cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15146/r31m36
title: Double digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

description: The phylogenetic and population genetic structure of symbiotic
 microorganisms may correlate with important ecological traits that can be
 difficult to directly measure, such as host preferences or dispersal
 rates. This study develops and tests a low-cost double digest restriction
 site-associated DNA sequencing (ddRADseq) protocol to reveal among- and
 within-species genetic structure for Lophodermium, a genus of fungal
 endophytes whose evolutionary analyses have been limited by the scarcity
 of informative markers. The protocol avoids expensive barcoded adapters
 and incorporates universal indexes for multiplexing. We tested for
 reproducibility and functionality by comparing shared loci from sample
 replicates and assessed the effects of numbers of ambiguous sites and
 clustering thresholds on coverage depths, number of shared loci among
 samples, and phylogenetic reconstruction. Errors between technical
 replicates were minimal. Relaxing the quality-filtering criteria increased
 the mean coverage depth per locus and the number of loci recovered within
 a sample, but had little effect on the number of shared loci across
 samples. Increasing clustering threshold decreased the mean coverage depth
 per cluster and increased the number of loci recovered within a sample but
 also decreased the number of shared loci across samples, especially among
 distantly-related species. The combination of low similarity clustering
 (70%) and relaxed quality-filtering (allowing up to 30 ambiguous sites per
 read) performed the best in phylogenetic analyses at both recent and deep
 genetic divergences. Hence, this method generated sufficient number of
 shared homologous loci to investigate the evolutionary relationships among
 divergent fungal lineages with small haploid genomes. The greater genetic
 resolution also revealed new structure within species that correlated with
 ecological traits, providing valuable insights into their cryptical life
 histories.
DOI: 10.5061/dryad.p8pq7fq
title: Data from: Vis/NIR reflectance spectroscopy for hybrid rice variety identification and chlorophyll content evaluation for different nitrogen fertilizer levels

description: Nitrogen is one of the most important nutrient indicator for the growth of
 crops, which is closely related to chlorophyll content of leaves and thus
 influences the photosynthetic ability of crops. In this study, visible and
 near infrared (vis/NIR) reflectance spectroscopy combined with
 multi-variate analysis was used to identify hybrid rice varieties and
 nitrogen fertilizer levels, as well as to detect chlorophyll content
 associated with nitrogen levels. The support vector machine (SVM)
 algorithm was applied to identify five varieties of hybrid rice and six
 levels of nitrogen fertilizer. The results demonstrated that different
 varieties of hybrid rice for each nitrogen level can be well distinguished
 except for the highest nitrogen level, and no nitrogen level for each rice
 variety can be completely identified from the other five nitrogen levels.
 Further, several spectral indices combined with partial least squares
 (PLS) analysis were applied for estimating chlorophyll content of rice
 leaves from plants subject to different nitrogen levels, and a coefficient
 of determination (R2) of 97.8% and a ratio of performance to deviation
 (RPD) of 4.6 for all rice varieties indicated this as a preferable
 procedure. Experimental results demonstrated that vis/NIR spectroscopy can
 have a great potential for identification of rice varieties and evaluation
 of nitrogen fertilizer levels.
description: Rice chlorophyll
 measurement
DOI: 10.6078/d12d5x
title: Berkeley High Resolution (BEHR) OMI NO2 - Gridded pixels, daily profiles

