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opencc-zeroDec 2020View details →

Data from: Ecological requirements drive the variable responses of wheat pests and natural enemies to the landscape context

1. Semi-natural habitats (SNH) are considered essential for pest suppressive landscapes, but their influence on crop pests and natural enemies can be highly variable. Instead of SNH per se, the availability of resources, such as pollen and nectar, may be more relevant for supporting pest control. 2. Here, we assessed the spatio-temporal variation of multiple insect pests (cereal leaf beetles and aphids) and natural enemies (predators and aphid parasitoids) in wheat fields and their responses to landscape context and flower availability. We combined detailed information on pollen use by natural enemies with the specific distribution of pollen-providing plants across a gradient of landscape composition and configuration. 3. The abundance of wheat pests was tightly linked to wheat development stage. Syrphids colonised the fields early in the season, while the abundance of other enemies increased later in the season. The responses of pests to landscape structure were variable and, while some pests had low abundances in landscapes with high edge density and SNH cover, Sitobion avenae abundance was positively associated with SNH cover. Lacewings, syrphids and cereal leaf beetles were abundant in landscapes with diverse and abundant flower resources, whereas the abundance of parasitoids and Nabis sp. was driven by aphid abundance. We detected no significant indirect effects of landscape on pests via natural enemies. 4. Synthesis and applications. Our findings highlight the need for conservation biological control to go beyond "one size fits all" and consider the specific ecology of the involved organisms. Landscapes with high edge density and flowering woody plants may support natural enemies, in particular syrphids, which colonised the fields early in the season. Incentives for pest-suppressive landscapes should focus on tailored strategies that disfavour pests and simultaneously enhance natural enemies according to their ecological requirements.

opencc-by-4.0Nov 2021View details →

Primary Versus Secondary Gravity Wave Responses at F-region Heights Generated by a Convective Source

Simulation outputs for the paper "Primary Versus Secondary Gravity Wave Responses at F-region Heights Generated by a Convective Source" by Heale et al. The .mat file consist of 3D (t,x,z) arrays of the temperature perturbation (K) for the full amplitude (T_fullamp), 1/4 amplitude (T_quarteramp), and 1/100th amplitude (T_hundrethamp) simulations. The time resolution is 60 seconds and the spatial resolution is 1km. The .mat file also included an x array and height array (km)

opencc-by-nc-4.0Oct 2024View details →

Data from: Process-based modelling of nonharmonic internal tides using adjoint, statistical, and stochastic approaches. Part II: adjoint frequency response analysis, stochastic models, and synthesis

Meta data updated after publication.

opencc-zeroOct 2022View details →

Ecological and metabolomic responses of plants to deer exclosure in a suburban forest

Trees and shrubs in suburban forests can be subject to chronic herbivory from abundant white-tailed deer, influencing survival, growth, secondary metabolites and ecological success in the community. We investigated how deer affect the size, cover, and metabolomes of four species in the understory of a suburban forest in central New Jersey, USA: the woody shrubs Euonymus alatus and Lindera benzoin, the tree Nyssa sylvatica, and the semi-woody shrub Rosa multiflora. For each species, we compared plants in 38 16 m2 plots with or without deer exclosure, measuring proportion cover and mean height after 6.5 years of fencing. We scored each species in all plots for deer browsing over eight years and assessed selection by deer among the species. We did untargeted metabolomics by sampling leaves from three plants of each species in an equal number of fenced and unfenced plots, conducting chloroform-methanol extractions followed by LC-MS/MS, and conducting statistical analysis on MetaboAnalyst. The proportion of a species browsed ranged from 0.24 to 0.35. Nyssa sylvatica appeared most selected by and susceptible to deer; in unfenced plots both its cover and mean height were significantly lower. Only cover or height was lower for E. alatus and L. benzoin in unfenced plots, while R. multiflora height was greater. The metabolomic analysis identified 2,333 metabolites, which clustered by species but not fencing treatment. However, targeted analysis of the top metabolites grouped by fencing for all samples and for each species alone, and was especially clear in N. sylvatica, which also grouped by fencing using all metabolites. The most significant metabolites that were upregulated in fenced plants include some involved in defense-related metabolic pathways, e.g. monoterpenoid biosynthesis. In overbrowsed suburban forests, variation of deer impact on species' ecological success, potentially mediated by metabolome-wide chemical responses to deer, may contribute to changes in community structure.

