gebhart/patrepeval huggingface dataset:
Virus Inhibition Activity of Effector Memory CD8 + T Cells Determines Simian Immunodeficiency Virus Load in Vaccinated Monkeys after Vaccine Breakthrough Infection (2012)

The goal of an effective AIDS vaccine is to generate immunity that will prevent human immunodeficiency virus 1 (HIV-1) acquisition. Despite limited progress toward this goal, renewed optimism has followed the recent success of the RV144 vaccine trial in Thailand. However, the lack of complete protection in this trial suggests that breakthroughs, where infection occurs despite adequate vaccination, will be a reality for many vaccine candidates. We previously reported that neutralizing antibodies elicited by DNA prime-recombinant adenovirus serotype 5 (rAd5) boost vaccination with simian immunodeficiency virus strain mac239 (SIVmac239) Gag-Pol and Env provided protection against pathogenic SIVsmE660 acquisition after repeated mucosal challenge. Here, we report that SIV-specific CD8(+) T cells elicited by that vaccine lowered both peak and set-point viral loads in macaques that became infected despite vaccination. These SIV-specific CD8(+) T cells showed strong virus-inhibitory activity (VIA) and displayed an effector memory (EM) phenotype. VIA correlated with high levels of CD107a mobilization and perforin expression in SIV-specific CD8(+) T cells. Remarkably, both the frequency and the number of Gag CM9-specific public clonotypes were strongly correlated with VIA mediated by EM CD8(+) T cells. The ability to elicit such virus-specific EM CD8(+) T cells might contribute substantially to an efficacious HIV/AIDS vaccine, even after breakthrough infection.
Supplementary Table 6 from Global Evaluation of Eph Receptors and Ephrins in Lung Adenocarcinomas Identifies EphA4 as an Inhibitor of Cell Migration and Invasion (2023)

&lt;p&gt;PDF file, 99K, Detailed mutations identified in the Eph receptors family in NSCLC.&lt;/p&gt;
Search for the doubly charmed baryon $\Omega_{cc}^+$ (2021)

Abstract: A search for the doubly charmed baryon Ωcc+ with the decay mode Ωcc+ → Ξc+K−π+ is performed using proton-proton collision data at a centre-of-mass energy of 13 TeV collected by the LHCb experiment from 2016 to 2018, corresponding to an integrated luminosity of 5.4 fb−1. No significant signal is observed within the invariant mass range of 3.6 to 4.0GeV/c2. Upper limits are set on the ratio R of the production cross-section times the total branching fraction of the Ωcc+ → Ξc+K−π+ decay with respect to the Ξcc++→Λc+K−π+π+ decay. Upper limits at 95% credibility level for R in the range 0.005 to 0.11 are obtained for different hypotheses on the Ωcc+ mass and lifetime in the rapidity range from 2.0 to 4.5 and transverse momentum range from 4 to 15 GeV/c.
Modeling Coating Flow and Surfactant Dynamics inside the Alveolar Compartment (2018)

We derive a new model for the coating flow inside the alveolar compartment, taking into account pulmonary surfactant production and recycling by Type 2 cells as well as its degradation. As the thickness of alveolar coating is much smaller than the average radius of the alveoli, we employ the classical lubrication approximation to describe the thin liquid film dynamics in the presence of pulmonary surfactant, which is a surface tension reducing agent and thus prevents the lungs from collapse. In the lubrication limit, we derive a degenerate system of two coupled parabolic partial differential equations that describe the time evolution of the thickness of the coating film inside the alveoli together with that of the surfactant concentration at the interface. We present numerical simulations using parameter values consistent with experimental measurements.
Adaptive Future Internet Applications (2017)

Adaptive capabilities are essential to guarantee the proper execution of Web services and service-oriented applications once dynamic changes are not exceptions but the rule. The importance of adaptive capabilities significantly increases in the context of Future Internet (FI) applications will have to autonomously adapt to changes on service provisioning, availability of things and content, computing resources, and network connectivity. Current solutions for adaptive Web services and adaptive service-based applications will be challenged in such a setting because they fall short to support essential characteristics of FI applications. This chapter analyzes and justifies the need for the transition from adaptive Web services and service-based applications to adaptive FI applications. Based on two real-world use cases from multimedia and logistics, the authors examine where current solutions fall short to properly address the adaptive needs of FI applications. They propose future research challenges that should be considered in adaptive FI applications.
High angular resolution Sunyaev-Zel’dovich observations of MACS J1423.8+2404 with NIKA: Multiwavelength analysis (2016)

