cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.79ntwr
title: Occurrence Download

description: A dataset containing 9959 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Agriornis lividus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 9959 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077502-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16625449
title: Subset BAM Files for Atf4 Locus (chr15:79481845–81029726, mm10) from RNA-seq

description: Data Description

This dataset contains subset BAM files corresponding to the genomic interval chr15:79,481,845–81,029,726 (mm10), which encompasses the Atf4, Rps19bp1, and Cacna1i loci and adjacent regions. These files were derived from:



Bulk RNA-seq data generated in our study investigating transcriptional readthrough and its impact on neighboring gene regulation during mouse embryonic heart development.

Re-analysis of public datasets that incorrectly utilized the Atf4 exon 2–3 cKO mouse model, a design known to abolish the endogenous polyadenylation signal and inevitably cause readthrough transcription. This leads to:



Downregulation of the downstream gene Rps19bp1 and subsequent p53 pathway activation;

Apparent upregulation of Cacna1i expression driven by Atf4–Cacna1i fusion transcripts, which inherently provide direct evidence of transcriptional readthrough (otherwise typically requiring nascent RNA sequencing).



The subset BAMs were extracted to facilitate focused visualization and analysis of:



Splicing junctions within the Atf4 locus;

Aberrant fusion transcripts (Atf4–Cacna1i);

Local transcriptional dynamics within this genomic region.





Associated Full RNA-seq Datasets (GEO) Generated in Our Study:



GSE303780: RNA-seq of Atf4 exon 3 frameshift knockout embryonic mouse hearts.

GSE303929: Comparative transcriptomic analysis of embryonic hearts in Atf4 exon 2 and exon 2–3 conditional knockout mice.

GSE303775: RNA-seq of Rps19bp1 cKO (Xmlc2-Cre) E11.5 mouse hearts.





Re-analyzed Published Public Datasets:



BioProject PRJEB26869 – Brain RNA-seq dataset (used to illustrate normal Cacna1i expression and splicing patterns).

GSE173578 (Mol Metab, 2021; PMID: 34303878)

GSE192990 (Sci Adv, 2022; PMID: 35895846)

GSE206760 (Cells, 2023; PMID: 37998373)

GSE212675 (GeroScience, 2023; PMID: 37014538)

GSE233677 (Blood, 2024; PMID: 38657191)
DOI: 10.5281/zenodo.16625450
title: Subset BAM Files for Atf4 Locus (chr15:79481845–81029726, mm10) from RNA-seq

description: Data Description

This dataset contains subset BAM files corresponding to the genomic interval chr15:79,481,845–81,029,726 (mm10), which encompasses the Atf4, Rps19bp1, and Cacna1i loci and adjacent regions. These files were derived from:



Bulk RNA-seq data generated in our study investigating transcriptional readthrough and its impact on neighboring gene regulation during mouse embryonic heart development.

Re-analysis of public datasets that incorrectly utilized the Atf4 exon 2–3 cKO mouse model, a design known to abolish the endogenous polyadenylation signal and inevitably cause readthrough transcription. This leads to:



Downregulation of the downstream gene Rps19bp1 and subsequent p53 pathway activation;

Apparent upregulation of Cacna1i expression driven by Atf4–Cacna1i fusion transcripts, which inherently provide direct evidence of transcriptional readthrough (otherwise typically requiring nascent RNA sequencing).



The subset BAMs were extracted to facilitate focused visualization and analysis of:



Splicing junctions within the Atf4 locus;

Aberrant fusion transcripts (Atf4–Cacna1i);

Local transcriptional dynamics within this genomic region.





Associated Full RNA-seq Datasets (GEO) Generated in Our Study:



GSE303780: RNA-seq of Atf4 exon 3 frameshift knockout embryonic mouse hearts.

GSE303929: Comparative transcriptomic analysis of embryonic hearts in Atf4 exon 2 and exon 2–3 conditional knockout mice.

GSE303775: RNA-seq of Rps19bp1 cKO (Xmlc2-Cre) E11.5 mouse hearts.





Re-analyzed Published Public Datasets:



BioProject PRJEB26869 – Brain RNA-seq dataset (used to illustrate normal Cacna1i expression and splicing patterns).

