cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8kprr4xr8
title: Implementing blended learning for clinician teachers: Identifying their needs and its impact on faculty development initiatives

description: Learning Technologies has been a fast-growing field in Health Professions
 Education (HPE). Approaches to teaching, learning and assessment has been
 increasingly influenced by learning technologies which requires HPE
 teachers to adapt their teaching practices and with that identify areas
 for professional development. The implementation of blended learning in
 HPE, has shown improvements in student performance. However, it seems as
 if there are challenges with the implementation of a blended learning
 approach and that there might be some needs that clinical teachers have
 that are not being addressed in order to implement blended learning
 successfully. We used a qualitative exploratory design to identify
 clinician teachers’ needs. Semi-structured, individual interviews were
 conducted with a total of eight (n=8) module coordinators in the third
 year of the MBChB programme, Stellenbosch University, Faculty of Medicine
 and Health Sciences. Results indicated the need for continuous technical
 and pedagogical support which refers to a longitudinal faculty development
 approach. Additionally, faculty development should include the support in
 structuring and rethinking the blended curriculum, as well as assisting in
 the clinicians’ development in their role and identity as a clinical
 teacher. These results reveal the importance of faculty development as a
 targeted longitudinal approach
description: Qualitative research design, based on the interpretative
 paradigm.
DOI: 10.5061/dryad.bnzs7h4dq
title: CT data for: Insight into the evolutionary assemblage of cranial kinesis from a Cretaceous bird

description: The independent movements and flexibility of various parts of the skull,
 called cranial kinesis, is an evolutionary innovation that is found in
 living vertebrates only in some squamates and crown birds and is
 considered to be a major factor underpinning much of the enormous
 phenotypic and ecological diversity of living birds, the most diverse
 group of extant amniotes. Compared to the postcranium, our understanding
 of the evolutionary assemblage of the characteristic modern bird skull has
 been hampered by sparse fossil records of early cranial materials, with
 competing hypotheses regarding the evolutionary development of cranial
 kinesis among early members of the avialans. Here, a detailed
 three-dimensional reconstruction of the skull of the Early Cretaceous
 enantiornithine Yuanchuavis kompsosoura allows for its in-depth
 description, including elements that are poorly known among early
 diverging avialans but are central to deciphering the mosaic assembly of
 features required for modern avian cranial kinesis. Our reconstruction of
 the skull shows evolutionary and functional conservation of the temporal
 and palatal regions by retaining the ancestral theropod dinosaurian
 configuration within the skull of this otherwise derived and volant bird.
 Geometric morphometric analysis of the palatine suggests that loss of the
 jugal process represents the first step in the structural modifications of
 this element leading to the kinetic crown bird condition. The mixture of
 plesiomorphic temporal and palatal structures together with a derived
 avialan rostrum and postcranial skeleton encapsulated in Yuanchuavis
 manifests the key role of evolutionary mosaicism and experimentation in
 early bird diversification.
description: <strong>X-ray computed
 tomography imaging</strong>. To optimize the scanning resolution, the skull
 and the two cranial vertebrae (atlas and axis) of the holotype of
 <em>Yuanchuavis kompsosoura</em> (IVPP V27883) were isolated
 from the slab. The skull was scanned using the industrial CT scanner
 Phoenix v-tome-x at the Key Laboratory of Vertebrate Evolution and Human
 Origins, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP,
 Beijing, China), with a beam energy of 140 kV and a flux of 150 μA at a
 resolution of 11.68 μm per pixel. The resulting scanned images were
 imported into Avizo (version 9.2.0) for digital segmentation, rendering,
 and reconstruction. The obtained three-dimensional models were optimized
 in MeshLab (version 2012.12).
DOI: 10.5061/dryad.z34tmpgh7
title: Data from: Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways

