Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic Effects of Acute Ultraviolet Radiation Exposure on Two Syntrichia Mosses

Ultraviolet radiation (UVR) is a major environmental stressor for terrestrial plants. Here we investigated genetic responses to acute broadband UVR exposure in the highly desiccation-tolerant mosses Syntrichia caninervis and Syntrichia ruralis, using a comparative transcriptomics approach. We explored whether UVR protection is physiologically plastic and induced by UVR exposure, addressing the following questions: (1) What is the timeline of changes in the transcriptome with acute UVR exposure in these two species? (2) What genes are involved in the UVR response? and (3) How do the two species differ in their transcriptomic response to UVR? There were remarkable differences between the two species after 10 and 30 min of UVR exposure, including no overlap in significantly differentially abundant transcripts (DATs) after 10 min of UVR exposure and more than twice as many DATs for S. caninervis as there were for S. ruralis. Photosynthesis-related transcripts were involved in the response of S. ruralis to UVR, while membrane-related transcripts were indicated in the response of S. caninervis. In both species, transcripts involved in oxidative stress and those important for desiccation tolerance (such as late embryogenesis abundant genes and early light-inducible protein genes) were involved in response to UVR, suggesting possible roles in UVR tolerance and cross-talk with desiccation tolerance in these species. The results of this study suggest potential UVR-induced responses that may have roles outside of UVR tolerance, and that the response to URV is different in these two species, perhaps a reflection of adaptation to different environmental conditions.
Agroecological Transitions: A Systematic Review of Research Approaches and Prospects for Participatory Action Methods

There have been many calls for an agroecological transition to respond to food shocks and crises stemming from conventional food systems. Participatory action research and transformative epistemologies, where communities are research actors rather than objects, have been proposed as a way to enhance this transition. However, despite numerous case studies, there is presently no overview of how participatory approaches contribute to agroecological transitions. The present article therefore aims to understand the effect of applying participatory action research (PAR) in agroecology. We undertook a systematic review of articles reporting methods and results from case studies in agroecological research. On the one hand, our systematic review of 347 articles shows that the agroecological research scope is broad, with all three types—as science, a set of practices and social movement—well-represented in the corpus. However, we can see a clear focus on agroecology “as a set of practices” as the primary type of use of the concept. On the other hand, we found a few case studies (23) with a participatory approach while most studies used extractive research methods. These studies show that understanding the drivers and obstacles for achieving an agroecological transition requires long-term research and trust between researchers and farmers. Such transformative epistemologies open doors to new questions on designing long-term PAR research in agroecology when confronted with a short-term project-based society.
Coronary Revascularization in Patients With Stable Coronary Artery Disease: The Role of Imaging

In the last decades, the effective management of some cardiovascular risk factors in the general population has led to a progressive decrease in the prevalence of coronary artery disease (CAD). Nevertheless, coronary heart disease remains the major cause of death in developed and developing countries and chronic coronary syndromes (CCS) are still a major target of utilization of non-invasive cardiac imaging and invasive procedures. Current guidelines recommend the use of non-invasive imaging in patients with CCS to identify subjects at higher risk to be referred for invasive coronary angiography and possible revascularization. These recommendations are challenged by two opposite lines of evidence. Recent trials have somewhat questioned the efficacy of coronary revascularization as compared with optimal medical therapy in CCS. As a consequence the role of imaging in these patients and in in patients with ischemic cardiomyopathy is under debate. On the other hand, real-life data indicate that a consistent proportion of patients undergo invasive procedure and are revascularized without any previous non-invasive imaging characterization. On top of this, the impact of COVID-19 pandemic on the sanitary systems caused a change in the current management of patients with CAD. In the present review we will discuss these conflicting data analyzing the evidence which has been recently accumulated as well as the gaps of knowledge which should still be filled.
Can Environmental Conditions at North Atlantic Deep-Sea Habitats Be Predicted Several Years Ahead? ——Taking Sponge Habitats as an Example

