gebhart/patrepeval huggingface dataset:
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift (2021)

The recently emerged SARS-CoV-2 Omicron variant harbors 37 amino acid substitutions in the spike (S) protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics. Here, we show that the Omicron RBD binds to human ACE2 with enhanced affinity relative to the Wuhan-Hu-1 RBD and acquires binding to mouse ACE2. Severe reductions of plasma neutralizing activity were observed against Omicron compared to the ancestral pseudovirus for vaccinated and convalescent individuals. Most (26 out of 29) receptor-binding motif (RBM)-directed monoclonal antibodies (mAbs) lost in vitro neutralizing activity against Omicron, with only three mAbs, including the ACE2-mimicking S2K146 mAb <sup>1</sup> , retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs recognizing antigenic sites outside the RBM, including sotrovimab <sup>2</sup> , S2X259 <sup>3</sup> and S2H97 <sup>4</sup> , neutralized Omicron. The magnitude of Omicron-mediated immune evasion and the acquisition of binding to mouse ACE2 mark a major SARS-CoV-2 mutational shift. Broadly neutralizing sarbecovirus mAbs recognizing epitopes conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.
3D-convolution based fast transient thermal model for 3D integrated circuits: methodology and applications (2015)

A thorough thermal analysis of integrated circuits (ICs) is essential to prevent temperature driven reliability issues, which might cause the failure of microelectronic devices. The classical analysis approach is based on finite element methods (FEM). However, in the last decades, other computational methodologies have been developed with the aim to obtain results more quickly and at a reasonable accuracy. In this paper, a transient fast thermal model (TFTM) methodology for 3DICs based on 3D-convolution and fast Fourier transform is presented. This methodology allows to quickly and accurately predict the temporal evolution of the chip temperature distribution, due to power dissipation that can be non-uniform both in time and space, in all tiers of the 3D package. In the first part of the paper the computational methodology is derived and described. Next, results are presented and validated with respect to conventional FEM simulations, showing good accuracy and computational time reduction. A realistic case, wherein different load switching scenarios are compared for a commercial floor-plan, is analyzed as an example of the applicability of the presented methodology. The speed of this algorithm, based on 3D-convolution, is compared with the one of previous work based on 2D-convolution and subseq uent time superposition.
Methods of obtaining active antisense compounds (2023)

Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.
The Effect of GHRH on Somatotrope Hyperplasia and Tumor Formation in the Presence and Absence of GH Signaling (2001)

Excessive GHRH stimulation leads to somatotrope hyperplasia and, ultimately, pituitary adenoma formation in the metallothionein promoter-driven human GHRH (hGHRH) transgenic mouse. This pituitary phenotype is similar to that observed in humans with ectopic production of GHRH. In both mice and man, GHRH hyperstimulation also results in dramatic increases in circulating GH and IGF-I. To determine whether GH/IGF-I modulates the development and growth rate of GHRH-induced pituitary tumors, pituitary growth and histology were evaluated in mice generated from cross-breeding metallothionein promoter-driven hGHRH transgenic mice with GH receptor binding protein (GHR) gene disrupted mice (GHR(-/-)). Expression of the hGHRH transgene in 2-month-old GHR intact (GHR(+)) mice resulted in the doubling of pituitary weight that was largely attributed to an increase in the number of GH-immunopositive cells. Pituitary weight of GHR(+) hGHRH mice did not significantly change between 2 and 6 months of age, whereas at 12 months, weights increased up to 100-fold those of GHR(+) pituitaries, and 70% of the glands contained grossly visible adenomas. All adenomas stained positively for GH, whereas some showed scattered PRL staining. Pituitaries of GHR(-/-) mice were half the size of those of GHR(+) mice. Although reduced in size, the histological features of GHR(-/-) mouse pituitaries were suggestive of somatotrope hyperplasia. Despite evidence of somatotrope hyperplasia, pituitaries from GHR(-/-) mice as old as 28 months of age were similar in size to those of 2-month-old mice and did not show signs of adenoma formation. Expression of the hGHRH transgene in GHR(-/-) mice did not significantly increase pituitary size between 2 and 6 months of age. However, at 12 months the majority of GHR(-/-), hGHRH pituitaries developed adenomas with mean pituitary weight and histological features similar to those of GHR(+), hGHRH mice. These observations demonstrate that intact GH signaling is not required for GHRH tumor formation. Although the majority of GHR(+), hGHRH and GHR(-/-), hGHRH pituitaries developed tumors by 12 months of age, a small subset remained morphologically indistinct from those at 2 months of age. These observations taken together with the fact that overt tumor formation is preceded by a static pituitary growth phase between 2 and 6 months, indicates that protective mechanisms are in place to maintain pituitary mass despite hGHRH hyperstimulation.
Mechanistic Studies of Diastereomeric Nickel(II)N-Glycoside Complexes Using Tandem Mass Spectrometry (1998)

