gebhart/patrepeval huggingface dataset:
The Synergy Peptide PHSRN and the Adhesion Peptide RGD Mediate Cell Adhesion through a Common Mechanism (2004)

This work reports on the role of the synergy peptide PHSRN in mediating the adhesion of cells. The attachment of baby hamster kidney cells and 3T3 Swiss fibroblasts to model substrates presenting either GRGDS or PHSRN was evaluated using self-assembled monolayers of alkanethiolates on gold presenting the peptide ligands mixed with tri(ethylene glycol) groups. These substrates permit rigorous control over the structures and densities of peptide ligands and at the same time prevent nonspecific interactions with adherent cells. Both cell types attached efficiently to monolayers presenting either the RGD or the PHSRN peptide but not to monolayers presenting scrambled peptide GRDGS or HRPSN. Cell attachment was comparable on substrates presenting either peptide ligand but less efficient than on substrates presenting the protein fibronectin. The degree of cell spreading, however, was substantially higher on substrates presenting RGD relative to PHSRN. Staining of 3T3 fibroblasts with anti-vinculin and phalloidin revealed clear cytoskeletal filaments and focal adhesions for cells attached by way of either RGD or PHSRN. Inhibition experiments showed that the attachment of 3T3 fibroblasts to monolayers presenting RGD could be inhibited completely by a soluble RGD peptide and partially by a soluble PHSRN peptide. IMR 90 fibroblast attachment to monolayers presenting PHSRN could be inhibited with anti-integrin alpha(5) or anti-integrin beta(1) antibody. This work demonstrates unambiguously that PHSRN alone can support the attachment of cells and that the RGD and PHSRN bind competitively to the integrin receptors.
Rapid Synthesis of Biotin-, Digoxigenin-, Trinitrophenyl-, and Fluorochrome-labeled Tyramides and Their Application for In Situ Hybridization Using CARD Amplification (1998)

A one-step procedure for the synthesis of different tyramide conjugates, which can be utilized in the catalyzed reporter deposition (CARD) amplification system, is described. Succinimidyl esters of biotin, digoxigenin, and of the fluorochromes fluorescein, rhodamine, aminomethylcoumarine acetic acid, and Cy3 were coupled to tyramine in dimethylformamide (DMF) adjusted to a pH of 7.0-8.0 with triethylamine (TEA). The coupling reaction can be performed within 2 hr and the reaction mixture can be applied without further purification steps. Furthermore, trinitrophenyl (TNP)-tyramide was prepared by adding 2,4,6,-trinitrobenzenesulfonic acid to tyramine dissolved in either MilliQ/DMF basified with TEA or in an NaHCO3 (pH 9.5) buffer. A subsequent precipitation of the TNP-tyramide resulted in a high-yield isolation of this conjugate. The synthesized tyramide conjugates were applied successfully in single- and multiple-target in situ hybridization (ISH) procedures to detect both repetitive and single-copy DNA target sequences in cell preparations with high efficiency. The described approach provides an easy and fast method to prepare a variety of tyramide conjugates in bulk amounts at relatively low cost.
Radioiodinated versus Radiometal-Labeled Anti–Carcinoembryonic Antigen Single-Chain Fv-Fc Antibody Fragments: Optimal Pharmacokinetics for Therapy (2007)

Antibody fragments with optimized pharmacokinetic profiles hold potential for detection and therapy of tumor malignancies. We studied the behavior of three anti-carcinoembryonic antigen (CEA) single-chain Fv-Fc (scFv-Fc) variants (I253A, H310A, and H310A/H435Q; Kabat numbering system) that exhibited differential serum persistence. Biodistribution studies done on CEA-positive tumor xenografted mice revealed that the 111In-labeled I253A fragment with the slowest clearance kinetics (T1/2beta, 27.7 h) achieved the highest tumor uptake (44.6% ID/g at 24 h), whereas the radiometal-labeled H310A/H435Q fragment with the most rapid elimination (T1/2beta, 7.05 h) reached a maximum of 28.0% ID/g at 12 h postinjection. The H310A protein was characterized by both intermediate serum half-life and tumor uptake. The 111In-based biodistribution studies showed that all three fragments were eliminated primarily through the liver, and hepatic radiometal activity correlated with the rate of fragment clearance. The 111In-labeled H310A/H435Q protein exhibited the highest liver uptake (23.5% ID/g at 24 h). Metabolism of the 125I-labeled scFv-Fc proteins resulted in low normal organ activity. Finally, the 125I/111In biodistribution data allowed for dose estimations, which suggest the 131I-labeled scFv-Fc H310A/H435Q as a promising candidate for radioimmunotherapy.
Non‐Invasive in vivo Imaging in Small Animal Research (2006)

