gebhart/patrepeval huggingface dataset:
SC5 mAb Represents a Unique Tool for the Detection of Extracellular Vimentin as a Specific Marker of Sezary Cells (2006)

Circulating malignant Sézary lymphocytes result from a clonal proliferation of memory/activated CD4(+)CD45RO(+) T lymphocytes primarily involving the skin. Recently, the CD158k/KIR3DL2 cell surface receptor has been identified to phenotypically characterize these cells. We previously described a mAb termed SC5 that identifies an unknown early activation cell membrane molecule. It is expressed selectively by T lymphocytes isolated from healthy individuals upon activation, and by circulating Sézary syndrome lymphocytes. In addition, we found that SC5 mAb was reactive with all resting T lymphocytes once permeabilized, indicating that SC5 mAb-reactive molecule might present distinct cellular localization according to the T cell activation status. In this study, we show for the first time that SC5 mAb recognizes the intermediate filament protein vimentin when exported to the extracellular side of the plasma membrane of viable Sézary malignant cells. We demonstrate that SC5 mAb is unique as it reacts with both viable malignant lymphocytes and apoptotic T cells. As vimentin is also detected rapidly at the cell membrane surface after normal T lymphocyte activation, it suggests that its extracellular detection on Sézary cells could be a consequence of their constitutive activation status. Finally, as a probable outcome of vimentin cell surface expression, autoantibodies against vimentin were found in the sera of Sézary syndrome patients.
Synthesis of the Bicyclic Core of CP‐225,917 and CP‐263,114 by an Intramolecular Diels–Alder Reaction (1997)

New lead compounds with promising biological activity are represented by CP-225,917 and CP-263,114. An approach based on an intramolecular Diels-Alder reaction for the total synthesis of these compounds is exemplified by the synthesis of racemic bicyclo[4.3.1]dec-1(9),4-dienes 2a,b from triene 1.
Protein interaction hot spots and engineered binding affinity within the smad4-ski interface (2008)

Protein-protein interactions underlie a dynamic range of cellular processes that are essential to biological organisms. As such, there is an increased desire to modify these interactions in order to elicit cellular responses. Proteins can be engineered to incorporate desired properties by using techniques from biology, chemistry, mathematics, and computer science. In this cross-disciplinary spirit, the work presented in this thesis explores the effects of mutations within protein interfaces through the use of computational and experimental methods. 
First, a machine learning approach is used to develop KFC—a knowledge-based model that improves the ability to predict binding or the subset of residues that account for most of the interface's binding free energy. KFC is based on two predictive models, one based on shape specificity features and the other based on biochemical contacts. Notably, KFC displays better overall predictive accuracy than computational alanine scanning (Robetta-Ala). Because these methods predict different subsets of known hot spots, a large and significant increase in accuracy is achieved by combining KFC and Robetta-Ala. The KFC analysis of two protein interface case studies indicates a strong correlation between KFC hot spot predictions and mutations that significantly reduce the binding affinity of the interface. 
Next, a protein engineering study that enhances the binding affinity of the Smad4-Ski protein complex is presented. A structure-based computational method is used to predict point mutations that may improve the binding affinity between Smad4 and Ski. Also, KFC is used to predict regions within the Smad4-Ski interface that may be sensitive to mutation. Then, an enzyme-linked immunosorbent assay (ELISA) is used to measure the relative changes in Ski-binding between the mutants predicted to improve binding affinity and wild-type Smad4. In addition to identifying several mutations that significantly enhance binding affinity, the mutational analysis highlights regions within the Smad4-Ski interface that can be optimized to improve binding and confirms that mutations in the region surrounding hot spot residues disrupt protein binding.
Low Zinc Intake During Exclusive Breast-Feeding Does Not Impair Growth (1994)

