Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

Malaysia had 10,219 confirmed cases of COVID-19 as of September 20, 2020. About 33% were associated with a Tablighi Jamaat religious mass gathering held in Kuala Lumpur between February 27 and March 3, 2020, which drove community transmission during Malaysia’s second wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to better understand the molecular epidemiology and spread. We obtained 58 SARS-CoV-2 whole genome sequences from patients in Kuala Lumpur and performed phylogenetic analyses on these and a further 57 Malaysian sequences available in the GISAID database. Nine different SARS-CoV-2 lineages (A, B, B.1, B.1.1, B.1.1.1, B.1.36, B.2, B.3 and B.6) were detected in Malaysia. The B.6 lineage was first reported a week after the Tablighi mass gathering and became predominant (65.2%) despite being relatively rare (1.4%) globally. Direct epidemiological links between lineage B.6 viruses and the mass gathering were identified. Increases in reported total cases, Tablighi-associated cases, and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly travel-associated and showed limited onward transmission. There were also temporally correlated increases in B.6 sequences in other Southeast Asian countries, India and Australia, linked to participants returning from this event. Over 95% of global B.6 sequences originated from Asia Pacific. We also report a nsp3-C6310A substitution found in 47.3% of global B.6 sequences which was associated with reduced sensitivity using a commercial diagnostic real-time PCR assay. Lineage B.6 became the predominant cause of community transmission in Malaysia after likely introduction during a religious mass gathering. This event also contributed to spikes of lineage B.6 in other countries in the Asia-Pacific. Mass gatherings can be significant causes of local and global spread of COVID-19. Shared genomic surveillance can be used to identify SARS-CoV-2 transmission chains to aid prevention and control, and to monitor diagnostic molecular assays. Clinical Trial Registration: COVID-19 paper.
Reference Values for Handgrip Strength in the Basque Country Elderly Population

Simple Summary Functional impairment is a growing global problem that increases with age and acute hospitalisations. Handgrip strength (HGS) is one of the tests used as a predictor of low skeletal muscle strength in the diagnosis of weakness. The aim of this study is to provide reference values of HGS in adults and older adults in the Basque Country by identifying cut-off points to measure weakness and compare the values with other populations. A health-promoting programme seems to be effective in obtaining better values as age increases with respect to the general population in the HGS test, delaying and even avoiding reaching the cut-off values for detecting weakness as a criterion for frailty. Despite the current findings available to health professionals for more effective detection of frailty, many of them have not been yet translated into clinical practice. Determining HGS values by population will allow to obtain clinically fast and effective cut-off values to detect weakness and probable risk in an ageing population. Abstract Strength training is currently the most recommended primary therapeutic strategy to prevent and reverse the decline of muscle mass, strength, and functional deterioration associated with age. The aim is to provide reference values of handgrip strength (HGS) in the Basque Country population and compare the values with other populations. A total of 1869 subjects from the health-promoting programme for adults and older adults run by the Bilbao City Council were assessed using HGS with a digital dynamometer and anthropometric data measured by Tanita to obtain the mean values according to age distribution. From the 1869 subjects, 87.5% were women and 12.5% men. The HGS was higher among men than women, 32.4 ± 6.6 versus 20.1 ± 4.7 kg, respectively, p < 0.001 at all ages. Weak HGS cut-off points by age groups ranged from 31.0 to 23.8 and from 18.9 to 12.4 in men and women, respectively. The sample data were compared (d, t, and α) with those of other populations in all age groups (group > 60 years at 95% df, p < 0.05). A health-promoting programme appears to be effective in the general population in obtaining better values in the HGS test as age increases.
Differences in Memory, Perceptions, and Preferences of Multimedia Consumer Medication Information: Experimental Performance and Self-Report Study

