Miracle-dz/UniFAR-FTUs huggingface dataset:
The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes

SARS-CoV-2 utilizes a number of strategies to modulate host responses to ensure efficient propagation. Here, we used ribosome profiling in SARS-CoV-2-infected cells to gain a deeper understanding of the translationally regulated events in infected cells. ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development. IMPORTANCE SARS-CoV-2 utilizes a number of strategies to modulate host responses to ensure efficient propagation. Here, we used ribosome profiling in SARS-CoV-2-infected cells to gain a deeper understanding of the translationally regulated events in infected cells. We found that although viral mRNAs are abundantly expressed, they are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy and alternative translation initiation sites that help increase the coding potential of its RNAs. In permissive cells, SARS-CoV-2 infection induced the translational repression of numerous innate immune mediators. Though the impact of SARS-CoV-2 on host mRNA translation was more subtle in primary airway cell cultures, we noted marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data provide new insight into how SARS-CoV-2 modulates innate host responses and highlight unique mechanisms for therapeutic intervention.
Symptoms of psychological distress amongst women during the COVID-19 pandemic in Saudi Arabia

Background Since the emergence of the COVID-19 pandemic in early 2020, several countries are still struggling to contain its spread. Apart from economic challenges, the pandemic has had a negative impact on the mental health and psychological well-being of millions of people worldwide. The effects of COVID-19 are disproportionate depending on sociodemographic characteristics. The aim of this study was to investigate the impact of COVID-19 on psychological distress among women in Saudi Arabia. Methods Data were extracted from an online cross-sectional self-reported questionnaire conducted to measure symptoms of psychological distress during the COVID-19 pandemic in Saudi Arabia from 3 May to 8 May 2020. The study included a sample of 1527 women. The questionnaire was based on the COVID-19 Peritraumatic Distress Index (CPDI) tool to categorise women who responded to the questionnaire as experiencing normal, mild, or severe levels of distress. Sociodemographic factors related to different levels of psychological distress among women were examined using descriptive analysis and multinomial logistic regression models. Results Overall, 44% of the respondents indicated symptoms of psychological distress due to the COVID-19 pandemic. Approximately 36% of women showed symptoms of mild psychological distress, with 8% of women experiencing a severe distress level. The results also revealed particularly high levels of psychological distress among younger women and female healthcare workers. Conclusion The COVID-19 pandemic highly contributes to psychological distress among women in Saudi Arabia. Therefore, it is essential to establish medium- and long-term strategies that target the most vulnerable women affected by the COVID-19 pandemic.
Job accommodation of people with disabilities in the construction industry: Analysis of production and absence

The purpose of this research was to evaluate production and absence of workers with and without disabilities in a construction work of a building. The survey was applied in the metropolitan region of Recife, in the state of Pernambuco, Brazil and there were eight workers with disabilities, one being a bricklayer and seven servants. The methods used in the field study were: direct observation of the activities and the environment, a video and photographic record of the tasks, semi-structured interviews with the workers with disabilities and their supervisor, and data was collected from the company about absences and worker’s production, with and without disabilities in order to make a comparative analysis. The results of the research show that in all cases, individuals with disabilities had lower production and more absences at work than individuals without disabilities.
Development and validation of nomograms for predicting adverse neonatal outcomes in women with polycystic ovary syndrome: a retrospective study

Abstract In our study, we retrospectively enrolled 606 women with newly diagnosed polycystic ovary syndrome. Participants were divided into two cohorts: development cohort (n = 424) and validation cohort (n = 182). Multivariate logistic regression analyses were used to identify predictive indicators, and nomograms were developed and validated. We found that waist hip rate (WHR), testosterone levels, and fasting blood glucose (FBG) levels (WTF) could predict the small for gestational age; BMI, WHR and modified Ferriman-Gallwey Score (BWM) correlated with low Apgar scores; and BMI, WHR, modified Ferriman-Gallwey Score, testosterone levels, and FBG levels (BWMTF) correlated with adverse neonatal outcomes. The BWMTF nomogram was established, revealing perfect discrimination with the area under the receiver operating characteristic curve (AUC) and stratified five-fold cross-validation in development cohort (AUC = 0.75, Mean AUC = 0.75) and validation cohort (AUC = 0.68, Mean AUC = 0.75). Calibration plots showed good calibration. We established and validated three models for predicting adverse perinatal effects to guide preventive treatment protocols. Impact statement What is already known on this subject? Many studies have identified a large number of predictors, but also lack a comprehensively quantified tool to predict adverse neonatal outcomes in women with PCOS to guide the development of clinical treatment programs. What do the results of this study add? This article screened the high risks factors of adverse neonatal outcomes in women with PCOS, and three nomograms were established and validated. Also, the area under the receiver operating characteristic curve (AUC) and stratified five-fold cross-validation in development cohort and validation cohort showed good discrimination; Calibration plots showed good calibration. What are the implications of these findings for clinical practice and/or further research? Our scoring system could help clinicians evaluate these risks and conduct proper screening, prevention, and management to ameliorate the risk of neonatal disease in these patients.
Italian Versions of the 12-Item Sexual Distress Scale (SDS) and the 5-Item Sexual Distress Scale-Short Form (SDS-SF): Psychometric Properties

