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1. Data from: Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

   https://doi.org/10.5281/zenodo.5102718  

   Mounger, Jeannie; Boquete, M. Teresa; Schmid, Marc W.; Granado, Renan; Robertson, Marta H.; Voors, Sandy A.; Langanke, Kristen L.; Alvarez, Mariano; Wagemaker, Cornelis A.M.; Schrey, Aaron W.; et al (January 2021, Zenodo)

   {"Abstract":["This record contains supplementary information for the article "Inheritance of DNA methylation differences in the mangrove Rhizophora mangle" published in Evolution&Development. It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. Short reads are available on SRA (PRJNA746695). Note that demultiplexing of the pooled reads (SRX11452376) will fail because the barcodes are already removed and the header information is lost during SRA submission. Instead, use the pre-demultiplexed reads that are as well linked to PRJNA746695.<\/p>\n\n\n <\/p>\n\nTable S13 (TableS13_DSSwithGeneAnnotation.offspringFams.csv.gz): <\/strong><\/p>\n\nDifferential cytosine methylation between families using the mother data set. The first three columns fragment number ("chr"), the position within the fragment ("pos"), and the sequence context ("context"). Columns with the pattern FDR_<X>_vs_<Y> contain false discovery rates of a test comparing population X with population Y. Average DNA methylation levels for each population are given in the columns "AC", "FD", "HI", "UTB", "WB", and "WI". The remaining columns contain the annotation of the fragment, for example whether it matches to a gene and if yes, the gene name ID and description are provided.<\/p>"]} 

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2. Source code: Basins modulate signatures of river salinization

   https://doi.org/10.5281/zenodo.11130548  

   Platt, Lindsay; Dugan, Hilary (May 2024, Zenodo)

   This resource contains source code and select data products behind the following Master's Thesis: Platt, L. (2024). Basins modulate signatures of river salinization (Master's thesis). University of Wisconsin-Madison, Freshwater and Marine Sciences. The source code represents an R-based data processing and modeling pipeline written using the R package "targets". Some of the folders in the source code zipfile are intentionally left empty (except for a hidden file ".placeholder") in order for the code repository to be setup with the required folder structure. To execute this code, download the zip folder, unzip, and open the salt-modeling-data.Rproj file. Then, reference the instructions in the README.md file for installing packages, building the pipeline, and examining the results. Newer versions of this repository may be updated in GitHub at github.com/lindsayplatt/salt-modeling-data. In addition to the source code, this resource contains three data files containing intermediate products of the pipeline. The first two represent data prepared for the random forest modeling. Data download and processing were completed in pipeline phases 1 - 5, and the random forest modeling was completed in phase 6 (see source code).  site_attributes.csv which contains the USGS gage site numbers and their associated basin attributes site_classifications.csv which contains the classification of a site for both episodic signatures ("Episodic" or "Not episodic") and baseflow salinization signatures ("positive", "none", "negative", or NA). Note that an NA in the baseflow classification column means that the site did not meet minimum data requirements for calculating a trend and was not used in the random forest model for baseflow salinization. site_attribute_details.csv contains a table of each attribute shorthand used as column names in site_attributes.csv and their names, units, description, and data source. 

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3. NSF COLDEX Ice Penetrating Radar Derived Grids of the Southern Flank of Dome A:Subtitle

   https://doi.org/10.18738/T8/M77ANK  

   Young, Duncan A; Paden, John P; Yan, Shuai; Kerr, Megan E; Singh, Shivangini; Vega_Gonzàlez, Alejandra; Kaundinya, Shravan; Greenbaum, Jamin S; Chan, Kristian; Blankenship, Donald D; et al (January 2025, Texas Data Repository)