The prototype of the NIKA2 camera, NIKA, is a dual-band instrument operating at the IRAM 30-m telescope, which can observe the sky simultaneously at 150 and 260 GHz. One of the main goals of NIKA (and NIKA2) is to measure the pressure distribution in galaxy clusters at high angular resolution using the thermal Sunyaev-Zel’dovich (tSZ) effect. Such observations have already proved to be an excellent probe of cluster pressure distributions even at intermediate and high redshifts. However, an important fraction of clusters host sub-millimeter and/or radio point sources, which can significantly affect the reconstructed signal. Here we report on <20 arcsec angular resolution observations at 150 and 260 GHz of the cluster MACS J1423.8+2404, which hosts both radio and sub-millimeter point sources. We examine the morphological distribution of the tSZ signal and compare it to other datasets. The NIKA data are combined with Herschel satellite data to study the spectral energy distribution (SED) of the sub-millimeter point source contaminants. We then perform a joint reconstruction of the intracluster medium (ICM) electronic pressure and density by combining NIKA, Planck, XMM-Newton, and Chandra data, focusing on the impact of the radio and sub-millimeter sources on the reconstructed pressureprofile. We find that large-scale pressure distribution is unaffected by the point sources because of the resolved nature of the NIKA observations. The reconstructed pressure in the inner region is slightly higher when the contribution of point sources are removed. We show that it is not possible to set strong constraints on the central pressure distribution without accurately removing these contaminants. The comparison with X-ray only data shows good agreement for the pressure, temperature, and entropy profiles, which all indicate that MACS J1423.8+2404 is a dynamically relaxed cool core system. The present observations illustrate the possibility of measuring these quantities with a relatively small integration time, even at high redshift and without X-ray spectroscopy. This work is part of a pilot study aiming at optimizing tSZ observations with the future NIKA2 camera.
assay information of the mouse qualitycontrol samples for HeliScopeCAGE (2017)

a tab delimited flat file (SDRF file) describing the experimental details for mouse quality control samples for the standard protocol of the HeliScopeCAGE protocol
Multiscale Structure of Starches Grafted with Hydrophobic Groups: A New Analytical Strategy (2020)

Starch, an abundant and low-cost plant-based glucopolymer, has great potential to replace carbon-based polymers in various materials. In order to optimize its functional properties for bioplastics applications chemical groups need to be introduced on the free hydroxyl groups in a controlled manner, so an understanding of the resulting structure-properties relationships is therefore essential. The purpose of this work was to study the multiscale structure of highly-acetylated (degree of substitution, 0.4 < DS ≤ 3) and etherified starches by using an original combination of experimental strategies and methodologies. The molecular structure and substituents repartition were investigated by developing new sample preparation strategies for specific analysis including Asymmetrical Flow Field Flow Fractionation associated with Multiangle Laser Light Scattering, Nuclear Magnetic Resonance (NMR), Raman and Time of Flight Secondary Ion Mass spectroscopies. Molar mass decrease and specific ways of chain breakage due to modification were pointed out and are correlated to the amylose content. The amorphous structuration was revealed by solid-state NMR. This original broad analytical approach allowed for the first time a large characterization of highly-acetylated starches insoluble in aqueous solvents. This strategy, then applied to characterize etherified starches, opens the way to correlate the structure to the properties of such insoluble starch-based materials.
Thin-domain modeling of mass transport in microchannels, with application to diffusive mixing (2004)

