gebhart/patrepeval huggingface dataset:
Electrochemistry as a surrogate for protein phosphorylation: voltage-controlled assembly of reflectin A1 (2020)

Phosphorylation is among the most widely distributed mechanisms regulating the tunable structure and function of proteins in response to neuronal, hormonal and environmental signals. We demonstrate here that the low-voltage electrochemical reduction of histidine residues in reflectin A1, a protein that mediates the neuronal fine-tuning of colour reflected from skin cells for camouflage and communication in squids, acts as an <i>in vitro</i> surrogate for phosphorylation <i>in vivo</i>, driving the assembly previously shown to regulate its function. Using micro-drop voltammetry and a newly designed electrochemical cell integrated with an instrument measuring dynamic light scattering, we demonstrate selective reduction of the imidazolium side chains of histidine in monomers, oligopeptides and this complex protein in solution. The formal reduction potential of imidazolium proves readily distinguishable from those of hydronium and primary amines, allowing unequivocal confirmation of the direct and energetically selective deprotonation of histidine in the protein. The resulting 'electro-assembly' provides a new approach to probe, understand, and control the mechanisms that dynamically tune protein structure and function in normal physiology and disease. With its abilities to serve as a surrogate for phosphorylation and other mechanisms of charge neutralization, and to potentially isolate early intermediates in protein assembly, this method may be useful for analysing never-before-seen early intermediates in the phosphorylation-driven assembly of other proteins in normal physiology and disease.
Carbon Nanotube and Semiconductor Nanorods Hybrids: Preparation, Characterization, and Evaluation of Photocurrent Generation (2017)

Carbon nanotubes (CNTs) and semiconductor nanocrystals (SCNCs) are known to be interesting donor-acceptor partners due to their unique optical and electronic properties. These exciting features have led to the development of novel composites based on these two nanomaterials and to their characterization for use in various applications, such as components in sensors, transistors, solar cells and biomedical devices. Two approaches based on covalent and noncovalent methods have been suggested for coupling the SCNCs to CNTs. Most covalent conjugation methods used so far were found to disrupt the electronic structure of the CNTs or interfere with charge transfer in the CNT-SCNC interface. Moreover, it offers random and poorly organized nanoparticle coatings. Therefore, noncovalent methods are considered to be ideal for better electronic coupling. However, a key common drawback of noncovalent methods is the lack of stability which hampers their applicability. In this article, a method has been developed to couple semiconductor seeded nanorods onto CNTs through π-π interactions. The CNTs and pyrene conjugated SCNC hybrid materials were characterized by both microscopic and spectroscopic techniques. Fluorescence and photocurrent measurements suggest the proposed pi-stacking approach results in a strong electronic coupling between the CNTs and the SCNCs leading to better photocurrent efficiency than that of a covalent conjugation method reported using similar SCNC material. Overall, the CNT-SCNC films reported in the present study open the scope for the fabrication of optoelectronic devices for various applications.
Experimental and Theoretical Charge Density Studies of 8-Hydroxyquinoline Cocrystallized with Salicylic Acid (2012)

The experimental electron density distribution (EDD) in 8-hydroxyquinoline cocrystallized with salicylic acid, 1, has been determined from a multipole refinement of high-resolution X-ray diffraction data collected at 100 K. The experimental EDD is compared with theoretical densities resulting from high-level ab initio and BHandH calculations using Atoms in Molecules theory. 1 crystallizes in the triclinic crystal system, and the asymmetric unit consists of a neutral salicylic acid molecule, a salicylate anion, and an 8-hydroxyquinolinium cation exhibiting a number of inter- and intramolecular hydrogen bonds and π-π interactions. Topological analysis reveals that π-π interactions are of the "closed-shell" type, characterized by rather low and flat charge density. In general, the agreement of the topological values (ρ(bcp) and ∇(2)ρ(bcp)) between experiment and theory is good, with mean differences of 0.010 e Å(-3) and 0.036 e Å(-5), respectively. The energetics of the π-π interactions have been estimated, and excellent agreement is observed between the relative energy and the strength of π-stacking derived from the Espinosa approach, with an average difference of only 4.4 kJ mol(-1).
Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy (2014)

The structural elasticity of metal-organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer.
The influence of pitch contour on vowel discrimination in infants (1999)

