Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative approaches to dispersing science: A case study of March Mammal Madness

Public engagement is increasingly viewed as an important pillar of scientific scholarship. For early career and established scholars, navigating the mosaic landscape of public education and science communication, noted for rapid “ecological” succession, can be daunting. Moreover, academics are characterized by diverse skills, motivations, values, positionalities, and temperaments that may differentially incline individuals to particular public translation activities.
Differential Proteomic Analysis of Astrocytes and Astrocytes-Derived Extracellular Vesicles from Control and Rai Knockout Mice: Insights into the Mechanisms of Neuroprotection

Reactive astrocytes are a hallmark of neurodegenerative disease including multiple sclerosis. It is widely accepted that astrocytes may adopt alternative phenotypes depending on a combination of environmental cues and intrinsic features in a highly plastic and heterogeneous manner. However, we still lack a full understanding of signals and associated signaling pathways driving astrocyte reaction and of the mechanisms by which they drive disease. We have previously shown in the experimental autoimmune encephalomyelitis mouse model that deficiency of the molecular adaptor Rai reduces disease severity and demyelination. Moreover, using primary mouse astrocytes, we showed that Rai contributes to the generation of a pro-inflammatory central nervous system (CNS) microenvironment through the production of nitric oxide and IL-6 and by impairing CD39 activity in response to soluble factors released by encephalitogenic T cells. Here, we investigated the impact of Rai expression on astrocyte function both under basal conditions and in response to IL-17 treatment using a proteomic approach. We found that astrocytes and astrocyte-derived extracellular vesicles contain a set of proteins, to which Rai contributes, that are involved in the regulation of oligodendrocyte differentiation and myelination, nitrogen metabolism, and oxidative stress. The HIF-1α pathway and cellular energetic metabolism were the most statistically relevant molecular pathways and were related to ENOA and HSP70 dysregulation.
IEDDA: An Attractive Bioorthogonal Reaction for Biomedical Applications

The pretargeting strategy has recently emerged in order to overcome the limitations of direct targeting, mainly in the field of radioimmunotherapy (RIT). This strategy is directly dependent on chemical reactions, namely bioorthogonal reactions, which have been developed for their ability to occur under physiological conditions. The Staudinger ligation, the copper catalyzed azide-alkyne cycloaddition (CuAAC) and the strain-promoted [3 + 2] azide–alkyne cycloaddition (SPAAC) were the first bioorthogonal reactions introduced in the literature. However, due to their incomplete biocompatibility and slow kinetics, the inverse-electron demand Diels-Alder (IEDDA) reaction was advanced in 2008 by Blackman et al. as an optimal bioorthogonal reaction. The IEDDA is the fastest bioorthogonal reaction known so far. Its biocompatibility and ideal kinetics are very appealing for pretargeting applications. The use of a trans-cyclooctene (TCO) and a tetrazine (Tz) in the reaction encouraged researchers to study them deeply. It was found that both reagents are sensitive to acidic or basic conditions. Furthermore, TCO is photosensitive and can be isomerized to its cis-conformation via a radical catalyzed reaction. Unfortunately, the cis-conformer is significantly less reactive toward tetrazine than the trans-conformation. Therefore, extensive research has been carried out to optimize both click reagents and to employ the IEDDA bioorthogonal reaction in biomedical applications.
Cytotoxicity of Essential Oil Cordia verbenaceae against Leishmania brasiliensis and Trypanosoma cruzi

