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delay"},{"subject":"survival analysis"},{"subject":"vaccine hesitancy"},{"subject":"vaccine uptake"}],"contributors":[{"name":"Center for Open 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Standard sociodemographic models leave substantial unexplained heterogeneity in vaccination delay: two individuals with identical demographic profiles may exhibit markedly different uptake timing. We hypothesize that this residual reflects structural delay — delay attributable to an individual's embedding in social network clusters where vaccine hesitancy is the norm, consistent with complex contagion theory.\nUsing the secure microdata environment of Statistics Netherlands (CBS), we reconstruct a whole-population multiplex network of approximately 17 million nodes across five administrative layers: household co-residence, family kinship, neighborhood proximity, school co-enrollment, and workplace co-employment. A two-stage analytic pipeline is applied. In Stage 1, a Cox Proportional Hazards model estimates time-to-first-vaccination as a function of individual demographics (age, sex, income, residence area, industry, school denomination, long-term care status), yielding sign-inverted deviance residuals as a continuous measure of structural delay. In Stage 2, node embeddings generated via DeepWalk and post-processed through the DINE interpretability framework are used as predictors in an XGBoost regression of structural delay. Predictive improvement is evaluated by out-of-sample RMSE reduction relative to a demographics-only baseline.\nThree pre-registered hypotheses are tested: (H1) structural delay is non-randomly clustered in the network; (H2) individual delay is positively associated with mean neighbor delay; (H3) this peer association strengthens with degree centrality. Extensive sensitivity analyses address CIMS consent-based missingness, the 4-month post-infection vaccination ineligibility window, and the identification of likely-abroad individuals in the registry.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://osf.io/q9dsz/","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-04-01T23:01:18Z","registered":"2026-04-01T23:01:19Z","published":null,"updated":"2026-04-08T06:57:18Z"},"relationships":{"client":{"data":{"id":"cos.osf","type":"clients"}}}},{"id":"10.15468/83ghy2","type":"dois","attributes":{"doi":"10.15468/83ghy2","identifiers":[{"identifier":"19c11f2a-4d9f-4d43-96c3-661695c4b62f","identifierType":"UUID"}],"creators":[{"name":"Meiling Ge","affiliation":[],"nameIdentifiers":[]},{"name":"Xu, Ningxia","nameType":"Personal","givenName":"Ningxia","familyName":"Xu","affiliation":[],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0009-0008-0975-5588","nameIdentifierScheme":"ORCID"}]},{"name":"Xuying Hu","affiliation":[],"nameIdentifiers":[]},{"name":"Tian, Xin","nameType":"Personal","givenName":"Xin","familyName":"Tian","affiliation":[],"nameIdentifiers":[]},{"name":"Xinlong Li","affiliation":[],"nameIdentifiers":[]},{"name":"Xu, Yu","nameType":"Personal","givenName":"Yu","familyName":"Xu","affiliation":[],"nameIdentifiers":[]},{"name":"Zongling Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Xuelei Zhang","affiliation":[],"nameIdentifiers":[]},{"name":"Xu, Qingzeng","nameType":"Personal","givenName":"Qingzeng","familyName":"Xu","affiliation":[],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-3036-5361","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"Systematics and biogeography of Chrysogorgiidae from the Indian Ocean: discovery of new species on deep-sea ridges"}],"publisher":"Zoosystematics and Evolution","container":{},"publicationYear":2026,"subjects":[{"subject":"Ninetyeast Ridge"},{"subject":"phylogeny"},{"subject":"Chrysogorgiidae"},{"subject":"taxonomy"},{"subject":"Carlsberg Ridge"}],"contributors":[{"name":"Sautter, Guido","nameType":"Personal","givenName":"Guido","familyName":"Sautter","affiliation":[],"contributorType":"RelatedPerson","nameIdentifiers":[]},{"name":"pensoft","affiliation":["Plazi"],"contributorType":"DataCurator","nameIdentifiers":[]}],"dates":[{"date":"2026-04-08","dateType":"Created"},{"date":"2026-04-08","dateType":"Updated"},{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"CHECKLIST","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Zero v1.0 Universal","rightsUri":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc0-1.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This dataset contains the digitized treatments in Plazi based on the original journal article Ge, Meiling, Xu, Ningxia, Hu, Xuying, Tian, Xin, Li, Xinlong, Xu, Yu, Wang, Zongling, Zhang, Xuelei, Xu, Qingzeng (2026): Systematics and biogeography of Chrysogorgiidae from the Indian Ocean: discovery of new species on deep-sea ridges. Zoosystematics and Evolution 102 (2): 621-647, DOI: 10.3897/zse.102.182492AbstractSpecies of the family Chrysogorgiidae are distributed worldwide in deep-sea environments. However, most recorded species of this family were from the Atlantic and Pacific Oceans, with only a few reports from the Indian Ocean, particularly from ridge regions. This study describes three new species and reports two known species from Indian Ocean ridges, integrating morphological and molecular analyses (mtMutS and 28 S rDNA). Chrysogorgia pugnioides Ge, Hu \u0026amp; Xu, sp. nov. is characterized by fist-like polyps; warty spindles in tentacles; flat and irregular spindles and elongate scales in the polyp body wall; and slender and smooth scales with toothed to irregular edges in the coenenchyme. Iridogorgia acutisclerita Ge, Zhang \u0026amp; Xu, sp. nov. resembles I. splendens but differs by possessing needles and pointed elongate scales in the polyp body wall. Iridogorgia levisquama Ge, Zhang \u0026amp; Xu, sp. nov. is differentiated from the congeneric I. squarrosa by slender and smooth scales with sharp ends in the polyp body wall and needles with fine wartiness in the tentacles. Parachrysogorgia chryseis and Metallogorgia melanotrichos are reported as new records for the Indian Ocean ridges. These findings expand the known biodiversity and biogeographic range of Chrysogorgiidae in the Indian Ocean ridges.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://www.gbif.org/dataset/19c11f2a-4d9f-4d43-96c3-661695c4b62f","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-04-08T06:47:00Z","registered":"2026-04-08T06:47:00Z","published":null,"updated":"2026-04-08T06:57:17Z"},"relationships":{"client":{"data":{"id":"gbif.gbif","type":"clients"}}}},{"id":"10.5281/zenodo.19466245","type":"dois","attributes":{"doi":"10.5281/zenodo.19466245","identifiers":[{"identifier":"oai:zenodo.org:19466245","identifierType":"oai"}],"creators":[{"name":"Chen, Shuang","nameType":"Personal","givenName":"Shuang","familyName":"Chen","affiliation":["Independent Scholar"],"nameIdentifiers":[{"nameIdentifier":"0009-0009-1516-1249","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"《山海经》神权空间认知新范式——第35篇:二元神权论视域下隐神-显神执行权划分与世俗权力的关系"},{"lang":"eng","title":"Systematic Reinterpretation of The Classic of Mountains and Seas: The Relationship Between the Division of Executive Power of Hidden Gods and Manifest Gods and Secular Power from the Perspective of Dual Theocracy Theory","titleType":"AlternativeTitle"}],"publisher":"Zenodo","container":{},"publicationYear":2026,"subjects":[{"subject":"Dual Theocracy Theory; Hidden Gods; Manifest Gods; Division of Executive Power; Secular Power; Direction of Productivity"},{"subject":"二元神权论;隐神;显神;执行权划分;世俗权力;生产力方向"}],"contributors":[],"dates":[{"date":"2026-04-08","dateType":"Issued"}],"language":"cmn","types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"CreativeWork","resourceType":"","resourceTypeGeneral":"Preprint"},"relatedIdentifiers":[{"relationType":"IsVersionOf","relatedIdentifier":"10.5281/zenodo.19466244","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution Non Commercial No Derivatives 4.0 International","rightsUri":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-nc-nd-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"Copyright (C) 2026 Chen Shuang.