cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17190/amf/1773399
title: AmeriFlux US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM)

description: This is the AmeriFlux version of the carbon flux data for the site US-xPU NEON Pu'u Maka'ala Natural Area Reserve (PUUM). Site Description - NEON's PUUM field site is located in the Pu'u Maka'ala Natural Area Reserve (NAR) on the eastern side of Hawaii’s “Big Island,” managed by the Hawaii Division of Forestry and Wildlife (DOFAW). More than 18,000 acres in size, the NAR is home to a rainforest with many native species, some of them endangered. It was established to protect some of the Big Island’s best wet native forest and unique geologic features.
DOI: 10.17190/amf/1671898
title: AmeriFlux US-xNW NEON Niwot Ridge Mountain Research Station (NIWO)

description: This is the AmeriFlux version of the carbon flux data for the site US-xNW NEON Niwot Ridge Mountain Research Station (NIWO). Site Description - The Niwot Ridge sits approximately 27 km west of Boulder, Colorado, and 6 km east of the Continental Divide. Topography, climate, and biota of the site are representative of Rocky Mountain alpine ecosystems, including extensive alpine tundra (mostly herbs, some shrubs and scree) and subalpine coniferous forests (Abies lasciocarpa and Picea engelmanii at higher elevations), talus slopes, wetlands and a variety of glacial landforms.

Characterized by cold and relatively long winters, Niwot Ridge has an average annual temperature of 1.5°C and average annual precipitation of 800 mm. Most precipitation falls as snow and summer precipitation falls primarily during afternoon thunderstorms. Located on the eastern side of the Continental Divide at 3,000-3,500 m elevation, the site best captures chemical inputs produced along the Front Range and is well situated to observe other east/west flows across the Southern Rockies in conjunction with other NEON sites.
DOI: 10.17190/amf/1579723
title: AmeriFlux US-xRM NEON Rocky Mountain National Park, CASTNET (RMNP)

description: This is the AmeriFlux version of the carbon flux data for the site US-xRM NEON Rocky Mountain National Park, CASTNET (RMNP). Site Description - NEON's Rocky Mountain National Park (RMNP) tower stands 12 km south of Estes Park, Colorado, representing a growing mosaic of urban and exurban areas. While the property is owned by RMNP, it is not contiguous with the core park boundaries.
As a mid-elevation site (2,750 m) on the east side of the Continental Divide, the site is aptly situated to investigate the chemical climate (i.e., pollution) generated along the Front Range as well as dust deposition produced and transported from the Great Basin to higher elevations. This is a particularly salient issue given recent estimates which project that an additional two million residents will inhabit the Front Range in twenty years.
DOI: 10.17190/amf/1671899
title: AmeriFlux US-xSB NEON Ordway-Swisher Biological Station (OSBS)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSB NEON Ordway-Swisher Biological Station (OSBS). Site Description - The Ordway-Swisher Biological Station (OSBS) is operated by the University of Florida and comprises over 9,300 acres. It is a year-round field station established for the long-term study and conservation of unique ecosystems through management, research and education. The Station is located approximately 20 miles east of Gainesville in Melrose (Putnam County, Florida). There are two aquatic arrays at Ordway-Swisher, representing the two dominant aquatic features on the landscape: 1) Suggs lake, a shallow surface water lake that is rich in taxa and biologically active in structure and function; and 2) Barco lake, a deep lake connected to ground water. The forest is maintained by fire and has a relatively open structure: it is managed with prescribed burns at a frequency of 3-4 years.
DOI: 10.17190/amf/1773400
title: AmeriFlux US-xRN NEON Oak Ridge National Lab (ORNL)

