Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of OSPM against air quality measurements in Brazil – the case study of Fortaleza, Ceará

ABSTRACT The contribution of vehicle emissions to air pollution is considered a large environmental and health problem in big Brazilian cities caused, among other factors, by slow renewal of the old vehicle fleet. Brazilian studies usually only consider traffic-related issues in transportation analysis, with minor assessments of emissions and close to non-existent assessment of air quality. On this background, this research aimed to calibrate and evaluate the Operational Street Pollution Model (OSPM®) to Brazilian conditions by implementing Brazilian emission factors. The urban background concentrations were modeled with the Urban Background Model (UBM) as part of the air quality system (THOR–AirPAS). In this case, we used meteorological data from a ground meteorological station outside Fortaleza processed by meteorological pre-processor and regional background concentrations from the Integrated Forecast System (IFS) as input to UBM. New air quality measurements were collected in busy streets of the city of Fortaleza during the year of 2017. The study collected samples of daily NO2 and PM10 concentrations to evaluate OSPM daily estimations. In addition, a transportation travel demand model (TRANUS) has been calibrated to the case study area with observed traffic data collected, in order to provide Annual Average Daily Traffic (AADT) as inputs to OSPM®. Two sets of emission factors were evaluated. Official Brazilian emission factors were applied to OSPM®, as well as adjusted emission factors derived in the project based on calibration that were higher than the official emission factors. Data showed that concentrations are significantly influenced by meteorological factors (such as temperature, wind speeds, wind directions), and especially precipitation for PM10 concentrations. OSPM® simulated results showed concentration levels and patterns close to air quality measurements with default emission factors and calibrated emission for UBM but large underestimations if official emissions were used for both UBM and OSPM. Implications: Busy urban streets in Brazilian cities with intense flow of diesel vehicles (such as buses and trucks) can significantly increase air pollution, especially for NO2 and PM10. With OSPM calibrated and evaluated to Brazilian conditions, the model system can be used by authorities to assess the impact of policy measures, such as vehicle access restrictions in Low Emission Zones, in order to consider not only traffic related issues, but also air pollution due to mobile sources with outdated emission technologies.
Prescription profile in patients with SARS-CoV-2 infection hospitalised in Aragon, Spain

Introduction On 14 March 2020, a state of alarm was declared in Spain because of the pandemic of coronavirus disease (COVID-19). After 12 weeks from the beginning of the pandemic, the number of confirmed cases stoods at 5781 in Aragon: 46% hospitalised, 5% admitted to intensive care unit, and 15% died. The absence of controlled trials in SARS-CoV-2 infection and the fast progression of the disease has promoted the use of treatments with unproven potential benefit. The objective of this study is to define the prescription profile in patients with SARS-CoV-2 infection hospitalised in Aragon, Spain during the pandemic and its adaptation to the official recommendations. Patients and methods Descriptive retrospective study of the consumption and inpatient dispensation of drugs in a sample of COVID-19 infected inpatients (with positive PCR test result) admitted to hospitals of Aragon, between 1 March and 8 May 2020. Data were collected by an inpatient dispensation software program. Results 1482 positive COVID-19 patients were analysed: 54.9% male, median age 75 years (IQR 62–85); 12% were admitted to the intensive care unit. Median prescription: 13 active ingredients per patient (IQR 9–19). 73% (1093 patients) received hydroxychloroquine, lopinavir/ritonavir, or azithromycin, 81% as combination therapy. 4.3% (52) received other antivirals. 46% received corticosteroids (84% methylprednisolone, 8.7% dexamethasone) and 2.2% tocilizumab. Discussion At the time of the study period there was not enough quality evidence to issue a recommendation on any treatment. There are several clinical trials ongoing to clarify what is the best treatment for patient with SARS-CoV-2 infection.
Efficacy and safety of sofosbuvir/velpatasvir in a real‐world chronic hepatitis C genotype 3 cohort

