cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4qz5
title: Turning turtle: Scaling relationships and self-righting ability in Chelydra serpentina

description: Testudines are susceptible to inversion and self-right using their necks,
 limbs, or both, to generate enough mechanical force to flip over. We
 investigated how shell morphology, neck length, and self-righting
 biomechanics scale with body mass during ontogeny in Chelydra
 serpentina, which uses neck-powered self-righting. We found that younger
 turtles flipped over twice as fast as older individuals. A simple
 geometric model predicted the relationships of shell shape and
 self-righting time with body mass. Conversely, neck force, power output,
 and kinetic energy increase with body mass at rates greater than
 predicted. These findings were correlated with relatively longer necks in
 younger turtles than would be predicted by geometric similarity.
 Therefore, younger turtles self-right with lower biomechanical costs than
 predicted by simple scaling theory. Considering younger turtles are more
 prone to inverting and their shells offer less protection, faster and less
 costly self-righting would be advantageous in overcoming the detriments of
 inversion.
description: The experimental setup consisted of a force plate, with a
 pressure pad on top, covered by a thin rubber mat. The force plate (3D
 Force Plate Type 9286B, Kistler® Instruments Ltd, Hook, Hampshire, UK) was
 used to measure the vertical reaction force exerted by a turtle during
 self-righting. Force data were recorded (at 420 Hz), using the BioWare®
 data-acquisition software (type 2812A, Kistler®). To measure the relative
 contributions of the neck and body to the vertical force, a pressure pad
 (Pressure Mapping Sensor 7101, Tekscan, Inc, South Boston, MA, USA) was
 placed on top of the force plate. The pressure pad data were recorded (at
 100 Hz) using the FootMat® Research software (v 7.1, Tekscan). A camera
 (Sony® Cyber-shot RX10 III) was used to record videos (at 100 fps) of the
 self-righting movements. The self-righting times were calculated from
 videos, using Tracker (https://physlets.org/tracker; The Open Source
 Physics Project). The self-righting time is defined as the duration from
 the moment a turtle’s head first contacted the pressure pad/force plate
 until the head was no longer in contact with the setup (see Fig.
 1A-D).
DOI: 10.5061/dryad.cjsxksn59
title: Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren

description: The existence of distinct traits in island versus mainland populations
 offers opportunities to gain insights into how eco-evolutionary processes
 operate under natural conditions. We used two island colonization events
 in the white-winged fairywren (Malurus leucopterus) to
 investigate the genomic and demographic origin of melanic plumage. This
 avian species is distributed across most of Australia, and males of the
 mainland subspecies (M. l. leuconotus) exhibit a blue nuptial plumage in
 contrast to males of two island subspecies – M. l.
 leucopterus on Dirk Hartog Island and M. l.
 edouardion Barrow Island – that exhibit a black nuptial plumage. We used
 reduced-representation sequencing to explore differentiation and
 demographic history in this species and found clear patterns of divergence
 between mainland and island populations, with additional substructuring on
 the mainland. Divergence between the mainland and Dirk Hartog was
 approximately 10 times more recent than the split between the mainland and
 Barrow Island, supporting two independent colonizations. In both cases,
 estimated gene flow between the mainland and the islands was low,
 contributing to signals of divergence among subspecies. Our results
 present demographic reconstructions of mainland-island dynamics and
 associated plumage variation in white-winged fairywrens, with broader
 implications regarding our understanding of convergent evolution in
 insular populations.
description: We obtained tissue samples from the Western Australian Museum,
 the South Australian Museum, and the Burke Museum as well as blood
 collected during fieldwork for 104 <i>M.
 leucopterus </i>individuals (see Table S1 in main
 manuscript). Genomic DNA was isolated using a DNeasy Extraction Kit
 (Qiagen, Valencia, California, USA) according to the manufacturer
 protocol. Double-digested restriction-site associated DNA markers
 (ddRADtags) were generated following the protocol of Peterson et
 al. (2012) with modifications described in Thrasher et al. (2018). All
 reads were trimmed to 97 bp and then filtered for quality using
 the FASTX-Toolkit(http://hannonlab.cshl.edu/fastx_toolkit). We removed
 sequences if a single base had a Phred quality score less than 10 and if
 more than 95% of bases had a Phred quality score less than 15. Sequences
 were assembled using a red-backed fairywren (<i>Malurus
 melanocephalus</i>) reference genome using stacks v 2.41. Sequences
 were aligned to the <i>M. melanocephalus </i>assembly
 with bowtie2 version 2.2.2 (Langmead et al. 2009). We required that a SNP
 be present in a minimum of 80% of the individuals and applied a minor
 allele frequency filter of 5%. We created a subset of SNPs that included
 only the first SNP per stack (6,497 SNPs). This data set was used for all
 analyses, with the exception of the PCA.
DOI: 10.5061/dryad.xwdbrv1cs
title: Host personality predicts cuckoo egg rejection in Daurian redstarts Phoenicurus auroreus

