gebhart/patrepeval huggingface dataset:
Copolymerization of carbon dioxide and epoxide (1969)

Journal of Polymer Science Part B: Polymer LettersVolume 7, Issue 4 p. 287-292 Article Copolymerization of carbon dioxide and epoxide Shohei Inoue, Shohei Inoue Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this authorHideomi Koinuma, Hideomi Koinuma Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this authorTeiji Tsuruta, Teiji Tsuruta Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this author Shohei Inoue, Shohei Inoue Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this authorHideomi Koinuma, Hideomi Koinuma Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this authorTeiji Tsuruta, Teiji Tsuruta Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Tokyo, JapanSearch for more papers by this author First published: April 1969 https://doi.org/10.1002/pol.1969.110070408Citations: 840AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume7, Issue4April 1969Pages 287-292 RelatedInformation
Gene overlap and site-specific attenuation of transcription of the viral polymerase L gene of human respiratory syncytial virus. (1987)

Sequence analysis of the gene encoding polymerase L protein of respiratory syncytial virus showed that L-gene transcription initiates within its upstream neighbor, the gene encoding the 22-kDa protein 22K. This is an exception to the canonical mode of sequential transcription of nonoverlapping genes described for other nonsegmented negative-strand RNA viruses. As a consequence of the gene overlap, the termination/polyadenylylation signal for the 22K gene is located at nucleotides 56-68 within the L gene. L-gene transcription yielded two RNAs: an abundant, truncated, polyadenylylated transcript resulting from termination at the internal signal and a markedly less abundant large polyadenylylated transcript representing the complete L gene. This result showed that the internal termination/polyadenylylation signal is an attenuator of L-gene transcription.
Soluble MHC-Peptide Complexes Induce Rapid Death of CD8+ CTL (2005)

Soluble MHC-peptide (pMHC) complexes, commonly referred to as tetramers, are widely used to enumerate and to isolate Ag-specific CD8(+) CTL. It has been noted that such complexes, as well as microsphere- or cell-associated pMHC molecules compromise the functional integrity of CTL, e.g., by inducing apoptosis of CTL, which limits their usefulness for T cell sorting or cloning. By testing well-defined soluble pMHC complexes containing linkers of different length and valence, we find that complexes comprising short linkers (i.e., short pMHC-pMHC distances), but not those containing long linkers, induce rapid death of CTL. This cell death relies on CTL activation, the coreceptor CD8 and cytoskeleton integrity, but is not dependent on death receptors (i.e., Fas, TNFR1, and TRAILR2) or caspases. Within minutes of CTL exposure to pMHC complexes, reactive oxygen species emerged and mitochondrial membrane depolarized, which is reminiscent of caspase-independent T cell death. The morphological changes induced during this rapid CTL death are characteristic of programmed necrosis and not apoptosis. Thus, soluble pMHC complexes containing long linkers are recommended to prevent T cell death, whereas those containing short linkers can be used to eliminate Ag-specific CTL.
Effectiveness of Generic Fixed-Dose Combinations of Highly Active Antiretroviral Therapy for Treatment of HIV Infection in India (2004)

Fixed-dose formulations of NVP-based combination therapy are safe and produced durable clinical and immunologic benefit.
Neuropilin-1 in Transplantation Tolerance (2013)

In the immune system, Neuropilin-1 (Nrp1) is a molecule that plays an important role in establishing the immunological synapse between dendritic cells (DCs) and T cells. Recently, Nrp1 has been identified as a marker that seems to distinguish natural T regulatory (nTreg) cells, generated in the thymus, from inducible T regulatory (iTreg) cells raised in the periphery. Given the crucial role of both nTreg and iTreg cells in the generation and maintenance of immune tolerance, the ability to phenotypically identify each of these cell populations in vivo is needed to elucidate their biological properties. In turn, these properties have the potential to be developed for therapeutic use to promote immune tolerance. Here we describe the nature and functions of Nrp1, including its potential use as a therapeutic target in transplantation tolerance.
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids (2010)

