cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6g97722
title: Data from: Wind pollination over 70 years reduces the negative genetic effects of severe forest fragmentation in the tropical oak Quercus bambusifolia

description: Whether wind pollination in trees can offset the negative genetic
 consequences of anthropogenic forest fragmentation is not clearly
 established. To answer this question, we examined the demographic genetics
 of Quercus bambusifolia over a 70-year recovery period in highly
 fragmented forests in Hong Kong. We sampled 1138 individuals from 37
 locations, and genetically analysed the chronosequence through the
 classification of tree diameters from the same populations using 13
 microsatellite markers. Our study reveals that severe fragmentation caused
 a significant genetic bottleneck with very few remaining but genetically
 diverse individuals. We observed an enhanced genetic diversity during
 demographic recovery. We found full-sibs within populations and half-sibs
 across the study range. This reflects a limited seed dispersal and
 extensive pollen flow. Despite reduced genetic structure both among and
 within populations, overall a strong persisting genetic differenti ation
 (F’ST = 0.240, P &lt; 0.01) and significant small-scale spatial
 genetic structure (F(1) = 0.13, Sp = 0.024, P &lt; 0.01) were
 observed. Existing bottlenecks and low effective population sizes within
 the temporal chronosequence suggest that the long-term effect of severe
 fragmentation cannot be entirely eliminated by wind pollination with
 demographic recovery in the absence of effective seed dispersal. Our
 results lead to recommendations for forest management.
description: SSR and DBH for Quercus
 bambusifoliaSSR for Quercus
 bambusifolia.xlsx
DOI: 10.5061/dryad.1s56s89
title: Data from: Trophic niche changes associated to habitat fragmentation in a Neotropical bat species

description: Habitat fragmentation could alter ecological traits including species
 trophic habits. Here, we used carbon and nitrogen stable isotope ratios to
 establish differences in isotopic niche width and food resource use
 between forest fragments and the continuous forest for the phyllostomid
 frugivorous bat Artibeus lituratus. Using mist nests, we captured bats
 from two forest fragments and two sites in continuous forest, and sampled
 from each individual captured three body tissues with contrasting turnover
 rates (skin, muscle and liver). Samples were collected between
 February-March (austral summer) and between August-September (austral
 winter). In addition, in each sampling site and season we collected
 potential food resources (fruits and insects) consumed by our A.
 lituratus. Our findings indicate that A. lituratus had a predominantly
 omnivorous diet, with high consumption of insects during summer in forest
 fragments. The increasing consumption of insects in these fragments seems
 to have led to a wider isotopic niche, in relation to the continuous
 forest. Because A. lituratus is typically a seed disperser, changes in
 trophic habits in the forest fragments from frugivory to insectivory may
 diminish their role in forest regeneration.
description: Muñoz-Lazo_S1_Dataset
DOI: 10.5061/dryad.pp77bs0
title: Data from: Short-term, but not long-term, increased daytime workload leads to decreased night-time energetics in a free-living song bird

description: Reproduction is energetically expensive and to obtain sufficient energy,
 animals can either alter their metabolic system over time to increase
 energy intake (increased-intake hypothesis) or reallocate energy from
 maintenance processes (compensation hypothesis). The first hypothesis
 predicts a positive relationship between basal metabolic rate (BMR) and
 energy expenditure (DEE) because of the higher energy demands of the
 metabolic system at rest. The second hypothesis predicts a trade-off
 between different body functions, with a reduction of the BMR as a way to
 compensate for increased daytime energetic expenditure. We experimentally
 manipulated the workload of wild pied flycatchers by adding or removing
 chicks when chicks were 2 and 11 days old. We then measured the feeding
 frequency (FF), DEE and BMR at day 11, allowing us to assess both short-
 and long-term effects of increased workload. The manipulation at day 2
 caused an increase in FF when broods were enlarged, but no response in DEE
 or BMR, while the manipulation at day 11 caused an increase in FF, no
 change in DEE and a decrease in BMR in birds with more chicks. Our results
 suggest that pied flycatchers adjust their workload but that this does not
 lead to a higher BMR at night (no support for the increased intake
 hypothesis). In the short term, we found that birds reallocate energy with
 a consequent reduction of BMR (evidence for the compensation hypothesis).
 Birds thus resort to short-term strategies to increase energy expenditure,
 which could explain why energy expenditure and hard work are not always
 correlated in birds.
description: Visser et al. 2019
 DataResults of the field
 experiment including measurements of the adult birds and chicks in
 relation to the treatments.Visser_etal_2019_Data.xlsx
DOI: 10.5061/dryad.j656q74
title: Data from: Selection on tropane alkaloids in native and non-native populations of Datura stramonium

