gebhart/patrepeval huggingface dataset:
Reduction of mdrl Gene Amplification in Human Multidrug-Resistant LoVo DX Cell Line Is Promoted by Triple Helix-Forming Oligonucleotides (1999)

We have demonstrated previously that the GT triplex-forming oligodeoxyribonucleotide (TFO) d(TGTGTTTTTGTTTTGTTGGTTTTGTTT), named TFO ID, targeted to a polypyrimidine-polypurine coding sequence located within human multidrug-resistance mdrl gene, specifically and significantly reduced mdrl mRNA levels in the drug-resistant T-leukemic CEM-VLB100 cell line. In this article, we demonstrate that TFO 1D is effective at inhibiting not only transcription but also replication of mdrl genes, leading to a loss of amplified gene copies in the drug-resistant colon adenocarcinoma LoVo DX cell line. In contrast, TFO ID does not alter replication of the constitutive mdrl gene copy in the corresponding parental sensitive LoVo 109 cell line. A specific reduction in mdrl gene amplification levels was also obtained with the pyrimidine TFO d(CTTTTTCTTTTCTTCCTTTTCTTT), named TFO 24TC, directed against the same polypyrimidine-polypurine sequence of the mdrl gene. We suggest that triple helix-forming oligonucleotides might affect the replication of unstable chromosomal elements as amplicons in actively replicating cells by causing a local impairment of DNA polymerase activity. This study lends support to the notion that TFO may be used to reduce gene amplification aiming to control neoplastic progression in cancer cells bearing amplified oncogenes.
Oral Cromolyn Sodium in Comparison with Elimination Diet in the Irritable Bowel Syndrome, Diarrheic Type Multicenter Study of 428 Patients (1995)

These results confirm the high prevalence of adverse reactions to foods in diarrheic irritable bowel syndrome and the usefulness of cromolyn sodium treatment in these patients.
Imaging arterial thrombosis: comparison of technetium-99m-labeled monoclonal antifibrin antibodies and indium-111-platelets. (1994)

In the large-vessel chronic arterial thrombi studied, the results of 99mTc-labeled monoclonal T2G1s antifibrin Fab' imaging were positive in only one-half of the patients studied, significantly less than the findings with platelet imaging, which were positive in all subjects. The higher rate of positive images with labeled platelets than with labeled antifibrin antibodies may be largely due to thrombus age, with continued platelet deposition but little active fibrin deposition.
The Synthesis of 2′-O-Methyl G-Clamp Containing Oligonucleotides and Their Inhibition of the HIV-1 Tat-TAR Interaction (2003)

We have synthesised a 2'-O-methyl riboside phosphoramidite derivative of the cytosine analogue 9-(2-aminoethoxy)-phenoxazine ('G-clamp') and successfully incorporated it into a series of small steric blocking 2'-O-methyl oligonucleotides targeting the stem-loop region of HIV-1 TAR RNA. The 'G-clamp' containing oligonucleotides show significant increases in binding to a model TAR RNA system when the 'G-clamp' is positioned opposite the loop region. The oligonucleotides also display dose-dependent inhibition of Tat-dependent transcription of an HIV DNA template in HeLa cell nuclear cell extract.
Exploratory biomarker analyses from OAM4558g: A placebo-controlled phase II study of erlotinib with or without MetMAb in patients with advanced non-small cell lung cancer (NSCLC). (2011)

