cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rfj6q57d0
title: Forecasting the publication and citation outcomes of Covid-19 preprints

description: The scientific community reacted quickly to the Covid-19 pandemic in 2020,
 generating an unprecedented increase in publications. Many of these
 publications were released on preprint servers such as medRxiv and
 bioRxiv. It is unknown however how reliable these preprints are, and if
 they will eventually be published in scientific journals. In this study,
 we use crowdsourced human forecasts to predict publication outcomes and
 future citation counts for a sample of 400 preprints with high Altmetric
 scores. Most of these preprints were published within one year of upload
 on a preprint server (70%), and 46% of the published preprints appeared in
 a high-impact journal with a Journal Impact Factor of at least 10. On
 average, the preprints received 162 citations within the first year. We
 found that forecasters can predict if preprints will be published after
 one year and if the publishing journal has high impact. Forecasts are also
 informative with respect to preprints’ rankings in terms of Google Scholar
 citations within one year of upload on a preprint server. For both types
 of assessment, we found statistically significant positive correlations
 between forecasts and observed outcomes. While the forecasts can help to
 provide a preliminary assessment of preprints at a faster pace than the
 traditional peer-review process, it remains to be investigated if such an
 assessment is suited to identify methodological problems in
 pre-prints. 
description: The dataset consists of survey responses collected through
 Qualtrix. Data was formatted and stored as .csv, and analysed with
 R.
DOI: 10.5061/dryad.zkh1893c8
title: Why and how we should join the shift from significance testing to estimation

description: A paradigm shift away from null hypothesis significance testing seems in
 progress. Based on simulations, we illustrate some of the underlying
 motivations. First, p-values vary strongly from study to study, hence
 dichotomous inference using significance thresholds is usually
 unjustified. Second, ‘statistically significant’ results have
 overestimated effect sizes, a bias declining with increasing statistical
 power. Third, ‘statistically non-significant’ results have underestimated
 effect sizes, and this bias gets stronger with higher statistical power.
 Fourth, the tested statistical hypotheses usually lack biological
 justification and are often uninformative. Despite these problems, a
 screen of 48 papers from the 2020 volume of the Journal of Evolutionary
 Biology exemplifies that significance testing is still used almost
 universally in evolutionary biology. All screened studies tested default
 null hypotheses of zero effect with the default significance threshold of
 p = 0.05, none presented a pre-specified alternative hypothesis, pre-study
 power calculation and the probability of ‘false negatives’ (beta error
 rate). The results sections of the papers presented 49 significance tests
 on average (median 23, range 0–390). Of 41 studies that contained verbal
 descriptions of a ‘statistically non-significant’ result, 26 (63%) falsely
 claimed the absence of an effect. We conclude that studies in ecology and
 evolutionary biology are mostly exploratory and descriptive. We should
 thus shift from claiming to ‘test’ specific hypotheses statistically to
 describing and discussing many hypotheses (possible true effect sizes)
 that are most compatible with our data, given our statistical model. We
 already have the means for doing so, because we routinely present
 compatibility (‘confidence’) intervals covering these hypotheses.
description: The code used for simulations and graphing is provided as plain
 txt file and is explained in the paper and in Appendix S1. The screening
 data set is provided as xlsx file and was generated by following the
 methods described in detail in the paper and in Appendix S1.
DOI: 10.5061/dryad.d2547d84p
title: Data set - Island area and historical geomorphological dynamics shape multifaceted diversity of barrier island floras

description: The influence of island dynamics and characteristics on taxonomic
 diversity, particularly species richness, are well studied. Yet, our
 knowledge on the influence of island dynamics and characteristics on other
 facets of diversity, namely functional and phylogenetic diversity, is
 limited, constraining our understanding of assembly processes on islands
 (e.g., biogeographic history, dispersal and environmental filtering, and
 species interactions). Using barrier islands, a highly dynamic and so far,
 understudied island type, we investigate how multiple facets of vascular
 plant diversity (functional, phylogenetic and taxonomic diversity) are
 shaped by island geomorphology, modern and historic area, and habitat
 heterogeneity. In line with our expectation, historical dynamics in island
 geomorphology affected phylogenetic and taxonomic diversity via habitat
 heterogeneity. However, island area was the best predictor across all
 facets of diversity. Specifically, larger islands had higher functional
 and phylogenetic diversity than expected by chance while most of the
 smaller islands had lower diversity. The influence of area on functional
 diversity acted via habitat heterogeneity, with habitat heterogeneity
 influencing negatively functional diversity. Our results suggest that
 larger islands accumulate functionally and phylogenetically unique
 species. Further, results for functional diversity pointed towards
 potential area-heterogeneity trade-offs, with these trade-offs likely
 resulting from increased interspecific competition favoring a specific set
 of trait values (of stronger competitors), particularly on smaller
 islands. Together, these results demonstrate that going beyond taxonomic
 diversity contributes to identifying underlying processes shaping
 diversity-area relationships.
DOI: 10.5061/dryad.vmcvdncvw
title: Virus classification for viral genomic fragments using PhaGCN2

