gebhart/patrepeval huggingface dataset:
Peptide Mapping of Bovine T‐Cell Epitopes for the 38 kDa Tuberculosis Antigen (1995)

Mycobacterium bovis infection in cattle continues to be a problem in several regions, partly due to inadequate diagnostic tests. The aim of this study was to use an experimental model of the natural disease to identify T-cell epitopes from the mycobacterial 38 kDa antigen as potentially specific diagnostic reagents. A panel of overlapping synthetic peptides (16-mers with a five-residue overlap) were produced from the published amino acid sequence. It was found that peripheral blood lymphocytes from at least three of four experimentally infected animals, which were considered to be in either Th1- or Th1/Th2-dominated stages of anti-mycobacterial immunity, proliferated in response to five epitopes (residues 1-27, 88-107, 122-138, 243-260 and 307-328). However, in vitro production of IFN-gamma was detected only in response to epitope 122-138, indicating a role in protective immunity. The peptides were not recognized by control, uninfected animals, but all epitopes showed various degrees of recognition by animals which were field reactors to intradermal tuberculin testing. Furthermore, epitopes 1-27, 88-107 and 122-138 were recognized by four breeds of cattle and by animals from separate herds, suggesting genetic permissiveness in recognition which would be essential in the development of a diagnostic test.
Impaired Angiogenesis After Hindlimb Ischemia in Type 2 Diabetes Mellitus (2007)

Deficient angiogenesis after ischemia may contribute to worse outcomes of peripheral arterial disease in patients with diabetes mellitus (DM). Vascular endothelial growth factor (VEGF) and its receptors promote angiogenesis. We hypothesized that in peripheral arterial disease, maladaptive changes in VEGF ligand/receptor expression could account for impaired angiogenesis in DM. Skeletal muscle from diet-induced, type 2 diabetic (DM) and age-matched normal chow (NC)-fed mice was collected at baseline and 3 and 10 days after hindlimb ischemia and analyzed for expression of VEGF (n=10 per group), full-length VEGF receptor (VEGFR)-1, soluble VEGFR-1, and markers of downstream VEGF signaling (n=20 per group) using ELISA, reverse transcriptase-polymerase chain reaction, and Western blots. In the absence of ischemia, DM mice had increased VEGF (NC versus DM: 26.6+/-2.6 versus 53.5+/-8.8 pg/mg protein; P<0.05), decreased soluble and membrane-bound VEGFR-1 (NC versus DM: 1.44+/-0.30 versus 0.85+/-0.08 and 1.03+/-0.10 versus 0.72+/-0.10, respectively; P<0.05), decreased phospho-AKT/AKT and phospho-endothelial NO synthase/endothelial NO synthase (NC versus DM: 0.76+/-0.2 versus 0.38+/-0.1 and 0.36+/-0.06 versus 0.25+/-0.04, respectively; P<0.05), and no change in VEGFR-2. After ischemia, both DM and NC had comparable increases in VEGF-A. VEGFR-1 and soluble VEGFR-1 expression increased in both groups, but the fold increase was significantly greater in DM. These data demonstrate that soluble VEGFR-1, an angiogenesis inhibitor, is regulated in skeletal muscle by type 2 DM and ischemia. In the absence of ischemia, despite reductions in both soluble VEGFR-1 and VEGFR-1, VEGF ligand signaling is lower in DM compared with controls. After ischemia, maladaptive upregulation of these receptors further reduces the capacity of VEGF to induce an angiogenic response, which may provide a novel target for therapy.
Service-delivery strategies: Three approaches to consulting for hospitality (2002)

Three Approaches to Consulting for HospitalityEffective consulting for hospitality involves going beyond applying mere expertise to solve a client's particular problem to being an empowering expert who focuses on ensuring that clients obtain the tools and resources needed to solve their own problems.by
Genotype calling in tetraploid species from bi-allelic marker data using mixture models (2011)

