gebhart/patrepeval huggingface dataset:
Tetraspanin 8 is an interactor of the metalloprotease meprin β within tetraspanin-enriched microdomains (2016)

Meprin β is a dimeric type I transmembrane protein and acts as an ectodomain sheddase at the cell surface. It was shown that meprin β cleaves the amyloid precursor protein (APP), thereby releasing neurotoxic amyloid β peptides and implicating a role of meprin β in Alzheimer's disease. In order to identify non-proteolytic regulators of meprin β, we performed a split ubiquitin yeast two-hybrid screen using a small intestinal cDNA library. In this screen we identified tetraspanin 8 (TSPAN8) as interaction partner for meprin β. Since several members of the tetraspanin family were described to interact with metalloproteases thereby affecting their localization and/or activity, we hypothesized similar functions of TSPAN8 in the regulation of meprin β. We employed cell biological methods to confirm direct binding of TSPAN8 to meprin β. Surprisingly, we did not observe an effect of TSPAN8 on the catalytic activity of meprin β nor on the specific cleavage of its substrate APP. However, both proteins were identified being present in tetraspanin-enriched microdomains. Therefore we hypothesize that TSPAN8 might be important for the orchestration of meprin β at the cell surface with impact on certain proteolytic processes that have to be further identified.
A Novel Compound ARN-3236 Inhibits Salt-Inducible Kinase 2 and Sensitizes Ovarian Cancer Cell Lines and Xenografts to Paclitaxel (2016)

<b>Purpose:</b> Salt-inducible kinase 2 (SIK2) is a centrosome kinase required for mitotic spindle formation and a potential target for ovarian cancer therapy. Here, we examine the effects of a novel small-molecule SIK2 inhibitor, ARN-3236, on sensitivity to paclitaxel in ovarian cancer.<b>Experimental Design:</b> SIK2 expression was determined in ovarian cancer tissue samples and cell lines. ARN-3236 was tested for its efficiency to inhibit growth and enhance paclitaxel sensitivity in cultures and xenografts of ovarian cancer cell lines. SIK2 siRNA and ARN-3236 were compared for their ability to produce nuclear-centrosome dissociation, inhibit centrosome splitting, block mitotic progression, induce tetraploidy, trigger apoptotic cell death, and reduce AKT/survivin signaling.<b>Results:</b> SIK2 is overexpressed in approximately 30% of high-grade serous ovarian cancers. ARN-3236 inhibited the growth of 10 ovarian cancer cell lines at an IC<sub>50</sub> of 0.8 to 2.6 μmol/L, where the IC<sub>50</sub> of ARN-3236 was inversely correlated with endogenous SIK2 expression (Pearson <i>r</i> = -0.642, <i>P</i> = 0.03). ARN-3236 enhanced sensitivity to paclitaxel in 8 of 10 cell lines, as well as in SKOv3ip (<i>P</i> = 0.028) and OVCAR8 xenografts. In at least three cell lines, a synergistic interaction was observed. ARN-3236 uncoupled the centrosome from the nucleus in interphase, blocked centrosome separation in mitosis, caused prometaphase arrest, and induced apoptotic cell death and tetraploidy. ARN-3236 also inhibited AKT phosphorylation and attenuated survivin expression.<b>Conclusions:</b> ARN-3236 is the first orally available inhibitor of SIK2 to be evaluated against ovarian cancer in preclinical models and shows promise in inhibiting ovarian cancer growth and enhancing paclitaxel chemosensitivity. <i>Clin Cancer Res; 23(8); 1945-54. ©2016 AACR</i>.
The Minimal Autoinhibited Unit of the Guanine Nucleotide Exchange Factor Intersectin (2010)

Intersectin-1L is a member of the Dbl homology (DH) domain guanine nucleotide exchange factors (GEF) which control Rho-family GTPase signaling. Intersectin-1L is a GEF that is specific for Cdc42. It plays an important role in endocytosis, and is regulated by several partners including the actin regulator N-WASP. Intact intersectin-1L shows low Cdc42 exchange activity, although the isolated catalytic DH domain shows high activity. This finding suggests that the molecule is autoinhibited. To investigate the mechanism of autoinhibition we have constructed a series of domain deletions. We find that the five SH3 domains of intersectin are important for autoinhibition, with the fifth domain (SH3(E)) being sufficient for the bulk of the autoinhibitory effect. This SH3 domain appears to primarily interact with the DH domain. We have determined the crystal structure of the SH3(E)-DH domain construct, which shows a domain swapped arrangement in which the SH3 from one monomer interacts with the DH domain of the other monomer. Analytical ultracentrifugation and gel filtration, however, show that under biochemical concentrations, the construct is fully monomeric. Thus we propose that the actual autoinhibited structure contains the related intramolecular SH3(E)-DH interaction. We propose a model in which this intramolecular interaction may block or distort the GTPase binding region of the DH domain.
<title>Point-to-point wireless communication using partially coherent optical fields</title> (2002)

