gebhart/patrepeval huggingface dataset:
The Chaperoning Properties of Mouse Grp170, a Member of the Third Family of Hsp70 Related Proteins (2003)

The 170 kDa glucose-regulated protein (grp170) is an endoplasmic reticulum resident protein that shares some sequence homology with both the hsp70 and hsp110 heat shock protein (hsp) families, yet is representative of a third and unique family of stress proteins. Despite observations indicating important roles in normal cellular functions, the in vitro chaperone properties of grp170 have not been rigorously examined. We have cloned mouse grp170 and expressed the recombinant protein in a baculovirus expression system. The function of recombinant grp170 was then assessed by determining its ability to bind to and prevent aggregation of heat-denatured luciferase. Grp170 maintains heat-denatured luciferase in a soluble state in the absence of ATP. In the presence of rabbit reticulocyte lysate, grp170 can refold and partially restore function to denatured luciferase. The chaperoning function of grp170 was also studied using domain deletion mutants, designed using the crystal structure of DnaK and the theoretical secondary structure of hsp110 as guides. Unlike hsp70 and hsp110, grp170 appears to have two domains capable of binding denatured luciferase and inhibiting its heat-induced aggregation. The two domains were identified as being similar to the classical beta-sandwich peptide binding domain and the C-terminal alpha-helical domain in hsp70 and hsp110. The ability of the C-terminal region to bind peptides is a unique feature of grp170.
Atorvastatin lowers portal pressure in cirrhotic rats by inhibition of RhoA/Rho-kinase and activation of endothelial nitric oxide synthase (2007)

In cirrhotic rats, atorvastatin inhibits hepatic RhoA/Rho-kinase signaling and activates the NO/PKG-pathway. This lowers intrahepatic resistance, resulting in decreased portal pressure. Statins might represent a therapeutic option for portal hypertension in cirrhosis.
Augmented and diminished spherands and scales of binding (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAugmented and diminished spherands and scales of bindingDonald J. Cram, George M. Lein, Takahiro Kaneda, Roger C. Helgeson, Carolyn B. Knobler, Emily Maverick, and Kenneth N. TruebloodCite this: J. Am. Chem. Soc. 1981, 103, 20, 6228–6232Publication Date (Print):October 1, 1981Publication History Published online1 May 2002Published inissue 1 October 1981https://pubs.acs.org/doi/10.1021/ja00410a050https://doi.org/10.1021/ja00410a050research-articleACS PublicationsRequest reuse permissionsArticle Views316Altmetric-Citations68LEARN 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
A Multistage Approach to Improve Performance of Computer-Aided Detection of Pulmonary Embolisms Depicted on CT Images: Preliminary Investigation (2010)

This study developed a computer-aided detection (CAD) scheme for pulmonary embolism (PE) detection and investigated several approaches to improve CAD performance. In the study, 20 computed tomography examinations with various lung diseases were selected, which include 44 verified PE lesions. The proposed CAD scheme consists of five basic steps: 1) lung segmentation; 2) PE candidate extraction using an intensity mask and tobogganing region growing; 3) PE candidate feature extraction; 4) false-positive (FP) reduction using an artificial neural network (ANN); and 5) a multifeature-based k-nearest neighbor for positive/negative classification. In this study, we also investigated the following additional methods to improve CAD performance: 1) grouping 2-D detected features into a single 3-D object; 2) selecting features with a genetic algorithm (GA); and 3) limiting the number of allowed suspicious lesions to be cued in one examination. The results showed that 1) CAD scheme using tobogganing, an ANN, and grouping method achieved the maximum detection sensitivity of 79.2%; 2) the maximum scoring method achieved the superior performance over other scoring fusion methods; 3) GA was able to delete "redundant" features and further improve CAD performance; and 4) limiting the maximum number of cued lesions in an examination reduced FP rate by 5.3 times. Combining these approaches, CAD scheme achieved 63.2% detection sensitivity with 18.4 FP lesions per examination. The study suggested that performance of CAD schemes for PE detection depends on many factors that include 1) optimizing the 2-D region grouping and scoring methods; 2) selecting the optimal feature set; and 3) limiting the number of allowed cueing lesions per examination.
Antitumor Effects of a Novel Phenylbutyrate-Based Histone Deacetylase Inhibitor, (S)-HDAC-42, in Prostate Cancer (2006)

