cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4r83
title: Mobility-assisted psuedo-MS3 sequencing of protein ions

description: The sequencing of intact proteins within a mass spectrometer has many
 benefits but is frequently limited by the fact that tandem mass
 spectrometry (MS/MS) techniques often generate poor sequence coverages
 when applied to protein ions. To overcome this limitation exotic MS/MS
 techniques that rely on lasers and radical chemistry have been developed.
 These techniques generate high sequence coverages, but they require
 specialized instrumentation, create products through multiple dissociation
 mechanisms, and often require long acquisition times. Recently, we
 demonstrated that protein ions can be dissociated in a trapped ion
 mobility spectrometry (TIMS) device prior to mobility separation in a
 commercial timsTOF. All generated product ions were distributed throughout
 the mobility dimension and this separation enabled deconvolution of
 complex tandem mass spectra and could enable facile pseudo-MS3
 interrogation of generated product ions with the downstream quadrupole and
 collision cell. A second activation step improves sequence coverage
 because the most labile bonds have been depleted during the first
 dissociation and subsequent dissociation events are more evenly
 distributed throughout the product ion backbone. In this work, we explore
 the potential of this mobility-assisted pseudo-MS3 (MAP) method on a
 commercial timsTOF and timsTOF Pro 2. We demonstrate that while MAP only
 generates 92% of the sequence coverage of the most effective MS/MS
 technique, it accomplished this feat in 1.5 mins and could be facilely
 integrated with liquid chromatographic separations.
description: Compressed Bruker data files with all mass spectra.
description: # Mobility-Assisted Psuedo-MS3 Sequencing of Protein Ions
 [https://doi.org/10.5061/dryad.mpg4f4r83](https://doi.org/10.5061/dryad.mpg4f4r83) In this deposit are the raw Bruker datafiles that were used to generate all figures found within the manuscript with the same title. The protein analyzed and the instrument utilized is explicitly indicated in the title of each data file. We recommend utilizing the software Bruker DataAnalysis to view both mass and mobility spectra, however, any software package capable of analyzing timsTOF data can be employed. The methods section in the accompanying manuscript describe in detail how the instrumental parameters are altered over the time course of the measurement.
DOI: 10.15468/dl.ewapwx
title: Occurrence Download

description: A dataset listing the 8011 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.25924 40.50165,-73.74719 40.58325,-73.76045 40.62201,-73.71251 40.7485,-73.79411 40.85866,-73.91447 40.91782,-74.07564 40.64853,-74.16948 40.64445,-74.25924 40.50165))",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 8011 records were derived from 181 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004027-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tmpg4f56x
title: Data from: Island biogeography and life-history traits stabilize island bird communities

description: Islands are model systems for testing and developing ecological theories.
 Despite extensive research on island biodiversity, the importance of the
 biogeographic context for biodiversity–stability relationships is poorly
 understood. We addressed this knowledge gap by integrating the Equilibrium
 Theory of Island Biogeography (ETIB) with a functional perspective to
 explore island biodiversity–stability relationships. We conducted annual
 breeding bird surveys across 36 land-bridge islands in eastern China over
 13 years. Using this long-term dataset, we quantified avian temporal
 community stability (and its components of population stability and
 population asynchrony) and tested how island biogeographic factors (i.e.,
 island area, isolation, colonization rates, and extinction rates) and
 biodiversity facets (i.e., species richness, average population size, and
 life-history traits) interact to influence stability. We found larger
 islands supported higher species richness due to colonization–extinction
 dynamics and habitat heterogeneity, which in turn promote both population
 stability and asynchrony. In addition, larger islands harbored larger and
 individually more stable populations over time. In contrast, island
 isolation had a weak net effect on stability, as its positive and negative
 influences through different pathways balanced each other out.
 Furthermore, species with ‘fast’ life-history traits, characterized by
 shorter generation times, contributed more to community stability. These
 findings clarify multiple pathways through which biogeographic factors
 shape avian community dynamics on islands. Our study thus illustrates how
 island biotas maintain community stability and provides insights for
 preserving biodiversity and ecosystem functioning in fragmented or
 island-like landscapes facing rapid biodiversity loss in an era of global
 change.
description: # Data from: Island biogeography and life-history traits stabilize island
 bird communities
 [https://doi.org/10.5061/dryad.tmpg4f56x](https://doi.org/10.5061/dryad.tmpg4f56x) **File:** Final_data.csv * Island ID, community stability (log-transformed; com.stab.log) * population stability (log-transformed; pop.stab.log) * population asynchrony (pop.asyn) * statistical-averaging effect (log-transformed; statistical.log) * compensatory effect (log-transformed; compensatory.log) * species richness (log-transformed; SR.log) * fast-slow trait diversity (FDis fast-slow) * fast-slow trait dominance (CWM fast-slow) * island area (log-transformed; A.log) * Isolation (distance to the mainland, Dm) * colonization rates (Col) * extinction rates (Ext) * community-weighted mean of hand-wing index (CWM HWI) * average population size (log-transformed; average_population_size.log) on 36 study islands in the Thousand Island Lake, China.
DOI: 10.15468/dl.4dvqt7
title: Occurrence Download

