gebhart/patrepeval huggingface dataset:
Silicon meta-APD integrated with InGaAsP meta-emitter for near-infrared (NIR) for active imaging and LIDAR (2023)

The detection of Nd: YAG laser emission at 1.064 microns is important for a number of applications such as active infrared imaging and space LIDAR. We propose a silicon avalanche photodiode (APD) based on micro-scaled photonic metastructures. In one approach, the metastructure contains a hexagonal hole array filled with SiO<sub>2</sub> to yield optical diffraction and trapping. With 3D electromagnetic modeling, we optimize the array dimensions and yield 26.0% theoretical absorption at 1.064 microns. It is 59 times larger than that of the planar structure with an additional 18% dark current reduction. In another approach, the metastructure contains a ring array fabricated on the top contact layer to excite localized surface plasmons. The theoretical QE is 52 times larger and the dark current is 8.6 times lower. In addition to active imaging and LIDAR, the present meta-APD designs are also useful for broadband passive imaging, in which I<sub>p</sub>/I<sub>d</sub> can be improved by 3.9 and 8.7 times, respectively. The ring metastructure can also be integrated with an InGaAsP light emitting diode to produce coherent, directional emission at 1.064 micron to further improve SWaP in active applications.
Detecting malicious network traffic using inverse distributions of packet contents (2005)

We study the problem of detecting malicious IP traffic in the network early, by analyzing the contents of packets. Existing systems look at packet contents as a bag of substrings and study characteristics of its base distribution B where B(i) is the frequency of substring i.We propose studying the inverse distribution I where I(f) is the number of substrings that appear with frequency f. As we show using a detailed case study, the inverse distribution shows the emergence of malicious traffic very clearly not only in its "static" collection of bumps, but also in its nascent "dynamic" state when the phenomenon manifests itself only as a distortion of the inverse distribution envelope. We describe our probabilistic analysis of the inverse distribution in terms of Gaussian mixtures, our preliminary solution for discovering these bumps automatically. Finally, we briefly discuss challenges in analyzing the inverse distribution of IP contents and its applications.
Potential antitumor agents. Part 43. Synthesis and biological activity of dibasic 9-aminoacridine-4-carboxamides, a new class of antitumor agent (1984)

The synthesis and biological activities of representatives of a new class of antitumor agent, the N-[2-(dialkylamino)ethyl ]-9-aminoacridine-4-carboxamides, are reported. Members of this class are stable and very water soluble with high levels of in vitro and in vivo antitumor activity. The compounds bind tightly to double-stranded DNA by intercalation, but the requirements for antitumor activity are more restrictive. They depend critically on the separation distance, positioning, and pKa values of the two cationic centers. For in vivo activity, significant bulk tolerance exists for lipophilic but not hydrophilic groups about the C-9 acridine position and for both lipophilic and hydrophilic groups on the side-chain cationic moiety. Significant attenuation of the pKa of the side-chain cationic center abolishes activity, as does alteration of either the disposition or separation distance of the side-chain charge with respect to the chromophore.
Stable-operation design and fabrication results of a battery-less wireless-sensor interface IC with a switched-capacitor frequency-locked-loop circuit (2023)

Abstract This paper describes a method of designing a wireless-sensor interface integrated circuit that operates without a battery. Stable operation at low power is realized by integrating three kinds of circuit techniques: (i) a radio-frequency backscatter circuit for wireless sensing without power consumption, (ii) a sensor interface circuit with a frequency-locked loop for stable operation, (iii) and an energy harvester circuit with a power management function for battery-less operation. The circuit was fabricated using 0.13 μ m CMOS process technology for design verification. We realized battery-less wireless sensing with intermittent operation and achieved high stability against process, voltage and temperature variations. The sensor information was obtained from the frequency variation of the radio-frequency backscatter signal. The integrated circuit was operated with radio-frequency signal power input exceeding −5 dBm. The integrated circuit dissipated less than 107.5 μ A. The communication distance was 0.8 m at 920 MHz for 250 mW equivalent isotopically radiated power.
Amine Elimination Reactions between Homoleptic Silylamide Lanthanide Complexes and an Isopropylidene-Bridged Cyclopentadiene−Fluorene System (2002)

