gebhart/patrepeval huggingface dataset:
Elucidation of the Small RNA Component of the Transcriptome (2005)

Small RNAs play important regulatory roles in most eukaryotes, but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new microRNAs (miRNAs) were among the most abundant of the nonredundant set of more than 75,000 sequences, whereas more than half represented lower abundance small interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs.
The expression of HSP60 and HSP10 in large bowel carcinomas with lymph node metastase (2005)

HSP60 and HSP10 may have diagnostic and prognostic significance in the management of this tumour and their overexpression in tumoral cells may be functionally related to tumoral progression. We hypothesise that their expression in follicular and medullary cells of lymph nodes may be induced by formation of metastases. Further studies based on these observations could lead to a better understanding of the HSPs involvement in colorectal cancer progression, as well as other neoplasms.
A simple LAN performance measure (1994)

A simple formula is presented for the assessment of the performance of LAN's. It is based on the most essential performance parameters only and is found to be a quite accurate, conservative estimate when compared to the classical closed queuing model of a time sharing system.
Effect of a chimeric anti-ganglioside GD2 antibody on cell-mediated lysis of human neuroblastoma cells. (1991)

An anti-GD2 ganglioside human/mouse chimeric monoclonal antibody, ch14.18, like its murine counterpart, 14.G2a, was shown to bind to human neuroblastoma cells. This chimeric antibody proved to be more effective than 14.G2a in mediating the lysis of neuroblastoma cells with human effector cells, such as granulocytes and natural killer cells within the peripheral blood mononuclear cell population. A comparison of these two effector cell populations isolated from the same donor revealed granulocytes to be more effective than peripheral blood mononuclear cells in lysing neuroblastoma cells, which were coated with monoclonal antibody ch14.18. Addition of recombinant human granulocyte-macrophage colony-stimulatory factor increased ch14.18-mediated lysis of neuroblastoma cells by granulocytes but not by peripheral blood mononuclear cells. In fact, granulocytes were effective in mediating lysis of neuroblastoma cells coated with ch14.18 irrespective of whether they were obtained from normal adults or from neuroblastoma patients.
Electron micrograph of diffuse plaques. Initial stage of senile plaque formation in the Alzheimer brain. (1989)

The ultrastructure of diffuse plaques (devoid of both amyloid core and swollen neurites) in the frontal cortex of an Alzheimer brain was examined, using paired routine electron microscopic ultrathin sections and adjacent 0.4-micron-thick semithin sections. The semithin sections, treated with formic acid and beta protein immunostain, showed abundant diffuse plaques. In the adjacent ultrathin section, diffuse plaques usually showed some scattered bundles of amyloid fibrils between focally blurred membranes of cell process. The diffuse plaques were nearly undetectable without the semithin beta protein immunostained preparations, because the neuropils within these plaques appeared almost normal morphologically. Capillaries, which rarely appeared in the center of the diffuse plaques, demonstrated no amyloid fibrils in their walls. These findings suggest that in the initial stages of senile plaque formation amyloid fibrils are formed sporadically between cell processes, but not around the capillaries.
Diagonal transforms suffice for color constancy (2002)

The main result is to show that under the conditions imposed by the Maloney-Wandell color constancy algorithm, color constancy can be expressed in terms of a simple independent adjustment of the sensor responses, so long as the sensor space is first transformed to a new basis. The overall goal is to present a theoretical analysis connecting many established theories of color constancy. For the case where surface reflectances are two-dimensional and illuminants are three-dimensional, it is proved that perfect color constancy can always be solved for by an independent adjustment of sensor responses, which means that the color constancy transform can be expressed as a diagonal matrix. In addition to purely theoretical arguments, results from simulations of diagonal-matrix-based color constancy, in which the spectra of real illuminants and reflectances along with the human cone sensitivity functions were used, are presented. The simulations demonstrate that when the cone sensor space is transformed to its new basis in the appropriate manner, a diagonal matrix supports close to optimal color constancy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functionalized Acenes and Heteroacenes for Organic Electronics (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFunctionalized Acenes and Heteroacenes for Organic ElectronicsJohn E. AnthonyView Author Information Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055 Cite this: Chem. Rev. 2006, 106, 12, 5028–5048Publication Date (Web):November 23, 2006Publication History Received30 March 2006Published online23 November 2006Published inissue 1 December 2006https://pubs.acs.org/doi/10.1021/cr050966zhttps://doi.org/10.1021/cr050966zresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views23827Altmetric-Citations2549LEARN 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 SUBJECTS:Aromatic compounds,Hydrocarbons,Mobility,Reaction products,Thin films Get e-Alerts
A Common Polymorphism in the Bile Acid Receptor Farnesoid X Receptor Is Associated with Decreased Hepatic Target Gene Expression (2007)

