gebhart/patrepeval huggingface dataset:
The production of foreign proteins in mammalian cells. (1988)

Expression systems for producing foreign proteins in mammalian cells are built from two components. One component is the DNA expression vector and the other is the mammalian host-cell line. Functional elements of DNA are better understood and generally easier to manipulate than complex mammalian cells. The standard approach, therefore, has been to manipulate the expression vectors to work well in convenient host cell lines. A wide variety of DNA regulatory signals for efficient transcription and translation have been tested in mammalian-cell-expression vectors. Many of the most successful and widely used regulatory signals are derived from eukaryotic viral DNAs. In addition to optimizing the vectors to give efficient transcription and translation of the foreign protein, higher expression levels can be achieved by increasing the number of foreign gene copies per cell. High gene copy number is usually attained by including an amplifiable gene, such as dhfr, in the expression vector, introducing the vector DNA into the host-cell lines, and then using a toxic agent to select for resistant cell lines containing high copy numbers of the amplifiable gene. Cells with amplified copy numbers of the selected gene generally also contain high copy numbers of the foreign gene and thus produce elevated levels of the foreign protein product. Although gene amplification has been most successful in creating cell lines producing high levels of foreign proteins, there are inherent instability problems with cell lines forced to carry extremely high copy numbers of foreign genes. One means of avoiding instability problems due to continuous high gene copy and continuous high foreign protein production, is to develop regulatable expression systems. The regulatable expression systems being developed are based either on regulating the gene copy number by regulating DNA replication or on regulating the level of transcription by using a regulatable promoter to transcribe the foreign protein coding cDNA. In addition to designing a good expression vector, it is important to consider the mammalian host cell. Although most potential mammalian host-cell lines are capable of post-translational processing and secretion, certain processing steps, such as gamma-carboxylation, may be done efficiently only in specialized cell types. It is also important to estimate how much of the foreign protein will be needed and to decide whether the proposed host-cell line can be easily and economically grown to produce that amount. Regulatory considerations are also important in choosing a host-cell line for commercial production. Many of the potential host-cell lines are tumorigenic and carry retroviruses.(ABSTRACT TRUNCATED AT 400 WORDS)
New Strategies for Enzyme Replacement Therapy for Lysosomal Storage Diseases (2010)

Enzyme replacement therapy is an established means of treating lysosomal storage diseases. Infused enzymes are normally targeted to the lysosomes of affected cells by interactions with cell-surface receptors that recognize carbohydrate moieties such as mannose and mannose 6-phosphate on the enzymes. Therefore, we have investigated alternative strategies to deliver the lysosomal enzyme beta-glucuronidase in the enzyme-deficient mucopolysaccharidosis type VII mouse model. Here we summarize our recent efforts to use nontraditional ways to deliver beta-glucuronidase. First, we used a chimeric protein of the insulin-like growth factor II (IGF-II) fused to beta-glucuronidase to deliver enzyme via the IGF-II binding site on the bifunctional IGF-II/mannose 6-phosphate receptor. Second, we used the 11-amino-acid human immunodeficiency virus (HIV) Tat domain fused to beta-glucuronidase to mediate uptake by absorptive endocytosis. Interaction with heparan sulfate on the cell surface internalizes and delivers the Tat-tagged enzyme to the lysosome via plasma membrane recycling. Third, we created a chimeric beta-glucuronidase fused to the Fc portion of human immunoglobulin G (IgG) Fc, which was transported by the neonatal Fc receptor from the maternal circulation across the placenta to sites of storage in fetal tissues. Finally, periodate treatment was used to eliminate interaction with carbohydrate receptors, creating an enzyme with increased plasma half-life, resulting in transport across the blood-brain barrier and clearance of storage in neurons. These strategies for delivering lysosomal enzymes could also be used to target nonlysosomal proteins or enzymes identified for bioremediation of other conditions.
Sindbis Virus: A Newly Recognized Arthropod-Transmitted Virus (1955)