GSE173578 (Mol Metab, 2021; PMID: 34303878)

GSE192990 (Sci Adv, 2022; PMID: 35895846)

GSE206760 (Cells, 2023; PMID: 37998373)

GSE212675 (GeroScience, 2023; PMID: 37014538)

GSE233677 (Blood, 2024; PMID: 38657191)
DOI: 10.25921/vpw6-8994
title: NOAA/WDS Paleoclimatology - Luckman - Small River - PCEN - ITRDB CANA450

description: A new network of 21 Picea engelmannii Parry ex Engelm. ring-width chronologies was developed from tree-line sites in the Canadian Rockies. These chronologies range in length from 297 to 648 years (mean 423 years) and have mean sensitivities between 0.16 and 0.20 (mean 0.18), first-order autocorrelations between 0.73 and 0.88 (mean 0.83), and subsample signal strengths >0.85 for 246-494 years (mean 324 years). Mean intersite correlations (A.D. 1700-1982) for chronologies with expressed population signals >0.85 are 0.46 and 0.63 for standard and residual chronologies, respectively. Standard ring-width chronologies are, in general, positively correlated with summer temperatures and negatively correlated with spring and previous summer temperatures. A regional June-September temperature reconstruction for the Banff-Jasper region (BJR; A.D. 1715-1982) was developed using multiple regression of three significant principal components from 14 standard ring-width chronologies. The first principal component contains 55% of the total chronology variance. The model reconstructs 38% of summer temperature variance during the calibration period (1888-1982). The BJR is the first regional temperature reconstruction for this area based on ring-width data from a network of sites. The reconstructed temperature patterns are broadly similar to other regional estimates of past temperatures. Above-average summer temperatures occurred in the mid-20th century and the late 1700s - early 1800s. Most of the 19th century was unusually cold, with the coldest conditions in the late 19th century. Detailed differences between BJR and previously developed reconstructions lie well within 2 sigma confidence limits and may reflect differences in tree species, modelling techniques, spatial coverage, and the seasonal temperature parameter reconstructed.
description: NOAA Template Raw Measurements file added 2019-02-04.
DOI: 10.25921/vg89-np65
title: NOAA/WDS Paleoclimatology - Esper - Atlas Mountains TZ - CDAT - ITRDB MORC023

description: Cedrus atlantica ring width data are used to reconstruct long-term changes in the Palmer Drought Severity Index (PDSI) over the past 953 years in Morocco, NW Africa. The reconstruction captures the dry conditions since the 1980s well and places this extreme period within a millennium-long context. PDSI values were above average for most of the 1450-1980 period, which let recent drought appear exceptional. However, our results also indicate that this pluvial episode of the past millennium was preceded by generally drier conditions back to 1049. Comparison of PDSI estimates with large-scale pressure field reconstructions revealed steady synoptic patterns for drought conditions over the past 350 years. The long-term changes from initially dry to pluvial to recent dry conditions are similar to PDSI trends reported from N America, and we suggest that they are related to long-term temperature changes, potentially teleconnected with ENSO variability and forced by solar irradiance changes.

description: Collection purpose: 
# dendrclimatology
# 
# Cores are stored at: 
# WSL
# 
# Notes: 
# Formerly  TIZ NOAA Template Raw Measurements file added 2019-05-01.
DOI: 10.25921/vqy1-hy67
title: NOAA/WDS Paleoclimatology - King - Chinese Garden - JUSC - ITRDB MT127

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description:  NOAA Template Chronology file added 2018-12-20. NOAA Template Raw Measurements file added 2019-02-08.
DOI: 10.25921/ve8y-c636
title: NOAA/WDS Paleoclimatology - Penny Ice Cap - Conductivity, Isotope, and Chemistry Data

description: Ice cores from Penny Ice Cap, Baffin Island, Canada, provide continuous Holocene records of oxygen isotopic composition (delta18O, proxy for temperature) and atmospheric impurities. A time scale was established with the use of altered seasonal variations, some volcanic horizons, and the age for the end of the Wisconsin ice age determined from the GRIP and GISP2 ice cores. There is pre-Holocene ice near the bed. The change in delta18O since the last glacial maximum (LGM) is at least 12.5 per mil, compared with an expected value of 7 per mil, suggesting that LGM ice originated at the much higher elevations of the then existing Foxe Dome and Foxe Ridge of the Laurentide Ice Sheet. The LGM delta18O values suggest thick ice frozen to the bed of Hudson Bay.
description: Snowpits were excavated in 1994 and 1995. 

