cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq4d
title: Data from: Host developmental stage effects on parasite resistance and tolerance

description: Hosts can defend themselves against parasites by either preventing or
 limiting infections (resistance), or limiting parasite-induced damage
 (tolerance). However, it remains underexplored how these defense types
 vary over host development with shifting patterns of resource allocation
 priorities. Here, we studied the role of developmental stage on resistance
 and tolerance in Atlantic salmon (Salmo salar). This anadromous fish has
 distinct life stages related to living in fresh and sea water. We
 experimentally exposed one-year old salmon, either at the freshwater stage
 or at the stage transitioning to the marine phase, to the trematode
 Diplostomum pseudospathaceum. Using 56 pedigreed families and multivariate
 animal models, we show that developmental transition is associated with
 reduced resistance, but does not affect tolerance. Furthermore, by
 comparing tolerance slopes (host fitness against parasite load) based on
 additive genetic effects among infected and unexposed control relatives,
 we observed that the slopes can be largely independent of the infection,
 that is they may not reflect tolerance. Together, our results suggest that
 the relative importance of different defense types may vary with host
 development and emphasize the importance of including control treatments
 for more confident interpretations of tolerance estimates.
DOI: 10.5061/dryad.x95x69pkb
title: An arachnid’s guide to being an ant: Morphological and behavioural mimicry in ant-mimicking spiders

description: Batesian mimicry imposes several challenges to mimics and evokes
 adaptations in multiple sensory modalities. Myrmecomorphy, morphological
 and behavioral resemblance to ants, is seen in over 2000 arthropod
 species. Ant-like resemblance is observed in at least 13 spider families
 despite spiders having a distinct body plan compared to ants. Quantifying
 the extent to which spiders’ shape, size, and behavior resemble model ants
 will allow us to comprehend the evolutionary pressures that have
 facilitated myrmecomorphy. Myrmaplata plataleoides are thought to closely
 resemble weaver ants, Oecophylla smaragdina. In this study, we quantify
 the speed of movement of model, mimic, and non-mimetic jumping spiders. We
 use traditional and geometric morphometrics to quantify traits such as
 foreleg and hindleg size and body shape between the model ant, mimic, and
 non-mimics. Our results suggest that while the mimics closely resemble the
 model ants in speed of movement, they occupy an intermediate morphological
 space compared to the model ants and non-mimics. We suggest that
 ant-mimicking spiders are better at mimicking ants’ locomotory movement
 than morphology and overall body shape. Our study provides a framework to
 understand the multimodal nature of mimicry and helps discern the relative
 contributions of such traits that drive mimetic accuracy in ant-mimicking
 spiders.
DOI: 10.5061/dryad.59zw3r28m
title: Dataset of Phylogenomics of the olive family Oleaceae

description: Deep-branching phylogenetic relationships are often difficult to resolve
 because phylogenetic signals are obscured by the long history and
 complexity of evolutionary processes, such as ancient
 introgression/hybridization, polyploidization and incomplete lineage
 sorting. Phylogenomics has been effective in providing information for
 resolving both deep- and shallow-scale relationships across all branches
 of the tree of life. Concatenated and coalescence trees based on the
 plastid genome, nuclear SNPs and multiple nuclear genes suggest events of
 incomplete lineage sorting and/or ancient introgression during the
 diversification of Oleaceae. Additionally, there was extreme heterogeneity
 in the plastid substitution rates across the tribes. Furthermore, our
 results supported that post-speciation introgression/hybridization, rather
 than ILS, is the main factor for phylogenetic discordance among the five
 tribes. The tribe Oleeae is especially prone to ancient hybridization and
 polyploidy, and its most likely parentages are the ancestral lineage of
 Jasmineae or its sister group, which is a “ghost lineage”, and
 Forsythieae. However, ILS and ancient introgression are mainly responsible
 for the phylogenetic discordance among the four subtribes of tribe Oleeae.
 This study showcases that using diverse phylogenomic methods can
 facilitate untangling long and complex evolutionary processes of ancient
 introgression, paleopolyploidization and ILS.
DOI: 10.5061/dryad.9s4mw6mhs
title: Effects of medication intake on the risk of haemorrhage in patients with sporadic cerebral cavernous malformations