The species Cordia verbenacea DC (Boraginaceae), known as the whaling herb and camaradinha, is a perennial shrub species native to the Atlantic Forest. Its leaves are used in folk medicine as an anti-inflammatory, analgesic, antiulcerogenic and curative agent, in the form of teas or infusions for internal or topical use. The present study aimed to verify the cytotoxicity of the essential oil and the leishmanicidal and trypanocidal potential of C. verbenacea. The essential oil was characterized by GC-MS. The in vitro biological activity was determined by anti-Leishmania and anti-Trypanosoma assays. The cytotoxixity was determined using mammalian fibroblasts. The C. verbenacea species presented α-pinene (45.71%), β-caryophyllene (18.77%), tricyclo[2,2,1-(2.6)]heptane (12.56%) as their main compounds. The essential oil exhibited strong cytotoxicity at concentrations below 250 μg/mL (LC50 138.1 μg/mL) in mammalian fibroblasts. The potent anti-trypanosome and anti-promastigote activities occurred from the concentration of 62.5 μg/mL and was considered clinically relevant. The results also demonstrate that at low concentrations (<62.5 μg/mL), the essential oil of C. verbenacea managed to be lethal for these activities. This can be considered an indication of the power used in daily human consumption. Therefore, it can be concluded that the essential oil of C. verbenacea contains a compound with remarkable antiparasitic activities and requires further research.
LPEATs Tailor Plant Phospholipid Composition through Adjusting Substrate Preferences to Temperature

Acyl-CoA:lysophosphatidylethanolamine acyltransferases (LPEATs) are known as enzymes utilizing acyl-CoAs and lysophospholipids to produce phosphatidylethanolamine. Recently, it has been discovered that they are also involved in the growth regulation of Arabidopsis thaliana. In our study we investigated expression of each Camelina sativa LPEAT isoform and their behavior in response to temperature changes. In order to conduct a more extensive biochemical evaluation we focused both on LPEAT enzymes present in microsomal fractions from C. sativa plant tissues, and on cloned CsLPEAT isoforms expressed in yeast system. Phylogenetic analyses revealed that CsLPEAT1c and CsLPEAT2c originated from Camelina hispida, whereas other isoforms originated from Camelina neglecta. The expression ratio of all CsLPEAT1 isoforms to all CsLPEAT2 isoforms was higher in seeds than in other tissues. The isoforms also displayed divergent substrate specificities in utilization of LPE; CsLPEAT1 preferred 18:1-LPE, whereas CsLPEAT2 preferred 18:2-LPE. Unlike CsLPEAT1, CsLPEAT2 isoforms were specific towards very-long-chain fatty acids. Above all, we discovered that temperature strongly regulates LPEATs activity and substrate specificity towards different acyl donors, making LPEATs sort of a sensor of external thermal changes. We observed the presented findings not only for LPEAT activity in plant-derived microsomal fractions, but also for yeast-expressed individual CsLPEAT isoforms.
Proteomics Analysis Reveals Altered Nutrients in the Whey Proteins of Dairy Cow Milk with Different Thermal Treatments

Thermal treatments of milk induce changes in the properties of milk whey proteins. The aim of this study was to investigate the specific changes related to nutrients in the whey proteins of dairy cow milk after pasteurization at 85 °C for 15 s or ultra-high temperature (UHT) at 135 °C for 15 s. A total of 223 whey proteins were confidently identified and quantified by TMT-based global discovery proteomics in this study. We found that UHT thermal treatment resulted in an increased abundance of 17 proteins, which appeared to show heat insensitivity. In contrast, 15 heat-sensitive proteins were decreased in abundance after UHT thermal treatment. Some of the heat-sensitive proteins were connected with the biological immune functionality, suggesting that UHT thermal treatment results in a partial loss of immune function in the whey proteins of dairy cow milk. The information reported here will considerably expand our knowledge about the degree of heat sensitivity in the whey proteins of dairy cow milk in response to different thermal treatments and offer a knowledge-based reference to aid in choosing dairy products. It is worth noting that the whey proteins (lactoperoxidase and lactoperoxidase) in milk that were significantly decreased by high heat treatment in a previous study (142 °C) showed no significant difference in the present study (135 °C). These results may imply that an appropriately reduced heating intensity of UHT retains the immunoactive proteins to the maximum extent possible.
HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data

The explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to assess the proteins associated with different non-coding DNA regions genome-wide. While the analysis of such data related to transcription factor binding is relatively straightforward, many modified histone variants, such as H3K27me3, are very important for the process of gene regulation but are very difficult to interpret. We propose a novel method, called HERON (HiddEn MaRkov mOdel based peak calliNg), for genome-wide data analysis that is able to detect DNA regions enriched for a certain feature, even in difficult settings of weakly enriched long DNA domains. We demonstrate the performance of our method both on simulated and experimental data.
Studies of Nature of Uncommon Bifurcated I–I···(I–M) Metal-Involving Noncovalent Interaction in Palladium(II) and Platinum(II) Isocyanide Cocrystals

