cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16533479
title: Complete Data, Models, and Results for: "A New Neural Wave Spectra Model"

description: Description

This Zenodo repository contains the complete dataset, pre-trained models, experimental results, and manuscript figures required to reproduce the findings presented in our paper: "A New Neural Wave Spectra Model".

This single archive provides all the necessary components to be used with our NeuralWave Mini code, which is publicly available on GitHub. The code repository contains all the Python scripts for modeling, inference, and figure generation.

Main Code Repository: https://github.com/GaryYang77/NeuralWave-Mini.git

Quick Start Guide

1.  Clone the Code Repository from GitHub:

git clone https://github.com/GaryYang77/NeuralWave-Mini.git
cd NeuralWave-Mini

2.  Download this archive from the current Zenodo page.

3.  Extract and Place all Folders into the root of the cloned NeuralWave_mini directory. Your final project structure should look like this:

NeuralWave-Mini/
├── datasets/                    # <--- From this Zenodo download
├── results/                     # <--- From this Zenodo download
├── paper_figures/               # <--- From this Zenodo download
├── welltrained_case_models/     # <--- From this Zenodo download
├── models/                      # (From GitHub)
├── figure_generation/           # (From GitHub)
└── ... (other code files)

4. Follow the Instructions in the GitHub repository's README.md file to set up the environment and run the experiments.

Contents of this Archive

This archive (.zip or .tar.gz) contains the following directories:



/datasets/: The complete training, validation, and test datasets.

/results/: The full set of model prediction results in NetCDF (.nc) format.

/paper_figures/: The final figures as they appear in the manuscript.

/welltrained_case_models/: All pre-trained model weights for NeuralWave, EarthFormer, and U-Net.
DOI: 10.5281/zenodo.16889873
title: Complete Data, Models, and Results for: "A New Neural Wave Spectra Model"

description: Description

This Zenodo repository contains the complete dataset, pre-trained models, experimental results, and manuscript figures required to reproduce the findings presented in our paper: "A New Neural Wave Spectra Model".

This single archive provides all the necessary components to be used with our NeuralWave Mini code, which is publicly available on GitHub. The code repository contains all the Python scripts for modeling, inference, and figure generation.

Main Code Repository: https://github.com/GaryYang77/NeuralWave-Mini.git

Quick Start Guide

1.  Clone the Code Repository from GitHub:

git clone https://github.com/GaryYang77/NeuralWave-Mini.git
cd NeuralWave-Mini

2.  Download this archive from the current Zenodo page.

3.  Extract and Place all Folders into the root of the cloned NeuralWave_mini directory. Your final project structure should look like this:

NeuralWave-Mini/
├── datasets/                    # <--- From this Zenodo download
├── results/                     # <--- From this Zenodo download
├── paper_figures/               # <--- From this Zenodo download
├── welltrained_case_models/     # <--- From this Zenodo download
├── models/                      # (From GitHub)
├── figure_generation/           # (From GitHub)
└── ... (other code files)

4. Follow the Instructions in the GitHub repository's README.md file to set up the environment and run the experiments.

Contents of this Archive

This archive (.zip or .tar.gz) contains the following directories:



/datasets/: The complete training, validation, and test datasets.

/results/: The full set of model prediction results in NetCDF (.nc) format.

/paper_figures/: The final figures as they appear in the manuscript.

/welltrained_case_models/: All pre-trained model weights for NeuralWave, EarthFormer, and U-Net.
DOI: 10.15468/dl.8rgakd
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Indonesia, Brunei Darussalam, Malaysia)",
 "OccurrenceStatus is Present",
 "TaxonKey is Phyllocladus",
 "Year 1970-2025"
 ]
}

 The dataset includes 270 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038281-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ua5n7t
title: Occurrence Download

description: A dataset containing 20426 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ageratina adenophora"
 ]
}

 The dataset includes 20426 records from 257 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038280-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17626003
title: KADASTR RAQAMLARINI SHAKLLANTIRISHDA GAT ASOSIDAGI AVTOMATLASHTIRILGAN ALGORITMLAR: AFZALLIKLARI VA CHEKLOVLARI
DOI: 10.5281/zenodo.17626004
title: KADASTR RAQAMLARINI SHAKLLANTIRISHDA GAT ASOSIDAGI AVTOMATLASHTIRILGAN ALGORITMLAR: AFZALLIKLARI VA CHEKLOVLARI
DOI: 10.14288/1.0406466
title: Discussions of the not-so-fit: how ableism limits diverse thought and investigative potential in evolutionary biology

