cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c866t1g5n
title: Tooth morphology elucidates shark evolution across the end-Cretaceous mass extinction

description: Sharks (Selachimorpha) are iconic marine predators that have survived
 multiple mass extinctions over geologic time. Their prolific fossil record
 is represented mainly by isolated shed teeth, which provide the basis for
 reconstructing deep time diversity changes affecting different
 selachimorph clades. By contrast, corresponding shifts in shark ecology,
 as measured through morphological disparity, have received comparatively
 limited analytical attention. Here, we use a geometric morphometric
 approach to comprehensively examine tooth morphologies in multiple shark
 lineages traversing the catastrophic end-Cretaceous mass extinction — this
 event terminated the Mesozoic Era 66 million years ago. Our results show
 that selachimorphs maintained virtually static levels of dental disparity
 in most of their constituent clades across the Cretaceous–Paleogene
 interval. Nevertheless, selective extinctions did impact apex predator
 species characterized by triangular blade-like teeth. This is particularly
 evident among lamniforms, which included the dominant Cretaceous
 anacoracids. Conversely, other groups, such as carcharhiniforms and
 orectolobiforms, experienced disparity modifications, while
 heterodontiforms, hexanchiforms, squaliforms, squatiniforms, and
 †synechodontiforms were not overtly affected. Finally, while some
 lamniform lineages disappeared, others underwent post-extinction disparity
 increases, especially odontaspidids, which are typified by narrow-cusped
 teeth adapted for feeding on fishes. Notably, this increase coincides with
 the early Paleogene radiation of teleosts as a possible prey source, and
 the geographic relocation of disparity sampling ‘hotspots’, perhaps
 indicating a regionally disjunct extinction recovery. Ultimately, our
 study reveals a complex morphological response to the end-Cretaceous mass
 extinction and highlights an event that influenced the evolution of modern
 sharks.
DOI: 10.15468/dl.p6hgnw
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-88.18951 -12.62741,-54.27682 -12.62741,-54.27682 0.94958,-77.79863 2.21044,-89.53536 2.95779,-88.18951 -12.62741))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Samanea saman"
 ]
}

 The dataset includes 140 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002722-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ksn02v735
title: Association of the systemic host immune response with acute hyperglycemia in mechanically ventilated septic patients

description: Hyperglycemia during sepsis is associated with increased organ dysfunction
 and higher mortality. The role of the host immune response in development
 of hyperglycemia during sepsis remains unclear. We performed a
 cross-sectional analysis of critically ill adult septic patients requiring
 mechanical ventilation (n=153) to study the relationship between
 hyperglycemia and ten markers of the host immune response measured on the
 first day of ICU admission (baseline). We determined associations between
 each biomarker and: (1) glucose, insulin, and c-peptide levels at the time
 of biomarker collection by Pearson correlation; (2) average glucose and
 glycemic variability in the first two days of ICU admission by linear
 regression; and (3) occurrence of hyperglycemia (blood
 glucose&gt;180mg/dL) by logistic regression. Results were adjusted for
 age, pre-existing diabetes mellitus, severity of illness, and total
 insulin and glucocorticoid dose. Baseline plasma levels of ST2 and
 procalcitonin were positively associated with average blood glucose and
 glycemic variability in the first two days of ICU admission in unadjusted
 and adjusted analyses. Additionally, higher baseline ST2, IL-1ra,
 procalcitonin, and pentraxin-3 levels were associated with increased risk
 of hyperglycemia. Our results suggest associations between the host immune
 response and hyperglycemia in critically ill septic patients particularly
 implicating the interleukin-1 axis (IL-1ra), the interleukin-33 axis
 (ST2), and the host response to bacterial infections (procalcitonin,
 pentraxin-3).
DOI: 10.5061/dryad.mcvdnck06
title: Season of prescribed fire determines grassland restoration outcomes after fire exclusion and overgrazing

