cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j3tx95xgf
title: Data from: Variations in bark structural properties affect both water loss and carbon economics in neotropical savanna trees in the Cerrado region of Brazil

description: Even after complete stomatal closure, plants lose water through the leaf
 cuticles and bark. This residual water conductance of leaves (gleaf-res)
 and stems (gbark) can negatively impact plant water balance and affect
 plant survival in seasonally dry environments. However, little is known
 about the costs and benefits associated with such water leaks, especially
 on stem level. Here, we characterized the structural and functional
 determinants of the variability in gbark across tropical savanna species
 to elucidate how variations in this trait are related to contrasting
 growth strategies. The high variability in gbark across species was
 associated with morphoantomical properties of the outer bark (thickness,
 density, and lenticel investment), and such characteristics influenced
 both stem transpiration and respiration, suggesting the existence of a
 trade-off between water conservation and oxygen permeability, which
 reflected contrasting growth and dehydration tolerance strategies. For
 instance, species with higher gbark and gleaf-res presented a fast
 resource acquisition strategy but were more prone to drought-induced
 mortality by hydraulic failure. However, model simulations revealed that
 the relative contribution of gleaf-res and gbark to overall water balance
 depended on whether leaves were less or more resistant to cavitation than
 the stems. Synthesis. By combining correlative studies, experimental
 results, and a modeling exercise, we provide a new understanding of the
 costs and benefits associated with the variability in gbark across
 tropical savanna species, and a new perspective for studies of water
 relations and carbon economics in species from a hyperdiverse savanna.
description: All methods and analyses are explicitely described and provided
 in the corresponding paper.
description: Please refer to the corresponding paper published in Journal of
 Ecology for further details.
DOI: 10.5061/dryad.j0zpc86gj
title: Labeled data for citation field extraction

description: Citations are an important part of scientific papers, and the proper
 handling of them is indispensable for the science of science. Citation
 field extraction is the task of parsing citations: given a citation
 string, extract authors, title, venue, doi etc. Since the number of
 citations is counted by hundreds millions, efficient computer based
 methods for this task are very important. The development of machine
 learning methods for citation field extraction requires ground truth: a
 large corpus of labeled citations. This dataset provides a very large
 (41M) corpus of labeled data obtained by the reverse process: we took
 structured citation lists and used BibTeX to generate labeled citation
 strings.
description: We extracted structure citation lists from a variety of sources
 (see the description in our paper referenced below) and retypeset them
 using a variety of BibTeX styles. The styles were modified to produce the
 labels corresponding to citation fields.
description: See README file for data description.
DOI: 10.5061/dryad.3bk3j9kmn
title: Towards bio-inspired polymer adhesives: Activation assisted via HOBt for grafting of dopamine onto poly(acrylic acid)

description: The design of bio-inspired polymers has long been an area of intense
 study, however applications to the design of concrete admixtures for
 improved materials performance have been relatively unexplored. In this
 work we functionalized poly(acrylic acid) (PAA), a simple analogue to
 polycarboxylate ether admixtures in concrete, with dopamine to form a
 catechol-bearing polymer (PAA-g-DA). Synthetic routes utilizing
 hydroxybenzotriazole (HOBt) as an activating agent were examined for their
 ability in grafting dopamine to the PAA backbone. Previous literature
 using the traditional coupling reagent
 1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to graft dopamine to
 PAA were found to be inconsistent and the sensitivity of EDC coupling
 reactions necessitated a search for an alternative. Additionally, HOBt
 allowed for greater control over percent functionalization of the
 backbone, is a simple, robust reaction, and showed potential for
 scalability. This finding also represents a novel synthetic pathway for
 amide bond formation between dopamine and PAA. Finally, we performed
 preliminary adhesion studies of our polymer on rose granite specimens and
 demonstrated a 56% improvement in the median adhesion strength over
 unfunctionalized PAA. These results demonstrate an early study on the
 potential of PAA-g-DA to be utilized for improving the bonds within
 concrete.
DOI: 10.5061/dryad.ht76hdrht
title: Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial

description: This dataset includes code, used and generated data for the experiments in
 the paper Analyzing Phylogenetic Trees with a Tree Lattice Coordinate
 System and a Graph Polynomial, and the supplementary material of the
 paper. The paper introduces representation and comparison methods for
 rooted unlabelled phylogenetic trees based on a tree lattice that serves
 as a coordinate system for rooted binary trees with branch lengths and a
 graph polynomial that fully characterizes tree shapes. The
 methods provide fast, accurate, likelihood-free, distance-based appraoches
 to analyzing phylogenetic trees and allow analysis for large trees with
 more than a thousand taxa.  The dataset has three sections. The
 first section is the implementation of the introduced methods for
 phylogenetic tree analysis as an R package, inlcuding the source code and
 the binary of the package. This packege provides basic functions for tree
 analysis and can be used or edited for related analysis. The secoond
 section includes all code for analyses performed in the the paper, and all
 the data used and generated in the analyses. The third section contains
 the supplementary material for the paper, which includes supplememntary
 results and figures. For details, please refer to the paper and the README
 file.
DOI: 10.15468/dl.cpxdd7
title: Occurrence Download

description: A dataset containing 3516 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence, Specimen, Material sample)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Monomorium floricola",
 "Year 1000-2025"
 ]
}

 The dataset includes 3516 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003055-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q83bk3jk8
title: Plant-soil feedback of the invasive Sorghum halepense on Hainan island, China

description: Sorghum halepense is a perennial invasive weed causing great harm
 worldwide, including various regions on Hainan island. In this study,
 using two approaches, we examined plant-soil feedback of different S.
 halepense populations. In the first, rhizosphere soil of S. halepense from
 the field was either sterilized or not to study the role of soil biota on
 S. halepense growth. In the second, we first let S. halepense plants
 condition the soil, and then regrow plants on these conditioned soil to
 study the role of overall changes in soil properties in plant-soil
 feedback. Sterilization increased the growth of S. halepense, indicating
 that soil biota inhibited the growth of S. halepense. Soil biota from some
 populations inhibited the growth of S. halepense more than that from
 others. In most cases, the relative response of a S. halepense population
 when associated with its own soil vs. when associated with other soils was
 similar to the relative response of other populations across the same
 soils. In the second approach, the effect of conditioning on most soil
 chemical properties were not different among populations. The interactive
 effect of conditioning population and replanting population on plant
 biomass was not significant, indicating that the performance of different
 S. halepense populations did not depend on the population of S. halepense
 that conditioned the soil. These results indicate that on Hainan island,
 S. halepense can outburst and proliferate despite negative feedback with
 soil biota, and populations of S. halepense differ little in their
 interactions with soil.
DOI: 10.5281/zenodo.18399388
title: Mortality and YLL costs attributable to PM2.5 and O3

description: Mortality and YLL costs attributable to PM2.5 and O3.
DOI: 10.5281/zenodo.18399389
title: Mortality and YLL costs attributable to PM2.5 and O3

description: Mortality and YLL costs attributable to PM2.5 and O3.
DOI: 10.5061/dryad.08kprr54f
title: Data on bird abundance in urban woodlands in 32 Swedish cities