It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.
Ionic Self-Assembled Redox-Active Polyelectrolyte−Ferrocenyl Surfactant Complexes:  Mesomorphous Structure and Electrochemical Behavior (2007)

Redox-active polyelectrolyte−surfactant complexes (PSC) were prepared via the ionic self-assembly of sodium poly(styrenesulfonate) (PSS) and ferrocenyl surfactant, n-alkyl (ferrocenylmethyl)ammonium bromide (Fcn, n = 8, 12, 16, where n is the carbon number of the alkyl chain), in solution. The PSS−Fcn complex exhibited an ordered lamellar mesomorphous structure with the long period of d = 2.49, 2.94, and 3.74 nm for PSS−Fc8, PSS−Fc12, and PSS−Fc16, respectively. With increasing the length of surfactant alkyl chain, the stacking order was improved. Interestingly, in the solid complex, the ferrocenyl moieties formed H-aggregation showing an increase in the π−π* energy transfer of cyclopentadienes in the ferrocene moieties as known from the blue shift in the UV spectrum. These complexes showed higher thermal stability compared with their components due to the ionic interaction. Cyclic voltammogram (CV) measurements indicated that the electrode process of these redox-active complex films was diffusion-controlled and almost reversible or quasi-reversible at scan rates ranging from 0.02 to 4 V/s. Though the reversibility of the electrode process became worse for the PSS−Fc12 and PSS−Fc16 films than that for the PSS−Fc8, the redox peak current |ip| increased with increasing surfactant tail length in the complex because the more ordered packing in the complex film formed by longer surfactant tails was more favorable for the electrolyte diffusion and charge transfer as judged on values of the surface charge-transfer coefficient αnα, standard rate constant Ks, and apparent diffusion coefficient Dapp reflecting the electrode kinetics. The present results demonstrate that the electrochemical activity of the redox-active poly(styrenesulfonate)−ferrocenyl surfactant complex can be easily tuned by changing the surfactant tail length. Our work provides a simple and facile approach to the preparation of redox-active polymers with ordered mesomorphous structure by the ionic self-assembly.
Klotho Gene Deficiency Causes Salt-Sensitive Hypertension via Monocyte Chemotactic Protein-1/CC Chemokine Receptor 2–Mediated Inflammation (2014)

Klotho (KL) is a newly discovered aging suppressor gene. In mice, the KL gene extends the lifespan when overexpressed and shortens the lifespan when disrupted. This study investigated if KL deficiency affects BP and salt sensitivity using KL mutant heterozygous (+/-) mice and wild-type (WT) mice (9 weeks of age, 16 mice per group). Notably, systolic BP in KL(+/-) mice began to increase at the age of 15 weeks, reached a peak level at the age of 17 weeks, and remained elevated thereafter, whereas systolic BP remained consistent in WT mice. High salt (HS) intake further increased BP in KL(+/-) mice but did not affect BP in WT mice. Blockade of CC chemokine receptor 2 (CCR2), involved in monocyte chemotaxis, by a specific CCR2 antagonist (INCB3284) abolished the HS-induced increase in BP in KL(+/-) mice. Furthermore, HS loading substantially increased the expression of monocyte chemotactic protein-1 and the infiltration of macrophages and T cells in kidneys in KL(+/-) mice, and treatment with INCB3284 abolished these effects. Treatment of KL(+/-) mice with INCB3284 also attenuated the increased renal expressions of serum glucocorticoid-regulated kinase 1, thiazide-sensitive NaCl cotransporter, and ATP synthase β along with the renal structural damage and functional impairment induced by HS loading. In conclusion, KL deficiency caused salt-sensitive hypertension and renal damage by CCR2-mediated inflammation.
β-Secretases, Alzheimer’s Disease, and Down Syndrome (2012)

