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opencc-by-4.0Apr 2024View details →

Unveiling the substrate-dependent dynamics of mycotoxin production in Fusarium verticillioides using an OSMAC-metabolomics approach

UHPLC-HRMS raw data files from the article : "Unveiling the substrate-dependent dynamics of mycotoxin production in Fusarium verticillioides using an OSMAC-metabolomics approach"

opencc-by-4.0Feb 2021View details →

Рис. 11. Зависимость чисΛенности Heterodera glycines от засоренности поΛей Fig. 11. Dependence of the number of Heterodera glycines on the field weediness in Reproductive potential of Soybean Cyst Nematode Heterodera glycines - quarantine pest of soybean - in Primorsky Region conditions

Рис. 11. Зависимость чисΛенности Heterodera glycines от засоренности поΛей Fig. 11. Dependence of the number of Heterodera glycines on the field weediness

opencc-zeroMay 2024View details →

Native plant diversity creates microbial legacies that either promote or suppress non-natives, depending on drought history

High-diverse native plant communities resist non-native plants more strongly than low-diverse communities, in part through resource competition. Yet, the role of soil biota is largely unknown, although non-native plants interact with soil biota. Here, we tested the responses of non-native plants to soil conditioned by different native plant diversities. We applied well-watered and dry treatments in the conditioning and response phases to explore the effects of historical and contemporary environmental stresses. Historical water conditions determined the effects of native diversity via soil biota on responding non-natives grown in well-watered environments. Non-native growth decreased with native species richness for well-watered soil inocula but increased for dry soil inocula. However, non-native growth in dry environments did not depend on conditioning native species richness of soil inocula. We provide a new understanding of mechanisms behind diversity-invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota, and non-native plants.

opencc-zeroMay 2024View details →

Data from: Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition

Antibiotic resistance genes (ARGs) benefit host bacteria in environments containing corresponding antibiotics, but it is less clear how they are maintained in environments where antibiotic selection is weak or sporadic. In particular, few studies have measured the effect of ARGs on host fitness in the absence of direct selection or determined if any costs are fixed or depend on the host strain, perhaps marking some ARG-host combinations as reservoirs that can maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in 11 diverse Escherichia spp. strains. Three ARGs (blaTEM-116, cat, and dfrA5, encoding resistance to β-lactams, chloramphenicol, and trimethoprim, respectively) imposed an overall cost but all ARGs had an effect in at least one host strain, reflecting a significant strain interaction effect. A simulation predicts these interactions cause the success of ARGs to depend on available host strains, and, to a lesser extent, for successful host strains to depend on the ARGs present in a community. These results indicate the importance of considering ARG effects over different host strains, especially the potential of reservoir strains that allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.

opencc-by-4.0Apr 2024View details →

Data from: The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin

<h4>Data package about haploid vs diploid adaptation to nystatin in yeast</h4> <div>This package contains files and scripts related to the publication "The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin". Raw data and analyses are included.</div>

opencc-zeroMay 2024View details →

Responsiveness to cold snaps by turtle embryos depends on exposure timing and duration

Characterizing how organisms respond to transient temperatures may further our understanding of their susceptibility to climate change. In animals with temperature-dependent sex determination (TSD), unusual transient temperatures during incubation result in sex bias and may therefore impair population breeding capacity. Past studies in the red-eared slider turtle (Trachemys scripta) have demonstrated that the timing and duration of heat exposure ("heat waves") can have major implications for the response of genes involved in gonadal development and the production of female hatchlings. Yet, no study has considered how the response of these genes to transient cold exposure ("cold snaps") may affect gene expression and influence the resulting production of males. We investigated how cold snap timing and duration affect gonadal gene expression in T. scripta embryos. Additionally, we explored the effect of early cold snap exposure duration on resulting hatchling sex ratios. Results show that responsiveness to cool temperatures changes rapidly across development, such that genes that responded to cold snaps when exposure began on incubation day 14 responded differently when cold exposure occurred just 4 to 8 days later. The sex ratio experiment revealed that embryos experiencing an early cold snap also require a long exposure (> 20 days) before most commit to testis development, further suggesting that early development under warm temperatures may lower their sensitivity to later cold snaps. These results highlight how individual responses to incubation temperature can change rapidly across development in turtles and have important effects on sex ratios. We discuss how variation in responsiveness to transient temperatures might help maintain mixed-sex ratios under variable thermal conditions in nature and may permit adaptive population responses to climate change.

