Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of prokaryotes at a shallow submarine vent of Panarea Island (Italy) by high-throughput sequencing

To determine microbial community composition and possible key microbial processes in the shallow-sea hydrothermal vent system off Panarea Island (Italy), we examined bacterial and archaeal communities of sediment and fluid samples from a hot vent by 16S rDNA Illumina sequencing technique. Both high abundant (>1% of total sequences), low abundant (from 0.1 to <1%) and rare (< 0.1%) phylogenetic groups were responsible for the distinct prokaryotic communities characterizing the heated sediment and fluid. The bacterial and archaeal communities from sediment were dominated by sequences affiliated with Rhodovulum genus ( Alphaproteobacteria ), including phototrophic ferrous-iron-oxidizing purple bacteria, Thiohalospira and Thiomicrospira ( Gammaproteobacteria ), typically involved in the sulphur cycle, and Methanococcus ( Euryarchaeota ). Fluid communities were dominated by anoxygenic phototrophic members of Chlorobium , followed by Thiomicrospira ( Gammaproteobacteria ), Sulfurimonas , Arcobacter and Sulfurospirillum ( Epsilonproteobacteria ), and Methanosarcina ( Euryarchaeota ). Obtained sequences were affiliated with prokaryotes taking a key part in the carbon, iron and sulphur cycling at the shallow hydrothermal system off Panarea Island. Despite the huge sequencing efforts, a great number of Bacteria and Archaea still remains unaffiliated at genus level, indicating that Black Point vent represents a hotspot of prokaryotic diversity.
Underweight, overweight or obesity, diabetes, and hypertension in Bangladesh, 2004 to 2018

Background and objectives Bangladesh is experiencing a nutrition transition with an increase in the double burden of malnutrition and non-communicable diseases (NCDs). This study sought to: 1) examine trends and differences in underweight, overweight/obesity, hypertension and diabetes by gender, area of residence, and wealth in Bangladesh from 2004 to 2018, 2) assess what factors contributed to changes in these outcomes. Methods We used data from five rounds of the Bangladesh Demographic and Health Surveys (n = 76,758 women 15-49y and 10,900 men 18-95y in total). We calculated differences, slope index of inequality (SII) and concentration index (CIX) to examine trends over time and differences in outcomes by wealth and residence. We identified determinants and estimated drivers of changes in outcomes using regression-based decomposition. Results Between 2004 and 2018, underweight prevalence decreased in both women (33% to 12%) and men (26% to 18%), whereas overweight/obesity increased (17% to 49% in women and 21% to 34% in men). Hypertension also increased in both women (31% to 44%) and men (19% to 33%) while diabetes changed marginally (11% to 14%). In all years, underweight was concentrated in poorer and rural households while overweight/obesity, diabetes and hypertension were concentrated in wealthier and urban households. Wealth inequity decreased over time for underweight, changed little for overweight/obesity, and increased for hypertension and diabetes among men. Increases in wealth explained 35% to 50% of the reduction in underweight and 30% to 57% of the increase in overweight/obesity. Conclusion Our findings imply that double duty actions are required to sustain the decrease in undernutrition and slow the increase in overweight/obesity and NCDs across diverse socioeconomic sections of the population in Bangladesh.
B0−B¯0mixing at next-to-leading order

We compute the perturbative corrections to the HQET sum rules for the matrix element of the \Delta B=2 operator that determines the mass shift of $B^0$, $\bar{B}^0$ states. Technically, we obtain analytically the non-factorizable contributions at order $\alpha_s$ to the bag parameter that first appear at the three-loop level. Together with the known non-perturbative corrections due to vacuum condensates and $1/m_b$ corrections, the full next-to-leading order result is now available. We present a numerical value for the renormalization group invariant bag parameter that is phenomenologically relevant and discuss comparison with recent lattice determinations.
Expression variation of OGG1 and HPRT gene and DNA damage in arsenic exposed industrial workers

