gebhart/patrepeval huggingface dataset:
Antibodies to the RNase H domain of hepatitis B virus P protein are associated with ongoing viral replication (1990)

Antibodies against the RNase H domain of human hepatitis B virus P protein(s) are frequent markers of acute and chronic virus infection (T. Weimer, K. Weimer, Z.-X. Tu, M.-C. Jung, G. R. Pape, and H. Will, J. Immunol. 143:3750-3756, 1989). In the present study, these antibodies were determined in serial serum samples of experimentally infected chimpanzees and naturally infected human patients with acute and chronic hepatitis B virus infection. Anti-P antibodies were found in the sera of both chimpanzees and humans early in infection shortly after the immunoglobulin M anti-HBc response; they persisted in chronic carriers with ongoing viral replication but declined and disappeared at the time of virus clearance from the sera. These data demonstrate that antibodies to the RNase H domain of the hepatitis B virus P protein are early markers of infection and a signal of ongoing virus replication. Falling titers indicate the decline or end of active virus production and may therefore be a prognostic sign of virus elimination in natural infection and after antiviral therapy.
Mechanism of Photolytic Decomposition of N-Halamine Antimicrobial Siloxane Coatings (2010)

Generally, antimicrobial N-halamine siloxane coatings can be rehalogenated repetitively upon loss of their biocidal efficacies, a marked advantage over coatings containing other antimicrobial materials. However, the N-halamine materials tend to slowly decompose upon exposure to ultraviolet irradiation as in direct sunlight. In this work the mechanism of photolytic decomposition for the N-halamine siloxanes has been studied using spectroscopic and theoretical methods. It was found that the N-chlorinated coatings slowly decomposed upon UVA irradiation, whereas the unhalogenated coatings did not. Model compound evidence in this work suggests that upon UVA irradiation, the N-Cl bond dissociates homolytically, followed by a Cl radical migration to the alkyl side chain connected to the siloxane tethering group. An alpha and/or beta scission then occurs causing partial loss of the biocidal moiety from the surface of the coated material, thus precluding complete rechlorination. NMR, FTIR, GCMS, and computations at the DFT (U)B3LYP/6-311++G(2d,p) level of theory have been employed in reaching this conclusion.
One-Bit Hybrid Precoding for Wideband Millimeter-Wave Massive MIMO Systems (2019)

Hybrid precoding is an effective method for millimeter-wave (mmWave) massive multiple input multiple output (MIMO) system to reduce the number of radio frequency (RF) chains without an obvious sum-rate loss. However, the current literature on hybrid precoding considers either the high resolution (HR) phase shifters (PSs) with high power consumption or the impractical narrowband mmWave channel model. To this end, in this paper, we investigate an energy-efficient hybrid precoding scheme using one-bit PSs for the practical frequency-selective wideband mmWave massive MIMO systems. Specifically, we provide energy consumption analysis to reveal the fact that the energy consumed by the one-bit PSs is much less as compared to the HR-PSs and the array gain loss incurred by using one-bit PSs is also very small. In addition, motivated by the cross- entropy optimization (CEO) algorithm evolved for machine learning, we propose the CEO-based hybrid precoding scheme to maximize the achievable sum- rate of the considered system. The performance evaluation demonstrates that our proposed scheme can obtain the near-optimal sum-rate and considerably higher energy efficiency than some existing works.
Reactive Oxygen Species Signaling in Response to Pathogens (2006)

The production of reactive oxygen species (ROS), via consumption of oxygen in a so-called oxidative burst, is one of the earliest cellular responses following successful pathogen recognition. Apoplastic generation of superoxide (O2−), or its dismutation product hydrogen peroxide (H2O2), has been
A novel effect of EGF on mRNA stability (1988)

Expression of the epidermal growth factor (EGF) receptor gene is stimulated by EGF and the phorbol ester, 4 beta-phorbol 12-myristate 13-acetate (PMA). PMA elevates EGF receptor mRNA levels in human KB epidermoid carcinoma cells, but does not significantly affect the half-life of this mRNA when its decay is examined after the addition of actinomycin D. In contrast, EGF greatly prolongs the half-life of EGF receptor mRNA suggesting a possible mechanism for the stimulatory effect of EGF on EGF receptor mRNA levels. EGF also stabilizes beta-tubulin and beta-actin mRNAs but has very little effect on the degradation of total mRNA.
Rationale for using insensitive quality control rules for today’s hematology analyzers (2010)