description: In species that are subject to brood parasitism, there is typically
 variation in individuals’ responses to parasitic eggs, with some rejecting
 the eggs while others do not. Whilst some factors, such as host age
 (breeding experience), the degree of egg matching and the level of
 perceived risk of brood parasitism have been shown to influence host
 decisions, a lot of the variation remains unexplained. The host
 personality hypothesis suggests that personality traits of the host
 influence its response to parasitic eggs, but few studies have tested
 this. We investigated the relationship between two personality traits
 (exploration and neophobia) and a physiological trait (breathing rate) of
 the host, and egg-rejection behaviour in a population of Daurian redstarts
 Phoenicurus auroreus in northeast China. We first show that exploratory
 behaviour and the response to a novel object are repeatable for individual
 females and show strong covariation, indicating distinct personality
 types. We then show that fast-exploring and less neophobic hosts were more
 likely to reject parasitic eggs than slow-exploring and more neophobic
 hosts. Variation in breathing rate – a measure of the stress-response –
 did not affect rejection behaviour. Our results demonstrate that host
 personality, along the bold-shy continuum, predicts the responses to
 parasitic eggs in Daurian redstarts, with bold hosts being more likely to
 reject parasitic eggs.
DOI: 10.15468/dl.k38dc4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Formanodendron doichangensis"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002764-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2z34tmpkq
title: Data from: Stay or fly away? Impact of human disturbance on shorebird individuals and populations

description: These data comprise the data of four chapters from the PhD thesis
 from van der Kolk (2021) entitled ‘Stay or fly away? Impact of human
 disturbance on shorebird individuals and populations.’ The thesis focusses
 on quantifying the impacts of human disturbance on oystercatchers. This
 dataset contains data from chapters 4, 5, 7 and 10. For Chapter 4 field
 observations were done to observe how shorebirds responded to aircraft
 overflights at different sites. The data provides an overview of the
 disturbance probability (i.e. the probability that birds took flight)
 following aircraft overflights, for different bird species, locations and
 aircraft types. These data were used to test whether there was a
 relationship between aircraft overflight frequency and disturbance
 probability. For Chapters 5 and 7 oystercatchers were equipped with GPS
 trackers to study the effects of disturbance on space use. The data of
 Chapter 5 provides GPS locations of oystercatchers in relation to the
 timings of military exercises. These data were used to quantify whether
 oystercatchers avoided the military training area during and immediately
 after military exercises. The data of Chapter 7 contains GPS locations of
 oystercatchers in relation to the moment of high tide and provides the
 roosting location. These data were used to study whether oystercatchers
 avoided a disturbed roost site in the tourist season. For Chapter 10 an
 individual based model was constructed that was used to quantify whether
 disturbance affected winter mortality of oystercatchers. The individual
 based model was written in Python. The data contains the full code of the
 model, as well as all input files needed to run the model. 
description: The data consists of a zip folder that contains the data of the
 four unpublished chapters of the PhD thesis (Chapters 4, 5, 7 and 10).
 Each folder contains data of one chapter and contains a readme file with
 information on the data provided.
DOI: 10.5281/zenodo.18396573
title: GENETIC MECHANISMS AND THE ROLE OF SUSCEPTIBILITY GENES IN AMYOTROPHIC LATERAL SCLEROSIS: PATHOGENIC PATHWAYS, CLINICAL IMPLICATIONS, AND EMERGING TARGETS