description: Fire exclusion and mismanaged grazing are globally important drivers of
 environmental change in mesic C4 grasslands and savannas. Although
 interest is growing in prescribed fire for grassland restoration, we have
 little long-term experimental evidence of the influence of burn season on
 the recovery of herbaceous plant communities, encroachment by trees and
 shrubs, and invasion by exotic grasses. We conducted a prescribed fire
 experiment (seven burns between 2001 and 2019) in historically
 fire-excluded and overgrazed grasslands of central Texas. Sites were
 assigned to one of four experimental treatments: summer burns (warm
 season, lightning season), fall burns (early cool season), winter burns
 (late cool season), or unburned (fire exclusion). To assess restoration
 outcomes of the experiment, in 2019, we identified old-growth grasslands
 to serve as reference sites. Herbaceous-layer plant communities in all
 experimental sites were compositionally and functionally distinct from
 old-growth grasslands, with little recovery of perennial C4 grasses and
 long-lived forbs. Unburned sites were characterized by several species of
 tree, shrub, and vine; summer sites were characterized by certain C3
 grasses and forbs; and fall and winter sites were intermediate in
 composition to the unburned and summer sites. Despite compositional
 differences, all treatments had comparable plot-level plant species
 richness (range 89–95 species/1000 m2). At the local-scale, summer sites
 (23 species/m2) and old-growth grasslands (20 species/m2) supported
 greater richness than unburned sites (15 species/m2), but did not differ
 significantly from fall or winter sites. Among fire treatments, summer and
 winter burns most consistently produced the vegetation structure of
 old-growth grasslands (e.g., mean woody canopy cover of 9%). But whereas
 winter burns promoted the invasive grass Bothriochloa
 ischaemum by maintaining areas with low canopy cover, summer
 burns simultaneously limited woody encroachment and
 controlled B. ischaemum invasion. Our results
 support a growing body of literature that shows that prescribed fire
 alone, without the introduction of plant propagules, cannot necessarily
 restore old-growth grassland community composition. Nonetheless, this
 long-term experiment demonstrates that prescribed burns implemented in the
 summer can benefit restoration by preventing woody encroachment while also
 controlling an invasive grass. We suggest that fire season deserves
 greater attention in grassland restoration planning and ecological
 research.
description: See Methods in:<br> Novak, E.N.,
 M. Bertelsen, D. Davis, D.M.
 Grobert, K.G. Lyons, J.P Martina, W.M. McCaw, M. O'Toole, and J.W.
 Veldman. 2021. Season of prescribed fire determines grassland resoration
 outcomes after fire exclusion and overgrazing. Ecosphere 12:
 e03730. 10.1002/ecs2.3730
DOI: 10.5061/dryad.z34tmpgc7
title: Temporal trends in case fatality, discharge destination, and admission to long-term care after acute stroke

description: Objective:  To determine contemporary trends in case fatality,
 discharge destination, and admission to long-term care after acute
 ischemic stroke and intracerebral hemorrhage (ICH) in a large,
 population-based cohort. Methods: We used linked administrative data to
 identify all emergency department visits and hospital admissions for
 first-ever ischemic stroke or ICH in Ontario, Canada from
 2003-2017.  We calculated crude and age/sex-standardized risk of
 death at 30 days and 1 year from stroke onset.  We stratified
 crude trends by stroke type, age, and sex and used the Kendall τ-b
 correlation coefficient to evaluate the significance of trends. 
 We determined trends in discharge home and to rehabilitation, and
 admission to long-term care at 1 year. We used Cox proportional hazard and
 logistic regression models to assess whether trends in outcomes persisted
 after adjustment for baseline factors, estimated stroke severity, and use
 of life-sustaining care.  Results: There were 163,574 people with
 acute ischemic stroke or ICH across the study period.  Between
 2003 and 2017, age/sex-standardized 30-day stroke case fatality decreased
 from 20.5% to 13.2% (7.3% absolute and 36% relative reduction) while that
 at 1 year decreased from 32.2 to 22.8 (9.3% absolute and 29% relative
 reduction).  Findings were consistent across age, sex, and stroke
 type, and after adjustment for comorbid conditions, stroke severity and
 use of life-sustaining care.  There was a reduction in long-term
 care admission after ischemic stroke, and an increase in discharge home or
 to rehabilitation for both stroke types. Conclusion:  We observed
 substantial reductions in acute stroke case fatality from 2003-2017 with a
 concurrent increase in discharge to home or rehabilitation and a decrease
 in long-term care admissions, suggesting continuous improvements in stroke
 systems of care.
DOI: 10.7280/d1t38t
title: Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior: S4 data, evidence for tuned inhibition in macaque superior colliculus

