cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h44j0zpqm
title: Additions to the knowledge of the genus Helvella in Europe: new records and de novo description of five species from the Nordic region

description: Helvella is a species-rich genus, forming a large variation of astounding
 ascocarps in many different habitats. During the last decade, molecular
 markers and morphological characters have been combined to delimit and
 identify cryptic species in this genus. We report on a list of 54 species
 of Helvella s.s. in the Nordic region and describe five new species, i.e.
 H. bresadolae, H. convexa, H. japonica, H. nordlandiae and H. oroarctica.
 The morphological and molecular characteristics of the new species and the
 emended / hypocrateriformis, / fibrosa-macropus, and / fallax-pezizoides
 lineages of Helvella s.s. are shortly commented upon. Further, we include
 a discussion of the distribution of species in the Nordic region based on
 a large set of studied collections. The ecological versatility and
 variable geographic patterns of these species indicate that cryptic
 species may have contrasting ecology in their local habitats.
description: DNA from individual specimens
 was extracted using the E.Z.N.A.®HP Fungal DNA Kit (Omega Biotek D3195),
 following the slightly modified procedure from Skrede et al. (2017). The
 three genetic markers, heat shock protein 90 (<em>hsp)</em>,
 RNApolymerase II second largest subunit (<em>rpb2</em>) and
 nuclear ribosomal large subunit DNA (LSU) were amplified using PuReTaq
 Ready-To-Go PCR Beads (GEhealthcare, Waukesha, WI), and purified with
 10´ ExoSAP-IT (GEhealthcare, Waukesha, WI). For
 primer sequences, detailed PCR conditions, and sequencing techniques, see
 the procedures in Skrede et al. (2017). In addition to sequences produced
 in the present study, sequences from a representative selection of
 <em>Helvella</em> species were downloaded from GenBank and
 included for reference. The sequences were automatically aligned using the
 MUSCLE v. 3.8.425 (Edgar 2004) plugin in Geneious Prime v. 2019.2.3
 (Biomatters, Auckland), followed by manual inspection.
description: The files are in fasta format and can be opened by any text
 editor.
DOI: 10.5061/dryad.7sqv9s4x3
title: Detecting ecological traps in human-altered landscapes: A case study of the thick-billed longspur nesting in croplands

description: Conversion of the North American prairies to cropland remains a prominent
 threat to grassland bird populations. Yet, a few species nest in these
 vastly modified systems. The thick-billed longspur (Rhynchophanes
 mccownii) is an obligate grassland bird whose populations have declined 4%
 annually during the past 50 years. Thick-billed longspurs historically
 nested in recently disturbed or sparsely vegetated patches within native
 mixed-grass prairie, but observations of longspurs in spring cereal and
 pulse crop fields during the breeding season in northeastern Montana, USA
 suggest such fields also provide cues for habitat selection. Maladaptive
 selection for poor-quality habitat may contribute to ongoing declines in
 longspur populations, but information on thick-billed longspur breeding
 ecology in crop fields is lacking. We hypothesized that these crop fields
 may function as ecological traps; specifically, we expected that crop
 fields may provide cues for territory selection, but frequent human
 disturbance and increased exposure to weather and predators would have
 negative consequences for reproduction. To address this hypothesis, we
 compared measures of habitat selection (settlement patterns and trends in
 abundance) and productivity (nest density, nest survival, and number of
 young fledged) between crop fields and native grassland sites during
 2020–21. Across both years, settlement patterns were similar between site
 types and occupancy ranged from 0.52 ± 0.17SE to 0.99 ± 0.01 on April 7
 and 30, respectively. Early season abundance differed by year, and changes
 in abundance during the breeding season appeared to be associated with
 precipitation-driven vegetation conditions rather than habitat type. While
 an index of nest density was lower in crop than native sites, the number
 of young fledged per successful nest (2.9 ± 0.18SE) and nest survival
 (0.24 ± 0.03 SE; n=222 nests) were similar for crop and native sites.
 Collectively, the data did not support our ecological trap hypothesis:
 longspurs did not exhibit a clear preference for crop sites and
 reproductive output was not significantly reduced. Our results indicate
 that croplands may provide alternative breeding habitat within a
 human-dominated landscape.
DOI: 10.5061/dryad.vmcvdncxs
title: Data From: Spot-fire distance increases disproportionately for wildfires compared to prescribed fires as grasslands transition to Juniperus woodlands

