cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8010643
title: Data for GECCO2023 Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness"

description: <strong>Data for Paper "Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness"</strong> <strong>instances.tar.xz</strong> contains 𝜌mnk-landscape instances <strong>metrics.csv</strong> contains the (C)PLOS-net metric-values <strong>performance.csv</strong> contains the performance of the different algorithms on each instance <strong>merged.csv</strong> contains the merged data from the 2 csv files above <strong>Reference</strong> Arnaud Liefooghe, Gabriela Ochoa, Sébastien Verel, and Bilel Derbel. 2023. <strong>Pareto Local Optimal Solutions Networks with Compression, Enhanced Visualization and Expressiveness</strong>. In Genetic and Evolutionary Computation Conference (GECCO ’23), July 15–19, 2023, Lisbon, Portugal. ACM, New York, NY, USA, 9 pages. https://doi.org/10.1145/3583131.3590474 <strong>Abstract</strong> The structure of local optima in multi-objective combinatorial optimization and their impact on algorithm performance are not yet properly understood. In this paper, we are interested in the representation of multi-objective landscapes and their multi-modality. More specifically, we revise and extend the network of Pareto local optimal solutions (PLOS-net), inspired by the well-established local optima network from single-objective optimization. We first define a compressed PLOS-net which allows us to enhance its perception while preserving the important notion of connectedness between local optima. We then study an alternative visualization of the (compressed) PLOS-net that focuses on good-quality solutions, improves the distinction between connected components in the network, and generalizes well to landscapes with more than 2 objectives. We finally define a number of network metrics that characterize the PLOS-net, some of them being strongly correlated with search performance. We visualize and experiment with small-size multi-objective nk-landscapes, and we disclose the effect of PLOS-net metrics against well-established multi-objective local search and evolutionary algorithms.
DOI: 10.5281/zenodo.7155803
title: Data for EMO2023 Paper "Feature-based Benchmarking of Distance-based Multi/Many-objective Optimisation Problems: A Machine Learning Perspective"

description: <strong>Data for Paper "Feature-based Benchmarking of Distance-based Multi/Many-objective Optimisation Problems: A Machine Learning Perspective"</strong> <br> The file <strong>dbmopp_dataset_perf.csv</strong> contains results from the 945 x 30 instances, with the following columns: <em>design_id</em>: problem identifier <em>n_var</em>: number of variables {2, ..., 20} <em>n_obj</em>: number of objectives {2, ..., 10} <em>nonident_ps</em>: non-identical Pareto sets {0 (no), 1 (yes)} <em>var_density</em>: varying density {0 (no), 1 (yes)} <em>n_discon_ps</em>: number of disconnected Pareto sets {0, ..., 6} <em>n_local_fronts</em>: number of local fronts {0, ..., 6} <em>n_resist_regions</em>: number of dominance resistance regions {0, ..., 6} <em>instance_id</em>: instance (fold) identifier {1, ..., 30} <em>budget</em>: number of evaluations performed by the algorithm {5000, 10000, 30000, 50000} <em>algo</em>: multi-objective evolutionary algorithm {NSGAII, IBEA, MOEAD, Random} <em>hypervolume</em>: hypervolume reached by the algorithm [0.0, 1.0] The file <strong>dbmopp_dataset_perf_aggregated.csv</strong> contains average results from the 945 problems, with the following columns: <em>design_id</em>: problem identifier <em>n_var</em>: number of variables {2, ..., 20} <em>n_obj</em>: number of objectives {2, ..., 10} <em>nonident_ps</em>: non-identical Pareto sets {0 (no), 1 (yes)} <em>var_density</em>: varying density {0 (no), 1 (yes)} <em>n_discon_ps</em>: number of disconnected Pareto sets {0, ..., 6} <em>n_local_fronts</em>: number of local fronts {0, ..., 6} <em>n_resist_regions</em>: number of dominance resistance regions {0, ..., 6} <em>budget</em>: number of evaluations performed by the algorithm {5000, 10000, 30000, 50000} <em>algo</em>: multi-objective evolutionary algorithm {NSGAII, IBEA, MOEAD, Random} <em>hypervolume_avg</em>: average hypervolume reached by the algorithm [0.0, 1.0] <em>best</em>: 1 if the corresponding algorithm obtains the best average hypervolume, 0 otherwise
DOI: 10.5281/zenodo.7155802
title: Data for EMO2023 Paper "Feature-based Benchmarking of Distance-based Multi/Many-objective Optimisation Problems: A Machine Learning Perspective"