description: This dataset contains online spike-sorted single-unit recordings from one
 Rhesus macaque who performed a dot-motion discrimination task while neural
 data was recorded with a 16-channel v-probe from superior colliculus
 neurons. Full methods for data collection, including description of the
 stimuli and task, surgical details, ethics statement, funding information,
 and other relevant details, are available in the above-referenced
 manuscript, section S4 Text.
description: <b>OVERVIEW</b> Eight days of data
 were examined for this study: 1 160720
 2 160909 3 160929 4
 161017 5 161019 6 161207
 7 161208 8 161209
   “Online sorted” sub-directories contain
 online spike-sorted into single-unit files. Files for Channel $X and Unit
 $Y recorded on $DATE contain raster data from ‘Preferred’ and ‘Preferred +
 Non-preferred’ trials.  
 <b>DATA STRUCTURE</b> Each Matlab
 .mat file contains a single structure, raster_data, which is n trials
 long, with n being the number of trials the money completed that
 day.    The relevant fields
 are:  
 <b>TGTON</b> Timestamp for target
 stimulus turning on  
 <b>CUEON</b> Timestamp for
 response cue onset Has a value in it if the trial was
 not aborted  
 <b>TGinRF</b> If 1, indicates
 target is in the cell’s response field  
 <b>SCOFF</b> If &gt; 0,
 indicates the sure choice is off  
 <b>SCON</b> If &gt; 0,
 indicates the sure choice is on  
 <b>SCinRF</b> If 1, indicates the
 sure choice is in the cell’s response field  
 <b>spikes</b> Times at which a
 spike occurred for this unit  
 <b>E1_7, E1_8, E0_7, E0_8</b> E1_X
 indicates presentation of a stimulus containing positive evidence (dot
 motion in the cell’s preferred direction) E0_X 
 indicates presentation of a stimulus containing negative evidence (dot
 motion in the cell’s non-preferred direction) A value
 (not NaN) in E1_7 and E0_7 on the same trial indicates a 100-preferred,
 0-nonpreferred trial A value (not NaN) in E1_8 and E0_8
 on the same trial indicates a 50-preferred, 50-nonpreferred
 trial Other E1_X and E0_X evidence levels were not used
 for this study
DOI: 10.5061/dryad.qbzkh18gd
title: Thermal profiles reveal stark contrasts in properties of biological membranes from heart among Antarctic notothenioid fishes which vary in expression of hemoglobin and myoglobin

description: Antarctic notothenioids are noted for extreme stenothermy, yet
 underpinnings of their thermal limits are not fully understood. We
 hypothesized that properties of ventricular membranes could explain
 previously observed differences among notothenioids in temperature onset
 of cardiac arrhythmias and persistent asystole. Microsomes were prepared
 using ventricles from six species of notothenioids, including four species
 from the hemoglobin-less (Hb−) family Channichthyidae (icefishes), which
 also differentially express cardiac myoglobin (Mb), and two species from
 the (Hb+) Nototheniidae. We determined membrane fluidity and structural
 integrity by quantifying fluorescence depolarization of
 1,6-diphenyl-1,3,5-hexatriene (DPH) and leakage of
 5(6)-carboxyfluorescein, respectively, over a temperature range from
 ambient (0 °C) to 20 °C. Compositions of membrane
 phospholipids and cholesterol contents were also quantified. Membranes
 from all four species of icefishes exhibited greater fluidity than
 membranes from the red-blooded species N.
 coriiceps. Thermal sensitivity of fluidity did not vary among
 species. The greatest thermal sensitivity to leakage occurred between 0
 and 5 °C for all species, while membranes from the
 icefish, Chaenocephalus aceratus (Hb−/Mb−) displayed
 leakage that was nearly 1.5-fold greater than leakage in N.
 coriiceps (Hb+/Mb+). Contents of phosphatidylethanolamine (PE)
 were approximately 1.5-fold greater in icefishes than in red-blooded
 fishes, and phospholipids had a higher degree of unsaturation in icefishes
 than in Hb + notothenioids. Cholesterol contents were
 lowest in Champsocephalus gunnari (Hb−/Mb−) and highest
 in the two Hb+/Mb + species, G.
 gibberifrons and N. coriiceps. Our results reveal marked
 differences in membrane properties and indicate a breach in membrane
 fluidity and structural integrity at a lower temperature in icefishes than
 in red-blooded notothenioids.
description: Animals were captured near Palmer Station, Antarctica. Tissues
 were collected on site and flash frozen for further analysis. Membranes
 were prepared from ventricular tissue and analyzed by GC-MS to determine
 membrane phospholipid distribution (Lipids). Fluoresecence depolarization
 of native membranes was quantified over a temperature range to determine
 membrane fluidity (Fluidity). Integrity of liposomes generated from
 prepared membranes were quantified over a temperature range to determine
 membrane leakage by fluorescent spectrophotometry (Leak). Lipid and
 fluidity data are raw. Leakage data has been normalized to maximal
 liposomal leakage at each respective temperature point. 
description: In the Excel sheet there are both a Read Me and Abbreviations tab
 to provide instruction to understand the data.
DOI: 10.5061/dryad.ncjsxkst8
title: Congestion reduction via personalized incentives

