gebhart/patrepeval huggingface dataset:
New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure (2021)

Abstract Simian-human immunodeficiency virus (SHIV) chimeras contain the HIV-1 envelope ( env ) gene embedded within an SIVmac proviral backbone. Previously, we showed that substitution of Env residue 375-Ser by bulky aromatic residues enhances Env binding to rhesus CD4 and enables primary or transmitted/founder (T/F) HIV-1 Envs to support efficient SHIV replication in rhesus macaques (RMs). Here, we test this design strategy more broadly by constructing and analyzing SHIVs containing ten strategically selected primary or T/F HIV-1 Envs corresponding to subtypes A, B, C, AE and AG, each with six allelic variants at position 375. All ten SHIVs bearing wildtype Env375 residues replicated efficiently in human CD4 + T cells, but only one of these replicated efficiently in rhesus CD4 + T cells. This was a SHIV whose subtype AE Env naturally contained a bulky aromatic His residue at position 375. Replacement of wildtype Env375 residues by Trp, Tyr, Phe or His in the other nine SHIVs uniformly led to efficient replication in rhesus CD4+ T in vitro and in RMs in vivo . Env375-Trp – the residue found most frequently among SIV strains infecting Old World monkeys – was favored for SHIV replication in RMs, although some SHIVs preferred Env375-Tyr, -His or -Phe. Nine SHIVs containing optimized Env375 alleles were grown large scale in primary activated rhesus CD4 + T cells to serve as challenge stocks in preclinical prevention trials. These virus stocks were genetically homogeneous, native-like in Env antigenicity and tier-2 neutralization sensitivity, transmissible by rectal, vaginal, penile, oral or intravenous inoculation routes, and exhibited acute and early replication kinetics that were indistinguishable from HIV-1 infection in humans. Finally, to expedite future SHIV constructions and eliminate short redundant elements in tat1 and env gp41 that were spontaneously deleted in chronically infected monkeys, we engineered a simplified second-generation SHIV design scheme and validated it in RMs. Overall, our findings demonstrate that SHIVs bearing primary or T/F Envs with bulky aromatic amino acid substitutions at position Env375 consistently replicate in RMs, recapitulating many features of HIV-1 infection in humans. We further show that SHIV challenge stocks grown in primary rhesus CD4 + T cells are efficiently transmitted by mucosal routes common to HIV-1 infection and can be used effectively to test for vaccine efficacy in preclinical monkey trials.
Shifting eye balance using monocularly directed attention in normal vision (2021)

In binocular vision, even without conscious awareness of eye of origin, attention can be selectively biased toward one eye by presenting a visual stimulus uniquely to that eye. Monocularly directed visual cues can bias perceptual dominance, as shown by studies using discrete measures of percept changes in continuous-flash suppression. Here, we use binocular rivalry to determine whether eye-based visual cues can modulate eye balance using continuous percept reporting. Using a dual-task versus single-task paradigm, we investigated whether the attentional load of these cues differentially modulates eye balance. Furthermore, both color-based and motion-based cue stimuli, non-overlaid and peripheral to the rivalry grating stimuli, were used to determine whether shifts in eye balance were stimulus specific. Aligned to cue stimulus onset, time series of percept reports were constructed and averaged across trials and participants. Specifically, for the monocular attention conditions, we found a significant shift in eye balance toward the cued eye and a significant difference in the time taken to switch from the dominating percept, regardless of whether the attention stimuli is color based or motion based. Although we did not find a significant main effect of attentional load, we found a significant interaction effect between the attentionally cued eye and attentional load on the shift in eye balance, indicating an influence of monocular attention on the shift in eye balance.
Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization (AP MALDI) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Extrinsic Tryptophans as NMR Probes of Allosteric Coupling in Membrane Proteins: Application to the A2A Adenosine Receptor (2018)