Individuals with Down Syndrome (DS), or trisomy 21, develop Alzheimer's disease (AD) pathology by approximately 40 years of age. Chromosome 21 harbors several genes implicated in AD, including the amyloid precursor protein and one homologue of the β-site APP cleaving enzyme, BACE2. Processing of the amyloid precursor protein by β-secretase (BACE) is the rate-limiting step in the production of the pathogenic Aβ peptide. Increased amounts of APP in the DS brain result in increased amounts of Aβ and extracellular plaque formation beginning early in life. BACE dysregulation potentially represents an overlapping biological mechanism with sporadic AD and a common therapeutic target. As the lifespan for those with DS continues to increase, age-related concerns such as obesity, depression, and AD are of growing concern. The ability to prevent or delay the progression of neurodegenerative diseases will promote healthy aging and improve quality of life for those with DS.
Endothelial Cell Culture (1996)

The aim of the Handbooks in Practical Animal Cell Biology is to provide practical workbooks for those involved in primary cell culture. Each volume addresses a different cell lineage, and contains an introductory section followed by individual chapters on the culture of specific differentiated cell types. The authors of each chapter are leading researchers in their fields and use their first-hand experience to present reliable techniques in a clear and thorough manner. Endothelial Cell Culture contains chapters on endothelial cells derived from 1) lung, 2) bone marrow, 3) brain, 4) mammary glands, 5) skin, 6) adipose tissue, 7) female reproductive system, and 8) synovium.
Enterococcus faecalis conjugative plasmid pAM373: complete nucleotide sequence and genetic analyses of sex pheromone response (2000)

pAM373 is a 36.7 kb conjugative plasmid in Enterococcus faecalis that encodes a response to a peptide sex pheromone, cAM373, secreted by plasmid-free (recipient) strains of enterococci. It was identified over 15 years ago as one of five plasmids in E. faecalis strain RC73 and was of interest because a related pheromone activity could be detected in culture supernatants of Staphylococcus aureus and Streptococcus gordonii. Because of increased clinical concern relating to the possibility of mobilizing vancomycin resistance determinants from enterococci, where they are becoming common, into pathogens such as S. aureus, efforts were initiated to characterize pAM373 further. The results of a complete nucleotide sequence determination of pAM373, as well as a genetic analysis of key genes related to regulation of the pheromone response, are reported here. With regard to determinants related to conjugation, the plasmid has a structural organization similar to other known pheromone-responsive plasmids such as pAD1, pCF10 and pPD1; however, there are several unique features. Although there are significant homologues relating to a pheromone-binding surface protein (TraC) and a negatively regulating protein (TraA), there is an absence of a determinant equivalent to traB of pAD1 (reduces endogenous pheromone) and a determinant for surface-exclusion protein. The precursor structure of the inhibitor peptide iAM373 was identified, and its determinant (iam373) was found to be about 500 nt upstream of an apparent transcription terminator t1. Tn917-lac insertion analyses provided interesting insights into aspects of control of the pheromone response and showed that, although the traA product is sensitive to pheromone, it appears to act differently from the traA homologue of pAD1.
A Novel Cytotoxin from Clostridium difficileSerogroup F Is a Functional Hybrid between Two Other Large Clostridial Cytotoxins (1999)

The large clostridial cytotoxins (LCTs) constitute a group of high molecular weight clostridial cytotoxins that inactivate cellular small GTP-binding proteins. We demonstrate that a novel LCT (TcdB-1470) from Clostridium difficile strain 1470 is a functional hybrid between "reference" TcdB-10463 and Clostridium sordellii TcsL-1522. It bound to the same specific receptor as TcdB-10463 but glucosylated the same GTP-binding proteins as TcsL-1522. All three toxins had equal enzymatic potencies but were equally cytotoxic only when microinjected. When applied extracellularly TcdB-1470 and TcdB-10463 were considerably more potent cytotoxins than TcsL-1522. The small GTP-binding protein R-Ras was identified as a target for TcdB-1470 and also for TcsL-1522 but not for TcdB-10463. R-Ras is known to control integrin-extracellular matrix interactions from inside the cell. Its glucosylation may be a major determinant for the cell rounding and detachment induced by the two R-Ras-attacking toxins. In contrast, fibroblasts treated with TcdB-10463 were arborized and remained attached, with phosphotyrosine containing structures located at the cell-to-cell contacts and beta3-integrin remaining at the tips of cellular protrusions. These components were absent from cells treated with the R-Ras-inactivating toxins. The novel hybrid toxin will broaden the utility of the LCTs for clarifying the functions of several small GTPases, now including also R-Ras.
Identification of Active Site Residues in the “GyrA” Half of Yeast DNA Topoisomerase II (1998)

