cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4f4qrfm1
title: Comparative analysis of time-based and quadrat sampling in seasonal population dynamics of intermediate hosts of human schistosomes

description: Background Despite their importance for designing and evaluating
 schistosomiasis control trials, little attention in the literature has
 been dedicated to sampling protocols for the parasite's snail
 intermediate hosts since their first development. We propose a comparative
 analysis of time-based and quadrat sampling protocols to quantify the
 seasonal variations in the abundance of these aquatic snail species of
 medical importance. Methodology/Principal Findings Snail populations were
 monitored during 42 consecutive months in three types of habitats
 (ephemeral pond, ephemeral river and permanent stream) in two sites
 covering different climatic zones in Burkina Faso. We employed both a
 widely used time-based protocol of 30min of systematic collection at a
 weekly interval, and a quadrat protocol of 8 replicates per sample at a
 monthly interval. The correspondence between the two protocols was
 evaluated using an ensemble of statistical models including linear and
 saturating-type functional forms as well as allowing for count
 zero-inflation. The quadrat protocol yielded on average a relative
 standard error of 40\%, for a mean snail density of 16.7 snails/m2 and
 index of dispersion of 1.51. Both protocols yielded similar seasonal
 patterns in snail abundance, confirming the asynchrony between permanent
 and ephemeral habitats with respect to the country's seasonal
 rainfall patterns. Formal model comparison of the link between time vs.
 quadrat counts showed strong support of saturation for the latter and
 measurement zero-inflation, providing important evidence for the presence
 of density feedbacks in the snail's population dynamics, as well as
 for spatial clustering. Conclusions/Significance In addition to the
 agreement with the time-based method, quadrat sampling provided insight
 into snail population dynamics and comparable density estimates across
 sites. The re-evaluation of these  "traditional"
 sampling protocols, as well as the correspondence between their outputs,
 is of practical importance for the design and evaluation of
 schistosomiasis control trials.
DOI: 10.5061/dryad.mpg4f4qtt
title: Using a custom mobile application for change management in an electronic health record implementation

description: Objectives Institutions cite managing the modification in infrastructure,
 technical support, and process change as substantial barriers to a
 successful electronic health record (EHR) implementation. In an effort to
 organize and centralize the complex scheduling, task completion and
 communication needs of a “big-bang” EHR go-live, we developed a unified
 communication system with the goal of improving implementation process
 efficiency. Our goal was to create a platform that would work across the
 medical enterprise. Materials and Methods We employed an agile process to
 design the application, called Hubbl, based on initial requirements and
 iteratively obtained stakeholder user. The final feature set included role
 specific organization, integrated communication, task and content
 management tooling, and embedded project information retrieval, all
 embedded into the end user’s day to day activities. Results User
 enrollment continually increased from launch in February of 2017 through
 go-live day. During the pre-go-live period, usage increased from an
 average of 7.37 events/user/day to 18.65 events/user/day with over 97
 communications sent across all periods. 5,400 unique users accessed tip
 sheets and information retrieval tools averaged 28.84 searches/user/day
 during the go-live period with an average high of 46.33 searches/user/day
 five days post go-live. User access during go-live and post-go-live
 averaged 12.82 accesses/user/day and decreased from 20.42 average accesses
 on day one of go live to 14.07 averaged accesses on day 60 of post go live
 with over 727 tasks monitored to completion during all periods. Conclusion
 Hubbl was an essential component of our communication, task coordination,
 and change management strategy, for our EHR go live. Institutions that
 choose a unified mobile and web based platform during a substantial IT
 (information technology) implementation can feasibly ensure task
 completion, project coordination, and timely information dissemination.
DOI: 10.5061/dryad.bk3j9kd6d
title: Data from: During hippocampal inactivation, grid cells maintain synchrony, even when the grid pattern is lost

description: The grid cell network in the medial entorhinal cortex (MEC) has been
 subject to thorough testing and analysis, and many theories for their
 formation have been suggested. To test some of these theories, we
 re-analyzed data from Bonnevie et al., 2013, in which the hippocampus was
 inactivated and grid cells were recorded in the rat MEC. We investigated
 whether the firing associations of grid cells depend on hippocampal
 inputs. Specifically, we examined temporal and spatial correlations in the
 firing times of simultaneously recorded grid cells before and during
 hippocampal inactivation. Our analysis revealed evidence of network
 coherence in grid cells even in the absence of hippocampal input to the
 MEC, both in regular grid cells and in those that became head-direction
 cells after hippocampal inactivation. This favors models, which suggest
 that phase relations between grid cells in the MEC are dependent on
 intrinsic connectivity within the MEC.
description: Data was originally collected for the following paper:
 Bonnevie T, Dunn B, Fyhn M, Hafting T, Derdikman D, Kubie JL,
 Roudi Y, Moser EI, Moser MB. Grid cells require excitatory drive from the
 hippocampus. Nature neuroscience. 2013 Mar;16(3):309 We
 have used Matlab to read and analyze the data.
description: The cells are uploaded as Matlab .mat files.
 We will supply code on Github for reading this data.
 (the link will be given in our published paper).
DOI: 10.5061/dryad.6djh9w0wn
title: Interfering with a memory without erasing its trace