opencc-by-4.0Oct 2022View details →

A systematic assessment of deep learning methods for drug response prediction: From in vitro to clinical applications

## GDSC dataset **GDSC_EXP.csv** GDSC gene expression profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol.   **GDSC_MUT.csv** GDSC gene mutation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.   **GDSC_CNV.csv** GDSC copy number variation profiles for 966 cancer cell lines, where each column represents a cell line in the form of its name and tissue collection site, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.   **GDSC_DR.csv** GDSC drug response data for 966 cancer cell lines and 282 drugs in the form of the natural logarithm of the IC50 readout. The first column shows the cell line name and tissue collection site, the second column shows the drug name, and the third column shows the drug response readout.   **GDSC_DrugAnnotation.csv** GDSC annotations for 282 drugs include drug name, PubChem CID, PubChem canonical SMILES, Rdkit canonical SMILES, Target Pathway, standard deviation, bimodality coefficient and density coverage. ## TCGA dataset **TCGA_EXP.csv** TCGA gene expression profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol.   **TCGA_MUT.csv** TCGA gene mutation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The wild type is coded as 1 and the wild type as 0.   **TCGA_CNV.csv** TCGA copy number variation profiles, where each column represents a patient in the form of TCGA patient ID, and each row represents a gene in the form of the HGNC symbol. The copy-neutral is coded as 0 and the deletion or amplification as 1.   **TCGA_DR.csv** TCGA clinical response data. The first column shows the TCGA patient ID, the second column shows the drug name, the third column shows the clinical response category, the fourth column shows the cancer type, and the last column shows the clinical label as responder or non-responder. ## PMID17185464 (Bortezomib) dataset **PMID17185464_EXP.csv** Bortezomib clinical trial gene expression profiles, where each column represents a patient in the form of patient ID, and each row represents a gene in the form of the HGNC symbol. **PMID17185464_DR.csv** Bortezomib clinical trial clinical response data. The first column shows the TCGA patient ID, the second column shows the drug name, the third column shows the clinical response category, and the last column shows the clinical label as responder or non-responder (NR: Non-responder, R: Responder).

Data for: Latent functional diversity may accelerate microbial community responses to temperature fluctuations

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically- and functionally-distinct communities emerge at each of these temperatures, with K-strategist taxa favoured under cooler conditions, and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation), is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to "switch on" at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.

Enhanced isohydric behavior decoupled the whole-tree sap flux response to leaf transpiration under nitrogen addition in a subtropical forest

Anthropogenic nitrogen deposition has the potential to change the leaf water-use strategy in the subtropical region of China. Nevertheless, the whole-tree level response crucial for ecosystem functions has not been well addressed over the past decades. In this study, the stem sap flux density (JS) was monitored for the whole-tree water transport capacity in two dominant species (Schima superba and Castanopsis chinensis) in a subtropical forest. To simulate the increased nitrogen deposition, the NH4NO3 solutions were sprayed onto the forest canopy at 25 kg ha-1 year-1 (CAN25) and 50 kg ha-1 year-1 (CAN50), respectively, since April 2013. The JS and microclimate (monitored since January 2014) derived from the whole-tree level stomatal conductance (GS) were used to quantify the stomatal behavior (GS sensitive to vapor pressure deficit, GS-VPD) in response to the added nitrogen. The maximum shoot hydraulic conductance (Kshoot-max) was also measured for both species. After one year of monitoring in January 2015, the mid-day (JS-mid) and daily mean (JS-mean) sap flux rates did not change under all the nitrogen addition treatments (p > 0.05). A consistent decline in the GS-VPD indicated an enhanced isohydric behavior for both species. In addition, the GS-VPD in the wet season was much lower than that in the dry season. S. superba had a lower GS-VPD and decreased JS-mid/JS-mean, implying a stronger stomatal control under the fertilization, which might be attributed to the low efficient diffuse-porous conduits and a higher JS. In addition, the GS for S. superba decreased and the GS-VPD increased more under CAN50 than that under CAN25, indicating that the high nitrogen dose restrains the extra nitrogen benefits. Our results indicated that the JS for both species was decoupled from the leaf transpiration for both species due to an enhanced isohydric behavior, and a xylem anatomy difference and fertilization dose would affect the extent of this decoupling relation.