7529 Background: MetMAb, a monovalent anti-cMet receptor antibody, inhibits HGF-mediated activation of c-Met. The Phase II study testing MetMAb in combination with erlotinib in patients with advanced NSCLC (n=128) demonstrated an OS benefit in Met Diagnostic (Dx)+ patients (n=65, defined as ≥50% of tumor cells staining 2+ or 3+ intensity for c-Met by IHC; HR=0.37, p=0.002). Methods: Exploratory tumor biomarkers related to c-Met and/or EGFR signaling were measured by FISH, qRT-PCR or various mutation detection techniques from archival tumor tissue specimens. Plasma HGF levels were measured by ELISA. Analyses with outcome were carried out independent of Met Dx status. Results: Baseline characteristics of patients with evaluable tumor or plasma specimens were generally comparable. MET gene copy number was evaluated in 96 specimens with a median mean copy number of 3.44 copies/cell (range 1.6–25.0) and true gene amplification was detected in 8%. Analysis of different copy number cutoffs revealed a non-significant trend toward improved OS when MET FISH-positivity was defined as ≥5 copies/cell (HR=0.47, p=0.19), but not at lower thresholds ≥4 copies (HR=0.89, p=0.82). An OS HR of 1.37 (95% CI: 0.43-4.36) was observed in 23 patients with both MET and EGFR FISH copy number gains (high polysomy or amplification). EGFR mutations were detected in 12% (13/112) of evaluable specimens; mutations were detected in 6 of 7 patients with objective responses. KRAS mutations were detected in 23% (26/112) of evaluable specimens and status did not affect OS for patients on MetMAb. High expression levels (≥median) of MET, HGF, EGFR, AREG or EREG mRNA did not independently predict an OS benefit. However, in the patient population for whom qRT-PCR data was available (n=67), the OS benefit in Met Dx+ patients was not as apparent (HR=0.69, p=0.48). A trend in improved OS on MetMAb was additionally observed in patients with low (<median) baseline plasma HGF levels (HR=0.46, p=0.11). Conclusions: The data continues to support c-Met IHC as a sensitive and independent predictor of OS benefit from MetMAb. Continued investigation of biomarkers is warranted in future clinical studies.
High-quality strain-relaxed SiGe alloy grown on implanted silicon–on–insulator substrate (2000)

We report on the growth and characterization of high-quality strain-relaxed SiGe alloys on a compliant silicon–on–insulator (SOI) substrate. The annealing temperature required for strain transfer has been reduced through boron implantation to the buried oxide, leading to a high quality SiGe alloy free from dislocations as evident from the near-band gap photoluminescence. Nearly complete strain relaxation (∼95%) for SiGe alloy of a thickness beyond the conventional critical thickness has been obtained.
Morphology‐Controlled Synthesis of SnO2 Nanotubes by Using 1D Silica Mesostructures as Sacrificial Templates and Their Applications in Lithium‐Ion Batteries (2009)

SnO(2) nanotubes with controllable morphologies are successfully synthesized by using a variety of one-dimensional (1D) silica mesostructures as effective sacrificial templates. Firstly, 1D silica mesostructures with different morphologies, such as chiral nanorods, nonchiral nanofibers, and helical nanotubes, are readily synthesized in aqueous solution by using the triblock copolymer Pluronic F127 and the cationic surfactant cetyltrimethylammonium bromide as binary templates. Subsequently, the obtained 1D silica mesostructures are used as sacrificial templates to synthesize SnO(2) nanotubes with preserved morphologies via a simple hydrothermal route, resulting in the formation of well-defined SnO(2) nanotubes with different lengths and unique helical SnO(2) nanotubes with a wealth of conformations. It is revealed that both of the short and long SnO(2) nanotubes showed much better performance as anode materials in lithium-ion batteries than normal SnO(2) nanopowders, which might be related to the hollow structure of the nanotubes that could alleviate the volume changes and mechanical stress during charging/discharging cycling. Moreover, the capacity and cycling performance of short nanotubes, which showed a specific discharge capacity of 468 mAh g(-1) after 30 cycles, are considerably better than those of long nanotubes because of the more robust structure of the short nanotubes.
Immunological Recognition of Peptides in Medicine and Biology (1995)

