cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rbnzs7hb2
title: Data from: Reproductive state influences the degree of risk tolerance for a seasonally breeding mesopredator

description: Abstract. The risk of predation can alter the way animals perceive costs
 and benefits in their environment, on which foraging decisions are made.
 To maximize fitness, animals with offspring show the most pronounced
 alteration in behavior because mothers experience increased nutritional
 requirements and increased vulnerability to predation. Therefore, the
 tolerance of risk is shaped, in part, by reproductive state. Like prey
 species, mesopredators balance a trade-off between food and predation to
 maximize fitness. However, few studies have acknowledged its importance.
 We investigated how mesopredators may alter their space use between
 periods when young are and are not vulnerable. Investigating the
 fine-scale space use of 19 packs of African wild dogs Lycaon pictus in the
 Kruger National Park, we found lower risk tolerance of denning packs; they
 re-visited area less frequently as lion and impala density increased and
 thus reduced the likelihood of risky encounters by avoiding areas where
 both risk and reward were high. By contrast, non-denning packs re-visited
 area less frequently as lion density increased and impala density
 decreased and thus avoided areas where reward was low, especially if risk
 was high. These results suggest that wild dogs shift their patterns of
 space use when the pack is most vulnerable. Ultimately, we found evidence
 of decreased risk tolerance by denning packs, likely because of increased
 vulnerability of lactating mothers and immobile pups. More broadly, our
 findings suggest that risk tolerance is dependent on reproductive state
 for mesopredators and should be considered as a possible mechanism for
 other mesopredators as well. 
description: Spatial and covariate data. The supporting
 file contains African wild dog pack locations and all covariate data used
 for analysis; denning season, lion density, impala density, terrain
 ruggedness, woody cover, and distance to den site as well as the two
 response variabes of number of visits and average duration of visit
 calculated with T-LoCoH. data.csv<br>
 README.txt
DOI: 10.5061/dryad.5qfttdz4f
title: Data: Foxes fertilize the subarctic forest and modify vegetation through denning

description: Ecosystem engineers modify habitats through processes other than trophic
 interactions, such as by regulating soil nutrients, and can influence
 resource availability and quality for other organisms. Predator-mediated
 elemental cycling may be especially important in determining plant
 diversity and growth in ecosystems where soil fertility and primary
 productivity are low. Red foxes (Vulpes vulpes L.), top predators
 in the Subarctic, could engineer local ecosystems through denning, which
 could create biogeochemical hotspots of nutrients due to continual input
 of feces, urine and prey remains. We examined soil and vegetation
 characteristics on red fox dens and paired control sites in woodland
 habitats near the Arctic treeline in Manitoba, Canada. The organic soil
 layer on den sites had 81% more inorganic nitrogen and 250% more
 extractable phosphorus than in control areas. Denning also increased soil
 respiration and pH in the organic layer, suggesting improved soil quality
 and nutrient availability for plants. By enriching nutrients and
 disturbing soils through digging, den sites had a higher plant
 species ß-diversity and a greater cover of erect woody
 shrubs (Salix spp.), grasses (Leymus mollis (Trinius)
 Pilger) and weedy ephemerals compared to control sites, resulting in a
 regional increase in plant species richness. Our research
 highlights the importance of considering impacts of predators other than
 through their consumption of prey, and provides insight into the role of
 red foxes in modifying plant diversity and productivity in the Subarctic.
DOI: 10.6084/m9.figshare.29039301
title: Using the descent direction in a method of centres algorithm for solving multi-objective programming problems

description: Interior-point methods, particularly the cutting-plane strategy, have emerged as interesting techniques in optimization. The main idea of the cutting-plane method is to cut off parts of the feasible set and shrink it by removing the points where optimality is surely not attained. The aim of this study is to improve the convergence speed of a newly developed modified cutting-plane method for multi-objective optimization problems. The effectiveness of the proposed approach is emphasized by its ability rapidly to shrink the feasible space, strengthen the optimal solution search method, and at the same time minimize the computational overhead. Additionally, it is demonstrated that the method is capable of achieving well-distributed efficient solutions on the efficient frontier by purposefully assigning weight vectors. The experimental analysis carried out confirms the effectiveness of the suggested method and offers a new promising perspective for addressing multi-objective optimization challenges.
DOI: 10.6084/m9.figshare.29039301.v1
title: Using the descent direction in a method of centres algorithm for solving multi-objective programming problems

