gebhart/patrepeval huggingface dataset:
Investigating Acquisition Performance on the Orbitrap Fusion When Using Tandem MS/MS/MS Scanning with Isobaric Tags (2017)

Methods for isobaric-tagged peptide analysis (e.g., TMT, iTRAQ), such as the synchronous precursor selection (SPS) tandem MS/MS/MS (MS<sup>3</sup>) approach, enable maintenance of reporter ion accuracy and precision by reducing the ratio compression caused by coisolated precursor ions. However, the decreased throughput of the MS<sup>3</sup> approach necessitates careful optimization of acquisition strategies and methods to ensure maximal proteome coverage. We present a systematic analysis of acquisition parameters used to analyze isobaric-tagged peptide samples on current generation Orbitrap mass spectrometer (MS) hardware. In contrast with previously reported works, we demonstrate the limited utility of acquiring reporter ion data in the ion trap analyzer; ion trap acquisition had only a minimal increase in identification depth and reduced quantification precision. We establish that despite the significantly increased scan rate afforded through the use of higher energy collisional dissociation (HCD) in MS<sup>3</sup>-based ion trap isobaric tag analyses, the reduced quantification precision and reporter ion yields negate the potential benefits in proteome coverage. Lastly, using optimized parameter sets, we further demonstrate the limited utility of the ion trap detector versus the Orbitrap for reporter ion detection in an in-depth analysis of a complex proteome sample. Together, these data will serve as a valuable resource to researchers undertaking analysis on current generation Orbitrap instrumentation with isobaric tags.
Gene Therapy for Pituitary Tumors (2003)

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Trapping of Acetylene by a Zirconocene Terminal Imido Complex (2000)

Treatment of the zirconocene terminal imido complex (CpR)2ZrNtBu(THF) (1a-THF: R = H; 1b-THF: R = Me) with acetylene results in the formation of a dinuclear product, [(CpR)2Zr]2(μ-CHCHNtBu)(μ-NtBu) (3a, R = H; 3b, R = Me), in which the zirconium centers are bridged by nitrogen and carbon. Upon heating, the dinuclear complex 3 is cleaved into the azametallacyclobutene (CpR)2Zr(η2-NtBuCHCH) (4) and the terminal imido complex (CpR)2ZrNtBu (1), which can be trapped with Lewis bases or alkynes. Heating 3 in the absence of traps cleanly produces the alkynyl-bridged species [(CpR)2ZrNHtBu]2(μ-C⋮C) (5). Kinetic data indicate that the dinuclear complex 3 fragments into the mononuclear species 4 and 1 prior to C−H activation to form 5. The X-ray structures of [Cp2Zr]2(μ-CHCHNtBu)(μ-NtBu) (3a) and [Cp2ZrNHtBu]2(μ-C⋮C) (5a) are reported; the structure of the dinuclear species [(Cp2Zr)((CpMe)2Zr)](μ-CHCHNtBu)(μ-NtBu) (3c) is included in the Supporting Information.
Association Between Polymorphism in the Chemokine Receptor CX3CR1 and Coronary Vascular Endothelial Dysfunction and Atherosclerosis (2001)