Site-directed mutagenesis was carried out at 10 highly conserved polar residues within the C-terminal half of yeast DNA topoisomerase II, which corresponds to the A subunit of bacterial DNA gyrase, to identify amino acid side chains that augment the active site tyrosine Tyr-782 in the breakage and rejoining of DNA strands. Complementation tests show that alanine substitution at Arg-690, Asp-697, Lys-700, Arg-704, or Arg-781, but not at His-735, His-736, Glu-738, Gln-750, or Asn-828, inactivates the enzyme in vivo. Measurements of DNA relaxation and cleavage by purified mutant enzymes show that these activities are abolished in the R690A mutant and are much reduced in the mutants D697A, K700A, R704A, and R781A. When a Y782F polypeptide with a phenylalanine substituting for the active site tyrosine was expressed in cells that also express the R690A polypeptide, the resulting heterodimeric yeast DNA topoisomerase II was found to nick plasmid DNA. Thus in a dimeric wild-type enzyme, Tyr-782 in one protomer and Arg-690 in the other cooperate in trans in the catalysis of DNA cleavage. For the residues D697A, K700A, R704A, and R781A, their locations in the crystal structures of type II DNA topoisomerase fragments suggest that Arg-781 and Lys-700 might be involved in anchoring the 5' and 3' sides of the broken DNA, respectively, and the roles of Asp-697 and Arg-704 are probably less direct.
Human chromosome 7 carries the beta 2 interferon gene. (1986)

A cDNA clone (pAE20-4) corresponding to the 1.3-kilobase human beta 2 interferon mRNA was used as a probe in blot-hybridization experiments of DNA from a panel of human-rodent somatic cell hybrids containing overlapping subsets of human chromosomes. The DNA hybridization experiments showed that the human beta 2 interferon gene is located on human chromosome 7. This assignment is consistent with previous experimental data in which the expression of the translationally active 1.3-kilobase beta 2 interferon mRNA was assayed in various somatic cell hybrids. Blot-hybridization experiments using DNA from different human cell strains and cell lines reveal distinct EcoRI restriction fragment length polymorphisms of the human beta 2 interferon gene.
Prostatic cell lineage markers: Emergence of BCL2 cells of human prostate cancer xenograft LuCaP 23 following castration (1996)

A model of prostate cancer progression based on the expression pattern of informative genes in the human prostate cancer xenograft LuCaP 23.1 is presented. Apparently, there are at least 2 tumor cell populations of LuCaP 23.1, representing 2 different phenotypes. One is NSE (neuron-specific enolase)-positive and the other NSE-negative. NSE-positive tumors were recovered after hormone-independent growth in castrated mice. These hormone-independent tumors also expressed BCL2, a gene product shown to inhibit apoptosis. With NSE, BCL2 and PSA (prostate-specific antigen) as identifying markers, the model specifies a putative progression sequence of the prostate cancer cell types. We also show a proposed lineage relationship among the 3 principal normal cell types found in the prostatic epithelium. © 1996 Wiley-Liss, Inc.
Macropinocytosis Is the Major Pathway Responsible for DNA Transfection in CHO Cells by a Charge-Reversal Amphiphile (2011)

