gebhart/patrepeval huggingface dataset:
Effects of the Δ67 Complex of Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase on Nucleoside Analog Excision (2004)

Long-term use of combination therapy against human immunodeficiency virus type (HIV-1) provides strong selective pressure on the virus, and HIV-1 variants that are resistant to multiple inhibitors have been isolated. HIV-1 variants containing amino acid substitutions within the coding region of HIV-1 reverse transcriptase (RT), such as the 3'-azido-3'-deoxythymidine (AZT)-resistant variant AZT-R (M41L/D67N/K70R/T215Y/K219Q) and a variant containing an insertion in the fingers domain (S69SGR70/T215Y), are resistant to the nucleoside RT inhibitor (NRTI) AZT because of an increase in the level of excision of AZT monophosphate (AZTMP) from the primer. While rare, variants have also been isolated which contain deletions in the RT coding region. One such virus, described by Imamichi et al. (J. Virol 74:10958-10964, 2000; J. Virol. 74:1023-1028, 2000; J. Virol. 75:3988-3992, 2001), contains numerous amino acid substitutions and a deletion of codon 67, which we have designated the Delta67 complex of mutations. We have expressed and purified HIV-1 RT containing these mutations. We compared the polymerase and pyrophosphorolysis (excision) activity of an RT with the Delta67 complex of mutations to wild-type RT and the two other AZT-resistant variants described above. All of the AZT-resistant variants we tested excise AZTMP and 9-[2-(R)-(phosphonomethoxy)propyl]adenine (PMPA [tenofovir]) from the end of a primer more efficiently than wild-type RT. Although the variant RTs excised d4TMP less efficiently than AZTMP and PMPA, they were able to excise d4TMP more efficiently than wild-type RT. HIV-1 RT containing the Delta67 complex of mutations was not able to excise as broad a range of NRTIs as the fingers insertion variant SSGR/T215Y, but it was able to polymerize efficiently with low concentrations of deoxynucleoside triphosphates and seems to be able to excise AZTMP and PMPA at lower ATP concentrations than AZT-R or SSGR/T215Y, suggesting that a virus containing the Delta67 complex of mutations would replicate reasonably well in quiescent cells, even in the presence of AZT.
<i>LYS3</i> encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat (2019)

ABSTRACT Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. HIGHLIGHTS LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. Wheat and barley LYS3 / PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. The down-stream target genes of PBF in wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism.
Frequency-comb infrared spectrometer for rapid, remote chemical sensing (2005)

We demonstrate real-time recording of chemical vapor fluc-tuations from 22m away with a fast Fourier-transform infrared (FTIR) spectrometer that uses a laser-like infrared probing beam generated from two 10-fs Ti:sapphire lasers. The FTIR's broad 9-12 microm spectrum in the "molecular fingerprint" region is dispersed by fast heterodyne self-scanning, enabling spectra at 2cm-1 resolution to be recorded in 70 micros snapshots. We achieve continuous acquisition at a rate of 950 IR spectra per second by actively manipulating the repetition rate of one laser. Potential applications include video-rate chemical imaging and transient spectroscopy of e.g. gas plumes, flames and plasmas, and generally non-repetitive phenomena such as those found in protein folding dynamics and pulsed magnetic fields research.
Role of microtubules in transferrin receptor transport from the cell surface to endosomes and the Golgi complex. (1993)

Transferrin receptor (TfR) follows complex pathways of transport after endocytosis from the cell surface. Most TfR is transported to endosomes and returns rapidly to the cell surface. In addition, approximately 10% of the internalized receptor recycles through the Golgi complex. To examine the role of microtubules in TfR traffic, K562 cultured human leukemia cells treated with nocodazole to depolymerize microtubules were studied. Nocodazole caused a 50% increase in the level of surface TfR, which was due to a change in receptor dynamics. The endocytosis rate in treated cells was 20% of control, indicating that TfR endocytosis via clathrin-coated vesicles was slowed, whereas the recycling of internalized receptors to the cell surface was unaffected. In contrast, nocodazole had little effect on the transport of TfR from the cell surface to the Golgi complex. Thus, the fragmentation and dispersal of the Golgi complex caused by microtubule depolymerization, which does not interrupt secretory traffic through this organelle, also does not block recycling through the Golgi. The decreased TfR endocytosis via coated vesicles and the increased TfR transport to the Golgi caused by nocodazole suggest that either (i) endocytosis via coated vesicles is not the rate-limiting step in transport to the Golgi or (ii) coated vesicles are not a part of this pathway. Finally, because nocodazole inhibits traffic from endosomes to lysosomes, surface-to-Golgi transport probably does not involve a lysosomal intermediate.
A Stack algorithm with limited tree-search (2009)

