cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q573n5tn5
title: Data and Code for: Resistance is futile: Weaker selection for resistance by abundant parasites increases prevalence and depresses host density

description: We model host evolution of costly resistance to infection and its
 dependence on environmental factors, such as nutrients. We find that
 higher nutrients can increase infection prevalence AND select for lower
 resistance. In turn, the model predicts that lower resistance drives
 infection prevalence even higher while depressing host density. The
 attached code performs the model analysis, produces the published figures,
 and conducts statistical analysis on the data (described below). We
 conducted a mesocosm experiment with mixtures of zooplankton host (Daphnia
 dentifera) genotypes, algal resources (Ankistrodesmus falcatus), and
 fungal parasites (Metschnikowia bicuspidata). Mesocosm populations were
 supplied with low or high nutrients (5 or 50 ug/L phosphorus and 100 or
 1000 ug/L nitrogen). We measured densities of hosts along with age class
 (juvenile or adult), sex, infections status, and egg number and
 chlorophyll densities; these data are a subset of data published
 previously Walsman et al. Functional Ecology
 (https://doi.org/10.1111/1365-2435.14030; data at
 https://doi.org/10.5061/dryad.mw6m905zg). For the first time, we also
 report genotype frequencies for the mixed genotype treatments.
 Importantly, we found that high nutrients increased infection prevalence
 as well as selecting for the host genotype less resistant to infection;
 the resulting host evolution increased infection prevalence further and
 depressed host density. These data and code may be reused with citation of
 the corresponding publication ("‘Resistance is futile’: Weaker
 selection for resistance by abundant parasites increases prevalence and
 depresses host density" in The American Naturalist).
DOI: 10.5061/dryad.v6wwpzh0c
title: Filtered phytoplankton movement data

description: A prerequisite for the survival and reproduction of organisms is to
 successfully navigate thermal environmental conditions that unfold over
 time and space. While effective movement behaviour has been highlighted as
 a key mechanism by which organisms and populations may persist amidst the
 backdrop of directional environmental warming, it remains unclear how
 behavioural plasticity may mediate such effects, particularly across
 timescales that span multiple generations. Here, we examine the capacity
 for transgenerational plasticity to alter the movement behaviour of the
 motile green algae Chlamydomonas reinhardtii in response to changes in
 thermal conditions. We first acclimated C. reinhardtii populations to
 thermal environments near (25°C), below (12.5°C), or above (37.5°C) the
 temperature range that maximizes population growth rates. Subsequently, we
 assayed the micro-spatial scale movement behaviour of these populations in
 thermally homogeneous environments across a period of two weeks in each
 respective environment, with the goal of evaluating the influence of
 thermal history on movement behaviour in a novel thermal environment.
 These results indicate that thermal history can mediate the movement
 patterns of C. reinhardtii individuals for up to ten generations and that
 the trajectory by which phenotypes converge on their acclimated values can
 be highly non-linear.  Subsequently, we demonstrated – using a
 dispersal assay in spatially variable environments – that thermal
 acclimation history can additionally alter movement patterns at
 ecologically relevant scales. Collectively these findings indicate the
 possibility for transgenerational plasticity to modify behaviour across
 extended timescales and converge on acclimated states via non-linear
 trajectories. Understanding the efficacy of behaviour for navigating novel
 thermal environments, such as environments anticipated amidst
 environmental warming, may thus require considering past as well as
 present environmental conditions.
DOI: 10.5061/dryad.z8w9ghxg9
title: Experiment results and codes for: A novel systems solution for accurate colorimetric measurement through smartphone-based augmented reality

description: This dataset includes the images, codes and Excel files of the results of
 2 synthetic and 2 real experiments in the Section "Experiment".
 This dataset also includes anonymous pH human reading records. In addtion,
 two new experiments for comments from reviewers are added.
description: Taking pictures with iPhone SE 2nd generation and iPhone XSMAX.
 Processing with Python script.
DOI: 10.6078/d1s72k
title: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat

