cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18344433
title: Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- MM285

description: Knowledgebases for the Mouse Methylation BeadChip (MM285)

This repository hosts curated knowledgebases for the Mouse Methylation BeadChip (MM285). These datasets are specifically formatted as RDS files for the knowYourCG Bioconductor package to facilitate functional enrichment analysis in murine studies.

1. Technical Metadata & Quality Control

Datasets defining the physical architecture and data cleaning parameters specific to the mouse array.





ProbeType — Infinium Type I vs Type II probe design.




InfiniumChemistry — Technical chemistry metadata for the MM285 platform.




ProbeCGnum — Number of CpGs queried by each probe.




Mask — Probes flagged for potential technical artifacts or SNPs.




Blacklist — Genomic regions known to produce poor quality or ambiguous data.



2. Genomic Context & Sequence Features

Mouse genomic landmarks and underlying DNA sequence characteristics.





Chromosome — Murine chromosomal assignments.




CGI — CpG Island (CGI) associations.




nFlankCG — Flanking sequence composition.




Tetranuc2 & Tetranuc4 — Tetranucleotide frequency signatures.




rmsk1 & rmsk2 — RepeatMasker repetitive elements in the mouse genome.



3. Epigenomic States & Regulatory Elements

Functional annotations based on mouse-specific chromatin and transcription factor data.





ChromHMM — Mouse-specific chromatin state models.




EnsRegBuild — Ensembl Regulatory Build annotations.




HM — Histone modification peaks for the mouse genome.




TFBSrm — Transcription Factor Binding Sites.




PMD — Partially Methylated Domains.



4. Biological Signatures

Knowledgebases summarizing gene-level and tissue-specific patterns.





MetagenePC — Principal components of gene-level methylation profiles in mice.





References & Documentation





Background Paper: Goldberg and Fu et al., Science Advances (2025)




Software: knowYourCG (Bioconductor)




User Guide: Usage for Mouse Methylation Array
DOI: 10.5281/zenodo.18180658
title: Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- MM285

description: Knowledgebases for the Mouse Methylation BeadChip (MM285)

This repository hosts curated knowledgebases for the Mouse Methylation BeadChip (MM285). These datasets are specifically formatted as RDS files for the knowYourCG Bioconductor package to facilitate functional enrichment analysis in murine studies.

1. Technical Metadata & Quality Control

Datasets defining the physical architecture and data cleaning parameters specific to the mouse array.





ProbeType — Infinium Type I vs Type II probe design.




InfiniumChemistry — Technical chemistry metadata for the MM285 platform.




ProbeCGnum — Number of CpGs queried by each probe.




Mask — Probes flagged for potential technical artifacts or SNPs.




Blacklist — Genomic regions known to produce poor quality or ambiguous data.



2. Genomic Context & Sequence Features

Mouse genomic landmarks and underlying DNA sequence characteristics.





Chromosome — Murine chromosomal assignments.




CGI — CpG Island (CGI) associations.




nFlankCG — Flanking sequence composition.




Tetranuc2 & Tetranuc4 — Tetranucleotide frequency signatures.




rmsk1 & rmsk2 — RepeatMasker repetitive elements in the mouse genome.



3. Epigenomic States & Regulatory Elements

Functional annotations based on mouse-specific chromatin and transcription factor data.





ChromHMM — Mouse-specific chromatin state models.




EnsRegBuild — Ensembl Regulatory Build annotations.




HM — Histone modification peaks for the mouse genome.




TFBSrm — Transcription Factor Binding Sites.




PMD — Partially Methylated Domains.



4. Biological Signatures

Knowledgebases summarizing gene-level and tissue-specific patterns.





MetagenePC — Principal components of gene-level methylation profiles in mice.