description: Theories of plant invasion based on enemy release in a new range assume
 that selection exerted by specialist herbivores on defence traits should
 be reduced, absent, or even selected against in the new environment. Here,
 we measured phenotypic selection on atropine and scopolamine concentration
 of Datura stramonium in eight native (Mexico) and 14 non-native (Spain)
 populations. Native populations produced between 20 and 40 times more
 alkaloid than non-native populations (atropine: 2.0171 vs. 0.0458 mg/g;
 scopolamine: 1.004 vs. 0.0488 mg/g, respectively). Selection on alkaloids
 was negative for atropine and positive for scopolamine concentration in
 both ranges. However, the effect sizes of selection gradients were only
 significant in the native range. Our results support the assumption that
 the reduction of plant defence in the absence of the plant’s natural
 enemies in invasive ranges is driven by natural selection.
description: tropane alkaloid
 concentration of native and non-native populations of Datura
 stramoniumData include leaf
 concentration of Atropine and Scopolamine in plants of Datura stramonium.
 Eight and fourteen populations from Mexico and Spain, respectively, are
 included. Also, seed production per plant is provided.
DOI: 10.5061/dryad.sh64br0
title: Data from: The effect of seepage and weak interlayer on the failure modes of surrounding rock - model tests and numerical analysis

description: The presence of weak interlayers and groundwater are common adverse
 geological conditions in tunnels. To investigate the modes of failure of
 rock masses surrounding tunnels owing to weak interlayers and groundwater,
 model tests and numerical simulations were conducted in this study based
 on two cases, and a model that considers only the weak interlayer was
 conducted for comparison. Based on the tests, differences between two
 models in terms of rock pressure, displacement, cracks and strain were
 analysed. The results reveal that the presence of groundwater has a
 significant effect on the space–time distribution of stress, displacement
 and cracks in the surrounding rock. Furthermore, based on the numerical
 model, the seepage field was analysed in terms of pore water pressure,
 permeability and the seepage process to understand the joint action of
 groundwater and weak interlayer on the failure mechanism of tunnels. The
 results show that the groundwater and interlayer complement each other to
 induce the failure mode of the surrounding rock. The water accelerates
 slip in the interlayer and the development of cracks. Conversely,
 low-strength, muddy weak interlayer serve as the channels of water flow,
 resulting in deformations and cracks at different locations and different
 failure modes.
description: Datas of Curves and Fish
 Language ProgramThis data file is
 consist of datas of curves in this paper obtained from model tests and
 numerical models. Besides, a Fish language program is also included to
 simulate dynamic permeability，during tunnel excavation.
DOI: 10.5061/dryad.q4t6h2b
title: Data from: Non-reproductive male cane toads (Rhinella marina) withhold sex-identifying information from their rivals

description: A male cane toad (Rhinella marina) that mistakenly clasps another male
 (rather than a female) in a sexual embrace (amplexus) can be induced to
 dismount by a male-specific “release call”. Although that sex-identifying
 system can benefit both males in that interaction, our standardised tests
 showed that one-third of male cane toads did not emit release calls when
 grasped. Most of those silent males were small, had small testes relative
 to body mass, and had poorly-developed secondary sexual characteristics.
 If emitting a release call is costly (e.g., by attracting predators), a
 non-reproductive male may benefit by remaining silent; other cues (such as
 skin rugosity) will soon induce the amplexing male to dismount, and the
 “opportunity cost” to being amplexed (inability to search for and clasp a
 female) is minimal for non-reproductive males. Hence, male toads may
 inform other males about their sexual identity only when it is beneficial
 to do so.
description: Kelehear and Shine
 dataInformation on behaviour
 and morphology of male cane toads in tropical Australia
DOI: 10.5061/dryad.382ps00
title: Data from: Reproductive conflict resolution in cooperative breeders

