gebhart/patrepeval huggingface dataset:
Chromosome 1q21 amplification and oncogenes in hepatocellular carcinoma (2010)

Hepatocellular carcinoma (HCC) is among the most lethal of human malignancies. During human multistep hepatocarcinogenesis, genomic gain represents an important mechanism in the activation of proto-oncogenes. In many circumstances, activated oncogenes hold clinical implications both as prognostic markers and targets for cancer therapeutics. Gain of chromosome 1q copy is one of the most frequently detected alterations in HCC and 1q21 is the most frequent minimal amplifying region (MAR). A better understanding of the physiological and pathophysiological roles of target genes within 1q21 amplicon will significantly improve our knowledge in HCC pathogenesis, and may lead to a much more effective management of HCC bearing amplification of 1q21. Such knowledge has long term implications for the development of new therapeutic strategies for HCC treatment. Our research group and others, focused on the identification and characterization of 1q21 target genes such as JTB, CKS1B, and CHD1L in HCC progression. In this review, we will summarize the current scientific knowledge of known target genes within 1q21 amplicon and the precise oncogenic mechanisms of CHD1L will be discussed in detail.
Unit Cell Constants of α-Copper Phthalocyanine (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnit Cell Constants of α-Copper PhthalocyanineMark T. Robinson and Gilbert E. KleinCite this: J. Am. Chem. Soc. 1952, 74, 24, 6294–6295Publication Date (Print):December 1, 1952Publication History Published online1 May 2002Published inissue 1 December 1952https://pubs.acs.org/doi/10.1021/ja01144a520https://doi.org/10.1021/ja01144a520research-articleACS PublicationsRequest reuse permissionsArticle Views272Altmetric-Citations58LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Program optimization using indexed and recursive data structures (2002)

This paper describes a systematic method for optimizing recursive functions using both indexed and recursive data structures. The method is based on two critical ideas: first, determining a minimal input increment operation so as to compute a function on repeatedly incremented input; second, determining appropriate additional values to maintain in appropriate data structures, based on what values are needed in computation on an incremented input and how these values can be established and accessed. Once these two are determined, the method extends the original program to return the additional values, derives an incremental version of the extended program, and forms an optimized program that repeatedly calls the incremental program. The method can derive all dynamic programming algorithms found in standard algorithm textbooks. There are many previous methods for deriving efficient algorithms, but none is as simple, general, and systematic as ours.
Le président de Brosses et les cultes de l'ancienne Égypte (1969)

David Madeleine-V. Le président de Brosses et les cultes de l'ancienne Égypte. In: Journal des savants, 1969, n°3. pp. 158-172.
Loss of membrane-dependent factor Va cleavage: a mechanistic interpretation of the pathology of protein CVermont (1994)

Clinical manifestations of arterial and venous thrombosis in a family with protein C deficiency was associated with two mutations in the light chain of protein C: Glu20-->Ala and Val34-->Met. Further studies showed that the mutation Glu20-->Ala which eliminated a gamma- carboxylation site was exclusively responsible for the anticoagulant defect of activated protein C (APC). Membrane-bound human factor Va is inactivated by APC after two sequential cleavages of the heavy chain at Arg506 and Arg306. Human factor Va inactivation by human recombinant APC (rAPC) and a mutant molecule with an alanine instead of a glutamic acid at position 20 (rAPC(gamma 20A)) was investigated in the presence and absence of phospholipid vesicles. During a 2-hour incubation period of the cofactor with either rAPC or rAPC(gamma 20A). In the absence of a membrane surface, factor Va is cleaved quantitatively at Arg506 and retains approximately 60% of its initial cofactor activity. After a 2- hour incubation period with rAPC membrane-bound factor Va has no cofactor activity, whereas in the presence of a membrane surface and rAPC(gamma 20A) factor Va retains 60% of its initial cofactor activity. The completed loss in factor Va cofactor activity upon incubation of the membrane-bound cofactor with phospholipid vesicles and rAPC is associated with cleavages at Arg506 and Arg306, whereas membrane-bound factor Va cleavage at Arg306 by rAPC(gamma 20A) is impaired, resulting in a cofactor that is cleaved at Arg506. Slow cleavage at Arg306 occurs when membrane-bound factor Va is incubated with rAPC(gamma 20A) and only small amounts of fragments of M(r) = 45,000 and 30,000 are noticed. Our data show that the genetic defect which leads to the absence of a gamma-carboxylation site at Glu20 impairs membrane binding of human APC, which in turn is required for cleavage of factor Va at Arg306 and inactivation of the cofactor. The consequence of impaired membrane-dependent cleavage at Arg306 is manifested in vivo by venous and arterial thrombosis.
Causes and effects of foaming in anaerobic sludge digesters (1997)