Tryptophan indole <sup>15</sup>N-<sup>1</sup>H signals are well separated in nuclear magnetic resonance (NMR) spectra of proteins. Assignment of the indole <sup>15</sup>N-<sup>1</sup>H signals therefore enables one to obtain site-specific information on complex proteins in supramacromolecular systems, even when extensive assignment of backbone <sup>15</sup>N-<sup>1</sup>H resonances is challenging. Here we exploit the unique indole <sup>15</sup>N-<sup>1</sup>H chemical shift by introducing extrinsic tryptophan reporter residues at judiciously chosen locations in a membrane protein for increased coverage of structure and function by NMR. We demonstrate this approach with three variants of the human A<sub>2A</sub> adenosine receptor (A<sub>2A</sub>AR), a class A G protein-coupled receptor, each containing a single extrinsic tryptophan near the receptor intracellular surface, in helix V, VI, or VII, respectively. We show that the native A<sub>2A</sub>AR global protein fold and ligand binding activity are preserved in these A<sub>2A</sub>AR variants. The indole <sup>15</sup>N-<sup>1</sup>H signals from the extrinsic tryptophan reporter residues show different responses to variable efficacy of drugs bound to the receptor orthosteric cavity, and the indole <sup>15</sup>N-<sup>1</sup>H chemical shift of the tryptophan introduced at the intracellular end of helix VI is sensitive to conformational changes resulting from interactions with a polypeptide from the carboxy terminus of the Gα<sub>S</sub> intracellular partner protein. Introducing extrinsic tryptophans into proteins in complex supramolecular systems thus opens new avenues for NMR investigations in solution.
Observation of Multiple Thresholds in the Many-Atom Cavity QED Microlaser (2004)

We report the observation of multiple laser thresholds in the many-atom cavity QED microlaser. Traveling-wave coupling and a supersonic atom beam are used to create a well-defined atom-cavity interaction. Multiple thresholds are observed as jumps in photon number due to oscillatory gain. Although the number of intra-cavity atoms is large, up to N~1000, the dynamics of the microlaser agree with a single atom theory. This agreement is supported by quantum trajectory simulations of a many-atom microlaser and a semiclassical microlaser theory. We discuss the relation of the microlaser with the micromaser and conventional lasers.
A Constrained Thermal Expansion Micro-Actuator (1998)

Abstract This paper describes a series of thermal micro-actuators fabricated from polycrystalline silicon. These actuators use geometric constraints to amplify motion from thermal expansion. Compliant mechanism theory, particularly the pseudo-rigid-body model, was used to aid in the visualization of the device’s behavior. Nonlinear finite element analysis was used to analyze the actuators and refine the designs. The resulting mechanisms were fabricated and tested. Maximum deflections of over 20 μm were obtained with a total cycle time faster than 4 milliseconds. A bi-directional actuator capable of 6 μm displacements in both directions is also described.
Usefulness of C-reactive protein in predicting early and late recurrences after atrial fibrillation ablation (2009)

We studied the C-reactive protein level and its predictive value for early and late arrhythmia recurrences after atrial fibrillation (AF) ablation. We analysed data from 125 consecutive patients (52% with paroxysmal AF) who underwent a first AF ablation. C-reactive protein level was determined at baseline and at Days 1, 2, and 3 post-AF ablation. An early recurrence (ER) was defined as any arrhythmia occurring within the first month following the index ablation. Sixty-eight patients (54%) experienced ER. Twenty-nine patients were re-ablated for ER within the first month and were not included for the long-term follow-up analysis. Of the remaining 96 patients, 59 (61%) experienced late recurrences. C-reactive protein level increased significantly after AF ablation with a peak (40 +/- 32 mg/L) occurring 2 days after the index procedure. Patients without ER had a significant higher C-reactive protein level (49 +/- 52 vs. 32 +/- 22 mg/L, P=0.02) compared with patients without ER. However, the C-reactive protein level was similar in patients with or without late recurrences. C-reactive protein level was the only independent predictor of ERs (P = 0.03). C-reactive protein level increased significantly after AF ablation. High C-reactive protein level was associated with fewer early arrhythmia recurrences. No relationship was found between C-reactive protein level and late arrhythmia recurrences.
Uniform accuracy of eigenpairs from a shift‐invert Lanczos method (2006)