Predicting the ambient environmental conditions in the coming several years to one decade is of key relevance for elucidating how deep-sea habitats, like for example sponge habitats, in the North Atlantic will evolve under near-future climate change. However, it is still not well known to what extent the deep-sea environmental properties can be predicted in advance. A regional downscaling prediction system is developed to assess the potential predictability of the North Atlantic deep-sea environmental factors. The large-scale climate variability predicted with the coupled Max Planck Institute Earth System Model with low-resolution configuration (MPI-ESM-LR) is dynamically downscaled to the North Atlantic by providing surface and lateral boundary conditions to the regional coupled physical-ecosystem model HYCOM-ECOSMO. Model results of two physical fields (temperature and salinity) and two biogeochemical fields (concentrations of silicate and oxygen) over 21 sponge habitats are taken as an example to assess the ability of the downscaling system to predict the interannual to decadal variations of the environmental properties based on ensembles of retrospective predictions over the period from 1985 to 2014. The ensemble simulations reveal skillful predictions of the environmental conditions several years in advance with distinct regional differences. In areas closely tied to large-scale climate variability and ice dynamics, both the physical and biogeochemical fields can be skillfully predicted more than 4 years ahead, while in areas under strong influence of upper oceans or open boundaries, the predictive skill for both fields is limited to a maximum of 2 years. The simulations suggest higher predictability for the biogeochemical fields than for the physical fields, which can be partly attributed to the longer persistence of the former fields. Predictability is improved by initialization in areas away from the influence of Mediterranean outflow and areas with weak coupling between the upper and deep oceans. Our study highlights the ability of the downscaling regional system to predict the environmental variations at deep-sea benthic habitats on time scales of management relevance. The downscaling system therefore will be an important part of an integrated approach towards the preservation and sustainable exploitation of the North Atlantic benthic habitats.
The Evasion of Antiviral Innate Immunity by Chicken DNA Viruses

The innate immune system constitutes the first line of host defense. Viruses have evolved multiple mechanisms to escape host immune surveillance, which has been explored extensively for human DNA viruses. There is growing evidence showing the interaction between avian DNA viruses and the host innate immune system. In this review, we will survey the present knowledge of chicken DNA viruses, then describe the functions of DNA sensors in avian innate immunity, and finally discuss recent progresses in chicken DNA virus evasion from host innate immune responses.
Histological Correlates of Neuroanatomical Changes in a Rat Model of Levodopa-Induced Dyskinesia Based on Voxel-Based Morphometry

Long-term therapy with levodopa (L-DOPA) in patients with Parkinson’s disease (PD) often triggers motor complications termed as L-DOPA-induced dyskinesia (LID). However, few studies have explored the pathogenesis of LID from the perspective of neuroanatomy. This study aimed to investigate macroscopic structural changes in a rat model of LID and the underlying histological mechanisms. First, we established the hemiparkinsonism rat model through stereotaxic injection of 6-hydroxydopamine (6-OHDA) into the right medial forebrain bundle, followed by administration of saline (PD) or L-DOPA to induce LID. Magnetic resonance imaging (MRI) and behavioral evaluations were performed at different time points. Histological analysis was conducted to assess the correlations between MRI signal changes and cellular contributors. Voxel-based morphometry (VBM) analysis revealed progressive bilateral volume reduction in the cortical and subcortical areas in PD rats compared with the sham rats. These changes were partially reversed by chronic L-DOPA administration; moreover, there was a significant volume increase mainly in the dorsolateral striatum, substantia nigra, and piriform cortex of the lesioned side compared with that of PD rats. At the striatal cellular level, glial fibrillary acidic protein-positive (GFAP+) astrocytes were significantly increased in the lesioned dorsolateral striatum of PD rats compared with the intact side and the sham group. Prolonged L-DOPA treatment further increased GFAP levels. Neither 6-OHDA damage nor L-DOPA treatment influenced the striatal expression of vascular endothelial growth factor (VEGF). Additionally, there was a considerable increase in synapse-associated proteins (SYP, PSD95, and SAP97) in the lesioned striatum of LID rats relative to the PD rats. Golgi-Cox staining analysis of the dendritic spine morphology revealed an increased density of dendritic spines after chronic L-DOPA treatment. Taken together, our findings suggest that striatal volume changes in LID rats involve astrocyte activation, enrichment of synaptic ultrastructure and signaling proteins in the ipsilateral striatum. Meanwhile, the data highlight the enormous potential of structural MRI, especially VBM analysis, in determining the morphological phenotype of rodent models of LID.
Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis

Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.
Recent Advances in Magnesia Blended Cement Studies for Geotechnical Well Construction—A Review