description: Woody encroachment is one of the greatest threats to grasslands globally,
 depleting a suite of ecosystem services, including forage production and
 grassland biodiversity. Recent evidence also suggests that woody
 encroachment increases wildfire danger, particularly in the Great Plains
 of North America, where highly volatile Juniperus spp. convert grasslands
 to an alternative woodland state. Spot-fire distances are a critical
 component of wildfire danger, describing the distance over which embers
 from one fire can cause a new fire ignition, potentially far away from
 fire suppression personnel. We assess changes in spot-fire distances as
 grasslands experience Juniperus encroachment to an alternative woodland
 state and how spot-fire distances differ under typical prescribed fire
 conditions compared to conditions observed during wildfire. We use
 BehavePlus to calculate spot-fire distances for these scenarios within the
 Loess Canyons Experimental Landscape, Nebraska, U.S.A., a 73,000-ha
 ecoregion where private-lands fire management is used to reduce woody
 encroachment and prevent further expansion of Juniperus fuels. We found
 prescribed fire used to control woody encroachment had lower maximum
 spot-fire distances compared to wildfires and, correspondingly, a lower
 amount of land area at risk to spot-fire occurrence. Under more extreme
 wildfire scenarios, spot-fire distances were 2 times higher in grasslands,
 and over 3 times higher in encroached grasslands and Juniperus woodlands
 compared to fires burned under prescribed fire conditions. Maximum
 spot-fire distance was 450% greater in Juniperus woodlands compared to
 grasslands and exposed an additional 14,000 ha of receptive fuels, on
 average, to spot-fire occurrence within the Loess Canyons Experimental
 Landscape. This study demonstrates that woody encroachment drastically
 increases risks associated with wildfire, and that spot fire distances
 associated with woody encroachment are much lower in prescribed fires used
 to control woody encroachment compared to wildfires.
description: This data was generated using BehavePlus software to calculate
 maximum spot-fire distance under multiple different wind speeds and woody
 encroachment scenarios. BehavePlus models were parameterized using wind
 speeds listed in the data set along with additional fuel parameters
 outlined in the associated manuscript (10.1371/journal.pone.0283816),
 which were used to represent 4 different encroachment scenarios: grassland
 state, encroached grassland, torching tree, and woodland. Prescribed fires
 were predicted to only occur under wind speeds between 0–20 mph while
 wildfires could occur between 0–80 mph.
description: BehavePlus (https://www.frames.gov/behaveplus/home) was used to generate the data included in this submission.
DOI: 10.25345/c5fj29s4s
title: MassIVE MSV000100612 - Optimizing nanoLC-TIMS-TOF and lipidomics sample preparation for low volume of plasma
title: These datasets correspond to the paper, "Optimizing nanoLC-TIMS-TOF and lipidomics sample preparation for low volume of plasma". In this study, two lipidomics extraction protocols suitable for nanoLC were compared. Effects of mobile phase buffer concentration to lipid coverage and overall nanoLC performance were also evaluated.
DOI: 10.5061/dryad.jwstqjqfd
title: Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2: Part 2

description: The Tec-family kinase Btk contains a lipid-binding Pleckstrin homology and
 Tec homology (PH-TH) module connected by a proline-rich linker to a “Src
 module”, an SH3-SH2-kinase unit also found in Src-family kinases and Abl.
 We showed previously that Btk is activated by PH-TH dimerization, which is
 triggered on membranes by the phosphatidyl inositol phosphate PIP3, or in
 solution by inositol hexakisphosphate (IP6) (Wang et al. 2015,
 https://doi.org/10.7554/eLife.06074). We now report that the ubiquitous
 adaptor protein growth-factor-receptor-bound protein 2 (Grb2) binds to and
 substantially increases the activity of PIP3-bound Btk on membranes. Using
 reconstitution on supported-lipid bilayers, we find that Grb2 can be
 recruited to membrane-bound Btk through interaction with the proline-rich
 linker in Btk. This interaction requires intact Grb2, containing both SH3
 domains and the SH2 domain, but does not require that the SH2 domain be
 able to bind phosphorylated tyrosine residues – thus Grb2 bound to Btk is
 free to interact with scaffold proteins via the SH2 domain. We show that
 the Grb2-Btk interaction recruits Btk to scaffold-mediated signaling
 clusters in reconstituted membranes. Our findings indicate that
 PIP3-mediated dimerization of Btk does not fully activate Btk, and that
 Btk adopts an autoinhibited state at the membrane that is released by
 Grb2.
description: The dataset was collected By TIRF microscopy, a description of
 the microscope is included in the manuscript Materials and
 Methods. For each TIFF, an associated set of single
 molecule tracks is included, processed via Trackmate (FIJI, Image
 J).
description: We suggest FIJI (Image J) for opening the included TIFF files.
 Any program capable of opening CSV format will work for the tracking data,
 however, Vim and Excel both work well.
DOI: 10.5061/dryad.m63xsj471
title: Experimental measurements and uncertainty analysis for validation of the Building Electrical Efficiency Analysis Model (BEEAM)