description: Interior-point methods, particularly the cutting-plane strategy, have emerged as interesting techniques in optimization. The main idea of the cutting-plane method is to cut off parts of the feasible set and shrink it by removing the points where optimality is surely not attained. The aim of this study is to improve the convergence speed of a newly developed modified cutting-plane method for multi-objective optimization problems. The effectiveness of the proposed approach is emphasized by its ability rapidly to shrink the feasible space, strengthen the optimal solution search method, and at the same time minimize the computational overhead. Additionally, it is demonstrated that the method is capable of achieving well-distributed efficient solutions on the efficient frontier by purposefully assigning weight vectors. The experimental analysis carried out confirms the effectiveness of the suggested method and offers a new promising perspective for addressing multi-objective optimization challenges.
DOI: 10.5061/dryad.2v6wwpzmh
title: Effect of Environmental Weathering on Biodegradation of Biodegradable Plastic Mulch Films under Ambient Soil and Composting Conditions

description: Plastic mulch films contribute to better crop production. Concerns for
 lack of sustainable disposal methods for conventional polyethylene (PE)
 mulch led to development of biodegradable plastic mulches (BDMs) that can
 be soil-incorporated or composted after use. Environmental weathering of
 BDMs during crop growth reduces their mechanical strength and alters the
 molecular structure of their polymeric components. However, the impact of
 weathering on BDMs’ biodegradability is not fully understood. The
 biodegradability of agriculturally weathered and unweathered BDMs in soil
 and compost was compared using standardized laboratory tests (ASTM D5988
 and D5338) using four BDMs (experimental polylactic acid and
 polyhydroxyalkanoate-based film [PLA/PHA] and three commercially available
 polybutyrate [PBAT]-based BDMs). In soil, biodegradation of weathered
 PLA/PHA was greater than its unweathered counterpart. For PBAT-based BDMs,
 the extent of biodegradation varied. A decrease of the weight-averaged
 molecular weight (Mw) of PBAT and PLA and thermostability of PLA, PHA,
 PBAT, and starch components was observed during biodegradation in the
 soil. The proportion of the minor components PHA and starch decreased
 during biodegradation, indicating preferential utilization of PHA over PLA
 and starch over PBAT by microbes. Bacterial abundance was significantly
 higher than fungal abundance in soil and was more prominent in soil
 adjacent to weathered than unweathered BDM treatments. Under composting
 conditions, unweathered PBAT-enriched mulches yielded higher CO2 evolution
 than their weathered counterpart. Together, these results suggest that
 environmental weathering enhances biodegradation of BDMs and mulch’s
 polymeric constituents also influence the microbial degradation, more so
 for bacterial than fungal communities.
description: Details are given in our paper. The majority of the data was
 obtained directly from instrumentation, with the exception of %
 biodegradation, which was determined through the instructions given in
 ASTM D5988 and D5338 for Fig 1 and Figs 6 +7, respectively
DOI: 10.5061/dryad.xksn02vfc
title: Data from: Experience, but not age, is associated with volumetric mushroom body expansion in solitary alkali bees

