Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the most important factors related to self-perceived health among older men in Sweden: a cross-sectional study using machine learning

Objective To evaluate which factors are the most strongly related to self-perceived health among older men and describe the shape of the association between the related factors and self-perceived health using machine learning. Design and setting This is a cross-sectional study within the population-based VAScular and Chronic Obstructive Lung disease study (VASCOL) conducted in southern Sweden in 2019. Participants A total of 475 older men aged 73 years from the VASCOL dataset. Measures Self-perceived health was measured using the first item of the Short Form 12. An extreme gradient-boosting model was trained to classify self-perceived health as better (rated: excellent or very good) or worse (rated: fair or poor) using self-reported data on 19 prevalent physician-diagnosed health conditions, intensity of 9 symptoms and 9 demographic and lifestyle factors. Importance of factors was measured in SHapley Additive exPlanations absolute mean and higher scores correspond to greater importance. Results The most important factors for classifying self-perceived health were: pain (0.629), sleep quality (0.595), breathlessness (0.549), fatigue (0.542) and depression (0.526). Health conditions ranked well below symptoms and lifestyle variables. Low levels of symptoms, good sleep quality, regular exercise, alcohol consumption and a body mass index between 22 and 28 were associated with better self-perceived health. Conclusions Symptoms are more strongly related to self-perceived health than health conditions, which suggests that the impacts of health conditions are mediated through symptoms, which could be important targets to improve self-perceived health. Machine learning offers a new way to assess composite constructs such as well-being or quality of life.
Genome-wide identification and expression analysis of the NAC transcription factor family in Saccharum spontaneum under different stresses

ABSTRACT The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The NAC family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the NAC gene family in the wild species Saccharum spontaneum has not been systematically studied. In this study, 115 SsNAC genes were identified in the S. spontaneum genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the SsNAC family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The SsNAC gene has different expression patterns at different developmental stages of stems and leaves. Further qRT–PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 SsNAC genes, indicating that these genes may play a key role in the resistance of S. spontaneum to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the NAC transcription factor family, providing a reference for further functional studies of the SsNAC gene.
NADPH oxidase 2 is necessary for chronic intermittent hypoxia‐induced sternohyoid muscle weakness in adult male mice

What is the central question of this study? Exposure to chronic intermittent hypoxia (CIH) evokes redox changes, culminating in impaired upper airway muscle function: what is the specific source of CIH‐induced reactive oxygen species? What is the main finding and its importance? Profound sternohyoid muscle dysfunction following exposure to CIH was entirely prevented by apocynin co‐treatment or NADPH oxidase 2 (NOX2) deletion. The results have implications for human obstructive sleep apnoea syndrome and point to antioxidant intervention, potentially targeting NOX2 blockade, as a therapeutic strategy.
A 77 Amino Acid Region in the N-Terminal Half of the HSV-1 E3 Ubiquitin Ligase ICP0 Contributes to Counteracting an Established Type 1 Interferon Response