Arsenic exposure alters redox balance, induces DNA damage, and deregulates many genes. OGG1 gene involved in base repair mechanism, for excision of 8-oxoguanine (8-oxoG) from DNA formed as a result of accumulation of ROS in cell. HPRT gene encode transferase enzymes involved in purine recycling mechanism. The main focus of the study was to evaluate the expression variation in HPRT, OGG1 gene expression, and DNA damage of industrial workers. Blood samples of 300 occupational workers were collected from welding, brick kiln, furniture, pesticide, and paint industry (n = 60/industry) to evaluate the expression variation in HPRT, OGG1 gene expression, and DNA damage in blood cells by comet assay along with age and gender matched 300 control individuals. Blood arsenic content was higher (P<0.001) in an industrial group compared to the control. OGG1 and HPRT expression were (P<0.05) downregulated in exposed workers compared to controls. Spearman correlation analysis showed a significant positive correlation between HPRT vs OGG1 (P< 0.0001) in exposed workers compared to controls. Altered expression of both genes was observed between workers with <25years and >25years of age as well as between workers with <10years and >10year exposure. Reduced expression (P<0.05) of both genes and a high extent of DNA damage was evident in exposed smokers compared to respective non-smokers. DNA fragmentation was higher (P<0.05) in the furniture, welding and brick kiln group compared to control, and other industries. The present study suggests that altered expression of OGG1 and HPRT gene induce oxidative stress, showed a negative impact on the recycling of purines leading to DNA damage which increase the vulnerability of workers to carcinogenicity.
EVLA OBSERVATIONS CONSTRAIN THE ENVIRONMENT AND PROGENITOR SYSTEM OF Type Ia SUPERNOVA 2011fe

We report unique Expanded Very Large Array observations of SN 2011fe representing the most sensitive radio study of a Type Ia supernova to date. Our data place direct constraints on the density of the surrounding medium at radii ∼1015–1016 cm, implying an upper limit on the mass loss rate from the progenitor system of (assuming a wind speed of 100 km s−1) or expansion into a uniform medium with density nCSM ≲ 6 cm−3. Drawing from the observed properties of non-conservative mass transfer among accreting white dwarfs, we use these limits on the density of the immediate environs to exclude a phase space of possible progenitor systems for SN 2011fe. We rule out a symbiotic progenitor system and also a system characterized by high accretion rate onto the white dwarf that is expected to give rise to optically thick accretion winds. Assuming that a small fraction, 1%, of the mass accreted is lost from the progenitor system, we also eliminate much of the potential progenitor parameter space for white dwarfs hosting recurrent novae or undergoing stable nuclear burning. Therefore, we rule out much of the parameter space associated with popular single degenerate progenitor models for SN 2011fe, leaving a limited phase space largely inhabited by some double degenerate systems, as well as exotic single degenerates with a sufficient time delay between mass accretion and SN explosion.
Connecting the Sun and the solar wind: the self-consistent transition of heating mechanisms

We have performed a 2.5 dimensional magnetohydrodynamic simulation that resolves the propagation and dissipation of Alfven waves in the solar atmosphere. Alfvenic fluctuations are introduced on the bottom boundary of the extremely large simulation box that ranges from the photosphere to far above the solar wind acceleration region. Our model is ab initio in the sense that no corona and no wind are assumed initially.The numerical experiment reveals the quasi-steady solution that has the transition from the cool to the hot atmosphere and the emergence of the high speed wind. The global structure of the resulting hot wind solution fairly well agree with the coronal and the solar wind structure inferred from observations. The purpose of this study is to complement the previous paper by Matsumoto & Suzuki (2012) and describe the more detailed results and the analysis method. These results include the dynamics of the transition region and the more precisely measured heating rate in the atmosphere. Particularly, the spatial distribution of the heating rate helps us to interpret the actual heating mechanisms in the numerical simulation.Our estimation method of heating rate turned out to be a good measure for dissipation of Alfven waves and low beta fast waves.
Physical parameters of late M-type members of Chamaeleon I and TW Hydrae Association: dust settling, age dispersion and activity

