cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15544560
title: DAO-CITO: A Dual Aggregation Optimization Method for Class Integration Test Order Generation

description: # Artifact for DAO-CITO: A Dual Aggregation Optimization Method for Class Integration Test Order Generation

This artifact contains data, figures, and code fragments used in the evaluation section of the paper.

## Contents

- `code/`: Key implementation code fragments (not fully runnable due to anonymization and project-specific dependencies).- `data_and_results/`: Data tables and result files used to generate all evaluation figures and tables.

This artifact is intended to support the reproducibility and transparency of our experimental results.

For double-blind review, all metadata and file contents have been anonymized. A complete version will be made available upon acceptance.
DOI: 10.5281/zenodo.16874857
title: Influence of Cabbage Farming Practice   and Potato Peel Addition on the Endpoint Microbial Community in Sauerkraut Fermentation

description: Microbiome experiment on the effects of farming practice and potato peel addition on sauerkraut microbiome and resistance towards Lister innocua inoculation.
DOI: 10.5281/zenodo.15804100
title: Data from: Sensory loss and its consequences: the role of compound eye in the induced anti-predation defense of Daphnia

description: In aquatic food webs, Daphnia detect predation risk through integrated visual and olfactory cues. To determine how the compound eye interacts with olfactory cues to mediate antipredator responses, we surgically removed the compound eye of Daphnia and assessed behavioral, physiological, and transcriptomic responses with or without fish kairomone. Our results revealed that eyeless Daphnia exhibited increased speed, reduced phototaxis, and larger body size. Eye loss weakened the kairomone-induced decrease in body size and tail spine elongation, whereas key behavioral defenses persisted. Transcriptomic profiling showed that eye removal suppressed the photoreceptor gene OPN4 and modulated the MAPK-centered defense module, while up-regulating transcripts associated with chitin synthesis, EIF2 translation and VEGF-driven growth; lacking visual priming, kairomone failed to activate the NPC2 and AKR1B response characteristic. These findings enhance our understanding of sensory integration and inducible defense mechanisms in zooplankton, highlighting the compound eye's critical role in mediating Daphnia's response to predation risk.
DOI: 10.5281/zenodo.15049603
title: Biochar production from vineyard pruning waste by oxidative torrefaction

description: The torrefaction process for producing biochar from waste biomass has garnered significant attention in recent years. However, economic constraints hinder the broader adoption of this process. One such constraint is the requirement for an inert atmosphere during torrefaction. This study aimed to evaluate the feasibility of torrefying vineyard pruning waste in an oxygen-rich environment. Torrefaction of waste vine shoots was conducted in a fixed-bed reactor, utilizing a carrier gas medium with varying O2 concentrations (0% to 21%) at process temperatures of 220, 250, and 280ºC. Proximate and elemental analyses revealed that the torrefaction temperature is the key variable influencing biochar yield. Moreover, under mild torrefaction conditions, an increase in the carrier gas O2 concentration had a lesser impact on product yield compared to process temperature. Thus, it can be inferred that combustion gases and gases generated under mild torrefaction conditions could serve as carrier gases for a more cost-effective torrefaction process. Under oxidative conditions, the total biomass energy recovery was measured at 87.3 ± 1.7% for low temperatures and short torrefaction durations.
DOI: 10.3886/e242033
title: Federal University, Lokoja 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Lokoja 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.5281/zenodo.14534942
title: Cultivation of Arthrospira platensis (ULC 0444) in varying concentrations of brewery influent wastewater

description: This dataset provides a comprehensive analysis of the cultivation, biomass productivity, pigment and lipid extraction, fatty acid composition, and wastewater treatment potential of Arthrospira platensis (ULC 0444) grown in diluted brewery wastewater. The dataset highlights the integration of wastewater treatment with microalgal biomass valorisation for sustainable bio-based applications.

Experimental Details:



Microalgal Strain: Arthrospira platensis (ULC 0444) sourced from the Belgian Coordinated Collections of Microorganisms (BCCM).

Cultivation Conditions:



Cultured in brewery wastewater (BWW) obtained from Brewery Omer Vander Ghinste, diluted to 0%, 25%, 50%, 75%, and 90% with demineralized water.

Supplemented with essential nutrients (NaNO₃, K₂SO₄, Na₂HPO₄, MgSO₄) to support growth.

Cultivated in transparent acrylic tubular reactors under full-spectrum white LED light (50 μmol·m⁻²·s⁻¹).

Aeration at 1000 mL·min⁻¹ using rotameters.



Growth Monitoring:



Optical density at 750 nm (OD₇₅₀).

Biomass dry weight (DW) correlation with OD measurements (Eq. 1).

