gebhart/patrepeval huggingface dataset:
VERNON HERBERT BLACKMAN SC.D. (CANTAB.), F.R.S. 1872–1967 (1968)

Journal Article VERNON HERBERT BLACKMAN SC.D. (CANTAB.), F.R.S. 1872–1967 Get access W. BROWN, F.R.S. W. BROWN, F.R.S. Search for other works by this author on: Oxford Academic PubMed Google Scholar Annals of Botany, Volume 32, Issue 2, April 1968, Pages 233–235, https://doi.org/10.1093/oxfordjournals.aob.a084203 Published: 01 April 1968
Activation of Multiple Interleukin-1β Converting Enzyme Homologues in Cytosol and Nuclei of HL-60 Cells during Etoposide-induced Apoptosis (1997)

Recent genetic and biochemical studies have implicated cysteine-dependent aspartate-directed proteases (caspases) in the active phase of apoptosis. In the present study, three complementary techniques were utilized to follow caspase activation during the course of etoposide-induced apoptosis in HL-60 human leukemia cells. Immunoblotting revealed that levels of procaspase-2 did not change during etoposide-induced apoptosis, whereas levels of procaspase-3 diminished markedly 2-3 h after etoposide addition. At the same time, cytosolic peptidase activities that cleaved DEVD-aminotrifluoromethylcoumarin and VEID-aminomethylcoumarin increased 100- and 20-fold, respectively; but there was only a 1. 5-fold increase in YVAD-aminotrifluoromethylcoumarin cleavage activity. Affinity labeling with N-(Nalpha-benzyloxycarbonylglutamyl-Nepsilon-biotin yllysyl)aspartic acid [(2,6-dimethylbenzoyl)oxy]methyl ketone indicated that multiple active caspase species sequentially appeared in the cytosol during the first 6 h after the addition of etoposide. Analysis on one- and two-dimensional gels revealed that two species comigrated with caspase-6 and three comigrated with active caspase-3 species, suggesting that several splice or modification variants of these enzymes are active during apoptosis. Polypeptides that comigrate with the cytosolic caspases were also labeled in nuclei of apoptotic HL-60 cells. These results not only indicate that etoposide-induced apoptosis in HL-60 cells is accompanied by the selective activation of multiple caspases in cytosol and nuclei, but also suggest that other caspase precursors such as procaspase-2 are present but not activated during apoptosis.
pH-Dependent membrane fusion and vesiculation of phospholipid large unilamellar vesicles induced by amphiphilic anionic and cationic peptides (1992)

We studied fusion induced by a 20-amino acid peptide derived from the amino-terminal segment of hemagglutinin of influenza virus A/PR/8/34 [Murata, M., Sugahara, Y., Takahashi, S., & Ohnishi, S. (1987) J. Biochem. (Tokyo) 102, 957-962]. To extend the study, we have prepared several water-soluble amphiphilic peptides derived from the HA peptide; the anionic peptides D4, E5, and E5L contain four and five acidic residues and the cationic peptide K5 has five Lys residues in place of the five Glu residues in E5. Fusion of egg phosphatidylcholine large unilamellar vesicles induced by these peptides is assayed by two different fluorescence methods, lipid mixing and internal content mixing. Fusion is rapid in the initial stage (12-15% within 20 s) and remains nearly the same or slightly increasing afterward. The anionic peptides cause fusion at acidic pH lower than 6.0-6.5, and the cationic peptide causes fusion at alkaline pH higher than 9.0. Leakage and vesiculation of vesicles are also measured. These peptides are bound and associated with vesicles as shown by Ficoll discontinuous gradients and by the blue shift of tryptophan fluorescence. They take an alpha-helical structure in the presence of vesicles. They become more hydrophobic in the pH regions for fusion. When the suspension is made acidic or alkaline, the vesicles aggregate, as shown by the increase in light scattering. The fusion mechanism suggests that the amphiphilic peptides become more hydrophobic by neutralization due to protonation of the carboxyl groups or deprotonation of the lysyl amino groups, aggregate the vesicles together, and interact strongly with lipid bilayers to cause fusion. At higher peptide concentrations, E5 and E5L cause fusion transiently at acidic pH followed by vesiculation.
A Flow Cytometry-Based Assay for Screening FimH Antagonists (2011)