description: The purpose of this research is to develop real-time algorithms to reduce
 traffic congestion and improve routing efficiency via offering
 personalized incentives to drivers. The incentives and alternative routes
 should be chosen smartly in order to maximize the probability of
 acceptance by drivers and to avoid the creation of new congestion in other
 areas of the network. To this end, we propose to exploit the
 wide-accessibility of smart communication devices and develop a real-time
 look-ahead incentive offering mechanism using individuals’ routing and
 aggregate traffic information. The proposed approach relies on historical
 data and state-of-the-art traffic prediction methodologies to continually
 predict congestion and traffic flow of the network. Using this prediction
 and based on individual preferences, the central controller offers
 personalized incentives to drivers with the goal of reducing the
 probability of congestion. The decisions about incentives are made via
 solving a series of carefully designed large-scale stochastic optimization
 problems. The performance of the proposed algorithms are evaluated using
 data from the Los Angeles area. Finally, we evaluate the performance of
 our method using data from the Los Angeles area. The Los Angeles region is
 ideally suited for being the validation area since there are a number of
 dedicated carpool lanes in the region and furthermore, there are portions
 of the freeway network where congestion pricing is employed with the added
 feature that ridesharing vehicles can travel on these lanes free of charge
 (e.g., I-110). Additionally, researchers at USC have developed the
 Archived Data Management System (ADMS) that collects, archives, and
 integrates a variety of transportation datasets from Los Angeles, Orange,
 San Bernardino, Riverside, and Ventura Counties.
description: The data is from the
 traffic data of the Los Angeles area. Researchers at USC have developed
 the Archived Data Management System (ADMS) that collects, archives, and
 integrates a variety of transportation datasets from Los Angeles, Orange,
 San Bernardino, Riverside, and Ventura Counties. ADMS includes access to
 real-time traffic datasets from i) 9500 highway and arterial loop
 detectors providing data approximately every 1 minute, and ii) 2500 bus
 and train GPS location (AVL) data operating throughout Los Angeles
 County. First, we
 export our data from the ADMS systems. Next, we preprocess the data based
 on our criteria such as the type of sensors, the time interval of data,
 and region. Also, we extract the graph of the network on Networkx.
 Finally, we use the data to do OD estimation and solve our optimization
 model. More
 details are provided in the readme.txt file.
description: Details are provided in the readme.txt file. We can share a
 sample of our run upon a reasonable request.
DOI: 10.5061/dryad.612jm642m
title: The impact of mistranslation on phenotypic variability and fitness