Background Electronic health resources are becoming prevalent. However, consumer medication information (CMI) is still predominantly text based. Incorporating multimedia into CMI (eg, images, narration) may improve consumers’ memory of the information as well as their perceptions and preferences of these materials. Objective This study examined whether adding images and narration to CMI impacted patients’ (1) memory, (2) perceptions of comprehensibility, utility, or design quality, and (3) overall preferences. Methods We presented 36 participants with CMI in 3 formats: (1) text, (2) text + images, and (3) narration + images, and subsequently asked them to recall information. After seeing all 3 CMI formats, participants rated the formats in terms of comprehensibility, utility, and design quality, and ranked them from most to least favorite. Results Interestingly, no significant differences in memory were observed (F2,70=0.1, P=0.901). Thus, this study did not find evidence to support multimedia or modality principles in the context of CMI. Despite the absence of effects on memory, the CMI format significantly impacted perceptions of the materials. Specifically, participants rated the text + images format highest in terms of comprehensibility (χ22=26.5, P<.001) and design quality (χ22=35.69, P<.001). Although the omnibus test suggested a difference in utility ratings as well (χ22=8.21, P=.016), no significant differences were found after correcting for multiple comparisons. Consistent with perception findings, the preference ranks yielded a significant difference (χ22=26.00, P<.001), whereby participants preferred the text + images format overall. Indeed, 75% (27/36) of participants chose the text + images format as their most favorite. Thus, although there were no objective memory differences between the formats, we observed subjective differences in comprehensibility, design quality, and overall preferences. Conclusions This study revealed that although multimedia did not appear to influence memory of CMI, it did impact participants’ opinions about the materials. The lack of observed differences in memory may have been due to ceiling effects, memory rather than understanding as an index of learning, the fragmented nature of the information in CMI itself, or the size or characteristics of the sample (ie, young, educated subjects with adequate health literacy skills). The differences in the subjective (ie, perceptions and preferences) and objective (ie, memory) results highlight the value of using both types of measures. Moreover, findings from this study could be used to inform future research on how CMI could be designed to better suit the preferences of consumers and potentially increase the likelihood that CMI is used. Additional research is warranted to explore whether multimedia impacts memory of CMI under different conditions (eg, older participants, subjects with lower levels of health literacy, more difficult stimuli, or extended time for decay).
Effect of Hydrophobic Treatments on Improving the Salt Frost Resistance of Concrete

Hydrophobic treatment is an important method to improve the waterproof properties of concrete. To evaluate the effectiveness of hydrophobic treatments on improving the salt frost resistance of concrete, two representative commercial ordinary water repellent agents of silane and organosilicone emulsion were selected, and concrete specimens with three water/cement ratios were fabricated. After the application of repellent agents on concrete surfaces, accelerated saline (5% MgCl2) freeze-thaw cycles were conducted on the specimens. The mass losses and relative dynamic modulus of elasticity (RDME) of concrete were tested periodically. The contact angles and water absorption ratios of concrete with and without hydrophobic treatments were also tested. Results showed that the repellent agents could substantially enhance the hydrophobicity of concrete and greatly reduce its water absorption. Different repellent agents exerted diverse improvements on concrete hydrophobicity. Meanwhile, the repellent agents could improve concrete resistance against salt scaling and RDME losses to a certain degree, and concrete with strong hydrophobicity showed relatively high salt frost resistance. However, the ordinary water repellent agents cannot achieve the same enhancement on salt frost resistance of concrete as that on the water hydrophobicity of concrete. With saline freezing and thawing cycles, the hydrophobic layer formed by the repellent agents on superficial concrete was destroyed gradually. As a result, the salt frost resistance of concrete from the hydrophobic treatments was ultimately lost.
Expression and Signaling of β-Adrenoceptor Subtypes in the Diabetic Heart

