cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tmpg4f8m
title: The Enterprise, a massive transposon carrying Spok meiotic drive genes

description: The genomes of eukaryotes are full of parasitic sequences known as
 transposable elements (TEs). Most TEs studied to date are relatively small
 (50 – 12000 bp), but can contribute to very large proportions of genomes.
 Here we report the discovery of a putative giant
 tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model
 fungus Podospora anserina. Previously, we described a large genomic
 feature called the Spok block which is notable due to the presence of
 meiotic drive genes of the Spok gene family. The Spok block ranges from
 110 kb to 247 kb and can be present in at least four different genomic
 locations within P. anserina, despite what is an otherwise highly
 conserved genome structure. We propose that the reason for its varying
 positions is that the Spok block is not only capable of meiotic drive, but
 is also capable of transposition. More precisely, the Spok block
 represents a unique case where the Enterprise has captured the Spoks,
 thereby parasitizing a resident genomic parasite to become a genomic
 hyperparasite. Furthermore, we demonstrate that Enterprise (without the
 Spoks) is found in other fungal lineages, where it can be as large as 70
 kb. Lastly, we provide experimental evidence that the Spok block is
 deleterious, with detrimental effects on spore production in strains which
 carry it. This union of meiotic drivers and a transposon has
 created a selfish element of impressive size in Podospora, challenging our
 perception of how TEs influence genome evolution and broadening the
 horizons in terms of what the upper limit of transposition may be.
description: This dataset contains the genome assembly and annotation files
 used for our study on the <em>Spok</em> block elements (i.e.
 the <em>Enterprises</em>). The assemblies of the strains
 CBS237.71m, PaWa137, PaWa139 were made from MinION Oxford Nanopore data
 assembled with Minimap2 v. 2.11 and Miniasm v. 0.2, and polished with
 Illumina HiSeq X data. The strain PaWa131 only has Illumina HiSeq X data,
 which was assembled with SPAdes v. 3.12.0. The <em>Spok</em>
 blocks were extracted from previously published genomes in the Spok paper
 dataset, where the assembly of CBS237.71m is also
 available. Folders included: -
 <strong>Genomes:</strong> genome assemblies and annotations.
 The assemblies are also available in the NCBI BioProject
 PRJNA685103.  -
 <strong>SpokBlocks:</strong> multifasta file with the
 sequences of all <em>Spok</em> blocks studied, along with
 their individual annotation files in gff formats. Notice that the
 annotation files are in the coordinates of the blocks, not of their native
 genomes. - <strong>Others</strong>: The
 repeat library of <em>Podospora </em>and the data file used
 for the fitness experiment.<br>  
description: Most of these files are already present in a GitHub repository, in an order that follows better the analyses themselves. Here instead there are files organized by type. <br>
DOI: 10.57761/amm5-1t88
title: Item Response Warehouse 2
DOI: 10.5061/dryad.rjdfn2z9f
title: Humpback whale song presence in the Atlantic sector of the Southern Ocean

description: Humpback whale song most likely fulfills a multi-purpose role in the
 humpback whale mating system including both inter- and intrasexual
 interactions. Humpback whale males produce most of their songs on the
 low-latitude breeding grounds, but evidences increase, showing that songs
 are also produced ‘off-season’ on the feeding grounds or during migration.
 This opens exciting opportunities to investigate migratory aggregations,
 study humpback whale behavioral plasticity and potentially even assign
 individual singers to specific breeding grounds. In this study, we
 analyzed passive acoustic data from 13 recording positions and multiple
 years (2011-2018) to investigate humpback whale song in a Southern Ocean
 feeding area comparing song presence, structure and complexity over
 spatial and temporal scales. Humpback whale song was detected at nine
 recording positions within the Atlantic sector of the Southern Ocean
 (ASSO) in five years. Most songs were recorded in May coinciding with the
 rapid increase in sea ice concentration at most recording positions. The
 spatio-temporal pattern in humpback whale singing activity on a Southern
 Ocean feeding ground is most likely shaped by the local prey availability
 and humpback whale migratory strategies. Furthermore, the comparative
 analyses of song structures clearly show a differentiation of two song
 groups, of which one was solely recorded at the western edge of the ASSO
 and the other song group was recorded throughout the spatial extent of the
 ASSO. This new finding suggests a common feeding ground occupation in the
 ASSO by multiple humpback whale populations, providing important baseline
 information for ecosystem and stock management.
DOI: 10.5061/dryad.brv15dv8j
title: Pharmacokinetics parameters, bioanalytical method underlying the manuscript: The effect of morning versus evening administration of empagliflozin on its pharmacokinetics and pharmacodynamics characteristics in healthy adults: a two-way crossover non-randomised trial

