Miracle-dz/UniFAR-FTUs huggingface dataset:
Early damage enhances compensatory responses to herbivory in wild lima bean

Damage by herbivores can induce various defensive responses. Induced resistance comprises traits that can reduced the damage, while compensatory responses reduce the negative effects of damage on plant fitness. Timing of damage may be essential in determining the patterns of induced defenses. Here, we tested how timing and frequency of leaf damage affect compensatory responses in wild lima bean plants in terms of growth and seed output, as well as their effects on induced resistance to seed beetles. To this end, we applied mechanical damage to plants at different ontogenetical stages, at one time point (juvenile stage only) or two time points (seedling and juvenile stage or juvenile and reproductive stage). We found that plants damaged at the seedling/juvenile stage showed higher compensatory growth, and seed output compared to plants damaged only at the juvenile stage or juvenile/reproductive stage. Seeds from plants damaged at the juvenile and juvenile/reproductive stages had fewer beetles than seeds from undamaged plants, however this was driven by a density dependent effect of seed abundance rather than a direct effect of damage treatments. We did not find differences in parasitism rate by parasitoid wasps on seed beetles among plant treatments. Our results show that damage at the seedling stage triggers compensatory responses which implies that tolerance to herbivory is enhanced or primed by early damage. Herbivory often occurs at several time points throughout plant development and this study illustrates that, for a full understanding of the factors associated with plant induced responses in a dynamic biotic environment, it is important to determine the multitrophic consequences of damage at more than one ontogenetical stage.
New models of Parkinson’s like neuroinflammation in human microglia clone 3: Activation profiles induced by INF-γ plus high glucose and mitochondrial inhibitors

Microglia activation and neuroinflammation have been extensively studied in murine models of neurodegenerative diseases; however, to overcome the genetic differences between species, a human cell model of microglia able to recapitulate the activation profiles described in patients is needed. Here we developed human models of Parkinson’s like neuroinflammation by using the human microglia clone 3 (HMC3) cells, whose activation profile in response to classic inflammatory stimuli has been controversial and reported only at mRNA levels so far. In fact, we showed the increased expression of the pro-inflammatory markers iNOS, Caspase 1, IL-1β, in response to IFN-γ plus high glucose, a non-specific disease stimulus that emphasized the dynamic polarization and heterogenicity of the microglial population. More specifically, we demonstrated the polarization of HMC3 cells through the upregulation of iNOS expression and nitrite production in response to the Parkinson’s like stimuli, 6-hydroxidopamine (6-OHDA) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), the latter depending on the NF-κB pathway. Furthermore, we identified inflammatory mediators that promote the pro-inflammatory activation of human microglia as function of different pathways that can simulate the phenotypic transition according to the stage of the pathology. In conclusion, we established and characterized different systems of HMC3 cells activation as in vitro models of Parkinson’s like neuroinflammation.
Characterization of the antagonistic potential of the glyphosate-tolerant Pseudomonas resinovorans SZMC 25872 strain against the plant pathogenic bacterium Agrobacterium tumefaciens

The utilization of microorganisms with biocontrol activity against fungal and bacterial pathogens of plants is recognized as a promising, effective, and environment-friendly strategy to protect agricultural crops. We report the glyphosate-tolerant Pseudomonas resinovorans SZMC 25872 isolate as a novel strain with antagonistic potential towards the plant pathogenic bacterium Agrobacterium tumefaciens. In our studies, the growth of the P. resinovorans SZMC 25872 and A. tumefaciens SZMC 14557 isolates in the presence of 74 different carbon sources, and the effect of 11 carbon sources utilized by both strains on the biocontrol efficacy was examined. Seven variations of media with different carbon sources were selected for the assays to observe the biocontrol potential of the P. resinovorans strain. Also, 50% concentrations of the cell-free culture filtrates (CCF) obtained from medium amended with L-alanine or succinic acid as sole carbon source were found to be effective for the growth suppression of A. tumefaciens by 83.03 and 56.80%, respectively. The effect of 7 media on siderophore amount and the activity of extracellular trypsin- and chymotrypsin-like proteases, as well as esterases were also evaluated. Significant positive correlation was found between the siderophore amount and the percentage of inhibition, and the inhibitory effect of the CCFs obtained from medium amended with succinic acid was eliminated in the presence of an additional iron source, suggesting that siderophores produced by P. resinovorans play an important role in its antagonistic potential. The metabolic profile analysis of the P. resinovorans SZMC 25872 strain, performed by high performance liquid chromatography - high resolution mass spectrometry (HPLC-HRMS), has identified several previously not reported metabolites that might play role in the antagonistic effect against A. tumefaciens. Based on our findings we suggest that the possible inhibition modes of A. tumefaciens SZMC 14557 by P. resinovorans SZMC 25872 include siderophore-mediated suppression, extracellular enzyme activities and novel bioactive metabolites.
The modeling of free-fall arch formation in granular flow through an aperture

