Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions

Plant surfaces are covered with cuticle wax and are the first barrier between a plant and environmental stresses. Eceriferum (CER) is an important gene family involved in wax biosynthesis and stress resistance. In this study, for the first time, 34 CER genes were identified in the passion fruit (Passiflora edulis) genome, and PeCER proteins varied in physicochemical properties. A phylogenetic tree was constructed and divided into seven clades to identify the evolutionary relationship with other plant species. Gene structure analyses revealed that conserved motifs ranged from 1 to 24, and that exons ranged from 1 to 29. The cis-element analysis provides insight into possible roles of PeCER genes in plant growth, development and stress responses. The syntenic analysis revealed that segmental (six gene pairs) and tandem (six gene pairs) gene duplication played an important role in the expansion of PeCER genes and underwent a strong purifying selection. In addition, 12 putative ped-miRNAs were identified to be targeting 16 PeCER genes, and PeCER6 was the most targeted by four miRNAs including ped-miR157a-5p, ped-miR164b-5p, ped-miR319b, and ped-miR319l. Potential transcription factors (TFs) such as ERF, AP2, MYB, and bZIP were predicted and visualized in a TF regulatory network interacting with PeCER genes. GO and KEGG annotation analysis revealed that PeCER genes were highly related to fatty acid, cutin, and wax biosynthesis, plant-pathogen interactions, and stress response pathways. The hypothesis that most PeCER proteins were predicted to localize to the plasma membrane was validated by transient expression assays of PeCER32 protein in onion epidermal cells. qRT-PCR expression results showed that most of the PeCER genes including PeCER1, PeCER11, PeCER15, PeCER17, and PeCER32 were upregulated under drought and Fusarium kyushuense stress conditions compared to controls. These findings provide a foundation for further studies on functions of PeCER genes to further facilitate the genetic modification of passion fruit wax biosynthesis and stress resistance.
H OUSEHOLD M ODELS : A N H ISTORICAL P ERSPECTIVE

This paper is a survey of the literature on theoretical models of the household, paying particular attention to some of the earlier contributions, and using them to place the current state of the theory in perspective. One of its aims is to suggest that the literature’s neglect of Samuelson’s proposal, that households can be modelled as if they maximised a form of social welfare function, was a mistake. However, the idea following directly from the Nash bargaining models, that the household’s preference ordering over the utility profiles of its members depends on exogenous variables, in particular wage rates and non-wage incomes, is an important one. Combined with Samuelson’s proposal, it can be made the basis for a general approach to modelling household decision taking, flexible enough to encompass noncooperative behaviour and Pareto inefficiencies arising out of the inevitable incompleteness and unenforceability of domestic agreements. We also point out the importance of household production and some of the implications of its neglect in modelling households. Above all, the aim is to provide a deeper understanding of the current theoretical literature on household economics by means of a survey of its history. JEL
CNNG: A Convolutional Neural Networks With Gated Recurrent Units for Autism Spectrum Disorder Classification

As a neurodevelopmental disorder, autism spectrum disorder (ASD) severely affects the living conditions of patients and their families. Early diagnosis of ASD can enable the disease to be effectively intervened in the early stage of development. In this paper, we present an ASD classification network defined as CNNG by combining of convolutional neural network (CNN) and gate recurrent unit (GRU). First, CNNG extracts the 3D spatial features of functional magnetic resonance imaging (fMRI) data by using the convolutional layer of the 3D CNN. Second, CNNG extracts the temporal features by using the GRU and finally classifies them by using the Sigmoid function. The performance of CNNG was validated on the international public data—autism brain imaging data exchange (ABIDE) dataset. According to the experiments, CNNG can be highly effective in extracting the spatio-temporal features of fMRI and achieving a classification accuracy of 72.46%.
Cyanobacteria as Candidates to Support Mars Colonization: Growth and Biofertilization Potential Using Mars Regolith as a Resource