Two isostructural trans-[MI2(CNXyl)2]·I2 (M = Pd or Pt; CNXyl = 2,6-dimethylphenyl isocyanide) metallopolymeric cocrystals containing uncommon bifurcated iodine···(metal–iodide) contact were obtained. In addition to classical halogen bonding, single-crystal X-ray diffraction analysis revealed a rare type of metal-involved stabilizing contact in both cocrystals. The nature of the noncovalent contact was studied computationally (via DFT, electrostatic surface potential, electron localization function, quantum theory of atoms in molecules, and noncovalent interactions plot methods). Studies confirmed that the I···I halogen bond is the strongest noncovalent interaction in the systems, followed by weaker I···M interaction. The electrophilic and nucleophilic nature of atoms participating in I···M interaction was studied with ED/ESP minima analysis. In trans-[PtI2(CNXyl)2]·I2 cocrystal, Pt atoms act as weak nucleophiles in I···Pt interaction. In the case of trans-[PdI2(CNXyl)2]·I2 cocrystal, electrophilic/nucleophilic roles of Pd and I are not clear, and thus the quasimetallophilic nature of the I···Pd interaction was suggested.
Prediction of Residual Stroke Risk in Anticoagulated Patients with Atrial Fibrillation: mCARS

Our ability to evaluate residual stroke risk despite anticoagulation in atrial fibrillation (AF) is currently lacking. The Calculator of Absolute Stroke Risk (CARS) has been proposed to predict 1-year absolute stroke risk in non-anticoagulated patients. We aimed to determine whether a modified CARS (mCARS) may be used to assess the residual stroke risk in anticoagulated AF patients from ‘real-world’ and ‘clinical trial’ cohorts. We studied patient-level data of anticoagulated AF patients from the real-world Murcia AF Project and AMADEUS clinical trial. Individual mCARS were estimated for each patient. None of the patients were treated with non-vitamin K antagonist oral anticoagulants. The predicted residual stroke risk was compared to actual stroke risk. 3503 patients were included (2205 [62.9%] clinical trial and 1298 [37.1%] real-world). There was wide variation of CARS for each category of CHA2DS2-VASc score in both cohorts. Average predicted residual stroke risk by mCARS (1.8 ± 1.8%) was identical to actual stroke risk (1.8% [95% CI, 1.3–2.4]) in the clinical trial, and broadly similar in the real-world (2.1 ± 1.9% vs. 2.4% [95% CI, 1.6–3.4]). AUCs of mCARS for prediction of stroke events in the clinical trial and real-world were 0.678 (95% CI, 0.598–0.758) and 0.712 [95% CI, 0.618–0.805], respectively. mCARS was able to refine stroke risk estimation for each point of the CHA2DS2-VASc score in both cohorts. Personalised residual 1-year absolute stroke risk in anticoagulated AF patients may be estimated using mCARS, thereby allowing an assessment of the absolute risk reduction of treatment and facilitating a patient-centred approach in the management of AF. Such identification of patients with high residual stroke risk could help target more aggressive interventions and follow-up.
A Teaching Kitchen Medical Groups Visit with an eHealth Platform for Hypertension and Cardiac Risk Factors: A Qualitative Feasibility Study.

