gebhart/patrepeval huggingface dataset:
Structural determinants and cellular environment define processed actin as the sole substrate of the N-terminal acetyltransferase NAA80 (2018)

N-terminal (Nt) acetylation is a major protein modification catalyzed by N-terminal acetyltransferases (NATs). Methionine acidic N termini, including actin, are cotranslationally Nt acetylated by NatB in all eukaryotes, but animal actins containing acidic N termini, are additionally posttranslationally Nt acetylated by NAA80. Actin Nt acetylation was found to regulate cytoskeletal dynamics and motility, thus making NAA80 a potential target for cell migration regulation. In this work, we developed potent and selective bisubstrate inhibitors for NAA80 and determined the crystal structure of NAA80 in complex with such an inhibitor, revealing that NAA80 adopts a fold similar to other NAT enzymes but with a more open substrate binding region. Furthermore, in contrast to most other NATs, the substrate specificity of NAA80 is mainly derived through interactions between the enzyme and the acidic amino acids at positions 2 and 3 of the actin substrate and not residues 1 and 2. A yeast model revealed that ectopic expression of NAA80 in a strain lacking NatB activity partially restored Nt acetylation of NatB substrates, including yeast actin. Thus, NAA80 holds intrinsic capacity to posttranslationally Nt acetylate NatB-type substrates in vivo. In sum, the presence of a dominant cotranslational NatB in all eukaryotes, the specific posttranslational actin methionine removal in animals, and finally, the unique structural features of NAA80 leave only the processed actins as in vivo substrates of NAA80. Together, this study reveals the molecular and cellular basis of NAA80 Nt acetylation and provides a scaffold for development of inhibitors for the regulation of cytoskeletal properties.
Responses of model cortical neurons to temporal interference stimulation and related transcranial alternating current stimulation modalities (2022)

<i>Objective.</i>Temporal interference stimulation (TIS) was proposed as a non-invasive, focal, and steerable deep brain stimulation method. However, the mechanisms underlying experimentally-observed suprathreshold TIS effects are unknown, and prior simulation studies had limitations in the representations of the TIS electric field (E-field) and cerebral neurons. We examined the E-field and neural response characteristics for TIS and related transcranial alternating current stimulation modalities.<i>Approach.</i>Using the uniform-field approximation, we simulated a range of stimulation parameters in biophysically realistic model cortical neurons, including different orientations, frequencies, amplitude ratios, amplitude modulation, and phase difference of the E-fields, and obtained thresholds for both activation and conduction block.<i>Main results</i>. For two E-fields with similar amplitudes (representative of E-field distributions at the target region), TIS generated an amplitude-modulated (AM) total E-field. Due to the phase difference of the individual E-fields, the total TIS E-field vector also exhibited rotation where the orientations of the two E-fields were not aligned (generally also at the target region). TIS activation thresholds (75-230 V m<sup>-1</sup>) were similar to those of high-frequency stimulation with or without modulation and/or rotation. For E-field dominated by the high-frequency carrier and with minimal amplitude modulation and/or rotation (typically outside the target region), TIS was less effective at activation and more effective at block. Unlike AM high-frequency stimulation, TIS generated conduction block with some orientations and amplitude ratios of individual E-fields at very high amplitudes of the total E-field (>1700 V m<sup>-1</sup>).<i>Significance</i>. The complex 3D properties of the TIS E-fields should be accounted for in computational and experimental studies. The mechanisms of suprathreshold cortical TIS appear to involve neural activity block and periodic activation or onset response, consistent with computational studies of peripheral axons. These phenomena occur at E-field strengths too high to be delivered tolerably through scalp electrodes and may inhibit endogenous activity in off-target regions, suggesting limited significance of suprathreshold TIS.
A Micromagnetic Study of Signal Propagations along MCA Data Channels (2008)

We present the results of micromagnetic studies on stability and bit propagation in the patterned nanodot chains. In particular, we discuss periodic results of long-array switching using a clocking field.
ChemInform Abstract: Systematic Design of Chemical Oscillators. Part 63. Kinetics and Mechanism of Pyrogallol Autoxidation: Calibration of the Dynamic Response of an Oxygen Electrode. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
STM Vizualization of Thiol‐Containing Peptide Dendrimers on Au(111) (2007)

