gebhart/patrepeval huggingface dataset:
Observation of Multiple, Identical Binding Sites in the Exchange of Carboxylic Acid Ligands with CdS Nanocrystals. (2014)

We study ligand exchange between the carboxylic acid group and 5.0 nm oleic-acid capped CdS nanocrystals (NCs) using fluorescence resonance energy transfer (FRET). This is the first measurement of the initial binding events between cadmium chalcogenide NCs and carboxylic acid groups. The binding behavior can be described as an interaction between a ligand with single binding group and a substrate with multiple, identical binding sites. Assuming Poissonian binding statistics, our model fits both steady-state and time-resolved photoluminescence (SSPL and TRPL, respectively) data well. A modified Langmuir isotherm reveals that a CdS nanoparticle has an average of 3.0 new carboxylic acid ligands and binding constant, Ka, of 3.4 × 10(5) M(-1).
High-throughput screen, using time-resolved FRET, yields actin-binding compounds that modulate actin–myosin structure and function (2018)

We have used a novel time-resolved FRET (TR-FRET) assay to detect small-molecule modulators of actin-myosin structure and function. Actin-myosin interactions play crucial roles in the generation of cellular force and movement. Numerous mutations and post-translational modifications of actin or myosin disrupt muscle function and cause life-threatening syndromes. Here, we used a FRET biosensor to identify modulators that bind to the actin-myosin interface and alter the structural dynamics of this complex. We attached a fluorescent donor to actin at Cys-374 and a nonfluorescent acceptor to a peptide containing the 12 N-terminal amino acids of the long isoform of skeletal muscle myosin's essential light chain. The binding site on actin of this acceptor-labeled peptide (ANT) overlaps with that of myosin, as indicated by (<i>a</i>) a similar distance observed in the actin-ANT complex as in the actin-myosin complex and (<i>b</i>) a significant decrease in actin-ANT FRET upon binding myosin. A high-throughput FRET screen of a small-molecule library (NCC, 727 compounds), using a unique fluorescence lifetime readout with unprecedented speed and precision, showed that FRET is significantly affected by 10 compounds in the micromolar range. Most of these "hits" alter actin-activated myosin ATPase and affect the microsecond dynamics of actin detected by transient phosphorescence anisotropy. We conclude that the actin-ANT TR-FRET assay enables detection of pharmacologically active compounds that affect actin structural dynamics and actomyosin function. This assay establishes feasibility for the discovery of allosteric modulators of the actin-myosin interaction, with the ultimate goal of developing therapies for muscle disorders.
追踪“幻术之旅”（上） (2009)

上月说到我们赶到罗恩家去搜查。罗恩家里积了厚厚的灰尘，看来她已经很久没有回来了。在阳台上，我们发现了很多魔术道具。难道罗恩也是一名魔术师？客厅里突然一阵响动，一名男子从柜子里钻了出来，飞快地向门外跑去。警察们很快追上并制服了他。
Application of 3D seismic attributes to optimize the placement of horizontal wells within a tight gas sand reservoir, Ordos Basin, China (2016)

ABSTRACT The Lower Permian Xiashihezi Formation in the Ordos Basin, China, is a quartz-sandstone reservoir with low porosity and low permeability. We have acquired 3D seismic data and well data from 18 vertical and four horizontal wells to indicate the potential of seismic attribute analyses in locating seismic sweet spots for lateral placement of horizontal wells. Using the analytic wavelet transform with a Morse wavelet, the integration of high tuning spectral components, high sweetness and high spectral attenuation helped us to estimate the distribution of gas-bearing tight sands in the Xiashihezi Formation. Our results revealed that the principal target of horizontal drilling and production was gas-bearing massive point bars in the braided river delta setting of the Ordos Basin. The integrated workflow of the seismic attribute analysis contributes to the optimal horizontal well planning by mining and exposing critical geological information of a tight gas sand reservoir from within 3D seismic data.
cDNA clone of hepatitis A virus encoding a virulent virus: induction of viral hepatitis by direct nucleic acid transfection of marmosets (1992)

