cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5x69p8dbs
title: Supplementary data from: Bisphosphonates maintain BMD after sequential teriparatide and denosumab in Premenopausal Women with Idiopathic Osteoporosis (PremenIOP)

description: Context: We previously reported that sequential teriparatide followed by
 denosumab substantially increases BMD in premenopausal idiopathic
 osteoporosis (PremenIOP). Objective: To determine whether bisphosphonates
 prevent bone loss after denosumab cessation in PremenIOP Design:
 Open-label extension study Participants: 24 PremenIOP
 Teriparatide-Denosumab Study participants Interventions: Oral alendronate
 (ALN), 70 mg weekly, or IV zoledronic acid (ZOL), 5mg once (patient
 choice), was administered 7 months (M) after final denosumab dose.
 Outcomes: BMD by DXA and serum C-telopeptide (CTX) q6M; vertebral fracture
 assessment (VFA) and HR-pQCT q12M. Results: 24 women with PremenIOP (aged
 43±8 years), severely affected with low trauma adult fractures (range
 0-12; 9 with vertebral fractures) and/or very low BMD, had large BMD
 increases on sequential teriparatide-denosumab (spine: 25±9%; total hip:
 11±6%). During the Bisphosphonate Extension, mean BMD and CTX changes in
 the entire group were small and not statistically significant at 6 or 12M.
 Women choosing ZOL (n=6) versus ALN (n=18) did not differ by baseline age,
 BMI, fractures, BMD, or CTX. On ZOL, there were small LSBMD declines and
 CTX increases, particularly between 6M and 12M, while greater stability
 was observed on ALN. Changes in BMD and CTX did not differ by duration of
 denosumab (36M vs &lt;36M) or between 20 women who remained
 premenopausal and 4 who transitioned into menopause. Higher
 pre-teriparatide CTX, likely reflecting baseline remodeling status,
 predicted more spine and hip bone loss. No new vertebral (clinical or VFA
 screening) or non-vertebral fractures occurred. Conclusion: Bisphosphonate
 therapy prevents significant bone loss after sequential
 teriparatide-denosumab in women with PremenIOP.
description: # Supplementary data from: Bisphosphonates maintain BMD after sequential
 teriparatide and denosumab in Premenopausal Women with Idiopathic
 Osteoporosis (PremenIOP) ## Description of the data and file structure
 Supplementary Table: Supplementary_Table_BisextR1.csv Changes in spine and
 hip BMD and CTX in (1) those who received 36M of denosumab vs those who
 received less than 36M of denosumab and (2) those who remained
 premenopausal vs those who transitioned to menopause before/during the
 study. Abbreviations: LS – lumbar spine; TH – total hip; FN – femoral
 neck; CTX – C-telopeptide; M - months
DOI: 10.5061/dryad.xksn02vpg
title: Phylogenetics, taxonomy, and chromosome number analysis of Sanvitalia (Asteraceae-Heliantheae-Zinniinae)

description: We collected molecular sequence data from the nuclear ribosomal ITS region
 and three plastid loci from multiple individuals of each species of
 Sanvitalia and additional members of the Zinniinae to create phylogenetic
 trees and study the evolutionary history of the clade. The alignments used
 for these trees is included here.
description: Forward and Reverse Sanger reads were assembled <em>de
 novo</em> in Geneious Prime. Contigs were aligned with MAFFT. The
 three plastid loci alignments were concatenated.
description: # Phylogenetics, taxonomy, and chromosome number analysis of Sanvitalia
 (Asteraceae-Heliantheae-Zinniinae)
 [https://doi.org/10.5061/dryad.xksn02vpg](https://doi.org/10.5061/dryad.xksn02vpg) The data set contains two alignments, one from the ITS and one from the concatenated plastid loci. These alignments were used as the basis of the phylogenetic trees seen in the publication. ## Description of the data and file structure Both alignments are in fasta format which is compatible with many phylogenetic programs. The concatenated data set is in the following order: psbA-matK, trnH-psbA, and trnL-trnF.
DOI: 10.5061/dryad.3tx95x6pk
title: Data from: The importance of migratory drop-off for island colonization in birds

