cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2mv
title: Prevalence of oral manifestations in patients with lupus erythematosus in a sample of Egyptian population, a hospital based cross-sectional study

description: Background: Several systemic diseases manifest themselves in the oral
 cavity. Oral manifestations of lupus erythematosus (LE) are associated
 with a significantly increased risk of cancer. Dentists who are unaware of
 these lesions will possibly miss them. This cross-sectional study aimed to
 assess the prevalence of oral manifestations in patients with LE in a
 sample of the Egyptian population. Methods: A descriptive study was
 performed on 189 patients attending the Internal Medicine Department,
 Rheumatology clinic in EL Qasr EL Ainy Hospital, Cairo University. Every
 patient was examined clinically after completing a questionnaire.
 Moreover, patients’ medical records were also evaluated. The oral
 manifestations were recorded according to the WHO guide to physical
 examination of the oral cavity and classified according to their
 morphologic aspects and localization. Results [DSL1] :
 Out of 198 patients, 182 females (96.3%) and 7 males (3.7%). The
 prevalence of oral lesions in LE patients was 55.6%. The most affected
 site was the tongue 25.7%. The most common clinical aspect was patches,
 53%. About 77.1% of the lesions were asymptomatic. 74.3% of the patients
 had oral candidiasis. The prevalence of skin lesions in LE patients was
 37.6%. The most common finding was malar rash 79%. Conclusions: The
 present study emphasizes the importance of early diagnosis of oral lesions
 to recognize patients with LE as the WHO considers oral manifestations of
 LE a widespread state associated with an increased risk of cancer. Also,
 implementation of oral hygiene measures and treatment to improve patients’
 nutritional state and health-related quality of life are recommended.
description: The study is an observational study. Demographic data and history
 were collected by in-depth interviews. A descriptive study was performed
 on 189 patients attending the Internal Medicine Department, Rheumatology
 clinic in EL Qasr EL Ainy Hospital, Cairo University. Every patient was
 examined clinically after completing a questionnaire. Moreover, patients’
 medical records were also evaluated. The oral manifestations were recorded
 according to the WHO guide to physical examination of the oral cavity and
 classified according to their morphologic aspects and
 localization.
DOI: 10.5061/dryad.hqbzkh1gs
title: Switch-like and persistent learning in individual Drosophila larvae

description: Associative learning allows animals to use past experience to predict
 future events. The circuits underlying memory formation support immediate
 and sustained changes in function, often in response to a single example.
 Larval Drosophila is a genetic model for memory formation that can be
 accessed at molecular, synaptic, cellular, and circuit levels, often
 simultaneously, but existing behavioral assays for larval learning and
 memory do not address individual animals, and it has been dicult to form
 long lasting memories, especially those requiring synaptic reorganization.
 We demonstrate a new assay for learning and memory capable of tracking the
 changing preferences of individual larvae. We use this assay to explore
 how activation of a pair of reward neurons changes the response to the
 innately aversive gas Carbon Dioxide (CO2). We conrm that when coupled to
 odor presentation in appropriate temporal sequence, optogenetic reward
 reduces avoidance of CO2. We nd that learning is switch-like: all-or-none
 and quantized in two states. Memories can be extinguished by repeated
 unrewarded exposure to CO2 but are stabilized against extinction by
 repeated training or overnight consolidation. Finally, we demonstrate
 long-lasting protein synthesis dependent and independent memory formation.
DOI: 10.5061/dryad.612jm6441
title: An integrated population model to project viability of a northern bobwhite population in Ohio [DATA]