Non-invasive real time in vivo molecular imaging in small animal models has become the essential bridge between in vitro data and their translation into clinical applications. The tremendous development and technological progress, such as tumour modelling, monitoring of tumour growth and detection of metastasis, has facilitated translational drug development. This has added to our knowledge on carcinogenesis. The modalities that are commonly used include Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), bioluminescence imaging, fluorescence imaging and multi-modality imaging systems. The ability to obtain multiple images longitudinally provides reliable information whilst reducing animal numbers. As yet there is no one modality that is ideal for all experimental studies. This review outlines the instrumentation available together with corresponding applications reported in the literature with particular emphasis on cancer research. Advantages and limitations to current imaging technology are discussed and the issues concerning small animal care during imaging are highlighted.
In vivo fluorescence of the ocular fundus exhibits retinal pigment epithelium lipofuscin characteristics. (1995)

Spectral characteristics, correlation with age, topographic distribution, and retinal location between the choriocapillaris and the photoreceptors suggest that the dominant fundus fluorophore is RPE lipofuscin. The minor fluorophore is probably in the neurosensory retina but has not been identified.
Glutamate receptor ligands as anxiolytics. (2001)

The glutamatergic system has received considerable attention over recent years as a potential target for anxiolytic drugs. In spite of the pronounced anxiolytic-like effects of competitive and non-competitive antagonists of NMDA receptors in animal models of anxiety, these substances can not be regarded as potential anxiolytic drugs, mainly due to their side-effect profiles (eg, ataxia, myorelaxation, impairment of learning and memory processes and psychotomimetic effects). Antagonists and partial agonists of the glycine, receptor inhibit function of the NMDA receptor complex and evoke in animals an anxiolytic-like response. Although data concerning anti-anxiety-like effects of glycine, receptor antagonists are not very promising, studies are underway to develop new, brain-penetrating agents devoid of side effects. Further developments are necessary to more fully elucidate the possible involvement of AMPA/kainate receptors in anxiety. The recent discovery of metabotropic glutamate receptors, which modulate the function of the glutamatergic system, offers new hope for discovery of a new generation of anxiolytics. MPEP, a highly selective, brain penetrable, noncompetitive mGlu5 receptor antagonist, evokes anxiolytic-like effects in several animal models of anxiety, remaining remarkably free of side effects. LY-354740, a selective brain-penetrable group II mGlu receptor agonist, evokes marked anxiolytic-like effects in animal models of anxiety. LY-354740 causes mild sedation in mice, does not disturb motor coordination and has no potential to cause dependence. Therefore mGlu receptor ligands may become the anxiolytics of the future, free from the side effects characteristic of benzodiazepines.
Electrochemically Assisted Microbial Production of Hydrogen from Acetate (2005)

Hydrogen production via bacterial fermentation is currently limited to a maximum of 4 moles of hydrogen per mole of glucose, and under these conditions results in a fermentation end product (acetate; 2 mol/mol glucose) that bacteria are unable to further convert to hydrogen. It is shown here that this biochemical barrier can be circumvented by generating hydrogen gas from acetate using a completely anaerobic microbial fuel cell (MFC). By augmenting the electrochemical potential achieved by bacteria in this MFC with an additional voltage of 250 mV or more, it was possible to produce hydrogen at the cathode directly from the oxidized organic matter. More than 90% of the protons and electrons produced by the bacteria from the oxidation of acetate were recovered as hydrogen gas, with an overall Coulombic efficiency (total recovery of electrons from acetate) of 60-78%. This is equivalent to an overall yield of 2.9 mol H2/mol acetate (assuming 78% Coulombic efficiency and 92% recovery of electrons as hydrogen). This bio-electrochemically assisted microbial system, if combined with hydrogen fermentation that produces 2-3 mol H2/mol glucose, has the potential to produce ca. 8-9 mol H2/mol glucose at an energy cost equivalent to 1.2 mol H2/mol glucose. Production of hydrogen by this anaerobic MFC process is not limited to carbohydrates, as in a fermentation process, as any biodegradable dissolved organic matter can theoretically be used in this process to generate hydrogen from the complete oxidation of organic matter.
High-power, high-efficiency 1.3 μm superluminescent diode with a buried bent absorbing guide structure (1989)