description: This dataset includes experimental measurements taken on a laboratory
 testbed at Colorado State University that was used for model validation of
 a software toolkit, the Building Electrical Efficiency Analysis Model
 (BEEAM). This toolkit was developed for comparing electrical efficiency of
 AC versus DC distribution systems in buildings. The testbed emulated loads
 found in a small office building and included laptop computer chargers,
 LED lighting systems, and miscellaneous DC and AC loads. Measurements were
 taken under AC and DC configurations in electrically balanced and
 unbalanced loading conditions. Also included in the dataset is an
 uncertainty analysis. A complete description of the testbed, hardware,
 measurements and uncertainty analysis is contained in the paper cited
 below.   Avpreet Othee, James Cale, Arthur Santos, Stephen Frank,
 Daniel Zimmerle, Omkar Ghatpande, Gerald Duggan and Daniel Gerber, “A
 Modeling Toolkit for Comparing AC and DC Electrical Distribution
 Efficiency in Buildings,” Energies, 2023 (accepted, publication in
 progress).
description: Data was collected using a Keysight multifunction switch
 measuring unit (MU) model 34980A with Keysight 34921T multiplexer and a
 Keysight PA2203A power analyzer.
DOI: 10.25338/b82w7q
title: Circularity of lithium-ion battery materials in electric vehicles

description: Batteries have the potential to significantly reduce greenhouse gas
 emissions from on-road transportation. However, environmental and social
 impacts of producing lithium-ion batteries, particularly cathode
 materials, and concerns over material criticality are frequently
 highlighted as barriers to widespread electric vehicle adoption. Circular
 economy strategies, like reuse and recycling, can reduce impacts and
 secure regional supplies. To understand the potential for circularity, we
 undertake a dynamic global material flow analysis of pack-level materials
 that includes scenario analysis for changing battery cathode chemistries
 and electric vehicle demand. Results are produced regionwise and through
 the year 2040 to estimate the potential global and regional circularity of
 lithium, cobalt, nickel, manganese, iron, aluminum, copper, and graphite,
 although the analysis is focused on the cathode materials. Under idealized
 conditions, retired batteries could supply 60% of cobalt, 53% of lithium,
 57% of manganese, and 53% of nickel globally in 2040. If the current mix
 of cathode chemistries evolves to a market dominated by NMC 811, a low
 cobalt chemistry, there is potential for 85% global circularity of cobalt
 in 2040. If the market steers away from cathodes containing cobalt, to an
 LFP-dominated market, cobalt, manganese, and nickel become less relevant
 and reach circularity before 2040. For each market to benefit from the
 recovery of secondary materials, recycling and manufacturing
 infrastructure must be developed in each region.
description: This data was collected through various sources, including from
 EV Volumes, International Energy Agency, Argonne National Lab, and
 published articles. A model was created with R to process the
 data. 
description: R is required to open the models.
DOI: 10.6084/m9.figshare.31169582
title: Phylogenomic insights into Taphrinomycotina and genomic features of <i>Saitoella coloradoensis</i> based on whole-genome sequencing at the chromosome level, with a proposal of the new class Saitoellomycetes

