gebhart/patrepeval huggingface dataset:
Population structure and molecular epidemiology of intestinal spirochaetes isolated from animals and man. (1997)

Serpulina hyodysenteriae and Serpulina pilosicoli are the respective antiological agents of swine dysentery and intestinal spirochaetosis. Both species have been shown to be genetically diverse but the mechanisms accounting for the variation have not been investigated. Originally, most bacterial species were thought to be clonal and although recombination occurred it was presumed to be too infrequent to disrupt linkage disequilibrium. The recent application of the index of association (Ia) to MEE data sets has shown that bacteria may occupy a spectrum of population structures. Whilst the majority of species are clonal, some naturally transformable species have been shown to be panmicitc (ie high levels of recombination have disrupted linkage disequilibrium) whilst others have an intermediate population structure. The Ia was applied to 231 S. hyodysenteriae isolates that were divided into 50 electrophoretic types (ETs), and the population structure was found to be epidemic (ie significant levels of background recombination occurring with a large number of isolates restricted to certain ETs that may have survival or virulence advantages). In contrast 145 S. pilosicoli isolates obtained from humans in the Highlands of PNG divided in 27 ETs had a completely panmictic population structure. The results may reflects the different epidemiological aspects of each disease. The potential mechanisms for recombination in each species require further investigation.
Interfacial Catalysis by Human 85 kDa Cytosolic Phospholipase A2 on Anionic Vesicles in the Scooting Mode (1997)

Analysis of phospholipases A2 on model phospholipid bilayers in which enzyme is essentially irreversibly bound at the lipid-water interface, termed "scooting mode", is a useful tool for studying the kinetic properties of interfacial enzymes. It is shown that human cytosolic 85 kDa phospholipase A2 (cPLA2) hydrolyzes sn-2-arachidonyl-containing phospholipids or the gamma-linolenoyl ester of 7-hydroxycoumarin (GLU) dispersed in vesicles of 1,2-dioleoyl-sn-glycero-3-phosphomethanol (L-DOPM) in the scooting mode. Trapping of cPLA2 on L-DOPM vesicles is rapid and independent of product formation. Slowing of cPLA2-catalyzed hydrolysis of substrates present in phosphatidylmethanol and phosphatidylcholine vesicles is primarily due to apparent inactivation rather than to substrate depletion. cPLA2 phosphorylated on serine 505 by mitogen-activated protein kinase displays a 30% increase in the rate of sn-2-arachidonylphosphatidylcholine hydrolysis in the scooting mode compared to that of the nonphosphorylated enzyme. Kinetic parameters of cPLA2 acting on a variety of different phosphatidylmethanol vesicles were evaluated, and the results are discussed in terms of active site affinities for substrates and of lateral organization of substrates in the bilayer. A key result is that the sigmoidal kinetics reported previously using 1,2-dimyristoyl-sn-glycero-3-phosphomethanol (DMPM) vesicles are most prominent near the phase transition temperature of DMPM. No sigmoidal kinetics was observed using L-DOPM vesicles. The results of kinetic experiments and the behavior of a fluorescent substrate analog are consistent with nonideal mixing of substrate in DMPM vesicles, but not in L-DOPM vesicles, suggesting that apparent saturation and sigmoidal kinetics are more a result of nonideal mixing of substrate in DMPM vesicles than of active site binding of substrate. The fluorescence assay described using L-DOPM/GLU vesicles is useful for evaluating the interfacial behavior of cPLA2, including its substrate preferences and the effect of active site-directed inhibitors.
The EBNA2-EBF1 complex promotes oncogenic MYC expression levels and metabolic processes required for cell cycle progression of Epstein-Barr virus-infected B cells (2021)