   <p>NSF COLDEX performed two airborne campaigns from South Pole Station over the Southern Flank of Dome A and 2022-23 and 2023-24, searching for a potential site of a continuous ice core that could sample the mid-Pleistocene transition. Ice thickness data extracted from the MARFA radar system has allow for a new understanding of this region.</p> <p>Here we generate crustal scale maps of ice thickness, bed elevation, specularity content, subglacial RMS deviation and fractional basal ice thickness with 1 km sampling, and 10 km resolution. We include both masked and unmasked grids.</p> <p> The projection is in the SCAR standard ESPG:3031 polar stereographic projection with true scale at 71˚S.</p> <p>These geotiffs were generated using performed using GMT6.5 (<a href="https://doi.org/10.1029/2019GC008515">Wessel et al., 2019</a>) using the pygmt interface, by binning the raw data to 2.5 km cells, and using the <a href="https://github.com/sakov/nn-c"> nnbathy </a> program to apply natural neighbor interpolation to 1 km sampling. A 10 km Gaussian filter - representing typical lines spacings - was applied and then a mask was applied for all locations where the nearest data point was further than 8 km. </p> Ice thickness, bed elevation and RMS deviation @ 400 m length scale (<a href="http://dx.doi.org/10.1029/2000JE001429">roughness</a>) data includes the following datasets: <ul> <li> UTIG/CRESIS <a href="https://doi.org/10.18738/T8/J38CO5">NSF COLDEX Airborne MARFA data</a></li> <li> British Antarctic Survey <a href="https://doi.org/10.5285/0f6f5a45-d8af-4511-a264-b0b35ee34af6">AGAP-North</a></li> <li> LDEO <a href="https://doi.org/10.1594/IEDA/317765"> AGAP-South </a></li> <li> British Antarctic Survey <a href="https://doi.org/10.5270/esa-8ffoo3e">Polargap</a></li> <li> UTIG Support Office for Airborne Research <a href="https://doi.org/10.15784/601588">Pensacola-Pole Transect (PPT) </a></li> <li> NASA/CReSIS <a href="https://doi.org/10.5067/GDQ0CUCVTE2Q"> 2016 and 2018 Operation Ice Bridge </a> </li> <li> ICECAP/PRIC <a href="https://doi.org/10.15784/601437"> SPICECAP Titan Dome Survey </a> </ul> <p>Specularity content (<a href="https://doi.org/10.1109/LGRS.2014.2337878">Schroeder et al. 2014</a>) is compiled from <a href="https://doi.org/10.18738/T8/KHUT1U"> Young et al. 2025a </a> and <a href="https://doi.org/10.18738/T8/6T5JS6"> Young et al. 2025b</a>.</p> <p>Basal ice fractional thickness is complied from manual interpretation by Vega Gonzàlez, Yan and Singh. </p> <p>Code to generated these grids can be found at <a href="https://github.com/smudog/COLDEX_dichotomy_paper_2025"> at github.com </a></p> 

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4. Model estimates of water yield and N yield under alternative N management practices across the Mississippi-Atchafalaya River basin during 1980-2017

   https://doi.org/10.25380/iastate.12779954.v1  

   Lu, Chaoqun; Zhang, Jien (August 2020, Iowa State University)

   This dataset contains maps of water yield and nitrogen (N) yield each year, covering the Mississippi/Atchafalaya River Basin (MARB) spanning from 1980 to 2017. These maps were reconstructed by aggregating from a daily model (Dynamic Land Ecosystem Model, DLEM) estimates and are at 5-min×5-min (0.08333° Lat × 0.08333° Lon) resolution. There are two subfolders, "TT" and "DT", within this folder. "TT" and "DT" respectively indicate "traditional timing" and "dynamic timing" of nitrogen fertilizer applications in regards to the model experiments in the main text. The "TT" folder contains the gridded model estimates of water yield (named by "Runoff") and nitrogen yield (named by "Nleach") at annual bases. TT reflects our best estimate of water and N fluxes within the context of multi-factor environmental changes including climate, atmospheric CO2 concentration, N deposition, land use, and human management practices (such as fertilizer use, tillage, tile drainage, etc.). The "DT" folder only contains the model estimates of nitrogen yield (“Nleach”) under an alternative N management practice. More details can be found in the linked publication. 

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5. Finding Missing Items Requires Strong Forms of Randomness

   https://doi.org/10.4230/LIPICS.CCC.2024.28  

   Chakrabarti, Amit; Stoeckl, Manuel (January 2024, Schloss Dagstuhl – Leibniz-Zentrum für Informatik)

   Santhanam, Rahul (Ed.)

   Adversarially robust streaming algorithms are required to process a stream of elements and produce correct outputs, even when each stream element can be chosen as a function of earlier algorithm outputs. As with classic streaming algorithms, which must only be correct for the worst-case fixed stream, adversarially robust algorithms with access to randomness can use significantly less space than deterministic algorithms. We prove that for the Missing Item Finding problem in streaming, the space complexity also significantly depends on how adversarially robust algorithms are permitted to use randomness. (In contrast, the space complexity of classic streaming algorithms does not depend as strongly on the way randomness is used.) For Missing Item Finding on streams of length 𝓁 with elements in {1,…,n}, and ≤ 1/poly(𝓁) error, we show that when 𝓁 = O(2^√{log n}), "random seed" adversarially robust algorithms, which only use randomness at initialization, require 𝓁^Ω(1) bits of space, while "random tape" adversarially robust algorithms, which may make random decisions at any time, may use O(polylog(𝓁)) random bits. When 𝓁 is between n^Ω(1) and O(√n), "random tape" adversarially robust algorithms need 𝓁^Ω(1) space, while "random oracle" adversarially robust algorithms, which can read from a long random string for free, may use O(polylog(𝓁)) space. The space lower bound for the "random seed" case follows, by a reduction given in prior work, from a lower bound for pseudo-deterministic streaming algorithms given in this paper. 

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