The CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein–ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate protein melt temperatures (Tm) and relative melt shifts from proteomics abundance data. Here, we report a user-friendly analysis of the melt shift calculation workflow where we describe the impact of each individual calculation step on the final output list of stabilized and destabilized proteins. This report also includes a description of how key steps in the analysis workflow quantitatively impact the list of stabilized/destabilized proteins from an experiment. We applied our findings to develop a more optimized analysis workflow that illustrates the dramatic sensitivity of chosen calculation steps on the final list of reported proteins of interest in a study and have made the R based program Inflect available for research community use through the CRAN repository [McCracken, N. Inflect: Melt Curve Fitting and Melt Shift Analysis. R package version 1.0.3, 2021]. The Inflect outputs include melt curves for each protein which passes filtering criteria in addition to a data matrix which is directly compatible with downstream packages such as UpsetR for replicate comparisons and identification of biologically relevant changes. Overall, this work provides an essential resource for scientists as they analyze data from TPP and CETSA experiments and implement their own analysis pipelines geared toward specific applications.

Yearly maps of onset of early melt (earliest observed melt conditions), melt (melt conditions observed throughout from this point until freeze), early freeze (earliest observed freeze conditions), and freeze (freeze conditions observed throughout from this point on) for the surface of sea ice derived from scanning multichannel microwave radiometer (SMMR) - special sensor microwave/imager (SSM/I) data. See [Markus et al. 2009] for further details. Original data prepared in a polar stereographic projection, with 25 km grid spacing; data has been reprojected into a northern hemispheric Equal-Area Scalable Earth (EASE) grid [see: http://nsidc.org/data/ease/ for further details] with 25 km grid spacing. Reference: Markus, T., J. C. Stroeve, and J. Miller (2009), Recent changes in Arctic sea ice melt onset, freezeup, and melt season length, J. Geophys. Res., 114, C12, doi:10.1029/2009JC005436.*****These data were compiled in conjunction with the Sunlight and the Arctic atmosphere-ice-ocean system (Synthesis of Arctic System Science, SASS) project.***** Data Citation: Eicken, H., R. Gradinger, T. Heinrichs, M. Johnson, A. Lovecraft, and M. Kaufman. (Jan. 5, 2010, Updated May 9, 2012). SMMR and SSM/I derived dates of Arctic sea ice surface melt/freeze (SIZONET). UCAR/NCAR – CISL – ACADIS. http://dx.doi.org/10.5065/D6KW5CXQ

No description is available. Visit https://dataone.org/datasets/doi%3A10.18739%2FA2SQ8QJ0F for complete metadata about this dataset.

The central Taupo Volcanic Zone (TVZ) is an actively rifting continental arc and is well known for its exceptionally high rate of rhyolitic magma generation and frequent caldera-forming eruptions. Two end-member types of rhyolites (R1 and R2) have been previously identified based on differences in their bulk-rock chemistry and mineral assemblage with hydrous phases crystallizing in the R1 type, which are not present or only rare in R2 rhyolites. Here we present new trace element and volatile data from rhyolitic melt inclusions measured in several representative eruptive deposits (R1 and R2 rhyolites) from the central TVZ to examine their volatile concentrations and origin. R1 and R2 show very distinct Cl concentrations, with R2 rhyolites being enriched in Cl by c. 1000 ppm. H2O is slightly higher in the R1 rhyolites, whereas CO2 concentrations are similar between the two end-member types. The origin of these volatile disparities between R1 and R2 melts is assigned to differences in the initial bulk volatile content of the parental magma, possibly associated with distinct input of fluids from the subduction zone. These disparities in bulk volatile concentrations can lead to variations in relative timing of exsolution of volatile phase(s) prior to melt inclusion entrapment.

The data used in the study Accuracy of Empirical Models of Debris-Covered Glaciers, A Winter-Billington, RD Moore and R Dadic, in prep. for submission to the Journal of Glaciology.

This dataset accompanies Zheng et al. (2023): Statistically parameterizing and evaluating a positive degree-day
model to estimate surface melt in Antarctica from 1979 to 2022, The Cryosphere.

This dataset contains annual PDD model output.