The current paper presents a literature review on the studies of incorporation of magnesia (magnesium oxide) into Portland cement material from the geotechnical well construction perspective. Starting with a comparison of application conditions between civil construction and geotechnical well cementing, this work reviewed the Portland cement categorizations, magnesia manufacturing routes at first. Then, the physical-chemical-mechanical properties were investigated which includes the reactivity of magnesia, expansion influence from its hydration, and carbonation/dehydroxylation of magnesia blended Portland cement. The development of cement material hydration modeling methods is also summarized. Moreover, the experimental characterization methods have also been elucidated including composition determination, particle size analysis, volumetric variation measurement, compressive strength testing, shear-bond strength testing, transition state analysis, etc. Meanwhile, the results and conclusions were extracted from the literature. Through this route, a comprehensive understanding of the scientific research progress on magnesia blended Portland cement development for geotechnical well construction is derived. Additionally, it is concluded that incorporating magnesia into Portland cement can provide benefits for this material utilization in geotechnical well constructions provided the reasonable tuning among the characteristics of magnesia, the downhole surrounding conditions, and the formulation of the cement slurry. Satisfying these pre-conditions, the effective expansion not only mitigates the micro-annulus issues but also increases the shear bonding strength at the cementing interfaces. Moreover, the caustic magnesia introduction into Portland cement has the potential advantage on carbon dioxide geological sequestration well integrity compared with the Portland cement sheath without it because of the denser in-situ porous matrix evolvement and more stable carbon fixation features of magnesium carbonate. However, since the impact of magnesia on Portland cement strongly depended on its properties (calcination conditions, particle size, reactivity) and the aging conditions (downhole temperature, pressure, contacting medium), it should be noted that some extended research is worth conducting in the future such as the synchronized hydration between magnesia and Portland cement, the dosage limit of caustic magnesia in Portland cement in terms of CO2 sequestration and the corresponding mechanical properties analysis, and the hybrid method (caustic magnesia, Portland cement, and other supplementary cementitious materials) targeting the co-existence of the geothermal environment and the corrosive medium scenario.
Adult Aging Moderates the Relationship Between Trait Cognitive Anxiety and Subjective Everyday Cognitive Difficulties

The present aim was to determine, across the adult lifespan, the extent to which different dimensions of trait anxiety might affect subjective cognitive difficulties in everyday life. Following Attentional Control Theory (ACT; Eysenck et al., 2007), we predicted that trait anxiety would have a greater effect on attention and verbal abilities than on visual abilities. We also expected trait cognitive anxiety to exhibit more robust relationships with cognition than trait somatic anxiety. Importantly, we predicted that effects of anxiety would be greater in older adults, in line with the Strength and Vulnerability Integration model (SAVI; Charles, 2010). The sample comprised 286 United Kingdom-based adults aged 18–93 years. Participants completed self-report measures of trait cognitive and somatic anxiety (the State-Trait Inventory for Cognitive and Somatic Anxiety; STICSA, Ree et al., 2008) and everyday cognitive difficulties (the Multiple Abilities Self-Report Questionnaire; MASQ, Seidenberg et al., 1994). Moderated regression models were constructed, including trait cognitive or somatic anxiety as a predictor of cognitive difficulties, and age as the moderator variable. Covariates included depression, stress (the Depression Anxiety Stress Scales—short form; DASS-21, Lovibond and Lovibond, 1995), gender, current mental health treatment status, and physical health status. When cognitive anxiety was the predictor variable, somatic anxiety was also included as a covariate, and vice-versa. Trait cognitive anxiety and age interacted to predict all MASQ subscales other than visual-perceptual ability. Difficulties with attention, verbal memory, and language abilities were significantly greater at higher levels of anxiety for all age groups, with the effect greatest in older adults. Difficulties with visual-spatial memory were significantly greater at higher levels of anxiety in middle-aged and older adults only. Higher trait somatic anxiety predicted difficulties with verbal memory and language ability independently of age, and interacted with age to predict language difficulties. Interestingly, age also significantly predicted less subjective difficulty with attention, independently of anxiety level. The results show that trait cognitive and somatic anxiety are both related to subjective, everyday cognitive difficulties. However, effects of trait cognitive anxiety are more robust across cognitive domains and tend to increase, or first appear, over the course of the adult lifespan.
Tannic Acid-Steeped Corn Grain Modulates in vitro Ruminal Fermentation Pattern and Microbial Metabolic Pathways