This contribution describes the amine elimination process as an alternative synthetic route to traditional salt metathesis for introducing the isopropylidene-bridged unsymmetrical ligand C5H5-CMe2-C13H9 (CpH-CMe2-FluH) onto group III-metal centers (Y, La, Nd) to give in turn the neutral, ate-complex-free ansa-lanthanidocenes. The reactions of homoleptic Ln[N(SiMe3)2]3 (Ln = Y (1), La (2), Nd (3)) with CpH-CMe2-FluH (4) in THF under mild conditions lead to the formation of ansa-complexes (η5,η5-Cp-CMe2-Flu)Ln(η5-Cp-CMe2-FluH) (Ln = Y (8), La (12), Nd (13)) in 70−84% isolated yields (based on 4). These reactions proceed via the rapidly formed bis(amido)lanthanide intermediates (η5-Cp-CMe2-FluH)Ln[N(SiMe3)2]2 (Ln = Y (5), La (9)), which undergo readily disproportionation/ligand redistribution reactions at 5−23 °C to give either a mono(amido)lanthanide complex (η5-Cp-CMe2-FluH)2Ln[N(SiMe3)2] (Ln = Y (6)) or another species assumed to be the binuclear complex (η5-Cp-CMe2-FluH)2Ln[μ-N(SiMe3)2]2Ln[N(SiMe3)2]2 (Ln = La (10)), respectively. Complexes 6 and 10 undergo an intramolecular amine elimination reaction under THF reflux to yield the corresponding ansa-complexes 8 and 12, respectively. The reversibility of the process has been investigated in the yttrium case: complex 8 converts back to 6 in the presence of (SiMe3)2NH in toluene at 90 °C with 50% conversion after 12 h. The effect of a noncoordinating apolar solvent on the reaction outcome of tris(amido) complexes 1−3 with 4 has been also studied using toluene, in which the low solubility presumably shifts the disproportionation equilibria and leads to the isolation of another class of compounds Ln(η5-Cp-CMe2-FluH)3 (Ln = Y (7), La (11)) in reasonable yields. Compounds 5−12 have been characterized in solution by 1D and 2D NMR techniques (1H, 13C, 1H−1H COSY, and 1H−13C HETCOR), and the solid state structures of 6 and of the mono(THF) adducts of ansa-lanthanidocenes 12 and 13 have been established by X-ray diffraction studies. The latter ansa-complexes feature very narrow Cp(centroid)−Ln−Flu(centroid) bite angles (Ln = La, 103.67(1)°; Ln = Nd, 105.08(1)°).
Blueshift of In0.2Ga0.8N/GaN single quantum well band gap energy by rapid thermal annealing (1999)

Up to 15 nm blueshift in the low-temperature photoluminescence (LT-PL) peak wavelength of Si-doped In0.2Ga0.8N/GaN single quantum well (SQW) is reported after rapid thermal annealing in atmospheric N2 ambient at temperatures below 1000 °C. We found that the thermal annealing not only blueshifts the LT-PL peak wavelength but it also improves the optical properties in terms of an increase in LT-PL peak intensity and a reduction in the spectrum width. Under the same thermal annealing conditions, however, a dielectric encapsulant layer (a spin-on silica layer) suppresses the blueshift of the LT-PL peak wavelength of the In0.2Ga0.8N/GaN QW. The effect of the thermal annealing temperature and time on the blueshift of the LT-PL peak wavelength is also reported. The possible mechanism responsible for the thermal annealing effect on the band gap energy of the In0.2Ga0.8N/GaN SQW is discussed.
Valency of CD3 binding and internalization of the CD3 cell-surface complex control T cell responses to second signals: distinction between effects on protein kinase C, cytoplasmic free calcium, and proliferation. (1986)

