gebhart/patrepeval huggingface dataset:
Targeted Delivery of Plasmid DNA to Myogenic Cells via Transferrin-Conjugated Peptide Nucleic Acid (2000)

We describe a novel approach to conjugate a targeting ligand to plasmid DNA without affecting either its supercoiled conformation or its ability to be efficiently transcribed. A 14-mer peptide nucleic acid (PNA) containing lysine and cysteine on each end was designed to target to a unique sequence located at the antibiotic resistance gene of the plasmid. The binding of PNA to the plasmid was found to be dose-dependent and sequence-specific and not to change the conformation of the plasmid. Transferrin (Tf) was conjugated with PNA via a reversible disulfide bond using N-succinimidyl-3-(2-pyridyldithio)propionate. Tf-PNA retained the ability to the plasmid in a sequence-specific manner. The efficiency of this bioconjugate for delivering plasmid was examined in cultured myoblasts and myotubes. Naked DNA and Tf-PNA/DNA showed no transfection activity in either myoblasts or myotubes. Polyethyleneimine (PEI) is required for significant increase of the transfection efficiency. At N:P ratio of 5, Tf-PNA enhanced gene transfection about fourfold over that of the DNA/PEI complex in both myoblasts and myotubes. This enhancement could be inhibited by excess free Tf, indicating that the enhancement of transfection was through Tf-mediated endocytosis. These findings suggest that this targeting system may have the potential for gene transfer to myogenic cells in vivo.
Two Synthetic Antibodies that Recognize and Neutralize Distinct Proteolytic Forms of the Ebola Virus Envelope Glycoprotein (2012)

Ebola virus (EBOV) is a highly pathogenic member of the Filoviridae family of viruses that causes severe hemorrhagic fever. Infection proceeds through fusion of the host cell and viral membranes, a process that is mediated by the viral envelope glycoprotein (GP). Following endosomal uptake, a key step in viral entry is the proteolytic cleavage of GP by host endosomal cysteine proteases. Cleavage exposes a binding site for the host cell receptor Niemann-Pick C1 (NPC1) and may induce conformational changes in GP leading to membrane fusion. However, the precise details of the structural changes in GP associated with proteolysis and the role of these changes in viral entry have not been established. Here, we have employed synthetic antibody technology to identify antibodies targeting EBOV GP prior to and following proteolysis (i.e. in the "uncleaved" [GP(UNCL)] and "cleaved" [GP(CL)] forms). We identified antibodies with distinct recognition profiles: Fab(CL) bound preferentially to GP(CL) (EC(50)=1.7 nM), whereas Fab(UNCL) bound specifically to GP(UNCL) (EC(50)=75 nM). Neutralization assays with GP-containing pseudotyped viruses indicated that these antibodies inhibited GP(CL)- or GP(UNCL)-mediated viral entry with specificity matching their recognition profiles (IC(50): 87 nM for IgG(CL); 1 μM for Fab(UNCL)). Competition ELISAs indicate that Fab(CL) binds an epitope distinct from that of KZ52, a well-characterized EBOV GP antibody, and from that of the luminal domain of NPC1. The binding epitope of Fab(UNCL) was also distinct from that of KZ52, suggesting that Fab(UNCL) binds a novel neutralization epitope on GP(UNCL). Furthermore, the neutralizing ability of Fab(CL) suggests that there are targets on GP(CL) available for neutralization. This work showcases the applicability of synthetic antibody technology to the study of viral membrane fusion, and provides new tools for dissecting intermediates of EBOV entry.
AnalysIs of the primary structure and promoter function of a pyruvate decarbozylase gene (PDCI) fromSaceharomyces cerevisiae (1986)

The PDC1 gene of Saccharomyces cerevisiae, encoding pyruvate decarboxylase was sequenced. The gene contains an open reading frame of 1647 base pairs. The codon usage shows the same strong bias as found for some other glycolytic enzymes. Transcription starts mainly at -30 and terminates 100 base pairs downstream of the termination codon. In some strains a second termination site, 46 base pairs upstream of the stop codon was observed. The function of the promoter region was analyzed by fusion to the bacterial structural gene encoding beta-lactamase (bla). On multicopy plasmid or integrated in the genome, the expression of the bla gene showed the regulation of the authentic PDC1 gene.
Alpha-naphthoflavone acts as an antagonist of 2,3,7, 8-tetrachlorodibenzo-p-dioxin by forming an inactive complex with the Ah receptor. (1991)

