gebhart/patrepeval huggingface dataset:
Decreased proteasomal cleavage at nitrotyrosine sites in proteins and peptides (2021)

Removal of moderately oxidized proteins is mainly carried out by the proteasome, while highly modified proteins are no longer degradable. However, in the case of proteins modified by nitration of tyrosine residues to 3-nitrotyrosine (NO<sub>2</sub>Y), the role of the proteasome remains to be established. For this purpose, degradation assays and mass spectrometry analyses were performed using isolated proteasome and purified fractions of native cytochrome c (Cyt c) and tyrosine nitrated proteoforms (NO<sub>2</sub>Y74-Cyt c and NO<sub>2</sub>Y97-Cyt c). While Cyt c treated under mild conditions with hydrogen peroxide was preferentially degraded by the proteasome, NO<sub>2</sub>Y74- and NO<sub>2</sub>Y97-Cyt c species did not show an increased degradation rate with respect to native Cyt c. Peptide mapping analysis confirmed a decreased chymotrypsin-like cleavage at C-terminal of NO<sub>2</sub>Y sites within the protein, with respect to unmodified Y residues. Additionally, studies with the proteasome substrate suc-LLVY-AMC (Y-AMC) and its NO<sub>2</sub>Y-containing analog, suc-LLVNO<sub>2</sub>Y-AMC (NO<sub>2</sub>Y-AMC) were performed, both using isolated 20S-proteasome and astrocytoma cell lysates as the proteasomal source. Comparisons of both substrates showed a significantly decreased proteasome activity towards NO<sub>2</sub>Y-AMC. Moreover, NO<sub>2</sub>Y-AMC, but not Y-AMC degradation rates, were largely diminished by increasing the reaction pH, suggesting an inhibitory influence of the additional negative charge contained in NO<sub>2</sub>Y-AMC secondary to nitration. The mechanism of slowing of proteasome activity in NO<sub>2</sub>Y-contaning peptides was further substantiated in studies using the phenylalanine and nitro-phenylalanine peptide analog substrates. Finally, degradation rates of Y-AMC and NO<sub>2</sub>Y-AMC with proteinase K were the same, demonstrating the selective inability of the proteasome to readily cleave at nitrotyrosine sites. Altogether, data indicate that the proteasome has a decreased capability to cleave at C-terminal of NO<sub>2</sub>Y residues in proteins with respect to the unmodified residues, making this a possible factor that decreases the turnover of oxidized proteins, if they are not unfolded, and facilitating the accumulation of nitrated proteins.
Intravesical combination treatment with antisense oligonucleotides targeting heat shock protein-27 and HTI-286 as a novel strategy for high-grade bladder cancer (2009)

Clinical results of current intravesical chemotherapeutics are insufficient, and novel and safe intravesical options for high-risk bladder cancer are required to prevent both recurrence and progression. In this study, we show promising efficacy of intravesical combination treatment using antisense oligonucleotides targeting heat shock protein-27 (Hsp27; OGX427) with HTI-286, a synthetic analogue of the marine sponge product hemiasterlin. The expression of Hsp27 in bladder cancer was examined using tissue microarray analysis. Then, four bladder cancer cell lines were screened for combination effects of OGX427 with HTI-286, and the molecular mechanisms underlying the synergic effect were analyzed. Chemosensitivity against HTI-286 was also compared between mock-transfected T24 (T24 mock) cells and Hsp27-overexpressing T24 (T24 Hsp27) cells. Furthermore, in vivo data were obtained in a bioluminescent orthotopic murine model of high-grade disease. Hsp27 is expressed at higher levels in bladder cancers compared with normal bladder epithelium. OGX427 significantly enhanced cytotoxicity of HTI-286. Combination treatment induced Akt inactivation and Bcl-2 down-regulation. T24 Hsp27 cells were more resistant to HTI-286 than T24 mock cells and showed stronger Akt activation after HTI-286 treatment. The protective effect of Hsp27 against HTI-286 was suppressed by LY294002, a phosphatidylinositol 3-kinase inhibitor, indicating that Hsp27-Akt interactions are key mechanisms to enhance chemosensitivity via OGX427. Intravesical combination therapy effectively inhibited orthotopic tumor growth without toxic side effects. Our results suggest that OGX427 enhances cytotoxicity of HTI-286 through Akt inactivation and provide strong preclinical proof-of-principle for intravesical administration of OGX427 in combination with HTI-286 for high-grade bladder cancer.
DOP-based PMD monitoring in optical subcarrier multiplexed systems by carrier/ sideband equalization (2003)