The 333.78m. P95 core was drilled to the bed in April-May 1995.
The 89m. P95.2 core was drilled adjacent to the P95 core (2.5 m. away) 
for evaluation of noise in the record. The d18O correlation between 
the two cores is .80.  

The 177.91m. P96 core also reached the bed.  It is located
approximately 16 km. from P95.  The P95-P96 correlation of d18O 
on 40-year segments is .3 to .5.

ADDITIONAL REFERENCES:
Fisher, D.A., R.M. Koerner, G.A. Zielinski, C.P. Wake, C.M. Zdanowicz, 
J.C. Bourgeois, P.A. Mayewski and N. Grummet, 2002,
The effects of flowline length evolution on chemistry-d18O profiles from 
Penny Ice Cap, Baffin Island, Canada
Annals of Glaciology, Volume 35, pp. 150-156.

Fisher, D. A., (2002).   High-resolution multiproxy climatic records 
from ice cores, tree-rings, corals and documentary sources using eigenvector 
techniques and maps: assessment of recovered signal and errors.
Holocene,  vol. 12, no. 4, pp. 401-420 

Grumet, N.S., Wake, C.P., Zielinski, G.A., Fisher, D.A. and Jacobs, J.D. 1998.  
Preservation of glaciochemical time-series in snow and ice records from the 
percolation zone of the Penny Ice Cap, Baffin Island. 
Geophysical Research Letters 25, 357-360.

Goto-Azuma, K., R.M. Koerner, and D.A. Fisher, 2002,
An ice-core record over the last two centuries from Penny Ice Cap, 
Baffin Island, Canada
Annals of Glaciology, Volume 35, pp. 29-35.
DOI: 10.25921/v7hq-me20
title: NOAA/WDS Paleoclimatology - Kauri NZ Tree ring width, PAGES Australasia 2k Version

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: Uploaded by R. Neukom, data obtained from original authors
	These are not raw data but processed and truncated chronologies. Details see (Neukom and Gergis 2011, The Holocene, DOI: 10.1177/0959683611427335). For the raws contact the authors or check ITRDB.
DOI: 10.25921/vbsq-kv49
title: NOAA/WDS Paleoclimatology - Lower Yangtze River 158 Year February-April Precipitation Reconstruction

description: February-April drought strongly affects agriculture and socio-economics in southeastern China, yet its long-term variability has not been assessed due to the shortness of instrumental records. In this study, we reported a 168-year tree-ring width chronology from a steep, low-elevation site with thin soil layers in the Xianxia Mountains, southeastern China. Contrary to the existing chronologies that are mostly temperature sensitive, this chronology contained a strong February-April precipitation signal, indicating great potential for tree-ring based precipitation reconstructions in southeastern China. The reconstruction explained 47.8% of the instrumental variance during 1951-2012. The full reconstruction indicated that there were 3 dry periods (1873-1896, 1924-1971, 1995-2012) and 2 wet periods (1856-1872, 1972-1994) during 1856-2013. The extreme drought in 2011 was not unprecedented for the past 168 years, and the recent severe droughts may be part of interdecadal variations in regional February-April precipitation. Our results also suggested that February-April precipitation in southeastern China was highly influenced by the tropical Pacific climate system, in particular El Niño-Southern Oscillation (ENSO).

description: Spring (February-April) 158 year precipitation reconstruction for the lower reaches of the Yangtze River, based on tree-ring data.
DOI: 10.25921/vwh6-2f47
title: NOAA/WDS Paleoclimatology - Samonil - Zofinsky prales - FASY - ITRDB CZEC004

description: We connected tree-census and dendrochronological research data (74.2 ha) in order to answer the following questions: How do we apply an individual-based approach, which allows us to abandon the traditional patch model, in the research of disturbance history through spatial scales? What is the disturbance history of the natural forest? How do we understand the influence of the Kyrill storm, which affected the reserve on 18 January 2007? How does the disturbance history in dendrochronological records correspond to real disturbances?
Location