description: In social insects, changes in behavior are often accompanied by structural
 changes in the brain. This neuroplasticity may come with experience
 (experience-dependent) or age (experience-expectant). Yet, the
 evolutionary relationship between neuroplasticity and sociality is
 unclear, because we know little about neuroplasticity in the solitary
 relatives of social species. We used confocal microscopy to measure brain
 changes in response to age and experience in a solitary halictid bee
 (Nomia melanderi). First, we compared the volume of individual brain
 regions among newly-emerged females, laboratory females deprived of
 reproductive and foraging experience, and free-flying, nesting females.
 Experience, but not age, led to significant expansion of the mushroom
 bodies—higher-order processing centers associated with learning and
 memory. Next, we investigated how social experience influences
 neuroplasticity by comparing the brains of females kept in the laboratory
 either alone or paired with another female. Paired females had
 significantly larger olfactory regions of the mushroom bodies. Together,
 these experimental results indicate that experience-dependent
 neuroplasticity is common to both solitary and social taxa, whereas
 experience-expectant neuroplasticity may be an adaptation to life in a
 social colony. Further, neuroplasticity in response to social chemical
 signals may have facilitated the evolution of sociality.
description: We conducted this study in Touchet,
 WA, USA between 27 May–19 June 2016 (Experiment 1) and 29 May–27 June 2018
 (Experiment 2). Newly-emerged (NE; &lt; 24-h old) female alkali bees
 were collected while leaving their natal nests by placing traps over bee
 beds. For Experiment 1, there were 3 treatment groups: 1) newly-emerged
 (NE), 2) lab-reared, and 3) reproductive females. NE females were
 sacrificed immediately (&lt; 24-h old) upon returning to the
 laboratory, whereas lab-reared females were housed individually in the
 laboratory for 10 d. Reproductive females (unknown age) were collected
 from bee beds and sacrificed upon returning to the laboratory. For
 Experiment 2, NE bees were randomly assigned to one of two treatment
 groups: 1) solo or 2) paired. Solo females were kept alone for 10 d, and
 paired females were given a nesting female cage-mate for the same
 duration. For paired bees, only the brains of focal females were used
 (i.e., we did not dissect the brains of cage-mates). The deposited datasets include raw
 volumetric measurements from separate brain regions. These volumes were
 obtained using autofluorescence-based confocal microscopy (Zeiss LMS 710,
 Jena, Germany) on whole-brain mounts to generate image stacks for all
 samples. Each structure and the whole brain were traced individually on
 each slice of the confocal stack. Experiment 1 and 2 trace intervals were
 every 5 µm
 and 10 µm
 optical slice, respectively. Volumetric measurements were generated using
 serial reconstruction.
DOI: 10.5061/dryad.x95x69phj
title: Plant‐eating carnivores: Multispecies analysis on factors influencing the frequency of plant occurrence in obligate carnivores

description: Plant-eating behavior is one of the greatest mysteries in obligate
 carnivores. Despite unsuitable morphological and physiological traits for
 plant consumption, the presence of plants in scat or stomach contents has
 been reported in various carnivorous species. However, researchers’
 interpretations of this subject are varied, and knowledge about it is
 scarce, without any multispecies studies. This study assessed the extent
 of variation in the frequency of plant occurrence in scat and stomach
 contents, as well as its relationship with various factors in 24 felid
 species using data from 213 published articles. Since the frequency of
 plant occurrence has not always been reported, we created two-part models
 and estimated parameters in a Bayesian framework. We found a significant
 negative relationship between the frequency of plant occurrence and body
 mass. This may be because plant-eating behavior reduces the energy loss
 caused by parasites and increases the efficiency of energy intake, which
 has a greater importance in smaller animals that have relatively high
 metabolic rates. This exploratory study highlights the importance of
 considering plant consumption in dietary studies on carnivorous species to
 understand the adaptive significance of this behavior and the relationship
 between obligate carnivores and plants.
description: Data collection methods are described in the main article. For
 details about the collection of environmental data, see the Appendix
 S2.
DOI: 10.5061/dryad.h44j0zpjf
title: Use of Deep Learning for structural analysis of CT-images of soil samples

description: Soil samples from several European countries were scanned using medical
 computer tomography (CT) device and are now available as CT images. The
 analysis of these samples was carried out using deep learning methods. For
 this purpose, a VGG16 network was trained with the CT-images (X). For the
 annotation (y) a new method for automated annotation,
 "surrogate'' learning, was introduced. The generated neural
 networks (NN) were subjected to a detailed analysis. Among other things,
 transfer learning was used to check whether the NN can also be trained to
 other y-values. Visually, the NN was verified using a gradient-based class
 activation mapping (grad-CAM) algorithm. These analyses showed that the NN
 was able to generalize, i.e. to capture the spatial structure of the soil
 sample. Possible applications of the models are discussed.
description: The dataset is provided in DICOM format. A set of Python scripts
 is provided to process the data.
DOI: 10.5061/dryad.x3ffbg7j4
title: Data for journal manuscript: Trait-based adaptability of Phragmites australis to the effects of soil water and salinity in the Yellow River Delta