Biomass productivity calculated using Eq. 2.



DW (g/L) = 9.9040 OD + 0.7440     (1).

P (g DW L−1 day−1) = (Xf-Xi)/(tf-ti)    (2)


Pigment Extraction and Analysis:Phycocyanin was extracted using freeze-thaw cycles and quantified spectrophotometrically using the Bennett and Bogorad method. Yield was calculated as the ratio of extracted phycocyanin to total biomass (Eq. 4 and Eq. 5).

Cpc =(A615-0.474.A652)/5.34  (4)Ypc=(Cpc.VPBS)/DW  (5)

Lipid Extraction and FAME Analysis:Lipids were extracted using the methanol-chloroform-water method and transesterified to fatty acid methyl esters (FAMEs). Analysis was conducted using an Agilent 7820A GC system with FID detection, calibrated with Supelco 37 Component FAME Mix.

Water Quality Analysis:



Turbidity measured with a HANNA Turbidimeter.

Chemical oxygen demand (COD), ammonium (NH₄⁺-N), total nitrogen (T-N), and phosphate (PO₄³⁻-P) concentrations determined using Hach test kits and Metrohm Eco IC.

Metal ions measured using ICP-OES.

pH monitored pre- and post-treatment.


Dataset Includes:



Cultivation data: OD, biomass dry weight, and productivity.

Phycocyanin content and yield.

FAME composition and biodiesel properties.

Water quality parameters pre- and post-treatment.


Statistical analysis:In the dataset provided, data were analyzed using a one-way ANOVA test in Microsoft Excel, followed by a post hoc Tukey test to compare group means.

Purpose:This dataset demonstrates the potential of Arthrospira platensis for simultaneous wastewater treatment and biomass production for bio-based applications, contributing to the circular bioeconomy.
DOI: 10.5281/zenodo.14535047
title: Cultivation of Arthrospira platensis (ULC 0444) in varying concentrations of brewery influent wastewater_biochar analysis

description: This dataset presents the results of hydrothermal carbonization (HTC) performed on residual microalgal biomass obtained after anaerobic digestion. The microalgal biomass, grown in 90% brewery wastewater (WW) and processed for pigment extraction, underwent HTC at three different temperatures (180°C, 210°C, and 240°C) to assess its potential for biochar production and liquid phase valorization.

Experimental Details:



Hydrothermal Carbonization (HTC):



Solid-to-liquid ratio: 1.5 g biomass per 32 mL anaerobically digested effluent.

HTC reactors: Small stainless-steel reactors (40 mL capacity) operated in a convection oven (Carbolite AX 30).

Reaction conditions: 180°C, 210°C, and 240°C for 3 hours.

Cooling method: Submerged in cold water post-reaction.



Biochar Recovery:



Separation: Filtration using Whatman filter paper.

Measurement: Dried biochar mass used to calculate yield.




Biochar Characterization:



Thermal Stability:



Evaluated through Thermogravimetric Analysis (TGA).



Elemental Analysis:



C, H, N, S measured using a Flash 2000 Elemental Analyzer.

Samples processed in duplicate for accuracy.



ICP Analysis (ICP-OES; iCap 7000 Series Thermo Scientific, USA):



Biochar digested in concentrated HNO₃ and analyzed via ICP for elemental composition.



FTIR Spectroscopy (Nicolet, USA):



Functional group analysis for potential applications in adsorption and soil amendments.




Liquid Phase Characterization:







Bio-oil extracted from the aqueous phase using ethyl acetate.




Data Analysis:



One-way ANOVA in Microsoft Excel was followed by a post hoc Tukey test to compare group means.


Data processing:FTIR data was smooshed using available code from "https://github.com/cran/signal/blob/master/R/sgolayfilt.R"

The FTIR data were smoothed using the Savitzky-Golay algorithm in RStudio to enhance signal clarity while preserving peak features. The code was already existed in "https://github.com/cran/signal/blob/master/R/sgolayfilt.R"The smoothing process involved the following steps:



The raw FTIR data, consisting of wavenumber and intensity values, were imported into RStudio.

The Savitzky-Golay filter was applied using the sgolayfilt() function from the signal package.

The filter was configured with a polynomial order of 3 and a window size of 201 points, ensuring an odd-length window for accurate filtering.

This method effectively reduced noise while retaining the integrity of spectral features, making the data suitable for further analysis.


Dataset Includes:



Biochar yield and thermal stability data.

Elemental composition results (C, H, N, S, and ICP analysis).

FTIR spectroscopy results for functional group identification.

Wastewater characteristics.