description: <strong>Data for Paper "Feature-based Benchmarking of Distance-based Multi/Many-objective Optimisation Problems: A Machine Learning Perspective"</strong> <br> The file <strong>dbmopp_dataset_perf.csv</strong> contains results from the 945 x 30 instances, with the following columns: <em>design_id</em>: problem identifier <em>n_var</em>: number of variables {2, ..., 20} <em>n_obj</em>: number of objectives {2, ..., 10} <em>nonident_ps</em>: non-identical Pareto sets {0 (no), 1 (yes)} <em>var_density</em>: varying density {0 (no), 1 (yes)} <em>n_discon_ps</em>: number of disconnected Pareto sets {0, ..., 6} <em>n_local_fronts</em>: number of local fronts {0, ..., 6} <em>n_resist_regions</em>: number of dominance resistance regions {0, ..., 6} <em>instance_id</em>: instance (fold) identifier {1, ..., 30} <em>budget</em>: number of evaluations performed by the algorithm {5000, 10000, 30000, 50000} <em>algo</em>: multi-objective evolutionary algorithm {NSGAII, IBEA, MOEAD, Random} <em>hypervolume</em>: hypervolume reached by the algorithm [0.0, 1.0] The file <strong>dbmopp_dataset_perf_aggregated.csv</strong> contains average results from the 945 problems, with the following columns: <em>design_id</em>: problem identifier <em>n_var</em>: number of variables {2, ..., 20} <em>n_obj</em>: number of objectives {2, ..., 10} <em>nonident_ps</em>: non-identical Pareto sets {0 (no), 1 (yes)} <em>var_density</em>: varying density {0 (no), 1 (yes)} <em>n_discon_ps</em>: number of disconnected Pareto sets {0, ..., 6} <em>n_local_fronts</em>: number of local fronts {0, ..., 6} <em>n_resist_regions</em>: number of dominance resistance regions {0, ..., 6} <em>budget</em>: number of evaluations performed by the algorithm {5000, 10000, 30000, 50000} <em>algo</em>: multi-objective evolutionary algorithm {NSGAII, IBEA, MOEAD, Random} <em>hypervolume_avg</em>: average hypervolume reached by the algorithm [0.0, 1.0] <em>best</em>: 1 if the corresponding algorithm obtains the best average hypervolume, 0 otherwise
DOI: 10.5281/zenodo.7998638
title: Data for "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"

description: This is the data associated with the following publication : "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"
DOI: 10.5281/zenodo.7998637
title: Data for "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"

description: This is the data associated with the following publication : "Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1"
DOI: 10.15129/9dbf7256-6c91-49a8-aae3-f9da1d54260f
title: Data for: "Estimating surface concentrations of Calanus finmarchicus using standardised eRGB imagery"

description: This dataset contains figures, MATLAB scripts and data required to apply the novel techniques developed in the paper. The 'ReadMe' file contrains more information about each of the files in the folder.
DOI: 10.6084/m9.figshare.22587031
title: Supplementary Material for: Distribution and clinical significance of HPV16 variants in head and neck squamous cell carcinomas: data from a Portuguese cohort and systematic review

description: Introduction: Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aims to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical-pathological characteristics and patient survival. Methods: We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing (NGS) was used to obtain whole-genome sequences and variants were established based on phylogenetic classification. Results: 74.% of samples clustered in lineage A, 5.7% lineage B, 2.9% C and 17.1% D. Comparative genome analysis revealed 243 single nucleotide variations (SNVs). Of these one hundred were previously reported, according to our systematic review. No significant associations with clinical-pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. Discussion/Conclusion: These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.
DOI: 10.6084/m9.figshare.22587031.v1
title: Supplementary Material for: Distribution and clinical significance of HPV16 variants in head and neck squamous cell carcinomas: data from a Portuguese cohort and systematic review