Peptide dendrimers assembled by solid-phase peptide synthesis using a branching diamino acid at every 2(nd) or 3(rd) position provide readily accessible synthetic model systems for proteins and enzymes. They adopt a globular shape by topology rather than by folding. Peptide dendrimers of 2(nd) and 3(rd) generation functionalized with a cysteine or cystine residue in the core were adsorbed on Au(111) surface and imaged by STM at air, under UHV, or in solution. The dendrimers appear as globular features with dimensions suggesting an extended flattened conformation, forming both single globules and ordered arrays on the surface. These images represent the first direct visualization of peptide dendrimer enzyme models.
Clinical and Immunologic Biomarkers for Histologic Regression of High-Grade Cervical Dysplasia and Clearance of HPV16 and HPV18 after Immunotherapy (2017)

<b>Purpose:</b> As previously reported, treatment of high-grade cervical dysplasia with VGX-3100 resulted in complete histopathologic regression (CR) concomitant with elimination of HPV16/18 infection in 40.0% of VGX-3100-treated patients compared with only 14.3% in placebo recipients in a randomized phase IIb study. Here, we identify clinical and immunologic characteristics that either predicted or correlated with therapeutic benefit from VGX-3100 to identify parameters that might guide clinical decision-making for this disease.<b>Experimental Design:</b> We analyzed samples taken from cervical swabs, whole blood, and tissue biopsies/resections to determine correlates and predictors of treatment success.<b>Results:</b> At study entry, the presence of preexisting immunosuppressive factors such as FoxP3 and PD-L1 in cervical lesions showed no association with treatment outcome. The combination of HPV typing and cervical cytology following dosing was predictive for both histologic regression and elimination of detectable virus at the efficacy assessment 22 weeks later (negative predictive value 94%). Patients treated with VGX-3100 who had lesion regression had a statistically significant >2-fold increase in CD137<sup>+</sup>perforin<sup>+</sup>CD8<sup>+</sup> T cells specific for the HPV genotype causing disease. Increases in cervical mucosal CD137<sup>+</sup> and CD103<sup>+</sup> infiltrates were observed only in treated patients. Perforin<sup>+</sup> cell infiltrates were significantly increased >2-fold in cervical tissue only in treated patients who had histologic CR.<b>Conclusions:</b> Quantitative measures associated with an effector immune response to VGX-3100 antigens were associated with lesion regression. Consequently, these analyses indicate that certain immunologic responses associate with successful resolution of HPV-induced premalignancy, with particular emphasis on the upregulation of perforin in the immunotherapy-induced immune response. <i>Clin Cancer Res; 24(2); 276-94. ©2017 AACR</i>.
Development of a Diamond Electron Source for Electron Optics Instruments and Evaluation of Energy Spread using the Source (2008)

Diamond that shows low or negative electron affinity has good electron emission properties. The authors are developing a diamond electron source, which is suited for electron optics instruments such as electron beam exposure systems and electron microscopes. As a result of thermionic emission evaluations, an electron emission current of practical level (116 μA at 600oC) was obtained. The energy spread of an electron beam generated by thermionic emission was measured as 0.23 eV (FWHM), the value of which was lower than those of a LaB6 cathode and a ZrO/W cathode measured together. The result of field emission evaluations, a practical beam current (459 pA) and stability (6%rms for 10 h) for scanning electron microscope (SEM) was obtained. The energy spread of over 200 pA of a high current electron beam generated by field emission was about the same as that of a tungsten field emission cathode. It was found that an unprecedentedly high current and high convergence electron source can be made by using diamond.
Generic Transport Functions (2000)

Some functionalities (e.g. fragmentation/reassembly and Encapsulating
Security Payload) provided by IPv6 can be viewed as independent of
IPv6 or even IP entirely. This document proposes to provide those
functionalities at different layers (e.g., MPLS, BIER or even
Ethernet) independent of IP.
Kontrollierte Bildung von polymeren Nanokapseln mit hoher Barriere und Vorhersage der Verkapselungseffizienz (2014)