Full scale anaerobic digesters treating mixed sludge containing primary sludge and thickened waste activated sludge were investigated for causes and effects of foaming. Sludge samples were collected from different depths of two full scale digesters, one gas-mixed, and the other mechanically-mixed, to determine the extent of foaming and its effects on anaerobic digestion; both digesters were fed the same feed sludge (3.4% TS) and at the same feed rate (about 2.2 kg TS/m3.day). The average depth of the surface foam layer in the gas-mixed and mechanically-mixed digester were 2.4 and 1.3 m respectively. Higher total solids concentrations were found at the surface (about 5% TS) than those found at the bottom (about 2% TS) in both gas-mixed and mechanically-mixed digesters, indicating an inverse total solids profile. Presence of excessive levels of Nocardia filaments (&gt;106 number/g VSS) in the activated sludge caused thicker foam layer at the surface, and this effect was more pronounced in the gas-mixed digester than in the mechanically-mixed digester. Gas-mixed digester (0.74 m3/kg VS destroyed) produced less sludge gas than the mechanically-mixed digester (0.93 m3/kg VS destroyed), however, gas-mixed digester (62% VS reduction) destroyed more volatile solids than the mechanically-mixed digester (54% VS reduction). These results indicate that gas-mixed digesters are more prone to foaming than mechanically-mixed digesters, and that the foaming can increase when excessive levels of Nocardia filaments are present in the feed sludge causing decreased digester performance.
Submicrometer fully self-aligned AlGaAs/GaAs Heterojunction bipolar transistor (1987)

A novel submicrometer fully self-aligned AlGaAs/GaAs heterojunction bipolar transistor (HBT) for reducing parasitic capacitances and resistances is proposed. The fabrication process utilizes SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> sidewalls for defining base electrode width and separating this electrode from both emitter and collector electrodes. Measured common-emitter current gain β for a fabricated HBT with 0.6 × 10-µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> emitter dimension and 0.7 × 10-µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> × 2 base dimension is 26 at 9 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> -A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> collector current density.
A Computational Study of Multicomponent Orbital Interactions during the Cyclization of Silyl, Germyl, and Stannyl Radicals onto C−N and C−O Multiple Bonds (2008)

BHandHLYP/6-311G** and BHandHLYP/DZP computations of the potential surface of Si-, Ge-, and Sn-radical cyclizations onto the imine double bond reveal that these reactions proceed through simultaneous SOMO --> pi*, LP(N) --> SOMO, and LP(N) --> sigma* interactions. Such multicomponent orbital interactions are responsible for the regioselectivity in these radical cyclizations, where the nucleophilic radical unexpectedly attacks the more electron-rich end of the pi system. Less nucleophilic heteroatoms, for example, the nitrogen atom in nitriles or the oxygen atom in carbonyl compounds, show reduced LP interactions with the radical center in the respective transition states, so that these reactions predominantly occur in the "classical" fashion and with the expected regioselectivities of nucleophilic radicals through SOMO --> pi* interactions. This supports the hypothesis that Si-, Ge- and, to a lesser extent, Sn-radicals are ambiphilic in nature and that the unpaired electron is not necessarily the most reactive site in a radical but can act as an observer of a nucleophilic attack at the radical center.
Human CD4<sup>+</sup> lymphocytes for antigen quantification: Characterization using conventional flow cytometry and mass cytometry (2012)