description: The adaptor protein (AP) complexes not only form the inner layer of
 clathrin coats but also have clathrin-independent roles in membrane
 traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester
 major histocompatibility complex class I (MHC-I), evading immune
 detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated
 membranes without clathrin and determined its structure. The coat
 assembles via Arf1 dimer interfaces. AP-1–positive tubules are enriched in
 cells upon clathrin knockdown. Nef localizes preferentially to AP-1
 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact
 residues are conserved across Arf isoforms and the Arf-dependent AP
 complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with
 Arf1 into tubular coats without clathrin or other scaffolding factors. The
 AP-1:Arf1 coat defines the structural basis of a broader class of
 tubulovesicular membrane coats as an intermediate in clathrin vesicle
 formation from internal membranes and as an MHC-I sequestration mechanism
 in HIV-1 infection.
description: Live-cell imaging was conducted
 on a Zeiss LSM900 with Airyscan 2.0 detection in SR-2Y mode, using the Zen
 Blue software. All imaging was conducted in an incubation chamber at 37°C
 and 5% CO<sub>2</sub>. 10um Z-stack movies with 140nm
 intervals were acquired for all analyzed cells. During multi-channel
 imaging, all channels were frame-sequentially acquired before moving to
 the next Z-slice to minimize crosstalk and time offset. Images were batch
 processed by ZEN Blue software for Airyscan reconstruction using filter
 strength setting 5 and 3D processing. To
 test for colocalization between Nef and AP1 signal, both channels from the
 same slice in a Z-stack was analyzed. Both channels were first background
 corrected using the 15 pixel median filtering as described above, and
 thresholded using the “Auto Threshold” Otsu and Li thresholds for the AP1
 and Nef channels respectively in imageJ. Particles less than 0.10 μm<sup>2 </sup>were
 filtered out. AP1 signal was then classified as “spheroid” if particles
 had circularity between 0.75 – 1.00 or as “tubule” if particles had
 circularity between 0 – 0.75 according to the “Analyze Particles”
 function. Using the thresholded images of AP1 and Nef, the Manders
 correlation coefficient was calculated for each type of AP1 structure
 using the JACoP plugin in imageJ. Specifically, the fraction of AP1 pixels
 overlapping with Nef pixels was reported for colocalization. To confirm
 that colocalization of AP1 and Nef was not random, the Van Steensel CCF
 function was generated using JACoP as well.
description: ImageJ is required to open the data files.
DOI: 10.5061/dryad.f1vhhmh15
title: Molecular dynamics simulations of the tripartite interface (Syt1_C2B—SNARE—Cpx Complex)

description: Synaptic transmission is mediated by an orchestra of presynaptic
 proteins that precisely control and trigger fusion between synaptic
 vesicles and the neuron terminal at the active zone upon an action
 potential. Critical to this process are the neuronal SNAREs (Soluble
 N-ethylmaleimide sensitive factor Attachment protein REceptor), the
 Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other
 factors. Here we present the data for molecular dynamics simulations of
 the tripartite interface bewteen these proteins. 
description: See README.md file.
description: See README.md file.
DOI: 10.5061/dryad.2v6wwpzs9
title: Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient

description: Aim: As anthropogenic stressors on the biosphere intensify, understanding
 how communities respond to disturbances is critical. Biodiversity is often
 thought to promote the stability of communities over time and enhance
 ecosystem functioning. However, results have been inconsistent, and the
 multifaceted linkages among diversity, stability, and functioning under
 acute disturbances remain poorly understood. We experimentally tested the
 responses of marine fish communities to disturbance (i.e., acute habitat
 loss) across a diversity gradient spanning 35º degrees of latitude in the
 western Atlantic Ocean to assess the diversity-stability relationship and
 the interplay between diversity, stability, and fish biomass recovery (as
 a proxy for function) in marine fish communities. Location: Western
 Atlantic Ocean (Maine, Massachusetts, North Carolina, Florida [USA],
 Belize, and Panama). Time period: 2016 – 2017 Major taxa studied: Small,
 bottom-dwelling (‘cryptobenthic’) fishes Results: Diversity showed a
 negative effect on community stability at both the regional (across docks)
 and local (within docks) scales. Similarly, local diversity was negatively
 correlated with ecosystem function. These effects are exacerbated by the
 habitat loss imposed via our experimental treatment. Main conclusions: Our
 results suggest that habitat loss may more intensively re-shuffle diverse,
 tropical communities, which impacts biomass recovery, our proxy of
 functioning. Contrary to ecological theory, in small-bodied,
 benthos-associated vertebrate communities, biodiversity may neither
 promote stability nor functioning, suggesting that human disturbances may
 be particularly impactful in tropical, high-diversity ecosystems.
description: We experimentally tested the response of marine fish communities
 to disturbance across a diversity gradient on human-made dock pilings. We
 holistically sampled cryptobenthic fish communities, then we imposed a
 severe disturbance by removing all benthic epifauna. We then compared the
 community stability, defined as the constancy in community composition, on
 disturbed and undisturbed pilings after one year.
DOI: 10.5061/dryad.95x69p8p8
title: Response to primary chemoradiotherapy of locally advanced oropharyngeal carcinoma is determined by the degree of cytotoxic T cell infiltration within tumor cell aggregates

description: Background: Effective anti-tumor immune responses are mediated by T cells
 and require organized, spatially coordinated interactions within the tumor
 microenvironment (TME). Understanding coordinated T-cell behavior and
 deciphering mechanisms of radiotherapy resistance mediated by tumor stem
 cells will advance risk stratification of oropharyngeal cancer (OPSCC)
 patients treated with primary chemoradiotherapy (RCTx).  Methods:
 To determine the role of CD8 T cells (CTL) and tumor stem cells in
 response to RCTx, we employed multiplex immunofluorescence stains on
 pre-treatment biopsy specimens from 86 advanced OPSCC patients and
 correlated these quantitative data with clinical parameters. Multiplex
 stains were analyzed at the single-cell level using QuPath and spatial
 coordination of immune cells within the TME was explored using the
 R-package Spatstat. Results: Our observations demonstrate that a strong
 CTL-infiltration into the epithelial tumor compartment (HR for overall
 survival, OS: 0.35; p&lt;0.001) and the expression of PD-L1 on CTL
 (HR: 0.36; p&lt;0.001) were both associated with a significantly
 better response and survival upon RCTx. As expected, p16 expression was a
 strong predictor of improved OS (HR: 0.38; p=0.002) and correlated with
 overall CTL infiltration (r: 0.358, p&lt;0.001). By contrast, tumor
 cell proliferative activity, expression of the tumor stem cell marker
 CD271 and overall CTL infiltration, regardless of the affected
 compartment, were not associated with response or survival. Conclusion: In
 this study, we could demonstrate the clinical relevance of the spatial
 organization and the phenotype of CD8 T cells within the TME. In
 particular, we found that the infiltration of CD8 T cells specifically
 into the tumor cell compartment was an independent predictive marker for
 response to chemoradiotherapy, which was strongly associated with p16
 expression. Meanwhile, tumor cell proliferation and the expression of stem
 cell markers showed no independent predictive effect in response to RCTx
 and require further study.
description: We retrospectively identified 86 patients with histologically
 confirmed diagnoses of oropharyngeal squamous cell carcinoma who have been
 treated with primary radiochemotherapy. Details on clinical-pathological
 parameters at initial diagnosis, subsequent treatments and survival data
 were collected from the patient´s medical records. We employed multiplex
 immunofluorescence stains on pre-treatment biopsy specimens from these 86
 patients with advanced OPSCC and correlated the resulting quantitative
 single-cell data with clinical parameters. Multiplex stains were analyzed
 at the single-cell level using QuPath and spatial coordination of immune
 cells within the TME was explored using the R-package Spatstat.
description: R, RStudio, Excel or other data editing program.
DOI: 10.5061/dryad.vt4b8gtw1
title: Videos of nest defense against cuckoo egg-laying from 2013 to 2022