description: Taphrinomycotina, a subphylum of the phylum Ascomycota, comprises fungi with diverse morphologies and ecologies. <i>Saitoella</i> and <i>Savitreella</i> are genera of red-colored yeasts within Taphrinomycotina, but their precise phylogenetic positions have remained controversial. In this study, we sequenced the whole genomes of <i>Saitoella coloradoensis</i> and <i>Savitreella phatthalungensis</i> in order to elucidate their phylogenetic relationships using a phylogenomic approach based on chromosome-level genome assemblies generated by long-read sequencing technologies. Our phylogenetic analyses suggest that <i>Saitoella</i> is distinct from all currently described classes within Taphrinomycotina, whereas <i>Savitreella</i> seems to belong to the class Taphrinomycetes. Furthermore, <i>Saitoella</i> shares high average amino acid identity with all other classes in Taphrinomycotina, suggesting that it retains ancient gene sequences. Our findings enable us to propose a new class, order, and family—namely, Saitoellomycetes, Saitoellales, and Saitoellaceae—automatically typified by the genus <i>Saitoella</i>. Our chromosome-level assembly reveals that <i>Saitoella coloradoensis</i> possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two <i>Saitoella</i> species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.
DOI: 10.6084/m9.figshare.31169582.v1
title: Phylogenomic insights into Taphrinomycotina and genomic features of <i>Saitoella coloradoensis</i> based on whole-genome sequencing at the chromosome level, with a proposal of the new class Saitoellomycetes

description: Taphrinomycotina, a subphylum of the phylum Ascomycota, comprises fungi with diverse morphologies and ecologies. <i>Saitoella</i> and <i>Savitreella</i> are genera of red-colored yeasts within Taphrinomycotina, but their precise phylogenetic positions have remained controversial. In this study, we sequenced the whole genomes of <i>Saitoella coloradoensis</i> and <i>Savitreella phatthalungensis</i> in order to elucidate their phylogenetic relationships using a phylogenomic approach based on chromosome-level genome assemblies generated by long-read sequencing technologies. Our phylogenetic analyses suggest that <i>Saitoella</i> is distinct from all currently described classes within Taphrinomycotina, whereas <i>Savitreella</i> seems to belong to the class Taphrinomycetes. Furthermore, <i>Saitoella</i> shares high average amino acid identity with all other classes in Taphrinomycotina, suggesting that it retains ancient gene sequences. Our findings enable us to propose a new class, order, and family—namely, Saitoellomycetes, Saitoellales, and Saitoellaceae—automatically typified by the genus <i>Saitoella</i>. Our chromosome-level assembly reveals that <i>Saitoella coloradoensis</i> possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two <i>Saitoella</i> species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.
DOI: 10.25338/b8z353
title: Toxoplasma gondii microscopy and PCR detection results between July, 2020 and August, 2022 in greater Monterey Bay, CA

description: Toxoplasma gondii is a zoonotic parasite that can cause severe morbidity
 and mortality in warm-blooded animals, including marine mammals such as
 sea otters. Free-ranging cats can shed environmentally resistant T. gondii
 oocysts in their feces, which are transported to water bodies through
 rain-driven surface runoff. Certain genotypes of T. gondii were found in
 otters that died from toxoplasmosis, however, the source of these
 parasites has not been determined. Despite their large population sizes
 and ability to contribute to environmental oocyst contamination, there is
 limited knowledge on the frequency of oocyst shedding and genotypes of
 oocysts shed by free-ranging cats. We aimed to determine the presence of
 T. gondii oocyst shedding in free-ranging domestic cats in central coastal
 California and identify genotypes shed in feces. We utilized a
 longitudinal field study of four free-ranging cat colonies to assess
 oocyst fecal shedding prevalence using microscopy and molecular
 confirmation with polymerase chain reaction (PCR). Initial DNA screening
 targeting the ITS1 locus confirmed presence of T. gondii and positive
 samples were further genotyped at the B1 locus. While oocysts were not
 visualized using microscopy (0/404), we detected T. gondii DNA in 25.9%
 (94/362) of fecal samples. We genotyped 27 samples at the B1 locus and
 characterized 13 samples at one or more loci using multi locus sequence
 typing (MLST). Parasite DNA detection was higher during the wet season
 (16.3%, 59/362) compared to the dry season (9.7%; 35/362), suggesting
 seasonal variation in T. gondii oocyst shedding. High diversity of T.
 gondii strains was characterized at the B1 locus in cat feces, including
 atypical strains previously associated with sea otter mortalities.
 Free-ranging cats may thus play an important role in the transmission of
 virulent parasite genotypes that cause morbidity and mortality in marine
 wildlife. Proper management of free-ranging cat colonies could reduce
 environmental contamination with oocysts and subsequent T. gondii
 infection in endangered marine mammals and people.
description: Four colonies in Gilroy (Santa Clara County), Moss Landing (Monterey County), Aptos (Santa Cruz County), and Santa Cruz (Santa Cruz County) were sampled monthly between July 2020 and August 2022 (24 months). Sampling did not occur in February or March 2021 due to COVID-19 restrictions, and sampling occurred twice in April 2022 due to the low sample size (n = 5) during the first collection trip earlier that month. Three sites were located directly on the coastline, and one (Gilroy) was located inland (25.4 km from coast) in the Uvas-Llagas watershed, which drains into Monterey Bay. Samples with confirmed <em>T. gondii</em> are indicated with a 1 under the "Toxoplasma confirmed" column, while samples without <em>T. gondii</em> DNA are listed as 0. Samples that were not tested with PCR are indicated by "NA".
description: CSV file can be opened by R or other statistical software.
DOI: 10.5061/dryad.8sf7m0ctd
title: Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2: Part 1