We studied zinc nutrition in exclusively breast-fed infants whose growth deviated from the norm. Their number fell from 200 at birth to 116 at the age of 6 months and 36 at the age of 9 months. The mothers received 0, 20, or 40 mg Zn++ as sulfate daily. Breast milk intake and concentrations of zinc in milk as well as in maternal and infant serum were measured. Individual zinc concentrations in milk showed channeling. The 20-mg supplement had no effect on the parameters measured. In contrast, 40 mg increased the maternal serum zinc concentration by 2 months and slowed the normal decline of milk zinc concentration by 6 months. Maternal supplementation had no effect on infant serum concentrations; they remained lower than adult levels throughout the 1st year of life. Zinc intake was low (about one-tenth of RDA), but it seemed to be adequate; the serum concentrations of the infants were stable after the age of 2 months. Low zinc concentrations in serum were not associated with impaired growth. On the contrary, the infants with the highest rates of growth had the lowest zinc concentrations. The infant serum zinc concentrations were channeled, but they were also influenced by the zinc intake. Reference values for breast-fed infants are given.
Drug-resistant catheter-associated urinary tract Infection (CAUTI): an enlightened therapeutic approach (Conference Presentation) (2019)

Catheter–associated urinary tract infections (CAUTIs) cause millions of infections in the US every year, with direct medical costs exceeding billions of dollars and resulting in > 1 million ER visits and hospitalizations, resulting in thousands of deaths. CAUTI is thought to be a major reservoir both containing and creating highly drug-resistant infections, due to the chronicity of infection, biofilm formation, and the setting of institutionalization with chronic exposure to antibiotics, thus enabling resistance. To reduce antibiotic resistance developing in this setting, we are attempting to apply both antimicrobial photodynamic therapy (aPDT), antimicrobial blue light (aBL), and combinations of both with minimal use of antibiotics. To this end, we established a rat model of UTI. In this model, we catheterized female rats, infected them with a standard uropathogenic E.Coli (UPEC; UTI89), infused the bladder with methylene blue (MB) and potassium Iodide (KI), and illuminated the bladder once with a diffusing fiber connected to a 1W 660nm laser. Multilog killing was observed, but given the transient nature of ROS generation, regrowth of UPEC was seen 24 hours later. To this end, we are experimenting with the combination of illumination with antibiotics. When tetracyclines are illuminated by aBL, we have found > 6 log(10) steps of microbial killing in vitro, and significant drops in the antibiotic MIC effected by the combination of light and drug. Multiple treatments with aBL and aPDT both with and without limited intravesical application of antimicrobials may light the way to solving this problem.
Resistance to Anti-PD-1 Therapy is mediated via the Microbiota-Th17-Prostoglandin E2 Axis in the LSLKrasG12D Lung Cancer Model (2022)

Abstract We previously demonstrated that anti-PD-1 antibody mediated activation of type 17 T-cells undermined checkpoint inhibitor therapy in the LSLKrasG12D murine lung cancer model. In this study we confirm that the Th17 subset is the primary driver of resistance to anti-PD-1; demonstrate that the ontogeny of dysplasia-associated Th17 cells is driven by microbiota-conditioned macrophages; and identify IL-17-COX-2/Prostoglandin E2 (PGE2) axis as the mediator of CD8+ cytotoxic T-lymphocyte (CTL) de-sensitization to checkpoint inhibitor therapy. Specifically, anti-PD-1 treatment of CD4+ T-cell RORc-deficient LSLKrasG12D mice resulted in a 50% increase in CTL cytotoxicity and a 2.2-fold reduction in tumor burden confirming the critical role of Th17 cells in resistance to therapy. Lung-specific depletion of microbiota reduced Th17 cell prevalence and tumor burden by ~2 and ~1.5 fold, respectively, establishing a link between microbiota and the Th17-driven tumorigenesis. Importantly, interstitial macrophages from microbiota sufficient, but not from microbiota-deficient, mice polarized naïve CD4+ T-cells towards a Th17 phenotype, highlighting their role in bridging microbiota and lung Th17 immunity. Neutralization of IL-17 diminished COX-2/PGE2 levels, whereas inhibition of COX-2 rescued CTL activity and restored tumor suppression in anti-PD-1 antibody-treated mice, revealing the molecular basis of IL-17-driven anti-PD-1 resistance. The clinical implications of these findings are discussed. Supported by grant from DOD grant (to N.E., OGMB190737) and in part through the NIH/NIGMS P20-GM135004 (1P20GM135005-01)
The synthesis of 9–10 Dibromo stearic acid glycidyl methacrylate and its use in vinyl ester resins (2007)