Summary 1. Studies on Sindbis virus, a newly recognized member of the arthropod-transmitted viruses, are described; these include data on its immunological characteristics, distribution in the Nile Valley, vertebrate host range, and transmissibility by arthropods. 2. The virus has been isolated from mosquitoes during three successive summers, and once from a juvenile hooded crow (Corvus corone sardonius). 3. It has been placed by Casals and Brown (1954) in Group A of the arthropod-transmitted viruses, but is distinguishable from other members of this group by the neutralization test. 4. Its particle size, estimated by gradacol membrane filtration, is between 40 and 48 mu. 5. On initial passages by brain-to-brain transfer it is fatal to infant mice but not to adult mice. 6. It is highly fatal to embryonated hens' eggs and is markedly cytopathogenic to outgrowths of fibroblastic cells in chick embryo tissue cultures. 7. Experimentally it is easily transmitted by Culex mosquitoes (Culex pipiens L. and Culex univittatus Theobald), and Ornithodoros savignyi (Audouin) ticks are infectible by parenteral puncture and will subsequently transmit the infection by feeding upon infant mice. 8. Antibody surveys imply a) a wide vertebrate host range including man, domestic quadrupeds, birds, and domestic fowl, and b) frequent human infection (27 per cent), particularly in the age group of 15 years and over (34 per cent), in the Nile Delta, and less frequent human infection (12 per cent) in the Southern Sudan. 9. No information is available on the symptomatology of natural infections.
Inhibition of immune reactionsin vivoby liposome associated transforming growth factor (TGF) type β1 (1991)

In view of its potent inhibitory capacity on immune cells in culture, we wished to determine the ability of transforming growth factor (TGF) beta 1 to down-regulate immune responses in vivo. Preliminary experiments suggested that, at the doses used, systemic injection of soluble TGF beta 1 could not affect bacterial-induced spleen enlargement in mice. Therefore, we sought to utilize a physiochemical property of this molecule, namely its high pI, to determine possible association between the ligand and preformed liposomes possessing an opposite charge. TGF beta 1 was preferentially associated with negatively charged, but not with neutral, liposomes. These TGF beta 1 associated liposomes were able to deliver a suppressive signal to indicator cells in vitro. Intravenous injection of TGF beta 1, associated with liposomes possessing an opposite charge, into mice immunized with heat-killed Corynebacterium parvum significantly reduced the size of the spleen as well as the number of splenocytes. Systemically administered TGF beta 1 associated liposomes could also inhibit delayed type hypersensitivity reactions to Listeria monocytogenes. These data suggest that appropriately administered, TGF beta 1 can inhibit immune responses in vivo.
Reversal of Hypermethylation and Reactivation of the RARβ2 Gene by Natural Compounds in Cervical Cancer Cell Lines (2010)

Reactivation of tumour suppressor genes that have been silenced by promoter methylation is a very attractive molecular target for cancer therapy. The treatment of a squamous cervical cancer cell line, SiHa, with 20 μM curcumin and genistein resulted in demethylation of promoter of the RARβ2 gene and led to the reactivation of the gene. The degree of methylation as observed by MSP decreased as the time period of treatment was increased from 72 h to 6 days. In HeLa cells (an adenocarcinoma cervical cancer cell line) there was also reversal of hypermethylation of the RARβ2 gene after six days of treatment with 20 μM curcumin. However, allyl sulphide treatment (20 μM) did not cause the reversal of hypermethylation until 72 h of treatment in the SiHa cell line. This is the first report to show the reversal of hypermethylation of the RARβ2 gene by genistein and curcumin in cervical cancer cell lines. Furthermore, these compounds acted as doublepronged agents as they caused apoptosis in the treated cervical cancer cell lines in addition to reversal of promoter hypermethylation.
Butelase 1: A Versatile Ligase for Peptide and Protein Macrocyclization (2015)

Macrocyclization is a valuable tool for drug design and protein engineering. Although various methods have been developed to prepare macrocycles, a general and efficient strategy is needed. Here we report a highly efficient method using butelase 1 to macrocyclize peptides and proteins ranging in sizes from 26 to >200 residues. We achieved cyclizations that are 20,000 times faster than sortase A, the most widely used ligase for protein cyclization. The reactions completed within minutes with up to 95% yields.
Outcomes of an Australian testing programme for epidermal growth factor receptor mutations in non‐small cell lung cancer (2014)