description: Viruses are the most ubiquitous and diverse entities in the biome. Due to
 the rapid growth of newly identified viruses, there is an urgent need for
 accurate and comprehensive virus classification, particularly for novel
 viruses. Here, we present PhaGCN2, which can rapidly classify the taxonomy
 of viral sequences at family level and supports the visualization of the
 associations of all families. We evaluate the performance of PhaGCN2 and
 compare it with the state-of-the-art virus classification tools, such as
 vConTACT2, CAT, and VPF-Class, using the widely accepted metrics. The
 results show that PhaGCN2 largely improves the precision and recall of
 virus classification, increases the number of classifiable virus sequences
 in the Global Ocean Virome dataset (v2.0) by 4 times, and classifies more
 than 90% of the Gut Phage Database. PhaGCN2 makes it possible to conduct
 high-throughput and automatic expansion of the database of the
 International Committee on Taxonomy of Viruses.
DOI: 10.5061/dryad.6t1g1jx1v
title: Island biogeography at the meso-scale: distance from forest edge affects choice of patch size by ovipositing treefrogs

description: Diversity in habitat patches is partly driven by variation in patch size,
 which affects extinction, and isolation, which affects immigration. Patch
 size also affects immigration as a component of patch quality. In wetland
 ecosystems, where variation in patch size and inter-patch distance is
 ubiquitous, relationships between size and isolation may involve
 trade-offs. We assayed treefrog oviposition at three patch sizes in arrays
 of two types, one where size increased with distance from forest
 (dispersed), and one with all patches equidistant from forest
 (equidistant), testing directly for an interaction between patch size and
 distance, which was highly significant. Medium patches in dispersed arrays
 received more eggs than those in equidistant arrays as use of typically
 preferred larger patches was reduced in dispersed arrays. Our results
 demonstrate a habitat selection trade-off between preferred large and
 less-preferred medium patches across small-scale variation in isolation.
 Such patch size/isolation relationships are critical to community assembly
 and to understanding how diversity is maintained within a metapopulation
 and metacommunity framework, especially as wetland habitat becomes
 increasingly rare and fragmented. These results bring lessons of Island
 Biogeography, writ large, to bear on questions at small scales where
 ecologists often work, and where habitat restoration is most often
 focused.
description: See manuscript and readme file.
DOI: 10.7272/q6vq30x9
title: Simulation and nurse-mentoring in a statewide nurse mentoring program in Bihar, India: diagnosis of postpartum hemorrhage and intrapartum asphyxia

description: Background: Mentoring programs that include simulation, bedside mentoring,
 and didactic components are becoming increasingly popular to improve
 quality. These programs are designed with little evidence to inform the
 ideal composition of mentoring activities that would yield the greatest
 impact on provider skills and patient outcomes. We examined the
 association of number of maternal and neonatal emergency simulations
 performed with the diagnosis of postpartum hemorrhage (PPH) and
 intrapartum asphyxia in real patients. Method: Prospective
 cohort. Between- and within-facility comparisons over time.
 Setting: 320 public facilities in the state of Bihar, India May
 2015 – 2017. Participants: Deliveries and livebirths.
 Interventions: Mobile nurse-mentoring program with simulations,
 teamwork and communication activities, didactic teaching, demonstrations
 of clinical procedures and bedside mentoring including conducting
 deliveries. Nurse mentor pairs visited each facility for one
 week, covering four facilities over a four-week period, for seven to nine
 consecutive months. Outcome measures: Diagnosis of PPH and
 intrapartum asphyxia. Results: Relative to the bottom one-third
 facilities that performed the fewest maternal simulations, facilities in
 the middle one-third group diagnosed 26% (IRR = 1.26, 95% CI: 1.00, 1.59)
 more cases of PPH in real patients. Similarly, facilities in the middle
 one-third group, diagnosed 25% (IRR = 1.25, 95% CI: 1.04, 1.50) more cases
 of intrapartum asphyxia relative to the bottom third group that did the
 fewest neonatal simulations. Facilities in the top one-third group (i.e.,
 performed the most simulations) did not have a significant difference in
 diagnosis of both outcomes, relative to the bottom one-third group.
 Conclusion: Findings suggest a complex relationship between
 performing simulations and opportunities for direct practice with
 patients, and there may be an optimal balance in performing the two that
 would maximize diagnosis of PPH and intrapartum asphyxia.
DOI: 10.26165/juelich-data/jpn8l6
title: Literature Review Data for Modeling Disruptive Events in Renewable Energy Supply: A Review

