cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57760/sciencedb.30818
title: HOLOLIFEX6: A Deterministic, Guardrailed Framework for Simulating and Measuring Emergent Consciousness via Higher-Order Thought Theory
title: HOLOLIFEX6: A Deterministic, Guardrailed Framework for Simulating and Measuring Emergent Consciousness via Higher-Order Thought Theory

description: This work introduces HOLOLIFEX6, a modular computational framework designed for the scientifically reproducible simulation of artificial consciousness. The system is architected around a "Strict Guardrailed Execution" model in Julia, which enforces deterministic behavior through isolated Random Number Generators (RNGs) and a non-interfering, streaming analysis pipeline. It models a complex adaptive system of autonomous entities and measures emergent integrated information (Φ) based on a synthesis of Integrated Information Theory (IIT) and Higher-Order Thought (HOT) Theory.We present experimental evidence demonstrating the successful emergence of a verifiable conscious state compliant with HOT Theory principles. Key discoveries include the identification of non-linear "islands of consciousness" at specific scales (16 and 256 entities) and the measurement of a U-shaped "cost of consciousness," revealing that the time required for emergence is non-monotonic with system scale. These results indicate that consciousness in this model is a product of organizational efficiency, not merely scale, and that the system autonomously evolves hierarchical strategies to overcome coordination overhead. HOLOLIFEX6 provides a stable, auditable digital laboratory for studying the fundamental conditions required for consciousness to arise from non-conscious components.
description: This work introduces HOLOLIFEX6, a modular computational framework designed for the scientifically reproducible simulation of artificial consciousness. The system is architected around a "Strict Guardrailed Execution" model in Julia, which enforces deterministic behavior through isolated Random Number Generators (RNGs) and a non-interfering, streaming analysis pipeline. It models a complex adaptive system of autonomous entities and measures emergent integrated information (Φ) based on a synthesis of Integrated Information Theory (IIT) and Higher-Order Thought (HOT) Theory.We present experimental evidence demonstrating the successful emergence of a verifiable conscious state compliant with HOT Theory principles. Key discoveries include the identification of non-linear "islands of consciousness" at specific scales (16 and 256 entities) and the measurement of a U-shaped "cost of consciousness," revealing that the time required for emergence is non-monotonic with system scale. These results indicate that consciousness in this model is a product of organizational efficiency, not merely scale, and that the system autonomously evolves hierarchical strategies to overcome coordination overhead. HOLOLIFEX6 provides a stable, auditable digital laboratory for studying the fundamental conditions required for consciousness to arise from non-conscious components.
DOI: 10.6075/j0dj5fzh
title: CIL:57187, Homo sapiens. In Cell Image Library

description: Imaging mode: scanning electron microscopy (SEM)
description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPESwas added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
DOI: 10.6075/j00g3jdd
title: CIL:725, Chlorocebus sabaeus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
description: COS 7 cell expressing Organelle LightsTM PM-GFP (Invitrogen)consisting of the myristoylation/palmitoylation sequence from Lck
tyrosine kinase. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505 emission filter. Image size is 1024 x 1024, pixel size is 0.14 µm x 0.14 µm and pixel time was set to 1.6 ¬µsec. Detector pinhole was set to collect 29 ~0.5 µm slices at 0.5 µm intervals.
DOI: 10.57760/sciencedb.30837
title: TRAMS 3.0 Model and SVD-3DEnVar Data Assimilation Framework Source Code
title: TRAMS 3.0 Model and SVD-3DEnVar Data Assimilation Framework Source Code

description: This source code package comprises two core components developed to enhance computational efficiency in SVD-3DEnVar data assimilation and its integration with the TRAMS 3.0 Model. It includes the full source code for both the TRAMS 3.0 Model (Tropical Regional Atmospheric Model System, Version 3.0) and the SVD-3DEnVar (Singular Value Decomposition-based 3D Ensemble Variational) Data Assimilation Framework.The TRAMS 3.0 Model is a specialized mesoscale atmospheric model designed to simulate tropical and subtropical atmospheric processes—such as mesoscale convective systems—and to support regional numerical prediction. The SVD-3DEnVar Framework combines singular value decomposition with ensemble-variational assimilation methods, with an emphasis on optimizing computational performance to meet the demands of efficient data assimilation in regional modeling. It processes observational data and refines initial conditions for numerical forecasts, enhancing the simulation capabilities of the TRAMS 3.0 Model.Structured for reproducibility, the code allows users to implement and test the SVD-3DEnVar scheme, integrate it with TRAMS 3.0, and validate computational gains. It is also designed for extensibility, supporting adaptation to other regional atmospheric models and further optimization of assimilation workflows.
description: This source code package comprises two core components developed to enhance computational efficiency in SVD-3DEnVar data assimilation and its integration with the TRAMS 3.0 Model. It includes the full source code for both the TRAMS 3.0 Model (Tropical Regional Atmospheric Model System, Version 3.0) and the SVD-3DEnVar (Singular Value Decomposition-based 3D Ensemble Variational) Data Assimilation Framework.The TRAMS 3.0 Model is a specialized mesoscale atmospheric model designed to simulate tropical and subtropical atmospheric processes—such as mesoscale convective systems—and to support regional numerical prediction. The SVD-3DEnVar Framework combines singular value decomposition with ensemble-variational assimilation methods, with an emphasis on optimizing computational performance to meet the demands of efficient data assimilation in regional modeling. It processes observational data and refines initial conditions for numerical forecasts, enhancing the simulation capabilities of the TRAMS 3.0 Model.Structured for reproducibility, the code allows users to implement and test the SVD-3DEnVar scheme, integrate it with TRAMS 3.0, and validate computational gains. It is also designed for extensibility, supporting adaptation to other regional atmospheric models and further optimization of assimilation workflows.
DOI: 10.6075/j0t72g8f
title: CIL:36049, Stentor coeruleus. In Cell Image Library

