gebhart/patrepeval huggingface dataset:
PTPH1 Is a Predominant Protein-tyrosine Phosphatase Capable of Interacting with and Dephosphorylating the T Cell Receptor ζ Subunit (2004)

Protein-tyrosine phosphatases (PTPases) play key roles in regulating tyrosine phosphorylation levels in cells, yet the identity of their substrates remains limited. We report here on the identification of PTPases capable of dephosphorylating the phosphorylated immune tyrosine-based activation motifs present in the T cell receptor zeta subunit. To characterize these PTPases, we purified enzyme activities directed against the phosphorylated T cell receptor zeta subunit by a combination of anion and cation chromatography procedures. A novel ELISA-based PTPase assay was developed to rapidly screen protein fractions for enzyme activity following the various chromatography steps. We present data that SHP-1 and PTPH1 are present in highly enriched protein fractions that exhibit PTPase activities toward a tyrosine-phosphorylated TCR zeta substrate (specific activity ranging from 0.23 to 40 pmol/min/microg). We also used a protein-tyrosine phosphatase substrate-trapping library comprising the catalytic domains of 47 distinct protein-tyrosine phosphatases, representing almost all the tyrosine phosphatases identified in the human genome. PTPH1 was the predominant phosphatase capable of complexing phospho-zeta. Subsequent transfection assays indicated that SHP-1 and PTPH1 are the two principal PTPases capable of regulating the phosphorylation state of the TCR zeta ITAMs, with PTPH1 directly dephosphorylating zeta. This is the first reported demonstration that PTPH1 is a candidate PTPase capable of interacting with and dephosphorylating TCR zeta.
Homology Modeling of the CG-specific DNA Methyltransferase SssI and its Complexes with DNA and AdoHcy (2004)

Prokaryotic DNA methyltransferase M.SssI recognizes and methylates C5 position of the cytosine residue within the CG dinucleotides in DNA. It is an excellent model for studying the mechanism of interaction between CG-specific eukaryotic methyltransferases and DNA. We have built a structural model of M.SssI in complex with the substrate DNA and its analogues as well as the cofactor analogue S-adenosyl-L-homocysteine (AdoHcy) using the previously solved structures of M.HhaI and M.HaeIII as templates. The model was constructed according to the recently developed "FRankenstein's monster" approach. Based on the model, amino acid residues taking part in cofactor binding, target recognition and catalysis were predicted. We also modeled covalent modification of the DNA substrate and studied its influence on protein-DNA interactions.
Multiple-dose tolerability, pharmacokinetics, and pharmacodynamics of ponesimod, an S1P1receptor modulator: Favorable impact of dose up-titration (2014)

This multiple-ascending-dose study investigated the safety, tolerability, pharmacokinetics, and pharmacodynamics of ponesimod, an S1P1 receptor modulator and a potential new treatment for autoimmune diseases. In part A, 10 healthy male and female subjects received once daily oral doses of ponesimod (5, 10, or 20 mg) or placebo for 7 days. Sinus bradycardia and, in some subjects, atrioventricular (AV) block occurred primarily on the first day of dosing, as desensitization developed to ponesimod-induced heart rate (HR) reduction and PR-prolongation. This elicited the design of an up-titration schedule in 17 subjects to a dose of 40 mg in part B. The up-titration regimen reduced HR and PQ/PR effects. Reported adverse events were mainly related to the cardiac and respiratory systems. Respiratory effects increased with higher doses. Ponesimod multiple-dose pharmacokinetics were slightly more than dose-proportional and characterized by a time to maximum concentration and an elimination half-life varying from 2.5 to 4.0 hours and 30.9 to 33.5 hours, respectively, and an accumulation of about 2.3-fold. Ponesimod caused a dose-dependent sustained decrease in total lymphocyte count, reversible within 7 days of discontinuation. A pharmacokinetic-pharmacodynamic model enabled comparing day 1 and steady-state conditions. These results warrant further investigation of ponesimod in patients.
Quantum electrodynamics and radiation reaction: Nonrelativistic atomic frequency shifts and lifetimes (1974)