Purpose:The dataset aims to evaluate the potential of HTC as a valorization pathway for residual microalgal biomass, supporting sustainable biochar production and the circular bioeconomy.
DOI: 10.5281/zenodo.17284207
title: The Multi-Phase Circumgalactic Medium of DESI Emission-Line Galaxies at z~1.5

description: Supplementary material to DESI's publication "The Multi-Phase Circumgalactic Medium of DESI Emission-Line Galaxies at z~1.5" to comply with the data management plan.
DOI: 10.5281/zenodo.18058235
title: GSK3β as a potential regulator in AML: a pan-cancer multi-omics analysis

description: Description: This dataset contains all underlying data supporting the findings in the aforementioned manuscript. It encompasses: (1) Bioinformatics data: Normalized gene expression matrices for GSK3 isoforms across 31 TCGA cancer types and GTEx normal tissues, corresponding immune cell enrichment scores (calculated via ssGSEA using the Bindea et al. gene signatures), and processed survival analysis data (Cox regression results). (2) In vitro experimental data: Raw flow cytometry files (.fcs format) for apoptosis and cell cycle analysis of human AML THP-1 cells treated with the GSK3 inhibitor CHIR-99021 or DMSO control, and the original, uncropped Western blot images for proteins including  c-Myc, and PARP1 (showing cleavage). The data were generated as part of a study to elucidate the pan-cancer landscape and therapeutic potential of GSK3β, with particular focus on acute myeloid leukemia (AML). These data can be reused for meta-analyses, computational validation, and comparative studies in oncology and hematology.
DOI: 10.5281/zenodo.14869226
title: Mitochondrial phylogeny and novel gene rearrangements in semiaquatic bugs (Hemiptera: Gerroidea)
DOI: 10.5281/zenodo.17186952
title: First principles band structure of interacting phosphorus and boron/aluminum δ-doped layers in silicon

description: Data supporting paper "

Silicon can be heavily doped with phosphorus in a single atomic layer (a δ layer), significantly altering the electronic structure of the conduction bands within the material. Recent progress has also made it possible to further dope silicon with acceptor-based δ layers using either boron or aluminum, making it feasible to create devices with interacting δ layers with opposite polarity. It is not known, however, how these δ layers will interact, particularly at small separation distances. Using Density Functional Theory, we calculate the electronic structure of a phosphorus-based δ layer interacting with a boron or aluminum δ layer, varying the distances between the δ layers. At separations 10 Å and smaller, the dopant potentials overlap and largely cancel each other out, leading to an electronic structure closely mimicking bulk silicon. At separations greater than 10 Å, the two layers behave independently of one another, forming a p-n diode with an intrinsic layer taking the place of the depletion region. One mechanism for charge transfer between δ layers at larger distances could be tunneling, where we see a greater than 3% probability for tunneling between a phosphorus and boron layer at 20 Å separation. This tunneling rate exceeds what would be seen for a standard silicon 1.1 eV triangular barrier, indicating that the interaction between delta layers creates enhanced tunneling at larger separation distances compared to a traditional junction. These calculations provide a foundation for the design of silicon-based electronics based on interacting δ layers.
DOI: 10.5281/zenodo.15759403
title: cartloader SeqScope Starter Tutorial Results

description: The repository is part of a cartloader public tutorial (https://seqscope.github.io/cartloader/vignettes/subregion_tutorials/seqscope/) based on the SeqScope Starter mouse datase. It showcases how to use cartloader (https://seqscope.github.io/cartloader/) toolkit to analyze and convert spatial transcriptomics data into web-optimized, spatially indexed PMTiles for downstream analysis, interactive web visualization, and data sharing across platforms. This repository provides PMTiles files for SGE dataset and its spatial factors from FICTURE analysis. These PMTiles files were generated using run_cartload2 from the cartloader toolkit.
DOI: 10.5281/zenodo.18090688
title: cartloader SeqScope Starter Tutorial Results

description: The repository is part of a cartloader public tutorial (https://seqscope.github.io/cartloader/vignettes/subregion_tutorials/seqscope/) based on the SeqScope Starter mouse datase. It showcases how to use cartloader (https://seqscope.github.io/cartloader/) toolkit to analyze and convert spatial transcriptomics data into web-optimized, spatially indexed PMTiles for downstream analysis, interactive web visualization, and data sharing across platforms. This repository provides PMTiles files for SGE dataset and its spatial factors from FICTURE analysis. These PMTiles files were generated using run_cartload2 from the cartloader toolkit.
DOI: 10.5281/zenodo.18089450
title: Molecular dynamics trajectories of selected protein-glycosaminoglycan systems with ff14SB/GLYCAM06j and CHARMM36m force fields