This paper analyzes the accuracy of the shift‐invert Lanczos iteration for computing eigenpairs of the symmetric definite generalized eigenvalue problem. We provide bounds for the accuracy of the eigenpairs produced by shift‐invert Lanczos given a residual reduction. We discuss the implications of our analysis for practical shift‐invert Lanczos iterations. When the generalized eigenvalue problem arises from a conforming finite element method, we also comment on the uniform accuracy of bounds (independent of the mesh size h).
Regulation of MHC I expression in lung epithelial cells during inflammation. (2022)

Infections of the respiratory tract are a perennial cause of death worldwide. These diseases typically affect the lung epithelium, composed of three main types of cells: alveolar type I (AT1), alveolar type 2 (AT2), and bronchiolar cells. These three epithelial cells (ECs) types express constitutively low levels of MHC I, representing less than 1% of the levels found in thymic ECs. This weak expression is surprising since it could disturb the elimination of infected or transformed cells. We hypothesized that lung ECs should be able to upregulate their MHC I expression swiftly when needed. We induced lung inflammation in mice using inhalation of LPS. We observed that AT1, AT2, and bronchiolar cells upregulated by 25 times their surface expression of MHC I during LPS-induced inflammation. The concerted production of the three IFN families, thanks to the factors Stat1, Stat2, and Nlrc5, drove this upregulation. The low expression of genes involved in the peptide loading of MHC I molecules nevertheless hampered MHC I upregulation in lung ECs. Discrete gene&nbsp;subsets were selectively differentially regulated by interferon signaling in each type of lung ECs. AT1 increased genes related to cytokine-mediated signaling pathway while AT2 and bronchiolar decreased genes involved in their specialized functions, essential to maintaining the integrity of lung epithelium (epithelium regeneration and cilium movement, respectively).&nbsp;Our results showed a balance between the expression of transcripts involved in immune defenses and transcripts maintaining lung epithelium integrity in lung ECs. It paves the way to a better understanding of antigen presentation in lung ECs, and the pathogenesis of lung inflammation.
The Use of Computer Navigation in Total Hip Arthroplasty Is Associated with a Reduced Rate of Revision for Dislocation (2021)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
An immersion scanner enabling 10 nm half pitch production and high productivity (2015)

Nikon's newly developed immersion scanner, NSR-S630D, provides exceptional performance in product overlay, CD uniformity, and productivity at 10 nm hp node and beyond. Generally, maintaining machine accuracy and productivity at a high level is difficult because they are in a trade-off relationship. The NSR-S630D is equipped with new features including an encoder servo-controlled reticle stage, reticle bending mechanism, optics with enhanced thermal aberration control, and thermally stable wafer stage. These features enable the NSR-S630D to deliver highest accuracy and productivity.
Basal body stability and ciliogenesis requires the conserved component Poc1 (2009)

Centrioles are the foundation for centrosome and cilia formation. The biogenesis of centrioles is initiated by an assembly mechanism that first synthesizes the ninefold symmetrical cartwheel and subsequently leads to a stable cylindrical microtubule scaffold that is capable of withstanding microtubule-based forces generated by centrosomes and cilia. We report that the conserved WD40 repeat domain-containing cartwheel protein Poc1 is required for the structural maintenance of centrioles in Tetrahymena thermophila. Furthermore, human Poc1B is required for primary ciliogenesis, and in zebrafish, DrPoc1B knockdown causes ciliary defects and morphological phenotypes consistent with human ciliopathies. T. thermophila Poc1 exhibits a protein incorporation profile commonly associated with structural centriole components in which the majority of Poc1 is stably incorporated during new centriole assembly. A second dynamic population assembles throughout the cell cycle. Our experiments identify novel roles for Poc1 in centriole stability and ciliogenesis.
Inhibition of Tumor Necrosis Factor Alpha by an Adenovirus-Encoded Soluble Fusion Protein Extends Transgene Expression in the Liver and Lung (1999)