Diverse approaches have been used to assure the analytical quality of automated hematology; as such, there is great variation in their error detection capabilities. We summarize the intralaboratory performance of a cohort of Sysmex XE-2100's running e-Check hematology quality control (QC). The imprecisions of a median performing (50th percentile imprecision) and more imprecise [15th percentile (15P) imprecision] Sysmex XE-2100 are compared with measures of total allowable error (regulatory and physiologically based) to obtain multiples of the usual imprecision that must be detected to prevent the hematology analyzer from producing medically unacceptable results. The resultant large multiples of the usual imprecision (s) demonstrate the need for insensitive QC rules employing very broad control ranges, control rules that have been implicitly supported by hematology analyzer manufacturers for the last several decades. For today's highly precise hematology analyzers, the following control rules are strongly advised: 1(3.5s) , 1(4s) and 1(4.5s) rules (violated if a single control observation exceeds either its ±3.5, ±4.0 and ±4.5s limits, respectively). In order for the hematology laboratory to totally embrace expanded QC limits, manufacturers must make available their instruments' usual and poorer (e.g. the 15P performance) imprecision's. Users of hematology analyzers that require more sensitive but less specific rules to prevent the reporting of clinically erroneous data are advised to acquire more precise (and thus more dependable) instrumentation.
Very Virulent Infectious Bursal Disease Virus in Southeastern Europe (2003)

Clinical outbreaks of severe acute infectious burial disease (IBD) were recorded since the mid- and late 1990s in several countries in the southeastern part of Europe. Epidemiologic data showed that both infectious bursal disease virus (IBDV)-vaccinated and IBDV-nonvaccinated chickens were affected with acute IBD and mortality up to 50% independent of the IBDV vaccination status of the appropriate parent flocks. For investigation of the causative agent of acute IBD, the variable region of VP2 was amplified, cloned, and sequenced. Nucleotide sequence analysis of polymerase chain reaction fragments showed several silent nucleotide exchanges in comparison with the sequence of the very virulent (vv) IBDV strain UK661. Also, restriction enzyme cleavage sites proposed specific for vvIBDV were present in all investigated strains. On the basis of clinical signs in affected flocks, recorded epidemiologic data, and sequence analysis, it is very likely the IBD-causing strains were of the vv phenotype.
Supplementary Figure 4 from Cancer-Induced Immunosuppression: IL-18–Elicited Immunoablative NK Cells (2023)

&lt;p&gt;PDF file - 111K, Phenotypic features of Kit+ NK cells compared with Kit- NK cells&lt;/p&gt;
Antisense approaches in prostate cancer (2004)

Patients with hormone refractory prostate cancer have limited treatment options and new therapies are urgently needed. Advances in the understanding of the molecular mechanisms implicated in prostate cancer progression have identified many potential therapeutic gene targets that are involved in apoptosis, growth factors, cell signalling and the androgen receptor (AR). Antisense oligonucleotides are short sequences of synthetic modified DNA that are designed to be complimentary to a selected gene's mRNA and thereby specifically inhibit expression of that gene. The antisense approach continues to hold promise as a therapeutic modality to target genes involved in cancer progression, especially those in which the gene products are not amenable to small molecule inhibition or antibodies. The current status and future direction of a number of antisense oligonucleotides targeting several genes, including BCL-2, BCL-XL, clusterin, the inhibitors of apoptosis (IAP) family, MDM2, protein kinase C-alpha, c-raf, insulin-like growth factor binding proteins and the AR, that have potential clinical use in prostate cancer are reviewed.
Quantitative isoform profiling and isoform convergence (2005)