Urinary tract infections (UTIs), including cystitis and pyelonephritis, affect a large proportion of the population and account for significant medical costs. In more than 80% of UTIs, uropathogenic Escherichia coli (UPEC) is the causative pathogen. The initial step in the pathogenesis of the infection is the adherence of UPEC to the human bladder epithelium, enabling the invasion into the host cells and the development of UTIs. This process is mediated by the lectin FimH located on type I pili and enables UPECs to attach to oligomannosides of the glycoprotein uroplakin Ia presented on uroepithelial cells. FimH antagonists such as α-d-mannopyranosides have been shown to interfere with the attachment of UPEC to their host cells, thus providing a novel therapeutic opportunity for the treatment and prevention of UTIs. In this article, we report a flow cytometry-based assay to evaluate the potential of FimH antagonists for the prevention of the infection of the human urinary bladder cell line 5637 by UPEC strain UTI89. The assay was optimized and validated, and the inhibitory potency of different α-d-mannopyranosides was determined. Finally, the IC(50) values measured by the flow cytometry-based assay were compared with those reported for other assay formats.
Studies on the Fischer indole synthesis: rearrangements of five-, six- and seven-membered cyclic hydrazones of pyrazoline, tetrahydropyridazine and tetrahydro-1,2-diazepine series in polyphosphoric acid (1991)

The rearrangements of a few cyclic phenylhydrazones structurally related to 1-phenyl-Δ2-pyrazoline, 1-phenyl-1,4,5,6-tetra hydropyridazine, and 1-phenyl-4,5,6,7-tetrahydro-1,2-diazepine in hot polyphosphoric acid (PPA) are described. The five-membered-ring substrates (the pyrazolines) did not undergo the [3,3] sigmatropic rearrangement typical of the Fischer indolization, the main reaction course being homolytic N–N bond cleavage, leading to benzidine and its 4-(2-benzoylethyl)-4′-(3-phenyl-Δ2-pyrazolin-1-yl) derivative. The six-membered heterocycles underwent two different reactions, both evolving the tautomeric enehydrazine form: the first one is the [3,3] sigmatropic rearrangement, expected for open-chain hydrazones, affording 4-acyl-1,2,3,4-tetrahydroquinoline derivatives; the second one is a retro-Diels–Alder reaction producing methyleneaniline and α,β-unsaturated carbonyl, compounds. The seven -membered -ring substrate gave a 5-acyltetrahydrobenz[b]azepine, resulting from the [3,3] rearrangement, together with both a pyrrolidine and a pyrazine by-product; their formation involves homolytic N–N bond cleavage of the ring, a δ hydrogen abstraction, followed by intramolecular or intermolecular ring closure. Chemical proofs are given for the new structures.
Using Search-Logs to Improve Query Tagging (2012)

Syntactic analysis of search queries is important for a variety of information-retrieval tasks; however, the lack of annotated data makes training query analysis models difficult. We propose a simple, efficient procedure in which part-of-speech tags are transferred from retrieval-result snippets to queries at training time. Unlike previous work, our final model does not require any additional resources at run-time. Compared to a state-ofthe-art approach, we achieve more than 20% relative error reduction. Additionally, we annotate a corpus of search queries with partof-speech tags, providing a resource for future work on syntactic query analysis. 1
Computational layout design optimization of frame structures (2017)

Engineers often expend considerable effort identifying the most efficient cross-section sizes for the individual structural members forming a structure, but may neglect to check whether members are optimally positioned, or are even needed at all. This can lead to far more material being used to form a building structure than is needed. To address this, layout optimization can potentially be used early in the design process to identify efficient arrangements of structural members. This paper introduces an interactive design approach that combines parametric modelling and layout optimization, using an adaptive ‘member adding’ technique to allow large scale problems to be solved on a standard desktop PC. Incorporation of the approach in Rhino-Grasshopper allows integration of geometric modelling and structural layout optimization within a single interactive modeling environment. This paper briefly outlines the underlying theory and implementation details, and then describes application of the approach to benchmark problems and a case study problem, a three-centred space frame arch roof. In this case it is shown that a 30% reduction in material usage can potentially be achieved through the use of a layout optimization-based approach, but that measures to improve the practicality of the solutions for use in practice are required. This is being addressed as part of a new collaborative research project involving the Universities of Bath, Sheffield and Edinburgh.
Murine CTLA4-IgG Treatment Inhibits Airway Eosinophilia and Hyperresponsiveness and Attenuates IgE Upregulation in a Murine Model of Allergic Asthma (1997)