Due to the capacity achievable, Multiple-Input Multiple-Output (MIMO) systems witnessed more interest in recent years. Several data detection algorithms are available for MIMO systems, especially the tree-search ones which offer lower complexity comparing to the ML receiver. In this paper, we are interested in one of tree-search algorithms, which is the Stack decoder. Nevertheless, the stack decoder is only proposed to decode MIMO systems employing finite constellations, as the QAM (Quadrature Amplitude Modulation). In this work, we introduce a new Stack decoder capable of decoding lattice and we call it the M-Stack decoder. The principle idea behind it is to generate M nodes at each tree-level and so to reduce the infinite alphabet of the lattice to only M components at each step. Then, we propose to adapt it to decode QAM constellations. This one is compared to the known QRD-Stack algorithm. While both visit the same number of nodes, the proposed M-Stack algorithm offers lower computational complexity and it is much faster than the QRD-Stack one.
C3, C4 and C5: the thioester site (1990)

Conference Article| December 01 1990 C3, C4 and C5: the thioester site ALEX S. K. LAW; ALEX S. K. LAW 1M.R.C. Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K. Search for other works by this author on: This Site PubMed Google Scholar ALISTER W. DODDS ALISTER W. DODDS 1M.R.C. Immunochemistry Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1990) 18 (6): 1155–1159. https://doi.org/10.1042/bst0181155 Article history Received: August 03 1990 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation ALEX S. K. LAW, ALISTER W. DODDS; C3, C4 and C5: the thioester site. Biochem Soc Trans 1 December 1990; 18 (6): 1155–1159. doi: https://doi.org/10.1042/bst0181155 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: α2M, α2-macroglobulin, AM, acceptor molecule, BE, binding efficiency This content is only available as a PDF. © 1990 Biochemical Society1990 Article PDF first page preview Close Modal You do not currently have access to this content.
Die durch Silberionen katalysierte Umlagerung von Propargyl‐phenyläther (1973)