Abstract Polymere Nanokapseln mit hoher Barriere wurden auf Basis einfacher thermodynamischer Überlegungen entwickelt. Eine gehinderte Diffusion des eingeschlossenen Materials führt zu hohen Verkapselungseffizienzen (EEs), was anhand der Verkapselung hoch flüchtiger Substanzen unterschiedlicher chemischer Beschaffenheit gezeigt wurde. Geringe Wechselwirkungen zwischen Kern‐ und Hüllenmaterial sind ausschlaggebend, um eine Phasenseparation sowie eine hohe Diffusionsbarriere der resultierenden Polymerhülle zu erzielen. Diese Wechselwirkungen können mittels der Hansen‐Löslichkeitsparameter charakterisiert und quantifiziert werden. Eine systematische Untersuchung unseres Copolymersystems offenbart einen linearen Zusammenhang zwischen den Hansen‐Löslichkeitsparametern für Wasserstoffbrücken ( δ h ) und den Verkapselungseffizienzen, was die Vorhersage des verkapselten Anteils für jedes beliebige Material ermöglicht. Zudem konnten EEs von vormals schlecht verkapselbaren Materialien durch Zugabe einer vermittelnden Substanz und gesamtheitlich verringerter δ h ‐Werte gesteigert werden.
Angle-resolved photoemission spectroscopy with a femtosecond high harmonic light source using a two-dimensional imaging electron analyzer (2007)

An experimental setup for time- and angle-resolved photoemission spectroscopy using a femtosecond 1 kHz high harmonic light source and a two-dimensional electron analyzer for parallel energy and momentum detection is presented. A selection of the 27th harmonic (41.85 eV) from the harmonic spectrum of the light source is achieved with a multilayer MoSi double mirror monochromator. The extinction efficiency of the monochromator in selecting this harmonic is shown to be better than 7:1, while the transmitted bandwidth of the selected harmonic is capable of supporting temporal pulse widths as short as 3 fs. The recorded E(k) photoelectron spectrum from a Cu(111) surface demonstrates an angular resolution of better than 0.6 degrees (=0.03 A(-1) at E(kin,e)=36 eV). Used in a pump-probe configuration, the described experimental setup represents a powerful experimental tool for studying the femtosecond dynamics of ultrafast surface processes in real time.
The Dependence of Alloy Composition of InGaAs Inserts in GaAs\n Nanopillars on Selective-Area Pattern Geometry (2013)

GaAs nanopillars with 150 nm - 200 nm long axial InGaAs inserts are grown by\nMOCVD via catalyst-free selective-area-epitaxy (SAE). The alloy composition of\nthe InGaAs region, as determined by room-temperature photoluminescence (PL),\ndepends critically on the pitch and diameter of the selective-area pattern\ngeometry. The PL emission varies based on pattern geometry from 1.0 \\{mu}m to\n1.25 \\{mu}m corresponding to a In to Ga ratio from 0.15 to &gt; 0.3. This In\nenrichment is explained by a pattern dependent change in the incorporation rate\nfor In and Ga. Capture coefficients for Ga and In adatoms are calculated for\neach pattern pitch. As the pitch decreases, these data reveal a contest between\na synergetic effect (related to nanopillar density) that increases the growth\nrate and a competition for available material that limits the growth rate.\nGallium is more susceptible to both of these effects, causing the observed\nchanges in alloy composition.\n
fMLP induces Hsp27 expression, attenuates NF-κB activation, and confers intestinal epithelial cell protection (2006)

