cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh189328g
title: Data from: Integrating 3D models with morphometric measurements to improve volumetric estimates in marine mammals

description: 1. Studies of body condition are key to understanding the health,
 bioenergetics, and ecological roles of marine mammals. Due to challenges
 in studying marine mammals at sea, body condition is often approximated
 using metrics representing the size of the dorsal surface visible from
 aerial imagery, but quantifying variability in body volume would enable a
 more holistic understanding of bioenergetics. Further, the number and
 location of measurements needed to accurately quantify body condition has
 received little attention. Three-dimensional (3D) models provide a
 promising tool for representing morphology and providing holistic
 estimates of marine mammal body condition when combined with field-based
 morphometric measurements. 2. We use humpback whales (Megaptera
 novaeangliae) to demonstrate the utility of 3D models for estimating body
 condition in marine mammals. We integrate morphometric measurements taken
 from Unoccupied Aerial Vehicles (UAVs) with scalable 3D models to generate
 estimates of humpback whale body volume. We assess which and how many
 morphometric measurements are required to accurately estimate body volume
 and compare the error between volume estimates derived from 3D models and
 previously developed models representing volume as a series of ellipses.
 Using UAV measurements, we assess the contribution of each morphometric
 measurement to volumetric estimates, and quantify the error produced by
 all combinations and numbers of morphometric measurements (131,072
 combinations). 3. Error in volume estimates from 3D models generated with
 as few as five width measurements was &lt;5% compared to the full
 models and was lower than the error produced when using five width
 measurements with the elliptical approach. We suggest that by conserving
 the external morphology of marine mammals, 3D models allow body volume and
 body condition to be estimated accurately with few measurements. 4. We
 provide code and guidelines for creating 3D models using the open-source
 software Blender and for assessing which measurements are needed to
 accurately capture the morphology of cetaceans. The 3D modeling approach
 we present will facilitate studies of intra- and interannual changes in
 body volume in marine mammals, which is vital to providing a more holistic
 understanding of bioenergetics and to assessing responses to environmental
 change and anthropogenic stressors.
description: See the associated manuscript for details.
description: Model scaling were done in Blender. Analyses
 were conducted in R.
DOI: 10.5061/dryad.d7wm37q45
title: Climbing flora of India

description: This dataset provides a comprehensive list of climber species in India.
 Species' names have been revised to reflect APG IV classification.
DOI: 10.5061/dryad.wm37pvmqm
title: Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species

description: 1. Juveniles are typically less resistant (more susceptible) to infectious
 disease than adults, and this difference in susceptibility can help fuel
 the spread of pathogens in age-structured populations. However
 evolutionary explanations for this variation in resistance across age
 remain to be tested. 2. One hypothesis is that natural selection has
 optimized resistance to peak at ages where disease exposure is greatest. A
 central assumption of this hypothesis is that hosts have the capacity to
 evolve resistance independently at different ages. This would mean that
 hosts populations have a) standing genetic variation in resistance at both
 juvenile and adult stages, and b) that this variation is not strongly
 correlated between age-classes so that selection acting at one age does
 not produce a correlated response at the other age 3. Here we evaluated
 the capacity of three wild plant species (Silene latifolia, S. vulgaris,
 and Dianthus pavonius) to evolve resistance to their anther-smut pathogens
 (Microbotryum fungi), independently at different ages. The pathogen is
 pollinator-transmitted, and thus exposure risk is considered to be highest
 at the adult flowering stage. 4. Within each species we grew families to
 different ages, inoculated individuals with anther smut, and evaluated the
 effects of age, family and their interaction on infection. 5. In two of
 the plant species, S. latifolia and D. pavonius, resistance to smut at the
 juvenile stage was not correlated with resistance to smut at the adult
 stage. In all three species, we show there are significant age*family
 interaction effects, indicating that age-specificity of resistance varies
 among the plant families. 6. Synthesis: These results indicate that
 different mechanisms likely underlie resistance at juvenile and adult
 stages and support the hypothesis that resistance can evolve independently
 in response to differing selection pressures as hosts age. Taken together
 our results provide new insight into the structure of genetic variation in
 age-dependent resistance in three well-studied wild host-pathogen systems.
description: For experimental setup and data collection methods please see the
 methods section of the manuscript.
description: Data files will work with microsoft excel, numbers, or any basic
 text editor.  R code files can be opened with the opensource software
 R.
DOI: 10.5061/dryad.931zcrjnz
title: Data for: Off-host survival of blacklegged ticks in eastern North America: A multi-stage, multi-year, and multi-site study