Because the harmonics are farther apart in high- than in low-pitched vowels, it was predicted that it should be difficult to extract the frequencies of the formant resonances, and therefore, to discriminate high-pitched vowels. Infant-directed speech is very high in pitch, yet studies showing that young infants can discriminate vowels have used low-pitched male voices. The present study showed that 6-month olds were able to discriminate /i/ and /I/ when the pitch was 240 Hz, but were unable to do so when the pitch was 340 Hz, demonstrating that the high pitch of infant-directed speech indeed impedes vowel discrimination. How, then, do infants learn vowel discrimination? The answer may lie with the large pitch contours that are also characteristic of infant-directed speech. Because the harmonic structure follows the frequency of the fundamental, but the formant structure remains relatively constant across frequency shifts, a second prediction was made: discrimination should be better for vowels containing pitch contours than for those with steady pitch. This is exactly what was found. The addition of a downward pitch contour at both high (440–340 Hz) and low (240–140 Hz) pitches significantly improved infants discrimination of /i/ and /I/. [Research supported by NSERC.]
Passively Mode Locked GHz Femtosecond Yb-Fiber Laser Using an Intra-Cavity Martinez Compressor (2011)

We demonstrate a 130fs, 3W, 1.3GHz fiber laser system based on a passively mode-locked Yb fiber soliton oscillator using an intra-cavity Martinez compressor with adjustable dispersion and bandwidth and a linear Yb-fiber amplifier.
DNAzyme Molecular Beacon Probes for Target-Induced Signal-Amplifying Colorimetric Detection of Nucleic Acids (2010)

A novel DNAzyme molecular beacon (DNAzymeMB) strategy was developed for target-induced signal-amplifying colorimetric detection of target nucleic acids. The DNAzymeMB, which exhibits peroxidase activity in its free hairpin structure, was engineered to form a catalytically inactive hybrid through hybridization with a blocker DNA. The presence of target DNA leads to dissociation of the DNAzymeMB from the inactive hybrid through hybridization with the blocker DNA. This process results in recovery of the catalytically active DNAzymeMB, which can catalyze a colorimetric reaction that signals the presence of the target DNA. In addition, a primer was rationally designed to anneal to the blocker DNA of the blocker/target DNA duplex and displace the bound target DNA during the extension reaction. The released target DNA triggers the next cycle involving hybridization with blocker DNA, DNAzymeMB dissociation, primer extension, and target displacement. This unique amplifying strategy leads to the generation of multiple numbers of active DNAzymeMB molecules from a single target molecule and gives a detection limit down to 1 pM, a value that is nearly 3 or 5 orders of magnitude lower than those of previously reported DNAzyme molecular beacon-based DNA detection methods.
Utility of (2,4-dioxo-1,4-dihydro-2H-quinazolin-3-yl)-acetic acid hydrazide in the synthesis of some heterocyclic nitrogen compounds (2013)

An efficient synthesis of (2,4-dioxo-1,4-dihydro-2 H -quinazolin-3-yl)-acetic acid hydrazide (3) has been achieved and described. The obtained hydrazide (3) was used in building of some interesting heterocycles such as, triazole, oxadiazole, pyrazole, phthalazine, and indol-2-one rings at position 3. The structures of the obtained compounds were confirmed by IR, 1 H NMR, 13 C NMR, MS spectral and elemental analysis.
INTERACTIVE VISUAL SALESFORCE ANALYTICS (2012)

We develop an integrated salesforce analytics application that combines enterprise data from human resources, compensation, and customer relationship management systems, produces predictive data-driven analytics insights to effectively manage organizations with many salespeople, and has an interactive visual interface that allows business users to explore the data and analytics at their own pace and under their control. Named SellerScope, this application addresses many shortcomings of existing salesforce management-related offerings, including the difficulty of use, the lack of interactivity, the lack of timeliness in information reaching stakeholders, and the limited combined analysis of disparate enterprise data. Te various data and analytics solutions are described in the paper. The interface is shown through screenshots in the paper, and also in animated form in an accompanying video. The business innovations of the application and the ways in which the visual interface facilitates understanding and trust by the user are discussed.
Collision complexes in the reactions of CH+3 with C2H4 and C2H2 (1986)

We present a crossed beam study of the reactions of CH+3 with ethylene and acetylene in the relative collision energy from 0.5 to 2.0 eV. Both systems involve condensation reactions proceeding through the formation of transient collision complexes living a fraction of a rotational period which decay through ejection of one or two molecules of H2. In addition, the ethylene system also yields CH4 + C2H+3 , nominally a hydride abstraction, but also proceeding through a long-lived collision complex. Isotopic scrambling in the CD+3 +C2H4 also confirms the presence of a transient collision complex in the reaction. The similarities accompanying the flux distributions for C2H+3 and C3H+5 production in the ethylene reaction suggest a common C3H+7 intermediate. Both the acetylene and ethylene reactions yield the condensation product C3H+3 , produced through transient intermediates. The flux distribution for the ethylene reaction suggests that C3H+3 formation proceeds by sequential ejection of two H2 molecules from the initial C3H+7 intermediate. The widths of the kinetic energy distributions for C3H+3 formation imply that at least 15% of the C3H+3 products must be the more stable cyclopropenium isomer.
Jejunal and ileal absorption in patients with chronic renal disease. Effect of 1alpha-hydroxycholecalciferol. (1976)