We use an optical filter to equalize the power of the carrier and one of the sidebands, enabling demonstration of a novel PMD monitor for both single-and double-sideband SCM systems using DOP as the monitoring signal.
Correction: Actin Cytoskeleton Regulates Hippo Signaling (2013)

[This corrects the article on p. e73763 in vol. 8.].
A linear prediction approach to two-dimensional spectral factorization and spectral estimation. (1978)

This thesis is concerned with the extension of the theory and computational techniques of time-series linear prediction to two-dimensional (2-D) random processes. 2-D random processes are encountered in image processing, array processing, and generally wherever data is spatially dependent. The fundamental problem of linear prediction is to determine a causal and causally invertible (minimum-phase), linear, shift-invariant whitening filter for a given random process. In some cases, the exact power density spectrum of the process is known (or is assumed to be known) and finding the minimum-phase whitening filter is a deter-ministic problem. In other cases, only a finite set of samples from the random process is available, and the minimum-phase whitening filter must be estimated. Some
Label-free detection of cellular drug responses by high-throughput bright-field imaging and machine learning (2017)

In the last decade, high-content screening based on multivariate single-cell imaging has been proven effective in drug discovery to evaluate drug-induced phenotypic variations. Unfortunately, this method inherently requires fluorescent labeling which has several drawbacks. Here we present a label-free method for evaluating cellular drug responses only by high-throughput bright-field imaging with the aid of machine learning algorithms. Specifically, we performed high-throughput bright-field imaging of numerous drug-treated and -untreated cells (N = ~240,000) by optofluidic time-stretch microscopy with high throughput up to 10,000 cells/s and applied machine learning to the cell images to identify their morphological variations which are too subtle for human eyes to detect. Consequently, we achieved a high accuracy of 92% in distinguishing drug-treated and -untreated cells without the need for labeling. Furthermore, we also demonstrated that dose-dependent, drug-induced morphological change from different experiments can be inferred from the classification accuracy of a single classification model. Our work lays the groundwork for label-free drug screening in pharmaceutical science and industry.
Intracellular Distribution of Lysozyme in Rat Alveolar Type II Epithelial Cells (1994)

This study investigated the intracellular distribution of lysozyme, a protein that is synthesized and secreted by rat alveolar type II epithelial (ATII) cells and alveolar macrophages, using a polyclonal antibody generated against purified rat lysozyme. Lysozyme was immunoprecipitated with this antibody from Triton X-100 lysates of ATII cells cultured on a basement membrane derived from Englebreth-Holme-Swarm mouse sarcoma (EHS) and radiolabeled with 35S-methionine. ATII cells cultured on EHS basement membrane for several days were fixed and labeled with antibodies to surfactant apoprotein A (SP-A) and lgp-120 (a lysosomal glycoprotein), or lysozyme and lgp-120, and studied by confocal microscopy. Organelles were identified that stained positively for either anti-lysozyme or anti-lgp-120; a second population of organelles contained both markers. Similarly, two populations of SP-A-containing organelles were identified; one contained the lysosomal glycoprotein lgp-120. In addition, confocal images demonstrated that both SP-A and lysozyme were secreted by ATII cells, as evidenced by the accumulation of secretory products within the lumen of the cyst-like aggregates. When the subcellular localization of SP-A and lysozyme was studied by analytical cell fractionation, two populations of organelles were identified that contained SP-A or lysozyme. The lighter population accounted for approximately 32% of SP-A and 33% of total intracellular lysozyme and was recovered in the same region of the gradient as secretory lamellar bodies. The more dense population co-localized with lysosomes and accounted for approximately 67% of both SP-A and lysozyme recovered. Western blots of cell fractions revealed intact lysozyme in all the cell fractions. The results of these experiments suggest that lysozyme has a similar intracellular distribution as surfactant apoprotein A in ATII cells. Lysozyme is found in fractions containing lamellar bodies where it is packaged for secretion, and in lysosomal fractions where it may undergo degradation.
<title>Spatial localization using interfering photon density waves: contrast enhancement and limitations</title> (1993)