References & Documentation





Background Paper: Goldberg and Fu et al., Science Advances (2025)




Software: knowYourCG (Bioconductor)




User Guide: Usage for Mouse Methylation Array
DOI: 10.14457/stou.the.2019.128
title: บทบาทการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียนของนักวิชาการส่งเสริมการเกษตรระดับอำเภอในพื้นที่รับผิดชอบของสำนักงานส่งเสริมและพัฒนาการเกษตรที่ 3

description: การวิจัยมีวัตถุประสงค์เพื่อศึกษาเกี่ยวกับบทบาทของนักวิชาการส่งเสริมการเกษตรระดับอำเภอในการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียน ประเด็นต่อไปนี้ (1) ความรู้และแหล่งความรู้ (2) บทบาทของนักวิชาการส่งเสริมการเกษตร (3) ความคิดเห็นและความต้องการของนักวิชาการส่งเสริมการเกษตร (4) ปัจจัยที่เกี่ยวข้องกับบทบาทการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียน และ (5) ปัญหาและข้อเสนอแนะในการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียน ประชากรที่ใช้ในการวิจัย คือ นักวิชาการส่งเสริมการเกษตรระดับอำเภอ จำนวน 275 คน กำหนดขนาดกลุ่มตัวอย่างตามสูตรของทาโร ยามาเน่ ที่ความคลาดเคลื่อน 5% ได้กลุ่มตัวอย่าง 163 คน สุ่มตัวอย่างแบบง่ายโดยวิธีการจับสลาก เครื่องมือที่ใช้เป็นแบบสอบถาม สถิติที่ใช้ในการวิเคราะห์ ได้แก่ ค่าความถี่ ค่าร้อยละ ค่าต่ำสุด ค่าสูงสุด ค่าเฉลี่ย ส่วนเบี่ยงเบนมาตรฐาน การจัดอันดับ และการวิเคราะห์ถดถอยพหุคูณ ผลการวิจัยพบว่า นักวิชาการส่งเสริมการเกษตรระดับอำเภอส่วนมากเป็นเพศหญิง อายุเฉลี่ย 36.83 ปี ส่วนมากจบการศึกษาระดับปริญญาตรี มีประสบการณ์การทำงานเฉลี่ย 11.06 ปี ได้รับเงินเดือนเฉลี่ย 22,414.93 บาท มีตำบลที่รับผิดชอบเฉลี่ย 1.83 ตำบล และกลุ่มยุวเกษตรกรที่รับผิดชอบเฉลี่ย 248 กลุ่ม (1) ความรู้และการได้รับความรู้ของนักวิชาการส่งเสริมการเกษตรในการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียนอยู่ในระดับปานกลาง (2) นักวิชาการส่งเสริมการเกษตรมีความคิดเห็นต่อบทบาทการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียนอยู่ในระดับมาก และมีระดับการปฏิบัติอยู่ในระดับปานกลาง (3) ความคิดเห็นในการส่งเสริมกลุ่มยุวเกษตรในโรงเรียนอยู่ในระดับมาก โดยเฉพาะความรู้และทักษะการจัดตั้งกลุ่มยุวเกษตรในโรงเรียน ส่วนความต้องการในการส่งเสริมกลุ่มยุวเกษตรในโรงเรียนอยู่ในระดับมาก โดยเฉพาะความต้องการงบประมาณสนับสนุนกิจกรรม (4) ปัจจัยที่เกี่ยวข้องกับบทบาทการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียน คือ จำนวนตำบลที่รับผิดชอบมีความสัมพันธ์ในทิศตรงกันข้าม แต่แหล่งความรู้ในการส่งเสริมกลุ่มยุวเกษตรในโรงเรียนมีความสัมพันธ์ในทิศทางเดียวกับบทบาทการส่งเสริมกลุ่มยุวเกษตรกรในโรงเรียน และ (5) ปัญหาที่พบมากที่สุด คือ นักวิชาการส่งเสริมการเกษตรมีงานภารกิจเร่งด่วนที่เข้าแทรกแซงงานประจำ ส่วนข้อเสนอแนะที่เห็นด้วยมากที่สุด คือ การพัฒนาสื่อเพื่อการเรียนรู้ด้านเกษตรที่ทันสมัยให้กับยุวเกษตรกรในโรงเรียน
DOI: 10.15468/dl.scdqf5
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.60111000000001 24.825288, 88.523742 24.819711, 88.4483 24.803119, 88.37665800000001 24.775923, 88.310596 24.738802, 88.251749 24.692676, 88.20157 24.638691, 88.161289 24.578185, 88.131891 24.512656, 88.11408299999999 24.443723, 88.10828600000001 24.373089, 88.11462299999999 24.302493, 88.132919 24.233672, 88.162705 24.168317, 88.20323399999999 24.108031, 88.25349900000001 24.054289, 88.31225999999999 24.008407, 88.378074 23.971505, 88.44932799999999 23.944484, 88.524283 23.928004, 88.60111000000001 23.922465, 88.677937 23.928004, 88.752892 23.944484, 88.824146 23.971505, 88.88996 24.008407, 88.94872100000001 24.054289, 88.998986 24.108031, 89.03951499999999 24.168317, 89.069301 24.233672, 89.087597 24.302493, 89.093934 24.373089, 89.088137 24.443723, 89.070329 24.512656, 89.040931 24.578185, 89.00064999999999 24.638691, 88.95047099999999 24.692676, 88.89162399999999 24.738802, 88.82556200000001 24.775923, 88.75391999999999 24.803119, 88.678478 24.819711, 88.60111000000001 24.825288))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005932-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30742691
title: Expecting the expected: an analytical framework to examine people’s expectations of robots

