Miracle-dz/UniFAR-FTUs huggingface dataset:
Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
An economic evaluation of an online computer-tailored smoking cessation intervention that includes message frame-tailoring: A randomized controlled trial

Evidence of economic evaluations of behaviour change interventions is scarce, but needed to guide policy makers’ decision-making. This study economically evaluated 4 versions of an innovative online computer-tailored smoking cessation intervention. The economic evaluation from a societal perspective was embedded in a randomized controlled trial among 532 smokers using a 2 (message frame-tailoring, i.e. how messages are presented: autonomy-supportive vs controlling) x 2 (content-tailoring, i.e. what content is presented: tailored vs. generic) design. Both kinds of tailoring, content-tailoring and message frame-tailoring, were based on a set of questions asked at baseline. Self-reported costs, prolonged smoking abstinence (cost-effectiveness) and quality of life (cost-utility) were assessed during a 6-month-follow-up. For cost-effectiveness analysis, costs per abstinent smoker were calculated. For cost-utility analysis, costs per QALY (i.e. quality-adjusted life year) gained were calculated. A willingness-to-pay (WTP) threshold of €20.000 was used. Bootstrapping and sensitivity analysis were conducted. Cost-effectiveness analysis showed that up to a WTP of €2.000, the combination of message frame- and content-tailoring dominated all study groups. From a WTP of €2.005, the content-tailored group dominated all study groups. Cost-utility analysis revealed that the combination of message frame-tailoring and content-tailoring had the highest probability of being the most efficient study group at all levels of the WTP. The combination of message frame-tailoring and content-tailoring in online smoking cessation programmes seemed to have high potential for cost-effectiveness (smoking abstinence) and cost-utility (quality of life), thus providing good value for money. Yet, when the WTP for each abstinent smoker is high (i.e., €2.005 or higher), the addition of message frame-tailoring might not be worth the effort and content-tailoring only is preferred.
Feasibility of evaluation of Polar H10 chest-belt ECG in patients with a broad range of heart conditions

Background: The chest-belt can be used to obtain a 1-lead ECG. Data from it have been validated for the determination of heart rate and for the possibility to detect atrial ﬁ brillation (AF) compared to ECG-Holter on a short ECG recording in selected patients. However, validation of the possibility to evaluate long ECG recordings in patients with a wide range of heart diseases has not yet been performed. Methodology and results: 54 hospitalized patients, 53 outpatients and 54 healthy controls were enrolled in the study (n = 161 in total). Using a Polar H10 chest-belt, 1–2 hours of ECG were recorded in all patients (1 153 229 heartbeats, average heart rate 76.6/min, 86.3% in sinus rhythm, 13.7% with atrial ﬁ brillation, 0.46% atrial premature beats, 0.49% ventricular premature beats). The presence of noise was 2.16% (A: 2.31%; B: 1.95%; C: 2.20%). 1 128 319 / 1 153 229 were evaluated as easy to interpret. Using ECG from the belt, the basic rhythm was reliably determined by the physician in majority of patients (51/54, 94.4% in hospitalized patients; in 100% of outpatients and healthy controls) when compared to 12-lead ECG. 3 ca- ses were evaluated as unclear; in all of these cases, all QRS complexes were stimulated by a pacemaker. In hospitalized patients, real-time ECG from the belt was comparable to telemetric ECG monitoring (match in 53/54, 98.1%). Conclusion: The ECG obtained from the chest-belt in hospitalized patients and outpatients with a wide range of cardiovascular diseases, as well as in healthy individuals, is usable in real practice for evaluation of baseline rhythm, atrial ﬁ brillation and premature contractions with a minimal proportion of difﬁ culties to interpret recordings due to artefacts. Caution should be exercised in interpretation of the ECG in patients with stimulated rhythm and in patients with atrial ﬂ utter. The chest belt can be used as a means for conti- nuous monitoring of ECG, evaluation of rhythm and screening of atrial ﬁ brillation.
The Effect of SARS-CoV-2 Vaccination on B-Cell Phenotype in Systemic Sclerosis Patients

