Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of direct PCR for phylogenetic analysis of Fusarium fujikuroi species complex isolated from rice seeds

Plant pathogenic fungi cause severe yield losses and mycotoxin contamination in crops. The precise and rapid detection of fungal pathogens is essential for effective disease management. Sequencing universal DNA barcodes has become the standard method for the diagnosis of fungal diseases, as well as for identification and phylogenetic analysis. A major bottleneck in obtaining DNA sequence data from many samples was the laborious and time-consuming process of sample preparation for genomic DNA. Here, we describe a direct PCR approach that bypasses the DNA extraction steps to streamline the molecular identification of fungal species. Using a direct PCR approach, we successfully sequenced the nuclear ribosomal internal transcribed spacer (ITS) region for the representatives of major fungal lineages. To demonstrate the usefulness of this approach, we performed a phylogenetic analysis of the Fusarium fujikuroi species complex, which causes bakanae (“foolish seedling”) disease of rice and mycotoxin contamination. A total of 28 candidate strains were isolated from rice seeds in the Republic of Korea, and the identity of the isolates was determined using the DNA sequence of both ITS and translation elongation factor 1-α regions. In addition, 17 F. fujikuroi isolates were examined for fumonisin (FB) production in rice medium using an enzyme-linked immunosorbent assay. Phylogenetic and toxigenic analyses showed that the F. fujikuroi strains could be distinguished into two groups: FB producers (B14-type) and non-producers (B20-type). These results will accelerate the molecular identification of fungal pathogens and facilitate the effective management of fungal diseases.
Osteocalcin serum concentrations and markers of energetic metabolism in pediatric patients. Systematic review and metanalysis

Background Osteocalcin plays a role in glucose metabolism in mice, but its relevance in human energetic metabolism is controversial. Its relationship with markers of energetic metabolism in the pediatric population has not been systematically addressed in infants and adolescents. Objective This study aims to assess the mean differences between tOC, ucOC, and cOC among healthy children and children with type 1 or type 2 diabetes (T1D or T2D) and the correlation of these bone molecules with metabolic markers. Methods A systematic review and metanalysis were performed following PRISMA criteria to identify relevant observational studies published in English and Spanish using PubMed, Scopus, EBSCO, and Web of Science databases. The risk of bias was assessed using New Castle–Ottawa scale. Effect size measures comprised standardized mean difference (SMD) and Pearson correlations. Heterogeneity and meta-regressions were performed. Results The 20 studies included were of high quality and comprised 3,000 pediatric patients who underwent tOC, cOC, or ucOC measurements. Among healthy subjects, there was a positive correlation of ucOC with WC and weight, a positive correlation of tOC with FPG, HDL-c, WC, height, and weight, and a negative correlation between tOC and HbA1c. Among diabetic subjects, a negative correlation of ucOC with HbA1c and glycemia in both T1D and T2D was found and a negative correlation between tOC and HbA1c in T1D but not in T2D. The ucOC concentrations were lower in T2D, T1D, and patients with abnormal glucose status than among controls. The serum concentrations of tOC concentrations were lower among T1D than in controls. The patient's age, altitude, and HbA1c influenced the levels of serum tOC. Conclusion Osteocalcin is involved in energy metabolism in pediatric subjects because it is consistently related to metabolic and anthropometric parameters. Systematic Review Registration https://www.crd. york.ac. uk/prospero/, identifier: CRD42019138283.
The positive psychology of challenge: Towards interdisciplinary studies of activities and processes involving challenges

Activities and processes involving challenges are a natural part of life for most people and are highlighted in times of rapid change and global issues. This article argues that more studies around activities and processes involving challenges should be conducted with a focus on the concept of challenge in the context of well-being and optimal functioning. The concept of challenge is important because it is explicitly embedded in many major themes of positive psychology and can be a key concept in creating perspectives and frameworks to connect and integrate multiple elements in positive psychology to promote advancements in the field. Studying activities and processes involving challenges is also important from the perspective of dialectically integrating the positive and negative elements encompassed in the concept of challenge. The article also proposes to label activities and processes involving challenges as “challengership” and that an interdisciplinary area to study “challengership” (named “challengership studies”) should be created, which can collaborate with positive psychology for mutual development. The positive psychology of challenge/challengership is likely to provide opportunities for further advancement of positive psychology by creating more integrated knowledge of how to flourish when faced with challenges individually and collectively. The knowledge created in these areas can also be applied to education, coaching, and training at schools and organizations to meet the needs of the times, where skills of challengership should be considered trainable.
Vietnam Association of Gastroenterology (VNAGE) consensus on the management of Helicobacter pylori infection