description: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive loss of upper and lower motor neurons, leading to paralysis and eventual respiratory failure. While the disease is clinically heterogeneous, genetic factors play a central role in its pathogenesis. Approximately 10% of ALS cases are familial (fALS), with mutations in several key genes including SOD1, C9orf72, TARDBP, and FUS. An increasing body of research has identified additional susceptibility genes and risk loci that contribute to sporadic ALS (sALS) through dysregulation of RNA metabolism, proteostasis, cytoskeletal integrity, and immune responses. This study critically examines the genetic architecture of ALS, explores molecular pathways impacted by pathogenic variants, and evaluates emerging genetic targets for therapeutic intervention. Through comprehensive genomic analysis, we identify novel genes implicated in ALS and provide an integrative model linking genetic variation to neurodegeneration.
DOI: 10.5281/zenodo.18396574
title: GENETIC MECHANISMS AND THE ROLE OF SUSCEPTIBILITY GENES IN AMYOTROPHIC LATERAL SCLEROSIS: PATHOGENIC PATHWAYS, CLINICAL IMPLICATIONS, AND EMERGING TARGETS

description: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive loss of upper and lower motor neurons, leading to paralysis and eventual respiratory failure. While the disease is clinically heterogeneous, genetic factors play a central role in its pathogenesis. Approximately 10% of ALS cases are familial (fALS), with mutations in several key genes including SOD1, C9orf72, TARDBP, and FUS. An increasing body of research has identified additional susceptibility genes and risk loci that contribute to sporadic ALS (sALS) through dysregulation of RNA metabolism, proteostasis, cytoskeletal integrity, and immune responses. This study critically examines the genetic architecture of ALS, explores molecular pathways impacted by pathogenic variants, and evaluates emerging genetic targets for therapeutic intervention. Through comprehensive genomic analysis, we identify novel genes implicated in ALS and provide an integrative model linking genetic variation to neurodegeneration.
DOI: 10.5061/dryad.zpc866t7p
title: Short-term treatment of golden retriever muscular dystrophy (GRMD) dogs with rAAVrh74.MCK.GALGT2 induces muscle glycosylation and utrophin expression but has no significant effect on muscle strength

description: We have examined the effects of intravenous (IV) delivery of
 rAAVrh74.MHCK7.GALGT2 in the golden retriever muscular dystrophy (GRMD)
 model of Duchenne Muscular Dystrophy (DMD). After baseline testing, GRMD
 dogs were treated at 3 months of age and reassessed at 6 months. This 3-6
 month age range is a period of rapid disease progression, thus offering a
 relatively short window to establish treatment efficacy.
  Measures analyzed included muscle AAV transduction, GALGT2
 transgene expression, GALGT2-induced glycosylation, muscle pathology, and
 muscle function.  A total of five dogs were treated, 4 at
 2x1014vg/kg and one at 6x1014vgkg. The 2x1014vg/kg dose led to
 transduction of regions of the heart with 1-3 vector genomes (vg) per
 nucleus, while most skeletal muscles were transduced with
 0.25-0.5vg/nucleus. GALGT2-induced glycosylation paralleled levels of
 myofiber vg transduction, with about 90% of cardiomyocytes having
 increased glycosylation versus 20-35% of all myofibers across the skeletal
 muscles tested. Conclusions from phenotypic testing were limited by the
 small number of dogs. Treated dogs had less pronounced fibrosis and
 overall lesion severity when compared to control groups, but surprisingly
 no significant changes in limb muscle function measures.
  GALGT2-treated skeletal muscle and heart had elevated levels of
 utrophin protein expression and GALGT2-induced expression of glycosylated
 a dystroglycan, providing further evidence of a treatment effect.
  No abnormalities were seen on serum chemistry, hematology, and
 cardiac testing, suggesting short-term safety. Cumulatively, these data
 show that short-term intravenous treatment of GRMD dogs with
 rAAVrh74.MHCK7.GALGT2 at high doses can induce muscle glycosylation and
 utrophin expression and may be safe over a short 3-month interval, but
 that such treatments have only modest effects on muscle pathology and do
 not significantly improve muscle strength.
DOI: 10.5061/dryad.6t1g1jwxv
title: Pervasive effects of Wolbachia on host activity