description: Increased variation in interannual weather due to climate change can exert
 a powerful influence on the population dynamics of a species.
 Understanding the influence of severe weather is important for managing
 weather-sensitive species. While best management practices target vital
 rates that are affected by weather, focusing on a single vital rate may
 not be sufficient if other vital rates are secondarily limiting. A
 comprehensive modeling framework to forecast future population dynamics
 while incorporating weather scenarios and vital rate variation within
 observed ranges that can be affected by management actions are necessary.
 A potential approach is to combine an integrated population model (IPM)
 with a population viability analysis (PVA) to generate novel insights
 about population dynamics. We used the northern bobwhite (Colinus
 virginianus), a rapidly declining gamebird sensitive to snowfall along the
 northern extents of the species’ range, to demonstrate the utility of a
 coupled IPM-PVA framework for projecting the response of a population to
 weather, management, and changes in vital rates. We created an IPM using
 two sources of count data spanning seven years, five years of winter
 survival data, and two years of breeding season demographics for a
 declining bobwhite population in southwestern Ohio during 2007–2015.
 Quasi-extinction probability at the end of the decadal projection during
 2019–2029 was 0.384–0.410 for mild, average, and severe winter weather
 scenarios. Quasi-extinction probability declined to 0.326 with 20%
 improvement in nest success and summer survival rates. A concurrent 20%
 increase in winter survival further reduced quasi-extinction probability
 to 0.263, which is a ~36% reduction in quasi-extinction probability
 compared to the baseline scenario with no changes in vital rates. These
 results suggest that long-term viability of this population may depend on
 extensive management of winter habitat to improve survival but will also
 require management actions to improve fecundity after severe winters. Our
 modeling approach demonstrated how IPMs can be used to project population
 responses to future weather conditions and overcome some of the pitfalls
 of traditional PVA. The coupled framework presented here can serve as a
 tool for managers to make climate informed management decisions.
description: Questions regarding dataset can be directed to:
 Connor Rosenblatt UC Davis, Department of
 Environmental Science and Policy
 connor.rosenblatt16@gmail.com
DOI: 10.5061/dryad.gxd2547mr
title: Winds aloft over three water bodies influence spring stopover distributions of migrating birds along the Gulf of Mexico coast

description: Migrating birds contend with dynamic wind conditions that ultimately
 influence most aspects of their migration, from broad-scale movements to
 individual decisions about where to rest and refuel. We used weather
 surveillance radar data to measure spring stopover distributions of
 northward migrating birds along the northern Gulf of Mexico coast and
 found a strong influence of winds over non-adjacent water bodies, the
 Caribbean Sea and Atlantic Ocean, along with the contiguous Gulf of
 Mexico. Specifically, we quantified the relative influence of meridional
 (north-south) and zonal (west-east) wind components over the three water
 bodies on weekly spring stopover densities along western, central, and
 eastern regions of the northern Gulf of Mexico coast. Winds over the
 Caribbean Sea and Atlantic Ocean were just as, or more, influential than
 winds over the Gulf of Mexico, with the highest stopover densities in the
 central and eastern regions of the coast following the fastest winds from
 the east over the Caribbean Sea. In contrast, stopover density along the
 western region of the coast was most influenced by winds over the Gulf of
 Mexico, with the highest densities following winds from the south. Our
 results elucidate the important role of wind conditions over multiple
 water bodies on region-wide stopover distributions and complement tracking
 data showing Nearctic-Neotropical birds flying non-stop from South America
 to the northern Gulf of Mexico coast. Smaller-bodied birds may be
 particularly sensitive to prevailing wind conditions during non-stop
 flights over water, with probable orientation and energetic consequences
 that shape subsequent terrestrial stopover distributions. In the future,
 the changing climate is likely to alter wind conditions associated with
 migration, so birds that employ non-stop over-water flight strategies may
 face growing challenges.
DOI: 10.5061/dryad.3bk3j9kkb
title: Beyond species richness and community composition: Using plant functional diversity to measure restoration success in jarrah forest