Coherent light launched into an atmospheric channel experiences substantial degradation in spatial coherence as it traverses the channel, resulting in beam wander and intensity scintillation at the receiver. Launching partially coherent light with well-defined 'beam-like' properties into the channel may exploit the spatial and frequency diversity properties of the atmospheric path so that acceptably low levels of system bit error rate performance can be obtained at fiber-optic data rates. To better understand the properties of partially coherent light in an atmospheric channel, here we develop an analytic expression for the second moment of a partially coherent lowest-order Gaussian beam propagating in the presence of isotropic, homogenous atmospheric turbulence. From the second moment equation expressions for the average intensity, beam size, complex degree of coherence, and lateral coherence length are derived. These results are valid for any beam type: focused, collimated, divergent, and the limiting cases of the plane and spherical wave. Expressions obtained here exactly reduce to the diffractive equivalents for a fully coherent beam when full coherence and the absence of turbulence are assumed. In addition, results correspond to expressions obtained previously for a partially coherent collimated beam in the absence of turbulence.
Determination of Burning Velocity and Flammability Limit of Methane/Air Mixture Using Counterflow Flames (1999)

NRC publication: No
Control of Film Morphology by Folding Hydrogen-Bonded Oligo(p-phenylenevinylene) Polymers in Solution (2005)

The film morphology of π-conjugated oligomers has been controlled by self-assembly in solution. To this end supramolecular hydrogen-bonded systems of oligo(p-phenylenevinylene) (OPV) carrying ureido-s-triazine hydrogen-bonding groups are used. Neutron scattering experiments in dodecane solutions show that columnar stacks are formed. Films with thicknesses on the order of 100 nm are made that have a supramolecular organization resembling the organization present in solution. Uniform rodlike morphological domains range over several hundreds of nanometers as shown by atomic force microscopy. The rodlike morphology of the OPVs was also preserved when blended with a C60 derivative, producing stable photovoltaic devices.
Ultra-Thin Film SOI/BOX Substrate Development, Its Application and Readiness (2011)

The Ultra-Thin SOI and BOX substrates are the foundation of Fully Depleted planar technology, a CMOS scaling solution for 20 nm node and beyond. Using the Smart CutTM technology, UTSOI substrates development, with SOI &amp; BOX thickness reduced down to 12 &amp; 25 nm respectively, is on the way to High Volume Manufacturing by the end of 2011. To improve device Vt variation control, SOI total layer thickness variation of less than +/- 1 nm for all the measured points and all the preproduction wafers is already achieved and +/- 0.5 nm variation is targeted. Tight SOI thickness variation at device scale and BOX thickness variation are also demonstrated.
Thermoplastic welding apparatus and related methods (2023)

Thermoplastic welding apparatus and related methods are disclosed. An example method includes providing a smart susceptor between composite parts that are to be joined via thermoplastic welding. The example method includes positioning the composite parts and the smart susceptor on a tooling surface within a cavity of a tooling apparatus and applying a seal to the composite parts and the tooling surface to form a vacuum chamber between the composite parts and the tooling surface at a welding joint of the composite parts; producing a magnetic field at the welding joint. The example method includes providing a vacuum in the vacuum chamber during a welding operation.
Autonomic function in gastroparesis and chronic unexplained nausea and vomiting: Relationship with etiology, gastric emptying, and symptom severity (2020)

Gastroparesis and CUNV may be a manifestation of GI autonomic dysfunction or imbalance, such that sympathetic dysfunction occurs early on in the manifestation of chronic upper GI symptoms, while parasympathetic dysfunction results in more severe symptoms and delayed gastric emptying.
Dynamic Consolidation of Combustion‐Synthesized Alumina‐Titanium Diboride Composite Ceramics (1996)

A mixture of TiO 2 , B2O 3 , and Al powders was reacted exo‐thermically to form a low‐density Al 2 O 3 –TiB 2 foamed product. After the cessation of the combustion synthesis reaction, this hot foam was densified by the pressure waves generated by the detonation of an explosive charge. The delay time between the initiation of the combustion synthesis and detonation of the explosive, the thickness of the explosive charge, and the strength of sample confinement were found to influence the effectiveness of the consolidation. Analysis of the combustion synthesis reaction temperature histories and microscopy of the reacted product sponge are used to develop additional information about this reaction/consolidation process. These results, and the microstructural properties of the combustion‐synthesized and dynamically consolidated products, are discussed.
Chemical Proportionality within Molecular Networks (2021)