We have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.
Multipass etalon cascade for high-resolution parallel spectroscopy (2021)

Spectral contrast, the ability to measure frequency components of vastly different intensity, is critical in optical spectroscopy. For high spectral contrast at high spectral resolution, scanning etalons are generally used, as they allow cascading multiple dispersive elements. However, scanning instruments are inherently limited in terms of acquisition speed. Here we report a single-shot cascaded spectrometer design, in which light is dispersed along a single dispersion direction at every stage and thus can be recirculated in the same etalon multiple times. Using this design principle, we demonstrate single-shot spectral measurements at sub-gigahertz resolution and unprecedented spectral contrast (∼80<i>d</i><i>B</i>).
3D interferometric optical tweezers using a single spatial light modulator (2005)

Hexagonal arrays of micron sized silica beads have been trapped in three-dimensions within an optical lattice formed by the interference of multiple plane-waves. The optical lattice design with sharply peaked intensity gradients produces a stronger trapping force than the traditionally sinusoidal intensity distributions of other interferometric systems. The plane waves were generated using a single, phase-only, spatial light modulator (SLM), sited near a Talbot image plane of the traps. Compared to conventional optical tweezers, where the traps are formed in the Fourier-plane of the SLM, this approach may offer an advantage in the creation of large periodic array structures. This method of pattern formation may also be applicable to trapping arrays of atoms.
Two Novel Mutations in Severe Factor VII Deficiency (2003)

Conference Abstract| April 01 2003 Two Novel Mutations in Severe Factor VII Deficiency Keith Gomez; Keith Gomez (1) Hacmostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar Michael A. Laffan; Michael A. Laffan (2) Department of Haematology, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar Geoffrey Kemball-Cook; Geoffrey Kemball-Cook (1) Hacmostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar John Pasi; John Pasi (3) Department of Pathology, Division of Haematology, School of Medicine, Robert Kilpatrick Clinical Sciences Building Leicester Royal Infirmary, Leicester LE2 7LX Search for other works by this author on: This Site PubMed Google Scholar Mark Layton; Mark Layton (2) Department of Haematology, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar Edward G.D. Tuddenham; Edward G.D. Tuddenham (1) Hacmostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar John McVey, II John McVey, II (1) Hacmostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 ONN Search for other works by this author on: This Site PubMed Google Scholar Clin Sci (Lond) (2003) 104 (s49): 30P. https://doi.org/10.1042/cs104030Pa Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Keith Gomez, Michael A. Laffan, Geoffrey Kemball-Cook, John Pasi, Mark Layton, Edward G.D. Tuddenham, John McVey; Two Novel Mutations in Severe Factor VII Deficiency. Clin Sci (Lond) 1 April 2003; 104 (s49): 30P. doi: https://doi.org/10.1042/cs104030Pa 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 JournalsClinical Science Search Advanced Search This content is only available as a PDF. © 2003 The Biochemical Society and the Medical Research Society2003 Article PDF first page preview Close Modal You do not currently have access to this content.
Sliding-Window RLS Low-Cost Implementation of Proportionate Affine Projection Algorithms (2014)

This paper addresses adaptive filtering for sparse identification. Proportionate affine projection algorithms (PAPAs) are known to be efficient techniques for this purpose. We show that the PAPA performance may improve with an increase in the projection order M (for example, such as M = 512), which, however, also results in an increased complexity; the complexity is in general O(M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> N) or at least O(MN) operations per sample, where N is the filter length. We show that PAPAs are equivalent to specific sliding-window recursive least squares (SRLS) adaptive algorithms with time-varying and tap-varying diagonal loading (SRLS-VDLs). We then propose an approximation to the SRLS-VDLs based on dichotomous coordinate descent (DCD) iterations with a complexity of O(N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</sub> N), which does not depend on M; it depends on the number of DCD iterations N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">u</sub> , which as we show can be significantly smaller than M, thus allowing a low-complexity implementation of PAPA adaptive filters.
Spectrally reconfigurable pixels for dual-color-mode imaging sensors (2012)