alpha-Naphthoflavone (ANF) has previously been shown to compete with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) for binding to the Ah receptor under conditions in vitro. However, ANF also prevents TCDD-elicited cytochrome P450lA1 induction, immunosuppression, and down-regulation of the estrogen receptor in vivo and within intact isolated cells. These data suggest that ANF is a TCDD antagonist. This study investigated the ability of ANF to transform the Ah receptor contained in rat hepatic cytosol or mouse hepatoma cells to a form that recognizes the dioxin-responsive enhancer element (DRE) upstream of the cytochrome P450lA1 gene. Gel retardation analysis indicated that TCDD- or beta-naphthoflavone (BNF)-bound receptor was able to bind to the DRE, whereas essentially no receptor-DRE complexes were observed using cytosol incubated with ANF concentrations as high as 1000 nM. Furthermore, an excess of ANF, when added to cytosol just before TCDD, blocked, in a concentration-dependent manner, the ability of TCDD to transform the receptor to a form that bound to the DRE. These studies indicated that ANF binds to the receptor and confers on it a conformation that cannot recognize the DNA recognition sequence contained in the DRE. Although an excess of the agonist 2,3,7,8-tetrachlorodibenzofuran (TCDF) readily reversed the inhibitory actions of ANF, ANF was unable to reverse the effects of TCDD, TCDF, or BNF on the receptor. These studies suggested that TCDD binding, unlike that of ANF, results in a receptor conformation that has higher affinity for the ligand. Treatment of mouse hepatoma Hepa 1c1c7 cells with TCDD or BNF resulted in receptor contained in nuclear extracts that bound to the DRE. Only a very minor ligand-dependent protein-DNA complex was detected when cells were treated with ANF. These data indicated that ANF acts as an antagonist of TCDD by directly binding to the Ah receptor and eliciting a protein conformation that has very low affinity for DNA.
Effects of Lead on Growth Plate Chondrocyte Phenotype (1996)

Lead toxicity is a major public health problem in the United States. The skeleton serves as the major reservoir for ingested lead, where it is incorporated into bone matrix during calcification. While lead in bone has been considered inactive, mounting clinical and epidemiological data has shown a strong correlation between lead exposure and adverse effects on stature in children. These epidemiologic data suggest a direct effect of lead on skeletal development, but whether it reflects a systemic effect, a specific effect on osteoblasts, or an effect on the epiphyseal growth plate is as yet unclear. This study examined the effects of lead on parameters of cartilage biology in isolated chondrocytes. Changes in growth plate chondrocyte phenotype were assessed utilizing an established avian growth plate chondrocyte model. Low, sublethal doses of lead caused specific and significant effects on a number of important markers of growth plate chondrocyte phenotype, including suppression of alkaline phosphatase and both type II and type X collagen expression at the protein and mRNA levels, and a decrease in thymidine incorporation. In contrast, proteoglycan synthesis was stimulated relative to controls in lead-treated cultures, suggesting that the alterations in collagen and DNA synthesis and alkaline phosphatase activity are not due to cytotoxity. The data demonstrate important regulatory effects of lead on growth plate chondrocytes in cell culture and suggest an inhibitory effect on the process of endochondral bone formation. The growth plate may be one of the key target tissues accounting for the adverse effects of chronic lead exposure on skeletal development.
Attachment of artificial cartilage to underlying bone (2003)

The key problem with artificial joint materials is obtaining quick and firm attachment onto the underlying bone. In developing artificial articular cartilage, composed of polyvinyl alcohol hydrogel (PVA-H), this problem was solved by using a composite osteo-chondral device (COD). This enables attachment within four weeks post-operation by massive bone ingrowth into the pores. The COD consists of PVA-H as an artificial cartilage and titanium fiber mesh (TFM) as porous artificial bone. In this study, the strength of the shear resistance force at the interface of the PVA-H and the TFM fabricated by injection molding and the changes in the mechanical properties of the PVA-H fabricated by high temperature during the injection-molding process were examined. The shear resistance force was strengthened markedly by using injection molding and no important deterioration of the PVA-H was found. Morphological examination of canine spines, to which artificial intervertebral discs made of the COD were implanted, showed good bonding of the COD with the vertebral bodies for an extended period of 30 months, and encouraged us to use the COD clinically.
N‐Heterocyclic Carbene and Phosphine Ruthenium Indenylidene Precatalysts: A Comparative Study in Olefin Metathesis (2007)