description: Female infanticide is common in animal societies where groups comprise
 multiple co-breeding females. To reduce the risk that their offspring are
 killed, mothers can synchronize breeding and pool offspring, making it
 hard for females to avoid killing their own young. However, female
 reproductive conflict does not invariably result in reproductive
 synchrony, and we lack a general hypothesis explaining the variation in
 conflict resolution strategies seen across species. Here, we investigate
 the fitness consequences of birth timing relative to other females and the
 prevalence of birth synchrony in cooperatively breeding Kalahari meerkats
 (Suricata suricatta). We show that, although there would be substantial
 benefits to females in synchronizing births and reducing their risk of
 infanticide, birth synchrony is rare. Since precise breeding synchrony has
 evolved in a related species with similar infanticidal female reproductive
 conflict, its absence in meerkats requires an evolutionary explanation. We
 therefore explore the costs and benefits of synchronizing breeding in two
 theoretical models, each of which contrasts synchrony with an alternative
 reproductive strategy: (i) breeding opportunistically and accepting
 fitness losses to infanticide or (ii) suppressing the reproduction of
 others to prevent infanticide. Our models show that the costs of synchrony
 constrain its development if subordinates breed infrequently, and that
 selection instead favours the suppression of subordinate reproduction by
 the dominant and opportunistic reproduction by subordinates. Together, our
 results suggest that the resolution of reproductive conflict in animal
 societies is shaped by differential breeding propensities among female
 group members, leading to divergent conflict resolution strategies even in
 closely-related species.
description: Cram et al Data for
 Analysis 01This file contains the
 data required to run the first empirical analysis in Cram et al 2019
 Behavioral Ecology: How does parturition timing, relative to other female
 group-mates, affect subordinate litter survival?Cram et al Data for
 Analysis 02This file contains the
 data required to run the second set of empirical analyses in Cram et al
 (2019) Behavioral Ecology: Do subordinate females synchronize parturition
 with the dominant female? Please note that negative values for the
 "days_since_dominant_parturition" field indicate that the
 subordinate gave birth before the dominant.
DOI: 10.5061/dryad.430hv4p
title: Data from: Strong but opposing effects of associational resistance and susceptibility on defense phenotype in an African savanna plant

description: The susceptibility of plants to herbivores can be strongly influenced by
 the identity, morphology, and palatability of neighboring plants. While
 the defensive traits of neighbors often determine the mechanism and
 strength of associational resistance and susceptibility, the effect of
 neighbors on plant defense phenotype remains poorly understood. We used
 field surveys and a prickle‐removal experiment in a semi‐arid Kenyan
 savanna to evaluate the efficacy of physical defenses against large
 mammalian herbivores in a common understory plant, Solanum campylacanthum.
 We then quantified the respective effects of spinescent Acacia trees and
 short‐statured grasses on browsing damage and prickle density in S.
 campylacanthum. We paired measurements of prickle density beneath and
 outside tree canopies with long‐term herbivore‐exclusion experiments to
 evaluate whether associational resistance reduced defense investment by
 decreasing browsing damage. Likewise, we compared defense phenotype within
 and outside pre‐existing and experimentally created clearings to determine
 whether grass neighbors increased defense investment via associational
 susceptibility. Removing prickles increased the frequency of browsing by
 ~25%, and surveys of herbivory damage on defended leaves suggested that
 herbivores tended to avoid prickles. As predicted, associational
 resistance and susceptibility had opposing effects on plant phenotype:
 individuals growing beneath Acacia canopies (or, analogously, within
 large‐herbivore exclosures) had a significantly lower proportion of their
 leaves browsed and produced ca 70–80% fewer prickles than those outside
 refuges, whereas plants in grass‐dominated clearings were more heavily
 browsed and produced nearly twice as many prickles as plants outside
 clearings. Our results demonstrate that associational resistance and
 susceptibility have strong, but opposing, effects on plant defense
 phenotype, and that variable herbivore damage is a major source of
 intraspecific variation in defense phenotype in this system.
description: Coverdale et al 2019
 DataData files associated
 with DOI 10.1111/oik.06644, "Strong but opposing effects of
 associational resistance and susceptibility on defense phenotype in an
 African savanna plant" by Tyler C. Coverdale et
 al.
DOI: 10.25934/00006008
title: Patterns of outcomes and the relevance surrogate endpoints in patients treated with immune checkpoint inhibitors