In most of the optical methods proposed for imaging an absorbing object embedded in a turbid medium, data is collected using a single source and detector scanned mechanically across the surface of the medium. In this study we exploited destructive interference of diffusive photon- density waves originating from two sources to localize one absorbing (or fluorescent) object in a scattering medium. A frequency-domain instrument is described for scanning several laser- beam spots across the surface of a turbid medium using 1D (or 2D) acousto-optical deflectors and detecting the signals with a gated, intensified CCD camera at a modulation frequency of 246 MHz. The localization of multiple objects arranged in the form of a spatial grating was investigated theoretically with an analytic model by combining the magnitude and phase of the signals detected from the objects. A novel grating pattern comprising several destructively interfering lines, which acts as spatial frequency filter, is discussed. The results were compared with those obtained using a single-source/single-detector scanning configuration. We show that the FWHM (full-width half-maximum) of the signal detected using the single- source/single-detector configuration establishes a limiting spatial scale over which multiple objects can be resolved. Beyond this limit the resolution can only be increased under severe penalty of contrast and signal loss.
Coupling SHS and SPS Processes (2014)

The consolidation of refractory ceramic powders at relatively milder conditions with respect to conventional methods represents an important target to achieve. Based on results recently reported in the literature, it is possible to state that the combination of the Self-propagating High-temperature Synthesis (SHS) with the Spark Plasma Sintering (SPS) technologies provides a useful contribution in this direction. Specifically, the two-steps processing route consisting in the synthesis of the ceramic powders by SHS and their subsequent densification by SPS is successfully utilized to obtain various dense MB 2 -based materials (M= Zr, Hf, Ta). In this regard, an important role is played by the SHS process, particularly for the synthesis of composite powders. Indeed, stronger interfaces are established among the different phases formed in-situ , so that diffusion phenomena are promoted during SPS. Additional benefits are produced by the use of the latter technology, due to the direct passage of the electric current through the powders undergoing sintering and the die containing them.
Myelodysplastic syndromes are induced by histone methylationâ€“altering ASXL1 mutations (2013)

Recurrent mutations in the gene encoding additional sex combs-like 1 (ASXL1) are found in various hematologic malignancies and associated with poor prognosis. In particular, ASXL1 mutations are common in patients with hematologic malignancies associated with myelodysplasia, including myelodysplastic syndromes (MDSs), and chronic myelomonocytic leukemia. Although loss-of-function ASXL1 mutations promote myeloid transformation, a large subset of ASXL1 mutations is thought to result in stable truncation of ASXL1. Here we demonstrate that C-terminal–truncating Asxl1 mutations (ASXL1-MTs) inhibited myeloid differentiation and induced MDS-like disease in mice. ASXL1-MT mice displayed features of human-associated MDS, including multi-lineage myelodysplasia, pancytopenia, and occasional progression to overt leukemia. ASXL1-MT resulted in derepression of homeobox A9 (Hoxa9) and microRNA-125a (miR-125a) expression through inhibition of polycomb repressive complex 2–mediated (PRC2-mediated) methylation of histone H3K27. miR-125a reduced expression of C-type lectin domain family 5, member a (Clec5a), which is involved in myeloid differentiation. In addition, HOXA9 expression was high in MDS patients with ASXL1-MT, while CLEC5A expression was generally low. Thus, ASXL1-MT–induced MDS-like disease in mice is associated with derepression of Hoxa9 and miR-125a and with Clec5a dysregulation. Our data provide evidence for an axis of MDS pathogenesis that implicates both ASXL1 mutations and miR-125a as therapeutic targets in MDS.
Low-threshold optical gain and lasing of colloidal nanoplatelets (2014)