We present a quantum electrodynamic treatment of radiative corrections in atoms which is patterned after Lorentz's classical work on radiation damping. Expressions for both radiative lifetimes and frequency shifts are calculated through second order in the electric charge for a fictitious two-level model atom and for a spinless one-electron atom with an infinite number of arbitrarily spaced energy levels. In order to apply the classical ideas of Lorentz to quantum-electrodynamic problems of this kind we work directly with the relevant dynamical variables of the atom and field. The calculations are carried out entirely in the Heisenberg picture by recognizing the importance of radiation reaction. The quantized-field operator equations are integrated with the aid of a Markov approximation. The part of the integrated field that arises from the atomic electron current operator, the radiation-reaction field, is shown to be solely responsible for the atom's linewidths and frequency shifts. It is clear that it is unnecessary to invoke vacuum fluctuations at any stage. The usual quantum electrodynamic exponential decay law is found to govern the expectation values of the energy and dipole moment of the atom as well as the radiated-field amplitude. The theory nevertheless remains unitary. The Heisenberg operator commutation relations are shown to be valid at all times, and the Markov approximation is justified for times longer than a reciprocal transition frequency.
Photochemically reactive polymers; synthesis and characterization of polyurethanes containing Cp2Mo2(CO)6 or Cp2Fe2(CO)4 molecules along the polymer backbone (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemically reactive polymers; synthesis and characterization of polyurethanes containing Cp2Mo2(CO)6 or Cp2Fe2(CO)4 molecules along the polymer backboneSteve C. Tenhaeff and David R. TylerCite this: Organometallics 1991, 10, 2, 473–482Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/om00048a026https://doi.org/10.1021/om00048a026research-articleACS PublicationsRequest reuse permissionsArticle Views293Altmetric-Citations74LEARN 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-Alertsclose Get e-Alerts
High open circuit voltage organic photovoltaic cells fabricated using 9,9′-bifluorenylidene as a non-fullerene type electron acceptor (2013)

We have found that 9,9'BF can be used as an electron acceptor for P3HT-based OPVs while similar devices using 4,4'BP do not show any photovoltaic effect. This can be related to the respective aromaticity and antiaromaticity of the reduced forms of 9,9'BF or 4,4'BP. The OPV device fabricated using P3HT and 9,9'BF exhibited a PCE of 2.28% with a V(oc) of 1.07 V, a J(sc) of 5.04 mA cm(-2), and a FF of 0.42.
Clock synchronization over networks using sawtooth models (2019)

Clock synchronization and ranging over a wireless network with low communication overhead is a challenging goal with tremendous impact. In this paper, we study the use of time-to-digital converters in wireless sensors, which provides clock synchronization and ranging at negligible communication overhead through a sawtooth signal model for round trip times between two nodes. In particular, we derive Cramér-Rao lower bounds for a linearitzation of the sawtooth signal model, and we thoroughly evaluate simple estimation techniques by simulation, giving clear and concise performance references for this technology.
Synthesis and characterisation of trigonal C2-chiral di- and tetra-substituted bis(oxazoline) alkyl zinc complexes and their reactivity towards protic reagents (2011)

