cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r7sqv9s7f
title: Data from: Mannose glycosylation is an integral step for human NIS localization and function in breast cancer cells

description: Chasing an intriguing biological question on the disparity of sodium
 iodide symporter (NIS or SLC5A5) expression and function in clinical
 scenario of breast cancer (BC), this study addresses key molecular defects
 involved. Human NIS expression is primarily recorded as a cytoplasmic
 protein, thus limiting its scope for targeted radio-iodine therapy. While
 developing NIS transgene over-expressing MCF-7 breast adenocarcinoma, a
 few unique clonal derivatives show predominant expression in plasma
 membrane, whereas majority others show cytosolic expression over long
 passages. The membrane lineage shows un-perturbed dynamic trafficking of
 NIS through secretory pathway organelles, when compared to cytoplasmic or
 parental cells. Further, treatment of membrane cells with specific
 glycosylation inhibitors highlights the importance of inherent
 glycosylation processing. The 84 gene signature glycosylation RT-Profiler
 array reveals that membrane clones cluster separately from the rest.
 Further, role of three differentially expressed genes i.e. MAN1B1, MAN1A1
 and MAN2A1 in regulation of NIS localization is confirmed by RNA
 interference. Thus, for the first time this study shows the important role
 of mannosidase in N-glycosylation processing for proper trafficking of NIS
 to the plasma membrane in BC cells
description: Data was collected by performing a q-RT PCR profiler array for 84
 genes involved in the process of N-linked glycosylation
DOI: 10.5061/dryad.crjdfn30n
title: Ultrasound-derived changes in thickness of human ankle plantar flexor muscles during walking and running are not homogeneous along the muscle mid-belly region

description: Skeletal muscle thickness is a valuable indicator of several aspects of a
 muscle’s functional capabilities. We used computational analysis of
 ultrasound images, recorded from 10 humans walking and running at a range
 of speeds (0.7 – 5.0 m s-1), to quantify interactions in thickness change
 between three ankle plantar flexor muscles (soleus, medial and lateral
 gastrocnemius) and quantify thickness changes at multiple muscle sites
 within each image. Statistical analysis of thickness change as a function
 of stride cycle (1d statistical parametric mapping) revealed significant
 differences between soleus and both gastrocnemii across the whole stride
 cycle as they bulged within the shared anatomical space. Within each
 muscle, changes in thickness differed between measurement sites but not
 locomotor condition. For some of the stride, thickness measures taken from
 the distal-mid image region represented the mean muscle thickness, which
 may therefore be a reliable region for these measures. Assumptions that
 muscle thickness is constant during a task, often made in musculoskeletal
 models, do not hold for the muscles and locomotor conditions studied here
 and researchers should not assume that a single thickness measure, from
 one point of the stride cycle or a static image, represents muscle
 thickness during dynamic movements.
description: Data are changes in muscle thickness obtained from segmentation
 of b-mode ultrasound image sequences, recorded from the lower leg muscles
 of human participants as they walked and ran on an instrumented
 treadmill. Full details of the image collection
 protocol are provided in Lai, A.<i> </i>Lichtwark, G.A.
 Schache, A.G. Lin, Y-C. Brown, N.A.T. Pandy, M.G. (2015) In vivo behavior
 of the human soleus muscle with increasing walking and running speeds.
 <i>Journal of Applied Physiology. </i><b>118</b>,
 1266-1275 Images were segmented using an active shape
 model approach described in Darby, J. Hodson-Tole, E.F, Costen, N., Loram,
 I. (2012) Automated regional analysis of B-mode ultrasound images of
 Skeletal Muscle Movement. <i>Journal of Applied
 Physiology.</i> <b>112</b>: 313-327
description: Data comprise three spreadsheet files, one for each muscle
 investigated: LG_Muscle_Thickness = measures from the
 lateral gastrocnemius muscle MG_Muscle_Thickness =
 measures from the medial gastrocnemius muscle
 SO_Muscule Thickness = measures from the soleus muscle
 In addition, the Read Me file provides explanation of the layout
 of data in the spreadsheet files
DOI: 10.5061/dryad.2280gb5n2
title: Incorporating evaporative water loss into bioenergetic models of hibernation to test for relative influence of host and pathogen traits on white-nose syndrome