description: Climatic conditions are widely thought to govern the distribution and
 abundance of ectoparasites, such as the blacklegged tick (Ixodes
 scapularis), vector of the agents of Lyme disease and other emerging human
 pathogens. However, translating physiological tolerances to distributional
 limits or mortality is challenging. Ticks may be able to avoid or tolerate
 unsuitable conditions, and what is lethal to one life history stage may
 not extend to others. Thus, even after decades of research there are clear
 gaps in our knowledge about how climatic conditions determine tick
 distributions or patterns of abundance. We present the results of a
 comprehensive, three-year study of the influence of local temperatures and
 vapor pressure deficits on the survival of each free-living, off-host
 stage of I. scapularis in semi-natural enclosures across three locations
 that span their current distribution in eastern North America. We found
 that only larvae are clearly sensitive to direct mortality from climatic
 conditions, specifically desiccating conditions, whereas mortality of
 nymphs and adults appears to stem from exhausted energy reserves. We also
 found strong evidence that key developmental transitions in the tick’s
 life cycle—fed larvae molting into to nymphs, fed nymphs molting into
 adults, and fed females producing larvae (via egg masses)—were all
 strongly temperature-dependent, though temperatures were not limiting in
 any of our sites. Collectively, our results suggest that climate is likely
 to impact I. scapularis largely through its impact on the larval stage.
description: Primary data consists of known numbers of ticks of a given life
 stage deployed in soil core enclosures (SCEs) and then the number
 recovered alive at a later date. This includes all flat (unfed) tick life
 stages as well as recently fed ticks molting (fed larvae and fed nymphs)
 or producing offspring (fed adults). These survivorship and life history
 transition data are paired with data on the daily ambient conditions
 (temperature and vapor pressure deficit) averaged across the roughly
 hourly readings of numerous iButton data loggers.
description: Data are in Excel format (xlsx or csv file types). Scripts are
 written in Rmd files and require an instalation of Rstan.
DOI: 10.5281/zenodo.12780053
title: AI classification of normal and malignant cells on the basis of their viscoelastic properties
DOI: 10.5281/zenodo.18401137
title: AI classification of normal and malignant cells on the basis of their viscoelastic properties
DOI: 10.5061/dryad.f4qrfj6zp
title: Early postoperative pain trajectories after posterolateral and axillary approaches for thoracic surgery: A prospective monocentric observational study

description: Less invasive thoracotomies may reduce early postoperative pain. The aims
 of this study were to identify pain trajectories from postoperative day 0
 to 5 after posterolateral and axillary thoracotomies and identify
 potential factors related to the worst" trajectory. Patients
 undergoing a posterolateral (92 patients) or axillary (89 patients)
 thoracotomy between July 2014 and November 2015 were analyzed in this
 prospective monocentric cohort study. The best-fitting model resulted in
 four pain trajectory groups: trajectory 1, the “worst”, with 29.8% of the
 patients with permanent significant pain; trajectory 2 with patients with
 low pain (32.6%), trajectory 3 with patients with a steep decrease in pain
 (22.7%), trajectory 4 with patients with a steep increase (14.9%).
 According to a multinomial logistic model multivariable analysis, some
 predictive factors allow differentiation between trajectory groups 1 and
 2. Risk factors for permanent pain are the existence of preoperative pain
 (OR =6.94, CI 95% [1.54-31.27]) and scar length (OR=1.20 [1.05-1.38])). In
 contrast, ASA class III is a protective factor to be in group 1 (OR=0.02
 [0.001-0.52]). In conclusion, early postoperative pain can be
 characterized by four trajectories and preoperative pain is the major
 factor for the worst trajectory of early postoperative pain.
description: eCRF
DOI: 10.5061/dryad.k3j9kd5b2
title: Python code generating the data of figures 2, 3, 4, 5 and 6 of the manuscript: The evolution of cooperation in the unidirectional linear division of labour of finite roles