Real‐world data on sofosbuvir/velpatasvir with and without ribavirin (SOF/VEL ± RBV), particularly among patients with genotype 3 (GT3) decompensated cirrhosis, prior treatment, coinfection, and hepatocellular carcinoma (HCC), are scarce. We aimed to assess the efficacy and safety of SOF/VEL ± RBV in a real‐world setting that included both community and incarcerated GT3 hepatitis C virus (HCV) patients.
Longitudinal associations of meaning in life and psychosocial adjustment to the COVID‐19 outbreak in China

Objective Literature suggests that ‘meaning in life’ may be a mental strength that enables individuals to function healthily and adaptively in the face of stress events. Therefore, this study aims to examine the longitudinal associations between meaning in life and psychosocial adjustment to the COVID‐19 outbreak among Chinese people. Methods A prospective design was adopted. 154 Chinese college students (Mean age = 20.41 ± 1.45 years) completed two waves of the assessment. Participants reported their meaning in life before the outbreak (Time 1) and their psychosocial adjustment 7 weeks later after the outbreak had occurred (Time 2). Results Participants’ meaning in life at Time 1 was positively related to life satisfaction and negatively related to depression, anxiety, stress, and negative emotions at Time 2. Additionally, levels of meaning in life at Time 1 were positively associated to COVID‐19‐related behavioural engagement – prosocial behaviour and information addiction at Time 2. Individuals’ perceptions of the outbreak and status of self‐quarantine did not moderate these relationships. Conclusion Findings suggest that individuals’ prior level of meaning in life may help them maintain a healthy psychosocial adjustment during disease outbreak, though cautions regarding the possibility to render an addiction to information about the outbreak are warranted.
The applicability of non-invasive methods for assessing liver fibrosis in hemodialysis patients with chronic hepatitis C

Background The accurate assessment of liver fibrosis among hemodialysis patients with chronic hepatitis C (CHC) is important for both treatment and for follow up strategies. Applying the non-invasive methods in general population with viral hepatitis have been successful but the applicability of the aminotransferase/platelet ratio index (APRI) or the fibrosis-4 index (FIB-4) in hemodialysis patients need further evaluation. Materials and methods We conducted a prospective, multi-center, uremic cohort to verify the applicability of APRI and FIB-4 in identifying liver fibrosis by reference with the standard transient elastography (TE) measures. Results There were 116 CHC cases with valid TE were enrolled in our analysis. 46 cases (39.6%) were classified as F1, 35 cases (30.2%) as F2, 11 cases (9.5%) as F3, and 24 cases (20.7%) as F4, respectively. The traditional APRI and FIB-4 criteria did not correctly identify liver fibrosis. The optimal cut-off value of APRI was 0.28 and of FIB-4 was 1.91 to best excluding liver cirrhosis with AUC of 76% and 77%, respectively. The subgroup analysis showed that female CHC hemodialysis patients had better diagnostic accuracy with 74.1% by APRI. And CHC hemodialysis patients without hypertension had better diagnostic accuracy with 78.6% by FIB-4. Conclusions This study confirmed the traditional category level of APRI and FIB-4 were unable to identify liver fibrosis of CHC hemodialysis patients. With the adjusted cut-off value, APRI and FIB-4 still showed suboptimal diagnostic accuracy. Our results suggest the necessary of TE measures for liver fibrosis in the CHC uremic population.
The Effects of ACA Medicaid Expansions on Health After 5 Years