PsPM-LSOA: Pupil size response, SCR, EMG, ECG and respiration measurement from a classical (Pavlovian) discriminant delay fear conditioning task

This dataset includes eye tracker (including pupillometry), skin conductance, EMG, ECG and respiratory measurements. Also included are task information, keypress responses, keypress response times and key correctness for each of 22 healthy unmedicated participants (13 females and 9 males aged 25.3 +/- 4.3 years) participating in a classical (Pavlovian) discriminant delay fear conditioning task. CS consists of two sine tones with constant frequency (135 Hz or 300 Hz). Assignment of CS frequency to CS-/CS+ is randomised across participants. US is a train of electric square pulses delivered with a constant current stimulator (Digitimer DS7A, Digitimer, Welwyn Garden City, UK) on participants' dominant forearm through a pin-cathode/ring-anode configuration. SOA betwen the CS and US is 7.5 s. The ITI is randomly determined on each trial to be 10.0 +/- 1.4 s.

Dataset and R code: Prior exposure to B. pertussis shapes the mucosal antibody response to acellular pertussis booster vaccination

The R code and dataset for the figures created in the Nature communications manuscript titled "Prior exposure to B. pertussis shapes the mucosal antibody response to acellular pertussis booster vaccination". contains: - excel dataset including the parameters needed for the figures - R code document with the code used to produce the figures and statistical analyses

Population-specific responses of an insect herbivore to variation in host-plant quality

Anthropogenic climate change poses a substantial challenge to many organisms, to which they need to respond to avoid fitness reductions. Investigating responses to environmental change is particularly interesting in herbivores, as they are potentially affected by indirect effects mediated via variation in host-plant quality. We here use the herbivorous insect Pieris napi to investigate geographic variation in the response to variation in food quality. We performed a common garden experiment using replicated populations from Germany and Italy, and manipulating host quality by growing host plants at different temperature and water regimes. We found that feeding on plants grown at a higher temperature generally diminished the performance of P. napi, evidenced by a prolonged development time and reduced larval growth rate, body mass, fat content, and phenoloxidase activity. Genotype by environment interactions (G x E) were present in several performance traits, indicating that Italian populations (1) respond more strongly to variation in host-plant quality and (2) are more sensitive to poor food quality than German ones. This may reflect a cost of the rapid lifestyle found in Italian populations. Consequently, German populations may be more resilient against environmental perturbations and may perhaps even benefit from warmer temperatures, while Italian populations will likely suffer from the concomitantly reduced host-plant quality. Our study thus exemplifies how investigating G x E may help to better understand the vulnerability of populations to climate change.

Belowground net primary productivity stability in response to a nitrogen addition gradient in an alpine meadow

1.Temporal stability of ecosystem productivity is important for providing reliable ecosystem services under global changes. Great efforts have been made to explore the response of aboveground net primary productivity (ANPP) stability to nitrogen (N) enrichment, yet how it affects belowground net primary productivity (BNPP) stability remains elusive, which hinders a comprehensive understanding of ecosystem stability from the view of a whole system. 2. Here, using a field manipulative experiment with six N addition rates (0, 2, 4, 8, 16, 32 g N m-2 year-1), we explored the response patterns and drivers of BNPP stability in the topsoil (0-20 cm) and subsoil (20-40 cm) in the alpine meadow. 3. The results showed that BNPP stability at both soil depths showed a unimodal response to increasing N addition rates. Specifically, for both the topsoil and subsoil, low-level N addition significantly promoted BNPP stability, while high doses of N addition had no significant impact on BNPP stability, suggesting that current low level of N deposition likely benefits the stable provision of belowground functioning. Furthermore, dominant species stability and species richness contributed most to the changes in BNPP stability in the topsoil, whereas only dominant species stability was the dominant driver of BNPP stability in the subsoil. 4. This study is among the first to illuminate the main mechanisms underlying the responses of BNPP stability to N enrichment at various soil depths, which will advance our current understanding of N addition effects on belowground processes and benefit the sustainable provision of ecosystem functioning in the context of atmospheric N deposition.

Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival

Specific leaf area (SLA) is one of the most important plant functional traits. It integrates multiple functions and reflects strategies of plants to obtain resources. How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood.This study aimed to explore the spatial variation in SLA and divergent adaptation of plants by changing SLA through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m2 kg–1, ranging from 0.9 to 110.2 m2 kg–1. SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, plants responded nonlinearly to environmental change by changing SLA. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, long-term adaptation of plants to environmental gradients and its short-term response to resource pulses through variation in SLA jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research.

GENEA Challenge 2022 User Study Raw Responses

This archive contains user-study response data in JSON format from the GENEA Challenge 2022 (https://youngwoo-yoon.github.io/GENEAchallenge2022/). Included in this data are the raw text responses on the questionnaire that was presented to participants after finishing the evaluation. If you use this material, please cite the following paper: Youngwoo Yoon, Pieter Wolfert, Taras Kucherenko, Carla Viegas, Teodor Nikolov, Mihail Tsakov, and Gustav Eje Henter. 2022. The GENEA Challenge 2022: A large evaluation of data-driven co-speech gesture generation. In Proceedings of the ACM International Conference on Multimodal Interaction (ICMI '22). ACM

Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs

Bacteria use a variety of systems to sense stress and mount an appropriate response to assure fitness and survival. Bacillus subtilis uses stressosomes—cytoplasmic multiprotein complexes—to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σB. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σB response profiles with respect to timing and intensity when facing an identical stressor. We used microfluidics and fluorescence microscopy to address the question of whether the σB responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σB with characteristic transient response timing irrespective of stressor but show varying response magnitude. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative and acid stress, implying that RsbR proteins can distinguish among stressors. To show this distinct timing, we quantified time-lapse image series of cells with a fluorescent σB transcriptional reporter. Representative videos of time-lapse image series and the results of our quantitation for each RsbR paralog in each stress condition are included in this dataset. We also probed the relative importance of each half of each RsbR paralog. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argued that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σB response timing. Time-lapse videos for each hybrid fusion protein and the corresponding quantification of these data are also included in the dataset.

Experimental gust response and flutter test of a wing with a fixed and a hinged wingtip

Gust responses and flutter test of a wing with a hinged and a fixed wingtip. The experiments were performed at the Swansea University wind tunnel by Davide Balatti as part of his research. Additional information in: [1] D. Balatti, H.H. Khodaparast, M.I. Friswell, & M. Manolesos (2022). Aeroelastic model validation through wind tunnel testing of a wing with hinged wingtip. In International Forum on Aeroelasticity and Structural Dynamics (IFASD), Madrid (https://www.researchgate.net/publication/361418631_AEROELASTIC_MODEL_VALIDATION_THROUGH_WIND_TUNNEL_TESTING_OF_A_WING_WITH_HINGED_WINGTIP) [2] Balatti, D., Khodaparast, H. H., Friswell, M. I., Manolesos, M., & Castrichini, A. Improving gust load alleviation performance of hinge wingtip using validated aeroelastic models. Available at SSRN 4258795.(https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4258795)

Recovery from heat-induced infertility: A study of reproductive tissue responses and fitness consequences in male Drosophila melanogaster

The predicted temperature increase caused by climate change is a threat to biodiversity. Across animal taxa, male reproduction is often sensitive to elevated temperatures leading to fertility loss and in more adverse scenarios, this can result in sterility when males reach their upper thermal fertility limit. Here we investigate temperature-induced changes in reproductive tissues, fertility reduction, sterility, and the associated fitness loss during the subsequent recovery phase in male Drosophila melanogaster. We heat-stressed males during development and either allowed them to recover or not in early adulthood, while measuring several determinants of male reproductive success. We found significant differences in recovery rate, organ sizes, sperm production, and other key reproductive traits among males from our different temperature treatments. Sperm maturation was impaired before reaching the upper thermal sterility threshold. While some effects were reversible, this did not compensate for the fitness loss due to damage imposed during development. Surprisingly, developmental heat stress was damaging to accessory gland growth, and female post-mating responses mediated by seminal fluid proteins were impaired regardless of the possibility of recovery. We suggest that sub-lethal thermal sterility and the subsequent fertility reduction is caused by a combination of inefficient functionality of both the accessory gland and testes.

