gebhart/patrepeval huggingface dataset:
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes (2014)

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome.
Design of a planar inverted-F Antenna with very wide impedance bandwidth (2006)

This letter presents a novel wideband planar inverted F-antenna, which covers GSM850/DCS1800/DCS1900/ IMT2000/WLAN/DMB services at the same time. The proposed antenna consists of a main patch with a pair of slant slits and L-shaped patch and occupies a total volume of 15/spl times/44/spl times/8mm/sup 3/. The triple frequency bands are obtained by changing the length and width of a slant slit 1 on the main patch. A very wide impedance bandwidth characteristic is achieved by optimizing not only the length and height of a L-shaped patch between the main patch and ground plane but also the length and width of a pair of slits on the main patch which is excited by the modified coplanar waveguide-feed. Good broadside radiation patterns are achieved for all six-frequency bands of interest.
The spectrum of cutaneous T-cell lymphomas: new insights into biology and therapy (2005)

This review provides an update of recent findings of immunologic, molecular, and cytogenetic features and treatment approaches for patients with cutaneous T-cell lymphoma with special emphasis on mycosis fungoides and Sezary syndrome.
Improved word recognition for observers with age-related maculopathies using compensation filters (1988)

A method for improving word recognition for people with age-related maculopathies, which cause a loss of central vision, is discussed. It is found that the use of individualized compensation filters based on an person's normalized contrast sensitivity function can improve word recognition for people with age-related maculopathies. It is shown that 27-70 pct more magnification is needed for unfiltered words compared to filtered words. The improvement in word recognition is positively correlated with the severity of vision loss.
All-optical switching of infrared optical radiation using isotropic liquid crystal (1995)

Experimental results of the transmission to total-internal reflection switching of a step-on CO/sub 2/ laser beam by a dielectric-clad, isotropic liquid crystal film is presented. The use of the isotropic phase allows for polarization independence of the processes, while maintaining a moderate thermal nonlinearity. Dependence of switching speed on incident angle and energy density is evaluated. Experimental observations of the nonlinear switching effect with microsecond CO/sub 2/ laser pulses are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pitch ranking ability of cochlear implant recipients: A comparison of sound-processing strategies (2005)

Pitch ranking of sung vowel stimuli, separated in fundamental frequency (F0) by half an octave, was measured with a group of eleven Nucleus 24 cochlear implant recipients using different sound coding strategies. In three consecutive studies, either two or three different sound coding strategies were compared to the Advanced Combinational Encoder (ACE) strategy. These strategies included Continuous Interleaved Sampling (CIS), Peak Derived Timing (PDT), Modulation Depth Enhancement (MDE), F0 Synchronized ACE (FOSync), and Multi-channel Envelope Modulation (MEM), the last four being experimental strategies. While pitch ranking results on average were poor compared to those expected for most normal hearing listeners, significantly higher scores were obtained using the MEM, MDE, and FOSync strategies compared to ACE. These strategies enhanced coding of temporal F0 cues by providing deeper modulation cues to F0 coincidentally in time across all activated electrodes. In the final study, speech recognition tests were also conducted using ACE, CIS, MDE, and MEM. Similar results among all strategies were obtained for word tests in quiet and between ACE and MEM for sentence tests in noise. These findings demonstrate that strategies such as MEM may aid perception of pitch and still adequately code segmental speech features as per existing coding strategies.
Regulation of Gene Expression by cGMP-dependent Protein Kinase (1996)

The cAMP/cAMP-dependent protein kinase (A-kinase) and Ca2+/calmodulin-dependent protein kinase (Cam-kinase) signal transduction pathways are well known to regulate gene transcription, but this has not been demonstrated directly for the cGMP/cGMP-dependent protein kinase (G-kinase) signal transduction pathway. Here we report that transfection of G-kinase into G-kinase-deficient cells causes activation of the human c-fos promoter in a strictly cGMP-dependent manner. The effect of G-kinase appeared to be mediated by several sequence elements, most notably the serum response element (SRE), the AP-1 binding site (FAP), and the cAMP response element (CRE). The magnitude of G-kinase transactivation of the fos promoter was similar to that of A-kinase, but there were significant differences between G-kinase and A-kinase activation of single enhancer elements and of a chimeric Gal4-CREB transcription factor. Our results indicate that G-kinase transduces signals to the nucleus independently of A-kinase or Ca2+, although it may target some of the same transcription factors as A-kinase and Cam-kinase.
Osteogenesis: bone development from primitive progenitors (1998)