description: Aim: The importance of restoring ecosystem functions to native systems
 that have been degraded, damaged or destroyed is increasingly recognised.
 Yet few studies have measured the effect of restoration efforts on
 ecosystem functioning or the functional diversity (FD) that underpins it.
 Here we assessed change in FD of restored assemblages one to 25 years
 after the onset of post-mine restoration. Location: Northern Jarrah
 (Eucalyptus marginata Donn ex Sm.) Forest bioregion of south-western
 Australia. Methods: Functional richness, evenness, divergence and
 dispersion were derived from five plant functional traits relevant to
 community reassembly. Effects of three explanatory variables (i.e., age,
 year restoration was initiated, and time since fire) on six response
 variables (i.e., four FD indices, species richness, and compositional
 similarity to nearby reference forest) were analysed using linear mixed
 models for a dataset with repeated measures of plots through time (n= 810
 plots), and linear models for a sub-set of one-time measures of different
 aged assemblages (i.e., space-for-time approach; n= 490 plots). Results:
 Functional evenness and functional dispersion increased with age, while
 functional divergence and functional richness decreased with age.
 Functional dispersion increased with time since fire, while functional
 richness decreased with time since fire. Species richness decreased with
 age, but at 25-years, species richness was comparable to that observed in
 reference forest. In contrast, similarity showed no relationship with age
 of restored forest, and at 25-years, similarity of restored forest to
 reference was low compared with similarity of reference forest to itself.
 Three of four FD indices had not reached those of reference jarrah forest
 25-years after restoration had been initiated. Conclusions: Reassembly of
 FD suggests importance of environmental filtering and high functional
 redundancy. A longer time frame may be needed to assess FD of restored
 assemblages, and in the meantime, species richness is not an adequate
 surrogate of FD.
description: The dataset was collected in the field via floristic surveys.
 Trait data for plant species were compiled. These data were used to derive
 indices of functional diversity (FD) using the R package FD (Laliberté
 & Legendre 2010). Code for models of FD are provided
 here. Laliberté, E., & Legendre, P. (2010). A distance-based framework for measuring functional diversity from multiple traits. <i>Ecology</i>, 91, 299–305. https://doi.org/10.1890/082244.1
description: Please see text file.
DOI: 10.5061/dryad.bzkh18999
title: Data from: Partial mycoheterotrophy in green plants forming Paris-type arbuscular mycorrhiza requires a thorough investigation

description: Recently, many green plants forming Paris-type arbuscular mycorrhiza (AM)
 have been suggested to receive fungal carbon (Giesemann et al. 2020b,
 2021). Whereas the enrichment of natural abundance of heavy stable
 isotopes (particularly 13C) has been considered as strong evidence for
 this ‘partial mycoheterotrophy,’ we show our own data on isotopic
 abundances and mycorrhizal colonization in Japanese plants and argue that
 the 13C-enrichment may not always be the result of acquiring carbon from
 AM fungi.
DOI: 10.7272/q66971tv
title: Provider and administrator-level perspectives on strategies to reduce fear and improve patient trust in the emergency department in times of heightened immigration enforcement

description: Heightened immigration enforcement may induce fear in undocumented
 patients when coming to the Emergency Department (ED) for care. Limited
 literature examining health system policies to reduce immigrant fear
 exists. In this multi-site qualitative study, we sought to assess provider
 and system-level policies on caring for undocumented patients in three
 California EDs. We recruited 41 ED providers and administrators from three
 California EDs (in San Francisco, Oakland, and Sylmar) with large
 immigrant populations. Participants were recruited using a trusted
 gatekeeper and snowball sampling. We conducted semi-structured interviews
 and analyzed the transcripts using constructivist grounded theory. We
 interviewed 10 physicians, 11 nurses, 9 social workers, and 11
 administrators, and identified 7 themes. Providers described existing
 policies and recent policy changes that facilitate access to care for
 undocumented patients. Providers reported that current training and
 communication around policies is limited, there are variations between who
 asks about and documents status, and there remains uncertainty around
 policy details, laws, and jurisdiction of staff. Providers also stated
 they are taking an active role in building safety and trust and see their
 role as supporting undocumented patients. This study introduces ED-level
 health system perspectives and recommendations for caring for undocumented
 patients. There is a need for active, multi-disciplinary ED policy
 training, clear policy details including the extent of providers’ roles,
 protocols on the screening and documentation of status, and continual
 reassessment of our health systems to reduce fear and build safety and
 trust with our undocumented communities.
description: Some parts of the interviews are redacted to protect the privacy
 and confidentiality of participants.
DOI: 10.5061/dryad.6t1g1jx01
title: The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant

description: Foraging trails of leafcutter colonies are iconic scenes in the
 Neotropics, with ants collecting freshly-cut plant fragments to provision
 a fungal food crop. We hypothesized that the fungus-cultivar’s
 requirements for macronutrients and minerals govern the foraging niche
 breadth of Atta colombica leafcutter ants. Analyses of plant fragments
 carried by foragers showed how nutrients from fruits, flowers, and leaves
 combine to maximize cultivar performance. While the most commonly foraged
 leaves delivered excess protein relative to the cultivar’s needs, in vitro
 experiments showed that the minerals P, Al, and Fe may expand the
 leafcutter foraging niche by enhancing the cultivar’s tolerance to
 protein-biased substrates. A suite of other minerals reduces cultivar
 performance in ways that may render plant fragments with optimal
 macronutrient blends unsuitable for provisioning. Our approach highlights
 how the nutritional challenges of provisioning a mutualist can govern the
 multidimensional realized niche available to a generalist insect
 herbivore.
DOI: 10.5061/dryad.sbcc2fr6w
title: Occurrence localities of Vipera ursinii subspecies

description: Occurrence dataset used for the analyses in "A step toward SDMs: a
 “couple-and-weigh” framework based on accessible data for biodiversity
 conservation and landscape planning" - Diversity and Distributions.
 Coordinates are in WGS84 - EPSG 4326.
description: A European dataset of all <em>Vipera ursinii
 </em>subspecies composed of both localities collected on the field
 and literature review.
DOI: 10.5061/dryad.2z34tmpn4
title: All data for: Megaherbivore impacts on ecosystem and Earth system functioning: The current state of the science

description: Megaherbivores (adult body mass &gt;1000 kg) are suggested to
 disproportionately shape ecosystem and Earth system functioning. We
 systematically reviewed the empirical basis for this general thesis and
 for the more specific hypotheses that (i) megaherbivores have
 disproportionately larger effects on Earth system functioning than their
 smaller counterparts, (ii) this is true for all extant megaherbivore
 species and (iii) their effects vary along environmental gradients. We
 furthermore explored possible biases in our understanding of megaherbivore
 impacts. We found that there are too few studies to quantitatively
 evaluate the general thesis or any of the hypotheses for all but the
 African savanna elephant. Following this finding, we performed a
 qualitative vote counting analysis. Our synthesis of this analysis
 suggests that megaherbivores can elicit strong impacts on e.g. vegetation
 structure, and biodiversity and all the elephant species promote seed
 dispersal. We were however unable to evaluate whether these effects are
 disproportionate to smaller large herbivores. Although environmental
 conditions can mediate megaherbivore impact, few studies quantified the
 effect of rainfall or soil fertility on megaherbivore impacts, precluding
 prediction of megaherbivore effects on the Earth system, particularly
 under future climates. Moreover, our review highlights major taxonomic,
 thematic and geographic biases in our understanding of megaherbivore
 effects. Most of the studies focused on African savanna elephant impacts
 on vegetation structure and biodiversity, with other megaherbivores and
 Earth system functions comparatively neglected. Studies were also biased
 towards semi-arid and relatively fertile systems, with the arid,
 high-rainfall and/or nutrient-poor parts of the megaherbivores’
 distribution ranges largely unrepresented. Our findings highlight that the
 empirical basis of our understanding of the ecological effects of extant
 megaherbivores is still limited for all species, except African savanna
 elephant, and that our current understanding is biased towards certain
 environmental and geographic areas. We further outline a detailed,
 urgently needed avenue for future research.
DOI: 10.5061/dryad.n8pk0p2w1
title: Echolocating toothed whales use ultra-fast echo-kinetic responses to track evasive prey