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"本文是《山海经》神权空间认知新范式系列研究的第35篇。二元神权论的核心是神权体系内部存在隐神与显神的二元划分。本文在二元神权论框架内,进一步明确:隐神与显神的早期区分,本质是“执行权”的划分。隐神掌握分配权(不做事),显神掌握执行权(做事)。显神在执行的过程中,必然要接触世俗。管事就有世俗权力。所以显神的权力必然带有世俗权力的色彩,而且是很大一部分。世俗权力不是从哪里“起源”的,它天生就有。本文认为,执行权的划分是理解神权与世俗权力关系的关键。三星堆与颛顼(陶寺)代表了执行权划分的两种路径:前者将生产力导向神权建设,后者将生产力导向世俗治理。两种路径的区别不是制度优劣,而是生产力方向不同。西方学界长期局限于神圣—世俗外部二分框架,未能揭示神权内部的执行权分化。本文以二元神权论突破这一局限,为理解早期神权与世俗权力的内生关系提供全新本土解释路径。\n\n \n\n \n\nThis manuscript is one of the serial research results on the systematic reinterpretation of The Classic of Mountains and Seas from the perspective of interdisciplinary integration of paleography, archaeology and ancient political system research. It is the 35th paper in the series “A New Paradigm of Theocratic Spatial Cognition in The Classic of Mountains and Seas.”\n\n \n\nThe core of Dual Theocracy Theory is the binary division between Hidden Gods and Manifest Gods within the theocratic system. This paper further clarifies that the early distinction between Hidden Gods and Manifest Gods is essentially the division of “executive power”. Hidden Gods hold the power of distribution (do not act), while Manifest Gods hold the power of execution (act). In the process of execution, Manifest Gods inevitably come into contact with the secular world. Whoever manages affairs has secular power. Therefore, the power of Manifest Gods necessarily carries the color of secular power, and to a large extent. Secular power does not have an external “origin”; it is innate. This paper argues that the division of executive power is the key to understanding the relationship between theocratic power and secular power. Sanxingdui and Zhuanxu (Taosi) represent two different paths of executive power division: the former oriented productivity toward theocratic construction, the latter oriented productivity toward secular governance. The difference between the two paths is not the superiority or inferiority of institutions, but the different directions of productivity. Western academia has long been confined to the external sacred/secular dichotomy, failing to reveal the division of executive power within the theocracy. This paper breaks through this limitation with Dual Theocracy Theory, providing a new indigenous interpretation path for understanding the endogenous relationship between early theocratic power and secular power.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19466245","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2026-04-08T06:57:07Z","registered":"2026-04-08T06:57:07Z","published":null,"updated":"2026-04-08T06:57:07Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.19466244","type":"dois","attributes":{"doi":"10.5281/zenodo.19466244","identifiers":[],"creators":[{"name":"Chen, Shuang","nameType":"Personal","givenName":"Shuang","familyName":"Chen","affiliation":["Independent Scholar"],"nameIdentifiers":[{"nameIdentifier":"0009-0009-1516-1249","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"《山海经》神权空间认知新范式——第35篇:二元神权论视域下隐神-显神执行权划分与世俗权力的关系"},{"lang":"eng","title":"Systematic Reinterpretation of The Classic of Mountains and Seas: The Relationship Between the Division of Executive Power of Hidden Gods and Manifest Gods and Secular Power from the Perspective of Dual Theocracy Theory","titleType":"AlternativeTitle"}],"publisher":"Zenodo","container":{},"publicationYear":2026,"subjects":[{"subject":"Dual Theocracy Theory; Hidden Gods; Manifest Gods; Division of Executive Power; Secular Power; Direction of Productivity"},{"subject":"二元神权论;隐神;显神;执行权划分;世俗权力;生产力方向"}],"contributors":[],"dates":[{"date":"2026-04-08","dateType":"Issued"}],"language":"cmn","types":{"ris":"GEN","bibtex":"misc","citeproc":"article","schemaOrg":"CreativeWork","resourceType":"","resourceTypeGeneral":"Preprint"},"relatedIdentifiers":[{"relationType":"HasVersion","relatedIdentifier":"10.5281/zenodo.19466245","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution Non Commercial No Derivatives 4.0 International","rightsUri":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-nc-nd-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"Copyright (C) 2026 Chen Shuang.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"本文是《山海经》神权空间认知新范式系列研究的第35篇。二元神权论的核心是神权体系内部存在隐神与显神的二元划分。本文在二元神权论框架内,进一步明确:隐神与显神的早期区分,本质是“执行权”的划分。隐神掌握分配权(不做事),显神掌握执行权(做事)。显神在执行的过程中,必然要接触世俗。管事就有世俗权力。所以显神的权力必然带有世俗权力的色彩,而且是很大一部分。世俗权力不是从哪里“起源”的,它天生就有。本文认为,执行权的划分是理解神权与世俗权力关系的关键。三星堆与颛顼(陶寺)代表了执行权划分的两种路径:前者将生产力导向神权建设,后者将生产力导向世俗治理。两种路径的区别不是制度优劣,而是生产力方向不同。西方学界长期局限于神圣—世俗外部二分框架,未能揭示神权内部的执行权分化。本文以二元神权论突破这一局限,为理解早期神权与世俗权力的内生关系提供全新本土解释路径。\n\n \n\n \n\nThis manuscript is one of the serial research results on the systematic reinterpretation of The Classic of Mountains and Seas from the perspective of interdisciplinary integration of paleography, archaeology and ancient political system research. It is the 35th paper in the series “A New Paradigm of Theocratic Spatial Cognition in The Classic of Mountains and Seas.”\n\n \n\nThe core of Dual Theocracy Theory is the binary division between Hidden Gods and Manifest Gods within the theocratic system. This paper further clarifies that the early distinction between Hidden Gods and Manifest Gods is essentially the division of “executive power”. Hidden Gods hold the power of distribution (do not act), while Manifest Gods hold the power of execution (act). In the process of execution, Manifest Gods inevitably come into contact with the secular world. Whoever manages affairs has secular power. Therefore, the power of Manifest Gods necessarily carries the color of secular power, and to a large extent. Secular power does not have an external “origin”; it is innate. This paper argues that the division of executive power is the key to understanding the relationship between theocratic power and secular power. Sanxingdui and Zhuanxu (Taosi) represent two different paths of executive power division: the former oriented productivity toward theocratic construction, the latter oriented productivity toward secular governance. The difference between the two paths is not the superiority or inferiority of institutions, but the different directions of productivity. Western academia has long been confined to the external sacred/secular dichotomy, failing to reveal the division of executive power within the theocracy. This paper breaks through this limitation with Dual Theocracy Theory, providing a new indigenous interpretation path for understanding the endogenous relationship between early theocratic power and secular power.