description: We present a novel framework for human-robot interaction designers to analyze and explore expectations of their robot designs. It consists of a model of how people form expectations of robots, and a taxonomy for classifying them. A known challenge in human-robot interactions is expectation discrepancy, in which the expectations people form when interacting with a social robot are not aligned with its actual capabilities. This can disappoint users and hinder interaction. Research has proposed ways to mitigate expectation discrepancy, but designers lack a systematic approach to analyzing and describing expectations. We developed a rigorous theoretical framework by drawing from theories and models from psychology and sociology on expectations between people, and by conducting a field review of expectations in human-robot interactions. We further propose methods for designers to leverage the framework in systematic analysis of how and why people form expectations of a given robot and what those expectations may be. This can empower designers with greater control over people’s expectations, enabling them to combat expectation discrepancy.
DOI: 10.15468/dl.4ape2r
title: Occurrence Download

description: A dataset containing 801 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Berneuxia"
 ]
}

 The dataset includes 801 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005933-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30742691.v2
title: Expecting the expected: an analytical framework to examine people’s expectations of robots

description: We present a novel framework for human-robot interaction designers to analyze and explore expectations of their robot designs. It consists of a model of how people form expectations of robots, and a taxonomy for classifying them. A known challenge in human-robot interactions is expectation discrepancy, in which the expectations people form when interacting with a social robot are not aligned with its actual capabilities. This can disappoint users and hinder interaction. Research has proposed ways to mitigate expectation discrepancy, but designers lack a systematic approach to analyzing and describing expectations. We developed a rigorous theoretical framework by drawing from theories and models from psychology and sociology on expectations between people, and by conducting a field review of expectations in human-robot interactions. We further propose methods for designers to leverage the framework in systematic analysis of how and why people form expectations of a given robot and what those expectations may be. This can empower designers with greater control over people’s expectations, enabling them to combat expectation discrepancy.
DOI: 10.6084/m9.figshare.31130086
title: Coral Reef Underwater Hyperspectral Dataset

description: The underwater hyperspectral dataset used for coral reef benthic classification experiments comprises three subsets (005, 006, and 019). Each subset includes the hyperspectral imagery and its corresponding ground truth data. The hyperspectral imagery consists of spectrally clipped data, with each clipped data cube containing 350 bands. The ground truth labels have been renumbered according to their respective categories. The original, unprocessed hyperspectral data and ground truth labels for all three subsets are publicly available at: https://doi.org/10.1594/PANGAEA.911300.
DOI: 10.6084/m9.figshare.31130086.v2
title: Coral Reef Underwater Hyperspectral Dataset