Kinetic studies on ring-closing metathesis of unhindered and hindered substrates using phosphine and N-heterocyclic carbene (NHC)-containing ruthenium-indenylidene complexes (first and second generation precatalysts, respectively) have been carried out. These studies reveal an appealing difference, between the phosphine and NHC-containing catalysts, associated with a distinctive rate-determining step in the reaction mechanism. These catalysts have been compared with the benzylidene generation catalysts and their respective representative substrates. Finally, the reaction scope of the two most interesting precatalysts, complexes that contain tricyclohexylphosphine and 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (SIMes), has been investigated for the ring-closing and enyne metathesis for a large range of olefins. Owing to their high thermal stability, the SIMes-based indenylidene complexes were more efficient than their benzylidene analogues in the ring-closing metathesis of tetrasubstituted dienes. Importantly, none of the indenylidene precatalysts were found to be the most efficient for all of the substrates, indeed, a complementary complex-to-substrate activity relationship was observed.
Rational Design of Peptide-Based HIV Proteinase Inhibitors (1990)

A series of peptide derivatives based on the transition-state mimetic concept has been designed that inhibit the proteinase from the human immunodeficiency virus (HIV). The more active compounds inhibit both HIV-1 and HIV-2 proteinases in the nanomolar range with little effect at 10 micromolar against the structurally related human aspartic proteinases. Proteolytic cleavage of the HIV-1 gag polyprotein (p55) to the viral structural protein p24 was inhibited in chronically infected CEM cells. Antiviral activity was observed in the nanomolar range (with one compound active below 10 nanomolar) in three different cell systems, as assessed by p24 antigen and syncytium formation. Cytotoxicity was not detected at 10 and 5 micromolar in C8166 and JM cells, respectively, indicating a high therapeutic index for this new class of HIV proteinase inhibitors.
A Directed Approach for Engineering Conditional Protein Stability Using Biologically Silent Small Molecules (2007)

The ability to regulate the function of specific proteins using cell-permeable molecules can be a powerful method for interrogating biological systems. To bring this type of "chemical genetic" control to a wide range of proteins, we recently developed an experimental system in which the stability of a small protein domain expressed in mammalian cells depends on the presence of a high affinity ligand. This ligand-dependent stability is conferred to any fused partner protein. The FK506- and rapamycin-binding protein (FKBP12) has been the subject of extensive biophysical analyses, including both kinetic and thermodynamic studies of the wild-type protein as well as dozens of mutants. The goal of this study was to determine if the thermodynamic stabilities (DeltaDeltaG(U-F)) of various amino acid substitutions within a given protein are predictive for engineering additional ligand-dependent destabilizing domains. We used FKBP12 as a model system and found that in vitro thermodynamic stability correlates weakly with intracellular degradation rates of the mutants and that the ability of a given mutation to destabilize the protein is context-dependent. We evaluated several new FKBP12 ligands for their ability to stabilize these mutants and found that a cell-permeable molecule called Shield-1 is the most effective stabilizing ligand. We then performed an unbiased microarray analysis of NIH3T3 cells treated with various concentrations of Shield-1. These studies show that Shield-1 does not elicit appreciable cellular responses.
Specificity and Biomineralization Activities of Ti-Binding Peptide-1 (TBP-1) (2005)

Numerous peptide aptamers that recognize inorganic materials have been isolated using in vitro peptide evolution systems. However, it remains unknown how peptides interact with inorganic materials or how specific those interactions are. We, therefore, assessed the target specificities of the peptide aptamer TBP-1 (RKLPDAPGMHTW) by monitoring its ability to bind 10 different metals. We found that phages displaying TBP-1 bound to Ti, Si, and Ag surfaces but not to Au, Cr, Pt, Sn, Zn, Cu, or Fe. As previously seen with Ti, binding to Si and Ag was diminished by R1A, P4A, or D5A mutation, suggesting that the same molecular mechanism underlies TBP-1 binding to all three materials. We also observed that a synthetic TBP-1 peptide mediated mineralization of both silica and Ag. It, thus, appears that although the overall chemical characteristics of Ti, Si, and Ag surfaces are dissimilar, they share a common subnanometric structure that is recognized by TBP-1.
Repeated Exposure of Tendon to Prostaglandin-E2 Leads to Localized Tendon Degeneration (2005)