The cellular and humoral immune responses to adenovirus (Ad) remain a major barrier to Ad-mediated gene therapy. We recently reported that mice deficient in tumor necrosis factor alpha (TNF-alpha) or Fas (APO-1, CD95) have prolonged expression of an Ad transgene expressing a foreign protein in the liver. To determine whether blockade of TNF-alpha or Fas would have the same effect in normal mice, we created transgenes that expressed soluble murine CD8 or CD8 fused to the extracellular regions of TNF receptor 1 (TNFR) or Fas and inserted into the left-end region of first-generation (E1/E3-) Ad vectors. Consistent with the results observed in TNF-deficient mice, expression of the TNFR-CD8 fusion protein was prolonged in vivo compared to that of control proteins. Not only did expression of TNFR-CD8 persist in the liver and the lung, but when coadministered with another first-generation vector, the protein provided "transprotection" for the companion vector and transgene. In addition, TNFR-CD8 attenuated the humoral immune response to the Ad. Together, these findings demonstrate that blockade of TNF-alpha is likely to be useful in extending the expression of an Ad-encoded transgene in a gene therapy application.
Structural Study of Cu Photodoped Ge-S Glasses (2007)

The products formed by Cu photodiffusion in GeS2 films are investigated. Rutherford backscattering spectrometry shows that for the experimental conditions used photodiffusion results in the introduction of 17.4 at. % Cu into the chalcogenide glass matrix. The diffusion product are analyzed by means of X-ray diffraction which reveals the formation of Cu2GeS3. Raman spectra show the considerable influence of Cu on the structure of the hosting glass which we relate to the incorporation of fourfold coordinated Cu into the glass matrix. Annealing of the films at 300°C and 430°C was also studied to determine the thermal stability of the ternary.
Overview of Boeing’s Shape Memory Alloy Based Morphing Aerostructures (2008)

The Boeing Company has a goal of creating aircraft that are capable of continuous optimization for all flight conditions. Toward this goal we have developed morphing-capable, adaptive structures based on Shape Memory Alloy (SMA) technology that enable component and system level optimization at multiple flight conditions. The SAMPSON Smart Inlet program showed that fully integrated SMA wire bundles could provide a fighter aircraft with a Variable Engine Inlet capability. The Reconfigurable Rotor Blade program demonstrated the ability of highly robust, controlled 55-Nitinol tube actuators to twist a rotor blade in a spin stand test to optimize aerodynamic characteristics. The Variable Geometry Chevrons program, which was the first use of 60-Nitinol for a major aerospace application, included a flight test and static engine test of GE90–115B engine fitted with controlled morphing chevrons that reduced noise and increased engine efficiency. The Deployable Rotor Tab employed tube actuators to deploy and retract small fences which are capable of significantly reducing blade vortex interaction generated noise on a rotorcraft. Most recently, the Variable Geometry Fan Nozzle program has built on the VGC technology to demonstrate improved jet engine performance. The Boeing Company continues to mature SMA technology in order to develop innovative applications and support their commercialization.
Quantitative Correlation of Solvent Polarity with the α‐/310‐Helix Equilibrium: A Heptapeptide Behaves as a Solvent‐Driven Molecular Spring (2003)

The long and the short of it: Just by changing the polarity of the solvent the highly folded heptapeptide Ac-[Aib-L-(αMe)Val-Aib]2-L-His-NH2 converts from an α into a 310 helix (see picture). The equilibrium constant between the two conformations correlates with the empirical solvent polarity parameter E. Molecular dynamics calculations show that the peptide elongates (310 helix) or shortens (α helix) on switching from one conformation to the other. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51015_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Monoclonal antibodies that demonstrate specificity for several types of human lung cancer. (1981)

