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Mechanisms of enhanced cardiorespiratory performance under hyperoxia differ with exposure duration in yellowtail kingfish

Hyperoxia has been shown to expand the aerobic capacity of some fishes, although there have been very few studies examining the underlying mechanisms and how they vary across different exposure durations. Here, we investigated cardiorespiratory function of yellowtail kingfish (Seriola lalandi) acutely (~20 hours) and chronically (3-5 weeks) acclimated to hyperoxia (~200 % air saturation). Our results show that aerobic performance of kingfish is limited in normoxia and increases with environmental hyperoxia. Aerobic scope was elevated in both hyperoxia treatments driven by a ~33% increase in maximum O2 uptake (MO2max), although the mechanisms differed across treatments. Fish acutely transferred to hyperoxia primarily elevated tissue O2 extraction, while increased stroke volume-mediated maximum cardiac output was the main driving factor in chronically acclimated fish. Still an improved O2 delivery to the heart in chronic hyperoxia was not the only explanatory factor as such. Here, maximum cardiac output only increased in chronic hyperoxia compared to normoxia when plastic ventricular growth occurred, as increased stroke volume was partly enabled by an ~8-12% larger relative ventricular mass. Our findings suggest that hyperoxia may be used long-term to boost cardiorespiratory function potentially rendering fish more resilient to metabolically challenging events and stages in their life-cycle.

Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention

Open the record for dataset details and reuse information.

opengpl-3.0-or-laterApr 2024View details →

Radarize: Enhancing Radar SLAM with Generalizable Doppler-Based Odometry

This is the dataset release for the <a href="https://www.sigmobile.org/mobisys/2024/" target="_blank" rel="noopener">ACM MobiSys 2024</a> paper "Radarize: Enhancing Radar SLAM with Generalizable Doppler-Based Odometry". <ul> <li>Project Website: <a href="http://radarize.github.io" target="_blank" rel="noopener">https://radarize.github.io</a></li> <li>Project Code: <a href="http://github.com/ConnectedSystemsLab/radarize_ae" target="_blank" rel="noopener">github.com/ConnectedSystemsLab/radarize_ae</a></li> </ul> If you found this useful, please cite  <pre><code>@inproceedings{sie2024radarize, author = {Sie, Emerson and Wu, Xinyu and Guo, Heyu and Vasisht, Deepak}, title = {Radarize: Enhancing Radar SLAM with Generalizable Doppler-Based Odometry}, booktitle = {The 22nd ACM International Conference on Mobile Systems, Applications, and Services (ACM MobiSys '24)}, year = {2024}, doi = {https://doi.org/10.1145/3643832.3661871}, }</code></pre>

Dataset for Direct comparison of different protocols to obtain Surface enhanced Raman spectra of human serum

This dataset contains all the spectra used in "Direct comparison of different protocols to obtain Surface enhanced Raman spectra of human serum ". Data are available in a compressed folder ("Dataset serum spectra") containing all the 75 TXT files (1 file=1 spectrum) of the same serum sample analyzed with the 5 protocols presented in the article.  The script employed for loading, preprocessing, and analyzing the dataset is named "Script for spectra analysis." Furthermore, the DOCX file ("Instructions") provides details concerning the metadata embedded within the title of each TXT file.

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol, and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency, and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomatoes. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

Payload-delivering engineered γδ T cells display enhanced cytotoxicity, persistence, and efficacy in preclinical models of osteosarcoma