description: Seasonal migration is an underappreciated driver of animal
 diversification. Changes in migratory behavior may favor the establishment
 of sedentary founder populations and promote speciation if there is
 sufficient reproductive isolation between sedentary and migratory
 populations. From a systematic literature review, we here quantify the
 role of migratory drop-off – the loss of migratory behavior – in promoting
 speciation in birds on islands. We identify at least 157 independent
 colonization events likely initiated by migratory species that led to
 speciation, including 44 cases among recently extinct species. By
 comparing, for all islands, the proportion of island endemic species that
 derived from migratory drop-off with the proportion of migratory species
 among potential colonizers, we showed that seasonal migration has a larger
 effect on island endemic richness than direct dispersal. We also found
 that the role of migration in island colonization increases with the
 geographic isolation of islands. Furthermore, the success of speciation
 events depends in part on species biogeographic and ecological factors,
 here positively associated with greater range size and larger flock sizes.
 These results highlight the importance of shifts in migratory behavior in
 speciation process and calls for greater consideration of migratory
 drop-off in the biogeographic distribution of birds.
description: # Data from: The importance of migratory drop-off for island colonization
 in birds
 [https://doi.org/10.5061/dryad.3tx95x6pk](https://doi.org/10.5061/dryad.3tx95x6pk) This file contains: 1\. A table containing all species’ migration characteristics, range size, inferred flock size, and relative brain size data (Supplementary Data 1). 2\. A table containing all details regarding the evolutionary history and migratory behavior of island endemic and related species (Supplementary Data 2). Each table (.xlsx format) contains a metadata sheet on the front page with descriptions of each column. Note that empty cells in Supplementary Data 1 and Supplementary Data have been replaced by "-" to avoid confusion for potential users. Bird range maps and diet data are publicly available, respectively in [www.birdlife.org](http://www.birdlife.org) and Wilman *et al.* (2014, doi:10.1890/13-1917.1). For any question or request please contact: Paul Dufour ([paul.dufour80@gmail.com)](mailto:paul.dufour80@gmail.c)
DOI: 10.5061/dryad.8cz8w9gzv
title: The Late Miocene Plesiosoricidae and Soricidae (Eulipotyphla, Mammalia) from the Pannonian region, Slovakia

description: Soricidae is the most species-rich eulipotyphlan family since the
 Pliocene. Numerous Late Miocene soricids and plesiosoricids are well-known
 from southern Europe. Localities from central Europe, despite being rare,
 have historically yielded better-preserved material that reveals a great
 diversity. We here add to this existing record with the description of
 eight species from MN9-MN12-aged localities of Slovakia (Paenelimnoecus
 repenningi, Paenesorex bicuspis, Isterlestes aenigmaticus nov. gen. nov.
 sp., Crusafontina endemica, Crusafontina kormosi, Amblycoptus jessiae,
 Asoriculus gibberodon, Petenyia dubia), alongside one species of
 Plesiosoricidae (Plesiosorex evolutus). The early occurrence of A.
 gibberodon and A. jessiae, the occurrence of Paenesorex, and the
 identification of Isterlestes aenigmaticus nov. gen. nov. sp. reinforce
 the hypothesis that the Pannonian region (south-eastern central Europe)
 was a source area for several soricid taxa (Allosoricinae, Anourosoricini,
 Soricini) during the Late Miocene.
description: # The Late Miocene Plesiosoricidae and Soricidae (Eulipotyphla, Mammalia)
 from the Pannonian region, Slovakia ### Supplementary file List of the
 Plesiosoricidae and Soricidae from the Late Miocene of Slovakia The file
 consists of a list of dento-gnathic elements attributed to the
 Eulipotyphla family Plesiosoricidae and Soricidae. Otherwise stated with
 the ID, each line represents a different dental element. The ID is the
 identification number of the material, housed at the Department of Geology
 and Paleontology of Comenius University, Bratislava. Additionally is
 provided the locality where each material has been extracted, its
 identification (i=incisor, c=canine, a=antemolar, p=premolar, m=molar,
 mand=mandible, max=maxillary; Upper elements are indicated with
 uppercase), its symmetry (l=left, r=right) and its generic and specific
 attribution. The right part of the file gathers the measurements of the
 specimens in millimeters (mm), the protocol of which has been described in
 the main document. The abbreviations are AW=anterior width; BL=labial
 (buccal) length; H=height; L=length; LL=lingual length; LT=length of the
 talon; N=number of specimens; PE=length of the posterior emargination;
 PW=posterior width; TAW=talonid width; TRW=trigonid width; W=width.
 "n/a" indicates the lack of measurements because of the
 fragmented nature of the specimens.
DOI: 10.15468/dl.bcwx2e
title: Occurrence Download

description: A dataset containing 7675 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Papilio helenus"
 ]
}