Cyanobacteria are indicated as organisms that can possibly support Mars colonization, contributing to the production of oxygen and other commodities therein. In this general context, the aim of this work was to evaluate the ability of three species of cyanobacteria (Anabaena cylindrica, Nostoc muscorum, and Arthrospira platensis) and a green microalga (Chlorella vulgaris) to grow using only the resources existing in Mars, i.e., water and Martian regolith stimulant (MGS-1), under an Earth-like atmosphere. A Martian regolith extract was produced and used as a culture medium to grow these species. Their growth was assessed during a period of 25 days, using optical density and fluorometric parameters. After this period, the possible contribution of end-of-life cyanobacteria/microalga as biofertilizing agents was also assessed, using the macrophyte Lemna minor as a vegetable model. Among the three species, N. muscorum showed the best growth performance when compared to the other species, while A. platensis and C. vulgaris were not able to thrive on Mars regolith extract. Therefore, N. muscorum should be the target of future studies not only due to their role in oxygen production but also due to their possible use as a food source, as many members of the Nostoc genus. Cyanobacteria and microalgae (A. platensis and C. vulgaris) showed good abilities as biofertilizing agents, i.e., they stimulated biomass (i.e., dry weight) production at levels comparable to the plants that grew on standard synthetic medium. The highest yield was reached with A. platensis, while the lowest was achieved using the media with N. muscorum. FTIR-ATR (Fourier transform infrared with attenuated total reflectance) spectroscopy showed that the differences between the plants grown on media with or without Martian regolith seem to be related mainly to polysaccharides.
Beneficial Changes in Growth Performance, Antioxidant Capacity, Immune Response, Hepatic Health, and Flesh Quality of Trachinotus ovatus Fed With Oedocladium carolinianum

The purpose of this study is to assess the feasibility of astaxanthin-rich Oedocladium carolinianum as an immunostimulant in the diet for Trachinotus ovatus. Three experimental diets containing 0% (OC0), 1% (OC1), and 5% (OC5) O. carolinianum powder were formulated for 6-week feeding trials. The results indicated that the OC5 diet boosted the growth performance through decreasing the feed conversion ratio and increasing digestive enzyme activities and intestinal villus length. Meanwhile, fish fed with the OC5 diet promoted antioxidant ability via stimulating the Nrf2-ARE signal pathway and enhancing antioxidant enzyme activities. Furthermore, the OC5 diet exerted hepatoprotective effects by suppressing the lipid deposition and inflammation response and enhancing the transport capacity of cholesterol. Besides, the OC5 diet improved the non-specific immunity by activating the lysozyme and complement system and increasing the nitric oxide content and total nitric oxide synthase activity. Dietary O. carolinianum supplementation promoted the deposition of astaxanthin in the whole body. Therefore, a diet supplemented with 5% O. carolinianum is recommended to boost the growth, antioxidant capacity, immune response, and flesh quality of T. ovatus.
Possible Effect of the use of Mesenchymal Stromal Cells in the Treatment of Autism Spectrum Disorders: A Review

Autism spectrum disorder (ASD) represents a set of heterogeneous neurodevelopmental conditions defined by impaired social interactions and repetitive behaviors. The number of reported cases has increased over the past decades, and ASD is now a major public health burden. So far, only treatments to alleviate symptoms are available, with still unmet need for an effective disease treatment to reduce ASD core symptoms. Genetic predisposition alone can only explain a small fraction of the ASD cases. It has been reported that environmental factors interacting with specific inter-individual genetic background may induce immune dysfunctions and contribute to the incidence of ASD. Such dysfunctions can be observed at the central level, with increased microglial cells and activation in ASD brains or in the peripheral blood, as reflected by high circulating levels of pro-inflammatory cytokines, abnormal activation of T-cell subsets, presence of auto-antibodies and of dysregulated microbiota profiles. Altogether, the dysfunction of immune processes may result from immunogenetically-determined inefficient immune responses against a given challenge followed by chronic inflammation and autoimmunity. In this context, immunomodulatory therapies might offer a valid therapeutic option. Mesenchymal stromal cells (MSC) immunoregulatory and immunosuppressive properties constitute a strong rationale for their use to improve ASD clinical symptoms. In vitro studies and pre-clinical models have shown that MSC can induce synapse formation and enhance synaptic function with consequent improvement of ASD-like symptoms in mice. In addition, two preliminary human trials based on the infusion of cord blood-derived MSC showed the safety and tolerability of the procedure in children with ASD and reported promising clinical improvement of core symptoms. We review herein the immune dysfunctions associated with ASD provided, the rationale for using MSC to treat patients with ASD and summarize the current available studies addressing this subject.
Ten-Year Experience of Chest Wall Reconstruction: Retrospective Review of a Titanium Plate MatrixRIB™ System