Semiconductor nanocrystals, which are also known as colloidal quantum dots (CQDs), are highly attractive materials for high performance optoelectronic device applications such as lasers. With their size, shape and composition tunable electronic structure and optical properties, CQDs are highly desired for achieving full-color, temperature-insensitive, low-threshold and solution-processed lasers [1, 2]. However, due to their small size, they suffer from the nonradiative multiexciton Auger Recombination (AR), where energy of a bound electron-hole pair is transferred to a third particle of either an electron or a hole instead of radiative recombination. Therefore, CQDs having suppressed AR are strongly required for achieving high quality CQD-based lasers. To address this issue, CQDs having different size, shape and electronic structure have been synthesized and studied extensively [3-5]. Generally, suppression of AR and lower optical gain thresholds are achieved via reducing the wavefunction overlap of the electron and hole in a CQD. However, the separation of the electron and hole wavefunctions will dramatically decrease the oscillator strength and optical gain coefficient, which is highly critical for achieving high performance lasers. Therefore, colloidal materials with suppressed AR and high gain coefficients are highly welcomed. Here, we study optical gain performance of colloidal quantum wells [6] of CdSe-core and CdSe/CdS core/crown nanoplatelets (NPLs) that demonstrate remarkable optical properties with ultra-low threshold one- and two-photon optical pumping. As a result of their giant oscillator strength, superior optical gain and lasing performance are achieved from these colloidal NPLs with greatly enhanced gain coefficient [7].
Investigation of effects of metalization on heat spreading in bump-bonded 3D systems (2015)

In three-dimensional integrated circuits (3DICs) aggressive wafer-thinning can lead to large thermal gradients, including spikes in individual device temperatures. In this paper we have simulated the impact of highly directionalized metallization on the transistor temperatures of a two-tier bump-bonded 3D system for various thicknesses of the top tier. A 90 μm × 90 μm area of active devices in the top tier dissipates power at 250 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , creating a hotspot. The maximum difference between temperatures in-line and out-of-line with the directional wiring is 4.5% for the 20 μm thick case and 17.3% for the 1 μm thick case.
On the transition between complementary medium and zero-refractive-index medium (2012)

It is known that complementary media which are constructed as slabs that optically cancel each other have optical properties that are different from materials with a zero refractive index. However, a zero-refractive-index material can be viewed as a special case of complementary media in which the constitutive parameters go to zero. This apparent inconsistency is resolved as we find that the optical property of a system can change from complementary-like to a zero-index-like as the system parameters change when absorption is considered properly and there is an intermediate regime in which the complementary system absorbs half of the incident light. The physical reason underlying this anomalous absorption is explained. © Copyright EPLA, 2012.
Sequences of Sets (2018)

Sequential behavior such as sending emails, gathering in groups, tagging posts, or authoring academic papers may be characterized by a set of recipients, attendees, tags, or coauthors respectively. Such "sequences of sets" show complex repetition behavior, sometimes repeating prior sets wholesale, and sometimes creating new sets from partial copies or partial merges of earlier sets.
A novel iterative calibration approach for thermal infrared cameras (2013)

