gebhart/patrepeval huggingface dataset:
Characterization of Novel Human Hepatoma Cell Lines with Stable Hepatitis B Virus Secretion for Evaluating New Compounds against Lamivudine- and Penciclovir-Resistant Virus (2000)

L-Nucleoside analogs are new therapeutic agents for treatment of chronic hepatitis B. However, their clinical application was limited by the emergence of viral resistance. It is important to develop a new system to evaluate drug cross-resistance and to test new agents that may overcome resistant virus. In this report, three cell lines HepG2-WT10, HepG2-SM1, and HepG2-DM2 are presented; these cell lines were established by transfection of HepG2 cells with unique fully functional 1.1x hepatitis B virus (HBV) genomes: wild-type HBV-adr and its L526M and L526MM550V variants, respectively. We have demonstrated that these genomes have different susceptibilities to lamivudine [L(-)SddC] and penciclovir (PCV). By examining HBV RNA transcription, antigen expression, progeny DNA replication, and viral susceptibilities to L(-)SddC, PCV, and other nucleoside analogs, it is concluded that the cell lines are able to stably produce L(-)SddC- and PCV-sensitive and -resistant HBV virions. In addition, the relative susceptibilities of the wild-type and mutant HBV produced from the stably transfected cell lines to several anti-HBV nucleoside analogs were also examined and found to be about the same as those found by using a transient infection system. PMEA [9-(2-phosphonylmethoxytehyl)-adenine] and QYL685 are able to suppress L(-)SddC- and PCV-resistant HBV. In conclusion, this cell culture system is a novel and useful tool for evaluating anti-HBV compounds and biologics.
The enterococci : pathogenesis, molecular biology, and antibiotic resistance (2002)

Table of Contents 1. History, Taxonomy, Biochemical Characteristics, and Antibiotic Susceptibility Testing of Enterococci, Richard R. Facklam, Maria da Gloria S. Carvalho, and Lucia M. Teixeira 2. Nonhuman Reservoirs of Enterococci, Frank M. Aarestrup, Patrick Butaye, and Wolfgang Witte 3. Enterococci as Members of the Intestinal Microflora of Humans, Gerald W. Tannock and Greg Cook 4. Physiology of Enterococci, Mark M. Huycke 5. Enterococcal Cell Wall, Jacques Coyette and Lynne E. Hancock 6. Plasmids and Transposons, Keith E. Weaver, Louis B. Rice, and Gordon Churchward 7. Conjugation and Genetic Exchange in Enterococci, Don B. Clewell and Gary M. Dunny 8. Enterococcal Virulence, Michael S. Gilmore, Phillip S. Coburn, Sreedhar R. Nallapareddy, and Barbara E. Murray 9. Acquired Antibiotic Resistances in Enterococci, Vivek Kak and Joseph W. Chow 10. Enterococcal Disease: Epidemiology and Treatment, Preeti N. Malani, Carol A. Kauffman, and Marcus J. Zervos 11. The Genome of Enterococcus faecalis V583: a Tool for Discovery, W. Michael McShan and Nathan Shankar
Influence of cellular trafficking on protein synthesis inhibition of immunotoxins directed against the transferrin receptor. (1995)

Previously, a quantitative analysis that related protein synthesis inhibition of transferrin-toxin conjugates to the cellular trafficking of transferrin was proposed (P.T. Yazdi and R. M. Murphy, Cancer Res., 54: 6387-6394, 1994). Here, this work is extended to evaluate cellular trafficking of anti-transferrin receptor antibodies and protein synthesis inhibition kinetics of immunotoxins constructed from the same antibodies and the toxin gelonin. Cellular trafficking models for two monoclonal anti-transferrin receptor antibodies (5E9 and OKT9) in HeLa cells were developed. The two mAbs had similar trafficking parameters, which differed significantly from those for transferrin. Protein synthesis inhibition kinetics for immunotoxins constructed from 5E9 or OKT9 and gelonin were measured. Analysis of the data using our previously proposed relationship between protein synthesis and cellular trafficking indicated that the relationship is also valid for these new systems. The protein synthesis inhibition constants for 5E9-gelonin and OKT9-gelonin conjugates were similar to those for the transferrin-gelonin conjugate. These results suggest that it may be possible to predict the efficacy of gelonin immunotoxins from knowledge of the trafficking of the corresponding targeting agent. A sensitivity analysis showed which cellular trafficking parameters have the greatest influence on immunotoxin efficacy and are, therefore, the most likely to be profitably manipulated.
Primary structure of bovine pituitary basic fibroblast growth factor (FGF) and comparison with the amino-terminal sequence of bovine brain acidic FGF. (1985)