A superluminescent diode (SLD) operating in the 1.3 μm wavelength region has been fabricated by the liquid phase epitaxial growth technique. Lasing is effectively suppressed by incorporating an unpumped buried bent guide structure for SLD operation. Devices with an antireflection coating on the front facet emit a high optical power of 11.5 mW at an injection current of dc 200 mA. The Fabry–Perot mode has been sufficiently suppressed over the entire emission spectral bandwidth of 40 nm. The transverse mode is stable and a beam divergence of 48°×33° has been achieved. A coupling power of 1 mW was achieved for the 1.9% Δn, and 2.8-μm-diam core single-mode fiber by butting.
Tunable Plasmonic Nanoparticles with Catalytically Active High-Index Facets (2014)

Noble metal nanoparticles have been of tremendous interest due to their intriguing size- and shape-dependent plasmonic and catalytic properties. Combining tunable plasmon resonances with superior catalytic activities on the same metallic nanoparticle, however, has long been challenging because nanoplasmonics and nanocatalysis typically require nanoparticles in two drastically different size regimes. Here, we demonstrate that creation of high-index facets on subwavelength metallic nanoparticles provides a unique approach to the integration of desired plasmonic and catalytic properties on the same nanoparticle. Through site-selective surface etching of metallic nanocuboids whose surfaces are dominated by low-index facets, we have controllably fabricated nanorice and nanodumbbell particles, which exhibit drastically enhanced catalytic activities arising from the catalytically active high-index facets abundant on the particle surfaces. The nanorice and nanodumbbell particles also possess appealing tunable plasmonic properties that allow us to gain quantitative insights into nanoparticle-catalyzed reactions with unprecedented sensitivity and detail through time-resolved plasmon-enhanced spectroscopic measurements.
A New Assay for the Enzymatic Degradation of Polylactic Acid (2003)

ABSTRACT: A new fluorescent assay for the degradation of polylactic acid was developed based on the reaction of the carboxyl groups of lactic acid and its soluble polymers with a fluorescent agent, o-phthalaldehyde, in the presence of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. The assay was used to show polylactic acid degradation catalyzed by proteinase K, subtilisin Carlsberg and subtilisin BPN′. The proteolytic degradation was shown to be activated or inhibited by the presence of detergent.
Total Synthesis of Everninomicin 13,384-1—Part 1: Retrosynthetic Analysis and Synthesis of the A1B(A)C Fragment (2000)

In this first of a series of four articles we introduce everninomicin 13,384-1 (1), a powerful antibiotic effective against drug resistant bacteria, as a target for total synthesis and discuss its retrosynthetic analysis. From the three defined fragments required for the synthesis (2: A1B(A)C fragment; 4: DE fragment; 5: FGHA2 fragment), we describe herein two approaches to the A1B(A)C block. The first strategy relied on an olefin metathesis reaction to construct a common intermediate for rings B and C, but was faced with final protecting group problems. The second, and successful approach, involved a 1,2-phenylsulfeno migration and a sulfur directed glycosidation procedure to link rings B and C, as well as an acyl fluoride intermediate to install the sterically hindered aryl ester moiety (ring A1). The final stages of the synthesis of the required 2-phenylseleno glycosyl fluoride 2 required introduction of a phenylseleno group at C-1 of ring C followed by a novel, DAST-promoted 1,2-migration to produce the desired 2-beta-phenylseleno glycosyl fluoride moiety.
Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution (2017)

