463 research outputs found
Trichopalpus nigribasis Curran 1927
No full textTrichopalpus nigribasis Curran, 1927 Trichopalpus nigribasis Curran, 1927: 255. HOLOTYPE: J, Canada,Alta.[= Alberta], Banff, 23.viii.1922, No. 2606, C. B. G. Garrett leg. (CNC). Chaetosa pilirostris Ringdahl, 1936: 178. HOLOTYPE: J, Norway, ‘im nördlichen Norwegen [= in northern Norway], Ein J vom Verf. bei Tromsö [= one male collected by the author near Tromsø]’ (probably MZLU). Synonymized by GORODKOV (1986: 28). Distribution. Finland (HACKMAN 1980: 131); Norway (NELSON & GREVE 2002: 46); Nearctic region (VOCKEROTH 1965: 836).Published as part of Šifner, František, 2008, A catalogue of the Scathophagidae (Diptera) of the Palaearctic region, with notes on their taxonomy and faunistics, pp. 111-196 in Acta Entomologica Musei Nationalis Pragae 48 (1) on pages 140-141, DOI: 10.5281/zenodo.534249
Addiction recovery stories: Neil Curran in conversation with Lisa Ogilvie
No full textPurpose This paper aims to explore the transition from addiction to recovery. It is the second in a series of recovery stories that examine candid accounts of addiction and recovery. Shared components of recovery are considered, along with the change and growth needed to support the transition. Design/methodology/approach The CHIME framework comprises five elements important to recovery (Connectedness, Hope, Identity, Meaning and Empowerment). It provides a standard to qualitatively study mental health recovery, having also been applied to addiction recovery. In this paper, an element for Growth is included in the model (G-CHIME), to consider both recovery, and sustained recovery. A first-hand account of addiction recovery is presented, followed by a semi-structured e-interview with the author of the account. This is structured on the G-CHIME model. Findings This paper shows that addiction recovery is a remarkable process that can be effectually explained using the G-CHIME model. The significance of each element in the model is apparent from the biography and e-interview presented. Originality/value Each account of recovery in this series is unique, and as yet, untold
MARQUIS: A multiplex method for absolute quantification of peptides and posttranslational modifications
No full textAbsolute quantification of protein expression and posttranslational modifications by mass spectrometry has been challenging due to a variety of factors, including the potentially large dynamic range of phosphorylation response. To address these issues, we have developed MARQUIS—Multiplex Absolute Regressed Quantification with Internal Standards—a novel mass spectrometry-based approach using a combination of isobaric tags and heavy-labelled standard peptides, to construct internal standard curves for peptides derived from key nodes in signal transduction networks. We applied MARQUIS to quantify phosphorylation dynamics within the EGFR network at multiple time points following stimulation with several ligands, enabling a quantitative comparison of EGFR phosphorylation sites and demonstrating that receptor phosphorylation is qualitatively similar but quantitatively distinct for each EGFR ligand tested. MARQUIS was also applied to quantify the effect of EGFR kinase inhibition on glioblastoma patient-derived xenografts. MARQUIS is a versatile method, broadly applicable and extendable to multiple mass spectrometric platforms.United States-Israel Binational Science FoundationNational Institutes of Health (U.S.) (Grant U54 CA112967)National Institutes of Health (U.S.) (Grant R01 CA118705)National Institutes of Health (U.S.) (Grant R01 CA096504)Mayo Brain Tumor SPORE CA10896
Computer aided manual validation of mass spectrometry-based proteomic data
No full textAdvances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics.National Institutes of Health (U.S.) (Grant R24DK090963)National Institutes of Health (U.S.) (Grant U54CA112967)National Cancer Institute (U.S.). Integrative Cancer Biology Program (Fellowship)Charles S. Krakauer FellowshipHugh Hampton Young Fellowshi
Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions
No full textProficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice
Early signaling dynamics of the epidermal growth factor receptor
