Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

SBF-SEM datasets related to the manuscript "Trans-cellular tunnels induced by the fungal pathogen Candida albicans facilitate invasion through successive epithelial cells without host damage" by Lachat et al, 2022.

11 serial block face- scanning electron microscopy (SBF-SEM) datasets described in the manuscript "Trans-cellular tunnels induced by the fungal pathogen Candida albicans facilitate invasion through successive epithelial cells without host damage" by Lachat et al, 2022. Resolution: 10 nm x,y, 100 nm Z. Datasets description and quantification can be found in the Supplementary information.

Adult facilitation becomes competition as juvenile soapberry bugs age

Intraspecific interactions can change from facilitative to competitive depending on the organism's ontogeny. In plant-feeding insects, host plant defenses can be strengthened or weakened by insect feeding, and can therefore be important for determining whether two insects feeding on the same plant help or harm each other's fitness. Here I conducted two experiments looking at the direct effect of a physical seed defense and the role of intraspecific facilitation in reducing the effects of that defense for juveniles of the red-shouldered soapberry bug. I demonstrate that juveniles are severely inhibited by the tough seed coat of their host plant, leading to high mortality early in development. Adults, in contrast, can create holes through which younger individuals could potentially feed. I manipulated whether or not seeds were fed on by adults on two host plant species: a well-defended native host and a poorly defended introduced host. Survival in the first week of development was dramatically improved by prior adult feeding and this facilitation was stronger on the well-defended host plant. However, the benefits of prior adult feeding ceased after the first week of development and shifted to having a negative effect on survival, development time, and body size. These results indicate that ontogeny is a key factor determining the effects of plant defenses and the strength and direction of intraspecific interactions across multiple host plant species.

opencc-zeroJun 2022View details →

Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation

Aims: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these plant communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime's CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what functional trade-offs they exhibit and how traits and functional diversity vary in response to bamboo presence/absence. Methods: To characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. isolated woody plants in the grasslands community) . Then, we used Mann Whitney test, t-test and variation partitioning to determine the effects of inside vs outside tree island and bamboo presence on community weighted means, woody species diversity and functional diversity. Results: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than in tree islands without bamboo. Conclusions: The observed functional assembly hints towards large-scale environmental abiotic filtering shaping stress-tolerant community strategy, and small-scale biotic interactions driving small-scale trait variation. We recommend experimental studies with fire, facilitation treatments, eco-physiological and recruitment traits to elucidate on tree island expansion and communities response to climate change.

DECIDO-professionals-barriers-facilitators

This study explored the barriers and facilitators to the implementation of a risk-based breast cancer screening program from the point of view of Spanish health professionals. A cross-sectional study with 220 Spanish health professionals was designed. Data were collected in 2020 via a web-based survey and included advantages and disadvantages of risk-based screening and barriers and facilitators for the implementation of the program. Descriptive statistics and Likert scale responses analyzed as category-ordered data were obtained. Risk-based screening was considered important or very important to reduce breast cancer mortality and promote a more proactive role for women in breast cancer prevention, to increase coverage for women under 50 years, to promote a breast cancer prevention strategy for women at high risk and to increase efficiency and effectiveness. Switching to a risk-based program from an age-based program was rated as important or very important by 85% of participants. As barriers for implementation, risk communication, workload of health professionals and limited human and financial resources were mentioned. Despite the barriers, there is good acceptance and it seems feasible, from the perspective of health professionals, to implement a risk-based breast cancer screening program in Spain. However, this poses a number of organizational and resource challenges.

ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA

One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.

Canopy gaps facilitate upslope shifts in montane conifers but not in temperate deciduous trees in the Northeastern United States

Many montane tree species are expected to migrate upslope as climate warms, but it is not clear if forest canopy gaps, which can facilitate tree seedling recruitment, serve as an important mechanism driving tree species range shifts. Patterns of tree seedling establishment can inform us about early stages of tree species migrations and are critical to examine in the context of global climate change. We contrasted elevational distributions of tree seedlings both within and outside of forest canopy gaps with the distributions of conspecific adults and saplings across the deciduous-coniferous ecotone on ten mountains in four states of the northeastern United States. We tested if seedling distributions of four dominant tree species (Abies balsamea, Picea rubens, Acer saccharum, and Fagus grandifolia) were shifted upslope of conspecific adult and sapling distributions. We also examined if this shift was facilitated by canopy gaps and what environmental drivers affected species distributions. There was limited seedling recruitment of dominant tree species at the temperate-coniferous ecotone, which we attributed to (i) an observed downslope shift of seedling distributions of the low-elevation deciduous species (Acer saccharum, Fagus grandifolia) and (ii) an upslope shift in seedling distributions of the high-elevation conifers (Abies balsamea, Picea rubens). The upslope shift of conifer seedlings contrasts with our previous research at these sites which observed downslope shifts of sapling distributions in Picea rubens, suggesting that seedlings may be responding to more recent climate warming. Canopy gaps in high-elevation conifer forests facilitated these upslope shifts by promoting conifer seedling recruitment. However, gaps at lower elevations did not play a significant role in seedling recruitment or the observed downslope shifts of the dominant deciduous species. Climate was the dominant predictor of adult tree distributions whereas both climate and soil were important predictors of seedling distributions. Synthesis. Our study illustrates that tree seedlings have the potential for monitoring the early stages of tree species migrations, and particularly so in canopy gaps in high-elevation conifer forests. Further, we stress that species range shifts are sensitive to local scale heterogeneity in light availability (i.e., canopy gaps) and other non-climatic factors.