Helicobacter pylori (H. pylori) infection is prevalent and has a rapidly increasing antibiotic resistance rate in Vietnam. Reinfection is quite common, and gastric carcinoma remains one of the most common malignancies, which is not uncommon to develop after successful eradication. The purpose of this consensus is to provide updated recommendations on the management of H. pylori infection in the country. The consensus panel consisted of 32 experts from 14 major universities and institutions in Vietnam who were invited to review the evidence and develop the statements using the Delphi method. The process followed the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. The consensus level was defined as ≥80% for agreement on the proposed statements. Due to the limited availability of high-quality local evidence, this consensus was also based on high-quality evidence from international studies, especially those conducted in other populations in the Asia–Pacific region. The panel finally reached a consensus on 27 statements after two voting rounds, which consisted of four sections (1) indications for testing and selection of diagnostic tests (2), treatment regimens, (3) post-treatment confirmation of H. pylori status, and (4) reinfection prevention methods and follow-up after eradication. Important issues that require further evidence include studies on third-line regimens, strategies to prevent H. pylori reinfection, and post-eradication follow-up for precancerous gastric lesions. We hope this consensus will help guide the current clinical practice in Vietnam and promote multicenter studies in the country and international collaborations.
English teachers’ perceptions of emergency remote teaching: Emotional attitudes, professional identity, and coping strategies

While the technology integration has been widely acknowledged, insufficient effort has been made to understand English teachers’ perceptions of emergency remote teaching (ERT). Given English is the primary foreign language in China and English teachers’ perceptions and adoptions of ERT impact the attainment of teaching and learning goals, this study inquired into experienced university English teachers’ emotional attitudes, perceptions of the reconstructed professional identity, and their strategies to cope with difficulties when conducting ERT in the Chinese English teaching context. Semi-structured interviews were conducted both online and face-to-face with five experienced universities English teachers in China. The findings indicated a trajectory of teachers’ attitudes toward ERT, namely, their attitudes were switched from doubt and rejection to fondness and attachment. Experienced English teachers adopted various strategies to cope with the difficulties and challenges they have encountered, including seeking support from their peers, students, and family, as well as self-regulated learning to sustain continuing professional development. During ERT, they have reconstructed their teacher identities. The study enriched peoples’ understandings of English teachers’ perceptions of the ERT by contextualizing the study in the Chinese educational context. Results can provide empirical evidence for policymakers and teacher trainers to make informed decisions regarding technical support and teachers’ continuing professional development.
The South Shetland Islands, Antarctica: Lithostratigraphy and geological map

Over the last few decades, numerous geological studies have been carried out in the South Shetland Islands, which have greatly contributed to a better understanding of its geological evolution. However, few attempts have been conducted to correlate the geological units throughout this archipelago. We present herein a review of the literature available in the South Shetland Islands, which we use to propose a lithostratigraphical correlation that constitutes a coherent stratigraphy for the main Mesozoic and Cenozoic rocks of the South Shetland Islands along with a new geological map. The lithostratigraphical correlation shows that the geological and environmental evolution comprises three main stages: 1) deep marine sedimentation from ∼164 to 140 Ma, 2) subaerial volcanism and sedimentation with a proliferation of plants and fauna from ∼140 to 35 Ma and 3) glacial and interglacial deposits from ∼35 Ma. The lithostratigraphical correlation also shows a broad geographical trend of decreasing age of volcanism from southwest to northeast, which has been previously suggested. However, this spatial age trend is disrupted by the presence of Eocene magmatism in Livingston Island, located in the centre of the archipelago. We suggest that the migration of volcanism occurred from the Late Cretaceous until the early Eocene. Subsequently, enhanced magmatic activity took place from the mid-Eocene until the Miocene, which we associate with processes related with the waning of subduction. Constraining the protolith age of the metamorphic complex of Smith Island remains challenging, yet holds key implications for the tectonic and accretionary evolution of the Antarctic Peninsula. The rocks recording the glaciation of this sector of Antarctica are well exposed in the northern South Shetland Islands and hold critical information for understanding the timings and processes that lead to the greenhouse to icehouse transition at the end of the Eocene. Finally, contemporaneous rocks to the breakup of Antarctic Peninsula from Patagonia that led to the opening of the Drake Passage and the development of the Scotia Sea are exposed in the centre and north of the South Shetland archipelago. Better constraints on the age and tectonic settings on these units may lead to further understanding the paleobiogeographical evolution of the region, which may have played an important role for speciation as a land bridge between South America and Antarctica. The dataset containing the geological map and associated information is shared as a shapefile or KML file.
fMRI evidence that hyper-caricatured faces activate object-selective cortex

