Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics

Funding Information: This work was supported by a research grant from the Danish Cardiovascular Academy, which is funded by the Novo Nordisk Foundation, grant number NNF20SA0067242 and the Danish Heart Foundation. Publisher Copyright: © 2023 The Authors. Proteomics published by Wiley-VCH GmbH.Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching. Protein identifications made by the spectral library search engine demonstrated a high degree of complementarity with the sequence database search engine, indicating the feasibility of increasing the number of protein identifications without additional pre-analytical sample preparation. The TMTpro-specific spectral library provides a resource for future plasma proteomics research and optimization of search algorithms for greater accuracy and speed in protein identifications in human plasma proteomics, and is made publicly available to the research community via ProteomeXchange with identifier PXD042546.publishersversionepub_ahead_of_prin

CHANG-ES VI: Probing Supernova Energy Deposition in Spiral Galaxies Through Multi-Wavelength Relationships

How a galaxy regulates its SNe energy into different interstellar/circumgalactic medium components strongly affects galaxy evolution. Based on the JVLA D-configuration C- (6 GHz) and L-band (1.6 GHz) continuum observations, we perform statistical analysis comparing multi-wavelength properties of the CHANG-ES galaxies. The high-quality JVLA data and edge-on orientation enable us for the first time to include the halo into the energy budget for a complete radio-flux-limited sample. We find tight correlations of $L_{\rm radio}$ with the mid-IR-based SFR. The normalization of our $I_{\rm 1.6GHz}/{\rm W~Hz^{-1}}-{\rm SFR}$ relation is $\sim$2-3 times of those obtained for face-on galaxies, probably a result of enhanced IR extinction at high inclination. We also find tight correlations between $L_{\rm radio}$ and the SNe energy injection rate $\dot{E}_{\rm SN(Ia+CC)}$, indicating the energy loss via synchrotron radio continuum accounts for $\sim0.1\%$ of $\dot{E}_{\rm SN}$, comparable to the energy contained in CR electrons. The integrated C-to-L-band spectral index is $\alpha\sim0.5-1.1$ for non-AGN galaxies, indicating a dominance by the diffuse synchrotron component. The low-scatter $L_{\rm radio}-{\rm SFR}$/$L_{\rm radio}-\dot{E}_{\rm SN (Ia+CC)}$ relationships have super-linear logarithmic slopes at $\sim2~\sigma$ in L-band ($1.132\pm0.067$/$1.175\pm0.102$) while consistent with linear in C-band ($1.057\pm0.075$/$1.100\pm0.123$). The super-linearity could be naturally reproduced with non-calorimeter models for galaxy disks. Using Chandra halo X-ray measurements, we find sub-linear $L_{\rm X}-L_{\rm radio}$ relations. These results indicate that the observed radio halo of a starburst galaxy is close to electron calorimeter, and a galaxy with higher SFR tends to distribute an increased fraction of SNe energy into radio emission (than X-ray).Comment: 16 pages, 6 figures, 1 table, MNRAS in pres

CHANG-ES IV: Radio continuum emission of 35 edge-on galaxies observed with the Karl G. Jansky Very Large Array in D-configuration, Data Release 1

We present the first part of the observations made for the Continuum Halos in Nearby Galaxies, an EVLA Survey (CHANG-ES) project. The aim of the CHANG-ES project is to study and characterize the nature of radio halos, their prevalence as well as their magnetic fields, and the cosmic rays illuminating these fields. This paper reports observations with the compact D configuration of the Karl G. Jansky Very Large Array (VLA) for the sample of 35 nearby edge-on galaxies of CHANG-ES. With the new wide bandwidth capabilities of the VLA, an unprecedented sensitivity was achieved for all polarization products. The beam resolution is an average of 9.6" and 36" with noise levels reaching approximately 6 and 30 microJy per beam for C- and L-bands, respectively (robust weighting). We present intensity maps in these two frequency bands (C and L), with different weightings, as well as spectral index maps, polarization maps, and new measurements of star formation rates (SFRs). The data products described herein are available to the public in the CHANG-ES data release available at www.queensu.ca/changes. We also present evidence of a trend among galaxies with larger halos having higher SFR surface density, and we show, for the first time, a radio continuum image of the median galaxy, taking advantage of the collective signal-to-noise ratio of 30 of our galaxies. This image shows clearly that a typical spiral galaxy is surrounded by a halo of magnetic fields and cosmic rays.Comment: 70 pages, of which 35 pages present the data of each galax