description: Background: Empagliflozin is an SGLT2 inhibitor approved for use in
 patients with Diabetes Mellitus type 2 (DMT2) with- or without other
 cardiovascular disease. Empagliflozin is taken once daily without
 rationale on the optimal timing for administration. This study
 aimed to determine the chronopharmacological effects of morning
 vs evening administration of empagliflozin 10 mg in Healthy Egyptian
 adults, by investigating the pharmacokinetics and
 pharmacodynamics parameters of empagliflozin depending on the intake
 time.  Methods: An open label, sequential,
 two‐way crossover trial comprised two periods with a washout period of 7
 days. Pharmacokinetics parameters (tmax (h),
 Cmax (ng/ml), AUC 0-t (ng.h/ml)) as primary
 endpoints, and (AUC 0 to ∞(ng.h/ml)) as secondary endpoint were
 assessed. Method validation was done prior to injection in
 LC/MS/MS and samples were processed by Liquid-Liquid extraction. The
 pharmacodynamic profile (UGE 0-24) was determined after method
 validation (glucose hexokinase method).
 Results: Tmax increased by (35%) in the evening
 phase compared to the morning phase,
 while Cmax decreased by (-6.5%)in the evening dose
 compared to the morning dose. Besides, AUC0 to
 ∞ increased in the evening phase by (8.25%) compared to the
 morning phase. The mean cumulative amount of glucose excreted;
 UGE (0-24) increased by (43%) in the evening dose compared to the
 morning dose Conclusion: Despite there was a significant
 difference between morning and evening doses, it didn't reach the
 significant level, thus, it can be concluded that there is no difference
 between the morning and evening doses.
DOI: 10.5061/dryad.k0p2ngf7b
title: Pharmacodynamics parameters underlying the manuscript: The effect of morning versus evening administration of empagliflozin on its pharmacokinetics and pharmacodynamics characteristics in healthy adults: a two-way crossover, non-randomised trial

description: Background: Empagliflozin is an SGLT2 inhibitor approved for use in
 patients with Diabetes Mellitus type 2 (DMT2) with- or without other
 cardiovascular disease. Empagliflozin is taken once daily without
 rationale on the optimal timing for administration. This study
 aimed to determine the chronopharmacological effects of morning
 vs evening administration of empagliflozin 10 mg in Healthy Egyptian
 adults, by investigating the pharmacokinetics and
 pharmacodynamics parameters of empagliflozin depending on the intake
 time.  Methods: An open label, sequential,
 two‐way crossover trial comprised two periods with a washout period of 7
 days. Pharmacokinetics parameters (tmax (h),
 Cmax (ng/ml), AUC 0-t (ng.h/ml)) as primary
 endpoints, and (AUC 0 to ∞(ng.h/ml)) as secondary endpoint were
 assessed. Method validation was done prior to injection in
 LC/MS/MS and samples were processed by Liquid-Liquid extraction. The
 pharmacodynamic profile (UGE 0-24) was determined after method
 validation (glucose hexokinase method).
 Results: Tmax increased by (35%) in the evening
 phase compared to the morning phase,
 while Cmax decreased by (-6.5%)in the evening dose
 compared to the morning dose. Besides, AUC0 to
 ∞ increased in the evening phase by (8.25%) compared to the
 morning phase. The mean cumulative amount of glucose excreted;
 UGE (0-24) increased by (43%) in the evening dose compared to the
 morning dose Conclusion: Despite there was a significant
 difference between morning and evening doses, it didn't reach the
 significant level, thus, it can be concluded that there is no difference
 between the morning and evening doses.
description: Urine samples were collected by urine collecting tube (1liter) for determination of UGE in g (urinary glucose excretion), which is the mean amount of glucose excreted in urine over the first 24 h after oral administration. Sampling intervals were 0 to 4, 4 to 8, 8 to 12 and 12 to 24 h after the administration of empagliflozin at the morning and evening doses. Samples were stored at -80°C before being sent to the clinical laboratory for analysis. Analysis was done by usin: Glucose hexokinase method. https://www.sciencedirect.com/science/article/abs/pii/S0308814615006172?via%3Dihub (link to Glucose hexokinase method)
DOI: 10.5061/dryad.7h44j0zt1
title: Protocol, case report(s), ethics approvals, informed consent, inclusion and exclusion criteria underlying: The effect of morning versus evening administration of empagliflozin on its pharmacokinetics and pharmacodynamics characteristics in healthy adults: a two-way crossover, non-randomised trial