description: The underwater hyperspectral dataset used for coral reef benthic classification experiments comprises three subsets (005, 006, and 019). Each subset includes the hyperspectral imagery and its corresponding ground truth data. The hyperspectral imagery consists of spectrally clipped data, with each clipped data cube containing 350 bands. The ground truth labels have been renumbered according to their respective categories. The original, unprocessed hyperspectral data and ground truth labels for all three subsets are publicly available at: https://doi.org/10.1594/PANGAEA.911300.
DOI: 10.6084/m9.figshare.31130086.v1
title: Coral Reef Underwater Hyperspectral Dataset

description: The underwater hyperspectral dataset used for coral reef benthic classification experiments comprises three subsets (005, 006, and 019). Each subset includes the hyperspectral imagery and its corresponding ground truth data. The hyperspectral imagery consists of spectrally clipped data, with each clipped data cube containing 350 bands. The ground truth labels have been renumbered according to their respective categories. The original, unprocessed hyperspectral data and ground truth labels for all three subsets are publicly available at: https://doi.org/10.1594/PANGAEA.911300.
DOI: 10.5281/zenodo.18344682
title: A Mechanical Infiltration Framework for Solid Tumor Reconditioning: Rethinking the Immune-Constructed Barrier

description: Conventional oncology models conceptualize the tumor capsule as a self-constructed shield by malignant cells. We propose a paradigm-shifting hypothesis: the solid tumor’s fibrotic barrier is primarily engineered by the host immune system as an emergency containment mechanism to restrict metastatic dissemination. This concept echoes the longstanding analogy of tumors as "wounds that do not heal," where the persistent fibrotic response mimics chronic wound healing processes driven by ongoing immune activation [Dvorak1986]. While protective, this barrier inadvertently creates a sealed biomechanical microenvironment characterized by elevated interstitial fluid pressure (IFP) and gas accumulation—key contributors to therapeutic resistance, including resistance to immunotherapy. This immune-constructed barrier also contributes to the classification of tumors as immunologically "cold," characterized by limited immune cell infiltration and poor response to immunotherapy. Here, we introduce a three-stage therapeutic protocol—decompression, infiltration and reprogramming (including immunotherapy integration), and extracorporeal purification—designed to leverage, rather than dismantle, this immune-constructed wall. By mechanically relieving internal pressure before intervention, we enable targeted drug delivery, cellular re-differentiation, and enhanced immunotherapy efficacy, while concurrent nanofilter-enhanced dialysis prevents systemic toxicity. This framework reframes solid tumor management from destruction to controlled reconditioning, with potential to convert "cold" tumors into more immunologically responsive states.
DOI: 10.5281/zenodo.18344683
title: A Mechanical Infiltration Framework for Solid Tumor Reconditioning: Rethinking the Immune-Constructed Barrier

description: Conventional oncology models conceptualize the tumor capsule as a self-constructed shield by malignant cells. We propose a paradigm-shifting hypothesis: the solid tumor’s fibrotic barrier is primarily engineered by the host immune system as an emergency containment mechanism to restrict metastatic dissemination. This concept echoes the longstanding analogy of tumors as "wounds that do not heal," where the persistent fibrotic response mimics chronic wound healing processes driven by ongoing immune activation [Dvorak1986]. While protective, this barrier inadvertently creates a sealed biomechanical microenvironment characterized by elevated interstitial fluid pressure (IFP) and gas accumulation—key contributors to therapeutic resistance, including resistance to immunotherapy. This immune-constructed barrier also contributes to the classification of tumors as immunologically "cold," characterized by limited immune cell infiltration and poor response to immunotherapy. Here, we introduce a three-stage therapeutic protocol—decompression, infiltration and reprogramming (including immunotherapy integration), and extracorporeal purification—designed to leverage, rather than dismantle, this immune-constructed wall. By mechanically relieving internal pressure before intervention, we enable targeted drug delivery, cellular re-differentiation, and enhanced immunotherapy efficacy, while concurrent nanofilter-enhanced dialysis prevents systemic toxicity. This framework reframes solid tumor management from destruction to controlled reconditioning, with potential to convert "cold" tumors into more immunologically responsive states.
DOI: 10.15468/dl.vfqz46
title: Occurrence Download

description: A dataset containing 10171 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Biancaea"
 ]
}