description: Introduction: Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aims to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical-pathological characteristics and patient survival. Methods: We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing (NGS) was used to obtain whole-genome sequences and variants were established based on phylogenetic classification. Results: 74.% of samples clustered in lineage A, 5.7% lineage B, 2.9% C and 17.1% D. Comparative genome analysis revealed 243 single nucleotide variations (SNVs). Of these one hundred were previously reported, according to our systematic review. No significant associations with clinical-pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. Discussion/Conclusion: These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.
DOI: 10.5281/zenodo.7758621
title: Data for "Reconciling the need of abandoned cropland in supporting both food security and climate change mitigation"

description: <strong>Data for "Reconciling the need of abandoned cropland in supporting both food security and climate change mitigation"</strong> <strong>All files will be made publicly accessible before publication.</strong> Content (spatial resolution, data info) Abandoned cropland map (10arcsec, 1 raster file) Suitabability of abanonded cropland for reforestation and recultivation (5arcmin, 3 raster files) Food production potential of global abandoned cropland (5arcmin,1 raster file) Climate change mitigation potential of global abandoned cropland (5arcmin, 1 raster file) outcomes of key scenarios 6 key Scenarios: Food production only, Climate change mitigation only, Maximizing food production, Maximizing climate change mitigation, Equal Allocation, Maximizing combined potential Data included in the output of each scenario: Land allocated for reforestation and recultivation (5arcmin/1arcdeg, 5 raster files) Climate change mitigation potential and food production potential (5arcmin/1arcdeg, 5 raster files) Emission for land clearing (5arcmin, 1 raster) Foregone climate change mitigation potential (5arcmin, 1 raster) Summary table Summary table for 6 key scenarios
description: Contact: Qiming Zheng Email: Qiming.zheng@outlook.com Personal Page: https://qmzheng09work.github.io/
DOI: 10.6084/m9.figshare.22269022.v1
title: Supplementary Material for: Evaluation of retinal microvascular features in patients with amblyopia based on optical coherence tomography angiography: a systematic review and Meta-analysis

description: Abstract Background: The performance of optical coherence tomography angiography (OCTA) in macular microvasculature of patients with amblyopia has been widely studied, but these studies have yielded different and controversial results. Objectives: To investigate retinal microvascular features in patients with amblyopia undergoing OCTA. Methods: PubMed, Embase, and Web of Science were searched for published articles comparing the retinal microvascular features between individuals with amblyopia and controls until April 2022. The mean difference with a 95% confidence interval was used to assess continuous variables. Results: The analysis included 17 studies. The whole vessel density of the superficial capillary plexus (SCPVD) was lower in amblyopic eyes (AE) than in normal control eyes (NE) in 3 × 3 mm2 scans, while the perifoveal vessel density of superficial and deep capillary plexus was lower in 6 × 6 mm2 scans. The whole parafoveal vessel density of deep capillary plexus (DCPVD) and parafoveal-SCPVD were lower in both scans. The comparison between amblyopic eyes and fellow eyes (FE) revealed no statistical difference in all quadrants except the parafoveal and perifoveal-SCPVD and the foveal-DCPVD. Additionally, SCPVD in all quadrants except the fovea and DCPVD in all quadrants except the parafoveal were higher in fellow eyes compared to normal control eyes. No significant difference was found in the foveal avascular area between AE and NE, AE and FE, or NE and FE. Conclusions: The retinal vessel density of superficial and deep capillary plexus in amblyopic and fellow eyes was lower than in normal controls, and differences were more likely discovered using 6 × 6 mm2 scans. Consequently, OCTA may be utilized as a diagnostic tool to identify and monitor patients with amblyopia.
DOI: 10.6084/m9.figshare.22822676
title: <strong>Disentangling particle composition to differentiate POC through remotely-sensed optical signatures in optically-complex estuarine and coastal waters</strong>