To transform the linear fluorescence intensity scale obtained with fluorescent microspheres to an antibody bound per cell (ABC) scale, a biological cell reference material is needed. Optimally, this material should have a reproducible and tight ABC value for the expression of a known clinical reference biomarker. In this study, we characterized commercially available cryopreserved peripheral blood mononuclear cells (PBMCs) and two lyophilized PBMC preparations, Cyto-Trol and PBMC-National Institute for Biological Standard and Control (NIBSC) relative to freshly prepared PBMC and whole blood samples. It was found that the ABC values for CD4 expression on cryopreserved PBMC were consistent with those of freshly obtained PBMC and whole blood samples. By comparison, the ABC value for CD4 expression on Cyto-Trol is lower and the value on PBMC-NIBSC is much lower than those of freshly prepared cell samples using both conventional flow cytometry and CyTOF™ mass cytometry. By performing simultaneous surface and intracellular staining measurements on these two cell samples, we found that both cell membranes are mostly intact. Moreover, CD4(+) cell diameters from both lyophilized cell preparations are smaller than those of PBMC and whole blood. This could result in steric interference in antibody binding to the lyophilized cells. Further investigation of the fixation effect on the detected CD4 expression suggests that the very low ABC value obtained for CD4(+) cells from lyophilized PBMC-NIBSC is largely due to paraformaldehyde fixation; this significantly decreases available antibody binding sites. This study provides confirmation that the results obtained from the newly developed mass cytometry are directly comparable to the results from conventional flow cytometry when both methods are standardized using the same ABC approach.
Carbonyl sulfide exchange in soils for better estimates of ecosystem carbon uptake (2016)

Abstract. Carbonyl sulfide (COS) measurements are one of the emerging tools to better quantify gross primary production (GPP), the largest flux in the global carbon cycle. COS is a gas with a similar structure to CO2; COS uptake is thought to be a proxy for GPP. However, soils are a potential source or sink of COS. This study presents a framework for understanding soil–COS interactions. Excluding wetlands, most of the few observations of isolated soils that have been made show small uptake of atmospheric COS. Recently, a series of studies at an agricultural site in the central United States found soil COS production under hot conditions an order of magnitude greater than fluxes at other sites. To investigate the extent of this phenomenon, soils were collected from five new sites and incubated in a variety of soil moisture and temperature states. We found that soils from a desert, an oak savannah, a deciduous forest, and a rainforest exhibited small COS fluxes, behavior resembling previous studies. However, soil from an agricultural site in Illinois, > 800 km away from the initial central US study site, demonstrated comparably large soil fluxes under similar conditions. These new data suggest that, for the most part, soil COS interaction is negligible compared to plant uptake of COS. We present a model that anticipates the large agricultural soil fluxes so that they may be taken into account. While COS air-monitoring data are consistent with the dominance of plant uptake, improved interpretation of these data should incorporate the soil flux parameterizations suggested here.
The Mechanism of Budding of Retroviruses from Cell Membranes (2009)

Retroviruses have evolved a mechanism for the release of particles from the cell membrane that appropriates cellular protein complexes, referred to as ESCRT-I, -II, -III, normally involved in the biogenesis of multivesicular bodies. Three different classes of late assembly (L) domains encoded in Gag, with core sequences of PPXY, PTAP, and YPXL, recruit different components of the ESCRT machinery to form a budding complex for virus release. Here, we highlight recent progress in identifying the role of different ESCRT complexes in facilitating budding, ubiquitination, and membrane targeting of avian sarcoma and leukosis virus (ASLV) and human immunodeficiency virus, type 1 (HIV-1). These findings show that retroviruses adopt parallel budding pathways by recruiting different host factors from common cellular machinery for particle release.
THE DEVELOPMENT OF SERUM‐FREE HORMONE‐SUPPLEMENTED MEDIA FOR PRIMARY KIDNEY CULTURES AND THEIR USE IN EXAMINING RENAL FUNCTIONS* (1981)