Ni(II) N-glycoside complexes of four diastereomeric monosaccharides were synthesized and analyzed by fast atom bombardment-mass spectrometry. The average kinetic energy release (KER) associated with the formation of a C2H4O2 neutral loss was indicative of stereochemical differences in the coordinated monosaccharide. Isotopic labeling studies and various linked scanning techniques were undertaken, suggesting multiple dissociation pathways from different reacting configurations, leading to the formation of isomeric [M-C2H4O2] product ions. Additionally, computational studies predict the presence of large structural differences between complexes possessing axial or equatorial C-2 substituents.
ATAC: A Manycore Processor with On-Chip Optical Network (2009)

Ever since industry has turned to parallelism instead of frequency scaling to improve processor performance, multicore processors have continued to scale to larger and larger numbers of cores. Some believe that multicores will have 1000 cores or more by the middle of the next decade. However, their promise of increased performance will only be reached if their inherent scaling and programming challenges are overcome. Meanwhile, recent advances in nanophotonic device manufacturing are making chip-stack optics a reality—interconnect technology which can provide significantly more bandwidth at lower power than conventional electrical analogs. Perhaps more importantly, optical interconnect also has the potential to enable new, easy-to-use programming models enabled by an inexpensive broadcast mechanism. This paper introduces ATAC, a new manycore architecture that capitalizes on the recent advances in optics to address a number of the challenges that future manycore designs will face. The new constraints—and opportunities— associated with on-chip optical interconnect are presented and explored in the design of ATAC. Furthermore, this paper introduces ACKwise, a novel directory-based cache coherence protocol that takes advantage of the special properties of ATAC to achieve high performance and scalability on large-scale manycores. Early performance results show that a 1000-core ATAC chip achieves a speedup of as much as 39 % when compared with a similarly sized manycore with an electrical mesh network. 1.
High-Reynolds-number turbulent boundary layer friction drag reduction from wall-injected polymer solutions (2009)

A set of controlled high-Reynolds-number experiments has been conducted at the William B. Morgan Large Cavitation Channel (LCC) in Memphis, Tennessee to investigate the friction drag reduction achieved by injecting aqueous poly(ethylene oxide) (PEO) solutions at three different mean molecular weights into the near-zero-pressure-gradient turbulent boundary layer that forms on a smooth flat test surface having a length of nearly 11m. The test model spanned the 3.05m width of the LCC test section and had an overall length of 12.9m. Skin-friction drag was measured with six floating-plate force balances at downstream-distance-based Reynolds numbers as high as 220 million and free stream speeds up to 20ms −1 . For a given polymer type, the level of drag reduction was measured for a range of free stream speeds, polymer injection rates and concentrations of the injected solution. Polymer concentration fields in the near-wall region (0 &lt; y + &lt; ~10 3 ) were examined at three locations downstream of the injector using near-wall planar laser-induced-fluorescence imaging. The development and extent of drag reduction and polymer mixing are compared to previously reported results using the traditional K -factor scaling. Unlike smaller scale and lower speed experiments, speed dependence is observed in the K -scaled results for the higher molecular weight polymers and it is postulated that this dependence is caused by molecular aggregation and/or flow-induced polymer degradation (chain scission). The evolution of near-wall polymer concentration is divided into three regimes: (i) the development region near the injector where drag reduction increases with downstream distance and the polymer is highly inhomogeneous forming filaments near the wall, (ii) the transitional mixing region where drag reduction starts to decrease as the polymer mixes across the boundary layer and where filaments are less pronounced and (iii) the final region where the polymer mixing and dilution is set by the rate of boundary layer growth. Unlike pipe-flow friction-drag reduction, the asymptotic maximum drag reduction (MDR) either was not reached or did not persist in these experiments. Instead, the nearest approach to MDR was transitory and occurred between the development and transitional regions. The length of the development region was observed to increase monotonically with increasing polymer molecular weight, injection rate, concentration and decreasing free stream speed. And finally, the near-wall polymer concentration is correlated to the measured drag reduction for the three polymer molecular weights in the form of a proposed empirical drag-reduction curve.
Large-Scale Synthesis of Polymer-Stabilized Silver Nanoparticles (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Ta2O5 Nanobars and Their Composites: Synthesis and Characterization (2008)