Conference Article| February 01 1998 Osteogenesis: bone development from primitive progenitors J. T. Triffitt; J. T. Triffitt 1MRC Bone Research Laboratory, University of Oxford, Nuffield Orthopaedic Centre, Oxford OX3 7LD, U.K. Search for other works by this author on: This Site PubMed Google Scholar C. J. Joyner; C. J. Joyner 1MRC Bone Research Laboratory, University of Oxford, Nuffield Orthopaedic Centre, Oxford OX3 7LD, U.K. Search for other works by this author on: This Site PubMed Google Scholar R. O. C. Oreffo; R. O. C. Oreffo 1MRC Bone Research Laboratory, University of Oxford, Nuffield Orthopaedic Centre, Oxford OX3 7LD, U.K. Search for other works by this author on: This Site PubMed Google Scholar A. S. Virdi A. S. Virdi 1MRC Bone Research Laboratory, University of Oxford, Nuffield Orthopaedic Centre, Oxford OX3 7LD, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Received: August 08 1997 Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1998 Biochemical Society1998 Biochem Soc Trans (1998) 26 (1): 21–27. https://doi.org/10.1042/bst0260021 Article history Received: August 08 1997 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J. T. Triffitt, C. J. Joyner, R. O. C. Oreffo, A. S. Virdi; Osteogenesis: bone development from primitive progenitors. Biochem Soc Trans 1 February 1998; 26 (1): 21–27. doi: https://doi.org/10.1042/bst0260021 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: BMP, bone morphogenetic protein, CFU-F, colony-forming unit fibroblastic, CBFA1, core-binding factor A1, FOP, fibrodysplasia ossificans progressiva, IL-1, interleukin 1, PGE2, prostaglandin E2, PPARγ2, peroxisome proliferator activated receptor γ2 This content is only available as a PDF. © 1998 Biochemical Society1998 Article PDF first page preview Close Modal You do not currently have access to this content.
Identification of farnesol as the non-sterol derivative of mevalonic acid required for the accelerated degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (1994)

The degradation of the microsomal enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase is highly regulated and is dependent on both a sterol and non-sterol derivative of mevalonic acid (MVA). We recently proposed that the non-sterol component is derived from farnesyl diphosphate (FPP), presqualene pyrophosphate, or squalene (Correll, C. C. and Edwards, P. A. (1994) J. Biol. Chem. 269, 633-638). In the current study, we have used digitonin-permeabilized cells to further define this MVA-derived non-sterol component required for the regulated degradation of HMG-CoA reductase. The addition of either FPP or farnesol to digitonin-permeabilized cells resulted in a rapid and dose-dependent degradation of HMG-CoA reductase. The effect of FPP, but not farnesol, was blocked by the phosphatase inhibitor sodium fluoride. The enhanced degradation of HMG-CoA reductase in permeabilized cells specifically required farnesol, since the addition of any of the structurally related isoprenoids geraniol, geranyl diphosphate, geranylgeranyl diphosphate, nerolidol, or all-cis-farnesol, or of the non-sterol squalene to the permeabilized cells did not stimulate enzyme degradation. The present studies demonstrate for the first time that the accelerated degradation of HMG-CoA reductase can be initiated in vitro. Further, since farnesol is shown to be specifically required for the enhanced degradation of the enzyme in vitro, we propose that this isoprenoid alcohol is important in this process in intact cells.
A phage‐based system to select multiple protein‐protein interactions simultaneously from combinatorial libraries (1998)