We examine the Affordable Care Act Medicaid expansion effects on self-rated health status over 5 years. The study uses data from the Behavioral Risk Factor Surveillance System for 2011-2018 and a difference-in-differences design. There is improvement in health status on a 1 to 5 point scale from poor to excellent health among individuals below 100% of the federal poverty line by 0.031, 0.068, 0.031, 0.064, and 0.087 points in 2014, 2015, 2016, 2017, and 2018, respectively. Changes in 2015, 2017, and 2018 are statistically significant (p < .05), and the 2014 change is marginally significant. The difference between 2014 and 2018 effects is statistically significant (p < .05). In most years, we cannot distinguish changes in days not in good physical or mental health from no effect. Overall, there is only minimal evidence for effects intensifying over time, suggesting that health gains thus far have mostly occurred early on due to unmet needs among those previously uninsured.
Fungal Shaker-like channels beyond cellular K+ homeostasis: A role in ectomycorrhizal symbiosis between Hebeloma cylindrosporum and Pinus pinaster

Potassium (K+) acquisition, translocation and cellular homeostasis are mediated by various membrane transport systems in all organisms. We identified and described an ion channel in the ectomycorrhizal fungus Hebeloma cylindrosporum (HcSKC) that harbors features of animal voltage-dependent Shaker-like K+ channels, and investigated its role in both free-living hyphae and symbiotic conditions. RNAi lines affected in the expression of HcSKC were produced and used for in vitro mycorrhizal assays with the maritime pine as host plant, under standard or low K+ conditions. The adaptation of H. cylindrosporum to the downregulation of HcSKC was analyzed by qRT-PCR analyses for other K+-related transport proteins: the transporters HcTrk1, HcTrk2, and HcHAK, and the ion channels HcTOK1, HcTOK2.1, and HcTOK2.2. Downregulated HcSKC transformants displayed greater K+ contents at standard K+ only. In such conditions, plants inoculated with these transgenic lines were impaired in K+ nutrition. Taken together, these results support the hypothesis that the reduced expression of HcSKC modifies the pool of fungal K+ available for the plant and/or affects its symbiotic transfer to the roots. Our study reveals that the maintenance of K+ transport in H. cylindrosporum, through the regulation of HcSKC expression, is required for the K+ nutrition of the host plant.
Same Involvement, Different Reasons: How Personality Factors and Organizations Contribute to Heavy Work Investment

The academic literature has drawn a clear distinction between a positive form (i.e., work engagement) and a negative form (i.e., workaholism) of heavy work investment (HWI). Nevertheless, the different weight of individual and situational factors contributing to their development was not thoroughly explored. This study aims to investigate the role of individual variables (i.e., obsessive–compulsive traits, achievement orientation, perfectionism, and conscientiousness) and situational factors (i.e., job demands and overwork climate) regarding engagement and workaholism simultaneously. Hypotheses were tested using a sample of 523 Italian employees. Results of structural equation modeling revealed that overwork climate and job demands were conversely related to engagement and workaholism, with job demand reporting the strongest association with workaholism. Furthermore, fear of failure was the only individual factor showing a significant and opposite relationship with workaholism and engagement. In contrast, perfectionism was positively associated with both forms of HWI. These results shed light on the potential effectiveness of intervention strategies focused on the employees and organizations in preventing workaholism and promoting engagement.
Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence

Background: Infections of the root canal space involve polymicrobial biofilms and lead to chronic, low grade inflammatory responses arising from the seeding of microbes and by-products. Acute exacerbation and/or disseminating infections occur when established microbial communities undergo sudden changes in phenotypic behaviour. Methods: Within clinical endodontic infections, we assessedcategorical determinants comprising, and changing microbial composition of, chronic polymicrobial infections and their association with amoebae. After standardised assessment, primary or secondary infections underwent sampling and DNA processing, targeting bacteria, fungi and amoebae, including 16S high-throughput sequencing. After taxonomic assignment, community composition was correlated with clinical signs and symptoms. Diversity and abundance analyses were carried out in relation to the presence of non-bacterial amplicons. Results: Clinical specimens revealed two distinct community clusters, where specific changes correlated with clinical signs. An association between the compositions of microbiomes was found between these groups and the presence of Entamoeba gingivalis in 44% of cases. When amoebae were present in endodontic infections, we demonstrate changes in microbial community structure that mirror those observed in treatment-resistant or recurrent infections. Conclusions: Amoeba are present in endodontic infections at a high prevalence, and may promote increased virulence by enrichment for phagocytosis-resistant bacteria.
An Improved Passive CR-39-Based Direct 222Rn/220Rn Progeny Detector