Novel Ta2O5 nanobars anchored on micron-sized carbon spheres were synthesized by the thermal decomposition of pentaethoxy tantalate, Ta(OEt)5. This one-step reaction was carried out using the RAPET (Reaction Under Autogenic Pressure at Elevated Temperature) method by dissociating Ta(OEt)5 at 800 degrees C for 3 h. The as-prepared Ta2O5/C nanobar-composite was annealed under air at 500 degrees C for 3 h (eliminating the carbon spheres), resulting in neat Ta2O5 nanobars. The products, Ta2O5/C and Ta2O5 nanobars, were characterized using methods such as electron microscopy (SEM, TEM, HRTEM, SAEDS, EA, EDX) and Powder-XRD. Transmission electron microscope (TEM) images indicated the particle size of the Ta2O5 nanobars coated on 40-60 nm carbon spheres. The optical properties of the Ta2O5/C nanobar-composite and the neat Ta2O5 nanobars were determined by UV-vis absorption spectrometry and their band gaps were found at 265 (4.7 eV) and 260 nm (4.8 eV), respectively. A PL band was also observed for a Ta2O5/C nanobar-composite and Ta2O5 nanobars. The above results indicate that Ta2O5 nanobars have a promising application in optical devices.
Glycogen synthase kinase-3 from rabbit skeletal muscle. Separation from cyclic-AMP-dependent protein kinase and phosphorylase kinase. (1980)

Publisher Summary This chapter discusses glycogen synthase kinase-3 from rabbit skeletal muscle. Glycogen synthase kinase-3 is one of the five glycogen synthase kinases that are identified in skeletal muscle, and is of major importance in determining the kinetic properties of glycogen synthase in vivo. It catalyzes the phosphorylation of three serine residues on glycogen synthase, converting the enzyme from a form that is almost fully active in the absence of glucose-6P, to one that is largely dependent on this allosteric activator. Glycogen synthase kinase-3 also has a second activity that is not shared by any other protein kinase—namely, the ability to activate an enzyme termed the MgATP-dependent protein phosphatase. Glycogen synthase may also contain traces of a modified form of phosphorylase kinase that has lost its sensitivity to regulation by calcium ions, and is therefore, no longer inhibited by ethylene glycol tetraacetic acid (EGTA). This is largely removed by passing glycogen synthase through phosphocellulose.
Abstract 1701: Improvement of tumor mutation burden measurement by removal of deaminated bases in FFPE DNA (2019)

Tumor mutation burden (TMB) is a positive predictive factor for response to immune-checkpoint inhibitors in certain types of cancer. The Oncomine™ Tumor Mutation Load Assay, a 1.7Mb targeted next generation sequencing (NGS) panel, measures TMB and detects mutations in 409 cancer genes. The TMB values obtained using targeted sequencing are positively correlated with TMB measured by whole exome sequencing in NSCLC, colorectal, endometrial and gastric cancers. TMB from these tumor samples are correlated with other phenotypes associated with genomic instability, specifically microsatellite instability (MSI) and mutations involved in mismatch repair and cancer related genes. Analysis of the Oncomine™ TML Assay results with Torrent Suite and Ion Reporter software uniquely measures the degree of deamination of cytosines to uracils in fixed tissues. FFPE preservation methods can lead to significant cytosine deamination of the isolated DNA, resulting in decreased sequencing quality. In these samples, uracils are propagated as thymines and result in false C>T substitutions. To minimize the influence that excess deamination has on TMB results, we have incorporated a UDG enzyme treatment to eliminate damaged targets and improve usable TMB values of DNA from damaged FFPE tumor tissue. The Oncomine™ TML assay for TMB on Ion GeneStudio™ S5 in conjunction with MSI detection is informative and potentially predictive for the use of checkpoint inhibitors in multiple cancer types.Citation Format: Warren Tom, Ruchi Chaudhary, Vinay Mittal, Dinesh Cyanam, Iris Casuga, Elaine Wong-Ho, Rob Bennett, Fiona Hyland, Seth Sadis, Janice Au-Young. Improvement of tumor mutation burden measurement by removal of deaminated bases in FFPE DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1701.
Thomson Reuters' Solution for Triple Ranking in the FEIII 2017 Challenge (2017)

In this paper we describe our approach to the triple ranking task of the FEIII 2017 challenge. Our method leveraged different machine learning classifiers in an ensemble as well as Thomson Reuters knowledge bases and information services to bring in external world knowledge of mentioned entities and extract information from the contextual sentences. Internal evaluation of our method was done by computing the Normalized Discounted Cumulative Gain (NDCG) as tracked by the challenge and classification accuracy. The official FEIII Challenge evaluation showed our system performed highly in single ranking of all triples, placing in 2nd or 3rd place out of 17 participants for 4 of 6 scoring variants; the system also performed above average in per role ranking for 4 of 6 average role NDCG scoring variants.
Characterization and laser performance of a new material: 2 at % Nd:YAG grown by the Czochralski method (2002)