An automated site located near Barrow, Alaska in the Chukchi Sea landfast ice records ice thickness, snow depth, ice temperature, sea level (as measured on floating ice), and air temperature at regular (typically 30 min.) intervals during the ice growth and early melt season from (typically) January through June each year. Data are collected as part of the Seasonal Ice Zone Observing Network (SIZONet) and the Alaska Ocean Observing System (AOOS), by the sea-ice research group at the Geophysical Institute, University of Alaska Fairbanks, P.O. Box 757320, Fairbanks, AK 99775-7320, USA (Project PI: Hajo Eicken, phone: (1)907-474-7280, e-mail: hajo.eicken@gi.alaska.edu, homepage: www.gi.alaska.edu/snowice/sea-lake-ice/eicken.html. Data Citation: Eicken, H., R. Gradinger, T. Heinrichs, M. Johnson, A. Lovecraft, and M. Kaufman. (Oct. 18, 2009, Updated May 9, 2012). Automated ice mass balance site (SIZONET). UCAR/NCAR -- CISL -- ACADIS. http://dx.doi.org/10.5065/D6MW2F2H

This archive documents all relevant output data and compute scripts of the publications (citation handles currently refer to preprint versions of the manuscript and will be updated at a later stage, when the manuscripts are published):

- part A:

Nicola, L., Reese, R., Kreuzer, M., Albrecht, T., and Winkelmann, R.: Oceanic gateways to Antarctic grounding lines – Impact of critical access depths on sub-shelf melt, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-2583, 2023.

- part B:

Kreuzer, M., Albrecht, T., Nicola, L., Reese, R., and Winkelmann, R.: Oceanic gateways in Antarctica – Impact of relative sea-level change on sub-shelf melt, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-2737, 2023.

It also includes the scripts used to produce the figures of the `part B` publication.

Here you will find the raw data (RawData.RData) and code (CHIVAS_SEROLOGY_Code.Rmd, an R Markdown file) for generating the analysis and figures for the following publication:

Streptococcus pyogenes pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.

Joshua Osowicki1,2,3 #, Hannah R Frost1 #, Kristy I Azzopardi1, Alana L Whitcombe4, Reuben McGregor4, Lauren H. Carlton4, Ciara Baker1, Loraine Fabri1,5,6, Manisha Pandey7, Michael F Good7, Jonathan R. Carapetis8,9,10, Mark J Walker11,12,13, Pierre R Smeesters1,2,5,6, Paul V Licciardi2,14, Nicole J Moreland4 *, Danika L Hill15 *, Andrew C Steer1,2,3 *

Provided in the RData file are the following items:

Dataframes:

"outcome" : clinical variables associated with human challenge for each participant

"data" : ELISA and functional antibody responses for human challenge participants. Each timepoint and isotype for each antigen as seperate column)

"data_long": Data equivalent to "data" file but in long format, i.e. One column for each antigen, timepoint and isotype as factors.

"data.melt" : Data equivalent to "data" file but in longer format , i.e. timepoint, isotype and antigen as factors, 'value' as ELISA AU.

"luminex" : IgG responses to 6 antigens analysed by luminex bead-based assay in human challenge participants.

"luminex.children" : IgG responses to 6 antigen analysed by luminex bead-based assay in children

Vectors:

"pharyngitis" : participant "id" for the 19 individuals that developed pharyngitis.

"Antigen.Order" : relates to "Main" antigen classification used in Figure 2

'additional" : relates to "Additional

Function:

"custom_theme" : used as a theme when using ggplot to graph.

Adobe Illustrator or Inkscape were used to generate the final image files for publication, with some graph editing to axes labels, font size, adding p-values etc.

Additional files:

3 .csv files have been included for download

"ELISA_data_wide_format.csv", a wide format data table of 25 human challenge individuals and 219 variables. Equivalent to the 'data' dataframe in the RData file

"CHIVAS_luminex.csv", a long format data table of 25 human challenge participants at 1 week, 1 month, and 3 months. Equivalent to the 'luminex' dataframe in the RData file.

"Luminex.children.csv", a datatable of 6 luminex variables for 39 children (healthy and post pharyngitis). Equivalent to the 'luminex.children' dataframe in the RData file.