cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vt4b8gtp0
title: Feeding preferences and nutritional niche of wild water buffalo (Bubalus arnee) in Koshi Tappu Wildlife Reserve, Nepal.

description: We sought to further the understanding of how an animal’s foraging ecology
 is influenced by their feeding preferences and nutritional composition of
 forage items. Our research identified these aspects of wild water
 buffalo’s (Bubalus arnee) foraging ecology in Nepal. First, we sought to
 describe the foraging preferences of wild water buffalo in terms of the
 relative abundance of functional forage groups (i.e., forbs, graminoids,
 and browse) in their diet. We observed signs of wild water buffalo
 foraging on 54 plant species. We found wild water buffalo consume
 graminoids and forbs 2-3 times more frequently than browse items. Then, we
 investigated the composition of nutrients (i.e., carbohydrates, proteins,
 and lipids) in wild water buffalo diets to develop an estimate of their
 realized nutrient niche. Of the 54 plant species foraged, we analyzed the
 nutritional composition of the 16 most frequently foraged species. We
 found the realized nutrient niche of wild water buffalo is dominated by
 carbohydrates, but there was a positive correlation between the relative
 frequency of foraged items and protein content. Our study contributes
 important information on the feeding preference and nutritional content of
 the endangered wild water buffalo. Our results can be used to inform
 conservation and management strategies of this species in wild. Selection
 of potential translocation sites should include key species that are
 higher in protein content and frequently forages by wild water buffalo
 (e.g., Typha elephantina) to help mitigate human-wildlife conflicts.
 Further, we provide valuable insight into the mechanisms influencing the
 foraging ecology of wild herbivores.
description: These data describe the relative frequency of plants foraged in
 Koshi Tappu Wildlife Reserve, Nepal and the macronutrient content of those
 plants. Fifty foraging plots were established throughout the reserve where
 signs of wild water buffalo (<em>Bablus arnee</em>) presence
 were observed. Plants that were foraged by buffalo were clipped and sent
 to Nepal Environmental and Scientific Services laboratory in Kathmandu,
 Nepal and proximate analysis estimated macronutrient content using
 standardized methods described by the Association of Official Agricultural
 Chemists. The authors then converted nutrients to units of metabolizable
 energy using conversion factors of 9 kcal/g for lipids, and 4 kcal/g for
 carbohydrates and proteins.
DOI: 10.5061/dryad.prr4xgxhm
title: Differences in oxidative stress across seasons and ability to cope with environmental mismatch in muscle and brain of black-capped chickadees (Poecile atricapillus) and rock pigeons (Columba livia)

description: Resident birds in temperate areas respond to seasonally fluctuating
 temperatures by adjusting their physiology so as to match thermogenic
 requirements of their environment. Climate change is predicted to increase
 the frequency of heat waves, increasing the likelihood that birds will
 face environmental mismatch. Changes in BMR due to seasonality or anomaly
 events should show effects to the oxidative stress system. We examined the
 effects of chronic and acute heat exposure on muscle and brain tissue
 total antioxidant capacity, enzymatic activities of catalase (CAT), and
 glutathione peroxidase (GPx) and lipid peroxidation (LPO) damage in two
 temperate bird species of differing body masses and ecological strategies,
 the black-capped chickadee (Poecile atricapillus) and the rock pigeon
 (Columba livia), across three seasons. We found that heat stress did not
 alter oxidative stress in either species or tissue. But, in muscle, rock
 pigeons and black-capped chickadees demonstrated similar seasonal changes
 where peroxyl scavenging capacity was highest in the fall, hydroxyl
 scavenging capacity was higher in fall and summer. CAT activity was lowest
 in the fall and highest in the summer, GPx activity was highest in the
 fall, and LPO damage was highest in the summer but lowest in the
 fall.  In brain, we found that scavenging capacity to hydroxyl
 radicals was highest in fall and summer for rock pigeons, whereas it was
 only elevated in the summer for black-capped chickadees. Our data suggest
 that the oxidative stress system is slow to change seasonally.
DOI: 10.5061/dryad.2rbnzs7jm
title: Ectopic expression of BBS1 rescues male infertility, but not retinal degeneration, in a BBS1 mouse model