description: This is the AmeriFlux version of the carbon flux data for the site US-xRN NEON Oak Ridge National Lab (ORNL). Site Description - Oak Ridge National Laboratory (ORNL) is located at the U.S. Department of Energy's Oak Ridge Reservation in Roane County, Tennessee. The ORNL reservation is situated within the borders of five parallel ridges and valleys to the north of the Clinch River that are part of the Ridge-and-Valley Appalachians physiographic province (Environmental Sciences Division n.d.). The NEON tower site and Walker Branch aquatic site at ORNL are located within the Walker Branch Watershed, a 100 ha area that has served as the site for long-term environmental studies by the Environmental Sciences Division at ORNL, NOAA, and many visiting university researchers.
DOI: 10.17190/amf/1617734
title: AmeriFlux US-xSE NEON Smithsonian Environmental Research Center (SERC)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSE NEON Smithsonian Environmental Research Center (SERC). Site Description - This site is operated at the Smithsonian Environmental Research Center, which is comprised of forests, wetlands, marshes and shoreline on the Chesapeake Bay
DOI: 10.17190/amf/1671900
title: AmeriFlux US-xSC NEON Smithsonian Conservation Biology Institute (SCBI)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSC NEON Smithsonian Conservation Biology Institute (SCBI). Site Description - The Smithsonian Conservation Biology Institute (SCBI) site is a mid-continent forested eastern deciduous site, species include Oaks, Hickories, and Ash, and contains well defined ground cover and understory strata.
DOI: 10.17190/amf/1617735
title: AmeriFlux US-xSL NEON North Sterling, CO (STER)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSL NEON North Sterling, CO (STER). Site Description - The North Sterling site, located outside of Sterling in Northeastern Colorado, is characterized by flat terrain and represents an agronomic site within urban and formerly urban areas.
The site is at the edge of a non-tilled experimental field that is used for the long-term sustainable Dryland Agroecosystems Project (DAP), which was initiated in 1985 at three sites in eastern Colorado (Sterling, Stratton, and Walsh) to evaluate the effects of cropping intensity on production, water use efficiency and selected soil chemical and physical properties. The DAP site was established in 1985 and was chosen because of representative soils present in the catena.
DOI: 10.17190/amf/1671901
title: AmeriFlux US-xSJ NEON San Joaquin Experimental Range (SJER)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSJ NEON San Joaquin Experimental Range (SJER). Site Description - Located at The San Joaquin Experimental Range, in the western foothills of the Sierra Nevada, this 18.2 kilometer terrestrial field site is a mix of open woodlands, shrubs and grasslands with low density cattle grazing.  SJER is an ecosystem research experimental area. It was originally conceived as a cooperative interdisciplinary research center to identify cost-effect methods of commercial livestock production in the annual grass-oak pine woodlands, while maintaining the integrity of the ecosystem. More recently, research objectives have expanded and diversified to include research projects making contributions to our knowledge of the patterns and processes working in this ecosystem.
DOI: 10.17190/amf/1579543
title: AmeriFlux US-xSR NEON Santa Rita Experimental Range (SRER)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSR NEON Santa Rita Experimental Range (SRER). Site Description - Santa Rita Experimental Range encompasses 21,000 hectares of upland Sonoran Desert, approximately 32 km south of Tucson, Arizona. Santa Rita Experimental Range was founded in 1903. It is the longest continuously active rangeland research facility and among the five oldest biological field stations in the United States. The site is broken into distinct pastures, through which cattle graze throughout the year in various densities and durations.
DOI: 10.17190/amf/1617736
title: AmeriFlux US-xSP NEON Soaproot Saddle (SOAP)

description: This is the AmeriFlux version of the carbon flux data for the site US-xSP NEON Soaproot Saddle (SOAP). Site Description - The Soaproot Saddle is a complex terrain of coarse hills, steep slopes and narrow drainages. With an elevation of 3274 - 4537’ this site encompasses 1438 acres of mixed conifer forests that are experiencing high levels of mortality due to native Pine beetles.  At the core of this site stands a 171’ tall flux tower that collects physical and chemical properties of atmosphere and related process. Soaproot Saddle also hosts an array of sensor measurements along with field observations collected by highly trained NEON staff. The automated instrument measurements and some of the terrestrial observational safor this field site are colocted with NEON's aquatic site, Upper Big Creek, which is located just north of Soaproot Saddle's site boundaries.
DOI: 10.17190/amf/1671902
title: AmeriFlux US-xTA NEON Talladega National Forest (TALL)

description: This is the AmeriFlux version of the carbon flux data for the site US-xTA NEON Talladega National Forest (TALL). Site Description - The TALL terrestrial field site covers 5300 hectares within the larger Oakmulgee District of the Talladega National Forest (475,000 hectares) in west-central Alabama. TALL is located within the Gulf Coastal Plain which is the dominant physiographic province (52%) of NEON's Domain 8: Ozarks Complex. It is also where the upper coastal plain gives rise to the Appalachian foothills. The lands of this region are rich a mosaic of forest types and habitats. Steep ridges to rolling hills fading to hardwood bottoms make up the diversity of forest conditions found in Oakmulgee. While known for its longleaf forests, over 40% of Oakmulgee is covered with a mixture of hardwoods and wetlands.
DOI: 10.17190/amf/1617737
title: AmeriFlux US-xST NEON Steigerwaldt Land Services (STEI)

