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1. A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data

   https://doi.org/10.1186/s12859-020-03752-7  

   Henning, Jessica ; Smith, Rob ( December 2020 , BMC Bioinformatics)

   null (Ed.)

   Abstract Background Mass spectrometry (MS) uses mass-to-charge ratios of measured particles to decode the identities and quantities of molecules in a sample. Interpretation of raw MS depends upon data processing algorithms that render it human-interpretable. Quantitative MS workflows are complex experimental chains and it is crucial to know the performance and bias of each data processing method as they impact accuracy, coverage, and statistical significance of the result. Creation of the ground truth necessary for quantitatively evaluating MS1-aware algorithms is difficult and tedious task, and better software for creating such datasets would facilitate more extensive evaluation and improvement of MS data processing algorithms. Results We present JS-MS 2.0, a software suite that provides a dependency-free, browser-based, one click, cross-platform solution for creating MS1 ground truth. The software retains the first version’s capacity for loading, viewing, and navigating MS1 data in 2- and 3-D, and adds tools for capturing, editing, saving, and viewing isotopic envelope and extracted isotopic chromatogram features. The software can also be used to view and explore the results of feature finding algorithms. Conclusions JS-MS 2.0 enables faster creation and inspection of MS1 ground truth data. It is publicly available with an MIT license at github.com/optimusmoose/jsms. 

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2. Evaluation and Comparison of Desktop Viewing and Headset Viewing of Remote Lectures in VR with Mozilla Hubs

   https://doi.org/10.2312/egve.20201259  

   Yoshimura, A. ; Borst, C.W. ( January 2020 , International Conference on Artificial Reality and Telexistence, and Eurographics Symposium on Virtual Environments (ICAT-EGVE), 2020)

   null (Ed.)
3. Brain responses to food viewing in women during pregnancy and post partum and their relationship with metabolic health: study protocol for the FOODY Brain Study, a prospective observational study

   https://doi.org/10.1136/bmjopen-2022-067013  

   Lesniara-Stachon, Anna ; Quansah, Dan Yedu ; Schenk, Sybille ; Retsa, Chrysa ; Halter, Ryan J ; Murray, Micah M ; Lacroix, Alain ; Horsch, Antje ; Toepel, Ulrike ; Puder, Jardena J ( April 2023 , BMJ Open)

   Food cravings are common in pregnancy and along with emotional eating and eating in the absence of hunger, they are associated with excessive weight gain and adverse effects on metabolic health including gestational diabetes mellitus (GDM). Women with GDM also show poorer mental health, which further can contribute to dysregulated eating behaviour. Food cravings can lead to greater activity in brain centres known to be involved in food ‘wanting’ and reward valuation as well as emotional eating. They are also related to gestational weight gain. Thus, there is a great need to link implicit brain responses to food with explicit measures of food intake behaviour, especially in the perinatal period. The aim of this study is to investigate the spatiotemporal brain dynamics to visual presentations of food in women during pregnancy and in the post partum, and link these brain responses to the eating behaviour and metabolic health outcomes in women with and without GDM.

   This prospective observational study will include 20 women with and 20 without GDM, that have valid data for the primary outcomes. Data will be assessed at 24–36 weeks gestational age and at 6 months post partum. The primary outcomes are brain responses to food pictures of varying carbohydrate and fat content during pregnancy and in the post partum using electroencephalography. Secondary outcomes including depressive symptoms, current mood and eating behaviours will be assessed with questionnaires, objective eating behaviours will be measured using Auracle and stress will be measured with heart rate and heart rate variability (Actiheart). Other secondary outcome measures include body composition and glycaemic control parameters.

   The Human Research Ethics Committee of the Canton de Vaud approved the study protocol (2021-01976). Study results will be presented at public and scientific conferences and in peer-reviewed journals.

    

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4. Why We Don’t Click: Interrogating the Relationship Between Viewing and Clicking in Social Media Contexts by Exploring the “Non-Click”

   https://doi.org/10.1093/jcmc/zmaa013  

   Ellison, Nicole B ; Triệu, Penny ; Schoenebeck, Sarita ; Brewer, Robin ; Israni, Aarti ( October 2020 , Journal of Computer-Mediated Communication)

   null (Ed.)

   Abstract Motivated by work that characterizes view-based social media practices as “passive use,” contrasting it with more desirable, interactive “active use,” this study explores how social media users understand their viewing and clicking practices and the empirical relationship between them. Employing a combination of eye tracking, survey, and interview methods, our study (N = 42) investigates the non-click—instances where people intentionally and thoughtfully do not click on content they spend time viewing. Counterintuitively, we find no difference in viewing duration to clicked versus non-clicked Facebook content. We find that use motivations and Facebook feed content are significant predictors of click behavior but measures of overall use, such as network size or minutes of use per day, are not. Our interview data reveal three audience-related concerns that contribute to deliberate non-clicking and illustrate how non-clicked content contributes to social connectedness when imported into other channels. We discuss implications for researchers, users, and designers. 

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5. Viewing river corridors through the lens of critical zone science

   https://doi.org/10.3389/frwa.2023.1147561  

   Wymore, Adam S. ; Ward, Adam S. ; Wohl, Ellen ; Harvey, Judson W. ( May 2023 , Frontiers in Water)

   River corridors integrate the active channels, geomorphic floodplain and riparian areas, and hyporheic zone while receiving inputs from the uplands and groundwater and exchanging mass and energy with the atmosphere. Here, we trace the development of the contemporary understanding of river corridors from the perspectives of geomorphology, hydrology, ecology, and biogeochemistry. We then summarize contemporary models of the river corridor along multiple axes including dimensions of space and time, disturbance regimes, connectivity, hydrochemical exchange flows, and legacy effects of humans. We explore how river corridor science can be advanced with a critical zone framework by moving beyond a primary focus on discharge-based controls toward multi-factor models that identify dominant processes and thresholds that make predictions that serve society. We then identify opportunities to investigate relationships between large-scale spatial gradients and local-scale processes, embrace that riverine processes are temporally variable and interacting, acknowledge that river corridor processes and services do not respect disciplinary boundaries and increasingly need integrated multidisciplinary investigations, and explicitly integrate humans and their management actions as part of the river corridor. We intend our review to stimulate cross-disciplinary research while recognizing that river corridors occupy a unique position on the Earth's surface.

    

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