cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9hfkv7q
title: Water temperature models, data and code for the Colorado, Green, San Juan, Yampa, and White rivers in the Colorado River basin

description: These data were compiled for a manuscript in which 1) we develop a water temperature model for the major river segments and tributaries of the Colorado River basin, including the Colorado, Green, Yampa, White, and San Juan rivers; 2) we link modeled water temperature to fish population data to predict the probability native and nonnative species will be common in the future in a warming climate; and 3) assess the degree to which dams create thermal discontinuity in summer in river segments across the western US. Per goal #1, we developed a water temperature model using data spanning 1985-2015 that predicts water temperature every 1 mile (1.6-km) in rivers both now and in the future due to the potential influence of climate change and human decisions on water storage in reservoirs that affect temperature. Data inputs to the water temperature model include air temperature, discharge, water temperature, and solar radiation. Base model data are included in the 'WaterT Model-Base Data' and 'WaterT Model-Base Summary' data tables, future air temperature predictions are included in the 'WaterT Model-CMIP AirT' data table, and reservoir elevations are included in the 'WaterT Model-Reservoir Storage' data table. These data were used to generate water temperature predictions used in Figures 1-4 in the associated manuscript. Per goal #2, we calculated the number of Thermally Suitable Days (TSDs) in each river segment for Colorado pikeminnow (Ptychocheilus lucius), razorback sucker (Xyrauchen texanus), humpback chub (Gila cypha), smallmouth bass (Micropterus dolomieu), red shiner (Cyprinella lutrensis), and channel catfish (Ictalurus punctatus) using species-specific thermal minimums, maximums, and optimums for growth ('TSD-TemperatureTolerance' data table) and mean monthly predicted water temperatures by reach from the base model ('TSD-WaterT' data table). We compare summarized decadal-scale endangered humpback chub population estimates from 1990-2018 for multiple populations relative to TSDs in the 'Humpback Chub PopEst' data table. We include endangered Colorado Pikeminnow population estimates from 2001-2018 relative to smallmouth bass removals in the 'Colorado Pikeminnow PopEst' data table. These are data presented in Figure 3 in the associated manuscript. Circle size is weighted to TSDs per data in the data table. Per goal #3, we take the difference between mean July air temperature and water temperature released from dams and compare this 'discontinuity' to the depth from which water was withdrawn from the reservoir in the 'Therm Discontinuity Data' data table. Data summarized for these 3 goals were obtained from the U.S. Geological Survey, National Water Information System, Glen Canyon Dam Monitoring and Research Center (USGS), U.S. Fish and Wildlife Service San Juan River Basin Recovery Implementation Program, NOAA National Climatic Data Center, National Solar Radiation Database, the USBR Hydromet Data System, and from published literature.
DOI: 10.5255/ukda-sn-854286
title: The Perspectives Study: From Evidence to Guidance on Patient Recruitment to Clinical Research in Intensive Care Units, 2016-2019

description: Data collection was conducted across three workstreams. In workstream (WS) 1, 17 ICU clinicians/researchers, and eight patient and public involvement (PPI) contributors with experience of working on ICU studies, took part in semi-structured telephone interviews about the problems and potential solutions in recruitment and consent to ICU studies. This informed the development of the survey for WS2. In WS2, 1453 participants from 14 ICUs in England took part in the survey, which explored experiences and views of ICU research recruitment and consent process. Forty-four surveys were either duplicates or had substantial missing data so 1409 surveys were included in the analysis. Of these, 333 surveys were from ICU patients, 488 from family members (of whom 63 were bereaved) and 588 were from healthcare practitioners. Thirty five percent (115/333) of patient surveys and 32% (157/488) of family member surveys were from individuals who reported having been approached about research in the ICU, while 44% (260/588) of healthcare practitioner surveys were from those who indicated they had a role in research. For WS3, a purposive sample of 60 participants, 54 of whom had completed the WS2 survey, took part in semi-structured interviews to explore their survey responses and their wider perspectives on ICU research in more depth. This included 13 patients, 30 family members (of whom 4 were bereaved before completing the survey, and 5 were bereaved since they or another family member completed the survey), and 17 healthcare practitioners. Of interviewed patients and family members, 25 had been approached about a study while in the ICU. Of healthcare practitioners, 12 had research roles at the time of their interview (3 doctors, 7 research nurses and 2 pharmacists). The six additional interviewees comprised: four family members of surveyed patients where the family member had visited the patient’s during their ICU stay; two ICU patients whose family members had completed a survey. Although these six interviewees had not completed the WS2 survey, the protocol permitted interviews with such individuals if they had close ties to WS2 participants.
DOI: 10.5281/zenodo.10037253
title: Pleiades snow dataset from stereo-images

