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Data for: Sierra Nevada mixed-conifer regeneration response to repeated burning varies by species

Fire-exclusion has acted as a major perturbation on dry conifer forests in the western U.S., increasing tree density and, in mixed-conifer forests, the dominance of shade-tolerant species. Restoration efforts aim to reverse these effects by reducing stand density, restoring relative proportions of tree species, and reintroducing recurrent fire, but there are limited long-term data on the effects of repeated burning on tree regeneration. We analyzed two decades of seedling and overstory data from the Teakettle Experimental Forest in the southern Sierra Nevada, California, USA to determine how thinning and repeated burning affect seedling establishment and overstory recruitment. The treatments included three levels of thinning (no thin, understory thin, overstory thin) crossed with two levels of burning (burn, no burn). Treatments were replicated three times in 4 ha treatment units. Seedlings were surveyed at gridpoints within the treatment units for the pre-treatment period (1999-2000), following the first-entry burn (2004-2006), at 10 years post-treatment (2011-2012), and before (2016-2017) and after (2018-2020) the second-entry burn. We analyzed seedling response using mixed models. Across treatments, pine seedling densities remained much lower than shade-tolerant seedling densities. We found that repeated burns led to modest increases in sugar pine (Pinus lambertiana) and substantial increases in incense-cedar (Calocedrus decurrens) seedling densities four years post-burn. No significant differences in seedling densities among repeated burning treatments were detected for Jeffrey pine (P. jeffreyi) or white fir (Abies concolor). We used overstory stem map data and seedling data to estimate recruitment into the mid-story and found that estimates of natural mid-story recruitment were much higher among white fir and incense-cedar than pines, even following treatments.

Functional responses of fisheries to hydropower dams in the Amazonian Floodplain of the Madeira River

1. Tropical river fisheries support food security for millions of people but are increasingly threatened by hydropower development. How dams affect these fisheries remains poorly known in most regions. Here, we used a functional traits approach to evaluate the extent to which the composition of fishery yields in the Madeira River Basin the largest sub-basin in the Amazon, respond to dam construction. We also explored how dams affected the monetary value of yields and fishing-based income of the communities. 2. We collected fishing data in 17 locations distributed more than 300 km across upstream, reservoir, and downstream zones during pre-and post-dam construction periods. We interviewed 711 fishers from 13 communities to assess fishing income during pre- and post-dam periods. 3. Catch-per-unit effort (CPUE) declined significantly, i.e., by 37%, after dam construction. Multivariate analysis yielded six species clusters according to trait syndromes related to life history, migration, swimming-performance/microhabitat-use and economic value that were associated with the environmental data characteristic of pre- and post-dam periods. Comparison of CPUE of each cluster indicated that large species with periodic life-history strategy and regional or long-distance migratory behavior were most affected by dam construction, with CPUE declining by, on average, 31%. Declines in yields and shifts in functional composition of the fishery yields resulted in average decline of 21% in the monetary of functional clusters and 30% in fishing income. 4. Synthesis and applications. Our study indicates that the implementation of the dams and associated changes in environmental conditions affected the functional composition of yields and reduced catches, negatively affecting the fishing-based income of the studied communities in the Madeira River.Whereas catches of all functional clusters declined after the dams, species possessing large body sizes, traits related to a periodic life history strategy, either with long-distance or regional migratory behaviors, and the greatest economic importance appeared to be particularly vulnerable. These results imply that hydropower expansion will cause detrimental effects for fisheries and the livelihoods they sustain. Our results underscore the urgent need for considering alternative sources of renewable energy (e.g., solar power and in-stream turbines) to avoid irreversible socio-environmental damages of large dam projects. In river reaches where dams are already in operation or under construction, minimizing impacts will require improving operational protocols to reduce hydrological alterations and developing research and technology to improve the functionality of fish passages. In these locations, addressing losses in fishery value and fishing-based income will also require the implementation of fair compensation measures. Maintaining fish production requires conserving flow pulses and free-flowing rivers and tributaries critical for completing life cycles of fish species with vulnerable traits.