ABSTRACT Epstein-Barr virus (EBV) is a human tumor virus, which preferentially infects resting human B cells. Upon infection in vitro , EBV activates and immortalizes these cells. The viral latent protein EBV nuclear antigen (EBNA) 2 is essential for B cell activation and immortalization; it targets and binds the cellular and ubiquitously expressed DNA binding protein CBF1, thereby transactivating a plethora of viral and cellular genes. In addition, EBNA2 uses its N-terminal dimerization (END) domain to bind early B cell factor (EBF) 1, a pioneer transcription factor specifying the B cell lineage. We found that EBNA2 exploits EBF1 to support key metabolic processes and to foster cell cycle progression of infected B cells in their first cell cycles upon activation. An α1-helix within the END domain was found to promote EBF1 binding. EBV mutants lacking the α1-helix in EBNA2 can infect and activate B cells efficiently, but the activated cells fail to complete the early S phase of their initial cell cycle. Expression of MYC , target genes of MYC and E2F as well as multiple metabolic processes linked to cell cycle progression are impaired in EBVΔα1 infected B cells. Our findings indicate that EBF1 controls B cell activation via EBNA2 and, thus, has a critical role in regulating the cell cycle of EBV infected B cells. This is a function of EBF1 going beyond its well-known contribution to B cell lineage specification. Significance statement Epstein-Barr virus (EBV) infects primary B cells and establishes life-long latent infection in these cells. EBV nuclear antigen (EBNA) 2 drives early processes of B cell activation and cell cycle entry. The surface of the N-terminal dimerization domain of EBNA2 exposes a five amino acid α-helix (α1) that recruits EBF1 to activate MYC and downstream targets of both MYC and E2F to support critical metabolic processes in infected B cells and to drive them through S phase in the first cell cycle post-infection. Our study demonstrates how EBNA2 exploits EBF1, a key factor of B cell lineage specification to initiate proliferation and high-lights the α1-helix as a potential Achilles heel of the virus at the stage when latent infection is established.
PTK6 Regulates IGF-1-Induced Anchorage-Independent Survival (2010)

These findings highlight PTK6 as a critical regulator of anchorage-independent survival of breast and ovarian tumor cells via modulation of IGF-1 receptor signaling, thus supporting PTK6 as a potential therapeutic target for multiple tumor types. The combined genomic and proteomic approaches in this report provide an effective strategy for identifying oncogenes and their mechanism of action.
Adaptive speech enhancement with varying noise backgrounds (2008)

We present a new approach for speech enhancement in the presence of non-stationary and rapidly changing background noise. A distributed microphone system is used to capture the acoustic characteristics of the environment. The input of each microphone is then classified either as speech or one of the predetermined noise types. Further enhancement of speech in respective microphones is carried out using a modified spectral subtraction algorithm that incorporates multiple noise models to quickly adapt to rapid background noise changes. Tests on real world speech captured under diverse conditions demonstrate the effectiveness of this method.
Moraxella -Dependent α1-Antichymotrypsin Neutralization (2007)

The acute phase reactant and protease inhibitor alpha(1)-antichymotrypsin is considered to play a protective role in the airways, but whether it interacts with respiratory bacteria is not known. We analyzed whether the common respiratory pathogens Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and other bacterial species interact with antichymotrypsin. M. catarrhalis was the only species that bound antichymotrypsin among 25 bacterial species tested by flow cytometry and direct binding assay. We compared a series of clinical isolates in addition to wild-type and ubiquitous surface protein-deficient Moraxella to study the nature of antichymotrypsin binding by the bacteria. Experiments with Moraxella mutants revealed that ubiquitous surface proteins A1 and A2 were responsible for the interaction, and using recombinant fragments, a consensus sequence within ubiquitous surface proteins A1 and A2 was defined. Binding of iodine-labeled antichymotrypsin was dose dependent and strong (dissociation constant [K(d)] 24.9-44.8 nM). Moreover, a chymotrypsin activity assay showed that antichymotrypsin, when bound to the bacterial surface, was neutralized. Moraxella antichymotrypsin neutralization is a novel microbial virulence mechanism that may induce excessive inflammation resulting in more exposed extracellular matrix that is beneficial for bacterial colonization.
PIC-based iterative SDR detector for OFDM systems in doubly-selective fading channels (2010)

