gebhart/patrepeval huggingface dataset:
Glycine 184 in Nonstructural Protein NS1 Determines the Virulence of Influenza A Virus Strain PR8 without Affecting the Host Interferon Response (2010)

The nonstructural protein NS1 of influenza A virus counteracts the interferon (IFN) system and thereby promotes viral replication. NS1 has acquired different mechanisms to limit induction of IFN. It prevents double-stranded RNA (dsRNA) and RIG-I-mediated activation of interferon regulatory factor 3 (IRF3), and it blocks posttranscriptional processing of cellular mRNAs by binding to the cleavage and polyadenylation specificity factor (CPSF). Using a mouse-adapted A/PR/8/34 virus and reverse genetics to introduce specific mutations in NS1 which eliminate one or both functions, we determined the relative contributions of these two activities of NS1 to viral virulence in mice. We found that a functional RNA-binding motif was required for IFN suppression and virulence. Restoration of CPSF binding in the NS1 protein of wild-type A/PR/8/34 virus, which cannot bind CPSF due to mutations in the central binding motif at positions 103 and 106, resulted in enhanced virulence. Surprisingly, if CPSF binding was abolished by substituting glycine for arginine at position 184 in the classical NS1-CPSF binding motif, the mutant virus replicated much more slowly in mice, although the mutated NS1 protein continued to repress the IFN response very efficiently. Our results show that a functional RNA-binding motif is decisive for NS1 of A/PR/8/34 virus to suppress IFN induction. They further demonstrate that in addition to its contribution to CPSF binding, glycine 184 strongly influences viral virulence by an unknown mechanism which does not involve the IFN system.
Evaluation of Specific Ultraviolet Absorbance as an Indicator of the Chemical Composition and Reactivity of Dissolved Organic Carbon (2003)

Specific UV absorbance (SUVA) is defined as the UV absorbance of a water sample at a given wavelength normalized for dissolved organic carbon (DOC) concentration. Our data indicate that SUVA, determined at 254 nm, is strongly correlated with percent aromaticity as determined by 13C NMR for 13 organic matter isolates obtained from a variety of aquatic environments. SUVA, therefore, is shown to be a useful parameter for estimating the dissolved aromatic carbon content in aquatic systems. Experiments involving the reactivity of DOC with chlorine and tetramethylammonium hydroxide (TMAH), however, show a wide range of reactivity for samples with similar SUVA values. These results indicate that, while SUVA measurements are good predictors of general chemical characteristics of DOC, they do not provide information about reactivity of DOC derived from different types of source materials. Sample pH, nitrate, and iron were found to influence SUVA measurements.
Potential synergies of drop‐in biofuel production with further co‐processing at oil refineries (2019)

Abstract Drop‐in biofuels have been defined as functionally equivalent to petroleum‐based transportation fuels and are fully compatible with the existing petroleum infrastructure. They will be essential in sectors such as aviation if we are to achieve emission reduction and climate mitigation goals. Currently, ‘conventional’ drop‐in biofuels, which are primarily based on upgrading of lipids / oleochemicals, are the only significant source of commercial volumes of drop‐in biofuels. However, the necessary increased, future volumes will likely come from ‘advanced’ drop‐in biofuels based on biomass feedstocks such as forest and agriculture residues. Biocrudes / bio‐oils produced from lignocellulosic feedstocks using thermochemical technologies such as gasification, pyrolysis, and hydrothermal liquefaction need to be further upgraded to drop‐in biofuels. However, advanced drop‐in biofuels have been slow to reach commercial maturity due to significant technical challenges, high capital costs, and the challenge of generally lower oil prices. It is likely that the co‐processing of drop‐in biofuels with conventional petroleum refining could considerably reduce capital costs. Initially, co‐processing is likely to be established through the upgrading of conventional / oleochemical feedstocks (lipids). Lipids are readily available in large volumes (global production in 2017 was ~185 million metric tonnes) and can be more easily integrated into oil‐refinery processes. In contrast, lignocellulose‐derived biocrudes / bio‐oils are not yet available in significant volumes and are more complex to co‐process in a refinery. The likely strategies for co‐processing of oleochemicals (lipids) and bio‐oil and biocrude feedstocks based on different insertion points within the refinery infrastructure are discussed. © 2019 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Chemical Industry and John Wiley &amp; Sons, Ltd.
Enhanced latitude for digital projection radiography (1999)