Modalities of Functional Peptide Characterization Synthetic Peptide Libraries for Research and Drug Discovery, C. Pinilla, J.R. Appel and R. A. Houghten Pepscan to Determine T and B Cell Epitopes, R.H. Meloen, W.C. Puijk, J.P.M. Langeveld, J.P.M. Langedijk, A. van Amerongen, and W.M.M. Schaaper Epitope Mapping Studies with Paper Disc-Bound Peptides, W. van 't Hof, M. van den Berg, and R.C. Aalberse Construction and Utilization of Peptide Libraries Displayed by Filamentous Bacteriophage, G. Cesareni, L. Castagnoli, L. Dente, G. Iannolo, C. Vetriani, F. Felici, A. Luzzago, P. Monaci, A. Nicosia, and R. Cortese The Analysis of Peptide Binding to MHC and of MHC Specificity, S. Buus, L. O. Pedersen, and A. Stryhn Promiscuity and Specificity of T Cell Epitopes, F. Sinigaglia, P. Panina-Bordignon, P. Valsasnini, and J. Hammer Processing of Proteins in the MHC Class II Pathway, J.M. van Noort Use of T Cell Epitopes in Raising Immune Responses, N. D. Zegers and W.J.A. Boersma Structure Function and Synthesis of Special, Derivatized Peptides Progress and Frontiers in Prediction of B and T Cell Epitopes, S. Modrow and H. Wolf Analysis of Peptide and Protein Structure, H.J. Dyson Synthesis, Analysis, and Conformation of Glycopeptides and Phosphopeptides, L. Otvos, Jr., G.I. Szendrei, L. Gorbics, and L. Urge Lipopeptides as Adjuvants and Integrated Adjuvanticity, G. Jung and W.G. Bessler Immunological Recognition of Peptides Optimization of Specific Anti-Peptide Responses: Immunization and Adjuvant, W.J.A. Boersma and Eric Claassen Epitope Specific Detection of Antibodies, E. Claassen and W.J.A. Boersma Multiple Antigen Peptides for Immunization, N.D. Zegers, E. Claassen, and W.J.A. Boersma Effects of Conformation, Amino Acid Sequence, and Carrier Coupling on the Immunological Recognition of Peptide and Protein Antigens, R. Jemmerson The Potency of Peptides in Immune Responses and in Immune Response Analysis: Single Amino Acid Specificity, N.D. Zegers, E. Claassen, and W.J.A. Boersma Preclinical and Experimental Clinical Applications of Peptides Peptide Vaccines, R. Arnon and M. Sela Cytotoxic Epitope-Based Peptide Vaccines, W.M. Kast, R.M.P. Brandt, and C.J.M. Melief Peptide Applications in Autoimmune Disease Research, K. Gerritse
Diabetes, Insulin Resistance, and Metabolic Syndrome in Horses (2012)

Analogous to the situation in human medicine, contemporary practices in horse management, which incorporate lengthy periods of physical inactivity coupled with provision of nutritional rations characterized by inappropriately high sugar and starch, have led to obesity being more commonly recognized by practitioners of equine veterinary practice. In many of these cases, obesity is associated with insulin resistance (IR) and glucose intolerance. An equine metabolic syndrome (MS) has been described that is similar to the human MS in that both IR and aspects of obesity represent cornerstones of its definition. Unlike its human counterpart, identification of the equine metabolic syndrome (EMS) portends greater risk for development of laminitis, a chronic, crippling affliction of the equine hoof. When severe, laminitis sometimes necessitates euthanasia. Unlike the human condition, the risk of developing type 2 diabetes mellitus and many other chronic conditions, for which the risk is recognized as increased in the face of MS, is less likely in horses. The equine veterinary literature has been replete with reports of scientific investigations regarding the epidemiology, pathophysiology, and treatment of EMS.
Experimental autoimmune encephalomyelitis (EAE) mediated by T cell lines: process of selection of lines and characterization of the cells. (1982)

This paper describes alternative ways of deriving lines of rat lymphocytes capable of mediating EAE. The cells were demonstrated to bear markers specific for T lymphocytes and to be negative for surface Ig, and for Fc and complement receptors. The line cells were found to proliferate in vitro specifically in response to myelin basic protein (BP) associated with accessory cells syngeneic at the major histocompatibility complex (MHC). This accessory cell function could not be provided by purified populations of adherent cells from spleen, peritoneal exudates, or bone marrow cultures alone.
Solution-Phase Surface Modification in Intact Poly(dimethylsiloxane) Microfluidic Channels (2006)

An improved approach composed of an oxidation reaction in acidic H2O2 solution and a sequential silanization reaction using neat silane reagents for surface modification of poly(dimethylsiloxane) (PDMS) substrates was developed. This solution-phase approach is simple and convenient for some routine analytical applications in chemistry and biology laboratories and is designed for intact PDMS-based microfluidic devices, with no device postassembly required. Using this improved approach, two different functional groups, poly(ethylene glycol) (PEG) and amine (NH2), were introduced onto PDMS surfaces for passivation of nonspecific protein absorption and attachment of biomolecules, respectively. X-ray electron spectroscopy and temporal contact angle experiments were employed to monitor functional group transformation and dynamic characteristics of the PEG-grafted PDMS substrates; fluorescent protein solutions were introduced into the PEG-grafted PDMS microchannels to test their protein repelling characteristics. These analytical data indicate that the PEG-grafted PDMS surfaces exhibit improved short-term surface dynamics and robust long-term stability. The amino-grafted PDMS microchannels are also relatively stable and can be further activated for modifications with peptide, DNA, and protein on the surfaces of microfluidic channels. The resulting biomolecule-grafted PDMS microchannels can be utilized for cell immobilization and incubation, semiquantitative DNA hybridization, and immunoassay.
Differential Regulatory Capacity of CD25+ T Regulatory Cells and Preactivated CD25+ T Regulatory Cells on Development, Functional Activation, and Proliferation of Th2 Cells (2004)