OFDM data detection in doubly-selective fading channels requires high complexity due to intercarrier interferences (ICI). We present a low-complexity receiver consisting of a semidefinite relaxation (SDR) based detector and parallel interference cancellation (PIC). The entire band is divided into clusters of adjacent subcarriers. SDR is applied on each cluster while PIC tackles ICI from other clusters. An upper bound of ICI power is derived and used to omit far-away clusters in performing PIC. Finally, an adaptive detector based on PIC, PIC-based SDR and the snap-shot SNR in channel is proposed to achieve a better tradeoff between complexity and performance.
Coordination-Dependent Chemical Reactivity of TFSI Anions at a Mg Metal Interface (2023)

Charge transfer across the electrode-electrolyte interface is a highly complex and convoluted process involving diverse solvated species with varying structures and compositions. Despite recent advances in in situ and operando interfacial analysis, molecular specific reactivity of solvated species is inaccessible due to a lack of precise control over the interfacial constituents and/or an unclear understanding of their spectroscopic fingerprints. However, such molecular-specific understanding is critical to the rational design of energy-efficient solid-electrolyte interphase layers. We have employed ion soft landing, a versatile and highly controlled method, to prepare well-defined interfaces assembled with selected ions, either as solvated species or as bare ions, with distinguishing molecular precision. Equipped with precise control over interfacial composition, we employed in situ multimodal spectroscopic characterization to unravel the molecular specific reactivity of Mg solvated species comprising (i.e., bis(trifluoromethanesulfonyl)imide, TFSI<sup>-</sup>) anions and solvent molecules (i.e., dimethoxyethane, DME/G1) on a Mg metal surface relevant to multivalent Mg batteries. In situ multimodal spectroscopic characterization revealed higher reactivity of the undercoordinated solvated species [Mg-TFSI-G1]<sup>+</sup> compared to the fully coordinated [Mg-TFSI-(G1)<sub>2</sub>]<sup>+</sup> species or even the bare TFSI<sup>-</sup>. These results were corroborated by the computed reaction pathways and energy barriers for decomposition of the TFSI<sup>-</sup> within Mg solvated species relative to bare TFSI<sup>-</sup>. Finally, we evaluated the TFSI reactivity under electrochemical conditions using Mg(TFSI)<sub>2</sub>-DME-based phase-separated electrolytes representing different solvated constituents. Based on our multimodal study, we report a detailed understanding of TFSI<sup>-</sup> decomposition processes as part of coordinated solvated species at a Mg-metal anode that will aid the rational design of improved sustainable electrochemical energy technologies.
Supplemental Video 3 from Visualization of Activated T Cells by OX40-ImmunoPET as a Strategy for Diagnosis of Acute Graft-versus-Host Disease (2023)

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Expression of a Functional Drosophila melanogaster CMP-sialic Acid Synthetase (2006)

CMP-N-acetylneuraminic acid is a critical metabolite in the generation of glycoconjugates that play a role in development and other physiological processes. Whereas pathways for its generation are firmly established in vertebrates, the presence and function of the relevant synthetic enzyme in insects and other protostomes is unknown. In this study, we characterize the first functional CMP-sialic acid synthase (DmCSAS) from any protostome lineage expressed from a D. melanogaster cDNA clone. Homologous genes were subsequently identified in other insect species. The gene is developmentally regulated, with expression first appearing at 12-24 h of embryogenesis, low expression through larval and pupal stages, and greatly enriched expression in the adult head, suggesting a possible role in the central nervous system. Activity of the enzyme was verified by an increase in in vitro and in vivo CMP-N-acetylneuraminic acid levels when expressed in a heterologous host. Unlike all known vertebrate CMP-sialic acid synthetase (CSAS) proteins that localize to the nucleus, the D. melanogaster CSAS protein was targeted to the Golgi compartment when expressed in both heterologous mammalian and insect cell lines. Replacement of the N-terminal leader sequence of DmCSAS with the human CSAS N-terminal sequence resulted in the redirection of the chimeric CSAS protein to the nucleus but with a concomitant loss of enzymatic activity. The localization of CSAS orthologs to different intracellular organelles represents, to our knowledge, the first example of differential protein targeting of orthologs in eukaryotes and reveals how the sialylation pathway diverged during the evolution of protostomes and deuterostomes.
Evolution of the Bifunctional Lead μ Agonist/δ Antagonist Containing the 2′,6′-Dimethyl-l-tyrosine−1,2,3,4-Tetrahydroisoquinoline-3-carboxylic Acid (Dmt−Tic) Opioid Pharmacophore (2009)