Nonlinear responses of metals and composites

Dataset composed of two main parts     1. Material characterization of a metal (from lab test)         Single file: `metal-tensile.txt`         Material characteristics:             - isotropic elastoplastic material with isotropic hardening             - poisson ratio = 0.3         Geometrical characteristics:             - specimen geometry: bar             - initial length = 1000 mm             - initial cross section = 35.28 mm^2         Loading characteristics:             - uniaxial tension     2. Composite open-hole substructure characterization (from FE simulations)         Multiple files: `EaX_EbY_EsZ.txt` (see README.txt for nomenclature)         Layup:             - [45/90/-45/0]s         Damage criterion:             - Hashin with cohesive damage propagation             - No delaminations considered         Loading characteristics:             - Homogenized strain loading over the plate edges             - In plane loading: different combinations of (eps_1, eps_2, eps_12)             - In plane response: (sig_1, sig_2, sig_12), i.e. homogenized stresses

Cell-type specific responses to associative learning in the primary motor cortex

The primary motor cortex (M1) is known to be a critical site for movement initiation and motor learning. Surprisingly, it has also been shown to possess reward-related activity, presumably to facilitate reward-based learning of new movements. However, whether reward-related signals are represented among different cell types in M1, and whether their response properties change after cue-reward conditioning remains unclear. Here, we performed longitudinal in vivo two-photon Ca2+ imaging to monitor the activity of different neuronal cell types in M1 while mice engaged in a classical conditioning task. Our results demonstrate that most of the major neuronal cell types in M1 showed robust but differential responses to both cue and reward stimuli, and their response properties undergo cell-type specific modifications after associative learning. PV-INs' responses became more reliable to the cue stimulus, while VIP-INs' responses became more reliable to the reward stimulus. PNs only showed robust response to the novel reward stimulus, and they habituated to it after associative learning. Lastly, SOM-IN responses emerged and became more reliable to both conditioned cue and reward stimuli after conditioning. These observations suggest that cue- and reward-related signals are represented among different neuronal cell types in M1, and the distinct modifications they undergo during associative learning could be essential in triggering different aspects of local circuit reorganization in M1 during reward-based motor skill learning.

Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors

R markdown files and source data to reproduce figures from the manuscript "Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors"

Data from: Symbiont-specific responses to environmental cues in a threesome lichen symbiosis

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We investigated differential gene expression in photosymbiodemes of the lichen Peltigera britannica at different temperatures representing mild and putatively stressful conditions and compared gene expression of thallus sectors containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts. Firstly, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Secondly, we quantified photobiont-mediated differences in fungal gene expression. High temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data. As expected, the expression of genes involved in photosynthesis was increased in both photobiont types at 15 and 25°C. The green algae exhibited thermal stress responses mainly at 25°C, and the fungus and the cyanobacteria already by 15°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima. Furthermore, photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression.

Data from: Explaining productivity variation in response to nitrogen addition and warming requires intraspecific variability

1. Recent studies have shown that intraspecific trait variability is an important source of total trait variation. However, the contribution of intraspecific variability to ecosystem functions in the face of global change remains unknown. 2. We measured plant height, leaf area, specific leaf area, leaf dry matter content and leaf thickness of 26 species at individual or leaf level and aboveground net primary productivity in 48 subplots subjected to 8 years of nitrogen addition and warming in a Tibetan alpine meadow. We split community weighted mean (CWM) and Rao's quadratic entropy (Rao) of individuals' traits within a given community into "fixed value" (only caused by interspecific difference of traits) and intraspecific variability (only caused by intraspecific difference), respectively, using a variance partitioning method. 3. We found that productivity showed a humped back response to nitrogen addition: it was highest at intermediate levels of nitrogen fertilization. The response trend was mediated by the changes of plant functional structure. Productivity was positive with fixed Rao of plant height and intraspecific variability of leaf area, i.e. community having higher fixed variability of plant height and individuals producing bigger leaf area can increase productivity via niche complementary and dominance effect. Warming reduced productivity directly and marginally decreased individuals' leaf area which suppresses productivity indirectly. 4. Our research suggests the non-negligible role of plant intraspecific trait variability in maintaining ecosystem functions, especially in the face of global change.