T cell-based cancer immunotherapy has typically relied on membrane-bound cytotoxicity enhancers such as chimeric antigen receptors expressed in autologous αβ T cells. These approaches are limited by tonic signaling of synthetic constructs and costs associated with manufacturing. γδ T cells are an emerging alternative for cellular therapy, possessing innate anti-tumor activity, potent antibody-dependent cellular cytotoxicity, and minimal alloreactivity. We present an immunotherapeutic platform technology built around the innate properties of the Vγ9Vδ2 T cell, harnessing specific characteristics of this cell type and offering an allo-compatible cellular therapy that recruits bystander immunity. We engineered γδ T cells to secrete synthetic tumor-targeting opsonins in the form of an scFv-Fc fusion protein and a mitogenic IL-15Ra–IL-15 fusion protein (stIL15). Using GD2 as a model antigen, we show that GD2-specific opsonin-secreting Vγ9Vδ2 T cells (stIL15-OPS-γδ T cells) have enhanced cytotoxicity and promote bystander activity of other lymphoid and myeloid cells. Secretion of stIL-15 abrogated the need for exogenous cytokine supplementation and further mediated activation of bystander natural killer cells. Compared to unmodified γδ T cells, stIL15-OPS-γδ T cells exhibited superior in vivo control of subcutaneous tumors and persistence in the blood. Moreover, stIL15-OPS-γδ T cells were efficacious against patient-derived osteosarcomas in animal models and in vitro, where efficacy could be boosted with the addition of zoledronic acid. Together the data identify stIL15-OPS-γδ T cells as a candidate allogeneic cell therapy platform combining direct cytolysis with bystander activation to promote tumor control.

Supplementary code and data for: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee

<div> <div> <div> Host-microbe interactions underlie the development and fitness of many macroorganisms, including bees. Whereas many social bees benefit from vertically transmitted gut bacteria, current data suggests that solitary bees, which comprise the vast majority of species diversity within bees, lack a specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of the ground-nesting solitary bee Anthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacterial genera (Streptomyces, Nocardiodes) and the fungus Moniliella spathulata. Dormant (diapausing) larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for diapausing bees. First, using isolated bacteria and fungi, we found that Streptomyces from brood cells inhibited the growth of multiple pathogenic filamentous fungi, suggesting a role in pathogen protection during overwintering, when bees face high pathogen pressure. Second, sugar alcohol composition changed in tandem with major changes in fungal abundance, suggesting links with bee cold tolerance or overwintering biology. We find that Anthophora bomboides hosts a conserved core microbiome that may provide key fitness advantages through larval development and diapause, which raises the question of how this microbiome is maintained and faithfully transmitted between generations. Our results suggest that focus on microbiomes of mature or active insect developmental stages may overlook stage-specific symbionts and microbial fitness contributions during host dormancy. </div> </div> </div>

Data from: Three-dimensional infrared scanning: An enhanced approach for spatial registration of probes for neuroimaging

Significance: Accurate spatial registration of probes (e.g., optodes and electrodes) for measurement of brain activity is a crucial aspect in many neuroimaging modalities. It may increase measurement precision and enable the transition from channel-based calculations to volumetric representations. Aim: This technical note evaluates the efficacy of a commercially available infrared three-dimensional (3D) scanner under actual experimental (or clinical) conditions and provides guidelines for its use. Method: We registered probe positions using an infrared 3D scanner and validated them against magnetic resonance imaging (MRI) scans on five volunteer participants. Results: Our analysis showed that with standard cap fixation, the average Euclidean distance of probe position among subjects could reach up to 43 mm, with an average distance of 15.25 mm [standard deviation (SD) = 8.0]. By contrast, the average distance between the infrared 3D scanner and the MRI-acquired positions was 5.69 mm (SD = 1.73), while the average difference between consecutive infrared 3D scans was 3.43 mm (SD = 1.62). The inter-optode distance, which was fixed at 30 mm, was measured as 29.28 mm (SD = 1.12) on the MRI and 29.43 mm (SD = 1.96) on infrared 3D scans. Our results demonstrate the high accuracy and reproducibility of the proposed spatial registration method, making it suitable for both functional near-infrared spectroscopy and electroencephalogram studies. Conclusions: The 3D infrared scanning technique for spatial registration of probes provides economic efficiency, simplicity, practicality, repeatability, and high accuracy, with potential benefits for a range of neuroimaging applications. We provide practical guidance on anonymization, labeling, and post-processing of acquired scans.