The two major mitogenic polypeptides for endothelial cells have been purified to homogeneity. The complete primary structure of bovine pituitary basic fibroblast growth factor (FGF) and the amino-terminal amino acid sequence of bovine brain acidic FGF have been established by gas-phase sequence analyses. Homogeneous preparations of these polypeptides are potent mitogens (basic FGF, ED50 approximately equal to 60 pg/ml; acidic FGF ED50 approximately equal to 6000 pg/ml) for many diverse cell types including capillary endothelial cells, vascular smooth muscle cells, and adrenocortical and granulosa cells; in vivo, basic FGF is a powerful angiogenic agent in the chick chorioallantoic membrane assay. The available protein sequence data demonstrate the existence of significant structural homology between the two polypeptides.
Characterization of Streptavidin Binding to Biotinylated, Binary Self-Assembled Thiol Monolayers—Influence of Component Ratio and Solvent (2010)

Many biosensor applications are based on streptavidin (SA) binding to partially biotinylated self-assembled thiol monolayers (SAMs). In our study, binary SAMs on gold were prepared from solutions containing 16-mercapto-1-hexadecanol (thiol I) and N-(8-biotinyl-3,6-dioxa-octanamidyl)-16-mercaptohexadecanamide (thiol II) in varying component ratios. Either chloroform or ethanol was used as solvent. After 24 h thiol incubation, SA was immobilized on the resulting SAMs using the strong SA-biotin interaction. The SA binding process was monitored by QCM-D (quartz crystal microbalance monitoring dissipation factor). It is shown that the Sauerbrey equation is valid to calculate the mass quantities of the immobilized SA layers. Under the chosen incubation conditions, marginal fractions of the biotinylated component II in chloroform ((n(I)/n(II))(solution) approximately = 1000) lead to SAMs which ensure a maximal SA binding quantity of m(Sauerbrey SA) approximately = 400 ng x cm(-2), being equivalent to a SA single-layer arrangement on the SAM surface. In case of incubations from ethanolic solutions, a complete SA layer formation needs significantly higher amounts of the biotinylated component II during SAM preparation ((n(I)/n(II))(solution) approximately = 50). X-ray photoelectron spectroscopy data show that the fraction of biotinylated thiol II in the SAM determines the amount of surface-bound SA. The SAM thiol ratio ((n(I)/n(II))(SAM)) not only depends on the corresponding component ratio in the incubation solution, but is also strongly influenced by the solvent. Using chloroform as solvent during SAM preparation significantly increased the fraction of biotinylated thiol II in the SAMs compared to ethanol.
Restoring Full Biological Activity to the Isolated Ectodomain of an Integral Membrane Protein (2006)

Integral membrane proteins, which include many cellular effector proteins and drug targets, can be difficult to produce, purify, and manipulate. Although the isolated ectodomains of many membrane proteins can be expressed as water soluble proteins, biological activity is frequently lost when these proteins are released from the membrane surface. An example is tissue factor, the integral membrane protein that triggers the blood clotting cascade and for which membrane anchoring is essential. Its isolated ectodomain (soluble tissue factor) can be expressed with high yield in bacteria but is orders of magnitude less active than the intact, membrane-anchored protein. We now report full restoration of biological activity to the isolated tissue factor ectodomain via the engineering of a hexahistidine tag onto its C-terminus and its use in combination with membrane bilayers containing nickel-chelating lipids. When soluble tissue factor was tethered to the membrane surface via such metal-chelating lipids, it bound factor VIIa with the same high affinity as wild-type tissue factor, and the resulting factor VIIa-tissue factor complexes supported factor X activation and factor VII autoactivation with essentially wild-type enzyme kinetic constants. Furthermore, when such bilayers were immobilized onto solid supports, they efficiently captured histidine-tagged soluble tissue factor directly from crude culture supernatants, with full biological activity, obviating the need for purification or laborious membrane reconstitution procedures. This strategy is rapid, efficient, scalable, and automatable and should be applicable to other integral membrane proteins, especially those with a single transmembrane domain. Applications include high-throughput screening of mutants or drugs, flow reactors, clinical assays, and point-of-care instrumentation.
Organocatalytic Enantioselective Cross-Dehydrogenative Coupling of N-Carbamoyl Cyclic Amines with Aldehydes (2016)

