gebhart/patrepeval huggingface dataset:
Replication of GB Virus C (Hepatitis G Virus) in Interferon-Resistant Daudi Cells (1999)

We previously reported that Daudi cells, a Burkitt's lymphoma cell line, were capable of supporting productive infection of hepatitis C virus (HCV). During continual cultivation after HCV infection, the culture became resistant to interferons (IFNs). This resistant cell line, coded as H-903, was used as host cells for replication of GB virus C (GBV-C), also known as hepatitis G virus. GBV-C RNA was detected in the culture by reverse transcription-PCR for more than 130 days after inoculation, while it was detected for 44 days but not later in the parental IFN-sensitive Daudi cells. Productive infection of GBV-C in the H-903 system was confirmed by serially inoculating supernatants from infected cultures into uninfected cells. The viral E2 antigen was detected by immunofluorescence in the cells inoculated with the fifth passage of GBV-C. The presumed capsid-coding region of the viral genome in the inoculum, in the serially passaged virus, or in the virus produced by a long-term culture was only 16 amino acids long, suggesting that the GBV-C with a short core sequence was replication competent.
Water-Solubilization of Nucleotides-Coated Single-Walled Carbon Nanotubes Using a High-Speed Vibration Milling Technique (2006)

[reaction: see text] Pristine single-walled carbon nanotubes (SWNTs) and nucleotides mixed using a mechanochemical high-speed vibration milling technique (HSVM) are soluble in an aqueous solution, and the solubilities of SWNTs depend significantly on the number of phosphate groups and the kinds of bases employed.
Targeting Superficial or Nodular Basal Cell Carcinoma with Topically Formulated Small Molecule Inhibitor of Smoothened (2011)

Our data highlight some of the challenges of translating preclinical experience into successful human results for a topical anticancer agent.
The Human Plasma Lipidome (2011)

Biochemical analyses reveal that plasma contains over 600 structural forms of lipid molecules. This review summarizes known correlations between levels of lipid moieties and disease and describes potential therapeutic targets relevant to CVD, cancer, and neurologic disease.
Signal peptides: exquisitely designed transport promoters (1994)

Prokaryotic proteins destined for transport out of the cytoplasm typically contain an N-terminal extension sequence, called the signal peptide, which is required for export. It is evident that many secretory proteins utilize a common export system, yet the signal sequences themselves display very little primary sequence homology. In attempting to understand how different signal peptides are able to promote protein secretion through the same pathway, the physical features of natural signal sequences have been extensively examined for similarities that might play a part in function. Experimental data have confirmed statistical analyses which highlighted dominant features of natural signal sequences in Escherichia coli: a net positive charge in the N-terminus increases efficiency of transport; the core region must maintain a threshold level of hydrophobicity within a range of length limitations; the central portion adopts an alpha-helical conformation in hydrophobic environments; and the signal cleavage region is ideally six residues long, with small side-chain amino acids in the -1 and -3 positions. This review focuses on the parallels between signal peptide physical features and their functions, which emerge when the results of a variety of experimental approaches are combined. The requirement for each property may be ascribed to a potential interaction that is critical for efficient protein export. The summation of the key physical features produces signal peptides with the flexibility to function in multiple roles in order to expedite secretion. In this way, nature has indeed evolved exquisitely tuned signal sequences.
Synthesis and Pharmacology of 6-Substituted Benztropines:  Discovery of Novel Dopamine Uptake Inhibitors Possessing Low Binding Affinity to the Dopamine Transporter (2005)

A series of 6alpha- and 6beta-substituted benztropines were synthesized. A marked enantioselectivity was observed for the 6beta-methoxylated benztropines, the (1R)-isomers being more potent than the corresponding (1S) compounds. The racemic 6alpha-methoxy-3-(4',4' '-difluorodiphenylmethoxy)tropane (5 g) was the most potent compound. It has been found that modifications at the 6-position of benztropine might reduce the DAT binding affinity, maintaining otherwise a significant dopamine uptake inhibitory activity. A reinvestigation of the absolute configuration of 6beta-methoxytropinone proved the 6R configuration for the (+)-enantiomer.
Order-picking industrial robot (1990)