opencc-zeroSep 2022View details →

Data from: Pitcher geometry facilitates extrinsically powered 'springboard trapping' in carnivorous Nepenthes gracilis pitcher plants

<div> Carnivorous pitcher plants capture insects in cup-shaped leaves that function as motionless pitfall traps. Nepenthes gracilis, evolved a unique 'springboard' trapping mechanism that exploits the impact energy of falling raindrops to actuate a fast pivoting motion of the canopy-like pitcher lid. We superimposed multiple computerized micro-tomography images of the same pitcher to reveal distinct deformation patterns in lid-trapping N. gracilis and closely related pitfall-trapping N. rafflesiana. We found prominent differences between downward and upward lid displacement in N. gracilis only. Downward displacement was characterised by bending in two distinct deformation zones while upward displacement was accomplished by evenly distributed straightening of the entire upper rear section of the pitcher. This suggests an anisotropic impact response, which may help to maximize initial jerk forces for prey capture, as well as the subsequent damping of the oscillation. Our results point to a key role of pitcher geometry for effective 'springboard' trapping in N. gracilis. </div>

opencc-by-4.0Sep 2022View details →

Data and Source codes: Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior

This repository provides access to the tracking data and analysis code used for the manuscript: Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behavior by Nobuaki Mizumoto1, Thomas Bourguignon1, and Nathan W. Bailey2 1 Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan 2 School of Biology, University of St Andrews, St Andrews, U.K. published in the Proceedings of the National Academy of Sciences of the United States of America.

opencc-zeroMay 2024View details →

Facilitated migration could bolster migrant passage through anthropogenically altered ecosystems

Anthropogenic habitat change frequently outpaces the adaptive capacity of migratory taxa, placing many species and populations at risk of extirpation or extinction due to the mismatch of natural migration phenology and suitable conditions. While dynamic protection can greatly benefit migratory species, it is contingent on the flexibility of relevant management actions. For regulated ecosystems where advanced management planning is required, we present a framework—facilitated migration—for actively matching natural migration phenology with suitable conditions for successful migrant passage. Using a case study of juvenile Chinook salmon (Oncorhynchus tshawytscha) oceanward migration in the Sacramento River, a major bottleneck to the recovery of imperiled populations in California, we show how the conditions associated with migration preparation, migration initiation, and successful migrant passage could be regulated to benefit migrants. Thermally shifted preparation, flow pulse-mediated initiation, and passage protection via increased flow, all accomplished by controlling the release of water from storage reservoirs, could increase the number of wild-origin Chinook salmon populations successfully migrating to the ocean by at least 18-212% compared to the status quo management scenario. To further inform expected outcomes, we find that the temporal scope and diversity of juvenile salmon lifestages studied via acoustic telemetry should be expanded, and that the range of flows and flow changes that juvenile salmon experience should be increased. Facilitated migration works by synchronizing migration—thus, a prudent course of action when implementing this strategy would be to favor event quality over event quantity. In forcing scientists and managers to critically evaluate how migrations can be supported and manipulated, facilitated migration will help migratory species persist in anthropogenically altered ecosystems.

Fig. 3 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice

Fig. 3 Th1 immune response acter CD8+T cells blockage in sitro. a. CD3+CD8+T cells were successcullv blocked. The blocking ecciciencv was more than 99.6 %. b, c. Percentages oc CD4+IFN-γ+ (Th1) in Tat-TPI (T-TPI), TPI stimulated splenocvtes with or without CD8+T-cell blockage. Data are presented as the means ± SEM crom cour independent experiments. (*P <0.05; **P <0.01)

Fig. 2 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice

Fig. 2 Immune responses in the draining popliteal lvmph nodes oc mice induced bv Tat-TPI (T-TPI) and TPI proteins. a and c. Percentages oc CD4+IFN-γ+ cells (Th1), CD8+IFN-γ+ cells (Tc1) analvsed bv FACS. b. The ratio oc CD4+ T cells to CD8+ T cells (CD4/CD8) in the draining popliteal lvmph nodes. Data are presented as the means ± SEM crom six mice in each group. (*P <0.05; **P <0.01)