description: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy because of their ability to induce tolerable and durable responses in advanced cancers. This can be attributed to the unique mechanism by which ICIs trigger a person’s immune system to reject cancer cells. The effects of ICIs in patients are different from those observed with conventional chemotherapies. For instance, while chemotherapy typically causes cancer cell death resulting in detectable shrinkage of cancers, ICIs may stop or slow cancer growth for long periods without evidence of cancer cell death. In several small studies, patients treated with ICIs have also been noted to have prolonged lives despite their cancers growing during ICI treatment. The different patterns of responses observed in patients treated with ICIs are important to recognize as they guide expectations of treatment outcomes for patients and may inform the design of clinical trials studying ICIs. However, atypical responses to ICIs have not been consistently defined in past studies or only assessed at the level of trials. This is also of clinical relevance as surrogate endpoints, substitute measures of overall survival, are frequently used in ICI trials to determine the advancement of treatment testing or for FDA approval.

Our primary objective is to assess how objective response categories, progression-free survival (PFS), duration of response (DUR), time to best response (TTBR), and depth of response (DepOR) are associated/correlated with overall survival (OS) in patients treated with ICIs.
DOI: 10.5061/dryad.16bc7f2
title: Data from: Overcoming the challenge of small effective sample sizes in home-range estimation

description: Technological advances have steadily increased the detail of animal
 tracking datasets, yet fundamental data limitations exist for many species
 that cause substantial biases in home‐range estimation. Specifically, the
 effective sample size of a range estimate is proportional to the number of
 observed range crossings, not the number of sampled locations. Currently,
 the most accurate home‐range estimators condition on an autocorrelation
 model, for which the standard estimation frame‐works are based on
 likelihood functions, even though these methods are known to underestimate
 variance—and therefore ranging area—when effective sample sizes are small.
 Residual maximum likelihood (REML) is a widely used method for reducing
 bias in maximum‐likelihood (ML) variance estimation at small sample sizes.
 Unfortunately, we find that REML is too unstable for practical application
 to continuous‐time movement models. When the effective sample size N is
 decreased to N ≤
 urn:x-wiley:2041210X:media:mee313270:mee313270-math-0001(10), which is
 common in tracking applications, REML undergoes a sudden divergence in
 variance estimation. To avoid this issue, while retaining REML’s
 first‐order bias correction, we derive a family of estimators that
 leverage REML to make a perturbative correction to ML. We also derive AIC
 values for REML and our estimators, including cases where model structures
 differ, which is not generally understood to be possible. Using both
 simulated data and GPS data from lowland tapir (Tapirus terrestris), we
 show how our perturbative estimators are more accurate than traditional ML
 and REML methods. Specifically, when
 urn:x-wiley:2041210X:media:mee313270:mee313270-math-0002(5) home‐range
 crossings are observed, REML is unreliable by orders of magnitude, ML home
 ranges are ~30% underestimated, and our perturbative estimators yield home
 ranges that are only ~10% underestimated. A parametric bootstrap can then
 reduce the ML and perturbative home‐range underestimation to ~10% and ~3%,
 respectively. Home‐range estimation is one of the primary reasons for
 collecting animal tracking data, and small effective sample sizes are a
 more common problem than is currently realized. The methods introduced
 here allow for more accurate movement‐model and home‐range estimation at
 small effective sample sizes, and thus fill an important role for animal
 movement analysis. Given REML’s widespread use, our methods may also be
 useful in other contexts where effective sample sizes are small.
description: GPS tracking data on
 lowland tapirtapir.zip
DOI: 10.25934/00005581
title: A Phase II, Multicenter, Single-Arm Study of Atezolizumab in Patients With Locally Advanced or Metastatic Urothelial Bladder Cancer