Abstract It is known that propargyl‐phenylethers rearrange at about 200° to 2 H ‐chromenes [1–4]. It is shown that this rearrangement occurs in benzene or chloroform at lower temperatures (20–80°) in the presence of silver‐tetrafluoroborate (or‐trifluoracetate). The ethers examined are presented in Scheme 1 . Thus in chloroform at 61° in the presence of AgBF 4 , phenyl‐propargylether ( 3 ) yields 2 H ‐chromene ( 13 ). With 0.78 molar equivalents AgBF 4 in benzene at 80° the same ether 3 yields a 3:1 mixture of 2‐methyl‐cumaron ( 14 ) and 2 H ‐chromene ( 13 ). From 1′‐methylpropargyl‐phenylether ( 4 ) and 2′‐butinyl‐3,5‐dimethylphenylether ( 5 ) under similar conditions the corresponding chromenes 16 and 17 resp. are obtained. Rearrangement of propargyl‐ and 2′‐butinyl‐1‐methyl‐2‐naphthylether ( 6 and 7 resp.) in benzene at 80° in the presence of AgBF 4 gives the corresponding allenyl‐naphthalenones 18 and 19 resp. Treatment of propargyl‐ and 2′‐butinyl‐mesityl‐ether ( 8 and 9 resp.), and propargyl‐ and l′‐methylpropargyl‐ 2 , 6 ‐dimethyl‐phenylether ( 10 and 11 resp.) in benzene at 80° with AgRF, yields as the only product the corresponding 3 ‐allenyl‐phenols 21 , 22 , 24 and 25 (Scheme 3). It is shown that in the presence of μ‐dichlor‐dirhodiuni (1)‐tetracarbonyl in benzene a t 80° the ether 4 rearranges to 2‐methyl‐2H‐chromene (16). However with this catalyst the predominant reaction is a cleavage to phenol. No reaction was observed when ethers 3 and 12 , (Scheme 7 ) were treated with the tris‐(trimethylsily1)‐ester of vanadic acid in benzene a t 80° (see also [8]). By analogy with the known mechanism for thc silver catalysis of the reversible propargylesterl/allenylester rearrangement [S], the silver (1)ion is assumed to form a pre‐equilibrium π‐complex with the C, C‐triplebond of the substrate. This complex then undergoes a [3s, 3s]‐sigmatropic rearrangement (Scheme 2). In the case of the others 6 , 7 and 12 the resulting allenyldienones were isolated. The 2,G‐dimethyl substituted ethers 8 , 9 , 10 and 11 resp. first give the usual allenyl‐ dienones (Scheme 3). These then undergo a novel silver catalysed dienon‐phenol‐rearrangement (Sclzenzu4) to give the 3‐allenylphenols 21 , 22 , 24 and 25 . Thc others 3 , 4 and 5 with free ortho positions presumably rearrange first to the non‐isolated 2‐allenyl‐phenols 15 , 42 and 43 resp.(Scheme 7). These then rearrange, either thermally or by silver (1)ion catalysis to the 2H‐chromenes 13 , 16 and 17 resp. The rate of the rearrangement of 2‐allenylphenol ( 15 ) to 13 at room temperature in benzene or chloroform is approximately doubled when silver ions are present as catalyst.
Programmed death ligand 1 as an indicator of pre-existing adaptive immune responses in human hepatocellular carcinoma (2016)

It is well known that the aberrant expression of programmed death ligand 1 (PD-L1) on tumor cells impairs antitumor immunity. To date, in hepatocellular carcinoma (HCC), the relationship between PD-L1 expression and host-tumor immunity is not well defined. Here, the expression levels of PD-L1 and CD8(+) T cell infiltration were analyzed by immunohistochemistry (IHC) in formalin fixed paraffin embedded (FFPE) specimens from 167 HCC patients undergoing resection. A significant positive association was found between PD-L1 expression and the presence of CD8(+) T cell (p < 0.0001). Moreover, constitutive PD-L1 protein expression was not detected by western blot in HepG2, Hep3B, and 7402 HCC cancer cell lines; but co-cultured these cell lines with INFγ, a cytokine produced by activated CD8(+) T cells, remarkably upregulated PD-L1 expression. In fresh frozen HCC specimens, INFγ was found to be significantly correlated with PD-L1 and CD8(+) gene expression, as evaluated by quantitative reverse transcriptase polymerase chain reaction (RT-PCR). These findings indicate that increased PD-L1 level may represent an adaptive immune resistance mechanism exerted by tumor cells in response to endogenous antitumor activity. Both increased intratumoral PD-L1 and CD8(+) were significantly associated with superior DFS (CD8(+): p = 0.03; PD-L1: p = 0.023) and OS (CD8(+): p = 0.001 and PD-L1: p = 0.059), but PD-L1 expression was not independently prognostic. In conclusions, PD-L1 upregulation is mainly induced by activated CD8(+) cytotoxic T cells pre-existing in HCC milieu rather than be constitutively expressed by the tumor cells, and it is a favorable prognostic factor for HCC.
Compressive strength and setting time determination of glass-ionomer cements incorporated with cetylpyridinium chloride and benzalkonium chloride. (2012)