Fig. 1 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice

Fig. 1 Expression, puricication and identicication oc the cusion proteins Tat-TPI and TPI. a. Puricication oc two cusion proteins detected bv Protein Gel Electrophoresis. M: molecular weight marker, Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI, Lane 3: the recombinant plasmid without puricication. b. Fusion proteins recognised bv His-Ab with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI. c. Fusion proteins recognised bv S. japonicum incected-mice serum with Western blotting. Lane 1: recombinant SjTat-TPI, Lane 2: recombinant SjTPI

Fig. 5 in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice

Fig. 5 Parasite burden and immune response were obsersed at 6 weeks acter S. japonicum incection in mice saccinated with T-TPI + IFA, TPI + IFA, IFA and PBS. a. Aserage number oc worms recosered. b. Aserage number oc eggs per gram (EPG) in the liser. c. Representatise granulomas with a single egg crom each group (100×). d. Aserage area oc single egg granulomas crom each group. e, f. Percentages oc CD3+CD4+IFN-γ+(Th1) and CD3+CD8+IFN-γ+(Tc1) gated crom CD3+ T cells analvsed bv FACS. Each bar represents the means ± SEM crom twelse mice per group. (*P <0.05; **P <0.01)

Fig. 4 T cell and antibodies responses acter three immunisations with T in SjTat-TPI facilitates adaptive T-cell responses and reduces hepatic pathology during Schistosoma japonicum infection in BALB/c mice

Fig. 4 T cell and antibodies responses acter three immunisations with T-TPI + IFA, TPI + IFA, IFA and PBS. a and b: Percentages oc CD3+CD4+IFN-γ+ (Th1) and CD3+CD8+IFN-γ+ (Tc1) gated crom CD3+ cells analvsed bv FACS. c. IgG, IgG1 and IgG2a lesels in mice sera were detected. Data are presented as the means ± SEM crom eight mice in each group. (*P <0.05; **P <0.01)

opencc-zeroJun 2024View details →

PRISMA-P: Facilitators and Barriers to Implementation of Financial Incentive Interventions for Health Behaviour Change

Prisma-P checklist for the systematic review titled: Facilitators and Barriers to Implementation of Financial Incentive Interventions for Health Behaviour Change.   This research was funded by the Health Research Board APA-2022-029.

opencc-by-4.0Jan 2020View details →

Figure 1 in Expert bioblitzes facilitate non-native fish tracking and interagency partnerships

Figure 1. Sampling locations for ten Fish Slam events (2012–2019). Counties shaded in green were sampled from 2012–2019; blue in 2017; purple and orange in 2019. Sampling in counties shaded in yellow is being planned for 2020.

opencc-by-4.0Feb 2024View details →

Adenosine deficiency facilitates CA1 synaptic hyperexcitability in the presymptomatic phase of a mouse KI model of Alzheimer disease.

All data points, statistical models and raw western blot images from "Adenosine deficiency facilitates CA1 synaptic hyperexcitability in the presymptomatic phase of a mouse KI model of Alzheimer disease" are available.

opencc-by-4.0Aug 2024View details →

Extended data of the article "Lockbox enrichment facilitates manipulative and cognitive activities for mice": Supplementary Figure

Figure and results of the distance traveled in the Free Exploratory Paradigm, Open Field Test, and Elevated Plus Maze Test during habituation are shown.

opencc-by-4.0May 2023View details →

Data archive for 'Convolutional neural networks facilitate river barrier detection and evidence severe habitat fragmentation in the Mekong River biodiversity hotspot'

This repository contains the code and databases used in the paper 'Convolutional neural networks facilitate river barrier detection and evidence severe habitat fragmentation in the Mekong River biodiversity hotspot'.  The 'Mekong River Barrier Database (MRBD)' folder contains the basin-scale barrier database developed in this study. This database contains more than 13,000 unique barriers, which were identified by using the convolutional neural networks-based object detection method from Google Earth’s satellite imagery. The 'FCOS' folder contains the barrier detection model (FCOS ResNext-101-FPN), trained for detecting river barriers from remotely sensed images within the MMDetection framework. The 'FCOS_x101_v2' folder contains the enhanced FCOS model. The 'R_script' folder contains R files used in the paper. Coordinate.R was used to extract coordinates from bounding boxes in each TIF image. CAFI.R was used to calculate the CAFI index in each sub-catchment. The 'Barrier image training set' folder contains over 10,000 river barrier satellite images and their associated JSON files, forming the 'training, validation, and test datasets' used during the model training process. This dataset is made available to the user community in raw, in the hope that others will contribute to its future development, thereby enhancing its use and utility. For more information on the MMDetection framework, refer to the following GitHub repository: <a href="https://github.com/open-mmlab/mmdetection">https://github.com/open-mmlab/mmdetection</a>