Antigen-specific T-cell activation requires the engagement of the T-cell receptor (TCR) with antigen as well as the engagement of appropriate costimulatory molecules. One of the most important pathways of costimulation is the interaction of CD28 on the T cell with B7-1/B7-2 on antigen-presenting cells. In the present study, we have examined the in vivo effects of blocking the CD28:B7 T-cell costimulatory pathway by administration of mCTLA4-IgG in a murine model of allergic asthma. Mice were sensitized with ovalbumin and exposed to repeated ovalbumin inhalation challenges. In mice treated with a control antibody at the time of ovalbumin challenge a significant increase in the number of eosinophils (12.8 +/- 4.3 x 10(3) cells, P < 0.05) in the bronchoalveolar lavage (BAL) fluid and airway hyperresponsiveness to methacholine (49 +/- 15%, P < 0.05) was observed. In addition, serum levels of ovalbumin-specific IgE were significantly (P < 0.01) increased after ovalbumin challenge compared with saline challenge (1,133 +/- 261 experimental units [EU]/ml and 220 +/- 63 EU/ml, respectively). In mice treated with mCTLA4-IgG at the time of ovalbumin challenge, the infiltration of eosinophils into BAL fluid and the development of airway hyperresponsiveness to methacholine were completely inhibited. The upregulation of ovalbumin-specific IgE levels in serum was attenuated by mCTLA4-IgG treatment. Furthermore, addition of mCTLA4-IgG to cultures of parabronchial lymph node cells from sensitized mice inhibited the ovalbumin-induced interleukin-4 production. These data indicate the therapeutic potential of blocking T-lymphocyte costimulation by CTLA4-IgG as a possible immunosuppressive treatment for patients with allergic asthma.
Relationship ofEGFRMutations, Expression, Amplification, and Polymorphisms to Epidermal Growth Factor Receptor Inhibitors in the NCI60 Cell Lines (2007)

These observations suggest that in addition to TK mutations, germ-line variability may also contribute to the pharmacodynamics of EGFR inhibitors, particularly when EGFR is genetically normal.
Early experience with laser disc decompression. A percutaneous method. (1992)

A study over an 18-month period involved 40 patients with a contained HNP who underwent laser-assisted percutaneous lumbar discectomy utilizing KTP/532. Access to the disc was via an 18-gauge probe followed by dilating cannulas under fluoroscopic control. A 400 um quartz fiber was utilized. The laser power was set between 10 and 15 watts and the exposure duration at 0.5 seconds and repeated with intervals of 0.5 seconds. Two of six patients required an open conventional L4-5 discectomy; four refused additional surgery. These failures are considered probably secondary to a subligamentous location of disc. Based upon early results, laser-assisted percutaneous lumbar discectomy with KTP laser appears to be a viable alternative to automated percutaneous discectomy in selected cases and perhaps an improvement over other techniques.
XPS Study and Optical Properties of Si Films Electrodeposited in a Room-Temperature Ionic Liquid (2008)

The binding state of Si in films electrodeposited in trimethyl-n-hexylammonium bis(trifluoromethylsulfonyl)imide containing 0.1 mol L −1 SiCl 4 was investigated by means of X-ray photoelectron spectroscopy (XPS). The bombardment of Ar + mainly causes the transition of spectrum shape from bimodal to broad in XPS spectra of Si 2p core level when Ar + etching is conducted. Angle-resolved XPS confirmed that the bimodal spectrum for the electrodeposited film surface is due to the oxidation in the air. The electrodeposited Si film was also characterized by reflectance and photoluminescence (PL) measurements. These measurements demonstrated that the electrodeposited film contains amorphous Si with the band gap of about 1.55 eV and a broad PL peak centered at the photon energy of 1.37 eV.
A vegetally localized T-box transcription factor in Xenopus eggs specifies mesoderm and endoderm and is essential for embryonic mesoderm formation (1997)