Objective: to assess the influence of SARS-CoV-2 mRNA vaccine on B-cell phenotypes in systemic sclerosis (SSc). Methods: peripheral blood B-cell subpopulations were evaluated before (t1) and 3 months (t3) after the second dose of vaccine in 28 SSc patients. Peripheral blood B-cell subpopulations were evaluated in 21 healthy controls (HCs) only at t1. Anti-spike IgG levels were evaluated at t3 in both cohorts. Results: SSc patients presented higher naive, double-negative, and CD21low B cells compared to HCs. IgM-memory and switched-memory B cells were lower in SSc patients than HCs. No differences in anti-spike IgG levels after vaccination were observed between SSc patients and HCs. Anti-spike IgG levels after vaccination were lower in SSc patients with increased CD21low B cells at baseline compared to SSc patients with normal CD21low B cells. A positive correlation was found between IgG levels and naive B cells. A negative linear correlation was shown between IgG levels and IgM-memory, switched-memory, double-negative, and CD21low B cells. Conclusions: SARS-CoV-2 mRNA vaccine response is normal in SSc patients not undergoing immunosuppressive therapy. The normal number of naive B cells is a positive marker of antibody response. The increased percentage of CD21low B cells represents a negative marker of antibody response.
High Levels of Zinc Affect Nitrogen and Phosphorus Transformation in Rice Rhizosphere Soil by Modifying Microbial Communities

Due to global industrialization in recent decades, large areas have been threatened by heavy metal contamination. Research about the impact of excessive Zn on N and P transformation in farmland has received little attention, and its mechanism is still not completely known. In this study, we planted rice in soils with toxic levels of Zn, and analyzed the plant growth and nutrient uptake, the N and P transformation, enzyme activities and microbial communities in rhizosphere soil to reveal the underlying mechanism. Results showed high levels of Zn severely repressed the plant growth and uptake of N and P, but improved the N availability and promoted the conversion of organic P into inorganic forms in rice rhizosphere soil. Moreover, high levels of Zn significantly elevated the activities of hydrolases including urease, protease, acid phosphatase, sucrase and cellulose, and dehydrogenase, as well as the abundances of Flavisolibacter, Sphingomonas, Gemmatirosa, and subgroup_6, which contributed to the mineralization of organic matter in soil. Additionally, toxic level of Zn repressed the nitrifying process by decreasing the abundance of nitrosifying bacteria Ellin6067 and promoted denitrification by increasing the abundance of Noviherbaspirillum, which resulted in decreased NO3− concentration in rice rhizosphere soil under VHZn condition.
Random and Free Positive Maps with Applications to Entanglement Detection

We apply random matrix and free probability techniques to the study of linear maps of interest in quantum information theory. Random quantum channels have already been widely investigated with spectacular success. Here, we are interested in more general maps, asking only for k-positivity instead of the complete positivity required of quantum channels. Unlike the theory of completely positive maps, the theory of k-positive maps is far from being completely understood, and our techniques give many new parametrized families of such maps. We also establish a conceptual link with free probability theory, and show that our construc- tions can be obtained to some extent without random techniques in the setup of free products of von Neumann algebras. Finally, we study the properties of our examples and show that for some parameters, they are indecomposable. In particular, they can be used to detect the presence of entanglement missed by the partial transposition test, that is, PPT entanglement. As an application, we considerably refine our understanding of PPT states in the case where one of the spaces is large whereas the other one remains small.
The dynamical ocean component of the Madden-Julian oscillation

At time scales between synoptic weather and the seasonal cycle, the Madden-Julian Oscillation (MJO) is the dominant cause of atmospheric variability in the tropics, modifying seasonal rainfall totals and influencing atmospheric circulation worldwide. It induces a large response in the tropical oceans through surface fluxes of heat and momentum. While the thermodynamic ocean-atmosphere interaction has been well studied, understanding is lacking on the dynamical ocean response to MJO-induced surface momentum fluxes. A comprehensive observational study of the nature of this response is undertaken. This indicates large amplitude and coherent dynamic variability consisting of equatorial ocean Kelvin and Rossby waves, along with coastally-trapped waves and extra-tropical responses. These processes have important implications for ocean circulation, chemistry and biology. Furthermore, it is shown that this response in the ocean dynamics can influence the behaviour of the MJO itself. The propagation of equatorial ocean Rossby waves into the western Indian Ocean causes deepening of the thermocline, positive temperature advection and thus positive sea surface temperature anomalies that trigger atmospheric convection. This constitutes a feedback that will modify the behaviour of the MJO, strengthening its low frequency component and enhancing its intermittent nature. The ocean dynamics can also trigger individual Madden-Julian (MJ) events through the same oceanic processes. This triggering mechanism is strongest for ‘primary’ MJ events that are not immediately preceded by other MJO activity, nor by any other triggers. A linearised ocean model is used to understand the fundamental principles behind the observed dynamical ocean component of the MJO. It is shown that the equatorial Rossby waveguide is more effective at transferring dynamic anomalies to the western Indian Ocean than the coastal Kelvin waveguide. Sensitivity studies demonstrate that westerly wind bursts with a broader latitudinal scale will be considerably more effective in generating a dynamical ocean response that can feed back onto the MJO. Crucially, it is shown that these dynamical ocean processes are predictable over periods of up to five months, far longer than the time scale over which the MJO can be predicted. It may therefore be possible to use observations of the ocean dynamics to improve forecasts of the MJO during periods of inactivity, when it has previously been most difficult to predict.
STRESS –STRAIN DIAGRAM OF SELF-CONSOLIDATING CONCRETE SUBJECTED TO CHEMICAL ATTACK