SUMMARY Order-picking, i.e. arranging work-pieces of different types on a pallet, which is nowadays often carried out manually, will in future be more and more automated for economic reasons. The industrial robot in combination with an intelligent gripper, a supporting palletizing and order-picking software and a suitably designed periphery will permit fully automated order-picking. The Fraunhofer-Institute for Manufacturing Engineering and Automation (F.R.G.) has developed such a system which takes advantage of the arrangement of the work-pieces in the compartment stack and simultaneously grips the work-pieces that are then arranged in a pattern on a pallet.
Major outer membrane proteins and proteolytic processing of RgpA and Kgp of Porphyromonas gingivalis W50 (2002)

Porphyromonas gingivalis is an anaerobic, asaccharolytic Gram-negative rod associated with chronic periodontitis. We have undertaken a proteomic study of the outer membrane of P. gingivalis strain W50 using two-dimensional gel electrophoresis and peptide mass fingerprinting. Proteins were identified by reference to the pre-release genomic sequence of P. gingivalis available from The Institute for Genomic Research. Out of 39 proteins identified, five were TonB-linked outer membrane receptors, ten others were putative integral outer membrane proteins and four were putative lipoproteins. Pyroglutamate was found to be the N-terminal residue of seven of the proteins, and was predicted to be the N-terminal residue of 13 additional proteins. The RgpA, Kgp and HagA polyproteins were identified as fully processed domains in outer membranes prepared in the presence of proteinase inhibitors. Several domains were found to be C-terminally truncated 16-57 residues upstream from the N-terminus of the following domain, at a residue penultimate to a lysine. This pattern of C-terminal processing was not detected in a W50 strain isogenic mutant lacking the lysine-specific proteinase Kgp. Construction of another W50 isogenic mutant lacking the arginine-specific proteinases indicated that RgpB and/or RgpA were also involved in domain processing. The C-terminal adhesin of RgpA, designated RgpA27, together with RgpB and two newly identified proteins designated P27 and P59 were found to migrate on two-dimensional gels as vertical streaks at a molecular mass 13-42 kDa higher than that calculated from their gene sequences. The electrophoretic behaviour of these proteins, together with their immunoreactivity with a monoclonal antibody that recognizes lipopolysaccharide, is consistent with a modification that could anchor the proteins to the outer membrane.
Expression of simian CETP in normolipidemic Fisher rats has a profound effect on large sized apoE-containing HDL (2002)

In order to investigate the direct effect of cholesteryl ester transfer protein (CETP) on the structure and composition of HDL in vivo, simian CETP was expressed in Fisher rat that spontaneously displays high plasma levels of HDL1. In the new CETPTg rat line, the production of active CETP by the liver induced a significant 48% decrease in plasma HDL cholesterol, resulting in a 34% decrease in total cholesterol level (P < 0.01 in both cases). Among the various plasma HDL subpopulations, the largest HDL were those mostly affected by CETP, with a 74% decrease in HDL1 versus a significantly weaker 38% decrease in smaller HDL2 (P < 0.0001). Apolipoprotein E (apoE)-containing HDL1 were selectively affected by CETP expression, whereas apoA content of HDL remained unmodified. The reduction in the apoE content of serum HDL observed in CETPTg rats compared to controls (53%, P < 0.02) suggests that apoE in HDL may constitute in vivo a major determinant of their ability to interact with CETP. These results bring new insight into the lack of HDL1 in plasma from CETP-deficient heterozygotes despite their substantial 50% decrease in CETP activity. In addition, they indicate that HDL1 constitute reliable and practicable sensors of very low plasma CETP activity in vivo.
Introduction to immunology (1983)

Introduction to Immunology , Introduction to Immunology , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Natural cytotoxicity to autologous antigen‐pulsed dendritic cells in multiple myeloma (2002)