description: Snow depth satellite observation datasets made from Pleiades stereo-images, used in the evaluation of the SURFEX/Crocus/SnowPappus simulation system.
Datasets are in the NETCDF4_CLASSIC format.
The observed snow depth field is named 'DSN_T_ISBA' with a 250m horizontal resolution.
Datasets projections are 'EPSG:2154' and is described in the Projection_Type field.
Datasets are CF Compliant.
DOI: 10.5281/zenodo.10079006
title: Non-methane volatile organic compound emissions over China estimated using TROPOMI HCHO retrievals

description: We used the Regional multi-Air Pollutant Assimilation System (RAPAS) with the EnKF algorithm to optimize daily NMVOC emissions in China by assimilating TROPOMI HCHO retrievals.  
airqual.qc.csv includes assimilated and verified surface NO2 observations.
HCHO.tar.gz includes assimilated TROPOMI HCHO retrievals.
posterior_emission_27km.nc and  posterior_emission_mg_27km.nc includes inferred daily posterior anthropogenic and biogenic NMVOC emissions respectively for August 2022.
DOI: 10.5281/zenodo.10266168
title: Bubona

description: Bubona is an international dataset of dental wear patterns and associated broad age stages observed in archaeological and modern cattle mandibles.
DOI: 10.5281/zenodo.10460562
title: Data for manuscript Measurement Report: Effects of transition metal ions on the optical properties of humic-like substances revealing structural preference

description: Data for our preprint manuscript Measurement Report: Effects of transition metal ions on the optical properties of humic-like substances revealing structural preference on EGU journal - Atmospheric Chemistry and Physics.
DOI: 10.5281/zenodo.10903574
title: A fine-grained dataset named iSOOD for sewage outfalls objective detection in natural environments

description: Basic Information:

The 10481 images in iSOOD were captured using UAVs and handheld cameras by individuals from the river basin in China. Our study has carefully annotated these images to ensure accuracy and consistency. The iSOOD has undergone technical validation utilizing the YOLOv5 objective detection model. The iSOOD have been publicly released after undergoing desensitization, with the goal of promoting interdisciplinary collaboration and accelerating advancements in the intelligence watershed management. We expect that the iSOOD dataset is anticipated to inspire further research on the SOs detection and the control of pollution migration paths, and serve as a fundamental resource for the use of advanced deep learning visual technology in environmental monitoring.

Usage Policy:If you plan to use our data in a scientific analysis paper, we strongly recommend contacting us in advance to seek opinions, and consider our contributions in the acknowledgments or as co-authors.
DOI: 10.5281/zenodo.1415369
title: Ultrafine Particle Dataset Collected By The Opensense Zurich Mobile Sensor Network

description: <strong>Ultrafine Particle Dataset Collected by the OpenSense Zurich Mobile Sensor Network</strong>

This dataset contains one year (2012/04- 2013/04, ~11Mio. samples) worth of ultra-fine particle (UFP) concentration measurements collected by a mobile senor network. The sensors are mounted on top of 10 streetcars in the city of Zurich, Switzerland.

<strong>Hardware:</strong>


	<strong>Ultrafine particle sensor</strong>: MiniDiSC (see also: Martin Fierz et al. Design, Calibration, and Field Performance of a Miniature Diffusion Size Classifier. Aerosol Science and Technology, Volume 45, 2011.)
	<strong>GPS receiver</strong>: u-blox EVK-6p


<strong>*.csv column format:</strong>


	Time of day: yyyy.mm.dd HH:MM
	Latitude WGS84
	Longitude WGS84
	HDOP: horizontal dillusion of precision, uncertainty of the GPS position
	Tram ID
	Number of particles [#/ccm]
	Average particle diameter [nm]
	LDSA: lung deposited surface area [um2 /cm3]


<strong>Data quality:</strong><br>
The data has been post-processed by performing a periodic null-offset calibration and  filtering samples during malfunction.