Abstract The study aimed to analyze the psychometric properties of the Italian versions of the 12-item Sexual Distress Scale (SDS) and the 5-item Sexual Distress Scale-Short Form (SDS-SF). A total sample of 2291 adults (1361 women, 930 men) participated through a web survey completing the SDS, the FSFI, the IIEF, the PANAS and the SCL-90-R. The results supported the adequacy of both the SDS and SDS-SF factor structures, good reliability (respectively, α = .96 and .92), discriminant validities and strong associations with satisfaction, fear, depression, and psychoticism. SDS and SDS-SF may facilitate the assessment of sexual distress for both clinical and research purposes.
Role of positive emotion regulation strategies in the association between childhood trauma and posttraumatic stress disorder among trauma-exposed individuals who use substances

ABSTRACT Background The co-occurrence of childhood trauma and posttraumatic stress disorder (PTSD) is highly prevalent and clinically significant. Existing research emphasizes the role of emotion regulation in the relation between childhood trauma and PTSD. Yet, research in this area has almost exclusively examined the influence of strategies aimed at regulating negative emotions, such as anger and sadness. Objective To extend existing research, the current study examined underlying roles of strategies for regulating positive emotions (i.e., self- and emotion-focused positive rumination and positive dampening) in the association between childhood trauma severity and PTSD symptoms. Participants and Setting Participants were 320 trauma-exposed community individuals who reported past 30-day substance use (Mage = 35.78, 50.3% men, 81.6% white). Method Analyses examined whether childhood trauma severity was indirectly related to PTSD symptoms through self-focused positive rumination, emotion-focused positive rumination, and positive dampening. Results Positive dampening, but not positive self- and emotion-focused positive rumination, indirectly explained associations between childhood trauma severity and PTSD symptoms (B = .17, SE = .03, 95% CI [.12, .24]). Conclusions These findings highlight the potential utility of targeting positive dampening in the treatment of PTSD symptoms among individuals who use substances with a history of childhood trauma.
Cell cycle heterogeneity as a regulator of epithelial bending during neural tube closure

During neurulation, the neural plate bends around the median hinge point (MHP), overlying the notochord. MHP cells spend more time in G1/S-phase of the cell cycle than lateral cells, and this is associated with adoption of a wedged cell shape due to interruption of interkinetic nuclear migration. Clustering of wedge shaped cells in the MHP is suggested to drive midline bending. To determine the mechanism underlying the prolonged cell cycle in the MHP, I examined the mRNA expression of cell cycle inhibitors, and found the cyclin-dependent-kinase-inhibitors (CDKIs), p21, p27 and p57, to be expressed in midline cells. p21-/- mice, which exhibit MHPs, show upregulation of p57 mRNA in midline cells, supporting the hypothesis of a redundant relationship between p21 and p57 during neural plate bending. Detailed cell cycle analysis was performed in p21-/- and p21+/+ embryos by sequential injections of two thymidine analogues, IdU and BrdU. p21-/- MHP cells spend significantly less time in S-phase compared to wild-type littermates, suggesting that p21 is responsible for the prolonged S-phase in the MHP. In the absence of p21, S-phase length in the MHP and lateral cells is equivalent. Overexpression of CIP/KIP genes in the midline of cultured embryos did not increase the proportion of basal nuclei, a measure of wedge shaped cells. Electroporation of p57 siRNA abolished p57 mRNA from the neural plate and notochord of p21-/- embryos but did not prevent MHP formation. Collectively, the results indicate that p21 is responsible for the prolongation of S-phase in the MHP but is not necessary for MHP formation. There is possible redundancy between p21 and p57 in the MHP. However, loss of both p21 and p57 is not sufficient to prevent MHP formation. Furthermore, a prolonged S-phase in the midline cells of the neural plate is not necessary for MHP formation.
Adolescent Baseball Pitchers With Ulnar Collateral Ligament Tears Exhibit a High Proportion of Partial Tears