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19466244","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":1,"versionOfCount":0,"created":"2026-04-08T06:57:07Z","registered":"2026-04-08T06:57:07Z","published":null,"updated":"2026-04-08T06:57:07Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.18096396","type":"dois","attributes":{"doi":"10.5281/zenodo.18096396","identifiers":[],"creators":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["Aurora initiative"],"nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"AURORA: A Conceptual Supervisory Architecture for the Control and Oversight of Intelligent Operating Systems."}],"publisher":"Zenodo","container":{},"publicationYear":2025,"subjects":[{"subject":"AI Safety, Supervisory Matrix"},{"subject":"Digital Conscience"},{"subject":"AI Governance"},{"subject":"Intelligent Operating"}],"contributors":[],"dates":[{"date":"2025-12-30","dateType":"Issued"},{"date":"2025-12-30","dateType":"Created","dateInformation":"The theoretical and conceptual part has been fully completed."}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"HasVersion","relatedIdentifier":"10.5281/zenodo.18096397","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"© Mostafa Abd Elsamie Abd El All Mohamed - 2025. All rights reserved.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"ntroduction: The Imperative for Autonomous Supervision in the Age of Intelligent Operating SystemsAs Artificial Intelligence (AI) transitions from narrow task-specific applications to highly autonomous Intelligent Operating Systems (IOS), the global community faces an unprecedented governance challenge. The rapid evolution of these systems has outpaced traditional regulatory frameworks, leading to what pioneers in the field describe as a \"loss of control\" or the \"black-box\" dilemma—where system outputs are logically consistent but fundamentally uninterpretable and unconstrained by human values.The AURORA Framework (Supervision and Control of Intelligent Operating Systems) emerges from a profound sense of social and technical responsibility. It addresses the critical gap between the accelerating intelligence of autonomous systems and the lagging mechanisms of human oversight. This research posits that for AI to be truly beneficial and safe, supervision must be an independent, parallel, and immutable layer that constrains risk without stifling the system's operational intelligence.At its core, AURORA is built upon the principle of Architectural Separation of Concerns. It moves beyond reactive monitoring to a proactive, multi-layered \"Supervisory Matrix\" consisting of 13 modular innovations. These range from predictive behavioral drift detection and tamper-proof distributed logging to the integration of a \"Digital Conscience Kernel\" that enforces ethical and legal constraints in real-time.This work is not merely a technical proposal; it is a conceptual bridge between the social sciences and advanced systems engineering. By encoding human values, legal constitutions, and ethical principles into a machine-enforceable architecture, AURORA provides a roadmap for a future where intelligent systems operate within a verifiable and accountable framework. This research serves as a foundational blueprint for developers, regulators, and stakeholders to ensure that the trajectory of autonomous intelligence remains aligned with human safety and societal integrity.\n\n \n\nThis research is the result of an independent, self-funded effort by Mostafa abd elsamie abd elall Mohamed, a social worker and researcher specializing in the intersection of technology and society. While the complexity of this architectural framework may seem unconventional for a social science background, it is rooted in the core mission of Social Work: the study and protection of the individual as the fundamental building block of society.potential loss of control over autonomous systems, the author felt a profound professional and ethical responsibility to act. In social sciences, any force that fundamentally alters human behavior or societal structures must be understood and governed. Therefore, rather than remaining a passive observer of the accelerating AI trajectory, the author leveraged his unique perspective on human values and social integrity to design a system that prioritizes safety and oversight.research laboratory, not a physical, technical, or experimental facility. It serves as a dedicated space for the development of high-level architectural blueprints and governance frameworks. This work represents a complete conceptual milestone, offered to the global scientific community as a foundation for future technical implementation and collaborative validation.\n\nALEXANDERIA UNIVERSITY \n\nTHE Higher Institute of Social work, Alexandria \n\nAURORA INITIATIVE \n\nEMIAL [ mostafasamy3021@gmail.com]\n\nMostafa abd elsamie abd elall Mohamed.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.18096396","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":1,"versionOfCount":0,"created":"2025-12-30T14:27:47Z","registered":"2025-12-30T14:27:47Z","published":null,"updated":"2026-04-08T06:56:58Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.18096397","type":"dois","attributes":{"doi":"10.5281/zenodo.18096397","identifiers":[{"identifier":"oai:zenodo.org:18096397","identifierType":"oai"}],"creators":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["Aurora initiative"],"nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"AURORA: A Conceptual Supervisory Architecture for the Control and Oversight of Intelligent Operating Systems."}],"publisher":"Zenodo","container":{},"publicationYear":2025,"subjects":[{"subject":"AI Safety, Supervisory Matrix"},{"subject":"Digital Conscience"},{"subject":"AI Governance"},{"subject":"Intelligent Operating"}],"contributors":[],"dates":[{"date":"2025-12-30","dateType":"Issued"},{"date":"2025-12-30","dateType":"Created","dateInformation":"The theoretical and conceptual part has been fully completed."}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsVersionOf","relatedIdentifier":"10.5281/zenodo.18096396","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"© Mostafa Abd Elsamie Abd El All Mohamed - 2025. All rights reserved.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"ntroduction: The Imperative for Autonomous Supervision in the Age of Intelligent Operating SystemsAs Artificial Intelligence (AI) transitions from narrow task-specific applications to highly autonomous Intelligent Operating Systems (IOS), the global community faces an unprecedented governance challenge. The rapid evolution of these systems has outpaced traditional regulatory frameworks, leading to what pioneers in the field describe as a \"loss of control\" or the \"black-box\" dilemma—where system outputs are logically consistent but fundamentally uninterpretable and unconstrained by human values.The AURORA Framework (Supervision and Control of Intelligent Operating Systems) emerges from a profound sense of social and technical responsibility. It addresses the critical gap between the accelerating intelligence of autonomous systems and the lagging mechanisms of human oversight. This research posits that for AI to be truly beneficial and safe, supervision must be an independent, parallel, and immutable layer that constrains risk without stifling the system's operational intelligence.At its core, AURORA is built upon the principle of Architectural Separation of Concerns. It moves beyond reactive monitoring to a proactive, multi-layered \"Supervisory Matrix\" consisting of 13 modular innovations. These range from predictive behavioral drift detection and tamper-proof distributed logging to the integration of a \"Digital Conscience Kernel\" that enforces ethical and legal constraints in real-time.This work is not merely a technical proposal; it is a conceptual bridge between the social sciences and advanced systems engineering. By encoding human values, legal constitutions, and ethical principles into a machine-enforceable architecture, AURORA provides a roadmap for a future where intelligent systems operate within a verifiable and accountable framework. This research serves as a foundational blueprint for developers, regulators, and stakeholders to ensure that the trajectory of autonomous intelligence remains aligned with human safety and societal integrity.