description: Data for a literature review on the modeling of disruptive events in renewable energy supply based on articles published between 2003 and September 2023. This datasheet provides a summary for each article reviewed, including the modeling technique used, the category of disruptive event identified, the demand sector applicable to the disruptive event, the spatial resolution of the study, and the technologies considered. This work was supported by the Helmholtz Association as part of the Platform for the Design of a Robust Energy System and Raw Material Supply (RESUR) and the program “Energy System Design”.
DOI: 10.5061/dryad.8w9ghx3pq
title: Cover crop and nitrogen rate management practices influence corn (Zea mays) NDVI and nitrogen content

description: Cover crops are rarely adopted in the northern Corn Belt because of short
 growing periods but could provide benefits when grown between wheat
 (Triticum aestivum L.) and corn (Zea mays L.). We evaluated corn NDVI
 (normalized difference vegetation index) and leaf N (at six leaf, ear
 leaf, 75% silk, and physiological maturity), over three growing seasons in
 response to factorial treatments of cover crop (annual ryegrass [Lolium
 perenne L. ssp. multiflorum (Lam.) Husnot], radish [Raphanus sativus L.],
 and no-cover control) and N rate (0X, 0.25X, 0.5X, and 1X) relative to the
 recommended rate based on pre-plant soil tests (157–190 kg N ha–1). Grain
 N was also measured in the last study year (2016) to evaluate if leaf N
 indicated grain N. Radish cover crop increased corn NDVI relative to the
 no-cover control, but annual ryegrass decreased NDVI relative to no-cover
 control. This response to cover crop treatment suggests that radish cover
 crop may improve corn nutritional status. Corn receiving 1X N rate had the
 slowest decrease in leaf N over the growing season, but 2016 data revealed
 that grain from all treatments receiving some level of N had similar N
 content. Root biomass was also highest in the 0.5X N rate treatment and
 could explain the previously reported result that 0.5X N rate results in
 highest corn yield. Taken together, these results suggest that half the
 recommended N fertilizer can be used with little effect on nutritional
 status of corn following spring wheat in the northern Corn belt.
DOI: 10.5061/dryad.c2fqz61b4
title: Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

description: Collateral sensitivity (CS), which arises when resistance to one
 antibiotic increases sensitivity towards other antibiotics, offers novel
 treatment opportunities to constrain or reverse the evolution of
 antibiotic resistance. The applicability of CS-informed treatments remains
 uncertain, in part because we lack an understanding of the generality of
 CS effects for different resistance mutations, singly or in combination.
 Here we address this issue in the Gram-positive pathogen Streptococcus
 pneumoniae by measuring collateral and fitness effects of
 clinically
 relevant gyrA and parC alleles, and
 their combinations, that confer resistance to fluoroquinolones. We
 integrated these results in a mathematical model which allowed us to
 evaluate how different in silico combination treatments
 impact the dynamics of resistance evolution. We identified common and
 conserved CS effects of different gyrA and parC alleles;
 however, the spectrum of collateral effects was unique for each allele or
 allelic pair. This indicated that allelic identity can impact the
 evolutionary dynamics of resistance evolution during monotreatment and
 combination treatment. Our model simulations, which included the
 experimentally derived antibiotic susceptibilities and fitness effects,
 and antibiotic-specific pharmacodynamics, revealed that both collateral
 and fitness effects impact the population dynamics of resistance
 evolution. Overall, we provide evidence that allelic identity and
 interactions can have a pronounced impact on collateral effects of
 different antibiotics and suggest that these need to be considered in
 models examining CS-based therapies.
DOI: 10.5061/dryad.41ns1rngs
title: Termite dispersal is influenced by their diet

description: Termites feed on vegetal matter at various stages of decomposition.
 Lineages of wood- and soil-feeding termites are distributed across
 terrestrial ecosystems located between 45°N and 45°S of latitude, a
 distribution they acquired through many transoceanic dispersal events.
 While wood-feeding termites often live in the wood on which they feed and
 are efficient at dispersing across oceans by rafting, soil-feeders are
 believed to be poor dispersers. Therefore, their distribution across
 multiple continents requires an explanation. Here, we reconstructed the
 historical biogeography and the ancestral diet of termites using
 mitochondrial genomes and δ13C and δ15N stable isotope measurements
 obtained from 324 termite samples collected in five biogeographic realms.
 Our biogeographic models showed that wood-feeders are better at dispersing
 across oceans than soil-feeders, further corroborated by the presence of
 wood-feeders on remote islands devoid of soil-feeders. However, our
 ancestral range reconstructions identified 33 dispersal events among
 biogeographic realms, 18 of which were performed by soil-feeders.
 Therefore, despite their lower dispersal ability, soil-feeders performed
 several transoceanic dispersals that shaped the distribution of modern
 termites.
DOI: 10.5061/dryad.76hdr7szr
title: A phylogenetic and morphological study of the Tectaria fuscipes group (Tectariaceae), with description of a new species

