gebhart/patrepeval huggingface dataset:
Acoustic Trapping in Biomedical Research (2014)

Herein a method that uses acoustically resonating glass capillaries and enables non-contact capture of micron-sized bioparticles, i.e. acoustic trapping, is described. A miniaturized ultrasonic transducer is used to locally actuate a cross-sectional resonance in the capillary. A 2000×200 µm2 capillary is typically operated around a resonance frequency of 4-MHz. Optimal design of the transducer for this purpose is investigated in detail, showing that mode-control in the transducer results in a more efficient device, and makes automatic frequency tracking possible. A system design that allows easy assembly and disassembly of the transducer and the capillary also demonstrates how a single-use device can be accomplished. A breakthrough for the presented acoustic trapping technology is the introduction of seed-particles. These enable trapping of submicron particles that would otherwise be impossible to capture in this kind of system. It is shown how controlled interaction with the larger seed particles can circumvent this limitation. Using this approach capture of 110 nm particles and Escherichia coli bacteria is demonstrated with 95% capture efficiency. The usefulness of the acoustic trapping device in biomedical research is demonstrated in applications such as; efficient washing of functionalised beads for biomarker detection in blood plasma, dynamic studies of cell-drug interactions, and purification and identification of microbes from infected blood. To enable these applications the acoustic trap an interface to a Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI MS) instrument has been devised. This is facilitated by designing the acoustic trap to operate in aspirate/dispense mode (like a pipette) depositing liquids in a microchip for solid phase extraction and subsequent MALDI MS analysis. Tracking and logging the system resonance frequency provides a new way to measure the amount of captured material as well as continuously adjusting the driving frequency to changes in the infused samples. Apart from providing a new measurement method, continuously adapting the resonance frequency enables samples with a wider range of acoustic properties to be processed. This is demonstrated in an assay for bacteria typing with MALDI MS in blood cultures. Here, acoustic trapping provides a faster and more automatable sample preparation method as compared to the one currently used in the clinical assay.
Expression of 3-Ketoacyl-Acyl Carrier Protein Reductase ( fabG ) Genes Enhances Production of Polyhydroxyalkanoate Copolymer from Glucose in Recombinant Escherichia coli JM109 (2005)

Polyhydroxyalkanoates (PHAs) are biologically produced polyesters that have potential application as biodegradable plastics. Especially important are the short-chain-length-medium-chain-length (SCL-MCL) PHA copolymers, which have properties ranging from thermoplastic to elastomeric, depending on the ratio of SCL to MCL monomers incorporated into the copolymer. Because of the potential wide range of applications for SCL-MCL PHA copolymers, it is important to develop and characterize metabolic pathways for SCL-MCL PHA production. In previous studies, coexpression of PHA synthase genes and the 3-ketoacyl-acyl carrier protein reductase gene (fabG) in recombinant Escherichia coli has been shown to enhance PHA production from related carbon sources such as fatty acids. In this study, a new fabG gene from Pseudomonas sp. 61-3 was cloned and its gene product characterized. Results indicate that the Pseudomonas sp. 61-3 and E. coli FabG proteins have different substrate specificities in vitro. The current study also presents the first evidence that coexpression of fabG genes from either E. coli or Pseudomonas sp. 61-3 with fabH(F87T) and PHA synthase genes can enhance the production of SCL-MCL PHA copolymers from nonrelated carbon sources. Differences in the substrate specificities of the FabG proteins were reflected in the monomer composition of the polymers produced by recombinant E. coli. SCL-MCL PHA copolymer isolated from a recombinant E. coli strain had improved physical properties compared to the SCL homopolymer poly-3-hydroxybutyrate. This study defines a pathway to produce SCL-MCL PHA copolymer from the fatty acid biosynthesis that may impact on PHA production in recombinant organisms.
Integrin-mediated Cell Adhesion Promotes Tyrosine Phosphorylation of p130Cas, a Src Homology 3-containing Molecule Having Multiple Src Homology 2-binding Motifs (1995)