<strong>References:</strong><br>
The dataset has been used and is described in more detail in the following publications:


	David Hasenfratz et al.<em> Pushing the Spatio-Temporal Resolution Limit of Urban Air Pollution Maps.</em> IEEE International Conference on Pervasive Computing and Communications (PerCom). Budapest, Hungary, March 2014. Best Paper Award. 
	David Hasenfratz et al. <em>Deriving High-Resolution Urban Air Pollution Maps Using Mobile Sensor Nodes. </em>Pervasive and Mobile Computing. Elsevier, 2015. 
	David Hasenfratz et al. <em>Demo Abstract: Health-Optimal Routing in Urban Areas.</em> ACM/IEEE International Conference on Information Processing in Sensor Networks (IPSN). Seattle, USA, April 2015.
	Michael Müller et al. <em>Statistical modelling of particle number concentration in Zurich at high spatio-temporal resolution utilizing data from a mobile sensor network. </em>Atmospheric Environment. Elsevier, 2016.


For further information, visit:  http://www.opensense.ethz.ch
DOI: 10.5281/zenodo.2542919
title: RAM Legacy Stock Assessment Database v4.44

description: RAM Legacy Stock Assessment Database version 4.44.
DOI: 10.5281/zenodo.3982670
title: Air pollution 01.2014 - 05.2020 (including COVID-19 lockdown) data from Graz, Austria

description: Please cite: https://doi.org/10.1016/j.envpol.2020.114587 Air quality by means of NO2, PM10 and O3 was measured at five sites in Graz, Austria (Süd (<em>eng. South</em>) - S, Nord (<em>eng. North</em>) - N, West (<em>eng. West</em>) - W, Don Bosco – D, Ost (<em>eng. East</em>) – O). In addition weather conditions like temperature, percipitation, relative humidity, pressure, wind speed and direction are added. The authors created binary temporal variables like weekday, month, season, year and day of year (numerical). The data consist of 2343 rows and 53 columns with a timestamp from January 2014 to May 2020 in a daily frequency. More details on measurement and the sites are available in Moser et al. [1] and [2]. The environmental data was provided by the Austrian government under the following license: CC-BY-4.0: Land Steiermark - data.steiermark.gv.at __________________ [1] Moser F, Kleb U, Katz H (2019) Statistische Analyse der Luftqualitätin Graz anhand von Feinstaub und Stickstoffdioxid. Graz [2] https://www.umwelt.steiermark.at/cms/ziel/2060750/DE/
DOI: 10.5281/zenodo.4037473
title: Precipitation and Temperature Data for the Sydney Catchment Area, Australia

description: This dataset contains time series for monthly precipitation over six sites (Blackheath, Braidwood, Darkes Forest, Goulburn, Lithgow and Moss Vale) in the Sydney Catchment Area (SCA) and monthly mean maximum and mean minimum temperature for three sites (Goulburn, Lithgow, and Moss Vale) in the SCA. This data was used in the study <em>Attribution and Prediction of Precipitation and Temperature Trends within the Sydney Catchment Using Machine Learning</em>. The data was originally from the Australian Bureau of Meteorology Climate Data Online (http://www.bom.gov.au/climate/data/index.shtml), but has been updated to have missing values (8% of data) filled using a moving average centred on the year for which the data is missing. <br> <br> Below is the abstract for the paper: Droughts in southeastern Australia can profoundly affect the water supply to Sydney, Australia's largest city. Increasing population, a warming climate, land surface changes, and expanded agricultural use increase water demand and reduce catchment runoff. Studying Sydney's water supply is necessary to manage water resources and lower the risk of severe water shortages. This study aims at understanding Sydney water supply by analysing precipitation and temperature trends across the catchment. A decreasing trend in annual precipitation was found across the Sydney catchment area. Annual precipitation also is significantly less variable, due to fewer years above the 80th percentile. These trends result from significant reductions in precipitation during spring and autumn, especially over the last 20 years. Wavelet analysis is applied to assess how the influence of climate drivers has changed over time. Attribute selection was carried out using linear regression and machine learning techniques including random forests and support vector regression. Drivers of annual precipitation included Niño3.4, SAM, DMI and measures of global warming such as the Tasman Sea Sea Surface temperature anomalies. The support vector regression model with a polynomial kernel achieved correlations of 0.921 and a skill score compared to climatology of 0.721. The linear regression model also performed well with a correlation of 0.815 and skill score of 0.567, highlighting the importance of considering both linear and non-linear methods when developing statistical models. Models were also developed on autumn and winter precipitation but performed worse than annual precipitation on prediction. For example, the best performing model on autumn precipitation, which accounts for approximately one quarter of annual precipitation, achieved an RMSE of 418.036 mm<sup>2</sup> on the testing data while annual precipitation achieved an RMSE of 613.704 mm<sup>2</sup>. However, the seasonal models provided valuable insight into whether the season would be wet or dry compared to the climatology.
DOI: 10.5281/zenodo.7413949
title: Example Dataset from BioMAX, MAX IV Laboratory