Sustained expression of cytoprotective intestinal epithelial heat shock proteins (Hsps), particularly Hsp27, depends on stimuli derived from bacterial flora. In this study, we examined the role of the bacterial chemotactic peptide fMLP in stimulating colonic epithelial Hsp expression at concentrations encountered in a physiological milieu. Treatment of the polarized human intestinal epithelial cell line Caco2bbe with physiological concentrations of fMLP (10-100 nM) induced expression of Hsp27, but not Hsp72, in a time- and concentration-dependent manner. Induction of Hsp27 by fMLP was specific since the fMLP analogs MRP and MLP were not effective. Hsp27 induction by fMLP was blocked by the fMLP-receptor antagonist BOC-FLFLF and was blocked when the dipeptide transporter PepT1, an entry pathway for fMLP, was silenced. fMLP activated both the p38 and ERK1/2 MAP kinase pathways in Caco2bbe cells, but not the SAPK/JNK pathway. The p38 inhibitor SB203580, but not the MEK-1 inhibitor PD98059, blocked Hsp27 induction by fMLP. fMLP treatment inhibited actin depolymerization and decreased transepithelial resistance caused by the oxidant monochloramine, and this inhibition was reversed by silencing Hsp27 expression. fMLP pretreatment also inhibited activation of proinflammatory transcription factor NF-kappaB by TNF-alpha in Caco2bbe cells, reducing induction of NF-kappaB target genes by TNF-alpha both in human intestinal biopsies and Caco2bbe cells. In conclusion, fMLP may contribute to the maintenance of intestinal homeostasis by mediating physiological expression of Hsp27, enhancing cellular protection, and negatively regulating the inflammatory response.
Widespread Endoscopic Mucosal Resection of the Esophagus with Strategies for Stricture Prevention: A Preclinical Study (2005)

Partial widespread EMR of the esophagus heals without stricture formation and does not require prophylactic intervention. The use of deep mural steroid injection following a circumferential resection does not appear to prevent strictures and may result in serious adverse events. Short-term use of esophageal stents is inadequate for stricture prevention. However, better results may be anticipated with longer term (at least 6 weeks) stent use.
Biosynthesis of the Escherichia coli K5 capsular polysaccharide (1999)

Conference Article| August 01 1999 Biosynthesis of the Escherichia coli K5 capsular polysaccharide G. Griffiths; G. Griffiths 1School of Biological Sciences, 1.800 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, U.K. Search for other works by this author on: This Site PubMed Google Scholar B. Barrett; B. Barrett 1School of Biological Sciences, 1.800 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, U.K. Search for other works by this author on: This Site PubMed Google Scholar N. Cook; N. Cook 1School of Biological Sciences, 1.800 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, U.K. Search for other works by this author on: This Site PubMed Google Scholar I. S. Roberts I. S. Roberts 1 1School of Biological Sciences, 1.800 Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, U.K. 1To whom correspondence should be addressed Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1999) 27 (4): 507–512. https://doi.org/10.1042/bst0270507 Article history Received: March 05 1999 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation G. Griffiths, B. Barrett, N. Cook, I. S. Roberts; Biosynthesis of the Escherichia coli K5 capsular polysaccharide. Biochem Soc Trans 1 August 1999; 27 (4): 507–512. doi: https://doi.org/10.1042/bst0270507 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: HCA, hydrophobic cluster analysis, Kdo, 3-deoxy-D-manno-2-octulosonic acid This content is only available as a PDF. © 1999 Biochemical Society1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Thermal Performance Comparison of Thick-Film Insulated Aluminum Substrates With Metal Core PCBs for High-Power LED Modules (2012)

Evolution of lumens per watt efficacy has enabled exponential growth in light-emitting diode (LED) lighting applications. However, heat management is a major challenge for an LED module design due to the necessity to conduct heat away from the LED chip. Elevated chip temperatures cause adverse effects on LED performance, lifetime, and color. This paper compares the thermal performance of high-power LED modules made with two types of circuit boards: novel substrates based on insulated aluminum material systems (IAMSs) technology that inherently allows using thermal vias under the LEDs and traditional metal core printed circuit boards (MCPCBs) commonly used with high-power LED applications. IAMS is a thick-film insulation system developed for aluminum that cannot handle temperature higher than 660 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C. The coefficient of thermal expansion of IAMS pastes is designed to match with aluminum, which minimizes any bowing. The thermal via underneath the LED enables excellent thermal performance. More than 7 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">°</sup> C reduction in LED junction temperature at 700-mA drive current and 27% reduction in the total thermal resistance from the LED junction to the bottom of the substrate were demonstrated for the IAMS technology when compared with MCPCB. When considering only the thermal resistance of the substrate, reductions of around 70% and 50% were obtained. This versatile and low-cost material system has the potential to make LEDs even more attractive in lighting applications.
Improving Implanted Glucose Sensor Performance - Designing the Next Generation of Sensors (2013)