Based on a renewed importance recently attributed to bi- or multifunctional opioids, we report the synthesis and pharmacological evaluation of some analogues derived from our lead μ agonist / δ antagonist, H-Dmt-Tic-Gly-NH-Bzl. Our previous studies focused on the importance of the C-teminal benzyl function in the induction of such bifunctional activity. The introduction of some substituents in the para position of the phenyl ring (-Cl, -CH(3), partially -NO(2), inactive -NH(2)) was found to give a more potent μ agonist / antagonist effect associated with a relatively unmodified δ antagonist activity (pA(2) = 8.28-9.02). Increasing the steric hindrance of the benzyl group (using diphenylmethyl and tetrahydroisoquinoline functionalities) substantially maintained the μ agonist and δ antagonist activities of the lead compound. Finally and quite unexpectedly D-Tic2, considered as a wrong opioid message now; inserted into the reference compound in lieu of L-Tic, provided a μ agonist / δ agonist better than our reference ligand (H-Dmt-Tic-Gly-NH-Ph) and was endowed with the same pharmacological profile.
Investigation of the adsorption of polystyrene by plasmon surface polaritons on metal gratings (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInvestigation of the adsorption of polystyrene by plasmon surface polaritons on metal gratingsJ. C. Loulergue, Y. Levy, and C. AllainCite this: Macromolecules 1985, 18, 2, 306–307Publication Date (Print):February 1, 1985Publication History Published online1 May 2002Published inissue 1 February 1985https://pubs.acs.org/doi/10.1021/ma00144a037https://doi.org/10.1021/ma00144a037research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations10LEARN 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
Conformance While Fracturing Tight Gas Formations (2008)

Abstract The industry is continuing to expand production from reservoirs that had previously been passed over because of less than desirable properties such as low porosity, permeability, high water saturations, and/or being in close proximity to water. Because of this, water production after a hydraulic fracturing operation is an even greater concern and can make stimulation of these intervals an uneconomical venture. This paper discusses how water production has been significantly reduced using a new conformance-while-fracturing (CWF) method that incorporates a hydrophobically modified water-soluble polymer (HMWSP) to function as a relative permeability modifier (RPM) incorporated into the fracturing treatment design. The purpose of the HMWSP is to reduce the effective permeability to the flow of water without significant changes to the flow of the hydrocarbon. A low gel loading borate crosslinking fluid is used to fracture stimulate the wells. The increase in water production with the CWF method is typically less than 50% that of offset wells that had been fracture stimulated with conventional methods. Additionally, the total production of the wells stimulated using the CWF method usually resulted in lower water-gas ratios. This paper describes the properties of the HMWSP, general CWF job-design considerations, field applications, and post-fracturing result comparisons of the CWF method with offset wells.
Low-rank + sparse (L+S) reconstruction for accelerated dynamic MRI with seperation of background and dynamic components (2013)

L+S matrix decomposition finds the low-rank (L) and sparse (S) components of a matrix M by solving the following convex optimization problem: min‖L‖<sub>*</sub>L+S matrix decomposition finds the low-rank (L) and sparse (S) components of a matrix M by solving the following convex optimization problem: ‖L ‖<sub>*</sub> + &lambda;‖S‖<sub>1</sub>, subject to M=L+S, where ‖L‖<sub>*</sub> is the nuclear-norm or sum of singular values of L and ‖S‖<sub>1</sub> is the 1<sub>1</sub>-norm| or sum of absolute values of S. This work presents the application of the L+S decomposition to reconstruct incoherently undersampled dynamic MRI data as a superposition of a slowly or coherently changing background and sparse innovations. Feasibility of the method was tested in several accelerated dynamic MRI experiments including cardiac perfusion, time-resolved peripheral angiography and liver perfusion using Cartesian and radial sampling. The high acceleration and background separation enabled by L+S reconstruction promises to enhance spatial and temporal resolution and to enable background suppression without the need of subtraction or modeling.
Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains (2019)