To analyse autologous lymphocyte cytolytic activities of potential importance for cell-based immunotherapy in multiple myeloma (MM), in vitro differentiated dendritic cells (DCs) loaded with patient-specific monoclonal immunoglobulin (mIg) were used as autologous target cellsin cytotoxicity assays. Effector populations consisted of purified natural killer (NK) cells (CD56+, CD3-) and T cells (CD3+). The MM patients' NK cells cultured in the presence of interleukin 2 (IL-2) showed pronounced cytotoxic activity towards autologous mature DCs. Autologous MM DC targets displayed similar susceptibility to NK cell lysis, compared with allogeneic control DC targets, despite high surface expression of self major histocompatibility complex (MHC) antigens. However, some degree of classic MHC class I-mediated negative regulation was implicated in the NK-DC interactions, as indicated by class I blocking experiments. NK-mediated lysis was also discerned towards primary autologous MM cells. The results indicated that the major effector mechanism was mediated through the perforin-granzyme exocytosis pathway. In conclusion, NK cells from MM patients displayed significant and consistent cytotoxicity towards autologous mature DCs, suggesting that innate immunity could be implicated in MM and may influence the outcome of the administration of tumour antigen-pulsed DCs in treatment trials.
Stress Under the Sun: Spotlight on Ultraviolet-B Responses (2003)

The UV-B spectral band (280–315 nm) contributes less than 2% of the short-wave photons received by terrestrial organisms in most natural environments. Concerns about potential impacts of stratospheric ozone depletion contributed to spark interest in studies of plant responses to enhanced UV-B
Modulation of gene expression by hypoxia in human umbilical cord vein endothelial cells: A transcriptomic and proteomic study (2004)

Hypoxia is a characteristic feature of many human pathologies, including cancer. The sustained proliferation rate of tumor cells leads to alterations of the tumor microenvironment, that progressively becomes more acidic, nutrient-deprived, and hypoxic. The reduced partial pressure of oxygen triggers the onset of an adaptive response, aimed at increasing the local oxygen concentration by several complementary actions. Although directly exposed to the blood stream, endothelial cells lining the vascular lumen in tumors also can be exposed to hypoxia and therefore can contribute to the onset of the adaptive response that leads to tumor angiogenesis. Aiming at getting a detailed insight into the oxygen-dependent regulation of the transcriptional program of vascular endothelial cells and at identifying new relevant markers that may be used as targets for therapeutic intervention in tumor angiogenesis, we have performed a broad-range transcriptomic analysis, using the Affymetrix HG-U133A Gene Chips, of mRNA expression levels in human umbilical cord vein endothelial cells (HUVEC), exposed in vitro to hypoxia for different time periods. The transcriptomic analysis was complemented by a semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of mRNA levels and alternative splicing for some selected extracellular matrix protein genes, and by a proteomic analysis, using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and tandem mass spectrometry for protein separation and identification, of hypoxic and normoxic HUVEC whole-cell lysates and subcellular fractions. Our analysis confirmed previous findings on genes whose expression is regulated by oxygen concentration but also identified new genes (e.g., CXCR4, claudin 3, CD24, tetranectin, Del-1, procollagen lysyl hydroxylase 1 and 2) which are transcriptionally upregulated in hypoxic conditions.
Enantiopure imidazolinium-dithiocarboxylates as highly selective novel organocatalysts (2008)

Asymmetric imidazolinium-dithiocarboxylates have been found for the first time to be highly selective catalysts; in the present case, the novel organocatalysts were able to catalyze the Staudinger reaction in up to 96% ee and 99% yield.
Electrochemical Patterning of Self-Assembled Monolayers onto Microscopic Arrays of Gold Electrodes Fabricated by Laser Ablation (1996)

This report demonstrates proof-of-concept application of two established electrochemical techniques affecting self-assembled monolayersthe thermodynamic control of monolayer assembly at gold and the electrochemical desorption of self-assembled monolayers from goldto pattern monolayers onto gold microelectrodes. When combined with a simple laser-based microfabrication technique, using commercially available microscope adaptations, to form arrays of individually-addressable gold microelectrodes from continuous thin gold films on glass, two new patterning methodologies result that enable fabrication of monolayer-based affinity arrays for potential use in chemical and biosensors. The described microfabrication technique is central to the success of these patterning methodologies because it allows SAM patterning of metal arrays immediately after their fabrication, so as to avoid problems associated with forming SAMs on commercially-supplied arrays. In this paper, each patterning methodology is used to fabricate an interdigitated microelectrode array in which one set of electrodes is modified with an active antibody and the other set of electrodes is resistant to nonspecific protein adsorption.
Are there several isoforms of Na,K-ATPase alpha subunit in the rabbit kidney? (1993)