Selectively infective phage (SIP) can be used to identify protein-protein interactions. SIP was modified to facilitate the simultaneous selection of interacting protein pairs from large combinatorial libraries. An interference-resistant phage was constructed which non-covalently, but stably links the genetic information of an interacting pair, encoded separately on phage and phagemid vectors, by co-packaging into heteropolyphages. In a model system, the interaction between a SIP-selected peptide and the intracellular domain of the p75 neurotrophin receptor was detected in the presence of a 10(4)-fold excess of a non-interacting control pair (jun leucine zipper and p75 intracellular domain) via SIP hetero-polyphage transductants. To minimize the redundancy of transductants and to minimize possible ligand exchange generated in a solution-based SIP screening, a filter-based in situ infectivity screening was developed. The combination of the above techniques may provide a powerful system for rapid screening of very large sequence spaces.
Causes and Consequences of MicroRNA Dysregulation (2012)

It is currently well recognized that microRNA deregulation is a hallmark of human cancer, and an aberrant expression of these tiny regulatory RNA molecules in several cell types is not just a random association, but it also plays a causal role in different steps of the tumorigenic process, from the initiation and development to progression toward the acquisition of a metastatic phenotype. Different regulatory mechanisms can control microRNA expression at a genetic or epigenetic level as well as involve the biogenesis machinery or the recruitment of specific transcription factors. The tumorigenic process implies a substantial alteration of these mechanisms, thus disrupting the equilibrium within the cell and leading to a global change in microRNA expression, with loss of oncosuppressor microRNAs and overexpression of oncomiRNAs. We review the main mechanisms regulating microRNAs and the consequences of their aberrant expression in cancer, with a glance at the possible implications at a clinical point of view.
Dynamic Determinants of Left Ventricular Early Diastolic Filling in Old Myocardial Infarction. (1992)

The determinants of left ventricular early diastolic filling were assessed in 15 patients with old myocardial infarction. The left atrial pressure (LAP) and left ventricular pressure (LVP) were simultaneously measured by a Millar's multisensor micromanometer with the pusled Doppler mitral inflow velocity at baseline and during angiotensin infusion (20 ng/kg/min). Cardiac output was measured by a thermodilution method. LV peak systolic pressure and end-diastolic pressure were significantly (p less than 0.001) increased during angiotensin infusion from 137 +/- 19 to 170 +/- 21 mmHg and from 13.3 +/- 5.9 to 20.4 +/- 6.2 mmHg, respectively. Cardiac index was significantly decreased during angiotensin infusion. Heart rate, diastolic time, and peak positive dP/dt were unchanged. Although the LA-LV peak pressure gradient[(LAP-LVP) max] was unchanged (from 2.8 +/- 1.0 to 3.0 +/- 1.4 mmHg), the pressure gradient interval (the interval between the first and second points of transmitral pressure crossover) was significantly (p less than 0.001) decreased from 154 +/- 38 to 117 +/- 26 msec during angiotensin infusion. Peak early diastolic mitral inflow velocity (peak E) and the time-velocity integral of E wave (Ei) were significantly decreased during angiotensin infusion from 51 +/- 10 to 45 +/- 11 cm/sec (p less than 0.002) and from 7.47 +/- 1.96 to 5.70 +/- 1.66 cm (p less than 0.001), respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Phorbol Esters: Structure, Biological Activity, and Toxicity in Animals (2007)

Phorbol esters are the tetracyclic diterpenoids generally known for their tumor promoting activity. The phorbol esters mimic the action of diacyl glycerol (DAG), activator of protein kinase C, which regulates different signal transduction pathways and other cellular metabolic activities. They occur naturally in many plants of the family Euphorbiacaeae and Thymelaeaceae. The biological activities of the phorbol esters are highly structure specific. The phorbol esters, even at very low concentrations, show toxicological manifestations in animals fed diets containing them. This toxicity limits the use of many nutritive plants and agricultural by-products containing phorbol esters to be used as animal feed. Therefore, various chemical and physical treatments have been evaluated to extract or inactivate phorbol esters so that seed meals rich in proteins could be used as feed resources. However, not much progress has been reported so far. The detoxifying ability has also been reported in some molluscs and in liver homogenate of mice. Besides, possessing antinutritional and toxic effects, few derivatives of the phorbol esters are also known for their antimicrobial and antitumor activities. The molluscicidal and insecticidal properties of phorbol esters indicate its potential to be used as an effective biopesticide and insecticide.
Phase III Randomized Trial of Cisplatin Plus Placebo Compared With Cisplatin Plus Cetuximab in Metastatic/Recurrent Head and Neck Cancer: An Eastern Cooperative Oncology Group Study (2005)