Introduction: Our Whole Lives-Hypertension (OWL-H) is an eHealth toolkit for hypertension and cardiac risks factors. It is a hybrid online self-management platform that teaches blood pressure (BP) self-monitoring and evidence-based lifestyle modifications combined with in-person teaching kitchen medical group visit. Qualitative feedback from participants regarding the facilitators and barriers of using OWL-H has been discussed in this article. Methods: The OWL-H platform was pilot tested in a pre-post trial with two cohorts of participants with hypertension (N = 24). The online intervention utilized OWL-H for teaching mindfulness meditation, the Dietary Approaches to Stop Hypertension nutrition plan, and evidence-based strategies for lifestyle modifications. Three in-person teaching kitchen medical group visits were held to demonstrate cooking skills to reinforce the online platform. Semi-structured focus group discussions (FGDs) were held after the intervention. Results: Fourteen of the 24 participants in the trial participated in the FGDs, and 1 participant provided feedback in a solo interview. Major themes that emerged included: (1) participants' request to tailor OWL-H's recipes and meal planning to suit their own dietary needs or preferences, to personalize the Home Practices (e.g., meditation) according to individual preferences (e.g., addition of nature sounds or guided visual imagery); (2) the strengths and weaknesses of OWL-H as a BP self-monitoring tool; (3) the need for community support in managing BP; and (4) participants noted lack of time, work and commute, Internet connectivity, stress, and sickness as obstacles in using OWL-H. Participants described feeling outpaced by the growth of technology and raised concerns of poor Internet connectivity hampering their use of OWL-H. Conclusion: OWL-H and the accompanying teaching kitchen medical group visit are potential tools to help reduce hypertension and cardiac risk factors. The intervention was found to have acceptability among people with lower income. Clinical Trials Registration#: NCT03974334.
Transcriptome-Based WGCNA Analysis Reveals Regulated Metabolite Fluxes between Floral Color and Scent in Narcissus tazetta Flower

A link between the scent and color of Narcissus tazetta flowers can be anticipated due to their biochemical origin, as well as their similar biological role. Despite the obvious aesthetic and ecological significance of these colorful and fragrant components of the flowers and the molecular profiles of their pigments, fragrant formation has addressed in some cases. However, the regulatory mechanism of the correlation of fragrant components and color patterns is less clear. We simultaneously used one way to address how floral color and fragrant formation in different tissues are generated during the development of an individual plant by transcriptome-based weighted gene co-expression network analysis (WGCNA). A spatiotemporal pattern variation of flavonols/carotenoids/chlorophyll pigmentation and benzenoid/phenylpropanoid/ monoterpene fragrant components between the tepal and corona in the flower tissues of Narcissus tazetta, was exhibited. Several candidate transcription factors: MYB12, MYB1, AP2-ERF, bZIP, NAC, MYB, C2C2, C2H2 and GRAS are shown to be associated with metabolite flux, the phenylpropanoid pathway to the production of flavonols/anthocyanin, as well as related to one branch of the phenylpropanoid pathway to the benzenoid/phenylpropanoid component in the tepal and the metabolite flux between the monoterpene and carotenoids biosynthesis pathway in coronas. It indicates that potential competition exists between floral pigment and floral fragrance during Narcissus tazetta individual plant development and evolutionary development.
Analysis of Sediment Reduction with VFS and Diversion Channel with Enhancements in SWAT Landuse-Subbasin Overland Flow and VFS Modules

In the last decade, many methods such as greet chamber, reservoir, or debris barrier, have been utilized to manage and prevent muddy water problem. The Vegetative Filter Strip (VFS) has been thought to be one of the most effective methods to trap sediment effectively. The VFS are usually installed at the edge of agricultural areas adjacent to stream or drainage ditches, and it has been shown that the VFS effectively removes pollutants transported with upland runoff. But, if the VFS is installed without any scientific analysis of rainfall-runoff characteristics, soil erosion, and sediment analysis, it may not reduce the sediment as much as expected. Although Soil and Water Assessment Tool (SWAT) model has been used worldwide for many hydrologic and Non-Point Source Pollution (NPSP) analysis at a watershed scale. but it has many limitations in simulating the VFS. Because it considers only 'filter strip width' when the model estimates sediment trapping efficiency, and does not consider the routing of sediment with overland flow option which is expected to maximize the sediment trapping efficiency from upper agricultural subbasin to lower spatially-explicit filter strip. Therefore, the SWAT overland flow option between landuse-subbasins with sediment routing capability was enhanced with modifications in SWAT watershed configuration and SWAT engine. The enhanced SWAT can simulate the sediment trapping efficiency of the VFS in the similar way as the desktop VFSMOD-w system does. Also it now can simulate the effects of overland flow from upper subbasin to reflect the increased runoff volume at the receiving subbasin, which is what is occurring at the field if no diversion channel is installed. In this study, the enhanced SWAT model was applied to small watershed located at Jaun-ri in South Korea to simulate diversion channel and spatially-explicit VFS. It was found that approximately sediment can be reduced by 31%, 65%, 68%, with diversion channel, the VFS, and the VFS with diversion channel, respectively.
The influence of age and development temperature on the temperature-related foraging risk of

