gebhart/patrepeval huggingface dataset:
Effects of Prostratin on T-Cell Activation and Human Immunodeficiency Virus Latency (2002)

Human immunodeficiency virus (HIV) replication is linked to cellular gene transcription and requires target cell activation. The latent reservoir of HIV-1 in quiescent T cells is thought to be a major obstacle to clearance of infection by highly active antiretroviral therapy (HAART). Thus, identification of agents that can induce expression of latent virus may, in the presence of HAART, allow elimination of the infected cells by the immune response. We previously used the SCID-hu (Thy/Liv) mouse model to establish that activation-inducible HIV can be generated at high frequency during thymopoiesis. Latently infected mature thymocytes can be exported into the periphery, providing an efficient primary cell model to determine cellular activation signals that induce renewed expression of latent virus. Here we characterized the effects of prostratin, a non-tumor-promoting phorbol ester, on primary human peripheral blood lymphocytes (PBLs) and assessed its ability to reactivate latent HIV infection from thymocytes and PBLs in the SCID-hu (Thy/Liv) model. Prostratin stimulation alone did not induce proliferation of quiescent PBLs; however, it could provide a secondary signal in the context of T-cell receptor stimulation or a primary activation signal in the presence of CD28 stimulation to induce T-cell proliferation. While prostratin alone was not sufficient to allow de novo HIV infection, it efficiently reactivated HIV expression from latently infected cells generated in the SCID-hu mouse. Our data indicate that prostratin alone is able to specifically reactivate latent virus in the absence of cellular proliferation, making it an attractive candidate for further study as an adjunctive therapy for the elimination of the latent HIV reservoir.
Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift (1994)

Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift Get access Andreas Wagner, Andreas Wagner Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Neil Blackstone, Neil Blackstone Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Paulyn Cartwright, Paulyn Cartwright Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Matthew Dick, Matthew Dick Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Bernhard Misof, Bernhard Misof Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Peter Snow, Peter Snow Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Gunter P. Wagner, Gunter P. Wagner Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Janet Bartels, Janet Bartels Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Mike Murtha, Mike Murtha Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar John Pendleton John Pendleton Department of Zoology, Center for Computational Ecology, Yale University,New Haven, Connecticut 06511, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Systematic Biology, Volume 43, Issue 2, June 1994, Pages 250–261, https://doi.org/10.1093/sysbio/43.2.250 Published: 01 June 1994 Article history Received: 18 December 1992 Accepted: 13 October 1993 Published: 01 June 1994
Effect of ration and seawater transfer on food consumption and growth of Atlantic salmon (Salmo salar) smolts (1996)

Chez les smolts de saumon de l'Atlantique auxquels on a administre des rations alimentaires correspondant a 0,5, 1,0 et 3,0 % de leur poids corporel par jour, la performance de la croissance en eau douce n'etait pas un parametre important de leur croissance ulterieure en eau salee (P > 0,05). On a utilise des radiographies pour mesurer le taux de consommation alimentaire de chaque poisson. Le taux de consommation des poissons recevant des rations faibles et intermediaires etait similaire en eau douce et en eau salee (P > 0,05). Toutefois, celui des poissons recevant une ration elevee etait deux fois plus grand en eau salee qu'en eau douce (P 0,05). Dans le cas des groupes recevant une ration intermediaire et elevee, les pentes etaient plus abruptes en eau salee par comparaison avec l'eau douce (P < 0,001).
GDF 15 as an anti-apoptotic, diagnostic and prognostic marker in oral squamous cell carcinoma (2012)