description: Phenotypic variation is widespread in natural populations, and can
 significantly alter their ecology and evolution. Phenotypic variation
 often reflects underlying genetic variation, but also manifests via
 non-heritable mechanisms. For instance, translation errors result in about
 10% of cellular proteins carrying altered sequences. Thus, proteome
 diversification arising from translation errors can potentially generate
 phenotypic variability, in turn increasing variability in the fate of
 cells or of populations. However, the link between proteome diversity and
 phenotypic variability remains unverified. We manipulated mistranslation
 levels in Escherichia coli, and measured phenotypic variability between
 single cells (individual level variation), as well as replicate
 populations (population level variation). Monitoring growth and survival,
 we find that mistranslation indeed increases variation across E. coli
 cells, but does not consistently increase variability in growth parameters
 across replicate populations. Interestingly, although any deviation from
 the wild type (WT) level of mistranslation reduces fitness in an optimal
 environment, the increased variation is associated with a survival benefit
 under stress. Hence, we suggest that mistranslation-induced phenotypic
 variation can impact growth and survival and has the potential to alter
 evolutionary trajectories.
description: All method details are given in the manuscript.
DOI: 10.5061/dryad.0k6djh9zq
title: Data from: Urbanization affects oak–pathogen interactions across spatial scales

description: The world is rapidly urbanizing, thereby transforming natural landscapes
 and changing the abundance and distribution of organisms. However,
 insights into the effects of urbanization on species interactions, and
 plant-pathogen interactions in particular, are lacking. We investigated
 the effects of urbanization on powdery mildew infection on Quercus robur
 at continental and within-city scales. At the continental scale, we
 compared infection levels between urban and rural areas of different-sized
 cities in Europe, and investigated whether plant traits, climatic
 variables and CO2 emissions mediated the effect of urbanization on
 infection levels. Within one large city (Stockholm, Sweden), we further
 explored whether local habitat features and spatial connectivity
 influenced infection levels during multiple years. At the continental
 scale, infection severity was consistently higher on trees in urban than
 rural areas, with some indication that temperature mediated this effect.
 Within Stockholm city, temperature had no effect, while local accumulation
 of leaf litter negatively affected powdery mildew incidence in one out of
 three years, and more connected trees had lower infection levels. This
 study is the first to describe the effects of urbanization on
 plant-pathogen interactions both within and among cities, and to uncover
 the potential mechanisms behind the observed patterns at each scale.
description: Dataset contains 2 field collections: Oak
 leaves collected in urban and rural areas at the continental scale (5
 trees per area), including small, medium and large cities in Spain,
 France, the Netherlands, Denmark, Sweden and Finland.
 Oak leaves collected within one large city (Stockholm, Sweden),
 during 3 years (2017-2019).  All oak leaves were scored
 for powdery mildew infection.
DOI: 10.5061/dryad.sf7m0cg56
title: DNA microarray of long-lived neutrophils versus control

description: The concept of plasticity of neutrophils is highlighted by studies showing
 their ability to transdifferentiate into antigen-presenting cells. In this
 regard, transdifferentiated neutrophils were found at inflammatory sites
 of autoimmune arthritis (AIA). Exposure of neutrophils to inflammatory
 stimuli prolongs their survival, thereby favoring the acquisition of
 pathophysiologically relevant phenotypes and functions. By using
 microarrays, qRT-PCR, and ELISAs, we showed that long-lived (LL)
 neutrophils obtained after 48 h of culture in the presence of GM-CSF, TNF,
 and IL-4 differentially expressed genes related to apoptosis, MHC class
 II, immune response, and inflammation. The expression of anti-inflammatory
 genes mainly of peptidase inhibitor families is upregulated in LL
 neutrophils. Among these, the PI3 gene encoding elafin was the most highly
 expressed. The de novo production of elafin by LL neutrophils depended on
 a synergism between GM-CSF and TNF via the activation and cooperativity of
 CCAAT/enhancer-binding protein ß and NF-κB pathways, respectively. Elafin
 concentrations were higher in synovial fluids (SF) of patients with AIA
 than in SF of osteoarthritis. SF neutrophils produced more elafin than
 blood counterparts. These results are discussed with respect to
 implications of neutrophils in chronic inflammation and the potential
 influence of elafin in AIA.
description: DNA microarray analyses were carried out with Affymetrix Human
 Transcriptome Array 2.0 (HTA 2.0) according to the Affymetrix standard
 protocol. To validate the results of our microarray
 data, the expression of selected genes in long-lived neutrophils were
 analyzed by qRT-PCR according to MIAME guidelines
description: This analysis allowed generating a gene list with the upregulated
 and downregulated genes in LL neutrophils with a fold change of at least
 2, with a <i>p </i>value &lt; 0,01 and an FDR value
 &lt; 0,1.