gebhart/patrepeval huggingface dataset:
Preclinical development of DNA vaccine candidates for the treatment of HPV16 induced malignancies (2012)

High-risk Human Papilloma Virus (HPV) induced malignancies are an interesting target for immunotherapy as they invariably express the viral proteins E6 and E7 that allow specific recognition of tumor cells without the risk of inducing autoimmunity. This thesis describes the preclinical development of pDNA vaccine candidates for the treatment of HPV16 induced malignancies. For this purpose gene-shuffled (SH) versions of HPV16 E6 and E7 were used to avoid the risk of transformation at the vaccination site. To improve the immunogenicity of E6SH and E7SH several optimizations strategies were evaluated. First it is shown that genetic fusion with Tetanus Toxin Fragment C (TTFC), results in a dramatic increase in immunogenicity. The resulting vaccine candidates TTFC-E6SH and TTFC-E7SH were also demonstrated to have lost their transforming potential. Secondly it is demonstrated that the mere addition of an endoplasmatic reticulum targeting sequence and a set of promiscuous CD4 helper epitopes results in an enormous increase of the immunogenicity of E6SH and E7SH. This design decreases the risk of raising competing carrier specific immune responses. Finally several nanoparticle based formulations of a model pDNA vaccine were evaluated and it is demonstrated that for in vivo applications it is essential to shield the cationic charge of such nanoparticles.
The Trade-off between Color Reproduction Accuracy and Image Sensor Noise (2008)

Image quality captured with five different spectral sensitivities were examined. Images were created with an image sensor model using four spectral images and three exposure index values. A psychophysical experiment was conducted and interval scales of preference were derived. It was shown that, as the exposure index increased, the preferred image sensor parameters shifted to better noise but less accurate color reproduction though strong image dependence was also shown. The interval scales were modeled using color difference, noise amplitude and their covariance. According to the fitting result, it was shown that even though both color difference and noise were measured in the same units, the effect of noise on the image quality was about 40% or less unless the high level perception of human visual system came into play.
Scanning tunneling microscopy study of a tunneling magneto-resistance device with coherent tunneling transports (2005)

The growth process and surface structure of a magnetic tunnel junction (MTJ) fabricated via molecular beam epitaxy is described. First, a stacking structure of Au(001) (40 nm)/Cr(001) (100 nm) was grown as a seed layer on a MgO(001) substrate at 300/spl deg/C. An Fe(001) layer with a thickness of 20 nm (bottom electrode) was deposited at room temperature and annealed at 300/spl deg/C to obtain a flat surface. Then, three atomic layers of aluminum were epitaxially grown on the bottom electrode using a Knudsen cell at room temperature. A streaky pattern from an epitaxial Al(001) layer was observed by reflection high energy electron diffraction. An Al-O barrier layer was formed by a natural oxidation in O/sub 2/ atmosphere with a pressure of 100 Torr for 15 minutes. Next, a top electrode of Fe (atomic layer) was grown at room temperature. Surface structure of each layer was probed by scanning tunneling microscopy.
Irradiation Wavelength Selective Surface Modification of a Triazeno Polymer (1996)

Standard spectroscopic and surface analysis techniques were used to study a triazeno polymer after laser treatment. Two different excimer lasers, KrF at 248 nm and XeCl at 308 nm, were applied as irradiation sources. For both excimer lasers fluences below and above the threshold of ablation were used. In the case of fluences below the threshold of ablation the irradiation led to a decrease of the absorption of the triazeno chromophore. From XPS spectrum and contact angle measurements a surface oxidation of the polymer is identified. After irradiation with fluences above the threshold of ablation for both irradiation wavelengths a different behavior is observed. Irradiation with the XeCl laser led to a less pronounced surface roughening as compared to KrF laser treatment. With the XPS and contact angle measurements, only slight changes could be detected. A totally different behavior was found for irradiation with the KrF excimer laser. The surface of the polymer turned black after the irradiation, and the oxygen and nitrogen content is drastically reduced, as determined from the XPS spectrum. The SEM pictures revealed the appearance of microstructures of about 5 μm size with some “treelike” structures at the top of the “naps”. Contact angle measurements show also the existence of a nonpolar surface. Spectroscopic techniques showed that there exists a clear difference between the irradiation of the triazeno polymer at the two wavelengths under ablation conditions. Excitation of the triazeno chromophore at 308 nm leads to clear ablation, whereas the irradiation with 248 nm introduces microstructures and a carbonized surface.
Multiplicity and transverse momentum evolution of charge-dependent correlations in pp, p–Pb, and Pb–Pb collisions at the LHC (2016)