Abstract In this study, 9–10 dibromo stearic acid glycidyl methacrylate (Di‐BrSAGMA) was synthesized from oleic acid and used as a replacement for styrene in vinyl ester (bisphenol A type VE (VE 828) and Novalac type VE (VE160)) to introduce fire retardance to these systems and to decrease the volatile organic compound (VOC) emissions caused by styrene. When the Di‐BrSAGMA was used as the comonomer, these resins exhibited too high viscosities, reduced modulus and glass transition temperature ( T g ) values compared to those of the styrene based systems. Thus, the Di‐BrSAGMA was used in the presence of styrene in these resins. The viscosities of the resins with various Di‐BrSAGMA contents were determined and the modulus and the T g values of the resulting polymers were measured via dynamic mechanical analysis (DMA) to determine the ideal formulations for each resin system. Similar analysis was performed, with similar oleic acid glycidyl methacrylate (OAGMA) contents, to determine the effect of the introduction of the bromine groups onto the network. Reactive diluent blends of the fatty acid based monomers with styrene, at styrene contents as low as 15–20 wt % at 35–45 wt % total comonomer content, in VE formulations were shown to have processable viscosities for liquid molding processes, and modulus and T g values that are comparable to those of the commercial VE‐styrene systems. The effect of the replacement of styrene by the Di‐BrSAGMA monomer on the thermal degradation behavior of the VE 828 and VE 160 networks was also explored by thermal gravimetric analysis (TGA). © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Crosstalk Analysis of 32-Core Dense Space Division Multiplexed System for Higher Order Modulation Formats Using an Integrated Cladding-Pumped Amplifier (2017)

We analyse the crosstalk performance of a fully integrated inline amplified 32-core link for 100G QPSK, 150G 8QAM, 200G 16-QAM, and 250G 32QAM in a recirculating loop. Transmission distances over 1000 km are confirmed for 8-QAM and QPSK channels.
Strain rate dependency of fractures of immature bone (2016)

Radiological features alone do not allow the discrimination between accidental paediatric long bone fractures or those sustained by child abuse. Therefore, there is a clinical need to elucidate the mechanisms behind each fracture to provide a forensic biomechanical tool for the vulnerable child. Four-point bending and torsional loading tests were conducted at more than one strain rate for the first time on immature bone, using a specimen-specific alignment system, to characterise structural behaviour at para-physiological strain rates. The bones behaved linearly to the point of fracture in all cases and transverse, oblique, and spiral fracture patterns were consistently reproduced. The results showed that there was a significant difference in bending stiffness between transverse and oblique fractures in four-point bending. For torsional loading, spiral fractures were produced in all cases with a significant difference in the energy and obliquity to fracture. Multiple or comminuted fractures were seen only in bones that failed at a higher stress or torque for both loading types. This demonstrates the differentiation of fracture patterns at different strain rates for the first time for immature bones, which may be used to match the case history given of a child and the fracture produced.
Armand-Frappier Outstanding Student Award — Role of ATP-dependent proteases in antibiotic resistance and virulence (2012)

ATP-dependent proteases are found in nearly all living organisms and are known to play important roles in protein quality control, including protein degradation and protein refolding. ATP-dependent proteases have been well characterized in Escherichia coli. However, in the opportunistic human pathogen Pseudomonas aeruginosa, the role of these proteases is only starting to be understood. This review will discuss the most recent research regarding the role of ATP-dependent proteases, particularly Lon and ClpP, in P. aeruginosa. These studies have revealed that despite the fact that they are not traditional regulators, these proteases are involved in regulating a multitude of processes, including antibiotic resistance and virulence, implicating a broad array of functions that these intracellular proteases have in Pseudomonas. These results are also relevant in the context of drug therapy, since ClpP and Lon are good candidates to become novel therapeutic targets to combat Pseudomonas infections.
Electroforming and Resistance Switching Characteristics of Silver-Doped MSQ With Inert Electrodes (2010)