\n\n \n\nThis research is the result of an independent, self-funded effort by Mostafa abd elsamie abd elall Mohamed, a social worker and researcher specializing in the intersection of technology and society. While the complexity of this architectural framework may seem unconventional for a social science background, it is rooted in the core mission of Social Work: the study and protection of the individual as the fundamental building block of society.potential loss of control over autonomous systems, the author felt a profound professional and ethical responsibility to act. In social sciences, any force that fundamentally alters human behavior or societal structures must be understood and governed. Therefore, rather than remaining a passive observer of the accelerating AI trajectory, the author leveraged his unique perspective on human values and social integrity to design a system that prioritizes safety and oversight.research laboratory, not a physical, technical, or experimental facility. It serves as a dedicated space for the development of high-level architectural blueprints and governance frameworks. This work represents a complete conceptual milestone, offered to the global scientific community as a foundation for future technical implementation and collaborative validation.\n\nALEXANDERIA UNIVERSITY \n\nTHE Higher Institute of Social work, Alexandria \n\nAURORA INITIATIVE \n\nEMIAL [ mostafasamy3021@gmail.com]\n\nMostafa abd elsamie abd elall Mohamed.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.18096397","contentUrl":null,"metadataVersion":3,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2025-12-30T14:27:47Z","registered":"2025-12-30T14:27:47Z","published":null,"updated":"2026-04-08T06:56:57Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.25919/thns-7d07","type":"dois","attributes":{"doi":"10.25919/thns-7d07","identifiers":[{"identifier":"csiro:73993","identifierType":"FedoraID"}],"creators":[{"name":"Lower, Marcus","nameType":"Personal","givenName":"Marcus","familyName":"Lower","affiliation":["Swinburne University of Technology, Australia"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0001-9208-0009","nameIdentifierScheme":"ORCID"}]},{"name":"Manchester, Dick","nameType":"Personal","givenName":"Dick","familyName":"Manchester","affiliation":["CSIRO Australia Telescope National Facility, Australia"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0001-9445-5732","nameIdentifierScheme":"ORCID"}]},{"name":"Dawson, Joanne","nameType":"Personal","givenName":"Joanne","familyName":"Dawson","affiliation":["Macquarie University, Australia"],"nameIdentifiers":[]},{"name":"Johnston, Simon","nameType":"Personal","givenName":"Simon","familyName":"Johnston","affiliation":["CSIRO Australia Telescope National Facility, Australia"],"nameIdentifiers":[]},{"name":"Weltevrede, Patrick","nameType":"Personal","givenName":"Patrick","familyName":"Weltevrede","affiliation":["University of Manchester, United Kingdom"],"nameIdentifiers":[]},{"name":"Kerr, Matthew","nameType":"Personal","givenName":"Matthew","familyName":"Kerr","affiliation":["Naval Research Laboratories, United States"],"nameIdentifiers":[]},{"name":"Shannon, Ryan","nameType":"Personal","givenName":"Ryan","familyName":"Shannon","affiliation":["Swinburne University of Technology, Australia"],"nameIdentifiers":[]},{"name":"Dai, Shi","nameType":"Personal","givenName":"Shi","familyName":"Dai","affiliation":["CSIRO Space and Astronomy, Australia"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0002-9618-2499","nameIdentifierScheme":"ORCID"}]},{"name":"Sobey, Charlotte","nameType":"Personal","givenName":"Charlotte","familyName":"Sobey","affiliation":["CSIRO Space and Astronomy, Australia"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0002-8950-7873","nameIdentifierScheme":"ORCID"}]},{"name":"Oswald, Lucy","nameType":"Personal","givenName":"Lucy","familyName":"Oswald","affiliation":["University of Oxford, United Kingdom"],"nameIdentifiers":[]},{"name":"Parthasarathy, Aditya","nameType":"Personal","givenName":"Aditya","familyName":"Parthasarathy","affiliation":["Max Planck Inst. fuer Radioastronomie, Bonn, Germany"],"nameIdentifiers":[]},{"name":"Roch, Sparrow","nameType":"Personal","givenName":"Sparrow","familyName":"Roch","affiliation":["Swinburne University of Technology, Australia"],"nameIdentifiers":[]},{"name":"Melfor, Selah","nameType":"Personal","givenName":"Selah","familyName":"Melfor","affiliation":["ASTRON, Netherlands"],"nameIdentifiers":[]},{"name":"Latkoczyova, Kristina","nameType":"Personal","givenName":"Kristina","familyName":"Latkoczyova","affiliation":["University of Southampton, United Kingdom"],"nameIdentifiers":[]}],"titles":[{"title":"Long-term project observations for project L100 semester 2026APRS_01"}],"publisher":"CSIRO","container":{},"publicationYear":2026,"subjects":[{"subjectScheme":"ANZSRC","classificationCode":"510199"}],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["56.15 GB"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"We request time to observe 270 pulsars on a regular basis in order to achieve three main science goals. The first is to understand pulsars: how do they spin down and what disrupts this process, how and why their profiles vary with time, whether they precess or have planetary mass companions, in short all the things that make pulsar timing noisier than the perfect clock. Secondly we want to understand the interstellar medium of our Galaxy through repeated monitoring of dispersion measure, rotation measure and flux density variations in conjunction with scintillation parameters. Finally, we provide these data as a community service both to the high-energy community where we have strong collaborative links (particularly to Fermi) and to the radio pulsar astronomers generally through the CSIRO archive. The project is on-going since 2007, we are (co-)authors on 107 papers arising from the P574 data. The data have contributed to the PhD theses of students from Bordeaux, Manchester, Oxford, Stanford, and Swinburne. We are seeking long-term project status with a view to continuing the project into the SKA era.