description: Objective: Recurrent intracerebral hemorrhage (ICH) poses a high risk for
 patients with cerebral cavernous malformations (CCMs). This study aimed to
 assess the influence of medication intake on hemorrhage risk in sporadic
 CCMs. Results: A total of 1116 patients with CCM were included. Logistic
 regression analysis showed a significant correlation (OR: 0.520, 95% CI:
 0.284–0.951, p = 0.034) between antithrombotic therapy and ICH as a mode
 of presentation. Cox regression analysis revealed no significant
 correlation between medication intake and occurrence of (re-)hemorrhage
 (hazard ratios: betablockers 1.270 [95% CI: 0.703–2.293], statins 0.543
 [95% CI: 0.194–1.526], antithrombotic therapy 0.507 [95% CI: 0.182–1.410],
 and thyroid hormones 0.834 [95% CI: 0.378–1.839]). Conclusion: In this
 observational study, antithrombotic treatment was associated with the
 tendency to a lower rate of ICH as a mode of presentation n a large cohort
 of patients with sporadic CCM. Intake of beta blockers, statins, and
 thyroid hormones had no eect on hemorrhage as a mode of presentation.
 During the 5-year follow-up period, none of the drugs aected the further
 risk Q7 of (re-)hemorrhage.
description: From a database of 1,409 consecutive patients with CCM (2003–
 2021), subjects with sporadic CCMs and complete magnetic resonance imaging
 data were included. We evaluated the presence of ICH as a mode of
 presentation, the occurrence of ICH during follow-up, and medication
 intake, including beta blockers, statins, antithrombotic therapy, and
 thyroid hormones. The impact of medication intake on ICH at presentation
 was calculated using univariate and multivariate logistic regression with
 age and sex adjustment. The longitudinal cumulative 5-year risk for
 (re-)hemorrhage was analyzed using the Kaplan–Meier curves and the Cox
 regression analysis.
DOI: 10.5061/dryad.d51c5b04q
title: Variation in the location and timing of experimental severing demonstrates that the persistent rhizome serves multiple functions in a clonal forest understory herb

description: 1. In clonal plants, persistent rhizomes can serve multiple purposes,
 including resource storage, modulation of heterogenous resource
 distributions, maintenance of bud banks and promotion of recovery from
 disturbance. Clonal plants are commonly long-lived and, in temperate
 zones, often exhibit organ preformation. Thus, investigations of how the
 timing of disturbance to the rhizome affects plant performance must occur
 over multiple growing seasons, but these types of studies are rare. 2. We
 conducted a field experiment to examine how the persistent rhizome
 supports the existing shoot, new ramet production, and recovery from
 damage using mayapple (Podophyllum peltatum; Berberidaceae), a common
 herbaceous perennial of low-light forest understories in Eastern North
 America. Mayapple maintains a long-lived rhizome and exhibits a
 developmentally-programmed seasonal pattern of resource transport and new
 ramet initiation. We varied both the position and timing of rhizome
 severing in rhizome systems with terminal sexual or vegetative shoots, and
 tracked plants for two years following severing. 3. The location and
 timing of severing affected both plant persistence (production of new
 shoots) and performance (leaf area), with effects differing for new shoots
 at the front vs. the back of the rhizome system. Across years, severing
 location and past years’ shoot size influenced plant persistence and
 performance, while the effect of timing of severing diminished; initial
 sexual status had little effect on rhizome system response that was not
 accounted for by initial leaf area. Severing generally led to the
 establishment of two independent rhizome systems. Relative to
 unmanipulated control systems, these two systems had more total leaf area,
 but less average leaf area per system. 4. Synthesis. Our results point to
 the rhizome as a resource integrator that affects plant responses to
 disturbance immediately following damage and in subsequent growing
 seasons. Rhizome bud age and/or subtending rhizome size, and developmental
 program influence responses to disturbance. While the effects of
 experimental disturbance on plant performance decreased two years after
 disturbance, further long-term investigation is needed to fully understand
 the demographic consequences of damage to persistent rhizomes. 
description: These data were collected in a field study of mayapple conducted
 in Indiana. We provide all data that were collected, including individuals
 where there were missing values that we excluded from our analyses. The
 data file is the raw data
description: We have included both the data file and an additional ReadMe file
 that contains descriptions of all of the columns present in the dataset,
 including the units and meanings of NA values for each othem.
DOI: 10.5061/dryad.wwpzgmskr
title: Risks for overwintering eggs of the dragonfly Sympetrum vicinum in aquatic and terrestrial environments