This paper reports on the resistance switching effect in silver-doped methylsilsesquioxane (MSQ) thin films with Pt top and bottom electrodes. Silver is thermally diffused into MSQ films for different times and the results prove that silver ions (or other oxidizable metal ions) are required in the system, but not necessarily as one of the two electrodes. SEM investigations at horizontal cells (gap width 15-100 nm) show the formation of metallic agglomerations in the gap. The forming process is found to be electric-field driven and the filament resistance is determined to be 30 Ω/nm. Under the assumption of conical-shaped filament growth, the diameter of a filament is calculated to 13.5 nm, which is in agreement with the SEM observations. Memory device related tests on 100 × 100 nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> cross junctions show unipolar switching up to 2000 times and retention at 85°C for at least 6 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> s.
Monochromator configurations for wavelength division multiplexing (1989)

Abstract : The purpose of this work was to investigate the application of modified Czerny-Turner spectrographic optical systems to high channel density wavelength division multiplexing. A breadboard test system was constructed using off-the-shelf components and system performance was measured and evaluated. The results found using the breadboard system will be used to further develop measurement techniques for WDM systems and also to increase the performance of other high density systems. In parallel with the breadboard fabrication/ evaluation, a series of lenses to increase system performance have been designed. (rrh)
Engineering of Voltage-Controlled Magnetic Anisotropy Magnetic Tunnel Junctions at Cryogenic Temperatures (2023)

We identified through numerical simulations the optimal condition to have a deterministic switching regime assisted by voltage-controlled magnetic anisotropy (VCMA). To minimize the write energy required to reach this regime, we measure the VCMA coefficient <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\xi $ </tex-math></inline-formula> on perpendicular magnetic tunnel junctions (pMTJ) with high resistance area (RA) product and varying thicknesses of the FeCoB storage layer and the naturally oxidized tunnel barrier. The VCMA coefficient is higher as the effective anisotropy decreases, which is the case for larger Mg and FeCoB thicknesses. The temperature dependence of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\xi $ </tex-math></inline-formula> was shown to increase from room temperature to 5 K, showing values up to 35 fJ/Vm at 10 K.
Results of multi-center clinical trials comparing four 18F PET amyloid-imaging agents: Preclinical to clinical correlations (2008)

133 Objectives: Develop 18F PET ligands for amyloid plaques in Alzheimer’s disease (AD). Methods: We have screened more than 200 fluorinated compounds to find an optimal 18F ligand for PET imaging of amyloid plaques. First results of an exploratory clinical trial with the tracer 18F-AV-1 (now known as BA94-9172) were previously presented by C. Rowe. Four new ligands, 18F-AV-19, 18F-AV-45, 18F-AV-138, and 18F-AV-144, were also selected for testing in human trials. We imaged a total of 94 subjects (38 mild to moderate AD and 56 healthy controls, HCs) across 12 centers. With each compound dosimetry, kinetic brain imaging and metabolism were obtained. Results: All four new compounds were well tolerated, showed acceptable dosimetry and were quickly metabolized. 18F-AV-45, 18F-AV-138, and 18F-AV-144 showed excellent amyloid-imaging properties, with clear separation between AD and HC. Distribution volume ratios and standardized uptake volume ratios were in the range of 1.5 – 2.5 in AD vs. 0.8 – 1.5 in HC. Kinetics of binding and brain washout varied across the compounds, and partially correlated with preclinical evaluations. Conclusions: Several 18F-AV-compounds successfully imaged amyloid plaques. Research Support: Avid Radiopharmaceuticals, Inc., NIH grants (SBIR to DMS; AG-022559 to HFK) *Additional contributors to this work include: Bradley Boeve, Robert Dannals, P. Murali Doraiswamy, Sudha Garg, Bradley Kemp, Mike Kilbourn, David Knopman, Rajesh Manchanda, Ronald Petersen, Michael Pontecorvo, Yaakov Stern, Zhude Tu, Ronald L. Van Heertum
Energy, Materials and Person-hour Savings through a New Decentralized Power Supply for HVAC in Large Buildings. A Case Study: A Shopping Center in Spain (2016)

