Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Identification of MATE Gene Family in Potato (Solanum tuberosum L.) and Expression Analysis in Heavy Metal Stress

A genome-wide identification and expression analysis of multidrug and toxic compound extrusion (MATE) gene family in potato was carried out to explore the response of MATE proteins to heavy meta stress. In this study, we identified 64 MATE genes from potato genome, which are located on 12 chromosomes, and are divided into I–IV subfamilies based on phylogenetic analysis. According to their order of appearance on the chromosomes, they were named from StMATE1–64. Subcellular location prediction showed that 98% of them are located on the plasma membrane as transporters. Synteny analysis showed that five pairs of collinearity gene pairs belonged to members of subfamily I and subfamily II had two pairs indicating that the duplication is of great significance to the evolution of genes in subfamilies I and II. Gene exon–intron structures and motif composition are more similar in the same subfamily. Every StMATE gene contained at least one cis-acting element associated with regulation of hormone transport. The relative expression levels of eight StMATE genes were significantly upregulated under Cu2+ stress compared with the non-stress condition (0 h). After Cd2+ stress for 24 h, the expression levels of StMATE33 in leaf tissue were significantly increased, indicating its crucial role in the process of Cd2+ stress. Additionally, StMATE18/60/40/33/5 were significantly induced by Cu2+ stress, while StMATE59 (II) was significantly induced by Ni2+ stress. Our study initially explores the biological functions of StMATE genes in the regulation of heavy metal stress, further providing a theoretical basis for studying the subsequent molecular mechanisms in detail.
Predicting Regional Variations in Nationalism With Online Expression of Disgust in China

Disgust is one of the basic emotions and is part of the behavioral immune system, which evolutionarily protects humans from toxic substances as well as from contamination threats by outgroup members. Previous works reveal that disgust not only activates humans’ defense against potential individual and collective threats, but also leads to severe moral judgments, negative intergroup attitudes, and even conservative political orientations. As is already known, nationalism is an ideology that features both negative feelings toward outgroups and beliefs about native superiority or privileges. Evidence from previous studies suggests that disgust is related to nationalism’s several components but lacks direct research on nationalism and disgust. The current study examines the relationship between disgust and nationalism in China at both individual and regional levels. In study 1, participants temporally induced disgust (vs. control) increasing the adoption of nationalism. In Study 2, we analyzed covariation in disgust expression in the Chinese micro-blog Weibo and the nationalism index as part of an online large-scale political survey http://zuobiao.me/ at the province level across Mainland China. The results show that online expression of disgust positively predicts nationalistic orientation at the regional level. Finally, we discuss how the findings shed light on research concerning online emotion expression and potential future directions.
RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

Downy mildew, caused by the oomycete Plasmopara viticola, is one of the diseases causing the most severe economic losses to grapevine (Vitis vinifera) production. To date, the application of fungicides is the most efficient method to control the pathogen and the implementation of novel and sustainable disease control methods is a major challenge. RNA interference (RNAi) represents a novel biotechnological tool with a great potential for controlling fungal pathogens. Recently, a candidate susceptibility gene (VviLBDIf7) to downy mildew has been identified in V. vinifera. In this work, the efficacy of RNAi triggered by exogenous double-stranded RNA (dsRNA) in controlling P. viticola infections has been assessed in a highly susceptible grapevine cultivar (Pinot noir) by knocking down VviLBDIf7 gene. The effects of dsRNA treatment on this target gene were assessed by evaluating gene expression, disease severity, and development of vegetative and reproductive structures of P. viticola in the leaf tissues. Furthermore, the effects of dsRNA treatment on off-target (EF1α, GAPDH, PEPC, and PEPCK) and jasmonic acid metabolism (COI1) genes have been evaluated. Exogenous application of dsRNA led to significant reductions both in VviLBDIf7 gene expression, 5 days after the treatment, and in the disease severity when artificial inoculation was carried out 7 days after dsRNA treatments. The pathogen showed clear alterations to both vegetative (hyphae and haustoria) and reproductive structures (sporangiophores) that resulted in stunted growth and reduced sporulation. Treatment with dsRNA showed signatures of systemic activity and no deleterious off-target effects. These results demonstrated the potential of RNAi for silencing susceptibility factors in grapevine as a sustainable strategy for pathogen control, underlying the possibility to adopt this promising biotechnological tool in disease management strategies.
Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population