description: The BEHR OMI NO2 product reprocesses tropospheric
 NO2 columns from the Ozone Monitoring Instrument (OMI) satellite
 using high resolution a priori NO2 profiles,
 surface reflectivity, and surface elevation data. This product uses
 NO2 profiles for the day retrieved, simulated by the WRF-Chem
 model at 12 km spatial resolution. The use of high spatial resolution
 NO2 profiles has been shown to better resolve urban/rural
 differences in NO2 column densities, and the use of day-to-day
 (rather than monthly average) profiles is especially important in
 applications that preferentially select observations upwind or downwind of
 a NOx source.
description: The methods for the BEHR product are described in detail in
 Laughner et al. (in prep). 
description: Each month of BEHR data is stored as a .tar.gz file (i.e. a tar
 archive compressed with gzip). These can be decompressed using 7zip or (on
 Mac/Linux) the command "tar -xzvf &lt;filename&gt;",
 e.g. "tar -xzvf OMI_BEHR-DAILY_US_v3-0A_200501.tar.gz" will
 expand OMI_BEHR-DAILY_US_v3-0A_200501.tar.gz  In
 addition to downloading the full dataset or manually downloading
 individual files, a Python program is available at https://github.com/CohenBerkeleyLab/BEHRDownloader that can perform bulk downloads of a subset of the files, as well as automatically uncompress the tar files. See the Readme in that repo for further usage information. For details on best practices for using the BEHR data, see the user guide PDF included in this repository.
DOI: 10.5061/dryad.vh8t993
title: Data from: High detectability with low impact: optimising large PIT tracking systems for cave-dwelling bats

description: Passive integrated transponder (PIT) tag technology permits the
 ‘resighting’ of animals tagged for ecological research without the need
 for physical re-trapping. While this is effective if animals pass within
 centimetres of tag readers, short-distance detection capabilities have
 prevented the use of this technology with many species. To address this
 problem, we optimised a large (15 m-long) flexible antenna system to
 provide a c. 8 m2 vertical detection plane for detecting animals in
 flight. We installed antennas at two roosting caves, including the primary
 maternity cave, of the critically endangered southern bent-winged bat
 (Miniopterus orianae bassanii) in south-eastern Australia. Testing of
 these systems indicated PIT-tags could be detected up to 105 cm either
 side of the antenna plane. Over the course of a three-year study, we
 subcutaneously PIT-tagged 2966 bats and logged over 1.4 million unique
 detections, with 97% of tagged bats detected at least once. The
 probability of encountering a tagged bat decreased with increasing
 environmental ‘noise’ (unwanted signal) perceived by the system. During
 the study we mitigated initial high noise levels by earthing both systems,
 which contributed to an increase in daily detection probability (based on
 the proportion of individuals known to be alive that were detected each
 day) from &lt;0.2 (noise level ≥30%) to 0.7-0.8 (noise level 5-15%).
 Conditional on a low (5%) noise level, model-based estimates of daily
 encounter probability were highest (&gt;0.8) during peak breeding
 season when both female and male southern bent-winged bats congregate at
 the maternity cave. In this paper we detail the methods employed and make
 methodological recommendations for future wildlife research using large
 antennas, including earthing systems as standard protocol and quantifying
 noise metrics as a covariate influencing the probability of detection in
 subsequent analyses. Our results demonstrate that large PIT antennas can
 be used successfully to detect small volant species, extending the scope
 of PIT technology and enabling a much broader range of wildlife species to
 be studied using this approach.
description: PIT data collected at
 Bat Cave, South AustraliaColumns are: yday (day
 of year), noise (mean daily noise level), detections (numbers of bats
 detected), ktba (number of bats known to be alive).suppData.csv
DOI: 10.6078/d1rw9g
title: MHD Field line tracing results

description: The zip files contain field line tracing results from a MHD simulation,
 which are used to create Figures 3 and 4 of a GRL paper,
 titled as "Investigation of Martian magnetic topology response to
 2017 September ICME."
DOI: 10.5061/dryad.p585k3p
title: Data from: A novel longitudinal framework aimed at improving the teaching of the neurologic examination