A series of zinc(ii) alkyl complexes stabilised by the C(2)-chiral bis(oxazoline) ligand ((R(1),R(2))BOX, with R(1) = (4S)-tBu, R(2) = H (a); R(1) = (4S)-Ph, R(2) = H (b); R(1) = (4R)-Ph, R(2) = (5S)-Ph (c)), has been synthesised and structurally characterised. ((R(1),R(2))BOX)H ligands react with ZnEt(2) in toluene to give the heteroleptic three-coordinate compounds of ((R(1),R(2))BOX)ZnEt, 1a, 1b and 1c in high yield. However, when the addition of (BOX)H ligands (a-b) over ZnEt(2) is "uncontrolled", the formation of homoleptic four-coordinate compounds are favoured (2a-b), but not for the more sterically crowded ligand (c). The zinc-ethyl derivatives (1a-c) react readily with protic reagents such as acetic acid (HOAc) and methanol (MeOH). For compounds 1a-c a redistribution of ligands is observed leading preferentially to homoleptic compounds, except for the bulkier ligand c providing a three-coordinate complex identified as ((Ph,Ph)BOX)Zn(OMe), 4c. The reaction of acetylacetone (acacH) with compounds 1a-c leads straightforwardly to the more stable four-coordinate compounds corresponding to ((R(1),R(2))BOX)Zn(η(2)-acac), 5a-c. The potential of these compounds as initiators for the copolymerisation of epoxides with CO(2) was investigated.
The crystal structure of some 2-oxo-1,3,2-dioxathiolanes (1984)

The trans diastereoisomers of 2-oxo-4(S)-phenyl-1,3,2-dioxathiolane and meso-2-oxo-4,5-diphenyl-1,3,2-dioxathiolane have been unambiguously identified by X-ray analysis; both adopt the half-chair conformation an differential endocyclic S–O bond lengths provide evidence for a stereoelectronic interaction with the SO group.
Predictors of joint damage in rheumatoid arthritis (1996)

Rheumatoid arthritis (RA) is the dominant form of destructive chronic arthritis with the potential to cause substantial disability and permanent functional impairment. The final extent and progression rate with time, however, varies markedly. In order to study effects of intervention and to support early aggressive and atoxic therapy in selected cases, predictive disease markers are needed. Recent advances regarding joint tissue composition and pathophysiology have defined a number of biological marker candidates which need to be explored for possible prognostic information. Some markers are characteristic for RA, such as rheumatoid factors and certain autoantibodies, which although they are more prevalent among patients with aggressive disease are not sensitive as predictors in early disease. Genetic susceptibility markers have been claimed to be good predictors of persisting arthritis in early synovitis clinics, but their role as severity markers in established disease is limited. Unspecific markers of inflammation, notably ESR or CRP when persistently elevated, are useful to monitor disease course and newer markers need to document their superiority over these. Another group of markers are attractive because of enriched or exclusive occurrence in joint tissue, and altered metabolism in joint disease. Thus, collagen type III propeptides, hyaluronates, and neopterin originating in the synovium could be useful, and, in particular, hyaluronate levels indeed do provide some predictive information. Highly tissue-specific cartilage metabolites include aggrecan fragments, collagen II fragments, cartilage oligomeric matrix protein (COMP) and the extraarticular cartilage matrix protein (CMP). When used alone or in combination in early disease some information can be obtained which may in the future facilitate prognostication. Bone metabolism can be monitored and there are different markers for synthesis and resorption. Meanwhile, whilst the new markers are essential research tools, their routine clinical usefulness remains to be proven.
Mother’s ‘genetic’ little helpers: microchimeric maternal cells promote reproductive fitness and survival of non-inherited traits (2016)

Abstract Reproductive success among outbred placental mammalian species requires active tolerance in mothers to foreign paternal antigens expressed by the developing fetus. Although this essential necessity for immunological tolerance has primarily been examined from the perspective of maternal responsiveness to foreign paternal antigens expressed by the developing fetus, exposure to maternal tissue during in utero development also imprints tolerance to genetically foreign non-inherited maternal antigens (NIMA) that persists into adulthood. Nonetheless, until now the biological advantages reinforcing conservation of tolerance to NIMA across eutherian mammals remained unclear. We show vertically transferred maternal cells that establish microchimerism in offspring promote systemic accumulation of regulatory T cells with NIMA specificity. In females, NIMA-specific regulatory T cells expand during pregnancies sired by males expressing alloantigens with overlapping NIMA specificity, thereby averting fetal wastage normally triggered by disruptions of fetal tolerance. Thus, reproductive fitness among females carrying embryos expressing paternally inherited antigens overlapping with NIMA is selectively enhanced. These findings demonstrate that genetic fitness, canonically thought to be restricted to Mendelian inheritance, is enhanced in female placental mammals through vertically transferred maternal cells that promote conservation of NIMA and enforce cross-generational reproductive benefits. Future studies will investigate the cellular and molecular phenotype of the microchimeric maternal cells to elucidate specific mechanisms that drive NIMA-specific regulatory T cell accumulation.
Maximizing the success rate of minimal model insulin sensitivity measurement in humans: the importance of basal glucose levels (2001)

