in many systems nitric oxide (NO) has been shown to protect cells from TNF-alpha-induced apoptosis. However, whether NO can be generated by the cytokine to down-regulate its own apoptotic program has never been studied. We have addressed this question in HeLa Tet-off cell clones stably transfected with the endothelial NO synthase under a tetracycline-responsive promoter. Endothelial NO synthase, induced about 100-fold in these cells by removal of the antibiotic, retained the characteristics of the native enzyme of endothelial cells, both in terms of intracellular localization and functional activity. Expression of the endothelial NO synthase was sufficient to protect from TNF-alpha-induced apoptosis. This protection was mediated by the generation of NO. TNF-alpha itself stimulated endothelial NO synthase activity to generate NO through a pathway involving its lipid messenger, ceramide. Our results identify a novel mechanism of regulation of a signal transduction pathway activated by death receptors and suggest that NO may constitute a built-in mechanism by which TNF-alpha controls its own apoptotic program.
Impact of liver failure on the circulating extracellular vesicle miRNA repertoire (2023)

This first comprehensive analysis to the best of our knowledge of patients with varying degrees and stages of liver failure demonstrates miRNA profiles specifically within the sEV compartment to be significantly altered in progressive liver disease and highlights the diagnostic and prognostic potential of sEV-miRNA in ACLF while also establishing downstream gene targets.
Exploiting Storage Class Memory to reduce energy consumption in mobile multimedia devices (2010)

Storage Class Memory (SCM) provides a valuable opportunity to merge main memory and secondary storage since it is not only non-volatile but also randomly accessible in byte unit. In this paper, we investigate four system configurations employing SCM and Flash memory storage and evaluate how much energy can be saved from each of them. According to experimental results measured in a real system, the most expensive combination of SDRAM memory and SCM storage increases performance dramatically. Also, the configuration using SCM for both memory and data storage lowers energy consumption to roughly an eighth, but decreases performance of compute intensive jobs to half, compared with the conventional SDRAM memory and Flash memory storage configuration.
<title>Mirror vs. the lens: What's the best for laser surgery?</title> (2002)

Many surgical procedures today are performed with lasers. Most medical laser companies produce a variety of lasers units, such as C02, Nd:YAG, Erbium, Excimer, Argon, and others. Each radiates a unique wavelength of light for use in a range of surgical procedures. Many of these wavelengths lie outside the visible spectrum. To allow surgeons to target the invisible beam, medical lasers transmit a secondary, low-power, visible aiming beam coincident with the high-power treatment beam. The laser delivery system's most important characteristic is the precision with which the size arid location ofthe aiming beam coincide with the size and location ofthe treatment beam at the surgical site.
Safety Evaluation of Titanium Middle Ear Prostheses at 3.0 Tesla (2005)

C-1.
Photonic-electronic integration with polysilicon photonics in bulk CMOS (2015)

Here, I review the development of a polysilicon photonic platform that is optimized for integration with electronics fabricated on bulk silicon wafers. This platform enables large-scale monolithic integration of silicon photonics with microelectronics. A single-polysilicon deposition and lithography mask were used to simultaneously define the transistor gate, the low-loss waveguides, the depletion modulators, and the photodetectors. Several approaches to reduce optical scattering and mitigate defect state absorption are presented. Waveguide propagation loss as low as 3 dB/cm could be realized in front-end polysilicon with an end-of-line loss as low as 10 dB/cm at 1280nm. The defect state density could be enhanced to enable all-silicon, infrared photodetectors. The resulting microring resonant detectors exhibit over 20% quantum efficiency with 9.7 GHz bandwidth over a wide range of wavelengths. A complete photonic link has been demonstrated at 5 Gbps that transfers digital information from one bulk CMOS photonics chip to another.
Performance Improvement of Li Ion Battery with Non-Flammable TMP Mixed Electrolyte by Optimization of Lithium Salt Concentration and SEI Preformation Technique on Graphite Anode (2014)

We fabricated a lithium ion battery with a non-flammable trimethyl phosphate (TMP) electrolyte, which has sufficient cycle properties (capacity retention was 97% at 50 cycles) and safety improvement due to the optimization of lithium salt concentration and a graphite anode with pre-formed solid electrolyte interphase (SEI). By dissolving highly concentrated LiPF6, i.e., above 2 M, into the TMP mixed electrolyte, lithium ion easily intercalated into the graphite anode. This was because the solvation number of TMP molecule to the lithium ion decreased. When a SEI film was formed using ethylene carbonate and diethyl carbonate solvents in advance without TMP, the decomposition of the non-carbonate solvent, such as TMP, was suppressed. Eventually, we found that a safe and high-performance lithium ion battery could be fabricated only with a combination of controlling the solvation number in the electrolyte and SEI pre-forming technology on the graphite anode
Possible mechanisms of screw loosening of rigid sternal fixation (2009)