description: Background: Empagliflozin is an SGLT2 inhibitor approved for use in
 patients with Diabetes Mellitus type 2 (DMT2) with- or without other
 cardiovascular disease. Empagliflozin is taken once daily without
 rationale on the optimal timing for administration. This study
 aimed to determine the chronopharmacological effects of morning
 vs evening administration of empagliflozin 10 mg in Healthy Egyptian
 adults, by investigating the pharmacokinetics and
 pharmacodynamics parameters of empagliflozin depending on the intake
 time.  Methods: An open label, sequential,
 two‐way crossover trial comprised two periods with a washout period of 7
 days. Pharmacokinetics parameters (tmax (h),
 Cmax (ng/ml), AUC 0-t (ng.h/ml)) as primary
 endpoints, and (AUC 0 to ∞(ng.h/ml)) as secondary endpoint were
 assessed. Method validation was done prior to injection in
 LC/MS/MS and samples were processed by Liquid-Liquid extraction. The
 pharmacodynamic profile (UGE 0-24) was determined after method
 validation (glucose hexokinase method).
 Results: Tmax increased by (35%) in the evening
 phase compared to the morning phase,
 while Cmax decreased by (-6.5%)in the evening dose
 compared to the morning dose. Besides, AUC0 to
 ∞ increased in the evening phase by (8.25%) compared to the
 morning phase. The mean cumulative amount of glucose excreted;
 UGE (0-24) increased by (43%) in the evening dose compared to the
 morning dose Conclusion: Despite the difference in
 pharmacokinetics parameters between evening and morning doses, Cmax,
 AUC0-t, AUC0-∞, didn’t differ on the bioequivalence level. In addition, as
 UGE (0-24) didn’t statistically differ, thus, we can conclude that there
 is no statistical significance between the morning and evening doses.
description: Informed consent were signed by all the participants before the
 begining of the study. Case reports were collected by
 the resident physician and the clinical pharmacist including their data,
 medical hstory, physical examination, any abnormal laboratory
 values,  eligible for inclusion and exclusion criteria, in addition to any
 comments from the physcian or the pharmacist.
DOI: 10.5061/dryad.gqnk98smc
title: Demographic data, reporting guidelines underlying the manuscript: The effect of morning versus evening administration of Empagliflozin on its pharmacokinetics and pharmacodynamics characteristics in healthy adults: a two way cross over, non-randomized trial

description: Background: Empagliflozin is an SGLT2 inhibitor approved for use in
 patients with Diabetes Mellitus type 2 (DMT2) with- or without other
 cardiovascular disease. Empagliflozin is taken once daily without
 rationale on the optimal timing for administration. This study
 aimed to determine the chronopharmacological effects of morning
 vs evening administration of empagliflozin 10 mg in Healthy Egyptian
 adults, by investigating the pharmacokinetics and
 pharmacodynamics parameters of empagliflozin depending on the intake
 time.  Methods: An open label, sequential,
 two‐way crossover trial comprised two periods with a washout period of 7
 days. Pharmacokinetics parameters (Tmax (h),
 Cmax (ng/ml), AUC 0-t (ng.h/ml)) as primary
 endpoints, and (AUC 0 to ∞(ng.h/ml)) as secondary endpoint were
 assessed. Method validation was done prior to injection in
 LC/MS/MS and samples were processed by Liquid-Liquid extraction. The
 pharmacodynamic profile (UGE 0-24) was determined after method
 validation (glucose hexokinase method).
 Results: Tmax increased by (35%) in the evening
 phase compared to the morning phase,
 while Cmax decreased by (-6.5%)in the evening dose
 compared to the morning dose. Besides, AUC0 to
 ∞ increased in the evening phase by (8.25%) compared to the
 morning phase. The mean cumulative amount of glucose excreted;
 UGE (0-24) increased by (43%) in the evening dose compared to the
 morning dose Conclusion: Despite the difference in
 pharmacokinetics parameters between evening and morning doses, Cmax,
 AUC0-t, AUC0-∞, didn’t differ on the bioequivalence level. In addition, as
 UGE(0-24) didn’t statistically differ, thus, we can conclude that there is
 no statistical significance between the morning and evening doses.
description: Demographic data were collected by taking participants'
 data, in addition to, blood tests to measure fasting blood sugar,
 triglycerides, high and low denisty lipo protein.
DOI: 10.5061/dryad.2z34tmpkp
title: Data from: Density-dependent and species-specific effects on self-organization modulate the resistance of mussel bed ecosystems to hydrodynamic stress