description: Previous research has shown that performance of a novice skill can be
 easily interfered with by subsequent training of another skill. We address
 the open questions whether extensively trained skills show the same
 vulnerability to interference as novice skills and which memory mechanism
 regulates interference between expert skills. We developed a recurrent
 neural network model of V1 able to learn from feedback experienced over
 the course of a long-term orientation discrimination experiment. After
 first exposing the model to one discrimination task for 3480 consecutive
 trials, we assessed how its performance was affected by subsequent
 training in a second, similar task. Training the second task strongly
 interfered with the first (highly trained) discrimination skill. The
 magnitude of interference depended on the relative amounts of training
 devoted to the different tasks. We used these and other model outcomes as
 predictions for a perceptual learning experiment in which human
 participants underwent the same training protocol as our model.
 Specifically, over the course of three months participants underwent
 baseline training in one orientation discrimination task for 15 sessions
 before being trained for 15 sessions on a similar task and finally
 undergoing another 15 sessions of training on the first task (to assess
 interference). Across all conditions, the pattern of interference observed
 empirically closely matched model predictions. According to our model,
 behavioral interference can be explained by antagonistic changes in
 neuronal tuning induced by the two tasks. Remarkably, this did not stem
 from erasing connections due to earlier learning but rather from a
 reweighting of lateral inhibition.
DOI: 10.15468/dl.ut4dvr
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-18.77217 28.26641,-17.11395 28.26641,-17.11395 28.92941,-18.77217 28.92941,-18.77217 28.26641))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gennaria diphylla",
 "Year 2025-2026"
 ]
}

 The dataset includes 20 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001926-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvzrq8
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus brosei"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001927-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8gtht76jg
title: Habitat type drives the distribution of non-indigenous species in fouling communities regardless of associated maritime traffic

description: Aim: Biological invasions and changes in land and sea use are amongst the
 five major causes of global biodiversity decline. Shipping and ocean
 sprawl (multiplication of artificial structures at the expense of natural
 habitats) are considered as the major forces responsible for marine
 invasions and biotic homogenization. And yet, there is little evidence of
 their interplay at multiple spatial scales. Here, we aimed to examine this
 interaction and the extent to which the type of artificial habitat alters
 the distribution of native and non-indigenous biodiversity. Location:
 Southeast Pacific - Central Chilean coastline Methods: Settlement plates
 were deployed upon two types of artificial habitats (floating or
 non-floating hard substrates) at a total of ten study sites, either
 exposed to international or local traffic. After colonization periods of
 three and thirteen months, plates were retrieved to determine their
 associated fouling sessile assemblages at an early and late stage of
 development, respectively. Putative confounding factors (temperature,
 metal concentrations) were taken into account. Results: While traffic type
 had no detectable effect, there were strong differences in community
 structure between habitats, consistent across the study region. These
 differences were driven by non-indigenous species which contributed to 58
 and 40% of the community structure in floating habitats after three and
 thirteen months, respectively – roughly 10 times greater than in their
 non-floating counterparts. Assemblages on floating structures also
 displayed a lower decline in similarity with increasing distance between
 sampling units, being thus more homogenous than non-floating habitats at
 the regional scale. Main conclusions: With the absence of international
 traffic effect, the colonization success by non-indigenous species appears
 to be mainly habitat-dependent and driven by local propagules. Floating
 structures not only provide specific niches but characteristics shared
 with major introduction and dispersal vectors (notably hulls), and in turn
 constitute important corridors to invasions and drivers of biotic
 homogenization at multiple scales.
description: cf. "Methods" section
description: The data file (.xls) is
 composed of 4 sheets: 1_DataSet (species x sample):
 Abundance (cover, %) matrix of each species across samples.
 2_Species indicators:
 Status/Type (Abiotic, Unassigned, Native, Cryptogenic, Non-Indigenous
 Species) and main trophic group considered for each species.
 3_Sample factors: Site and
 experimental factors (Habitat, Traffic, Age, Experimental Unit, Replicate,
 nested within site) corresponding to each sample. 4_Site description: Full name,
 coordinate and description of each study site (traffic, substratum
 etc.).
DOI: 10.21223/p3/skydrt
title: Dataset for: Parental value for tuber yield in potato clones with resistance to late blight and heat tolerance, under high temperatures conditions (SET 1)