The goal of this study was to compare the performance of cancellous and cortical screws for plate and screw fixation of the sternum. Pelvic bone plates were fixated to osteoporotic sternum in both unicortical and bicortical configurations and then loaded transversely (0-50N at 2Hz) for 15,000 cycles. The resulting plate displacement was measured continuously. In the first 10 cycles bicortical screw purchase demonstrated less loosening (p=0.015), while differences between screw type was insignificant. After the 15,000 cycles, cortical screws had less loosening (p=0.039) than cancellous, while the number of cortices fixated was insignificant to loosening. These initial findings indicate that both number of cortices fixated and type of screw are both important in designing and optimized system for sternal fixation. It appears that the cortical shell regions allow more screw purchase than the osteoporotic cancellous regions, while bicortical screw purchase appears to minimize the loosening of the screws.
Effects of Doping on the Morphology and Infrared Radiative Properties of Black Silicon (2019)

For the first time, we show that the density of nanostructures on Black Silicon obtained by wafer-level cryogenic plasma processing increases with a high level of doping, extending the spectral range of its very high absorptivity from near-infrared to far-infrared. We have found experimentally and confirmed by simulations that, for highly doped Black Silicon, a high absorptivity is observed till 15 μm. Subsequent processing of SEM images reveals that these noteworthy radiative properties are probably due to particular morphological features of heavily doped Black Silicon at the nano-scale. These features are quantified through statistical image processing. Reported results pave the way to highly integrated and effective infrared sources using Black Silicon.
Recent progress in InGaN-based laser diodes fabricated on nonpolar/semipolar substrates (2011)

We report recent progress for InGaN-based lasers diodes fabricated on nonpolar/semipolar substrates. We demonstrate single-mode green lasers operating with >;3.5% wall-plug-efficiency and 100mW output power. In the blue regime we demonstrate single-mode lasers with >;23% wall-plug-efficiency and high power lasers with >;1.4W of output power.
Light distribution and thermal effects in the rat brain under optogenetic stimulation (2015)

Optical brain stimulation gained a lot of attention in neuroscience due to its superior cell-type specificity. In the design of illumination strategies, predicting the light propagation in a specific tissue is essential and requires knowledge of the optical properties of that tissue. We present the estimated absorption and reduced scattering in rodent brain tissue using non-destructive contact spatially resolved spectroscopy (cSRS). The obtained absorption and scattering in the cortex, hippocampus and striatum are similar, but lower than in the thalamus, leading to a less deep but broader light penetration profile in the thalamus. Next, the light distribution was investigated for different stimulation protocols relevant for fiber-optic based optogenetic experiments, using Monte Carlo simulation. A protocol specific analysis is proposed to evaluate the potential of thermally induced side effects.
FPGA-based nand flash memory error characterization and solid-state drive prototyping platform (abstract only) (2011)

NAND Flash memory has been widely used for data storage due to its high density, high throughput, low cost, and low power. However, as the storage cells become smaller and with more bits programmed per cell, they are expected to suffer from reduced reliability and limited endurance. Wear-leveling and signal processing can significantly improve both reliability and endurance. However, finding optimal algorithms would require a quick and accurate characterization of Flash memory providing an insight into the error patterns. To this end, we have designed and implemented an FPGA-based framework for quick, accurate, and comprehensive characterization of Flash memories to allow efficient algorithm explorations.
Identification and energy calibration of hadronically decaying tau leptons with the ATLAS experiment in pp collisions at √s = 8 TeV (2015)

