cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tmpg4f9g
title: Data from: Observing frugivores or collecting scats: A method comparison to construct quantitative seed dispersal networks

description: Mutualistic interactions form the basis for many ecological processes and
 are often analyzed within the framework of ecological networks. These
 interactions can be sampled with a range of methods and first analyses of
 pollination networks sampled with different methods showed differences in
 common network metrics. However, it is yet unknown if metrics of seed
 dispersal networks are similarly affected by the sampling method and if
 different methods detect a complementary set of frugivores. This is
 necessary to better understand the (dis-)advantages of each method and to
 identify the role of each frugivore for the seed dispersal process. Here,
 we compare seed removal networks based on the observation of 2,189
 frugivore visits on ten focal plant species with seed deposition networks
 constructed by DNA barcoding of plant seeds in 3,094 frugivore scats. We
 were interested in whether both methods identify the same disperser
 species and if species-level network metrics of plant species were
 correlated between network types. Both methods identified the same avian
 super-generalist frugivores, which accounted for the highest number of
 dispersed seeds. However, only with DNA barcoding, we detected elusive but
 frequent mammalian seed dispersers. The overall networks created by both
 methods were congruent but the plant species’ degree, their interaction
 frequency, and their specialization index (d’) differed. Our study
 suggests that DNA barcoding of defecated and regurgitated seeds can be
 used to construct quantitative seed deposition networks similar to those
 constructed by focal observations. To improve the overall completeness of
 seed dispersal networks it might be useful to combine both methods to
 detect interactions by both birds and mammals. Most importantly, the DNA
 barcoding method provides information on the post-dispersal stage and thus
 on the qualitative contribution of each frugivore for the plant community
 thereby linking species interactions to regeneration dynamics of
 fleshy-fruited plant species.
description: Short summary: Along transects, we collected
 scats of frugivores which contained seeds of the fleshy-fruited plant
 community in Białowieża Forest, Poland. We used DNA barcoding to identify
 the frugivore and were thereby able to obtain quantitative seed deposition
 data. Further, we
 used focal observations to catch feeding interactions between
 fleshy-fruited plant and their frugivore partners. Additionally, we counted the
 number of ripe fruits along the transects and determined the crop size of
 observed plant individuals.  
description: This data package contains data from Schlautmann, Jan; Rehling,
 Finn; Albrecht, Jörg; Jaroszewicz, Bogdan; Schabo, Dana G. &
 Farwig, Nina (2021) Observing frugivores or collecting scats: A method
 comparison to construct quantitative seed dispersal networks, Oikos.
 Please refer to the readMe.txt file for details on the dataset.
DOI: 10.5061/dryad.5tb2rbp3w
title: Data from: Male and female reproductive fitness costs of an immune response in natural populations

description: Parasites can mediate host fitness both directly, via effects on survival
 and reproduction, or indirectly by inducing host immune defense with
 costly side-effects.  The evolution of immune defense is
 determined by a complex interplay of costs and benefits of parasite
 infection and immune response, all of which may differ for male and female
 hosts in sexual lineages.  Here, we examine fitness
 costs associated with an inducible immune defense in a fish-cestode
 host-parasite system.  Cestode infection induces
 peritoneal fibrosis in threespine stickleback (Gasterosteus aculeatus),
 constraining cestode growth and sometimes encasing and killing the
 parasite. Surveying two wild populations of stickleback, we confirm that
 the presence of fibrosis scar tissue is associated with reduced parasite
 burden in both male and female fish. However, fibrotic fish had lower
 foraging success and reproductive fitness (reduced female egg production
 and male nesting success), indicating strong costs of the lingering
 immunopathology.  Consistent with substantial
 sexually-concordant fitness effects of immune response, we find alignment
 of multivariate selection across the sexes despite sexual antagonism over
 morphological shape. Although both sexes experienced costs of fibrosis,
 the net impacts are unequal because in the two study populations females
 had higher cestode exposure. To evaluate whether this difference in risk
 should drive sex-specific immune strategies, we analyze a quantitative
 genetic model of host immune response to a trophically transmitted
 parasite. The model and empirical data illustrate how shared costs and
 benefits of immune response lead to shared evolutionary interests of male
 and female hosts, despite unequal infection risks across the
 sexes.
DOI: 10.5061/dryad.gtht76hm6
title: Multidimensional trophic niche revealed by complementary approaches: gut content, digestive enzymes, fatty acids and stable isotopes in Collembola