Previous pharmacologic and kinetic studies have demonstrated the axial heterogeneity of the rabbit kidney tubule with regard to Na,K-ATPase. To evaluate whether this heterogeneity might reflect the presence of distinct isoforms of the alpha subunit of Na,K-ATPase, we used two monoclonal antibodies, IIC9 and IIE2 (G8), specific for the alpha 1 and alpha 3 isoforms, respectively, as probes for changes in the specific activity of Na,K-ATPase at the level of successive segments of the rabbit nephron. Single, well defined nephron segments were obtained by microdissection of collagenase-treated kidney. Results indicate that IIC9 antibody inhibited Na,K-ATPase activity by > 90% in all the segments of the nephron except the collecting duct. Conversely, IIE2 (G8) antibody abolished Na,K-ATPase activity in the collecting duct, whereas it had no effect in other nephron segments. These findings suggest that the rabbit collecting duct preferentially expresses a distinct isoform of Na,K-ATPase catalytic subunit, which is presumably alpha 3-like, in agreement with previous pharmacologic and kinetic observations, whereas other nephron segments would express the alpha 1 isoform.
Spin Labeled Bovine Serum Albumin, Spin Labeled Bovine Serum Albumin Chelating Agents and Their Gadolinium Complexes. Potential Contrast Enhancing Agents for Magnetic Resonance Imaging (1986)

Abstract Bovine Serum Albumin (BSA) was spin labeled using the active esters 3 and 5 containing a nitroxyl radical to give the spin labeled BSA derivatives 4 and 6. Spin labeled C D TA , DTPA and TTHA chelating agents 10, 13 and 16 and the corresponding BSA derivatives 17, 18 and 19 and their gadolinium complexes 20, 21 and 22 were synthesized. All these BSA derivatives were evaluated as possible contrast enhancing agents for NMR imaging by measurement of spin-lattice (T 1 ) and spin-spin (T 2 ) relaxations and by calculations of relaxivities i.e., slopes of 1/T 1 versus concentration plots. The spin labeled BSA-complexon-gadolinium conjugates 20, 21 and 22 were found to have better relaxation times and relaxivities than the BSA spin labeled derivatives 4, 6, 17, 18 and 19. The spin count for the BSA derivatives 4, 6, 17, 18 and 19 and for their gadolinium conjugates 20, 21 and 22 was found to be between 9 -1 0 spins/molecule of the protein. The gadolinium conjugates 20, 21 and 22 of spin labeled BSA possess high relaxivities combined with a nitroxyl marker that could be used with EPR to assess pharmacokinetic behaviors of these potential contrast agents
Regulation of the production of extracellular pectinase, cellulase, and protease in the soft rot bacterium Erwinia carotovora subsp. carotovora: evidence that aepH of E. carotovora subsp. carotovora 71 activates gene expression in E. carotovora subsp. carotovora, E. carotovora subsp. atroseptica, and Escherichia coli (1994)