Molecular networking of non-targeted tandem mass spectrometry data connects structurally related molecules based on similar fragmentation spectra. Here we report the Chemical Proportionality contextualization of molecular networks. ChemProp scores the changes of abundance between two connected nodes over sequential data series which can be displayed as a direction within the network to prioritize potential biological and chemical transformations or proportional changes of related compounds. We tested the ChemProp workflow on a ground truth data set of defined mixture and highlighted the utility of the tool to prioritize specific molecules within biological samples, including bacterial transformations of bile acids, human drug metabolism and bacterial natural products biosynthesis. The ChemProp workflow is freely available through the Global Natural Products Social Molecular Networking environment.
40-Gb/s Optical Packet Buffer Using Conversion/Dispersion-Based Delays (2009)

We experimentally demonstrate a continuously tunable, all-optical packet buffer based on conversion dispersion delays. 40-Gb/s asynchronous transfer mode (ATM) packets with return-to-zero on-off keying data are buffered up to ten-packet length (116 ns). The packet buffer performance is characterized for several delay values. Power penalties of 3, 2, and 0.5 dB for zero-packet, five-packet, and ten-packet delays are achieved, respectively, at a bit error rate (BER) of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> . Reconfiguration of the packet buffer is also investigated and reconfiguration times as fast as 25 ps are shown by using a high-speed optical switch to toggle between wavelength conversion pumps. The reconfiguration is also demonstrated for a 1 ns guard time between the packets. It is observed that reconfiguration with this method results in ~1.1 and ~2 dB extra power penalty at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> BER for 1 and 25 ps guard times, respectively.
How much feedback is required in MIMO Broadcast Channels? (2006)

In this paper, a downlink communication system, in which a base station (BS) equipped with M antennas communicates with N users each equipped with K receive antennas is considered. We study the minimum required amount of feedback at the BS, in order to achieve the maximum sum-rate capacity. First, we define the amount of feedback as the average number of users who send information to the BS. In the asymptotic case of N rarr infin, we show that with finite amount of feedback, it is not possible to achieve the maximum sum-rate. Indeed, in order to reduce the gap between the achieve sum-rate and the optimum value to zero, a minimum feedback of ln ln ln N is asymptotically necessary. Then, we consider a practical scenario, in which the amount of feedback is defined as the average number of bits which is sent to the BS. We show that to achieve the maximum sum-rate, infinite amount of feedback is required. Moreover, the minimum amount of feedback, in order to reduce the gap to the optimum sum-rate to zero, scales as otimes(ln ln ln N), which is achievable by the random beam-forming scheme proposed in M. Sharif and B. Hassibi, (2005)
DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 (1993)

The design and synthesis of high-affinity FKBP12 ligands is described. These compounds potently inhibit the cis-trans-peptidylprolyl isomerase (rotamase) activity catalyzed by FKBP12 with inhibition constants (K i,app ) as low as 1 nM, yet they possess remarkable structural simplicity relative to FK506 and rapamycin, from which they are conceptually derived. The atomic structures of three FKBP12-ligand complexes and of one unbound ligand were determined by X-ray crystallography and are compared to the FKBP12-FK506 and FKBP12-rapamycin complexes
Access to 1,2-diketones by an unusual radical cascade (2011)

An unusual radical fragmentation of an unstrained cyclohexane structure was observed leading to complex 1,2-diketones.
A recent bottleneck of Y chromosome diversity coincides with a global change in culture (2015)

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Identification of the major capsid protein gene of human cytomegalovirus (1989)

The coding region for the major capsid protein (MCP) of human cytomegalovirus (HCMV) was identified by comparing the protein sequence with the respective sequences of herpes simplex virus (HSV), Epstein-Barr virus, and varicella-zoster virus. The predicted length of the HCMV MCP was 1,370 amino acids. Comparison of the MCP sequences of the different human herpesviruses showed a homology of 25% to the MCP of HSV type 1, a homology of 29% to the MCP of Epstein-Barr virus, and a homology of 23% to the MCP of varicella-zoster virus. A subfragment of the HSV type 1 KpnI i fragment encoding the MCP VP5 cross-hybridized with the HCMV HindIII U fragment containing part of the MCP gene. Northern (RNA) blot analyses with subclones out of the coding region for the HCMV MCP detected one large transcript of about 8 kilobases. A portion of the open reading frame was expressed in Escherichia coli plasmid pBD2 IC2OH as a beta-galactosidase fusion protein and was used to generate polyclonal antibodies in New Zealand White rabbits. The obtained antisera reacted in Western immunoblots with the MCP of purified HCMV virions. A monoclonal antibody against the human MCP and a monospecific rabbit antiserum against strain Colburn of simian cytomegalovirus detected the fusion protein as well as the MCP of purified virions in immunoblots.
Density gradients at hydrogel interfaces for enhanced cell penetration (2015)