description: Phragmites australis is the dominant species in the Yellow River Delta and
 plays an important role in wetland ecosystems. Ecological responses of the
 P. australis community to soil properties were investigated in 96 areas
 along the coastal-inland regions in the Yellow River Delta of China. The
 aim was to evaluate the relationship between phenotypic variation and
 environmental factors, reveal which functional traits could well respond
 to changes in electrical conductivity and soil water content, and the
 ecological strategies of P. australis. Within the range of soil water
 content (9.39–36.92%) and electrical conductivity (0.14–13.29 ms/cm), the
 results showed that the effects of soil water content and salinity were
 not equally important for the characterization of the morphological and
 physiological variability, and that plant functional traits including leaf
 traits and stem traits responded more strongly to soil salinity than soil
 water content. Our results suggested that salinity leads to reduced
 average height, specific leaf area, leaf area, and base stem diameter, but
 increased leaf water content and leaf thickness. The relationships between
 functional traits and electrical conductivity were generally linear and
 logarithmic. The coefficients of variation of morphological traits showed
 more phenotypic plasticity than the physiological traits. Salinity also
 led to the stress tolerator/competitor-stress tolerator (S/CS) strategies
 of P. australis; with the decrease of environmental stress, the main
 strategy gradually moved to the competitor (C) strategy, making P.
 australis the dominant species in the Yellow River Delta.
DOI: 10.5061/dryad.qrfj6q5f2
title: Core genome phylogenetic tree of two Campylobacter novaezeelandiae and four unclassified thermophilic Campylobacter isolates from Canadian agricultural surface water

description: This dataset includes 1) concatenated alignment of 135 core gene
 sequences and 2) phylogenomic tree of the 38 currently described
 Campylobacter spp., including Campylobacter novaezeelandiae and four
 additional novel Campylobacter species isolated from agricultural water in
 Canada. The original alignment of 120 kb was produced by
 Roary v.3.13.0. Gblocks v.0.91b was used to
 remove ambiguous alignments and phylogenetically uninformative positions.
 The final alignment (110 kb) was used as input to RAxML-NG
 v.0.9.0 to infer a phylogenetic tree under the GTR+G substitution model
 with 100 bootstrap replicates.
description: Isolates CW4409, CW4516, CW4519, and CW4600 were sequenced as
 part of the GenomeTrakr Project at Texas Department of State Health
 Services (Austin, Texas), and<b> </b>isolates CW4087 and
 CW4073 were sequenced at the Center for Biotechnology & Genomics,
 Texas Tech University (Lubbock, Texas). The rest of the Campylobacter spp.
 genomes (fasta files) were downloaded from GenBank. All
 genomes were annotated using Prokka v.1.13.3 and the .gff files were used
 as input to Roary v.3.13.0 to create a core gene alignment using the
 following parameters: -e -n -i 55; where "-e" creates a
 multiFASTA alignment of core genes using Prank; "-n" - fast core
 gene alignment with Mafft, used with -e; and "-i 55" is
 the minimum percentage identity for blastp. The resulting
 "core_gene_alignment.fasta" file (120 kb) was edited in Gblocks
 v.0.91b with the following parameters: minimum length of a block set to
 minimum and positions where at least 50% of the sequences had a gap were
 treated as a gap position. The resulting
 alignment "core_gene_alignment_Gblocks.fasta (110 kb) was used by
 RAxML v.0.9.0 to infer a phylogenetic tree under the GTR+G substitution
 model with 100 bootstrap replicates ("Tree.raxml.support-core_with
 accessions.newick").
DOI: 10.5061/dryad.dncjsxkzm
title: Data from: Decay classes of coarse woody debris in a lowland Dipterocarp forest: implications for volume, density and carbon estimates