We report on two-particle charge-dependent correlations in pp, p-Pb, and Pb-Pb collisions as a function of the pseudorapidity and azimuthal angle difference, [Formula: see text] and [Formula: see text] respectively. These correlations are studied using the balance function that probes the charge creation time and the development of collectivity in the produced system. The dependence of the balance function on the event multiplicity as well as on the trigger and associated particle transverse momentum ([Formula: see text]) in pp, p-Pb, and Pb-Pb collisions at [Formula: see text] 7, 5.02, and 2.76 TeV, respectively, are presented. In the low transverse momentum region, for [Formula: see text] GeV/<i>c</i>, the balance function becomes narrower in both [Formula: see text] and [Formula: see text] directions in all three systems for events with higher multiplicity. The experimental findings favor models that either incorporate some collective behavior (e.g. AMPT) or different mechanisms that lead to effects that resemble collective behavior (e.g. PYTHIA8 with color reconnection). For higher values of transverse momenta the balance function becomes even narrower but exhibits no multiplicity dependence, indicating that the observed narrowing with increasing multiplicity at low [Formula: see text] is a feature of bulk particle production.
Faculty Opinions recommendation of Modulation of synaptic plasticity and memory by Reelin involves differential splicing of the lipoprotein receptor Apoer2. (2005)

Apolipoprotein E receptor 2 (Apoer2), a member of the LDL receptor gene family, and its ligand Reelin control neuronal migration during brain development. Apoer2 is also essential for induction of long-term potentiation (LTP) in the adult brain. Here we show that Apoer2 is present in the postsynaptic densities of excitatory synapses where it forms a functional complex with NMDA receptors. Reelin signaling through Apoer2 markedly enhances LTP through a mechanism that requires the presence of amino acids encoded by an exon in the intracellular domain of Apoer2. This exon is alternatively spliced in an activity-dependent manner and is required for Reelin-induced tyrosine phosphorylation of NMDA receptor subunits. Mice constitutively lacking the exon perform poorly in learning and memory tasks. Thus, alternative splicing of Apoer2, a novel component of the NMDA receptor complex, controls the modulation of NMDA receptor activity, synaptic neurotransmission, and memory by Reelin. PMID: 16102539 Funding information This work was supported by: NHLBI NIH HHS, United States Grant ID: R37 HL063762 NINDS NIH HHS, United States Grant ID: NS43408 NIMH NIH HHS, United States Grant ID: MH57014 NHLBI NIH HHS, United States Grant ID: HL20948 NHLBI NIH HHS, United States Grant ID: HL63762
Scene change detection on H.264/AVC compressed video using intra mode distribution histogram based on intra prediction mode (2007)

Abstract:- This paper presents a novel scene change detection method using complexity and edge direction based on intra prediction mode in H.264/AVC compressed video. When scene change occurs, there is less temporal correlation between consecutive frames. Therefore, most of macro-blocks are encoded in intra mode. Using this property, the proposed method calculates the percentage of intra mode blocks in each predictive frame in order to get candidates of scene change frames. To detect accurate scene change frames, we generate the Intra Mode Distribution Histogram (IMDH) representing edge directionality and image roughness. By similarity matching of consecutive two IMDHs, we decide scene change frames. The distance between two IMDHs is measured using χ 2-statistic. The experimental results show that our method is efficient and robust. Key-Words: Scene Change Detection, H.264/AVC, Intra Mode Distribution Histogram. 1
Excited State Dynamics and Structures of Functionalized Phthalocyanines. 1. Self-Regulated Assembly of Zinc Helicenocyanine (2005)