Growth-differentiation factor 15 (GDF 15) is involved in tumor pathogenesis and its expression is increased in many types of cancers. Functional effects of GDF 15 on oncogenesis of oral squamous cell carcinoma (OSCC) remain unclear. Therefore, the aim of this study was to examine the apoptotic characteristics of GDF 15 in OSCC cell lines in vitro and to analyze serum GDF 15 concentrations as a diagnostic and prognostic tumor marker for OSCC in vivo. Caspase activity was assessed in OSCC cell lines with the Caspase-Glo 3/7 system. Serum GDF 15 concentrations from 64 patients with histopathological proven OSCC and from 30 healthy volunteers were measured using an enzyme-linked immunosorbent assay. In 21 patients, serum GDF 15 was also analyzed postoperatively. In vitro, treatment of OSCC cell lines with GDF 15 reduced Caspase 3/7 activity significantly (p<0.05). In vivo, serum GDF 15 concentrations of the OSCC patients in all stages of OSCC were significantly higher than those of the healthy subjects (p<0.0001). After surgery, GDF 15 concentrations declined significantly from 1545±774pg/ml preoperative to 953±438pg/ml postoperative (p=0.003). The median survival time of OSCC patients with GDF 15 levels below 875pg/ml was significantly higher than of OSCC patients with GDF 15 levels above or equal 875pg/ml (p=0.031). Determination of receiver operating characteristic curves (ROC) showed a respective area under the ROC curve (AUC) of 0.943. The anti-apoptotic effect of GDF 15 in OSCC cell lines was shown in vitro. In vivo, significant elevated serum GDF 15 levels with prognostic value in OSCC-patients were seen for the first time. The results indicate that GDF15 may be used as a potential marker for diagnosis and prognosis of this entity.
Molten salt chemistry in nitrate salt storage systems: Linking experiments and modeling (2018)

Sensible heat storage in molten nitrate salts is a key technology when it comes to thermal energy storage in combination with concentrating solar power (CSP) plants. Currently, a mixture of sodium and potassium nitrate called Solar Salt is used at temperatures between 280 and 560 °C. Our research approaches comprise an improvement of Solar Salt stability at temperatures above 560 °C, which comes along with a broadening of the operating temperature range. In this way, a higher storage capacity and efficiency, as well as economic advances can be achieved. Numerous publications about the chemistry of molten nitrate salt mixtures reveal the formation of chemical species such as nitrite ions, nitrous gases and oxide ions and carbonate ions. Among these, the reversible reaction of nitrate to nitrite with release of oxygen is the predominant reaction at temperatures below 560 °C. So far, there is a lack of literature that pays particular attention on the contributions of reaction kinetics and mass transport effects on the reaction velocity of the nitrate/nitrite-reaction. However, understanding of these physico-chemical phenomena is essential, because further decomposition reactions build on the nitrate/nitrite-reaction. In this study, experiments at different scales (50 mg to 100 g) are compared with regard to the reduction reaction velocity at 500 °C. A data treatment procedure for thermogravimetric analysis experiments successfully eliminates effects of salt evaporation on the measured mass changes. The chemical equilibrium of the salt samples turned out to be reasonable, when compared to literature values. It was found, that the surface-to-volume ratio of the salt melt samples significantly affects the evaporation rates and the reaction velocity. The time period that is needed until chemical equilibrium is reached at 500 °C clearly increases when the surface-to-volume ratio decreases. The thermogravimetric analysis apparatus enables experiments, which measure reaction kinetics without mass transport limitations. It is demonstrated that a simulation model adapted from literature displays a reaction velocity that incorporates both reaction kinetics and mass transport without differentiation of the two phenomena.
Marburg I polymorphism of factor VII–activating protease is associated with idiopathic venous thromboembolism (2004)

The factor VII-activating protease (FSAP) variant Marburg I is known to attenuate the profibrinolytic system in vitro and was recently shown to be a significant predictor for the evolution and progression of carotid stenosis. The objective of this case-control study was to assess FSAP Marburg I's role in the occurrence of venous thromboembolism (VTE). The frequency of FSAP Marburg I was significantly increased in patients with a history of VTE (17 of 213 patients, 8.0%, P = .014) or idiopathic VTE (12 of 103 patients, 11.7%, P = .002) compared to healthy controls (5 of 213 controls, 2.3%). Logistic regression analysis confirmed FSAP Marburg I to be an independent risk factor for VTE (odds ratio, 3.5; 95% confidence interval [CI], 1.2-10.0) and idiopathic VTE (odds ratio, 6.2; 95% CI, 2.0-18.9).
Scroll, tilt or move it (2009)

