gebhart/patrepeval huggingface dataset:
A New Strategy for Large-Scale Preparation of High-Titer Recombinant Adeno-Associated Virus Vectors by Using Packaging Cell Lines and Sulfonated Cellulose Column Chromatography (1996)

The extensive testing of adeno-associated virus (AAV) as a vector for human gene therapy has been hampered by low efficiency of the current packaging system, which is based on transient transfection with plasmid DNAs and infection with adenovirus in permissive cells. In an effort to resolve this problem, HeLa cell-based packaging cell lines were established. These packaging cells carry multiple copies of the AAV genome lacking the inverted terminal repeat (ITR) sequences. The AAV genes were silent in these cells but inducibly expressed by adenovirus infection. When the AAV vector plasmid containing the neoR gene flanked by the ITRs was also integrated into these cells, efficient production of the recombinant AAV particles occurred after adenovirus infection. AAV vector particles in cell lysates could be concentrated by sulfonated cellulose column chromatography. Using the packaging cells and the column chromatography technique, it is possible to prepare AAV vectors with the titer of higher than 10(8) cfu/ml or 5 x 10(10) particles/ml. This new strategy should be useful for testing AAV vectors in vivo.
Novel Selective Agents for the Degradation of Androgen Receptor Variants to Treat Castration-Resistant Prostate Cancer (2017)

Androgen receptor (AR) mediates the growth of prostate cancer throughout its course of development, including in abnormal splice variants (AR-SV)-driven advanced stage castration-resistant disease. AR stabilization by androgens makes it distinct from other steroid receptors, which are typically ubiquitinated and degraded by proteasomes after ligand binding. Thus, targeting AR in advanced prostate cancer requires the development of agents that can sustainably degrade variant isoforms for effective therapy. Here we report the discovery and characterization of potent selective AR degraders (SARD) that markedly reduce the activity of wild-type and splice variant isoforms of AR at submicromolar doses. Three SARDs (UT-69, UT-155, and (R)-UT-155) bind the amino-terminal transcriptional activation domain AF-1, which has not been targeted for degradation previously, with two of these SARD (UT-69 and UT-155) also binding the carboxy-terminal ligand binding domain. Despite different mechanisms of action, all three SARDs degraded wild-type AR and inhibited AR function, exhibiting greater inhibitory potency than the approved AR antagonists. Collectively, our results introduce a new candidate class of next-generation therapeutics to manage advanced prostate cancer. <i>Cancer Res; 77(22); 6282-98. ©2017 AACR</i>.
A Tale of Two Compartments: Interstitial Versus Blood Glucose Monitoring (2009)

Self-monitoring of blood glucose was described as one of the most important advancements in diabetes management since the invention of insulin in 1920. Recent advances in glucose sensor technology for measuring interstitial glucose concentrations have challenged the dominance of glucose meters in diabetes management, while raising questions about the relationships between interstitial and blood glucose levels. This article will review the differences between interstitial and blood glucose and some of the challenges in measuring interstitial glucose levels accurately.
Propagating Intensity Disturbances in Fan-like Coronal Loops: Flows or Waves? (2012)

Quasi-periodic intensity disturbances propagating upward along the coronal structure have been extensively studied using EUV imaging observations from SOHO/EIT and TRACE. They were interpreted as either slow mode magnetoacoustic waves or intermittent upflows. In this study we aim at demonstrating that time series of spectroscopic observations are critical to solve this puzzle. Propagating intensity and Doppler shift disturbances in fanlike coronal loops are analyzed in multiple wavelengths using the sit-and-stare observations from Hinode/EIS. We find that the disturbances did not cause the blue-wing asymmetry of spectral profiles in the warm (∼1.5 MK) coronal lines. The estimated small line-of-sight velocities also did not support the intermittent upflow interpretation. In the hot (∼2 MK) coronal lines the disturbances did cause the blue-wing asymmetry, but the double fits revealed that a high-velocity minor component is steady and persistent, while the propagating intensity and Doppler shift disturbances are mainly due to variations of the core component, therefore, supporting the slow wave interpretation. However, the cause for blueward line asymmetries remains unclear.
Converting sets of polygons to manifold surfaces by cutting and stitching (1998)