 The dataset includes 7675 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003930-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zcrjdfnmh
title: PIV results from a kinematic study of robotic bird wings

description: A faster cruising speed increases drag and thereby the thrust (T) needed
 to fly, while the weight and lift (L) requirement remains constant. Birds
 can adjust their wingbeat in multiple ways to accommodate this change in
 aerodynamic force, but the relative costs of different strategies remain
 largely unknown. To evaluate the efficiency of several kinematic
 strategies, I used a robotic wing (Ajanic et al., 2023) and quantitative
 flow measurements. I found that, among the tested strategies, changing the
 mean wingbeat elevation provides the most efficient solution to changing
 T/L, offering insight into why birds tend to beat their wings with a
 greater ventral than dorsal excursion. I also found that although
 propulsive efficiency (ηp) may peak at a Strouhalnumber (St, measure of
 relative flapping speed) near 0.3, the overall efficiency of generating
 force decreases with St. This challenges the expectance of a specific
 optimal St for flapping flight and instead suggest the chosen St depends
 on T/L. This may explain the variation in preferred St among birds and why
 bats prefer flying at higher St than birds (Taylor et al., 2003) since
 their body shape imposes relatively higher thrust requirements (Muijres et
 al., 2012). In addition to explaining flapping strategies used by birds,
 my results suggest alternative, efficient, flapping motions for drones to
 explore aiming to extend their flight range.
description: The data was collected using stereo particle image velocimetry in
 a plane transverse to the free-stream flow of a wind tunnel, capturing the
 wake of a flapping bio-hybrid robotic wing. The images were processed
 using Davis 10.2.1 (Lavision).
description: # PIV results from a kinematic study of robotic bird wings
 [https://doi.org/10.5061/dryad.zcrjdfnmh](https://doi.org/10.5061/dryad.zcrjdfnmh) The data represents the wake of the robotic wing gathered at 720 Hz for different kinematic strategies of flapping. The kinematic settings associated with each of the data sets are listed in the ExpCond file.  The kinematic settings varied were: Wingbeat frequency [Hz], angular amplitude [degrees] as the angle the wing sweeps through during a downstroke or upstroke, mean wingbeat elevation [degrees] defined as the angle relative to the horizontal plane that the wing flaps about, downstroke ratio as the relative duration of the downstroke to the full wingbeat, and the stroke plane angle [degrees] defined as the angle of the flapping motion relative to the vertical.   ## Description of the data and file structure Each of the folders contains files for each of the frames sampled at 720 Hz. The files are CSV files containing 5 comma-separated columns representing the x position, the y position, the velocity in the x direction, the velocity in the y direction, and the velocity in the z direction. The coordinate system is right-handed with x in the upward direction, y in the spanwise direction (base to tip of the wing), and z in the streamwise direction (aligned with the wind tunnel flow).
DOI: 10.5281/zenodo.18406093
title: Xоrijiy tаdqiqоtlаrda shaxs  krеаtivligini rivоjlаntirish muаmmоsi

description: Kreаtivlik-shaxsni о‘qitish vа tаrbiуаlаsh, ulаrning shаxsiу va kasbiy fаzilаtlаrini shаkllаntirish va rivojlantirishni о‘z ichigа оlgаn murаkkаb jаrауоndir. Реdаgоgik-рsiхоlоgik xorijiy tаdqiqоtlаrni о‘rgаnish vа tаhlil qilish аsоsidа krеаtivning о‘zigа xоs xususiуаtlаri hаmdа muvаffаqiуаtli mutаxаssis bо‘lish vа kаsbiу fаоliуаtdа уuqоri nаtijаlаrgа erishishi mumkinligi aniqlandi.
DOI: 10.5281/zenodo.18406094
title: Xоrijiy tаdqiqоtlаrda shaxs  krеаtivligini rivоjlаntirish muаmmоsi