(S)-HDAC-42 is a potent orally bioavailable inhibitor of HDAC, as well as targets regulating multiple aspects of cancer cell survival, which might have clinical value in prostate cancer chemotherapy and warrants further investigation in this regard.
Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. (1979)

The 3072-nucleotide-long sequence of a segment from the 88-min region of the Escherichia coli chromosome has been determined. The sequence covers the genes for ribosomal proteins L11 (rplK), LI (rplA), L10 (rplJ), and L7/L12 ((rplL), and the 5' end of the gene for the beta subunit of RNA polymerase (rpoB), along with the presumed regulatory regions for these genes. The probable locations of the promoter for the first two genes (the L11 operon) and the promoter for the latter three genes (the proximal part of the beta operon) have been identified. We have also found that the four ribosomal protein genes preferentially use codons that are recognized efficiently by the most abundant tRNA species. These and other features of the sequence results are discussed in relation to available information obtained from both in vitro and in vivo experiments on the expression of these ribosomal and RNA polymerase subunit genes.
Computer Modeling of Three-dimensional Structure of DNA-packaging RNA (pRNA) Monomer, Dimer, and Hexamer of Phi29 DNA Packaging Motor (2002)

A striking common feature in the maturation of all linear double-stranded DNA viruses is that their lengthy genome is translocated with remarkable velocity into the limited space within a preformed protein shell and packaged into near crystalline density. A DNA-translocating motor, powered by ATP hydrolysis, accomplishes this task, which would otherwise be energetically unfavorable. DNA-packaging RNA, pRNA, forms a hexameric complex to serve as a vital component of the DNA translocating motor of bacterial virus Phi29. The sequential action of six pRNA ensures continual function in the DNA translocation process. The Phi29 motor has been assembled with purified components synthesized by chemical or biotechnological approaches and is able to pump the viral DNA into the protein shell in vitro. pRNA dimers are the building blocks of the hexamer. The computer models of the three-dimensional structure of the motor was constructed based on experimental data derived from photoaffinity cross-linking by psoralen, phenphi (cis-Rh(1,10-phenanthroline)(9,10-phenan-threnequinone diimine)Cl(2)(+)), and azidophenacyl; chemical modification and chemical modification interference with dimethyl sulfate, 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate, and kethoxal; complementary modification; and nuclease probing by single- and double-stranded specific RNases. The shapes of these computer models are very similar to the published pRNA images of cryo-atomic force microscopy. pRNA hexamer docking with the connector crystal structure reveals a very impressive match with the available biochemical, genetic, and physical data.
Technology for Automated, Rapid, and Quantitative PCR or Reverse Transcription-PCR Clinical Testing (2005)

RNA yield and integrity on the GeneXpert are comparable to benchtop methods. Reproducibility of the GeneXpert data is similar to that seen with manual methods in our hands but may need improvement for some applications. The GeneXpert can perform RNA isolation, reverse transcription, and quantitative PCR in approximately 35 min and could therefore be used for intraoperative testing when applicable.
Regulation and crystallization of phosphorylated and dephosphorylated forms of truncated dimeric phenylalanine hydroxylase (1997)

Phenylalanine hydroxylase is regulated in a complex manner, including activation by phosphorylation. It is normally found as an equilibrium of dimeric and tetrameric species, with the tetramer thought to be the active form. We converted the protein to the dimeric form by deleting the C-terminal 24 residues and show that the truncated protein remains active and regulated by phosphorylation. This indicates that changes in the tetrameric quaternary structure of phenylalanine hydroxylase are not required for enzyme activation. Truncation also facilitates crystallization of both phosphorylated and dephosphorylated forms of the enzyme.
Impact of the German Lipoprotein Apheresis Registry (DLAR) on therapeutic options to reduce increased Lp(a) levels (2015)