description: As the first line of defense in avian brood parasitism, nest defense plays
 an important role in reducing nest parasitism and increasing host fitness.
 However, systematic studies on its effectiveness (i.e., on whether it
 successfully prevents cuckoo parasitism) are lacking. Based on 214 video
 recordings from 10 years of field observations, we evaluated the
 effectiveness of nest defenses of the Oriental reed warbler (Acrocephalus
 orientalis) in deterring common cuckoo (Cuculus canorus) parasitism. The
 results revealed that, under a breeding pair situation (≤ 2 host
 individuals), nest defenses of the warbler were hardly effective in
 resisting the egg-laying behavior of the cuckoo, and many of the cuckoos
 under attack were able to complete the parasitic process without being
 harmed. However, when hosts were ≥ 3 host individuals, the trigger value
 was reached, and the warbler was able to effectively thwart the
 cuckoo's parasitism and cause lethal damage to the cuckoo. This
 indicated that the host group was effective in resisting the cuckoo, which
 fully demonstrates the importance of cooperation and socially transmitted
 defenses among host neighbors in resisting cuckoo parasitism.
DOI: 10.5061/dryad.3ffbg79n7
title: Data from: The selective advantage of a mast-flowering behavior in Veratrum album subsp. oxysepalum: Implications of the predator satiation hypothesis

description: Premise: The synchronous highly variable flower or seed production among
 years within a population– i.e., masting – has been reported in numerous
 perennial plants. Although ecological advantages of masting are recognized
 as the enhancement of pollination efficiency and/or escape from predator
 attack, little is known about the degree of these advantages and the
 variation in masting behavior among populations of conspecific plants.
 Methods: We observed flowering ramet density and reproductive
 success (fruit-set success and herbivorous damage) of a perennial herb,
 Veratrum album subsp. oxysepalum, across six lowland and six alpine
 populations in northern Japan during 2–3 years. We then analyzed the
 relationship between floral density and reproductive success to clarify
 the ecological significance of mast flowering. Furthermore, flowering
 intervals of individual plants were estimated by counting annual scars on
 rhizomes. Results: Mast flowering was observed in most
 populations, but flowering intervals of individual plants were shorter in
 the alpine populations compared with the lowland populations. Floral
 damage by stem borers (dipteran larvae) and seed predation by lepidopteran
 larvae were intense in the lowland populations. The seed production of
 individual ramets increased with higher floral density owing to the
 effective avoidance of floral-stem damage and seed predation. Although
 stem borers were absent in alpine habitat, seed predation decreased with
 higher floral density also in the alpine populations. Pollination success
 was independent of floral density in both the alpine and lowland
 populations.  Conclusions: These results strongly
 support the predator satiation hypothesis for the mast flowering behavior
 in this species.
description: The data file of Excel includes four sheets 1)
 Yearly variation of flowering ramets 2) Comparison of
 flowering intervals among populations  3) Relationship
 between reproductive success and flowering ramet density
 4) Relationship between stem border No and damege score of the
 herbivory
DOI: 10.5061/dryad.fn2z34tz5
title: Multiple social benefits drive the formation of mixed-species groups of Australian humpback and Indo-Pacific bottlenose dolphins