The identification of optimal drug administration schedules to battle the emergence of resistance is a major challenge in cancer research. The existence of a multitude of resistance mechanisms necessitates administering drugs in combination, significantly complicating the endeavor of predicting the evolutionary dynamics of cancers and optimal intervention strategies. A thorough understanding of the important determinants of cancer evolution under combination therapies is therefore crucial for correctly predicting treatment outcomes. Here we developed the first computational strategy to explore pharmacokinetic and drug interaction effects in evolutionary models of cancer progression, a crucial step towards making clinically relevant predictions. We found that incorporating these phenomena into our multiscale stochastic modeling framework significantly changes the optimum drug administration schedules identified, often predicting nonintuitive strategies for combination therapies. We applied our approach to an ongoing phase Ib clinical trial (TATTON) administering AZD9291 and selumetinib to EGFR-mutant lung cancer patients. Our results suggest that the schedules used in the three trial arms have almost identical efficacies, but slight modifications in the dosing frequencies of the two drugs can significantly increase tumor cell eradication. Interestingly, we also predict that drug concentrations lower than the MTD are as efficacious, suggesting that lowering the total amount of drug administered could lower toxicities while not compromising on the effectiveness of the drugs. Our approach highlights the fact that quantitative knowledge of pharmacokinetic, drug interaction, and evolutionary processes is essential for identifying best intervention strategies. Our method is applicable to diverse cancer and treatment types and allows for a rational design of clinical trials. <i>Cancer Res; 77(14); 3908-21. ©2017 AACR</i>.
Procedure for production of hybrid genes and proteins and its use in assessing significance of amino acid differences in homologous tryptophan synthetase alpha polypeptides. (1981)

Hybrid tryptophan synthetase alpha and beta polypeptides were produced by genetic recombination between the trpB--trpA regions of Escherichia coli and Salmonella typhimurium contained on compatible, multicopy plasmids. Intragenic recombination was decreased but still evident in recA cells. Genetic exchange occurred at many sites within trpA, but every recombinant gene produced a functional alpha polypeptide despite many amino acid differences from one or the other of the parental polypeptides. The five hybrid tryptophan synthetase alpha subunits examined resembled the parental polypeptides in catalytic function but differed in thermostability. The stability differences suggest that, as amino acid changes occurred in these proteins during the course of evolution, subsequent changes were limited to those that would allow retention of a desired protein conformation.
Fractionation of Glycopeptides by Affinity Column Chromatography on Concanavalin A-Sepharose1 (1975)

Using [3H]-labeled oligosaccharides, we found that the presence of at least two alpha-mannosyl residues with free hydroxyl groups at C-3, 4, and 6 is required for oligosaccharides to be related by a concanavalin A-Sepharose column. This finding is also applicable to N-[14C]acetylated glycopeptides. Thus, the concanavalin A-Sepharose column might become a useful tool for structural studies of glycopeptides and oligosaccharides and for their fractionation. Glycopeptides prepared from the trypsinate of rat fibroblasts, which has been purified by paper electrophoresis, were further separated into two fractions by chromatography on a concanavalin A-Sepharose column.
On the inhibition of bud development and other functions of growth substance in vicia faba (1934)

Abstract It is well known that when the growing point of a young dicotyledonons plant is removed, the axillary buds lower down the stem grow out strongly, and eventually take the place of main stem. The presence of the terminal bud thus exercises an inhibiting action on the development of the lateral buds, causing them to remain dormant. To a smaller extent the leaves also inhibit the development of buds in their axils, as was shown by Dorsál (1909). The phenomenon has been studied by many workers, among others by Snow, who found (1929, a) that the rapidly growing young leaves in the terminal bud were the most active in inhibiting development of the axilllaries. It appears also, from our experiments, that the rapid growth of a lateral bud is accompanied by inhibition of the bud immediately below it, and a similar behaviour of opposite buds was observed by Dorsál (1926). In a brief preliminary communication (Thimann and Skoog, 1933) it was shown that the inhibiting action of the terminal bud can be imitated by applying the growth substance ("auxin" or "Wuchsstoff") to decapitated plants. These experiments, and others, will now be described more fully; further, the relation between the growth promoting action of growth substance and its effect on bud inhibition will be considered. The first evidence that the inhibition of lateral bud development might be caused by a special substance was brought forward by Snow (1929, b). The work to be described here proves that inhibition can be caused in this way, and shows that the inhibiting substance is almost certainly identical with the hgrowth substance. Literature on the growth substance need not be discussed here (see Nielsen, 1930; du Buy and Nuernbergk, 1932; Thimann and Bonner , 1933); it is only necessary to mention that the substance promotes growth by cell elongation and not by cell division. On this account it has been principally studied in the Avena coleoptile, in which it is produced in the tip and transported in a polar manner towards the base.
A dual axis gas gyroscope utilizing low-doped silicon thermistor (2005)

