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What's Changed Fix subroutines with array arguments by @jcjaskula-aws in https://github.com/openqasm/oqpy/pull/77 Update CITATION.cff to include v0.3.2 authors by @karalekas in https://github.com/openqasm/oqpy/pull/79 Bump version to 0.3.3 by @jcjaskula-aws in https://github.com/openqasm/oqpy/pull/78 Full Changelog: https://github.com/openqasm/oqpy/compare/v0.3.2...v0.3.3

Perl Scripts used in the bioinformatics pipeline Example Command lines: perl ./NG_typing_high_coverage_R9_v3.pl barcode01.filtered.fastq 60 10 0.8 perl ./NG_typing_high_coverage_R10_v3.pl barcode01.filtered.fastq 60 10 0.8 Before running: Locations of the following softwares, scripts and ref seqs should be given in the Line 23-36 of the main script (NG_typing_high_coverage_R9/R10_v3.pl). Scripts (provided here): NG_typing_extraction_v1.pl, cal_blast_coverage_and_filter.pl, extract_reads_with_high_coverage.pl, vcfqualfilter_R9/R10.pl, trim_porB1a4MAST.pl, trim_porB1b4MAST.pl, trim_tbpB4MAST.pl Softwares: blastn (blast+), minimap2 ref seqs: blast database(NG_typing_16p_v1.fasta), ref seqs used for mapping and generating consensus (Reference sequences v2 for NG-typing ) Parameters: barcode01.filtered.fastq: input demultiplexed fastq files, need to QC first 60: the number of reads in subset for downstream analysis 10: the minimum supporting observations to consider a variant (for FreeBayes) 0.8: the threshold of coverage Tips: Different scripts can be run according to the flowcell used. The only difference is the threshold used for calling deletion variants, R9.4: 100; R10.3: 50 for ref seqs, need to index first

Minor release for Zenodo archiving. Code for ADJUST: A Dictionary-Based Joint Reconstruction and Unmixing Method for Spectral Tomography For a full description, please visit https://github.com/mzeegers/ADJUST

Zenodo changed API, some keys had to be updated Python 3.12 support access token support for private repositories

Recent additions log: https://stereopipeline.readthedocs.io/en/latest/news.html

Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts. Funding provided by: Environment and Climate Change CanadaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100008638Award Number:

This is the code to create and host a web-based database for the entry, management and dissemination of biological traits data (see https://univie.ac.at/arctictraits) for an example of a running instance. The web interface is written in php and javascript, the database runs in MySQL. Instructions for installation are contained in the README file. Idea: Renate DegenDesign and code/database implementation: Sarah FaulwetterIf you download and use the code please drop me an e-mail at sarahfaulwetter@gmail.com so that I can inform you on any new versions, bugfixes, etc.

Correct json data for Actions

Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services