The use of full color-sensitive photodetectors with three electrically tunable spectral responses allows the design of sensors that can be real-time reconfigured for different color acquisition modes. All the (physically identical) pixels can be biased in the same way, each giving the same set of RGB spectral responses: in this situation the conversion from the sensor color space to a reference color space can be implemented as usual, giving typical color errors ΔE(a,b) in the order of 2-3. Alternatively, pixels can be biased in two different ways (e.g., row by row), forming pairs: by joining the information from adjacent pixels, the sensor has six spectral responses, with a reduced resolution. By exploiting this plurality of spectral responses, color reproduction accuracy can be increased. In this work, an improved design of the Transverse Field Detector, a filterless and tunable three-color pixel, is used as the experimental device to propose a dual-color-mode reconfigurable sensor.
0210 Measurement of Low/High Intensity Focused Ultrasound in Water Uniformly Containing Lipid Microbubbles (2013)

We constructed an experimental setup of focused ultrasound Field for water with uniformly distributed lipid microbubbles, and measured nonlinear propagation properties caused by oscillations of microbubbles. An ultrasound transducer with a concave PZT ceramic element with a focal length of 40 mm was fixed in a water tank. The therapeutic sensitizer Sonazoid with a diameter of 2 to 3 μm was used. A 30 mm thick polyacrylamide gel containing microbubbles was fixed to include the focus to suppress bubble mobility during the measurement. Elements with four center frequencies l, 2.23, 3.35, and 4.32 MHz, and a moderately weak ultrasound intensity (focal pressure 0.15 MPa) that suppresses the destruction of microbubbles, were used. Then, we conducted one-dimensional measurement and the results showed that the waveform attenuated with the increasing incident frequency and void fraction, which indicates the nonlinearity of the oscillations of microbubbles. Higher harmonics were generated at low frequencies. While focal-pressure increased with the applied voltage to the transducer at high frequencies (near resonance), no increase in focal-pressure was observed in the case of low frequencies.
A Computationally Scalable Speaker Recognition System (2015)

Publication in the conference proceedings of EUSIPCO, Tampere, Finland, 2000
Physiological and Horticultural Effects of Sweet Cherry Chemical Blossom Thinners (2006)

This article reports on the physiological effects and horticultural benefits of chemical blossom thinners on 9-year-old and 12-year-old `Bing'/`Gisela®5′ sweet cherry trees in 2004 and 2005, respectively. Chemical thinning agents were applied at 20% and 80% full bloom (FB) by air-blast sprayer and were comprised of: 2% ammonium thiosulphate (ATS), 4% vegetable oil emulsion (VOE), 2% fish oil + 2.5% lime sulfur (FOLS), 1% tergitol, and an untreated control. Leaf gas exchange, leaf SPAD meter readings, chlorophyll fluorescence parameters, fruit yield, and fruit quality were evaluated. FOLS, tergitol, VOE, and ATS suppressed leaf net CO 2 exchange rate (NCER) by 33%, 30%, 28%, and 18%, respectively, over a variable length recovery period directly after 80% FB treatment. Leaf NCER recovered fully from every thinning treatment. Reductions in leaf NCER were unrelated to g S . VOE reduced estimated leaf chlorophyll content the greatest, suppressing overall levels by 11% for 23 days after treatment. All blossom thinners reduced constant fluorescence (Fo). No thinning agent reduced fruit set or yield in 2004. ATS, FOLS, and tergitol reduced fruit set in 2005. VOE was ineffective as a thinner yet exhibited significant leaf phytotoxicity. Among thinners, there was no relationship between inhibition of leaf NCER and thinning efficacy.
High-Resolution Mapping and Dynamics of the Transcriptome, Transcription Factors, and Transcription Co-Factor Networks in Classically and Alternatively Activated Macrophages (2018)

