Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the PLAC8 Gene in Mexican Women With and Without Preeclampsia and Obesity

Preeclampsia (PE) is a leading cause of maternal-fetal mortality worldwide, and obesity is an important risk factor. Genes associated with pathophysiological events common to preeclampsia and obesity, such as PLAC8, remain to be studied; therefore, the aim of the present study was to evaluate this gene in the placentas of women affected with preeclampsia and healthy pregnant women. This case-controlled study included 71 healthy and 64 preeclampsia pregnancies. Gene expression was evaluated in primary human cytotrophoblasts (PHCT) from six normal and six preeclampsia pregnancies, and protein expression was verified in placentas from five healthy and six preeclampsia pregnancies. The whole coding and 5′ regions of the PLAC8 gene were sequenced from healthy (n = 10) and preeclamptic (n = 10) pregnancies. The presence of the observed nucleotide variations was analyzed by RT-PCR in the total population. Statistical analyses were performed accordingly. Obesity was associated with severe preeclampsia (SPE) (OR = 3.34; CI 95% 1.3–8.2, p < 0.01). Significantly higher mRNA and protein expression was observed in preeclamptic vs. healthy placentas (p < 0.05). After sequencing, a single nucleotide variation was identified in 10 cases and one control (p < 0.01), which was then evaluated in the total population showing no association with preeclampsia. This preliminary study confirms the association of SPE with obesity and suggests higher expression of PLAC8 mRNA and protein in placentas from preeclampsia. No differences in nucleotide variations between cases and controls of the whole population were observed. Further research is required to evaluate the implications of higher gene/protein expression in preeclampsia and the causes of such variation.
An Integrated Analysis of the Identified PRPF19 as an Onco-immunological Biomarker Encompassing the Tumor Microenvironment, Disease Progression, and Prognoses in Hepatocellular Carcinoma

Background: Targeting the mRNA splicing process has been identified as a therapeutic strategy for human cancer. PRPF19 is an RNA binding protein that is involved in pre-mRNA processing and repairing DNA damage; the aberrant expression of PRPF19 is potentially associated with carcinogenesis. However, the biological role of PRPF19 in hepatocellular carcinoma (HCC) is still elusive. Methods: Data obtained from TCGA, Oncomine, and GEO were used to investigate the PRPF19 expression level and its role in tumor immune infiltration, prognosis, and the tumor progression of cohorts from HCC. Using various databases and tools (UALCAN, TIMER, TISMO, and PathCards), we presented the potential mechanisms of PFPF19 upregulation, PRPF19-related pathways, and its biological functions in liver cancer. Results: For HCC, PRPF19 expression was found upregulated both in single tumor cells and tissues. Furthermore, the increased expression of PRPF19 was significantly correlated to clinical characteristics: advanced stage, vascular invasion, high AFP, and poor prognosis of HCC. According to the tumor-immunological analysis, we found that PRPF19 is positively correlated with infiltrating myeloid-derived suppressor cells (MDSCs). Moreover, the microenvironment of HCC tissues with high expression of PRPF19 is highly immunosuppressive (lower T-lymphocytes, multiple immune checkpoints upregulated). Patients with high expression of PRPF19 and high MDSCs had a worse survival prognosis as well. TP53 mutation may have a positive effect on PRPF19 expression via decreased promoter methylation of PRPF19. By TF-mRNA network analysis, key transcription factors (TFs) in TC-NER and PCS pathways (PRPF19 involved) were identified. Conclusion: This work implied that PRPF19 is associated with tumor immune evasion and progression, and serves as a prognostic marker for worse clinical outcomes with HCC. Thus, this critical regulator could serve as a potential therapeutic target of HCC.
Genome-Wide Analysis of the Gene Structure, Expression and Protein Interactions of the Peach (Prunus persica) TIFY Gene Family