description: Bardet-Biedl syndrome (BBS) is a rare ciliopathy for which there are no
 current effective treatments. BBS is a genetically heterogeneous disease,
 though the M390R mutation in BBS1 is involved in approximately 25% of all
 genetic diagnoses of BBS. The principle features of BBS include retinal
 degeneration, obesity, male infertility, polydactyly, intellectual
 disability, and renal abnormalities. Patients with mutations in BBS genes
 often present with night blindness within the first decade of life, which
 progresses to complete blindness. This is due to progressive loss of
 photoreceptor cells. Male infertility is caused by a lack of spermatozoa
 flagella, rendering them immobile. In this study, we have crossed the
 wild-type human BBS1 gene, driven by the CAG promoter, onto the
 Bbs1M390R/M390R mouse model to determine if ectopic expression of BBS1
 rescues male infertility and retinal degeneration. qRT-PCR indicates that
 the BBS1 transgene is expressed in multiple tissues throughout the mouse,
 with the highest expression seen in the testes, and much lower expression
 in the eye and hypothalamus. Immunohistochemistry of the transgene in the
 eye showed little if any expression in the photoreceptor outer nuclear
 layer. When male Bbs1M30R/M390R;BBS1TG+mice are housed with WT females,
 they are able to sire offspring, indicating that the male infertility
 phenotype of BBS is rescued by the transgene. Using electroretinography
 (ERGs) to measure retinal function and optical coherence tomography to
 measure retinal thickness, we show that the transgene does not confer
 protection against retinal degeneration in Bbs1M300R/M390R;BBS1TG+ mice.
description: Missing values for eyes in OCT data sheet are due to un-readable
 images. In the case where there is only data for one eye, that value was
 used for analysis. Otherwise, the average of two eyes was used in our
 analyses.
DOI: 10.5061/dryad.k0p2ngf4z
title: Controlled packing and single-droplet resolution of 3D-printed functional synthetic tissues

description: 3D-printing networks of droplets connected by interface bilayers is a
 powerful platform to build synthetic tissues, in which functionality
 relies on precisely ordered structures. However, the structural precision
 and consistency in assembling these structures is currently limited, which
 restricts intricate designs and the complexity of functions performed by
 synthetic tissues. Here, we report that the equilibrium contact angle
 (θDIB) between a pair of droplets is a key parameter that dictates the
 tessellation and precise positioning of hundreds of picolitre droplets
 within 3D-printed, multi-layer networks. When θDIB approximates the
 geometrically-derived critical angle (θc) of 35.3º, the resulting networks
 of droplets arrange in regular hexagonally close-packed (hcp) lattices
 with the least fraction of defects. With this improved control over
 droplet packing, we can 3D-print functional synthetic tissues with
 single-droplet-wide conductive pathways. Our new insights into 3D droplet
 packing permit the fabrication of complex synthetic tissues, where
 precisely positioned compartments perform coordinated tasks.
description: The files are labelled in the format:
 SILXX_POPCYY_NetNumber_Process.tif
 Where: "SILXX_POPCYY" indicates the
 volume fraction of silicone oil
 (<i>φ<sub>SIL</sub></i>) and molar fraction of
 POPC (<i>x<sub>POPC</sub></i>) at which the
 network was printed (e.g. "SIL55_POPC13" corresponds to
 <i>φ<sub>SIL</sub> = 0.55
 </i>and<i> x<sub>POPC</sub> =
 0.13</i>) "NetNumber" indicates the
 repeat number of the specific printed network (e.g. "net3"
 indicates the 3rd network printed at a specific condition)
 "Process" indicates the type of processing visualised
 in the image. This can be: " " :
 Raw confocal image "Network": Segmented
 image showing automatic identification of the lipid bilayers in droplet
 networks "Network_Corrected": Manually
 corrected image after automatic segmentation
 "LinkClasses": Segmented image showing classification
 of lipid bilayers and lipid monolayers
 "Overlay": Overlay of the confocal image and
 corresponding packing classification based on Delaunay
 triangulation.
DOI: 10.5061/dryad.zw3r22859
title: Mate-finding Allee effects can be exacerbated or relieved by sexual cannibalism