description: A dataset containing 361 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spratelloides gracilis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 361 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004045-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3ffbg79s8
title: Paradoxes in the co-evolution of contagions and institutions

description: Epidemic models study the spread of undesired agents through populations,
 be it infectious diseases through a country, misinformation in social
 media, or pests infesting a region. In combating these epidemics, we rely
 neither on global top-down interventions, nor solely on individual
 adaptations. Instead, interventions commonly come from local institutions
 such as public health departments, moderation teams on social media
 platforms, or other forms of group governance. Classic models, which are
 often individual or agent-based, are ill-suited to capture local
 adaptations. We leverage developments of institutional dynamics based on
 cultural group selection to study how groups attempt local control of an
 epidemic by taking inspiration from the successes and failures of other
 groups. Incorporating institutional changes into epidemic dynamics reveals
 paradoxes: a higher transmission rate can result in smaller outbreaks as
 does decreasing the speed of institutional adaptation. When groups
 perceive a contagion as more worrisome, they can invest in improved
 policies and, if they maintain these policies long enough to have impact,
 lead to a reduction in endemicity. By looking at the interplay between the
 speed of institutions and the transmission rate of the contagions, we find
 rich co-evolutionary dynamics that reflect the complexity of known
 biological and social contagions.
description: # Paradoxes in the co-evolution of contagions and institutions
 [https://doi.org/10.5061/dryad.3ffbg79s8](https://doi.org/10.5061/dryad.3ffbg79s8) We use group-based models as set of master equations to study the impact of institutional policies on contagion. We find that incorporating institutional changes into epidemic dynamics reveals paradoxes: a higher transmission rate can result in smaller outbreaks as does decreasing the speed of institutional adaptation. See README.md within the included zip file for more details.  ## Code/Software The code to reproduce the results of this paper can be found at [jstonge/hello-gmes/src/examples](https://github.com/jstonge/hello-gmes/tree/main/src/examples). The code depends on the Git submodule [jstonge/InstitutionalDynamics.jl, ](https://github.com/jstonge/InstitutionalDynamics.jl)which contain the model written in [Julia](https://julialang.org/). Make sure to follow the instructions on the README to get started. In addition to the script to reproduce the results of the paper, the repository contains code to run the associated [Observable Framework](https://observablehq.com/framework/) app (a live version can be found [here](https://joint-lab.observablehq.cloud/hello-gmes/)). If you are interested in the full data pipeline of the project, please consult the [Makefile](https://github.com/jstonge/hello-gmes/blob/main/Makefile) where we keep track in details of the flow of our data.
DOI: 10.15468/dl.cazrep
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-66.12437 0.33359,-65.8395 -1.31869,-64.35814 -1.63205,-60.51232 -5.24998,-57.60658 -4.30989,-56.8659 -2.91399,-58.91701 -2.23029,-61.82275 -1.11928,-62.05065 0.19115,-66.12437 0.33359))",
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyhypopomus hendersoni"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004049-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n8pk0p34d
title: Data from: The breath shape controls intonation of mouse vocalizations

description: Intonation in speech is the control of vocal pitch to layer expressive
 meaning to communication, like increasing pitch to indicate a question.
 Also, stereotyped patterns of pitch are used to create distinct sounds
 with different denotations, like in tonal languages and, perhaps, the ten
 sounds in the murine lexicon. A basic tone is created by exhalation
 through a constricted laryngeal voice box, and it is thought that more
 complex utterances are produced solely by dynamic changes in laryngeal
 tension. But perhaps, the shifting pitch also results from altering the
 swiftness of exhalation. Consistent with the latter model, we describe
 that intonation in most vocalization types follows deviations in
 exhalation that appear to be generated by the re-activation of the
 cardinal breathing muscle for inspiration. We also show that the brainstem
 vocalization central pattern generator, the iRO, can create this breath
 pattern. Consequently, ectopic activation of the iRO not only induces
 phonation, but also the pitch patterns that compose most of the
 vocalizations in the murine lexicon. These results reveal a novel
 brainstem mechanism for intonation.
description: # The breath shape controls intonation of mouse vocalizations
 [https://doi.org/10.5061/dryad.n8pk0p34d](https://doi.org/10.5061/dryad.n8pk0p34d) The contents of the data sets include the data files for each experiment (airflow trace, sounds file, opto pulse timestmaps, and EMG). ## Description of the data and file structure Airflow for baseline vocalization recordings:   The plethysmography chamber was modified to accommodate a microphone to record vocalizations (CM16/CMPA, Avisoft Bioacoustics) and the airflow in the chamber was measured by a spirometer (FE141, AD instruments). Both data streams were acquired through a DAQ board (PCI-6251, National Instruments) and written to disk for offline analysis. Sound was acquired at 400 kHz and airflow at 1 kHz. Files are annotated with the date_cage number_animal ID_trial number .wav file – waveform audio file of the sound spectrogram .txt file – breathing airflow sampled at 1 kHz. \--&gt; When these recordings are combined with optogenetics, an additional .txt file is included \_opto that shows when the light signal is provided (values &gt; 1). \--&gt; When recordings are combined with EMGs, the files are annotated with the channel used for acquisition and the corresponding muscle.  \_ch1_larynx_ch2_dia indicates that the channel 1 recordings is of the laryngeal muscle and channel 2 is the diaphragm muscle. \--&gt; Empty cells have 'null' values. ## Sharing/Access information Please contact Kevin Yackle if more information is needed to analyze the data. ## Code/Software The code for analysis is available on the Yackle Lab Github
DOI: 10.15468/dl.36hzmz
title: Occurrence Download