Large and public displays mostly provide little interactivity due to technical constraints, making it difficult for people to capture interesting information or to influence the screen's content. Through the combination of largescale visual output and the mobile phone as an input device, bidirectional interaction with large public displays can be enabled. In this paper, we propose and compare three different interaction techniques (Scroll, Tilt and Move) for continuous control of a pointer located on a remote display using a mobile phone. Since each of these techniques seemed to have arguments for and against them, we conducted a comparative evaluation and discovered their specific strengths and weaknesses. We report the implementation of the techniques, their design and results of our user study. The experiment revealed that while Move and Tilt can be faster, they also introduce higher error rates for selection tasks.
Metallic microstructures fabricated using photosensitive polyimide electroplating molds (1993)

A polyiimide-based process for the fabrication of thick (1-150 mu m), sharp-sidewall, high-aspect-ratio electroplated microstructures is presented. This process is a low-cost alternative to the LIGA process for microstructure fabrication. Although this process cannot match the performance of the LIGA process, it uses ordinary optical masks and ultraviolet light exposure, resulting in simple and inexpensive equipment requirements. Using this technology, structures made of a variety of electroplated metals can be fabricated. Vertically integrated structures that exploit the multilayer ability of the polyimides used can also be realized. Surface micromachining with this process can be used to fabricate movable electroplated microactuators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cutting Edge: The Membrane Type Matrix Metalloproteinase MMP14 Mediates Constitutive Shedding of MHC Class I Chain-Related Molecule A Independent of A Disintegrin and Metalloproteinases (2010)

Engagement of tumor cell surface MHC class I chain-related molecule A (MICA) to NKG2D stimulates NK and T cell antitumor immunity. Shedding of MICA by tumor cells facilitates tumor immune evasion, which may in part contribute to tumor progression. Thus, elucidating the mechanisms by which tumors shed MIC is of great importance for therapy to reinforce NK and T cell antitumor immunity. In this study, we report that the membrane type matrix metalloproteinase (MMP)14 mediates MICA shedding. Suppression of MMP14 expression blocks MICA shedding. Concomitantly, overexpression of MMP14 enhances MICA shedding. The regulation of MICA shedding by MMP14 is independent of the activity of a disintegrin and metalloproteinases, which have been reported to mediate MICA shedding. Finally, MMP14 expression in MICA-positive tumor cells regulates the sensitivity of tumor cells to NK cell killing. These findings suggest that MMP14 may be a new target for tumor immune therapy.
PD-1 and CTLA-4 Inhibitory Cosignaling Pathways in HIV Infection and the Potential for Therapeutic Intervention (2009)

The balance between proinflammatory mechanisms and the dampening of excessive immune activation is critical for successful clearance of a pathogen without harm to the host. In particular, molecules of the B7:CD28 family play a critical role in regulating T cell activation and peripheral tolerance. Chronic pathogens like HIV, which is characterized by ongoing viral replication despite detectable virus-specific T cell responses, and cancer cells have exploited these pathways to attenuate Ag-specific T cell immunity. This review summarizes evidence that molecules of the B7:CD28 family, PD-1, CTLA-4, and their ligands, play an active and reversible role in virus-specific T cell exhaustion associated with HIV infection in humans and in the SIV model in macaques. We discuss the potential for immunotherapeutic interventions based on manipulation of these inhibitory networks, the promising data obtained with blockade of the PD-1 pathway in animal models, and the challenges to such therapies.
Phonon Tracing for Auralization and Visualization of Sound (2006)

We present a new particle tracing approach for the simulation of mid- and high-frequency sound. Inspired by the photorealism obtained by methods like photon mapping, we develop a similar method for the physical simulation of sound within rooms. For given source and listener positions, our method computes a finite-response filter accounting for the different reflections at various surfaces with frequency-dependent absorption coefficients. Convoluting this filter with an anechoic input signal reproduces a realistic aural impression of the simulated room. We do not consider diffraction effects due to low frequencies, since these can be better computed by finite elements. Our method allows the visualization of a wave front propagation using color-coded blobs traversing the paths of individual phonons.
Learning and Relearning in Boltzmann Machines (2001)