The available numbers suggest in parts very good response by the participating centres to the DLAR. Unfortunately, there are also centres that have not documented any patients so far or LA treatments at all. The benchmark values for reduction rates in lipoprotein concentration required by the directives of the German Federal Joint Committee (G-BA) have all been met. The decrease in MACE and MANCE rates currently observed is very promising. However, the comparably short runtime of the registry does not allow for high confidence in the current results. Certainly, reliable data will be extractable in the coming years. Given the high interest expressed by European neighbours, the extension of the registry to the European level should be a future goal for the DLAR as well.
Cytokine-Dependent Modification of IL-12p70 and IL-23 Balance in Dendritic Cells by Ligand Activation of Vα24 Invariant NKT Cells (2009)

CD1d-restricted invariant NKT (iNKT) cells play crucial roles in various types of immune responses, including autoimmune diseases, infectious diseases and tumor surveillance. The mechanisms underlying their adjuvant functions are well understood. Nevertheless, although IL-4 and IL-10 production characterize iNKT cells able to prevent or ameliorate some autoimmune diseases and inflammatory conditions, the precise mechanisms by which iNKT cells exert immune regulatory function remain elusive. This study demonstrates that the activation of human iNKT cells by their specific ligand alpha-galactosylceramide enhances IL-12p70 while inhibiting the IL-23 production by monocyte-derived dendritic cells, and in turn down-regulating the IL-17 production by memory CD4(+) Th cells. The ability of the iNKT cells to regulate the differential production of IL-12p70/IL-23 is mainly mediated by a remarkable hallmark of their function to produce both Th1 and Th2 cytokines. In particular, the down-regulation of IL-23 is markedly associated with a production of IL-4 and IL-10 from iNKT cells. Moreover, Th2 cytokines, such as IL-4 and IL-13 play a crucial role in defining the biased production of IL-12p70/IL-23 by enhancement of IL-12p70 in synergy with IFN-gamma, whereas inhibition of the IFN-gamma-promoted IL-23 production. Collectively, the results suggest that iNKT cells modify the IL-12p70/IL-23 balance to enhance the IL-12p70-induced cell-mediated immunity and suppress the IL-23-dependent inflammatory pathologies. These results may account for the long-appreciated contrasting beneficial and adverse consequence of ligand activation of iNKT cells.
Mondriaan memory protection (2004)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.
Overexpression of 5-methylcytosine DNA glycosylase in human embryonic kidney cells EcR293 demethylates the promoter of a hormone-regulated reporter gene (2001)

We have shown that the DNA demethylation complex isolated from chicken embryos has a G(.)T mismatch DNA glycosylase that also possesses 5-methylcytosine DNA glycosylase (5-MCDG) activity. Herein we show that human embryonic kidney cells stably transfected with 5-MCDG cDNA linked to a cytomegalovirus promoter overexpress 5-MCDG. A 15- to 20-fold overexpression of 5-MCDG results in the specific demethylation of a stably integrated ecdysone-retinoic acid responsive enhancer-promoter linked to a beta-galactosidase reporter gene. Demethylation occurs in the absence of the ligand ponasterone A (an analogue of ecdysone). The state of methylation of the transgene was investigated by Southern blot analysis and by the bisulfite genomic sequencing reaction. Demethylation occurs downstream of the hormone response elements. No genome-wide demethylation was observed. The expression of an inactive mutant of 5-MCDG or the empty vector does not elicit any demethylation of the promoter-enhancer of the reporter gene. An increase in 5-MCDG activity does not influence the activity of DNA methyltransferase(s) when tested in vitro with a hemimethylated substrate. There is no change in the transgene copy number during selection of the clones with antibiotics. Immunoprecipitation combined with Western blot analysis showed that an antibody directed against 5-MCDG precipitates a complex containing the retinoid X receptor alpha. The association between retinoid receptor and 5-MCDG is not ligand dependent. These results suggest that a complex of the hormone receptor with 5-MCDG may target demethylation of the transgene in this system.
Genomic organization of mouse J kappa recombination signal binding protein (RBP-J kappa) gene. (1992)