The farnesoid X receptor (FXR or NR1H4) is an important bile-acid-activated, transcriptional regulator of genes involved in bile acid, lipid, and glucose homeostasis. Accordingly, interindividual variations in FXR expression and function could manifest as variable susceptibility to conditions such as cholesterol gallstone disease, atherosclerosis, and diabetes. We performed an FXR polymorphism discovery analysis of European-, African-, Chinese-, and Hispanic-Americans and identified two rare gain-of-function variants and a common single nucleotide polymorphism resulting in a G-1T substitution in the nucleotide adjacent to the translation initiation site (FXR*1B) with population allelic frequencies ranging from 2.5 to 12%. In cell-based transactivation assays, FXR*1B (-1T) activity was reduced compared with FXR*1A (-1G). This reduced activity for FXR*1B resulted from neither decreased translational efficiency nor the potential formation of a truncated translational variant. To further define the relevance of this polymorphism, gene expression was examined in a human liver bank to reveal that levels of the FXR target genes small heterodimer partner and organic anion transporting polypeptide 1B3 were significantly reduced in livers harboring an FXR*1B allele. These findings are the first to identify the presence of a common genetic variant in FXR with functional consequences that could contribute to disease risk or therapeutic outcomes.
Structure and function of the CD16:zeta:gamma complex expressed on human natural-killer cells. (1992)

Natural-killer (NK) cells are large granular lymphocytes involved in host defense against tumor cells and virally-infected cells. In addition to natural cytotoxicity, NK cells can effect antibody-dependent cytotoxicity mediated by CD16 (Fc gamma RIIIA alpha). It has recently been shown that CD16 is associated with disulfide-linked dimers composed of 2 homologous sub-units, zeta and gamma. These transducing molecules are also associated with other multimeric cell-surface receptors such as the T-cell antigen receptor (CD3:TCR) complex (zeta and gamma) and the high-affinity Fc receptor for IgE (Fc epsilon RI) expressed on basophils and mast cells (gamma). These results show that distinct cell-surface receptors utilize common transducing sub-units, and emphasize the homology between the CD16, Fc epsilon RI and CD3:TCR complexes. However within the lymphoid cells, the gamma-gamma homodimer is preferentially expressed in NK cells and cytotoxic T cells, suggesting that specific combinations of these transducing dimers might sub-serve distinct signal-transducing functions, and contribute to lymphocyte heterogeneity.
The pattern of activation antigen expression on T-lymphocyte subpopulation in infectious mononucleosis. (1991)

The peripheral blood mononuclear cells of patients with infectious mononucleosis (IM) have been characterized by the determination of activation antigens using a panel of 11 monoclonal antibodies (MoAbs) belonging to 9 clusters. The activation of CD8+ peripheral blood mononuclear cells of IM patients was found to be determined by HLA-DR and CD45RO MoAbs. The antibodies of the CD30, CD40 and CD70 termed antigens also showed an increased expression as compared to the controls. In contrast, the CD25, CD69, CD71, and CD45 antigens were expressed at a low rate on the surface of the CD8+ cells. We found, on the other hand, a very low percentage of B lymphocytes in the peripheral blood, which reflects on the virus caused antigen modulation and on the effectivity of activated CD8 cells with the characteristic expression of the above outlined markers in IM. In six asymptomatic patients, the percentage of CD8+HLA-DR+, as well as of CD8+CD45RO+ cells proved to be lower than that in the active phase of the disease. The number of B cells showed normal value in the clinically asymptomatic cases.
Macromol. Chem. Phys. 2/2013 (2013)

Back Cover: Polymer molecules (represented by the yellow lines) are coarse-grained into chains of fluctuating soft spheres (represented by the red blobs). They correspond to density clouds representing the spatial distribution of segments of the underlying microscopic sub-chains. Thus the nonbonded interactions can be efficiently calculated from the cloud overlap via a grid (the grey mesh). Further details can be found in the article by G. Zhang, K. C. Daoulas, and K. Kremer* on page 214.
Kinetic resolution of unnatural and rarely occurring amino acids: enantioselective hydrolysis of N-acyl amino acids catalyzed by acylase I (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic resolution of unnatural and rarely occurring amino acids: enantioselective hydrolysis of N-acyl amino acids catalyzed by acylase IH. Keith Chenault, Juergen Dahmer, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1989, 111, 16, 6354–6364Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://doi.org/10.1021/ja00198a055RIGHTS & PERMISSIONSArticle Views4917Altmetric-Citations261LEARN 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 InReddit PDF (1 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Application of American Land Use and Environmental Planning Techniques to Environmental Recovery in Emerging Economies: Fundamental Foundations from the New World to the Old (1992)