The trade-off between contrast and latitude is a well-known and long-standing image quality limitation in projection radiography. With the introduction of electronic acquisition, it is possible to capture a wide range of x-ray exposures in a single image. However, the problem of rendering and displaying images, such that information outside the normal expected latitude is visualized while maintaining adequate contrast for diagnostic details, has remained. The enhanced visualization processing (EVP) algorithm described in this paper addresses this problem. A clinical study is reported utilizing 70 images, including 5 images of each of 14 examination types selected from a large data base of diagnostic computed radiography images. For each image, a control rendering was produced by means of a state-of-the-art automated tone scaling algorithm. A test rendering was produced by applying EVP to the control image. Ten radiologists independently rated the 140 resulting images on a 9-point diagnostic quality scale. EVP provided increased exposure latitude without objectionable loss of detail contrast. In many images, EVP substantially reduced the loss of information in normally under-penetrated areas, while reducing the need for 'bright lighting' in over- penetrated areas. The diagnostic quality ratings of both EVP and control images were, on average, high. However, the median rating for EVP images was one full rating category higher than that of the control images. Viewing the images as pairs, 76 percent of the EVP images were rated 1 or more categories superior to the corresponding control image while only 6 percent of the control images were rated as superior to the corresponding EVP image. Similar results were obtained across all 14 examination-types studied.
Comparison of Inhaled Corticosteroids (1998)

Delivery systems can significantly affect both topical and systemic activity of inhaled corticosteroids. More direct comparative studies between agents are required to firmly establish comparative topical to systemic activity ratios. The preponderance of evidence suggests that the agents are not equipotent on a microgram basis.
Segment Routing Recursive Information (2017)

Segment Routing (SR) allows for a flexible definition of end-to-end
paths within IGP topologies by encoding paths as sequences of
topological sub-paths, called segments. These segments are
advertised by the link-state routing protocols (IS-IS and OSPF).
There are use cases where it is desirable to utilize a SID associated
with a given node in order to transport traffic destined to different
local services supported by such node. This document defines the
mechanism to do so and illustrates it.
Language-Based Therapies for the Young Child Stutterer (1982)

This paper explores the rationale for using language-based therapy for young stutterers. The ways in which knowledge of the structure of language and knowledge of language acquisition sequences may be used to facilitate fluency are discussed. Current therapies for young stutterers, those of Ryan and Van Kirk, Stocker, Gregory and Hill, and Wall and Myers, are described. Each of the therapies employs techniques requiring the manipulation of linguistic variables in order to increase the child's fluency.
Localization in human interleukin 2 of the binding site to the alpha chain (p55) of the interleukin 2 receptor. (1991)

Human interleukin 2 (IL-2) analogs with defined amino acid substitutions were used to identify specific residues that interact with the 55-kDa subunit (p55) or alpha chain of the human IL-2 receptor. Analog proteins containing specific substitutions for Lys-35, Arg-38, Phe-42, or Lys-43 were inactive in competitive binding assays for p55. All of these analogs retained substantial competitive binding to the intermediate-affinity p70 subunit (beta chain) of the receptor complex. The analogs varied in ability to interact with the high-affinity p55/p70 receptor. Despite the lack of binding to p55, all analogs exhibited significant biological activity, as assayed on the murine CTLL cell line. The dissociation constants of Arg-38 and Phe-42 analogs for p70 were consistent with intermediate-affinity binding; the Kd values were not significantly affected by the presence of p55 in binding to the high-affinity IL-2 receptor complex. These results confirm the importance of the B alpha-helix in IL-2 as the locus for p55-receptor binding and support a revised model of IL-2-IL-2 receptor interaction.
Mirk/Dyrk1B Maintains the Viability of Quiescent Pancreatic Cancer Cells by Reducing Levels of Reactive Oxygen Species (2009)