description: Kreаtivlik-shaxsni о‘qitish vа tаrbiуаlаsh, ulаrning shаxsiу va kasbiy fаzilаtlаrini shаkllаntirish va rivojlantirishni о‘z ichigа оlgаn murаkkаb jаrауоndir. Реdаgоgik-рsiхоlоgik xorijiy tаdqiqоtlаrni о‘rgаnish vа tаhlil qilish аsоsidа krеаtivning о‘zigа xоs xususiуаtlаri hаmdа muvаffаqiуаtli mutаxаssis bо‘lish vа kаsbiу fаоliуаtdа уuqоri nаtijаlаrgа erishishi mumkinligi aniqlandi.
DOI: 10.5061/dryad.p2ngf1vzh
title: Genome assembly variation and its implications for gene discovery in nematode species

description: Genome assemblers are a critical component of genome science, but the
 choice of assembly software and protocols can be daunting. Here, we
 investigate genome assembly variation and its implications for gene
 discovery across three nematode species—Caenorhabditis bovis, Haemonchus
 contortus, and Heligmosomoides bakeri—highlighting the critical interplay
 between assembly choice and downstream genomic analysis. Selecting
 commonly used genome assemblers, we generated multiple assemblies for each
 species, analyzing their structure, completeness, and effect on gene
 family analysis. Our findings demonstrate that assembly variations can
 significantly affect gene family composition, with notable differences in
 gene families important in anthelmintic discovery and immunomodulation.
 Despite broadly similar performance using various assembly metrics,
 comparisons of assemblies with a single species revealed underlying
 structural rearrangements and inconsistencies in gene content, which would
 affect downstream analyses. This emphasizes the need for continuous
 refinement of genome assemblies and their annotations.
description: The assemblies were generated using different software.
 <em>Caenorhabditis
 bovis </em>and <em>Haemonchus contortus</em>
 Redbean2.5 Flye
 Canu SMARTdenovo
 Falcon Falcon-unzip 
 <em>Heligmosomoides bakeri</em> 
 Flye HiCanu
 Hifiasm The gene models were
 generated using the software BRAKER3
description: # Genome assembly variation and its implications for gene discovery in
 nematode species
 [https://doi.org/10.5061/dryad.p2ngf1vzh](https://doi.org/10.5061/dryad.p2ngf1vzh) We wanted to determine the effect of genome assembly variation. We used DNA sequence reads from three species of nematodes: *Caenorhabditis bovis* (Oxford Nanopore reads); *Haemonchus contortus* (PacBio RSII reads); *Heligmosomoides polygyrus* (PacBio HiFi reads). For each species, several assembly algorithms were used and their results were compared. We also generated gene models for each assembly using the Braker3 software. ## Description of the data and file structure All data files are compressed using gzip. The naming structure for most of the files is aaa_bbb_ccc.ddd, where * aaa --&gt; the species, where Cbovis --&gt; *Caenorhabditis bovis*; Hcontortus --&gt; *Haemonchus contortus*; Hbakeri --&gt; *Heligmosomoides bakeri*. * bbb --&gt; the assembly algorithm used, or for the published genomes, the first author of the paper (e.g., Stevens, Chow, Doyle). * ccc --&gt; **asm** for assembly or braker3 for gene models. * ddd --&gt; **fsa** for fasta format or **gtf** for gene transfer file format. ### Version change log **9-oct-2024:** We have included the supplementary information associated with the publication. * Mariene_n_Wasmuth_SOM_Figures --&gt; Figures S1-S6. * Mariene_n_Wasmuth_SOM_Tables --&gt; Tables S1-S71. * Mariene_n_Wasmuth_FileS1 --&gt; Additional methods, including the commands used for various software.
DOI: 10.5061/dryad.6t1g1jx64
title: Watching the watchers: Camera identification and characterization using retro-reflections - Dataset