These data demonstrate that individuals infected with similar viral strains can generate partially similar antibody responses, but these do not drastically differ from those in individuals infected with relatively unrelated strains.
Parameter Estimation for MRF Stereo (2005)

This paper presents a novel approach for estimating parameters for MRF-based stereo algorithms. This approach is based on a new formulation of stereo as a maximum a posterior (MAP) problem, in which both a disparity map and MRF parameters are estimated from the stereo pair itself. We present an iterative algorithm for the MAP estimation that alternates between estimating the parameters while fixing the disparity map and estimating the disparity map while fixing the parameters. The estimated parameters include robust truncation thresholds, for both data and neighborhood terms, as well as a regularization weight. The regularization weight can be either a constant for the whole image, or spatially-varying, depending on local intensity gradients. In the latter case, the weights for intensity gradients are also estimated. Experiments indicate that our approach, as a wrapper for existing stereo algorithms, moves a baseline belief propagation stereo algorithm up six slots in the middlebury rankings.
Wide steering angle optical phased array based on silicon nano-membrane (2009)

We present a new approach to wide angle optical beam steering based on nano-membrane-based phased array structures with unequally spaced elements. In our approach, the array elements are positioned in such way that grating lobes associated with different sub-arrays do not overlap. Therefore, we reduce the side-lobe-level of the array radiation pattern and at the same time we can avoid the optical coupling between adjacent waveguides by relaxing the half-wavelength spacing requirement for large angle beam steering. By optimizing the optical waveguide structure for the maximum full-width at half-maximum of the single radiator's radiation pattern we discuss the optimum performance achievable using the Unequally-spaced Waveguide Arrays.
Abstract 376: Downregulation of Endogenous Apelinergic Axis Mediates Endothelial and Organismal Senescence (2016)

Background: Apelinergic signaling is a recently discovered GPCR mediated pathway. Endothelial cells are the main source of endogenous apelin (apln) while apelin receptor (aplnr) is present on multiple cell types. Since the role of endogenous apelinergic pathway within the context of senescence is largely unknown, we ask if levels of apln- aplnr vary with aging. We also investigate the effects of downregulated apln- aplnr on cellular and organismal aging. Approach and Results: To assess variations in endogenous apln- aplnr with aging, we compared their levels in 1 month (young) and 1 year old (old) WT mice. We noticed significant downregulation of apln- aplnr with chronological senescence in multiple tissues. Expression of apelin was also reduced with replicative senescence of endothelial cells. L-NAME administration, a model of stress induced senescence, also repressed aortic and cardiac apln. To address the mechanism involved in downregulation of apln- aplnr, we administered young wild type mice with Ang II. After a week of Ang II, there was significant downregulation of aortic apln and aplnr. Ang II and TGF-β also repressed apln and aplnr in vitro . Next we investigated the effects of downregulated apln on endothelial cells. In response to shRNA mediated apelin knockdown, cells exhibited slower proliferation and upregulated senescence associated markers. We observed similar results when endothelial aplnr was blocked with an antagonist, ML221. In addition, apln and aplnr deficient mice also exhibited features of cardiovascular aging, including ventricular hypertrophy and lower EF. Importantly, aplnr deficient mice at eight months of age were also hypertensive. Conclusion: We provide a systematic assessment of senescence associated variation in levels of apln- aplnr. We demonstrate the role of Ang II- TGF-β axis in downregulating apln- aplnr during chronological and stress induced senescence in vivo and in vitro . We propose a novel model of Ang II- TGF-β induced senescence. Where in, with aging Ang II and TGF-β repress endogenous apln- aplnr. Downregulation of endogenous apln- aplnr axis decreases beneficial “youthful” effects of apelin, resulting in endothelial dysfunction and accelerated organismal aging.