Diabetes is a chronic, endocrine disorder that effects millions of people worldwide. Cardiovascular complications are the major cause of diabetes-related morbidity and mortality. Cardiac β1- and β2-adrenoceptor (AR) stimulation mediates positive inotropy and chronotropy, whereas β3-AR mediates negative inotropic effect. Changes in β-AR responsiveness are thought to be an important factor that contributes to the diabetic cardiac dysfunction. Diabetes related changes in β-AR expression, signaling, and β-AR mediated cardiac function have been studied by several investigators for many years. In the present review, we have screened PubMed database to obtain relevant articles on this topic. Our search has ended up with wide range of different findings about the effect of diabetes on β-AR mediated changes both in molecular and functional level. Considering these inconsistent findings, the effect of diabetes on cardiac β-AR still remains to be clarified.
Hydrogen Peroxide Emission and Fate Indoors during Non-bleach Cleaning: A Chamber and Modeling Study.

Activities such as household cleaning can greatly alter the composition of air in indoor environments. We continuously monitored hydrogen peroxide (H2O2) from household non-bleach surface cleaning in a chamber designed to simulate a residential room. Mixing ratios of up to 610 ppbv gaseous H2O2 were observed following cleaning, orders of magnitude higher than background levels (sub-ppbv). Gaseous H2O2 levels decreased rapidly and irreversibly, with removal rate constants (kH2O2) 17-73 times larger than air change rate (ACR). Increasing the surface-area-to-volume ratio within the room caused peak H2O2 mixing ratios to decrease and kH2O2 to increase, suggesting that surface uptake dominated H2O2 loss. Volatile organic compound (VOC) levels increased rapidly after cleaning and then decreased with removal rate constants 1.2-7.2 times larger than ACR, indicating loss due to surface partitioning and/or chemical reactions. We predicted photochemical radical production rates and steady-state concentrations in the simulated room using a detailed chemical model for indoor air (the INDCM). Model results suggest that, following cleaning, H2O2 photolysis increased OH concentrations by 10-40% to 9.7 × 105 molec cm-3 and hydroperoxy radical (HO2) concentrations by 50-70% to 2.3 × 107 molec cm-3 depending on the cleaning method and lighting conditions.
Faraday Rotation of Dy2O3, CeF3 and Y3Fe5O12 at the Mid-Infrared Wavelengths

The relatively narrow choice of magneto-active materials that could be used to construct Faraday devices (such as rotators or isolators) for the mid-infrared wavelengths arguably represents a pressing issue that is currently limiting the development of the mid-infrared lasers. Furthermore, the knowledge of the magneto-optical properties of the yet-reported mid-infrared magneto-active materials is usually restricted to a single wavelength only. To address this issue, we have dedicated this work to a comprehensive investigation of the magneto-optical properties of both the emerging (Dy2O3 ceramics and CeF3 crystal) and established (Y3Fe5O12 crystal) mid-infrared magneto-active materials. A broadband radiation source was used in a combination with an advanced polarization-stepping method, enabling an in-depth analysis of the wavelength dependence of the investigated materials’ Faraday rotation. We were able to derive approximate models for the examined dependence, which, as we believe, may be conveniently used for designing the needed mid-infrared Faraday devices for lasers with the emission wavelengths in the 2-μm spectral region. In the case of Y3Fe5O12 crystal, the derived model may be used as a rough approximation of the material’s saturated Faraday rotation even beyond the 2-μm wavelengths.
Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage

Acinetobacter baumannii isolate ATCC 19606 was recovered in the US prior to 1948. It has been used as a reference and model organism in many studies involving antibiotic resistance and pathogenesis of A. baumannii, while, until recently, a complete genome of this strain was not available. Here, we present an analysis of the complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina) and long-read sequencing (MinION), and show it contains two small cryptic plasmids and a novel complete prophage of size 41.2 kb. We also characterised several regions of the ATCC 19606 genome, leading to the identification of a novel cadmium/mercury transposon, which was named Tn6551. ATCC 19606 is an antibiotic-sensitive strain, but a comparative analysis of all publicly available ST52 strains predicts a resistance to modern antibiotics by the accumulation of antibiotic-resistance genes via plasmids in recent isolates that belong to this sequence type.
High MERS-CoV seropositivity associated with camel herd profile, husbandry practices and household socio-demographic characteristics in Northern Kenya

