cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25740/xq853fr8935
title: SARS-CoV2 seroprevalence in Placer county, Preliminary Report (submitted 6/29/21; data collected 10/20-4/21)

description: CA-FACTS (The Californians Fighting Against Coronavirus Together Study), Placer County is a collaboration between Stanford University and the County of Placer, with data collected from October 2020 to April of 2021.  A preliminary report was submitted to the county in June 2021, before all data had been received and cleaned. We found that among a representative sample of county residents who both provided a blood spot for testing and completed a survey on demographics and behaviors, seroprevalence increased from 1.2% in January 2021 to 43.6% in March 2021, due in part to an increasing proportion of the population being vaccinated. The data used for this preliminary report are provided here, along with a data dictionary.  A revised updated and cleaned final dataset and final report will be posted when available.
DOI: 10.25740/zf117dn1545
title: Data on alpha and delta SARS-CoV-2 mutations in settled solids from 2 POTW in northern CA 2020-2021

description: Measured concentrations of SARS-CoV-2 variant mutations in wastewater settled solids
DOI: 10.3535/3gb-83v-fwa
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qkf-m6m-ntt
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0yt-qcw-l2p
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e08-ewt-cy4
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/xn861qv4853
title: Data/Code for "High-frequency and long-term observations of endangered salmonid eDNA in a coastal stream: temporal dynamics, relationships with environmental factors, and comparisons to conventional observations"

description: Data and Python Code for the Scott Creek eDNA study conducted in 2019 and 2020. Datasets include Environmental Sample Processor (ESP) logs,  qPCR output and standards, eDNA concentrations, environmental data, and fish trap counts. Code used to aggregate and analyze data for the manuscript.

Collaboration between the Monterey Bay Aquarium Research Institute (MBARI), the Monterey Bay Aquarium, Stanford University, and the National Atmospheric and Oceanic Administration (NOAA).
DOI: 10.3535/rjv-twz-4ls
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/qy007jv4648
title: Better tired than lost: turtle ant trail networks favor coherence over short edges. 2021. Chandrasekhar, A., Marshall, J. A. R., Austin, C., Navhlakha, S. ,Gordon, D. M. PLoS Computational Biology.

description: Creating a routing backbone is a fundamental problem in both biology and engineering. The routing backbone of the trail networks of arboreal turtle ants (Cephalotes goniodontus) connects many nests and food sources using trail pheromone deposited by ants as they walk. Unlike species that forage on the ground, the trail networks of arboreal ants are constrained by the vegetation. We examined what objectives the trail networks meet by comparing the observed ant trail networks with networks of random, hypothetical trail networks in the same surrounding vegetation and with trails optimized for four objectives: minimizing path length, minimizing average edge length, minimizing number of nodes, and minimizing opportunities to get lost. The ants’ trails minimized path length by minimizing the number of nodes traversed rather than choosing short edges. In addition, the ants’ trails reduced the opportunity for ants to get lost at each node, favoring nodes with 3D configurations most likely to be reinforced by pheromone. Thus, rather than finding the shortest edges, turtle ant trail networks take advantage of natural variation in the environment to favor coherence, keeping the ants together on the trails.
DOI: 10.3535/8t5-x68-9ek
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qvb-azt-d5q
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/hd852bg4538
title: Data supporting the publication entitled Reproducibility of Cerebrovascular Reactivity Measurements: A Systematic Review of Neuroimaging Techniques

description: Cerebrovascular reactivity (CVR), the capacity of the brain to increase cerebral blood flow (CBF) to meet changes in physiological demand, is an important biomarker to evaluate brain health. Typically, this brain “stress test” is performed by using a medical imaging modality to measure the CBF change between two states: at baseline and after vasodilation. However, since there are many imaging modalities and many ways to augment CBF, a wide range of CVR values have been reported. An understanding of CVR reproducibility is critical to determine the most reliable methods to measure CVR as a clinical biomarker. This review focuses on CVR reproducibility studies using neuroimaging techniques in 32 articles comprising 427 total subjects. The literature search was performed in PubMed, Embase, and Scopus. The review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We identified 5 factors of the experimental subjects (such as sex, blood characteristics, and smoking) and 9 factors of the measuring technique (such as the imaging modality, the type of the vasodilator, and the quantification method) that have strong effects on CVR reproducibility.  Based on this review, we recommend several best practices to improve the reproducibility of CVR quantification in neuroimaging studies.
DOI: 10.25740/tm725vs8229
title: Data for: Unusual magnetotransport in twisted bilayer graphene