description: A dataset containing 34470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Machine Observation)",
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Aedes albopictus",
 "Year 2000-2025"
 ]
}

 The dataset includes 34470 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004046-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f1vhhmh4s
title: Tulaneia amabilia, a new erniettomorph from the Wood Canyon Formation, Nevada and the age of the Ediacaran-Cambrian transition in the Great Basin

description: Specimens of Tulaneia amabilia n. gen n. sp. [previously Ernietta
 plateauensis Pflug] discovered by RJH in 1991 at a site in the Montgomery
 Mountains near Johnnie, Nevada, are described for the first time. All of
 the material from the original locality was from float, but its
 stratigraphic position was clearly within the lowest siliciclastic to
 dolostone interval of the lower member of the Wood Canyon Formation
 (LMWCF); this was confirmed by subsequent discoveries. As the upper part
 of the LMWCF contains Treptichnus pedum (Seilacher), the
 Ediacaran-Cambrian boundary has long been drawn at its first appearance.
 However, in the Esmeralda Member of the Deep Spring Formation in the
 White-Inyo Mountains, California and at Mount Dunfee, Nevada, another
 Cambrian ichnofossil—‘Plagiogmus’ [now Psammichnites gigas arcuatus
 (Roedel)]—is found just beneath the nadir of the basal Cambrian isotope
 excursion (BACE). As the nadir of the BACE excursion is older than ~539 Ma
 in Mexico, the oldest occurrences of Treptichnus pedum in the LMWCF are
 latest—not earliest— Fortunian in age, and there is no need to reduce the
 age of the eon boundary from ~539 to ~533 Ma. Tulaneia resembles Ernietta
 and other erniettomorphs in being composed of tubular modules with planar
 common surfaces, but its overall shape was tabular and unidirectional
 rather than sack or frond shaped. We also illustrate and briefly describe
 other trace and body fossils from the LMWCF and re-illustrate previously
 published specimens of Psammichnites gigas arcuatus in order to document
 its earliest occurrence in the Great Basin.
description: # Tulaneia amabilia, a new erniettomorph from the Wood Canyon Formation,
 Nevada and the age of the Ediacaran-Cambrian transition in the Great Basin
 [https://doi.org/10.5061/dryad.f1vhhmh4s](https://doi.org/10.5061/dryad.f1vhhmh4s) ## Description of the data and file structure Tabulated stratigraphic measurements and occurrences of key fossils and other geological criteria in sections through the Ediacaran-Cambrian lower member of the Wood Canyon Formation (LMWCF) in California and Nevada, presented as a Microsoft Excel file saved as a pdf. The columns filled with numbers represent measured stratigraphic sections, labeled and referenced accordingly; the gray-shaded cells refer to specimens that are illustrated in this work or in the literature, as shown in order from left to right, respectively. The stratigraphic heights of the three main dolostones of the LMWCF are highlighted in orange to enable visual correlation of the measured sections; heights in sections are in meters and are taken from the authors' field records and/or the cited references. Unfilled data cells mean that no information pertaining to this stratigraphic level and/or taxon is available. ## Sharing/Access information Links to other publicly accessible locations of the data: None. Data was derived from the following sources: Measured stratigraphic sections, literature.
DOI: 10.15468/dl.xjupkp
title: Occurrence Download

description: A dataset containing 11328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyotum"
 ]
}

 The dataset includes 11328 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004048-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xmqy46
title: Occurrence Download

description: A dataset containing 649996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 649996 records from 269 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004015-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ck57j5
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-109.52601 34.78921,-104.0367 34.78921,-104.0367 44.89273,-109.52601 44.89273,-109.52601 34.78921))",
 "HasCoordinate is true",
 "TaxonKey is Satyrium liparops"
 ]
}