description: Hibernation consists of extended durations of torpor interrupted by
 periodic arousals. The ‘dehydration hypothesis’ proposes that hibernating
 mammals arouse to replenish water lost through evaporation during torpor.
 Arousals are energetically expensive, and increased arousal frequency can
 alter survival throughout hibernation. Yet we lack a means to assess the
 effect of evaporative water loss (EWL), determined by animal physiology
 and hibernation microclimate, on torpor bout duration and subsequent
 survival. White-nose syndrome (WNS), a devastating disease impacting
 hibernating bats, causes increased frequency of arousals during
 hibernation and EWL has been hypothesized to contribute to this increased
 arousal frequency. WNS is caused by a fungus, which grows well in humid
 hibernaculum environments and damages wing tissue important for water
 conservation. Here, we integrated the effect of EWL on torpor expression
 in a hibernation energetics model, including the effects of fungal
 infection, to determine the link between EWL and survival. We collected
 field data for Myotis lucifugus, a species that experiences high mortality
 from WNS, to gather parameters for the model. In saturating conditions, we
 predicted healthy bats experience minimal mortality. Infected bats,
 however, suffer high fungal growth in highly saturated environments,
 leading to exhaustion of fat stores before spring. Our results suggest
 that host adaptation to humid environments leads to increased arousal
 frequency from infection, which drives mortality across hibernaculum
 conditions. Our modified hibernation model provides a tool to assess the
 interplay between host physiology, hibernaculum microclimate, and diseases
 such as WNS on winter survival.
DOI: 10.5061/dryad.0gb5mkkwp
title: Do infants and preschoolers quantify probabilities based on proportions?

description: Most statistical problems encountered throughout life require the ability
 to quantify probabilities based on proportions. Recent findings on the
 early ontogeny of this ability have been mixed: For example, when
 presented with jars containing preferred and less preferred items,
 12-month-olds, but not 3- and 4-years-olds, seem to rely on the
 proportions of objects in the jars to predict the content of samples
 randomly drawn out of them. Given these contrasting findings, it remains
 unclear what the probabilistic reasoning abilities of young children are
 and how they develop. In our study, we addressed this question and tested,
 with identical methods across age groups and similar methods to previous
 studies, whether 12-months-olds and 3- and 4-years-olds rely on
 proportions of objects to estimate probabilities of random sampling
 events. Results revealed that neither infants nor preschoolers do. While
 preschoolers’ performance is in line with previous findings, infants’
 performance is difficult to interpret given their failure in a control
 condition in which the outcomes happened with certainty rather than a
 graded probability. More systematics studies are needed to explain why
 infants succeeded in a previous study but failed in our study.
description: Children were recruited
 from a database of families who had voluntarily registered and agreed to
 participate. They were from mixed socioeconomic backgrounds and some
 family were plurilingual. Each child underwent a preference
 test, a probability condition and a baseline condition. In the preference
 test, the experimenter presented children with two different Kinder eggs
 capsules, one empty and white and the other containing a fingerpuppet and
 blue. She hid both objects in separate cups and let subjects choose a cup
 (only subject choosing the cup containing the blue egg were kept in the
 final sample). In the probability condition, the experimenter presented
 subjects with two populations of Kinder eggs, one containing a higher
 proportion of blue eggs and the other a higher proportion of white eggs.
 She secretly drew one object out of each population, hid them in separet
 cups and let subjects choose between both cups. The same procedure was
 repeated in the baseline condition, in which one population only contained
 blue eggs and the other only white eggs.  Every session was video recorded.
 Children's choices were coded from the videos. We coded it as a
 success when children chose the sample drawn out of the population with a
 higher proportion of blue eggs and as a failure when they chose the other
 sample.
DOI: 10.5061/dryad.c866t1g32
title: The biomolecular characterisation of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark

description: We present the analysis of an osseous finger ring from a predominantly
 early Neolithic context in Denmark. To characterise the artefact and
 identify the raw material used for its manufacture, we performed
 micro-computed tomography (Micro CT) scanning, zooarchaeology by mass
 spectrometry (ZooMS) peptide mass fingerprinting, as well as protein
 sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS).
 We conclude that the ring was made from long bone or antler due to the
 presence of osteons (Haversian canals). Subsequent ZooMS analysis of
 collagen I and II indicated that it was made from Alces alces or Cervus
 elaphus material. We then used LC-MS/MS analysis to refine our species
 identification, confirming that the ring was made from Cervus elaphus, and
 to examine the rest of the proteome. This study demonstrates the potential
 of ancient proteomics for species identification of prehistoric artefacts
 made from osseous material.
description: Micro CT was used to examine the ring using the commercial Zeiss
 Xradia410 versa system. The ring was rotated 360 degrees in 1601 steps
 taking a picture at each step using a pre-voltage of 80kV and a power of
 10W. Two measurements with different pixel resolutions were performed at
 32.3 and 13.5 µm. The 3D volume was reconstructed using the software
 provided with the instrument system “Reconstructor”, which is based on a
 Feldkamp-Davis-Kress algorithm (Feldkamp, Davis and Kress 1984). The
 resulting 3D volumes are cylinders with a diameter and height of 3.2 cm
 and 1.35 cm respectively corresponding to the different pixel resolutions,
 containing different amounts of the object. Visualisation was performed
 using ‘Avizo 9.7’ (Thermo Fisher Scientific). The volume investigated with
 high resolution X-ray micro CT, has been segmented into elements of the
 bone (shown in transparent gray) and porosity in the bone (shown in blue).
 The different levels of blue are a result of the amount of
 transparency.
DOI: 10.5061/dryad.8cz8w9gk6
title: Factors influencing fall departure phenology in migratory birds that bred in northeastern North America

description: The phenology of migrating birds is shifting with climate change. For
 instance, short-distance migrants wintering in temperate regions tend to
 delay their migration in fall during spells of warmer temperature.
 However, some species do not show strong shifts, and the factors
 determining which species will react to temperature changes by delaying
 their migration are poorly known. In addition, it is not known whether a
 slower migration or a postponed departure creates the observed delays in
 fall migration because most studies occur far south of the boreal breeding
 areas making it difficult to separate those two mechanisms. We used 22
 years of data at a northern observatory in eastern North America, at the
 southern edge of the boreal forest, to examine how 21 short-distance
 migrants responded to changing temperatures. We investigated if those
 species responding to temperature share life history features (i.e. diet,
 size, total migration distance, breeding habitat, timing of migration).
 The period of migration in each species was, by far, the most important
 factor predicting the response of a species to temperature. Eight of the
 13 species migrating in October changed their migration onset with
 temperature (usually by delaying migration by 1-2d/°C), while the
 migration timing of none of the eight species migrating in September was
 dependent on temperature. Furthermore, the absence of a greater migration
 delay by birds breeding farther from the study site (i.e. Arctic breeding
 birds) suggests the mechanism is a postponed departure rather than a
 slower migration. We conclude that temperature variations in late fall
 influence the conditions on the breeding grounds, so that birds still
 present at that time might benefit more from postponing their departure in
 warm weather.
description: All data was collected between 1996 and 2017 at the Observatoire
 d’oiseaux de Tadoussac (48.15ºN, 69.66ºW), Québec, Canada. The main
 observation point is situated 55 m above sea level, on sand dunes
 surrounded by boreal forest and adjacent to the estuary of the St.
 Lawrence River. Due to the microhabitat of the dunes being unfavourable
 for breeding birds, the area is visited mostly by migrating birds passing
 through. The funnel effect created by the estuary, where birds migrating
 south follow the shoreline, creates a high density of migrants passing
 through the region (Ibarzabal 1999), The open habitat of the dunes,
 cleared from vegetation every year, facilitates detection for observers.
 Stationary observations were carried out daily by at least one experienced
 birdwatcher from August 24 to November 25 in each year. The observations
 started approximately one hour after sunrise and lasted five hours or more
 depending on the migration flow. Only heavy rain or snow prematurely ended
 the observations
DOI: 10.15468/dl.drvjah
title: Occurrence Download