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://data.csiro.au/collection/csiro%3A73993v1","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-04-08T06:56:54Z","registered":"2026-04-08T06:56:55Z","published":null,"updated":"2026-04-08T06:56:55Z"},"relationships":{"client":{"data":{"id":"csiro.repo","type":"clients"}}}},{"id":"10.5281/zenodo.19432553","type":"dois","attributes":{"doi":"10.5281/zenodo.19432553","identifiers":[],"creators":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["AURORA RESEARCH INITIATIVE"],"nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"AURORA _ One Body_An Integrated Theoretical and Technical Framework for the Governance of Intelligent Operating Systems"}],"publisher":"Zenodo","container":{},"publicationYear":2026,"subjects":[{"subject":"AI Governinc"},{"subject":"AI safety"},{"subject":"AI Ethics"},{"subject":"Social technology research"},{"subject":"Socio-tecnology"},{"subject":"Social worker"},{"subject":"Higher institute of social work, alexanderia"}],"contributors":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["AURORA RESEARCH INITIATIVE"],"contributorType":"RightsHolder","nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"dates":[{"date":"2026-04-05","dateType":"Issued"}],"language":null,"types":{"ris":"THES","bibtex":"phdthesis","citeproc":"thesis","schemaOrg":"Thesis","resourceType":"","resourceTypeGeneral":"Dissertation"},"relatedIdentifiers":[{"relationType":"HasVersion","relatedIdentifier":"10.5281/zenodo.19432554","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"© Mostafa Abd Elsamie Abd El All Mohamed - 2026. All rights reserved.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"AURORA – ONE BODY\n\nAn Integrated Theoretical and Technical Framework for Embedded Governance of Intelligent Operating Systems\n\nAuthor: Mostafa Abd Elsamie Abd Elall MohammadDate: April 2026Version: 1.0\n\n---\n\nIntroduction \n\nThis compendium presents the complete specification of AURORA, a first‑of‑its‑kind, four‑layer supervisory architecture for the embedded governance of Intelligent Operating Systems (IOS) . Unlike traditional oversight mechanisms that remain external and reactive, AURORA integrates supervision as a structural architectural layer – operating continuously, proportionally, and accountably at machine speed.\n\nGrounded in Risk Society Theory (Beck) , Actor‑Network Theory (Latour) , and Socio‑Technical Systems Theory, the framework addresses the fundamental governance gap across three dimensions: scale (millions of concurrent decisions), speed (millisecond cycles), and structural opacity (non‑interpretable logic). The AURORA architecture closes this gap through 24 modular innovations distributed across four hierarchical layers:\n\n· Layer 1 (Sensory): Data collection, traceability, and immutable logging (DTL, IBTL, DAL)· Layer 2 (Analytical): Detection, correlation, and risk assessment (BDDM, MACE, CARCE, ADF, RFADA, TDIMS)· Layer 3 (Governance): Policy application, ethics, and legal compliance (PTDM, SIT, CECM, DCK, ACEE, ACTS, AVCS)· Layer 4 (Enforcement): Action control, containment, and human oversight (CAAA, PCGD, DCU, HILOA, HOGD, KSLC, AFAS, AAISS)\n\nEach innovation is specified with core functionality, operational logic, pseudocode, dependencies, and measurable performance targets. The compendium includes theoretical foundations, scope definitions, architectural specifications, a complete supervisory matrix, practical deployment guidelines, and a compliance dossier aligned with ISO/IEC 42001:2023, NIST AI RMF 1.0, and IEEE 7000.\n\nTarget audience: AI governance researchers, autonomous systems engineers, regulatory bodies, and compliance professionals.\n\nOriginal work. Sole author. Not previously published.\n\n---\n\nQuick Metadata for Zenodo Upload\n\nField ValueTitle AURORA – One Body: An Integrated Theoretical and Technical Framework for Embedded Governance of Intelligent Operating SystemsAuthor Mostafa Abd Elsamie Abd Elall MohammadPublication Date 2026-04-05Version 1.0Language EnglishLicense CC BY‑NC‑ND 4.0 (or as preferred)Keywords AI governance, intelligent operating systems, supervisory architecture, embedded supervision, risk society theory, ISO/IEC 42001, NIST AI RMF, autonomous systems, ethical AI, kill‑switch, accountability logging, behavioral drift detection","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19432553","contentUrl":null,"metadataVersion":9,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":1,"versionOfCount":0,"created":"2026-04-05T21:55:51Z","registered":"2026-04-05T21:55:51Z","published":null,"updated":"2026-04-08T06:56:02Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.19432554","type":"dois","attributes":{"doi":"10.5281/zenodo.19432554","identifiers":[{"identifier":"oai:zenodo.org:19432554","identifierType":"oai"}],"creators":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["AURORA RESEARCH INITIATIVE"],"nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"AURORA _ One Body_An Integrated Theoretical and Technical Framework for the Governance of Intelligent Operating Systems"}],"publisher":"Zenodo","container":{},"publicationYear":2026,"subjects":[{"subject":"AI Governinc"},{"subject":"AI safety"},{"subject":"AI Ethics"},{"subject":"Social technology research"},{"subject":"Socio-tecnology"},{"subject":"Social worker"},{"subject":"Higher institute of social work, alexanderia"}],"contributors":[{"name":"abd elall, Mostafa abd elsamie","nameType":"Personal","givenName":"Mostafa abd elsamie","familyName":"abd elall","affiliation":["AURORA RESEARCH INITIATIVE"],"contributorType":"RightsHolder","nameIdentifiers":[{"nameIdentifier":"0009-0002-2948-9092","nameIdentifierScheme":"ORCID"}]}],"dates":[{"date":"2026-04-05","dateType":"Issued"}],"language":null,"types":{"ris":"THES","bibtex":"phdthesis","citeproc":"thesis","schemaOrg":"Thesis","resourceType":"","resourceTypeGeneral":"Dissertation"},"relatedIdentifiers":[{"relationType":"IsVersionOf","relatedIdentifier":"10.5281/zenodo.19432553","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"},{"rights":"© Mostafa Abd Elsamie Abd El All Mohamed - 2026. All rights reserved.","rightsUri":"http://rightsstatements.org/vocab/InC/1.0/"}],"descriptions":[{"description":"AURORA – ONE BODY\n\nAn Integrated Theoretical and Technical Framework for Embedded Governance of Intelligent Operating Systems\n\nAuthor: Mostafa Abd Elsamie Abd Elall MohammadDate: April 2026Version: 1.0\n\n---\n\nIntroduction \n\nThis compendium presents the complete specification of AURORA, a first‑of‑its‑kind, four‑layer supervisory architecture for the embedded governance of Intelligent Operating Systems (IOS) . Unlike traditional oversight mechanisms that remain external and reactive, AURORA integrates supervision as a structural architectural layer – operating continuously, proportionally, and accountably at machine speed.\n\nGrounded in Risk Society Theory (Beck) , Actor‑Network Theory (Latour) , and Socio‑Technical Systems Theory, the framework addresses the fundamental governance gap across three dimensions: scale (millions of concurrent decisions), speed (millisecond cycles), and structural opacity (non‑interpretable logic). The AURORA architecture closes this gap through 24 modular innovations distributed across four hierarchical layers:\n\n· Layer 1 (Sensory): Data collection, traceability, and immutable logging (DTL, IBTL, DAL)· Layer 2 (Analytical): Detection, correlation, and risk assessment (BDDM, MACE, CARCE, ADF, RFADA, TDIMS)· Layer 3 (Governance): Policy application, ethics, and legal compliance (PTDM, SIT, CECM, DCK, ACEE, ACTS, AVCS)· Layer 4 (Enforcement): Action control, containment, and human oversight (CAAA, PCGD, DCU, HILOA, HOGD, KSLC, AFAS, AAISS)\n\nEach innovation is specified with core functionality, operational logic, pseudocode, dependencies, and measurable performance targets. The compendium includes theoretical foundations, scope definitions, architectural specifications, a complete supervisory matrix, practical deployment guidelines, and a compliance dossier aligned with ISO/IEC 42001:2023, NIST AI RMF 1.0, and IEEE 7000.