The TIFY family is a plant-specific gene family involved in regulating many plant processes, such as development and growth, defense and stress responses, fertility and reproduction, and the biosynthesis of secondary metabolites. The v2.0 peach (Prunus persica) genome, which has an improved chromosome-scale assembly and contiguity, has recently been released, but a genome-wide investigation of the peach TIFY family is lacking. In this study, 16 TIFY family genes from the peach genome were identified according to the peach reference genome sequence information and further validated by cloning sequencing. The synteny, phylogenetics, location, structure, and conserved domains and motifs of these genes were analyzed, and finally, the peach TIFY family was characterized into 9 JAZ, 1 TIFY, 1 PPD and 5 ZML subfamily members. Expression profiles of peach JAZ, PPD, and ZML genes in various organs and fruit developmental stages were analyzed, and they showed limited effects with fruit ripening cues. Four TIFY members were significantly affected at the mRNA level by exogenous treatment with MeJA in the peach epicarp, and among them, PpJAZ1, PpJAZ4 and PpJAZ5 were significantly correlated with fruit epicarp pigmentation. In addition, the TIFY family member protein interaction networks established by the yeast two-hybrid (Y2H) assay not only showed similar JAZ-MYC2 and JAZ homo- and heterodimer patterns as those found in Arabidopsis but also extended the JAZ dimer network to ZML-ZML and JAZ-ZML interactions. The PpJAZ3-PpZML4 interaction found in this study suggests the potential formation of the ZML-JAZ-MYC complex in the JA-signaling pathway, which may extend our knowledge of this gene family’s functions in diverse biological processes.
Are Machine Learning Algorithms More Accurate in Predicting Vegetable and Fruit Consumption Than Traditional Statistical Models? An Exploratory Analysis

Machine learning (ML) algorithms may help better understand the complex interactions among factors that influence dietary choices and behaviors. The aim of this study was to explore whether ML algorithms are more accurate than traditional statistical models in predicting vegetable and fruit (VF) consumption. A large array of features (2,452 features from 525 variables) encompassing individual and environmental information related to dietary habits and food choices in a sample of 1,147 French-speaking adult men and women was used for the purpose of this study. Adequate VF consumption, which was defined as 5 servings/d or more, was measured by averaging data from three web-based 24 h recalls and used as the outcome to predict. Nine classification ML algorithms were compared to two traditional statistical predictive models, logistic regression and penalized regression (Lasso). The performance of the predictive ML algorithms was tested after the implementation of adjustments, including normalizing the data, as well as in a series of sensitivity analyses such as using VF consumption obtained from a web-based food frequency questionnaire (wFFQ) and applying a feature selection algorithm in an attempt to reduce overfitting. Logistic regression and Lasso predicted adequate VF consumption with an accuracy of 0.64 (95% confidence interval [CI]: 0.58–0.70) and 0.64 (95%CI: 0.60–0.68) respectively. Among the ML algorithms tested, the most accurate algorithms to predict adequate VF consumption were the support vector machine (SVM) with either a radial basis kernel or a sigmoid kernel, both with an accuracy of 0.65 (95%CI: 0.59–0.71). The least accurate ML algorithm was the SVM with a linear kernel with an accuracy of 0.55 (95%CI: 0.49–0.61). Using dietary intake data from the wFFQ and applying a feature selection algorithm had little to no impact on the performance of the algorithms. In summary, ML algorithms and traditional statistical models predicted adequate VF consumption with similar accuracies among adults. These results suggest that additional research is needed to explore further the true potential of ML in predicting dietary behaviours that are determined by complex interactions among several individual, social and environmental factors.
Comparison of Thermal Seed Treatments to Control Snow Mold in Wheat and Loose Smut of Barley