The kinase Mirk/dyrk1B mediated the clonogenic growth of pancreatic cancer cells in earlier studies. It is now shown that Mirk levels increased 7-fold in SU86.86 pancreatic cancer cells when over a third of the cells were accumulated in a quiescent G(0) state, defined by Hoechst/Pyronin Y staining. Depletion of Mirk by a doxycycline-inducible short hairpin RNA increased the G(0) fraction to approximately 50%, suggesting that Mirk provided some function in G(0). Mirk reduced the levels of reactive oxygen species (ROS) in quiescent cultures of SU86.86 cells and of Panc1 cells by increasing transcription of the antioxidant genes ferroxidase, superoxide dismutase (SOD)2, and SOD3. These genes were functional antioxidant genes in pancreatic cancer cells because ectopic expression of SOD2 and ferroxidase in Mirk-depleted cells lowered ROS levels. Quiescent pancreatic cancer cells quickly lost viability when depleted of Mirk because of elevated ROS levels, exhibiting up to 4-fold less colony-forming activity and 4-fold less capability for dye exclusion. As a result, reduction of ROS by N-acetyl cysteine led to more viable cells. Mirk also destabilizated cyclin D1 and D3 in quiescent cells. Thus, quiescent pancreatic cancer cells depleted of Mirk became less viable because they were damaged by ROS, and had increased levels of G(1) cyclins to prime cells to escape quiescence.
Quantitative description of radiofrequency (RF) power‐based ratiometric chemical exchange saturation transfer (CEST) pH imaging (2015)

Chemical exchange saturation transfer (CEST) MRI holds great promise for the imaging of pH. However, routine CEST measurement varies not only with the pH-dependent chemical exchange rate, but also with CEST agent concentration, providing pH-weighted information. Conventional ratiometric CEST imaging normalizes the confounding concentration factor by analyzing the relative CEST effect from different exchangeable groups, requiring CEST agents with multiple chemically distinguishable labile proton sites. Recently, a radiofrequency (RF) power-based ratiometric CEST MRI approach has been developed for concentration-independent pH MRI using CEST agents with a single exchangeable group. To facilitate quantification and optimization of the new ratiometric analysis, we quantified the RF power-based ratiometric CEST ratio (rCESTR) and derived its signal-to-noise and contrast-to-noise ratios. Using creatine as a representative CEST agent containing a single exchangeable site, our study demonstrated that optimized RF power-based ratiometric analysis provides good pH sensitivity. We showed that rCESTR follows a base-catalyzed exchange relationship with pH independent of creatine concentration. The pH accuracy of RF power-based ratiometric MRI was within 0.15-0.20 pH units. Furthermore, the absolute exchange rate can be obtained from the proposed ratiometric analysis. To summarize, RF power-based ratiometric CEST analysis provides concentration-independent pH-sensitive imaging and complements conventional multiple labile proton group-based ratiometric CEST analysis.
Nerve growth factor induces protein-tyrosine phosphorylation. (1988)

When the sympathetic nerve-like cell line PC12 is exposed to nerve growth factor (NGF), there is a rapid and transient phosphorylation of tyrosine residues in cellular proteins, as demonstrated by immunoblotting of cell extracts with high-affinity polyclonal antibodies specific for phosphotyrosine residues. Epidermal growth factor (EGF), which does not cause the morphological differentiation of PC12 cells that is produced by NGF, also induces protein-tyrosine phosphorylation. The methyltransferase inhibitor, 5'-methylthioadenosine, which is known to block the NGF-mediated morphological differentiation of PC12 cells, also inhibits the induction of protein-tyrosine phosphorylation by NGF. 5'-Methylthioadenosine has no effect, however, on EGF-stimulated phosphorylation of tyrosine residues in cellular proteins. In addition, low temperature markedly slows the rate of protein-tyrosine phosphorylation stimulated by NGF, but it has no effect on the time course of protein-tyrosine phosphorylation induced by EGF. These data suggest that NGF and EGF induce protein-tyrosine phosphorylation in PC12 cells by different mechanisms.
Automated measurement system for 1- Omega standard resistors using a modified Wheatstone bridge (2002)