We report that stiffness gradients facilitate infiltration of cells through otherwise cell-impermeable hydrogel interfaces. By enabling the separation of hydrogel manufacturing and cell seeding, and by improving cell colonization of additively manufactured hydrogel elements, interfacial density gradients present a promising strategy to progress in the creation of 3D tissue models.
Tetraferrocenylethylene, a Chiral, Organometallic Propeller: Synthesis, Structure, and Electrochemistry (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTetraferrocenylethylene, a Chiral, Organometallic Propeller: Synthesis, Structure, and ElectrochemistryBenno Bildstein, Peter Denifl, Klaus Wurst, Max Andre, Martin Baumgarten, Jan Friedrich, and Ernst Ellmerer-MuellerCite this: Organometallics 1995, 14, 9, 4334–4342Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/om00009a042https://doi.org/10.1021/om00009a042research-articleACS PublicationsRequest reuse permissionsArticle Views302Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Modes in amorphous silicon (1998)

Abstract We discuss how the vibrational modes in an amorphous material can be characterized by various correlation functions. The spectrum of modes can be expected to contain both extended and localized states separated by mobility edges. The inverse participation ratio can be used as a measure of localization. To examine the vibrational modes in more detail, we propose to study moduli of Fourier transforms of powers of the eigenvector components. We have applied the analysis to vibrational modes of amorphous silicon. The structural and potential models that we use are based on the Wooten—Winer—Weaire bond-switching algorithm and Stillinger—Weber classical potential. The structural models are cubic supercells, periodically repeated. Whereas models ranging in size from 216 to 4096 atoms have been studied, only the 4096-atom model results are included here. In the analysis, we employ only q vectors that are consistent with the boundary conditions used to obtain the modes. Upon averaging over q-vector direction, systematic dependences result. The structural aspects of the model are briefly considered. In particular, no unusual structural ordering has been detected in the pair distribution function for the 4096-atom model.
A four-pixel matched collimator for high-sensitivity SPECT imaging (2013)

We propose a wide aperture parallel-hole collimator that we call a 4-pixel matched collimator (4-PMC) for high-sensitivity SPECT imaging. The hole size of the 4-PMC is matched to four detector pixels; that is, there are four (2 × 2) pixels per collimator hole. By contrast, a 1-pixel matched collimator (1-PMC) is defined as a collimator whose hole size is matched to one detector pixel. We evaluated four types of collimator (high-resolution collimator versions and high-sensitivity collimator versions of both 4-PMC and 1-PMC) by simulation. SPECT images of a cylindrical phantom with cold spots in the noise-free condition demonstrated that the 4-PMC provided a higher-contrast image than the 1-PMC for the same collimator version. In addition, SPECT images at the noise level corresponding to a human cerebral blood flow study suggested that the high-sensitivity version of the 4-PMC provided the highest contrast image among the four collimator types. In conclusion, the high-sensitivity SPECT system using the 4-PMC can improve the trade-off between spatial resolution and sensitivity and will consequently provide improved image contrast for clinical studies of the human brain compared with the SPECT system using the 1-PMC.
Accelerating diagnosis of Parkinson’s disease through risk prediction (2021)

Overall, our machine learning approach allows for both guiding clinical decisions such as the initiation of neuroprotective interventions and importantly, the possibility of earlier diagnosis for clinical trials for disease modifying therapies.
CCR4 expressing cells cultured adherently on a capillary wall and formaldehyde fixed as the stationary phase for ligand screening by ACE (2012)

We have developed an on-line screening method for CC chemokine receptor 4 (CCR4) ligands, in which the whole cells expressed with CCR4 were cultured adherently and immobilized on the inner wall of the capillary as the stationary phase for the first time. Moreover, in this method it is unnecessary to isolate and purify the target receptors from cell membranes. Therefore, it is possible to almost completely preserve the native conformation of the target receptors. The binding activities of the immobilized CCR4 did not change. A known antagonist of CCR4, compound A, was employed to validate the bioactivity of the cell layer and stability of this method. The intraday, interday, and batch-to-batch reproducibilities were investigated (RSD ≤ 13.9%). Nonlinear chromatography was used to calculate the binding constant between the compound A and CCR4 (6.4 × 10(4)/M, RSD = 4.96%). Using this method, the qualitative and quantitative characterizations of 23 computer-aided drug design compounds were achieved and the kinetic parameters (K, k(a), k(d), and k') were obtained by nonlinear chromatography. Three active compounds were screened out, which also showed activity in chemotaxis inhibition assay. The experimental results show that this method is simple, sensitive, and efficient for drug screening. Moreover, it offered a novel way to detect the nonspecific interactions between ligands and cell membrane.