Direct inoculation of marmoset livers with an in vitro transcription mixture containing cDNA and full-length genomic RNA transcripts of hepatitis A virus resulted in acute viral hepatitis. Elevations in serum levels of liver enzymes were correlated with appearance of antibody to hepatitis A virus. Genomes of infectious hepatitis A virus isolated from the feces of transfected marmosets contained the same mutation as the cDNA template used for transfection. Liver biopsies confirmed that the virus encoded by the cDNA clone induced histopathological changes equivalent to those caused by virulent wild-type virus.
Lung Inflammation and Epithelial Changes in a Murine Model of Atopic Asthma (1996)

A murine model of allergen-induced airway inflammation and epithelial phenotypic change, and the time-courses of these events, are described. Mice were sensitized to ovalbumin using an adjuvant-free protocol, and challenged by multiple intratracheal instillations of ovalbumin by a non-surgical technique. Many of the characteristic features of human atopic asthma were seen in the mice. A marked eosinophilic infiltration of lung tissue and airways followed allergen challenge, and its severity increased with each challenge, as did the number of eosinophils in the blood. Lymphocytes, neutrophils, and monocytes also invaded the lungs. Airway macrophages showed signs of activation, their appearance resembling those recovered from antigen-challenged human asthmatic airways. The airway epithelium was thickened and displayed a marked goblet cell hyperplasia in terminal bronchioles and larger airways. After repeated challenges, the reticular layer beneath the basement membrane of the airway epithelium showed fibrosis, reproducing a commonly observed histologic feature of human asthma. Goblet cell hyperplasia began to appear before eosinophils or lymphocytes had migrated across the airway epithelium, and persisted for at least 11 days after the third intratracheal challenge with ovalbumin, despite the number of inflammatory cells in the lungs and airways having decreased to near-normal levels by 4 days. Plugs of mucus occluded some of the airways. These results indicate that some of the phenotypic changes in airway epithelium that follow an allergic response in the lung can be initiated before the migration of eosinophils or lymphocytes across the epithelial layer.
Large‐scale preparation of T4 endonuclease VII from over‐expressing bacteria (1990)

Endonuclease VII is the product of gene 49 of phage T4 and was the first enzyme shown to resolve Holliday structures in vitro [Mizuuchi, K. et al. (1982) Cell 29 , 357–365]. Low amounts of the enzyme were originally purified from phage‐infected cells [Kemper, B. &amp; Garabett, M. (1981) Eur. J. Biochem. 115 , 123–131]. We now report a purification procedure for milligram amounts of cloned endonuclease VII expressed in Escherichia coli with gene 49 under the control of a temperature‐inducible promoter on a plasmid system [Tomaschewski, J. (1988) PhD Thesis, University of Bochum, FRG]. The protein was purified 500‐fold from crude extracts in five steps with a recovery of 15%. The steps include (a) poly(ethyleneglycol)/dextran two‐phase separation; (b) DEAE‐cellulose; (c) single‐stranded DNA‐agarose; (d) Mono‐Q and (e) Mono‐S chromatography. The final protein was more than 98% pure as estimated from SDS/PAGE analysis. The protein has an apparent molecular mass of 17.8 kDa on SDS‐containing polyacrylamide gels and 36 kDa when determined by gel filtration or sedimentation through sucrose gradients in the presence of high salt (600 mM NaCl). In the absence of additional salt, the enzyme has a tendency to aggregate and products of molecular masses differing in steps of about 18 kDa appear on SDS‐containing polyacrylamide gels.
Inhibition of Cell Cycle Progression by the Alternatively Spliced Integrin β 1C (1995)

Integrins regulate cell growth, differentiation, and behavior in many systems. Integrin beta 1C (beta 1S) is an alternatively spliced variant of integrin beta 1 with a specific cytoplasmic domain and is expressed in several human tissues. Human beta 1c transiently expressed in mouse 10T1/2 fibroblasts showed a diffuse pattern of cell surface staining, whereas beta1 localized to focal adhesions. Moderate concentrations of beta 1C had no effect on actin stress fibers or focal adhesions, but markedly inhibited DNA synthesis. Inhibition by beta 1C mapped to the late G1 phase of the cell cycle, near the G1-S boundary. Thus, alternative splicing of beta1 results in transmission of distinct signals that may regulate growth in vivo.
Advantage of the Mark-III FEL for biophysical research and biomedical applications (2003)