Fractalkine, a chemokine expressed by inflamed endothelium, induces leukocyte adhesion and migration via the receptor CX3CR1, and the CX3CR1 polymorphism V249I affects receptor expression and function. Here we show that this polymorphism is an independent risk factor for atherosclerotic coronary artery disease (CAD). Genotyping of the CX3CR1-V249I polymorphism was performed in a cohort of 339 white individuals who underwent cardiac catheterization (n=197 with and n=142 without CAD, respectively). In 203 patients, intracoronary acetylcholine 15 microg/min) and sodium nitroprusside (20 microg/min) were administered to test endothelium-dependent and -independent coronary vascular function, respectively. Change in coronary vascular resistance (DeltaCVR) was measured as an index of microvascular dilation. An association was observed between presence of the CX3CR1 I249 allele and reduced prevalence of CAD, independent of established CAD risk factors (odds ratio=0.54 [95% confidence interval, 0.30 to 0.96], P=0.03). Angiographic severity of CAD was also lower in these subjects (P=0.01). Furthermore, endothelium-dependent vasodilation was greater in these individuals compared with individuals homozygous for the CX3CR1-V249 allele (DeltaCVR during acetylcholine = -46+/-3% versus -36+/-3%, respectively, P=0.02), whereas DeltaCVR with sodium nitroprusside was similar in both groups (-55+/-2% versus -53+/-2%, P=0.45). The association between CX3CR1 genotype and endothelial function was independent of established risk factors and presence of CAD by multivariate analysis (P=0.02). Thus, the CX3CR1 I249 allele is associated with decreased risk of CAD and improved endothelium-dependent vasodilation. This suggests that CX3CR1 may be involved in the pathogenesis of CAD.
Dispersion-based pulse shaping for multiplexed two-photon fluorescence microscopy (2010)

We demonstrate selective two-photon excited fluorescence microscopy with shaped pulses produced with a simple yet efficient scheme based on dispersive optical components. The pulse train from a broadband oscillator is split into two subtrains that are sent through different amounts of glass. Beam recombination results in pulse-shape switching at a rate of 150MHz. Time-resolved photon counting detection then provides two simultaneous images resulting from selective two-photon excitation, as demonstrated in a live embryo. Although less versatile than programmable pulse-shaping devices, this novel arrangement significantly improves the performance of selective microscopy using broadband shaped pulses while simplifying the experimental setup.
Rank-Independent Codebook Design from a Quaternary Alphabet (2007)

Single-user as well as multi-user MIMO systems employ codebook-based feedback to customize the signal transmission to the current channel conditions. The two competing metrics for evaluating a codebook are packet-error-rate/throughput performance and codebook search complexity at the mobile. To address this issue structured unitary codebooks are proposed where each codebook entry is restricted to a power of i and a single codebook is optimized for all ranks. Such codebooks are shown to perform favorably with the best known (unconstrained) codebooks in terms of distance measures and are also shown to perform well in multi-user MIMO link-level simulations.
Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G.cntdot.T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G) (1982)

The relaxation lifetimes of imino protons from individual base pairs were measured in (I) a perfect helix, d(C-G-C-G-A-A-T-T-C-G-C-G), (II) this helix with a G . C base pair replaced with a G . T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and (III) the perfect helix with an extra adenine base in a mismatch, d(C-G-C-A-G-A-A-T-T-C-G-C-G). The lifetimes were measured by saturation recovery proton nuclear magnetic resonance experiments performed on the imino protons of these duplexes. The measured lifetimes of the imino protons were shown to correspond to chemical exchange lifetimes at higher temperatures and spin-lattice relaxation times at lower temperatures. Comparison of the lifetimes in these duplexes showed that the destabilizing effect of the G . T base pair in II affected the opening rate of only the nearest-neighbor base pairs. For helix III, the extra adenine affected the opening rates of all the base pairs in the helix and thus was a larger perturbation for opening of the base pairs than the G . T base pair. The temperature dependence of the exchange rates of the imino proton in the perfect helix gives values of 14-15 kcal/mol for activation energies of A . T imino protons. These relaxation rates were shown to correspond to exchange involving individual base pair opening in this helix, which means that one base-paired imino proton can exchange independent of the others. For the other two helices that contain perturbations, much larger activation energies for exchange of the imino protons were found, indicating that a cooperative transition involving exchange of at least several base pairs was the exchange mechanism of the imino protons. The effects of a perturbation in a helix on the exchange rates and the mechanisms for exchange of imino protons from oligonucleotide helices are discussed.
Rotor end losses in multi-phase fractional-slot concentrated-winding permanent magnet synchronous machines (2010)