description: The expansion of urban areas is increasingly contributing to biodiversity
 declines. Several studies have analyzed the effect of increasing
 urbanization on bird diversity, but few have differentiated effects of
 urban landscapes (matrix) from changes in focal habitat quality at
 multiple spatial scales. In this study we analyzed the effect of
 urbanization on bird communities in individual (local scale) and across
 multiple (regional scale) cities while controlling for the quality of
 sampled natural habitats. We conducted bird point counts and habitat
 quality mapping of trees, dead wood and shrubs in 459 forest remnants
 along an urbanization gradient in 32 cities in Sweden. We then analyzed
 how the degree of urbanization affected species richness of
 woodland-breeding bird and red-listed bird species at a regional and local
 scale. We also analyzed how urbanization affected beta-diversity and
 dissimilarity between communities at the different spatial scales, and if
 dissimilarities in species communities along the urbanization gradient
 were driven by species nestedness or turnover. We found that urbanization
 decreased species richness, and the number of red-listed species, at both
 the regional and local scale. Dissimilarities in woodland-breeding bird
 communities among urban, semi-urban and peri-urban areas at the local
 scale were particularly due to turnover, and at the regional scale to
 nestedness. Since there was no difference in habitat quality among
 woodlands across the urbanization gradient, we conclude that landscape
 urbanization systematically causes poorer and more homogeneous bird
 communities. However, despite that natural habitats in cities contribute
 less to the regional diversity, they are critical to maintain the local
 bird communities of individual cities and their surroundings.
DOI: 10.48804/n94q4s
title: Replication Data for: Abnormal carnitine concentrations in critical illness associated with compromised outcome

description: Carnitine deficiency affects mitochondrial and muscle function, but its relevance during critical illness remains unknown. Our aim was to investigate the relationship between plasma free carnitine concentrations and outcome in prolonged critical illness.
In this secondary analysis of the EPaNIC randomised controlled trial, abnormal plasma free carnitine concentrations, measured on ICU-day-6 (N = 1600), were defined by their association with a lower likelihood of an earlier alive ICU discharge (the primary endpoint) in a Cox proportional hazards model. Subsequently, they were binned based on their distribution and partial residuals in the Cox-model. Adjusted multivariable Cox-model and logistic regression analysed both association of abnormal carnitinemia with acute and long-term morbidity and mortality, and predictive risk factors.
DOI: 10.5061/dryad.ns1rn8pvn
title: Negative E-cadherin expression on bone marrow myeloma cell membranes is associated with extramedullary disease

description: Background: The loss of E-cadherin expression and the induction of
 N-cadherin are known as hallmarks of the epithelial-to-mesenchymal
 transition, an essential initial step in the process of metastasis in
 solid tumors. Although several studies have reported expressions of these
 cadherins in patients with multiple myeloma (MM), their clinical
 significance is unknown as MM cells are non-epithelial. Methods: In this
 study, we examined the expression of E- and N-cadherins by
 immunohistochemistry using bone marrow (BM) biopsy specimens from 31 newly
 diagnosed MM patients and in subsequent biopsy specimens from six of
 these. Results: Negative E-cadherin expression on BM myeloma cell
 membranes was significantly associated with the presence of soft-tissue
 masses arising from bone lesions and breaking through the cortical bone,
 referred to as extramedullary disease (EMD). Conclusions: Given the
 aggressive nature of EMD, our study suggests that screening for E-cadherin
 using BM immunohistochemistry is one measure that could predict the
 development of EMD in patients with MM.
DOI: 10.5061/dryad.59zw3r297
title: The role of hemostatic agents following dental extractions: a systematic review and meta-analysis