Calcium absorption in 30-cm segments of small intestine was measured by constant perfusion of test solutions containing different concentrations of calcium gluconate. In both the jejunum and ileum, calcium absorption rates increased progressively as luminal calcium concentration was increased stepwise between 1 and 20 mM. Although calcium transport was not saturable within these limits, unidirectional flux ratios of calcium (47Ca) suggest that calcium absorption is active in both the jejunum and ileum. Calcium absorption in patients with chronic renal disease was markedly depressed in both regions of the small intestine. This was due to decreased flux out of the lumen; flux in the reverse direction was normal. Flux ratios in the renal disease patients showed no evidence for active calcium transport. Treatment of these patients for 1 wk within 2 mug/day of 1alpha-hydroxycholecalciferol [1alpha-(OH)-D3] restored net calcium absorption and unidirectional calcium flux out of the lumen to normal values in the jejunum; in the ileum, 1alpha-(OH)-D3 increased calcium absorption 60-83% of normal at the various luminal calcium concentrations. 1alpha(OH)-D3 had no effect on unidirectional calcium flux into the lumen or on xylose and electrolyte absorption in either area of the small intestine.
Silicon-Chip-Based Octave-Spanning Frequency Comb (2012)

We demonstrate an octave-spanning frequency comb via parametric four-wave mixing in a monolithic, high-Q silicon nitride microring resonator. The comb is generated from a single-frequency pump laser and spans 180 THz with a 226-GHz spacing.
Synthesis of 3-(1-hydroxyethyl)-2-azetidinones via ester-imine condensations (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of 3-(1-hydroxyethyl)-2-azetidinones via ester-imine condensationsDuane A. Burnett, Judith C. Gallucci, and David J. HartCite this: J. Org. Chem. 1985, 50, 25, 5120–5123Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/jo00225a028https://doi.org/10.1021/jo00225a028research-articleACS PublicationsRequest reuse permissionsArticle Views192Altmetric-Citations22LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Mapping Pieris rapae granulosis virus transcripts and their in vitro translation products (1988)

Poly(A)+ RNA was isolated from Pieris rapae granulosis virus (PrGV)-infected P. rapae larvae at times early (40 h postinoculation) and late (88 h postinoculation) in larval infection. Using Northern (RNA) blot analysis, we determined the sizes, relative abundances, and map locations of over 100 PrGV transcripts. Differences were found in the transcripts which had accumulated at the two time points. Splicing of these transcripts was not detected. Evidence for the expression of overlapping RNAs in PrGV was obtained. A minimum of 35 PrGV translation products were detected via hybrid selection of poly(A)+ RNA with specific PrGV restriction endonuclease fragments, followed by in vitro translation.
Positional specificity of different transcription factor classes within enhancers (2018)

Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
MEDIUM ACCESS CONTROL PROTOCOLS AND ROUTING STRATEGIES FOR WIRELESS LOCAL AND PERSONAL AREA NETWORKS (2003)

Routing Strategies for Wireless Local
Spectroscopic studies and a structural model for blue copper centers in proteins. (1976)

Low temperature absorption, circular dichroism, and magnetic circular dichroism spectral studies of the blue copper proteins Rhus vernicifera stellacyanin, bean plastocyanin, and Pseudomonas aeruginosa azurin have been made. Low energy bands attributable to the d-d transitions 2B2 leads to 2E and 2B2 leads to 2B1 in a flattened tetrahedral (D 2d) copper-(II) center are observed in these proteins at about 5000 and 10,000 cm-1, respectively. The band positions accord well with ligand field calculations based on a tetrahedral structure that is distorted approximately 6 degrees toward a square plane. The ligands in this flattened tetrahedral coordination unit in bean plastocyanin are identified from various spectroscopic experiments as His-38, Cys-85, His-88, and a deprotonated peptide nitrogen (N) a few residues above His-38.
Superbanana orbits in stellarator geometries (1979)

The presence of superbanana orbit types localized to either the interior or the exterior of stellarators and torsatrons is numerically investigated for 3.5 MeV alpha particles. The absence of the interior superbanana in both geometries is found to be due to non-conservation of the action. Exterior superbananas are found in the stellarator only, as a consequence of the existence of closed helical magnetic wells. No superbananas of either type are found in the torsatron.
Wide Dynamic Range, High Precision, Lossless Layered Coding Method (2006)