This paper describes the trigger and offline reconstruction, identification and energy calibration algorithms for hadronic decays of tau leptons employed for the data collected from pp collisions in 2012 with the ATLAS detector at the LHC center-of-mass energy s√=8 TeV. The performance of these algorithms is measured in most cases with Z decays to tau leptons using the full 2012 dataset, corresponding to an integrated luminosity of 20.3 fb−1. An uncertainty on the offline reconstructed tau energy scale of 2% to 4%, depending on transverse energy and pseudorapidity, is achieved using two independent methods. The offline tau identification efficiency is measured with a precision of 2.5% for hadronically decaying tau leptons with one associated track, and of 4% for the case of three associated tracks, inclusive in pseudorapidity and for a visible transverse energy greater than 20 GeV. For hadronic tau lepton decays selected by offline algorithms, the tau trigger identification efficiency is measured with a precision of 2% to 8%, depending on the transverse energy. The performance of the tau algorithms, both offline and at the trigger level, is found to be stable with respect to the number of concurrent proton--proton interactions and has supported a variety of physics results using hadronically decaying tau leptons at ATLAS.
Constitutive activation of Jak‐2 and Tyk‐2 in a v‐Src‐transformed human gallbladder adenocarcinoma cell line (1998)

It is well known that v-Src phosphorylates various substrates on tyrosine residue and associates with tyrosine-phosphorylated proteins as well as proline-rich ligands through its SH2 and SH3 domains, respectively, thereby inducing oncogenic transformation. A signal pathway from the cell surface to genes in the nucleus, the Jak/STAT (signal transducers and activators of transcription) pathway, has been shown to be involved in the signal transduction mechanism mediated by many cytokines and growth factors. Although a member of the STAT family, STAT3 has been reported to be constitutively activated in several v-Src-transformed cells, and it still remains unknown whether Jak molecules, which act upstream of STATs, are involved in the v-Src-induced activation mechanism of STAT3. In this study, we analyzed activations of both Jak and STAT molecules using v-Src-transformed HAG-1 cells derived from a human gallbladder adenocarcinoma. STAT3 was found to be constitutively activated in v-Src-transformed HAG-1 cells, but not in either non-transformed mock-transfected or activated c-H-ras-transfected HAG-1 cells, even though the other known STAT molecules are expressed. Furthermore, both Jak-2 and Tyk-2 were constitutively activated only in v-Src-transformed HAG-1 cells. Association of v-Src with either STAT3 or the Jak molecules was not observed. No change of this activation was detected by either interferon (IFN)-α2a or IFN-γ, which had shown inhibitory effects on the growth of v-Src-transformed HAG-1 cells. These results raise the possibility that Jak-2 and Tyk-2 are both activated by v-Src, thereby contributing to the constitutive activation of STAT3 in the v-Src-transformed cells. J. Cell. Physiol. 175:220–228, 1998. © 1998 Wiley-Liss, Inc.
All-optical write/read memory for 20 Gbit/s datapackets (2000)

A writable all-optical memory for variable length, 20 Gbit/s data packets is demonstrated. The memory uses an ultrafast nonlinear interferometer (UNI) gate and does not perform data inverting in each pass. Regenerative storage with low switching energies is verified.
Targeting the SREBP-1/Hsa-Mir-497/SCAP/FASN Oncometabolic Axis Inhibits the Cancer Stem-like and Chemoresistant Phenotype of Non-Small Cell Lung Carcinoma Cells (2022)

Targeting the SREBP-1/hsa-miR-497 signaling axis is a potentially effective anticancer therapeutic strategy for NSCLC.
What Words Really Mean: Exploring Possible Worlds in the Real World (2017)

Lexical semantics is a notoriously difficult topic, with no consensus yet on the best method for categorization. In his famous Twin Earth thought experiment, Putnam (1975) showed extension by reference can prevail over assumed definitions: if cats were revealed as robots controlled from Mars (and not animals at all), we would likely change our definition of CAT to preserve reference rather than realizing cats do not exist. Thus cats cannot be defined as inherently being animals even in ordinary circumstances.&#13;\nBut we need not invoke imaginary possible worlds to investigate the limits of categories. In fact, we can observe real world changes in lexical usage patterns that reveal pre-existing bias in lexical meaning. For example, Putnam mentions two similar examples of words changing meaning following scientific advancement: GOLD and JADE. In the case of GOLD, once methods were discovered to distinguish fool’s gold (pyrite) from GOLD, the narrower meaning prevailed. However, in the case of JADE, mineral analysis revealed that JADE in fact referred to two distinct minerals, and that wider meaning prevailed. We could consider these to be instances of semantic change, but another possibility is to view them as tests of the true, original lexical meaning. When circumstances change in the world, usage patterns adjust, but at least to some extent, it is the original meaning (or at least most salient aspects of that original meaning) that prevails. WHAT IF becomes WHAT NEXT?&#13;\nThis paper explores the extent to which we can study lexical meaning by observing changes in usage. By imagining plausible possible worlds, we may even be able to make predictions about future usage. In synchronic usage, even obvious components of definitions may turn out to be optional. Consider HUSBAND, defined in the first edition of the Oxford English Dictionary (1899) as: “a man joined to a woman by marriage. Correlative of WIFE.” Only recently in the OED’s third edition (2016) was the entry updated to account for new usage following legalized gay marriage: “male partner in a marriage.” This paper considers the OED’s first definition inaccurate: HUSBAND has always meant MALE SPOUSE rather than (MALE) SPOUSE OF WOMAN, but recognizing that nuance required changes in culture and law because earlier context did not disambiguate the definition. Similar lexical meanings are presented from the perspective of changing contexts, including a survey of speaker’s judgments to refine assumed definitions, hinting at possible future usage and dictionary definitions.
Friction between Brush Layers of Charged and Neutral Bottle-Brush Macromolecules. Molecular Dynamics Simulations (2011)