The oral microbiota has been observed to be influenced by cigarette smoking and linked to several human diseases. However, research on the effect of cigarette smoking on the oral microbiota has not been systematically conducted in the Chinese population. We profiled the oral microbiota of 316 healthy subjects in the Chinese population by 16S rRNA gene sequencing. The alpha diversity of oral microbiota was different between never smokers and smokers (P = 0.002). Several bacterial taxa were first reported to be associated with cigarette smoking by LEfSe analysis, including Moryella (q = 1.56E-04), Bulleidia (q = 1.65E-06), and Moraxella (q = 3.52E-02) at the genus level and Rothia dentocariosa (q = 1.55E-02), Prevotella melaninogenica (q = 8.48E-08), Prevotella pallens (q = 4.13E-03), Bulleidia moorei (q = 1.79E-06), Rothia aeria (q = 3.83E-06), Actinobacillus parahaemolyticus (q = 2.28E-04), and Haemophilus parainfluenzae (q = 4.82E-02) at the species level. Two nitrite-producing bacteria that can increase the acidity of the oral cavity, Actinomyces and Veillonella, were also enriched in smokers with FDR-adjusted q-values of 3.62E-06 and 1.10E-06, respectively. Notably, we observed that two acid production-related pathways, amino acid-related enzymes (q = 6.19E-05) and amino sugar and nucleotide sugar metabolism (q = 2.63E-06), were increased in smokers by PICRUSt analysis. Finally, the co-occurrence analysis demonstrated that smoker-enriched bacteria were significantly positively associated with each other and were negatively correlated with the bacteria decreased in smokers. Our results suggested that cigarette smoking may affect oral health by creating a different environment by altering bacterial abundance, connections among oral microbiota, and the microbiota and their metabolic function.
Radiomic Analysis of Contrast-Enhanced Mammography With Different Image Types: Classification of Breast Lesions

Objective: A limited number of studies have focused on the radiomic analysis of contrast-enhanced mammography (CEM). We aimed to construct several radiomics-based models of CEM for classifying benign and malignant breast lesions. Materials and Methods: The retrospective, double-center study included women who underwent CEM between November 2013 and February 2020. Radiomic analysis was performed using high-energy (HE), low-energy (LE), and dual-energy subtraction (DES) images from CEM. Datasets were randomly divided into the training and testing sets at a ratio of 7:3. The maximum relevance minimum redundancy (mRMR) method and least absolute shrinkage and selection operator (LASSO) logistic regression were used to select the radiomic features and construct the best classification models. The performances of the models were assessed by the area under the receiver operating characteristic curve (AUC) with a 95% confidence interval (CI). Leave-group-out cross-validation (LGOCV) for 100 rounds was performed to obtain the mean AUCs, which were compared by the Wilcoxon rank-sum test and the Kruskal–Wallis rank-sum test. Results: A total of 192 women with 226 breast lesions (101 benign; 125 malignant) were enrolled. The median age was 48 years (range, 22–70 years). For the classification of breast lesions, the AUCs of the best models were 0.931 (95% CI: 0.873–0.989) for HE, 0.897 (95% CI: 0.807–0.981) for LE, 0.882 (95% CI: 0.825–0.987) for DES images and 0.960 (95% CI: 0.910–0.998) for all of the CEM images in the testing set. According to LGOCV, the models constructed with the HE images and all of the CEM images showed the highest mean AUCs for the training (0.931 and 0.938, respectively; P < 0.05 for both) and testing sets (0.892 and 0.889, respectively; P = 0.55 for both), which were significantly higher than those of the two models constructed with the LE and DES images in the training (0.912 and 0.899, respectively; all P < 0.05) and testing sets (0.866 and 0.862, respectively; all P < 0.05). Conclusions: Radiomic analysis of CEM images was valuable for classifying benign and malignant breast lesions. The use of HE images or all three types of CEM images can achieve the best performance.
Perception and Evaluation of 23 Positive Emotions in Hong Kong and the Netherlands

Positive emotions are linked to numerous benefits, but not everyone appreciates the same kinds of positive emotional experiences. We examine how distinct positive emotions are perceived and whether individuals’ perceptions are linked to how societies evaluate those emotions. Participants from Hong Kong and Netherlands rated 23 positive emotions based on their individual perceptions (positivity, arousal, and socially engaging) and societal evaluations (appropriate, valued, and approved of). We found that (1) there were cultural differences in judgments about all six aspects of positive emotions; (2) positivity, arousal, and social engagement predicted emotions being positively regarded at the societal level in both cultures; and (3) that positivity mattered more for the Dutch participants, although arousal and social engagement mattered more in Hong Kong for societal evaluations. These findings provide a granular map of the perception and evaluation of distinct positive emotions in two cultures and highlight the role of cultures in the understanding how positive emotions are perceived and evaluated.
Parental Stress and Satisfaction in Parents With Pre-school and School Age Children