Self-consolidating concrete (SCC) is increasingly used in a number of concrete applications, some of which are highly susceptible to attack by sulfuric acid. This work aimed to study the resistance of a wide range of different SCCs to sulfuric attack. The main variables studied included binder material type (highly reactive materials), limestone powder, and hybrid fibers in this work, compaction, L-box, and V-hopper were performed for the new mixtures. In this study, the specimens were immersed in a solution of sulfuric acid at a concentration (0.5%) for up to 289 days after normal curing for 28 days. Laboratory results show that concrete containing pozzolanic material has reduced mechanical properties compared to a mixture containing only limestone powder. The study also showed that there was an improvement in the resistance of concrete to acid solutions when hybrid fibers were added to the concrete mix. From the stress graph, the strain at given axial stress will be less than once the failure becomes more severe, it will become less rigid than immersing the specimen for six months.
Embryonic Exposure to Cigarette Smoke Extract Impedes Skeletal Development and Evokes Craniofacial Defects in Zebrafish

Exposure to cigarette smoke represents the largest source of preventable death and disease in the United States. This may be in part due to the nature of the delayed harmful effects as well as the lack of awareness of the scope of harm presented by these products. The presence of “light” versions further clouds the harmful effects of tobacco products. While active smoking in expectant mothers may be reduced by educational and outreach campaigns, exposure to secondhand smoke is often involuntary yet may harm the developing embryo. In this study, we show that the main component of secondhand smoke, sidestream cigarette smoke, from several brands, including harm-reduction versions, triggered unsuccessful hatching at 3 dpf and reduced overall survival at 6 dpf in developing zebrafish. At non-lethal concentrations, craniofacial defects with different severity based on the cigarette smoke extract were noted by 6 dpf. All tested products, including harm-reduction products, significantly impacted cartilage formation and/or bone mineralization in zebrafish embryos, independent of whether the bones/cartilage formed from the mesoderm or neural crest. Together, these results in a model system often used to detect embryonic malformations imply that exposure of a woman to secondhand smoke while pregnant may lead to mineralization issues in the skeleton of her newborn, ultimately adding a direct in utero association to the increased fracture risk observed in children of mothers exposed to cigarette smoke.
Cross-Cultural Comparison of ICD-11 Adjustment Disorder Prevalence and Its Risk Factors in Japanese and Lithuanian Adolescents

Background: Although there is increasing knowledge about adjustment disorder (AjD) based on the new diagnostic criteria of the International Classification of Diseases (ICD-11), less is known on AjD in adolescents. This study aimed to examine the prevalence of AjD and its risk factors in Japanese and Lithuanian adolescents. Methods: The cross-sectional study sample comprised 1745 adolescents from Japan (n = 913) and Lithuania (n = 832). AjD was assessed using the Adjustment Disorder New Module-8 (ADNM-8). We compared the prevalence of AjD in Japanese and Lithuanian adolescents. Using multinominal logistic regression analysis, we examined the effects of age, gender, socioeconomic status, and cumulative stressors as societal and cultural factors, resilience as an intrapersonal factor, and loneliness and perceived support as interpersonal factors on adolescent AjD. Results: The prevalence of probable AjD was 11.7% in Lithuanian adolescents and 6.9% in Japanese adolescents. Gender, socioeconomic status, cumulative stressors, resilience, loneliness, and perceived positive social support were each significantly associated with AjD risk. Conclusions: This cross-cultural comparative study revealed characteristics of the stressors and prevalence of AjD among Japanese and Lithuanian adolescents. In terms of the socio-interpersonal framework model for the stress–response syndrome, sociocultural, intrapersonal, and interpersonal factors were found to be risk factors associated with AjD in adolescents.
Evaluation of Hydroxyapatite and Hydroxyapatite Combined with Platelet-Rich Plasma Graft in Treatment of Intrabony Periodontal Defect - A Comparative Study.