\n\nTarget audience: AI governance researchers, autonomous systems engineers, regulatory bodies, and compliance professionals.\n\nOriginal work. Sole author. Not previously published.\n\n---\n\nQuick Metadata for Zenodo Upload\n\nField ValueTitle AURORA – One Body: An Integrated Theoretical and Technical Framework for Embedded Governance of Intelligent Operating SystemsAuthor Mostafa Abd Elsamie Abd Elall MohammadPublication Date 2026-04-05Version 1.0Language EnglishLicense CC BY‑NC‑ND 4.0 (or as preferred)Keywords AI governance, intelligent operating systems, supervisory architecture, embedded supervision, risk society theory, ISO/IEC 42001, NIST AI RMF, autonomous systems, ethical AI, kill‑switch, accountability logging, behavioral drift detection","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19432554","contentUrl":null,"metadataVersion":9,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2026-04-05T21:55:50Z","registered":"2026-04-05T21:55:51Z","published":null,"updated":"2026-04-08T06:56:01Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.58132/gqccqt","type":"dois","attributes":{"doi":"10.58132/gqccqt","identifiers":[],"creators":[{"name":"Ko, Gabriel","nameType":"Personal","givenName":"Gabriel","familyName":"Ko","affiliation":["University of Warsaw"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0001-7266-5739","nameIdentifierScheme":"ORCID"}]},{"name":"Krokosz, Wiktor","nameType":"Personal","givenName":"Wiktor","familyName":"Krokosz","affiliation":["University of Warsaw"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0002-9958-0214","nameIdentifierScheme":"ORCID"}]},{"name":"Mazelanik, Mateusz","nameType":"Personal","givenName":"Mateusz","familyName":"Mazelanik","affiliation":["University of Warsaw"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0001-5498-7486","nameIdentifierScheme":"ORCID"}]},{"name":"Wasilewski, Wojciech","nameType":"Personal","givenName":"Wojciech","familyName":"Wasilewski","affiliation":["University of Warsaw"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-3030-3187","nameIdentifierScheme":"ORCID"}]},{"name":"Parniak, Michał","nameType":"Personal","givenName":"Michał","familyName":"Parniak","affiliation":["University of Warsaw"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0002-6849-4671","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"Replication data for: Calibrated electric-field imaging with Rydberg-state fluorescence and Autler-Townes splitting"}],"publisher":"Dane Badawcze UW","container":{},"publicationYear":2026,"subjects":[],"contributors":[{"name":"Krokosz, Wiktor","nameType":"Personal","givenName":"Wiktor","familyName":"Krokosz","affiliation":["University of Warsaw"],"contributorType":"ContactPerson","nameIdentifiers":[]}],"dates":[{"date":"2026","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[{"description":"Data StructureReplication data for said article is provided in the form of a HDF5 file with the NetCDF4 file format. This choice allows us to embed the metadata and hierarchical structure right within the dataset. The data is best read with the use of the `xarray` Python library, with minimal examples below showcasing usage and code segments for replicating article plots.DependenciesPythonnumpymatplotlibxarraycolorcetlmfitUsageAs mentioned, the data structure has been carefully prepared for top transparency and ease of exploration in mind. Its loading can be done as follows:import xarray as xrdt = xr.open_datatree(\"ARTICLE_DATA.h5\")print(dt)and gives us an immediate overview of the entire data structure:Group: /├── Group: /HWP│    Dimensions:       (θ: 8, z: 3420, uncertainty: 2, Δ1269: 80)│    Coordinates:│     * θ          (θ) int64 64B -24 -12 0 12 24 36 48 60│     * z          (z) float64 27kB -19.3 -19.29 -19.28 ... 18.79 18.8│     * uncertainty     (uncertainty) int64 16B 0 1│     * Δ1269        (Δ1269) float64 640B -58.5 -57.0 -55.5 ... 58.5 60.0│    Data variables:│      Rabi Fits      (θ, z, uncertainty) float64 438kB ...│      Points to Evaluate (z) float64 27kB ...│      Fluorescence    (θ, Δ1269, z) uint16 4MB ...└── Group: /REFLECTOR    Dimensions:    (mirror_d: 14, z: 3420, uncertainty: 2, Δ1269: 80)    Coordinates:     * mirror_d   (mirror_d) float64 112B -1.2 -0.9 -0.45 -0.3 ... 0.9 1.05 1.2     * z       (z) float64 27kB -19.3 -19.29 -19.28 ... 18.77 18.79 18.8     * uncertainty  (uncertainty) int64 16B 0 1     * Δ1269     (Δ1269) float64 640B -58.5 -57.0 -55.5 ... 57.0 58.5 60.0    Data variables:      Rabi Fits   (mirror_d, z, uncertainty) float64 766kB ...      Fluorescence (mirror_d, Δ1269, z) float32 15MB ...In interactive environments, for example a Jupyter notebook, the data structure features rich HTML previews with interacting controls, making this a recommended environment for processing the attached dataset.The HWP group features a dataset with fluorescence data for half waveplate attenuated measurements. This includes both the fluorescence data from the camera, after dark count subtraction and vertical averaging, as well as master equation Rabi fits results performed with the methodology from the article. The fits have and added uncertainty flag dimension, as we store both the nominal value as well as its uncertainty obtained from the fit.Similarily, the REFLECTOR group contains analogus data, but with the HIPS mirror position being varied instead of the half waveplate angle.All of the parameters are preserved as Xarray coordinates, with long names and units for plotting.Importsimport matplotlib.pyplot as pltimport matplotlib as mplimport numpy as npimport xarray as xrfrom lmfit import Model, Parameters, minimizedt = xr.open_datatree(\"ARTICLE_DATA.h5\")Figure 3 plotpoints_to_evaluate = dt[\"HWP/Points to Evaluate\"].dropna(\"z\")dt[\"HWP/Rabi Fits\"].sel(uncertainty=0, z=slice(-15, 15)).plot.line(hue=\"θ\")for z in points_to_evaluate: plt.axvline(z.item())plt.show()Figure 4 plotThis example showcases also the multifit of a composite model. As described in the article, the model components share all parameters apart from the scaling so a custom objective function is required.points_to_evaluate = dt[\"HWP/Points to Evaluate\"].dropna(\"z\")da_at_points = dt[\"HWP/Rabi Fits\"].sel(z=points_to_evaluate).isel(uncertainty=0)err_at_points = dt[\"HWP/Rabi Fits\"].sel(z=points_to_evaluate).isel(uncertainty=1)def objective(params: Parameters, da: xr.DataArray, err_da: xr.DataArray, model: Model): \"\"\"Calculate total residual for fits of a model sum to several data sets.\"\"\" resid = xr.zeros_like(da) # make residual per data set for i in range(da.z.size): components = model.components[i].eval(params=params, angle=da.