In this study, to predict the formation of the free-fall arch via granular flow through an aperture, an analytical model has been developed based on the particle-scale force equilibrium. This model calculates the size and location of the meta-stable arch and can be extended to predict the granular flow rate. According to the developed analytical model, the formation of a free-fall arch is independent of granular height and stress state above the arch, where only granular particle size, aperture size, and granular friction influence the development of the arch. Besides, this proposed model can predict the formation of the meta-stable arch without empirical parameters. In comparison with experimental results, the predicted granular flow rate based on the model exhibits high accuracy for uniform-sized granular flow. According to numerical simulations, the free-fall arch appears above the aperture; however, the particle velocity at the arch is low and can be considered negligible. Gravity will cause the granular particles under the arch to fall freely. This mathematical model offers an efficient method to predict the formation of the free-fall arch and calculate the granular flow rate through an aperture.
Prognostic analysis of m6A-related genes as potential biomarkers in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options. N6-methyladenosine (m6A) is a reversible RNA modification and has been implicated in various biological processes. However, there are few studies on m6A in IPF. This project mainly explores the prognostic value of m6A-related genes as potential biomarkers in IPF, in order to establish a set of accurate prognostic prediction model. In this study, we used GSE28042 dataset in GEO database to screen out 218 m6A-related candidate genes with high IPF correlation and high differential expression through differentially expressed gene analysis, WGCNA and m6A correlation analysis. The genes associated with the prognosis of IPF were screened out by univariate Cox regression analysis, LASSO analysis, and multivariate Cox regression analysis, and the multivariate Cox model of prognostic risk of related genes was constructed. We found that RBM11, RBM47, RIC3, TRAF5 and ZNF14 were key genes in our model. Finally, the prognostic prediction ability and independent prognostic characteristics of the risk model were evaluated by survival analysis and independent prognostic analysis, and verified by the GSE93606 dataset, which proved that the prognostic risk model we constructed has a strong and stable prediction efficiency.
Arbuscular mycorrhiza induces low oxidative burst in drought-stressed walnut through activating antioxidant defense systems and heat shock transcription factor expression

Arbuscular mycorrhizal fungi (AMF) have important roles in enhancing drought tolerance of host plants, but it is not clear whether and how AMF increase drought tolerance in walnut (Juglans regia). We hypothesized that AMF could activate antioxidant defense systems and heat shock transcription factors (Hsfs) transcription levels to alleviate oxidative damage caused by drought. The walnut variety ‘Liaohe No. 1’ was inoculated with Diversispora spurca and exposed to well-watered (WW, 75% of the maximum soil water capacity) and drought stress (DS, 50% of the maximum soil water capacity) for 6 weeks. Plant growth, antioxidant defense systems, and expressions of five JrHsfs in leaves were studied. Such drought treatment inhibited root mycorrhizal colonization, while plant growth performance was still improved by AMF inoculation. Mycorrhizal fungal inoculation triggered the increase in soluble protein, glutathione (GSH), ascorbic acid (ASC), and total ASC contents and ascorbic peroxidase and glutathione reductase activities, along with lower hydrogen peroxide (H2O2), superoxide anion radical (O2 •−), and malondialdehyde (MDA) levels, compared with non-inoculation under drought. Mycorrhizal plants also recorded higher peroxidase, catalase, and superoxide dismutase activities than non-mycorrhizal plants under drought. The expression of JrHsf03, JrHsf05, JrHsf20, JrHsf22, and JrHsf24 was up-regulated under WW by AMF, while the expression of JrHsf03, JrHsf22, and JrHsf24 were up-regulated only under drought by AMF. It is concluded that D. spurca induced low oxidative burst in drought-stressed walnut through activating antioxidant defense systems and part Hsfs expressions.
Case report: Plasmablastic neoplasm with multinucleated giant cells—Analysis of stemness of the neoplastic multinucleated giant cells