description: This is the AmeriFlux version of the carbon flux data for the site US-xST NEON Steigerwaldt Land Services (STEI).
DOI: 10.17190/amf/1617738
title: AmeriFlux US-xTE NEON Lower Teakettle (TEAK)

description: This is the AmeriFlux version of the carbon flux data for the site US-xTE NEON Lower Teakettle (TEAK). Site Description - The site encompasses 5,138 hectares (12,696 acres) of mixed conifer and red fir forest, ranging in elevation from 1,990 to 2,807 m (6,529 – 9,209ft). The varied terrain is typical of the Sierra Nevada, with rugged mountains, meadows and prominent granite outcrops. TEAK has been designated as one of two relocatable terrestrial sites for the Pacific Southwest domain. The core aquatic site, Teakettle Creek, is just south of the terrestrial site.
DOI: 10.5281/zenodo.17457151
title: Cell Behavior Science (CBS): A Physically Grounded Framework Integrating Non-Equilibrium Thermodynamics, Active Matter Theory, Mechanobiology, Gene Regulatory Networks, Metabolic Fluxes, and Extracellular Matrix Remodeling

description: Cell Behavior Science (CBS) introduces a unified, physically grounded framework for predicting cellular dynamics, integrating non-equilibrium thermodynamics, active matter hydrodynamics, cytoskeletal mechanobiology, gene regulatory networks, dynamic flux balance analysis, and extracellular matrix remodeling with durotactic feedback. The cell is modeled as an open dissipative system driven by ATP hydrolysis, enabling quantitative simulations from femtosecond vibrational coherences to organotypic scales. Core hypotheses include the Coherent Vibrational Network (CVN), with ultrafast oscillations (10 fs–1.2 ps) enhancing catalysis (coherence integrals >0.35 ps, τ_c >0.8 ps), and Mechano-Geometric Memory (MGM), encoding deformations in eigenmodes (<10 Hz) to modulate epigenetics (r>0.88, τ_v~100 s). The Entropic Flux Model (EFM) quantifies entropy production while incorporating mechanotransduction, metabolic shifts (e.g., Warburg: v_gly ≥2 v_OXPHOS +0.5 M_MGM), and durotaxis (v_duro = v_0 ∇E / ||∇E|| tanh(||∇E|| / E_c)). Implementation combines agent-based modeling, graph neural networks (AUROC>0.94), and proximal policy optimization for therapeutic optimization (45% acceleration). Benchmarks across invasion (RMSE 1.35±0.06 μm/h), organoids (AUC 0.948±0.008), resistance (91.2±0.8%), contractility (R²=0.89±0.02), and fibrosis (RMSE 0.85±0.04) outperform baselines by 18–52% (p<10^{-5}). Sensitivity analyses (Sobol S_i<0.05) confirm robustness. CBS is falsifiable via spectroscopic, genomic, calorimetric, fluxomic, and migratory assays, advancing precision therapeutics (e.g., 32% AAV enhancement, 40% fibrosis reduction).
DOI: 10.17190/amf/1617739
title: AmeriFlux US-xTL NEON Toolik (TOOL)

description: This is the AmeriFlux version of the carbon flux data for the site US-xTL NEON Toolik (TOOL). Site Description - The Toolik field site is located in a remote wilderness area at the Toolik Field Station which is on land managed by the Bureau of Land Management. The area is underlain by continuous permafrost, which exerts a major influence on hydrology and the distribution, structure, and function of terrestrial and aquatic ecosystems. Because of its location between the Brooks Range and the coastal plain, the vegetation and soils at TOOL are representative of much of the Alaskan foothills tundra.

This terrestrial field site is collocated with NEON’s Toolik Lake aquatic site. The closest city, Fairbanks, Alaska is 400 miles away. The Dalton Highway (also known as the Haul Road or Pipeline Road), which traverses the middle of the state from Fairbanks to Prudhoe Bay, provides access to the area.
DOI: 10.5281/zenodo.17253442
title: Cell Behavior Science (CBS): A Physically Grounded Framework Integrating Non-Equilibrium Thermodynamics, Active Matter Theory, Mechanobiology, Gene Regulatory Networks, Metabolic Fluxes, and Extracellular Matrix Remodeling