Blueberries infected with the fungal pathogen Colletotrichum fioriniae release odors that repel Drosophila suzukii

Spotted-wing drosophila, Drosophila suzukii, is a serious pest of thin-skinned fruits. Alternative methods to control this pest are needed to reduce insecticide use, including new repellents. Previous research demonstrated that D. suzukii adults use odor cues to avoid blueberries infected with the fungal pathogen Colletotrichum fioriniae, which causes the disease anthracnose. To identify novel D. suzukii repellents, we investigated the volatile emission from experimentallyinfected fruit, which were inoculated with C. fioriniae isolates in the laboratory, and from field-collected fruit, which were naturally infected and harvested from a field. We then tested the pathogen-induced volatiles on D. suzukii adult behavior.hanks to Arthur Rudolph for his help operating the GC–MS during pandemic work restrictions, Chelsea Abegg for providing field-collected blueberry fruit infected with anthracnose, to Mustafa Wasti, Robert Holdcraft, and Vera Kyryczenko-Roth for technical assistance. Authors CCR and JJB were supported by USDA ARS CRIS 6036-224300-001-000D and CR-S and AQ were supported by USDA SCRI 2020-51181-32140, The Sridhar Polavarapu Memorial Endowment for Vaccinium Research, and USDA Sustainable Agriculture Research and Education (grant no. LNE22-455R).info:eu-repo/semantics/publishedVersio

CHANG-ES X: Spatially-resolved Separation of Thermal Contribution from Radio Continuum Emission in Edge-on Galaxies

We analyze the application of star formation rate (SFR) calibrations using H$\alpha$ and 22 micron infrared imaging data in predicting the thermal radio component for a test sample of 3 edge-on galaxies (NGC 891, NGC 3044, and NGC 4631) in the Continuum Halos in Nearby Galaxies -- an EVLA Survey (CHANG-ES). We use a mixture of H$\alpha$ and 24 micron calibration from Calzetti et al. (2007), and a linear 22 micron only calibration from Jarrett et al. (2013) on the test sample. We apply these relations on a pixel-to-pixel basis to create thermal prediction maps in the two CHANG-ES bands: L- and C-band (1.5 GHz and 6.0 GHz, respectively). We analyze the resulting non-thermal spectral index maps, and find a characteristic steepening of the non-thermal spectral index with vertical distance from the disk after application of all methods. We find possible evidence of extinction in the 22 micron data as compared to 70 micron Spitzer Multband Imaging Photometer (MIPS) imaging in NGC 891. We analyze a larger sample of edge-on and face-on galaxy 25 micron to 100 micron flux ratios, and find that the ratios for edge-ons are systematically lower by a factor of 1.36, a result we attribute to excess extinction in the mid-IR in edge-ons. We introduce a new calibration for correcting the H$\alpha$ luminosity for dust when galaxies are edge-on or very dusty.Comment: Accepted for publication in ApJ on December 24, 2017, 23 pages, 19 figure

A Threat Assessment and Security Analysis of the Three Sports Facilities of Indiana University-Purdue University, Indianapolis NCAA Softball Fields, Carroll Stadium, and the IU Natatorium

This research report provides a security assessment of the Softball Fields, Carroll Stadium, and the Natatorium Complex at Indiana University-Purdue University Indianapolis (IUPUI). The purpose of this report is to prevent and mitigate harm to visitors and these facilities which resulting from human-made or natural disasters. Research is guided by the hypothesis that these facilities- due to their respective importance, locations, and attendance patterns are in harm’s way; and that certain strategies of prevention, protection, and mitigation coupled with effective preparedness, response, and recovery can lessen risk, improve security and provide A THREAT ASSESSMENT AND SECURITY ANALYSIS 5 added resilience. Further, “harm’s way” is considered to be either a natural disaster or a human-made disaster, accident, active provocation, or act of terrorism. Methods of analysis include applied research; predominantly utilizing qualitative data with some quantitative investigation. Results of this assessment illustrate that these venues possess numerous vulnerabilities to both natural and human-made threats that if exposed, could result in serious consequences. The two most likely natural hazards identified include straight-line winds and tornadoes. Further, the most likely human threats to these facilities arise from a potential terrorist vehicle attack (TVA) and an active shooter. This project also identifies a specific need for additional planning to prevent an IED or VBIED attack on the Natatorium. Common themes from the attached three case studies reveal that given theses vulnerabilities, the following safety and security adjustments are recommended: Surveillance equipment Metal detectors Security bollards or other temporary barriers Evacuation routes and shelter in place plans Special event security procedures Weather related technology and protocols Staff training for emergency situation