Cancer stem cells have the capability of self-renewal and multipotency and are, therefore, associated with tumor heterogeneity, resistance to chemoradiation therapy, and metastasis. The hypothesis that multinucleated giant cells, which often emerge following chemo- and/or radiotherapy, serve as cancer stem cells has not been fully evaluated. Although a previous study demonstrated that these cells functioned as stem cells, only low levels of Yamanaka factors were expressed, contrasting with the high expression seen from their gestated first-generation mononuclear cells. Herein, we report a case of a plasmablastic neoplasm with multinucleated giant cells that were analyzed for stemness to test the above hypothesis. The patient was a male in his 80s who had a plasmablastic neoplasm that was not easily distinguishable as plasmablastic lymphoma versus plasma cell myeloma of plasmablastic type. Lymph node biopsy showed predominant mononuclear cell proliferation with admixed multinucleated giant cells. Immunohistochemistry and in situ hybridization showed that both multinucleated and mononuclear cells had the same profile: CD138(+), light chain restriction of κ>λ, cyclin D1(+), CD68(-), EBER-ISH (+). These results suggested that both cell types were neoplastic. In accordance with the previous study, the multinucleated giant cells showed low expression of Yamanaka factors, which were highly expressed in some of the mononuclear cells. Furthermore, the multinucleated giant cells showed a much lower proliferative activity (Mib1/Ki67 index) than the mononuclear cells. Based on these results, the multinucleated giant cells were compatible with cancer stem cells. This case is expected to expand the knowledge base regarding biology of cancer stem cells.
Mutational analysis and protein profiling predict drug sensitivity in multiple myeloma cell lines

Introduction Multiple myeloma (MM) is a heterogeneous disease where cancer-driver mutations and aberrant signaling may lead to disease progression and drug resistance. Drug responses vary greatly, and there is an unmet need for biomarkers that can guide precision cancer medicine in this disease. Methods To identify potential predictors of drug sensitivity, we applied integrated data from drug sensitivity screening, mutational analysis and functional signaling pathway profiling in 9 cell line models of MM. We studied the sensitivity to 33 targeted drugs and their association with the mutational status of cancer-driver genes and activity level of signaling proteins. Results We found that sensitivity to mitogen-activated protein kinase kinase 1 (MEK1) and phosphatidylinositol-3 kinase (PI3K) inhibitors correlated with mutations in NRAS/KRAS, and PI3K family genes, respectively. Phosphorylation status of MEK1 and protein kinase B (AKT) correlated with sensitivity to MEK and PI3K inhibition, respectively. In addition, we found that enhanced phosphorylation of proteins, including Tank-binding kinase 1 (TBK1), as well as high expression of B cell lymphoma 2 (Bcl-2), correlated with low sensitivity to MEK inhibitors. Discussion Taken together, this study shows that mutational status and signaling protein profiling might be used in further studies to predict drug sensitivities and identify resistance markers in MM.
Single-cell RNA-sequencing in asthma research

Asthma is a complex and heterogeneous disease with multicellular involvement, and knowledge gaps remain in our understanding of the pathogenesis of asthma. Efforts are still being made to investigate the immune pathogenesis of asthma in order to identify possible targets for prevention. Single cell RNA sequencing (scRNA-seq) technology is a useful tool for exploring heterogeneous diseases, identifying rare cell types and distinct cell subsets, enabling elucidation of key processes of cell differentiation, and understanding regulatory gene networks that predict immune function. In this article, we provide an overview of the importance of scRNA-seq for asthma research, followed by an in-depth discussion of the results in recent years, in order to provide new ideas for the pathogenesis, drug development and treatment of asthma.
SDG-11 and smart cities: Contradictions and overlaps between social and environmental justice research agendas