description: 1. Allee effects occur when individual or population survival decreases
 due to populations being small or sparse. A key mechanism underlying Allee
 effects is difficulty in finding mates at low densities. Species may be
 particularly vulnerable to mate-finding Allee effects if females rely on
 an abundance of males to reproduce successfully. In sexually cannibalistic
 species, females may consume males before or after copulation, potentially
 reducing the supply of males to the point where a mate-finding Allee
 effect occurs. 2. In this study, we investigate the extent to which sexual
 cannibalism can modulate mate-finding Allee effects, and the conditions
 under which sexual cannibalism is likely to be particularly detrimental to
 population viability. 3. We created an individual-based model that tracked
 specific females throughout the breeding season and used extinction risk
 and per capita growth rate to measure the strength of the Allee effects.
 We varied both founder population size and mate encounter rate
 independently of each other to expose the mechanism driving the Allee
 effects. We also analysed how cannibalism-derived female fecundity
 benefits affected extinction risk. 4. We found that sexual cannibalism
 could lead to high extinction risk, particularly when cannibalism occurred
 before copulation, founder population size was small, and mate encounter
 rates were low. However, post-copulatory cannibalism reduced extinction
 risk, if cannibalism increased female fecundity enough. We found that
 there were strong threshold effects, in which small changes in encounter
 rate could strongly alter population extinction risk. 5. We find that
 sexual cannibalism is likely to negatively impact population survival as
 population size and mate encounter rate decrease. This may be exacerbated
 if male quality declines and female hunger increases in declining
 populations. As many top invertebrate predators, such as spiders and
 mantids are sexually cannibalistic, this may have ecosystem-wide impacts.
 We also suggest that other reproductive behaviours, such as rejecting all
 but high quality mates or requiring multiple mates to ensure fertility,
 are also likely to cause mate-finding Allee effects when habitat quality
 degrades. 03-Mar-2020
description: A function that simulates a single day of a sexually
 cannibalistic breeding system.
DOI: 10.5061/dryad.931zcrjgm
title: Data from: Cu-Al mixed oxide-catalysed multicomponent synthesis of gluco- and allofuranose-linked 1,2,3-triazole derivatives

description: A series of carbohydrate linked-1,2,3-triazole derivatives were
 synthetized in good yields from glucofuranose and allofuranose
 diacetonides using as key step a three-component 1,3-dipolar azide-alkyne
 cycloaddition catalyzed by a Cu-Al mixed oxide. In this multicomponent
 reaction, Cu-Al mixed oxide/sodium ascorbate system serves as highly
 reactive, recyclable and efficient heterogeneous catalyst for
 regioselective synthesis of 1,4-disubstituted 1,2,3-triazoles. The
 reported protocol has significant advantages over classical CuI/DIPEA or
 CuSO4/sodium ascorbate conditions in terms of efficiency and reduced
 synthetic complexity. In addition, the selective deprotection of
 synthesized di-O-isopropylidene derivatives was also carried out leading
 to the corresponding mono-O-isopropylidene products in moderate yields.
 Some of the synthesized triazole glycoconjugates were tested for their in
 vitro antimicrobial activity using the disk diffusion method against
 Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis),
 Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa), as
 well as fungus (Aspergillus niger) and yeast (Candida utilis). The results
 revealed that these compounds exhibit moderate to good antimicrobial
 activity mainly against Gram-negative bacteria.
description: NMR spectra were recorded on a
 Bruker Ascend-400 (400 MHz) and Bruker Avance DMX-500 (500 MHz)
 spectrometers in CDCl<sub>3 </sub>or
 acetone-d<sub>6</sub> and chemical shifts are given in ppm
 with TMS as the reference.
description: Raw NMR data (including <sup>1</sup>H,
 <sup>13</sup>C, COSY, HSQC and HMBC experiments) for new
 synthetized compounds.
DOI: 10.5061/dryad.tmpg4f4vt
title: Population asynchrony alone does not explain stability in species rich soil animal assemblages: the stabilising role of forest age on oribatid mite communities