The production of pectolytic enzymes (pectate lyase [Pel] and polygalacturonase [Peh]), cellulase (Cel), and protease (Prt) is activated in the soft rot bacterium Erwinia carotovora subsp. carotovora by aepA (activator of extracellular protein production) and celery extract (Y. Liu, H. Murata, A. Chatterjee, and A. K. Chatterjee, Mol. Plant-Microbe Interact. 6:299-308, 1993). We recently isolated a new class of mutants of strain E. carotovora subsp. carotovora 71 which overproduces Pel, Peh, Cel, and Prt. From the overproducing strain AC5034, we identified an activator locus, designated aepH*, which stimulated Pel, Peh, Cel, and Prt production in E. carotovora subsp. carotovora 71 or its derivatives. The nucleotide sequence of the aepH* DNA segment revealed an open reading frame of 141 bp that could encode a small (5.45-kDa) highly basic (pI 11.7) protein of 47 amino acid residues. Analyses of deletions and MudI insertions indicated that the activator function required the 508-bp DNA segment which contains this open reading frame. The wild-type locus, aepH+, is localized within a DNA segment upstream of aepA. An AepH- strain constructed by exchanging aepH+ with aepH*::MudI was deficient in Pel, Peh, Cel, and Prt production; exoenzyme production was restored upon the introduction of a plasmid carrying aepH+ or aepH*. Plasmids carrying either aepH+ or aepH* activated the production of Pel-1, Peh-1, and Cel in Escherichia coli HB101 carrying the cognate genes. The aepH effect in E. coli was due to the activation of transcription, as indicated by assays of pel-1 and peh-1 mRNAs. The aepH+ and aepH* plasmids also stimulated Pel, Peh, Cel, and Prt production in other wild-type E. carotovora subsp. carotovora strains as well as in E. carotovora subsp. atroseptica. Although the stimulatory effect was generally more pronounced with aepH* than with aepH+, the extent of activation in the wild-type strains depended upon the bacterial strain and the growth medium. Southern blot hybridization revealed the presence of aepH homologs in E. carotovora subsp. carotovora and E. carotovora subsp. atroseptica, and provided physical evidence for linkage between aepA and aepH homologs in genomes of these bacteria. We conclude that aepH-mediated activation of exoprotein gene expression is a feature common to most strains of E. carotovora.
Specific Regulation of E2F Family Members by Cyclin-Dependent Kinases (1997)

The transcription factor E2F-1 interacts stably with cyclin A via a small domain near its amino terminus and is negatively regulated by the cyclin A-dependent kinases. Thus, the activities of E2F, a family of transcription factors involved in cell proliferation, are regulated by at least two types of cell growth regulators: the retinoblastoma protein family and the cyclin-dependent kinase family. To investigate further the regulation of E2F by cyclin-dependent kinases, we have extended our studies to include additional cyclins and E2F family members. Using purified components in an in vitro system, we show that the E2F-1-DP-1 heterodimer, the functionally active form of the E2F activity, is not a substrate for the active cyclin D-dependent kinases but is efficiently phosphorylated by the cyclin B-dependent kinases, which do not form stable complexes with the E2F-1-DP-1 heterodimer. Phosphorylation of the E2F-1-DP-1 heterodimer by cyclin B-dependent kinases, however, did not result in down-regulation of its DNA-binding activity, as is readily seen after phosphorylation by cyclin A-dependent kinases, suggesting that phosphorylation per se is not sufficient to regulate E2F DNA-binding activity. Furthermore, heterodimers containing E2F-4, a family member lacking the cyclin A binding domain found in E2F-1, are not efficiently phosphorylated or functionally down-regulated by cyclin A-dependent kinases. However, addition of the E2F-1 cyclin A binding domain to E2F-4 conferred cyclin A-dependent kinase-mediated down-regulation of the E2F-4-DP-1 heterodimer. Thus, both enzymatic phosphorylation and stable physical interaction are necessary for the specific regulation of E2F family members by cyclin-dependent kinases.
SOH Balancing Control Method for the MMC Battery Energy Storage System (2017)

The recycled batteries can be assumed for the cost-effective grid energy storage (ES) applications, where the state of health (SOH) of recycled batteries are hard to make equal when reassembling them in one ES system. Therefore, when implementing the traditional state-of-charge balancing control methods, the batteries integrated into the same ES system will demonstrate the SOH deviation characteristics during the long-term operation due to the different degradation they suffered, which will reduce the mean time to repair, increase the maintenance duty, and shorten the life time of the ES system. Alternatively, this paper proposes an SOH balancing control method for the modular multilevel-converter-based battery energy storage system (MMC BESS) by fully using the unique modular configuration. The relationship among SOH, depth of discharge, and life cycles is analyzed in the theory, which builds the criteria for power distribution among battery packs in the MMC BESS. In addition, instead of estimating the specific SOH value, a relative SOH evaluation method is presented for easier practical implementation. And then, multiple control loops are designed for achieving the expected operational performance. MATLAB simulation and experimental results are presented to verify the proposed control method.