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Evolutionary biology and many of its foundational concepts are grounded in a history of ableism and eugenics. The field has not made a concerted effort to divest our concepts and investigative tools from this fraught history and as a result, an ableist investigative lens has persisted into present-day evolutionary research, limiting the scope of research and harming the ability to communicate and synthesize knowledge about evolutionary processes. This failure to divest from our eugenicist and ableist history has harmed progress in evolutionary biology and allowed principles from evolutionary biology to continue to be weaponized against marginalized communities in the modern-day. To rectify this problem, scholars in evolutionary research must come to terms with how the history of the field has influenced their investigations and work to establish a new framework for defining and investigating concepts, such as selection and fitness.&lt;/p&gt;
DOI: 10.14288/1.0406473
title: Ventilatory parameters measured in Madagascar hissing cockroaches during continuous gas exchange and DGCs

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;This dataset is presented in the manuscript titled: 'Discontinuous gas exchange in Madagascar hissing cockroaches is not a consequence of hysteresis around a fixed PCO&lt;sub&gt;2&lt;/sub&gt; threshold'; published in JEB. The primary purpose of this investigation was to test if discontinuous gas exchange cycles (DGCs) were caused by PCO&lt;sub&gt;2&lt;/sub&gt; fluctuations around ventilatory setpoints. Madagascar hissing cockroaches were exposed to normoxic acapnia and treatments of either hypoxic acapnia, and normoxic hypercapnia, while displaying continious gas exchange, and DGCs. Hemolymph PO&lt;sub&gt;2 &lt;/sub&gt;and PCO&lt;sub&gt;2&lt;/sub&gt; were measured in conjunction with ventilatory frequency and VCO&lt;sub&gt;2 &lt;/sub&gt;released. This data displays the changes in ventilatory parameters observed during ambient gas manipulations.&lt;/p&gt;
DOI: 10.14288/1.0400468
title: Parental population range expansion before secondary contact promotes heterosis

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.&lt;/p&gt;
DOI: 10.14288/1.0406462
title: Madagascar Hissing Cockroach hemolymph PO2, PCO2, and gas exchange parameters

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;This data set contains &lt;em&gt;in vivo &lt;/em&gt;measurements of&lt;em&gt; &lt;/em&gt;hemolymph PO&lt;sub&gt;2&lt;/sub&gt; and PCO&lt;sub&gt;2&lt;/sub&gt; made on Madagascar hissing cockroaches (&lt;em&gt;Gromphadorhina portentosa&lt;/em&gt;) using implanted micro fiber optic sensors (optodes). In addition, rate of CO&lt;sub&gt;2&lt;/sub&gt; release, ventilation frequency, and durations of the tri-phasic discontinuous gas exchange cycle associated with these measurements are also recorded. All measurements were performed while the cockroaches were breathing either normoxic and normocapnic air, hypoxic air (10 kPa PO&lt;sub&gt;2&lt;/sub&gt;), or hypercapnic air (2 kPa PCO&lt;sub&gt;2&lt;/sub&gt;) at 22 ºC.&lt;/p&gt;
DOI: 10.14288/1.0406464
title: Oncorhynchus kisutch genetic stock ID SNP baseline

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Genetic stock identification (GSI) &lt;span style="background:white;"&gt;using genotypes produced from genotyping-by-sequencing of SNP loci&lt;/span&gt; has become the gold standard for stock identification in Pacific salmon, which are found in mixed stocks in the ocean. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and promise real-time, in-field stock identification on variable batch sizes. Here we evaluate utility and comparability to established GSI platforms of at-sea stock identification of coho salmon &lt;i&gt;Oncorhynchus kisutch&lt;/i&gt; based on targeted SNP amplicon sequencing on the minION platform during a high-sea winter expedition to the Gulf of Alaska. As long read sequencers are not optimized for short amplicons, we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach by providing mobile small batch genotyping to diverse stakeholders.&lt;/p&gt;
DOI: 10.14288/1.0406362
title: Replication Data for: "Improving litterfall production prediction in China under variable environmental conditions using machine learning algorithms"