Monoclonal antibodies with selectivity for human lung cancer were produced by immunizing BALB/c mice with an established line of human small cell lung cancer (NCI-H69) and fusing the mouse spleen cells to mouse myeloma line X63-Ag8.653. The resulting hybrid cells were initially screened by immunoautoradiography for production of antibodies that would react with NCI-H69 and another small cell lung cancer line (NCI-H128) but not its autologous B-lymphoblastoid line (NCI-H128BL). Stable monoclonal antibody-producing lines were isolated by repeated cloning. Three independently derived monoclonal antibodies, designated 525A5, 534F8, and 538F12, were found to react with three of the major types of human lung cancer (small cell, adenocarcinoma, and squamous carcinoma). They did not react with bronchioloalveolar and large cell lung cancers, myeloma, lymphomas, leukemias, osteogeneic sarcoma, mesothelioma, hypernephroma, malignant melanoma, simian virus 40-transformed human fetal lung cells, skin fibroblast lines, human B-lymphoblastoid lines, human erythrocytes, and rodent cells. Interestingly, these antibodies also bound to three out of three human neuroblastomas and two out of three breast cancers but failed to react with mouse neuroblastoma and rat pheochromocytoma. The monoclonal antibodies reacted with human small cell lung cancer tumors obtained at autopsy, but had insignificant reactions with normal human lung, liver, spleen, and skeletal muscle. We conclude that monoclonal antibodies have been generated that react with common antigenic determinants expressed on several human lung cancer types, neuroblastoma, and some breast cancers, but are not detectable by our current assays on a variety of other human tumors or normal adult human tissues. Such antibodies are of potential clinical and biological importance.
Spontaneous photon emission from 32 nm and 14 nm SOI FETs (2016)

The very faint spontaneous near-infrared photon emission of scaled SOI FETs fabricated in 32 nm planar and 14 nm FinFET technologies is characterized and modeled for the first time. A high sensitivity and low noise detector is leveraged to measure emission at low voltages, including sub-threshold and linear regions that are extremely faint. Furthermore, the effect of device threshold is studied and modeled for the first time by comparing the emission from FETs with different Vt.
N,N′-Bis-(2-(cyano)ethoxycarbonyl)-2-methyl-2-thiopseudourea: A Guanylating Reagent for Synthesis of 2′-O-[2-(Guanidinium)ethyl]-Modified Oligonucleotides (2007)

A guanylating reagent, N,N'-bis-(2-(cyano)ethoxycarbonyl)-2-thiopseudourea, was synthesized and used for synthesis of 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modified oligonucleotides. A convenient deprotection method for the 2'-O-GE oligonucleotides was developed.
Rate constants and Arrhenius parameters for the reactions of some carbon-centered radicals with tris(trimethylsilyl)silane (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRate constants and Arrhenius parameters for the reactions of some carbon-centered radicals with tris(trimethylsilyl)silaneC. Chatgilialoglu, J. Dickhaut, and B. GieseCite this: J. Org. Chem. 1991, 56, 22, 6399–6403Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/jo00022a035https://doi.org/10.1021/jo00022a035research-articleACS PublicationsRequest reuse permissionsArticle Views452Altmetric-Citations82LEARN 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
Accuracy of power Doppler angiography for the assessment of arterial stenoses (2003)

This study, performed in an in vitro flow model under pulsatile flow, compares 4 segmentation algorithms. These algorithms are applied to 3D power Doppler flow angiograms for quantifying the cross-sectional area of the lumen of a simulated artery with a stenosis of 80% area reduction. Results show that all four algorithms overestimate the cross-sectional area of the arterial lumen, but two of them provide accurate estimates of the percentage of area reduction within the stenosis.