Many real world polygonal surfaces contain topological singularities that represent a challenge for processes such as simplification, compression, smoothing, etc. We present an algorithm for removing such singularities, thus converting non manifold sets of polygons to manifold polygonal surfaces (orientable if necessary). We identify singular vertices and edges, multiply singular vertices, and cut through singular edges. In an optional stitching phase, we join surface boundary edges that were cut, or whose endpoints are sufficiently close, while guaranteeing that the surface is a manifold. We study two different stitching strategies called edge pinching and edge snapping; when snapping, special care is required to avoid re-creating singularities. The algorithm manipulates the polygon vertex indices (surface topology) and essentially ignores vertex coordinates (surface geometry). Except for the optional stitching, the algorithm has a linear complexity in the number of vertices edges and faces, and require no floating point operation.
Isolation of a Common Receptor for Coxsackie B Viruses and Adenoviruses 2 and 5 (1997)

A complementary DNA clone has been isolated that encodes a coxsackievirus and adenovirus receptor (CAR). When transfected with CAR complementary DNA, nonpermissive hamster cells became susceptible to coxsackie B virus attachment and infection. Furthermore, consistent with previous studies demonstrating that adenovirus infection depends on attachment of a viral fiber to the target cell, CAR-transfected hamster cells bound adenovirus in a fiber-dependent fashion and showed a 100-fold increase in susceptibility to virus-mediated gene transfer. Identification of CAR as a receptor for these two unrelated and structurally distinct viral pathogens is important for understanding viral pathogenesis and has implications for therapeutic gene delivery with adenovirus vectors.
Is the Formation of AL-Type Amyloid Promoted by Structural Peculiarities of Immunoglobulin L-Chains? Primary Structure of an Amyloidogenic λ-L-Chain (BJP-ZIM) (1987)

A Bence-Jones protein (Protein ZIM) was isolated from the urine of a patient with myeloma-associated amyloidosis. The amino-acid sequence of the variable region of the carboxymethylated protein was established by automatic stepwise degradation of the enzymatically deblocked protein and tryptic peptides thereof. The protein is of the lambda-type of human immunoglobulin L-chains and is closely homologous to subgroup I. In the course of the tryptic digestion a precipitate was formed which showed properties characteristic of amyloid, such as staining with Congo red and green birefringence in polarized light. High-performance liquid chromatography was applied to separate these peptides. The precipitate consists of two peptides which coincide with position 19-45 of the variable and 129-140 of the constant part, respectively. Possible implications of this finding are discussed in the context of amyloid formation after limited proteolytic digestion.
Substrate Nucleotide-Determined Non-Templated Addition of Adenine by Taq DNA Polymerase: Implications for PCR-Based Genotyping and Cloning (1996)

The Applied Biosystems PRISM fluorescence-based genotyping system as well as the Invitrogen TA Cloning vector system are influenced by the tendency of Taq DNA polymerase to add an adenine nucleotide to the 3' end of PCR products after extension. Incomplete addition of adenine to a majority of PCR product strands creates problems in allele-calling during genotyping and potentially diminishes the cloning efficiency of such products. Experiments reported here show that certain terminal nucleotides can either inhibit or enhance adenine addition by Taq and that PCR primer design can be used to modulate this activity. The methods we propose can substantially improve allele-calling for problematic microsatellite markers when using GENOTYPER software.
Platelet Factor 4 Modulates Fibroblast Growth Factor 2 (FGF-2) Activity and Inhibits FGF-2 Dimerization (1998)