This study investigated the effects of tannic acid (TA)-treated corn on changes in ruminal fermentation characteristics and the composition of the ruminal bacterial community in vitro. Ruminal fluid was obtained from three rumen-fistulated goats fed a 60:40 (forage/concentrate) diet. The batch cultures consisted of 25 ml of strained rumen fluid in 25 ml of an anaerobic buffer containing 0.56 g of ground corn, 0.24 g of soybean meal, 0.10 g of alfalfa, and 0.10 g of oat grass. Ground corn (2 mm) was steeped in an equal quantity (i.e., in a ratio of 1:1, w/v) of water alone (Con), 15 (TA15), 25 (TA25), and 35 g/l (TA35) TA solution for 12 h. After incubation for 24 h, TA-treated corn linearly increased (P <0.05) ruminal pH and the molar proportion of acetate, but linearly reduced (P <0.05) total volatile fatty acids and the molar proportion of butyrate compared with the Con treatment. Illumina MiSeq sequencing was used to investigate the profile changes of the ruminal microbes. A principal coordinates analysis plot based on weighted UniFrac values revealed that the structure of the ruminal bacterial communities in the control group was different from that of the TA-treated corn groups. The results of changes in the rumen bacterial communities showed that TA-treated corn linearly enriched (P <0.05) Rikenellaceae_RC9_gut_group, but linearly reduced (P <0.05) Ruminococcaceae_NK4A214_group, Ruminococcus_2, and unclassified_o__Clostridiales. Functional prediction of ruminal microbiota revealed that the TA-treated corn linearly decreased ruminal microbiota function of utilizing starch through pyruvate metabolism. In conclusion, TA-treated corn can modulate the rumen fermentation characteristics, microbial composition, and metabolic pathways, which may be potentially useful for preventing the occurrence of ruminal acidosis.
The Population Genetics, Virulence, and Public Health Concerns of Escherichia coli Collected From Rats Within an Urban Environment

The co-existence of rats and humans in urban environments has long been a cause for concern regarding human health because of the potential for rats to harbor and transmit disease-causing pathogens. Here, we analyze whole-genome sequence (WGS) data from 41 Escherichia coli isolates collected from rat feces from 12 locations within the city of Chicago, IL, United States to determine the potential for rats to serve as a reservoir for pathogenic E. coli and describe its population structure. We identified 25 different serotypes, none of which were isolated from strains containing significant virulence markers indicating the presence of Shiga toxin-producing and other disease-causing E. coli. Nor did the E. coli isolates harbor any particularly rare stress tolerant or antimicrobial resistance genes. We then compared the isolates against a public database of approximately 100,000 E. coli and Shigella isolates of primarily food, food facility, or clinical origin. We found that only one isolate was genetically similar to genome sequences in the database. Phylogenetic analyses showed that isolates cluster by serotype, and there was little geographic structure (e.g., isolation by distance) among isolates. However, a greater signal of isolation by distance was observed when we compared genetic and geographic distances among isolates of the same serotype. This suggests that E. coli serotypes are independent lineages and recombination between serotypes is rare.
Meaning Reflectivity in Later Life: The Relationship Between Reflecting on Meaning in Life, Presence and Search for Meaning, and Depressive Symptoms in Older Adults Over the Age of 75

Background: Over the last decades, there is growing attention for the importance of meaning in life for older adults. However, there is virtually no insight into the mental processes that contribute to this experience. Some scholars recently called for an investigation of meaning reflectivity, or the process of reflecting on issues specifically related to meaning in life. In this study, we explored to what extent older adults talk and think about issues of meaning in life, and how this meaning reflectivity is related to the search for and presence of meaning in life, and to depressive symptoms. Method: In this cross-sectional observational study, 282 community-residing older adults (75 or older) in Belgium filled in paper questionnaires on meaning in life (presence and search), depressive symptoms, and meaning reflectivity (categorical item). ANOVA analyses were used to explore differences in meaning in life and depressive symptoms across the meaning reflectivity categories. Regression and negative binomial models investigated the association between meaning reflectivity and presence, search and depressive symptoms. Finally, an exploratory structural equation model examined whether presence of meaning statistically mediated the relationship between meaning reflectivity and depressive symptoms. Results: The majority of participants (42.4%) indicated that they had thought about meaning in life before, 23.2% indicated that they had talked about it before, 18% indicated that they hadn’t thought about it before but found it interesting, and 16.4% indicated that they were indifferent/unconcerned about meaning in life. The latter group reported lower levels of presence of meaning and search for meaning and higher levels of depressive symptoms. Belonging to this category was also associated with lower presence and search in regression analyses, but not with depressive symptoms above the effect of presence of meaning. Exploratory mediation analyses suggested that presence of meaning may be a mediator between meaning reflectivity and depressive symptoms. Conclusion: Meaning reflectivity is an important process to consider in the context of the experience of meaning in life for older adults. Those older adults who are indifferent about issues of meaning in life might be more vulnerable to experience a lack of meaning and depressive symptoms.