Currently, heating and cooling systems used for achieving thermal comfort in commercial buildings represent a significant energy consumption. Traditionally, power supply installations of these Heating, Ventilation and Air Conditioning Systems (HVAC) present low efficiency. In these installations the power is supplied from the substation to the HVAC system by low voltage cables. Due to the long distances of the power distribution, the system suffers considerable energy losses. This paper proposes a decentralized power supply installation based on a power distribution at medium voltage, which achieves not only significant energy savings, but also important savings in material and person-hours. These improvements entail substantial savings in cost and CO2 emissions.
A deblending strategy using alternating constant delay simultaneous source data (2014)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2014A deblending strategy using alternating constant delay simultaneous source dataAuthors: Gordon Poole*Damien RussierKent StevensThomas MenschRisto SiliqiGordon Poole*CGG, Damien RussierCGG, Kent StevensCGG, Thomas MenschCGG, and Risto SiliqiCGGhttps://doi.org/10.1190/segam2014-0765.1 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Abstract This paper introduces a deblending strategy for simultaneous source data using alternating constant delays. The technique uses uncontaminated data to generate a cross-talk noise estimate for deblending. The effectiveness of the strategy is demonstrated on a broadband dual source marine dataset acquired offshore Indonesia. Keywords: algorithm, interpolation, sources, separation, signal processingPermalink: https://doi.org/10.1190/segam2014-0765.1FiguresReferencesRelatedDetailsCited byAcquisition and separation of coherent simultaneous sources: Theory and an application to data acquired in the Sultanate of OmanZijian Tang and Xander Campman13 December 2018 | GEOPHYSICS, Vol. 84, No. 1 SEG Technical Program Expanded Abstracts 2014ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2014 Pages: 5183 publication data© 2014 Published in electronic format with permission by the Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 05 Aug 2014 CITATION INFORMATION Gordon Poole*, Damien Russier, Kent Stevens, Thomas Mensch, and Risto Siliqi, (2014), "A deblending strategy using alternating constant delay simultaneous source data," SEG Technical Program Expanded Abstracts : 4335-4339. https://doi.org/10.1190/segam2014-0765.1 Plain-Language Summary Keywordsalgorithminterpolationsourcesseparationsignal processingPDF DownloadLoading ...
O2‐02‐01: HIGH RESOLUTION STRUCTURE OF AMYLOID‐β(1‐42) FIBRILS (2018)

Several lines of evidence suggest a central role of the amyloid-β protein (Aβ) in the pathogenesis of Alzheimer's disease (AD). Structural details of Aβ assemblies will help to understand their roles during pathology and will elucidate consequences of mutations within the Aβ amino acid sequence for its aggregation. We used cryo-electron microscopy, solid state NMR spectroscopy and x-ray diffraction to obtain high resolution structural information of fibrils grown from recombinantly expressed Aβ(1-42). We determined the structure of an Aβ(1-42) fibril composed of two intertwined protofilaments determined by cryoelectron microscopy (cryo-EM) to 4.0-Ångstrom resolution, complemented by solid-state nuclear magnetic resonance experiments [1]. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall “LS”-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed “groove” and “ridge,” leading to different binding pathways on both fibril ends, which has implications for fibril growth. The β strands are staggered with relation to one another in a zipper-like manner. At both fibril ends, the binding site for the addition of subunit i contains contributions of subunits i-1, i-2, i-3, i-4, and i-5, or i+1, i+2, i+3, i+4, and i+5, respectively. Therefore, five Aβ(1-42) subunits are required to provide the full interface for monomer addition. For a fragment of six subunits, the capping subunits would have the same full contact interface as those in an extended fibril. We define this structural element of six subunits as the minimal fibril unit. This minimal fibril unit may also be the minimal seed size for nucleation as suggested by results from Aβ aggregation studies monitored by small angle neutron scattering and analytical ultracentrifugation. High resolution structural details help to understand the role of amino acid side chains within Aβ for fibril formation and growth. [1] Gremer et al., Science 358, 116–119 (2017).