We have studied the relationship of valency of CD3 stimulation and modulation of the CD3 receptor complex with biochemical and proliferative responses of T cells. Anti-CD3 Fab, as well as F(ab')2 and whole antibody caused rapid modulation of the CD3 antigen, whereas anti-CD3 conjugated to Sepharose did not. In the absence of monocytes, T cells stimulated with anti-CD3 Fab, F(ab')2, or F(ab')2-Sepharose showed differences in their ability to respond to second signals given by PMA, IL 1, IL 2, or antibodies to Tp67 and Tp44. None of the anti-CD3 signals alone caused resting T cells to produce IL 2, and only the Sepharose-bound anti-CD3 F(ab')2 caused T cells to express high levels of functional IL 2 receptors. Anti-CD3 F(ab')2-Sepharose-stimulated T cells produced IL 2 and proliferated in response to each of the second signals. Because anti-CD3-Sepharose did not cause modulation of the CD3 antigen, the ability of the Sepharose-bound antibody to induce T cells to express IL 2 receptors and to respond to individual second signals may be related to lack of modulation rather than valency of binding. Anti-CD3 Fab-stimulated T cells responded to PMA but required combinations of other second signals. T cells stimulated with unmodified anti-CD3 antibody or F(ab')2 fragments responded to PMA but did not respond to any other second signals alone or in combination. Stimulations that resulted in modulation (i.e., anti-CD3 whole antibody, anti-CD3 F(ab')2, or anti-CD3 Fab fragments) caused an increase in cytoplasmic calcium levels in resting T cells but blocked proliferation of T cells in response to mitogenic lectins or CD2 stimulation. Anti-CD3 F(ab')2 on Sepharose, however, did not block T cell proliferation. Whole bivalent anti-CD3 antibody or F(ab')2 fragments, but not monovalent Fab fragments, caused a rapid translation of protein kinase C activity from cytosol to membrane in the Jurkat T cell line. Because all of these modulate the receptor, these data indicate that the functional difference between monovalent and bivalent binding to CD3 is related to antibody valency and not to antigenic modulation. The use of Fab anti-CD3 stimulation that requires combinations of second signals for proliferation allowed an analysis of the functional relationships between IL 1, anti-Tp67, and anti-Tp44.
Rate- and Site-Dependent Effects of Propafenone, Dofetilide, and the NewIKs-Blocking Agent Chromanol 293b on Individual Muscle Layers of the Intact Canine Heart (1999)

At the heart rates applied, the in vivo canine heart does not exhibit regional differences in electrophysiological properties. Given the homogeneity of antiarrhythmic drug effects, induction of local gradients of refractoriness is obviously not a common mechanism of proarrhythmia in normal hearts.
3D analysis of vapor and liquid phase of GDI injectors using laser induced exciplex fluorescence tomography in a high pressure/high temperature spray chamber (2007)

&lt;div class="htmlview paragraph"&gt;The quality of mixture formation in gasoline direct injection (GDI) engines has a significant influence on combustion, emissions and mileage. A new measurement technique was set up at an optically accessible high pressure / high temperature spray chamber to investigate the spatial mass distribution of vapor and liquid phase in order to optimize the stratified engine operation mode. Therefore a laser light sheet is traversed through the spray, the exciplex fluorescence is detected and the tomography results are quantified by the global information of the injected mass, which allows detailed spray investigations with λ-charts. For spray homogeneity analysis a new method based on histogram calculation is presented allowing grid independent comparison of different injector types.&lt;/div&gt;
Supplementary Table S3 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map (2023)

&lt;p&gt;Supplementary Table S3. Chemical-genetic interaction scores derived in this study&lt;/p&gt;
Preparing Fission Yeast for Electron Microscopy (2017)

Freezing samples while simultaneously subjecting them to a rapid increase in pressure, which inhibits ice crystal formation, is a reliable method for cryofixing fission yeast. The procedure consists simply of harvesting cells and loading them into a high-pressure freezer (HPF), and then operating the device. If equipment for high-pressure freezing is not available, fission yeast can be frozen by plunging a monolayer of cells into a liquid cryogen, usually ethane or propane. Unlike the HPF, where relatively large volumes of cells can be frozen in a single run, plunge freezing requires cells to be dispersed in a layer <20 µm thick. Unless frozen cells are to be imaged in the vitreous state, they must be fixed, dehydrated, and embedded for subsequent study by transmission electron microscopy; warming frozen cells without fixation badly damages cell structure. Fixation is best accomplished by freeze-substitution, a process in which frozen water is removed from samples by a water-miscible solvent that is liquid at a temperature low enough to prevent the cellular water from recrystallizing. Low concentrations of chemical fixatives and stains are generally added to this solvent such that they permeate the cells as the water is replaced. The activity of these additives is quite limited at the low temperatures required for minimizing ice crystal formation, but they are in the right place to react effectively as the cells warm up. Step-by-step protocols for HPF, plunge freezing, and freeze-substitution are provided here.
Controlling the Nucleation Morphology of Lithium Using ALD-Grown TiO2 (2020)