p130Cas (Cas) has been recently identified as a 130-kDa protein that is highly phosphorylated on tyrosine residues and is stably associated with p47v-crk (v-Crk) and p60v-src (v-Src) oncogene products in cells transformed by the respective genes. Cas is a novel signaling molecule having a single Src homology (SH) 3 domain and a cluster of multiple SH2-binding motifs. While the tight association of Cas with v-Crk and v-Src is strongly suggestive of a significant role in regulating cellular transformation, the function of Cas in normal untransformed cells is totally unknown. We report here that cell adhesion to fibronectin rapidly promotes tyrosine phosphorylation of Cas in human and rat fibroblast cell lines. The response was equally induced by cell adhesion to plates coated with vitronectin, laminin, and collagen but not by cell attachment to nonspecific substrate poly-L-lysine. The kinetic profile of Cas phosphorylation was almost identical with that of tyrosine phosphorylation of focal adhesion kinase pp125FAK (Fak), which is well known to be activated subsequent to integrin-mediated cell adhesion. Adhesion-dependent Cas phosphorylation was completely inhibited by treating cells with cytochalasin D, an agent that disrupts polymerization of actin stress fibers. These results suggest that tyrosine phosphorylation of Cas is stimulated by normal cell adhesion in close association with Fak phosphorylation and the formation of actin stress fibers. In v-Src- or v-Crk-transformed cells, however, the tyrosine phosphorylation of Cas is markedly increased in an adhesion-independent manner that is insensitive to treatment with cytochalasin D. Thus, Cas plays a role in signaling pathways mediated by cell adhesion as well as by transformation. We propose that Cas may amplify and propagate integrin-mediated signals by interacting with SH2-containing molecule(s).
Bis(fluoroxy)difluoromethane, CF2(OF)2 (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBis(fluoroxy)difluoromethane, CF2(OF)2Frederick A. Hohorst and Jean'ne M. ShreeveCite this: J. Am. Chem. Soc. 1967, 89, 8, 1809–1810Publication Date (Print):April 1, 1967Publication History Published online1 May 2002Published inissue 1 April 1967https://pubs.acs.org/doi/10.1021/ja00984a009https://doi.org/10.1021/ja00984a009research-articleACS PublicationsRequest reuse permissionsArticle Views128Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Blind Equalization Techniques for xDSL using Channel Coding and Precoding (1999)

A new concept for digital communication over severe in- tersymbol interference producing channels, e.g., high-rate digital transmission over twisted pair lines (xDSL techniques) is proposed including channel coding, precoding, equalization, and synchroniza- tion. Channel coding improves data reliability or tolerable signal attenuation, e.g., field length, whereas a nonlinear predistortion method, a modification of the well-known T omlinson-Harashima precoding (THP) including signal shaping and dynamics limitation at the receiver side, is used in order to cope with intersymbol inter- ference. In contrast to prior approaches, a fixed compromise pre- coder together with a linear blind adaptive fine tuning equalizer at the receiver side is proposed in order to avoid any retransmission of channel measurement data to the receiver. By this, neither a block- ing of bidirectional communication can happen nor sophisticated start-up protocols are necessary. For this purpose new algorithms for blind adaptive equalization are introduced which are able to op- erate at very low signal-to-noise ratios due to channel coding and for highly correlated data sequences, typically for the application of precoding techniques. Additionally, methods for symbol timing syn- chronization are proposed.
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization (2009)

ToppGene Suite (http://toppgene.cchmc.org; this web site is free and open to all users and does not require a login to access) is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. A P-value of each annotation of a test gene is derived by random sampling of the whole genome. The protein-protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method). We demonstrate the utility of ToppGene Suite using 20 recently reported GWAS-based gene-disease associations (including novel disease genes) representing five diseases. ToppGene ranked 19 of 20 (95%) candidate genes within the top 20%, while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%.
The Antimicrobial Acitvity and Quantitative Structure - Biological Activity Relationships Evaluation of Some Novel 2-Hydroxybenzamide Derivatives (2008)