description: The evolution of cooperation is an unsolved mystery, which we see in many
 social and biological systems. In the study titled "The evolution of
 cooperation in the unidirectional linear division of labour of finite
 roles", we investigate under which sanction systems and how the
 evolution of cooperation happens in the linear division of
 labour.  This python code has been used to produce the results of
 Figures 2, 3, 4, 5, and 6 of the manuscript. This code shows the evolution
 of cooperation among the population of various different groups which have
 different roles to play in the linear division of labour, on the basis of
 numerical analysis of a partial differential equation system, which
 originates from the replicator equations used in the evolutionary game
 theory.  We find the locally stable equilibria using this code,
 which shows the ultimate results of the dynamics in the system under given
 parameters. Figures 3, 5, and 6 are direct products of the code, showing
 the dynamics of a system, and figures 2 and 4 are the end results of those
 dynamics.  We found that in a social dilemma situation,
 cooperation never evolves in the system without punishment. However, with
 sanction systems by introducing a suitable amount of punishment, while
 having a suitable findability of the defector, and a suitable initial
 population structure, cooperation can evolve. These results can be found
 with this code. We have no legal or ethical concerns regarding this data
 as this is a numerical analysis based on theoretical equations. 
description: These are python codes for numerical simulation of replicator
 equations to generate figures 2, 3, 4, 5, and 6 of the study titled
 "The evolution of cooperation in the unidirectional linear division
 of labour of finite roles". For making the code easier to read, .pdf
 version is given.
DOI: 10.5061/dryad.t4b8gtj4v
title: Flooding triggers increased surface activity in a bottom-dwelling turtle

description: Mexican giant musk turtles (Staurotypus triporcatus) are large,
 bottom-dwelling turtles in Central America. Following a flooding event,
 they were frequently seen at the surface, wherease they were never seen
 prior to the flooding. The data were collected using a motorized canoe to
 search for turtles at the surface. When possible, notes were made about
 size. In some cases, it was possible to capture the turtles and measure
 them. Observations of times, dates, sexes, and sizes of turtles are
 presented, as well as a measure of search effort (times of day searched
 and distance of creek searched). Missing values are reported as NA.
description: The data are dates, sizes, and sizes of turtles we observed. The
 data are explained in the file.
DOI: 10.5061/dryad.xsj3tx9jj
title: Divergent trait responses to nitrogen addition in tall and short species

description: Asymmetrical light competition and direct detrimental effect of nitrogen
 have been proposed as two main mechanisms driving species richness
 declines following nitrogen (N) addition. N addition is also known to
 alter functional trait composition towards increased dominance of tall and
 fast-growing species. However, whether trait changes vary between species
 and, in particular, how the traits of tall and short species respond to N
 addition has rarely been studied. Understanding whether different trait
 changes occur for tall and short species would provide insight into
 mechanisms underlying N addition effects. Based on a long-term N addition
 experiment, we measured the natural height of 44 plant species and the
 photosynthetic active radiation (PAR) at seven heights in the vegetation
 and identified a clear stratification of the plant community into tall
 species (&gt;30cm tall), which experienced high light conditions, and
 short species that grew under the canopy. We also measured four functional
 traits, including maximum plant height, specific leaf area, leaf dry
 matter content and leaf thickness, on 35 species that occurred in
 fertilized and unfertilized plots. Structural equation modelling revealed
 that nitrogen (N) addition significantly reduced species richness by
 enhancing light asymmetry and had no direct effects, suggesting that N
 detrimental effects are negligible in our system. Consistent with this, we
 found different responses of traits and diversity for the tall and short
 species. Specifically, N addition reduced the number of short species but
 increased the number of tall species. In addition, specific leaf area
 increased, and leaf dry matter content decreased, for short species only,
 suggesting that they shifted to a fast growth strategy to cope with lower
 light levels. In contrast, tall species increased their height further to
 capture more light at the top of the canopy.   Synthesis. The
 divergent trait responses observed for tall and short species show that
 although certain traits, like height and leaf traits, show correlated
 responses at the whole community level, these correlations may not be
 consistent across all species. Together, our results highlight that light
 competition is the main mechanism driving species loss following N
 addition gradient.
DOI: 10.5061/dryad.h44j0zpp5
title: Species richness and phylogenetic structure of 249 global islands