An improved passive CR-39-based direct 222Rn/220Rn progeny detector with 3 detection channels was designed and tested in this study to measure and calculate equilibrium equivalent concentration (EEC) of both 222Rn and 220Rn without the equilibrium factor. A theoretical model was established to calculate the EEC with optimization. Subsequently, an exposure experiment was carried out to test the performance of this detector, and we compared the chamber experiment and the theoretical model by estimating and measuring various parameters. The deposition flux of progeny derived from the prediction agreed well with the value measured in the exposure chamber. The energy-weighted net track density (NTD) measured by this detector is much more reliable to reflect the linear relation between NTD and time-integrated EEC. Since the detector is sensitive to the exposure environmental condition, it is recommended to apply the detector to measure the EEC after its calibration in a typical indoor environment.
Free water: A marker of age-related modifications of the cingulum white matter and its association with cognitive decline

Diffusion MRI is extensively used to investigate changes in white matter microstructure. However, diffusion measures within white matter tissue can be affected by partial volume effects due to cerebrospinal fluid and white matter hyperintensities, especially in the aging brain. In previous aging studies, the cingulum bundle that plays a central role in the architecture of the brain networks supporting cognitive functions has been associated with cognitive deficits. However, most of these studies did not consider the partial volume effects on diffusion measures. The aim of this study was to evaluate the effect of free water elimination on diffusion measures of the cingulum in a group of 68 healthy elderly individuals. We first determined the effect of free water elimination on conventional DTI measures and then examined the effect of free water elimination on verbal fluency performance over 12 years. The cingulum bundle was reconstructed with a tractography pipeline including a white matter hyperintensities mask to limit the negative impact of hyperintensities on fiber tracking algorithms. We observed that free water elimination increased the ability of conventional DTI measures to detect associations between tissue diffusion measures of the cingulum and changes in verbal fluency in older individuals. Moreover, free water content and mean diffusivity measured along the cingulum were independently associated with changes in verbal fluency. This suggests that both tissue modifications and an increase in interstitial isotropic water would contribute to cognitive decline. These observations reinforce the importance of using free water elimination when studying brain aging and indicate that free water itself could be a relevant marker for age-related cingulum white matter modifications and cognitive decline.
Challenges in estimating HIV prevalence trends and geographical variation in HIV prevalence using antenatal data: Insights from mathematical modelling

Background HIV prevalence data among pregnant women have been critical to estimating HIV trends and geographical patterns of HIV in many African countries. Although antenatal HIV prevalence data are known to be biased representations of HIV prevalence in the general population, mathematical models have made various adjustments to control for known sources of bias, including the effect of HIV on fertility, the age profile of pregnant women and sexual experience. Methods and findings We assessed whether assumptions about antenatal bias affect conclusions about trends and geographical variation in HIV prevalence, using simulated datasets generated by an agent-based model of HIV and fertility in South Africa. Results suggest that even when controlling for age and other previously-considered sources of bias, antenatal bias in South Africa has not been constant over time, and trends in bias differ substantially by age. Differences in the average duration of infection explain much of this variation. We propose an HIV duration-adjusted measure of antenatal bias that is more stable, which yields higher estimates of HIV incidence in recent years and at older ages. Simpler measures of antenatal bias, which are not age-adjusted, yield estimates of HIV prevalence and incidence that are too high in the early stages of the HIV epidemic, and that are less precise. Antenatal bias in South Africa is substantially greater in urban areas than in rural areas. Conclusions Age-standardized approaches to defining antenatal bias are likely to improve precision in model-based estimates, and further recency adjustments increase estimates of HIV incidence in recent years and at older ages. Incompletely adjusting for changing antenatal bias may explain why previous model estimates overstated the early HIV burden in South Africa. New assays to estimate the fraction of HIV-positive pregnant women who are recently infected could play an important role in better estimating antenatal bias.
A Sardinian founder mutation in glycoprotein Ib platelet subunit beta (GP1BB) that impacts thrombocytopenia