opencc-by-4.0Feb 2024View details →

Raw data for "Enhancing fluidity and mechanical properties in LC3 binders with one-third Portland clinker content"

Raw data for "Enhancing fluidity and mechanical properties in LC3 binders  with one-third Portland clinker content" The raw data include thermal analysis, isothermal calorimetry, laboratory X-ray powder diffraction (LXRPD) and mercury intrusion porosimetry

Assessing moss transplant methods to enhance Sphagnum moss recovery in post-wildfire hydrophobic peat

Wildfire is the dominant disturbance in northern peatlands and can release large quantities of carbon to the atmosphere through combustion. Post-fire peat hydrophobicity can inhibit moss regeneration, thereby decreasing the potential for post-fire carbon sequestration. To investigate how to enhance post-fire recovery we assessed two moss restoration methods (plugs and fragments) in an Alberta poor fen two and three years following wildfire. Post-fire peat hydrophobicity and moss regeneration was characterized in four surface cover types: Severely Burned Feather moss hollows (SB-F), Severely Burned Sphagnum fuscum hummocks (SB-S), Lightly Burned S. fuscum hummocks (LB-S), and Lightly Burned Feather moss lawns (LB-F). We then conducted experiments testing the success of moss plugs and fragments of varying moss species at LB-F and SB-F surface covers, which had high hydrophobicity and low post-fire moss recovery.

Integrating pigment and fatty acid profiles for enhanced estimation of seston community composition

Climate change, nutrition pollution, and land use alterations influence the primary production of lakes. While light-microscopy counting remains the standard for estimating phytoplankton community composition, its expense and time-consuming nature necessitate cost-effective alternatives for seston analysis. Furthermore, estimating the contribution of seston constituents other than primary producers, or non-algal particles, is not possible with light-microscopy counting. Biotracer approach using computational methods and chemotaxonomic biomarkers such as carotenoid pigments and fatty acids have been utilised as an alternative in seston analysis when species-level taxonomy is not required. However, a comprehensive testing of how well carotenoid and fatty acids can be utilised in estimating a wide range of seston phytoplankton communities using different estimation methods is lacking. To assess the accuracy of a suite of state-of-the-art biotracer-based computational methods, namely CHEMTAX, FASTAR (Fatty Acid Source-Tracking Algorithm in R), MixSIAR, and QFASA (Quantitative Fatty Acid Signature Analysis), lake water samples were collected in 2016, 2018, 2019, 2020, and 2021 for seston composition analysis in a boreal eutrophic lake with light-microscopy counting serving as the reference for seston composition. Absolute errors between the biotracer-based estimates were calculated to evaluate method performance. A small laboratory experiment to assess the reliability of estimating the contribution of non-algal particles using the computational methods with fatty acids was also conducted. The closest alignment to light-microscopy counting in terms of absolute error was achieved when both carotenoids and fatty acids were utilised together in the QFASA method. For CHEMTAX, FASTAR, and MixSIAR utilising carotenoids alone produced the closest results. Additionally, the estimation methods accurately assessed the proportion of non-algal particles in the seston when utilising fatty acid profiles, a capability not possible with light-microscopy counting. Our findings demonstrate that the biotracer approach provides a viable and cost-effective alternative to light-microscopy counting when group-level information of phytoplankton community composition suffices. Furthermore, we show that non-algal particles can be effectively estimated together with phytoplankton when utilising fatty acids.

Dataset for Enhancing nitrogen reduction reaction through formation of 2D hybrid heterostructures of MoS2@rGO

Dataset for publication  Enhancing nitrogen reduction reaction through formation of 2D2D hybrid heterostructures of MoS2@rGO. All details about how to work with the dataset is included within the readme file.

RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing

This dataset accompanies the study "RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing". The study introduces RepliChrom, a computational framework designed to predict enhancer–promoter interactions (EPIs) by leveraging multi-scale replication timing (RT) signals. This approach addresses the fundamental challenge of distinguishing gene targets regulated by distal enhancers from those activated by proximal transcriptional activity-a key problem in understanding the causal basis of complex diseases. Despite recent advances in high-throughput technologies such as Hi-C, ChIA-PET, and Hi-TrAC that allow genome-wide reconstruction of 3D chromatin architecture, the role of DNA replication timing in mediating these spatial interactions remains underexplored. RepliChrom fills this gap by using cell-type-specific RT profiles as predictive features for chromatin interaction inference. To support model development, training, and evaluation, we provide a comprehensive multi-omics dataset covering six human cell lines (K562, GM12878, HeLaS3, IMR90, NHEK, and HUVEC ), encompassing: Hi-C datasets: Processed chromatin interaction loops used to define positive and negative enhancer–promoter interaction pairs. ChIA-PET datasets: Interaction data anchored around transcription factor binding, including POLR2A and CTCF, used for model validation across different interaction types. Hi-TrAC datasets: Targeted chromatin accessibility-derived interaction data, offering complementary validation of the model on alternate platforms. Replication Timing (RT) data: Processed RT signal profiles for each cell line, used to extract multi-scale temporal features as inputs for RepliChrom. These datasets enable reproducibility of the model training process and serve as benchmark resources for future research into DNA replication–mediated regulation of 3D genome architecture. Included Files Hi-C_datasets.zip (2.23 MB): Processed Hi-C interaction pairs for six cell types. ChIA-PET_datasets.zip (818.18 KB): CTCF and POLR2A ChIA-PET interactions across multiple lines. Hi-TrAC_datasets.zip (196 bytes): Hi-TrAC-based chromatin interaction training datasets across multiple lines. Cellline_RT_data.zip (86.17 MB): Replication timing signal data across multiple human cell types for multi-scale replication timing feature extraction. Usage All datasets are intended for academic, non-commercial use. The provided files can be directly used to reproduce the training and evaluation of RepliChrom, and may also support broader applications in enhancer–promoter modeling, replication-timing analysis, and 3D genomics studies. For detailed usage instructions and code implementation, please refer to the GitHub repository: https://github.com/DaoFuying/RepliChrom

Enhancing Climate Model Performance through Improving Volcanic Aerosol Representation Dataset and model source codes

Enhancing Climate Model Performance through Improving Volcanic Aerosol Representation: Dataset and codes used in the study

opencc-zeroDec 2023View details →

Coronary Circulation Enhances the Aerobic Performance of Pacific Salmon, Particularly for Females

Female Pacific salmon often experience higher mortality than males during their once-in-a-lifetime up-river spawning migration, particularly when exposed to secondary stressors (e.g. high temperatures). However, the underlying mechanisms remain unknown. One hypothesis is that female Pacific salmon hearts are more oxygen-limited than males and are less able to supply oxygen to the body's tissues during this demanding migration. Such oxygen limitations can develop from naturally occurring coronary blockages (i.e., coronary arteriosclerosis) found in mature salmon hearts. To test this hypothesis, we measured resting (RMR) and maximum metabolic rate (MMR), aerobic scope (AS) and acute upper thermal tolerance in coho salmon (Oncorhynchus kisutch) with an intact or artificially blocked coronary oxygen supply. We also assessed venous blood oxygen and chemistry (cortisol, ions, and metabolite concentrations) at different time intervals during recovery from exhaustive exercise. We found that coronary blockage impaired MMR, but to a greater extent in females than males. Thus, coronary oxygen supply is more important in females than males to support peak metabolism, which is essential during upriver swimming. Furthermore, the coronary blockage reduced AS and PvO2 during exercise recovery but did not differ between sexes. Coronary ligation lowered acute upper thermal tolerance by 1.1°C. Our findings highlight the importance of coronary blood supply for mature salmon and show evidence that elevated female mortality may be linked to cardiac limitation, particularly during warm water conditions.

opencc-by-4.0Jun 2024View details →

Other Supplementary Material for 'Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks' by Xu et al.