description: The following repository contains trajectory data from 1-microsecond MD simulations of the Fibroblast Growth Factor 2-heparin hexamer (PDB ID: 1BFC), Fibroblast Growth Factor 1-heparin hexamer (PDB ID: 2AXM) and Cathepsin K-chondroitin 4-sulfate hexamer (PDB ID: 4N8W) complexes using the ff14SB/GLYCAM06j and CHARMM36m force fields. For each system and each force field, three independend runs are provided. For ff14SB/GLYCAM06j files in AMBER format are provided, while for CHARMM36m in GROMACS format.
DOI: 10.5281/zenodo.18089451
title: Molecular dynamics trajectories of selected protein-glycosaminoglycan systems with ff14SB/GLYCAM06j and CHARMM36m force fields

description: The following repository contains trajectory data from 1-microsecond MD simulations of the Fibroblast Growth Factor 2-heparin hexamer (PDB ID: 1BFC), Fibroblast Growth Factor 1-heparin hexamer (PDB ID: 2AXM) and Cathepsin K-chondroitin 4-sulfate hexamer (PDB ID: 4N8W) complexes using the ff14SB/GLYCAM06j and CHARMM36m force fields. For each system and each force field, three independend runs are provided. For ff14SB/GLYCAM06j files in AMBER format are provided, while for CHARMM36m in GROMACS format.
DOI: 10.3886/e242034
title: Federal University, Ndifu-Alike 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Ndifu-Alike 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.5281/zenodo.18090720
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by John Spencer Womersley, http://www.wikidata.org/entity/Q21394699. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21394699
DOI: 10.5281/zenodo.8137445
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by John Spencer Womersley, http://www.wikidata.org/entity/Q21394699. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21394699
DOI: 10.3886/e242035
title: Federal University, Otuoke 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Otuoke 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.15468/dl.4gk66s
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Panama",
 "OccurrenceStatus is Present",
 "TaxonKey is Myiopsitta monachus"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068856-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e242036
title: Federal University, Oye-Ekiti 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Oye-Ekiti 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.3886/e242037
title: Federal University, Wukari 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Wukari 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.5281/zenodo.15612514
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Johannes Leendert van Soest, http://www.wikidata.org/entity/Q21447526. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21447526
DOI: 10.5281/zenodo.18090759
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Johannes Leendert van Soest, http://www.wikidata.org/entity/Q21447526. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21447526
DOI: 10.5281/zenodo.18090787
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by James Bowie, http://www.wikidata.org/entity/Q6130052. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6130052
DOI: 10.5281/zenodo.8149148
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by James Bowie, http://www.wikidata.org/entity/Q6130052. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6130052
DOI: 10.26180/29441996
title: PDF_CB-Conceptual-Framework_FULL_1Jul25.pdf

description: This Circular Building conceptual framework is shown in Figure. 7.1 of Fernando Pavez's PhD thesis.
DOI: 10.26180/29441996.v1
title: PDF_CB-Conceptual-Framework_FULL_1Jul25.pdf

description: This Circular Building conceptual framework is shown in Figure. 7.1 of Fernando Pavez's PhD thesis.
DOI: 10.15468/dl.44z2rt
title: Occurrence Download

description: A dataset containing 114368 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemiphaga novaeseelandiae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-180 -90, 180 -90, 180 90, -180 90, -180 -90))"
 ]
}

 The dataset includes 114368 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068852-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e242038
title: Federal University, Birnin Kebbi 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542

description: Federal University, Birnin Kebbi 2026/2027 IJMB Form, JUPEB Form Is Out Call 07076040542 To Apply and further admission assistance. Call Prof. Ben +2347076040542
DOI: 10.5281/zenodo.18090375
title: CPDB
title: CPDB_omics_ppi_embeddings_2048

description: Gene association graph
description: We introduce PISGE (Pathway-Informed Spectral Gene Embeddings), a spectral graph learning framework that unifies multi-omics feature extraction with topology-aware representation learning. PISGE employs a two-stage training strategy. In the pretraining stage, spectral embeddings are learned independently for each omics modality?gene expression, DNA methylation, copy number alteration, somatic mutation?and for network topology, enabling the model to capture modality-specific molecular and structural patterns. In the fine-tuning stage, these embeddings are integrated and refined using curated cancer driver annotations to optimize predictive performance. To enhance transparency, PISGE incorporates attention-based attribution and saliency-driven spectral biclustering, uncovering coherent gene?pathway modules supported by enrichment analysis. Across multiple tumor datasets, PISGE achieves strong predictive accuracy and reveals biologically consistent pathway-level organization through interpretable cluster?feature relationships.