Addition of cetuximab to cisplatin significantly improves response rate. There was a survival advantage for the development of rash. Progression-free and overall survival were not significantly improved by the addition of cetuximab in this study.
Functional Testing and Characterisation of ISFETs on Wafer Level by Means of a Micro-droplet Cell (2006)

A wafer-level functionality testing and characterisation system for ISFETs (ion-sensitive field-effect transistor) is realised by means of integration of a specifically designedcapillary electrochemical micro-droplet cell into a commercial wafer prober-station. Thedeveloped system allows the identification and selection of “good” ISFETs at the earlieststage and to avoid expensive bonding, encapsulation and packaging processes for non-functioning ISFETs and thus, to decrease costs, which are wasted for bad dies. Thedeveloped system is also feasible for wafer-level characterisation of ISFETs in terms ofsensitivity, hysteresis and response time. Additionally, the system might be also utilised forwafer-level testing of further electrochemical sensors.
Fabrication of Reflective Holographic PDLC for Blue (2001)

Abstract Reflective holographic polymer dispersed liquid crystals(HPDLCs) have been fabricated with a ternary monomer system composed of dipentaerythritol hydroxy penta acrylate(DPHPA)/trimethylol propane triacylate(TMPTA)/N-vinylpyrrolidone(NVP)=7/2/1 by weight. Gratings were written by irradiating with an Ar-ion laser(λ=488 nm) at various intensities(20–200 mW/cm2) on LC/monomers composite films of various composition(25/75, 30/70, 35/65, 38/62, 40/60). Polarized optical micrography(POM) images of gratings and UV-visible spectra were taken and reflection efficiency-irradiation intensity-film composition relatioriships are subsequently obtained in three dimensional plot which showed that maximum reflection moves from high LC content (38wt%) at low irradiation intensity (20 mW/cm2) to low LC content(25wt%) at high irradiation intensity (200 mW/cm2).
Isotope Effect Studies on the Cytochrome P450 Enzymes (1995)

Isotope effect experiments provide a powerful tool for study of the fundamental aspects of the enzymology of the cytochrome P450 enzymes. Competition between alternate pathways not only allows P450 isotope effects to be observed, but also provides mechanistic information on both oxygen activation and substrate oxidation. Indeed, the kind of knowledge that isotope effect studies can provide is not readily obtainable by other methodologies.
Antitumor Effects of a Human Dimeric Antibody Fragment 131I-AFRA-DFM5.3 in a Mouse Model for Ovarian Cancer (2011)

AFRA-DMF5.3 is a human antibody fragment that, as a dimer, specifically binds to the a-folate receptor (FR) on ovary cancer cells. Pharmacokinetic and biodistribution parameters of 131 I-AFRA-DFM5.3 after intravenous administration in animal models support its potential therapeutic use. We evaluated its preclinical specificity and therapeutic efficacy in tumor models. Methods: A negative control, AFRA-DFM6.1, was obtained by protein engineering. The activity and specificity of 131 I-AFRA-DFMs were evaluated by systemic administration (intravenous) in subcutaneous tumor xenograft-bearing nude mice. Pharmacokinetics, biodistribution, and efficacy were assessed by intraperitoneal administration of 131 I-AFRA-DFM5.3 in nude mice bearing 2 different intraperitoneal ovarian carcinoma xenografts. Treatments were tested at different doses and as single or double administrations 1 wk apart. Results: In subcutaneous models, 131 I-AFRA-DFM5.3, but not the negative control, was found to reside on FR-positive tumor masses and significantly reduced tumor growth. In intraperitoneal models, early accumulation on free-floating clumps of ovarian cancer cells and solid peritoneal masses was evident after 1 h, and tumor uptake was stable for up to 3 h. The high tumor uptake determined the efficacy of 131 I-AFRA-DFM5.3. The best antitumor activity, with more than 50% of treated animals cured, was achieved with 2 locoregional treatments of intraperitoneally growing tumors on days 2 and 9. Conclusion: These results suggest that radioimmunotherapy with 131 I-AFRA-DFM5.3 is feasible and leads to significantly prolonged survival. These preclinical data provide the basis for the rationale design of therapeutic treatments of ovarian cancer patients with a radiolabeled anti-FR antibody fragment.
Bmp signaling is necessary and sufficient for ventrolateral endoderm specification in Xenopus (2008)