Chest wall tumor resection can result in a large defect that can pose a challenge in reconstruction in restoring chest wall contour, maintaining respiratory mechanics, and improving cosmesis. Titanium plates were first introduced for treating a traumatic flail chest, which yielded promising results in restoring chest wall stability. Subsequently, the applications of titanium plates in chest wall reconstruction surgery were demonstrated in case reports and series. Our center has adopted this technique for a decade, and patients are actively followed up after operation. Here, we retrospectively analyze our 10-year experience of using titanium plates and other reconstruction approaches for chest wall reconstruction, in terms of clinical outcomes, complications, and reasons for reoperation to determine long-term safety and efficacy. Thirty-eight patients who underwent chest wall resection and reconstruction surgery were identified. Of these, 11 had titanium plate insertion, 11 had patch repair or flap reconstruction, and the remaining 16 had primary closure of defects. Chest wall reconstruction using titanium plate(s) and patch repair (with or without flap reconstruction) was associated with larger chest wall defects and more sternal resections than primary closure. Subgroup analysis also showed that reconstruction by the titanium plate technique was associated with larger chest wall defects than patch repair or flap reconstruction [286.80 cm2 vs. 140.91 cm2 (p = 0.083)]. There was no 30-day hospital mortality. Post-operative arrhythmia was more commonly seen following chest wall reconstruction compared with primary closure (p = 0.041). Furthermore, more wound infections were detected following the use of titanium plate reconstruction compared with the patch repair (with or without flap reconstruction) approach (p = 0.027). In conclusion, the titanium plate system is a safe, effective, and robust approach for chest wall reconstruction surgery, especially in tackling larger defect sizes.
Investigation of Functional Synergism of CENPF and FOXM1 Identifies POLD1 as Downstream Target in Hepatocellular Carcinoma

Background Lines of evidence implicate CENPF and FOXM1 may have novel co-operative roles in driving hepatocellular carcinoma (HCC). Objective We investigated the clinicopathological correlation, functional characterization, molecular mechanism and translational significance of CENPF and FOXM1. Methods We carried out integrative studies investigating functional synergism of CENPF and FOXM1 in HCC and its metastasis. Human HCC samples, HCC cell lines and mouse model were used in the studies. Stable knockdown, q-PCR, Western blotting, whole-transcriptomic sequencing (RNA-seq), as well as cell and mouse assays were performed. Results Upon clinicopathological correlation, we found that co-overexpression of CENPF and FOXM1 in human HCCs was associated with more aggressive tumor behavior including presence of venous invasion, tumor microsatellite formation, and absence of tumor encapsulation. Moreover, co-silencing FOXM1 and CENPF using shRNA approach in HCC cell lines resulted in significantly reduced cell proliferation. Furthermore, our RNA-seq and differential gene expression analysis delineated that CENPF and FOXM1 co-regulated a specific set of target genes in various metabolic processes and oncogenic signaling pathways. Among them, POLD1, which encodes the catalytic subunit of DNA polymerase δ, was ranked as the top downstream target co-regulated by CENPF and FOXM1. POLD1 expression was positively correlated with that of FOXM1 and CENPF in HCCs. In addition, POLD1 expression was significantly upregulated in HCC tumors. Functionally, in vivo orthotopic injection model showed that stable knockdown of POLD1 in HCC cells suppressed tumor incidence and tumorigenicity and had a trend of diminished lung metastasis. Conclusion Taken together, our data suggest that CENPF and FOXM1 could synergistically support hepatocarcinogenesis via the regulation of POLD1. CENPF and FOXM1 may represent new vulnerabilities to novel drug-based therapy in HCC.
Glutamine Availability Regulates the Development of Aging Mediated by mTOR Signaling and Autophagy

Glutamine is a conditionally essential amino acid involved in energy production and redox homeostasis. Aging is commonly characterized by energy generation reduction and redox homeostasis dysfunction. Various aging-related diseases have been reported to be accompanied by glutamine exhaustion. Glutamine supplementation has been used as a nutritional therapy for patients and the elderly, although the mechanism by which glutamine availability affects aging remains elusive. Here, we show that chronic glutamine deprivation induces senescence in fibroblasts and aging in Drosophila melanogaster, while glutamine supplementation protects against oxidative stress-induced cellular senescence and rescues the D-galactose-prompted progeria phenotype in mice. Intriguingly, we found that long-term glutamine deprivation activates the Akt-mTOR pathway, together with the suppression of autolysosome function. However, the inhibition of the Akt-mTOR pathway effectively rescued the autophagy impairment and cellular senescence caused by glutamine deprivation. Collectively, our study demonstrates a novel interplay between glutamine availability and the aging process. Mechanistically, long-term glutamine deprivation could evoke mammalian target of rapamycin (mTOR) pathway activation and autophagy impairment. These findings provide new insights into the connection between glutamine availability and the aging process.
Coupling Coordination Analysis of Natural Resource Utilization Benefits in Beijing From 1978 to 2018