Macrophages are the prime innate immune cells of the inflammatory response, and the combination of multiple signaling inputs derived from the recognition of host factors [e.g., interferon-g (IFN-γ)] and invading pathogen products (e.g., toll-like receptors (TLRs) agonists) are required to maintain essential macrophage function. The profound effects on biological outcomes of inflammation associated with IFN-γ pretreatment ("priming") and TLR4 ligand bacterial lipopolysaccharide (LPS)-induced macrophage activation (M1 or classical activation) have long been recognized, but the underlying mechanisms are not well defined. Therefore, we analyzed gene expression profiles of macrophages and identified genes, transcription factors (TFs), and transcription co-factors (TcoFs) that are uniquely or highly expressed in IFN-γ-mediated TLR4 ligand LPS-inducible versus only TLR4 ligand LPS-inducible primary macrophages. This macrophage gene expression has not been observed in macrophage cell lines. We also showed that interleukin (IL)-4 and IL-13 (M2 or alternative activation) elicited the induction of a distinct subset of genes related to M2 macrophage polarization. Importantly, this macrophage gene expression was also associated with promoter conservation. In particular, our approach revealed novel roles for the TFs and TcoFs in response to inflammation. We believe that the systematic approach presented herein is an important framework to better understand the transcriptional machinery of different macrophage subtypes.
Glia modulate the response of murine cortical neurons to excitotoxicity: glia exacerbate AMPA neurotoxicity (1995)

We have developed "pure" neuronal cultures (< 1% astrocytes) from mouse neocortex to study the effect of glial cells on the response of neurons to injury. Cortical neurons were found to require glial-conditioned medium to survive. Immature neurons, 2-4 d in vitro, deprived of glial-conditioned medium, underwent apoptosis over 48 hr, as suggested by condensed nuclear morphology, DNA fragmentation, and protection by inhibition of macromolecular synthesis. Apoptosis induced by trophic factor deprivation has been described for other neuronal populations, such as superior cervical ganglion and dorsal root ganglion cells. Cortical neurons in pure culture provide another neuronal population for the study of apoptosis induced by trophic factor deprivation. We then studied the interaction of neurons and glia under excitotoxic conditions. Experiments on mature cultures showed that pure neuronal cultures were at least 10-fold more sensitive to acute glutamate exposure than were neuronal-glial ("mixed") cocultures. The difference in sensitivity between pure neurons and mixed cultures was reduced when mixed cultures were treated with the glutamate uptake inhibitor, L-trans-pyrrolidine-2,4-dicarboxylic acid (trans-PDC). In 24 hr exposure to N-methyl-D-aspartate (NMDA), or oxygen, glucose deprivation, pure neurons were more sensitive than mixed cultures; trans-PDC again increased the sensitivity of mixed cultures to nearly that of pure neuronal cultures. In contrast, mixed and pure neuronal cultures exposed to NMDA for 10 min, or to kainate for 24 hr, had similar injury dose-response curves, suggesting that glial glutamate uptake is a less important protective mechanism in these excitotoxic injuries. Surprisingly, pure neurons were less sensitive than mixed cultures to (RS)-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) toxicity at concentrations up to 100 microM. This does not reflect astrocyte toxicity, as AMPA at concentrations to 1 mM did not injure astrocyte cultures. Glial cultures showed increased levels of glutamate in the extracellular medium in response to exposure to AMPA, but not NMDA or kainate. However, pure neuronal and mixed cultures exposed to the same concentration of AMPA did not have elevated levels of glutamate in the media. We found that glia were generally neuroprotective under excitotoxic conditions, likely through their ability to clear extracellular glutamate. However, the presence of glia exacerbated AMPA neurotoxicity.
High Density 3D Pre-Stack Q Estimation (2004)