Many brain imaging studies have looked at the cortical responses to object categories and faces. A popular way to manipulate face stimuli is by using a “face space,” a high dimensional representation of individual face images, with the average face located at the origin. However, how the brain responds to faces that deviate substantially from average has not been much explored. Increasing the distance from the average (leading to increased caricaturing) could increase neural responses in face-selective regions, an idea supported by results from non-human primates. Here, we used a face space based on principal component analysis (PCA) to generate faces ranging from average to heavily caricatured. Using functional magnetic resonance imaging (fMRI), we first independently defined face-, object- and scene-selective areas with a localiser scan and then measured responses to parametrically caricatured faces. We also included conditions in which the images of faces were inverted. Interestingly in the right fusiform face area (FFA), we found that the patterns of fMRI response were more consistent as caricaturing increased. However, we found no consistent effect of either caricature level or facial inversion on the average fMRI response in the FFA or face-selective regions more broadly. In contrast, object-selective regions showed an increase in both the consistency of response pattern and the average fMRI response with increasing caricature level. This shows that caricatured faces recruit processing from regions typically defined as object-selective, possibly through enhancing low-level properties that are characteristic of objects.
Uterine NK cells underexpress KIR2DL1/S1 and LILRB1 in reproductive failure

A significant proportion of recurrent miscarriage, recurrent implantation failure and infertility are unexplained, and these conditions have been proposed to have an etiology of immunological dysfunction at the maternal-fetal interface. Uterine Natural Killer cells (uNK) comprise three subsets and are the most numerous immune cells found in the uterine mucosa at the time of implantation. They are thought to play an important role in successful pregnancy by regulation of extravillous trophoblast (EVT) invasion and spiral artery remodelling. Here, we examine the frequency, phenotype and function of uNK1-3 from the uterine mucosa of 16 women with unexplained reproductive failure compared to 11 controls with no reproductive problems, during the window of implantation. We report that KIR2DL1/S1 and LILRB1 expression is lower in the reproductive failure group for both uNK (total uNK, uNK 2 and 3) and pNK. We also show that degranulation activity is significantly reduced in total uNK, and that TNF-α production is lower in all uNK subsets in the reproductive failure group. Taken together, our findings suggest that reproductive failure is associated with global reduction in expression of uNK receptors important for interaction with HLA-C and HLA-G on EVT during early pregnancy, leading to reduced uNK activation. This is the first study to examine uNK subsets during the window of implantation in women with reproductive failure and will serve as a platform to focus on particular aspects of phenotype and function of uNK subsets in future studies. Further understanding of uNK dysregulation is important to establish potential diagnostic and therapeutic targets in the population of women with unexplained reproductive failure.
An Assessment of Reliability of Future Projections by Multi-Model Ensemble Based on a New Method Measuring Contribution of External Forcings to Total Variance

This study estimates the effect of greenhouse gases (GHGs) on future climate projections produced by multi-model ensembles (MMEs) using twenty-one coupled Atmosphere-Ocean general circulation models. In this study, potential predictability (P) is applied to assess the reliability of GHGs effects on future climate projections. P is a ratio of external variance to total variance, which is used to measure the impact of external forcing. When the internal variance is very small, P will be close to 1, and the ensemble is highly predictable, indicating that the variation is largely controlled by external forcing. P reveals that future climate changes in the 21st century due to the GHGs effect are statistically more significant over higher latitudes than lower latitudes, and over land rather than ocean for the surface air temperature (SAT). For precipitation (PCP), most regions show that P is less than 0.5, except for the South African, North Eastern Pacific, North Atlantic, Central South American, and East Asian regions. It is clearly shown that the strong regions of correlation between MME and the observation where P is strong have a small inter-model difference. This study suggests that an analysis method such as P provides credibility to signals in projection of the SAT and PCP changes.
Improving care for SUD patients with complex trauma–relationships between childhood trauma, dissociation, and suicidal behavior in female patients with PTSD and SUD

Background Posttraumatic disorders are among the most frequent co-occurring diagnoses in patients with substance use disorders (SUD). Individuals with this dual diagnosis often present with special treatment needs, especially after childhood traumatic experiences (CT). Along with posttraumatic stress disorder (PTSD) and dissociative symptoms, suicidal behaviors belong to the clinical challenges in this group of patients and may influence the course and outcome of SUD treatment. Therefore, a better understanding of the relationships between different forms of CT, psychopathology and suicidal behaviors seems to be important to tailor adequate concepts of care. Materials and methods We examined 343 female patients with SUD and Posttraumatic stress disorder (PTSD). All patients completed the Childhood Trauma Questionnaire (CTQ), the Dissociative Experiences Scale-Taxon (DES-T) and the Structured Clinical Interview Axis I Disorders (SCID-I). To determine relationships between different symptoms with potential importance for concepts of treatment, we conducted analyses of moderated mediation for different models. We examined the direct and indirect effects of associations between the type of CT, dissociation and suicidal behavior, as well as the moderation effect of PTSD. Results All participants met DSM-criteria for either full PTSD (75.2%) or subsyndromal PTSD (24.8%). Almost all (94.5%) received at least one substance dependence diagnosis and the remaining 5.5% met substance abuse criteria. Most participants (93.3%) reported at least one type of childhood trauma. In all models, dissociation was a risk factor for suicidal ideation (SI) and for suicide attempts (SA). In both, participants with subsyndromal PTSD and participants with full PTSD, dissociation mediated the relationship between childhood sexual abuse and SI as well as SA. Moreover, we report direct effects between different childhood traumas and SI and SA. Furthermore, emotional abuse was a significant predictor of dissociation. Discussion In our sample of female patients with SUD and co-occurring PTSD, dissociation significantly increased suicidal behavior and served as a mediator of the relationship between childhood sexual abuse and suicidal behavior. Our findings underline the need to include interventions to address dissociative symptoms and other more complex consequences of childhood trauma into concepts of care for patients with SUD.
Adverse drug reactions in an ageing PopulaTion (ADAPT) study: Prevalence and risk factors associated with adverse drug reaction-related hospital admissions in older patients