Minimal model analysis of glucose and insulin concentrations in the intravenous glucose tolerance test (IVGTT) has been widely used to obtain a measure of insulin sensitivity in humans. Issues of model validity and IVGTT protocol have been explored extensively. Less attention has been paid, however, to the computer programming protocol for estimating the model parameters (programming implementation). Minimal model analysis of data from an IVGTT protocol involving a high glucose dose (0.5 g/kg) and a reduced sample schedule, employed in healthy pre- or post-menopausal women, healthy men or men with coronary heart disease or chronic heart failure (20 in each group), was undertaken according to 12 different programming implementations using a commercially available model-equation-solving program. The ability of the program to arrive at an acceptable solution to the model equations gave a success rate of between 39% and 96%, depending on the implementation. Variation in basal glucose assignment significantly affected the magnitude of estimates of insulin sensitivity. The maximum modelling success rate was achieved by introduction of an imputed glucose measurement at 360 min from the glucose injection, taking the basal glucose level as the fasting glucose concentration, and overweighting the initial glucose measurement after a delay for mixing. Use of this implementation to analyse data from a study comparing insulin sensitivities obtained using the minimal model and a euglycaemic clamp reference gave a correlation of 0.80 (P<0.001) between the two methods. Straightforward variations in programming implementation, involving appropriate assignment of the basal glucose concentration and use of an imputed glucose measurement signifying re-establishment of basal glucose levels following the IVGTT, can considerably improve modelling success rate.
A super junction SiGe low-loss fast switching power diode (2009)

This paper proposes a novel super junction (SJ) SiGe switching power diode which has a columnar structure of alternating p− and n− doped pillar substituting conventional n− base region and has far thinner strained SiGe p+ layer to overcome the drawbacks of existing Si switching power diode. The SJ SiGe diode can achieve low specific on-resistance, high breakdown voltages and fast switching speed. The results indicate that the forward voltage drop of SJ SiGe diode is much lower than that of conventional Si power diode when the operating current densities do not exceed 1000 A/cm2, which is very good for getting lower operating loss. The forward voltage drop of the Si diode is 0.66 V whereas that of the SJ SiGe diode is only 0.52 V at operating current density of 10 A/cm2. The breakdown voltages are 203 V for the former and 235 V for the latter. Compared with the conventional Si power diode, the reverse recovery time of SJ SiGe diode with 20 per cent Ge content is shortened by above a half and the peak reverse current is reduced by over 15%. The SJ SiGe diode can remarkably improve the characteristics of power diode by combining the merits of both SJ structure and SiGe material.
Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational–Experimental Platform (2018)

Novel approaches are needed to combat antibiotic resistance. Here, we describe a computational-experimental framework for the discovery of novel cryptic antimicrobial peptides (AMPs). The computational platform, based on previously validated antimicrobial scoring functions, indicated the activation peptide of pepsin A, the main human stomach protease, and its N- and C-terminal halves as antimicrobial peptides. The three peptides from pepsinogen A3 isoform were prepared in a recombinant form using a fusion carrier specifically developed to express toxic peptides in Escherichia coli. Recombinant pepsinogen A3-derived peptides proved to be wide-spectrum antimicrobial agents with MIC values in the range 1.56-50 μM (1.56-12.5 μM for the whole activation peptide). Moreover, the activation peptide was bactericidal at pH 3.5 for relevant foodborne pathogens, suggesting that this new class of previously unexplored AMPs may contribute to microbial surveillance within the human stomach. The peptides showed no toxicity toward human cells and exhibited anti-infective activity in vivo, reducing by up to 4 orders of magnitude the bacterial load in a mouse skin infection model. These peptides thus represent a promising new class of antibiotics. We envision that computationally guided data mining approaches such as the one described here will lead to the discovery of antibiotics from previously unexplored sources.
Orbital angular momentum modes of high-gain parametric down-conversion (2017)