Here we show that Bmp signaling is necessary and sufficient for the specification of ventral endoderm in Xenopus embryos. Overexpression of Bmp4 in ectoderm induces markers of endoderm, including Sox17beta, Mixer, and VegT, but cannot induce the expression of the dorsoanterior markers, Xhex and Cerberus. Furthermore, knockdown approaches using overexpression of Bmp antagonists and morpholinos designed against Bmp4, Bmp2, and Bmp7 demonstrate that Bmp signaling is critical for ventral, but not dorsoanterior endoderm formation. This activity is not simply a result of embryonic dorsalization as markers for dorsal endoderm are not expanded. We further show that endodermal cells of either ventral or dorsal character do not form when both Wnt and Bmp signals are abolished. Overall, this report strongly suggests that Bmp plays an essential role in ventral endoderm specification.
Toward Fully Synthetic Carbohydrate-Based HIV Antigen Design:  On the Critical Role of Bivalency (2004)

Synthetic gp120331-335 glycopeptide fragments carrying hybrid and high-mannose type N-linked glycans were evaluated for binding to broadly neutralizing antibody 2G12 using surface plasmon resonance technology. None of the hybrid-type constructs demonstrated binding to 2G12. In the high-mannose series, the "Cys dimer" construct, presenting two undecasaccharide glycans, showed significantly higher binding than the Cys-protected monomer. The binding of the dimeric structure was further investigated in competition with recombinant gp120. The data suggest that gp120 and its designed synthetic epitope construct bind to the same site on 2G12.
High-contrast step-index waveguides in borate nonlinear laser crystals by 3D laser writing (2011)

We report the ultrafast fabrication of high-contrast step-index channel waveguides in Nd(3+):YCa(4)O(BO(3))(3) borate laser crystals by means of 3D direct laser writing. Guiding up to 3.4 μm wavelength is demonstrated for the first time in a laser written crystalline waveguide. Modeling the measured fundamental modes at the wavelengths of 1.9 µm and 3.4 µm allowed us to estimate the high laser-induced refractive index increments (index contrasts) to be 0.010 (0.59%), and 0.005 (0.29%), respectively. Confocal µ-Raman spectral imaging of the waveguides cross-sections confirmed that the cores have very well defined step profiles, and that the increase in the refractive index can be linked to the localized creation of permanent intrinsic defects. These results indicate that this crystalline waveguides are a potential candidate for the development of 3D active waveguide circuits, due to the laser and electro-optic properties of rare earth doped borate crystals.
Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (μFACS) (2010)

We demonstrate a high performance microfabricated FACS system with highly integrated microfluidics, optics, acoustics, and electronics. Single cell manipulation at a high speed is made possible by the fast response time (approximately 0.1 ms) of the integrated PZT actuator and the nozzle structure at the sorting junction. A Teflon AF-coated optofluidic waveguide along the microfluidic channel guides the illumination light, enabling multi-spot detection, while a novel space-time coding technology enhances the detection sensitivity of the microFACS system. The real-time control loop system is implemented using a field-programmable-gate-array (FPGA) for automated and accurate sorting. The microFACS achieves a high purification enrichment factor: up to approximately 230 fold for both polystyrene microbeads and suspended human mammalian cells (K562) at a high throughput (>1000 cells s(-1)). The sorting mechanism is independent of cell properties such as size, density, and shape, thus the presented system can be applied to sort out any pure sub-populations. This new lab-on-a-chip FACS system, therefore, holds promise to revolutionize microfluidic cytometers to meet cost, size, and performance goals.