description: Cell Behavior Science (CBS) introduces a unified, physically grounded framework for predicting cellular dynamics, integrating non-equilibrium thermodynamics, active matter hydrodynamics, cytoskeletal mechanobiology, gene regulatory networks, dynamic flux balance analysis, and extracellular matrix remodeling with durotactic feedback. The cell is modeled as an open dissipative system driven by ATP hydrolysis, enabling quantitative simulations from femtosecond vibrational coherences to organotypic scales. Core hypotheses include the Coherent Vibrational Network (CVN), with ultrafast oscillations (10 fs–1.2 ps) enhancing catalysis (coherence integrals >0.35 ps, τ_c >0.8 ps), and Mechano-Geometric Memory (MGM), encoding deformations in eigenmodes (<10 Hz) to modulate epigenetics (r>0.88, τ_v~100 s). The Entropic Flux Model (EFM) quantifies entropy production while incorporating mechanotransduction, metabolic shifts (e.g., Warburg: v_gly ≥2 v_OXPHOS +0.5 M_MGM), and durotaxis (v_duro = v_0 ∇E / ||∇E|| tanh(||∇E|| / E_c)). Implementation combines agent-based modeling, graph neural networks (AUROC>0.94), and proximal policy optimization for therapeutic optimization (45% acceleration). Benchmarks across invasion (RMSE 1.35±0.06 μm/h), organoids (AUC 0.948±0.008), resistance (91.2±0.8%), contractility (R²=0.89±0.02), and fibrosis (RMSE 0.85±0.04) outperform baselines by 18–52% (p<10^{-5}). Sensitivity analyses (Sobol S_i<0.05) confirm robustness. CBS is falsifiable via spectroscopic, genomic, calorimetric, fluxomic, and migratory assays, advancing precision therapeutics (e.g., 32% AAV enhancement, 40% fibrosis reduction).
DOI: 10.15468/dl.rytzqp
title: Occurrence Download

description: A dataset containing 476 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Romerolagus diazi"
 ]
}

 The dataset includes 476 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003023-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17190/amf/1617740
title: AmeriFlux US-xUK NEON The University of Kansas Field Station (UKFS)

description: This is the AmeriFlux version of the carbon flux data for the site US-xUK NEON The University of Kansas Field Station (UKFS). Site Description - Along an eastern deciduous forest and tallgrass prairie transition zone just north of Lawrence, Kansas, this 6 km2 terrestrial field site is located at the University of Kansas Field Station. A 116' tall flux tower rises out of a mixed hardwood forest dominated by white ash trees. Field obdservations of plants, animals, soils and microbes are collected around the tower and in the nearby tallgrass prairie.
DOI: 10.17190/amf/1634886
title: AmeriFlux US-xTR NEON Treehaven (TREE)

description: This is the AmeriFlux version of the carbon flux data for the site US-xTR NEON Treehaven (TREE). Site Description - Treehaven, situated between Rhinelander and Tomahawk, WI, is one of two relocatable sites located in NEON’s Great Lakes Domain. The Treehaven property spans 1400 acres and is owned and operated by the University of Wisconsin-Stevens Point (UWSP), College of Natural Resources. UWSP uses the property and conference center for summer field techniques courses but welcomes other educators, researchers, and the public to use and enjoy their forests, trails, and facility.
DOI: 10.17190/amf/1579724
title: AmeriFlux US-xWD NEON Woodworth (WOOD)

description: This is the AmeriFlux version of the carbon flux data for the site US-xWD NEON Woodworth (WOOD). Site Description - The Northern Plains-Woodworth site (Woodworth), is a restored prairie in an undulating matrix of small lakes, ponds and ephemeral water bodies (re. prairie potholes). The site is administered by the Department of the Interior (DOI), National Fish and Wildlife, National Wildlife Refuge. The Northern Plains-Woodworth site is located at ~ 3 miles SE of the town of Woodworth, ND.  The Northern Plains-Woodworth site is part of the Chase Lake National Wildlife Refuge and is at the center of one of the largest roadless blocks of native prairie left in the Upper Great Plains.
DOI: 10.17190/amf/1617741
title: AmeriFlux US-xUN NEON University of Notre Dame Environmental Research Center (UNDE)

description: This is the AmeriFlux version of the carbon flux data for the site US-xUN NEON University of Notre Dame Environmental Research Center (UNDE). Site Description - NEON's Domain 5 core site is located at the University of Notre Dame Environmental Research Center (UNDERC) East. Straddling the border between Northern Wisconsin and Michigan’s Upper Peninsula, the UNDERC property comprises approximately 7500 acres and is maintained as an environmental education and research facility. UNDERC also has 30 lakes comprising 1350 acres, including Crampton Lake, a NEON aquatics site. Region-wide logging for pine in the late 1800s and early to mid-1900's led to clear cutting of most forested areas on the property. The main parcel was donated to the University in the 1930s. Timber harvest continued into the 1950s and later, leaving a mixture of successional forest regrowth. Since the 1970s, the site has been minimally managed to maintain access for recreational, educational and research goals.
DOI: 10.17190/amf/1617743
title: AmeriFlux US-xYE NEON Yellowstone Northern Range (Frog Rock) (YELL)