description: Coarse woody debris (CWD) is a critical structural and functional
 component of forest ecosystems. In tropical forests, developing a
 decomposition classification is required for vigorous estimates of the
 role of CWD in carbon (C) and nutrient cycling and habitat diversity. This
 study considered the relationship between decay class, termite
 infestation, wood density, and C content of CWD in a lowland Dipterocarp
 forest in Southern Vietnam. The termite infestation averaged 73% by number
 and 32% by volume of all CWD pieces. Microbial and termite-driven
 decomposition was separated in the suggested decay classification system.
 Five decay classes were assigned to CWD items based on the proportion of
 wood consumed by invertebrates, as well as softness and moisture of the
 remaining wood. The proportion of wood volume consumed by termites in the
 1st, 2nd, 3rd, 4th, and 5th decay classes averaged 2, 5, 15, 48 and 77%,
 respectively. The bulk density of wood of the 1st, 2nd, 3rd, 4th, and 5th
 decay classes averaged 0.628, 0.501, 0.332, 0.169 and 0.071 g cm-3,
 respectively. The C concentration in wood averaged 42% and did not depend
 on decay class. The total C content in CWD decreased with decomposition
 and averaged 0.259, 0.199, 0.121, 0.037, and 0.009 g cm-3 in the CWD of
 the 1st, 2nd, 3rd, 4th, and 5th decay classes, respectively. We conclude
 that in Dipterocarp forests the inventories of CWD by decay classes should
 include estimates of proportions of wood, termite soil substrate, and wood
 voids.
DOI: 10.5061/dryad.cc2fqz65k
title: Annual killifish embryo ecology

description: Embryo-environment interactions are of paramount importance during the
 development of all organisms, and impacts during this period can echo far
 into later stages of ontogeny. African annual fish of the genus
 Nothobranchius live in temporary pools and their eggs survive the dry
 season in the dry bottom substrate of the pools by entering a facultative
 developmental arrest termed diapause. Uniquely among animals, the embryos
 (encased in eggs) may enter diapause at three different developmental
 stages. Such a system allows for the potential to employ different
 regulation mechanisms for each diapause. We sampled multiple
 Nothobranchius embryo banks across the progressing season, species and
 populations. We present important baseline field data and examine the role
 of environmental regulation in the embryonic development of this unique
 system. We describe the course of embryo development in the wild and find
 it to be very different from the typical development under laboratory
 conditions. Development across the embryo banks was synchronized within
 and across the sampled populations with all embryos entering diapause I
 during the rainy season, and diapause II during the dry season. Asynchrony
 occurred at transient phases of the habitat, during the process of habitat
 desiccation and at the end of the dry season. Our findings reveal the
 significance of considering wild environmental conditions in understanding
 the importance of the serial character of the annual fish diapauses.
DOI: 10.5061/dryad.fttdz08s0
title: Data from: A unique, large-sized stem-Odonata (Insecta) found in the early Pennsylvanian of New Brunswick (Canada)

description: A stem-relative of dragon- and damselflies, Brunellopteron norradi
 Béthoux, Deregnaucourt and Norrad gen. et spec. nov., is documented based
 on a specimen found at Robertson Point (Grand Lake, New Brunswick, Canada;
 Sunburry Creek Formation; early Moscovian, Pennsylvanian) and preserving
 the basal half of a hindwing. A comparative analysis of the evolution of
 wing venation in early odonates demonstrates that it belongs to a yet
 poorly documented subset of species. Specifically, it displays a MP+CuA
 fusion, a CuA+CuP fusion, and a CuP+AA fusion, but lacks the ‘extended’
 MP+Cu/CuA fusion and the ‘extended’ (CuP/CuA+CuP)+AA fusion which
 occurrence is typical of most Odonata, including Meganeura-like species.
 The occurrence of intercalary veins suggests that its closest relative
 might be Gallotypus oudardi Nel, Garrouste and Roques, 2008, from the
 Moscovian of northern France.
description: The two reflectance transformation imaging (RTI) files provided
 in this dataset document the specimen NBMG 21589, deposited at the New
 Brunswick Museum (Palaeontology collection; Saint John, New Brunswick,
 Canada). Each RTI file was generated using 42 photographs, themselves
 taken using a ca. 30-cm diameter automated light dome driving a digital
 camera Canon EOS 5D Mark III coupled to a Canon MP-E 65 mm macro lens
 (Canon, Tokyo, Japan) . Original photographs were optimized using Adobe
 Photoshop CS6 (Adobe Systems, San Jose, CA, USA) before RTI-processing,
 itself achieved using the RTIbuilder software (Cultural Heritage
 Imaging).
DOI: 10.17605/osf.io/nwz32
title: From past to partnership: the interplay of autobiographical memory and social value orientation in adolescent cooperation

description: The datasets used for analyses in study 1 and study 2.