Žofínský Prales (48 °40′ N, 14 °42′ E, 735-830 m a.s.l., granite, Czech Republic)
Methods

Repeated tree-censuses (>20 000 trees) were carried out in 1975, 1997 and 2008. These surveys served as the basis of dendrochronological research, during which 3 020 trees were sampled. A boundary line (BL) approach and geostatistical techniques were used to detect disturbance intensity and its spatial pattern.
Results

The mean disturbance rate was 11.0% canopy loss per decade (maximum 33.7%) in the core zone. Bordering forests were directly affected by humans after 1800. A maximum of nine disturbance events were recorded per tree, but there were also 3% of non-suppressed trees without records of disturbance events. The Kyrill storm represented a singular event in the forest history from the point of view of its exceptional spatial pattern (ranges up to 320.0 m), but not from the perspective of disturbance intensity. The relationship between disturbance intensity (y) and the range of spatial autocorrelation (x) can be explained by the equation y = 10.6863 + 0.0783*x (R2 = 0.546, P = 0.009). The spatial variability of releases ≥50% of BL corresponds to real disturbance events, while the insertion of weak releases led to the overestimation of range. The frequency of releases was affected by a decrease in air pollution at the beginning of the 1990s.
Conclusions

Effects of small-scale disturbances predominate in forest dynamics. Disturbance intensity was often not directly in accordance with the range of spatial autocorrelation. The ecological role of disturbance is therefore biased if disturbance intensity is used as the sole criterion. The results suggest the importance of historical and geographical contingency in ecosystem development.
description:  NOAA Template Chronology file added 2018-12-19. NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.25921/vzys-1280
title: NOAA/WDS Paleoclimatology - Global Holocene Mean Surface Temperature Reconstructions

description: An extensive new multi-proxy database of paleo-temperature time series (Temperature 12k) enables more robust analysis of global mean surface temperature (GMST) and associated uncertainties than was previously available. We applied five different statistical methods to reconstruct the GMST of the past 12,000 years (Holocene). Each method used different approaches to averaging the globally distributed time series and to characterizing various sources of uncertainty, including proxy temperature, chronology and methodological choices. The results were aggregated to generate a multi-method ensemble of plausible GMST and latitudinal-zone temperature reconstructions with a realistic range of uncertainties. The warmest 200-year-long interval took place around 6500 years ago when GMST was 0.7C (0.4, 1.8) warmer than the 19th Century (median, 5th, 95th percentiles). Following the global thermal maximum, GMST cooled at an average rate -0.08C per 1000 years (-0.24, -0.05). The multi-method ensembles and the code used to generate them highlight the utility of the Temperature 12k database, and they are now available for future use by studies aimed at understanding Holocene evolution of the Earth system.
description: Global mean surface temperature (GMST) and associated uncertainties for the past 12,000 years using five different statistical methods. The reconstructions are based on v1.0 of the Temperature 12k Database available at: 
https://www.ncdc.noaa.gov/paleo/study/27330
DOI: 10.25921/vrmr-gd04
title: NOAA/WDS Paleoclimatology - Combined NGRIP-Cariaco Basin 56,000 Year d18O Record

description: The mechanisms of Late Pleistocene megafauna extinctions remain fiercely contested, with human impact or climate change cited as principal drivers. Here, we compare ancient DNA and radiocarbon data from 31 detailed time series of regional megafaunal extinctions/replacements over the past 56,000 years with standard and new combined records of Northern Hemisphere climate in the Late Pleistocene. Unexpectedly, rapid climate changes associated with interstadial warming events are strongly associated with the regional replacement/extinction of major genetic clades or species of megafauna. The presence of many cryptic biotic transitions prior to the Pleistocene/Holocene boundary revealed by ancient DNA confirms the importance of climate change in megafaunal population extinctions and suggests that metapopulation structures necessary to survive such repeated and rapid climatic shifts were susceptible to human impacts. 
description: North Greenland Ice Sheet Project (NGRIP) oxygen isotope (d18O) data at 20-year resolution, combined with the Cariaco Basin chronology.
DOI: 10.25921/v2vp-2f15
title: NOAA/WDS Paleoclimatology - Burial Lake, Alaska 34,000 Year Organic Geochemical Data