Climate change and the subsequent increase of global temperature are the most current and important threats to biodiversity. Despite the importance of temperature, our knowledge about the level of behavioural and physiological adaptations of ant species from temperate regions to cope with high temperatures is limited compared to the broad knowledge of typical thermal specialists from warmer regions. In the current study, we investigated the temperature-related foraging risk of xerothermic ant species from the temperate climate in Europe, Formica cinerea. Our aims were to check how an increase in external soil temperature affects the foraging activity of workers and how the temperature during development and worker age affects foraging activity in high temperatures. Based on our results, we can draw the following conclusions: (1) the majority of workers utilize a risk-aversive strategy in relation to foraging in high surface temperatures; (2) pupal development temperature affects the risk taken by adult workers: workers that developed in a higher temperature forage more often but for shorter intervals compared to workers that developed in a lower temperature; (3) age is an important factor in temperature-related foraging activity, as with increasing age, workers forage significantly longer at the highest temperatures. Our study is one of the first to assess the potential factors that can affect the foraging risk of ants from a temperate climate in high ambient temperatures. Significance statement Our study is the first direct test of workers’ age and the development temperature of pupae on the thermal-related foraging strategy of adult F. cinerea workers. It shows that worker age and the development temperature of pupae interact to promote tolerance of thermal stress. We found that with increasing age, workers are prone to forage significantly longer at the highest and riskiest temperatures. Workers that developed in the high temperature (28°C) foraged more often but for shorter intervals compared to workers that developed in the lower temperature (20°C). Interestingly, the factor of age is more significant for ants that developed in the higher temperature of 28°C; the foraging time of these ants significantly increased with their age.
Interactive comment on “Carbonyl Sulfide: Comparing a Mechanistic Representation of the Vegetation Uptake in a Land Surface Model and the Leaf Relative Uptake Approach” by

[1] Maignan et al., develop a parameterization for including OCS uptake within a well-known land surface model (ORCHIDEE ). Since OCS has been proposed as a proxy for GPP (currently not observable at large scales), this work is an important step towards estimating global GPP. The authors do a very thorough job of combing the OCS literature for published values of leaf relative uptake (LRU) and validating modeled uptake at two temperate sites where OCS flux is measured. I think this work should eventually be published in Biogeosciences. However I am currently a little confused with regard to how the paper is framed. The authors pose their formulation of OCS flux using a conductance based approach against the well-known LRU based relationship between FOCS and GPP. The LRU approach is also based on conductance, with simple assumptions regarding the relative role of mesophyll and stomatal conductances (Seibt et al., 2010). Thus the differences in flux resulting between the two approaches are not surprising, and don’t really manifest themselves once transported and compared against OCS flask measurements from NOAA. This is an interesting finding, but I think the authors must focus on a more scientific question. Answer: We thank the Referee for this analysis. We must precise here that what we call the “LRU approach” in this study, is based on a former work with ORCHIDEE (Launois et al., 2015b), which does not consider a varying LRU as modelled in Seibt et al. (2010, their equation (8)), but uses constant values for each Plant Functional Type (PFT). We have thus clarified the context of this study and formulated our goal in a more scientific way: “In a former study, Launois et al. (2015b) simply defined the COS uptake by vegetation as the CO2 gross uptake simulated by LSMs, scaled with a constant LRU value for each large vegetation class. The goal of this study is to now simulate the uptake of atmospheric COS by continental vegetation in a more complex and realistic way using a mechanistic approach within an LSM, and apply this model to evidence the shortcomings or pertinence of the LRU concept, depending on the studied scales”. In the revised manuscript we have thus emphasized the study of the LRU variability both at hourly and site scales, and at monthly and global scales. This can be seen in more details through our answers to both Referees’ comments.