Lithium (Li) metal batteries are desirable as rechargeable storage devices due to their high energy density; however, their practical implementation is hindered by the difficulty in controlling the Li metal plating microstructure. Artificial solid-electrolyte interphases (SEIs) have shown the potential to curtail the electrochemical instabilities of lithium, and atomic layer deposition (ALD) is commonly employed for the synthesis of thin-film artificial SEIs such as Al 2 O 3 and alucone. However, these films quickly become delaminated as a result of their innate resistance to the cyclic shuttling of Li ions, resulting in marginal improvements in cell performance. Herein, we detail the use of ALD-grown TiO 2 as a nucleation layer, rather than as an artificial SEI. We show that by depositing TiO 2 directly on the Cu current collector, we can control the deposition morphology of Li in the widely studied ether-based electrolyte - 1M LiTFSi in an equal volume mixture of 1,3 dioxolane and 1,2 dimethoxyethane, with 1 weight percent of lithium nitrate as an additive. By optimizing the thickness of TiO 2 , we reveal that lithium nucleates into large deposits atop the TiO 2 film under significantly reduced overpotential, resulting in a reduction in contact surface area with the electrolyte and an increase in cell performance. We report substantial improvements in cycling efficiency with an average Coulombic efficiency of 96% after 150 cycles at a current density of 1 mA cm -2 in Li/Cu cells. In comparison to the pristine cells, voltage profiles for the champion TiO 2 -modified cell display negligible loss in charge capacity in the mid and late-stage electrochemical cycles, indicating an improvement in the reversibility of lithium stripping and plating. Using X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectroscopy (EDS), we establish that lithium plates atop TiO 2 , rather than beneath it, suggesting that the presence of TiO 2 supports the enhanced reversibility of Li stripping and plating. Also, we utilize coulometry and transmission electron microscopy (TEM) measurements to establish the effects of the TiO 2 film. All performance and characterization data will be presented and discussed.
Performance of a hardened x-ray streak camera at Lawrence Livermore National Laboratory’s National Ignition Facility (2022)

Electron tubes continue to provide the highest speeds possible for recording dynamics of hot high-energy density plasmas. Standard streak camera drive electronics and CCD readout are not compatible with the radiation environment associated with high DT fusion yield inertial confinement fusion experiments >10<sup>13</sup> 14 MeV DT neutrons or >10<sup>9</sup> n cm<sup>-2</sup> ns<sup>-1</sup>. We describe a hardened x-ray streak camera developed for the National Ignition Facility and present preliminary results from the first experiment on which it has participated, recording the time-resolved bremsstrahlung spectrum from the core of an inertial confinement fusion implosion at more than 40× the operational neutron yield limit of the previous National Ignition Facility x-ray streak cameras.
Slowing down light to 300  km/s in a deuterium-loaded fiber Bragg grating (2015)

We report light propagation with a group velocity of only 300 km/s, a group index of 1010, and a group delay of 42 ns, in a strong apodized fiber Bragg grating 12.5 mm in length. The grating was fabricated in a deuterium-loaded fiber using a femtosecond laser and a phase mask, followed by annealing to reduce residual losses. Data analysis indicates a strong index modulation of 1.98×10(-3) and an ultra-low single-pass power loss of 0.010 dB.
Overview of computational simulations for PDT treatments based on optimal choice of singlet oxygen (2017)

Effective photodynamic therapy (PDT) treatment planning and treatment monitoring requires computer simulations of both light transport in tissue and photosensitizer (PS) photophysics to accurately estimate singlet oxygen. Simply using fixed prescribed values of light dose (fluence) or PDT dose (the time integral of ‘PS concentration’ times the ‘fluence rate’) – one value for all patients – does not account for differences in the amount of singlet oxygen formed when fluence rates change or patient tissue parameters change. We will focus on singlet oxygen dose which is calculated by solving the photokinetics rate equations and which determines the effectiveness of the subsequent reactions of singlet oxygen with the cancer target and the negative effect of PS photobleaching.
The impact of bilateral or unilateral cataract surgery on visual functioning: when does second eye cataract surgery benefit patients? (2012)

Bilateral cataract surgery was associated with greater visual functioning over unilateral cataract surgery when the fellow eye had a significant cataract or poor presenting visual acuity, supporting the current practice of second eye surgery depending on the fellow eye's cataract status and visual acuity.
The selectivity of responses to red‐green colour and achromatic contrast in the human visual cortex: an fMRI adaptation study (2015)