description: Mussels self-organize to form large regularly-patterned biogenic
 structures that modify the biotic and abiotic environment and provide
 numerous ecosystem functions and services. We used two mussel species
 which form mono-specific and mixed beds to investigate
 how species-specific behaviour affects self-organization
 and resistance to wave stress.  For these results, the
 laboratory dataset was used. Perna perna has strong
 attachment, but low motility, while Mytilus
 galloprovincialis shows the reverse. At low density the
 less motile P. perna has limited spatial
 self-organization compared to M. galloprovincialis while
 when co-existing, the two species formed random spatial patterns.
 At high density, the two species self-organized in similar ways while, in
 coexistence, patterns were less strong.  Spatial pattern
 formations significantly shaped resistance to
 hydrodynamic stress. For these results, the field dataset was
 used. At low density, P. perna beds with strong
 attachment and M. galloprovincialis beds with strong
 spatial organisation showed higher retention rates than mixed beds. At
 high density, the presence of strongly attached P.
 perna significantly increased retention in mixed and P.
 perna beds compared to M.
 galloprovincialis beds. Our study emphasises the importance of
 the interplay of species-specific behaviours to spatial self-organization
 and stress tolerance in natural communities.
DOI: 10.5061/dryad.ffbg79ctf
title: Phenotypic data for M. edulis responses to warming and ocean acidification

description: 1. In mosaic marine habitats, such as intertidal zones, ocean
 acidification (OA) is exacerbated by high variability of pH, temperature,
 and biological CO2 production. The non-linear interactions among these
 drivers can be context-specific and their effect on organisms in these
 habitats remains largely unknown, warranting further investigation. 2. We
 were particularly interested in Mytilus edulis (the blue mussel) from
 intertidal zones of the Gulf of Maine (GOM), USA for this study. GOM is a
 hot spot of global climate change (average Sea Surface Temperature (SST)
 increasing by &gt; 0.2 °C y−1 ) with &gt; 60% decline in mussel
 population over the past 40 years. 3. Here, we utilize bioenergetic
 underpinnings to identify limits of stress tolerance in M. edulis from GOM
 exposed to warming and OA. We have measured whole-organism oxygen
 consumption rates and metabolic biomarkers in mussels exposed to control
 and elevated temperatures (10 vs. 15 °C, respectively) and current and
 moderately elevated PCO2 levels (~ 400 vs. 800 µatm, respectively). 4. Our
 study demonstrates that adult M. edulis from GOM are metabolically
 resilient to the moderate OA scenario but responsive to warming as seen in
 changes in metabolic rate, energy reserves (total lipids), metabolite
 profiles (glucose and osmolyte dimethyl amine) and enzyme activities
 (carbonic anhydrase and calcium-ATPase). 5. Our results are in agreement
 with recent literature that OA scenarios for the next 100-300 years do not
 affect this species, possibly as a consequence of maintaining its in vivo
 acid−base balance.
DOI: 10.5061/dryad.sxksn0329
title: Data from: Telenomus nizwaensis (Hymenoptera: Scelionidae), an important egg parasitoid of the pomegranate butterfly Deudorix livia Klug (Lepidoptera: Lycaenidae) in Oman

description: The pomegranate butterfly Deudorix (=Virachola) livia is the major pest of
 pomegranate, a crop of economic importance, in Oman. A species of
 parasitoid wasp in the hymenopteran family Scelionidae is responsible for
 high levels of mortality of its eggs. This wasp is described herein as
 Telenomus nizwaensis Polaszek sp. n. based on morphology and DNA sequence
 data. Telenomus nizwaensis is currently known only from D. livia, which is
 also a pest of economic importance on other crops in North Africa, the
 Arabian Peninsula, and the Mediterranean. We summarise current knowledge
 of T. nizwaensis life-history and its potential to provide biological pest
 control.
description: Data collection: nucleotide sequences were downloaded from
 GenBank. Data processing: multiple sequence alignments
 were generated with MAFFT. Phylogenetic analyses were conducted with
 IQ-TREE.
description: The reader is referred to the accompanying README file for an
 explanation of the datasets.
DOI: 10.5061/dryad.m63xsj41b
title: Data from: Network ecology in dynamic landscapes