Pattern formation in early embryogenesis is guided by maternal, localized determinants and by inductive interactions between cells. In Xenopus eggs, localized molecules have been identified and some, such as Vg1 and Xwnt-11, can specify cell fates by functioning as inducers or patterning agents. We have used differential screening to identify new Xenopus genes that regulate mesodermal patterning, and we have isolated a new member of the T-box family of transcription factors. This gene, named Brat, is expressed maternally and its transcripts are localized to the vegetal hemisphere of the egg. During early embryonic cleavage, Brat mRNA becomes partitioned primarily within vegetal cells that are fated to form the endoderm. Zygotic expression of Brat begins at the onset of gastrulation within the presumptive mesoderm of the marginal zone. Consistent with its zygotic expression pattern, Brat induces, in a dose-dependent manner, a full spectrum of mesodermal genes that mark tissues across the dorsal-ventral axis, from the blood through the Spemann organizer. Brat also induces endoderm, consistent with its vegetal localization, making Brat a good candidate for a maternal determinant of the endoderm. We tested whether endogenous Brat is required for mesoderm formation by expressing a dominant-negative, transcriptional repressor form of Brat in embryos. This treatment inhibited mesoderm formation and severely disrupted normal development, thereby establishing that Brat plays a critical role in embryonic mesoderm formation and body patterning.
Apoptosis and the cell cycle (1995)

In this review, we consider apoptosis as a process intimately linked to the cell cycle. There are several reasons for thinking of apoptosis as a cell cycle phenomenon. First, within the organism, apoptosis is almost exclusively found in proliferating tissues. Second, artificial manipulation of the cell cycle can either prevent or potentiate apoptosis, depending on the point of arrest. Data from such studies have suggested that molecules acting late in G1 are required for apoptosis. Since passage through late G1 into S phase in mammalian cells is known to be regulated by p53 and by activation of cyclin-dependent kinases, we also examine recent studies linking these molecules to the apoptotic pathway.
Natriuretic Peptides, Their Receptors, and Cyclic Guanosine Monophosphate-Dependent Signaling Functions (2005)

Natriuretic peptides are a family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. The mammalian members are atrial natriuretic peptide, B-type natriuretic peptide, C-type natriuretic peptide, and possibly osteocrin/musclin. Three single membrane-spanning natriuretic peptide receptors (NPRs) have been identified. Two, NPR-A/GC-A/NPR1 and NPR-B/GC-B/NPR2, are transmembrane guanylyl cyclases, enzymes that catalyze the synthesis of cGMP. One, NPR-C/NPR3, lacks intrinsic enzymatic activity and controls the local concentrations of natriuretic peptides through constitutive receptor-mediated internalization and degradation. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure, whereas homozygous inactivating mutations in human NPR-B cause a form of short-limbed dwarfism known as acromesomelic dysplasia type Maroteaux. The physiological effects of natriuretic peptides are elicited through three classes of cGMP binding proteins: cGMP-dependent protein kinases, cGMP-regulated phosphodiesterases, and cyclic nucleotide-gated ion channels. In this comprehensive review, the structure, function, regulation, and biological consequences of natriuretic peptides and their associated signaling proteins are described.
Prototype Fabrication and PreliminaryIn VitroTesting of a Shape Memory Endovascular Thrombectomy Device (2007)