Resource manipulation reveals interactive phenotype-dependent foraging in free-ranging lizards

Recent evidence suggests that individuals differ in foraging tactics and this variation is often linked to an individual's behavioural type (BT). Yet, while foraging typically comprises a series of search and handling steps, empirical investigations have rarely considered BT-dependent effects across multiple stages of the foraging process, particularly in natural settings. In our long-term sleepy lizard (Tiliqua rugosa) study system, individuals exhibit behavioural consistency in boldness (measured as an individual's willingness to approach a novel food item in the presence of a threat) and aggressiveness (measured as an individual's response to an 'attack' by a conspecific dummy). These BTs are only weakly correlated and have previously been shown to have interactive effects on lizard space use and movement, suggesting that they could also affect lizard foraging performance, particularly in their search behaviour for food. To investigate how lizards' BTs affect their foraging process in the wild, we supplemented food in 123 patches across a 120-ha study site with three food abundance treatments (high, low, and no-food-controls). Patches were replenished twice a week over the species' entire spring activity season and feeding behaviours were quantified with camera traps at these patches. We tracked lizards using GPS to determine their home range (HR) size and repeatedly assayed their aggressiveness and boldness in designated assays. We hypothesised that bolder lizards would be more efficient foragers while aggressive ones would be less attentive to the quality of foraging patches. We found an interactive BT effect on overall foraging performance. Individuals that were both bold and aggressive ate the highest number of food items from the foraging array. Further dissection of the foraging process showed that aggressive lizards in general ate the fewest food items in part because they visited foraging patches less regularly, and because they discriminated less between high and low-quality patches when revisiting them. Bolder lizards, in contrast, ate more tomatoes because they visited foraging patches more regularly, and ate a higher proportion of the available tomatoes at patches during visits. Our study demonstrates that BTs can interact to affect different search and handling components of the foraging process, leading to within-population variation in foraging success. Given that individual differences in foraging and movement will influence social and ecological interactions, our results highlight the potential role of BT's in shaping individual fitness strategies and population dynamics.

Fig. 2 in Temperature Dependence Of The Breeding Parametres Of The Collared Flycatcher (Passeriformes, Muscicapidae) In The National Park Homilshanski Lisy (Ne Ukraine)

Fig. 2. First spring records and first-egg day of Collared Flycatcher at investigation plots in 2006–2017.

Fig. 5 in Temperature Dependence Of The Breeding Parametres Of The Collared Flycatcher (Passeriformes, Muscicapidae) In The National Park Homilshanski Lisy (Ne Ukraine)

Fig. 5. Model-averaged coefficients of the predictor variables from the subset of best-fitting models for the clutch size (eggs).

Fig. 1 in Temperature Dependence Of The Breeding Parametres Of The Collared Flycatcher (Passeriformes, Muscicapidae) In The National Park Homilshanski Lisy (Ne Ukraine)

Fig. 1. Map of boundaries of the Collared Flycatcher subpopulation study area (Keller et al., 2020).

Fig. 3 in Temperature Dependence Of The Breeding Parametres Of The Collared Flycatcher (Passeriformes, Muscicapidae) In The National Park Homilshanski Lisy (Ne Ukraine)

Fig. 3. Model-averaged importance of the predictor variables from the subset of best-fitting models for the first egg date (FED).

opencc-by-4.0Jul 2022View details →

Fig. 2 in Retrieving climate change dependent Sea Surface Temperature (SST) in Southern Turkey by using Landsat thermal imagery

Fig. 2 — The four sections of the sampling site Table 1 — Landsat images features (29) Product Type Pixel size (collected) Pixel size (resampled) Thermal band Landsat 4-5 TM L1 120-meters 30-meters Band 6 Landsat 7 ETM+ L1 60-meters 30-meters Band 6 Landsat 8 OLI/TIRS L1 100-meters 30-meters Band 10/ Band11

opencc-by-4.0Jul 2022View details →

Fig. 3 in Retrieving climate change dependent Sea Surface Temperature (SST) in Southern Turkey by using Landsat thermal imagery

Fig. 3 — SST anomalies: a) T1 Cross-section, b) T2 Cross-section, c) T3 Cross-section, and d) T4 Cross-section

opencc-by-4.0Nov 2021View details →

Figure 1 in Developing biosecurity plans for non-native species in marine dependent areas: the role of legislation, risk management and stakeholder engagement

Figure 1. Five-stage approach for risk assessment management of NNS in Shetland, adapted from the ecosystem-based risk management framework (Cormier et al. 2013).

Self Consistent Recurrent Neural Network for Path Dependent Deformation

Data and Machine Learning codes for the paper: <ul> <li>Title : Self Consistent Recurrent Neural Network for Path Dependent Deformation</li> </ul> Abstract : Current neural network (NN) structures can learn patterns from data points with historical dependence. Specifically, in natural language processing (NLP), sequential learning has transitioned from recurrence-based architectures to transformer-based architectures. However, it is not known in advance which NN architectures will perform best on datasets containing deformation history due to mechanical loading. Thus, this study ascertains the appropriateness of 1D-convolutional, recurrent, and transformer-based architectures for predicting material failure based on the earlier states in the form of deformation history. Following this investigation, the crucial issues arising from the mathematical computation process of the best-performing NN architectures and the physical properties of the deformation paths are examined in detail. Additionally, we propose a novel and adaptable RNN approach to address the fundamental challenges of truncation and consistency related to obtaining estimations that are compatible with the natural physical properties of deformation paths. This study will serve as a foundation for localization estimation and pave the way for future endeavors to propose further solutions to encountered challenges.

Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster

To survive adverse environments, many animals enter a dormant state such as hibernation, dauer, or diapause. Various Drosophila species undergo adult reproductive diapause in response to cool temperatures and/or short day-length. While it is known that flies are less active during diapause, an in-depth understanding of diapause effects on circadian rhythms and sleep is lacking. Here we show that, in diapause-inducing conditions, Drosophila melanogaster exhibit altered circadian activity profiles, including a severely reduced morning activity peak and an advanced evening activity peak. Consequently, the flies have a single activity peak at a time similar to when non-diapausing flies have a siesta. Temperatures ≤15 °C, rather than short day-length, primarily drive the behavior. At cool temperatures, flies also rapidly enter a deep sleep state that lacks the sleep cycles of flies at higher temperatures and requires particularly high levels of stimulation for arousal. Furthermore, we show that at 18–25 °C, flies prefer to siesta in the shade, a preference that is virtually eliminated at 10 °C. Resting in the shade is driven by an aversion to blue light, sensed by rhodopsin 7 (Rh7) outside of the eyes. Flies at 10 ˚C show neuronal markers of elevated sleep pressure, including increased expression of Bruchpilot and elevated Ca2+ in the R5 ellipsoid body neurons. Therefore, sleep pressure might overcome blue light aversion. Thus at temperatures known to cause reproductive arrest, preserve germline stem cells, and extend lifespan, Drosophila melanogaster are prone to deep sleep and exhibit dramatically altered - yet rhythmic - daily activity patterns.

opencc-by-4.0May 2024View details →

Dataset for: Methodology to identify and quantify flight path dependent bird strike scenarios over aircraft

<h1>ScenarioGenerator</h1> <h2>Description</h2> This project is a Python project containing a demonstrations of the methodology developed by J. Bertholdt.  The code takes stl files and flight path data in order to create bird strike impact scenarios for each cell.  With this data it is possible to approximate the impact intensity and create heat maps over the geometry. <h2>Features</h2> - Data processing: The code creates scenarios (impact vector, angle, velocity and bird data) for hit areas and estimates peak pressure and total impulse.    - Data saving: The code saves the data in forms of csv files. - Data reader: The code can read the csv files and recreate the processed data and mesh. - Data visualization: The code contains examples for data filtering and plotting.  <h2>Installation</h2> 1. Download Code 2. Adjust directories in data_reader_demo.py and stl_processing_demo. 3. Create a virtual environment: <h3>Required packages:</h3> - numpy - birdpressure - matplotlib - pyvista

Data from: Meta-analytical evidence for frequency-dependent selection across the tree of life

Explaining the maintenance of genetic variation in fitness related traits within populations is a fundamental challenge in ecology and evolutionary biology. Frequency-dependent selection (FDS) is one mechanism that can maintain such variation, especially when selection favours rare variants (negative FDS). However, our general knowledge about the occurrence of FDS, its strength and direction remain fragmented, limiting general inferences about this important evolutionary process. We systematically reviewed the published literature on FDS and assembled a database of 747 effect sizes from 101 studies to analyse the occurrence, strength, and direction of FDS, and the factors that could explain heterogeneity in FDS. Using a meta-analysis, we found that overall, FDS is more commonly negative, although not significantly when accounting for phylogeny. An analysis of absolute values of effect sizes, however, revealed the widespread occurrence of modest FDS. However, negative FDS was only significant in laboratory experiments and non-significant in mesocosms and field-based studies. Moreover, negative FDS was stronger in studies measuring fecundity and involving resource competition over studies using other fitness components or focused on other ecological interactions. Our study unveils key general patterns of FDS and points in future promising research directions that can help us understand a long-standing fundamental problem in evolutionary biology and its consequences for demography and ecological dynamics.

Data for: Serial dependence: a matter of memory load

The dataset of each experiment is stored in csv format for each experiment separately. Tables are stored in long format, with rows coding the event in each trial, and columns coding variables. The subject identifier (number) is coded by the variable obs. theta is orientation of the presented gabor, error is calculated as the acute angle between the reported and true orientations, expressed in degrees. nitems: (1) load trial, (0) no load trial. The meaning of the other variables should be self-explanatory by the column headers name. Additional information on each variable is described in the method section.

Data from: Status-dependent metabolic effects of social interactions in a group-living fish

Social interactions can sometimes be a source of stress, but social companions can also ameliorate and buffer against stress. Stress and metabolism are closely linked, but the degree to which social companions modulate metabolic responses during stressful situations—and whether such effects differ depending on social rank—is poorly understood. To investigate this question, we studied Neolamprologus pulcher, a group-living cichlid fish endemic to Lake Tanganyika, and measured the metabolic responses of dominant and subordinate individuals when they were either visible or concealed from one another. When individuals could see each other, subordinates had lower maximum metabolic rates and tended to take longer to recover following an exhaustive chase compared to dominants. In contrast, metabolic responses of dominants and subordinates did not differ when individuals could not see one another. These findings suggest that the presence of a dominant individual has negative metabolic consequences for subordinates, even in stable social groups with strong prosocial relationships.