<div> Other Supplementary Material for "Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks" by Xu, Rutkowski, Rebowski, Boczkowska, Pollard, Dominguez, Vavylonis, and Ostap, bioRxiv, <a href="https://doi.org/10.1101/2024.02.09.579714" rel="nofollow">https://doi.org/10.1101/2024.02.09.579714</a>    </div>

opencc-zeroJun 2024View details →

Data from: Earthworms promote crop growth by enhancing the connections among soil microbial communities

Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities, and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community, and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal, and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal, and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers. Synthesis and applications: Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.

opencc-by-4.0Jun 2024View details →

Enhancing Automated Tools: Reporting Improvements and Bugs with Bug Builder

Qualitative Research Part I - Manual Process Task: Open a Issue for some automated test tool Geneva Emotion Wheel  List of emotions (Anger, Interest, Amusement, Pride, Joy, Pleasure, Contentment, Love, Admiration, Relief, Compassion, Sadness, Guilt, Regret, Shame, Disappointment, Fear, Disgust, Contempt, Hate) What are the causes of these feelings? Part II - Bug Builder Task: Open a Issue for some automated test tool Geneva Emotion Wheel  List of emotions (Anger, Interest, Amusement, Pride, Joy, Pleasure, Contentment, Love, Admiration, Relief, Compassion, Sadness, Guilt, Regret, Shame, Disappointment, Fear, Disgust, Contempt, Hate) What are the causes of these feelings? Part III - Semi-Structured Experience Interview 1. How do you feel about opening a task to the automation team using the manual process? 2. What situations do you face when opening a bug manually to the automation team? 3. What were your first impressions of Bug Builder? 4. Do you feel that Bug Builder meets your needs for reporting automation bugs? Why? 5. Which Bug Builder features did you find most useful? 6. Which Bug Builder features did you find least useful or unnecessary? 7. How intuitive do you find the Bug Builder interface? 8. Has Bug Builder helped increase the efficiency of opening bugs? How? 9. Have you noticed any improvements in the speed of opening a bug since implementing Bug Builder? 10. Have you encountered any technical difficulties when using Bug Builder? If so, what? 11. What would you do differently if you had to implement Bug Builder again? 12. Have you received sufficient training to use Bug Builder effectively? 13. How effective was the team support provided during the Bug Builder deployment? 14. What additional support would you like to see? 15. Are you satisfied with the Builder? Why? 16. Would you recommend the Bug Builder to other testing teams? Why? 17. Are there any other tools or features that you think could complement or replace the Bug Builder? 18. Is there anything else you would like to share about your experience with the tool? 19. Are there any specific improvements you would like to see in the Bug Builder?

opencc-zeroJun 2024View details →

Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation

High-density lipoprotein (HDL) nanoparticles promote endothelial cell (EC) function and suppress inflammation, but their utility in treating EC dysfunction has not been fully explored. Here, we describe a fusion protein named ApoA1-ApoM (A1M) consisting of apolipoprotein A1 (ApoA1), the principal structural protein of HDL that forms lipid nanoparticles, and ApoM, a chaperone for the bioactive lipid sphingosine 1-phosphate (S1P). A1M forms HDL-like particles, binds S1P, and is signaling competent. Molecular dynamic simulations showed that the S1P-bound ApoM moiety in A1M efficiently activated the EC surface receptors. Treatment of human umbilical vein endothelial cells (HUVECs) with A1M-S1P stimulated barrier function either alone or cooperatively with other barrier-enhancing molecules, including the stable prostacyclin analog iloprost, and suppressed cytokine-induced inflammation. A1M-S1P injection into mice during sterile inflammation suppressed neutrophil influx and inflammatory mediator secretion. Moreover, systemic A1M administration led to a sustained increase in circulating HDL-bound S1P and suppressed inflammation in a murine model of LPS-induced endotoxemia. We propose that A1M administration may enhance vascular endothelial barrier function, suppress cytokine storm, and promote resilience of the vascular endothelium.