We have demonstrated the primary kidney cultures and defined medium can be used for several purposes. First, primary kidney cultures can be examined in defined medium to evaluate the physiological significance of studies made with established kidney cell lines. Secondly, new kidney epithelial cell culture systems can be developed, using primary cultures and defined medium. The studies presented here have demonstrated several possible approaches towards these ends. First, a hormone-supplemented serum-free medium (Medium K-1) developed for an established dog kidney epithelial cell line (MDCK) was used to grow primary cultures of baby mouse kidney epithelial cells without fibroblast overgrowth. The primary cultures of baby mouse cells not only grew in response to each of the five supplements in Medium K-1, but also possessed several of the differentiated kidney functions observed in the MDCK cell line. Secondly, defined media were developed for primary cultures of rabbit kidney epithelial cells directly. The rabbit cells were shown to require a different set of supplements than MDCK cells to attain optimal growth. Furthermore primary cultures derived from purified rabbit proximal tubules required a different set of supplements than primary cultures derived from unpurified rabbit kidney tissue. These new primary culture systems should prove invaluable in examining renal transport functions in vitro.
压缩空气供应系统的现代化改造——利用热再生干燥器使企业能够利用高效、节能的设备进行生产 (2009)

厂址位于德国BrunsbQtteI市的Sasol公司是一家生产脂肪醇和氧化铝的企业，在他们的许多流程生产工艺中需要的是纯净且干燥的压缩空气。目前，Sasol公司正在投资扩大企业的生产能力，同时也在仔细的考察如何提高能源利用率。因此在他们新建的空压机站中新增了一台10000m^3／h的涡轮压缩机和具有热再生的吸附式干燥器。
An Antiviral Peptide Inhibitor That Is Active against Picornavirus 2A Proteinases but Not Cellular Caspases (2006)

The replication of many viruses is absolutely dependent on proteolytic cleavage. Infected cells also use this biological mechanism to induce programmed cell death in response to viral infection. Specific inhibitors for both viral and cellular proteases are therefore of vital importance. We have recently shown that the general caspase inhibitor zVAD.fmk inhibits not only caspases, but also the 2Apro of human rhinoviruses (HRVs) (L. Deszcz, J. Seipelt, E. Vassilieva, A. Roetzer, and E. Kuechler, FEBS Lett. 560:51-55, 2004). Here, we describe a derivative of zVAD.fmk that inhibits HRV2 2Apro but that has no effect on caspase 9. This gain in specificity was achieved by replacing the aspartic acid of zVAD.fmk with methionine to generate zVAM.fmk. Methionine was chosen because an oligopeptide with methionine at the P1 position was a much better substrate than an oligopeptide with an alanine residue, which is found at the P1 position of the wild-type HRV2 2Apro cleavage site. zVAM.fmk inhibits the replication of HRV type 2 (HRV2), HRV14, and HRV16. In contrast to zVAD.fmk, however, zVAM.fmk did not inhibit apoptosis induced by puromycin in HeLa cells. zVAM.fmk inhibited in vitro the intermolecular cleavage of eukaryotic initiation factor 4GI (eIF4GI) by HRV2 2Apro at nanomolar concentrations. However, much higher concentrations of zVAM.fmk were required to inhibit HRV14 2Apro cleavage of eIF4GI. In contrast, intramolecular self-processing of HRV14 2Apro was much more susceptible to inhibition by zVAM.fmk than that of HRV2 2Apro, suggesting that zVAM.fmk inhibits HRV2 and HRV14 replication by targeting different reactions of the same proteinase.
Statin Use and Microbleeds in Patients With Spontaneous Intracerebral Hemorrhage (2012)

Statin use in patients with ICH is independently associated with MB, especially csMB. Future studies are needed to confirm our findings and to investigate whether csMB can serve as a surrogate marker for ICH risk in statin-treated patients.
Differential expression of related HLA class II DQ beta genes caused by nucleotide variation in transcriptional regulatory elements (1992)

HLA class II genes comprise a large multigene family with intra- and interlocus variation in structure and expression. Within this family of related genes, the HLA-DX alpha and beta loci (HLA DQA2 and DQB2) are highly homologous to functional HLA-DQ loci (HLA DQA1 and DQB1) but are frequently termed pseudogenes because DX gene transcription has not been observed, even in cells expressing HLA-DQ. Analysis of upstream transcriptional regulatory elements for the DX beta and DQ beta genes identified a high degree of nucleotide homology, consistent with their derivation from a common ancestral class II gene. However, transient expression assays with plasmids utilizing promoter elements from the DX beta gene had no activity in transfected human B cells, in contrast to homologous DQ beta sequences. Reciprocal exchange of specific sequences from the DQ beta gene with those of the DX beta gene restored expression to wild-type DQ beta levels, as did mutagenesis of only three DX-specific nucleotides in the upstream regulatory region. These three nucleotides mark two binding sites for distinct nuclear DNA-binding proteins that differentially recognize DQ beta and DX beta sequences. Transcription of these genes is critically dependent on interactions between these two upstream regulatory region sites which distinguish DX beta from its closely related homologue, DQ beta.
Ultra-Efficient Epitaxial Liftoff Solar Cells Exploiting Optical Confinement in the Wave Limit (1999)