Due to increasing demands to reduce chemical plant protection products, including prophylactic chemical seed treatments, there is a renewed interest in thermal seed treatments for cereal crops. We carried out contemporary evaluations of various alternative seed treatments for economically relevant cereal diseases in Switzerland. Thermal seed treatments were evaluated for effectiveness against two seed-borne diseases, snow mold (Microdochium spp.) and loose smut of barley (Ustilago nuda), commonly found in Swiss cereal production. Field trials testing seed treatments against Microdochium spp. , including M. majus and M. nivale, on wheat were conducted across four growing seasons from 2016/17 to 2019/20 and against U. nuda on barley across three growing seasons from 2016/17 to 2018/19. The foci of these trials were primarily on thermal seed treatments, including steam, hot air, and warm water. Additionally, a Cerall® treatment, based on the microorganism Pseudomonas chlororaphis strain MA 342, was included in two of the trials focusing on Microdochium spp. Steam, warm water, and hot air showed high efficacy against Microdochium spp. , while Cerall® showed no disease reduction. In the Microdochium spp. 2018/19 trial, a combination of poor field conditions, low quality seed, and high disease pressure reduced seed germination. The 2019/20 Microdochium spp. field trial, which occurred during less challenging field conditions than those in 2018/19 and included the same seed lot from 2018/19 and a less diseased second lot, showed an improved efficacy of the steam treatments. The warm water treatments were found to be the only effective thermal treatment against U. nuda. Our results demonstrate that the steam treatments more readily affected germination rate in a highly diseased seed lot, while warm water treatments showed limited damage to the seed. Warm water was found to be the most consistently effective thermal treatment against both diseases, and constraints in implementing such a treatment are discussed. If the steam treatment parameters are correctly set to minimize damage to the plant, it offers effective protection against some seed-borne diseases. Overall, the results from this study give more information about effectiveness of alternative seed treatments under various field conditions.
Economic Recession and the Long Term Risk of Psychiatric Disorders and Alcohol Related Diseases—A Cohort Study From Eastern Finland

Background Long-term development of psychiatric disorders and alcohol-related diseases after economic recessions is insufficiently studied. We investigated the overall impact of the economic recession between 1991 and 1994 in Finland on the long-term incidence of psychiatric and alcohol-related diseases. Methods A population-based sample of 1,774 women and men aged 53–73 years were examined between 1998 and 2001 from the Kuopio Ischemic Heart Disease Risk Factor Study (KIHD). Participants completed comprehensive questionnaires on the possible impact of the 1990s recession in Finland on their lives. They were followed-up until 2018. Cox proportional hazards regression was used to estimate hazard ratios (HR) of new incident psychiatric and alcohol-related disorders during the 20-years follow-up after linkage to the National Hospital Registry. Logistic regression was used to estimate odds ratios (OR) of psychiatric disorders at baseline. Results At baseline, 93 participants had psychiatric disorders. During 20-years follow-up, 138 new psychiatric disorders and 45 alcohol-related diseases were developed. The covariate-adjusted risk of psychiatric disorders was over twice higher among men who experienced recession-induced hardships compared to those who did not (HR = 2.20, 95%CI = 1.04–4.70, p = 0.04). The risk of alcohol-related diseases was more than four times higher among men with hardships (HR = 4.44, 95%CI = 1.04–18.90, p = 0.04). No such associations were observed among women. No association was observed between recession-induced hardships and having psychiatric disorders at baseline in both genders (multivariate-adjusted p = 0.63 for women, multivariate-adjusted p = 0.36 for men). Conclusion Long-term risk of psychiatric disorders and alcohol-related diseases was increased after the 1990s economic recession in Finland, but only among middle-age and older men.
A Generative Adversarial Network-based Framework for Fruit and Vegetable Occlusion Detection in Smart Refrigerators

With the development of deep learning, image recognition technology has made great progress. However, there is often occlusion in the image recognition task. Object occlusion not only loses part of the target information, but also introduces additional interference, thus exacerbating the difficulty of image recognition. This paper aims to improve the recognition rate of fruits and vegetables in the presence of occlusion, so as to alert people to the timely disposal of food in the refrigerator when it is nearing its expiration date. To this end, this paper employs the Alexnet architecture and revises it for better feature extraction, and combines it with a generative adversarial network (GAN), which trains a generator and a discriminator with pairs of occluded and non-occluded images, and finally recover the occluded images. Experimental results show that the proposed system improves the accuracy of fruit and vegetable recognition, and can be better used in smart refrigerators to remind the shelf life of fruits and vegetables.
Improving Sustainable Field-Grown Wheat Production With Azospirillum brasilense Under Tropical Conditions: A Potential Tool for Improving Nitrogen Management