description: The fern species Tectaria fuscipes and morphologically
 similar species, which are common in tropical and subtropical mainland
 Asia, constitute a taxonomically confusing group. To better understand
 species boundaries and relationships within the T.
 fuscipes group, we conducted phylogenetic analyses of five
 plastid regions and morphological observations of herbarium specimens and
 living plants. As a result, we produced a generally well-resolved
 phylogeny of the T. fuscipes group and morphologically similar
 species in Asia. The phylogenetic analyses supported the T.
 fuscipes group including T. dissecta, T.
 fuscipes, T. ingens, T. paradoxa, T.
 setulosa, T. subfuscipes, T. subsageniacea and
 a new species, but excluding T. kusukusensis.
 However, T. fuscipes, T.
 subfuscipes and T. subsageniacea are almost
 indistinguishable in morphology, which form a complex characterized by the
 black linear-lanceolate stipe scales. The new species found in southern
 China and Vietnam is described here as T. fungii. It is similar
 to the T. fuscipes complex and T. kusukusensis,
 but differs from the former mainly by its brown-castaneous
 lanceolate stipe scales and from the latter by having nearly hairless
 laminae (versus frond axes abaxially bearing copious hairs).
DOI: 10.5061/dryad.3bk3j9kmx
title: Warming may extend tree growing seasons and compensate for reduced carbon uptake during dry periods

description: 1. Warming and drought alter plant phenology, photosynthesis and growth
 with important consequences for the global carbon cycle and the earth’s
 climate. Yet, few studies have attempted to tease apart their effects on
 tree phenology, particularly leaf senescence, and on source and sink
 activity. 2. We experimentally assessed the single and combined effects of
 warming and reduced soil moisture on the phenology (leaf-out and
 senescence date, growing season length) and aboveground sink (height and
 diameter growth, leaf area and Huber values) and source activity (net
 photosynthesis, photosynthetic efficiency, chlorophyll concentration and
 total carbon (C) uptake) of two tree species with distinct strategies to
 deal with drought: European beech and pubescent oak. 3. Warming advanced
 leaf-out, irrespective of soil moisture levels, particularly in oak and to
 a lower extent in beech, leading to a prolonged growing season in oak but
 not beech. No impacts of warming on senescence timing were found for both
 species. Reduced moisture had little impact on the phenology of both
 species. Warming-induced advances in phenology and higher photosynthetic
 efficiency increased the annual C uptake for oak and compensated for the
 reduced photosynthetic activity in the presence of reduced moisture.
 Conversely, for beech, source activity, including yearly C uptake, was
 lower in all treatments than the control, indicating no compensation of
 the C budget by phenological shifts. 4. Synthesis. Our results demonstrate
 that a warming-driven earlier activity and higher photosynthetic
 efficiency compensates for reduced photosynthesis during hot and dry
 periods, but only for pubescent oak, which is a rather drought tolerant
 species. Current predictions of warming-induced mitigation effects through
 extended C uptake seem incorrect for beech. --
description: The methods are described in full in the manuscript.
DOI: 10.5061/dryad.ncjsxksx6
title: Multitrophic diversity and biotic associations influence subalpine forest ecosystem multifunctionality

description: Biodiversity across multiple trophic levels is required to maintain
 multiple ecosystem functions. Yet, it remains unclear how multitrophic
 diversity and species interactions regulate ecosystem multifunctionality.
 Here, combining data from nine different trophic groups (including trees,
 shrubs, herbs, leaf mites, small mammals, bacteria, pathogenic fungi,
 saprophytic fungi and symbiotic fungi) and 13 ecosystem functions related
 to supporting, provisioning and regulating services, we used a
 multitrophic perspective to evaluate the effects of elevation, diversity
 and network complexity on scale-dependent subalpine forest
 multifunctionality. Our results demonstrate that elevation and soil pH
 significantly modified species composition and richness across
 multitrophic groups and influenced multiple functions simultaneously. We
 provide evidence that species richness across multiple trophic groups had
 stronger effects on multifunctionality than species richness at any single
 trophic level. Moreover, biotic associations, indicating the complexity of
 trophic networks, were positively associated with multifunctionality. The
 relative effects of diversity on multifunctionality increased at the scale
 of the larger community compared to a scale accounting for neighbouring
 interactions. Our results highlight the paramount importance of scale- and
 context- dependent multitrophic diversity and interactions for a better
 understanding of mountain ecosystem multifunctionality in a changing
 world.
description: Data was collected at both neighbourhood scale and community
 scale.
description: The nine groups from different trophic levels, 13 important
 ecosystem functions, and abiotic variables were collected at both
 neighbourhood and community scale.