description: 1. The importance of microbial and plant communities in the control of the
 diversity and structure of soil animal communities has been clarified over
 the last decade. Previous research focused on abiotic factors, niche
 separation and spatial patterns. Significant gaps still exist in our
 knowledge of the factors that control the stability of these communities
 over time. 2. We analysed a nine-year data set form the national Long-term
 Ecological Research Network of Latvia. We focused on 117 oribatid species
 from three Scots pine forests of different age (&lt;40 yrs, 65 yrs,
 and &gt;150 yrs) and structure. For each forest type, 100 samples were
 collected each year, providing very high replication and long of time
 series for a soil community. We assessed different aspects of stability:
 we used a dynamic null model, parametrised on observed growth rates, to
 test the hypothesis that asynchrony in species populations stabilises
 total community size; we also analysed alpha and beta diversity over time
 to test the hypothesis that temporal variation in species composition and
 relative abundances is controlled by forest attributes. 3. Real
 communities can be more stable than their stochastic counterparts if
 species are asynchronous, confirming for the first time the role of
 asynchrony in stabilising soil communities. Yet, while some real
 communities were more stable and had higher abundance and growth rates
 than others, they were not necessarily more asynchronous than the less
 stable communities. Species composition and relative abundances were also
 less variable in the more stable communities. 4. Species asynchrony
 generally stabilises species rich communities but is not sufficient to
 explain different levels of stability between forests. Forest age is a key
 factor explaining different levels of overyielding and so stability. Data
 suggests that both asynchrony and high diversity of microhabitat structure
 of Scots pine forests promote stability of soil animal communities.
description: This dataset can be analysed with the R script
 "StabilityMetrics.R" provided in the original
 publication
DOI: 10.5061/dryad.nzs7h44nj
title: Data from: The clinical, histological, and genotypic spectrum of SEPN1-related myopathy: A case series

description: Objective: To clarify the prevalence, long-term natural history and
 severity determinants of SEPN1-related myopathy (SEPN1-RM), we analyzed a
 large international case series. Methods: Retrospective clinical,
 histological and genetic analysis of 132 pediatric and adult patients
 (2-58 years) followed-up for several decades. Results: The clinical
 phenotype was marked by severe axial muscle weakness, spinal rigidity and
 scoliosis (86.1%, from 8.9±4 years), with relatively-preserved limb
 strength and previously-unreported ophthalmoparesia in severe cases. All
 patients developed respiratory failure (from 10.1±6 years), 81.7%
 requiring ventilation while ambulant. Histopathologically, 79 muscle
 biopsies showed large variability, partly determined by site of biopsy and
 age. Multi-minicores were the most common lesion (59.5%), often associated
 with mild dystrophic features and occasionally with eosinophilic
 inclusions. Identification of 65 SEPN1 mutations, including 32 novel ones
 and the first pathogenic CNV, unveiled exon 1 as the main mutational
 hotspot and revealed the first genotype-phenotype correlations, bi-allelic
 null mutations being significantly associated with disease severity
 (p=0.017).  SEPN1-RM was more severe and progressive than
 previously thought, leading to loss of ambulation in 10% cases, systematic
 functional decline from the end of the third decade and reduced lifespan
 even in mild cases. The main prognosis determinants were
 scoliosis/respiratory management, SEPN1 mutations and body mass
 abnormalities, which correlated with disease severity. Finally, we propose
 a set of severity criteria, provide quantitative data for outcome
 identification and establish a need for age stratification. Conclusion:
 Our results inform clinical practice, improving diagnosis and management,
 and represent a major breakthrough for clinical trial readiness in this
 not-so-rare disease.
description: We included 132 patients with
 <i>SEPN1</i> mutations identified between 2001 and 2017.
 Thirty-one were previously reported. <i>SEPN1/SELENON</i> was analyzed on genomic DNA from peripheral blood using Sanger sequencing or Next Generation Sequencing-based gene panels [NGS]. Variants were reported according to Human Genome Variation Society recommendations (http://varnomen.hgvs.org/) using the complete <i>SEPN1/SELENON</i> transcript (NM_020451.2; NP_065184.2). Genome Aggregation (http://gnomad.broadinstitute.org/) and Clinvar (http://www.ncbi.nlm.nih.gov/clinvar/) databases were interrogated to identify previously-reported mutations and to determine variant frequency in the population. Alamut-Batch-UI v1.11® (Interactive Biosoftware, North Seattle, WA) was used to predict variant impact.
description: Supplementary Table 1: Comprehensive summary of mutation data. rsID: Reference SNP cluster ID from dbSNP database. ClinVarID: ID from ClinVar database. N: number of patients carrying the mutation.
DOI: 10.5061/dryad.7pvmcvdpz
title: Disconnects between ecological theory and data in phenological mismatch research