We report on the optical quality and laser performance of Czochralski-grown 2-at. %-doped Nd:YAG. Using a diode pumped laser in an end pumped configuration, we compare the laser performance of this material with the performance of 1-at. %-doped Nd:YAG and 0.7-at. %-doped Nd:YVO4 crystals. Experimental results show the superior performance of 2-at. % Nd:YAG over Nd:YVO4. With a pump power of 25.7 W, a maximum output power of 12.3 W with a slope efficiency of 57% and an optical-to-optical efficiency of 48% were achieved.
Cadmium and Peripheral Arterial Disease: Gender Differences in the 1999–2004 US National Health and Nutrition Examination Survey (2010)

Gender differences in the association of blood and urine cadmium concentrations with peripheral arterial disease (PAD) were evaluated by using data from 6,456 US adults aged ≥40 years who participated in the 1999-2004 National Health and Nutrition Examination Survey. PAD was defined as an ankle-brachial blood pressure index of <0.9 in at least one leg. For men, the adjusted odds ratios for PAD comparing the highest with the lowest quintiles of blood and urine cadmium concentrations were 1.82 (95% confidence interval (CI): 0.82, 4.05) and 4.90 (95% CI: 1.55, 15.54), respectively, with a progressive dose-response relation and no difference by smoking status. For women, the corresponding odds ratios were 1.19 (95% CI: 0.66, 2.16) and 0.56 (95% CI: 0.18, 1.71), but there was evidence of effect modification by smoking: among women ever smokers, there was a positive, progressive dose-response relation; among women never smokers, there was a U-shaped dose-response relation. Higher blood and urine cadmium levels were associated with increased prevalence of PAD, but women never smokers showed a U-shaped relation with increased prevalence of PAD at very low cadmium levels. These findings add to the concern of increased cadmium exposure as a cardiovascular risk factor in the general population.
High-Speed and High-Resolution Interrogation of a Strain and Temperature Random Grating Sensor (2018)

High-speed and high-resolution interrogation of a random fiber grating sensor based on spectral shaping and wavelength-to-time (SS-WTT) mapping, and pulse compression for simultaneous measurement of strain and temperature is proposed and demonstrated. In the proposed system, an ultrashort pulse is spectrum shaped by a high-birefringence (Hi-Bi) random grating (HBRG) to generate two orthogonally polarized spectra with a wavelength difference determined by the birefringence of the HBRG, which are then fed to a dispersive optical loop in which a linearly chirped fiber Bragg grating (LCFBG) is incorporated, to perform linear WTT mapping, to generate two temporally separated optical pulses, which are converted to two random electrical waveforms at a photodetector). Random pulse compression is then performed to increase the interrogation resolution. By measuring the time shifts of the temporally compressed pulses, the strain and temperature information is retrieved. An experiment is performed. The experimental results show that the proposed random grating sensor and its interrogation system can provide a strain and temperature resolution of 7.1 μϵ and 0.79 °C at an ultrahigh speed of 20 MHz.
Effect of lipolytic acyl hydrolase on the activity for six carbon aldehyde formation in tea chloroplasts (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of lipolytic acyl hydrolase on the activity for six carbon aldehyde formation in tea chloroplastsJiro Sekiya, Tadahiko Kajiwara, Masaya Imoto, Satoshi Inouye, and Akikazu HatanakaCite this: J. Agric. Food Chem. 1982, 30, 1, 183–185Publication Date (Print):January 1, 1982Publication History Published online1 May 2002Published inissue 1 January 1982https://pubs.acs.org/doi/10.1021/jf00109a040https://doi.org/10.1021/jf00109a040research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-Citations6LEARN 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
Postoperative Paralysis From Thoracic Ossification of Posterior Longitudinal Ligament Surgery Risk Factor of Neurologic Injury (2016)

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ChemInform Abstract: Stereochemistry of the Core Structure of the Mycolactones. (2001)

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.
Preclinical dosimetric studies of 177Lu‐scFvD2B and comparison with 177Lu‐PSMA‐617 and 177Lu‐iPSMA endoradiotherapeutic agents (2021)

In this preclinical study, we demonstrated the potential of <sup>177</sup> Lu-scFvD2B as a therapeutic agent for PSMA-expressing tumors, due to its higher tumor-absorbed dose when compared with <sup>177</sup> Lu-LMW agents.