EGFR gene mutation testing is feasible on local and interstate lung cancer samples. The rate of valid test outcomes is high, but FNA samples are associated with more frequent test failure.
Deletions within the amino-terminal half of the c-src gene product that alter the functional activity of the protein. (1989)

To examine how amino acid sequences outside of the catalytic domain of pp60c-src influence the functional activity of this protein, we have introduced deletion mutations within the amino-terminal half of pp60c-src. These mutations caused distinct changes in the biochemical properties of the c-src gene products and in the properties of cells infected with retroviruses carrying these mutant c-src genes. Cells expressing the c-srcNX protein, which contains a deletion of amino acids 15 to 89, displayed a refractile, spindle-shaped morphology, formed intermediate-sized, tightly packed colonies in soft agar, and contained elevated levels of cellular phosphotyrosine-containing proteins. Thus, deletion of amino acids 15 to 89 can activate the kinase activity and transforming potential of the c-src gene product. Deletion of amino acids 112 to 225, however, did not increase the kinase activity or transforming ability of pp60c-src; indeed, deletion of these sequences in c-srcHP suppressed phenotypic alterations induced by pp60c-src. Cells expressing the c-srcNP or c-srcBS gene products (containing deletions of amino acids 15 to 225 and 55 to 169, respectively) displayed a fusiform, refractile morphology and formed diffuse colonies in soft agar; the mutant proteins displayed an increased in vitro protein-tyrosine kinase activity. However, only a few cellular proteins contained elevated levels of phosphotyrosine in vivo. Thus, deletions downstream of amino acid 89 severely restricted the ability of c-src to phosphorylate cellular substrates in vivo without affecting the intrinsic tyrosine kinase activity of the c-src gene product. These results suggest the existence of at least two modulatory regions within the amino-terminal half of pp60c-src that are important for the regulation of tyrosine kinase activity and for the interaction of pp60c-src with cellular substrates.
RETRACTED: Selective inhibition of the platelet-derived growth factor signal transduction pathway by a protein-tyrosine kinase inhibitor of the 2-phenylaminopyrimidine class. (1995)

The platelet-derived growth factor (PDGF) receptor is a member of the transmembrane growth factor receptor protein family with intrinsic protein-tyrosine kinase activity. We describe a potent protein-tyrosine kinase inhibitor (CGP 53716) that shows selectivity for the PDGF receptor in vitro and in the cell. The compound shows selectivity for inhibition of PDGF-mediated events such as PDGF receptor autophosphorylation, cellular tyrosine phosphorylation, and c-fos mRNA induction in response to PDGF stimulation of intact cells. In contrast, ligand-induced autophosphorylation of the epidermal growth factor (EGF) receptor, insulin receptor, and the insulin-like growth factor I receptor, as well as c-fos mRNA expression induced by EGF, fibroblast growth factor, and phorbol ester, was insensitive to inhibition by CGP 53716. In antiproliferative assays, the compound was approximately 30-fold more potent in inhibiting PDGF-mediated growth of v-sis-transformed BALB/c 3T3 cells relative to inhibition of EGF-dependent BALB/Mk cells, interleukin-3-dependent FDC-P1 cells, and the T24 bladder carcinoma line. When tested in vivo using highly tumorigenic v-sis- and human c-sis-transformed BALB/c 3T3 cells, CGP 53716 showed antitumor activity at well-tolerated doses. In contrast, CGP 53716 did not show antitumor activity against xenografts of the A431 tumor, which overexpresses the EGF receptor. These findings suggest that CGP 53716 may have therapeutic potential for the treatment of diseases involving abnormal cellular proliferation induced by PDGF receptor activation.
The pharmacokinetics of clotting factor therapy (2003)