A modified Wheatstone bridge that has four detectors to sense the imbalances in the circuit and a digitally controlled feedback system to balance it automatically with a resolution of a few parts in 10/sup 9/ is described, and its operating principle is briefly explained. The performance of the fully automated measurement system using the bridge is examined. Data were taken with a measuring current of 50 mA through each resistor. The total integration time of 120 s for each feedback cycle corresponds to an effective noise bandwidth of 3.3 mHz, so that the estimated voltage resolution is 35 pV using the experimentally determined noise power spectrum of 0.61 nV/ square root Hz. Combining this with the voltage drop of 50 mV at each resistor, a resolution of 1.43 n Omega is expected for each feedback cycle, and 0.28 n Omega for each relative resistance ratio. The average standard deviation from the linear fits is 0.31 n Omega , which is in good agreement with the estimated value and is only a factor of four larger than the ultimate sensitivity determined by thermal noise of 1- Omega standard resistors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
TCP big window and NAK options (1989)

Two extensions to the TCP protocol are described in this RFC in order to provide a more efficient operation over a network with a high bandwidth*delay product. The main issue that still needs to be solved is congestion versus noise. This issue is touched on in this memo, but further research is still needed on the applicability of the extensions in the Internet as a whole infrastructure and not just high bandwidth*delay product networks. Even with this outstanding issue, this document does describe the use of these options in the isolated satellite network environment to help facilitate more efficient use of this special medium to help off load bulk data transfers from links needed for interactive use.
Experimental Investigation of a Morphing Nacelle Ducted Fan (2005)

The application of Circulation Control to the nacelle of a shrouded fan is proposed as a means to enhance off-design performance of the shrouded fan. Typically, a fixed geometry shroud is efficient at a single operating condition. Modifying circulation about the fixed geometry is proposed as a means to virtually morph the shroud without moving surfaces. This approach will enhance off-design-point performance with minimal complexity, weight, and cost. Termed the Morphing Nacelle, this concept provides an attractive propulsion option for Vertical Take-off and Landing (VTOL) aircraft, such conceptual Personal Air Vehicle (PAV) configurations proposed by NASA. An experimental proof of concept investigation of the Morphing Nacelle is detailed in this paper. A powered model shrouded fan model was constructed with Circulation Control (CC) devices integrated in the inlet and exit of the nacelle. Both CC devices consisted of an annular jet slot directing a jet sheet tangent to a curved surface, generally described as a Coanda surface. The model shroud was tailored for axial flight, with a diffusing inlet, but was operated off-design condition as a static lifting fan. Thrust stand experiments were conducted to determine if the CC devices could effectively improve off-design performance of the shrouded fan. Additional tests were conducted to explore the effectiveness of the CC devices a means to reduce peak static pressure on the ground below a lifting fan. Experimental results showed that off-design static thrust performance of the model was improved when the CC devices were employed under certain conditions. The exhaust CC device alone, while effective in diffusing the fan exhaust and improving weight flow into shroud inlet, tended to diminish performance of the fan with increased CC jet momentum. The inlet CC device was effective at reattaching a normally stalled inlet flow condition, proving an effective means of enhancing performance. A more dramatic improvement in static thrust was obtained when the inlet and exit CC devices were operated in unison, but only over a limited range of CC jet momentum. Operating the nacelle inlet and exit CC devices together proved very effective in reducing peak ground plane static pressure, while maintaining static thrust. The Morphing Nacelle concept proved effective at enhancing off-design performance of the model; however, additional investigation is necessary to generalize the results.
(<sup>3</sup>H/<sup>14</sup>C)Beta‐methylheptadecanoic acid subcellular distribution and lipid incorporation in mouse heart (1990)

Beta-methylfatty acids are transported into myocardial cells as other fatty acids would be, but are incapable, for example, of undergoing complete catabolism. Our previous studies have established the structure-location relationship and the imaging characteristics of these analogs. In the present study in mouse myocardium, microautoradiography and electron microscopy were used to show the distribution of [7,8-3H] beta-methylheptadecanoic acid [( 3H]BMHA) in mitochondria and lipid droplets. Thin-layer chromatography demonstrated the presence of [1-14C] beta-methylheptadecanoic acid [( 14C]BMHA) and its metabolites in various lipid pools. These studies complement our earlier findings which showed that similarities exist in the initial metabolic fate of BMHA and physiological fatty acids.
CD38 and CD100 lead a network of surface receptors relaying positive signals for B-CLL growth and survival (2004)