description: The pericarp is the predominant tissue determining the structural
 characteristics of most fruits. However, the molecular and genetic
 mechanisms controlling pericarp development remain only partially
 understood. Previous studies have identified that CLASS-II KNOX genes
 regulate fruit size, shape, and maturation in Arabidopsis thaliana and
 Solanum lycopersicum. Here we characterized the roles of the
  Solanum lycopersicum CLASS-II KNOX (TKN-II) genes in pericarp
 development via a detailed histological, anatomical, and karyotype
 analysis of the TKN-II knockdown (35S:amiR-TKN-II) fruits. We identify
 that 35S:amiR-TKN-II pericarps contain more cells around their equatorial
 perimeter and fewer cell layers than the control. In addition, the cell
 sizes but not the ploidy levels of these pericarps were dramatically
 reduced. Further, we demonstrate that fruit shape and pericarp layer
 number phenotypes of the 35S:amiR-TKN-II fruits can be overridden by the
 procera mutant, known to induce a constitutive response to the plant
 hormone gibberellin. However, neither the procera mutation nor exogenous
 gibberellin application can fully rescue the reduced pericarp width and
 cell size phenotype of 35S:amiR-TKN-II pericarps. Our findings establish
 that  TKN-II  genes regulate tomato fruit anatomy,
 acting via gibberellin to control fruit shape but utilizing a
 gibberellin-independent pathway to control the size of pericarp cells.
description: Raw measurements of the carpel length, width, and perimeter were
 performed from the carpel sterioscope images using the Image J
 software.  Raw measurements
 of the mature fruits and their pericarp width were done with the 0-2000g
 scale (MRS) and digital caliper.
DOI: 10.5061/dryad.4tmpg4fd1
title: Data from: Phylogenetic structure of the extinction and biotic factors explaining differential survival of terrestrial notosuchians at the Cretaceous-Palaeogene crisis

description: Although the clade Crocodylomorpha is represented by few extant species
 (Crocodylia), it has a rich fossil record. Hundreds of species adapted to
 terrestrial, semi-aquatic and marine environments, have existed over more
 than 200 million years. Numerous studies have attempted to characterize
 the factors driving the diversification and extinction events of
 Crocodylomorpha, resulting in ambiguous and even contradictory
 conclusions, which points to the need for phylogenetically and temporally
 smaller-scaled studies. Here, we focus on differential survival at the
 Cretaceous-Palaeogene crisis of Notosuchia, a diverse clade of mostly
 terrestrial Crocodylomorpha that achieved great diversity during the
 Cretaceous. More precisely, we tested the effect of body size and
 palaeotemperatures on notosuchian survival probability during the K-Pg
 crisis as well as the effect of diet on the evolution of their body size.
 We find that Notosuchia showed an evolutionary trend towards larger body
 sizes through time, associated with a shift from an omnivorous to a
 carnivorous diet. This may explain why sebecids were the only notosuchians
 to survive the K-Pg crisis. We also corroborate conclusions of previous
 studies that detected a Lagerstätten effect occurring in the Adamantina
 Formation (Upper Cretaceous, Brazil, Bauru Group). This work confirms the
 value of more finely-scaled macroevolutionary studies for understanding
 the history of a rich and complex group such as Crocodylomorpha.
description: All the data have been collected either from the literature or
 from the Paleobiology Database.
description: R is the only software needed to open one file (the R script).
 All other files are .csv.
DOI: 10.5061/dryad.h44j0zpp6
title: Where have all the lions gone? Establishing realistic baselines to assess decline and recovery of African lions