description: Objective: This study critically evaluated the role of hemostatic agents
 following dental extractions, and the benefits they add over conventional
 hemostatic measures. Materials and methods: a literature search was
 conducted, including publications that fulfilled the criteria developed
 based on the PICOS guidelines; Population: patients who receive simple or
 surgical tooth extractions, Intervention: the use of hemostatic agents
 following dental extraction, Control: any type of conventional hemostatic
 measures (i.e. suture, gauze pressure), Outcome: time to achieve
 hemostasis following tooth removal, postoperative pain, swelling, or
 bleeding events, and Study design: randomized/controlled clinical trials.
 Results: Twenty-eight articles met the inclusion criteria, and 24 were
 meta-analyzed. Several types of hemostatic agents were used, namely tissue
 adhesives made from cyanoacrylate or fibrin, tranexamic acid,
 hemocoagulase, collagen membrane, HemCon dental dressing, epsilon
 aminocaproic acid, Surgicel, sponges or plugs composed of gelatin,
 oxidized cellulose, and fibrin. Newer hemostatic agents were also applied,
 such as Ankaferd blood stopper, and feracrylum. Hemostatic agents
 demonstrated significantly shorter time to achieve hemostasis and fewer
 bleeding events in patients on antithrombotic drugs or with bleeding
 disorders (WMD= -2.12, 95% CI -2.63 to -1.61, P &lt; 0.00001, and RR
 0.61, 95% CI 0.43 to 0.86; P= 0.005, respectively). Furthermore, the use
 of these agents resulted in significantly less postoperative pain
 following 3rd molar surgery in healthy patients (WMD= -0.33, 95% CI -0.65
 to -0.02, P = 0.04). Conversely, they did not have any effect on
 postoperative swelling (WMD= -0.11, 95% CI -0.31 to 0.08, P = 0.26). The
 time needed to finish the surgical procedure when hemostatic agents were
 used was shorter but with no significant difference (MD= -78.93, 95% CI
 -187.35 to 29.49, P = 0.15). Conclusion: Included studies differ in their
 methods of reporting bleeding, pain, and swelling. Thus, the results of
 this article should be confirmed in future research. Within these
 limitations, it is concluded that hemostatic agents lead to faster
 hemostasis and fewer postoperative bleeding incidences, compared to
 conventional hemostatic measures. Their use is highly recommended
 following dental extractions in patients on antithrombotic drugs or with
 bleeding disorders, who are likely to develop postoperative hemorrhage
 events.
DOI: 10.7280/d19h6j
title: Forward entrainment in pitch discrimination (data analysis)

description: The Matlab programs uploaded here generate 5 figures (3 primary and 2
 supplemental), 2 videos, and 4 audio files associated with a reanalysis of
 findings by Lin et al. (2021), Eur. J. Neurosci,
 https://doi.org/10.1111/ejn.15208.  Several studies have
 demonstrated psychophysical forward entrainment in a pitch-discrimination
 task. Lin et al. (2021) has challenged these findings by demonstrating
 that a sequence of 4 entraining pure tones does not affect the ability to
 determine whether an FM pulse, presented after termination of the
 entraining sequence, has swept up or down in frequency.  They
 conclude that rhythmic sequences do not facilitate pitch discrimination.
 Here we provide data analysis that shows several methodological and
 stimulus design confounds in Lin et al.’s study that may explain their
 failure to observe forward entrainment in pitch discrimination.
DOI: 10.5061/dryad.sj3tx966n
title: Measurement of male and female morphologies in Mercurialis annua

description: We provide a dataset documenting the changes in male and female
 morphological traits after evolution at low- and high-density during three
 generations in the dioecious plant species Mercurialis annua. Our dataset
 corresponds to results from an experimental evolution protocol in which we
 have measured male and female traits after the evolution of ten
 experimental independent populations at the two contrasting densities.
 Seeds were initially collected in various populations of the species range
 and grown for three generations in a common garden, which aim was to build
 a seed bank with large genetic variance for experimental evolution. The
 seeds resulting from this initial generation (G0) have than been grown to
 build ten experimental populations (POP in the dataset) that were affected
 either to low or high density (TREAT in the dataset). Each population was
 grown separately from the other populations and its assigned density was
 applied during the last four weeks of growth. After three generations of
 evolution at their assigned density, seeds resulting from the third
 generation of evolution were grown in a common garden with two spatial
 blocks (BLOCK in the dataset) in which we recorded the spatial position of
 each plants (x and y in the dataset) measured vegetative and reproductive
 traits in male and female plants.
description: A README file is provided as well as a description of the dataset
 directly within the datafile.
DOI: 10.6084/m9.figshare.31167997
title: DataSet RME

description: Dataset Research Fractal in Class
DOI: 10.6084/m9.figshare.31167997.v1
title: DataSet RME

description: Dataset Research Fractal in Class
DOI: 10.5061/dryad.98sf7m0kr
title: Species-level CWM values mask contrasting intra- vs interspecific trait shifts at subtropical forest edges