Cost of managing an episode of relapse in multiple sclerosis in the United States

BACKGROUND: The purpose of this study was to determine the direct medical US cost of managing multiple sclerosis relapses. METHODS: Direct data analysis and cost modeling were employed to derive typical resource use profiles and costs in 2002 US dollars, from the perspective of a third-party payer responsible for comprehensive health-care. The location and scope of health care services provided over a 90-day period were used to define three levels of relapse management. Hospitalization and resulting subsequent care was defined as high intensity management. A medium level of intervention was defined as either use of the emergency room, an observational unit, or administration of acute treatments, such as intravenous methylprednisolone in an outpatient or home setting. The lowest intensity of care comprised physician office visits and symptom-related medications. Data were obtained from many sources including all payer inpatient, ambulatory and emergency room databases from several states, fee schedules, government reports, and literature. All charges were adjusted using cost-to-charge ratios. RESULTS: Average cost per person for high management level was $12,870, based on analysis of 4,634 hospital cases (mean age 48 years, 73$1,847 and mild episode $243. CONCLUSIONS: Management strategies leading to a reduction in the frequency and severity of a relapse, less reliance on inpatient care, or increased access to steroid infusions in the home, would have a substantial impact on the economic consequences of managing relapses

Adapting effects of emotional expression in anxiety: evidence for an enhanced late positive potential

An adaptation paradigm was used to investigate the influence of a previously experienced visual context on the interpretation of ambiguous emotional expressions. Affective classification of fear-neutral ambiguous expressions was performed following repeated exposure to either fearful or neutral faces. There was a shift in the behavioural classification of morphs towards ‘fear’ following adaptation to neutral compared to adaptation to fear with a non-significant trend towards the high anxiety group compared to the low being more influenced by the context. The event-related potential (ERP) data revealed a more pronounced late positive potential (LPP), beginning at ~400 ms post-stimulus onset, in the high but not the low anxiety group following adaptation to neutral compared to fear. In addition, as the size of the behavioural adaptation increased there was a linear increase in the magnitude of the late-LPP. However, context-sensitivity effects are not restricted to trait anxiety, with similar effects observed with state anxiety and depression. These data support the proposal that negative moods are associated with increased sensitivity to visual contextual influences from top-down elaborative modulations, as reflected in an enhanced late positive potential deflection

The perils of project-based work: Attempting resistance to extreme work practices in video game development

This article examines two blogs written by the spouses of game developers about extreme and exploitative working conditions in the video game industry and the associated reader comments. The wives of these video game developers and members of the game community decry these working conditions and challenge dominant ideologies about making games. This article contributes to the work intensification literature by challenging the belief that long hours are necessary and inevitable to make successful games, discussing the negative toll of extreme work on workers and their families, and by highlighting that the project-based structure of game development both creates extreme work conditions and inhibits resistance. It considers how extreme work practices are legitimized through neo-normative control mechanisms made possible through project-based work structures and the perceived imperative of a race or ‘crunch’ to meet project deadlines. The findings show that neo-normative control mechanisms create an insularity within project teams and can make it difficult for workers to resist their own extreme working conditions, and at times to even understand them as extreme

Stellar Astrophysics and Exoplanet Science with the Maunakea Spectroscopic Explorer (MSE)

The Maunakea Spectroscopic Explorer (MSE) is a planned 11.25-m aperture facility with a 1.5 square degree field of view that will be fully dedicated to multi-object spectroscopy. A rebirth of the 3.6m Canada-France-Hawaii Telescope on Maunakea, MSE will use 4332 fibers operating at three different resolving powers (R ~ 2500, 6000, 40000) across a wavelength range of 0.36-1.8mum, with dynamical fiber positioning that allows fibers to match the exposure times of individual objects. MSE will enable spectroscopic surveys with unprecedented scale and sensitivity by collecting millions of spectra per year down to limiting magnitudes of g ~ 20-24 mag, with a nominal velocity precision of ~100 m/s in high-resolution mode. This white paper describes science cases for stellar astrophysics and exoplanet science using MSE, including the discovery and atmospheric characterization of exoplanets and substellar objects, stellar physics with star clusters, asteroseismology of solar-like oscillators and opacity-driven pulsators, studies of stellar rotation, activity, and multiplicity, as well as the chemical characterization of AGB and extremely metal-poor stars.Comment: 31 pages, 11 figures; To appear as a chapter for the Detailed Science Case of the Maunakea Spectroscopic Explore