description: The International Potato Center (CIP) has developed a population named LBHT, obtaining new clones that are more tolerant to high temperatures, resistant to late blight, virus and early maturity, and they are available for use by developing countries for the selection of varieties or as parents in their breeding programs. The potato is highly heterozygozus crop, the most important economical characters are governed by additive and non-aditive genes. Therefore, the parental value of a clone cannot be assessed from phenotypic value alone. It is very important to know its combining ability as an indicator of parental value. Combining ability analysis is a method very useful for choosing better parents, and in the formulation of a crossing plan for a plant breeding program. During 2012 and 2013, 19 advanced clones of LBHT population, were crossed using line x tester mating design, where the clones were used as female parents (lines) and as male parents (testers). The varieties, Katahdin (Solanum tuberosum spp tuberosum), Huagalina (Solanum tuberosum spp andigena) and clone CIP398098.204 were used in this experiment. Furthermore, during 2013 - 2014, 57 progenies were evaluated under field conditions in three locations in Peru: La Molina, San Ramon and Majes. All experiments were conducted using statistical design of randomized complete block with three replications of 40 plants per plot. At harvest, the number and weight of marketable and non-marketable tubers were recorded. Then, the average weight of tubers, weight of marketable and total tubers per hectare in tons were calculated The analysis of variance for line by tester mating desing and determination of the effects of general combining ability (GCA) for these characters were performed using statistical software, SAS V. 9.4 (SAS Institute Inc., Cary, NC, USA).
DOI: 10.5061/dryad.280gb5mkz
title: Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

description: Geographic isolation substantially contributes to species endemism on
 oceanic islands when speciation involves the colonisation of a new island.
 However, less is understood about the drivers of speciation within
 islands. What is lacking is a general understanding of the geographic
 scale of gene flow limitation within islands, and thus the geographic
 scale and drivers of geographical speciation within insular contexts.
 Using a community of beetle species, we show that when dispersal ability
 and climate tolerance are restricted, microclimatic variation over
 distances of only a few kilometres can maintain strong geographic
 isolation and drive incipient speciation. Further to this, we demonstrate
 congruent diversification with gene flow across species, mediated by
 Quaternary climate oscillations that have facilitated a dynamic of
 isolation and secondary contact. The unprecedented scale of parallel
 species responses to a common environmental driver for evolutionary change
 has profound consequences for understanding past and future species
 responses to climate variation.
description: This files contains all DNA and topoclimate data from the
 manuscript. The file README contains additional data for each
 individual.
DOI: 10.15468/dl.8py57w
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-18.76749 28.20479,-16.97627 28.20479,-16.97627 28.92098,-18.76749 28.92098,-18.76749 28.20479))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Habenaria tridactylites",
 "Year 2025-2026"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001924-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.15dv41ns9
title: The diverse nature of island isolation and its effect on land-bridge insular faunas

description: Aim Isolation is a key factor in island biology. It is usually defined as
 the distance to the geographically nearest mainland, but multiple
 alternatives exist. We explored how testing different isolation indices
 affects the inference of isolation effects on faunal characteristics. We
 focused on land-bridge islands and compared the relationships of multiple
 spatial and temporal (i.e., through time) isolation indices with
 community-, population-, and individual-level characteristics (species
 richness, population density, and body size, respectively). Location
 Aegean Sea islands, Greece. Time period: current. Taxon Multiple animal
 taxa. Methods We estimated 21 isolation indices for 205 islands, and
 recorded species-richness data for 15 taxa (invertebrates and
 vertebrates). We obtained body size data for seven lizard species and
 population density data for three. We explored how well indices predict
 each characteristic, in each taxon, by conducting a series of OLS
 regressions (controlling for island area when needed), and a
 meta-analysis. Results Isolation was significantly (and negatively)
 associated with species richness in ten of 15 taxa. It was significantly
 (and positively) associated with body size in only one of seven species,
 and was not associated with population density. The effect of isolation on
 species richness was much weaker than island area, regardless of the index
 tested. Spatial indices generally outperformed temporal indices, and
 indices directly related to the mainland outperformed those related mainly
 to neighbouring islands. No index was universally superior to others,
 including the distance to the geographically nearest mainland. Main
 Conclusions The choice of index can alter our perception of the effects of
 isolation on biological patterns. The nearly automatic, ubiquitous, use of
 distance to the geographically nearest mainland misrepresents the
 complexity of isolation effects. We recommend to simultaneously test
 multiple indices, that represent different aspects of isolation, to
 produce more constructive and thorough investigations and avoid imprecise
 inference.
DOI: 10.5061/dryad.6q573n5v5
title: Red oak seedlings as indicators of deer browse pressure: gauging the outcome of different white-tailed deer management approaches