Among the technologies for integrating GaAs devices with Si VLSI chips, epitaxial liftoff (ELO) is conspicuous for maintaining the quality of the single crystal epitaxial GaAs films. Traditionally, ELO is implemented in aqueous HF solution. It would be cleaner and simpler if ELO could be implemented in a vapor process. In this article, we will present the potential improvements in the epitaxial liftoff process by using a vapor phase etch to undercut thin films.
Hepatic acute phase induction of murine  -galactoside  2,6 sialyltransferase (ST6Gal I) is IL-6 dependent and mediated by elevation of Exon H--containing class of transcripts (1999)

Hepatic expression of CMP-NeuAc:Galβ1,4GlcNAc α2,6-sialyltransferase (ST6Gal I) is induced as part of the acute phase response in mammals by mechanisms that remain poorly understood. Previous work suggests that murine liver ST6Gal I mRNA contains an additional and novel region that is not found on ST6Gal I mRNA from human HepG2 hepatoma cells and from rat liver. This novel region, residing 5′ of the common Exon I sequence, is encoded by a discrete upstream exon, Exon H. Here we provide evidence that the Exon H—containing transcript is the murine counterpart of the human and rat ST6Gal I mRNAs transcribed from the hepatic-specific promoter, P1. Exon H—containing ST6Gal I mRNA is expressed in all three mice strains examined: balb/c, C57B46, and 129Sv. Furthermore, murine RNA tissue survey indicates that presence of Exon H—containing transcripts is restricted to the liver. When mice are subjected to subcutaneous injection of turpentine to elicit the hepatic acute phase response, greater than 4-fold elevation in liver ST6Gal I mRNA was observed. Consistent with the view that Exon H—containing transcripts is regulated by the murine P1 promoter, 5′-RACE analysis indicates that the majority of these transcripts contains the Exon H sequence. This is consistent with the view that Exon H—containing transcripts are regulated by the murine P1 region. To assess the mechanism of ST6Gal I response in the hepatic acute phase reaction, mice harboring lesions in both alleles of the IL-6 gene were examined. IL-6(−/−) animals expressed normal levels of ST6Gal I mRNA in liver, with Exon H—containing transcripts remaining the predominant mRNA isoform. However, hepatic ST6Gal I is not elevated upon turpentine injection in the IL-6(−/−) animals. These results indicate that ST6Gal I induction in mouse liver during the acute phase reaction is mediated predominantly by the IL-6 pathway, and results in the induction of the Exon H—containing class of ST6Gal I mRNA that is specific to the liver.
Generation of a Recombinant, Membrane-targeted Form of the Complement Regulator CD59 (2003)

Inappropriate activation of complement contributes to pathology in diverse inflammatory diseases. Soluble recombinant forms of the natural cell membrane regulators of complement are effective in animal models and some human diseases. However, their use is limited for reasons related to cost, short half lives, and propensity to cause unwanted systemic effects. Some of these limitations may be overcome by use of bacterial expression systems, specific targeting moieties, and judicious choice of regulator. Here we describe the application of these strategies to the generation of a membrane-targeted form of CD59. A recombinant soluble form of rat CD59, comprising the first 71 residues of the mature protein and missing the membrane-anchoring signal, was expressed in bacteria, purified, and refolded in a fully active form. The protein was coupled through its carboxyl terminus to a short, synthetic address tag that confers membrane binding activity. Attachment of the membrane address tag markedly increased complement-inhibitory activity assessed in vitro in hemolysis assays. Intra-articular administration of the tagged agent markedly suppressed disease in a model of rheumatoid arthritis in Lewis rats. This novel type of agent, termed sCD59-APT542, offers for the first time the prospect of efficient and specific inhibition of membrane attack complex activity in vivo.