description: Objective To develop an educational framework basis for improving
 the teaching of the neurologic examination (NE) by asking German
 neurologists to (1) identify the basic elements of the screening NE and
 (2) nominate the steps they would deem mandatory for medical students to
 master. Methods We conducted a questionnaire-based survey among
 neurologists working in a hospital or ambulatory setting in southwest
 Germany. To define the screening NE, neurologists were asked to list the
 NE components they normally use in clinical encounters with patients in
 whom neurologic findings are unlikely. Furthermore, they were asked to
 identify additional elements of the NE which they would consider mandatory
 for students to master. Results Our neurologists nominated a set
 of 23 elements as being essential for a screening NE. There was high
 consensus among the 2 groups, and the results were concordant with
 international data. Furthermore, nearly 60 additional maneuvers of the NE
 were deemed obligatory for students to master. Conclusion Our
 results reinforce the international consensus for screening NE components
 and confirm a large set of additional examination steps that medical
 students should master, thereby indicating the need for an educational NE
 teaching concept. To solve this educational challenge, we propose a
 longitudinal curriculum that incorporates the “core + clusters” framework,
 thus combining the screening NE (core) with hypothesis-driven sets of
 maneuvers (clusters). Based on our data, we provide an initial proposal
 for the core and neurologic diagnostic clusters which is applicable to
 both novice and advanced learners across the continuum of training.
description: e-QuestionnaireOriginal German and translated English version of the survey instrumente-questionnaire.docxTable e-1. StudypopulationCharacteristics of respondents of the surveytable e-1_studypopulation.docx
DOI: 10.15468/dl.wqw4h3
title: Occurrence Download

description: A dataset containing 503984 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Swiss National Fauna Databank"
 ]
}

 The dataset includes 503984 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001869-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1gd48
title: STET modeling output files for 2017 Sept solar flare study at Mars

description: The zip file contains 9 STET output files for the 2017 Sept solar
 flare study at Mars. File names with 'pre',
 'pek', and 'pst' correspond to the pre-flare,
 peak-flare, and post-peak flare periods, respectively. File names with
 'atm', 'all', and 'dep' include background
 inputs for the STET model, electron differential number flux for different
 altitudes and pitch angles, and ion production rates,
 respectively.
DOI: 10.6078/d16085
title: Interview Proceedings with Delbert Anderson

description: The following are the proceedings of an interview between Hunter Hall
 (interviewer) and Delbert Anderson (interviewee). The text has been
 transcribed from email to this document for legibility. The interview
 occurred on May 3rd, 2018 and was conducted with intentions to use as
 primary evidence for Hall’s final paper due for the Music R1B (Spring
 2018) course at the University of California, Berkeley.
DOI: 10.7280/d1cd4c
title: Supporting Information: Toward learned chemical perception of force field typing rules

description: The Open Force Field Initiative seeks to to automate force field
 development in order to advance force fields and improve accuracy
 (openforcefield.org). An important part of this effort includes automating
 the determination of chemical perception --- that is, the way force field
 parameters are assigned to a molecule based on chemical environment. We
 developed a novel technology for this purpose, termed SMARTY.
 It generalizes atom typing by using direct chemical perception
 with SMARTS strings adopting a hierarchical approach to
 type assignment. The SMARTY technology enables creation of a move set in
 atom-typing space that can be used in a Monte Carlo optimization. We
 demonstrate the power of this approach with a fully automated procedure
 that is able to re-discover human-defined atom types in the traditional
 small molecule force field parm99/parm@Frosst. We furthermore extend this
 tool to direct chemical perception of valence types (bonds, angles, and
 torsions) via SMIRKS strings to create SMIRKY, and, again, assess
 how well the automated Monte Carlo scheme can discover the valence
 parameters in smirnoff99Frosst without human intervention. This repository
 contains input files, output files, anlysis results, and the required
 scripts to perform that analysis for a series of tests with SMARTY and
 SMIRKY. All tests were performed on three molecule sets: AlkEthOH
 is a simple set of 42 molecules with only alkanes, ethers, and
 alcohols; PhEthOH was created as an extension of this set to
 include aromatic carbons in addition to the alkanes for a total of 200
 molecules; and lastly, MiniDrugBank was created to mimic the
 complexity of the DrugBank database with a minimal number of molecules
 containing 371 druglike molecules in the final set
 (github.com/openforcefield/MiniDrugBank).  For more information
 on SMARTY and SMIRKY including the source code for these tools,
 instructions on their use, and detailed examples for implementation
 checkout the relevant github
 repository: github.com/openforcefield/smarty
description: These results were collected from SMARTY and SMIRKY simulations
 on three different molecule sets.  For details on these
 tools see our github
 repository: <strong>github.com/openforcefield/smarty</strong>
description: This repository includes input files, output files, and score vs.
 iteration plots for all SMARTY and SMIRKY simulations with every molecule
 set. <br> This also includes molecule files that are human and
 machine readable. <br> It contains heat map results shared here as
 images and as computer readable csv files. <br> This also includes
 all of the python scripts used to analyze these results and to create the
 figures in this paper. For more details on organization
 and contents see the internal README files
DOI: 10.5061/dryad.k6t1rj8
title: Quantum supremacy using a programmable superconducting processor