Interferons (IFNs) are secreted cellular factors that are induced by viral infection and limit replication. HSV-1 is largely refractory to the antiviral effects of type 1 IFNs, which are synthesized shortly after viral infection, in part through the activities of the viral regulatory protein, ICP0. ABSTRACT Herpes simplex virus 1 (HSV-1) is a human pathogen capable of establishing lifelong latent infections that can reactivate under stress conditions. A viral immediate early protein that plays important roles in the HSV-1 lytic and latent infections is the viral E3 ubiquitin ligase, ICP0. ICP0 transactivates all temporal classes of HSV-1 genes and facilitates viral gene expression. ICP0 also impairs the antiviral effects of interferon (IFN)-β, a component of host innate defenses known to limit viral replication. To begin to understand how ICP0 allows HSV-1 to disarm the IFN-β response, we performed genetic analyses using a series of ICP0 truncation mutants in the absence and presence of IFN-β in cell culture. We observed that IFN-β pretreatment of cells significantly impaired the replication of the ICP0 truncation mutants, n212 and n312, which code for the first 211 and 311 amino acids of ICP0, respectively; this effect of IFN-β correlated with decreased HSV-1 early and late gene expression. This increased sensitivity to IFN-β was not as apparent with the ICP0 mutant, n389. Our mapping studies indicate that loss of 77 amino acids from residues 312 to 388 in the N-terminal half of ICP0 resulted in a virus that was significantly more sensitive to cells pre-exposed to IFN-β. This 77 amino acid region contains a phospho-SUMO-interacting motif or -SIM, which we propose participates in ICP0’s ability to counteract the antiviral response established by IFN-β. IMPORTANCE Interferons (IFNs) are secreted cellular factors that are induced by viral infection and limit replication. HSV-1 is largely refractory to the antiviral effects of type 1 IFNs, which are synthesized shortly after viral infection, in part through the activities of the viral regulatory protein, ICP0. To understand how ICP0 impedes the antiviral effects of type 1 IFNs, we used a series of HSV-1 ICP0 mutants and examined their viral replication and gene expression levels in cells stimulated with IFN-β (a type 1 IFN). Our mapping data identifies a discrete 77 amino acid region in the N-terminal half of ICP0 that facilitates HSV-1 resistance to IFN-β. This region of ICP0 is modified by phosphorylation and binds to the posttranslational modification SUMO, suggesting that HSV, and potentially other viruses, may counteract type 1 IFN signaling by altering SUMO and/or SUMO modified cellular proteins.
Breast Cancer Physical Activity Mobile Intervention: Early Findings From a User Experience and Acceptability Mixed Methods Study

Background Physical activity (PA) is the most well-established lifestyle factor associated with breast cancer (BC) survival. Even women with advanced BC may benefit from moderate PA. However, most BC symptoms and treatment side effects are barriers to PA. Mobile health coaching systems can implement functionalities and features based on behavioral change theories to promote healthier behaviors. However, to increase its acceptability among women with BC, it is essential that these digital persuasive systems are designed considering their contextual characteristics, needs, and preferences. Objective This study aimed to examine the potential acceptability and feasibility of a mobile-based intervention to promote PA in patients with BC; assess usability and other aspects of the user experience; and identify key considerations and aspects for future improvements, which may help increase and sustain acceptability and engagement. Methods A mixed methods case series evaluation of usability and acceptability was conducted in this study. The study comprised 3 sessions: initial, home, and final sessions. Two standardized scales were used: the Satisfaction with Life Scale and the International Physical Activity Questionnaire–Short Form. Participants were asked to use the app at home for approximately 2 weeks. App use and PA data were collected from the app and stored on a secure server during this period. In the final session, the participants filled in 2 app evaluation scales and took part in a short individual interview. They also completed the System Usability Scale and the user version of the Mobile App Rating Scale. Participants were provided with a waist pocket, wired in-ear headphones, and a smartphone. They also received printed instructions. A content analysis of the qualitative data collected in the interviews was conducted iteratively, ensuring that no critical information was overlooked. Results The International Physical Activity Questionnaire–Short Form found that all participants (n=4) were moderately active; however, half of them did not reach the recommended levels in the guidelines. System Usability Scale scores were all >70 out of 100 (72.5, 77.5, 95, and 80), whereas the overall user version of the Mobile App Rating Scale scores were 4, 4.3, 4.4, and 3.6 out of 5. The app was perceived to be nice, user-friendly, straightforward, and easy to understand. Recognition of achievements, the possibility of checking activity history, and the rescheduling option were positively highlighted. Technical difficulties with system data collection, particularly with the miscount of steps, could make users feel frustrated. The participants suggested improvements and indicated that the app has the potential to work well for survivors of BC. Conclusions Early results presented in this study point to the potential of this tool concept to provide a friendly and satisfying coaching experience to users, which may help improve PA adherence in survivors of BC.
Changes in epigenetic features in legumes under abiotic stresses

Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress‐resilient crops is crucial for ensuring global food security. Because of their nitrogen‐fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next‐generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.
What makes a violent mind? The interplay of parental rearing, dark triad personality traits and propensity for violence in a sample of German adolescents

Machiavellianism, narcissism and psychopathy are socially aversive personality traits that are strongly linked to the propensity of violence. A central determinate of aggression and violence is parental rearing. Interestingly, while the origin of the development of Dark Triad is not yet entirely understood, next to genetic and environmental factors, literature points towards an influence of parenting styles to the development of dark traits. Therefore, in a sample of 1366 9th grade students (mean age 14.89,), we assessed the interplay between parental rearing, dark triad traits, observation of violence among peers and their propensity for violence. The sample has a good representativeness on school types. Results reveal a positive association between the experience of parental rejection by both parents and punishment as well as parental control and overprotection and Machiavellianism, narcissism and psychopathy. Parental emotional warmth was associated negatively with Machiavellianism and psychopathy while no significant association with narcissism was seen. In a path model, parental rearing, dark triad traits and observation of violence among peers significantly contributed to the propensity of violence. However, differences between the experienced parenting behaviour of mothers and fathers should be noted. Both rejection and overly harsh punishments by fathers and emotional warmth by mothers have no significant influence on the dark triad. It is interesting that the effects regarding maternal parenting behaviour are stronger overall than the effects regarding paternal parenting behaviour. These results underline the importance of parental rearing on the development of Machiavellianism, narcissism and psychopathy and suggest a significant role of parental rearing and the dark triad traits on propensity for violence in adolescents. Parenting trainings and family interventions may be a promising starting point to prevent antisocial behavior linked to the dark triad and to prevent violent behavior in future generations
Restorative rehabilitation robotics to promote function, independence and dignity: users’ perspectives on clinical applications

Abstract People with mobility impairments have reported that improving their walking is one of the most important goals of their rehabilitation. Novel robotic technologies using powered exoskeletons for the lower limb could potentially offer efficient and less labour-intensive approaches to rehabilitation with shorter recovery times. To gather users’ and carers’ perspectives of assistive device use to provide information to design personalised and safe mobility rehabilitation technology. Semi-structured interviews were carried out with people with experience of mobility impairments. Iterative data collection was used to gather information about the social phenomena surrounding patient interaction and requirements for assistive devices for mobility impairments. Cycles of continuous data collection and thematic analysis using a theoretical, semantic approach was used to develop key themes within the data. We interviewed eight people: six people with mobility impairments and two carers. We identified five main themes: relationship with assistive technology, requirements for assistive technology, function and goal setting, personal factors to assistive device use and psychosocial factors to assistive device use. There was variability in the importance placed on each theme, particularly in the trade-off between the function and comfort of assistive technology. Patients emphasised the need for assistive technology to be personalised; they reported the ability to stand, control spasticity and involvement in community roles as key goals of their rehabilitation. These results highlight the variation in requirements for assistive technology between people with different mobility impairments; individuals’ experiences are unique and future prototypes need to account for different levels of impairments and personal goals. These findings will also inform the user evaluation stage of assistive device testing. The acceptability of assistive devices is dependent upon a number of factors, including personalisation, comfort and function. Future pilot studies should gather qualitative data to determine the acceptability of actual device use.
Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.
Genome-wide association studies in non-anxiety individuals identified novel risk loci for depression