Although 6.45 micro m is not the strongest absorption band of biological tissues in the mid-infrared, a Mark-III free-electron laser (FEL) tuned to this wavelength can efficiently ablate tissue while minimizing collateral damage. A model has previously been presented that explains this wavelength dependence as a competition between two dynamic processes--explosive vaporization of saline and denaturation of structural proteins. Here it is shown that this model predicts a 'sweet-spot' for each wavelength, i.e. a region of parameter space (incident intensity and pulse width) in which explosive vaporization is preceded by substantial protein denaturation. This sweet-spot is much larger for wavelengths where protein is the dominant chromophore. At other wavelengths, collateral damage may be minimized within the sweet-spot, but the maximum intensities and pulse widths in these regions are insufficient to remove tissue at surgically relevant rates.
Phospho‐olivines as Positive‐Electrode Materials for Rechargeable Lithium Batteries (1997)

Reversible extraction of lithium from (triphylite) and insertion of lithium into at 3.5 V vs. lithium at 0.05 mA/cm2 shows this material to be an excellent candidate for the cathode of a low‐power, rechargeable lithium battery that is inexpensive, nontoxic, and environmentally benign. Electrochemical extraction was limited to ∼0.6 Li/formula unit; but even with this restriction the specific capacity is 100 to 110 mAh/g. Complete extraction of lithium was performed chemically; it gave a new phase, , isostructural with heterosite, . The framework of the ordered olivine is retained with minor displacive adjustments. Nevertheless the insertion/extraction reaction proceeds via a two‐phase process, and a reversible loss in capacity with increasing current density appears to be associated with a diffusion‐limited transfer of lithium across the two‐phase interface. Electrochemical extraction of lithium from isostructural (M = Mn, Co, or Ni) with an electrolyte was not possible; but successful extraction of lithium from was accomplished with maximum oxidation of the occurring at x = 0.5. The couple was oxidized first at 3.5 V followed by oxidation of the couple at 4.1 V vs. lithium. The interactions appear to destabilize the level and stabilize the level so as to make the energy accessible.
Monoclonal antibody solution hybridization assay for detection of mouse hepatitis virus infection (1992)

A monoclonal antibody solution hybridization (MASH) assay was developed to detect fecal excretion of mouse hepatitis virus (MHV). The assay used a biotinylated cDNA probe to detect viral RNA target sequences by hybridization in solution, capture of hybrids on the solid phase with antibiotin antibody, and immunoassay with an enzyme-labelled monoclonal antibody specific for DNA-RNA hybrids. The MASH assay was used to monitor the time course of enterotropic MHV excretion after oronasal inoculation. Infectivity of the inoculated mice was simultaneously monitored with sentinel animals. The MASH assay detected MHV excretion in all inoculated mice, with the highest mean excretion levels occurring from day 3 through day 9 postinoculation. Mean excretion then decreased gradually to below detection limits by day 21 postinoculation. Sentinels became infected on exposure to inoculated mice up to but not after day 21 postinoculation. Infected sentinel mice showed a time course of virus excretion similar to that of inoculated mice. These results indicate that the MASH assay is useful for rapid, sensitive, and specific detection of MHV in clinical specimens from laboratory mice.
A simple method for direct cloning and sequencing cDNA by the use of a single specific oligonucleotide and oligo(dT) in a polymerase chain reaction (PCR) (1989)

Journal Article A simple method for direct cloning and sequencing cDNA by the use of a single specific oligonucleotide and oligo(dT) in a polymerase chain reaction (PCR) Get access Martin W. Berchtold Martin W. Berchtold Institute of Pharmacology and Biochemistry, University Zürich-Irchel8057 Zürich, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 1, 11 January 1989, Page 453, https://doi.org/10.1093/nar/17.1.453 Published: 11 January 1989 Article history Received: 17 November 1988 Published: 11 January 1989
New Markers of Pancreatic Cancer Identified Through Differential Gene Expression Analyses: Claudin 18 and Annexin A8 (2008)

Claudin 18 and annexin A8 are frequently highly overexpressed in infiltrating ductal adenocarcinomas when compared with normal reactive ducts, suggesting a role for these molecules in pancreatic ductal adenocarcinomas. Furthermore, these may serve as diagnostic markers, as screening tests and as therapeutic targets.
Tyrosine Kinase Inhibitors. 15. 4-(Phenylamino)quinazoline and 4-(Phenylamino)pyrido[d]pyrimidine Acrylamides as Irreversible Inhibitors of the ATP Binding Site of the Epidermal Growth Factor Receptor (1999)