Background: Ulnar collateral ligament (UCL) tears in the throwing elbow are classified according to grade and location using magnetic resonance arthrography (MRA). However, the frequency of each tear type and the association to age, competition level, and radiographic findings in adolescent baseball pitchers are unknown. Purposes: The primary purpose of this study was to use MRA to characterize the severity, location, and UCL tear type in adolescent pitchers. The second aim was to describe the relationship between the UCL tear type and age, competition level, and plain radiographic findings. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Records of adolescent pitchers with a UCL tear treated by the senior author between 2007 and 2016 were retrospectively reviewed. MRA scans were reviewed and tears were classified according to the Joyner-Andrews classification. Low-grade partial tears are classified as type I, high-grade partial tears as type II, complete full-thickness tears as type III, and tear pathology in >1 region in the UCL as type IV. Each type of tear also has a location designated at the midsubstance, ulna (U), or humerus (H). Patient characteristics, competition level, and associated plain radiographic abnormalities were recorded. Univariate analyses were performed to examine the relationships between tear types and age, competition level, and plain radiographic findings. Results: A total of 200 adolescent pitchers (mean ± SD age, 17.2 ± 1.5 years) with MRA scans were reviewed. Type II-H (n = 62), type II-U (n = 51), and type III-U (n = 28) were the most common tear types observed. Type II tears comprised 64.5% of adolescent UCL tears, with type II-H being the most common. Plain radiographs were abnormal in 32% of patients, with calcifications (10.5%) and olecranon osteophytes (12.5%) being the most common findings. There were no significant relationships between tear type and age (P = .25), competition level (P = .23), or radiographic abnormalities (P = .75). Conclusion: Humeral-sided high-grade partial tears were the most common tear type in adolescent pitchers. There was no relationship between UCL tear type and age competition level, and plain radiographic abnormalities.
Japanese Encephalitis Virus NS4A Protein Interacts with PTEN-Induced Kinase 1 (PINK1) and Promotes Mitophagy in Infected Cells

The JEV-infected mammalian cells show an enhanced mitophagy flux with a concomitant decline in the mitochondrial mass. We show that the NS4A protein of JEV localized to the mitochondria and interacted with PINK1 in Huh7 cells during infection with the virus and demonstrate that JEV-NS4A alone is sufficient to induce mitophagy. The study provides the first evidence of mitochondrial quality control dysregulation during JEV infection, largely mediated by its NS4A protein. ABSTRACT The nonstructural protein 4A (NS4A) of flaviviruses has been implicated as a “central organizer” of the membrane-bound replication complex during virus replication. However, its role in the host responses to virus infection is not understood. Using the yeast-two-hybrid library screen, we identified a multitude of host proteins interacting with the Japanese encephalitis virus (JEV) NS4A protein. Several of these interacting proteins are known to localize to the mitochondria. One of these proteins was PTEN-induced kinase 1 (PINK1), a serine/threonine-protein kinase known for its role in mitophagy. Here, we demonstrate the JEV-NS4A localization to the mitochondria and its interaction with PINK1 in Huh7 cells during JEV infection. The JEV-infected cells showed an enhanced mitophagy flux with a concomitant decline in the mitochondrial mass. We present data showing that JEV-NS4A alone was sufficient to induce mitophagy. Interference with mitochondrial fragmentation and mitophagy resulted in reduced virus propagation. Overall, our study provides the first evidence of mitochondrial quality control dysregulation during JEV infection, largely mediated by its NS4A protein. IMPORTANCE The JEV-infected mammalian cells show an enhanced mitophagy flux with a concomitant decline in the mitochondrial mass. We show that the NS4A protein of JEV localized to the mitochondria and interacted with PINK1 in Huh7 cells during infection with the virus and demonstrate that JEV-NS4A alone is sufficient to induce mitophagy. The study provides the first evidence of mitochondrial quality control dysregulation during JEV infection, largely mediated by its NS4A protein.
Fractional Exponential Feedback Control for Finite-Time Stabilization and its Application in a Spin-Exchange Relaxation-Free Comagnetometer