Because of the significance of diffusion on the microfluidic length scale, diffusion-based mixers are a valuable and popular component in lab-on-a-chip designs, with many variations emerging. The design of such mixers, however, is limited by existing simulation tools, which are often slow and poorly suited to the special geometry of microchannels. In this article, we derive the necessary conditions for a reduced-dimension model of flow and diffusion in a thin (i.e., height much less than width) channel. We subsequently show that the resulting mass transport equation can be solved in a streamfunction-pressure coordinate system, providing a simpler, more accurate, and more stable solution than is possible using standard methods in the x–y coordinate system. Simulations by this method were fast, requiring less than 30 min even for complex domains; the bulk of the time was spent on noncomputational tasks such as mesh generation. The approach was applied to three problems: a simple mixer based on the T sensor of Yager and co-workers, and then two variations on the base case in which obstructions were introduced to increase the available diffusion time. Although the obstructions changed the flow pattern significantly, there was little effect on the outlet concentration profile. It was observed from the model equations that if the flow rate is unchanged, the improvement in mixing can be expressed in terms of an upper bound based on the increase in pressure drop. In the case studied, the pressure drop change was small, so the mixing was not improved very much.
Is there evidence to use kinematic/kinetic measures clinically in low back pain patients? A systematic review (2018)

The literature to date offers limited and inconsistent evidence of kinematic/kinetic measures in low back pain patients that could be used clinically.
Monolithic integration of Sb-based photopumped lasers on Si (2005)

This study demonstrates monolithic integration and filamentary photopumped lasing from an InGaSb quantum well based laser structure. The device is grown on Si(100) using an AlSb quantum dot nucleation layer.
Development and Characterization of In Vitro Human Oral Mucosal Equivalents Derived from Immortalized Oral Keratinocytes (2016)

Tissue-engineered oral mucosal equivalents (OME) are being increasingly used to measure toxicity, drug delivery, and to model oral diseases. Current OME mainly comprise normal oral keratinocytes (NOK) cultured on top of a normal oral fibroblasts-containing matrix. However, the commercial supply of NOK is limited, restricting widespread use of these mucosal models. In addition, NOK suffer from poor longevity and donor-to-donor variability. Therefore, we constructed, characterized, and tested the functionality of OME based on commercial TERT2-immortalized oral keratinocytes (FNB6) to produce a more readily available alternative to NOK-based OME. FNB6 OME cultured at an air-to-liquid interface for 14 days exhibited expression of differentiation markers cytokeratin 13 in the suprabasal layers and cytokeratin 14 in basal layer of the epithelium. Proliferating cells were restricted to the basal epithelium, and there was immuno-positive expression of E-cadherin confirming the presence of established cell-to-cell contacts. The histology and expression of these structural markers paralleled those observed in the normal oral mucosa and NOK-based models. On stimulation with TNFα and IL-1, FNB6 OME displayed a similar global gene expression profile to NOK-based OME, with increased expression of many common pro-inflammatory molecules such as chemokines (CXCL8), cytokines (IL-6), and adhesion molecules (ICAM-1) when analyzed by gene array and quantitative PCR. Similarly, pathway analysis showed that both FNB6 and NOK models initiated similar intracellular signaling on stimulation. Gene expression in FNB6 OME was more consistent than NOK-based OME that suffered from donor variation in response to stimuli. Mucosal equivalents based on immortalized FNB6 cells are accessible, reproducible and will provide an alternative animal experimental system for studying mucosal drug delivery systems, host-pathogen interactions, and drug-induced toxicity.
Dependence of thin-oxide films quality on surface microroughness (1992)

The effects of silicon surface microroughness on electrical properties of thin-oxide films, such as breakdown electric field intensity (E/sub BD/) and time-dependent dielectric breakdown (Q/sub BD/), have been studied, where the microroughnesses of silicon and silicon dioxide surfaces are evaluated by the scanning tunneling microscope (STM) and the atomic force microscope (AFM), respectively. An increase of surface microroughness has been confirmed to severely degrade the E/sub BD/ and Q/sub BD/ characteristics of thin-oxide films with thicknesses of 8-10 nm and to simultaneously decrease channel electron mobility. An increase of surface microroughness has been demonstrated to originate mainly from wet chemical cleaning processing based on the RCA cleaning concept, particularly the ammonium-hydrogen-peroxide cleaning step. In order to keep the surface microroughness at an initial level, the content ratio of NH/sub 4/OH/H/sub 2/O/sub 2//H/sub 2/O solution has been set at 0.05:1:5 and the room-temperature DI water rinsing has been introduced right after the NH/sub 4/OH/H/sub 2/O/sub 2//H/sub 2/O cleaning step in conventional RCA cleaning procedure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High Efficiency N-Type Emitter-Wrap-Through Silicon Solar Cells (2011)