Data from: Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons

This dataset is originally used in: I. Silva Barreto, M. Pierantoni, M. Hammerman, E. Törnquist, S. Le Cann, A. Diaz, J. Engqvist, M. Liebi, P. Eliasson, H. Isaksson, Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons, Matrix Biology (2022), doi:https://doi.org/10.1016/j.matbio.2022.11.006 Abstract: The specific viscoelastic mechanical properties of Achilles tendons are highly dependent on the structural characteristics of collagen at and between all hierarchical levels. Research has been conducted on the deformation mechanisms of positional tendons and single fibrils, but knowledge about the coupling between the whole tendon and nanoscale deformation mechanisms of more commonly injured energy-storing tendons, such as Achilles tendons, remains sparse. By exploiting the highly periodic arrangement of tendons at the nanoscale, in situ loading of rat Achilles tendons during small-angle X-ray scattering acquisition was used to investigate the collagen structural response during load to rupture, cyclic loading and stress relaxation. The fibril strain was substantially lower than the applied tissue strain. The fibrils strained linearly in the elastic region of the tissue, but also exhibited viscoelastic properties, such as an increased stretchability and recovery during cyclic loading and fibril strain relaxation during tissue stress relaxation. We demonstrate that the changes in the width of the collagen reflections could be attributed to strain heterogeneity and not changes in size of the coherently diffracting domains. Fibril strain heterogeneity increased with applied loads and after the toe region, fibrils also became increasingly disordered. Additionally, a thorough evaluation of radiation damage was performed. In conclusion, this study clearly displays the simultaneous structural response and adaption of the collagen fibrils to the applied tissue loads and provide novel information about the transition of loads between length scales in the Achilles tendon. Any queries related to the data set or the publication may be directed to Hanna Isaksson by email (hanna.isaksson@bme.lth.se).

EEG and eyetracking response to static and moving stimuli

This dataset contains processed EEG and eyetracking recordings from an experiment in which twelve participants viewed a black disk either flashed in one position or moving in a straight line in one of six directions. Static stimuli were presented at nodes on a hexagonal grid, while moving stimuli moved in straight lines along the axes of the grid.

opencc-zeroDec 2022View details →

Bison movement response to weather

Animal movement patterns are affected by complex interactions between biotic and abiotic landscape conditions, and these patterns are being altered by weather variability associated with a changing climate. Some animals, like the American plains bison (Bison bison L.; hereafter, plains bison), are considered keystone species, thus their response to weather variability may alter ecosystem structure and biodiversity patterns. Many movement studies of plains bison and other ungulates have focused on point‐pattern analyses (e.g., resource‐selection) that have provided information about where these animals move, but information about when or why these animals move is limited. For example, information surrounding the influence of weather on plains bison movement in response to weather is limited but has important implications for their conservation in a changing climate. To explore how movement distance is affected by weather patterns and drought, we utilized 12‐min GPS data from two of the largest plains bison herds in North America to model their response to weather and drought parameters using generalized additive mixed models. Distance moved was best predicted by air temperature, wind speed, and rainfall. However, air temperature best explained the variation in distance moved compared to any other single parameter we measured, predicting a 48% decrease in movement rates above 28°C. Moreover, severe drought (as indicated by 25‐cm depth soil moisture) better predicted movement distance than moderate drought. The strong influence of weather and drought on plains bison movements observed in our study suggests that shifting climate and weather patterns will likely affect plains bison movement patterns, further complicating conservation efforts for this wide‐ranging keystone species. Moreover, changes in plains bison movement patterns may have cascading effects for grassland ecosystem structure, function, and biodiversity. Plains bison and grassland conservation efforts need to be proactive and adaptive when considering the implications of a changing climate on bison movement patterns.