With the acceleration of economic and social development, the demand for natural resources has increased. To realize the sustainable utilization of natural resources (SUNRs), it is necessary to seek ways to improve natural resource utilization benefits (NRUBs) and promote the coordinated development of economic, social, and ecological benefits. This study explores the coupling coordination relationships of NRUBs in Beijing from 1978 to 2018 and analyzes the influencing factors. We first establish a comprehensive evaluation index system covering economic, social, and ecological benefits to quantify NRUBs. Then, a coupling coordination degree (CCD) model is applied to reveal the evolution characteristics of the coupling coordination relationships among the NRUB system. Finally, the main factors affecting the coordinated development of NRUBs are identified through gray relational analysis (GRA). Three main results are found: 1) from 1978 to 2018, the economic, social, ecological, and comprehensive benefits all have been significantly improved, although with some fluctuations. 2) The coupling coordination relationships of NRUBs show upward trends during the study period, and their coordination types transform from imbalance to coordination. 3) Urbanization, industrial structure, technology innovation, economic development, and environmental awareness all have significant impacts on the coupling coordination relationships of NRUBs. Measures such as transformation of the economic development mode, improvement of public facilities, construction of spiritual culture, ecological protection, and technological innovation need to be recognized to achieve coordinated development. This study can provide a reference for other comprehensive evaluations of natural resources and the formulation of natural resource utilization policies.
The Atrium in Atrial Fibrillation – A Clinical Review on How to Manage Atrial Fibrotic Substrates

Atrial fibrillation (AF) is the most common sustained arrhythmia in the population and is associated with a significant clinical and economic burden. Rigorous assessment of the presence and degree of an atrial arrhythmic substrate is essential for determining treatment options, predicting long-term success after catheter ablation, and as a substrate critical in the pathophysiology of atrial thrombogenesis. Catheter ablation of AF has developed into an essential rhythm-control strategy. Nowadays is one of the most common cardiac ablation procedures performed worldwide, with its success inversely related to the extent of atrial structural disease. Although atrial substrate evaluation remains complex, several diagnostic resources allow for a more comprehensive assessment and quantification of the extent of left atrial structural remodeling and the presence of atrial fibrosis. In this review, we summarize the current knowledge on the pathophysiology, etiology, and electrophysiological aspects of atrial substrates promoting the development of AF. We also describe the risk factors for its development and how to diagnose its presence using imaging, electrocardiograms, and electroanatomic voltage mapping. Finally, we discuss recent data regarding fibrosis biomarkers that could help diagnose atrial fibrotic substrates.
Comprehensive Network-Based Analyses Reveal Novel Renal Function-Related Targets in Acute Kidney Injury

Background: Acute kidney injury (AKI) is a common clinical syndrome with limited methods of treatment and diagnosis. Although several molecules associated with AKI have been discovered, molecular mechanisms underlying AKI still remain unclear. Weighted gene co-expression network analysis (WGCNA) is a novel method to uncover the relationship between co-expression genes and clinical traits at the system level. Methods: First, by employing WGCNA in transcriptional data on 30 patients with well/poor functioning kidney graft, we identified two co-expression modules that were significantly related to serum creatinine (SCr). Second, based on the modules, potential small molecular compound candidates for developing targeted therapeutics were obtained by connectivity map analysis. Furthermore, multiple validations of expression in space/time were carried out with two classical AKI models in vivo and other five databases of over 152 samples. Results: Two of the 14 modules were found to be closely correlated with SCr. Function enrichment analysis illustrated that one module was enriched in the immune system, while the other was in the metabolic process. Six key renal function-related genes (RFRGs) were finally obtained. Such genes performed well in cisplatin-induced or cecal ligation and puncture-induced AKI mouse models. Conclusion: The analysis suggests that WGCNA is a proper method to connect clinical traits with genome data to find novel targets in AKI. The kidney tissue with worse renal function tended to develop a “high immune but low metabolic activity” expression pattern. Also, ACSM2A, GLYAT, CORO1A, DPEP1, ALDH7A1, and EPHX2 are potential targets of molecular diagnosis and treatment in AKI.
The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes

The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.