description: After decades of high deer populations, North America forests have lost
 much of their previous biodiversity.  Any landscape-level
 recovery requires substantial reductions in deer herds, but modern
 societies and wildlife management agencies appear unable to devise
 appropriate solutions to this chronic ecological and human health
 crisis.  We evaluated the effectiveness of fertility control
 hunting in reducing deer impacts at Cornell University.  We
 estimated spring deer populations and planted Quercus rubra seedlings to
 assess deer browse pressure, rodent attack, and other factors compromising
 seedling performance.  Oak seedlings protected in cages grew
 well, but deer annually browsed ≥ 60% of unprotected seedlings. 
 Despite female sterilization rates of &gt; 90%, the deer population
 remained stable. Neither sterilization nor recreational hunting reduced
 deer browse rates and neither appears able to achieve reductions in deer
 populations or their impacts.  We eliminated deer sterilization
 and recreational hunting in a core management area in favor of allowing
 volunteer archers to shoot deer over bait, including at night. 
 This resulted in a substantial reduction in the deer population and a
 linear decline in browse rates as a function of the spring deer abundance.
  Public trust stewardship of North American landscapes will
 require a fundamental overhaul in deer management to may provide for a
 brighter future, and oak sentinels may be a promising metric to assess
 changes.  These changes will require intense public debate and
 may require new approaches such as regulated commercial hunting and the
 natural dispersal or intentional release of important deer predators
 (e.g., wolves and mountain lions).  Such drastic changes in deer
 management will be highly controversial, and at present, likely difficult
 to implement in North America.  However, the future of our forest
 ecosystems and associated biodiversity will depend on evidence and guided
 change in landscape management and stewardship.
DOI: 10.5061/dryad.0rxwdbrv4
title: Biocontrol potential of a novel endophytic bacterium from Mulberry (Morus) tree

description: Mulberry (Morus) is an economically important woody tree that is suitable
 for use in sericulture as forage and in medicine. However, this
 broad-leaved tree is facing multiple threats ranging from phytopathogens
 to insect pests. Here, a Gram-positive, endospore-forming bacterium (ZJU1)
 was frequently isolated from healthy mulberry plants by screening for
 foliar endophytes showing antagonism against pathogens and pests.
 Whole-genome sequencing and annotation resulted in a genome size of 4.06
 Mb and classified the bacterium as a novel strain of Bacillus
 amyloliquefaciens that has rarely been identified from tree leaves. An
 integrative approach combining traditional natural product chemistry,
 activity bioassays, and high-resolution mass spectrometry confirmed that
 strain ZJU1 uses a blend of antimicrobials including peptides and volatile
 organic compounds to oppose Botrytis cinerea, a major phytopathogenic
 fungus causing mulberry gray mold disease. We showed that the inoculation
 of endophyte-free plants with ZJU1 significantly decreased both leaf
 necrosis and mortality under field conditions. In addition to the direct
 interactions of endophytes with foliar pathogens, in planta studies
 suggested that the inoculation of endophytes also induced plant systemic
 defense, including high expression levels of mulberry disease resistance
 genes. Moreover, when applied to the generalist herbivore Spodoptera
 litura, ZJU1 was sufficient to reduce the pest survival rate below 50%. A
 previously undiscovered crystal toxin (Cry10Aa) could contribute to this
 insecticidal effect against notorious lepidopteran pests. These unique
 traits clearly demonstrate that B. amyloliquefaciens ZJU1 is promising for
 the development of successful strategies for biocontrol applications. The
 search for new plant-beneficial microbes and engineering microbiomes is
 therefore of great significance for sustainably improving plant
 performance.
description: The samples were diluted in methanol:water (1:1, dilution 1/10,
 UHPLC-grade CHEMSOLUTE<sup>®</sup>), and 1 μL was injected
 into a C-18 column (Kinetex, 100 × 2.1 mm, 2.6 μm, Thermo Accucore) and
 analyzed with a UHPLC-HR-MS (UltiMate 3000 UHPLC, Dionex, USA) coupled to
 a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific,
 Dreieich, Germany). The mass spectrometry analysis was performed in both
 positive- and negative-ion mode with a scan range of
 <i>m</i>/<i>z</i> 100–1,500 for both the full-scan
 and the targeted data-dependent mass spectrometry experiment (ddMS, Top
 N). The peak resolutions were set at 70,000 and 17,500 for the full-scan
 and ddMS analyses, respectively. The MS/MS experiments were conducted with
 an isolation window of 0.4 <i>m</i>/<i>z</i> at a
 peak resolution of 35,000 (average NCE 15, 30, 45). The maximum ion time
 was set to 200 ms, and the AGC target was set to 3e6. The analytical
 standard was prepared in methanol:water (1:1), and a 10 μL aliquot was
 injected under similar conditions to those mentioned above.