description: Altered microclimatic conditions and higher disturbance at forest edges
 create environmental stress and modify resource gradients from edge to
 interior, changing the selection pressures acting on individuals. Although
 community-weighted trait-mean (CWM) shifts along edge gradients have been
 widely documented at the species level, it is unclear how edge effects act
 at the individual level, and whether the direction of intraspecific trait
 shifts mirrors that of CWM shifts in response to edge effects. On 20
 islands in the Thousand Island Lake, China, we established 484 plots (2×2
 m) in a stratified random design across distances of 0 – 128 m from the
 forest edge. Within each plot, we sampled leaves (n=34,768) from within
 and among all 2,993 individuals of 68 species and measured five leaf
 traits (leaf area, LA; specific leaf area, SLA; leaf dry matter content,
 LDMC; thickness, LT; chlorophyll content, LCC). Using generalized linear
 mixed models, we found that different leaf traits exhibited contrasting
 shifts in inter- vs. intraspecific trait variation in response to edge
 effects. For SLA, LT, and LCC, negative covariance between inter- and
 intraspecific trait shifts resulted in dampening of community-wide trends
 compared to CWM response to edge effects. In contrast, the community-wide
 trend for LDMC was reinforced due to positive covariance between inter-
 and intraspecific trait shifts, while for LA the direction of covariance
 shifted from negative to positive on small vs. large islands. Together,
 edge effects alter selection regimes in reassembling plant communities.
 Predicting the community-wide consequences depends on the degree to which
 there is negative vs. positive covariance between species sorting and
 within-species adaptation. The widely-used CWM approach can mask
 contrasting trait selection pressures acting on individuals within local
 populations. Individual-level trait variation can improve understanding of
 community re-assembly trajectories in response to global environmental
 change.
DOI: 10.5061/dryad.cc2fqz67j
title: Relating wing morphology and immune function to patterns of partial and differential bat migration using stable isotopes

description: Migration is energetically expensive and is predicted to drive similar
 morphological adaptations and physiological trade-offs in migratory bats
 and birds. Previous studies suggest that fixed traits like wing morphology
 vary among species and individuals according to selective pressures on
 flight, while immune defenses can vary flexibly within individuals as
 energy is variably reallocated throughout the year. We assessed
 intraspecific variation in wing morphology and immune function in
 silver-haired bats (Lasionycteris noctivagans), a species that follows
 both partial and differential migration patterns. We hypothesized that if
 bats experience energy constraints associated with migration, then wing
 morphology and immune function should vary based on migratory tendency
 (sedentary or migratory) and migration distance. We predicted that
 long-distance migrants would have reduced immune function and more
 migration-adapted wing shapes compared to resident or short-distance
 migrating bats. We estimated breeding latitude of spring migrants using
 stable hydrogen isotope techniques. Our sample consisted primarily of male
 bats, which we categorized as residents, long-distance northern migrants,
 short-distance northern migrants, and southern migrants (apparent breeding
 location south of capture site). Controlling for individual condition and
 capture date, we related wing characteristics and immune indices among
 groups. Some, but not all, aspects of wing form and immune function varied
 between migrants and residents. Long-distance northern migrants had larger
 wings than short-distance northern migrants and lower wing loading than
 southern migrants. Compared with resident bats, short-distance northern
 migrants had reduced IgG while southern migrants had heightened
 neutrophils and neutrophil-to-lymphocyte ratios. Body fat, aspect ratio,
 wing tip shape, and bacteria killing ability did not vary with migration
 status or distance. In general, male silver-haired bats do not appear to
 mediate migration costs by substantially downregulating immune defenses or
 to be under stronger selection for wing forms adapted for fast,
 energy-efficient flight. Such phenotypic changes may be more adaptive for
 female silver-haired bats, which migrate farther and are more constrained
 by time in spring than males. Adaptations for aerial hawking and the use
 of heterothermy by migrating bats may also reduce the energetic cost of
 migration and the need for more substantial morphological and
 physiological trade-offs.