There is an increased role Information and Communications Technology (ICT) plays in the achievement of Sustainable Development Goals (SDGs). This paper focuses specifically on SDG-11 “Make cities and human settlements inclusive, safe, resilient and sustainable” and how cities are increasingly incorporating ICT toward this goal. The public discourse on Smart Cities suggests economic, social and environmental benefits are possible through the use of Information and Communication Technology (ICT). However, the increased deployment and use of digital infrastructure and processes in the name of sustainability and optimization itself is the focus of a growing body of critical literature on Smart Cities. This mini-review collates critical literature on digital infrastructures and processes related to SDG-11 and Smart Cities to identify areas of significance for further research. Although many Smart City projects discuss sustainability benefits, the distribution of benefits and risks across different communities is rarely examined. An increased use of ICT in Smart City projects can provide environmental benefits to some communities, while shifting the burden of risks to other communities. An increased use of ICT has its own energy and resource impacts that has implications for sustainability beyond the geography of individual cities to global impacts. The lifecycle and supply chain impacts of advanced ICT projects are being identified and documented. The end user of the Smart City projects may benefit significantly from the increased use of ICTs, while the environmental costs are often borne by disparate communities. In some cases, within the same city where a Smart City project is deployed, the inequities in distribution of environmental resources and services are exacerbated by layering new ICT implementations on top of existing socio-economic inequities. Therefore, this paper combines a broad view of Smart City environmental impacts, as well as a deep examination of the intersection of social justice and environmental justice issues to create more wholistic approaches for analysis of governance of Smart City projects. A more wholistic approach for governance of Smart City projects is required that includes combined social justice and environmental justice frameworks, toward achievement of SDG-11 goals.
Costs and effects of telerehabilitation in neurological and cardiological diseases: A systematic review

Introduction Telerehabilitation in neurological and cardiological diseases is an alternative rehabilitation that improves the quality of life and health conditions of patients and enhances the accessibility to health care. However, despite the reported benefits of telerehabilitation, it is necessary to study its impact on the healthcare system. Methods The systematic review aims to investigate the costs and results of telerehabilitation in neurological and cardiological diseases. MEDLINE and EMBASE databases were searched from 2005 to 2021, for studies that assess the costs and results of telerehabilitation compared to traditional rehabilitation (center-based programs) in neurological and cardiological diseases. A narrative synthesis of results was carried out. Results A total of 8 studies (865 participants) of 430 records were included. Three studies were related to the costs and results of telerehabilitation in neurological diseases (specifically in stroke). In total, five studies assessed telerehabilitation in cardiological diseases (chronic heart failure, coronary heart disease, acute coronary syndrome, and cardiovascular diseases). The duration of the telerehabilitation ranged from 6 to 48 weeks. The studies included cost-analysis, cost-benefit, cost-effectiveness, or cost-utility. In total, four studies found significant cost/savings per person between $565.66 and $2,352.00 (p < 0.05). In contrast, most studies found differences in costs and clinical effects between the telerehabilitation performed and the rehabilitation performed at the clinic. Just one study found quality-adjusted life years (QALY) significant differences between groups [Incremental cost-effectiveness ratio (ICER) per QALY ($−21,666.41/QALY). Discussion Telerehabilitation is an excellent alternative to traditional center rehabilitation, which increases the accessibility to rehabilitation to more people, either due to the geographical situation of the patients or the limitations of the health systems. Telerehabilitation seems to be as clinical and cost-effective as traditional rehabilitation, even if, generally, telerehabilitation is less costly. More research is needed to evaluate health-related quality of life and cost-effectiveness in other neurological diseases. Systematic review registration [https://figshare.com/articles/journal_ contribution/Review_Protocol_Costs_and_effects_of_Telerehabilitation_in_ Neurological_and_Cardiological_Diseases_A_Systematic_Review/19619838], identifier [19619838].
Proper modulation of AHR signaling is necessary for establishing neural connectivity and oligodendrocyte precursor cell development in the embryonic zebrafish brain