description: The Tec-family kinase Btk contains a lipid-binding Pleckstrin homology and
 Tec homology (PH-TH) module connected by a proline-rich linker to a “Src
 module”, an SH3-SH2-kinase unit also found in Src-family kinases and Abl.
 We showed previously that Btk is activated by PH-TH dimerization, which is
 triggered on membranes by the phosphatidyl inositol phosphate PIP3, or in
 solution by inositol hexakisphosphate (IP6) (Wang et al. 2015,
 https://doi.org/10.7554/eLife.06074). We now report that the ubiquitous
 adaptor protein growth-factor-receptor-bound protein 2 (Grb2) binds to and
 substantially increases the activity of PIP3-bound Btk on membranes. Using
 reconstitution on supported-lipid bilayers, we find that Grb2 can be
 recruited to membrane-bound Btk through interaction with the proline-rich
 linker in Btk. This interaction requires intact Grb2, containing both SH3
 domains and the SH2 domain, but does not require that the SH2 domain be
 able to bind phosphorylated tyrosine residues – thus Grb2 bound to Btk is
 free to interact with scaffold proteins via the SH2 domain. We show that
 the Grb2-Btk interaction recruits Btk to scaffold-mediated signaling
 clusters in reconstituted membranes. Our findings indicate that
 PIP3-mediated dimerization of Btk does not fully activate Btk, and that
 Btk adopts an autoinhibited state at the membrane that is released by
 Grb2.
description: The dataset was collected By TIRF microscopy, a description of
 the microscope and imaging settings is included in the manuscript
 Materials and Methods. All files are 15-second time lapses except data
 collected for Figure 2 Supplement 1, which are 10-second time
 lapses.
description: We suggest using FIJI (Image J) to view TIFF files. We used the
 Measure Z stack function to determine the average intensity across the
 stack.
DOI: 10.15468/dl.enu7u2
title: Occurrence Download

description: A dataset containing 1373950 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ukraine",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 1373950 records from 260 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002918-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30821443.v1
title: Optimizing Pediatric Dose Finding: A Phase I/II Design Integrating Adult Data

description: Precision dose selection in pediatric trials is imperative given children’s distinct profiles, yet constrained by ethical barriers and recruitment challenges that could be strategically mitigated through adult trial data integration. To address the limitations of existing methods, we propose the pp-BOIN12 and pp-TITE-BOIN12 designs based on the Power prior framework to identify optimal biological dose (OBD) and address delayed outcomes. These designs adaptively quantify dose-level similarity between adult and pediatric cohorts using Hellinger distance to calibrate real-time borrowing weights. Numerical simulations demonstrate that pp-BOIN12 improves the percentage of correct OBD selection while reducing patient assignments to doses above maximum tolerated dose (MTD). pp-TITE-BOIN12 maintains comparable accuracy with minimal performance degradation while significantly shortening trial duration. This work provides an adaptive and safe method for incorporating adult data into pediatric extrapolation trials.