description: The tantalizing promise of quantum computers is that certain computational
 tasks might be executed exponentially faster on a quantum processor than
 on a classical processor. A fundamental challenge is to build a
 high-fidelity processor capable of running quantum algorithms in an
 exponentially large computational space. Here, we report using a processor
 with programmable superconducting qubits to create quantum states on 53
 qubits, corresponding to a computational state-space of dimension 2^53 ∼
 10^16. Measurements from repeated experiments sample the corresponding
 probability distribution, which we verify using classical simulations.
 While our processor takes about 200 seconds to sample one instance of a
 quantum circuit 1 million times, a state-of-the-art supercomputer would
 require approximately 10,000 years to perform the equivalent task. This
 dramatic speedup relative to all known classical algorithms provides an
 experimental realization of quantum supremacy on a computational task and
 heralds the advent of a much-anticipated computing paradigm.
description: This dataset defines the Random Quantum Circuits (RQCs) used in
 our quantum supremacy demonstration and lists the bitstrings observed in
 the experimental executions of the circuits on the Sycamore
 processor.
description: Please see Readme file.
DOI: 10.25338/b83886
title: Temperature-Dependent Dynamics of Molecular Dopant in Conjugated Polymer

description: Understanding the nature of dopant dynamics in the solid state is critical
 for improving the longevity and stability of organic electronic devices
 and for optimizing the dopinginduced solubility control (DISC) patterning
 method. In this work, we use quasi-elastic neutron scattering (QENS) to
 study the dynamics of the soluble p-type molecular dopant
 tetrafluoromethyloxycarbonyltricyanoquinodimethane (F4MCTCNQ) in the
 semiconductive polymer poly(3-hexylthiophene-2,5-diyl)
 (P3HT). Specifically, fast dynamics (ps−ns) of the dopant, such
 as the methyl and the methoxycarbonyl group rotations, are observed in
 QENS experiments.
description: QENS measurements were performed on the backscattering
 spectrometer called BASIS at the Spallation Neutron Source (SNS) at Oak
 Ridge National Laboratory (ORNL) with an energy resolution of 3.5 μeV
 (full width at half-maximum, fwhm), a dynamic range of ±170 μeV, and a
 scattering wavevector Q range from 0.3 to 2.0 Å−1. The elastic scans were
 obtained from 50 to 375 K at a heating rate of 1 K/min, and the high
 statistical QENS spectra were recorded at 273, 323, and 373 K. The spectra
 collected at 50 K were used as the instrument resolution function, and all
 the data were corrected for detector efficiency using a vanadium
 standard. To prepare the blend sample for QENS
 measurements, solutions of F4MCTCNQ and d-P3HT in deuterated chlorobenzene
 were first mixed to achieve a 17% mole fraction of dopant to polymer. The
 blend solution was then drop-cast onto a clean glass slide.  The sample
 was placed into a vacuum chamber to completely evaporate the solvent. The
 resulting blend layer was scraped from the glass slide using a clean razor
 blade. Both blend and neat samples were ground to a power using a mortar
 and pestle for 15 min and then weighed prior to being loaded into a 0.5 mm
 thick flat aluminum container for further analysis.<br>
DOI: 10.5061/dryad.38100f6
title: Data from: Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA (eDNA) metabarcoding