description: A dataset containing 1659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, United States of America)",
 "Geometry POLYGON((-119.09557 13.3905,-92.81334 13.3905,-92.81334 36.84823,-119.09557 36.84823,-119.09557 13.3905))",
 "TaxonKey is Canis lupus baileyi"
 ]
}

 The dataset includes 1659 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001965-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dz08kprst
title: Late Cretaceous domatia reveals the antiquity of plant–mite mutualisms in flowering plants

description: Mite houses, or acarodomatia, are found on the leaves of over 2,000 living
 species of flowering plants today. These structures facilitate tri-trophic
 interactions between the host plant, its fungi or herbivore adversaries,
 and fungivorous or predaceous mites by providing shelter for the
 consumers. Previously, the oldest acarodomatia were described on a
 Cenozoic Era fossil leaf dating to 49 million years in age. Here, we
 report the first occurrence of Mesozoic Era acarodomatia in the fossil
 record from leaves discovered in the Late Cretaceous Kaiparowits Formation
 (76.6–74.5 Ma) in southern Utah, USA. This discovery extends the origin of
 acarodomatia by &gt;25 million years, and the antiquity of this
 plant–mite mutualism provides important constraints for the evolutionary
 history of acarodomatia on angiosperms.
description: NA
DOI: 10.5061/dryad.m0cfxpnz9
title: Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy

description: Genes in plant secondary metabolic pathways enable the biosynthesis of a
 range of medically and industrially important compounds, and are often
 clustered on chromosomes. Here, we study genomic clustering in the
 benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver
 somniferum), exploring relationships between gene expression, copy number
 variation, and metabolite production. We use Hi-C to improve the existing
 draft genome assembly, yielding chromosome-scale scaffolds that include 35
 previously unanchored BIA genes. We find that co-expression of BIA genes
 is increased within clusters and identify novel candidates with unknown
 function based on clustering and covariation in expression and alkaloid
 production. Copy number variation in critical BIA genes correlates with
 stark differences in alkaloid production, linking noscapine production
 with an 11-gene deletion, and increased thebaine/decreased morphine
 production with deletion of a T6ODM cluster. Our results show that the
 opium poppy genome is still dynamically evolving in ways that contribute
 to medically and industrially important phenotypes.
DOI: 10.5061/dryad.vx0k6djmq
title: Data from:TRPC3 determines osmosensitive [Ca2+]i signaling in the collecting duct and contributes to urinary concentration

description: It is well-established that the kidney collecting duct (CD) plays a
 central role in regulation of systemic water homeostasis. 
 Aquaporin 2 (AQP2)-dependent water reabsorption in the CD critically
 depends on the arginine vasopressin (AVP) antidiuretic input and the
 presence of a favorable osmotic gradient at the apical plasma membrane
 with tubular lumen being hypotonic compared to the cytosol.  This
 osmotic difference creates a mechanical force leading to an increase in
 [Ca2+]i in CD cells.  The significance of the osmosensitive
 [Ca2+]i signaling for renal water transport and urinary concentration
 remain unknown.  To examine molecular mechanism and physiological
 relevance of osmosensitivity in the CD, we implemented simultaneous direct
 measurements of [Ca2+]i dynamics and the rate of cell swelling as a
 readout of the AQP2-dependent water reabsorption in freshly isolated
 split-opened CDs of wild type and genetically manipulated animals and
 combined this with immunofluorescent detection of AVP-induced AQP2
 trafficking and assessment of systemic water balance.  We
 identified the critical role of the Ca2+-permeable TRPC3 channel in
 osmosensitivity and water permeability in the CD.  We further
 demonstrated that TRPC3 -/- mice exhibit impaired urinary concentration,
 larger urinary volume and a greater weight loss in response to water
 deprivation despite increased AVP levels and AQP2 abundance. 
 TRPC3 inhibition/deletion interfered with AQP2 translocation to the plasma
 membrane in response to AVP and water deprivation.  In summary,
 we provide compelling multicomponent evidence in support of a critical
 contribution of TRPC3 in the CD for osmosensitivity and renal water
 handling.
DOI: 10.5061/dryad.n02v6wwsd
title: Linking community assembly and structure across scales in a wild mouse parasite community