description: Trophic niche differentiation may explain coexistence and shape functional
 roles of species. In complex natural food webs, however, trophic niche
 parameters depicted by single and isolated methods may simplify the
 multidimensional nature of consumer trophic niches, which includes feeding
 processes such as food choice, ingestion, digestion, assimilation and
 retention. Here we explore the correlation and complementarity of trophic
 niche parameters tackled by four complementary methodological approaches,
 i.e., visual gut content-, digestive enzyme-, fatty acid- and stable
 isotope analyses – each assessing one or few feeding processes, and
 demonstrate the power of method combination. Focusing on soil ecosystems,
 where many omnivore species with cryptic feeding habits co-exist, we chose
 Collembola as an example. We compiled fifteen key trophic niche parameters
 for 125 species from 40 studies. We assessed correlations among trophic
 niche parameters and described variation of these parameters in different
 Collembola species, families and across life forms, which represent
 microhabitat specialisation. Correlation between trophic niche parameters
 was weak in 45 out of 64 pairwise comparisons, pointing at complementarity
 of the four methods. Jointly, the results indicated that fungal- and
 plant-feeding Collembola assimilate storage, rather than structural
 polysaccharides, and suggested bacterial feeding as a potential
 alternative feeding strategy. Gut content and fatty acid analyses
 suggested alignment between ingestion and assimilation/retention processes
 in fungal- and plant-feeding Collembola. From the fifteen trophic niche
 parameters, six were related to Collembola family identity, suggesting
 that not all trophic niche dimensions are phylogenetically structured.
 Only three parameters were related to the life forms, suggesting that
 species use various feeding strategies when living in the same
 microenvironments. Consumers can meet their nutritional needs by varying
 their food choices, ingestion and digestion strategies, with the
 connection among different feeding processes being dependent on the
 consumed resource and consumer adaptations. Multiple methods reveal
 different dimensions, together drawing a comprehensive picture of the
 trophic niche. Future studies applying the multidimensional trophic niche
 approach will allow us to trace trophic complexity and reveal niche
 partitioning of omnivorous species and their functional roles, especially
 in cryptic environments such as soils, caves, deep ocean or benthic
 ecosystems.
DOI: 10.5061/dryad.00000003g
title: Cost of step time asymmetry and step length asymmetry in human walking

description: The metabolic cost of walking in healthy individuals increases with
 spatiotemporal gait asymmetries. Pathological gait, such as post-stroke,
 often has asymmetry in step lengths and step times which may contribute to
 an increased energy cost. But paradoxically, enforcing step length
 symmetry does not reduce metabolic cost of post-stroke walking. The
 isolated and interacting costs of asymmetry in step times and step lengths
 remain unclear, because previous studies did not simultaneously enforce
 spatial and temporal gait asymmetries. Here, we delineate isolated costs
 of asymmetry in step times and step lengths in healthy human walking. We
 first show that the cost of step length asymmetry is predicted by the cost
 of taking two non-preferred step lengths (one short and one long), but
 that step time asymmetry adds an extra cost beyond the cost of
 non-preferred step times. The metabolic power of step time asymmetry is
 about 2.5 times greater than the cost of step length asymmetry.
 Furthermore, the costs are not additive when walking with asymmetric step
 times and step lengths: metabolic power of concurrent asymmetry in step
 lengths and step times is driven by the cost of step time asymmetry alone.
 The metabolic power of asymmetry is explained by positive mechanical power
 produced during single support phases to compensate for a net loss of
 center of mass power incurred during double support phases. These data may
 explain why metabolic cost remains invariant to step length asymmetry in
 post-stroke walking and suggests how effects of asymmetry on energy cost
 can be attenuated.
DOI: 10.5061/dryad.8kprr4xnm
title: Seed predation and dispersal by small mammals in a landscape of fear: effects of personality, predation risk, and land-use change