description: Figure 414 from Chapter 16 (Cytoplasmic matrix and cytoskeleton) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Transverse section of a portion of the cortex of a partially extended Stentor coerulus shows a cilium flanked by two microtubule arrays in cross section. The microtubules are interconnected by short bridges to form ribbons that are attached to basal bodies of neighboring cilia. During extension, the overlapping ribbons of stiff microtubules slide with respect to on another, decreasing their degree of overlap and causing the organism to elongate. Underlying myonemes contract to shorten the organism. From Huang and Pitelka, J. Cell Biol. 57:704-728, 1973 (PMID:4633444). A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain
Data qualification: Processed
DOI: 10.6075/j0pz57fx
title: CIL:28737. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.45 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j06t0mrw
title: CIL:39664, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.15468/dl.deezw6
title: Occurrence Download

description: A dataset containing 3749 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, United Kingdom of Great Britain and Northern Ireland)",
 "Geometry POLYGON((-16.00243 47.89191,12.09689 47.89191,12.09689 59.14191,-16.00243 59.14191,-16.00243 47.89191))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Martes martes (Linnaeus, 1758)",
 "Year 2019-2025"
 ]
}

 The dataset includes 3749 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006943-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id346690.1
title: StrainInfo SI-ID 346690.1

description: StrainInfo dataset 346690 about a strain of Paulschulzia pseudovolvox. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346576.1
title: StrainInfo SI-ID 346576.1

description: StrainInfo dataset 346576 about a strain of Chloridella. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346577.1
title: StrainInfo SI-ID 346577.1

description: StrainInfo dataset 346577 about a strain of Pseudocharaciopsis ovalis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346578.1
title: StrainInfo SI-ID 346578.1

description: StrainInfo dataset 346578 about a strain of Neocystis mucosa. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/ghykki
title: Données espèces - Expertise IQE - Ecuelles - 2013

description: L’Indice de Qualité Ecologique (IQE) repose sur un inventaire de terrain relativement complet et permet une évaluation en profondeur de la qualité écologique d’un site dans sa globalité. Les inventaires se déroulent sur 6 journées, incluant un passage crépusculaire et nocturne, échelonnées du début du printemps à la fin de l’été.
Ces données espèces sont issues des Expertises IQE en lien avec la convention Eurovia.
iqe-patrinat.mnhn.fr
DOI: 10.60712/si-id346667.1
title: StrainInfo SI-ID 346667.1

description: StrainInfo dataset 346667 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346668.1
title: StrainInfo SI-ID 346668.1

description: StrainInfo dataset 346668 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346669.1
title: StrainInfo SI-ID 346669.1

description: StrainInfo dataset 346669 about a strain of Pleodorina californica. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.yfoeip
title: Occurrence Download

description: A dataset containing 249904 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Gabon"
 ]
}

 The dataset includes 249904 records from 396 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004324-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id346670.1
title: StrainInfo SI-ID 346670.1

description: StrainInfo dataset 346670 about a strain of Spondylosium pulchellum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346691.1
title: StrainInfo SI-ID 346691.1

description: StrainInfo dataset 346691 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346692.1
title: StrainInfo SI-ID 346692.1

description: StrainInfo dataset 346692 about a strain of Pandorina morum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346693.1
title: StrainInfo SI-ID 346693.1

description: StrainInfo dataset 346693 about a strain of Pandorina morum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346694.1
title: StrainInfo SI-ID 346694.1

description: StrainInfo dataset 346694 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346671.1
title: StrainInfo SI-ID 346671.1

description: StrainInfo dataset 346671 about a strain of Staurodesmus dejectus. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346672.1
title: StrainInfo SI-ID 346672.1

description: StrainInfo dataset 346672 about a strain of Xanthidium subhastiferum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346673.1
title: StrainInfo SI-ID 346673.1

description: StrainInfo dataset 346673 about a strain of Xanthidium subhastiferum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346695.1
title: StrainInfo SI-ID 346695.1

description: StrainInfo dataset 346695 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346696.1
title: StrainInfo SI-ID 346696.1

description: StrainInfo dataset 346696 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346697.1
title: StrainInfo SI-ID 346697.1

description: StrainInfo dataset 346697 about a strain of Chlorella salina. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346786.1
title: StrainInfo SI-ID 346786.1

description: StrainInfo dataset 346786 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.byfvxk
title: Occurrence Download

description: A dataset containing 170715 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "Year 1950-2018",
 "Geometry POLYGON((-97.81 17.528,-96.687 17.528,-96.687 18.877,-97.81 18.877,-97.81 17.528))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 170715 records from 335 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008930-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id346787.1
title: StrainInfo SI-ID 346787.1

description: StrainInfo dataset 346787 about a strain of Cricosphaera. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346788.1
title: StrainInfo SI-ID 346788.1

description: StrainInfo dataset 346788 about a strain of Chrysotila carterae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id346674.1
title: StrainInfo SI-ID 346674.1

description: StrainInfo dataset 346674 about a strain of Xanthidium subhastiferum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.