description: Aim: Predict empirically the current and recent-historical (c. 1970)
 landscape connectivity and population size of the African lion as a
 baseline against which to assess conservation of the species. Location:
 Continental Africa. Methods: We compiled historical records of lion
 distribution to generate a recent-historical range for the species.
 Historical population size was predicted using a generalised additive
 model. Resistant kernel and factorial least-cost path analyses were used
 to predict recent-historical landscape connectivity and compare this with
 contemporary connectivity at continental, regional and country scales.
 Results: We estimate a baseline population of ~92,054 (83,017 – 101,094
 95% CI) lions in c1970, suggesting Africa’s lion population has declined
 by ~75%, over the last five decades. Although greatly reduced from
 historical extents (c. 1500 AD), recent-historical lion habitat was
 substantially connected. However, in comparison, contemporary population
 connectivity has declined dramatically, with many populations now
 isolated, as well as large declines within remaining population core
 areas. This decline was most marked in the West and Central region, with a
 90% decline in connected habitat, and in the Congo Basin where connected
 habitat is reduced to 17% of its c. 1970 level. The Eastern and Southern
 regions have experienced lower, though significant, declines in connected
 habitat (44% and 55% respectively). Contemporary populations are connected
 by three non-core habitat linkages and 15 potential corridors (spanning
 unconnected habitat) that may allow dispersal and gene flow. Declining
 connectivity mirrors recent studies showing loss of genetic diversity and
 increasing genetic isolation of lion populations. Main conclusions: We
 provide an empirically derived baseline for African lion population size,
 habitat extent and connectivity in c. 1970 and at present against which to
 evaluate contemporary conservation of the species, avoiding a shifting
 baseline syndrome where conservation success/failure is measured only
 against recent population size or range. We recommend priorities for
 conservation of existing habitat to avoid further fragmentation.
DOI: 10.7291/d1xx09
title: Diverge and conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

description: The archipelagos of Wallacea extend between the Sunda and Sahul Shelves,
 serving as a semi-permeable two-way filter influencing faunal exchange
 between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are
 widespread throughout southern Wallacea and exhibit complex clinal,
 ontogenetic, sexual, and seasonal morphological variation rendering
 species delimitation difficult. We screened a mitochondrial marker for 245
 Sphenomorphus specimens from this area to inform the selection of 104
 samples from which we used targeted sequence-capture to generate a dataset
 of 1154 nuclear genes (~1.8 Mb) plus complete mitochondrial genomes.
 Phylogenomic analyses recovered many deeply divergent lineages, three of
 which are now sympatric, that began to diversify in the late Miocene
 shortly after the oldest islands are thought to have become emergent. We
 infer a complex and non-stepping-stone pattern of island colonization,
 with the group having originated in the Sunda Arc islands before using
 Sumba as a springboard for colonization of the Banda Arcs. Estimates of
 population structure and gene flow across the region suggest total
 isolation except between two Pleistocene Aggregate Island Complexes that
 become episodically land-bridged during glacial maxima. These historical
 processes have resulted in at least 11 Sphenomorphus species in the
 region, nine of which require formal description. This fine-scale
 geographic partitioning of undescribed species highlights the importance
 of utilizing comprehensive genomic studies for defining biodiversity
 hotspots to be considered for conservation protection.
description: See supplementary methods for a detailed description of the
 datasets, which include mitochondrial ND4 sequence data (GenBank accession
 numbers MW291696–291940), and a targeted sequence capture dataset that
 includes 1,154 nuclear loci and complete mitochondrial genomes for 104
 samples. The targeted capture dataset was sequenced on the Illumina
 platform with paired end 100 bp reads that have been deposited in the NCBI
 sequence read archive under accession number PRJNA682772.
DOI: 10.5061/dryad.7pvmcvdwq
title: Data for: Stool biomarkers as measures of enteric pathogen infection in infants from Addis Ababa informal settlements