Based on our studies of the biological activity of 2-hydroxybenzamide derivatives, we evaluated the antimicrobial activity of some novel compounds from this class (esters, hydrazides, hydrazones), against bacterial (Escherichia coli, Staphylococcus aureus, Bacillus subtilis, Bacillus cereus) and fungical (Sacharomyces cerevisiae, Candida albicans) strains using the disc-diffusion method under standard conditions. It was found that all tested compounds present a good activity against the tested microorganisms and they were more active against Candida albicans. The established minimum inhibitory concentration (MIC) values were ranged between 10-2- 3.6�10-4 mol/L and were used to obtain some quantitative structure-biological activity relationships using HyperChem 5.01 program for molecular modelling and conformational analysis. The established equations using different parameters present correlation coefficients statistically ensured.
Laminar optical tomography: demonstration of millimeter-scale depth-resolved imaging in turbid media (2004)

Laminar optical tomography (LOT) is a new technique that combines the advantages of diffuse optical tomography image reconstruction and a microscopy-based setup to allow noncontact imaging with 100-200-microm resolution effective over depths of 0-2.5 mm. LOT is being developed primarily for multispectral imaging of rat cortex, for which resolving functional dynamics in various layers of the brain's cortex (to depths of 1500 microm) is of increasing interest to neurophysiologists. System design and image reconstruction techniques are described, along with simulation and phantom results that demonstrate the characteristics and limitations of system accuracy and resolution.
Interaction of Tau Isoforms with Alzheimer's Disease Abnormally Hyperphosphorylated Tau and in VitroPhosphorylation into the Disease-like Protein (2001)

The microtubule-associated protein tau is a family of six isoforms that becomes abnormally hyperphosphorylated and accumulates in neurons undergoing neurodegeneration in the brains of patients with Alzheimer disease (AD). We investigated the isoform-specific interaction of normal tau with AD hyperphosphorylated tau (AD P-tau). We found that the binding of AD P-tau to normal human recombinant tau was tau4L > tau4S > tau4 and tau3L > tau3S > tau3, and that its binding to tau4L was greater than to tau3L. AD P-tau also inhibited the assembly of microtubules promoted by each tau isoform and caused disassembly when added to preassembled microtubules. This inhibition and depolymerization of microtubules by the AD P-tau corresponded directly to the degree of its interaction with the different tau isoforms. In vitro hyperphosphorylation of recombinant tau (P-tau) conferred AD P-tau-like characteristics. Like AD P-tau, P-tau interacted with and sequestered normal tau and inhibited microtubule assembly. These studies suggest that the AD P-tau interacts preferentially with the tau isoforms that have the amino-terminal inserts and four microtubule binding domain repeats and that hyperphosphorylation of tau appears to be sufficient to acquire AD P-tau characteristics. Thus, lack of amino-terminal inserts and extra microtubule binding domain repeat in fetal human brain might be protective from Alzheimer's neurofibrillary degeneration.
High activity of N-alpha-benzyloxycarbonyl-L-lysine thiobenzyl ester serine esterase and cytolytic perforin in cloned cell lines is not demonstrable in in-vivo-induced cytotoxic effector cells. (1987)

Recent observations have suggested striking similarities between complement-mediated and cell-mediated lysis. Both pathways share the terminal insertion of channels into target membranes, and unique esterases have been postulated to participate in the activation of cytolytic effector molecules. Since killer-specific esterases and channel-forming proteins can be demonstrated in in vitro cell lines, it is important to ascertain that the described esterase and channel-forming proteins are also present in killer cells from in vivo sources. Results presented here show that killer-cell-specific N alpha-benzyloxycarbonyl-L-lysine thiobenzyl ester serine esterase is induced in vitro concomitant with the sensitization of cytotoxic effector cells. In contrast, in-vivo-primed cytotoxic T cells or natural killer (NK) cells fail to express high levels of this enzyme. Assay of different cytotoxic effector cells reveals the presence of N alpha-benzyloxycarbonyl-L-lysine thiobenzyl ester serine esterase in clones with T killer and NK activity, but enzyme levels do not correlate with cytolytic activity nor does inhibition of esterase activity interfere with granule-mediated cell lysis. A similar result is seen with granule-mediated cytolytic activity. Cloned NK and T killer cell lines possess granules that are able to lyse erythrocyte targets. However, T killer cells sensitized in mixed lymphocyte culture or in vivo have no detectable cytotoxic granules. Cytotoxic granules are also not detected in NK cells isolated from animals.
Mcl-1 cleavage and sustained phosphorylation of c-Jun -N-terminal kinase mediate melanoma apoptosis induced by 2-acetyl furanonaphthoquinone : Roles of bcl-2 and p53 (2008)