description: Risk-spreading behaviour is often exhibited by animals as a response to
 unpredictably variable environments. Using field and laboratory studies,
 we tested the hypothesis that Sympetrum vicinum dragonflies spread the
 risks of winter environments by laying eggs across a terrestrial–aquatic
 gradient. Sympetrum vicinum eggs that overwintered in terrestrial and
 benthic-limnetic habitats had significantly higher hatching success
 compared with eggs that overwintered in littoral sites. Low success may
 have been caused by hypoxia due to excess sediment in the littoral samples
 in the lab. While hypoxia experienced under winter conditions (4°C) had no
 negative effect on hatching success, hatching in hypoxic and anoxic water
 significantly decreased hatching success. Opportunistic egg predation by a
 winter-active caddisfly significantly decreased egg hatching success.
 Because S. vicinum eggs have a relatively low supercooling point (−
 26.25°C), freezing may not be a significant source of mortality in
 terrestrial or aquatic sites. By ovipositing in both terrestrial and
 aquatic environments, female dragonflies may be balancing the
 unpredictable risks of both the failure to inundate the eggs and egg
 predation. Our research highlights the potential for biotic interactions
 during winter to shape the behaviour and life-history of aquatic
 invertebrates.
description: See paper for description of data collection methods and
 analysis. Paper is available fully formated through the publisher or open
 access (unformatted) through the University of Toronto's
 T-Space. 
description: Notes explaing data are available in a README_.txt document. The
 same notes explaining data are available on each tab of the excel file.
 One extra tab of data is included here but was not used in our paper. Data
 uploaded here is raw unless otherwise indicated.
DOI: 10.25338/b8r04t
title: Transit payment preferences of unbanked passengers

description: Throughout California, using public transit often requires moving between
 operators with different payment mediums and scheduling specifications.
 While some metropolitan regions offer integrated payment options they
 don’t work for all travelers and still require a transit agency issued
 card and/or account. At the same time, when connecting to services not
 within the integrated portion, travelers must have a second, third or even
 additional means of payment for each transit system use. The California
 Integrated Travel Project aims to allow transit users to pay for transit
 throughout the state of California with whichever card based, or
 electronic means of payment they prefer. However, for some passengers some
 of these options are not available. In this study we explore how
 these un and underbanked passengers will be able to access open payment
 systems. We collected intercept survey data at transit stops in the
 Davis-Sacramento-Woodland area of California to assess the potential for
 un and underbanked passengers to use digital payment tools, such as tap
 cards, and smartphone-based apps. We find that these riders typically pay
 with cash now but have some interest in payments with prepaid debit cards,
 and other means of payments. Accessibility for un and underbanked
 passengers is a known priority of Cal-ITP, and as the state takes the next
 steps towards open payments systems throughout California’s transit
 systems, the outcomes of this study will help ensure the needs of these
 passengers are met.
description: This dataset was collected through an intercept survey at public
 transit stops in the Sacramento area of California.
 Incomplete cases have been removed, identifying information has
 been removed. Other processing is limited to recoding variables based on
 participant responses, and creating binary variables from those that
 allowed "check all that appy" responses.
description: There are missing values due to item non-response for some
 variables. These are primarily coded as NA for use in the data processing
 and analysis environment R. Many variables have been
 converted to factors, applying an order to the values, that might not
 otherwise have them or that would not be represented by text descriptions
 of the levels. This includes things like "no", and
 "yes", or more complex sets of valued text data such as
 "high school", "associates", "bachelors",
 "masters", "graduate degree".
DOI: 10.5061/dryad.f7m0cfxxj
title: Calis-p 2.1 a software for protein-based stable isotope fingerprinting (Protein-SIF) and probing (Protein-SIP)

description: Calis-p (The CALgary approach to ISotopes in proteomics) is a java
 application to estimate isotopic composition (e.g. delta13C or delta15N)
 of individual species in a microbial community from a proteomic dataset.
 Calis-p 2.1 handles both natural isotope abundances and data from
 labelling experiments such as stable isotope probing (SIP). It requires a
 mzIdent (or target spectrum match) and mzML files as the input and
 requires about 1 min per mzML file with 10 threads and needs &lt;10 Gb
 of RAM. It has been tested with data from various nano liquid
 chromatography/Orbitrap platforms. For successful SIP, it is extremely
 sensitive, but requires the 13C fraction to remain below 10%. Detailed
 documentation can be found in the Wiki
 on https://sourceforge.net/p/calis-p/wiki/Home/ and the research
 article.
description: The files are either tables in tab-delimited or comma-delimited
 format and can be opened with a text editor or they are in Microsoft Excel
 format and can be opened with Excel or Open Office.
DOI: 10.5061/dryad.mkkwh711p
title: Berberine protects against sepsis-related acute lung injury in rats