The existing catalytic enantioselective cross-dehydrogenative coupling of cyclic amines predominantly focused on reactive N-aryl tetrahydroisoquinolines, which typically suffered from limited substrate generality and synthetic utility, and required the use of metal catalyst. Herein, a metal-free catalytic enantioselective cross-dehydrogenative coupling of N-carbamoyl cyclic amines and aldehydes has been reported for the first time. Employing an easily installed and functionalized acyl protecting group rather than the widely adopted aryl moiety endows the enantioselective process with better substrate generality and broader synthetic utility.
Aneuploidy: Instigator and Inhibitor of Tumorigenesis (2007)

Aneuploidy, an aberrant chromosome number, has been recognized as a common characteristic of cancer cells for more than 100 years and has been suggested as a cause of tumorigenesis for nearly as long. However, this proposal had remained untested due to the difficulty of selectively generating aneuploidy without causing other damage. Using Cenp-E heterozygous animals, which develop whole chromosome aneuploidy in the absence of other defects, we have found that aneuploidy promotes tumorigenesis in some contexts and inhibits it in others. These findings confirm that aneuploidy can act oncogenically and reveal a previously unsuspected role for aneuploidy as a tumor suppressor.
Transport Barriers in Transscleral Drug Delivery for Retinal Diseases (2007)

Transscleral delivery has emerged as an attractive method for treating retinal disorders because it offers localized delivery of drugs as a less invasive method compared to intravitreal administration. Numerous novel transscleral drug delivery systems ranging from microparticles to implants have been reported. However, transscleral delivery is currently not as clinically effective as intravitreal delivery in the treatment of retinal diseases. Transscleral drug delivery systems require drugs to permeate through several layers of ocular tissue (sclera, Bruch's membrane-choroid, retinal pigment epithelium) to reach the neuroretina. As a result, a steep drug concentration gradient from the sclera to the retina is established, and very low concentrations of drug are detected in the retina. This steep gradient is created by the barriers to transport that hinder drug molecules from successfully reaching the retina. A review of the literature reveals 3 types of barriers hindering transscleral drug delivery: static, dynamic and metabolic. While static barriers have been examined in detail, the literature on dynamic and metabolic barriers is lacking. These barriers must be investigated further to gain a more complete understanding of the transport barriers involved in transscleral drug delivery.
A Probe Technique for Determining the Thermal Conductivity of Tissue (1972)

A small needle-like probe has been developed for the determination of the thermal conductivity of either in-vitro or in-vivo tissue. This probe consists of a copper cylinder having a diameter of 1.5 mm and a length of 22.5 mm. Constantan and copper leads are attached to the center and top of the cylinder, respectively, and as a consequence the probe acts as a thermocouple. The distinguishing characteristic of this probe is that when it is suddenly embedded into a medium at a different temperature, the duration of its temperature–time response is such that it can be related to the thermal properties of the medium. This is accomplished by a match with an analytically determined response curve which accounts for metabolic heat generation, blood flow, and conductive effects. By nondimensionalizing the governing equations for the probe–tissue system, three nondimensional groups for time, temperature, and blood flow emerge. The results of a parametric study of these effects are presented in tabular form. Initially, the probe technique was used to determine the thermal conductivity of a 1 percent agar–water mixture and the results were within 5 percent of water. Subsequently, experimental thermal-conductivity data were obtained on the following in-vitro human organs: liver, kidney, heart, spleen, whole brain, brain gray matter, and brain white matter. In addition, density, specific-heat, and water-content measurements were also obtained on these organs. In-vivo conductivity data have recently been obtained for canine liver with and without blood flow. These data indicate that the in-vivo value without blood flow is approximately the same as the in-vitro value after the organ had been removed and refrigerated for 24 hr. Blood flow, if not considered, resulted in apparent conductivities which were 15 to 25 percent higher than that of the tissue.
Cold Fusion: Training Seq2Seq Models Together with Language Models (2018)