description: Heritable symbionts have diverse effects on the physiology, reproduction,
 and fitness of their hosts. Maternally
 transmitted Wolbachia are one of the most common
 endosymbionts in nature, infecting about half of all insect species. We
 test the hypothesis that Wolbachia alter host behavior
 by assessing the effects of 14
 different Wolbachia strains on the locomotor activity of
 nine Drosophila host species. We find
 that Wolbachia alter the activity of six different host
 genotypes, including all hosts in our assay infected
 with wRi-like Wolbachia strains
 (wRi, wSuz, wAur), which have rapidly spread
 among Drosophila species in only the last 13,000 years.
 While Wolbachia effects on host activity were common,
 the direction of these effects varied unpredictably and sometimes depended
 on host sex. We hypothesize that the prominent effects
 of wRi-like Wolbachia may be explained by
 patterns of Wolbachia titer and localization within host
 somatic tissues, particularly in the central nervous system. Our findings
 support the view that Wolbachia have wide-ranging
 effects on host behavior. The fitness consequences of these behavioral
 modifications are important for understanding the evolution of
 host-symbiont interactions, including
 how Wolbachia spread within host populations.
DOI: 10.5061/dryad.0cfxpnw1k
title: Evidence for a fungal loop in shrublands

description: 1. Dryland communities may mitigate the loss of limited resources by
 exchanging nutrients through subterranean fungal connections, termed
 fungal loops. In arid grasslands, fungal loops can influence community
 composition and primary productivity, yet their ecological significance
 across dryland systems remains unexplored. We investigated the functional
 role of fungal loops in nutrient translocation in a North American
 shrubland ecosystem. 2. We traced the movement of 15N from moss-dominated
 biocrusts to the dominant xeric shrub Larrea tridentata, and the movement
 of 13C from L. tridentata to biocrusts in plots established in situ in the
 Sonoran Desert. Measurements occurred at three time points spanning one
 week following a simulated 2.5 mm rainfall event, and at distances up to 1
 m from tracer application. We also used ITS sequencing to investigate
 changes in fungal community composition in soils over the one-week period.
 3. We discovered movement of 15N from biocrusts into L. tridentata foliage
 as well as 15N movement to other spatially isolated moss-dominated
 biocrust patches, yet this movement did not occur until 4-6 days
 post-rainfall, when significantly higher δ15N was observed in L.
 tridentata and biocrusts compared to previous days. We did not observe
 consistent patterns of 13C movement from L. tridentata into neighboring
 shrubs or biocrusts, suggesting differential environmental drivers for
 carbon movement in this system. Fungal communities exhibited a decrease in
 alpha diversity on the last day of the study, indicative of a delayed
 community response to rainfall concomitant with nutrient translocation.
 Fungal endophyte orders Pleosporales and Pezizales dominated all plot
 soils, and order Pleosporales was significantly more abundant in 15N
 enriched plots, suggesting that dark-septate endophytic fungi were
 involved in nitrogen translocation. The delay in nutrient translocation
 may reflect a rainfall-triggered rebuilding of mycelial networks between
 community members following drought. 4. Synthesis: Our results point to
 fungal-mediated nutrient exchange pathways in a previously uninvestigated
 vegetation type, shrublands, where nutrients are translocated between
 moss-dominated biocrusts and nearby shrubs. We provide the first evidence
 that nutrient transfer may be delayed up to six days following rainfall,
 consistent with pulse-dynamic responses in drylands, and that
 moss-dominated biocrusts play a role in fungal loops.
description: These data were collected and processed following the protocols
 outlined in Carvajal Janke & Coe, 2021. 
description: Feature tables and metadata are in relation to fungal community
 analysis, and Combined Data (along with Combined Data Outliers Removed)
 are a combination of the isotope concentration data provided in the COIL
 spreadsheet as well as in situ data collected per sample.
DOI: 10.5061/dryad.vt4b8gtrg
title: RIP2 interacts with REL1 to control leaf architecture by modulating brassinosteroid signaling in rice

