cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gmsbcc2mh
title: Pinpointing the neural signatures of single-exposure visual recognition memory

description: Memories of the images that we have seen are thought to be reflected in
 the reduction of neural responses in high-level visual areas such as
 inferotemporal (IT) cortex, a phenomenon known as repetition suppression
 (RS). We challenged this hypothesis with a task that required rhesus
 monkeys to report whether images were novel or repeated while ignoring
 variations in contrast, a stimulus attribute that is also known to
 modulate the overall IT response. The monkeys’ behavior was largely
 contrast-invariant, contrary to the predictions of an RS-inspired decoder,
 which could not distinguish responses to images that are repeated from
 those that are of lower contrast. However, the monkeys’ behavioral
 patterns were well-predicted by a linearly decodable variant in which the
 total spike count was corrected for contrast modulation. These results
 suggest that the IT neural activity pattern that best aligns with
 single-exposure visual recognition memory behavior is not RS but rather
 “sensory referenced suppression (SRS)”: reductions in IT population
 response magnitude, corrected for sensory modulation.
DOI: 10.5061/dryad.r4xgxd2bq
title: DNA metabarcoding of prey reveals spatial, temporal, and diet partitioning of an island ecosystem by four invasive wasps

description: 1. Invasive alien species can cause detrimental changes in native
 ecosystems, but our understanding of the interactions between multiple
 exotic species is limited. To evaluate the joint effect of multiple
 sympatric invaders on an ecosystem, we must first understand how they
 interact with each other. 2. Here, we quantified the spatial distribution,
 dietary composition and overlap of four invasive generalist vespid species
 (two Vespula and two Polistes) that co-occur on Ahuahu off the north-east
 coast of New Zealand. We used DNA metabarcoding of larval faecal material
 to identify prey species, and mapped the locations of nests. 3. We
 observed clear spatial partitioning, with different wasp species
 aggregating in different habitats. Diet differed both among wasp species
 (diet partitioning) and among seasons (temporal partitioning). There was
 stronger competition (highest diet overlap) between V. germanica and V.
 vulgaris than between other wasp species, but partitioning resources
 minimised spatial and diet overlap between the four species. 4.
 Additionally, we obtained high-resolution diet inventories that help
 assess the combined ecological impact of invasion by multiple wasps. These
 species consumed mostly native and endemic invertebrates from multiple
 trophic levels, but particularly herbivores (Lepidoptera). We provide
 direct evidence that in combination they exploited a wide range of endemic
 invertebrates. 5. Synthesis and applications. Our study demonstrates
 resource partitioning among four invasive wasps, facilitating coexistence
 of these generalist invaders. We conclude that coexistence probably
 amplifies their ecological impact. Quantifying how multiple invaders
 exploit and partition resources provides insights into how communities
 assemble and helps to assess the cumulative effects of multiple invaders
 on the recipient community.08-Feb-2021
description: See publication.
description: See publication.
DOI: 10.5061/dryad.h70rxwdhr
title: A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown

description: Several studies reported the rapid evolution of avirulence (Avr) genes to
 escape R-mediated plant immunity and identified a variety of mechanisms
 leading to virulence. The poplar rust fungus Melampsora larici-populina is
 the most damaging pathogen of poplars. A major adaptive event occurred in
 1994 with the breakdown of RMlp7 resistance gene in poplar. Population
 genomics studies identified a locus in the genome of M. larici-populina,
 which likely corresponds to the AvrMlp7 candidate avirulence gene. We used
 a population genetics approach combined with dedicated qPCR assays on a
 comprehensive set of 281 isolates, covering 27 years (encompassing the
 resistance breakdown event), to validate the candidate locus and to assess
 its polymorphism. We found two mechanisms, a point mutation and a
 deletion, that allowed the pathogen to escape RMlp7-mediated resistance.
 Six diploid genotypes were thus characterized at the candidate locus
 (three avirulent and three virulent). In addition, a temporal analysis
 revealed that the two virulence alleles pre-existed (harboured as
 avirulent heterozygous genotypes) since the early samplings and were found
 in association (as virulent genotypes) at the time of the resistance
 breakdown.These molecular analyses were complemented by a population
 genetic analysis of those temporal samples, using 22 microsatellite
 markers.
description: 281 isolates were chosen from a historical collection maintained
 at INRAE Grand-Est – Nancy, France, which ranges from 1989 to 2016. This
 collection included most samples from a previous study of Persoons et al.
 (2017) but extended the time-period covered by the analysis (see Table S1,
 Supporting information). Virulence factor of all
 isolates were confirmed upon inoculation of a poplar cultivar carrying
 <i>RMlp7</i> resistance gene (<i>P. × interamericana
 </i>‘Beaupré’) and a universal cultivar susceptible to all poplar
 rust isolates (<i>P. × euramericana ‘</i>Robusta’), as a
 positive control. Genotyping was performed using 22
 microsatellite markers (Xhaard et al., 2011). Two
 assays based on TaqMan® real-time PCR were used to detect two types of
 mutations at the <i>AvrMlp7</i> locus: a deletion of the locus
 containing the gene and a non-synonymous SNP in the coding
 sequence.
DOI: 10.6084/m9.figshare.30519259
title: Symptom burden in the first four years following hospitalization after mild traumatic brain injury