description: Frequent enteric infections in children may be an important cause of
 growth faltering; however, we do not fully understand the mechanisms by
 which pathogen infections and the physiological responses to these
 infections result in poorer growth. Commonly used protein fecal biomarkers
 (anti-alpha trypsin, neopterin, and myeloperoxidase) provide broad
 immunological information on an inflammatory response; however, they do
 not provide information on non-immune processes (e.g., gut integrity) that
 may be important indicators of chronic end states such as environmental
 enteric dysfunction (EED). To explore how additional biomarkers will
 better inform which physiological pathways (both immune and non-immune)
 are impacted by pathogen exposure we added to the traditional panel of 3
 protein fecal biomarkers 4 novel fecal mRNA transcript biomarkers (sucrase
 isomaltase, caudal homeobox 1, S100A8, and mucin 12) and analyzed stool
 samples from infants living in informal settlements in Addis Ababa,
 Ethiopia. To test how this expanded biomarker panel captures distinct
 pathogen exposure processes we used two different scoring systems. First,
 we used a theory-based approach to assign each biomarker to specific
 physiological attributes based on prior understanding of each biomarker.
 Second, we used data reduction methods to categorize biomarkers and then
 assign physiological attributes to those categories. We used linear models
 to examine the association between the derived biomarker scores (based on
 mRNA and protein levels) and stool pathogen gene counts to determine
 pathogen-specific effects on gut physiology and immune responses.
 Inflammation scores were positively associated with Shigella and
 enteropathogenic E. coli (EPEC) infection, while gut integrity scores were
 negatively associated with Shigella, EPEC, and shigatoxigenic E. coli
 (STEC) infection. Our expanded panel of biomarkers hold promise as tools
 to measure systemic outcomes of enteric pathogen infection. mRNA
 biomarkers complement established protein biomarkers by providing
 important cell-specific physiological and immunological consequences of
 pathogen carriage that can lead to chronic end states such as EED.
DOI: 10.15468/dl.htysg8
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dolichos fangitsa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 122 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003174-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vq83bk3w9
title: Data from: Single, but not dual, attack by a biotrophic pathogen and sap-sucking insect affects the oak leaf metabolome

description: Plants interact with a multitude of microorganisms and insects, both
 belowand above ground, which might influence plant metabolism. Despite
 this, we lack knowledge of the impact of natural soil communities and
 multiple aboveground attackers on the metabolic responses of plants, and
 whether plant metabolic responses to single attack can predict responses
 to dual attack. We used untargeted metabolic fingerprinting (gas
 chromatographymass spectrometry, GC-MS) on leaves of the pedunculate oak,
 Quercus robur, to assess the metabolic response to different soil
 microbiomes and aboveground single and dual attack by oak powdery mildew
 (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus).
 Distinct soil microbiomes were not associated with differences in the
 metabolic profile of oak seedling leaves. Single attacks by aphids or
 mildew had pronounced but different effects on the oak leaf metabolome,
 but we detected no difference between the metabolomes of healthy seedlings
 and seedlings attacked by both aphids and powdery mildew. Our findings
 show that aboveground attackers can have species-specific and non-additive
 effects on the leaf metabolome of oak. The lack of a metabolic signature
 detected by GC-MS upon dual attack might suggest the existence of a
 potential negative feedback, and highlights the importance of considering
 the impacts of multiple attackers to gain mechanistic insights into the
 ecology and evolution of species interactions and the structure of
 plant-associated communities, as well as for the development of
 sustainable strategies to control agricultural pests and diseases and
 plant breeding.
description: This dataset contains the metabolite annotation of Quercus robur
 leaves under single or dual attack (by aphids and powdery mildew),
 obtained by GCMS. At SMC, sample preparation for GC-MS
 was performed according to Gullberg et al. (2004). More specifically, 750
 µL of extraction buffer (20/20/60 v/v/v chloroform:water:methanol)
 including internal standards were added to each sample. The sample was
 shaken with a tungsten bead in a mixer mill at 30 Hz for 3 min, after
 which the bead was removed and the sample was centrifuged at 4◦C and
 14,000 rpm, for 10 min. 200 µL of supernatant were transferred to a
 microvial and solvents were evaporated. Derivatization was performed
 according to Gullberg et al. (2004). More specifically, 30 µL of
 methoxyamine (15 µg/µL in pyridine) were added to the dry sample and the
 sample was shaken vigorously for 10 min before being left to react in room
 temperature. After 16 h, 30 µL of MSTFA and 30 µL of heptane were added
 and the sample was shaken and left to react for 1 h in room temperature.
 30 µL of methyl stearate (15 ng/µL in heptane) were added before
 analysis.
DOI: 10.25338/b8v34s
title: Relative rate kinetics aqueous sulfate radical reaction with some atmospherically relevant compounds