description: This Phase II, single-arm study is designed to evaluate the effect of atezolizumab treatment in participants with locally advanced or metastatic urothelial bladder cancer. Participants will be enrolled into 1 of 2 cohorts. Cohort 1 will consist of participants who are treatment-naïve and ineligible for cisplatin-containing chemotherapy. The results of Cohort 1 & 2 are reported separately (NCT02951767 and NCT02108652, respectively). Cohort 2 will contain participants who have progressed during or following a prior platinum-based chemotherapy regimen. Participants in both cohorts will be given a 1200 milligrams (mg) intravenous (IV) dose of atezolizumab on Day 1 of 21-day cycles. Treatment of participants in Cohort 1 will continue until disease progression per Response Evaluation Criteria in Solid Tumors Version 1.1 (RECIST v1.1) or unmanageable toxicity. Treatment of participants in Cohort 2 will continue until loss of clinical benefit or unmanageable toxicity.
DOI: 10.25934/00005598
title: A Phase III, Open-Label, Multicenter, Randomized Study to Investigate the Efficacy and Safety of Atezolizumab (Anti-PD-L1 Antibody) Compared With Chemotherapy in Patients With Locally Advanced or Metastatic Urothelial Bladder Cancer After Failure With Platinum-Containing Chemotherapy

description: This is a Phase III, global, multicenter, open-label, two-arm, randomized, controlled study designed to evaluate the efficacy and safety of atezolizumab compared with chemotherapy in participants with locally advanced or metastatic urothelial bladder cancer (UBC) who have progressed during or following a platinum-containing regimen. The anticipated time on study treatment is based on continued clinical benefit, i.e., until disease progression or unacceptable toxicity. The target sample size is 931 participants.
DOI: 10.25934/00005599
title: A Phase II, Randomized Study of Atezolizumab (Anti-PD-L1 Antibody) Administered as Monotherapy or in Combination With Bevacizumab Versus Sunitinib in Patients With Untreated Advanced Renal Cell Carcinoma

description: This multicenter, randomized, open-label study will evaluate the efficacy, safety and tolerability of atezolizumab as monotherapy or in combination with bevacizumab versus sunitinib in participants with histologically confirmed, inoperable, locally advanced or metastatic renal cell carcinoma who have not received prior systemic therapy either in the adjuvant or metastatic setting.
DOI: 10.25934/00005791
title: A Phase II, Multicenter, Single-arm Study of MPDL3280A in Patients With PD-L1-Positive Locally Advanced or Metastatic Non-small Cell Lung Cancer

description: This multicenter, single-arm study will evaluate the efficacy and safety of atezolizumab (MPDL3280A) in participants with PD-L1-positive locally advanced or metastatic NSCLC. Participants will receive an intravenous (IV) dose of 1200 milligrams (mg) atezolizumab (MPDL3280A) on Day 1 of 21-day cycles until disease progression. Eligible participants will be categorized in to three groups as follows:   1. Participants with no prior chemotherapy for advanced disease;   2. Participants who progress during or following a prior-platinum based chemotherapy regimen for advanced disease (2L+participants);   3. Participants who are 2L+ and previously treated for brain metastases.
DOI: 10.25934/00005793
title: A Phase II, Open-label, Multicenter, Randomized Study to Investigate the Efficacy and Safety of MPDL3280A (Anti−PD-L1 Antibody) Compared With Docetaxel in Patients With Non−Small Cell Lung Cancer After Platinum Failure

description: This multicenter, open-label, randomized study will evaluate the efficacy and safety of Atezolizumab compared with docetaxel in participants with advanced or metastatic non-small cell lung cancer after platinum failure. Participants will be randomized to receive either Atezolizumab 1200 milligram (mg) intravenously every 3 weeks or docetaxel 75 milligram per meter square (mg/m^2) intravenously every 3 weeks. Treatment with Atezolizumab may be continued as long as participants are experiencing clinical benefit as assessed by the investigator, i.e., in the absence of unacceptable toxicity or symptomatic deterioration attributed to disease progression.