Background: Older people experience greater morbidity with a corresponding increase in medication use resulting in a potentially higher risk of adverse drug reactions (ADRs). Objectives: The aim of this study was to; 1) determine the prevalence and characteristics of ADR-related hospital admissions among older patients (≥65 years) in Ireland; and 2) identify the risk factors associated with ADR-related hospital admissions. Methods: A cross-sectional study of ADR prevalence in patients aged ≥65 years admitted acutely to hospital in Ireland over a 8 month period (November 2016- June 2017). A multifaceted review of each hospital admission was undertaken to assess the likelihood of an ADR being a reason for admission (cause of admission or contributing to admission) in the context of the patient’s medication, clinical conditions, comorbidities and investigations. A number of decision aids were applied by two independent reviewers to assess ADR causality, avoidability and severity. A random sample of patients, determined not to have a suspected ADR on screening, were assigned to a non-ADR control group. Multivariable logistic regression was used to assess the association between potential risk factors for ADR-related admissions compared with non-ADR-related admissions. Results: In total, 3,760 hospital admission episodes (in 3,091 patients) were screened and 377 admissions were considered ADR-related (10.0%, 95% CI 9.1%, 11.0%). 219 (58.1%) ADR-related admissions were caused by an ADR, while ADRs contributed to 158 (41.9%) admissions. 268 (71.1%) of all ADR-related admissions were deemed definitely or possibly preventable/avoidable. 350 (92.8%) ADRs were classified as being of moderate severity, with 27 (7.2%) classified as severe. Antithrombotic agents, mainly aspirin and warfarin, were the drugs most frequently associated with ADR-related admissions (gastrointestinal and vascular haemorrhagic disorders). In multivariable analysis, immobility, frailty, having delirium or ulcer disease and taking anticoagulant and antiplatelet medication on admission were significantly associated with an ADR-related hospital admission. Conclusion: One in ten hospital admissions, among those aged 65 + years, were considered ADR-related, with approximately 70% potentially avoidable. Reliable and validated ADR detection and prediction tools are needed to develop prevention strategies.
Development of rapid and precise approach for quantification of bacterial taxa correlated with soil health

The structure and dynamic of soil bacterial community play a crucial role in soil health and plant productivity. However, there is a gap in studying the un−/or reclaimed soil bacteriome and its impact on future plant performance. The 16S metagenomic analysis is expensive and utilize sophisticated pipelines, making it unfavorable for researchers. Here, we aim to perform (1) in silico and in vitro validation of taxon-specific qPCR primer-panel in the detection of the beneficial soil bacterial community, to ensure its specificity and precision, and (2) multidimensional analysis of three soils/locations in Egypt (‘Q’, ‘B’, and ‘G’ soils) in terms of their physicochemical properties, bacteriome composition, and wheat productivity as a model crop. The in silico results disclosed that almost all tested primers showed high specificity and precision toward the target taxa. Among 17 measured soil properties, the electrical conductivity (EC) value (up to 5 dS/m) of ‘Q’ soil provided an efficient indicator for soil health among the tested soils. The 16S NGS analysis showed that the soil bacteriome significantly drives future plant performance, especially the abundance of Proteobacteria and Actinobacteria as key indicators. The functional prediction analysis results disclosed a high percentage of N-fixing bacterial taxa in ‘Q’ soil compared to other soils, which reflects their positive impact on wheat productivity. The taxon-specific qPCR primer-panel results revealed a precise quantification of the targeted taxa compared to the 16S NGS analysis. Moreover, 12 agro-morphological parameters were determined for grown wheat plants, and their results showed a high yield in the ‘Q’ soil compared to other soils; this could be attributed to the increased abundance of Proteobacteria and Actinobacteria, high enrichment in nutrients (N and K), or increased EC/nutrient availability. Ultimately, the potential use of a taxon-specific qPCR primer-panel as an alternative approach to NGS provides a cheaper, user-friendly setup with high accuracy.