description: Biological surveys based on visual identification of the biota are
 challenging, expensive, and time consuming, yet crucial for effective
 biomonitoring. DNA metabarcoding is a rapidly developing technology that
 can also facilitate biological surveys. This method involves the use of
 next generation sequencing technology to determine the community
 composition of a sample. However, it is uncertain as to what biological
 substrate should be the primary focus of metabarcoding surveys. This study
 aims to test multiple sample substrates (soil, scat, plant material and
 bulk arthropods) to determine what organisms can be detected from each and
 where they overlap. Samples (n = 200) were collected in the Pilbara (hot
 desert climate) and Swan Coastal Plain (hot mediterranean climate) regions
 of Western Australia. Soil samples yielded little plant or animal DNA,
 especially in the Pilbara, likely due to conditions not conducive to
 long-term preservation. In contrast, scat samples contained the highest
 overall diversity with 131 plant, vertebrate, and invertebrate Families
 detected. Invertebrate and plant sequences were detected in the plant (86
 Families), pitfall (127 Families), and vane trap (126 Families) samples.
 In total 278 Families were recovered from the survey, 217 in the Swan
 Coastal Plain and 156 in the Pilbara. Aside from soil, 22-43% of the
 Families detected were unique to the particular substrate and community
 composition varied significantly between substrates. These results
 demonstrate the importance of selecting appropriate metabarcoding
 substrates when undertaking terrestrial surveys. If the aim is to broadly
 capture all biota then multiple substrates will be required.
description: DADA_trnL
 Demultiplexed
 sequences from the trnL (plants) assay. Includes samples from pitfall
 traps, vane traps, soil, scat, and plant material samples. Prepared for
 DADA2 script.   
 DADA_12SV5
 Demultiplexed
 sequences from the 12SV5 (vertebrates) assay. Includes scat samples only.
 Prepared for DADA2 script.   
 DADA_rbcL
 Demultiplexed
 sequences from the rcbL (plant) assay. Includes only plant material
 samples. Prepared for DADA2 script.   
 DADA_ZBJArt
 Demultiplexed
 sequences from the ZBJ-Art (arthropod) assay. Includes pitfall trap, vane
 trap, soil, scat, and plant material samples. Prepared for DADA2
 script   
 DADA_Ant236
 Demultiplexed
 sequence files of the Ant236 Assay. Contains pitfall trap, vane trap,
 scat, and plant samples. Prepared for DADA2 script.   
 mapping_files
 Sample
 descriptions, divided by the assays. Identifies the sequencing run, Sample
 ID, Substrate, and Site of each sample.   
 DADA2_script_dryad Example R script for sequence analysis using DADA2. This script was run separately for each assay.   <strong>DADA_Summary</strong>   This folder contains the summaries from the DADA2 workflow, which shows the number of sequences removed in the filtering and denoising steps.
DOI: 10.5061/dryad.6n2c2n2
title: Data from: A threat to loyalty: Fear of missing out (FOMO) leads to reluctance to repeat current experiences

description: We investigate a popular but underresearched concept, the fear of missing
 out (FOMO), on desirable experiences of which an individual is aware, but
 in which they do not partake. Through laboratory and field studies, we
 establish FOMO’s pervasiveness as a psychological phenomenon, present
 real-life contexts wherein FOMO may be experienced, and explore its
 behavioral consequences. Specifically, we show that FOMO poses a threat to
 loyalty by decreasing one’s intentions to repeat a current experience and
 may decrease the valuation of the current experience.
description: Study 1A_summer school
 lab study Data used in our
 analysis of Study 1A summer school lab study.   
 Study 1B_office field
 study Data used in study 1B
 office field study.   
 Study1C_museum field
 study Data used in study 1C museum field
 study
DOI: 10.15468/dl.hc635q
title: Occurrence Download

description: A dataset listing the 16711 species recorded in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "StateProvince is one of (Indiana, Illinois, Michigan, Wisconsin, Ohio, Pennsylvania, Maryland, Delaware, New York, Maine, Rhode Island, Vermont, MAssachusetts, New Hampshire, New Jersey, Connecticut, New Brunswick, Ontario, Nova Scotia, Quebec)",
 "TaxonKey is Coleoptera"
 ]
}

 The dataset's 16711 records were derived from 267 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001861-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.