description: Mengyu Li<sup>1</sup>, Fang Shen<sup>1, *</sup>, Emanuele Organelli<sup>2</sup>, Wei Luo<sup>1</sup>, Xuerong Sun<sup>1</sup>, Xiaodao Wei<sup>1</sup> <br> <sup>1</sup> State Key Laboratory of Estuarine and Coastal Research, Center for Blue Carbon Science and Technology, East China Normal University, Shanghai, China <sup>2</sup> National Research Council (CNR), Institute of Marine Sciences (ISMAR), Via Fosso del Cavaliere 100, Rome, Italy * Corresponding author. Email: fshen@sklec.ecnu.edu.cn;
DOI: 10.6084/m9.figshare.22822676.v3
title: <strong>Disentangling particle composition to differentiate POC through remotely-sensed optical signatures in optically-complex estuarine and coastal waters</strong>

description: Mengyu Li<sup>1</sup>, Fang Shen<sup>1, *</sup>, Emanuele Organelli<sup>2</sup>, Wei Luo<sup>1</sup>, Xuerong Sun<sup>1</sup>, Xiaodao Wei<sup>1</sup> <br> <sup>1</sup> State Key Laboratory of Estuarine and Coastal Research, Center for Blue Carbon Science and Technology, East China Normal University, Shanghai, China <sup>2</sup> National Research Council (CNR), Institute of Marine Sciences (ISMAR), Via Fosso del Cavaliere 100, Rome, Italy * Corresponding author. Email: fshen@sklec.ecnu.edu.cn;
DOI: 10.6084/m9.figshare.22643041
title: Supplementary Material for: HBV DNA Integration into Telomerase or MLL4 Genes and TERT Promoter Point Mutation as Three Independent Signatures in Subgrouping HBV-related HCC with distinct features

description: Introduction: A set of genetic mutations to classify hepatocellular carcinoma (HCC) useful to clinical studies is an unmet need. Hepatitis B virus-related HCC (HBV-HCC) harbors a unique genetic mutation, namely the HBV integration, among other somatic endogenous gene mutations. We explored a combination of HBV DNA integrations and common somatic mutations to classify HBV-HCC by using a capture-sequencing platform. Methods: A total of 153 HBV-HCCs after surgical resection were subjected to capture-sequencing to identify HBV integrations and three common somatic mutations in genomes. Three mutually exclusive mutations, HBV DNA integration into the TERT promoter, HBV DNA integration into MLL4, or TERT promoter point mutation, were identified in HBV-HCC. Results: They were used to classify HBV-HCCs into four groups: G1 with HBV-TERT integration (25.5%); G2 with HBV-MLL4 integration (10.5%); G3 with TERT promoter mutation (30.1%); and G4 without these three mutations (34.0%). Clinically, G3 has the highest male-to-female ratio, cirrhosis rate and associated with higher early recurrence and mortality after resection, but G4 has the best outcome. Transcriptomic analysis revealed a grouping different from the published ones, and G2 with an active immune profile related to immune checkpoint inhibitor response. Analysis of integrated HBV DNA provided clues for HBV genotype and variants in carcinogenesis of different HCC subgroup. This new classification was also validated in another independent cohort. Discussion/Conclusion: A simple and robust genetic classification was developed to aid in understanding HBV-HCC and in harmonizing clinical studies.
DOI: 10.6084/m9.figshare.22643041.v1
title: Supplementary Material for: HBV DNA Integration into Telomerase or MLL4 Genes and TERT Promoter Point Mutation as Three Independent Signatures in Subgrouping HBV-related HCC with distinct features