Abstract Background Depression is a debilitating mental disorder that often coexists with anxiety. The genetic mechanisms of depression and anxiety have considerable overlap, and studying depression in non-anxiety samples could help to discover novel gene. We assess the genetic variation of depression in non-anxiety samples, using genome-wide association studies (GWAS) and linkage disequilibrium score regression (LDSC). Methods The GWAS of depression score and self-reported depression were conducted using the UK Biobank samples, comprising 99,178 non-anxiety participants with anxiety score <5 and 86,503 non-anxiety participants without self-reported anxiety, respectively. Replication analysis was then performed using two large-scale GWAS summary data of depression from Psychiatric Genomics Consortium (PGC). LDSC was finally used to evaluate genetic correlations with 855 health-related traits based on the primary GWAS. Results Two genome-wide significant loci for non-anxiety depression were identified: rs139702470 (p = 1.54 × 10−8, OR = 0.29) locate in PIEZO2, and rs6046722 (p = 2.52 × 10−8, OR = 1.09) locate in CFAP61. These associated genes were replicated in two GWAS of depression from PGC, such as rs1040582 (preplication GWAS1 = 0.02, preplication GWAS2 = 2.71 × 10−3) in CFAP61, and rs11661122 (preplication GWAS1 = 8.16 × 10−3, preplication GWAS2 = 8.08 × 10−3) in PIEZO2. LDSC identified 19 traits genetically associated with non-anxiety depression (p < 0.001), such as marital separation/divorce (rg = 0.45, SE = 0.15). Conclusions Our findings provide novel clues for understanding of the complex genetic architecture of depression.
The design of an automated data-analysis system for robotic telescopes and its application to Be stars

A method of drilling in which drill string sections are added to a drill string with minimal loss of drilling fluid. A valve sub is located below the kelly and the outer housing of the valve sub comprises the valve actuator. In disassembling the sub from a pipe string, gripping of the sub while relatively rotating the pipe string will cause the valve to be closed before the joint is broken. In reconnecting the sub to the string, the valve will be opened as the connection is made.
Nipah Virus Detection at Bat Roosts after Spillover Events, Bangladesh, 2012–2019

Knowledge of the dynamics and genetic diversity of Nipah virus circulating in bats and at the human-animal interface is limited by current sampling efforts, which produce few detections of viral RNA. We report a series of investigations at Pteropus medius bat roosts identified near the locations of human Nipah cases in Bangladesh during 2012–2019. Pooled bat urine was collected from 23 roosts; 7 roosts (30%) had >1 sample in which Nipah RNA was detected from the first visit. In subsequent visits to these 7 roosts, RNA was detected in bat urine up to 52 days after the presumed exposure of the human case-patient, although the probability of detection declined rapidly with time. These results suggest that rapidly deployed investigations of Nipah virus shedding from bat roosts near human cases could increase the success of viral sequencing compared with background surveillance and could enhance understanding of Nipah virus ecology and evolution.
Epidemiological and genetic characteristics of clinical carbapenem-resistant Acinetobacter baumannii strains collected countrywide from hospital intensive care units (ICUs) in China

ABSTRACT Acinetobacter baumannii is one of the key Gram-negative pathogens that can cause serious nosocomial infections. In China, a large proportion of clinical A. baumannii strains are multidrug resistant, among which strains resistant to carbapenems are particularly worrisome, as infections caused by such strains may limit the choice of existing antibiotics. We conducted a nationwide and genome-based surveillance on the prevalence and antibiotic susceptibility profile of carbapenem-resistant A. baumannii (CRAB) strains collected from intensive care units (ICUs) in hospitals in different provinces and investigated the routes of transmission and mechanism of resistance by whole-genome sequencing and phylogenetic analysis. We found that CRAB strains were prevalent in 71.4% (55/77) of the ICUs surveyed. Clonal spread of CRAB was found in 37.6% (29/77) of ICUs and a total of 22 different clones were identified. Most clones were transmissible within one ICU, but up to six clones could be detected in at least three hospitals. In addition, carbapenem-hydrolysing class D β-lactamases (CHDL) were found to be mainly responsible for carbapenem-resistance in A. baumannii and the ST2 global-clone is the predominant type of CRAB in China. Importantly, we found that CRAB isolates currently exhibited an extremely low rate of resistance to colistin (0.4%) and tigecycline (2.5%), but a high rate of resistance to ceftazidime–avibactam (70.2%). Findings in this work shall facilitate development of appropriate antimicrobial regimens for treatment of CRAB infections. Further surveillance and research on the evolutionary and epidemiological features of clinical CRAB strains are necessary.