description: Data: "data_updated_0618-empty rows removed-3-2.xlsx" contains 968 records of total annual litterfall production (Mg/ha/yr) collected at 314 forest sites covering the full geographical range of Chinese forests. The sites were distributed across various climatic zones, spanning latitudes from 18.26° to 51.50° N, longitudes from 82.25° to 129.53° E, altitudes from 0 to 4115 m above sea level, mean annual temperatures (MAT) from −5.4 to 25.4 °C, and mean annual precipitation (MAP) levels from 370 to 2800 mm. In addition to the geographical location and climate conditions, associated stand information is also included, such as forest type, stand origin, stand age, mean diameter at breast height (DBH), mean tree height, and stand density. Trap size (i.e., the surface area of the litter traps) is also included as it is a potentially important factor affecting litter collection. Code: "Litterfall v1.2_[total]_public release.ipynb" contains a complete pipeline of data parsing, cleaning, preprocessing, model training, and prediction.
DOI: 10.14288/1.0406475
title: Seminatural habitat surrounding farms promotes multifunctionality in avian ecosystem services

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Farmland birds can suppress insect pests, but may also consume beneficial insects, damage crops, and potentially carry foodborne pathogens. As bird communities shift in response to farming practices, so too do the benefits (services) and costs (disservices) from birds. Understanding how and why ecosystem services and disservices covary can inform management interventions that enhance synergies, avoid tradeoffs, and promote multifunctionality.&lt;/p&gt; &lt;p&gt;We investigated how farmland diversification practices influence the services and disservices provided by wild birds on 21 California strawberry farms. Specifically, we coupled 285 bird surveys, metabarcoding, and other molecular analyses of ~1,000 fecal samples representing 55 bird species (mostly passerines) to determine which individuals consumed pests, natural enemies, and crops and carried foodborne pathogens. Then, we explored how farming practices shape ecosystem service bundles, or suites of consistently co-occurring services/disservices.&lt;/p&gt; &lt;p&gt;Avian services and disservices were shaped by interactions between local farming practices and landscape context. We found that the amount of seminatural habitat surrounding each farm was the single most important driver of ecosystem services, with the best outcomes (highest multifunctionality) occurring on farms surrounded by seminatural habitat.&lt;/p&gt; &lt;p&gt;Bundles were primarily influenced by landscape context. Increasing seminatural habitat around farms was associated with more multifunctional bird communities that maximized services and minimized disservices. However, not all tradeoffs were minimized in landscapes with more seminatural habitat, suggesting that specific farming contexts can exacerbate or mitigate tradeoffs as bird communities shift in response to diversification practices.&lt;/p&gt; &lt;p&gt;Synthesis and applications: Though growers are often pressured to remove noncrop habitat to reduce food-safety risks, our work suggests that conserving habitat can support bird conservation, mitigate food-safety risks, and decrease crop damage from birds. More broadly, by considering the multiple roles that communities play in ecosystems, managers can simultaneously maximize services and minimize disservices to achieve multifunctionality.&lt;/p&gt;
DOI: 10.14288/1.0406561
title: Future climatic suitability of native tree species in restoration sites in Northwestern Ecuador

description: Climatic suitability of 10 tree species in 1237 restoration sites in Northwest Ecuador under baseline climatic conditions (1960-1990) and two climate scenarios (RCP 4.5 and 8.5) in the 2030s, 2050s, and 2070s. We built bioclimatic niche models to obtain the climatic suitability values for the species at each restoration site. The suitability values ranged from 0 (unsuitable) to 1 (suitable). Suitability thresholds (i.e., MaxSS, MTP, 10% TP) per species are provided to categorize species as "suitable" or "unsuitable" at the restoration sites. We used this dataset on species climatic suitability in restoration sites to assess the species climatic viability (i.e., persistance over time). Obtain further detail on this dataset's content in the file "AA_README.txt" in English, or "AA_README_Español.txt" in Spanish. Geographical data on the restoration sites location is not publicly available due to privacy restrictions from the government of Ecuador under the permit (MAE-SG-2018-6447-E).
DOI: 10.14288/1.0406467
title: The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (&lt;i&gt;Zostera marina&lt;/i&gt;) spanning 30º of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions, and traits can help us predict how communities may respond to environmental change.&lt;/p&gt;
DOI: 10.14288/1.0412732
title: Supplementary material for: Invited review: Risk factors for transition period disease in intensive grazing and housed dairy cattle