Clotting factor preparations are expensive and not readily available in all parts of the world. We are still facing shortages due to limited production. Thus, it is obvious that clotting factor therapy should be optimised as far as possible. The judicious use of pharmacokinetic principles should be one of the fundaments of dosing. There are several pitfalls in studies of clotting factor pharmacokinetics, such as discrepancies between assays, inadequate blood sampling protocols, problems to define the administered dose, uncertainty in the estimation of plasma volume for in vivo recovery calculation, and post-infusion activation of the clotting factor. Thus, while the pharmacokinetics of factor VIII is well characterised there are some discrepancies in the literature on factor IX. Recombinant factor VIIa is useful to treat haemorrhages in haemophilia complicated by inhibitors. The pharmacokinetics of VIIa has been investigated, however, the relationship between plasma level of VIIa and effect needs further exploration. Important applications of clotting factor pharmacokinetics include optimising the treatment and improving its cost-effectiveness during long-term prophylaxis as well as during bleeding episodes and surgery.
Targeting anti-HIV drugs to the CNS (2009)

The development of antiretroviral drugs over the past couple of decades has been commendable owing to the identification of several new targets within the overall HIV replication cycle. However, complete control over HIV/AIDS is yet to be achieved. This is because the current anti-HIV drugs, although effective in reducing plasma viral levels, cannot eradicate the virus completely from the body. This occurs because most anti-HIV drugs do not accumulate in certain cellular and anatomical reservoirs including the CNS. Insufficient delivery of anti-HIV drugs to the CNS is attributed to their low permeability across the BBB. Hence, low and sustained viral replication within the CNS continues even during prolonged antiretroviral drug therapy. Therefore, developing novel approaches that are targeted at enhancing the CNS delivery of anti-HIV drugs are required. In this review, we discuss the potential of nanocarriers and the role of cell-penetrating peptides in enhancing drug delivery to the CNS. Such drug delivery approaches could also lead to higher drug delivery to other cellular and anatomical reservoirs where the virus harbors than with conventional treatment, thus providing an effective therapy to eliminate the virus completely from the body.
Emerging technologies for fiber network survivability (1995)

Reducing network protection costs, while maintaining an acceptable level of survivability, has become an important challenge for network planners and engineers. This article will review technology and architectures that may be used to implement cost effective survivable fiber networks for each transport layer, and discuss the interworking system between survivability mechanisms across different layers and associated open issues. Standards development, product availability and the current status of deployment will also be reviewed. The first section reviews a class of survivable fiber network architectures that has been deployed or is scheduled to be deployed. Next is a review of emerging technologies for these survivable architecture implementations. These emerging technologies include SONET, ATM, and passive optical technology. Finally the issue of multiple layer interworking on SONET/ATM networks is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Epstein-Barr Virus Nuclear Antigen 2 Binds via Its Methylated Arginine-Glycine Repeat to the Survival Motor Neuron Protein (2003)

Here we provide evidence that EBNA2 is methylated in vivo and that methylation of EBNA2 is a prerequisite for binding to SMN. We present SMN as a novel binding partner of EBNA2 by showing that EBNA2 colocalizes with SMN in nuclear gems and that both proteins can be coimmunoprecipitated from cellular extract. Furthermore, in vitro methylation of either wild-type EBNA2 or a glutathione S-transferase-EBNA2 fusion protein encompassing the arginine-glycine (RG) repeat element is necessary for in vitro binding to the Tudor domain of SMN. The recently shown functional cooperation of SMN and EBNA2 in transcriptional activation and the previous observation of a severely reduced transformation potential yet strongly enhanced transcriptional activity of an EBNA2 mutant lacking the RG repeat indicate that binding of SMN to EBNA2 is a critical step in B-cell transformation by Epstein-Barr virus.
Nitric oxide synthase inhibitor reduces the apoptotic change in the cisplatin-treated cochlea of guinea pigs (2000)

Cisplatin is known to cause inner ear damage. The role of nitric oxide (NO) in the cochlea of the guinea pigs after injections of cisplatin or a combination of cisplatin and NO synthase (NOS) inhibitor [N(G)-nitro-L-arginine methyl ester (L-NAME)] i.p. was examined by means of immunohistochemistry. Three days after injection, the cochleas were examined immunohistochemically for single-stranded DNA (ssDNA). We found that ssDNA was expressed in the stria vascularis and spiral ganglion cells of the cisplatin-treated cochlea. In the L-NAME/cisplatin-treated cochlea, the number of cells that exhibited positive staining for ssDNA was markedly reduced. High NO levels lead to inner ear dysfunction under pathological conditions. Our results indicate that NO mediates the ototoxicity of cisplatin.
ChemInform Abstract: Interactions of NO with Rh/TiO2 and TiO2‐Promoted Rh/SiO2. (1986)