 The dataset includes 132 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004052-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.280gb5mz5
title: ZAP affects Zika virus RNA interactome - Table S1-ChIRP-MS data

description: One of the most recent advances in the analysis of viral RNA–cellular
 protein interactions is the Comprehensive Identification of RNA-binding
 Proteins by Mass Spectrometry (ChIRP-MS). Here, we used ChIRP-MS in
 mock-infected and Zika-infected wild-type cells and cells knockout for the
 zinc finger CCCH-type antiviral protein 1 (ZAP). We characterized
 “ZAP-independent” and “ZAP-dependent” cellular protein interactomes
 associated with flavivirus RNA and found that ZAP affects cellular
 proteins associated with Zika virus RNA. The ZAP-dependent interactome
 identified with ChIRP-MS provides potential ZAP co-factors for antiviral
 activity against Zika virus and possibly other viruses. Identifying the
 full spectrum of ZAP co-factors and mechanisms of how they act will be
 critical to understanding the ZAP antiviral system and may contribute to
 the development of antivirals.
description: # ZAP affects Zika virus RNA interactome - Table S1-ChIRP-MS data
 [https://doi.org/10.5061/dryad.280gb5mz5](https://doi.org/10.5061/dryad.280gb5mz5) Supplementary data ## Description of the data and file structure **Table S1** **- ChIRP-MS data** Table S1 ChIRP_MS data, **sheet** “**C Extended Zika interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. RNA helicases are highlighted in yellow. Table S1 ChIRP_MS data, **sheet** “**D Reference Ooi et al., 2019**” – The same proteins in both studies are highlighted in red. Table S1 ChIRP_MS data, **sheet** “**F ZAP-independent interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. Table S1 ChIRP_MS data, **sheet** “**H ZAP-dependent interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. RNA helicases are highlighted in yellow. The empty cells in files are a result of the programs used.
DOI: 10.5061/dryad.gb5mkkwzs
title: Decomposition of bark beetle-attacked trees after mortality varies across forests

description: Data are from a 2 year experiment examining differences in decomposition
 processes between bark beetle-attacked trees and trees not attacked by
 bark beetles in three sites spanning a broad geographic area.
 Specifically, in Honduras, and Mississippi and Arizona, USA, we felled one
 recently bark beetle-attacked and one apparently healthy conspecific tree
 at each site that was cut into 120 experimental logs. Logs of each tree
 (attacked or unattacked) were assigned one of three metal mesh covering
 treatments: 1) fully covered to exclude all macroinvertebrates, 2) covered
 from above to exclude secondary bark beetle colonization, 3) no cover to
 allow all detrital food web organisms. Half of all logs at each site was
 collected after 1 and 2 years and the density loss, insect visual damage
 rating, and abundance of termites, ants, and beetles
 was measured.
description: # Decomposition of bark beetle-attacked trees after mortality varies
 across forests
 [https://doi.org/10.5061/dryad.gb5mkkwzs](https://doi.org/10.5061/dryad.gb5mkkwzs) In Honduras, and Mississippi and Arizona, USA, Trees were felled and cut into sixty 10 cm sections (hereafter referred to as logs). Logs from both attacked and unattacked trees were randomly assigned to one of three covering treatments (n =20 per treatment/ tree type) to determine the relative contributions of microbes and invertebrates to decomposition rates: 1) fully covered (hereafter: FC), 2) covered from above (hereafter: HC (i.e., Half Covered), and 3) no covering (hereafter: NC). FC and HC logs were outfitted with stainless steel fine-mesh metal cloth (mesh size 0.26 ×0.47 mm). Half of all logs at each site was collected after ~1 and 2 years and the density loss, insect visual damage rating, and abundance of termites, ants, and beetles was measured. Insects were extracted using hanging cloth Berlese Funnels over 5 days with a 40W halogen light. Ants, Termites, and Beetles (order level) were then separated and counted. Wood density was determined after insect extraction, by cutting two ~8 cm3 cube subsamples of the logs (~2 cm × 2 cm x 2 cm) from the log sapwood (SW) and dried at 105 ◦C for 48 h before weighing. Visual insect damage rating (hereafter VIDR) was also assessed from wood cube subsamples based on an adapted AWPA E1 scale: Briefly, 6 indicated wood was very severely attacked and easily broken and 0 indicated no damage (detailed methods are in Supplementary material). ## Description of the data and file structure Each column in the data file is described on the metadata sheet of the excel file. ## Sharing/Access information Data was derived from the following sources: * [https://doi.org/10.1016/j.foreco.2023.121636](https://doi.org/10.1016/j.foreco.2023.121636)