Abstract Despite high exposure to Middle East respiratory syndrome coronavirus (MERS-CoV), the predictors for seropositivity in the context of husbandry practices for camels in Eastern Africa are not well understood. We conducted a cross-sectional survey to describe the camel herd profile and determine the factors associated with MERS-CoV seropositivity in Northern Kenya. We enrolled 29 camel-owning households and administered questionnaires to collect herd and household data. Serum samples collected from 493 randomly selected camels were tested for anti-MERS-CoV antibodies using a microneutralisation assay, and regression analysis used to correlate herd and household characteristics with camel seropositivity. Households reared camels (median = 23 camels and IQR 16–56), and at least one other livestock species in two distinct herds; a home herd kept near homesteads, and a range/fora herd that resided far from the homestead. The overall MERS-CoV IgG seropositivity was 76.3%, with no statistically significant difference between home and fora herds. Significant predictors for seropositivity (P ⩽ 0.05) included camels 6–10 years old (aOR 2.3, 95% CI 1.0–5.2), herds with ⩾25 camels (aOR 2.0, 95% CI 1.2–3.4) and camels from Gabra community (aOR 2.3, 95% CI 1.2–4.2). These results suggest high levels of virus transmission among camels, with potential for human infection.
TLR-9 agonist and CD40-targeting vaccination induces HIV-1 envelope-specific B cells with a diversified immunoglobulin repertoire in humanized mice

The development of HIV-1 vaccines is challenged by the lack of relevant models to accurately induce human B- and T-cell responses in lymphoid organs. In humanized mice reconstituted with human hematopoietic stem cells (hu-mice), human B cell-development and function are impaired and cells fail to efficiently transition from IgM B cells to IgG B cells. Here, we found that CD40-targeted vaccination combined with CpG-B adjuvant overcomes the usual defect of human B-cell switch and maturation in hu-mice. We further dissected hu-B cell responses directed against the HIV-1 Env protein elicited by targeting Env gp140 clade C to the CD40 receptor of antigen-presenting cells. The anti-CD40.Env gp140 vaccine was injected with CpG-B in a homologous prime/boost regimen or as a boost of a NYVAC-KC pox vector encoding Env gp140 clade C. Both regimens elicited Env-specific IgG-switched memory hu-B cells at a greater magnitude in hu-mice primed with NYVAC-KC. Single-cell RNA-seq analysis showed gp140-specific hu-B cells to express polyclonal IgG1 and IgG3 isotypes and a broad Ig VH/VL repertoire, with predominant VH3 family gene usage. These cells exhibited a higher rate of somatic hypermutation than the non-specific IgG+ hu-B-cell counterpart. Both vaccine regimens induced splenic GC-like structures containing hu-B and hu-Tfh-like cells expressing PD-1 and BCL-6. We confirmed in this model that circulating ICOS+ memory hu-Tfh cells correlated with the magnitude of gp140-specific B-cell responses. Finally, the NYVAC-KC heterologous prime led to a more diverse clonal expansion of specific hu-B cells. Thus, this study shows that CD40-targeted vaccination induces human IgG production in hu-mice and provides insights for the development of a CD40-targeting vaccine to prevent HIV-1 infection in humans.
Fiscal Expenditures on Science and Technology and Environmental Pollution: Evidence from China