description: We present transport measurements of bilayer graphene with 1.38° interlayer twist and apparent
additional alignment to its hexagonal boron nitride cladding. As with other devices with twist
angles substantially larger than the magic angle of 1.1°, we do not observe correlated insulating
states or band reorganization. However, we do observe several highly unusual behaviors in magne-
totransport. For a large range of densities around half filling of the moire bands, magnetoresistance
is large and quadratic. Over these same densities, the magnetoresistance minima corresponding
to gaps between Landau levels split and bend as a function of density and field. We reproduce
the same splitting and bending behavior in a simple tight-binding model of Hofstadter’s butterfly
on a square lattice with anisotropic hopping terms. These features appear to be a generic class of
experimental manifestations of Hofstadter’s butterfly and may provide insight into the emergent
states of twisted bilayer graphene.
DOI: 10.3535/vd9-5ls-zvm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/ps241xy4214
title: Conducting Second Language Reading Research: A Methodological Guide Resources

description: This database had its inception in 1991 with the publication of Reading Development in a Second Language (Bernhardt, 1991). Influenced by Guthrie, Seifert, and Mosberg (1983), the 1991 database was constructed from a review of an array of journals frequently referenced by teachers and researchers in the English-speaking world as well as from a set of edited volumes. It resulted in a collation of 121 published research studies. Nine thematic categories resulted: word recognition; background knowledge factors; text-structure analyses; oral-aural factors; syntactic features; cross-lingual processing strategies; metacognitive strategies; testing methods; and instruction. Within each of the nine categories, number of subjects as well as the language of focus; independent variables; dependent variables; and findings were distilled.

Over the years, several expansions of the database have been conducted. By 2011, 25 journals had been explored. These include The Modern Language Journal, Applied Linguistics, TESOL Quarterly, Foreign Language Annals, Language Learning, Reading Research Quarterly, Journal of Literacy Behavior, NABE Journal, Die Unterrichtspraxis, Hispania, French Review, ADFL Bulletin, CALICO Journal, AERJ, Journal of Research in Reading, Research and Reading Instruction, Reading and Writing, Studies in Second Language Acquisition, Second Language Research, Journal of Adolescent & Adult Literacy, Reading Teacher, Reading Improvement, RELC Journal, Reading in a Foreign Language, and The Reading Matrix.. Searching through the years 1998-2008 yielded over 200 studies for analysis and several additional journal titles (The Language Learning Journal, Applied Psycholinguistics, Scientific Studies of Reading, and Reading Psychology). The resulting spreadsheet includes a total of 776 individual articles as of 2019. Each article is coded according to general theme of the research; number of subjects, languages, and tasks. A brief list of findings is included.
DOI: 10.25740/wb240vf5537
title: Music manuscript facsimiles list (14th-17th centuries)

description: Music manuscript facsimiles (14th-17th centuries) found in Stanford Libraries are organized by century, and then by country of origin. Includes links to SearchWorks records for sources where available.
DOI: 10.3535/v5l-q8y-lzn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vmq-9t0-s8z
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/ny927zd1474
title: Lully Project microform inventory

description: Microforms assembled for the Lully Project, a repository of extant sources of music scores of ballets, operas, and other works.
DOI: 10.25740/vk278sy7516
title: Data repository for Development and Application of a 1D Compaction Model to Understand 65 Years of Subsidence in the San Joaquin Valley

description: Repo contains input data for the modelling in the paper Development and Application of a 1D Compaction Model to Understand 65 Years of Subsidence in the San Joaquin Valley, as well as the 10080 simulations used for that paper. This repo contains the well completion reports, head data and resistivity log data used in the study. The head data are in the repository but are 'hidden' because they are not publicly available. Please contact mlees@stanford.edu if you need to see these data.
DOI: 10.3535/akm-tjp-l9l
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x0t-bf7-tlk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/sz403bn0186
title: Rainfall, neighbors and foraging: the dynamics of a population of red harvester ant colonies 1988-2019. Sundaram, Steiner, Gordon. 2021. Ecological Monographs