description: Our understanding of the timing of human arrival to the Americas remains fragmented, despite decades of active research and debate. Genetic research has recently led to the 'Beringian standstill hypothesis' (BSH ), which suggests an isolated group of humans lived somewhere in Beringia for millennia during the Last Glacial, before a subgroup migrated southward into the American continents about 14 ka. Recently published organic geochemical data suggest human presence around Lake E5 on the Alaskan North Slope during the Last Glacial; however, these biomarker proxies, namely faecal sterols and polycyclic aromatic hydrocarbons (PAH s), are relatively novel and require replication to bolster their support of the BSH. We present new analyses of these biomarkers in the sediment archive of Burial Lake (latitude 68 26'N, longitude 159 10'W, 460 m a.s.l.) in northwestern Alaska. Our analyses corroborate that humans were present in Beringia during the Last Glacial and that they likely promoted fire activity. Our data also suggest that humans coexisted with Ice Age megafauna for millennia prior to their eventual extinction at the end of the Last Glacial. Lastly, we identify fire as an overlooked ecological component of the mammoth steppe ecosystem.
description: Fecal sterol and Polycyclic Aromatic Hydrocarbon (PAHs) data from sediments collected in Burial Lake, Alaska, for the past 34,000 years
DOI: 10.25921/vbzy-fz96
title: NOAA/WDS Paleoclimatology - Touchan - Rocky Ridge - JUOC - ITRDB CA698

description: Snowpack in the Sierra Nevada Mountains accounts for around one-third of California's water supply. Melting snow provides water into dry summer months characteristic of the region's Mediterranean climate. As climate changes, understanding patterns of snowpack, snowmelt, and biological response is critical in this region of agricultural, recreational, and ecological value. Here we investigated the relationships between tree rings of montane conifer trees (Tsuga mertensiana, Abies magnifica, Abies concolor, Calocedrus decurrens, Juniperus occidentalis, and Pinus ponderosa) and regional climate indices with the goal of reconstructing April 1 snow-water equivalent (SWE) in the North Fork American River watershed of the Sierra Nevada. Chronologies were positively correlated with April 1 SWE of the year prior to ring formation. Temporal trends in correlation between tree-ring chronologies and climate indices indicate strengthening tree growth response to climate over time. We developed a skillful, nested reconstruction for April 1 SWE, 1661-2013. Variability of the reconstruction is within the envelope of 20th and 21st-century variability; however, the 2015 record low snowpack is unprecedented in the tree-ring record, as in results from previous studies. Future research should focus on integrating modern snow sensor data into paleoclimate research and understanding mechanistic linkages between snow and tree growth response.
description:  NOAA Template Chronology file added 2020-07-08.
DOI: 10.25921/vb53-5v61
title: NOAA/WDS Paleoclimatology - Eastern Labrador Sea Stable Isotope, Trace Metal and SST Data over the last 1250 Years

description: Despite the relative climate stability of the present interglacial, it has been punctuated by several centennial-scale climatic oscillations; the latest of which are often colloquially referred to as the Medieval Climatic Anomaly (MCA) and the Little Ice Age (LIA). The most favored explanation for the cause of these anomalies is that they were triggered by variability in solar irradiance and/or volcanic activity and amplified by ocean-atmosphere-sea ice feedbacks. As such, changes in the strength of the Atlantic Meridional Overturning Circulation (AMOC) are widely believed to have been involved in the amplification of such climatic oscillations. The Labrador Sea is a key area of deep water formation. The waters produced here contribute approximately one third of the volume transport of the deep limb of the AMOC and drive changes in the North Atlantic surface hydrography and subpolar gyre circulation. In this study, we present multiproxy reconstructions from a high-resolution marine sediment core located south of Greenland that suggest an increase in the influence of polar waters reaching the Labrador Sea close to MCA-LIA transition. Changes in freshwater forcing may have reduced the formation of Labrador Sea Water and contributed toward the onset of the LIA cooling.
description: Provided Keywords: Last millennium, Labrador Sea