P004 HIGH DENSITY 3D PRE-STACK Q ESTIMATION Summary 1 EAGE 66th Conference &amp; Exhibition — Paris France 7 - 10 June 2004 S. J. LANCASTER &amp; M. C. TANIS BP Exploration EPTG Chertsey Road Sunbury-upon-Thames Middlesex TW16 7LN England For optimum resolution after pre-stack depth migration amplitude phase and bandwidth distortions need to be corrected first. Here we describe a novel approach to estimating an offset space and time varying Q field in 3D based on monochromatic spectral decay. The method is demonstrated on data from the Southern Caspian Basin where gas accumulations in the overburden above the Shah Deniz
A quantitative automated immunoassay for fibrinogen/fibrin degradation products. (1985)

Abstract We describe a prototype quantitative automated assay for fibrin and fibrinogen degradation products, a particle-enhanced turbidimetric inhibition immunoassay (PETINIA) in the Du Pont aca discrete clinical analyzer. This assay involves a latex particle reagent with covalently bound fibrinogen and a polyclonal antiserum raised in rabbits against human fibrinogen. A special secondary sample-collection tube quantitatively removes fibrinogen from citrated plasma and inhibits further fibrinolysis, independent of heparin concentration. The assay range is 0-100 mg/L, in fibrinogen equivalents. The CV for the assay is less than 10% when performed with the aca. Nonclottable fibrin and fibrinogen fragments are measured by the assay, the greatest sensitivity being directed at the E domain of the fibrinogen molecule. We illustrate with case studies the potential of this assay for providing clinical information not obtainable with currently available qualitative and semi-quantitative assays.
Sinonasal Sarcoidosis: Diagnosis and Management (2002)

Sinonasal sarcoidosis is a fairly uncommon, yet clinically challenging, manifestation of this systemic disease. The diagnosis is often difficult to establish, treatment options are often unclear, and ultimate clinical responses can be quite variable. This article discusses the varied clinical presentations of this unusual nasal inflammatory process, as well as various treatment options, from simple local nasal hygiene measures to more aggressive systemic therapy. Although the role of surgical intervention is controversial, a simple review of some of the indications for surgery in these patients helps to clarify this somewhat cloudy clinical area. Aggressive clinical management in conjunction with long-term surveillance can often produce dramatic clinical responses for these difficult patients with sarcoidosis in the sinonasal area.
A phase I dose-escalation study to a predefined dose of a transforming growth factor-β1 monoclonal antibody (TβM1) in patients with metastatic cancer (2014)

Transforming growth factor β (TGF-β) plays an important role in cancer. Monoclonal antibodies (mAb) designed to specifically block the TGF-β ligands, are expected to inhibit tumor progression in patients with metastatic cancer. TβM1 is a humanized mAb optimized for neutralizing activity against TGF-β1. The objective of this clinical trial was to assess the safety and tolerability of TβM1 in patients with metastatic cancer. In this phase I, uncontrolled, non-randomized, dose-escalation study, 18 eligible adult patients who had measurable disease per RECIST and a performance status of ≤ 2 on the ECOG scale were administered TβM1 intravenously over 10 min at doses of 20, 60, 120 and 240 mg on day 1 of each 28-day cycle. Safety was assessed by adverse events (as defined by CTCAE version 3.0) and possible relationship to study drug, dose-limiting toxicities and laboratory changes. Systemic drug exposure and pharmacodynamic (PD) parameters were assessed. TβM1 was safe when administered once monthly. The pharmacokinetic (PK) profile was consistent with a mAb with a mean elimination half-life approximately 9 days. Although anticipated changes in PD markers such as serum VEGF, bFGF and mRNA expression of SMAD7 were observed in whole-blood, suggesting activity of TβM1 on the targeted pathway, these changes were not consistent to represent a PD effect. Additionally, despite the presence of an activated TGF-β1 expression signature in patients' whole blood, the short dosing duration did not translate into significant antitumor effect in the small number of patients investigated in this study.