Abstract not Available.
Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions atsNN=2.76  TeV (2011)

The centrality dependence of the charged-particle multiplicity density at midrapidity in Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV is presented. The charged-particle density normalized per participating nucleon pair increases by about a factor of 2 from peripheral (70%-80%) to central (0%-5%) collisions. The centrality dependence is found to be similar to that observed at lower collision energies. The data are compared with models based on different mechanisms for particle production in nuclear collisions.
Predicting Chemotherapy Sensitivity Profiles for Breast Cancer Cell Lines with and Without Stem Cell-Like Features (2014)

Our current understanding of cancer-stem cells (CSCs) is that they are slow growing, generally mesenchymallike cells capable of generating tumors. Convincing evidence for the existence of such cells comes from recent lineage tracing experiments. CSCs have been reported as being resistant to conventional drug treatment and have been considered as being responsible for failure of chemotherapy. Recently, several databases aiming the genetic characterization of a large number of cancer cell lines have been made publicly available. In addition to gene expression data, these databases contain cytotoxicity information for all cell lines for a number of drugs as well. It is possible to classify known cell lines derived from a given tumor, based on how similar they are to CSCs, or in other words, to define their stem-ness, using gene-lists that define such cells. Using two such, independently generated, gene lists we found that breast cancer cell lines could be categorized into two distinct groups which we designate CSC-like and non-CSC-like. We then identified drugs to which the two groups were most sensitive to. We also generated sensitivity profiles for all drugs, within one such database, to identify chemotherapeutics with preferential action on breast cancer. We believe this is a straight-forward approach for swiftly identifying drugs that would selectively target a subpopulation of cells for any given tumor type. Keywords: Cancer, cancer stem cells, chemotherapy, cytotoxicity, database mining, lapatinib, LBW242, TKI258.
Confiding in and Listening to Virtual Agents: The Effect of Personality (2018)

We present an intelligent virtual interviewer that engages with a user in a text-based conversation and automatically infers the user's psychological traits, such as personality. We investigate how the personality of a virtual interviewer influences a user's behavior from two perspectives: the user's willingness to confide in, and listen to, a virtual interviewer. We have developed two virtual interviewers with distinct personalities and deployed them in a real-world recruiting event. We present findings from completed interviews with 316 actual job applicants. Notably, users are more willing to confide in and listen to a virtual interviewer with a serious, assertive personality. Moreover, users' personality traits, inferred from their chat text, influence their perception of a virtual interviewer, and their willingness to confide in and listen to a virtual interviewer. Finally, we discuss the implications of our work on building hyper-personalized, intelligent agents based on user traits.
Mutational analysis of a critical signaling domain of the human interleukin 4 receptor. (1994)

The human interleukin 4 receptor (hIL-4R) is a member of a superfamily of cytokine receptors defined by conserved features of their extracellular domains. The intracellular domains of the hIL-4R and of other members of this family lack any recognizable enzymatic motifs, though ligand-dependent tyrosine phosphorylation of these receptors has been observed. Recent studies have suggested that serine-rich and acidic domains within the cytoplasmic portions of cytokine receptors might be required for signal transduction. Using deletion and truncation mutants of the hIL-4R, we have explored an essential 39-amino acid signaling domain that is rich in acidic amino acid residues and in serine residues that form consensus phosphorylation sites for known serine/threonine kinases. To assess the contribution of these motifs to signaling, we engineered site-directed mutants of these residues. Surprisingly, cells expressing mutant hIL-4R lacking either the serine or the acidic amino acids retain the ability of cells expressing the wild-type receptor to proliferate in hIL-4. Furthermore, receptors in which all six cytoplasmic tyrosines are absent can function, suggesting that tyrosine phosphorylation of the receptor may be an epiphenomenon rather than a requisite event in signaling.