θ.values) resid.isel(z=i).values[:] = (da.isel(z=i).values - components) / err_da.isel( z=i ).values # now flatten this to a 1D array, as minimize() needs return resid.values.flatten()def hwp_sine(angle, amplitude, shift, c): return amplitude * (np.sin(4 * np.deg2rad(angle) + shift) + c)model_arr = [Model(hwp_sine, prefix=f\"z{i}_\") for i in range(da_at_points.z.size)]model = sum(model_arr[1:], start=model_arr[0])fit_params = model.make_params()for i in range(da_at_points.z.size): fit_params.add( f\"z{i}_amplitude\", value=( da_at_points.isel(z=i).max().item() - da_at_points.isel(z=i).min().item() ) / 2, ) if i == 0: fit_params.add(f\"z{i}_shift\", value=1.93) fit_params.add( f\"z{i}_c\", value=3.5, # vary=False, ) else: fit_params.add(f\"z{i}_shift\", expr=\"z0_shift\") fit_params.add(f\"z{i}_c\", expr=\"z0_c\")out = minimize( objective, fit_params, args=( da_at_points, err_at_points, model, ), nan_policy=\"omit\",)hwp_space = np.linspace(da_at_points.θ.min().item(), da_at_points.θ.max().item(), 200)components = model.eval_components(params=out.params, angle=hwp_space) for i in range(da_at_points.z.size): color = mpl.rcParams[\"axes.prop_cycle\"].by_key()[\"color\"][i % len(mpl.rcParams[\"axes.prop_cycle\"])] plt.plot( hwp_space, components[f\"z{i}_\"], color=color, ) plt.errorbar( da_at_points.θ, da_at_points.isel(z=i), yerr=err_at_points.isel(z=i), fmt=\".\", label=f\"z={da_at_points.z.isel(z=i).item():.2f} mm\", markersize=5, ecolor=\"grey\", elinewidth=1, capsize=2, color=color, )plt.legend(title=r\"$\\mathcal{R}(θ, z)$ [MHz]\")plt.xlabel(r\"HWP Angle $\\Theta$ [deg]\")plt.ylabel(r\"$\\hat\\mathcal{R}(θ, z)$ [MHz]\")plt.show()Figure 5This code cell needs to be executed after figure 4 as it reuses the fit data.for i in range(da_at_points.z.size): plt.plot( sorted( model.components[i].eval(params=out.params, angle=da_at_points.θ.values) ), sorted(da_at_points.isel(z=i).values), label=f\"z={da_at_points.z.isel(z=i).item():.2f} mm\", )plt.legend()plt.show()Figure 6fig, axs = plt.subplots( nrows=2, ncols=2, sharey=\"row\", sharex=True, height_ratios=[1, 1], layout=\"constrained\",)# Pick mirror positions to plotds_min = dt[\"REFLECTOR\"].sel(mirror_d=1.05)ds_max = dt[\"REFLECTOR\"].sel(mirror_d=-0.3)for i, ds in enumerate([ds_min, ds_max]): fax, eax = axs.T[i] # Fluorescence map pcm = ds[\"Fluorescence\"].plot.imshow( ax=fax, interpolation=\"nearest\", add_colorbar=False, cmap=cm.rainbow4 ) fax.set_xlabel(\"\") # AT fits eax.errorbar( ds.z, ds[\"Rabi Fits\"].sel(uncertainty=0), yerr=ds[\"Rabi Fits\"].sel(uncertainty=1), label=\"Rabi fit\", ) eax.set_xlabel(\"Distance from camera focus point [mm]\") axs.T[i][0].set_title(f\"HIPS mirror position: {ds.mirror_d.item():.2f} mm\")fig.colorbar(pcm, ax=axs[0, :], label=\"Fluorescence [a.u.]\")axs[1, 0].set_ylabel(r\"$\\Omega_{\\text{mm}}$ [MHz]\")axs[0, 1].set_ylabel(\"\")axs[1, 0].legend()fig.show()Figure 7mirror_slice = dt[\"REFLECTOR/Rabi Fits\"].sel(mirror_d=[-0.3, 0.9, 1.2], uncertainty=0)mirror_slice.plot.line(x=\"z\", hue=\"mirror_d\")plt.show()FundingThis research was funded in whole or in part by National Science Centre, Poland grants No. 2021/43/D/ST2/03114 and No. 2024/53/N/ST7/02730. The \"Quantum Optical Technologies\" (FENG.02.01-IP.05-0017/23) project is carried out within the Measure 2.1 International Research Agendas programme of the Foundation for Polish Science co-financed by the European Union under the European Funds for Smart Economy 2021-2027 (FENG).","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[{"schemeUri":"https://ror.org","funderName":"Polish Science Foundation","awardNumber":"FENG.02.01-IP.05-0017/23","funderIdentifier":"https://ror.org/048zd9m77","funderIdentifierType":"ROR"},{"schemeUri":"https://ror.org","funderName":"National Science Centre (Poland)","awardNumber":"2021/43/D/ST2/03114","funderIdentifier":"https://ror.org/03ha2q922","funderIdentifierType":"ROR"},{"schemeUri":"https://ror.org","funderName":"National Science Centre 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La Living Key est une cle USB custom (8GB+) qui contient TOUT: l installeur Cherie OS, la cle HMAC (32 bytes), l identite ORCID, le boot loader. No LK = no boot. La LK EST l OS installable. Flow: branche LK, installe Cherie OS sur PC, call home licence (HMAC+ORCID), retire LK, OS tourne. Reboot = LK requise 2 sec pour recharger HMAC en RAM. Pas de cache disque, pas de licence stockee. La RAM meurt au reboot, la LK recharge. Un objet physique non copiable = installeur + licence + identite + activation LIVE DOI + ZK-Proof + authentification reseau. Modeles custom USB avec gravure logo Cherie OS. Branding persona cosmétique (QUEEN, MARCEL, REQUIN). Cout: ~5-10 euros par cle USB custom. Remplace la licence Windows, la carte SABAM, et le certificat d identite en un seul objet. Toutes variantes et evolutions futures couvertes. All Rights Reserved.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19466336","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":1,"versionOfCount":0,"created":"2026-04-08T06:54:54Z","registered":"2026-04-08T06:54:55Z","published":null,"updated":"2026-04-08T06:54:55Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.19466337","type":"dois","attributes":{"doi":"10.5281/zenodo.19466337","identifiers":[{"identifier":"oai:zenodo.org:19466337","identifierType":"oai"}],"creators":[{"name":"Ochej, Stephane","nameType":"Personal","givenName":"Stephane","familyName":"Ochej","nameIdentifiers":[{"nameIdentifier":"0009-0000-8201-5537","nameIdentifierScheme":"ORCID"}],"affiliation":[]}],"titles":[{"title":"Living Key (LK) — Cle USB Souveraine: Installeur + Licence + Identite + LIVE DOI (Cherie OS)"}],"publisher":"Zenodo","container":{},"publicationYear":2026,"subjects":[{"subject":"Living Key"},{"subject":"USB souveraine"},{"subject":"installeur OS"},{"subject":"licence physique"},{"subject":"HMAC"},{"subject":"Cherie OS"},{"subject":"LIVE DOI"},{"subject":"ZK-Proof"},{"subject":"All Rights Reserved"}],"contributors":[],"dates":[{"date":"2026-04-08","dateType":"Issued"}],"language":null,"types":{"ris":"RPRT","bibtex":"article","citeproc":"article-journal","schemaOrg":"ScholarlyArticle","resourceType":"Working paper","resourceTypeGeneral":"Text"},"relatedIdentifiers":[{"relationType":"IsVersionOf","relatedIdentifier":"10.5281/zenodo.19466336","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[{"rights":"Other (Not Open)","rightsIdentifier":"other-closed"}],"descriptions":[{"description":"Declaration PI. La Living Key est une cle USB custom (8GB+) qui contient TOUT: l installeur Cherie OS, la cle HMAC (32 bytes), l identite ORCID, le boot loader. No LK = no boot. La LK EST l OS installable. Flow: branche LK, installe Cherie OS sur PC, call home licence (HMAC+ORCID), retire LK, OS tourne. Reboot = LK requise 2 sec pour recharger HMAC en RAM. Pas de cache disque, pas de licence stockee. La RAM meurt au reboot, la LK recharge. Un objet physique non copiable = installeur + licence + identite + activation LIVE DOI + ZK-Proof + authentification reseau. Modeles custom USB avec gravure logo Cherie OS. Branding persona cosmétique (QUEEN, MARCEL, REQUIN). Cout: ~5-10 euros par cle USB custom. Remplace la licence Windows, la carte SABAM, et le certificat d identite en un seul objet. Toutes variantes et evolutions futures couvertes. All Rights Reserved.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19466337","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2026-04-08T06:54:54Z","registered":"2026-04-08T06:54:54Z","published":null,"updated":"2026-04-08T06:54:54Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.19449520","type":"dois","attributes":{"doi":"10.5281/zenodo.19449520","identifiers":[{"identifier":"oai:zenodo.org:19449520","identifierType":"oai"},{"identifier":"10201/188989","identifierType":"Handle"}],"creators":[{"name":"JORDA GARCIA, R.","nameType":"Personal","familyName":"JORDA GARCIA, R.","affiliation":["Universidad de Murcia"],"nameIdentifiers":[{"nameIdentifier":"0009-0005-8655-8789","nameIdentifierScheme":"ORCID"}]},{"name":"SANCHEZ HERNÁNDEZ, R.","nameType":"Personal","familyName":"SANCHEZ HERNÁNDEZ, R.","affiliation":["Universidad de Murcia"],"nameIdentifiers":[]}],"titles":[{"title":"Capítulo undécimo. 