description: Network ecology is an emerging field that allows researchers to
 conceptualize and analyze ecological networks and their dynamics. Here, we
 focus on the dynamics of ecological networks in response to environmental
 changes. Specifically, we formalize how network topologies constrain the
 dynamics of ecological systems into a unifying framework in network
 ecology that we refer to as the “ecological network dynamics framework”.
 This framework stresses that the interplay between species interaction
 networks and the spatial layout of habitat patches is key to identifying
 which network properties (number and weights of nodes and links).
 Determining how effective ecological networks change through space and
 time can help reveal their complex dynamics in a changing world. We used
 directed graphlets to analyze changes in species interaction networks from
 a forest site (forest web), an edge site (edge web), and both sites
 together (meta web) at two time periods.
description: Species interactions in food-webs from forested landscapes were
 extracted from a database online and converted into directed binary
 interactions. 
description: Filename 
 Description 
 Forest1.csv Forest web: binary species interactions
 at time 1 
 Edge1.csv Edge web: binary species interactions
 at time 1 
 ForestEdge1.csv Meta web: binary species interactions
 at time 1 
 Forest2.csv Forest web: binary species interactions
 at time 2 
 Edge2.csv Edge web: binary species interactions
 at time 2 
 ForestEdge2.csv Meta web: binary species interactions
 at time 2
DOI: 10.5061/dryad.vt4b8gtrd
title: Nitrogen budget data

description: Input-output estimates of nitrogen (N) on cropland are essential for
 improving N management and better understanding the global N cycle. Here,
 we compare 13 N budget datasets covering 115 countries and regions over
 1961-2015. Though most datasets showed similar spatiotemporal patterns,
 some annual estimates varied widely among them, resulting in large ranges
 and uncertainty. In 2010, global medians (in Tg N yr-1) and associated
 min-max ranges were 73 (64-84) for global harvested crop N; 161 (139-192)
 for total N inputs; 86 (68-97) for N surplus; and 46% (40%-53%) for
 nitrogen use efficiency. Some of the most uncertain N budget terms by
 country showed ranges as large as their medians, revealing areas for
 improvement. A benchmark N budget dataset, derived from central tendencies
 of the original datasets, can be used in model comparisons and inform
 sustainable N management in food systems.
description: Each budget term is saved in a 13*55*115 matrix that includes 13
 estimates, for a 55-year period (1961-2015), for 115 countries or regions,
 using a subset of those defined by FAOSTAT. For names
 of 13 data sources see "Data_source_13". For names of 115
 countries/regions see "Country_name_115".
 Unit: area, km<sup>2</sup>; others, kg N per
 year. Harvested area: areah_3d_readout
 Fertilizer input: nfer_3d_readout Manure
 input: nman_3d_readout Fixation
 input: nfix_3d_readout Deposition
 input: ndep_3d_readout Harvested
 nitrogen: nyld_3d_readout USSR represents Former Soviet
 Union (FSU).
DOI: 10.5061/dryad.f7m0cfxv7
title: Sequence alignments of Corallicolids, apicomplexan symbionts of coral

description: Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host
 to a widespread and diverse group of intracellular symbionts of the phylum
 Apicomplexa. These symbionts, colloquially called ‘corallicolids’, are
 mostly known through molecular analyses, and no formal taxonomy has been
 proposed. Another apicomplexan, Gemmocystis cylindrus (described from the
 coral Dendrogyra cylindrus), may be related to corallicolids, but lacks
 molecular data. Here, we isolate and describe motile trophozoite (feeding)
 corallicolids cells using microscopic (light, SEM, and TEM) and molecular
 phylogenetic analysis to provide the basis for a formal description.
 Phylogenetic analyses using nuclear and plastid rRNA operons, and three
 mitochondrial protein sequences derived from single-cell transcriptomes,
 all confirm that these organisms fall into a discrete deep-branching clade
 within the Apicomplexa not closely related to any known species or major
 subgroup. As a result, we assign this clade to a new order, Corallicolida
 ord. nov., and family, Corallicolidae fam. nov. We describe a type
 species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp.
 host, and also describe a second species, Anthozoaphila gnarlus gen. nov.
 sp. nov., from the coral host Madracis mirabilis. Finally, we propose
 reassigning the incertae sedis taxon G. cylindrus from the order
 Agamococcidiorida to the Corallicolida, based on similarities in
 morphology and host localization to that of the corallicolids.