CD25+ T regulatory (Treg) cells play a central role regarding the maintenance of peripheral tolerance via suppression of autoaggressive CD4+ T cells, CD8+ T cells, and Th1 cells. In this study we demonstrate that CD25+ Treg cells can also suppress the differentiation of murine conventional CD4+ T cells toward Th2 cells in a contact-dependent manner. However, the cytokine production and proliferation of established Th2 cells could not be inhibited by freshly isolated CD25+ Treg cells, whereas a strong inhibition of differentiated Th2 cells by in vitro preactivated CD25+ Treg cells could be observed. Inhibition of both conventional CD4+ T cells and Th2 cells is accompanied by a strong enhancement of the expression of FoxP3 in the suppressed T cells. Hence, our study indicates that CD25+ Treg cells have a therapeutic potential for Th2-mediated diseases and suggests a novel mechanism of suppression mediated by the transcriptional repressor FoxP3.
Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. (1992)

Control elements of the tetracycline-resistance operon encoded in Tn10 of Escherichia coli have been utilized to establish a highly efficient regulatory system in mammalian cells. By fusing the tet repressor with the activating domain of virion protein 16 of herpes simplex virus, a tetracycline-controlled transactivator (tTA) was generated that is constitutively expressed in HeLa cells. This transactivator stimulates transcription from a minimal promoter sequence derived from the human cytomegalovirus promoter IE combined with tet operator sequences. Upon integration of a luciferase gene controlled by a tTA-dependent promoter into a tTA-producing HeLa cell line, high levels of luciferase expression were monitored. These activities are sensitive to tetracycline. Depending on the concentration of the antibiotic in the culture medium (0-1 microgram/ml), the luciferase activity can be regulated over up to five orders of magnitude. Thus, the system not only allows differential control of the activity of an individual gene in mammalian cells but also is suitable for creation of "on/off" situations for such genes in a reversible way.
Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway (2012)

Most organisms are simply diamagnetic, while magnetotactic bacteria and migratory animals are among organisms that exploit magnetism. Biogenic magnetization not only is of fundamental interest, but also has industrial potential. However, the key factor(s) that enable biogenic magnetization in coordination with other cellular functions and metabolism remain unknown. To address the requirements for induction and the application of synthetic bio-magnetism, we explored the creation of magnetism in a simple model organism. Cell magnetization was first observed by attraction towards a magnet when normally diamagnetic yeast Saccharomyces cerevisiae were grown with ferric citrate. The magnetization was further enhanced by genetic modification of iron homeostasis and introduction of ferritin. The acquired magnetizable properties enabled the cells to be attracted to a magnet, and be trapped by a magnetic column. Superconducting quantum interference device (SQUID) magnetometry confirmed and quantitatively characterized the acquired paramagnetism. Electron microscopy and energy-dispersive X-ray spectroscopy showed electron-dense iron-containing aggregates within the magnetized cells. Magnetization-based screening of gene knockouts identified Tco89p, a component of TORC1 (Target of rapamycin complex 1), as important for magnetization; loss of TCO89 and treatment with rapamycin reduced magnetization in a TCO89-dependent manner. The TCO89 expression level positively correlated with magnetization, enabling inducible magnetization. Several carbon metabolism genes were also shown to affect magnetization. Redox mediators indicated that TCO89 alters the intracellular redox to an oxidized state in a dose-dependent manner. Taken together, we demonstrated that synthetic induction of magnetization is possible and that the key factors are local redox control through carbon metabolism and iron supply.
A Transverse Flow Repetitive Dye Laser (1970)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Boiteux and O. de Witte, "A Transverse Flow Repetitive Dye Laser," Appl. Opt. 9, 514-515 (1970) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
TAZ, a Transcriptional Modulator of Mesenchymal Stem Cell Differentiation (2005)