2-acetyl furanonaphthoquinone (FNQ) is a naturally occurring drug with enhanced toxicity versus glucose-starved tumor cells, which frequently show topoisomerase II drug resistance. Since loss of p53 tumor suppressor function or overexpression of the anti-apoptotic bcl-2 gene can decrease susceptibility to some cancer therapies, we now investigated the effect of FNQ against genetically matched C8161 melanoma cell lines transduced to express unequal levels of Bcl-2, or engineered to harbour a functional wt p53 for comparison with dominant-negative mutant p53 R175H. Cells with differing p53 genotype showed susceptibility to FNQ. However, this response was attenuated in those overexpressing mutant p53, although a brief p53 induction was early seen in FNQ-treated wt p53 cells. Cells susceptible to FNQ showed cleavage of anti-apoptotic Mcl-1, sustained activation of the c-Jun N-terminal Kinase (p-JNK), and apoptosis-associated PARP fragmentation, all of which were counteracted in bcl-2 overexpressing cells. Suppression of JNK activation with the specific inhibitor, SP600125 also prevented FNQ-mediated cell death. Our data suggests that Bcl-2, persistent JNK phosphorylation and cleavage of anti-apoptotic Mcl-1 are key events controlling susceptibility to FNQ.
Ethylene Bis(2-indenyl) Zirconocenes:  A New Class of Diastereomeric Metallocenes for the (Co)Polymerization of α-Olefins (2001)

Sequential additions of NaOEt and benzyl chloride (BzCl) to diethyl adipate in THF afforded EtOOCCH(Bz)CH2CH2CH(Bz)COOEt (3) in high yield via successive Dieckmann condensations. This was converted to CH2CH2(2-indene)2 (2) using standard synthetic methodology, from which 436 g of CH2CH2(2-indenyl)2ZrCl2 (1) was prepared. Incorporation of a 1-alkyl substituent gave rac and meso isomers CH2CH2(1-R-2-indenyl)2ZrCl2 (R = Me, 12r, 12m; R = Et, 14r, 14m). Methylation gave rac- and meso-CH2CH2(1-Me-2-indenyl)2ZrMe2 (15r, 15m) and CH2CH2(2-indenyl)2ZrMe2 (16). CH2CH2(4-Ph-2-indene)2 (20) was prepared similarly to 2 using 2-phenyl benzylbromide and diethyladipate/NaOEt, from which rac- and meso-CH2CH2(4-Ph-2-indenyl)2ZrCl2 (19r and 19m) were prepared. Alkylation of 19m gave meso-CH2CH2(4-Ph-2-indenyl)2ZrMe2 (23m). The 4-phenyl metallocenes rac- and meso-CH2CH2(1-Me-4-Ph-2-indenyl)2ZrCl2 (25r and 25m) were prepared via 20. C2-symmetric CH2CH2(1,3-Me2-2-indenyl)2ZrCl2 (29) was prepared to compare its polymerization behavior with 1. These zirconocenes displayed activities of up to 4320 kg PE/(g Zr·h) for the polymerization of ethylene (9.6 bar, 80 °C, hexane) to linear PE. The activity was much lower (2−20 kg/(g Zr·h); liquid propylene, 50 °C) for the polymerization of propylene to low molecular weight atactic polypropylene. Alkyl groups in the 1- and/or 3-positions led to a significant reduction of 2,1-insertions from 9.4% in the polymer from 1/MAO, and 9.9% from 19/MAO, to 0.1−0.4%. Attempts to prepare an isospecific catalyst were unsuccessful; substituent variation i.e., 4-phenyl in 19, did not provide effective enantiomorphic site control. Addition of H2 has a dramatic activation effect (>100-fold) in propylene polymerization and afforded saturated propylene oligomers with activities up to 6240 kg/(g Zr·h). The low polymer molecular weights allowed detailed NMR analysis of the end groups, which enabled the chain transfer and metallocene activation mechanisms to be identified. Copolymerization of ethylene and propylene (in liquid propylene at 50 °C with 6 mol % ethylene) afforded copolymers with activities of 1300−12500 kg/(g Zr·h). Reactivity ratios (rE = 41−98, rP = 0.0025−0.0084, rErP = 0.1−0.7) indicate a very high preference for sequential ethylene insertions. Copolymerization of ethylene and 1-hexene (4.4 bar ethylene, heptane, 70 °C) gave copolymers with activities of up to 1100 kg/(g Zr·h) using 12r/MAO. The copolymer microstructure showed highly preferential sequential ethylene incorporation: rE = ca. 200, rH = 0.004.
A Color Atlas of Endovascular Surgery (1991)