An electromechanical microactuator comprised of shape memory polymer (SMP) and shape memory nickel-titanium alloy (nitinol) was developed and used in an endovascular thrombectomy device prototype. The microactuator maintains a straight rod shape until an applied current induces electro-resistive (Joule) heating, causing the microactuator to transform into a corkscrew shape. The straight-to-corkscrew transformation geometry was chosen to permit endovascular delivery through (straight form) and retrieval of (corkscrew form) a stroke-causing thrombus (blood clot) in the brain. Thermal imaging of the microactuator during actuation in air indicated that the steady-state temperature rise caused by Joule heating varied quadratically with applied current and that actuation occurred near the glass transition temperature of the SMP (86 degrees C). To demonstrate clinical application, the device was used to retrieve a blood clot in a water-filled silicone neurovascular model. Numerical modeling of the heat transfer to the surrounding blood and associated thermal effects on the adjacent artery potentially encountered during clinical use suggested that any thermal damage would likely be confined to localized areas where the microactuator was touching the artery wall. This shape memory mechanical thrombectomy device is a promising tool for treating ischemic stroke without the need for infusion of clot-dissolving drugs.
Custom‐made root analogue titanium implants placed into extraction sockets. An experimental study in monkeys. (1997)

The aim of this investigation was to evaluate clinically and histologically a new custom-made, root analogue titanium implant placed into extraction sockets in monkeys (Macaca fascicularis). Three adult monkeys were used in this investigation. After raising full thickness flaps on the buccal and lingual side, the upper central and lateral incisors were extracted. Each tooth root was machine copied to 1 titanium analogue using a new CAD/CAM-system. The implants were installed in the respective extraction sockets and the flaps sutured back. After 6 months of healing biopsies were taken and processed according to the cutting-grinding technique. The percentage of mineralized bone-to-implant contact was measured as a fraction of the rough implant surface using computer-assisted analysis. The main clinical problem that occurred during implant placement was the fracture of the buccal alveolar wall. The histometric evaluation showed a mean mineralized bone-to-implant contact of 41.2 +/- 20.6%. In this investigation it could be shown that implants fabricated by laser copying will osseointegrate. The presented data encourage the performance of clinical and experimental trials evaluating the new system utilizing improved second generation CAD/CAM equipment. Such studies are currently underway.
Biosynthesis and Action of Ethylene (1985)

Abstract Ethylene is a plant hormone which regulates many aspects of growth, development, and senescence (1). Depending upon where and when ethylene occurs, it may be beneficial or harmful to harvested horticultural crops. Efficient postharvest technology therefore requires the ability to control ethylene effects to suit our practical needs. Before ethylene can exert such responses, it has to be biosynthesized by the plants or supplies from external sources. As in the case of other hormones, ethylene is thought to bind to a receptor, forming an activated complex which in turn triggers the primary reaction. The primary reaction then initiates the chain of reactions, including modification of gene expression, and leading to a wide variety of physiological responses (Fig. 1). Thus, there are 4 levels of manipulation we can use to regulate ethylene responses: (a) control the level of ethylene in the tissue by addition or removal of ethylene, (b) regulate the level of ethylene in the tissue by stimulating or inhibiting ethylene biosynthesis, (c) modify the binding characteristics of ethylene to the receptor, or modify the amount of the receptor, and (d) manipulate the ethylene-dependent gene expression.
Virus-associated human tumors: cervical carcinomas and papilloma viruses. (2000)

The latest experimental data on the role of viruses in the origin of human tumors are discussed. This group of viruses consists of T-cell leukemia virus type 1 (HTLV 1), herpes viruses (HHV 8 and Epstein-Barr virus), hepatitis B virus, and human papilloma viruses. The most typical feature of this group of viruses is a very long latent period from the initial infection to the development of the disease that varies between 10 and 40 years. The mechanism of malignant cell conversion is specific for each viral type but is mainly associated with a disruption of functions of cellular genes participating in the control of cell division and proliferation. It can be a direct inactivation of tumor suppressor genes by their interaction with viral gene products (papilloma viruses), or a trans-activation of cellular genes modulating cell proliferation by viral gene products (hepatitis B virus and HTLV 1). Viruses play an initiative role and additional genetic changes in the genome of infected cells are necessary for complete expression of the oncogenic potential of the viral genes. Only these cells will give rise to a monoclonal cell population with uncontrolled proliferation. New approaches for the creation of vaccines against cancers associated with hepatitis B virus and papilloma viruses (hepatocellular carcinomas and cervical tumors, respectively) are in progress. These vaccines have been found to be effective in prevention of the disease in the experimental models and are now beginning to be used for human vaccination.