description: To study how the phylogenetic composition of native island floras
 influences naturalized alien species richness, we assembled a dataset of
 249 global islands from the global inventory of floras and traits (GIFT,
 Weigelt et al., 2020) and the Global Naturalized Alien Flora database
 (GloNAF, van Kleunen et al. 2019). The dataset contains naturalized and
 native species number, island area (km²) geological information from these
 sources. Additionally, we calculated three phylogenetic community metrics
 (Faith's PD, MPD and MNTD) using a global seed plant phylogeny (Smith
 and Brown, 2018) with different source pools, unstandardized Faith's
 PD with global island species pool, global island and mainland species
 pool and without missing species added to the phylogeny (pd, pd.matched),
 standardized measures with global island species pool and missing species
 added into the phylogeny (pd.ses, mpd.ses, mntd.ses), standardized
 measures with global island and mainland species pool and missing species
 added into the phylogeny (pd.ses.all, mpd.ses.all, mntd.ses.all) and
 standardized measures with global island species pool and missing species
 added into the phylogeny (pd.ses.matched, mpd.ses.matched,
 mntd.ses.matched). We also included biogeographical and socio-economical
 variables for the islands: mean annual precipitation (mm) and temperature
 (°C) (Karger et al., 2017), distance to closest mainland in km (Weigelt
 and Kreft 2013 and Moser et al., 2018) and terrain ruggedness index (Riley
 et al., 1999, USGS 2011). Finally, we included gross domestic product and
 number of ports (World Port index 2019) and airports (Open Flights 2015).
DOI: 10.5061/dryad.g4f4qrft1
title: Development of chronic pain after posterolateral and axillary approaches for thoracic surgery: A prospective monocentric observational study

description: Mini-invasive thoracotomies may reduce chronic pain and pain-related
 functional impairment. The aims of part 2 of the study were to assess
 their incidence after posterolateral and axillary thoracotomies and to
 identify potential factors of chronic pain. Patients undergoing a
 posterolateral (79 patients) or axillary (79 patients) thoracotomy between
 July 2014 and November 2015 were analyzed in this prospective monocentric
 cohort study. At the 4-month assessment, more patients had chronic pain in
 the posterolateral group (60.8% vs 40.5%; p=0.017).  There was a
 significant difference between groups favoring the axillary group: less
 level of catastrophism (p=0.021) and less impact of pain on daily
 activities (globally, p=0.009; routine activities subscore, p=0.010,
 chosen activity subscore, p=0.030). According to a multinomial logistic
 model multivariable, three factors are associated with the presence of
 chronic pain: the presence of pain before surgery (OR=2.36, CI 95%
 [1.03-5.39]), a large posterolateral incision (OR=4.14 [1.25-13.72]) and
 the intensity of pain during mobilization of the ipsilateral shoulder at
 postoperative day 6 (OR=1.37 [1.10-1.70]). In conclusion, chronic pain is
 less frequent after an axillary approach than after a posterolateral one.
 Identified risk factors for chronic pain should lead to more aggressive
 management of preoperative and early postoperative pain and favor the
 mini-invasive approach.
description: eCRF
DOI: 10.5061/dryad.2547d7wt5
title: Data from: A causal role of anterior prefrontal-putamen circuit for response inhibition revealed by transcranial ultrasound stimulation in humans

description: Stopping an inappropriate response requires the involvement of the
 prefrontal-subthalamic hyperdirect pathway. However, how the
 prefrontal-striatal indirect pathway contributes to stopping is poorly
 understood. In this study, transcranial ultrasound stimulation is used to
 perform interventions in a task-related region in the striatum. Functional
 magnetic resonance imaging (MRI) reveals activation in the right anterior
 part of the putamen during response inhibition, and ultrasound stimulation
 to the anterior putamen, as well as the subthalamic nucleus, results in
 significant impairments in stopping performance. Diffusion imaging further
 reveals prominent structural connections between the anterior putamen and
 the right anterior part of the inferior frontal cortex (IFC), and
 ultrasound stimulation to the anterior IFC also shows significant impaired
 stopping performance. These results demonstrate that the right anterior
 putamen and right anterior IFC causally contribute to stopping and suggest
 that the anterior IFC-anterior putamen circuit in the indirect pathway
 serves as an essential route for stopping.
description: The files (X.dtseries.nii / X.dlabel.nii) can be viewed by using
 wb_view in Connectome Workbench
 (https://www.humanconnectome.org/software/connectome-workbench).
DOI: 10.5061/dryad.dncjsxm2v
title: Estimating global GPP from the plant functional type perspective using a machine learning approach