description: Changing climatic conditions are shaping how density mediates resource competition. Colonies of the seed-eating red harvester ant, Pogonomyrmex barbatus, live for up to about 30 years in desert grassland. They compete with conspecific neighbors for foraging area in which to search for seeds. This study draws on a long-term census of a population of about 300 colonies from 1988-2019 at a site near Rodeo, New Mexico, USA. Rainfall was high in the first decade of the study, and then declined as a severe drought began in about 2001-03. We examine the effects on colony survival and recruitment of the spatial configuration of the local neighborhood of conspecific neighbors, using Voronoi polygons as a measure of a colony's foraging area, and consider how changing rainfall influences the effects of local neighborhoods. The results show that a colony's chances of surviving to the next year depend on its age and on the foraging area available in its local neighborhood. Recruitment, measured as a founding colony's chance of surviving to be 1 year old, depends on rainfall. In the earlier years of the study, when rainfall was high, colony numbers increased, and then began to decline after about 1997-99, apparently due to crowding. As rainfall decreased, beginning in about 2001-03, recruitment declined, and so did colony survival, leading to a trend towards earlier colony death which was most pronounced in 2016.  As rainfall declined, apparently decreasing food availability, more foraging area was needed to sustain a colony: although numbers of colonies declined, the impact of crowding by intraspecific neighbors increased. These processes maintain overdispersion on the scale of about 8 meters, with transient clustering at larger spatial scales. In addition, other factors besides crowding, such as the colony's regulation of foraging activity to manage water loss, appear to contribute to a colony's survival. The adaptive capacity for selection on the collective behavior that regulates foraging activity may determine how the population responds to ongoing climate change and drought.
DOI: 10.25740/zb133qp4049
title: Occupancy models for coral reef oases

description: Identifying relatively intact areas within ecosystems, and determining the conditions favoring their existence, is necessary for effective management in the context of widespread environmental degradation. In this study, we used 3,766 surveys of randomly selected sites in the United States and U.S. Territories to identify the correlates of sites categorized as ‘oases’ (defined as sites with relatively high total coral cover). We used occupancy models to evaluate the influence of ten environmental predictors on the probability that an area (21.2 km2 cell) would harbor coral oases defined at four spatial extents: cross-basin, basin, region, and sub-region. Across all four spatial extents, oases were more likely to occur in habitats with high light attenuation. The influence of the other environmental predictors on the probability of oasis occurrence were less consistent and varied with the scale of observation. Oases were most likely in areas of low human population density, but this effect was evident only at the cross-basin and sub-regional extents. At the regional and sub-regional extents oases were more likely where sea-surface temperature was more variable, whereas at the larger spatial extents the opposite was true. By identifying the correlates of oasis occurrence, the model can inform the prioritization of reef areas for management. Areas with biophysical conditions that confer corals with physiological resilience, as well as limited human impacts, likely support coral reef oases across spatial extents. Our approach is widely applicable to the development of conservation strategies to protect biodiversity and ecosystems in an era of magnified human disturbance.
DOI: 10.3535/hw3-qbh-mn3
title: Tethysbaena aiakos Wagner, 1994

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/fn197fc3696
title: Nutrient and isotope data from ETNP, Costa Rica Dome, Cruise MV1008

description: Nutrient concentration and isotope data published in Buchwald et al (2015), Global Biogeochemical Cycles 29: 2061-2081.
DOI: 10.25740/yc041mz9691
title: Airborne Electromagnetic Data Acquired at Kaweah Subbasin in the Central Valley of California, U.S.A.

description: Kaweah Subbasin in the Central Valley of California is one of the over-drafted water basins. Over-pumping of groundwater resources due to the latest droughts and the high level of water demand to support agricultural activities threatens the water security of the region. Developing management practices to use groundwater resources in a sustainable way is urgent and important. However, without seeing under the ground where groundwater is stored and flows, it is not possible to pursue sustainable groundwater management. Traditionally, well-based approaches have been used for this imaging purpose. While these approaches provide accurate point information about hydrogeology of the subsurface, low spatial density and coverage of the wells result in a large data gap between the wells. Therefore, a new approach is needed to fill in this data gap for mapping out hydrogeology of the subsurface with high spatial density and coverage. This was the motivation of the acquisition of the AEM data covering Kaweah Subbasin. For this AEM experiment, SkyTEM 312 system was used; a total of 800 line-km AEM data was obtained. Acquired AEM data were processed by Aqua Geo Framework. Noisy data due to man-made noise sources (e.g., powerlines) were first omitted, then standard processing schemes (e.g., stacking, harmonic noise reduction, trapezoidal filtering) were applied using Aarhus Workbench Software. Provided AEM data in this repository are the processed AEM data, which is ready to be inverted to recover a resistivity distribution of the subsurface.
DOI: 10.3535/ekp-xqg-9jm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/taf-9ay-4r5
title: Tethysbaena stocki Wagner, 1994