Using molecular dynamics simulations, we study the lubricating properties of neutral and charged bottle-brush coatings as a function of the compression and shear stresses and brush grafting density. Our simulations have shown that in charged bottle-brush systems under shear there is a layer with excess counterions located in the middle between brush-bearing surfaces. The main deformation mode of the charged bottle-brush layers is associated with the backbone deformation, resulting in the backbone deformation ratio, α, and shear viscosity, η, being universal functions of the Weissenberg number. In the case of neutral bottle-brush systems, in addition to the backbone deformation there is also side chain deformation. The coupling between backbone and side chain deformation violates universality in the deformation ratio, α, dependence on the Weissenberg number and results in scaling exponents varying with the compression stress and brush grafting density. The existence of different length scales controlling deformation of neutral bottle brushes manifests itself in the shear viscosity, η, dependence on the shear rate, ̇γ. Shear viscosity, η, as a function of the shear rate, ̇γ, has two plateaus and two shear thinning regimes. The low shear rate plateau and shear thinning regime correspond to the backbone deformation, while the second plateau and shear thinning regime at moderate shear rates are due to side chain deformation. For both systems the value of the friction coefficient increases with increasing shear rate. The values of the friction coefficient for charged bottle-brush systems are about ten times smaller than corresponding values for neutral systems at the same shear rate.
Conical dispersions induced interface states in two-dimensional photonic crystals (2016)

In our previous work, we use accidental degeneracy to realize conical dispersions at Γ point (k = 0) in two-dimensional (2D) photonic crystals (PCs) [1]. The conical dispersion consists of a triply degenerate state with two linear bands touching at the Dirac-like point and an additional flat band intersecting it at the same frequency. If the conical dispersion is derived from monopole and dipole excitations, the system can be described as a zero-refractive-index material with effective permittivity and permeability equal to zero simultaneously at the Dirac-like point frequency. Generally speaking, there is no guarantee that interface states can be found at the boundary of 2D PCs. Recently, we found that if an interface is formed by two semi-infinite PCs with the system parameters slightly perturbed from the condition of conical dispersion formation, there are always interface states [2]. The conical dispersion guarantees the existence of gaps both below and above the Dirac-like point in the projected band structure, a necessary condition for the formation of interface states. Meanwhile, the quasi-longitudinal flat band in the conical dispersion ensures that these two gaps have different signs of surface impedances, which can be obtained by the layer-by-layer multiple scattering theory. Since there is a relationship between the sign of the surface impedance and the geometric phase of the bulk band, the existence of interface states can be also explained by the geometric phases of the bulk bands. The presence of interface states in such systems is verified by the microwave experiment [3].
Fluorescence diffuse optical tomography with structural a priori information (2008)

Fluorescence diffuse optical tomography (FT) is an emerging molecular imaging technique that can spatially resolve both fluorophore concentration and lifetime parameters. In this study, we investigated the performance of a frequency domain FT system for inclusions with various sizes and contrast levels. Due to the ill-posedness of the FT problem, the fluorescence parameters can not be recovered accurately. The reconstructed fluorescence parameters depend on the signal to background contrast and size of the compartments containing the fluorophores. Recently, imaging with multiple modalities has become a popular trend. Different modalities give different information on the subject under investigation. Here, we evaluated the improvement in FT reconstruction when structural a priori information from a second imaging modality was incorporated. The results demonstrated that the structural a priori information was crucial to be able to recover both parameters with high accuracy. Without such a priori information, the same fluorophore concentration for different object sizes could not be recovered to the same value. On the other hand, when the structural a priori information was available, both fluorescence parameters could be recovered within 15% error for all the cases.