Because of the relatively frequent occurrence of recurrent caries after a restorative treatment, and because of the huge number of cariogenic microorganisms present in the oral cavity, which present a potential risk factor regarding the development of new carious lesions, attention has increasingly been directed towards the therapeutic antimicrobial effects of restorative materials. The glass ionomer cements distinguish themselves as the most acceptable restorative materials possessing the positive characteristics of fluorine in the processes of remineralisation and antimicrobial action. In addition to the release of fluoride ions, GICs can potentially be used as templates for the release of other active antimicrobial components. The addition of antimicrobial compounds in the glass ionomer cements and analysis of their physical characteristics are very important especially for use in the posterior region of milk teeth. The aim of this study was to analyse the physical characteristics of ChemFlex and Fuji IX, conventional glass ionomer cements incorporated with the antimicrobial components Cetylpyridinium Chloride and Benzalkonium Chloride, through measurements of their setting times, and determination of their compressive strengths. Five samples of each glass ionomer with no antimicrobial compounds added were prepared--to serve as a control group; and collections of five samples of each cement with different concentrations of Cetylpyridinium Chloride and Benzalkonium Chloride--1%, 2% and 3%--added to them were also prepared--a total of 60 samples. The results of the analysis point out that it is possible to incorporate these antimicrobial agents in conventional GICs, and this is especially true when the added amount of the antimicrobial agents is 1%.
Effect of gap length on effective field strength (2002)

A micro-channel plate (MCP) was used to measure the minute emission current within the range of 1*10/sup -19/ A to 1*10/sup -14/ A in a high vacuum (1.3*10/sup -5/ Pa). By a Fowler-Nordheim plot, it is found that the effective field strength for initial electron emission is mostly constant between 10/sup 7/ and 10/sup 8/ V/cm under any gap length. The effective field strength is held constant between 10/sup 7/ and 10/sup 8/ V/cm, independent of the current under any gap length. With this result, a model which shows the choice of minute projection is suggested. In order to certify this model, an MCP phosphor-anode is used. As a result, it is found that the minute projections which emit electrons melt with heat and are chosen when the voltage rises. >
The Neuroprotective Effect of Klotho is Mediated via Regulation of Members of the Redox System (2014)

Generation of reactive oxygen species (ROS), leading to oxidative damage and neuronal cell death, plays an important role in the pathogenesis of neurodegenerative disorders, including Alzheimer disease. The present study aimed to examine the mechanism by which the anti-aging protein Klotho exerts neuroprotective effects against neuronal damage associated with neurodegeneration and oxidative stress. Pretreatment of rat primary hippocampal neurons and mouse hippocampal neuronal cell line HT22 with recombinant Klotho protected these cells from glutamate and oligomeric amyloid β (oAβ)-induced cytotoxicity. In addition, primary hippocampal neurons obtained from Klotho-overexpressing mouse embryos were more resistant to both cytotoxic insults, glutamate and oAβ, compared with neurons from wild-type littermates. An antioxidative stress array analysis of neurons treated with Klotho revealed that Klotho significantly enhances the expression of the thioredoxin/peroxiredoxin (Trx/Prx) system with the greatest effect on the induction of Prx-2, an antioxidant enzyme, whose increase was confirmed at the mRNA and protein levels. Klotho-induced phosphorylation of the PI3K/Akt pathway, a pathway important in apoptosis and longevity, was associated with sustained inhibitory phosphorylation of the transcription factor forkhead box O3a (FoxO3a) and was essential for the induction of Prx-2. Down-regulation of Prx-2 expression using a lentivirus harboring shRNA almost completely abolished the ability of Klotho to rescue neurons from glutamate-induced death and significantly, but not completely, inhibited cell death mediated by oAβ, suggesting that Prx-2 is a key modulator of neuroprotection. Thus, our results demonstrate, for the first time, the neuroprotective role of Klotho and reveal a novel mechanism underlying this effect.
Radiation forces on a dielectric sphere produced by highly focused cylindrical vector beams (2003)

Radiation forces on a dielectric sphere produced by highly focused generalized cylindrical vector beams are numerically studied in the Rayleigh scattering regime. Simulation results demonstrate that a highly focused radially polarized beam can be used to trap particles with index of refraction higher than the ambient, while a highly focused azimuthally polarized beam can be applied to trap particles with index of refraction lower than the ambient.
A Faraday current sensor using a novel multi-optical-loop sensing element (1995)