description: Dataset collected at BioMAX beamline, MAX IV Labortory, Sweden, of thaumatin. Data collection parameters: Data collected: 30 November 2022 Wavelength: 0.9763 Å (12.7 keV) Beamline: BioMAX, MAX IV Laboratory Detector: DECTRIS EIGER 16M File format: HDF5 in EIGER Nexus format Number of frames: 1800 Oscillation per frame: 0.1°, 180° total Resolution at detector corners: 2 Å Estimated flux: 1.68e11 ph/s Beamline parameters: <strong>Synchrotron Name</strong> MAX IV <strong>Focusing Optics</strong> K-B Mirror <strong>Detector Type</strong> Hybrid Pixel Counting Detector <strong>Beamline name</strong> BioMAX <strong>Monochromator<br> Type</strong> Si(111) <strong>Detector Model </strong> EIGER 16M <strong>Synchrotron Current</strong> 297.0 mA <strong>Beam Shape</strong> ellipse <strong>Detector Manufacturer</strong> DECTRIS <strong>Undulator type</strong> <strong>Beam size at sample Horiz/vert (µm)</strong> 50/50 <strong>Detector pixel size (um)</strong> 75 <strong>Undulator gap</strong> 5.04 mm <strong>Beam divergence<br> Horiz/vert (µrad)</strong> 6/104 <strong>Beam polarization</strong> 0.99 Crystals of thaumatin were grown from solutions of thaumatin (20-50 mg/mL) in NaK-tartrate (1.0 M), HEPES pH 7 (100 µM), and 25% glycerol.
DOI: 10.5281/zenodo.8237324
title: Dataset associated with "Constraints on the subsecond modulation of striatal dynamics by physiological dopamine signaling"

description: This repository contains behavioral data, dLight photometry measurements, smoothed spiking data from recorded striatal neurons, and miniscope recordings. Text files with further explanation are provided to assist with replication of the main analyses. Matlab code to perform key analyses can be found in the accompanying GitHub repository (https://github.com/sotmasman/Dopamine-constraints)
DOI: 10.6073/pasta/336c992d04a16d589a24297d96af35f6
title: LTREB Biological Limnology at Lake Myvatn 2012-2020

description: These data are part of a long-term monitoring program at Lake Myvatn, Iceland. The program was designed to characterize import benthic and pelagic variables across years as chironomid midge populations varied in abundance. Starting in 2012 samples were taken at roughly ten-day intervals during June, July, and August at a central location in the lake. Starting in 2015, additional five sites representing dominant habitat types were sampled generally three times each year. The dataset also includes occasional winter samples under ice.
DOI: 10.6084/m9.figshare.24746898
title: Supplementary Material for: Clinical Impact of Early Tumour Shrinkage in Metastatic or Unresectable Oesophageal Cancer Treated with Pembrolizumab plus Chemotherapy

description: Introduction: Metastatic or unresectable locally advanced oesophageal cancer remains a disease with high mortality. More recently, pembrolizumab plus chemotherapy has been indicated as the first-line treatment for those patients, but the predictive factors for treatment efficacy remain controversial. This study investigated the clinical utility of early tumour shrinkage (ETS) and depth of response (DpR) in metastatic or unresectable oesophageal cancer treated with pembrolizumab plus CF therapy. 
Methods: ETS and DpR, defined as the percent decreases at the second evaluation and the percentage of the maximal tumour shrinkage during treatment, were measured in 53 eligible patients. The ETS and DpR cut-off values were 20% and 30%, respectively, based on survival outcomes. 
Results: Twenty-seven patients (51%) were treatment-naïve, while 26 (49%) had received any treatment before initiating pembrolizumab plus CF therapy. The median progression-free survival (PFS) and overall survival (OS) for ETS ≥20% and &lt;20% were 12.7 and 5.5 months and 14.4 and 8.2 months, and 12.7 and 4.9 months and 14.4 and 8.0 months for DpR ≥30% and &lt;30%, respectively. ETS &lt;20% showed early tumour growth, whereas ETS ≥20% had a good response rate with sufficient longer response duration. In addition, an ETS cut-off of 20% predicted the best overall response and was not associated with prior treatment. In multivariable analysis, ETS ≥20% and DpR ≥30% were independent factors of longer PFS. 
Conclusion: Our findings suggest that an ETS is a promising on-treatment marker for early prediction of further sensitivity to pembrolizumab plus CF therapy.
DOI: 10.6084/m9.figshare.25127711
title: Supplementary Material for: Prevalence of Renal Neoplasia in Autosomal Dominant Polycystic Kidney Disease: Systematic Review and Meta-analysis