This chapter contains sections titled: Relaxation Searches, Easy and Hard Learning, The Boltzmann Machine Learning Algorithm, An Example of Hard Learning, Achieving Reliable Computation with Unreliable Hardware, An Example of the Effects of Damage, Conclusion, Acknowledgments, Appendix: Derivation of the Learning Algorithm, References
Impact of FcγRIIa-FcγRIIIa Polymorphisms and KRAS Mutations on the Clinical Outcome of Patients With Metastatic Colorectal Cancer Treated With Cetuximab Plus Irinotecan (2009)

Combined FcgammaRIIa/FcgammaRIIIa polymorphisms are prognostic factors for disease progression in mCRC patients treated with cetuximab plus irinotecan. As these polymorphisms are also clinically relevant in mutated-KRAS mCRC, an important role of ADCC in cetuximab efficacy is presumed.
Transient, lectin-like association of calreticulin with folding intermediates of cellular and viral glycoproteins. (1995)

The soluble, calcium-binding protein calreticulin shares high sequence homology with calnexin, a transmembrane chaperone of glycoprotein folding. Our experiments demonstrated that calreticulin, like calnexin, associated transiently with numerous newly synthesized proteins in the endoplasmic reticulum. The population of proteins that bound to calreticulin was partially overlapping with those that bound to calnexin. Hemagglutinin (HA) of influenza virus was shown to associate with both calreticulin and calnexin. Using HA as a model substrate, it was found that both calreticulin- and calnexin-bound HA corresponded primarily to incompletely disulfide-bonded folding intermediates and conformationally trapped forms. Binding of all substrates was oligosaccharide-dependent and required the trimming of glucose residues from asparagine-linked core glycans by glucosidases I and II. In vitro, alpha-mannosidase digestion of calreticulin-bound HA indicated that calreticulin was specific for monoglucosylated glycans. Thus, calreticulin appeared to be a lectin with similar oligosaccharide specificity as its membrane-bound homologue, calnexin. Both are therefore likely to play an important role in glycoprotein maturation and quality control in the endoplasmic reticulum.
Ursodeoxycholic acid — adverse effects and drug interactions (2003)

Ursodeoxycholic acid is generally well tolerated. Drug absorption interactions with anion exchange resins deserve consideration. Metabolic interactions with compounds metabolized by cytochrome P4503A are to be expected.
Confocal and two-photon microscopy : foundations, applications, and advances (2001)

Foreword (G. Brakenhoff). Preface. Acknowledgements. Contributors. The Generalized Microscope (C. Sheppard). Confocal Microscopy: Basic Principles and Architectures (T. Wilson). Two--Photon Microscopy: Basic Principles and Architectures (A. Diaspro & C. Sheppard). Cross--Sections of Fluorescent Molecules in Multiphoton Microscopy (C. Xu). Resolution and Contrast in Confocal and Two--Photon Microscopy (J. Jonkman and E. Stelzer). The Role of Pinhole Size in High--Aperture Two--and Three--Photon Microscopy (P. Torok & C. Sheppard). Aberrations and Penetration in In--Depth Confocal and Two--Photon--Excitation Microscopy (C. de Grauw, et al.). Group Velocity Dispersion and Fiber Delivery in Multiphoton Laser Scanning Microscopy (R. Wolleschensky, et al.). Cellular and Subcellular Perturbations During Multiphoton Microscopy (K. Konig & U. Tirlapur). Pracitcal Multiphoton Microscopy (J. Girkin & D. Wokosin). Sampling, Resolution and Digital Image Processing in the Spatial and Fourier Domains (K. Castleman). Image--Restoration Methods: Basics and Algorithms (P. Boccacci & M. Bertero). Two--Photon Excitation Fluorescence Microscopy Imaging in Xenopus and Transgenic Mouse Embryos (A. Periasamy, et al.). Multiple Color Fluorescence Imaging in Microscopy (K. Castleman). Stereological Methods for Estimating Geometrical Parameters of Microscopic Structure by Three--Dimensional Imaging (L. Kubinova, et al.). Imaging Live Cells in 3D Using Wide--Field Microscopy with Image Restoration (W. Carrington). Confocal Microscopy in the Study of the Cell Nucleus (L. Neri, et al.). Confocal Imaging of Neuronal Growth and Morphology in Brain Slices (I. Skaliora & S. Pagakis). FISH Imaging (M. Kozubek). Two--Photon Imaging of Tissue Physiology based on Endogenous Fluorophores (L. Hsu, et al.). Two--Photon Near--Infrared Femtosecond Laser Scanning Microscopy in Plant Biology (U. Tirlapur & K. Konig). Two--Photon Excitation Microscopy for Image Spectroscopy and Biochemistry of Tissues, Cells, Organelles, and Lipid Vesicles Under Physiological Conditions (T. Parasassi, et al.). Real--Time In Situ Calcium Imaging with Single-- and Two--Photon Confocal Microscopy (K. Fujita & T. Takamatsu). Superresolution in Fluorescence Confocal Microscopy and in DVD Optical Storage (R. Pike). Photobleaching by Confocal Microscopy (J. McNally & C. Smith). Two--Photon Laser Scanning Microscopy for Characterization of Integrated Circuits and Optoelectronics (C. Xu). Index.
Hematologic Profile of Sepsis in Neonates: Neutrophil CD64 as a Diagnostic Marker (2007)