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dyh-3em-g7r
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wzd-gyl-r3m
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/gz610dt4642
title: Dynamic three-dimensional maps of solute concentration and solute arrival times in synthetic and geologic porous media

description: Experimental and training data associated with the publication entitled ‘Three-Dimensional Permeability Inversion Using Convolutional Neural Networks and Positron Emission Tomography’ (published in WRR, DOI: 10.1029/2021WR031554). The dataset contain three-dimensional maps of various properties on four geologic rock cores obtained from X-ray Computed Tomography and Positron Emission Tomography imaging measurements. The synthetic training dataset used in the publication is also attached. An additional 'Readme.txt' file is provided that contains detailed description of the dataset.
DOI: 10.25740/kd763fh7892
title: SARS-CoV-2 RNA concentrations in matched influent and solids samples from 5 POTW across the United States

description: Data use in the manuscript by Kim et al. entitled: SARS-CoV-2 RNA is enriched by orders of magnitude in solid relative to liquid wastewater at publicly owned treatment works
DOI: 10.3535/p2l-7wk-vwj
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rvc-85x-qcn
title: Thermosbaena mirabilis Monod, 1924

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2s2-6et-agt
title: Tethysbaena aiakos Wagner, 1994

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.21227/g9f4-q411
title: "RTS"

description: "The intensification of retrogressive thaw slumps (RTSs) across permafrost regions in reaction to anthropogenic climate change presents critical challenges to infrastructure and ecosystems. This begs the question of quantifying disaster triggers and regional-scale spatial susceptibility of RTS. Presented here, an innovative multi-methodological framework combining multivariate environmental factor analysis, deep learning-enhanced feature extraction, and ensemble modeling to evaluate RTS susceptibility. It was performed in permafrost regions of Hoh Xil, Qinghai-Tibet Plateau, where unique geography engendered a proliferation of RTSs. Analysis revealed hydrothermal dynamics as the primary trigger of RTS activation, particularly when encountering extreme rainfall and anomalous freeze-thaw degree days. Ground ice content and fine-grained soil composition constitute essential material prerequisites for failure development. Besides, negative sampling via clustering with geological similarity constraints effectively mitigated sample imbalance and enhanced model generalizability. The integration of convolutional neural networks (CNNs) effectively captured terrain-induced signatures associated with RTS initiation, enabling the generation of operationally susceptible maps with enhanced spatial precision. The heterogeneous ensemble modeling comparison demonstrated that the Boosting-integrated framework achieved optimal predictive performance, yielding an accuracy of 0.9853, significantly outperforming base models. The integrated deep learning and geostatistics approach decodes complex RTSs triggers and delivers scalable solutions for climate-adaptive engineering planning in permafrost regions."
DOI: 10.25740/sk226xw9348
title: Data for "Expanding the momentum field of view in angle-resolved photoemission systems with hemispherical analyzers"

description: This archive contains the data that supports the findings of "Expanding the momentum field of view in angle-resolved photoemission systems with hemispherical analyzers" authored by Nicolas Gauthier, Jonathan A. Sobota, Heike Pfau, Alexandre Gauthier, Hadas Soifer, Maja D. Bachmann, Ian R. Fisher, Zhi-Xun Shen and Patrick S. Kirchmann. Preprint available at https://arxiv.org/abs/2108.08772
DOI: 10.25740/yd752gv9649
title: Hana to yume supplements

description: Hana to yume supplements.
DOI: 10.3535/8ps-a1a-fjh
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qnn-hf9-cy9
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/wb705qc9592
title: Identifying and Measuring Excessive and Discriminatory Policing

description: This collection contains police stop and population data for Chicago, Nashville, New York City and Philadelphia. This data was collected to analyze racial disparities in policing for the above jurisdictions and comes from a range of sources (publicly available, census data, by request). All record-level data do not include personal information to preserve privacy.
The data is structured to reproduce the analyses in "Identifying and Measuring Excessive and Discriminatory Policing", "Empirical Approaches to Identify Systemic Discrimination in Policing", and "Precinct or Prejudice? Understanding Racial Disparities in New York City's Stop-and-Frisk Policy". Our analysis code and further documentation are available at the GitHub repositories below. Clean files are available in .rds and .rdata formats while raw data is available in .csv, .rds, and shapefile formats.
DOI: 10.3535/yhr-dv1-cgb
title: Decapoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/57x-cf7-99e
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hvd-b4r-vnp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25740/ck044th0182
title: Respiratory Syncytial Virus (RSV) RNA in wastewater settled solids at two Bay Area, CA wastewater treatment plants

description: Data to on RSV RNA in wastewater solids
DOI: 10.3535/enc-y61-pgp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lfd-yyh-n11
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.