In the ALBA-II project, Q-Cells SE, Bitterfeld-Wolfen, Germany, and the Institute for Solar Energy Research Hamelin, Emmerthal, Germany, are developing high-efficiency emitter-wrap-through (EWT) solar cells on n-type silicon wafers. N-type silicon grown by the Czochralski (Cz) method forms the basis of this high-efficiency solar cell development as it offers high bulk carrier lifetimes. The EWT device structure allows us to employ a simplified process sequence compared with interdigitated back-contact back-junction solar cells. High open-circuit voltages of our solar cells are achieved by different passivation layers for base and emitter surfaces and picosecond laser ablated contact openings. An optimization of the resistances along the current paths in base and emitter leads to an improvement in fill factor (FF) over former EWT solar cells. Together with the inherently high current densities of EWT solar cells, we achieve on our small-area (4-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , designated area without busbars) cells a short-circuit current density J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SC</sub> of 40.4 mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , an open-circuit voltage V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OC</sub> of 661 mV, FFs well above 80%, and, thus, cell efficiencies of up to 21.6%.
Transmission power variance constrained power allocation for iterative frequency domain multiuser SIMO detector (2014)

Transmission power variance constrained power allocation in single carrier multiuser (MU) single-input multiple-output (SIMO) systems with iterative frequency domain (FD) soft cancelation (SC) minimum mean squared error (MMSE) equalization is considered in this paper. It is known in the literature that peak to average power ratio (PAPR) at the transmitter can be decreased by reducing the variance of the transmit power. In this paper, we derive a power variance constraint to statistically control the PAPR. This constraint is plugged into a convergence constrained power allocation (CCPA) problem and successive convex approximation (SCA) approach via series of geometric programs (GP) is developed. Numerical results are presented in the form of complementary cumulative distribution functions (CCDFs) to demonstrate the effectiveness of the proposed method.
Grasping Field: Learning Implicit Representations for Human Grasps (2020)

Robotic grasping of house-hold objects has made remarkable progress in recent years. Yet, human grasps are still difficult to synthesize realistically. There are several key reasons: (1) the human hand has many degrees of freedom (more than robotic manipulators); (2) the synthesized hand should conform to the surface of the object; and (3) it should interact with the object in a semantically and physically plausible manner. To make progress in this direction, we draw inspiration from the recent progress on learning-based implicit representations for 3D object reconstruction. Specifically, we propose an expressive representation for human grasp modelling that is efficient and easy to integrate with deep neural networks. Our insight is that every point in a three-dimensional space can be characterized by the signed distances to the surface of the hand and the object, respectively. Consequently, the hand, the object, and the contact area can be represented by implicit surfaces in a common space, in which the proximity between the hand and the object can be modelled explicitly. We name this 3D to 2D mapping as Grasping Field, parameterize it with a deep neural network, and learn it from data. We demonstrate that the proposed grasping field is an effective and expressive representation for human grasp generation. Specifically, our generative model is able to synthesize high-quality human grasps, given only on a 3D object point cloud. The extensive experiments demonstrate that our generative model compares favorably with a strong baseline and approaches the level of natural human grasps. Our method improves the physical plausibility of the hand-object contact reconstruction and achieves comparable performance for 3D hand reconstruction compared to state-of-the-art methods.
Low-load expander deactivation studies for a light-duty single-shaft piston-compounded engine (2019)