description: The long-term monitoring of gross primary production (GPP) is crucial to
 the assessment of the carbon cycle of terrestrial ecosystems. In this
 study, a well-known machine learning model (Random Forest, RF) is
 established to reconstruct the global GPP dataset named ECGC_GPP. The
 model distinguished nine functional plant types, including C3 and C4
 crops, using eddy fluxes, meteorological variables, and leaf area index as
 training data of the RF model. Based on ERA5_Land and the corrected GEOV2
 data, the global monthly GPP dataset at a 0.05-degree resolution from 1999
 to 2019 was estimated. The results showed that the RF model could explain
 74.81% of the monthly variation of GPP in the testing dataset, of which
 the average contribution of Leaf Area Index (LAI) reached 41.73%. The
 average annual and standard deviation of GPP during 1999–2019 were 117.14
 ± 1.51 Pg C yr-1, with an upward trend of 0.21 Pg C yr-2 (p &lt;
 0.01). By using the plant functional type classification, the
 underestimation of cropland is improved. Therefore, ECGC_GPP provides
 reasonable global spatial patterns and long-term trends of annual GPP.
description: We unified the ERA5_Land and
 the corrected GEOV2 datasets to 0.05 degree and monthly scales. The
 meteorological and remote sensing datasets were classified by the eight
 PFTs to estimate the GPP of different PFT. Particularly, we established
 site-level PFT training models for CRO_C3 and CRO_C4, respectively, due to
 their significant differences. The CRO cells were a mixture of CRO_C3 and
 CRO_C4. Therefore, trained CRO_C3 and CRO_C4 models were both applied to
 the CRO cells and multiplied by their respective proportions to generate
 the final GPP estimation of CRO. This is what we designed to improve the
 current situation of GPP underestimation over CRO_C4 dominated regions. In
 this way, we generated a 0.05 degree and monthly scales global GPP dataset
 (ECGC_GPP) from 1999 to 2019.
description: The ECGC_GPP dataset is stored in .nc file format and can be
 opened using Matlab or Python.
DOI: 10.5061/dryad.5tb2rbp6k
title: Data for: Osteocytes regulate senescence of bone and bone marrow

description: The skeletal system contains a series of sophisticated cellular lineages
 arisen from the mesenchymal stem cells (MSCs) and hematopoietic stem cells
 (HSCs), that determine the homeostasis of bone and bone marrow. Here we
 reasoned that osteocyte may exert a function in regulation of these
 lineage cell specifications and tissue homeostasis. Using a mouse model of
 conditional deletion of osteocytes by the expression of diphtheria toxin
 subunit ? (DTA) in dentin matrix protein 1 (DMP1) positive
 osteocytes, we demonstrated that partial ablation of DMP1 positive
 osteocytes caused severe sarcopenia, osteoporosis and degenerative
 kyphosis, leading to shorter lifespan in these animals. Osteocytes'
 reduction altered mesenchymal lineage commitment resulting in impairment
 of osteogenesis and induction of osteoclastogensis. Single cell RNA
 sequencing further revealed that hematopoietic lineage was mobilized
 towards myeloid lineage differentiation with expanded myeloid progenitors,
 neutrophils and monocytes, while the lymphopoiesis was impaired with
 reduced B cells in the osteocyte ablation mice. The acquisition of a
 senescence-associated secretory phenotype (SASP) in both osteoprogenic and
 myeloid lineage cells was the underlying cause. Together, we showed that
 osteocytes play critical roles in regulation of lineage cell
 specifications in bone and bone marrow through mediation of senescence.