Sequence-to-sequence (Seq2Seq) models with attention have excelled at tasks which involve generating natural language sentences such as machine translation, image captioning and speech recognition. Performance has further been improved by leveraging unlabeled data, often in the form of a language model. In this work, we present the Cold Fusion method, which leverages a pre-trained language model during training, and show its effectiveness on the speech recognition task. We show that Seq2Seq models with Cold Fusion are able to better utilize language information enjoying i) faster convergence and better generalization, and ii) almost complete transfer to a new domain while using less than 10% of the labeled training data.
Laser Desorption/in Situ Chemical Ionization Aerosol Mass Spectrometry for Monitoring Tributyl Phosphate on the Surface of Environmental Particles (2000)

The possibility of using real-time aerosol mass spectrometry (RTAMS) for the detection of surface-adsorbed tributyl phosphate (TBP) as an alkali metal adduct has been investigated. Environmental particles contain variable amounts of easily ionizable alkali metals. During laser desorption of surface-adsorbed TBP molecules, Na+ and K+ ions are generated by the interaction of the laser radiation with the particle's material. The alkali metal ions serve as in situ chemical ionization reagents of the neutral analyte molecules. The effect of laser fluence on the signal intensities of the potassium ion and cationized TBP was also studied. The best performance of the instrument was observed with laser fluences that produce high abundances of K+ but low abundances of ions from the particle's bulk material. The relatively low laser fluence, necessary to produce potassium ions, prevents the excessive fragmentation of the analyte. The instrument is capable of real-time monitoring of submonolayer coverage of TBP on the surface of micron-sized particles.
De maakindustrie is terug (2014)

De maakindustrie, is dat nog iets voor Nederland? Absoluut, vindt Egbert-Jan Sol van TNO. Daarbij moeten we echter niet meer denken aan rokende schoorstenen, maar aan slimme fabrieken die complexe producten afleveren in kleine series. Op de Hannover Messe vorige week presenteerden het Ministerie van Economische Zaken, FME-CWM, TNO en VNO-NCW het visiedocument 'Smart industry' aan bondskanselier Angela Merkel en premier Mark Rutte. Een samenvatting.
Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients (2020)

Given the ongoing SARS-CoV-2 pandemic, identification of immunogenic targets against the coronavirus spike glycoprotein will provide crucial advances towards the development of sensitive diagnostic tools and potential vaccine candidate targets. In this study, using pools of overlapping linear B-cell peptides, we report two IgG immunodominant regions on SARS-CoV-2 spike glycoprotein that are recognised by sera from COVID-19 convalescent patients. Notably, one is specific to SARS-CoV-2, which is located in close proximity to the receptor binding domain. The other region, which is localised at the fusion peptide, could potentially function as a pan-SARS target. Functionally, antibody depletion assays demonstrate that antibodies targeting these immunodominant regions significantly alter virus neutralisation capacities. Taken together, identification and validation of these neutralising B-cell epitopes will provide insights towards the design of diagnostics and vaccine candidates against this high priority coronavirus.
Cloning and Expression of a Novel Mammalian Homolog ofDrosophila Transient Receptor Potential (Trp) Involved in Calcium Entry Secondary to Activation of Receptors Coupled by the Gq Class of G Protein (1997)

Hormonal stimulation of Gq-protein coupled receptors triggers Ca2+ mobilization from internal stores. This is followed by a Ca2+ entry through the plasma membrane. Drosophila Trp and Trpl proteins have been implicated in Ca2+ entry and three mammalian homologues of Drosophila Trp/Trpl, hTrp1, hTrp3 and bTrp4 (also bCCE) have been cloned and expressed. Using mouse brain RNA as template, we report here the polymerase chain reaction-based cloning and functional expression of a novel Trp, mTrp6. The cDNA encodes a protein of 930 amino acids, the sequence of which is 36.8, 36.3, 43.1, 38.6, and 74. 1% identical to Drosophila Trp and Trpl, bovine Trp4, and human Trp1 and Trp3, respectively. Transient expression of mTrp6 in COS.M6 cells by transfection of the full-length mTrp6 cDNA increases Ca2+ entry induced by stimulation of co-transfected M5 muscarinic acetylcholine receptor with carbachol (CCh), as seen by dual wavelength fura 2 fluorescence ratio measurements. The mTrp6-mediated increase in Ca2+ entry activity was blocked by SKF-96365 and La3+. Ca2+ entry activity induced by thapsigargin was similar in COS cells transfected with or without the mTrp6 cDNA. The thapsigargin-stimulated Ca2+ entry could not be further stimulated by CCh in control cells but was markedly increased in mTrp6-transfected cells. Records of whole cell transmembrane currents developed in response to voltage ramps from -80 to +40 mV in control HEK cells and HEK cells stably expressing mTrp6 revealed the presence of a muscarinic receptor responsive non-selective cation conductance in Trp6 cells that was absent in control cells. Our data support the hypothesis that mTrp6 encodes an ion channel subunit that mediates Ca2+ entry stimulated by a G-protein coupled receptor, but not Ca2+ entry stimulated by intracellular Ca2+ store depletion.
ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets (2014)