It is known that human tendon fibroblasts produce PGE(2) in vitro and in vivo in response to repetitive mechanical loading. This study demonstrates that repetitive exposure of the tendon to PGE(2) can result in degenerative changes within the tendon. Therefore, PGE(2) produced by tendon fibroblasts in response to repetitive mechanical loading in vivo might contribute to the development of exercise-induced tendinopathy.
EFFECTS OF 6‐[p‐(4‐PHENYLACETYLPIPERAZIN‐1‐YL)PHENYL]‐4,5‐DIHYDRO‐3(2H)PYRIDAZINONE (CCI 17810) AND ASPIRIN ON PLATELET AGGREGATION AND ADHESIVENESS (1981)

1. The effects of 6-[p-(4-phenylacetylpiperazin-1-yl)]-4,5-dihydro-3(2H)pyridazinon (CCI 17810) on platelet aggregation and adhesiveness have been investigated and compared with those of aspirin. 2. In vitro, CCI 17810 was a potent inhibitor of the aggregation of human platelets induced by collagen, adenosine 5'-diphosphate (ADP) (primary response), thrombin and arachidonic acid, with EC50 values in the range 0.5 to 10 micrograms/ml. The second phase of the response to adrenaline was blocked by concentrations in the range 15 to 25 micrograms/mg. Platelets from rats, rabbits and dogs were as sensitive as human platelets to the effects of CCI 17810. Aspirin was nearly as effective as CCI 17810 against collagen, and adrenaline but about 10 times less active against arachidonic acid; it did not inhibit the primary response to ADP and was only a weak inhibitor of thrombin-induced aggregation. 3. In mice, single oral doses of CCI 17810 in the range 12.5 to 100 mg/kg inhibited collagen-induced thrombocytopenia. Arachidonic acid-induced mortality was markedly reduced by 10 mg/kg and possibly slightly reduced by 1 mg/kg. Aspirin was considerably less active than CCI 17810 in inhibiting collagen-induced thrombocytopenia but was almost as active as CCI 17810 in reducing arachidonic acid-induced mortality. 4. In vitro, CCI 17810 reduced the adhesiveness of human platelets to glass beads (retention of platelets in glass bead columns). Single oral doses of CCI 17810 in the range 25 to 200 mg/kg reduced mouse platelet adhesiveness; rat platelet adhesiveness was reduced by doses in the range 12.5 to 100 mg/kg. Aspirin (20 or 200 mg/kg) slightly increased mouse platelet adhesiveness.
A Novel Temporal Access Control Scheme for Outsourced Data in Cloud with User Revocation (2017)

E-governance can be implemented very effectively using the cloud computing technologies. Security and privacy of data are the major challenges in cloud-based e-governance systems. With proper access control and user revocation schemes, we can protect the privacy and security of data stored in cloud servers used for e-governance. There are a lot of techniques to achieve the controlled access in cloud computing. In some applications of e-government, the users should be allowed to access data, only for a specific period of time. In this paper, we introduce a temporal access control scheme based on attribute-based encryption (ABE), which allows users to access the data according to their access policy and for a specific time period only. Our model includes both the temporal access scheme and a time-based proxy re-encryption scheme to allow a user's access right to expire automatically.
Adenovirus-directed Expression of Dominant Negative Estrogen Receptor Induces Apoptosis in Breast Cancer Cells and Regression of Tumors in Nude Mice (2001)

These results indicate that dominant negative ER mutants have the potential to induce apoptosis of T47D cells and regression of tumors. The delivery of dominant negative ERs by adenoviral vectors may provide a useful tool for targeted therapy of ER-positive breast cancer.
Security and QoS Self-Optimization in Mobile Ad Hoc Networks (2008)

Network quality-of-service and network security have been considered as separate entities and research in these areas have largely proceeded independently. However, security impacts overall QoS and it is therefore essential to consider both security and QoS together when designing protocols for ad hoc environments as one impacts the other. In this paper we propose a mechanism for a distributed dynamic management system which aims to maximize QoS and/or security while maintaining a minimum user acceptable level of QoS and/or security even as network resource availability change. In order to achieve this objective, we propose three basic frameworks: a policy based plug-in security framework, multi-layer QoS guided routing and a proportional integral derivative (PID) controller. Simulation results indicate the proposed PID optimized security and QoS algorithm produce similar performance as non-secure QoS routing protocols under various traffic loads.
Genetic Analysis of a Poliovirus/Hepatitis C Virus Chimera: New Structure for Domain II of the Internal Ribosomal Entry Site of Hepatitis C Virus (2001)