As we move into the twentieth century, environmental problems continue to receive a great deal of international attention and concern. It is recognized that the ongoing degradation of the world's natural resources combined with pollution and other environmental problems threatens the well being of us all. This article begins by exploring a number of regional environmental problems and looks particularly at the decay of the world's urban centers. An examination of the development of the planning process employed modernly in the United States follows. The authors propose that the application of the American land use planning techniques may lessen the environmental problems faced by the world's urban centers and that planning can play a substantial role in the remediation of environmental problems. In addition, the use of the planning techniques discussed by emerging economic regions, such as portions of Eastern Europe and Asia, will provide protection for the environment and natural resources without stifling the emerging communities economic development.
Transcriptional autoregulation by quorum sensing Escherichia coli regulators B and C (QseBC) in enterohaemorrhagic E. coli (EHEC) (2005)

The cell-to-cell communication system referred to as quorum sensing (QS) is based on the principle that bacteria secrete hormone-like compounds referred to as autoinducers. Upon reaching a threshold concentration, these autoinducers interact with transcription factors to regulate gene expression. We previously reported that enterohaemorrhagic Escherichia coli (EHEC), which is responsible for outbreaks of bloody diarrhoea, utilizes a QS system to regulate gene transcription. We have also previously shown that the quorum sensing E. coli regulators B and C (QseBC) may act as a two-component system to transcriptionally regulate the expression of flagella and motility. Here, using a reverse transcription polymerase chain reaction (RT-PCR), we show that qseBC are transcribed in an operon. Furthermore, using a qseBC::lacZ transcriptional fusion, we observed that QseB autoactivates its own transcription. In addition, the transcriptional start site of the qseBC promoter responsive to QseBC was mapped, and single-copy and multicopy deletion analyses were performed to determine the minimal region necessary for QseB transcriptional activation. These data allowed us to map an additional transcriptional start site for the qseBC promoter which may allow for a basal level of QseBC expression. Finally, electrophoretic mobility shift assays, competition experiments and DNase I footprints were performed and demonstrated that QseB directly binds to two sites in its own promoter. These results indicate that QseB may act to autoregulate its own transcription through binding to low- and high-affinity sites found in its promoter.
Cytokine Response Modifier A (CrmA) Inhibits Ceramide Formation in Response to Tumor Necrosis Factor (TNF)-α: CrmA and Bcl-2 Target Distinct Components in the Apoptotic Pathway (1997)

Proteases are now firmly established as major regulators of the "execution" phase of apoptosis. Here, we examine the role of proteases and their relationship to ceramide, a proposed mediator of apoptosis, in the tumor necrosis factor-alpha (TNF-alpha)-induced pathway of cell death. Ceramide induced activation of prICE, the protease that cleaves the death substrate poly(ADP-ribose) polymerase. Bcl-2 inhibited ceramide-induced death, but not ceramide generation. In contrast, Cytokine response modifier A (CrmA), a potent inhibitor of Interleukin-1 beta converting enzyme and related proteases, inhibited ceramide generation and prevented TNF-alpha-induced death. Exogenous ceramide could overcome the CrmA block to cell death, but not the Bcl-2 block. CrmA, however, did not inhibit the activation of nuclear factor (NF)-kappa B by TNF-alpha, demonstrating that other signaling functions of TNF-alpha remain intact and that ceramide does not play a role in the activation of NF-kappa B. These studies support a distinct role for proteases in the signaling/activation phase of apoptosis acting upstream of ceramide formation.
Swan-Ganz Catheter-Induced Severe Complications in Cardiac Surgery: Right Ventricular Perforation, Knotting, and Rupture of a Pulmonary Artery (2006)

The incidence of serious Swan-Ganz catheter complications in our patient population is comparable to the incidence reported in the literature. Based on these results the use of Swan-Ganz catheters in cardiac surgery is still justified since the rate of associated serious complications is extremely low. Despite the rare occurrence of serious complications and the infrequent fatal outcomes, the benefit of its use in selected cases of cardiac surgery overweight its associated complications.
Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics (2009)