Recently synthesized zinc helicenocyanine (ZnHc), where four helicene groups are fused with a phthalocyanine (Pc) core through all-carbon linkages, exhibits an unusually strong tendency of forming soluble molecular aggregates in organic solvents. The aggregation results in a strong optical absorption across most of the visible region, which is drastically different from that of its monomer. The aggregation is suppressed by dissolving ZnHc in a liquid crystal, octylbiphenylcarbonitrile (OBCN), where the monomer ZnHc dominates and exhibits a typical optical absorption spectrum of monomeric zinc phthalocyanine, except red shift in both Q- and B- bands due to pi-conjugation expansion. This study correlates optical properties and excited state dynamics of ZnHc with intra- and intermolecular electronic interactions, using quantum mechanical calculations and ultrafast transient absorption spectroscopy. Structural details of the aggregates are revealed by small-angle X-ray scattering (SAXS) to be uniformly dimers with alkoxy chains wrapped around the core of a face-to-face dimer. The results suggest that while the peripheral helicene moieties in ZnHc are electronically coupled to the Pc core via expansion of the pi-conjugation of the macrocycle, the coupling is attenuated by the "lock washer" conformation of the nonplanar peripheral helicenes which prevents pi-conjugation throughout the entire macrocycle. The interplay between pi-conjugation expansion in the macrocyle plane and the pi-pi stacking out of the macrocyle plane produces a structure that facilitates the unique optical properties and self-regulated assembly into nanoscale structures in solution. These novel optical properties are explored for potential applications in various areas.
Prion Pathogenesis is Independent of Caspase-12 (2007)

The pathogenic mechanism(s) underlying neurodegenerative diseases associated with protein misfolding is unclear. Several studies have implicated ER stress pathways in neurodegenerative conditions, including prion disease, amyotrophic lateral sclerosis, Alzheimer's disease and many others. The ER stress response and upregulation of ER stress-responsive chaperones is observed in the brains of patients affected with Creutzfeldt-Jacob disease and in mouse models of prion diseases. In particular, the processing of caspase-12, an ER-localized caspase, correlates with neuronal cell death in prion disease. However, the contribution of caspase-12 to neurodegeneration has not been directly addressed in vivo. We confirm that ER stress is induced and that caspase-12 is proteolytically processed in a murine model of infectious prion disease. To address the causality of caspase-12 in mediating infectious prion pathogenesis, we inoculated mice deficient in caspase-12 with prions. The survival, behavior, pathology and accumulation of proteinase K-resistant PrP are indistinguishable between caspase-12 knockout and control mice, suggesting that caspase-12 is not necessary for mediating the neurotoxic effects of prion protein misfolding.
Involvement of the CD95 (APO-1/Fas) receptor and ligand system in Helicobacter pylori-induced gastric epithelial apoptosis. (1998)

Helicobacter pylori infection is associated with chronic gastritis, peptic ulceration, and gastric carcinoma. The potential role of CD95-mediated apoptosis was investigated in a panel of gastric biopsies obtained from patients with H. pylori-associated chronic gastritis (n = 29) and with noninfected normal mucosa (n = 10). Immunohistochemistry revealed increased CD95 receptor expression in epithelial and lamina propria cells in chronic gastritis. By in situ hybridization, CD95 ligand mRNA was absent or low in normal mucosa but expressed at high levels in lamina propria lymphocytes and, unexpectedly, in epithelial cells in chronic gastritis. Apoptotic cells were rare in normal mucosa but were observed regularly in chronic gastritis in close proximity to CD95 ligand mRNA expression throughout the epithelial and lamina propria cells. In a functional analysis gastric epithelial cell lines were incubated with supernatants of H. pylori. Treatment with the cytotoxic isolate H. pylori 60190 but not with the noncytotoxic isolate Tx30a upregulated CD95 in up to 50% of gastric epithelial cells and induced apoptosis in these cells. H. pylori-induced apoptosis was partially prevented by blocking CD95, demonstrating the functional role of the CD95 system. These findings suggest that H. pylori-associated chronic gastritis involves apoptosis of gastric epithelial cells by activation of the CD95 receptor and ligand system.
Cervical wart virus infection, intraepithelial neoplasia and carcinoma; an immunohistological study using a panel of monoclonal antibodies (1983)