A single-shaft, piston-compounded engine has shown great potential for improvements in efficiency over current state-of-the-art light-duty engines through the use of an efficient second expansion process to more fully recover energy still present in the exhaust gasses. This process inherently works well at mid to high loads where the displacement ratio of the piston expander can be maximized and fully utilized, but the positive-displacement nature of piston compounding creates a liability in efficiency and exhaust gas temperature at low loads. This study examined the trade-offs in efficiency, exhaust temperature, and engine design for various methods of mitigating the low-load deficiencies of the piston-compounded design. An optimum solution was identified, and these results were then used to guide the design of an experimental piston-compounded engine.
Quenching Method and Performance of High Voltage Layered Lithium Rich Nickel Manganese Oxides (2020)

Due to their promise of high specific capacity layered lithium rich nickel manganese oxide materials have a large body of literature dedicated to their structure, and electrochemical behaviors [1–5] . Yet these materials have often been marred by significant capacity losses, rate capability limitations, and structural instability over the course of cycling. Several techniques involving surface and structural modifications have been used to mitigate these capacity losses [6–8] . In this work we used a hybrid acetate/nitrate precursors and sol-gel/combustion synthesis to conduct an unprecedented combined survey of the composition of Li(Ni x Li (1/3-2x/3) Mn (2/3-x/3) )O 2 , and synthetic quench rates to elucidate the effects of these variables on electrochemical cycling behavior, bulk morphology, and surface morphology of the layered lithium rich manganese oxides. We find that the electrochemical behavior of these materials is dependent on both the nickel content as well as the quenching method, with a lower limit on the nickel content beyond which the effects of quenching are minimal. Despite XRD revealing loss of super lattice peaks indicating a loss of transition metal ordering, often associated with capacity loss, galvanostatic cycling of samples saw improved capacities over the course of cycling. SEM found bulk morphology of cathodes differs across nickel contents, yet it did not experience large changes over the course of cycling. The use of TEM found that the surfaces of Li(Ni x Li (1/3-2x/3) Mn (2/3-x/3) )O 2 powders is highly sensitive to quenching method, and comparison of surfaces over the course of cycling provided incites into the effects of quenching and nickel content on electrochemical cycling behaviors of the cathode materials. This investigation reveals that careful considerations in synthesis are required for the realization of high-performance layered lithium rich nickel manganese oxides. [1] Y. J. Park, Y.-S. Hong, X. Wu, K. S. Ryu, S. H. Chang, J. Power Sources 2004 , 129 , 288. [2] Z. Lu, L. Y. Beaulieu, R. A. Donaberger, C. L. Thomas, J. R. Dahn, J. Electrochem. Soc. 2002 , 149 , A778. [3] Z. Lu, J. R. Dahn, J. Electrochem. Soc. 2002 , 149 , A1454. [4] M. Jiang, B. Key, Y. S. Meng, C. P. Grey, Chem. Mater. 2009 , 21 , 2733. [5] J. Bréger, N. Dupré, P. J. Chupas, P. L. Lee, T. Proffen, J. B. Parise, C. P. Grey, J. Am. Chem. Soc. 2005 , 127 , 7529. [6] D. Eum, B. Kim, S. J. Kim, H. Park, J. Wu, S. P. Cho, G. Yoon, M. H. Lee, S. K. Jung, W. Yang, W. M. Seong, K. Ku, O. Tamwattana, S. K. Park, I. Hwang, K. Kang, Nat. Mater. 2020 , 19 , 419. [7] H. Z. Zhang, Q. Q. Qiao, G. R. Li, S. H. Ye, X. P. Gao, J. Mater. Chem. 2012 , 22 , 13104. [8] Y. Wu, A. Manthiram, Solid State Ionics 2009 , 180 , 50.
Characterization of severe acute respiratory syndrome coronavirus membrane protein (2006)

The coronavirus membrane protein (M) is the key player in the assembly of virions at intracellular membranes between endoplasmic-reticulum and Golgi-complex. Using a newly established human monoclonal anti-M antibody we detected glycosylated and nonglycosylated membrane-associated M in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infected cells and in purified virions. Further analyses revealed that M contained a single N-glycosylation site at asparagine 4. Recombinant M was transported to the plasma membrane and gained complex-type N-glycosylation. In SARS-CoV infected cells and in purified virions, however, N-glycosylation of M remained endoglycosidase H-sensitive suggesting that trimming of the N-linked sugar side chain is inhibited.