description: Dairy cows in both grazing and zero-grazing systems are at risk of disease in the weeks around calving. In this review, we highlight the factors associated with the development of diseases common during this period and discuss how different production systems face different challenges in improving cow health; some risks (including some associated with lameness) appear easier to address in grazing systems, but some nutritional issues are easier to manage in zero-grazing systems. We conclude that system specific solutions are required. In the supplementary material you will find a list of the research compiled to estimate the disease prevalence of dairy cattle under grazing and zero-grazing dairies.
DOI: 10.57745/0t7dll
title: R512331003_projection_datasheet.pdf
DOI: 10.57745/2qr5oo
title: Notice_fiche_synthèse.pdf

description: :unav
DOI: 10.57745/48kxm5
title: R616461001_projection_datasheet.pdf
DOI: 10.57745/5gbww4
title: Notice_fiche_synthÃ¨se_Explore2.pdf
DOI: 10.57745/5yog1z
title: R202001002_projection_datasheet.pdf
DOI: 10.57745/69dkuq
title: R413001300_projection_datasheet.pdf

description: :unav
DOI: 10.57745/831vl5
title: R618291001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/8ag3t9
title: R502331002_projection_datasheet.pdf
DOI: 10.57745/8wpblh
title: R125001001_projection_datasheet.pdf
DOI: 10.57745/9ttbhi
title: R011001002_projection_datasheet.pdf
DOI: 10.57745/aeujcg
title: R502331002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/agkttj
title: R212001101_projection_datasheet.pdf

description: :unav
DOI: 10.57745/at872x
title: R002001002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/cay5us
title: R411001001_projection_datasheet.pdf
DOI: 10.57745/eknuyq
title: R608001003_projection_datasheet.pdf

description: :unav
DOI: 10.57745/fr2akg
title: R406000101_projection_datasheet.pdf

description: :unav
DOI: 10.57745/gn6jbk
title: R202001002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/gopbq0
title: R713001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/gpcrlq
title: R618291001_projection_datasheet.pdf
DOI: 10.57745/j8a4pl
title: R314001002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/klfx4h
title: R125001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/lacqy1
title: R614291001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/lhrdq1
title: R616461001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/lntf9k
title: R413001300_projection_datasheet.pdf
DOI: 10.57745/mpwaio
title: R118001001_projection_datasheet.pdf
DOI: 10.57745/nzjsxc
title: R118001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/p4kxb7
title: R025001001_projection_datasheet.pdf
DOI: 10.57745/p98g0s
title: R103001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/pggwos
title: R022001002_projection_datasheet.pdf
DOI: 10.57745/rkmrot
title: R222001001_projection_datasheet.pdf
DOI: 10.57745/ry6gda
title: R212001101_projection_datasheet.pdf
DOI: 10.57745/setera
title: R025001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/susrbc
title: R002001002_projection_datasheet.pdf
DOI: 10.57745/tgguub
title: R523001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/ts684v
title: R222001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/u7dy8v
title: R713001001_projection_datasheet.pdf
DOI: 10.57745/uaxdwi
title: R523001001_projection_datasheet.pdf
DOI: 10.57745/wlmbrd
title: R011001002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/wn4lrj
title: R411001001_projection_datasheet.pdf

description: :unav
DOI: 10.57745/xafykw
title: R608001003_projection_datasheet.pdf
DOI: 10.57745/xhqqbx
title: R406000101_projection_datasheet.pdf
DOI: 10.57745/xvnks1
title: R022001002_projection_datasheet.pdf

description: :unav
DOI: 10.57745/yifczs
title: Notice_fiche_synthese.pdf
DOI: 10.57745/zkvsln
title: R512331003_projection_datasheet.pdf

description: :unav
DOI: 10.14288/1.0406545
title: OpenLCA tutorial with a free database

description: This is a step-by-step tutorial for getting started with OpenLCA software. This tutorial contains 1 database (.zolca), 2 handouts, and 2 accompanying lecture slides. [Disclaimer] the database used for this tutorial is compiled from two open-access databases (ELCD database and USDA crop database v1.1).
DOI: 10.57745/iecnaz
title: Notice_fiche_synthese_Explore2.pdf
DOI: 10.57745/jaoga8
title: R314001002_projection_datasheet.pdf
DOI: 10.57745/pxsekh
title: R614291001_projection_datasheet.pdf
DOI: 10.57745/qlbwgj
title: R103001001_projection_datasheet.pdf
DOI: 10.14288/1.0407254
title: Smart Triage Jinja Data De-identification

description: This dataset contains de-identified data with an accompanying data dictionary and the R script for de-identification procedures.