This article is the first work to propose a series of control strategies for the longitudinal electron spin polarization of the spin-exchange relaxation-free comagnetometer system to ensure its ultrastable measurement. Two types of finite-time control strategies are presented for a nonlinear system with affine input. The first control strategy is finite-time fractional exponential feedback control (FEFC), which ensures that the trajectories of an autonomous system converge to an equilibrium state in a finite time that can be specified. The second control strategy is finite-time robust FEFC, which provides a finite-time stability of a nonautonomous system with unknown structures under disturbance and perturbations, and its upper bound of the settling time can be estimated. The theoretical results are supported by numerical simulations.
Reliability-based design of spread footings on clays reinforced with aggregate piers

ABSTRACT The economical and safe design of footings supported on aggregate-pier-reinforced clay could benefit from the implementation of a reliability-based approach that incorporates the different sources of uncertainty. Monte Carlo simulations are conducted to quantify the probability distribution of the ultimate bearing capacity for practical design scenarios. A reliability analysis is then conducted to propose design charts that yield the required factor of safety as a function of the major input parameters. The novelty in the proposed methodology is the incorporation of a lower bound shear strength that is based on the remoulded undrained shear strength in the reliability analysis.
Regret-Theoretic Multiattribute Decision-Making Model Using Three-Way Framework in Multiscale Information Systems

The existing multiattribute decision-making (MADM) methods on multiscale information systems (MSISs) are generally studied from the utility point of view, which may cause two problems: 1) the objects are strictly classified into good or bad, which may lead to misclassification and 2) the risk attitude and psychological behaviors of decision makers are difficult to be reflected. In light of this, this article proposes a wide three-way decision (3WD) model on an MSIS, which combines 3WD theory and regret theory and can precisely make up for these two shortcomings. First, by virtue of regret theory, an outranking relation on the comprehensive MSIS is constructed according to the regret-rejoicing index. Second, objects in the outranking relation are classified into three different domains by a clustering method. In each domain, the ranking of objects can be calculated by using the relative closeness coefficient. Finally, we use the cases in the database to simulate the experiment to verify the decision-making effect of the proposed model. Comparative analysis and experimental analysis also show the effectiveness, superiority, and stability of the proposed model.
Does Bystander Intervention Training Work? When Employee Intentions and Organisational Barriers Collide

Scholars have recently begun to consider the role of bystander intervention training in countering workplace incivility and bullying. Given the scarce empirical evidence of bystander training outcomes in occupational settings, this study set out to evaluate the effectiveness of a bystander intervention training in a large healthcare organisation, by assessing changes to levels of psychological safety, bystander efficacy, intent and behaviours over time. One hundred and forty employees in a large healthcare organisation in New Zealand attended the training and were asked to complete three surveys, one conducted at baseline, one carried out 2 weeks following the training and the last survey conducted 2 months later. The qualitative and qualitative findings of this study show that the bystander intervention training resulted in significant improvements to bystander attitudes and beliefs, which were ascribed to the quality of training materials, the facilitator and opportunities to role-play bystander intervention strategies. However, the positive bystander beliefs, attitudes and intent to intervene declined in the months following the training. The qualitative findings shed a light on these results and suggest that the participants required support for training transfer in the form of updated and accessible information about negative acts and bystander intervention strategies, leadership support and role modelling of bystander behaviours and civility, and the implementation of accountability systems that ensure the ongoing development of a civility culture.
PRC1 chromatin factors strengthen the consistency of neuronal cell fate specification and maintenance in C. elegans

In the nervous system, the specific identity of a neuron is established and maintained by terminal selector transcription factors that directly activate large batteries of terminal differentiation genes and positively regulate their own expression via feedback loops. However, how this is achieved in a reliable manner despite noise in gene expression, genetic variability or environmental perturbations remains poorly understood. We addressed this question using the AIY cholinergic interneurons of C. elegans, whose specification and differentiation network is well characterized. Via a genetic screen, we found that a loss of function of PRC1 chromatin factors induces a stochastic loss of AIY differentiated state in a small proportion of the population. PRC1 factors act directly in the AIY neuron and independently of PRC2 factors. By quantifying mRNA and protein levels of terminal selector transcription factors in single neurons, using smFISH and CRISPR tagging, we observed that, in PRC1 mutants, terminal selector expression is still initiated during embryonic development but the level is reduced, and expression is subsequently lost in a stochastic manner during maintenance phase in part of the population. We also observed variability in the level of expression of terminal selectors in wild type animals and, using correlation analysis, established that this noise comes from both intrinsic and extrinsic sources. Finally, we found that PRC1 factors increase the resistance of AIY neuron fate to environmental stress, and also secure the terminal differentiation of other neuron types. We propose that PRC1 factors contribute to the consistency of neuronal cell fate specification and maintenance by protecting neurons against noise and perturbations in their differentiation program.