2,3,7,8-tetrachlorodibenzo-[p]-dioxin (TCDD) is a persistent global pollutant that exhibits a high affinity for the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. Epidemiological studies have associated AHR agonist exposure with multiple human neuropathologies. Consistent with the human data, research studies using laboratory models have linked pollutant-induced AHR activation to disruptions in learning and memory as well as motor impairments. Our understanding of endogenous AHR functions in brain development is limited and, correspondingly, scientists are still determining which cell types and brain regions are sensitive to AHR modulation. To identify novel phenotypes resulting from pollutant-induced AHR activation and ahr2 loss of function, we utilized the optically transparent zebrafish model. Early embryonic TCDD exposure impaired embryonic brain morphogenesis, resulted in ventriculomegaly, and disrupted neural connectivity in the optic tectum, habenula, cerebellum, and olfactory bulb. Altered neural network formation was accompanied by reduced expression of synaptic vesicle 2. Loss of ahr2 function also impaired nascent network development, but did not affect gross brain or ventricular morphology. To determine whether neural AHR activation was sufficient to disrupt connectivity, we used the Gal4/UAS system to express a constitutively active AHR specifically in differentiated neurons and observed disruptions only in the cerebellum; thus, suggesting that the phenotypes resulting from global AHR activation likely involve multiple cell types. Consistent with this hypothesis, we found that TCDD exposure reduced the number of oligodendrocyte precursor cells and their derivatives. Together, our findings indicate that proper modulation of AHR signaling is necessary for the growth and maturation of the embryonic zebrafish brain.
The atrial secondary tricuspid regurgitation is associated to more favorable outcome than the ventricular phenotype

Aim We sought to evaluate the differences in prognosis between the atrial (A-STR) and the ventricular (V-STR) phenotypes of secondary tricuspid regurgitation. Materials and methods Consecutive patients with moderate or severe STR referred for echocardiography were enrolled. A-STR and V-STR were defined according to the last ACC/AHA guidelines criteria. The primary endpoint was the composite of all-cause death and heart failure (HF) hospitalizations. Results A total of 211 patients were enrolled. The prevalence of A-STR in our cohort was 26%. Patients with A- STR were significantly older and with lower NYHA functional class than V-STR patients. The prevalence of severe STR was similar (28% in A-STR vs. 37% in V-STR, p = 0.291). A-STR patients had smaller tenting height (TH) (10 ± 4 mm vs. 12 ± 7 mm, p = 0.023), larger end-diastolic tricuspid annulus area (9 ± 2 cm2 vs. 7 ± 6 cm2/m2, p = 0.007), smaller right ventricular (RV) end-diastolic volumes (72 ± 27 ml/m2 vs. 92 ± 38 ml/m2; p = 0.001), and better RV longitudinal function (18 ± 7 mm vs. 16 ± 6 mm; p = 0.126 for TAPSE, and −21 ± 5% vs. −18 ± 5%; p = 0.006, for RV free-wall longitudinal strain, RVFWLS) than V-STR patients. Conversely, RV ejection fraction (RVEF, 48 ± 10% vs. 46 ± 11%, p = 0.257) and maximal right atrial volumes (64 ± 38 ml/m2 vs. 55 ± 23 ml/m2, p = 0.327) were similar between the two groups. After a median follow-up of 10 months, patients with V-STR had a 2.7-fold higher risk (HR: 2.7, 95% CI 95% = 1.3–5.7) of experiencing the combined endpoint than A-STR patients. The factors related to outcomes resulted different between the two STR phenotypes: TR-severity (HR: 5.8, CI 95% = 1, 4–25, P = 0.019) in A-STR patients; TR severity (HR 2.9, 95% CI 1.4–6.3, p = 0.005), RVEF (HR: 0.97, 95% CI 0.94–0.99, p = 0.044), and RVFWLS (HR: 0.93, 95% CI 0.85–0.98, p = 0.009) in V-STR. Conclusion Almost one-third of patients referred to the echocardiography laboratory for significant STR have A-STR. A-STR patients had a lower incidence of the combined endpoint than V-STR patients. Moreover, while TR severity was the only independent factor associated to outcome in A-STR patients, TR severity and RV function were independently associated with outcome in V-STR patients.