Studying the driving factors of environmental pollution is of great importance for China. Previous literature mainly focused on the cause of national aggregate emission changes. However, research about the effect of fiscal expenditures on science and technology (FESTs) on environmental pollution is rare. Considering the large gap among cities in China, it is necessary to investigate whether and how FESTs affect environmental pollution among cities. We adopted three kinds of typical environmental pollutants including sulfur dioxide (SO2) emissions, wastewater emission, and atmospheric particulate matter less than 2.5 micrometers in diameter (PM2.5). Using the data of 260 prefecture-level cities over ten years in China, we found that FESTs play a significantly positive role in reducing sulfur dioxide (SO2) emissions and PM2.5 concentrations, but fail to alleviate wastewater emissions. Specifically, for every 1% increase in FESTs, SO2 emissions were reduced by 5.317% and PM2.5 concentrations were reduced by 5.329%. Furthermore, we found that FESTs reduced environmental pollution by impeding fixed asset investments and by promoting research and development activities (R&D). Moreover, the impacts of FESTs on environmental pollution varied across regions and sub-periods. Our results are robust to a series of additional checks, including alternative econometric specifications, generalized method of moments (GMM) analysis and overcoming potential endogeneity with an instrumental variable. Our findings confirm that government efforts can be effective on pollution control in China. Hence, all governments should pay more attention to FESTs for sustainable development and environmental quality improvements.
Impact of COVID-19 Pandemic on the Overall Diagnostic and Therapeutic Process for Patients of Emergency Department and Those with Acute Cerebrovascular Disease

(1) Background: During a pandemic, patients and processes in the emergency department (ED) change. These circumstances affect the length of stay (LOS) or degree of crowding in the ED. The processes for patients with acute critical illness, such as cerebrovascular disease (CVD), can be also delayed. Using the process mining (PM) method, this study aimed to evaluate LOS, ED processes for CVD, and delayed processes during the coronavirus disease 2019 (COVID-19) pandemic. (2) Methods: Data were collected from the Clinical Data Warehouse of a medical center. Phase 1 included patients who visited the ED before the COVID-19 outbreak. In Phase 2, post-COVID-19 ED patients were divided into the COVID-19 tested group (CTG) and COVID-19 not tested group (CNTG) according to whether polymerase chain reaction test was performed. We analyzed patients’ ED processes before and after COVID-19 using the PM method. We analyzed patients with acute CVD separately to determine whether the process and LOS of patients with acute critical illness were changed or delayed. (3) Results: After the COVID-19 outbreak, the overall LOS was delayed and all processes in CTG patients were delayed. Registration to triage and triage were delayed in both CTG and CNTG patients. The brain imaging process for CTG patients with acute CVD was also delayed. (4) Conclusion: After a pandemic, some processes were changed, new processes were developed, and processes for patients with acute CVD who needed proper time management were not exempted.
Development of a novel magnetite–chitosan composite for the removal of fluoride from drinking water: adsorption modeling and optimization

Magnetic nanoparticles (MNPs) have recently been adopted by researchers in the field of adsorption/biosorption for separation of pollutants from aqueous solutions. In this paper, chitosan was impregnated with magnetite nanoparticles through a chemical co-precipitation method to fabricate hybrid adsorbents of Fe3O4–chitosan. The physicochemical and structural properties of the adsorbent were characterized, and then the performance of the adsorbent was evaluated for fluoride removal from water. The operational factors affecting the adsorption process, including pH, contact time, adsorbent dosage, initial fluoride concentration, and temperature, were studied. Various isotherm and kinetic models were also used to evaluate the fit of the experimental data with the modeled results. The equilibrium data were well described by the Freundlich model. The kinetics of the adsorption process followed the pseudo-second-order model. Recycling results suggested that the Fe3O4–chitosan particles maintain a great reusability potential for five consecutive cycles. Findings also showed that the Fe3O4–chitosan can be easily regenerated via acid treatment. The results of the present work highlighted the potential of using the Fe3O4–chitosan magnetic composite for the removal of fluoride from water. In conclusion, Fe3O4–chitosan can be considered as an appropriate adsorbent for fluoride removal from water, because it can be separated both quickly and easily, it has high efficiency, and it does not lead to secondary pollution.