The pattern of epithelial antigen expression has been examined in normal and disordered cervical squamous epithelium using immunohistological methods and a range of monoclonal antibodies. It was demonstrated that wart virus infection (WVI) is associated with disordered staining for a keratin-associated component and for HLA-DR antigen. Furthermore, wart-infected epithelium shows strong labelling for carcinoembryonic antigen (CEA) and for human milk fat globule antigens 1 and 2 (HMFG1 and 2). In addition these antigens (CEA, HMFG1 and 2) are also expressed in mixed WVI and cervical intraepithelial neoplasia (CIN), CIN III and in carcinoma. While these findings do not allow immunohistological discrimination between non-neoplastic and neoplastic cervical epithelia, they do provide support for the view that cellular proliferation of the type induced by papilloma virus may represent an initiator stage in the process of neoplastic transformation.
SSDNeRF: Semantic Soft Decomposition of Neural Radiance Fields (2022)

Neural Radiance Fields (NeRFs) encode the radiance in a scene parameterized by the scene's plenoptic function. This is achieved by using an MLP together with a mapping to a higher-dimensional space, and has been proven to capture scenes with a great level of detail. Naturally, the same parameterization can be used to encode additional properties of the scene, beyond just its radiance. A particularly interesting property in this regard is the semantic decomposition of the scene. We introduce a novel technique for semantic soft decomposition of neural radiance fields (named SSDNeRF) which jointly encodes semantic signals in combination with radiance signals of a scene. Our approach provides a soft decomposition of the scene into semantic parts, enabling us to correctly encode multiple semantic classes blending along the same direction -- an impossible feat for existing methods. Not only does this lead to a detailed, 3D semantic representation of the scene, but we also show that the regularizing effects of the MLP used for encoding help to improve the semantic representation. We show state-of-the-art segmentation and reconstruction results on a dataset of common objects and demonstrate how the proposed approach can be applied for high quality temporally consistent video editing and re-compositing on a dataset of casually captured selfie videos.
Microstructure changes in superplastically deformed ultrafine-grained Al-3Mg-0.2Sc alloy (2015)

Experiments were conducted on an ultrafine-grained Al-3wt.%Mg-0.2wt.%Sc alloy to characterize the microstructure changes occurring during large tensile deformation at elevated temperature within a transition between superplasticity and creep. The coarse-grained material was subjected to equal-channel angular pressing at room temperature using a die which had a 90° angle between the channels. The billets were rotated by 90° in the same sense between each pass in the processing route Bc. The billets were subsequently pressed by 2 and 8 passes. Microstructure was investigated by scanning electron microscope equipped with an electron back scatter diffraction unit. Microstructure analysis showed that the movement of dislocations and the growth of grains were restricted by Al3Sc coherent precipitates formed during stabilizing annealing at 623 K for 1h. It was found that deformation behaviour of investigated Al alloy was influenced by inhomogeneity of microstructure and deformation-induced coarsening of grains. The fracture behaviour was affected by cavity formation due to high local concentration of plastic deformation at the triple points and inefficient accommodation processes of grain boundary sliding. The results showed that total tensile deformation is a consequence of a various mechanisms occurring at different stages of tensile deformation. The superplastic tensile deformation was predominantly realized by grain boundary sliding and formation of mesoscopic shear bands. The role played by grain boundary sliding is discussed.
trans-Chlorohydridobis(triethylphosphine)platinum(II) (2001)

[20436-52-6] C12H31ClP2Pt (MW 467.87) InChI = 1S/2C6H15P.ClH.Pt.H/c2*1-4-7(5-2)6-3;;;/h2*4-6H2,1-3H3;1H;;/q;;;+1;/p-1 InChIKey = SPGVJLOIUZTFML-UHFFFAOYSA-M (trans) [16842-17-4] InChI = 1S/2C6H15P.ClH.Pt.H/c2*1-4-7(5-2)6-3;;;/h2*4-6H2,1-3H3;1H;;/q;;;+1;/p-1 InChIKey = SPGVJLOIUZTFML-UHFFFAOYSA-M (catalyst for nitrile hydration1) Physical Data: mp 81–82 °C; bp 130 °C/0.01 mmHg; sublimes at 75 °C/0.01 mmHg. Solubility: sol organic solvents, incl. pentane (avoid chlorinated solvents). Form Supplied in: white solid; commercially available. Analysis of Reagent Purity: mp, NMR, IR. Preparative Method: prepared in three steps from PtCl2.2 Handling, Storage, and Precautions: air stable as the solid.
Long-term outcomes of IMiD-based trials in patients with immunoglobulin light-chain amyloidosis: a pooled analysis (2020)