Alternative pre-messenger RNA splicing is a crucial step in eukaryotic gene expression, and therefore it is subject to tight regulation. Given its importance in conferring protein diversity, alternative splicing is sensitive to changes in cellular states including malignancy. We present a new paradigm by which to quantitatively study the alternative splicing of any molecule through the presented methods of quantitative exon profiling and quantitative isoform profiling which take advantage of a single-molecule based technology [Mit99]. Furthermore, we extend this paradigm to include a novel unified platform---called Isoform Convergence---to qualify particular isoforms as candidate diagnostic markers, potential therapeutic targets, and perhaps even as precursor therapeutics themselves. We apply this paradigm to quantitatively investigate the alternative splicing of CD44 in two leukemias. CD44 is an alternatively spliced cell surface receptor, which is generally implicated in cancer though the specifics are mired in controversy. In this work, we suggest several corrections to previously made claims about the presence of specific CD44 exons and of specific CD44 isoforms in leukemia as well as in non-diseased cells. Furthermore, we provide not only the first comprehensive characterization of CD44's (or any molecule's) alternative exon splicing in human cells, but also its resulting quantities of exons and isoforms to an average resolution on the order of 1.E+06 molecules. Finally, we identify specific isoforms in each leukemia that may serve as candidate markers or possibly as therapeutic targets. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Seasonal storage and alternative carriers: A flexible hydrogen supply chain model (2017)

A viable hydrogen infrastructure is one of the main challenges for fuel cells in mobile applications. Several studies have investigated the most cost-efficient hydrogen supply chain structure, with a focus on hydrogen transportation. However, supply chain models based on hydrogen produced by electrolysis require additional seasonal hydrogen storage capacity to close the gap between fluctuation in renewable generation from surplus electricity and fuelling station demand. To address this issue, we developed a model that draws on and extends approaches in the literature with respect to long-term storage. Thus, we analyse Liquid Organic Hydrogen Carriers (LOHC) and show their potential impact on future hydrogen mobility. We demonstrate that LOHC-based pathways are highly promising especially for smaller-scale hydrogen demand and if storage in salt caverns remains uncompetitive, but emit more greenhouse gases (GHG) than other gaseous or hydrogen ones. Liquid hydrogen as a seasonal storage medium offers no advantage compared to LOHC or cavern storage since lower electricity prices for flexible operation cannot balance the investment costs of liquefaction plants. A well-to-wheel analysis indicates that all investigated pathways have less than 30% GHG-emissions compared to conventional fossil fuel pathways within a European framework.
SNF Interim Storage Canister Corrosion and Surface Environment Investigations (FY2020 Status Report) (2020)

This progress report describes work performed during FY20 at Sandia National Laboratories (SNL) to assess the localized corrosion performance of container/cask materials used in the interim storage of spent nuclear fuel (SNF). Of particular concern is stress corrosion cracking (SCC), by which a through-wall crack could potentially form in a canister outer wall over time intervals that are shorter than possible dry storage times. Work in FY20 further defined our understanding of the potential chemical and physical environment present on canister surfaces, evaluated the relationship between the environment and the resultant corrosion that occurs, and initiated crack growth rate testing under relevant environmental conditions. In FY20, work to define dry storage canister surface environments included several tasks. First, collection of dust deposition specimens from independent spent fuel storage installation (ISFSI) site locations helped to establish a more complete understanding of the potential chemical environment formed on the canister. Second, the predicted evolution of canister surface relative humidity RH) values was estimated using ISFSI site weather data and the horizontal canister thermal model used by the SNL probabilistic SCC model. These calculations determined that for typical ISFSI weather conditions, seasalt deliquescence to produce MgCl2-rich brines could occur in less than 20 years at the coolest locations on the canister surface, and, even after nearly 300 years, conditions for NaCl deliquescence (75% RH) are not reached. This work illustrates the importance of understanding the stability of MgCl2-rich brines on the heated canister surface, and the potential impact of brine composition on corrosion processes, including pitting and stress corrosion cracking. In an additional study, the description of the canister surface environment was refined in order to define more realistic corrosion testing environments including diurnal cycles, soluble salt chemistries, and inert mineral particles. The potential impacts of these phenomena on canister corrosion are being evaluated experimentally. Finally, work over the past few years to evaluate the stability of magnesium chloride brines continued in FY20. MgCl2 degassing experiments were carried out, confirming that MgCl2 brines slowly degas HCl on heated surfaces, converting to less deliquescent magnesium hydroxychloride phases and potentially leading to brine dryout.
Optimized Decoding-Energy-Aware Encoding In Practical VVC Implementations (2022)