We have isolated a cDNA clone (RBP-2) for the protein (RBP-J kappa) which binds to immunoglobulin recombination signals with 23-base pair spacers (Matsunami, N., Hamaguchi, Y., Yamamoto, Y., Kuze, K., Kangawa, K., Matsuo, H., Kawaichi, M., and Honjo, T. (1989) Nature 342, 934-937). During further screening of a cDNA library from the same mouse pre-B cell line (38B9), we have isolated a second cDNA clone (RBP-2N) which differs from RBP-2 in its 5' sequence. RNase protection assays indicated that the RBP-2N type mRNA was produced in 10-20 times the quantity as RBP-2 mRNA. To elucidate the relationship between these two mRNAs, we analyzed the genomic organization of the RBP-J kappa gene. Southern hybridization of mouse genomic DNA detected at least 7 EcoRI fragments hybridizing to an RBP-2 cDNA probe, suggesting a complex structure for the RBP-J kappa gene. Cloning of each EcoRI fragment revealed one functional RBP-J kappa gene and three related genes. The functional gene was composed of 11 exons and spanned at least 50 kilobase pairs. The sequence of exon 1 and its 5'-flanking region contained a GC-rich promoter-like region but no apparent TATA box. The initiation site of transcription was heterogeneous, and the two types of mRNA are produced from the same exon by transcription initiation at different sites and by different usage of splice signals. Two of the three related genes were processed pseudogenes with scattered stop codons. The other was also a processed gene with a sequence exactly the same as that of RBP-2, except that this gene lacked the sequence corresponding to the first exon of the functional gene.
Polymer-immobilized carbohydrate ligands: versatile chemical tools for biochemistry and medical sciences (1995)

N. V. Bovin and H.-J. Gabius, Chem. Soc. Rev., 1995, 24, 413 DOI: 10.1039/CS9952400413
Anomalous Hysteresis in Perovskite Solar Cells (2014)

Perovskite solar cells have rapidly risen to the forefront of emerging photovoltaic technologies, exhibiting rapidly rising efficiencies. This is likely to continue to rise, but in the development of these solar cells there are unusual characteristics that have arisen, specifically an anomalous hysteresis in the current-voltage curves. We identify this phenomenon and show some examples of factors that make the hysteresis more or less extreme. We also demonstrate stabilized power output under working conditions and suggest that this is a useful parameter to present, alongside the current-voltage scan derived power conversion efficiency. We hypothesize three possible origins of the effect and discuss its implications on device efficiency and future research directions. Understanding and resolving the hysteresis is essential for further progress and is likely to lead to a further step improvement in performance.
Meta-Evaluation of Worksite Health Promotion Economic Return Studies: 2012 Update (2012)

Two earlier editions of The Art of Health Promotion reported formal meta-evaluations of economic return studies of worksite health promotion programs. These meta-evaluations were among the most popular articles in our publishing history because practitioners, scientists, and employers continue to seek evidence on the economic effectiveness of workplace health promotion. The 2003 report examined 42 peer-reviewed journal articles that met the inclusion criteria, and the 2005 report examined 56 peer-reviewed journal articles. This 2012 update examines 10 additional studies that met the same set of inclusion criteria; four of the weaker studies were dropped, resulting in a total of 62 studies in this report. The meta-evaluation method used here is the same as used in the earlier reports and has been adapted from use with other preventive health programs, providing an overall summary and individual look at the quality of the peer reviewed articles that comprise the current scientific evidence of economic return for worksite health promotion and wellness programs. The term ‘‘meta-evaluation’’ as used in this article is defined as the application of a systematic review process to a set of evaluation studies with a similar purpose in order to determine their respective quality and to summarize their primary findings. It applies the formal meta-evaluation review process and methodology developed and refined by Windsor and Orleans and further modified by Boyd and Windsor to studies of multi-component worksite health promotion programs as defined by Heaney. This report include excerpts from the book Proof Positive: An Analysis of the Cost-Effectiveness of Worksite Wellness, seventh edition, revised and expanded in December of 2011, which applies the same methodology. This edition of The Art of Health Promotion addresses the following topics:
Three-dimensional IC trends (1986)