description: Scatter-hoarding small mammals act as both seed predators and seed
 dispersers in forest ecosystems. Their choices regarding consuming or
 caching seeds must balance the risk of predation with the energy rewards
 gained from immediate or delayed consumption of seeds. Several factors
 influence their interaction with seeds, including the individual’s
 personality. Little is known about how personality affects foraging
 decisions in response to predation risk. This missing information is
 critical because if foraging decisions differ among individuals in
 response to perceived risk, then varying combinations of personality types
 in a population (and varying risks of predation across forest types) may
 have diverse effects on forest regeneration. Further, land-use change may
 influence the interplay of personality, risk perception, and foraging
 decisions by altering the perceived risk and the distribution of
 personality types in the landscape. To contribute to filling these
 knowledge gaps, we designed a large-scale field experiment to evaluate how
 personality, perceived predation risk, and land-use change affect the
 interaction of small mammals and seeds. Using infrared cameras, we
 recorded the choices of individuals of known personality at paired
 experimental sites with high vs. low perceived predation risk (N=2389
 observations from 74 individuals). We found that personality influenced
 multiple foraging decisions, and perceived risk affected how individuals
 with different personalities responded to those decisions. Specifically,
 exploration/activity influenced seed choice, boldness affected the number
 of seeds selected, and docility influenced both foraging site selection
 and whether mice consumed or removed seeds. Our results show that land-use
 change erased the effects of variation in risk perception, as the effects
 of personality on foraging site selection were seen only in the unmanaged
 forest sites. We demonstrate the importance of considering personality on
 foraging decisions under varying levels of risk, and more generally,
 underscore the importance of considering individual variation in affecting
 ecological processes.
description: See methods in paper
description: Scripts are commented
DOI: 10.5061/dryad.t1g1jwt27
title: Data from: Evolution of shade tolerance is associated with attenuation of shade avoidance and reduced phenotypic plasticity in North American milkweeds

description: Premise: Mismatches between light conditions and light-capture strategy
 can reduce plant performance and prevent colonization of novel habitats.
 Although light-capture strategies tend to be highly conserved among
 closely related species, evolutionary transitions from shaded to unshaded
 habitats (and vice versa) occur in numerous plant lineages. Methods: We
 combined phylogenetic approaches with field and greenhouse experiments to
 investigate evolutionary constraints on light-capture strategy in North
 American milkweeds (genus Asclepias) and to determine whether colonization
 of shaded habitats in this heliophilic clade is associated with reduced
 plasticity and attenuation of the shade avoidance response. Results:
 Colonization of shaded habitats has occurred at least 10 times in this
 genus, including at least once in each major North American clade.
 Evolutionary transitions between habitats exhibit strong directional bias,
 with shifts from full-sun to shaded habitats occurring at least three
 times as often as the opposite transition. In field and greenhouse
 experiments, sun species responded to shade by increasing internode
 length, height, and specific leaf area, consistent with the shade
 avoidance response; paired shade species exhibited reduced plasticity
 overall, and only one trait (specific leaf area) responded to experimental
 shade. Conclusions: Our results suggest that milkweeds colonized shaded
 environments numerous times using a light-capture strategy distinct from
 the ancestral (putatively shade avoidant) strategy, including a general
 attenuation of plasticity in response to variable light conditions. This
 pattern bolsters the notion that shade avoidance and tolerance represent
 divergent evolutionary strategies for maximizing performance under
 qualitatively different types of shade.
description: See README file for details
DOI: 10.5061/dryad.gmsbcc2n7
title: Accompanied versus unaccompanied walking for continuous oxygen saturation measurement during 6-min walk test in COPD: A randomised cross-over study