The accurate geometric calibration of thermal infrared (IR) cameras is of vital importance in many computer vision applications. In general, the calibration procedure consists of localizing a set of calibration points within a calibration image. This set is subsequently used to solve for the camera parameters. However, due to the physical limitations of the IR acquisition process, the localization of the calibration points often poses difficulties, subsequently leading to unsatisfying calibration results. In this work a novel IR camera calibration approach is introduced. It is able to localize the calibration points within the images of a conventional calibration board consisting of miniature light-bulbs with improved accuracy. Our algorithm models the radiation pattern of each light bulb as an ellipse and considers the center of mass of the extracted ellipsoidal region as the starting calibration point, which is refined iteratively using alternating mappings to and from an undistorted grid model. The proposed processing chain leads to a significantly reduced calibration error when compared to the state-of-the-art. Furthermore, the proposed methodology can also be used to calibrate visible-light cameras thus being suitable for the calibration of multiple camera rigs involving both visible-light and IR cameras.
Characterization of Hydrogen in Epitaxial Silicon Films Grown at Very Low Temperatures (1998)

Experimental and theoretical analyses of hydrogen atoms incorporated in epitaxial silicon films grown at very low temperatures were investigated using a high resolution X-ray diffractometer (HRXRD) and an ab-initio total energy calculation. We found that the lattice constant of the epitaxial films was expanded by the H atoms and this lattice expansion occurred only in a direction normal to the surface. We proposed the Si–H–Si configuration as a model to explain the lattice expansion phenomenon. The results of the calculation supported this model and also suggested that the microscopic stress was introduced by the H atom in the configuration. In B-doped epitaxial Si films, the B atoms were 100% neutralized by the H atoms and activated by thermal annealing. We increased the growth temperature to overcome these H related problems and succeeded in controlling the H incorporation. The B-doped Si film with a hole concentration of 1.7×10 19 cm -3 was obtained at a growth temperature of 240°C.
Comparative evaluation of three-phase isolated matrix-type PFC rectifier concepts for high efficiency 380VDC supplies of future telco and data centers (2014)

Due to the high energy consumption in data and telco centers, the use of 380V or 400V DC facility-level distribution has been proposed as an alternative to the conventional AC distribution for a more efficient power delivery structure. The DC voltage is powered from the three-phase mains by a PFC rectifier and in many cases a mains transformer is used to provide galvanic isolation. In order to achieve a high efficiency in the DC voltage generation and to implement the required isolation, a single-stage concept, such as a matrix-type rectifier that enables PFC functionality and galvanic isolation in a single conversion, can be beneficial. In addition, due to the fact that with the matrix-type rectifier the galvanic isolation is performed with a high-frequency transformer, this results in a more compact rectifier system compared to conventional systems where the mains-frequency isolation transformer is located at the input of the PFC rectifier. In this paper, an overview of isolated matrix-type PFC rectifier topologies is given and a new converter circuit is proposed, analyzed and comparatively evaluated against another promising PFC rectifier concept, the phase-modular IMY-rectifier.
Structural Diversity of Host–Guest and Intercalation Complexesof Fullerene C60 (2005)

Abstract Pristine fullerene C 60 has a fcc structure. Crystallisation of the fullerene in a variety of solvents can lead to inclusion complexes, as well as discrete host–guest complexes in the presence of cavitands and porphyrins, and related molecules. The complexes retain varying degrees of fullerene ··· fullerene interactions at the van der Waals limit, except in a limited number of cases where the fullerenes are completely shrouded by one or more included/host molecule. Analysis of the fullerene ··· fullerene interactions in these complexes reveals a diverse structural arrangement of the fullerenes. They can be organised into dimers, single linear columns or zigzag chains, double columns, spectacular fivefold Z‐shaped columnar arrays, hexagonal close‐packed layers, corrugated sheets, honeycomb motifs, non‐close‐packed layers and complex three‐dimensional networks. Disorder of the fullerenes in the solid state is common, although structures with close‐packed planar arrangements of C 60 molecules and/or with symmetry matching between the host molecule and the fullerene (two‐, three‐ and fivefold symmetry) tend to have less disorder of the fullerene. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)