description: 1) Describe clinically significant symptoms over 4 years following hospitalization after mild traumatic brain injury (mTBI); 2) examine quality of life (QoL), social participation, and healthcare service use in relation to symptom burden. Longitudinal cohort study in which 142 adults (ages 18–65) hospitalized following mTBI were assessed 4, 8, 12, 24, 36, and 48 months post-injury. Questionnaires and interviews evaluated fatigue, insomnia, cognitive complaints, anxiety, depression, headaches, dizziness, QoL, social participation, and healthcare service use for mTBI symptoms. The number of clinically significant symptoms (based on validated cutoff scores) was totaled for each participant; QoL, social participation, and healthcare services were examined in relation to the number of symptoms. At each timepoint, ≥45% of the participants experienced 3+ symptoms and ≥15% experienced 5+. The mean number of symptoms was similar over time (2.48–2.79; <i>p</i> = 0.32). The presence of 3+ symptoms was associated with poor QoL and social participation, including lower rates of return-to-work. Healthcare service use was not universal, even among individuals with 5+ symptoms. Clinicians should be alert to the long-term presence of multiple symptoms following hospitalization after mTBI, as these affect a significant proportion of individuals and are associated with poorer outcomes.
DOI: 10.6084/m9.figshare.30519259.v1
title: Symptom burden in the first four years following hospitalization after mild traumatic brain injury

description: 1) Describe clinically significant symptoms over 4 years following hospitalization after mild traumatic brain injury (mTBI); 2) examine quality of life (QoL), social participation, and healthcare service use in relation to symptom burden. Longitudinal cohort study in which 142 adults (ages 18–65) hospitalized following mTBI were assessed 4, 8, 12, 24, 36, and 48 months post-injury. Questionnaires and interviews evaluated fatigue, insomnia, cognitive complaints, anxiety, depression, headaches, dizziness, QoL, social participation, and healthcare service use for mTBI symptoms. The number of clinically significant symptoms (based on validated cutoff scores) was totaled for each participant; QoL, social participation, and healthcare services were examined in relation to the number of symptoms. At each timepoint, ≥45% of the participants experienced 3+ symptoms and ≥15% experienced 5+. The mean number of symptoms was similar over time (2.48–2.79; <i>p</i> = 0.32). The presence of 3+ symptoms was associated with poor QoL and social participation, including lower rates of return-to-work. Healthcare service use was not universal, even among individuals with 5+ symptoms. Clinicians should be alert to the long-term presence of multiple symptoms following hospitalization after mTBI, as these affect a significant proportion of individuals and are associated with poorer outcomes.
DOI: 10.5061/dryad.v9s4mw6tz
title: Camera traps Red deer exhibit spatial and temporal responses to hiking activity

description: Outdoor recreation has the potential to impact the spatial and temporal
 distribution of animals. We explore interactions between red deer (Cervus
 elaphus) and hikers along a popular hiking path in the Scottish Highlands.
 We placed camera traps in transects at different distances (25, 75 and 150
 metres) from the path to study whether distance from hiker activity
 influences the number of deer detected. We compared this with the
 detection of red deer in an additional, spatially isolated area (one km
 away from any other transects and the hiking path). We collected count
 data on hikers at the start of the path and explored hourly (red deer
 detection during the day), daily, diurnal (day vs night), and monthly
 spatial distributions of red deer. Using Generalized Linear Mixed Models
 with forward model selection, we found that the distribution of deer
 changed with the hiking activity. We found that fewer red deer were
 detected during busy hourly hiking periods. We found that during the day,
 more red deer were detected at 150m than at 25m. Moreover, during the day,
 red deer were detected at a greater rate in the isolated area than around
 the transects close to the path and more likely to be found close to the
 path at night. This suggests that avoidance of hikers by red deer, in this
 study area, takes place over distances greater than 75m and that red deer
 are displaced into less disturbed areas when the hiking path is busy. Our
 results suggest that the impact of hikers is short-term, as deer return to
 the disturbed areas during the night.
description: See in the corresponding paper, Marion et al 2021:
 "Data collection occurred over three periods: from the
 beginning of August to mid-November 2017, from mid-June to the end of
 October 2018 and from the end of May to end of October 2019, for a total
 of 7077 camera trap survey effort days. [...] The spatiotemporal
 distribution of red deer along the hiking path was quantified using
 transects of three camera traps at distances of 25, 75 and 150 m on one
 side of the hiking path (the transects were perpendicular to the path).
 [...] The transects were set up in three different
 points along the hiking path: East (TE), West (TW) and North (TN) in all
 three years (2017–2018–2019). A separate transect (in 2019 only) was set
 up in an isolated area of the landscape with no path nearby (the closest
 distance to the hiking path was 1 km). [...]"
 Moreover, the dataset also includes information about the hiking
 activity in the study area, per hour and per day. These data were
 collected using a laser counter at the entrance of the hiking
 path. We processed these data in the software
 R.
description: See the ReadMe file.
DOI: 10.5061/dryad.6djh9w10z
title: Data from: Sperm performance limits the reproduction of an invasive fish in novel salinities