description: This is the AmeriFlux version of the carbon flux data for the site US-xYE NEON Yellowstone Northern Range (Frog Rock) (YELL). Site Description - Located 100 kilometers southeast of Bozeman, the YELL site is within the northern reaches of Yellowstone National Park. The terrain consists of rolling hills with small wetlands in the bottom of the depressions. The field site is a mosaic of pine-dominated forest mixed with open swaths of sage and grass.  This site is also within one of the Park’s bear management areas which includes seasonal closure (early March to early June) to minimize bear-human interactions.
DOI: 10.17190/amf/1617742
title: AmeriFlux US-xWR NEON Wind River Experimental Forest (WREF)

description: This is the AmeriFlux version of the carbon flux data for the site US-xWR NEON Wind River Experimental Forest (WREF). Site Description - Located in an old growth Pacific Northwest forest west of the Cascade Range, Wind River Experimental Forest has a rich history of research and timber management since the early 1900s. The area is best known for its old-growth forests of Douglas-fir and western hemlock. 

Data collected at this site provides an interesting comparison to NEON’s ABBY site which is located Yacolt Burn State Forest, a relatively young growth industrial timber production forest.
DOI: 10.17190/amf/2331385
title: AmeriFlux US-YK2 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Unburned

description: This is the AmeriFlux version of the carbon flux data for the site US-YK2 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Unburned. Site Description - Tower installed in the Yukon-Kuskokwin Delta in September 2019. Discontinuos permafrost zone in a wetland tundra ecosystem characterized by peat plateaus and wetlands.
DOI: 10.17190/amf/2331384
title: AmeriFlux US-YK1 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Burned 2015

description: This is the AmeriFlux version of the carbon flux data for the site US-YK1 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Burned 2015. Site Description - Tower installed in the Yukon-Kuskokwim Delta in July 2019, in an area that was burned in year 2015. Discontinuous permafrost zone in a wetland tundra ecosystem characterized by peat plateaus and wetlands
DOI: 10.17190/amf/2507523
title: AmeriFlux US-YNS North Star Yedoma

description: This is the AmeriFlux version of the carbon flux data for the site US-YNS North Star Yedoma. Site Description - Dry hillslope underlain by ice rich permafrost and now covered with native grasses and managed as a rustic golf course.  The land clearing performed decades ago has caused permafrost thawing, surface subsidence, and development of thermokarst mounds or baidjarahks.  No foreign fill materials, pesticides or fertilizers have been used, and the area is not irrigated.  The area outside the flux footprint is second growth deciduous forest with similar soil conditions.
DOI: 10.5281/zenodo.17456775
title: 4DN Joint Analysis – Chromatin Loop Benchmark and Transcription Association

description: This repository contains the scripts and input data used to analyze and generate all major figures for two sections of the 4D Nucleome (4DN) Consortium marker paper, “An integrated view of the structure and function of the human 4D nucleome” (Nature, 2025).



Benchmarking of 3D genomic assays — evaluating the performance of different experimental platforms (Hi-C, Micro-C, CTCF ChIA-PET, RNAPII ChIA-PET, and H3K4me3 PLAC-Seq) in detecting various classes of chromatin loops.

Loop–transcription association analysis — assessing how 3D genome organization at the loop level correlates with gene transcriptional activity.


If you use the scripts or data in this repository, please cite:

4D Nucleome Consortium et al. An integrated view of the structure and function of the human 4D nucleome. Nature. 2025.
DOI: 10.5281/zenodo.17456776
title: 4DN Joint Analysis – Chromatin Loop Benchmark and Transcription Association

description: This repository contains the scripts and input data used to analyze and generate all major figures for two sections of the 4D Nucleome (4DN) Consortium marker paper, “An integrated view of the structure and function of the human 4D nucleome” (Nature, 2025).



Benchmarking of 3D genomic assays — evaluating the performance of different experimental platforms (Hi-C, Micro-C, CTCF ChIA-PET, RNAPII ChIA-PET, and H3K4me3 PLAC-Seq) in detecting various classes of chromatin loops.

Loop–transcription association analysis — assessing how 3D genome organization at the loop level correlates with gene transcriptional activity.


If you use the scripts or data in this repository, please cite:

4D Nucleome Consortium et al. An integrated view of the structure and function of the human 4D nucleome. Nature. 2025.