There is controversy as to how responses to colour in the human brain are organized within the visual pathways. A key issue is whether there are modular pathways that respond selectively to colour or whether there are common neural substrates for both colour and achromatic (Ach) contrast. We used functional magnetic resonance imaging (fMRI) adaptation to investigate the responses of early and extrastriate visual areas to colour and Ach contrast. High-contrast red-green (RG) and Ach sinewave rings (0.5 cycles/degree, 2 Hz) were used as both adapting stimuli and test stimuli in a block design. We found robust adaptation to RG or Ach contrast in all visual areas. Cross-adaptation between RG and Ach contrast occurred in all areas indicating the presence of integrated, colour and Ach responses. Notably, we revealed contrasting trends for the two test stimuli. For the RG test, unselective processing (robust adaptation to both RG and Ach contrast) was most evident in the early visual areas (V1 and V2), but selective responses, revealed as greater adaptation between the same stimuli than cross-adaptation between different stimuli, emerged in the ventral cortex, in V4 and VO in particular. For the Ach test, unselective responses were again most evident in early visual areas but Ach selectivity emerged in the dorsal cortex (V3a and hMT+). Our findings support a strong presence of integrated mechanisms for colour and Ach contrast across the visual hierarchy, with a progression towards selective processing in extrastriate visual areas.
Biochemical analysis of the interaction of fibronectin with IgG and localization of the respective binding sites (1996)

Fibronectin (Fn), a mosaic protein composed of multiple copies of three different module types (Fl, F2 and F3), has been found associated with circulating immune complexes (ICs) and immunoglobulin (Ig) aggregates in a variety of IC diseases and myeloproliferative disorders. We have previously shown that a proteolytic fragment of Mr = 25,900 Da, from the NH2-terminal domain of Fn, composed of five type 1 modules (1Fl -5Fl) binds to the major Ig classes under physiologic conditions, suggesting that the presence of Fn in ICs and cryoglobulins results from a physicochemical binding interaction between these two molecules. Using an ELISA, we now show that the interaction between Fn and IgG is: (1) not influenced by any other constituent of plasma; (2) unaffected by temperature; and (3) has an estimated Kd of 3.77 x 10(-9) M. In addition, we have further delineated the respective sites involved in the interaction between Fn and IgG. Recombinant type l module pairs (1Fl.2Fl and 4Fl.5Fl) from the NH2-terminus of Fn, expressed in yeast, were employed in an ELISA and affinity chromatography and compared with the 25.9 kDa (1Fl - 5Fl) fragment and intact Fn for binding to IgG. The 4Fl.5Fl and the 25.9 kDa fragment bound to immobilized IgG and inhibited Fn binding to IgG to nearly the same extent as the intact molecule (IC50: Fn = 6.77 x 1O(-9) M; 25.9 kDa fragment = 5 x 10(-9) M; 4Fl.5Fl = 7.6 x 10(-9) M). Thus, the binding site for IgG on the Fn molecule is localized to and completely conferred by the 4Fl.5Fl module pair (residues 151-244). Similar experiments using papain-generated Fab and Fc fragments of IgG localized the Fn binding site on IgG to the Fe region of the IgG molecule. Fn bound to the Fc fragment with a nearly identical Kd of 3.69 x 10(-9) M, as to intact IgG (3.77 x 10(-9) M). These studies support the hypothesis that the interaction between Fn and Ig may contribute to the pathophysiology of immune complex related disorders.
DJ-1 Protects Against Dopamine Toxicity: Implications for Parkinson's Disease and Aging (2012)

Parkinson's disease (PD) is a common age-related neurodegenerative disorder. Dopamine neurotoxicity, mediated through oxidative stress, is implicated in disease pathogenesis. The vesicular monoamine transporter-2 (VMAT2) transfers dopamine into synaptic vesicles preparing it for exocytotic release and preventing its cytoplasmic oxidation. DJ-1 mutations cause early-onset familial PD. Here, we show that DJ-1 protects dopaminergic neurons and controls the vesicular sequestration of dopamine by upregulating VMAT2. Overexpression of DJ-1 protected cells against dopamine toxicity, reduced oxidative stress, and increased VMAT2 expression and function. Reduced DJ-1 levels resulted in opposite effects. Dopamine vesicular sequestration and its release upon depolarization were dependent on DJ-1 levels. Transcriptional regulation of VMAT2 expression by DJ-1 was confirmed by chromatin immunoprecipitation assay. The results were corroborated in vivo using 6-hydroxydopamine hemiparkinsonian mouse model and transgenic DJ-1 knockout mice. Our experimental data point to a novel potential protective function of DJ-1, which could be used as a therapeutic tool.