The cellular uptake of a functional charge-reversal amphiphile:DNA lipoplex is described. First, pharmacological inhibitors were applied to block different endocytosis pathways. By examining the resulting transfection activities, it was found that endocytosis was the pathway leading to transfection in Chinese hamster ovary (CHO) cells. When the specific pathway of macropinocytosis was inhibited, β-galactosidase expression was significantly depleted (90%); meanwhile the inhibition of clathrin-mediated pathway only brought a 30% decrease in expression; and the inhibition of caveolae-mediated pathway did not affect expression. Furthermore, a transfection kinetics study revealed that the cellular uptake responsible for gene expression was a slower process compared to clathrin-mediated endocytosis, consistent with fluid-phase uptake compared to receptor-mediated uptake. Next, a fluorescence colocalization study was used to visualize the DNA lipoplex uptake pathways. The colocalization of the DNA lipoplex and Cascade Blue, a fluid-phase uptake marker, was observed. Meanwhile, the colocalization of the DNA lipoplex and transferrin, a clathrin-mediated endocytosis marker, was also seen. However, no colocalization was observed with the endosome/lysosome marker Lysotracker. Our results indicate that macropinocytosis, not the commonly seen clathrin-mediated endocytosis for cationic lipids, is the major pathway leading to gene transfection in CHO cells for this charge-reversal amphiphile.
First Results From A Multi-Ion Beam Lithography And Processing System At The University Of Florida (2011)

The University of Florida (UF) have collaborated with Raith to develop a version of the Raith ionLiNE IBL system that has the capability to deliver multi‐ion species in addition to the Ga ions normally available. The UF system is currently equipped with a AuSi liquid metal alloy ion source (LMAIS) and ExB filter making it capable of delivering Au and Si ions and ion clusters for ion beam processing. Other LMAIS systems could be developed in the future to deliver other ion species. This system is capable of high performance ion beam lithography, sputter profiling, maskless ion implantation, ion beam mixing, and spatial and temporal ion beam assisted writing and processing over large areas (100 mm2)—all with selected ion species at voltages from 15–40 kV and nanometer precision. We discuss the performance of the system with the AuSi LMAIS source and ExB mass separator. We report on initial results from the basic system characterization, ion beam lithography, as well as for basic ion‐solid interactions.
Immersion, presence and performance in virtual environments (1996)

This paper describes an experiment to assess the influence of immersion on performance in immersive virtual environments. The task involved Tri-Dimensional Chess, and required subjects to reproduce on a real chess board the state of board learned from a sequence of moves witnessed in a virtual environment. Twenty four subjects were allocated to a factorial design consisting of two levels of immersion (exocentric screen based, and egocentric HMD based), and two kinds of environment (plain and realistic). The results suggest that egocentric subjects performed better than exocentric, and those in the more realistic environment performed better than those in the less realistic environment. Previous knowledge of chess, and amount of virtual practice were also significant, and may be considered as control variables to equalise these factors amongst the subjects. Other things being equal, males remembered the moves better than females, although female performance improved with higher spatial ability test score. The paper also attempts to clarify the relationship between immersion, presence and performance, and locates the experiment within such a theoretical framework.
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap (2008)

SNAP server is available at http://www.broad.mit.edu/mpg/snap/.
<title>Transferring automation for large-scale development and production of Invader SNP assays</title> (2000)

The Human Genome Project has led to the discovery of hundreds of thousands of single nucleotide polymorphisms (SNPs). SNPs can act as genetic markers to create high- density maps of the human genome for large-scale genetic analysis for evaluating links between genetic mutations and human diseases and for performing association studies. To create those maps, assays capable of detecting many different SNPs must be developed rapidly, as additional SNPs are discovered. When both the design of and the technology used in the assays can be partially or fully automated, the development process and the time to results can be accomplished quickly and efficiently. Invader<SUP>TM</SUP> technology offers a highly sensitive signal amplification system that detects and quantifies mutations and SNPs from unamplified human genomic DNA in two sequential steps.