Abstract Temp.‐programmed desorption spectroscopic studies show that while the chemisorption of NO is suppressed with increasing catalyst reduction temp. in a manner similar to that for H 2 and C0 chemisorption, the amount of NO adsorbed is always greater than that of H 2 or C0.
Measurement of low-temperature specific heat (1983)

The measurement of low-temperature specific heat (LTSH) (0.1 K&amp;lt;T&amp;lt;60 K) has seen a number of breakthroughs both in design concepts and instrumentation in the last 15 years—particularly in small sample calorimetry. This review attempts to provide an overview of both large and small sample calorimetry techniques at temperatures below 60 K, with sufficient references to enable more detailed study. A comprehensive review is made of the most reliable measurements of the LTSH of 84 of the elements to illustrate briefly some of the problems of measurements and analysis, as well as to provide additional references. More detail is devoted to three special areas of low-temperature calorimetry that have seen rapid development recently—(1) measurement of the specific heat of highly radioactive samples, (2) measurement of the specific heat of materials in high magnetic fields (18 T), and (3) measurement of the specific heat of very small (100 μg) samples. The review ends with a brief discussion of the frontier research currently underway on microcalorimetry for nanogram sample weights.
TLR8: the forgotten relative revindicated (2012)

The endosomal Toll-like receptors (TLRs) TLR3, TLR7, TLR8 and TLR9 are important in sensing foreign nucleic acids encountered by phagocytes. Because TLR8 was initially thought to be non-functional in mice, less is known about TLR8 than the genetically and functionally related TLR7. Originally associated with the recognition of single-stranded RNA of viral origin, there is now evidence that human TLR8 is also able to sense bacterial RNA released within phagosomal vacuoles, inducing the production of both nuclear factor (NF)-κB-dependent cytokines and type I interferons (IFNs), such as IFN-β. The functions of TLR8 extend beyond the recognition of foreign pathogens and include cross-talk with other endosomal TLRs, a process that may also have a role in the generation of autoimmunity.
Tissue-specific expression of herpes simplex virus thymidine kinase gene delivered by adeno-associated virus inhibits the growth of human hepatocellular carcinoma in athymic mice (1997)

About 70% of hepatocellular carcinomas are known to express alpha-fetoprotein, which is normally expressed in fetal but not in adult livers. To induce herpes simplex virus-thymidine kinase expression in these cancer cells, we constructed an adeno-associated viral vector containing the HSV-TK gene under the control of the alpha-fetoprotein enhancer and albumin promoter. We previously demonstrated in vitro that although this vector can transduce a variety of human cells, only transduced AFP and albumin-expressing hepatocellular carcinoma cell lines were sensitive to killing by ganciclovir (GCV). In the present study, we explored the effect of this vector on hepatocellular carcinoma cells in vivo. Subcutaneous tumors generated in nude mice by implanting hepatocellular carcinoma cells previously transduced with this vector shrank dramatically after treatment with GCV. Bystander effect was also observed on the tumors generated by mixing transduced and untransduced cells. To test whether the tumor cells can be transduced by the virus in vivo, we injected the recombinant adeno-associated virus into tumors generated by untransduced hepatocarcinoma cell line. Tumor growth were retarded after treatment with GCV. These experiments demonstrate the feasibility of in vivo transduction of tumor cell with rAAV.
Enhanced Levels of CD154 (CD40 Ligand) on Platelets in Patients with Chronic Heart Failure (2003)

Our pilot study demonstrates significantly enhanced levels of CD154 on platelets in patients with CHF. This suggests that the CD40-CD154 axis may contribute to the proinflammatory milieu, which exists in CHF and thus may play a pathogenic role in the development and progression of CHF.