This paper presents the design, simulation and fabrication of a dual axis semiconductor gas gyroscope. The sensor configuration consists of a piezoelectric pump and a micro thermal sensing element, packaged in an aluminum case with diameter and length of 14mm and 25mm, respectively. Good agreement between the sensitivity simulation results and the experimental data has been realized. This sensor is to be applied in ship anti-rolling and stabilization systems.
Expression and costimulatory effects of the TNF receptor superfamily members CD134 (OX40) and CD137 (4-1BB), and their role in the generation of anti-tumor immune responses (2002)

This study addresses the relative importance of CD134 (OX40) and CD137 (4-1BB) in the costimulation of CD4+ and CD8+ T cells under comparable conditions of antigenic stimulation. We demonstrate that CD134 is capable of directly costimulating CD8+ T cells. However, costimulation of CD8+ T cells by CD134 is less potent than that triggered by CD137. The higher costimulatory activity of CD137, when compared with CD134, correlates well with its faster expression kinetics and higher levels on CD8+ T cells. Furthermore, induction of CD137 expression on CD8+ T cells is highly sensitive to low levels of TCR stimulation, which is in contrast with CD134. Conversely, CD134 is more effective than CD137 in costimulating CD4+ T cells. This, however, could not be attributed to differential expression. We also demonstrate that the transient nature of CD134 and CD137 expression on activated CD4+ T cells is the resultof proteolytic shedding. Consistent with the greater ability of CD137 to costimulate CD8+ T cells, stimulation of CD137 in vivo is considerably more effective than CD134 in augmenting anti-tumor immune responses. Therefore, agents that stimulate signaling via CD137 are likely to be more useful in clinical conditions where highly effective CD8+ CTL responses are required.
Differential and cell type specific expression of murine alpha-interferon genes is regulated on the transcriptional level (1988)

In mouse cells induced with virus infection or dsRNA, the relative levels of alpha-4 interferon mRNA were higher than the levels of alpha-1 and alpha-6 mRNAs; the ratio between relative levels of alpha-4 and alpha-1 or alpha-6 mRNA was, however, dependent on the cell type. Recombinant plasmids, in which the expression of chloramphenicol acetyltransferase (CAT) gene was directed by the promoter regions of alpha-1, alpha-4 or alpha-6 interferon genes were constructed and their inducible expression was studied either in transient assay or in permanently transfected mouse cells. The highest levels of CAT activity and CAT mRNA were observed with alpha-4 CAT plasmid, while the expression of alpha-1 CAT was consistently higher than that coded by alpha-6 CAT plasmid; the ratio between CAT activities coded by alpha-4 CAT and alpha-1 CAT was dependent on cell type. However, in heterologous Vero cells, the transfected alpha-1 and alpha-4 genes were expressed constitutively, and the levels of mRNAs were comparable. These results show that the difference in the relative levels of individual alpha-1 and alpha-4 mRNAs reflects the transcriptional inducibility of the respective promoter regions.
Hemophilia gene therapy: Update (2002)

Gene transfer is an exciting and potentially important treatment approach for hemophilia A and B. Four phase I clinical trials of the safety of gene transfer in hemophilia A or B have been completed and two more trials are currently underway. The results of these trials indicate that gene transfer in hemophilia with the vectors and doses used is safe and well tolerated. Efforts continue to understand the basic biology and improve the efficiency of gene transfer.