description: Aim: To assess the therapeutic effects of berberine in experimentally
 induced lung sepsis.  Examining its effects on selected
 cytokines, gene and protein expression and the histopathological findings.
 Results: Berberine significantly reduced the wet/dry lung ratio, the BALF
 protein, cell, and neutrophils percentage & the BALF cytokines
 levels. In addition, pretreatment with berberine decreases the
 myeloperoxidase and MDA levels and decreases gene expression of NFKB, MCP
 -1 and the ICAM - 1 by RT - PCR analysis. Thus, suggesting an antioxidant
 and anti-inflammatory mode of the action. Western blot analysis revealed
 increased PPAR – Υ expression in the berberine pretreated group compared
 to the CLP group. Histopathological examination revealed improved
 histopathological parameters, in the berberine pretreated group, compared
 to the CLP group. Conclusion: Berberine improves the outcome in sepsis via
 antioxidant and anti-inflammatory effects, modulation of cytokine levels,
 upregulation of PPAR - Υ protein expression, and histopathological
 amelioration.
description: # Berberine protects against sepsis-related acute lung injury in rats
 Give a brief summary of
 dataset contents, contextualized in experimental procedures and results.
 ## Description of the data and file structure One data file
 **statistics.docx** with tables and figures.
DOI: 10.5281/zenodo.17980227
title: Limits of the Arrhenius–Kramers Model Revealed by Studies of Friction-Generating Sliding Proteins

description: The uploaded archive contains data that support the findings of the "Limits of the Arrhenius–Kramers Model Revealed by Studies of Friction-Generating Sliding Proteins" article. The contents of this archive are organized as follows:



README.txt — contains description of the archive files.

figues/data/ — folder with data presented in figures.

results/ — folder with analysis and computation results.

simulations/ — folder with raw output from Brownian simulations.
DOI: 10.5281/zenodo.17980228
title: Limits of the Arrhenius–Kramers Model Revealed by Studies of Friction-Generating Sliding Proteins

description: The uploaded archive contains data that support the findings of the "Limits of the Arrhenius–Kramers Model Revealed by Studies of Friction-Generating Sliding Proteins" article. The contents of this archive are organized as follows:



README.txt — contains description of the archive files.

figues/data/ — folder with data presented in figures.

results/ — folder with analysis and computation results.

simulations/ — folder with raw output from Brownian simulations.
DOI: 10.5061/dryad.vq83bk3td
title: Data and code from: A review of cisco form diversity and lake depth

description: Cisco form diversity overlaps with glacial lake coverage in North America.
 A recent hypothesis proposes that secondary contact among refugial cisco
 lineages during retreat of the Laurentide Ice Sheet was the basis for the
 geography of cisco diversity in North American lakes. Glacial lake
 coverage in North America is also a map of Mysis diluviana distribution, a
 glacial relic species found in lakes including the Laurentian Great Lakes.
 The presence of Mysis increases isotopic niche size of cisco, a necessary
 condition for Mysis to be a key element of cisco clade diversification. We
 reviewed literature on cisco forms in North American lakes to determine if
 cisco diversity is related to an ecological opportunity gradient, maximum
 lake depth with the presence of Mysis. Cisco form diversity increases with
 lake maximum depth in North America in the presence of Mysis with deeper
 lakes increasingly likely to hold multiple forms. Lakes without Mysis had
 only one cisco form and were shallower in general. We hypothesize that
 Mysis is the basis for the relationship between lake depth and cisco form
 diversity because of the complex behavior and distribution of Mysis that
 stems from increasing lake depth. We propose the geography of cisco
 diversity in North America results from within lake predator–prey
 processes as a function of lake depth under the Mysis hypothesis vs.
 secondary contact priming genetic diversity. The two hypotheses are not
 mutually exclusive. Analysis of a lake set covering both cisco and Mysis
 ranges points to more lakes having multiple cisco forms.
description: The data sources and methods of collection in this Dryad
 submission are described in detail in the associated manuscript and readme
 file.
description: Missing values are identified with n/a's in the associated
 datasets.
DOI: 10.5061/dryad.rbnzs7hcf
title: Climate warming causes photobiont degradation and C starvation in a boreal climate sentinel lichen

description: The long-term potential for acclimation by lichens to warming climates is
 poorly known, despite their prominent roles in forested ecosystems.
 Although often considered "extremophiles", lichens may not
 readily acclimate to novel climates well beyond historical norms. In a
 previous study (Smith et al. 2018), Evernia mesomorpha transplants in a
 whole-ecosystem climate change experiment showed drastic mass loss after
 one year of warming. We examined the causes of this warming-induced mass
 loss by measuring physiological, functional, and reproductive attributes
 of lichen transplants. Severe loss of mass and physiological function
 occurred above +2ºC of warming. Loss of algal symbionts (“bleaching”) and
 turnover in algal community compositions increased with temperature and
 were the clearest impacts of experimental warming. Enhanced CO 2 had no
 significant physiological or symbiont composition effects. The functional
 loss of algal photobionts led to significant loss of mass and specific
 thallus mass (STM), which in turn reduced water-holding capacity (WHC).
 Although algal genotypes remained detectable in thalli exposed to higher
 temperatures, within-thallus photobiont communities shifted in composition
 towards greater diversity. Analogous to the effects of climate change on
 corals, the balance of symbiont carbon metabolism in lichens is central to
 their resilience to changing conditions.