The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements.
Progesterone for the prevention of preterm birth in women with multiple pregnancies: the AMPHIA trial (2007)

Current Controlled Trials ISRCTN40512715.
Differential contribution of necrosis and apoptosis in myocardial ischemia-reperfusion injury (2004)

Necrosis and apoptosis differentially contribute to myocardial injury. Determination of the contribution of these processes in ischemia-reperfusion injury would allow for the preservation of myocardial tissue. Necrosis and apoptosis were investigated in Langendorff-perfused rabbit hearts (n = 47) subjected to 0 (Control group), 5 (GI-5), 10 (GI-10), 15 (GI-15), 20 (GI-20), 25 (GI-25), and 30 min (GI-30) of global ischemia (GI) and 120 min of reperfusion. Myocardial injury was determined by triphenyltetrazolium chloride (TTC) staining, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL), bax, bcl2, poly(ADP)ribose polymerase (PARP) cleavage, caspase-3, -8, and -9 cleavage and activity, Fas ligand (FasL), and Fas-activated death domain (FADD). The contribution of apoptosis was determined separately (n = 42) using irreversible caspase-3, -8, and -9 inhibitors. Left ventricular peak developed pressure (LVPDP) and systolic shortening (SS) were significantly decreased and infarct size and TUNEL-positive cells were significantly increased (P < 0.05 vs. Control group) at GI-20, GI-25, and GI-30. Proapoptotic bax, PARP cleavage, and caspase-3 and -9 cleavage and activity were apparent at GI-5 to GI-30. Fas, FADD, and caspase-8 cleavage and activity were unaltered. Irreversible inhibition of caspase-3 and -9 activity significantly decreased (P < 0.05) infarct size at GI-25 and GI-30 but had no effect on LVPDP or SS. Myocardial injury results from a significant increase in both necrosis and apoptosis (P < 0.05 vs. Control group) evident by TUNEL, TTC staining, and caspase activity at GI-20. Intrinsic proapoptotic activation is evident early during ischemia but does not significantly contribute to infarct size before GI-25. The contribution of necrosis to infarct size at GI-20, GI-25, and GI-30 is significantly greater than that of apoptosis. Apoptosis is significantly decreased by caspase inhibition during early reperfusion, but this protection does not improve immediate postischemic functional recovery.
Xenon Provides Faster Emergence from Anesthesia than Does Nitrous Oxide-sevoflurane or Nitrous Oxide-isoflurane (1997)

Emergence from xenon anesthesia is two or three times faster than that from equal-MAC N2O+isoflurane or N2O+sevoflurane anesthesia.
Effects of Vinyl Ethylene Carbonate Additive on Elevated-Temperature Performance of Cathode Material in Lithium Ion Batteries (2008)

The addition of 2% vinyl ethylene carbonate (VEC) into LiPF6/EC + DMC electrolyte can significantly improve the cyclic performance of a LiNi0.8Co0.2O2/Li cell at elevated temperatures such as 50 °C. In situ electrochemical mass spectrometry (EMS) was used to investigate the gas evolution spectroscopy in the cell during a charge/discharge process with and without VEC additive. Fourier transform infrared (FTIR), ultraviolet−visible (UV−vis), and liquid nuclear magnetic resonance (NMR) spectroscopies were also carried out to investigate the reactions between various electrolyte components and VEC without the electrochemical reaction. We propose the possible polymerized products based on the spectroscopy and the acting mechanism of the VEC additives.
Mutation of the ptsG Gene Results in Increased Production of Succinate in Fermentation of Glucose by Escherichia coli (2001)

Escherichia coli NZN111 is blocked in the ability to grow fermentatively on glucose but gave rise spontaneously to a mutant that had this ability. The mutant carries out a balanced fermentation of glucose to give approximately 1 mol of succinate, 0. 5 mol of acetate, and 0.5 mol of ethanol per mol of glucose. The causative mutation was mapped to the ptsG gene, which encodes the membrane-bound, glucose-specific permease of the phosphotransferase system, protein EIICB(glc). Replacement of the chromosomal ptsG gene with an insertionally inactivated form also restored growth on glucose and resulted in the same distribution of fermentation products. The physiological characteristics of the spontaneous and null mutants were consistent with loss of function of the ptsG gene product; the mutants possessed greatly reduced glucose phosphotransferase activity and lacked normal glucose repression. Introduction of the null mutant into strains not blocked in the ability to ferment glucose also increased succinate production in those strains. This phenomenon was widespread, occurring in different lineages of E. coli, including E. coli B.