description: Visual predators rely on fast-acting optokinetic responses to
 track and capture agile prey. Most toothed whales, however, rely on
 echolocation for hunting and have converged on biosonar
 clicking rates reaching 500/s during prey pu rsuits. If echoes
 are processed on a click by click basis, as assumed, neural
 responses 100x faster than those in vision are required to keep pace with
 this information flow. Using high resolution bio-logging of wild
 predator prey interactions we show that toothed whales adjust
 clicking rates to track prey movement within 50 200 ms of prey escape
 responses. Hypothesising that these stereotyped biosonar adjustments are
 elicited by sudden prey accelerations, we measured echo kinetic responses
 from trained harb our porpoises to a moving target and found
 similar latencies. High biosonar sampling rates are, therefore, not
 supported by extreme speeds of neural processing and muscular
 responses. Instead, the neuro kinetic response times in
 echolocation are similar to those of tracking responses in
 vision, suggesting a common neural underpinning.
description: See 'Materials and Methods' section of Vance et al
 (2021).  
description: This data set is divided into wild harbour porpoise data (files
 beginning with hp), wild beaked whale data (files beginning with md)
 and trained harbour porpoise data (files beginning with either Freja17 or
 Sif17). The wild data represent the echolocation responses of harbour
 porpoise and beaked whales to their prey in the wild. The trained harbour
 porpoise data represents echolocation responses to a moving aluminium
 sphere target in a captive setting. Each file contains an individual prey
 encounter/moving target trial.  The data is presented
 in a NetCDF format and includes additional metadata within each data
 structure. The structures included are 1) X -the sound envelope 2) CL -
 the timing of echolocation clicks relative to the start of the sound
 envelope 3) R- the time of prey/target movement relative to start of sound
 extract and distance from prey/target during movement 4) info- an
 information structure for the tag deployment and 5) for trained harbour
 porpoise trials only, A - the two axes acceleration of the aluminum target
 sphere.  We have further included several MATLAB
 scripts which will allow users to plot echograms of the acoustic data, the
 same as those presented in Vance et al (2021). Additional information on
 how to use these is included within the help information for each
 script.
DOI: 10.5061/dryad.9ghx3ffhz
title: SI dataset S1 - knuckle-walking biomechanical strategies

description: African apes engage in a distinct form of locomotion called
 knuckle-walking, but there is much ambiguity as to when and how this
 locomotor behaviour evolved. This study aims to elucidate potential
 differences in knuckle-walking elbow posture and loading in African apes
 through the study of trabecular bone. Using a whole-epiphysis approach, we
 quantified variation in trabecular structure of the distal humerus of
 chimpanzees, western lowland gorillas, and mountain gorillas in comparison
 to orang-utans, siamangs and a sample of Old and New World monkeys.
 Results demonstrate differences in the distribution of trabecular bone
 within the distal humerus that are consistent across taxa that habitually
 use a flexed-elbow posture in comparison to those that use an
 extended-elbow during locomotion. Western lowland gorillas show an
 extended-elbow pattern consistent with the straight forelimb position
 during knuckle-walking, whereas chimpanzees show a flexed-elbow pattern.
 Unexpectedly, mountain gorillas show an intermediate pattern between their
 western counterparts and chimpanzees. The differences found in elbow joint
 posture between chimpanzees and gorillas, and between gorilla species,
 point to diversification in the knuckle-walking biomechanical strategies
 among African apes, which has implications in the debate regarding the
 locomotor behaviour from which human bipedalism arose.
description: Medtool 4.2 (www.dr-pahr.at) was used to quantify trabecular bone
 throughout the distal epiphysis of the humerus using a Holistic
 Morphometric Analysis (HMA) following the methods described in Gross et
 al. (2014) and Tsegai et al. (2013). Briefly, cortical bone is separated
 from the trabeculae (SI Fig. S2) by casting rays at different angles from
 the outer cortical shell and terminating them on contact with background
 voxels. The inner structure is then closed with a spherical kernel the
 size of the average trabecular thickness in that bone (Pahr and Zysset,
 2009), and the 3D edge of this inner structure defines the boundary
 between subchondral trabecular and cortical bone (Gross et al., 2014).
 Bone volume fraction (BV/TV), quantified as a ratio of bone volume to
 total volume, and degree of anisotropy (DA), quantified following the mean
 intercept length (MIL) method and bounded between 0 (isotropy) and 1
 (anisotropy), were measured throughout the distal epiphysis using a
 sampling sphere with a 5-mm diameter on a 2.5- mm background
 grid.
description: The data used in this article are vector (categorical variables)
 and numerical (measures) values. There are no missing values. There is a
 comprehensive README xls file with detaild explanations on the data
 collected and calculated used as the basis of the article to be downloaded
 with the dataset.