A series of 6- and 7-acrylamide derivatives of the 4-(phenylamino)quinazoline and -pyridopyrimidine classes of epidermal growth factor receptor (EGFR) inhibitors were prepared from the corresponding amino compounds by reaction with either acryloyl chloride/base or acrylic acid/1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride. All of the 6-acrylamides, but only the parent quinazoline 7-acrylamide, were irreversible inhibitors of the isolated enzyme, confirming that the former are better-positioned, when bound to the enzyme, to react with the critical cysteine-773. Quinazoline, pyrido[3,4-d]pyrimidine, and pyrido[3,2-d]pyrimidine 6-acrylamides were all irreversible inhibitors and showed similar high potencies in the enzyme assay (likely due to titration of the available enzyme). However the pyrido[3,2-d]pyrimidine analogues were 2-6-fold less potent than the others in a cellular autophosphorylation assay for EGFR in A431 cells. The quinazolines were generally less potent overall toward inhibition of heregulin-stimulated autophosphorylation of erbB2 (in MDA-MB-453-cells), whereas the pyridopyrimidines were equipotent. Selected compounds were evaluated in A431 epidermoid and H125 non-small-cell lung cancer human tumor xenografts. The compounds showed better activity when given orally than intraperitoneally. All showed significant tumor growth inhibition (stasis) over a dose range. The poor aqueous solubility of the compounds was a drawback, requiring formulation as fine particulate emulsions.
CD review (2007)

Perfect posture for the dental team, P. Ellis and Smile-on Ltd, Smile-on Ltd, £199.00 + VAT.
Transduction Profiles of Recombinant Adeno-Associated Virus Vectors Derived from Serotypes 2 and 5 in the Nigrostriatal System of Rats (2004)

We compared the transduction efficiencies and tropisms of titer-matched recombinant adeno-associated viruses (rAAV) derived from serotypes 2 and 5 (rAAV-2 and rAAV-5, respectively) within the rat nigrostriatal system. The two serotypes (expressing enhanced green fluorescent protein [EGFP]) were delivered by stereotaxic surgery into the same animals but different hemispheres of the striatum (STR), the substantia nigra (SN), or the medial forebrain bundle (MFB). While both serotypes transduced neurons effectively within the STR, rAAV-5 resulted in a much larger EGFP-expressing area than did rAAV-2. However, neurons transduced with rAAV-2 vectors expressed higher levels of EGFP. Consistent with this result, EGFP-positive projections emanating from transduced striatal neurons covered a larger area of the SN pars reticulata (SNr) after striatal delivery of rAAV-5, but EGFP levels in fibers of the SNr were higher after striatal injection of rAAV-2. We also compared the potentials of the two vectors for retrograde transduction and found that striatal delivery of rAAV-5 resulted in significantly more transduced dopaminergic cell bodies within the SN pars compacta and ventral tegmental area. Similarly, EGFP-transduced striatal neurons were detected only after nigral delivery of rAAV-5. Furthermore, we demonstrate that after striatal AAV-5 vector delivery, the transduction profiles were stable for as long as 9 months. Finally, although we did not target the hippocampus directly, efficient and widespread transduction of hippocampal neurons was observed after delivery of rAAV-5, but not rAAV-2, into the MFB.
On-line sample preconcentration in capillary electrophoresis, focused on the determination of proteins and peptides (2001)

This overview highlights the possibilities of on- or in-line preconcentration procedures in combination with a CZE separation, focused on the determination of peptides and proteins. The discussed methods, including sample stacking, field-amplified injection, isotachophoresis, solid phase extraction, membrane preconcentration, electroextraction, supported liquid membranes, hollow fibers, immunoaffinity, and molecularly imprinted polymers technology preconcentration are categorized in electrophoresis-based and chromatography-based preconcentration. The chromatography-based preconcentration is subdivided in low-specificity and high-specificity methods. A number of preconcentration methods are available, however, this paper demonstrates that various compounds in different media (aqueous solutions, urine, and plasma) require different preconcentration systems. The preconcentration techniques of first choice in general seem to be solid-phase extraction and membrane preconcentration, because of their high concentration ability, multiapplicability, relative simplicity and clean-up capability. For the future, hollow fibers seem to hold a great potential as preconcentration technique, yielding high concentration factors, using simple designs. New techniques, such as hollow fibers, molecularly imprinted polymers technology and supported liquid membranes may have the potential to supersede the conventional preconcentration techniques in some cases. The larger the arsenal of preconcentration techniques becomes, the more efficiently peptides and proteins may be analyzed in the future. These techniques, in some cases, require pre-cleanup procedures, to ensure the purity of the samples to concentrate.
Microwave Synthesis of Nanoporous Materials (2006)