ROVER can facilitate rapid and accurate genetic variant calling for a broad range of PCR-MPS users.
Presentation of the Section for Chemical Research (SCR) of the New Swiss Chemical Society (NSCS) (1998)

The Section for Chemical Research (SCR) of the NSCS intends to provide a forum for chemists active in research, so as to promote exchange of ideas and collaboration. The SCR organizes or supports symposia, seminars, and scientific meetings, with a special emphasis on the Fall Meeting of the NSCS, which is de facto the largest annual forum of Swiss chemistry. Particular attention is paid by the SCR to the promotion of research results obtained by young chemists so as to help them starting their career. At present, the SCR membership stands at 465 members.
Focal manifestations of diffuse liver disease at MR imaging. (1992)

Detection and exclusion of focal liver lesions is especially difficult in patients with diffuse liver disease. Magnetic resonance (MR) imaging may be particularly valuable in these patients. By judicious comparison of appropriate pulse sequences, normal and hypertrophic liver may be distinguished from atrophic, neoplastic, or otherwise abnormal hepatic parenchyma. Chemical shift (lipid-sensitive) techniques allow definitive identification of fatty liver, including focal fatty infiltration or focal sparing. T2-weighted and T2*-weighted images allow identification of iron overload, depicting malignancies as focal masses without iron. Analysis of signal intensity and internal morphology allows confident distinction between regenerative nodules and hepatocellular carcinoma in most instances, and allows diagnosis of early carcinoma within regenerative nodules. MR imaging provides capabilities for noninvasive characterization of liver tissue beyond those available with other noninvasive modalities.
A nerve cuff technique for selective excitation of peripheral nerve trunk regions (1990)

Numerical modeling and experimental testing of a nerve cuff technique for selective stimulation of superficial peripheral nerve trunk regions is presented. Two basic electrode configurations ("snug" cuff monopolar and tripolar longitudinally aligned dots) have been considered. In addition, the feasibility of "steering" excitation into superficial nerve trunk regions using subthreshold levels of current flow from an electrode dot located on the opposite side of the nerve has been tested. Modeling objectives were to solve for the electric field that would be generated within a representative nerve trunk by each electrode configuration; and to use a simple nerve cable model to predict the effectiveness of each configuration in producing localized excitation. In three acute experiments on cat sciatic nerve the objective was to characterize the effectiveness of each electrode configuration in selectively activating only the medial gastrocnemius muscle. Modeling and experimentation both suggest that longitudinally aligned tripolar dot electrodes on the surface of a nerve trunk, and bounded by a layer of insulation (such as a nerve cuff), will restrict excitation to superficial nerve trunk regions more successfully than will monopolar dot electrodes. Excitation "steering" will improve the spatial selectivity of both monopolar and tripolar electrode configurations.
Anti‐BDCA‐4 (neuropilin‐1) antibody can suppress virus‐induced IFN‐alpha production of plasmacytoid dendritic cells (2007)

Plasmacytoid dendritic cells (PDC) in human blood are the main source of virus-induced interferon (IFN)-alpha. They exhibit a lineage-negative phenotype but all express BDCA-4, which is homologous to the neuronal receptor neuropilin-1. Specific staining with anti-BDCA-4 antibody is used for positive isolation of PDC from blood by magnetic cells sorting. Here, it is demonstrated that these positively selected PDC showed reduced or completely abolished IFN-alpha release compared to unstained PDC, which were negatively selected by magnetic depletion of lineage-positive blood mononuclear cells. In addition, treatment of these unstained PDC with anti-BDCA-4 mAb also resulted in at least two-fold lower or reduced virus-induced IFN-alpha production. It is shown that the antibody not only affects cell survival or block virus attachment but also reduces IFN-alpha release induced by non-viral CpG oligodeoxynucleotides. In conclusion, data suggest an immunoregulatory role for BDCA-4 on PDC as demonstrated for IFN-alpha response to virus.