No full textDespite extensive study of the EGF receptor (EGFR) signaling network, the immediate posttranslational changes that occur in response to growth factor stimulation remain poorly characterized; as a result, the biological mechanisms underlying signaling initiation remain obscured. To address this deficiency, we have used a mass spectrometry-based approach to measure system-wide phosphorylation changes throughout the network with 10-s resolution in the 80 s after stimulation in response to a range of eight growth factor concentrations. Significant changes were observed on proteins far downstream in the network as early as 10 s after stimulation, indicating a system capable of transmitting information quickly. Meanwhile, canonical members of the EGFR signaling network fall into clusters with distinct activation patterns. Src homology 2 domain containing transforming protein (Shc) and phosphoinositol 3-kinase (PI3K) phosphorylation levels increase rapidly, but equilibrate within 20 s, whereas proteins such as Grb2-associated binder-1 (Gab1) and SH2-containing tyrosine phosphatase (SHP2) show slower, sustained increases. Proximity ligation assays reveal that Shc and Gab1 phosphorylation patterns are representative of separate timescales for physical association with the receptor. Inhibition of phosphatases with vanadate reveals site-specific regulatory mechanisms and also uncovers primed activating components in the network, including Src family kinases, whose inhibition affects only a subset of proteins within the network. The results presented highlight the complexity of signaling initiation and provide a window into exploring mechanistic hypotheses about receptor tyrosine kinase (RTK) biology.National Institutes of Health (U.S.) (Grants U54CA112967, R01CA118705, and R01CA096504)National Institutes of Health (U.S.) (Biotechnology Training Grant T32GM008334
Promoting Diversity and Pluralism in Contemporary Communication Policies in the United States and the United Kingdom
No full textTime-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases
No full textWhile the affinities and specificities of SH2 domain-phosphotyrosine interactions have been well characterized, spatio-temporal changes in phosphosite availability in response to signals, and their impact on recruitment of SH2-containing proteins in vivo, are not well understood. To address this issue, we used three complementary experimental approaches to monitor phosphorylation and SH2 binding in human A431 cells stimulated with epidermal growth factor (EGF): 1) phospho-specific mass spectrometry; 2) far-Western blotting; and 3) live cell single-molecule imaging of SH2 membrane recruitment. Far-Western and MS analyses identified both well-established and previously undocumented EGF-dependent tyrosine phosphorylation and binding events, as well as dynamic changes in binding patterns over time. In comparing SH2 binding site phosphorylation with SH2 domain membrane recruitment in living cells, we found in vivo binding to be much slower. Delayed SH2 domain recruitment correlated with clustering of SH2 domain binding sites on the membrane, consistent with membrane retention via SH2 rebinding.National Institutes of Health (U.S.) (Grant U01CA154966
Detailed optical and near-infrared polarimetry, spectroscopy and broad-band photometry of the afterglow of GRB 091018 : polarization evolution
No full textFollow-up observations of large numbers of gamma-ray burst (GRB) afterglows, facilitated by the Swift satellite, have produced a large sample of spectral energy distributions and light curves, from which their basic micro- and macro-physical parameters can in principle be derived. However, a number of phenomena have been observed that defy explanation by simple versions of the standard fireball model, leading to a variety of new models. Polarimetry can be a major independent diagnostic of afterglow physics, probing the magnetic field properties and internal structure of the GRB jets. In this paper we present the first high-quality multi-night polarimetric light curve of a Swift GRB afterglow, aimed at providing a well-calibrated data set of a typical afterglow to serve as a benchmark system for modelling afterglow polarization behaviour. In particular, our data set of the afterglow of GRB 091018 (at redshift z = 0.971) comprises optical linear polarimetry (R band, 0.13-2.3d after burst); circular polarimetry (R band) and near-infrared linear polarimetry (Ks band). We add to that high-quality optical and near-infrared broad-band light curves and spectral energy distributions as well as afterglow spectroscopy. The linear polarization varies between 0 and 3per cent, with both long and short time-scale variability visible. We find an achromatic break in the afterglow light curve, which corresponds to features in the polarimetric curve. We find that the data can be reproduced by jet break models only if an additional polarized component of unknown nature is present in the polarimetric curve. We probe the ordered magnetic field component in the afterglow through our deep circular polarimetry, finding P circ < 0.15per cent (2σ), the deepest limit yet for a GRB afterglow, suggesting ordered fields are weak, if at all present. Our simultaneous R- and Ks-band polarimetry shows that dust-induced polarization in the host galaxy is likely negligible
A systems theoretical perspective on data-driven modeling and simulation
No full textHarvestSystem Engineerin
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