Studies in the last decade suggest that microwave energy may have a unique ability to influence chemical processes. These include chemical and materials syntheses as well as separations. Specifically, recent studies have documented a significantly reduced time for fabricating zeolites, mixed oxide and mesoporous molecular sieves by employing microwave energy. In many cases, microwave syntheses have proven to synthesize new nanoporous structures. By reducing the times by over an order of magnitude, continuous production would be possible to replace batch synthesis. This lowering of the cost would make more nanoporous materials readily available for many chemical, environmental, and biological applications. Further, microwave syntheses have often proven to create more uniform (defect-free) products than from conventional hydrothermal synthesis. However, the mechanism and engineering for the enhanced rates of syntheses are unknown. We review the many studies that have demonstrated the enhanced syntheses of nanoporous oxides and analyze the proposals to explain differences in microwave reactions. Finally, the microwave reactor engineering is discussed, as it explains the discrepancies between many microwave studies.
Long‐term Survival of Retina Optic Nerve Section in Adult Ganglion Cells Following bcl‐2 Transgenic Mice (1996)

The bcl-2 gene codes for a protein that acts as a powerful inhibitor of active cell death. Since the transection of the optic nerve in adult mammalians starts a massive process of degeneration in retinal ganglion cells, we investigated whether the overexpression of bcl-2 in adult transgenic mice can protect the axotomized ganglion cells. We performed intracranial optic nerve transection on both wild type and transgenic adult mice, and we tested cell survival 2 or 3.5 months after axotomy. The percentage of surviving ganglion cells after optic nerve section was computed by combining the counts of the optic nerve fibres in intact nerves with the cell density measures of the ganglion cell layer of axotomized retinae. From these data we found that in transgenic mice approximately 65% of ganglion cells survived 3.5 months after axotomy. In contrast, 2 months after surgery, < 10% of ganglion cells were left in wild type retinae. We have also examined the morphology and fine structure of the proximal stump of the sectioned optic nerves by light and electron microscopy. In the transgenic mice a very large number of axons survived after surgery and they still exhibited fairly normal morphology and ultrastructure. On the other hand the wild type transected nerves had only a few visible axons that displayed clear signs of degeneration. We conclude that the overexpression of Bcl-2 protein in central neurons is a very effective strategy to ensure long-term survival in axotomized cells.
The flt3/flk-2 ligand: receptor distribution and action on murine haemopoietic cell survival and proliferation. (1995)

In this study the distribution and quantitation of the flt3/flk-2 receptor was examined on bone marrow cells and defined haemopoietic subpopulations. Undifferentiated cells expressed the greatest numbers of flt3/flk-2 receptors: 19% of primitive lin-kit+sca-1+ bone marrow cells and 16% of fetal liver lin-aa4.1+ cells exhibited over 15 000 receptors per cell as determined by binding of the radiolabeled cognate ligand (flt3/flk-2 ligand, FL). Moderate binding was demonstrated on early B lymphocyte subsets (4400 receptors per cell) and very low levels were detected on monocytes. Binding was not detected on promyelocytes, myelocytes, promonocytes, metamyelocytes, polymorphonuclear cells, eosinophils or nucleated erythroid cells. FL enhanced the survival of primitive lin kit+sca-1+ cells with an efficacy s with an efficacy equivalent to stem cell factor (SCF). FL stimulated predominantly blast and granulocyte-macrophage colony formation in cultures of bone marrow cells by both direct and indirect mechanisms. Marked synergistic effects of FL with combinations of colony stimulating factors (CSFs) or interleukin-6 occurred in the proliferation of primitive lin-kit+sca-1+ cells, but not lin-kit+sca-1- progenitor cells. Surprisingly, recloning experiments revealed that FL plus IL-3 increased the generation of progenitor cells by lin-kit a-1- cells compared with SCF plus IL-3. Thus FL functions as a factor with both direct and indirect stimulatory activities directed to the expansion, maintenance of clonogenic potential, and possibly limited self-renewal, of early haemopoietic cells.