description: BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited condition, however its relationship with renal cell carcinoma (RCC) remains unclear. This paper aims to establish the prevalence of RCC and its subtypes amongst ADPKD patients. 

METHODS: A database search was conducted to retrieve studies reporting RCC occurrence within ADPKD patients until July 2023. Key outcomes included number and subtype of RCC cases, and number of RCCs presenting incidentally. A random-effects meta-analysis was performed.
 
RESULTS: Our search yielded 569 articles, 16 met the inclusion criteria. Nephrectomy specimens from 1,147 ADPKD patients were identified. Of studies reporting per-kidney results (n = 13), 73 RCCs were detected amongst 1,493 kidneys, equating to a per-kidney prevalence of 4.3% (95% CI, 3.1 to 5.7, I2 = 15.7%). 75 ADPKD patients were found to have RCC (75/1147), resulting in a per-person prevalence of 5.7% (95% CI, 3.7 to 7.9, I2 = 40.3%) (n = 16). As 7 patients had bilateral disease, 82 RCCs were detected in total. Of these, 39 were clear cell RCC, 35 were papillary and 8 were other. As such, papillary RCCs made up 41.1% (95% CI, 25.9 to 56.9, I2 = 18.1%) of detected cancers. The majority of RCCs were detected incidentally (72.5% [95% CI, 43.7 to 95.1, I2 = 66.9%]). 
 
CONCLUSION: ADPKD appears to be associated with the papillary RCC subtype. The clinical implications of these findings are unclear, however may become apparent as outcomes and life expectancy amongst APDKD patients improve.
DOI: 10.6084/m9.figshare.25240684
title: <b>Transcriptomic approach on </b><b><i>Villorita cyprinoides</i></b><b> (black clam)</b>

description: <i>Villorita cyprinoides</i> is an ecologically and aquaculturally significant endemic species. This project aims to create reference transcriptomes that will provide a baseline for advancing studies to address the species localized habitat, underlying response mechanisms to various environmental stressors, and to improve genetically enhanced stress and disease-resistant individuals.
DOI: 10.6084/m9.figshare.25506865
title: Supplementary Material for: Sex-dependent differences in the neural correlates of cocaine and emotional cue-reactivity in regular cocaine users and non-drug using controls: understanding the role of duration and severity of use

description: Introduction: The development of cocaine use disorder (CUD) in females is suggested to be more strongly related to neural mechanisms underlying stress-reactivity, whereas in males it is suggested to be more strongly related to neural mechanisms underlying drug cue-reactivity. Existing evidence, however, is based on neuroimaging studies that either lack a control group and/or have very small sample sizes that do not allow to investigate sex differences. Methods: The main objective of the current study was to investigate sex differences in the neural correlates of cocaine and negative emotional cue-reactivity within high-risk intranasal cocaine users (CUs: 31 males and 26 females) and non-cocaine-using controls (non-CUs: 28 males and 26 females). A region of interest (ROI) analysis was applied to test for the main and interaction effects of group, sex, and stimulus type (cocaine cues versus neutral cocaine cues and negative emotional cues versus neutral emotional cues) on activity in the dorsal striatum (DS), ventral striatum (VS), amygdala, and dorsal anterior cingulate cortex (dACC). 
Results: There were no significant sex or group differences in cocaine cue-reactivity in any of the ROIs. Results did reveal significant emotional cue-reactivity in the amygdala and VS, but these effects were not moderated by group or sex. Exploratory analyses demonstrated that emotional cue-induced activation of the dACC and VS was negatively associated with years of regular cocaine use in female CUs, while this relationship was absent in male CUs. 
Conclusions: While speculative, the sex-specific associations between years of regular use and emotional cue-reactivity in the dACC and VS suggest that, with longer years of use, female CUs become less sensitive to aversive stimuli, including the negative consequences of cocaine use, which could account for the observed “telescoping effect” in female CUs.