Mesenchymal stem cells (MSCs) are a pluripotent cell type that can differentiate into several distinct lineages. Two key transcription factors, Runx2 and peroxisome proliferator-activated receptor gamma (PPARgamma), drive MSCs to differentiate into either osteoblasts or adipocytes, respectively. How these two transcription factors are regulated in order to specify these alternate cell fates remains a pivotal question. Here we report that a 14-3-3-binding protein, TAZ (transcriptional coactivator with PDZ-binding motif), coactivates Runx2-dependent gene transcription while repressing PPARgamma-dependent gene transcription. By modulating TAZ expression in model cell lines, mouse embryonic fibroblasts, and primary MSCs in culture and in zebrafish in vivo, we observed alterations in osteogenic versus adipogenic potential. These results indicate that TAZ functions as a molecular rheostat that modulates MSC differentiation.
Improved tumor targeting with chemically cross-linked recombinant antibody fragments. (1994)

The construction and use of recombinant chimeric and later fully humanized (CDR-grafted) antibodies to tumor-associated antigens has reduced the immune response generated to these antibodies in clinical studies. However, their long circulating half-life is a disadvantage for tumor imaging and therapy. Fragments such as F(ab')2, Fab', Fv and single chain Fv (scFv) offer faster blood clearance but also lower overall tumor doses. We have examined the tumor targeting of several novel fragments produced by chemical cross-linking of Fab' or scFv to dimeric and trimeric species. To facilitate cross-linking of Fab' fragments, a chimeric B72.3 Fab' fragment has been expressed with a hinge sequence containing a single cysteine residue. B72.3 scFv was also produced with a similar hinge region peptide attached to the COOH terminus to allow cross-linking. These fragments, Fab' delta Cys and scFv' delta Cys were cross-linked with linkers containing two or three maleimide groups to produce dimeric and trimeric molecules with increased avidity for antigen. Cross-linkers were also designed to contain a 12-N-4 macrocycle capable of stable radiolabeling with 90Y. This allowed the production of site-specifically-labeled, fully immunoreactive proteins. Biodistribution studies in the nude mouse LS174T xenograft model with scFv, di-scFv, and tri-scFv demonstrated that these fragments clear extremely rapidly from the circulation and give rise to only low levels of activity accumulated at the tumor. Di-Fab (DFM) and tri-Fab (TFM) however, accumulated relatively high levels of activity at the tumor with high tumor:blood ratios generated, demonstrating improved targeting compared to IgG. cB72.3 90Y-labeled tri-Fab was found not to accumulate in the kidney or the bone, resulting in an attractive antibody fragment for tumor therapy.
Piezoelectric transducer design for a miniaturized injectable acoustic transmitter (2015)

Acoustic telemetry has been an important tool in the last 20 years for studying fish survival and migration behaviors during and after dam passage. This technology uses implantable acoustic transmitters as tags to three-dimensionally track the movement of fish. However, the relatively large weights and sizes of commercially available transmitters limit the populations of fish that could be studied. The surgical implantation procedures required may also injure fish and also incur a significant amount of labor. Therefore, a smaller, lighter, and injectable tag was needed, and similar or better acoustic performance and service life over that provided by existing commercial tags was desired. To develop such a small transmitter, a number of technical challenges, including design optimization of the piezoelectric transducer, needed to be overcome. The goal of our efforts to optimize the transducer focused on improving the average source level in the 180° range in which the transmitter was facing the receiving hydrophone, so as to increase the transmitter’s detection probability. This paper reports the techniques that were explored and developed to achieve this goal. We found that a novel off-center tube transducer improved the average source level of the front half of the transducer by 1.5 dB. An acoustic reflector attached to the back of the transducer also improved the source level by 3 dB when the transducer was pointed toward the receiving hydrophone, although the source level on the sides of the transducer was reduced. We found that too small a gap between the transducer and the component placed behind it resulted in distortion of the beam pattern. To overcome that issue, we connected a tuning inductor in series with the transducer to help optimize the source level. Furthermore, the findings and techniques developed in this work contributed to the successful development and implementation of a new injectable transmitter.