description: FPKM (Fragments per kilobase of exon model per million mapped fragments)
 value of all detected genes in in WT, rel1, rip2, and rel1 rip2 mutants.
 ZH11_1, ZH11_2, ZH11_3 represent samples were collected from ZH11 with
 three independent biological replicates. rel1_1, rel1_2, rel1_3 represent
 samples were collected from rel1 mutants with three independent biological
 replicates. rip2_1, rip2_2, rip2_3 represent samples were collected from
 rip2 mutant with three independent biological replicates. rel1rip2_1,
 rel1rip2_2, rel1rip2_3 represent samples were collected from rel1rip2
 double mutant with three independent biological replicates.
description: Three replicates of ZH11, rel1, rip2, and
 <i>rel1rip2</i> mutant during the seedling stage were used for
 RNA-sequencing. Leaves of samples were harvested, preserved in liquid
 nitrogen, and stored at -80 ºC. Transcriptome data were collected by
 Beijing Novogene Bioinformatics Technology Company. Raw data (raw reads)
 in fastq format were first processed through in-house perl scripts. In
 this step, clean data (clean reads) were obtained by removing reads
 containing adapters, poly-N, and low-quality reads from the raw data. At
 the same time, quality parameters of the clean data, including Q20, Q30,
 GC content, and sequence duplication level, were used for data filtering.
 All subsequent analyses were conducted using high-quality clean data.
 Reference genome and gene model annotation files were downloaded from The
 MSU Rice Genome Annotation Project Database website at
 http://rice.plantbiology.msu.edu/.
DOI: 10.5061/dryad.ncjsxkstm
title: Data from manuscript: Assessment of the 7075-T6-aluminum-alloy/microalloyed-dual-phase-steel joint for automotive chassis

description: The corrosion behavior of a 7075-T6 Aluminum Alloy sample (AA7075-T6) and
 a low-Carbon low-Manganese microalloyed dual-phase steel sample (MADPS)
 were studied by electrochemical impedance spectroscopy (EIS) and
 potentiodynamic polarization (PP). The galvanic corrosion resulting from
 their assembly within a dissimilar joint, was studied by the
 zero-resistance ammeter technique (ZRA). The tests were conducted at room
 temperature and pressure (Mexico City) using an aqueous solution of 3%
 NaCl as electrolyte (pH 5.3) and without deaereating the solution. All
 tests were repeated more than twice to check the reproducibility.
 Electrochemical impedance spectroscopy (EIS) and potentiodynamic
 polarization were conducted using a BioLogic VMP3 potentiostat with EC-Lab
 software. The samples were pasted to the side of an acrylic cell. Circular
 sections of 1 cm2 on top of the samples were cut off from the cell to
 allow electrolyte contact. A typical three-electrode cell arrangement was
 used, with the samples connected as working electrode (WE), an Ag/AgCl
 (3.5 M KCl) electrode as the reference electrode (RE), and a platinum wire
 or mesh as counter electrode (CE). The samples were allowed to contact the
 electrolyte during 1 h before each electrochemical measurement to allow
 open circuit potential (OCP) stabilization. Impedance measurements were
 performed in the frequency range from 100 kHz to 10 mHz, with a 10 mV
 voltage amplitude from the OCP, acquiring the data at a resolution of 10
 points per decade. Potentiodynamic polarization curves were carried out
 with a potential scanning rate of 0.5 mV/s from - 250 mV to +250 mV vs.
 (Ag/AgCl) to ensure steady-state conditions. The zero-resistance ammeter
 (ZRA) technique was conducted using the BioLogic VMP3
 potentiostat. The galvanic couple was set in a coplanar
 configuration with the samples contacting each other along one of their
 sides. The samples were pasted to the bottom of the acrylic cell. The
 MADP-steel sample was connected as WE, while the AA was connected as CE,
 and an Ag/AgCl (3.8M KCl) was employed as RE (set at a height of 4 mm from
 the samples surface). The galvanic current and the galvanic potential were
 measured every 0.5 s during 4 h. The galvanic current was further divided
 by the electrode area to calculate the galvanic current density.