description: Is there is a difference in the 6-Minute Walk Test (6MWT) distance when
 the assessor accompanies the patient to continuously measure oxygen
 saturation (SpO2) compared to the patient walking unaccompanied? We
 conducted a randomised cross-over study to evaluate the impact of the
 assessor walking with the patient during 6MWT (6MWTwith) versus patient
 walking alone (6MWTwithout). At the end of a pulmonary rehabilitation
 programme, each patient performed two 6MWTs in random order and separated
 by 30 minutes rest. 49 COPD patients (GOLD II-IV) were included. In a
 regression model adjusting for period and subject, accompanying the
 patient resulted in a lower walking distance (mean difference -9.1 m,
 [95%CI, -13.9 to -4.3], p=0.0004). Notably, six patients walked more than
 30m further (minimal important difference, MID) in one of the two
 conditions (6MWTwith: n=1, 6MWTwithout: n=5). There were no
 betweensequence-group differences in heart rate, dyspnoea and leg-fatigue,
 and SpO2. The median (interquartile range) number and duration of SpO2
 signal artefacts were high but not different between the experimental
 conditions (6MWTwith: 17 [4, 24], 34s [7, 113], 6MWTwithout: 11 [3, 26],
 24s [4, 62]). On a study population level, we observed a statistically
 significant difference in 6MWT distance between the two experimental
 conditions, however, the magnitude of difference is small and may not be
 considered clinically relevant. Nevertheless, in a clinical setting,
 unaccompanied walking resulted in a substantially higher walking distance
 in individual patients, pointing towards strictly standardised testing
 methodology, in particular in pre-post study designs.
DOI: 10.5061/dryad.nzs7h44rd
title: Herbaceous production and soil nitrogen after mesquite mortality

description: In the mixed C3/C4 grassland of the southern Great Plains, USA, the
 invasive woody legume, honey mesquite (Prosopis glandulosa), affects grass
 production and composition differently beneath the canopy (subcanopy) than
 in spaces between trees (intercanopy) due in part to the dominant presence
 of C3 Texas wintergrass (Nassella leucotricha) beneath the mesquite canopy
 and soil enrichment from N-fixation by mesquite. This arrangement, unlike
 most Prosopis systems worldwide that have C4 grass or C3 subshrub
 understories, uniquely affects grass production spatially and seasonally
 during mesquite expansion and possibly after anthropogenic removal of
 mesquite. We compared herbaceous and soil N responses in subcanopy and
 intercanopy microsites during the first 2 years following a root-killing
 herbicide mesquite treatment. Perennial grass (PGR) and total herbaceous
 (THB) production were greater in treated than untreated intercanopy and
 subcanopy microsites at 1-yr post-treatment, with Texas wintergrass
 comprising the largest portion of PGR. In year 2, PGR production declined
 in both treated microsites with no differences between treatments.
 However, THB production remained greater in treated than untreated
 microsites due mainly to increased annual forb production that supplanted
 PGR production from year 1. Increased annual forb production in treated
 microsites in year 2 was likely due to high rainfall in fall of year 1
 that stimulated forb seed germination, increased light from the loss of
 shading by mesquite, and soil inorganic N that increased from year 1 to
 year 2. Pre-treatment spatial heterogeneity of herbaceous composition and
 soil N, caused by mesquite, affected post-treatment patterns of herbaceous
 production. The unexpected replacement of PGR by annual forbs in year 2
 revealed that grass forage production following brush control can deviate
 markedly from predicted models under certain conditions.  
description: Data collected by field sampling and lab analysis
DOI: 10.5061/dryad.vq83bk3s8
title: Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit

description: Spatially distributed excitation and inhibition collectively shape a
 visual neuron’s receptive field (RF) properties. In the
 direction-selective circuit of the mammalian retina, the role of strong
 null-direction inhibition of On-Off direction-selective ganglion cells
 (ON-OFF DSGCs) on their direction selectivity is well-studied. However,
 how excitatory inputs influence the On-Off DSGC’s visual response is
 underexplored. Here, we report that On-Off DSGCs have a spatially
 displaced glutamatergic receptive field along their horizontal
 preferred-null motion axes. This displaced receptive field contributes to
 DSGC null-direction spiking during interrupted motion trajectories.
 Theoretical analyses indicate that population responses during interrupted
 motion may help populations of On-Off DSGCs signal the spatial location of
 moving objects in complex, naturalistic visual environments. Our study
 highlights that the direction-selective circuit exploits separate sets of
 mechanisms under different stimulus conditions, and these mechanisms may
 help encode multiple visual features.
description: Dataset has electrophysiology data files and calcium imaging data
 files. Whole-cell recordings are .abf files. These are associated with
 stimulus files. Data files of spiking activity for
 moving bar and occluded bar stimuli are in .mat files. These .mat files
 include information about spike times and spike number to stimuli in
 different motion directions.  Calcium imaging datasets
 include the fluoresence of the cell in the first column, and the
 background value in the second column. This data set also include a
 stimulus file, and a file containing the timing information of the voltage
 steps triggering the presentation of each stimulus.
 README file called 'README Ding et al eLife' give more
 detail about individual files.
DOI: 10.5061/dryad.s7h44j16j
title: Asperity level characterisation of abrasive wear using atomic force microscopy

description: Using an Atomic Force Microscope (AFM) a nanoscale wear characterisation
 method has been applied to a commercial steel substrate AISI 52100, a
 common bearing material. Two wear mechanisms were observed by the
 presented method: atom attrition and elastoplastic ploughing. It is shown
 that not only friction can be used to classify the difference between
 these two mechanisms, but also the ‘degree of wear’. Archard’s Law of
 Adhesion shows good conformity to experimental data at the nanoscale for
 the elastoplastic ploughing mechanism. However, there is a distinct
 discontinuity between the two identified mechanisms of wear and their
 relation to the load and the removed volume. The length scale effect of
 the material’s hardness property plays an integral role in the
 relationship between the ‘degree of wear’ and load. The transition between
 wear mechanisms is hardness dependent, as below a load threshold limited
 plastic deformation in the form of pile up is exhibited. It is revealed
 that the presented method can be utilised as a rapid wear characterisation
 technique, but additional work is necessary to project individual asperity
 interaction observations to macroscale contacts.  
description: The data was collected by a combinated of nanoindentation, and
 using AFM in contact mode. The AFM was used to scratch a steel substrate
 AISI52100 with varying applied load and measure the topography of the
 susbtrate. 
description: Figure 4A: Nanoindentation depth with respect to load
 Figure 4B: Meyer's Hardness from nano indentation with
 respect to load Figure 6A: AFM Scratch methodology -
 wear volume with respect to the number of passes of the AFM tip
 Figure 7: AFM Scratch-Topography Interrupted Methodology (total
 40 passes) - Trace-retrace averaged coefficient of friction with respects
 to the number of passes Figure 8: AFM
 Scratch-Topography Continuous Methodology (total 40 passes) -
 Trace-retrace averaged coefficient of friction with respects to the number
 of passes  Figure 10: AFM Scratches Continuous
 Methodology  (total 2000 passes) - Pile up and removed volume with
 respects to applied normal load Figure 12: Degree of
 Wear versus normal applied load  Figure 13A: AFM
 Scratch-Topography Continuous Methodology (total 2000 passes) -
 Trace-retrace averaged coefficient of friction with respects to the number
 of passes and various applied normal loads  Figure 13B:
 Comparison of AFM Scratch-Topography Continuous Methodology (total 2000
 passes) maximum and steady state friction  versus applied normal
 load