Introduction: periodontitis is an inflammatory disease of the supporting tissues of the teeth caused by specific micro-organisms or a group of specific micro-organisms, resulting in progressive destruction of the periodontal ligament and alveolar bone with pocket formation, recession, or both. Aim of the study: The present study aimed to assess the effect of hydroxyapatite and hydroxyapatite combined with platelet-rich plasma graft in treatment of intrabony periodontal defects. Subjects and Methods: 24 periodontitis patients with intra-bony periodontal defects participated in this clinical trial and treated with full thickness mucoperiosteal flap surgical technique and Hydroxyapatite bone graft (goup I) or full thickness mucoperiosteal flap surgical technique and Hydroxyapatite bone graft combined with platelet-rich plasma graft (group II ). Clinical outcomes included plaque index (PI), gingival index (GI), probing depth (PD) and clinical attachment level (CAL). Bone defect area was measured by digital periapical radiographs and bone density was calculated by Digora program. Measurements at baseline, 3-months and 6-months postoperatively were subjected to statistical analysis. Results : Both of hydroxyapatite bone graft (HA group) and hydroxyapatite bone graft with platelet-rich plasma (HA+ PRP group) resulted in statistically significant improvement in all clinical and radiographic parameters from baseline to 3-months and 6-months. But no significant difference was observed between both groups. After 3-months, HA group showed 5.05±. 37 PD reduction and 6.65±1.11 CAL gain, while HA+PRP group showed 4.95±. 96 PD reduction and 6.30±0.86 CAL gain. After 6-months HA group showed 3.50±. 62 PD reduction and 4.60±1.17 CAL gain, while HA+PRP group showed 3.35±. 67 PD reduction and 4.70±0.67 CAL gain. Conclusion : Both hydroxyapatite bone graft group and hydroxyapatite bone graft combined with platelet-rich plasma group showed significant reduction in clinical and radiographic outcomes after 6 months with no statistically significant difference between them . Both treatment modalities are successful procedures for treating intrabony defects
One year of European premiers leadership and empathy in times of global pandemic: a Twitter sentiment analysis

Abstract After over a year of the COVID-19 pandemic, we observe very different health and economic outcomes across countries. Has this also been the case for the communication of their leaders? Has the communication of the political leaders of most affected countries shown higher levels of sentiment? This study uses Twitter to test whether a sample of European leaders exhibited empathy in their unmediated communications, as advocated by neo-charismatic leadership theories. We find that leaders do show emotions in their communications. However, there are no significant differences between them, leading us to reject the hypothesis that leaders of the most affected countries displayed more empathy than those of the least affected.
Research Scenarios of Autonomous Vehicles, the Sensors and Measurement Systems Used in Experiments

Automated and autonomous vehicles are in an intensive development phase. It is a phase that requires a lot of modelling and experimental research. Experimental research into these vehicles is in its initial state. There is a lack of findings and standardized recommendations for the organization and creation of research scenarios. There are also many difficulties in creating research scenarios. The main difficulties are the large number of systems for simultaneous checking. Additionally, the vehicles have a very complicated structure. A review of current publications allowed for systematization of the research scenarios of vehicles and their components as well as the measurement systems used. These include perception systems, automated response to threats, and critical situations in the area of road safety. The scenarios analyzed ensure that the planned research tasks can be carried out, including the investigation of systems that enable autonomous driving. This study uses passenger cars equipped with highly sophisticated sensor systems and localization devices. Perception systems are the necessary equipment during the conducted study. They provide recognition of the environment, mainly through vision sensors (cameras) and lidars. The research tasks include autonomous driving along a detected road lane on a curvilinear track. The effective maintenance of the vehicle in this lane is assessed. The location used in the study is a set of specialized research tracks on which stationary or moving obstacles are often placed.
Using Decision Trees to Examine Environmental and Behavioural Factors Associated with Youth Anxiety, Depression, and Flourishing

Modifiable environmental and behavioural factors influence youth mental health; however, past studies have primarily used regression models that quantify population average effects. Decision trees are an analytic technique that examine complex relationships between factors and identify high-risk subgroups to whom intervention measures can be targeted. This study used decision trees to examine associations of various risk factors with youth anxiety, depression, and flourishing. Data were collected from 74,501 students across Canadian high schools participating in the 2018–2019 COMPASS Study. Students completed a questionnaire including validated mental health scales and 23 covariates. Decision trees were grown to identify key factors and subgroups for anxiety, depression, and flourishing outcomes. Females lacking both happy home life and sense of connection to school were at greatest risk for higher anxiety and depression levels. In contrast with previous literature, behavioural factors such as diet, movement and substance use did not emerge as differentiators. This study highlights the influence of home and school environments on youth mental health using a novel decision tree analysis. While having a happy home life is most important in protecting against youth anxiety and depression, a sense of connection to school may mitigate the negative influence of a poor home environment.