Neutrophil CD64 is a highly sensitive marker for neonatal sepsis. Prospective studies incorporating CD64 into a sepsis scoring system are warranted.
Comprehensive comparison of three different animal models for systemic inflammation (2017)

The LPS model of systemic inflammation revealed to be most suitable when being interested in the impact of new therapies for acute inflammation. When using the CLP model to mimic human sepsis more closely, a longer time course should be employed, as the treatment induces delayed development of systemic inflammation.
Dislocation filtering in SiGe and InGaAs buffer layers grown by selective lateral overgrowth method (1995)

A quantitative analysis based on the Luryi and Suhir model [Appl. Phys. Lett. 49, 140 (1986)] has shown that the growth of strain relaxed and low dislocation density SixGe1−x and InxGa1−xAs buffer layers on Si and GaAs substrates, respectively, is feasible despite the layer/substrate lattice mismatch. A successful growth of such layers is possible on partially masked substrates by selective lateral overgrowth method. In this case, the buffer layer/substrate misfit stress is of limited lateral extent, in accordance with Saint-Venant’s principle, and its effective length does not exceed 15% of the seeding window width even for very thick buffer layers. High threading dislocation density in the buffer layer can be avoided by reducing the window width such that the effective stress zone length is comparable with the critical layer thickness for misfit dislocation formation. However, a thin alloy layer deposited by molecular beam epitaxy or metalorganic chemical vapor deposition on both the Si and GaAs substrates, prior to coating with SiO2 mask and patterning with oxide-free seeding windows, is required for a quite broad range of alloy compositions
Parkinsonism in HIV infected patients during antiretroviral therapy – data from a Brazilian tertiary hospital (2016)

These findings suggest that HIV infected individuals might be at a higher risk for developing parkinsonism as a manifestation of early neurodegeneration. Prospective and larger studies are needed to address this particular association and its characteristics.
Small‐Molecule Diversification from Iterated Branching Reaction Pathways Enabled by DNA‐Templated Synthesis (2005)

Two unique features of DNA-templated synthesis were integrated to prepare complex small molecules by using iterated branching reaction pathways: the direction of multiple, otherwise “incompatible”, reaction types in one reaction vessel and the direction of sequence-programmed subsets of reaction intermediates to appropriate reagents. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z502899_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.
Invited commentary: targeting of 125I-labeled B lymphocyte stimulator. (2003)

B lymphocyte stimulator (BLyS), also identified as TALL-1 (TNF and apoptosis ligand-related leukocyte-expressed ligand 1), BAFF (B cell activating factor belonging to the tumor necrosis factor family), THANK (tumor necrosis factor homologue that activates apoptosis, nuclear factor-κB, and c-Jun NH2