Although mid-to-late type M dwarfs are the most common stars in our stellar neighborhood, our knowledge of these objects is still limited. Open questions include the evolution of their angular momentum, internal structures, dust settling in their atmospheres, age dispersion within populations. In addition, at young ages, late-type Ms have masses below the hydrogen burning limit and therefore are key objects in the debate on the brown dwarf mechanism of formation. In this work we determine and study in detail the physical parameters of two samples of young, late M-type sources belonging to either the Chamaeleon I Dark Cloud or the TW Hydrae Association and compare them with the results obtained in the literature for other young clusters and also for older, field, dwarfs. We used multi-wavelength photometry to construct and analyze SEDs to determine general properties of the photosphere and disk presence. We also used low resolution optical and near-infrared spectroscopy to study activity, accretion, gravity and effective temperature sensitive indicators. We propose a VO-based spectral index that is both temperature and age sensitive. We derived physical parameters using independent techniques confirming the already common feature/problem of the age/luminosity spread. In particular, we highlight two brown dwarfs showing very similar temperatures but clearly different surface gravity (explained invoking extreme early accretion). We also show how, despite large improvement in the dust treatment in theoretical models, there is still room for further progress in the simultaneous reproduction of the optical and near-infrared features of these cold young objects.
A simple version of resting‐state heart rate variability interpretation for patients with affective disorders: A four‐pattern perspective

Heart rate variability (HRV) is often considered as a biomarker reflecting well‐being, but the clinical meaning of short‐term resting‐state HRV is not sufficiently defined. We assume that combining several common HRV indices as “HRV patterns” and using the patterns for screening purposes are meaningful approaches. Resting‐state 5‐min HRV data of 424 subjects were analyzed. Four of the most commonly used HRV indices were considered: standard deviation of normal–to–normal RR intervals, low‐frequency power, high‐frequency power and the ratio of low‐frequency to high‐frequency power. According to these indices, four HRV patterns were defined: normal pattern, low HRV pattern, relatively high sympathetic pattern, and relatively high vagal pattern. The associations between the demographics, lifestyles, personality traits, psychological states, and HRV patterns were explored: the low HRV pattern was positively associated with age, body mass index, and depression; the relatively high sympathetic pattern was positively associated with age and negatively associated with exercise habit; and the relatively high vagal pattern was negatively associated with having a steady job and novelty seeking. The pattern perspective may provide a convenient and evidence‐based way to interpret resting‐state HRV for patients with affective disorders.
The Microstructure of Turbulent Flow

In 1941 a general theory of locally isotropic turbulence was proposed by Kolmogoroff which permitted the prediction of a number of laws of turbulent flow for large Reynolds numbers. The most important of these laws, the dependence of the mean square of the difference in velocities at two points on their distance and the dependence of the coefficient of turbulence diffusion on the scale of the phenomenon, were obtained by both Kolmogoroff and Obukhoff in the same year. At the present time these laws have been experimentally confirmed by direct measurements carried out in aerodynamic wind tunnels in the laboratory, in the atmosphere, and also on the ocean. In recent years in the Laboratory of Atmospheric Turbulence of the Geophysics Institute of the Soviet Academy of Sciences, a number of investigations have been conducted in which this theory was further developed. The results of several of these investigations are presented.
Optimized Informed Consent for Psychotherapy: Protocol for a Randomized Controlled Trial