The optimization of the energy demand is crucial for modern video codecs. Previous studies show that the energy demand of VVC decoders can be improved by more than 50% if specific coding tools are disabled in the encoder. However, those approaches increase the bit rate by over 20% if the concept is applied to practical encoder implementations such as VVenC. Therefore, in this work, we investigate VVenC and study possibilities to reduce the additional bit rate, while still achieving low-energy decoding at reasonable encoding times. We show that encoding using our proposed coding tool profiles, the decoding energy efficiency is improved by over 25% with a bit rate increase of less than 5% with respect to standard encoding. Furthermore, we propose a second coding tool profile targeting maximum energy savings, which achieves 34% of energy savings at bitrate increases below 15%.
Analysis of a Game Theory-based Model of Vehicle-Pedestrian Interaction at Uncontrolled Crosswalks (2020)

The paper deals with a detailed analysis of a game theory-based vehicle-pedestrian interaction model adopted from literature. For the sake of simplicity only single-vehicle/single-pedestrian model is considered. The adopted model is extended with a stochastic component that accounts for variability in pedestrian/driver behaviors and influence of multi-agent environment. The model is generalized for scenarios where pedestrian appears at different distances relative to crosswalk. The analysis study is organized as follows. First, an off-line analysis of model-derived probability distributions and corresponding crossing decisions is conducted to gain initial insights. Next, large-scale simulations of the model are conducted for a wide set of randomly generated initial conditions and stochastic component tunings. Finally, the obtained simulation results are analyzed and discussed.
A CMOS Ultra-Wideband Impulse Radio Transceiver for 1-Mb/s Data Communications and&lt;tex&gt;$pm$&lt;/tex&gt;2.5-cm Range Finding (2006)

A CMOS ultra-wideband impulse radio (UWB-IR) transceiver was developed in 0.18-/spl mu/m CMOS technology. It can be used for 1-Mb/s data communications as well as for precise range finding within an error of /spl plusmn/2.5 cm. The power consumptions of the transmitter and receiver for data communication are 0.7 and 4.0 mW, respectively. When an LNA operates intermittently through bias switching, the power consumption of the transceiver is only 1 mW. The range for data communication is 1 m with BER of 10/sup -3/. For ranging applications, the transmitter can reduce the power to 0.7 /spl mu/W for 1k pulses per second, and the receiver consumes little power. The transceiver design, all-digital transmitter, and intermittent circuit operation at the receiver reduce the power consumption dramatically, which makes the transceiver well suited for applications like sensor networks. The electronic field intensity is lower than 35 /spl mu/V/m, and thus the UWB system can be operated even under the current Japan radio regulations.
Predicting moderate earthquake and studying seismic activity of small earthquake cluster with S Method (2002)

In this paper,we study the data of mobile geomagnetic survey with S method and compare the results with the seismic active frequency of small earthquake cluster.It is found that when the anomaly of s value appears, the seismic active frequency of small earthquake cluster increases within one year.Otherwise,it decreases.If there is anomalous s value in the mobile geomagnetic survey line,an earthquake M S4 0 may occur in the adjacent area.So S method is practical to predict the medium- short term earthquake in the area with few earthquakes.
A 5.1GHz 0.34mm<sup>2</sup> Router for Network-on-Chip Applications (2007)

A five-port two-lane pipelined packet-switched router core with phase-tolerant mesochronous links forms the key communication fabric for an 80-tile network-on-chip (NoC) architecture. The 15FO4 design combines 102 GB/s of raw bandwidth with low fall-through latency of 980 ps. A shared crossbar architecture with a double-pumped crossbar switch enables a compact 0.34 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> router layout. In a 65nm eight-metal CMOS process, the router contains 210K transistors and operates at 5.1GHz at 1.2 V, while dissipating 945 mW.
Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock (2005)

Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an alternative splicing factor that is mainly nuclear, although it shuttles rapidly between nuclear and cytoplasmic compartments. Cells stressed by osmotic shock (OSM) activate the mitogen-activated protein kinase kinase(3/6)-p38 signaling pathway, which in turn results in accumulation of hnRNP A1 in the cytoplasm. This effect modulates alternative splicing regulation in vivo and correlates with increased hnRNP A1 phosphorylation. We have characterized the molecular mechanism involved in the cytoplasmic accumulation of hnRNP A1 in NIH 3T3 cells subjected to OSM. This treatment results in serine-specific phosphorylation within a C-terminal peptide, dubbed the "F-peptide," which is adjacent to the M9 motif that mediates bidirectional transport of hnRNP A1. Analysis of mutants in which the F-peptide serines were replaced by aspartic acids or alanines showed that F-peptide phosphorylation is required for the subcellular redistribution of hnRNP A1 in cells subjected to OSM. Furthermore, F-peptide phosphorylation modulates the interaction of hnRNP A1 with transportin Trn1. Our findings suggest that the phosphorylation of F-peptide by cell-signaling pathways regulates the rate of hnRNP A1 nuclear import.
Adenylate cyclase activity of NIH 3T3 cells morphologically transformed by ras genes (1986)

The observed homology between G-proteins which regulate adenylate cyclase and ras proteins and the suggested role of ras in the regulation of adenylate cyclase in yeast prompted us to examine the regulation of adenylate cyclase in three cell lines: (i) NIH 3T3 cells, (ii) NIH 3T3 cells transformed by high levels of the normal rasH gene product and (iii) NIH 3T3 cells transformed by a mutated rasH gene product. We found that the regulation of adenylate cyclase by G-proteins is identical in the three cell lines, although the response of the transformed NIH 3T3 cells to agonists is strongly attenuated. Our data suggest that mammalian ras products do not interact directly with adenylate cyclase, although their increased expression may indirectly inhibit the interaction of adenylate cyclase stimulatory receptors with G-proteins.
Assessment of PD-L1 expression across breast cancer molecular subtypes, in relation to mutation rate, BRCA1-like status, tumor-infiltrating immune cells and survival (2018)

To better understand the expression pattern of programmed death-ligand 1 (PD-L1) expression in different breast cancer types, we characterized PD-L1 expression in tumor and tumor-infiltrating immune cells, in relation to mutation rate, <i>BRCA1</i>-like status and survival. We analyzed 410 primary treatment-naive breast tumors comprising 162 estrogen receptor-positive (ER+) and HER2-, 101 HER2+ and 147 triple-negative (TN) cancers. Pathologists quantified tumor-infiltrating lymphocytes (TILs) and PD-L1 expression in tumor cells and TILs using whole slides and tissue microarray. Mutation rate was assessed by DNA sequencing, <i>BRCA1</i>-like status using multiplex ligation-dependent probe amplification, and immune landscape by multiplex image analyses of CD4, CD68, CD8, FOXP3, cytokeratin, and PD-L1. Half of PD-L1 scores evaluated by tissue microarray were false negatives compared to whole slide evaluations. We observed at least 1% of PD-L1-positive (PD-L1+) cells in 53.1% of ER+HER2-, 73.3% of HER2+, and 84.4% of TN tumors. PD-L1 expression was higher in ductal compared to lobular carcinomas, also within ER+HER2- tumors (p = 0.04). High PD-L1+ TILs score (> 50%) was independently associated with better outcome in TN tumors (HR = 0.27; 95%CI = 0.10-0.69). Within TN tumors, PD-L1 and TIL scores showed a modest but significant positive association with the number of silent mutations, but no association with <i>BRCA1</i>-like status. Multiplex image analyses indicated that PD-L1 is expressed on multiple immune cells (CD68+ macrophages, CD4+, FOXP3+, and CD8+ T cells) in the breast tumor microenvironment, independent of the PD-L1 status of the tumor cells. We found no evidence that levels of PD-L1+ TILs in TN breast cancer are driven by high mutation rate or <i>BRCA1</i>-like status.
Recent Advances in the Solid‐Phase Combinatorial Synthetic Strategies for the Quinoxaline‐, Quinazoline‐ and Benzimidazole‐Based Privileged Structures (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.