Part 1 Natural history of the atherosclerotic lesions: the atherosclerotic lesion relationship of the distribution of lesions and the application and development of interventional methods. Part 2 Angioplasty devices techniques and applications: intraluminal access techniques balloon angioplasty lasers atherectomy stents additional endovascular techniques. Part 3 Angioscopy. Part 4 Additional imaging techniques and guidance methods: angiography ultrasound spectroscopy. Part 5 Evolving related technologies in vascular surgery: laser endarterectomy laser vascular tissue fusion.
Preparative enzymatic synthesis and hydrophobic chromatography of acyl-acyl carrier protein. (1979)

We have used purified preparations of acyl-acyl carrier protein synthetase to prepare pure, native acyl-acyl carrier proteins (acyl-ACP) ranging in chain lengths from C10:0 to C delta 9 18:1. Factors affecting yield are explored and reaction conditions are presented that yield 0.8 to 0.9 mg of C16:0-ACP/ml of reaction mix. Ohter acyl groups, such as C10:0 and C delta 9 18:1 are poorer substrates and gave correspondingly lower yields. Acyl-Acp synthetase may be recovered from the reaction mixture using blue-Sepharose CL-6B and recycled. ACP and acyl-ACP are separated by hydrophobic chromatography on octyl-Sepharose CL-4B. Mixtures of acyl-ACPs could be resolved according to acyl chain length using octyl-Sepharose CL-4B columns eluted with a 2-propanol gradient. The high resolution obtained using 2-propanol gradients to separate acyl-ACP species suggests that similar techniques would be applicable to the chromatography of protein mixtures on hydrophobic supports.
Influence of Electrical Potential Distribution, Charge Transport, and Recombination on the Photopotential and Photocurrent Conversion Efficiency of Dye-Sensitized Nanocrystalline TiO2 Solar Cells:  A Study by Electrical Impedance and Optical Modulation Techniques (2000)

The role of electrical potential, charge transport, and recombination in determining the photopotential and photocurrent conversion efficiency (IPCE) of dye-sensitized nanocrystalline solar cells was studied. Electrostatic arguments and electrical impedance spectroscopy (EIS) are used to obtain information on the electrical and electrochemical potential distribution in the cell. It is shown that on the macroscopic level, no significant electrical potential drop exists within the porous TiO2 when it contacts the electrolyte and that the electrical potential drop at the transparent conducting oxide substrate (TCO)/TiO2 interface occurs over a narrow region, one or two layers of TiO2. Analyses of EIS and other data indicate that both the photopotential of the cell and the decrease of the electrical potential drop across the TCO/TiO2 interface are caused by the buildup of photoinjected electrons in the TiO2 film. The time constants for the recombination and collection of the photoinjected electrons are measured by EIS and intensity-modulated photocurrent spectroscopy (IMPS). As the applied bias is varied from short-circuit to open-circuit conditions at 1 sun light intensity, recombination becomes faster, the collection of electrons becomes slower, and the IPCE decreases. The decrease of IPCE correlates directly with the decline of the charge-collection efficiency ηcc, which is obtained from the time constants for the recombination and collection of the photoinjected electrons. Significantly, at open circuit, ηcc is only 45% of its short-circuit value, indicating that the dye-sensitized nanocrystalline TiO2 solar cell behaves as a nonideal photodiode.