Internal ribosomal entry sites (IRESs) of certain plus-strand RNA viruses direct cap-independent initiation of protein synthesis both in vitro and in vivo, as can be shown with artificial dicistronic mRNAs or with chimeric viral genomes in which IRES elements were exchanged from one virus to another. Whereas IRESs of picornaviruses can be readily analyzed in the context of their cognate genome by genetics, the IRES of hepatitis C virus (HCV), a Hepacivirus belonging to Flaviviridae, cannot as yet be subjected to such analyses because of difficulties in propagating HCV in tissue culture or in experimental animals. This enigma has been overcome by constructing a poliovirus (PV) whose translation is controled by the HCV IRES. Within the PV/HCV chimera, the HCV IRES has been subjected to systematic 5' deletion analyses to yield a virus (P/H710-d40) whose replication kinetics match that of the parental poliovirus type 1 (Mahoney). Genetic analyses of the HCV IRES in P/H710-d40 have confirmed that the 5' border maps to domain II, thereby supporting the validity of the experimental approach applied here. Additional genetic experiments have provided evidence for a novel structural region within domain II. Arguments that the phenotypes observed with the mutant chimera relate solely to impaired genome replication rather than deficiencies in translation have been dispelled by constructing novel dicistronic poliovirus replicons with the gene order [PV]cloverleaf-[HCV]IRES-Deltacore-R-Luc-[PV]IRES-F-Luc-P2,3-3'NTR, which have allowed the measurement of HCV IRES-dependent translation independently from the replication of the replicon RNA.
Short term methotrexate therapy in psoriasis. (1994)

Data on 82 psoriatics (62 males and 20 females) with either chronic recalcitrant, erythrodermic, generalized pustular or severe palmoplantar psoriasis treated with methotrexate (MTX) have been reviewed. MTX was given in a single oral weekly dose of 3.75-30 mg based on body weight. Seven patients with a relative contraindication for MTX use were also treated safely with MTX. An attempt was made to withdraw MTX as quickly as possible with the intention of providing drug free period of 4-6 months coinciding this period with the seasonal remissions in disease activity. MTX could be withdrawn in up to 90 per cent patients within an average of 25 wk. The total cumulative dose could also be reduced by this method as also the need to repeat liver biopsies.
Circulating selectins, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1 in hyperthyroidism. (1995)

Serum concentrations of soluble intercellular adhesion molecule-1 (sICAM-1), soluble vascular cell adhesion molecule-1 (sVCAM-1), soluble E-selectin (sE-selectin), soluble P-selectin, and soluble L-selectin (sL-selectin), tumor necrosis factor-alpha, and interleukin-6 were measured in patients with Graves' disease (GD) (n = 33), in patients with toxic nodular goiter (n = 34), and in a group of healthy controls (n = 36). The serum levels of sICAM-1, sVCAM-1, sE-selectin, and sL-selectin were markedly elevated in patients with GD and in patients with toxic nodular goiter before treatment with methimazole (P < 0.05 for all). After 8 weeks of therapy, serum concentrations of sVCAM-1 and sE-selectin normalized, whereas serum levels of sL-selectin and sICAM-1 remained elevated. Hormone concentrations normalized after 2 weeks, clearly preceding falling levels of circulating adhesion molecules. Serum concentrations of soluble P-selectin, TNF-alpha, and interleukin-6 did not differ among patients with GD and toxic nodular goiter and healthy subjects. Serum levels of sVCAM-1 and sICAM-1 correlated with the serum concentrations of TSH receptor antibodies (n = 33; r = 0.921 and r = 0.792, respectively) and thyroid peroxidase antibodies (n = 33; r = 0.682 and r = 0.761, respectively) but not thyroglobulin antibodies. However, no correlation between serum levels of sE-selectin, sL-selectin, and soluble P-selectin or cytokines and serum levels of thyroid peroxidase antibodies, TSH receptor antibodies, or thyroglobulin antibodies, respectively, was found. In addition, no correlation between serum levels of adhesion molecules or cytokines and thyroid hormones was seen. We conclude that both the action of thyroid hormones and the autoimmune process in GD may contribute to elevated levels of soluble adhesion molecules.