description: Aim: The few fish species able to reproduce across wide osmotic ranges
 either plastically acclimate sperm performance to, or are locally adapted
 to, different salinities. The invasive round goby (Neogobius melanostomus)
 is spreading in Eurasia and the Americas, into both fresh and brackish
 water. We aim to understand if reproduction in different salinities is
 affected an ability to acclimate. Location: Brackish and freshwater
 systems of northern Europe and the Baltic Sea. Methods: We cross-exposed
 round gobies from freshwater and brackish origin to 0 and 16 practical
 salinity units (PSU), and the fish were given nest boxes to spawn. After
 four weeks, we measured their sperm performance in both 0 and 16 PSU,
 fertilization success of each clutch was measured through visual analysis
 of eggs. Clutches were split and allowed to develop in both 0 and 16 PSU
 salinity, and reproductive success (zygote development) was measured 20±1
 days later. Responses were analyzed using generalized mixed models.
 Results: After a month, the fish showed no plasticity in sperm performance
 to their acclimation salinity, regardless of their origin. Sperm velocity
 was highest in the salinity similar to the males’ origin. Significantly
 lower fertilization success was measured for individuals that reproduced
 outside their salinity of origin despite recurring spawning events in all
 treatment groups. Among fertilized eggs, zygote development was similar
 regardless of salinity treatment of either eggs or parents. Main
 Conclusions: Short-term acclimation to new salinities does not affect
 sperm performance in the round goby. Alternative hypotheses such as local
 adaption should be further investigated. Limits to the species’
 reproductive success, and therefore invasion processes, are likely
 dependent on environment-phenotype matches. Fish of brackish origin
 spawned successfully in freshwater, pointing to an increased risk of
 introducing populations of brackish origin into freshwater.
description: See associated Open Access paper for methodology.
description: Please see ReadMe file.
DOI: 10.5061/dryad.tqjq2bvz3
title: Whole genome resequencing of males and females of three Daphnia magna genotypes

description: Mechanisms of sex determination (SD) differ widely across the tree of
 life. In genotypic sex determination (GSD), genetic elements determine
 whether individuals are male or female, while in environmental sex
 determination (ESD), external cues control the sex of the offspring. In
 cyclical parthenogens, females produce mostly asexual daughters, but
 environmental stimuli such as crowding, temperature or photoperiod may
 cause them to produce sons. In aphids, sons are induced by ESD, even
 though GSD is present, with females carrying two X chromosomes and males
 only one (X0 SD system). In contrast, although ESD exists in Daphnia, the
 two sexes were suggested to be genetically identical, based on a 1972
 study on Daphnia magna (2n=20) that used three allozyme markers. This
 study cannot, however, rule out an X0 system, as all three markers may be
 located on autosomes. Motivated by the life cycle similarities of Daphnia
 and aphids, and the absence of karyotype information for Daphnia males, we
 tested for GSD (homomorphic sex chromosomes and X0) systems in D. magna
 using a whole genome approach by comparing males and females of three
 genotypes. Our results confirm the absence of haploid chromosomes or
 haploid genomic regions in D. magna males as well as the absence of
 sex-linked genomic regions and sex-specific single nucleotide
 polymorphisms. Within the limitations of the three populations studied
 here and the methods used, we suggest that our results make the
 possibility of genetic differences among sexes in the widely used Daphnia
 model system very unlikely.
DOI: 10.15468/dl.3pyyya
title: Occurrence Download

description: A dataset containing 3072 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Litoria littlejohni"
 ]
}