Dataset supporting publication: "Geothermal Power: Monitoring the Building Response During Installation"

Dataset supporting publication: “Geothermal Power: Monitoring the Building Response During Installation” (publication available for download: <a href="https://zenodo.org/record/4244246#.X6KWq1CCHIU">GEOFIT Zenodo</a>) The European project GEOFIT (Deployment of novel GEOthermal systems, technologies and tools for energy efficient building retrofitting) is gathering more than 20 partners from all around Europe. Its main objective is to deploy and to integrate advanced methods of worksite inspection, ground research, and building structural monitoring, drilling and worksite characterization into advanced geothermal based retrofitting methods. This contribution reports the experimental results to be achieved within GEOFIT at the location of specific case studies. In particular standard accelerometric measurements will be collected and compared with the information collected by the geo-radar system made available by one of the partners. This paper focuses on the structural monitoring of a two-story masonry building. The results of a preliminary data collection in the absence of drilling are also reported.

Source data for - Bidirectional alterations in brain temperature profoundly modulate spatiotemporal neurovascular responses in-vivo: Implications for theragnostics

Neurovascular coupling (NVC) is a mechanism that, amongst other known and latent critical functions, ensures activated brain regions are adequately supplied with oxygen and glucose. This biological phenomenon underpins non-invasive perfusion-related neuroimaging techniques, and recent reports have implicated NVC impairment in several neurodegenerative disorders. Yet, much remains unknown regarding NVC in health and disease, and only recently has there been burgeoning recognition of a close interplay with brain thermodynamics. Accordingly, we developed a novel multi-modal approach to systematically modulate cortical temperature and interrogate the spatiotemporal dynamics of sensory-evoked NVC. We show that changes in cortical temperature profoundly and intricately modulate NVC, with low temperatures associated with diminished oxygen delivery, and high temperatures inducing a distinct vascular oscillation. These observations provide novel insights into the relationship between NVC and brain thermodynamics, with important implications for brain-temperature-related therapies, functional biomarkers of elevated brain temperature, and in-vivo methods to study neurovascular coupling.

Behavioral responses of a large, heat-sensitive mammal to climatic variation at multiple spatial scales

1. Climate warming creates energetic challenges for endothermic species by increasing metabolic and hydric costs of thermoregulation. Although endotherms can invoke an array of behavioral and physiological strategies for maintaining homeostasis, the relative effectiveness of those strategies in a climate that is becoming both warmer and drier is not well understood. 2. In accordance with the heat dissipation limit theory, which suggests that allocation of energy to growth and reproduction by endotherms is constrained by the ability to dissipate heat, we expected that patterns of habitat use by large, heat-sensitive mammals across multiple scales are critical for behavioral thermoregulation during periods of potential heat stress and that they must invest a large portion of time to maintain heat balance. 3. To test our predictions, we evaluated mechanisms underpinning the effectiveness of bed sites for ameliorating daytime heat loads and potential heat stress across the landscape while accounting for other factors known to affect behavior. We integrated detailed data on microclimate and animal attributes of moose Alces alces, into a biophysical model to quantify costs of thermoregulation at fine and coarse spatial scales. 4. During summer, moose spent an average of 67.8% of daylight hours bedded, and selected bed sites and home ranges that reduced risk of experiencing heat stress. For most of the day, shade could effectively mitigate the risk of experiencing heat stress up to 10°C, but at warmer temperatures (up to 20℃) wet soil was necessary to maintain homeostasis via conductive heat loss. Consistent selection across spatial scales for locations that reduced heat load underscores the importance of the thermal environment as a driver of behavior in this heat-sensitive mammal. 5. Moose in North America have long been characterized as riparian-obligate species because of their dependence on woody plant species for food. Nevertheless, the importance of dissipating endogenous heat loads conductively through wet soil suggests riparian habitats also are critical thermal refuges for moose. Such refuges may be especially important in the face of a warming climate in which both high environmental temperatures and drier conditions will likely exacerbate limits to heat dissipation, especially for large, heat-sensitive animals.