The design and the performance of an optically based, Faraday current sensing system employing a novel sensing element, using the so-called 'complementary reflections' scheme, is reported. This new design not only increases the overall sensitivity of the device by a factor of three, but also makes it easy to align the current measuring element in the system. With the use of this new optical element, a sensitivity of 6.57*10-5 rad A-1 and a minimum detectable current of 11.3 mA Hz-1/2 have been achieved.
Ambiguity Function Analysis for Orthogonal-LFM Waveform Based Multistatic Radar (2021)

Over the last decade, research on multistatic radar waveform design has attracted significant consideration among the radar system designers.Among the waveform design techniques, linear frequency modulated waveforms are widely used, but the problem associated with it is range Doppler coupling and complexity in achieving adequate pulse-to-pulse diversity. In this letter, an orthogonal linear frequency modulated (OLFM) waveform has been used as the transmitted waveforms, which has good correlation properties and large time bandwidth product. The ambiguity function (AF), which is the output of the matched filter, is used to analyze the target resolution capabilities of the OLFM waveforms. The mathematical expressions of the AF with OLFM waveforms for the multistatic architecture are represented based on the target fluctuations observed at the receiver. These expressions allow the ambiguity in resolving target position and velocity vectors for any transmitted waveform in the multistatic topology. The normalized cross-correlation value of the LFM waveforms is compared with the OLFM waveforms, which signify the isolation factor between two transmitted waveforms at the receiver. A performance comparison has been made based on the probability of target detection for various multistatic scenarios under numerous signal-to-noise ratio (SNR) conditions.
Binding of Human Immunodeficiency Virus Type I to the C3b/C4b Receptor CRt (CD35) and Red Blood Cells in the Presence of Envelope-Specific Antibodies and Complement (1994)

Immune complexes formed in vitro by incubating cell-free human immunodeficiency virus type 1 (HIV-1) with sera from infected or gp160-vaccinated persons, together with normal human serum as a source of complement, readily bound to K562 cells expressing recombinant human complement receptor type 1 (CR1). However, antibodies from seronegative persons had little or no effect. This effect was absent in the presence of heat-inactivated or C3-depleted normal human sera or when wild type K562 cells were used, confirming a requirement for complement and CR1. In additional experiments, complement alone targeted HIV-1 to CR1 on red blood cells, and envelope-specific antibodies increased this effect. These results demonstrate that envelope-specific antibodies promote HIV-1 immune complex formation with complement and that these complexes readily bind CR1 on cell surfaces.
Endothelial Function in Obstructive Sleep Apnea and Response to Treatment (2003)

Impaired endothelium-dependent vascular relaxation is a prognostic marker of atherosclerosis and cardiovascular disease. We evaluated endothelium-dependent flow-mediated dilation (FMD) and endothelium-independent nitroglycerin (NTG)-induced dilation of the brachial artery with Doppler ultrasound in 28 men with obstructive sleep apnea (OSA) and 12 men without OSA. Subjects with OSA (apnea-hypopnea index; mean +/- SD, 46.0 +/- 14.5) had lower FMD compared with subjects without OSA (5.3 +/- 1.7% vs. 8.3 +/- 1.0%, p < 0.001), and major determinants of FMD were the apnea-hypopnea index and age. There was no significant difference in NTG-induced dilation. Subjects with OSA were randomized to nasal continuous positive airway pressure (nCPAP) or observation for 4 weeks. Subjects on nCPAP had significant increase in FMD, whereas those on observation had no change (4.4% vs. -0.8%, difference of 5.2%, p < 0.001). Neither group showed significant change in NTG-induced vasodilation. Eight subjects who used nCPAP for over 3 months were reassessed on withdrawing treatment for 1 week. On nCPAP withdrawal, FMD became lower than during treatment (p = 0.02) and were similar to baseline values. Our findings demonstrated that men with moderate/severe OSA have endothelial dysfunction and treatment with nCPAP could reverse the dysfunction; the effect, however, was dependent on ongoing use.