description: Introduction: A set of genetic mutations to classify hepatocellular carcinoma (HCC) useful to clinical studies is an unmet need. Hepatitis B virus-related HCC (HBV-HCC) harbors a unique genetic mutation, namely the HBV integration, among other somatic endogenous gene mutations. We explored a combination of HBV DNA integrations and common somatic mutations to classify HBV-HCC by using a capture-sequencing platform. Methods: A total of 153 HBV-HCCs after surgical resection were subjected to capture-sequencing to identify HBV integrations and three common somatic mutations in genomes. Three mutually exclusive mutations, HBV DNA integration into the TERT promoter, HBV DNA integration into MLL4, or TERT promoter point mutation, were identified in HBV-HCC. Results: They were used to classify HBV-HCCs into four groups: G1 with HBV-TERT integration (25.5%); G2 with HBV-MLL4 integration (10.5%); G3 with TERT promoter mutation (30.1%); and G4 without these three mutations (34.0%). Clinically, G3 has the highest male-to-female ratio, cirrhosis rate and associated with higher early recurrence and mortality after resection, but G4 has the best outcome. Transcriptomic analysis revealed a grouping different from the published ones, and G2 with an active immune profile related to immune checkpoint inhibitor response. Analysis of integrated HBV DNA provided clues for HBV genotype and variants in carcinogenesis of different HCC subgroup. This new classification was also validated in another independent cohort. Discussion/Conclusion: A simple and robust genetic classification was developed to aid in understanding HBV-HCC and in harmonizing clinical studies.
DOI: 10.6084/m9.figshare.23302055
title: Table S3

description: Data summary of the pollinator visitation measurements performed in "Polyploidy-induced floral changes lead to unexpected pollinator behavior in <em>Arabidopsis arenosa</em>" by Schmickl et al (2023).
DOI: 10.15151/esrf-es-1108935046
title: Phason mode in the i-AlCuRu quasicrystal

description: We propose to measure phason modes in the i-AlCuRu quasicrystal using diffuse scattering on an absolute scale. This measurement will be interpreted using the hydrodynamic theory of quasicrystal and phason elastic constant. This will be the first phason elastic constant determination in the i-AlCuRu quasicrystal that is isostructural to i-AlPdMn.
DOI: 10.6084/m9.figshare.22683268.v1
title: Supplementary Material for: Changes in Visual Long-term Potentiation Show Preserved Cyclicity in Human Females Taking Combined Oral Contraceptives

description: Introduction: The combined oral contraceptive pill (COC) is often employed to address physical and neurological symptoms in menstrual cycle-related disorders by suppressing shifts in endogenous gonadal hormone fluctuations. Symptom persistence, especially in the lead up to the hormone free interval (HFI) suggests an underlying neurobiological mechanism of preserved cycling. Our study utilised a non-invasive method of visually inducing long-term potentiation (LTP) to index changes in neural plasticity in the absence of hormonal fluctuations. Methods: Visually induced LTP was recorded using electroencephalography in 24 healthy female COC users across three sessions; day 3 and 21 during active hormone pills, and day 24 during the HFI. The Daily Record of the Severity of Problems (DRSP) questionnaire tracked premenstrual symptoms. Dynamic causal modelling (DCM) was used to elucidate the neural connectivity and receptor activity changes associated with LTP across different days of COC. Results: Visually induced LTP was greater on day 21 than day 3 (p=0.011) and was localised to the P2 visually evoked potential. There was no effect of the HFI (day 24) on LTP. DCM of differences between day 3 and 21 showed changes to inhibitory interneuronal gating of LTP in cortical layer VI. The DRSP only showed a significant increase in symptoms in the HFI, meaning the LTP result appeared more sensitive to cyclicity. Conclusions: This study provides objective evidence of preserved cyclicity in COC users through enhanced LTP on day 21 compared to day 3 of a 28-day COC regimen, indicating that relatively higher excitation in the brain despite peripheral gonadal suppression may underlie and exacerbate menstrual cycle-related disorders.
DOI: 10.25549/pcra-c14-52844
title: Redemption tidings, vol. 34, nos. 1-52, 3 Jan. - 25 Dec. 1958

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.hkb5n3
title: Occurrence Download

description: A dataset containing 1780 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cnemarchus erythropygius (P.L.Sclater, 1853)"
 ]
}

 The dataset includes 1780 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0379368-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jofug
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Penaeus vannamei Boone, 1931"
 ]
}

 The dataset includes 120 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002454-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7zdnwg
title: Occurrence Download

description: A dataset containing 1586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombyx mori Linnaeus, 1758"
 ]
}

 The dataset includes 1586 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0379355-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.