Antelope space-use and behaviour indicate multi-level responses to varying anthropogenic influences in a highly human-dominated landscape

A primary means of conserving a species or a habitat in a human-dominated landscape is through promoting coexistence with humans while minimizing conflict. For this, we should understand how wildlife are impacted by direct and indirect human activities. Such information is rare from areas with high human densities. To investigate how animals respond to altered ecological conditions in human-dominated landscapes, we focussed on a wild herbivore of conservation concern in Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck, Antilope cervicapra, a generalist grazer, lives in refugia located in a growing human population. We studied the impacts of humans on habitat use and behaviour of blackbuck. We laid 250 x 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat use assessment. We observed herds of blackbuck for 89 hours in different habitat types using scan sampling methods. Our habitat-use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high-quality forage was available. Habitat openness was the major predictor of habitat-use inside the core area, where levels of human activities were low. We also found a positive correlation between habitat use by blackbuck and livestock. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human-wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land use will impact long-term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where human activities are relatively low.

opencc-by-4.0Feb 2023View details →

Sleep Architecture in Response to a Late Evening Competition in Team-Sport Athletes

Purpose: The aim of this study was to assess the effect of a late evening competition on sleep characteristics and perceived recovery in team-sport players using a validated self-applicable and portable polysomnographic device. Methods: Sixteen teamsport players (age: 25.4 [1.4] y; body mass index: 23.6 [0.5] kg/m2) completed the study. Objective and subjective sleep data were collected for 4 consecutive nights: 2 nights before (PRE2 and PRE1) and the 2 nights after an eveningmatch (POST1), performed between 6:00 PM and 9:00 PM. Total quality of recovery values were also collected in the morning. Results: A significantly delayed bedtime (P < .0001; η2p = .68, large) was observed in the first night after the competition (2 h 29 min [1 h 15 min]) compared both to PRE2 (+88 min; P < .0001), PRE1 (+98 min; P < .0001), and POST1 (+100 min; P < .0001), and similar results were observed for wake-up time (P = .033; η2p = .39, large): Players woke up significantly later in evening match (9 h 20 min [1 h 55 min]) compared with PRE2 (+85 min; P = .050) and POST1 (+85 min; P = .049). Conversely, total sleep time; sleep efficiency; sleep onset latency; wake after sleep onset; cortical arousals; N1, N2, N3, and REM (rapid eye movement) percentages; total quality of recovery values; and scores of subjective sleep quality did not vary among the 4 study nights. Conclusions: Team-sport players had delayed bedtime and wake up time following an evening competition; however, sleep quality, duration, and subjective scores of recovery were not affected by the evening match. The delayed wake-up time seems to protect athletes’ sleep efficiency/duration against the evening-match-induced delayed bedtime.

opencc-by-4.0Jun 2022View details →

Tundra soil viruses mediate the responses of microbial communities to climate warming

The dataset of this study contains the information of metagenomic data, environmental factors, GeoChip data,  vOTUs table, mOTUs tables, and the viral and microbial sequences. If this study dataset is useful, please cite: Ji M, et al. Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming[J]. Mbio, 2023: e03009-22. For any other dataset/analysis inquiries, please contact me: jimengzhi@mail.sdu.edu.cn.

NDVI-based monitoring of long-term vegetation dynamics and responses to multi-time scales droughts in Inner Mongolia

The characteristics of vegetation and drought for different seasons between 1982 and 2015 in Inner Mongolia were studied based on the Normalized Difference Vegetation Index (NDVI) and the Standardized Precipitation Evapotranspiration Index (SPEI). The response of vegetation to drought over various time scales for different seasons and vegetation types was investigated using the maximum Pearson correlation, allowing a discussion about the possible causes of any changes. The results indicate that the vegetation NDVI in Inner Mongolia showed an increasing trend in different seasons, with spring vegetation NDVI (April to May) having the largest significant increasing rate, followed by the growing season (April to October), autumn (September to October), and summer (June to August). Accordingly, the proportion of stations with decreasing SPEI was, in descending order, summer, growing season, autumn, and spring. Additionally, the magnitude of the SPEI decrease was greater in eastern Inner Mongolia. NDVI and SPEI were positively correlated in most regions of Inner Mongolia, indicating that changes in vegetation in most parts of this region were affected by the spatial and temporal characteristics of drought, the correlation being them being strongest in the growing season, followed by summer, then spring and autumn. Considering the different types of vegetation, forests were less affected by drought, with broadleaf forests more affected than coniferous forests. The meadow steppes and typical steppes were more affected by 12-month droughts in the growing season and summer, 6-month droughts in spring, and 3-month droughts in autumn, with desert steppes mainly affected by 3-month droughts. The shrubs, sandy vegetation, and cropland were mostly affected by droughts in summer, and show a greater response to 3-month droughts in autumn. Finally, the water balance was found to be the most important factor affecting the response of vegetation to drought in Inner Mongolia.