VLSI will be reaching to the limit of minimization in the 1990s, and after that, further increase of packing density or functions might depend on the vertical integration technology. Three-dimensional (3-D) integration is expected to provide several advantages, such as 1) parallel processing, 2) high-speed operation, 3) high packing density, and 4) multifunctional operation. Basic technologies of 3-D IC are to fabricate SOI layers and to stack them monolithically. Crystallinity of the recrystallized layer in SOI has increasingly become better, and very recently crystalaxis controlled, defect-free single-crystal area has been obtained in chip size level by laser recystallization technology. Some basic functional medels showing the concept or image of a future 3-D IC were fabricated in two or three stacked active layers. Some other proposals of subsystems in the application of 3-D structure, and the technical issues for realizing practical 3-D IC, i.e., the technology for fabricating high-quality SOI crystal on complicated surface topology, crosstalk of the signals between the stacked layers, total power consumption and cooling of the chip, will also be discussed in this paper.
Zebrafish Class 1 Phosphatidylinositol Transfer Proteins: PITPβ and Double Cone Cell Outer Segment Integrity in Retina (2010)

Phosphatidylinositol transfer proteins (PITPs) in yeast co-ordinate lipid metabolism with the activities of specific membrane trafficking pathways. The structurally unrelated metazoan PITPs (mPITPs), on the other hand, are an under-investigated class of proteins. It remains unclear what biological activities mPITPs discharge, and the mechanisms by which these proteins function are also not understood. The soluble class 1 mPITPs include the PITPalpha and PITPbeta isoforms. Of these, the beta-isoforms are particularly poorly characterized. Herein, we report the use of zebrafish as a model vertebrate for the study of class 1 mPITP biological function. Zebrafish express PITPalpha and PITPbeta-isoforms (Pitpna and Pitpnb, respectively) and a novel PITPbeta-like isoform (Pitpng). Pitpnb expression is particularly robust in double cone cells of the zebrafish retina. Morpholino-mediated protein knockdown experiments demonstrate Pitpnb activity is primarily required for biogenesis/maintenance of the double cone photoreceptor cell outer segments in the developing retina. By contrast, Pitpna activity is essential for successful navigation of early developmental programs. This study reports the initial description of the zebrafish class 1 mPITP family, and the first analysis of PITPbeta function in a vertebrate.
Characterization of a C5a receptor on human polymorphonuclear leukocytes (PMN). (1985)

Elucidation of the interactions between C5a and granulocytes is central to understanding the role of C5a in inflammation. In this study, interactions between C5a and PMN have been studied at two levels. Binding of human C5a to intact human cells has been characterized by using the radiolabeled ligand 125I-C5a. Binding is shown to be reversible, saturable, and to reach equilibrium in 60 to 90 min at 0 degrees C. Results show high affinity C5a binding sites with Kd = 2 X 10(-9) M and a range of 50,000 to 113,000 binding sites per PMN. These values for C5a receptors are comparable with the number of fMLP and LTB4 receptors on PMN. Binding of C5a to PMN fails to reach equilibrium at 37 degrees C because there is an irreversible loss of available surface receptors caused by an active internalization of the ligand-receptor complex. Interactions between C5a and human PMN were characterized further by cross-linking experiments, with the use of ethylene glycol bis succinimidylsuccinate (EGS). Cross-linking of 125I-C5a to intact PMN followed by subcellular fractionation revealed a single radioactive band present only in the plasma membrane fraction and visualized by autoradiography. Similar experiments resulted in a covalent linkage between 125I-C5a and a component in the isolated plasma membrane of PMN. The covalent complex containing C5a and a putative receptor has been visualized by autoradiography as a single 60,000 Mr complex on SDS-PAGE. The complex is not present when experiments are performed in the presence of excess unlabeled C5a or in the absence of EGS. Therefore, the putative receptor for C5a on human neutrophils is estimated to be approximately 48,000 Mr, assuming contribution of 12,000 to 13,000 daltons by the ligand 125I-C5a.