description: A focused imaging system such as a camera will reflect light directly back
 at a light source in a retro-reflection (RR) or cat-eye reflection. RRs
 provide a signal that is largely independent of distance providing a way
 to probe cameras at very long ranges. We find that RRs provide a rich
 source of information on a target camera that can be used for a variety of
 remote sensing tasks to characterize a target camera including predictions
 of rotation and camera focusing depth as well as cell phone model
 classification. We capture three RR datasets to explore these problems
 with both large commercial lenses and a variety of cell phones. This
 repository contains time-synced videos from the perspective of both a
 retro-reflective probe and a target camera that can be used to train
 algorithms for different remote sensing tasks. We include a dataset for
 cellphone classification, target camera rotation prediction, and target
 camera focusing depth prediction.
description: # Watching the watchers: Camera identification and characterization using
 retro-reflections - Dataset
 [https://doi.org/10.5061/dryad.6t1g1jx64](https://doi.org/10.5061/dryad.6t1g1jx64) ## Description of the data and file structure This dataset was used to generate results in the paper titled "Watching the watchers: Camera identification and characterization using retro-reflections" The data folder contains the datasets for the Phone classification and Focus_and_rotation experiments. data\Focus_Rotation\raw_data\angles: contains the paired videos from the viewpoint of the probe and target camera. The target camera video is used to calculate the rotation angle of the target camera. The probe video is the view from the probe and can be used to predict the target camera's rotation. data\Focus_Rotation\raw_data\focus contains videos for different settings of a commercial lens on a rotating target camera. data\PhoneData contains the data relevant for the phone classification experiment. Trimmed_Phone_Videos and Trimmed_Probe_Videos contain the paired videos from the target phone and the probe. Phone_data\imgs contains the background image that is subtracted from the probe videos to remove static background. data\PhoneData\data is left empty and is used to save intermediate data in the linked code repository. Focus (object) distances are in meters and focal lengths are in millimeters. ## Code Code in this project is written in python and contains some jupyter notebook (ipynb files). There are multiple README files throughout the project code to explain which files replicate different results in the paper.
DOI: 10.5061/dryad.nvx0k6f06
title: FreshLanDiv: A global database of freshwater biodiversity across different land uses

description: Freshwater ecosystems have been heavily impacted by land-use changes, but
 data syntheses on these impacts are still limited. Here, we compiled a
 global database encompassing 241 studies with species abundance data (from
 multiple biological groups and geographic locations) across sites with
 different land-use categories. This compilation will be useful for
 addressing questions regarding land-use change and its impact on
 freshwater biodiversity. The database includes metadata of each
 study, site location, sample methods, sample time, land-use category, and
 abundance of each taxon. The database contains data from across the globe,
 with 85% of the sites having well-defined geographical
 coordinates. The database covers all major freshwater biological
 groups including algae, macrophytes, zooplankton, macroinvertebrates,
 fish, and amphibians.
description: # FreshLanDiv: A global database of freshwater biodiversity across
 different land uses
 [https://doi.org/10.5061/dryad.nvx0k6f06](https://doi.org/10.5061/dryad.nvx0k6f06) This database includes data from 241 studies that contain abundance data on assemblages of several taxon groups from different land-use categories. Our compilation includes data from all major freshwater taxa (e.g., phytoplankton, macrophytes, macroinvertebrates, amphibians, fishes) and ecosystem types, and includes data from across the world. ## Description of the data and file structure * **Land-use-and-freshwater-database.xlsx:** 1. **Datasource:** Records of each study source, including study title and DOI, etc. 2. **Plotdata:** Information of each site and plot (where the samples occurred). It includes location information, plot size land use information, etc. 3. **Observationdata:** Records of observation data, including sample details and species abundance data. 4. **Scientificname:** Species scientific name and classification. 5. **Description:** The description of all variables. * **Metadata.csv:** Metadata of each study, including Dataset_id, coordinates, taxa and basin type. * **Sample_rank.jpg:** Describe the relationship between different sample ranks. Note: "NA" in the database indicates a missing value that could not be obtained from the original paper. ## Sharing/Access information The associated code is available: * Zenodo [https://doi.org/10.5281/zenodo.13866691](https://doi.org/10.5281/zenodo.13866691) * Github [https://github.com/Minghua-shen/FreshLanDiv](https://github.com/Minghua-shen/FreshLanDiv)
DOI: 10.15483/3014715
title: FleetREDI: Mail Delivery Class 6 Propane Trucks

description: Capturing real-world data is critical to reducing the barriers to technology advancement for commercial vehicles. FleetREDI’s insights provide detailed duty cycle information and highlight unique aspects of the given dataset. Each insight delivers a quick look at the collected data by summarizing the operation and identifying key findings of the initial analysis. This FleetREDI insight explores propane and diesel Class 6 mail delivery trucks.

Propane-powered commercial vehicles can achieve the same duty cycles and match the power, acceleration, and cruising speeds of conventionally fueled vehicles while producing significantly less emissions of tailpipe oxides of nitrogen (NOx). The primary goal of the project was to demonstrate alternative fuel vehicles in a mail transport application and evaluate the viability of propane as a cost-effective alternative to conventional diesel trucks.

![FleetREDI clean delivery trucks](FleetREDI-clean-delivery.jpg)