Gene expression responses of Bactrocera tryoni larvae feeding on different ripening stages of tomato fruit

Bactrocera tryoni larvae rearing in immature-green, color-break, and fully-ripe tomato fruit's RSEM, DGE, Trinity Fasta file, Trinity Fasta gene to transcript map, and Trinotate annotation report data.

Machine learning deconvolution of the immune response to dengue

Machine learning deconvolution of the immune response to dengue - dataset of antibody repertoire sequencing

Plant responses to hypergravity: a comprehensive review [Dataset]

These are the datasets used to generate the keyword co-occurrence network and the mapping of hypergravity treatments in the literature for the review article titled "Plant responses to hypergravity: a comprehensive review".  Article Citation: Hosamani, R., Swamy, B.K., Dsouza, A. et al. Plant responses to hypergravity: a comprehensive review. Planta 257, 17 (2023). <a href="https://doi.org/10.1007/s00425-022-04051-6">https://doi.org/10.1007/s00425-022-04051-6</a>

Arbuscular mycorrhizal fungi improve the growth and drought tolerance of Cinnamomum migao by enhancing physio-biochemical responses

Drought is the main limiting factor for plant growth in karst areas with a fragile ecological environment. Cinnamomum migao H. W. Li is an endemic medicinal woody plant present in the karst areas of southwestern China, and it is endangered due to poor drought tolerance. Arbuscular mycorrhizal fungi (AMF) are known to enhance the drought tolerance of plants. However, few studies have examined the contribution of AMF in improving the drought tolerance of Cinnamomum migao seedlings. Therefore, we conducted a series of experiments to determine whether a single inoculation and coinoculation of AMF (Claroideoglomus lamellosum and Claroideoglomus etunicatum) enhanced the drought tolerance of Cinnamomum migao. Further, we compared the effects of single inoculation and coinoculation with different inoculum sizes (20, 40, 60, and 100 g; four replicates per treatment) on mycorrhizal colonization rate, plant growth, photosynthetic parameters, antioxidant enzyme activity, and malondialdehyde (MDA) and osmoregulatory substance contents. The results showed that compared with nonmycorrhizal plants, AMF colonization significantly improved plant growing status; net photosynthetic rate; superoxide dismutase, catalase, and peroxidase activities; and soluble sugar, soluble protein, and proline contents. Further, AMF colonization increased relative water content and reduced MDA content in cells. These combined cumulative effects of AMF symbiosis ultimately enhanced the drought tolerance of seedlings and were closely related to the inoculum size. With an increase in inoculum size, the growth rate and drought tolerance of plants first increased and then decreased. The damage caused by drought stress could be reduced by inoculating 40–60 g of AMF, and the effect of co-inoculation was significantly better than that of single inoculation at 60 g of AMF, while the effect was opposite at 40 g of AMF. Additionally, the interaction between AMF and inoculum sizes had a significant effect on drought tolerance. In conclusion, the inoculation of the AMF Claroideoglomus lamellosum and Claroideoglomus etunicatum improved photosynthesis, activated antioxidant enzymes, regulated cell osmotic state, and enhanced the drought tolerance of Cinnamomum migao, enabling its growth in fragile ecological environments.

Dataset of the questionaries' responses

These datasets were produced as part of a Master's thesis. The study aimed at analysing, as from an integration of DeLone and McLean's (2003) Information Systems Success Model with Davis' (1989) Technology Acceptance Model, the factors that influence the satisfaction and the intention of continuity of use, of students and teachers, regarding the use of Moodle. These are the data sets with the responses of students and teachers to the respective questionnaires.