Fractional-slot concentrated-windings (FSCW) have been gaining a lot of interest in Permanent Magnet (PM) synchronous machines. This is due to the advantages they provide including shorter non-overlapping end turns, higher efficiency, higher power density, higher slot fill factor, lower manufacturing cost, better flux-weakening capability resulting in wider constant power vs. speed range, and fault-tolerance. This paper focuses on eddy current losses in the rotor clamping rings. Losses in the non-magnetic shaft with the option of i) metallic, ii) nonmetallic, and iii) metallic with shielding laminations clamping rings are analyzed. The study is based on Finite Element Analysis (FEA). Desirable slot/pole combinations for different number of phases with both single- and double-layer windings are investigated. Experimental results for a 3-phase 12slot/10pole design will be presented to confirm that the losses in the rotor clamping rings can be very significant in case of FSCW and should not be overlooked during the design phase.
ChemInform Abstract: Synthesis and Crystallographic Characterization of a Platinadehydrobenzo[19]annulene. (1998)

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.
SU-E-T-711: Normal Tissue Tolerance Evaluation Tool for Clinical Protocols (2013)

Purpose: We developed Graphic User Interface (GUI) to evaluate and verify whether Dose Volume Histogram (DVH) parameters meet clinical protocol criteria. Methods: A graphical application to import and evaluate DVH parameters was developed by using Matlab (version R2012a, Mathworks). Two DVH text files which were exported from Eclipse treatment planning system (Varian, USA) could be imported, and it automatically depicts DVH values and arranges dose statistics in Eclipse manner (Figure 1). Additionally, it is possible to evaluate not only KIRAMS dose constraint protocol but also currently well-known normal tissue constraint protocol such as American Association of Physicists in Medicine (AAPM), Radiation Therapy Oncology Group (RTOG) and Quantitative Analyses of Normal Tissue Effects in the Clinic (QUANTEC). Those protocols were able to be simultaneously depicted on the DVH so that dose constraints were easily distinguishable. Results: DVH data analyzed for all organ parameters with the application was faster than manually looking for points using the treatment planning system. Also, since a protocol-specific marker used for evaluating dose constraint, the software was easily able to verify each depicted DVH for different types of patient plans whether under the protocol suggested dose or not (Figure 2). Conclusion: This software can help the planner to easily decide how much computer-calculated DVH was over/under estimated on the basis of the dose constraints that clinical protocols suggested. Acknowledgement : This research was supported by the Ministry of education, Science and Technology(MEST)
UPMAC: A Localized Load-Adaptive MAC Protocol for Underwater Acoustic Networks (2015)

Unlike terrestrial networks that mainly rely on radio waves for communications, underwater networks utilize acoustic waves, which have comparatively lower loss and longer range in underwater environments. However, acoustic waves incurs long propagation delays that typically lead to low throughput and higher energy cost of transmission than reception. Thus, collision and retransmission should be reduced in order to reduce energy cost and improve throughput. Receiver-based protocols, like receiver-initiated packet train and cluster-based on-demand time sharing, can significantly reduce collision and retransmission. But they are either time-consuming or energy consuming because nodes are controlled to turn into receiver mode by control packets or a timer regardless of load. In this paper, we propose an underwater practical MAC protocol (UPMAC), whose objective is to be adaptive to the network load conditions by providing two modes (high and low load modes) and switching between them based on different offered load. Turn-around time overhead is reduced and it is less vulnerable to control packet corruption by using the technique of piggyback. UPMAC uses receiver-based approach in high load mode, leading to a low data collision rate in both one-hop and multihop situation. Extensive simulations show that UPMAC can achieve better performance in both general and Sea Swarm topologies.
Essentials of molecular photochemistry (1991)