Background Informed consent is a legal and ethical prerequisite for psychotherapy. However, in clinical practice, consistent strategies to obtain informed consent are scarce. Inconsistencies exist regarding the overall validity of informed consent for psychotherapy as well as the disclosure of potential mechanisms and negative effects, the latter posing a moral dilemma between patient autonomy and nonmaleficence. Objective This protocol describes a randomized controlled web-based trial aiming to investigate the efficacy of a one-session optimized informed consent consultation. Methods The optimized informed consent consultation was developed to provide information on the setting, efficacy, mechanisms, and negative effects via expectation management and shared decision-making techniques. A total of 122 participants with an indication for psychotherapy will be recruited. Participants will take part in a baseline assessment, including a structured clinical interview for Diagnostic and Statistical Manual of Mental Disorders-fifth edition (DSM-5) disorders. Eligible participants will be randomly assigned either to a control group receiving an information brochure about psychotherapy as treatment as usual (n=61) or to an intervention group receiving treatment as usual and the optimized informed consent consultation (n=61). Potential treatment effects will be measured after the treatment via interview and patient self-report and at 2 weeks and 3 months follow-up via web-based questionnaires. Treatment expectation is the primary outcome. Secondary outcomes include the capacity to consent, decisional conflict, autonomous treatment motivation, adherence intention, and side-effect expectations. Results This trial received a positive ethics vote by the local ethics committee of the Center for Psychosocial Medicine, University-Medical Center Hamburg-Eppendorf, Hamburg, Germany on April 1, 2021, and was prospectively registered on June 17, 2021. The first participant was enrolled in the study on August 5, 2021. We expect to complete data collection in December 2022. After data analysis within the first quarter of 2023, the results will be submitted for publication in peer-reviewed journals in summer 2023. Conclusions If effective, the optimized informed consent consultation might not only constitute an innovative clinical tool to meet the ethical and legal obligations of informed consent but also strengthen the contributing factors of psychotherapy outcome, while minimizing nocebo effects and fostering shared decision-making. Trial Registration PsychArchives; http://dx.doi. org/10.23668/psycharchives.4929 International Registered Report Identifier (IRRID) DERR1-10.2196/39843
Linear models of dissipation whose Q is almost frequency independent

Laboratory experiments and field observations indicate that tlie Q of many non ferromagnetic inorganic solids is almost frequency independent in the range 10' to 10~2 cps; although no single substance has been investigated over the entire frequency spectrum. One of the purposes of this investigation is to find the analytic expression of a linear dissipative mechanism whose Q is almost frequency independent over large frequency ranges. This will be obtained by introducing fractional derivatives in the stress strain relation. Since the aim of this research is to also contribute to elucidating the dissipating mechanism in the earth free modes, we shall treat the cases of dissipation in the free purely torsional modes of a shell and the purely radial vibration of a solid sphere. The theory is checked with the new values determined for the Q of the spheroidal free modes of the earth in the range between 10 and 5 minutes integrated with the Q of the Railegh waves in the range between 5 and 0.6 minutes. Another check of the theory is made with the experimental values of the Q of the longitudinal waves in an alluminimi rod, in the range between 10-5 and 10-3 seconds. In both clicks the theory represents the observed phenomena very satisfactory.
Synovial fibroblasts assume distinct functional identities and secrete R-spondin 2 in osteoarthritis