description: Climate change may lead to phenological mismatches, where the timing of
 critical events between interacting species becomes de-synchronized, with
 potential negative consequences. Evidence documenting negative impacts on
 fitness is mixed. The Cushing match-mismatch hypothesis, the most common
 hypothesis underlying these studies, offers testable assumptions and
 predictions to determine consequences of phenological mismatch when
 combined with a pre-climate change baseline. Here, we highlight how
 improved approaches could rapidly advance mechanistic understanding. We
 find that currently no study has collected the data required to test this
 hypothesis well, and 71% of studies fail to define a baseline. Experiments
 that clearly link timing to fitness and test extremes, integration across
 approaches, and null models would aid robust predictions of shifts with
 climate change.
description: We located papers relating phenological data from trophic
 interactions to fitness and/or performance of the consumer and/or the
 resource by conducting keyword searches in ISI Web of Science published up
 to June 2017. Keywords included phenolog* AND mismatch* OR synchron* AND
 interact* AND (fitness* OR performance*). If more than one measure of
 phenology was included, we chose the one used by the authors to calculate
 mismatch and examine its impact on performance. Our final review included
 42 studies with 45 pair-wise species interactions (3 studies had 2
 interactions). Based on the type of data collected for the consumer and
 resource, we classified studies as life history (i.e. one that collected
 data at the individual level) or one that collected data at the population
 or community (i.e., across species). To determine whether studies had the
 potential to define pre-climate change baselines, we measured the study’s
 time span and years of data based on the years where phenology data was
 available for both the consumer and resource, and consumer performance
 data was available.
description: Each observation is an individual pair-wise species
 interaction.
DOI: 10.15468/dl.m4jz75
title: Occurrence Download

description: A dataset containing 4591 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is WII Herbarium Dataset"
 ]
}

 The dataset includes 4591 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002231-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4tmpg4f66
title: Microsite conditions in retrogressive thaw slumps may facilitate increased seedling recruitment in the Alaskan Low Arctic

description: In Low Arctic tundra, thermal erosion of ice‐rich permafrost soils
 (thermokarst) has increased in frequency since the 1980s. Retrogressive
 thaw slumps (RTS) are thermokarst disturbances forming large open
 depressions on hillslopes through soil wasting and vegetation
 displacement. Tall (&gt;0.5 m) deciduous shrubs have been observed in
 RTS a decade after disturbance. RTS may provide conditions suitable for
 seedling recruitment, which may contribute to Arctic shrub expansion. We
 quantified in situ seedling abundance, and size and viability of soil
 seedbanks in greenhouse trials for two RTS chronosequences near lakes on
 Alaska's North Slope. We hypothesized recent RTS provide microsites
 for greater recruitment than mature RTS or undisturbed tundra. We also
 hypothesized soil seedbanks demonstrate quantity–quality tradeoffs;
 younger seedbanks contain smaller numbers of mostly viable seed that
 decrease in viability as seed accumulates over time. We found five times
 as many seedlings in younger RTS as in older RTS, including birch and
 willow, and no seedlings in undisturbed tundra. Higher seedling counts
 were associated with bare soil, warmer soils, higher soil available
 nitrogen, and less plant cover. Seedbank viability was unrelated to size.
 Older seedbanks were larger at one chronosequence, with no difference in
 percent germination. At the other chronosequence, germination was lower
 from older seedbanks but seedbank size was not different. Seedbank
 germination was positively associated with in situ seedling abundance at
 one RTS chronosequence, suggesting postdisturbance revegetation from
 seedbanks. Thermal erosion may be important for recruitment in tundra by
 providing bare microsites that are warmer, more nutrient‐rich, and less
 vegetated than in undisturbed ground. Differences between two
 chronosequences in seedbank size, viability, and species composition
 suggest disturbance interacts with local conditions to form seedbanks. RTS
 may act as seedling nurseries to benefit many Arctic species as climate
 changes, particularly those that do not produce persistent seed.
description: This dataset is based on field sampling of soil seedbanks, in
 situ seedling counts and greenhouse germination trials. Material was
 harvested from 1x1 m plots along 50m transects. 4 transects per site, two
 sites consisting of thermokarst-disturbed lakes of different ages on
 Alaska's North Slope
description: There are no missing values in this dataset.