Platelet factor 4 (PF-4) inhibits angiogenesis in vitro and in vivo. The mechanism of inhibition is poorly understood. We have investigated the mechanism of inhibition by examining the interaction of PF-4 and the fibroblast growth factor-2 (FGF-2)/fibroblast growth factor receptor (FGFR) system. PF-4 inhibited the binding of FGF-2 to high-affinity and low-affinity binding sites in murine microvascular endothelial cells (LEII cells) and proliferation. Maximum inhibition of binding to endothelial FGF receptors was observed at PF-4 concentrations between 5 and 10 microg/mL (half maximum inhibition at 0.6 micro/mL), and proliferation was completely inhibited at 2 microg/mL. At this concentration, PF-4 reduced internalization of 125I-FGF-2 by threefold and delayed degradation. To gain insight into the mechanism of inhibition, we have analyzed the interaction of PF-4 with FGF-2/FGFR by using mutant heparan sulfate-deficient Chinese hamster ovary (CHO) cells transfected with the FGFR-1 cDNA (CHOm-FGFR-1) and by examining the direct interaction with FGF-2. In the absence of heparin, PF-4 inhibited binding of 125I-FGF-2 to CHOm-FGFR-1 cells in a concentration-dependent manner, although not completely. In the presence of heparin, PF-4 abolished totally the stimulatory effect of heparin. Furthermore, PF-4 complexed to FGF-2 and inhibited endogenous or heparin-induced FGF-2 dimerization. These results indicate that PF-4 interacts with FGF-2 by complex formation, inhibiting FGF-2 dimerization, binding to FGF receptors, and internalization. This mechanism most likely contributes to the antiangiogenic properties of PF-4.
Modulation of biomarkers of inflammation and bone turnover and associations with bone mineral density in ankylosing spondylitis (AS) patients treated with infliximab (2007)

Oregon Hlth & Sci Univ, Portland, OR 97201 USA. Rheumazentrum Ruhrgebiet, Herne, Germany. Univ Hosp Maastricht, Maastricht, Netherlands. Centocor Inc, Res & Dev, Malvern, PA 19355 USA. Univ Hasselt, Diepenbeek, Belgium.
Determination of carrier density of ZnO nanowires by electrochemical techniques (2006)

The carrier density of ZnO nanowires has been determined by means of electrochemical impedance spectroscopy. A model taking into account the geometry of ZnO nanowires has been developed and the differences with the standard flat model, as curved Mott-Schottky plots, are discussed. The as-grown electrodeposited samples present a high donor density of 6.2×1019cm−3, dramatically reduced by two orders of magnitude after an annealing in air at 450°C during 1h. The results show that the surface of the ZnO nanowires is active; therefore this system appears as a useful structure to support a functionalized nanostructured devices.
Ehrlichia chaffeensisExpresses Macrophage- and Tick Cell-Specific 28-Kilodalton Outer Membrane Proteins (2004)

ABSTRACT Ehrlichia chaffeensis , a tick-transmitted rickettsial agent, causes human monocyte/macrophage-tropic ehrlichiosis. In this study, proteomic approaches were used to demonstrate host cell-specific antigenic expression by E. chaffeensis . The differentially expressed antigens include those from the 28-kDa outer membrane protein (p28-Omp) multigene locus. The proteins expressed in infected macrophages are the products of p28-Omp19 and p28-Omp20 genes, whereas in tick cells, the protein expressed is the p28-Omp14 gene product. The differentially expressed proteins are posttranslationally modified by phosphorylation and glycosylation to generate multiple expressed forms. Host cell-specific protein expression is not influenced by growth temperatures and is reversible. Host cell-specific protein expression coupled with posttranslational modifications may be a hallmark for the pathogen's adaptation to a dual-host life cycle and its persistence.
Preventive Treatment with Ketamine Attenuates the Ischaemia-Reperfusion Response in a Chronic Postischaemia Pain Model (2015)

Ischemia and inflammation may be pathophysiological mechanisms of complex regional pain syndrome (CRPS). Ketamine has proposed anti-inflammatory effects and has been used for treating CRPS. This study aimed to evaluate anti-inflammatory and analgesic effects of ketamine after ischaemia-reperfusion injury in a chronic postischaemia pain (CPIP) model of CRPS-I. Using this model, ischemia was induced in the hindlimbs of male Sprague-Dawley rats. Ketamine, methylprednisolone, or saline was administered immediately after reperfusion. Physical effects, (oedema, temperature, and mechanical and cold allodynia) in the bilateral hindpaws, were assessed from 48 hours after reperfusion. Fewer (56%) rats in the ketamine group developed CPIP at the 48th hour after reperfusion (nonsignificant). Ketamine treated rats showed a significantly lower temperature in the ischaemic hindpaw compared to saline (P < 0.01) and methylprednisolone (P < 0.05) groups. Mechanical and cold allodynia were significantly lower in the ischaemic side in the ketamine group (P < 0.05). Proinflammatory cytokines TNF-α and IL-2 were significantly lower at the 48th hour after reperfusion in ketamine and methylprednisolone groups, compared to saline (all P < 0.05). In conclusion, immediate administration of ketamine after an ischaemia-reperfusion injury can alleviate pain and inflammation in the CPIP model and has potential to treat postischaemic pain.
High-velocity microprojectiles for delivering nucleic acids into living cells. 1987. (1992)