Molecular photochemistry The electronic structure of molecules Radiation and molecular orbitals Molecular photophysics Photochemical reactions Photochemical reactions of ethenes, polyenes and ethynes Photochemical reactions of the carbonyl chromophore Aromatic photochemistry Photochemical reactions of nitrogen-containing chromophores The photochemistry of other organic chromophores Photo-oxidation reactions
Flow-Aware Service Function Embedding Algorithm in Programmable Data Plane (2020)

Service function chaining (SFC) is an indispensable technique for Internet service providers to efficiently manage their networks. However, SFC poses requirements of additional processing time of service functions (SFs) and increased routing time owing to detoured paths. In this paper, we introduce the use of a programmable data plane (PDP) to reduce the additional processing and routing times in SFC. We first classify the existing PDP-empowered SFC schemes and analyze their pros and cons. An optimization problem, to find the optimal SF embedding strategy minimizing the SFC completion time while efficiently utilizing the PDP switch resources, is formulated and a flow-aware SF embedding (FASE) algorithm that complementarily combines the redundant SF and re-circulation approaches is devised. FASE is implemented over a commercial PDP switch and experimental results demonstrate that FASE can reduce the SFC completion time by up to 33% compared with conventional approaches while utilizing the switch resources efficiently.
Systemic hyperkalemia and mild hypothermia for valve surgery in patients with patent internal mammary artery graft (2010)

Myocardial protection is compromised in patients with a patent internal mammary artery (IMA) graft. We assessed the advantages of systemic hyperkalemia with mild hypothermia for valve surgery in patients with a patent IMA graft. Nine patients (mean age 71.5+/-7.0 years) with a patent IMA graft underwent valve surgery from May 2004 to July 2009. Of those, eight underwent aortic valve replacement and one mitral repair, with two double-valve surgery. Antegrade and retrograde blood cardioplegia were performed intermittently, and systemic potassium was given to all. The lowest bladder temperature was 27.2+/-2.4 degrees C, and the initial and peak systemic potassium levels were 6.8+/-1.4 and 8.0+/-1.6 mEq/l, respectively, while potassium at the end of the cardiopulmonary bypass procedure after sufficient modified ultrafiltration was reduced to 5.5+/-0.6 mEq/l. There was one hospital death due to ischemic colitis. Cardiac arrest was easily achieved in each patient without IMA or aortocoronary graft injury. The postoperative peak creatine kinase-MB level was 33+/-17 IU/l, with no ST changes seen in electrocardiogram findings or new asynergy seen in echocardiogram findings. Systemic hyperkalemia and mild hypothermia for valve surgery in patients with a patent IMA graft is a good option to reduce graft and myocardial injuries.
Acousto-optic modulation in a Si-waveguide (2021)

We demonstrate acousto-optic modulation (V<inf>&#x03C0;</inf>L ~3.6 Vcm) in a Si waveguide circuit by integrating a photonic compatible PZT film on the SOI chip. We then fabricated a small footprint inter-digital transducer (IDT) on the film to piezoelectrically actuate acoustic waves at GHz frequencies.
Biological Activity of Cannabis sativa L. Extracts Critically Depends on Solvent Polarity and Decarboxylation (2020)