Sustainable intensification of cropping systems requires to increase productivity and nutrients use efficiency while reducing negative impacts of agricultural management practices on ecosystem and environment. Plant growth-promoting rhizobacteria (PGPR) inoculations are considered one of the most promising and safe strategy to alleviate environmental alterations in context of climatic extremes to improve plant nutrition while reducing dependency of nitrogen (N) fertilizer application. This study investigated the interactive effects of N levels and inoculation with A. brasilense on plant biomass, grain yield, agronomic efficiency (AE) of applied N, apparent N-fertilizer recovery (AFR) and N content in plant targeting economic feasibility of wheat production system. The field trial tested 4 N application levels applied in side-dressing (control, low, average and high; named 0, 50, 100 and 200 kg N ha−1) and two inoculations (without and with A. brasilense seed inoculation). The results exhibited that inoculation with A. brasilense enhanced AE, AFR and N uptake in wheat plants with increased root and shoot N accumulation and grain N accumulation under average and high N application levels. In addition, inoculation increased root and shoot biomass, leading to a yield increase of 10.3% compared with non-inoculated plants. Wheat plant inoculation associated with application of the average N level provided the greatest profitability. Furthermore, results showed that reducing N fertilization from 100 to 50 kg N ha−1 along A. brasilense inoculation led to an increase in operating profit of 10.5%. In view of low economic cost, ease of application, and high probability of a positive response by wheat crops, even associated with different N application levels, the inoculation with A. brasilense prone to be a key sustainable management practice to improve wheat production under tropical conditions. This practice has the potential to increase wheat grain yield, N use and uptake, and overall farm profitability.
Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation

Neutrophils in the tumor microenvironment exhibit altered functions. However, the changes in neutrophil behavior during tumor initiation remain unclear. Here we used Translating Ribosomal Affinity Purification (TRAP) and RNA sequencing to identify neutrophil, macrophage and transformed epithelial cell transcriptional changes induced by oncogenic RasG12V in larval zebrafish. We found that transformed epithelial cells and neutrophils, but not macrophages, had significant changes in gene expression in larval zebrafish. Interestingly, neutrophils had more significantly down-regulated genes, whereas gene expression was primarily upregulated in transformed epithelial cells. The antioxidant, thioredoxin (txn), a small thiol that regulates reduction-oxidation (redox) balance, was upregulated in transformed keratinocytes and neutrophils in response to oncogenic Ras. To determine the role of thioredoxin during tumor initiation, we generated a zebrafish thioredoxin mutant. We observed an increase in wound-induced reactive oxygen species signaling and neutrophil recruitment in thioredoxin-deficient zebrafish. Transformed keratinocytes also showed increased proliferation and reduced apoptosis in thioredoxin-deficient larvae. Using live imaging, we visualized neutrophil behavior near transformed cells and found increased neutrophil recruitment and altered motility dynamics. Finally, in the absence of neutrophils, transformed keratinocytes no longer exhibited increased proliferation in thioredoxin mutants. Taken together, our findings demonstrate that tumor initiation induces changes in neutrophil gene expression and behavior that can impact proliferation of transformed cells in the early tumor microenvironment.
The Contribution of Working Memory Areas to Verbal Learning and Recall in Primary Progressive Aphasia