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En este capítulo se analiza su Asamblea General (competencias, clases de asambleas, convocatoria y constitución, adopción de acuerdos y su documentación e impugnación).","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://zenodo.org/doi/10.5281/zenodo.19449520","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":1,"created":"2026-04-07T07:34:16Z","registered":"2026-04-07T07:34:16Z","published":null,"updated":"2026-04-08T06:54:40Z"},"relationships":{"client":{"data":{"id":"cern.zenodo","type":"clients"}}}},{"id":"10.5281/zenodo.19449519","type":"dois","attributes":{"doi":"10.5281/zenodo.19449519","identifiers":[{"identifier":"10201/188989","identifierType":"Handle"}],"creators":[{"name":"JORDA GARCIA, R.","nameType":"Personal","familyName":"JORDA GARCIA, R.","affiliation":["Universidad de Murcia"],"nameIdentifiers":[{"nameIdentifier":"0009-0005-8655-8789","nameIdentifierScheme":"ORCID"}]},{"name":"SANCHEZ HERNÁNDEZ, R.","nameType":"Personal","familyName":"SANCHEZ HERNÁNDEZ, R.","affiliation":["Universidad de Murcia"],"nameIdentifiers":[]}],"titles":[{"title":"Capítulo undécimo. 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Using multi-scale molecular dynamics simulations, we were able to explore the conformational space of the disordered conformations of both types of protein under biological conditions in an affordable amount of computational time. 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Here, we report that proteolytic digestion of the \u003ci\u003eBacillus thuringiensis\u003c/i\u003e insecticidal protoxin in the insect gut releases free L-serine. This amino acid acts not as a nutritive source but as a critical metabolic cue that reprograms a newly discovered species of gut bacteria, \u003ci\u003eEnterococcus\u003c/i\u003e. Through integrated metabolomic, transcriptomic, and phenotypic analyses, we demonstrate that L-serine induces a state of enhanced stress resistance that triggered robust biofilm formation in \u003ci\u003eEnterococcus\u003c/i\u003e by upregulating pathways including the phosphotransferase system and LPXTG-motif adhesion proteins. This enables opportunistic pathogenic\u003ci\u003e Enterococcus\u003c/i\u003e to thrive in the dysbiotic gut environment, translocate systemically, and ultimately accelerate host mortality. Our findings reveal a new mechanism by which exotic protoxin-derived metabolic signals can directly modulate gut microbial behavior, converting a commensal into a pathobiont. This paradigm extends our understanding of microbiome-mediated disease etiology, suggesting that similar metabolite-mediated functional shifts may underpin dysbiotic states in diverse host ecosystems triggered by dietary or immune protein degradation.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"url":"https://figshare.com/articles/dataset/Protoxin-derived_L-serine_drives_pathogenicity_of_gut_bacteria_i_Enterococcus_i_through_biofilm_induction/30939236/1","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-04-08T06:53:50Z","registered":"2026-04-08T06:53:50Z","published":null,"updated":"2026-04-08T06:54:02Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}}}},{"id":"10.13130/rd_unimi/8hslti/aocrzx","type":"dois","attributes":{"doi":"10.13130/rd_unimi/8hslti/aocrzx","identifiers":[],"creators":[{"name":"Tiana, Guido","nameType":"Personal","givenName":"Guido","familyName":"Tiana","affiliation":["University of Milan"],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0001-9868-1809","nameIdentifierScheme":"ORCID"}]}],"titles":[{"title":"topol_HIV_buffer.tpr"}],"publisher":"UNIMI Dataverse","container":{"type":"DataRepository","identifier":"10.13130/RD_UNIMI/8HSLTI","identifierType":"DOI"},"publicationYear":2024,"subjects":[],"contributors":[],"dates":[{"date":"2024-10-22","dateType":"Available"},{"date":"2026-04-08","dateType":"Updated"},{"date":"2024","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsPartOf","relatedIdentifier":"10.13130/rd_unimi/8hslti","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["1803700"],"formats":["application/octet-stream"],"version":"3.0","rightsList":[{"rightsUri":"info:eu-repo/semantics/openAccess"},{"lang":"en","rights":"Creative Commons Zero v1.0 Universal","rightsUri":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc0-1.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://dataverse.unimi.it/file.xhtml?persistentId=doi:10.13130/RD_UNIMI/8HSLTI/AOCRZX","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":1,"versionCount":0,"versionOfCount":0,"created":"2024-10-22T08:53:49Z","registered":"2024-10-22T08:53:49Z","published":null,"updated":"2026-04-08T06:54:02Z"},"relationships":{"client":{"data":{"id":"crui.unimi","type":"clients"}}}},{"id":"10.6084/m9.figshare.30939236","type":"dois","attributes":{"doi":"10.6084/m9.figshare.30939236","identifiers":[],"creators":[{"name":"Wang, Zeyu","givenName":"Zeyu","familyName":"Wang","nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-0087-8123","nameIdentifierScheme":"ORCID"}],"affiliation":[]}],"titles":[{"title":"Protoxin-derived L-serine drives pathogenicity of gut bacteria \u003ci\u003eEnterococcus\u003c/i\u003e through biofilm induction"}],"publisher":"figshare","container":{},"publicationYear":2026,"subjects":[{"subject":"Bacteriology","schemeUri":"http://www.abs.gov.au/ausstats/abs@.nsf/0/6BB427AB9696C225CA2574180004463E","subjectScheme":"ANZSRC Fields of Research","classificationCode":"310701"}],"contributors":[],"dates":[{"date":"2026-04-08","dateType":"Created"},{"date":"2026-04-08","dateType":"Updated"},{"date":"2026-04-08","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["347634 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Environmental stressors can disrupt the delicate balance between host and gut microbiota, yet the molecular signals that drive pathogenicity of midgut bacteria remain poorly understood. Here, we report that proteolytic digestion of the \u003ci\u003eBacillus thuringiensis\u003c/i\u003e insecticidal protoxin in the insect gut releases free L-serine. This amino acid acts not as a nutritive source but as a critical metabolic cue that reprograms a newly discovered species of gut bacteria, \u003ci\u003eEnterococcus\u003c/i\u003e. Through integrated metabolomic, transcriptomic, and phenotypic analyses, we demonstrate that L-serine induces a state of enhanced stress resistance that triggered robust biofilm formation in \u003ci\u003eEnterococcus\u003c/i\u003e by upregulating pathways including the phosphotransferase system and LPXTG-motif adhesion proteins. This enables opportunistic pathogenic\u003ci\u003e Enterococcus\u003c/i\u003e to thrive in the dysbiotic gut environment, translocate systemically, and ultimately accelerate host mortality. Our findings reveal a new mechanism by which exotic protoxin-derived metabolic signals can directly modulate gut microbial behavior, converting a commensal into a pathobiont. 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