Rarity of light-chain amyloidosis (AL) makes randomized studies challenging. We pooled three phase II studies of immunomodulatory drugs (IMiDs) to update survival, toxicity, and assess new response/progression criteria. Studies included were lenalidomide-dexamethasone (Len-Dex) (n = 37; years: 2004-2006), cyclophosphamide-Len-Dex (n = 35; years: 2007-2008), and pomalidomide-Dex (n = 29; years: 2008-2010) trial. Primary endpoint was hematologic response. Overall survival (OS) was calculated from registration to death and progression-free survival (PFS) was calculated from registration to progression or death. Hematologic, cardiac, and renal response/progression was assessed using the modern criteria. Analysis included 101 patients, with a median age of 65 years, 61% male, 37 newly diagnosed (ND), and 64 relapsed/refractory (RR). Median follow-up was 101 months (range 17-150) and 78% of patients died. OS and PFS for pooled cohort were 31 and 15 months, respectively. Forty-eight patients achieved a hematologic response; for ND, 10 patients (28%) achieved ≥VGPR (very good partial response) and 8 (14%) among the RR. Only cardiac stage was prognostic for OS. Common grade ≥3 toxicities were hematologic, fatigue, and rash, and were similar among studies. Hematologic and renal responses occurred more frequently and rapidly using modern response criteria; cardiac response was less frequent but occurred quickly. IMiDs can result in long progression-free intervals/survival with tolerable toxicities. The new response/progression criteria were rapid and allows for tailoring therapy.
Qualitative and quantitative determination of poloxamer surfactants by mass spectrometry (2001)

Poloxamers are polyethylene-polypropylene glycol linear co-polymers. A simple matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) method has been developed for the determination of the average molecular weight of poloxamers. The molecular mass of five standard poloxamers determined by MALDI closely corresponds to that specified by the manufacturers, and no mass distribution effects were observed. Quantitation of distributions based on the molecular mass envelope using electrospray (ES) ionization was unsuccessful. To overcome this problem, quantitation was based on fragment ions (m/z 45 and 59) which gave reproducible signals using a very high orifice voltage ( approximately 200 eV). Poloxamer concentrations were determined accurately with a good linear response using the standard addition method. We believe that the use of very small fragment ions for quantitation of polymers may become a widely applicable general technique.
Mobile phone location in dedicated and idle modes (2002)

The possibility to determine the geographical position of a cellular mobile phone has become more and more important. One main reason for this, is that location of mobile phones in the case of emergency calls becomes mandatory in the US. Also commercial markers of mobile phone location are expected to grow fast in the near future. Emergency call location and some commercial applications require location, when a mobile phone is in the dedicated mode, whereas other applications do not require call to be on. This article describes a GSM 900 trial location system, that is based on the observed time difference (OTD) location method. The first location results are presented with a test mobile phone both in the idle and dedicated modes.
Modulation Transfer Function (2009)

<strong>2.1 Introduction</strong> <br/> An optical system's image quality can be characterized in the spatial domain using the impulse response (spot size) of the system, or in the spatial-frequency domain using the Fourier transform of the impulse response, the transfer function. An ideal system would form a point image of a point object. But, because of diffraction and aberrations, a real system has an impulse response of nonzero width. The impulse response of a system is the two-dimensional image formed in response to a delta-function object, and is denoted by the symbol h(x,y). The actual image, g, formed by the system is the ideal image, f (an exact replica of the object with appropriate size scaling), convolved with the impulse response, h: f(x,y)**h(x,y)=g(x,y), where the double asterisk denotes a two-dimensional convolution. A narrower impulse response gives better image quality than a wide impulse response. Alternately, we can consider the imaging process in the spatial-frequency domain. In this context, we are concerned with the imaging of sinusoids of different frequencies, rather than the imaging of point objects. The irradiance distribution of an object can be thought of as composed of "spatial frequency" components, in the same way as a time-domain electrical signal is composed of various temporal frequencies by means of a Fourier analysis. First, consider an irradiance distribution as a function of x and y, as seen in Fig. 2.1. This irradiance distribution can represent either an object or an image. From a one-dimensional profile of the distribution, we obtain a single-variable function that can be Fourier decomposed into its constituent spatial frequencies (cycles/mm).