The author's previous paper “High Quality, Wide Dynamic Range, Compression System”, which was presented at SMPTE Pasadena in Oct 2004, described a highly layered precision lossy coding system. That paper introduced the concept that “visually lossless” lossy coding could be achieved by ensuring that the amplitude of quantization coding errors is always less than the inherent original image noise floor. In general, the original image noise floor is a function of brightness and color, and is sometimes a function of regions within a frame. This noise floor will also usually vary between shots and scenes.
DeepSol: a deep learning framework for sequence-based protein solubility prediction (2018)

Supplementary data are available at Bioinformatics online.
Cell death mechanisms in ALS (1996)

Mutations in copper-zinc superoxide dismutase (CuZnSOD) that are associated with familial ALS (FALS) are dominant, gain-of-function mutations, but the nature of the function gained has not been identified. In addition to catalyzing the dismutation of superoxide, copper-zinc superoxide dismutase also displays peroxidase activity. Whereas mutants A4V and G93A retained superoxide dismutase activity, they demonstrated a markedly enhanced copper-dependent peroxidase activity in comparison with that of the wild type enzyme as detected by the spin trap 5,5'-dimethyl-1-pyrroline N-oxide (DMPO) in electron paramagnetic resonance measurements. Two copper chelators, diethyldithiocarbamate and penicillamine, inhibited the mutants' peroxidase activity, but not that of the wild type enzyme, at stoichiometric concentrations; furthermore, these copper chelators enhanced neural survival in a cell-culture model of ALS but did not alter survival of cells expressing only wild type copper-zinc superoxide dismutase. These observations suggest that oxidative reactions catalyzed by mutant copper-zinc superoxide dismutases may initiate the neuropathologic changes of FALS.
Different channel coding strategies for OFDM-CDMA (2002)

The performance of different channel coding schemes are presented for an OFDM-CDMA system. The different channel coding schemes are shown for a receiver using equal gain combining on the carriers in a multipath channel. As such the only information needed at the receiver is the phase of the sub-carriers. Two new channel coding schemes for OFDM-CDMA are presented, orthogonal and super orthogonal convolutional coding. These are compared against a 1/2 rate K=7 convolutional code and a 3/4 rate K=7 punctured convolutional code. A comparison is made of the spectral efficiency of the different coding schemes, the bandwidth required and the receiver complexity tradeoffs.
Identification of signaling pathways involved in the mechanism of action of the immunomodulatory peptide gamma-D-glutamyl-L-tryptophan. (2011)

5591 Background: Gamma-D-glutamyl-L-tryptophan (SCV-07) is being studied for attenuation of oral mucositis (OM) in head and neck cancer patients receiving chemoradiation therapy. In a pilot study SCV-07-treated subjects had delayed onset of ulcerative OM (Adkins 2009) which correlated with changes in circulating cytokines (Alterovitz 2010). In animal studies SCV-07 inhibits growth of different xenografted tumor types. SCV-07 acts via immune modulation; initial evaluation of SCV-07 signaling demonstrated inhibition of cytokine induced STAT3 transcriptional activity. In this study we explored further the molecular mechanisms by which SCV-07 interferes with mucositis pathobiology and concurrently exhibits anti-tumor activity. Methods: Tyrosine phosphorylated STAT3 (STAT3 PY) was evaluated by Western blot of Jurkat or CD45 mutant Jurkat cells with or without IL-10 or IFNα stimulation and SCV-07. Global phosphorylation profiles were analyzed using phosphoprotein detection array kits. C57/B6 mice inoculated with B16F0 tumor cells were treated with vehicle or SCV-07 and plasma cytokines analyzed by multiplex assay when tumor inhibition was evident. Results: SCV-07 significantly inhibited IL-10- and IFNα-induced STAT3 PY in Jurkat cells which was blocked by pervanadate treatment, implicating tyrosine phosphatase activity. Phosphatase CD45 was not required since STAT3 PY inhibition was seen in CD45 mutant Jurkat cells. However, SCV-07 induced activating phosphorylation of the phosphatase SHP-2 and altered phosphorylation of Src family kinases and STAT5a/b, known substrates for SHP-2. SCV-07 also decreased IFNα stimulated phosphorylation of SHP-2 associated immunoreceptors Siglec3 (CD33) and SIRPbeta1 (CD172B). SCV-07-treatment of B16 bearing mice slowed tumor growth and significantly decreased the STAT3-induced cytokines MCP-1 and IL-12p40 which are implicated in immune pathology. Conclusions: These data suggest a model where SCV-07, via SHP-2 activation and STAT3 inhibition, could shift macrophage subsets from M2 to M1 and T cells from Th2 to Th1, thereby promoting an immune regulatory environment that inhibits both mucositis and tumor progression.