Light beams with orbital angular momentum (OAM) are convenient carriers of quantum information. They can be also used for imparting rotational motion to particles and provide high resolution in imaging. Due to the conservation of OAM in parametric down-conversion (PDC), signal and idler photons generated at low gain have perfectly anti-correlated OAM values. It is interesting to study the OAM properties of high-gain PDC, where the same OAM modes can be populated with large, but correlated, numbers of photons. Here we investigate the OAM spectrum of high-gain PDC and show that the OAM mode content can be controlled by varying the pump power and the configuration of the source. In our experiment, we use a source consisting of two nonlinear crystals separated by an air gap. We discuss the OAM properties of PDC radiation emitted by this source and suggest possible modifications.
Nontraditional University Research Partners That Facilitate Service Learning And Graduate Research For Sustainable Development (2020)

Her area of interests include the development of treatment technologies for inorganic contaminant remediation with a special emphasis on arsenic in drinking water and in landfill leachate; investigating the effect of climate change on mercury fate in aquatic environments; and understanding the effect of water storage containers on water quality in developing countries. She has an ongoing interest in multidisciplinary projects that encourage sustainable development and provide affordable and efficient technology to developing areas, especially with respect to improving water quality and reducing the incidence of water borne diseases and water related diseases and other health complications. She believes in holistic approaches to providing engineering solutions which incorporate women's perspectives and needs and which build local capacity.
Dielectric image line leaky wave antenna for broadside radiation (1983)

A dielectric image line leaky wave antenna is presented, capable of efficient operation at broadside. The stopband phenomenon at broadside is avoided by using pairs of radiator elements at 90° phase quadrature (quarter-wave spacing).
Calculated gain and spontaneous spectra of multi-quantum-well lasers (1985)

Optical gain and spontaneous spectra of multi-quantum-well (MQW) lasers are investigated theoretically. A band-to-band radiative recombination rate is calculated using an energy-dependent density of states and k-selection rule. It is found that the gain and spontaneous spectra are significantly dependent upon degrees of two-dimensionality of subbands created in MQW structure.
A comparative study on cell disruption methods for release of aspartase from E. coli K-12. (2013)

Applicability of different mechanical cell disruption techniques namely sonication, bead milling and French press for the release of aspartase from E. coli K-12 was compared. Various operating parameters of each technique were optimized to obtain maximum aspartase release. The efficiency of aspartase release and cell disruption by all the methods was also compared under optimal conditions. The maximum release of aspartase (98.22%) and maximum cell breakage (84.25%) was observed using French press, while 92% of aspartase release was obtained by both sonication and bead milling. The order of cell disruption constant (k) for aspartase release by these methods was French press > bead milling > sonication. Disruption of cells using French press also demonstrated maximum protein release (14.12 mg/mL). The crude enzyme preparations can be further used for purification and its applications.
Amplified 2-<formula formulatype="inline"><tex Notation="TeX">$\mu{\rm m}$</tex></formula> Thulium-Doped All-Fiber Mode-Locked Figure-Eight Laser (2013)

We report the first mode-locked, thulium-doped fiber figure-eight laser. The mode-locked oscillator produces 1.5-ps pulses with 63 pJ of pulse energy at a 10.4-MHz repetition rate with a 3-nm bandwidth at a center wavelength of 2034 nm. After amplification, the pulses are compressed to 370 fs with ~ 50 nJ of pulse energy. The oscillator can also operate in a square pulse regime, yielding stable pulses from ~ 100 ps to 20 ns long with ~ 100 nJ per pulse after amplification.