A method is described in which DNA or RNA is delivered into plant cells using small tungsten particles (microprojectiles; 4 µm diameter) at high velocity. After acceleration, the particles pierce the cell walls and membranes and enter the intact cells without killing them. Using this method, 1 cm² sections of Allium cepa epidermis were bombarded with tungsten particles coated with plasmid p35S-CAT, containing a gene that encodes chloramphenicol acetyltransferase (CAT). Extracts subsequently obtained from the tissue revealed expression of the gene, in the form of very high levels of CAT activity; controls showed negligible activity. It is suggested that the method can be used to study the transient expression of foreign genes in intact tissue and can possibly provide a broadly applicable means of transformation capable of circumventing the host range restrictions of Agrobacterium tumefaciens and the regeneration problems associated with protoplasts
Regulation of hyaluronan synthase-2 expression in human intestinal mesenchymal cells: mechanisms of interleukin-1β-mediated induction (2005)

Elevated levels of hyaluronan are associated with numerous inflammatory diseases including inflammatory bowel disease. The purpose of this study was to determine whether a cause and effect relationship might exist among proinflammatory cytokines, IL-1beta, TNF-alpha, IFN-gamma, or transforming growth factor-beta (TGF-beta) and hyaluronan expression in human JDMC and, if so, to identify possible mechanisms involved in the induction of hyaluronan expression. TGF-beta, TNF-alpha, and IFN-gamma had little or no effect on hyaluronan production by these cells. Treatment with IL-1beta induced an approximate 30-fold increase in the levels of hyaluronan in the medium of human jejunum-derived mesenchymal cells. Ribonuclease protection analysis revealed that steady-state transcript levels for hyaluronan synthase (HAS)2 were present at very low levels in untreated cells but increased as much as 18-fold in the presence of IL-1beta. HAS3 transcript levels were also increased slightly by exposure of these cells to IL-1beta. Expression of HAS1 transcripts was not detected under any condition in these cells. IL-1beta induction of hyaluronan expression was inhibited in cells transfected with short interfering RNA corresponding to HAS2 transcripts. Inhibitors of the p38 and ERK1/2 mitogen-activated pathways but not JNK/SAPK blocked the IL-1beta-mediated induction of hyaluronan expression and the increase in HAS2 transcript expression. These results suggest that IL-1beta induction of HAS2 expression involves multiple signaling pathways that act in concert, thus leading to an increase in expression of hyaluronan by jejunum-derived mesenchymal cells.
Substantial overproduction of antibodies by applying osmotic pressure and sodium butyrate (1993)

Much of the current cell technology has enabled increased antibody production levels due to judicious nutrient feeding to raise cell densities and design better bioreactors. This study demonstrates that hybridomas can be hyperstimulated to produce higher immunoglobulin (lg) levels by suppressing cell growth and increasing culture longevity through adaptation to higher osmolarity media and addition of sodium butyrate. Prior to adaptation, cells placed in higher osmotic pressures (350 and 400 mOsm) were severely suppressed in growth down to 25% of the control (300 mOsm), although total lg titers achieved were similar to the control, approximately 140 mg/L. After a week of adaptation to 350 and 400 mOsm media, cell growth was not as dramatically suppressed, but considerably higher lg levels were attained at these elevated osmolarities. The highest yield of 265 mg/L was obtained at 350 mOsm compared to 140 mg/L at 300 mOsm, while maximum viable cell numbers dropped from 35 x 10(5) cells/mL to 31 x 10(5) cells/mL and culture longevity was extended by 20 h more than the control. Sodium butyrate, known to enhance protein production in other cell types, was then supplemented at a range of concentrations between 0.01 and 0.4 mM to the 350 mOsm culture to further enhance the lg levels. Butyrate at a concentration of 0.1 mM, in combination with osmotic pressure at 350 mOsm, further elevated the lg levels to 350 mg/L. Concomitantly, maximum viable cell numbers were reduced to 22 x 10(5) cells/mL, but culture longevity was extended by 40 h in the 0.1 mM butyrate supplemented culture compared to the control condition. Specific antibody productivity, q(Mab), continued to stay high during the stationary phase and was further elevated during the decline phase: thus, overall lg levels can be increased by 2.3 times by combining osmotic pressure and butyrate treatment.
Rapid Identification of Intact Whole Bacteria Based on Spectral Patterns using Matrix-assisted Laser Desorption/Ionization with Time-of-flight Mass Spectrometry (1996)

Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was investigated as a method for the rapid identification of whole bacteria, either by comparison with archived reference spectra or by co-analysis with cultures of known bacteria. Bacteria were sampled from colonies on an agar plate, mixed with the matrix, air-dried, and introduced in batches into the mass spectrometer for analysis. In the first experiment, both bacterial strains that had been previously analyzed to obtain reference spectra and other strains that had not been analyzed were blind-numbered and their spectra were obtained. Those strains that matched reference spectra were found to be correctly identified. A second experiment involved co-analysis of reference strains and bind-numbered strains under identical conditions; species-specific identification was demonstrated by comparison of spectra of the blind-numbered strains with those of the standards. In all of the spectra obtained in these experiments, each bacterial strain showed a few characteristic high-mass ions which are thought to be derived from bacterial proteins. This work represents the first reported instance of successful bacterial chemotaxonomy by MALDI-TOFMS analysis of whole cells. For the strains tested, the method is rapid and simple.
ANTIGEN RECOGNITION AND THE IMMUNE RESPONSE (1972)

The low molecular weight compound L-tyrosine-azobenzenearsonate (RAT) induces a cellular immune response in guinea pigs. The contribution of the side chain of tyrosine to the immunogenicity of RAT and the structural requirements at that position for immunogenicity were assessed by synthesizing a series of analogs of RAT containing modifications in the side chain of tyrosine and employing them as immunogens. Removal of either the carboxyl or amino group did not markedly affect immunogenicity, measured by the induction of delayed cutaneous sensitivity, whereas deletion of both completely abolished it. However, a charged group was not required since side chains containing a polar hydroxyl group could substitute for chains bearing an amino or carboxyl group. The size of the side chain exerted a pronounced influence; the charged or polar substituent had to be extended from the phenolic ring by at least two carbon atoms in order to confer immunogenicity.
Importance of L3T4+ and Lyt-2+ cells in the immunologic control of infection with Mycobacterium bovis strain bacillus Calmette-Guérin in mice. Assessment by elimination of T cell subsets in vivo. (1987)

The course of infection after injection of small doses of bacillus Calmette-Guérin (BCG) was studied in mice which were depleted in vivo of T cell subsets by administration of either anti-L3T4 or anti-Lyt-2 mAb. The results presented herein strongly suggest that the L3T4+ subpopulation play a pivotal role in the immunologic control of BCG infection because the depletion of L3T4+ cells led to a dramatic increase in the number of viable bacteria. Depletion of Lyt-2+ cells had no significant effect on the course of infection. These results were confirmed by using adoptive transfer experiments which showed that protective immunity was mediated by L3T4+ cells generated in the spleen as a result of infection. Moreover, T cells capable of controlling the recurrence of BCG multiplication from residual bacteria remaining in organs after the recovery from infection were shown to belong to the L3T4+ subpopulation.
Detection of DNA hybridization by a field‐effect transistor with covalently attached catcher molecules (2006)

Abstract Electronic DNA sensors based on field‐effect transistor (FET) arrays operating in liquid environments offer an alternative method for the detection of biomolecular binding events without the requirement to label the analyte molecules. In order to obtain reproducible signals from such sensors, the attachment of the probe molecules to the gate area of the transistor chips requires a well‐controlled supramolecular architecture. The FET chips used in this work are non‐metallized, 8‐channel transistor devices with micrometer dimensions of the gate structures, which are encapsulated to be dipped into an analyte solution. Two identical chips were functionalized with DNA catcher molecules of different sequences and read out in a differential measurement approach. In this article, we describe the details of the surface modification and covalent attachment of the catcher DNA. The surface modification was characterized by XPS, Fourier transform infrared spectroscopy (FT‐IR), fluorescence microscopy and imaging ellipsometry. Electrical FET recordings of the immobilization and hybridization of DNA molecules are presented. Copyright © 2006 John Wiley &amp; Sons, Ltd.