 The dataset includes 10171 records from 341 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005935-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9r23p
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.60111000000001 24.825288, 88.523742 24.819711, 88.4483 24.803119, 88.37665800000001 24.775923, 88.310596 24.738802, 88.251749 24.692676, 88.20157 24.638691, 88.161289 24.578185, 88.131891 24.512656, 88.11408299999999 24.443723, 88.10828600000001 24.373089, 88.11462299999999 24.302493, 88.132919 24.233672, 88.162705 24.168317, 88.20323399999999 24.108031, 88.25349900000001 24.054289, 88.31225999999999 24.008407, 88.378074 23.971505, 88.44932799999999 23.944484, 88.524283 23.928004, 88.60111000000001 23.922465, 88.677937 23.928004, 88.752892 23.944484, 88.824146 23.971505, 88.88996 24.008407, 88.94872100000001 24.054289, 88.998986 24.108031, 89.03951499999999 24.168317, 89.069301 24.233672, 89.087597 24.302493, 89.093934 24.373089, 89.088137 24.443723, 89.070329 24.512656, 89.040931 24.578185, 89.00064999999999 24.638691, 88.95047099999999 24.692676, 88.89162399999999 24.738802, 88.82556200000001 24.775923, 88.75391999999999 24.803119, 88.678478 24.819711, 88.60111000000001 24.825288))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005937-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14588134
title: ONCO-360 | DATASUS | INCA | CNES | SIOPS
DOI: 10.15468/dl.zemvcz
title: Occurrence Download

description: A dataset containing 545 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Festuca ovina",
 "Year 1970-2000"
 ]
}

 The dataset includes 545 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005936-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ag2h3b
title: Occurrence Download

description: A dataset containing 51956 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fagopyrum esculentum Moench",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Occurrence evidence)"
 ]
}

 The dataset includes 51956 records from 321 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013773-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57724/jci_20250228_meridian_sf
title: MERIDIAN: Snow fences in Byers Peninsula (Livingston Is.)
DOI: 10.15468/dl.3w6yyx
title: Occurrence Download

description: A dataset containing 139821 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Spain, France, Italy, Portugal, Greece, Morocco)",
 "TaxonKey is Arbutus unedo L."
 ]
}

 The dataset includes 139821 records from 556 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009586-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.561rp
title: Data from: Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): uncovering a history of reticulate evolution and implications for infrageneric classification

description: Reticulate evolution often leads to incongruence between nuclear and
 plastid phylogenies and comparisons between them have been used as a first
 approximation to disentangle patterns of hybridization. Because other
 processes like incomplete lineage sorting and phylogenetic error also
 produce similar incongruence patterns, additional sources of evidence must
 be incorporated. Here we focus on reconstructing the phylogeny of genus
 Lachemilla using nuclear ribosomal ITS and plastid trnL-F DNA sequences,
 and explore widespread patterns of cytonuclear discordance in this group.
 Lachemilla is a highly morphologically variable group of perennial herbs
 and shrubs, and a nearly ubiquitous member of the diverse Neotropical
 high-altitude grasslands. Our analyses identified four major clades within
 Lachemilla that are in part congruent with previous morphological
 classifications of the group. Furthermore, using multiple sources of
 evidence, including a procrustean approach to cophylogeny estimation,
 coalescent-based simulations, phylogenetic networks, chromosome counts,
 and genome size estimations, we also revealed a large-scale pattern of
 incongruence between the plastid and nuclear phylogenies in Lachemilla,
 which is mainly the result of widespread hybridization and polyploidy. We
 also estimated that the origin of Lachemilla in South America (~14.5 mya)
 predates the "rapid-uplift" diversification model that has been
 suggested for other high species-richness Andean plant clades, but
 following the formation of the high-elevation Andean grasslands during the
 last 5 mya, a rapid accumulation of particular nested lineages occurred
 has contributed to the ubiquitous presence of Lachemilla in these biomes.
description: Data_from_Morales-Briones_et_al_Sys_Bio_RETICULATE_HISTORY_OF LACHEMILLAData_from_Morales-Briones_et_al_Sys_Bot_RETICULATE_HISTORY_OF LACHEMILLA.zip