Objectives Synovium is acutely affected following joint trauma and contributes to post-traumatic osteoarthritis (PTOA) progression. Little is known about discrete cell types and molecular mechanisms in PTOA synovium. We aimed to describe synovial cell populations and their dynamics in PTOA, with a focus on fibroblasts. We also sought to define mechanisms of synovial Wnt/β-catenin signalling, given its emerging importance in arthritis. Methods We subjected mice to non-invasive anterior cruciate ligament rupture as a model of human joint injury. We performed single-cell RNA-sequencing to assess synovial cell populations, subjected Wnt-GFP reporter mice to joint injury to study Wnt-active cells, and performed intra-articular injections of the Wnt agonist R-spondin 2 (Rspo2) to assess whether gain of function induced pathologies characteristic of PTOA. Lastly, we used cultured fibroblasts, macrophages and chondrocytes to study how Rspo2 orchestrates crosstalk between joint cell types. Results We uncovered seven distinct functional subsets of synovial fibroblasts in healthy and injured synovium, and defined their temporal dynamics in early and established PTOA. Wnt/β-catenin signalling was overactive in PTOA synovium, and Rspo2 was strongly induced after injury and secreted exclusively by Prg4hi lining fibroblasts. Trajectory analyses predicted that Prg4hi lining fibroblasts arise from a pool of Dpp4+ mesenchymal progenitors in synovium, with SOX5 identified as a potential regulator of this emergence. We also showed that Rspo2 orchestrated pathological crosstalk between synovial fibroblasts, macrophages and chondrocytes. Conclusions Synovial fibroblasts assume distinct functional identities during PTOA in mice, and Prg4hi lining fibroblasts secrete Rspo2 that may drive pathological joint crosstalk after injury.
Health sector readiness for the prevention and control of non-communicable diseases: A multi-method qualitative assessment in Nepal

In Nepal, deaths attributable to NCDs have increased in recent years. Although NCDs constitute a major public health problem, how best to address this has not received much attention. The objective of this study was to assess the readiness of the Nepalese health sector for the prevention and control of NCDs and their risk factors. The study followed a multi-method qualitative approach, using a review of policy documents, focus group discussions (FGDs), and in-depth interviews (IDIs) conducted between August and December 2020. The policy review was performed across four policy categories. FGDs were undertaken with different cadres of health workers and IDIs with policy makers, program managers and service providers. We performed content analysis using the WHO health system building blocks framework as the main categories. Policy documents were concerned with the growing NCD burden, but neglect the control of risk factors. FGDs and IDIs reveal significant perceived weaknesses in each of the six building blocks. According to study participants, existing services were focused on curative rather than preventive interventions. Poor retention of all health workers in rural locations, and of skilled health workers in urban locations led to the health workers across all levels being overburdened. Inadequate quantity and quality of health commodities for NCDs emerged as an important logistics issue. Monitoring and reporting for NCDs and their risk factors was found to be largely absent. Program decisions regarding NCDs did not use the available evidence. The limited budget dedicated to NCDs is being allocated to curative services. The engagement of non-health sectors with the prevention and control of NCDs remained largely neglected. There is a need to redirect health sector priorities towards NCD risk factors, notably to promote healthy diets and physical activity and to limit tobacco and alcohol consumption, at policy as well as community levels.
Amphibian loss alters periphyton structure and invertebrate growth in montane streams

Abstract Amphibians are declining worldwide due to a combination of stressors such as climate change, invasive species, habitat loss, pollution and emergent diseases. Although their losses are likely to have important ecological consequences on the structure and functioning of freshwater ecosystems, this issue has been scarcely explored. We conducted an experiment in three montane streams—where primary production is the main source of energy and carbon—to assess the effects of amphibian disappearance (i.e. presence or absence of the common midwife toad Alytes obstetricans, a common species found in pools of these streams) on several aspects of ecosystem functioning and structure: periphyton biomass and chlorophyll a concentration, algal assemblage structure, and growth of macroinvertebrate grazers. We compared four types of experimental enclosures: (i) without macroinvertebrates or amphibians; (ii) with larvae of the caddisfly Allogamus laureatus; (iii) with A. obstetricans tadpoles; and (iv) with both A. laureatus larvae and A. obstetricans tadpoles. The absence of tadpoles increased periphyton biomass, but did not cause differences on inorganic sediment accrual. The algal assemblage had a higher diversity in the absence of tadpoles, and their characteristic taxa differed from the assemblages in presence of tadpoles. A. laureatus presented higher mass in presence of tadpoles; however, tadpole length was not affected by presence of macroinvertebrates. Our results suggest that presence of tadpoles is a driver of periphyton accrual and assemblage structure, acting as top‐down control and with key potential consequences on the functioning of montane stream ecosystems.