description: Understanding what processes drive community structure is fundamental to
 ecology. Many wild animals are simultaneously infected by multiple
 parasite species, so host parasite communities can be valuable tools for
 investigating connections between community structures at multiple scales,
 as each host can be considered a replicate parasite community. Like
 free-living communities, within-host parasite communities are
 hierarchical; ecological interactions between hosts and parasites can
 occur at multiple scales (e.g. host community, host population, parasite
 community within the host), therefore both extrinsic and intrinsic
 processes can determine parasite community structure. We combine analyses
 of community structure and assembly at both the host population and
 individual scales using extensive datasets on wild wood mice (Apodemus
 sylvaticus) and their parasite community. An analysis of parasite
 community nestedness at the host population scale provided predictions
 about the order of infection at the individual scale, which were then
 tested using parasite community assembly data from individuals hosts from
 the same populations. Nestedness analyses revealed parasite communities
 were significantly more structured than random. However, observed
 nestedness did not differ from null models in which parasite species
 abundance was kept constant. We did not find consistency between observed
 community structure at the host population scale and within-host order of
 infection. Multistate-Markov models of parasite community assembly showed
 that a host’s likelihood of infection with one parasite was not impacted
 by previous parasite infection, suggesting there is not a deterministic
 order of infection among the species we investigated in wild wood mice.
 Our results demonstrate that patterns at one scale (i.e. host population)
 do not reliably predict processes at another scale (i.e. individual host),
 and that neutral or stochastic processes may be driving the patterns of
 nestedness observed in these communities. We suggest that experimental
 approaches that manipulate parasite communities are needed to better link
 processes at multiple ecological scales.
DOI: 10.15468/dl.6qh2u6
title: Occurrence Download

description: A dataset containing 2254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, United States of America)",
 "TaxonKey is Canis lupus baileyi"
 ]
}

 The dataset includes 2254 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001967-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6m905qfvs
title: Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest

description: In boreal systems, soil profiles typically consist of distinct stratified
 horizons, with organic layers at the surface overlying deeper mineral
 horizons providing microhabitat variation along a depth gradient, and
 vertical stratification of fungal communities along such soil profiles is
 commonly observed. We studied fungal community structure in a coastal pine
 forest along a gradient of decreasing influence from the coast. In this
 system, the vertical stratification pattern of soil microhabitats (defined
 here as organic, mineral with roots, and mineral without roots; O, MR, and
 MN, respectively) is non-uniform; organic horizons are sometimes buried
 under drifting sand dunes. Our results show that soil microhabitats are
 distinct with respect to physiochemical characteristics, community
 composition, and OTU richness. While community composition was partly
 related to depth and distance from the coastal forest edge, microhabitat
 appeared to have the strongest influence. A closer inspection of the OTUs
 with the highest relative sequence abundance within each microhabitat
 revealed that microhabitats support functionally distinct fungal
 communities with respect to trophic mode and growth morphology. These
 results suggest that in coastal pine forests, variation in soil
 microhabitats contributes to the high fungal diversity found below-ground
 and may play an important role in optimizing nutrient cycling.