Parenting is a transforming experience for the life of parents that brings joy and satisfaction as well as challenges, frustration, and demands. The aim of this study was to determine the relationship between “parental stress and satisfaction” and work-home conflict, perceived social support, and global satisfaction with life, and to determine the moderating role of the parent's gender. A sample of 244 participants was studied: 49.6% (121) mothers and 50.4% (123) fathers with children between 2 and 12 years of age. The data was analysed by means of multiple linear regression models and Beta regression for stress and parental satisfaction, respectively, and they were complemented with general and conditional dominance analyses to estimate the relevance of the predictors. Mothers presented higher levels of parental stress and satisfaction than fathers. Being female, having two children, and home-work conflict were predictors of a higher parental stress. Age was also a predictor, as younger parents and also those older than 37 years of age showed more parental stress. Having no partner and being male was associated to lower parental satisfaction. In conclusion, parental stress and satisfaction emerge as clearly differentiated dimensions of parenting experience. The gender gap in parental stress could be linked to the persistence of traditional roles regarding the care of the children, in agreement with the findings in other research.
Derivation and Validation of a Prognostic Scoring Model Based on Clinical and Pathological Features for Risk Stratification in Oral Squamous Cell Carcinoma Patients: A Retrospective Multicenter Study

Objective To develop and validate a simple-to-use prognostic scoring model based on clinical and pathological features which can predict overall survival (OS) of patients with oral squamous cell carcinoma (OSCC) and facilitate personalized treatment planning. Materials and Methods OSCC patients (n = 404) from a public hospital were divided into a training cohort (n = 282) and an internal validation cohort (n = 122). A total of 12 clinical and pathological features were included in Kaplan–Meier analysis to identify the factors associated with OS. Multivariable Cox proportional hazards regression analysis was performed to further identify important variables and establish prognostic models. Nomogram was generated to predict the individual’s 1-, 3- and 5-year OS rates. The performance of the prognostic scoring model was compared with that of the pathological one and the AJCC TNM staging system by the receiver operating characteristic curve (ROC), concordance index (C-index), calibration curve, and decision curve analysis (DCA). Patients were classified into high- and low-risk groups according to the risk scores of the nomogram. The nomogram-illustrated model was independently tested in an external validation cohort of 95 patients. Results Four significant variables (physical examination-tumor size, imaging examination-tumor size, pathological nodal involvement stage, and histologic grade) were included into the nomogram-illustrated model (clinical–pathological model). The area under the ROC curve (AUC) of the clinical–pathological model was 0.687, 0.719, and 0.722 for 1-, 3- and 5-year survival, respectively, which was superior to that of the pathological model (AUC = 0.649, 0.707, 0.717, respectively) and AJCC TNM staging system (AUC = 0.628, 0.668, 0.677, respectively). The clinical–pathological model exhibited improved discriminative power compared with pathological model and AJCC TNM staging system (C-index = 0.755, 0.702, 0.642, respectively) in the external validation cohort. The calibration curves and DCA also displayed excellent predictive performances. Conclusion This clinical and pathological feature based prognostic scoring model showed better predictive ability compared with the pathological one, which would be a useful tool of personalized accurate risk stratification and precision therapy planning for OSCC patients.
In vivo Dominant-Negative Effect of an SCN5A Brugada Syndrome Variant

Loss-of-function mutations in the cardiac Na+ channel α-subunit Nav1.5, encoded by SCN5A, cause Brugada syndrome (BrS), a hereditary disease characterized by sudden cardiac death due to ventricular fibrillation. We previously evidenced in vitro the dominant-negative effect of the BrS Nav1.5-R104W variant, inducing retention of wild-type (WT) channels and leading to a drastic reduction of the resulting Na+ current (INa). To explore this dominant-negative effect in vivo, we created a murine model using adeno-associated viruses (AAVs). Methods Due to the large size of SCN5A, a dual AAV vector strategy was used combining viral DNA recombination and trans-splicing. Mice were injected with two AAV serotypes capsid 9: one packaging the cardiac specific troponin-T promoter, the 5′ half of hSCN5A cDNA, a splicing donor site and a recombinogenic sequence; and another packaging the complementary recombinogenic sequence, a splicing acceptor site, the 3′ half of hSCN5A cDNA fused to the gfp gene sequence, and the SV40 polyA signal. Eight weeks after AAV systemic injection in wild-type (WT) mice, echocardiography and ECG were recorded and mice were sacrificed. The full-length hSCN5A-gfp expression was assessed by western blot and immunohistochemistry in transduced heart tissues and the Na+ current was recorded by the patch-clamp technique in isolated adult GFP-expressing heart cells. Results Almost 75% of the cardiomyocytes were transduced in hearts of mice injected with hNav1.5 and ∼30% in hNav1.5-R104W overexpressing tissues. In ventricular mice cardiomyocytes expressing R104W mutant channels, the endogenous INa was significantly decreased. Moreover, overexpression of R104W channels in normal hearts led to a decrease of total Nav1.5 expression. The R104W mutant also induced a slight dilatation of mice left ventricles and a prolongation of RR interval and P-wave duration in transduced mice. Altogether, our results demonstrated an in vivo dominant-negative effect of defective R104W channels on endogenous ones. Conclusion Using a trans-splicing and viral DNA recombination strategy to overexpress the Na+ channel in mouse hearts allowed us to demonstrate in vivo the dominant-negative effect of a BrS variant identified in the N-terminus of Nav1.5.
Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses

Background The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development. Methods We therefore performed a comprehensive comparative study, analyzing RNA-Seq data of infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different types of cells as well as COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses. Results and Conclusion First, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.
Development and external validation of a diagnostic multivariable prediction model for a prompt identification of cases at high risk for SARS-COV-2 infection among patients admitted to the emergency department

Background: An urgent need exists for an early detection of cases with a high-risk of SARS-CoV-2 infection, particularly in high-flow and -risk settings, such as emergency departments (EDs). The aim of this work is to develop and validate a predictive model for the evaluation of SARS-CoV-2 infection risk, with the rationale of using this tool to manage ED patients. Methods: A retrospective study was performed by cross-sectionally reviewing the electronical case records of patients admitted to Niguarda Hospital or referred to its ED in the period 15 March to 24 April 2020. Derivation sample was composed of non-random inpatients hospitalized on 24 April and admitted before 22 April 2020. Validation sample was composed of consecutive patients who visited the ED between 15 and 25 March 2020. The association between the dichotomic outcome and each predictor was explored by univariate analysis with logistic regression models. Results: A total of 113 patients in the derivation sample and 419 in the validation sample were analyzed. History of fever, elder age and low oxygen saturation showed to be significant predictors of SARS-CoV-2 infection. The neutrophil count improves the discriminative ability of the model, even if its calibration and usefulness in terms of diagnosis is unclear. Conclusion: The discriminatory ability of the identified models makes the overall performance suboptimal; their implementation to calculate the individual risk of infection should not be used without additional investigations. However, they could be useful to evaluate the spatial allocation of patients while awaiting the result of the nasopharyngeal swab.
Assessment of mesalamine in the alterations of metabolic parameters in comorbid ulcerative colitis and metabolic syndrome patients: A retrospective study

BACKGROUND & AIMS: It is unclear how the gut targeting medication mesalamine alters metabolic parameters associated with Metabolic Syndrome (MetS). We completed a retrospective analysis on ulcerative colitis (UC) and MetS comorbid patients receiving mesalamine to examine the effects of mesalamine on the metabolic risk factors associated with MetS. METHODS: We performed a retrospective chart review using Cerner Health Facts (from July 2007 to July 2017). We identified UC patients with a MetS comorbidity and who were prescribed mesalamine within +/- 7 days of an encounter in which they were diagnosed with UC. We then collected the patients blood pressure, labs, and body measurement index (BMI) for each of these patient at the index date and the closest values to 12 months after the index date. We used analysis of covariance (ANCOVA) to determine the effect of mesalamine therapy in patients with both UC and MetS on the metabolic parameters after 12 months of treatment compared to baseline. RESULTS: Our search of Cerner Health Facts identified 6,197 UC patients with concomitant MetS who were prescribed mesalamine. Of these individuals, 48% were female and 52% were male and within this cohort 88.3% received oral mesalamine and 11.7% received mesalamine via the rectal route. Oral mesalamine reduced fasting glucose levels and increased HDL cholesterol in these patients. C-reactive protein levels and erythrocyte sedimentation rate were also significantly reduced. Rectal mesalamine only reduced BMI. Further analysis revealed several MetS conditions risk factors were further improved when mesalamine was taken in the absence of medication for hypertension, hyperglycemia or dyslipidemia. CONCLUSION: In a retrospective chart study of UC-MetS patients, we found oral mesalamine improved several metabolic parameters associated with MetS. Our findings suggest the PPAR agonist mesalamine that targets the gastrointestinal tract could prove beneficial in improving hypertension, hyperglycemia and dyslipidemia.
Understanding the Impact of Image Quality in Face Processing Algorithms

: Face processing algorithms are becoming more popular in recent days due to the great domain of application they can be used in. As a consequence, research about the quality of face images is also increasing. Several papers concluded that image quality does impact the performance of face processing algorithms, with low-quality images having a detrimental effect on performance. However, there is still a need for a comprehensive understanding of the extent of the impact of specific distortions like noise, blur, JPEG compression, and brightness. We’ve conducted a study evaluating the performance of three face processing algorithms with images under different levels of the aforementioned distortions. The study’s results placed noise and blur with Gaussian distributions, as the main distortions affecting performance. A detailed description of the adopted methodology, as well as the results obtained from the study, is presented in this paper.