Minor cannabinoid and non-cannabinoid molecules have been proposed to significantly contribute to the pharmacological profile of cannabis extracts. Phytoplant Research has developed highly productive cannabis cultivars with defined chemotypes, as well as proprietary methods for the extraction and purification of cannabinoids. Here, we investigate the effect of solvent selection and decarboxylation on the composition and pharmacological activity of cannabis extracts. A library of forty cannabis extracts was generated from ten different cannabis cultivars registered by Phytoplant Research at the EU Community Plant Variety Office. Plant material was extracted using two different solvents, ethanol and hexane, and crude extracts were subsequently decarboxylated or not. Cannabinoid content in the resulting extracts was quantified, and biological activity was screened in vitro at three molecular targets involved in hypoxia and inflammation (NF-κB, HIF-1α and STAT3). Changes in transcriptional activation were strongly associated to solvent selection and decarboxylation. Two decarboxylated extracts prepared with hexane were the most potent at inhibiting NF-κB transcription, while HIF-1α activation was preferentially inhibited by ethanolic extracts, and decarboxylated extracts were generally more potent at inhibiting STAT3 induction. Our results indicate that solvent selection and proper decarboxylation represent key aspects of the standardized production of cannabis extracts with reproducible pharmacological activity.
Quenching of fluorescence of bleomycins by ferrous ion and its correlation with DNA-breakage activity (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuenching of fluorescence of bleomycins by ferrous ion and its correlation with DNA-breakage activityCheng-Hsiung Huang, Louis Galvan, and Stanley T. CrookeCite this: Biochemistry 1979, 18, 13, 2880–2887Publication Date (Print):June 26, 1979Publication History Published online1 May 2002Published inissue 26 June 1979https://pubs.acs.org/doi/10.1021/bi00580a032https://doi.org/10.1021/bi00580a032research-articleACS PublicationsRequest reuse permissionsArticle Views47Altmetric-Citations7LEARN 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
Modeling of friction-induced deformation and microstructures. (2006)

Frictional contact results in surface and subsurface damage that could influence the performance, aging, and reliability of moving mechanical assemblies. Changes in surface roughness, hardness, grain size and texture often occur during the initial run-in period, resulting in the evolution of subsurface layers with characteristic microstructural features that are different from those of the bulk. The objective of this LDRD funded research was to model friction-induced microstructures. In order to accomplish this objective, novel experimental techniques were developed to make friction measurements on single crystal surfaces along specific crystallographic surfaces. Focused ion beam techniques were used to prepare cross-sections of wear scars, and electron backscattered diffraction (EBSD) and TEM to understand the deformation, orientation changes, and recrystallization that are associated with sliding wear. The extent of subsurface deformation and the coefficient of friction were strongly dependent on the crystal orientation. These experimental observations and insights were used to develop and validate phenomenological models. A phenomenological model was developed to elucidate the relationships between deformation, microstructure formation, and friction during wear. The contact mechanics problem was described by well-known mathematical solutions for the stresses during sliding friction. Crystal plasticity theory was used to describe the evolution of dislocation content in the worn material, which in turn provided an estimate of the characteristic microstructural feature size as a function of the imposed strain. An analysis of grain boundary sliding in ultra-fine-grained material provided a mechanism for lubrication, and model predictions of the contribution of grain boundary sliding (relative to plastic deformation) to lubrication were in good qualitative agreement with experimental evidence. A nanomechanics-based approach has been developed for characterizing the mechanical response of wear surfaces. Coatings are often required to mitigate friction and wear. Amongst other factors, plastic deformation of the substrate determines the coating-substrate interface reliability. Finite element modeling has been applied to predict the plastic deformation for the specific case of diamond-like carbon (DLC) coated Ni alloy substrates.
A Standalone Approach for Ultra-Tightly Coupled High Sensitivity GNSS Receiver (2014)

The tracking threshold in conventional scalar-based GNSS receivers limits the performance of ML bit decoding, which is paramount to ML based bit wipe-off. In this paper, a standalone approach, that is, in the absence of aiding information, is proposed for the ultratightly coupled high sensitivity GNSS receiver. The benefits are analyzed and determined of using ultratightly coupled GNSS receiver in the standalone mode to improve bit decoding and navigation solutions. The results show the ultra-tight receiver is more robust than the GNSS-only receivers. In the context of GPS L1 C/A signals, the field test results show ultra-tight receiver can improve the successful decoding rate (SDR) compared to scalar-based receiver. Compared to the vector-based receiver, the ultra-tight receiver is more immune to the high BER problem in extending coherent integration time. The position and velocity accuracy of the standalone ultra-tight receiver has been improved more than 40% after extending coherent integration time in the vehicular navigation test in urban canyon. A newly proposed signal power based update observation selection strategy has helped to mitigate multipath impacts.