description: The sulfate anion radical (SO4)  is a reactive oxidant formed in
 the autoxidation chain of sulfur dioxide. Recently, other formation
 pathways to SO4 for have been reported. This work investigated the
 second-order rate coefficients for the aqueous oxidation of some important
 organic aerosol compounds by the aqueous SO4 oxidation (kSO4).
 2-methyltetrol, 2-methyl-1,2,3-trihydroxy-4-sulfate,
 2-methyl-1,2-dihydroxy-3-sulfate, 1,2-dihydroxyisoprene,
 2-methyl-2,3-dihydroxy-1,4-dinitrate, 2-methyl-1,2,4-trihydroxy-3-nitrate,
 2-methylglyceric acid and 2-methylglycerate,  lactic acid and
 lactate, and pyruvic acid and pyruvate. The rate coefficients of unknowns
 are determined against that of erythritol in pure water in a temperature
 range of 298 – 322 K. The decays of each reagent were measured with
 nuclear magnetic resonance (NMR) and high-performance liquid
 chromatography-high resolution mass spectrometry
 (HPLC-HRMS). Incorporations of additional SO4 reactions into
 models may aid in the understanding of organosulfate formation, radical
 propagation, and aerosol mass sinks.
description: See Read Me file for detaled methods.
description: Need Microsoft Excel (proprietary) or these open source
 softwares: LibreOffice, Google Sheets, MS Excel Online (free), Apache Open
 Office, Zoho Sheets.
DOI: 10.5061/dryad.fj6q573z1
title: Nutrient balance and energy-acquisition effectiveness: Do birds adjust their fruit diet to achieve intake targets?

description: 1. According to diet-regulation hypotheses, animals select food to
 regulate the intake of macronutrients or maximise energy feeding
 efficiency. Specifically, the nutrient balance model proposes that
 foraging is primarily a process of balancing multiple nutrients to achieve
 a nutritional intake target, while the energy maximisation model proposes
 that foraging aims to maximise energy. 2. Here, we evaluate the adjustment
 of fruit diets (the fruit-derived component of the diets) to nutritional
 and energy intake targets, characterizing the nutrient balance and energy
 maximisation strategies across fruit-eating bird species with different
 fruit-handling behaviours ("gulpers", which swallow whole
 fruits, and "mashers", which process the fruit in the beak) in
 subtropical Andean forests. Food-handling behaviour determines the food
 intake rate and, consequently, influences animal efficiency to obtain
 nutrients and energy. 3. We used extensive field data from the diet of
 fruit-eating birds to test how species adjust their food intake. We used
 nutritional geometry to explore macronutrient balance and the
 effectiveness framework to explore energy-acquisition effectiveness. 4.
 Observed diets showed a good fit with predictions of a diet balanced in
 macronutrient proportions. With few exceptions, diets clustered near an
 optimal macronutrient mixture and did not differ from each other in terms
 of maximising energy intake. Moreover, when comparing our results with a
 random diet based on local fruit availability, birds tended to fit better
 to the nutritional target, and less to the energy target, than expected
 from a random diet. Fruit-handling behaviour did not affect the ability of
 bird species to reach a nutritional target but it affected species energy
 acquisition, which was lower in mashers than in gulpers. 5. This study
 explores for the first time different diet-regulation strategies in wild
 fruit-eating birds, and supports the argument that the diet reflects a
 specific regulation of macronutrients. Understanding why birds select
 fruits is a complex question requiring multiple considerations. The
 nutrient balance model explains the relevance of nutrient composition in
 the fruit selection by fruit-eating birds, although it is still necessary
 to determine its relative importance with respect to other dietary
 drivers.
description: For details on data collection and processing refer to the main
 text.
description: Data needed to run the R script present in Appendix S7.
 R Commander or R Studio are required.