description: Mixed-species groups are common amongst diverse taxa including fishes,
 birds, and mammals. Antipredator, foraging, and social benefits have been
 proposed as functional explanations for mixed-species group formation.
 Amongst delphinids, mixed-species groups are widespread, but little is
 known about their function. To investigate the potential benefits of
 delphinid mixed-species groups, we compared the number of individuals, the
 age composition, and the behaviour of single- and mixed-species sightings
 of Australian humpback (Sousa sahulensis) and Indo-Pacific bottlenose
 dolphins (Tursiops aduncus) observed around the North West Cape, Western
 Australia. We found no difference in the number of individuals or the age
 composition of humpback dolphins present in single- and mixed-species
 sightings, whereas bottlenose dolphins were present in larger numbers in
 single-species sightings than in mixed-species sightings due to a higher
 number of adults. Socialising was the initial observed behavioural state
 of 36.1% of mixed-species sightings, compared to only 5.1% and 10.3% of
 humpback and bottlenose dolphin single-species sightings, respectively.
 Furthermore, both species travelled and foraged less frequently when in
 mixed-species groups. Of 93 mixed-species groups observed during a focal
 follow of ≥10 minutes, 32 (34.4%) involved aggressive and/or sexual
 behaviours typically initiated by bottlenose dolphins towards humpback
 dolphins while the remaining 61 (65.6%) involved only neutral and
 affiliative behaviours. The results of this study suggest that the
 observed mixed-species groups provide multiple social benefits,
 particularly those pertaining to socio-sexual behaviours and the
 development and care of young.
DOI: 10.5061/dryad.zgmsbccg0
title: A general approach for quantifying microbial effects on plant competition

description: Purpose  A growing perspective in plant ecology highlights the
 ways that microbial interactions can promote or hinder plant coexistence.
 Towards this aim, recently-proposed approaches provide ways to empirically
 quantify how microbes affect the outcome of competition between plants.
 One such approach experimentally measures competition coefficients by
 comparing biomass performance of plants growing individually or with
 competitors, then quantifies microbial effects by comparing with a
 sterilization treatment. Nonetheless, the complexity of plant-microbe
 interactions presents general challenges when linking observations of
 microbial effects to underlying models. Results  We show how the
 implementation of a density gradient design can help quantify potential
 nonlinearities and facilitative interactions in plant-soil microbe
 interactions, which are properties once thought to hinder the
 quantification of the microbial impact of plant competitive outcome. We
 provide guidelines for setting up the experiment and accurately
 interpreting the results. Conclusion  We argue that future
 studies should aim to parameterize suitable demographic models to
 characterize the contribution of soil microbes to plant
 coexistence. 
description: Building on insights from modern coexistence theory, we propose a
 comprehensive density gradient design to quantify the combined impact of
 plant-plant competition and plant-soil microbe interactions on plant
 coexistence patterns.
DOI: 10.5061/dryad.dbrv15f4m
title: Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

description: Understanding historical range shifts and population size variation
 provides important context for interpreting contemporary genetic
 diversity. Methods to predict changes in species distributions and model
 changes in effective population size (Ne) using whole genomes make it
 feasible to examine how temporal dynamics influence diversity across
 populations. We investigate Ne variation and climate-associated range
 shifts to examine the origins of a previously observed latitudinal
 heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson
 (Hymenoptera: Apidae: Bombus Latreille) in western North America. We
 analyze whole genomes from a latitude-elevation cline using sequentially
 Markovian coalescent models of Ne through time to test whether relatively
 low diversity in southern high-elevation populations is a result of
 long-term differences in Ne. We use Maxent models of the species range
 over the last 130,000 years to evaluate range shifts and stability. Ne
 fluctuates with climate across populations, but more genetically diverse
 northern populations have maintained greater Ne over the late Pleistocene
 and experienced larger expansions with climatically favorable time
 periods. Northern populations also experienced larger bottlenecks during
 the last glacial period which matched the loss of range area near these
 sites, however, bottlenecks were not sufficient to erode diversity
 maintained during periods of large Ne. A genome sampled from an island
 population indicated a severe postglacial bottleneck, indicating that
 large recent post-glacial declines are detectable if they have occurred.
 Genetic diversity was not related to niche stability or glacial-period
 bottleneck size. Instead, spatial expansions and increased connectivity
 during favorable climates likely maintain diversity in the north while
 restriction to high elevations maintains relatively low diversity despite
 greater stability in southern regions. Results suggest genetic diversity
 gradients reflect long-term differences in Ne dynamics and also emphasize
 the unique effects of isolation on insular habitats for bumble bees.
 Patterns are discussed in the context of conservation under climate
 change.
description: Spreadsheet program (Excel, Open Office, etc), text editor,
 decompression software.