 The dataset includes 3072 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002785-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bvq83bk86
title: Response of vegetation to coffee pulp addition

description: Applying nutrient-rich agricultural by-products, such as fruit peels and
 pulp, to degraded land has been proposed as a strategy to overcome a
 number of barriers to tropical forest recovery. While such linkages
 between agroindustry and restoration represent win-win scenarios,
 practical applications remain largely unexplored. In this case study, we
 tested coffee pulp as an amendment to catalyze forest succession on
 post-agricultural land in southern Costa Rica. A 0.5-m-deep layer of
 coffee pulp was deposited across a 35 × 40-m area and an adjacent
 similar-sized control plot (no coffee pulp addition) was delineated. Over
 two years, we measured changes in soil nutrients, ground cover, understory
 vegetation, tree establishment, and canopy cover across both coffee pulp
 and control treatments. Our results show that soil carbon, nitrogen,
 phosphorous were significantly elevated in the coffee pulp compared to
 control treatment after two years. Coffee pulp addition significantly
 altered the ground cover characteristics, eliminating pasture grasses,
 facilitating establishment of herbaceous plants, and increasing the
 percent area covered by leaf litter. Early-successional trees and shrubs
 established quickly in coffee pulp treatment, reaching 30-fold greater
 mean basal area and 20-fold greater woody stem density (&gt;1-cm-dbh)
 compared to the control treatment. Structural metrics showed 4-fold
 greater mean canopy height in the coffee pulp compared to control
 treatment and &gt;80% canopy cover overall. Canopy height &gt;5 m
 was ~40% in the coffee pulp but was negligible in the control treatment.
 Our study highlights the significant potential for using agricultural
 waste, like coffee pulp, to jump start forest succession on degraded
 tropical lands and encourages further research to optimize linkages
 between agroindustry and restoration.
DOI: 10.15468/dl.ydh25w
title: Occurrence Download

description: A dataset containing 3280 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Balanidae, Serpulidae, Watersiporidae, Styelidae, Pennariidae, Mytilidae, Teredinidae, Ulvaceae, Caulerpaceae, Bougainvilliidae, Syllidae, Hydractiniidae, Varunidae, Bolinopsidae)",
 "Geometry POLYGON ((33.925781 30.297018, 30.849609 30.221102, 36.738281 17.978733, 42.539063 11.867351, 46.054688 9.362353000000001, 53.613281 12.297068, 64.6875 21.616579, 66.269531 25.403585, 65.302734 29.993002, 50.976563 32.398516, 33.925781 30.297018))"
 ]
}

 The dataset includes 3280 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002786-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1c59zw3tw
title: Code for: Comparison and interpretability of machine learning models to predict severity of chest injury

description: Objective: Trauma quality improvement programs and registries
 improve care and outcomes for injured patients. Designated trauma centers
 calculate injury scores using dedicated trauma registrars; however, many
 injuries arrive at non-trauma centers, leaving a substantial amount of
 data uncaptured. We propose automated methods to identify severe chest
 injury using machine learning (ML) and natural language processing (NLP)
 methods from the electronic health record (EHR) for quality reporting.
 Materials and Methods: A level I trauma center was queried for
 patients presenting after injury between 2014 and 2018. Prediction
 modeling was performed to classify severe chest injury using a reference
 dataset labeled by certified registrars. Clinical documents from trauma
 encounters were processed into concept unique identifiers for inputs to ML
 models: logistic regression with elastic net regularization (EN), extreme
 gradient boosted machines (XGB), and convolutional neural networks (CNN).
 The optimal model was identified by examining predictive and face validity
 metrics using global explanations. Results: Of 8,952 encounters,
 542 (6.1%) had a severe chest injury. CNN and EN had the highest
 discrimination, with an area under the receiver operating characteristic
 curve of 0.93 and calibration slopes between 0.88 and 0.97. CNN had better
 performance across risk thresholds with fewer discordant cases.
 Examination of global explanations demonstrated the CNN model had better
 face validity, with top features including “contusion of lung” and
 “hemopneumothorax.”  Discussion: The CNN model featured
 optimal discrimination, calibration, and clinically relevant features
 selected.  Conclusion: NLP and ML methods to populate
 trauma registries for quality analyses are feasible.
description: This is a script for R used for the analysis for our manuscript.
 The source data cannot be shared as it is electronic health record data
 that is protected under the Health Insurance Portability and
 Accountability Act.
description: This script could be used with cTAKES analysis on institutional
 data to generate similar results.
DOI: 10.5061/dryad.34tmpg4jp
title: An alternative and highly efficient synthetic protocol of Osimertinib

description: Osimertinib, a third generation potent and specific EGFR inhibitor is an
 important drug against many forms of cancer. It was synthesized by an
 improved and highly efficient protocol, revisiting the classical synthetic
 process and modifying parameters, such as solvents, temperature, reagents,
 and reaction time. A cost-effective, environmentally friendly methodology
 for the synthesis of Osimertinib was established, which gave shorter
 reaction times, saved labor by eliminating purification steps through
 column chromatography, and enhanced yields. Four of the seven steps in
 total, were proceeded quantitatively or almost quantitatively (~ 98%).
 This synthetic protocol provides a very high overall yield, up to 68%. In
 addition, the entire approach enables the preparation of Osimertinib
 analogues and could be extended in the synthesis of other structurally
 similar bioactive compounds.