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Strategy for high-accuracy-and-precision retrieval of atmospheric methane from the mid-infrared FTIR network

Abstract. We present a strategy (MIR-GBM v1.0) for the retrieval of column-averaged dry-air mole fractions of methane (XCH4) with a precision MIR-GBM v1.0 is using HITRAN 2000 (including the 2001 update release) and 3 spectral micro windows (2613.70–2615.40 cm−1, 2835.50–2835.80 cm−1, 2921.00–2921.60 cm−1). A first-order Tikhonov constraint is applied to the state vector given in units of per cent of volume mixing ratio. It is tuned to achieve minimum diurnal variation without damping seasonality. Final quality selection of the retrievals uses a threshold for the goodness of fit (χ2 MIR-GBM v1.0 is the optimum of 24 tested retrieval strategies (8 different spectral micro-window selections, 3 spectroscopic line lists: HITRAN 2000, 2004, 2008). Dominant errors of the non-optimum retrieval strategies are systematic HDO/H2O-CH4 interference errors leading to a seasonal bias up to ≈5%. Therefore interference errors have been quantified at 3 test sites covering clear-sky integrated water vapor levels representative for all NDACC sites (Wollongong maximum = 44.9 mm, Garmisch mean = 14.9 mm, Zugspitze minimum = 0.2 mm). The same quality ranking of the 24 strategies was found for all 3 test sites with one optimum, i.e. MIR-GBM v1.0. Seasonality of XCH4 above the Zugspitze (47° N) shows a minus-sine shape with a minimum in March/April, a maximum in September, and an amplitude of 16.2 ± 2.9 ppb (0.94 ± 0.17%). This agrees well with the WFM-DOAS v2.0 scientific XCH4 retrieval product. A conclusion from this paper is that improved spectroscopic parameters for CH4, HDO, and H2O in the 2613–2922 cm−1 spectral domain are urgently needed. If such become available with sufficient accuracy, at least two more spectral micro windows could be utilized leading to another improvement in precision. The absolute inter-calibration of NDACC MIR-GBM v1.0 XCH4 to TCCON data is subject of ongoing work.
A Prototype QSP Model of the Immune Response to SARS‐CoV‐2 for Community Development

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic requires the rapid development of efficacious treatments for patients with life‐threatening coronavirus disease 2019 (COVID‐19). Quantitative systems pharmacology (QSP) models are mathematical representations of pathophysiology for simulating and predicting the effects of existing or putative therapies. The application of model‐based approaches, including QSP, have accelerated the development of some novel therapeutics. Nevertheless, the development of disease‐scale mechanistic models can be a slow process, often taking years to be validated and considered mature. Furthermore, emerging data may make any QSP model quickly obsolete. We present a prototype QSP model to facilitate further development by the scientific community. The model accounts for the interactions between viral dynamics, the major host immune response mediators and tissue damage and regeneration. The immune response is determined by viral activation of innate and adaptive immune processes that regulate viral clearance and cell damage. The prototype model captures two physiologically relevant outcomes following infection: a “healthy” immune response that appropriately defends against the virus, and an uncontrolled alveolar inflammatory response that is characteristic of acute respiratory distress syndrome. We aim to significantly shorten the typical QSP model development and validation timeline by encouraging community use, testing, and refinement of this prototype model. It is our expectation that the model will be further advanced in an open science approach (i.e., by multiple contributions toward a validated quantitative platform in an open forum), with the ultimate goal of informing and accelerating the development of safe and effective treatment options for patients.