Recent evidence of domain-specific working memory (WM) systems has identified the areas and networks which are involved in phonological, orthographic, and semantic WM, as well as in higher level domain-general WM functions. The contribution of these areas throughout the process of verbal learning and recall is still unclear. In the present study, we asked, what is the contribution of domain-specific specialized WM systems in the course of verbal learning and recall? To answer this question, we regressed the perfusion data from pseudo-continuous arterial spin labeling (pCASL) MRI with all the immediate, consecutive, and delayed recall stages of the Rey Auditory Verbal Learning Test (RAVLT) from a group of patients with Primary Progressive Aphasia (PPA), a neurodegenerative syndrome in which language is the primary deficit. We found that the early stages of verbal learning involve the areas with subserving phonological processing (left superior temporal gyrus), as well as semantic WM memory (left angular gyrus, AG_L). As learning unfolds, areas with subserving semantic WM (AG_L), as well as lexical/semantic (inferior temporal and fusiform gyri, temporal pole), and episodic memory (hippocampal complex) become more involved. Finally, a delayed recall depends entirely on semantic and episodic memory areas (hippocampal complex, temporal pole, and gyri). Our results suggest that AG_L subserving domain-specific (semantic) WM is involved only during verbal learning, but a delayed recall depends only on medial and cortical temporal areas.
Depressive and Anxious Temperaments as Predictors of Late Onset Bipolar Disorder? Preliminary Results of a “Real World” Exploratory Study

Introduction Bipolar disorder (BD) onset typically occurs between 15 and 30 years, being diagnosed under the age of 50 in 90% of cases, named “non-late onset BD” (non-LOBD). However, clinical observation of late-onset BD (LOBD) raised some concern regarding a differential psychopathological pattern, outcomes and treatment, including a specific affective temperament vulnerability. Therefore, an exploratory study in the “real world” was carried out by investigating psychopathological and temperamental features of a psychogeriatric cohort of LOBD and non-LOBD subjects. Methods A total of 180 patients affected with BD-I, BD-II, and Cyclothymic Disorder were screened in a Mood Disorder Outpatient Service, during the timeframe January 2019-August 2021. Out of 78 enrolled outpatients, 66 (33 non-LOBD, 33 LOBD) were recruited, by the retrospective collection of sociodemographic, cognitive, psychopathological and clinical assessment, including the short-version of the Temperament Evaluation of Memphis, Pisa, and San Diego (TEMPS-M). Results LOBD is significantly associated with higher rates of BD-II diagnosis (χ2 = 27.692, p < 0.001), depressive episodes (p = 0.025), mixed states (p = 0.009), predominant depressive and anxious affective temperaments (p < 0.001). Non-LOBD is significantly associated with higher endocrinological (χ2 = 6.988, p = 0.008) and metabolic comorbidity (χ2 = 5.987, p = 0.014), a diagnosis of BD-I, manic episodes, and predominant hyperthymic affective temperaments (p = 0.001). GDS (p < 0.001) and MSRS (p = 0.005) scores were significantly higher in LOBD. Conclusion Further longitudinal studies with larger sample sizes and a control group are needed to determine whether LOBD may represent a distinct psychopathological entity from non-LOBD and evaluate differences (if any) in terms of prognosis and treatment between non-LOBD and LOBD.
Effect of Nonequilibrium Transient Electronic Structures on Lattice Stability in Metals: Density Functional Theory Calculations

The electronic structures of metals undergo transient nonequilibrium states during the photoexcitation process caused by isochoric heating of X-ray free-electron laser, and their lattice stability is, thus, significantly affected. By going beyond frozen core approximation, we manually introduced nonequilibrium electron distribution function in finite-temperature density functional theory with the framework of Kohn–Sham–Mermin to investigate such transient states, and their effect on lattice stability in metals is demonstrated by phonon dispersion calculated using the finite displacement method. We found that the perfect lattice of a metal collapses due to the exotic electronic structure of nonequilibrium transient state created by isochoric heating of X-ray free-electron laser. Further increase of the number of holes created in the sample (i.e., an increase of laser fluence) still results in lattice instability for aluminum, while for copper, it results in phonon hardening. The potential energy surface is calculated for the extreme case of both Al and Cu with exactly one hole created in its inner shell for each one of the atoms. A double-well structure is clearly observed for Al, while the potential energy surface becomes steeper for Cu.