This work addresses the question whether CD38, a negative prognostic marker in B-cell chronic lymphocytic leukemia (B-CLL), plays a role in neoplastic B-cell growth and survival. We show that CD38+ B-CLL cells bind to murine fibroblasts transfected with the CD31 ligand. The interaction triggers an extensive remodeling of the B-CLL membrane, with relocalization of BCR/CD19 to the CD38/CD31 contact areas, and it also increases cell survival and proliferation. A second event is the up-modulation of the survival receptor CD100, restricted to proliferating cells, and a concomitant decrease of CD72 (low-affinity CD100 ligand and negative regulator of immune responses). The most efficient signals are delivered through sequential interactions between CD38/CD31 and CD100/plexin-B1 (high-affinity CD100 ligand), as inferred by coculture experiments using specific transfectants and blocking monoclonal antibodies (mAbs). The finding that nurselike cells from B-CLL patients express CD31 and plexin-B1, which deliver growth and survival signals to CD38+/CD100+ B-CLL cells, further confirms the model proposed. These findings show that a set of normal receptors and ligands ruling physiologic signaling pathways in B lymphocytes becomes detrimental when expressed in the context of B-CLL cells, ultimately leading to the generation of a tumor reservoir.
The Extracellular Matrix and Inflammation (2005)

Components that propagate inflammation in joint disease may be derived from cartilage since the inflammation resolves after joint replacement. We found that the cartilage component fibromodulin has the ability to activate an inflammatory cascade, i.e. complement. Fibromodulin and immunoglobulins cause comparable deposition of C1q, C4b, and C3b from human serum. Using C1q and factor B-deficient sera in combination with varying contents of metal ions, we established that fibromodulin activates both the classical and the alternative pathways of complement. Further studies revealed that fibromodulin binds directly to the globular heads of C1q, leading to activation of C1. However, deposition of the membrane attack complex and C5a release were lower in the presence of fibromodulin as compared with IgG. This can be explained by the fact that fibromodulin also binds complement inhibitor factor H. Factor H and C1q bind to non-overlapping sites on fibromodulin, but none of the interactions is mediated by the negatively charged keratan sulfate substituents of fibromodulin. C1q but not factor H binds to an N-terminal fragment of fibromodulin previously implicated to be affected in cartilage stimulated with the inflammatory cytokine interleukin 1. Taken together our observations indicate fibromodulin as one factor involved in the sustained inflammation of the joint.
<i>Pneumocystis</i> Cell Wall β-Glucans Stimulate Alveolar Epithelial Cell Chemokine Generation through Nuclear Factor-κB–Dependent Mechanisms (2005)

Exuberant inflammatory responses are associated with respiratory failure during Pneumocystis pneumonia. Alveolar epithelial cells (AECs) promote Pneumocystis attachment and proliferation, but also contribute prominently to host cytokine-mediated inflammation during pneumonia. Recent investigations indicate that AECs produce macrophage inflammatory protein-2 (MIP-2) and tumor necrosis factor-alpha (TNF-alpha) following challenge with Pneumocystis carinii. Nuclear factor-kappaB (NF-kappaB) is a ubiquitous transcription factor critical for regulation of proinflammatory cytokine expression. Herein, we assess rat AEC NF-kappaB responses to challenge with a P. carinii beta-glucan cell wall component (PCBG). Prominent nuclear translocation of p65 NF-kappaB was demonstrated following PCBG challenge. NF-kappaB activation was in part mediated through Protein Kinase C (PKC) signaling pathways. PCBG challenge of AECs was also shown to induce MIP-2 and TNF-alpha mRNA production, a response that was ameliorated by NF-kappaB inhibition. MIP-2 protein expression was also dramatically increased by PCBG challenge, in a manner that was significantly attenuated by both PKC and NF-kappaB inhibition. The data further demonstrate that AEC chemokine responses were not mediated by the recently described dectin-1 receptor, but instead involved participation of cell surface lactosylceramide. These data support a significant role for AECs in host responses during Pneumocystis pneumonia, and further indicate that beta-glucan induces inflammatory cytokine production through NF-kappaB-dependent mechanisms.
Biology of the Prokaryotes (1998)

Bacteriology paved the way to cell biology - a historical account the procaryotic cell basic prerequisites for cellular life diversity of metabolic pathways the genetics of the prokaryotes and their viruses gene expression and regulatory mechanism cell growth and differentiation diversity and systematics prokaryotes in the biosphere applied microbiology.