Miracle-dz/UniFAR-FTUs huggingface dataset:
Organization of Sodium Dodecyl Sulfate at the Graphite−Solution Interface

The aggregated structure of sodium dodecyl sulfate (SDS) adsorbed to the graphite−solution interface has been determined. Atomic force microscopy reveals that SDS adsorbs in periodic structures when the solution concentration is in the range 2.8−81 mM. Using previously obtained adsorption isotherms, we deduce that these structures are hemicylindrical, but we are not able to determine their length. The long axes of the hemicylinders lie parallel in grains which typically extend over (500 nm)2 to (1000 nm)2, but the grain size can be reduced by adsorption of other species from solution. Two basic types of grain boundaries have been identified: broad boundaries, where the periodicity of both grains continue into the boundary for several periods, and narrow boundaries, where one or both of the hemicylindrical arrays terminate within a short distance. The period within each grain decreases when the concentration of SDS or the concentration of added NaCl is increased and approaches the diameter of bulk micelle.
Monitoring of Lignin and Hemicelluloses in Spent Cooking Liquor during Kraft Delignification

Summary A direct and rapid method for determining the average molecular weight (MW) and content of lignin and hemicelluloses in spent cooking liquor by high performance size-exclusion chromatography (HPSEC) using a cartridge glass column and 2.5 mM NaOH as an eluent was developed. A Uv290 detector in line with a RI detector was applied to characterise lignin and hemicelluloses, respectively, from liquor during the kraft cooking of grey and black alder wood. During the main delignification stage, the concentration of high-MW wood components in liquor changed through the maximum. The MW values of hemicelluloses in the liquor decreased to DPn = 30 ± 5 and DPw = 55 ± 5. The M̄ n and M̄ w of lignin in spent kraft cooking liquor during the main and final delignification stages did not exceed 3000 and 5000, respectively.
Gold nanoparticles for naked-eye DNA detection: smart designs for sensitive assays

Methods allowing colorimetric (instrument-free) detection of biomarkers at clinically relevant concentrations are highly desirable for point-of-care diagnostics. Gold nanoparticles (AuNPs) can fulfill such a scope in several ways. This review describes different schemes for AuNPs-based colorimetric detection of nucleic acid biomarkers, with a particular focus on factors, sometimes overlooked, which can help in the design of sensitive assays. These include AuNPs multivalency, ligand density on the surface of functionalized particles, and proper combination of AuNPs and enzymes, these latter being used for both signal amplification and PCR-free target amplification.
Influence of odd and even number of Stone–Wales defects on the fracture behaviour of an armchair single-walled carbon nanotube under axial and torsional strain

Using Brenner's bond-order potential to represent the interaction of the in-plane C–C bond, an armchair (8,8) single-walled carbon nanotube is investigated by molecular dynamics simulation under axial loading and twist, both for perfect and imperfect lattices introducing an increasing number of Stone–Wales (SW) defects. The Young modulus, shear modulus, tensile strength, shear strength, ductility, stiffness and toughness are computed. All the mechanical characteristics are found to change appreciably by the inclusion of SW defects. Two distinct patterns of fracture mode are observed with odd and even numbers of defects. A clear evidence of the defect–defect interaction is observed when more than one defect is included.
Increased Risk of Autopsy-Proven Pneumonia with Sex, Season and Neurodegenerative Disease

There has been a markedly renewed interest in factors associated with pneumonia, a leading cause of death worldwide, due to its frequent concurrence with pandemics of influenza and Covid-19 disease. Reported predisposing factors to both bacterial pneumonia and pandemic viral lower respiratory infections are wintertime occurrence, older age, obesity, pre-existing cardiopulmonary conditions and diabetes. Also implicated are age-related neurodegenerative diseases that cause parkinsonism and dementia. We investigated the prevalence of autopsy-proven pneumonia in the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND), a longitudinal clinicopathological study, between the years 2006 and 2019 and before the beginning of the Covid-19 pandemic. Of 691 subjects dying at advanced ages (mean 83.4), pneumonia was diagnosed postmortem in 343 (49.6%). There were 185 subjects without dementia or parkinsonism while clinicopathological diagnoses for the other subjects included 319 with Alzheimer disease dementia, 127 with idiopathic Parkinson disease, 72 with dementia with Lewy bodies, 49 with progressive supranuclear palsy and 78 with vascular dementia. Subjects with one or more of these neurodegenerative diseases all had higher pneumonia rates, ranging between 50 and 61%, as compared to those without dementia or parkinsonism (40%). In multivariable logistic regression models, male sex and a non-summer death both had independent contributions (ORs of 1.67 and 1.53) towards the presence of pneumonia at autopsy while the absence of parkinsonism or dementia was a significant negative predictor of pneumonia (OR 0.54). Male sex, dementia and parkinsonism may also be risk factors for Covid-19 pneumonia. The apolipoprotein E4 allele, as well as obesity, chronic obstructive pulmonary disease, diabetes, hypertension, congestive heart failure, cardiomegaly and cigarette smoking history, were not significantly associated with pneumonia, in contradistinction to what has been reported for Covid-19 disease.
Folate (MTHFR C677T and MTRR A66G) gene polymorphisms and risk of prostate cancer: a case-control study with an updated meta-analysis

Introduction: Methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR) are the key enzymes of the folate pathway, which involved in the DNA methylation. DNA methylation may affect the stability and integrity of DNA, that supposed to play a pivotal role in carcinogenesis. So, we aimed to investigate the association of MTHFR C677T and MTRR A66G gene polymorphisms with susceptibility to prostate cancer in North Indian population. We also performed meta-analyses of published literatures on these polymorphisms to evaluate their association with prostate cancer. Methods: We genotyped MTHFR C677T and MTRR A66G gene polymorphisms in 147 prostate cancer cases and 147 healthy controls using PCR-RFLP methods. Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated for risk estimation. For meta-analysis different databases were searched and all statistical analysis were performed using Open Meta-Analyst software. Results: The present case control study revealed that the T allele (OR= 1.67; 95% CI: 0.99-2.84, p= 0.05), CT genotype (OR= 1.92; 95% CI: 1.06-3.48, p= 0.02), and dominant (TT+CT) model (OR= 1.85; 95% CI: 1.05-3.30, p= 0.03) of MTHFR C677T gene polymorphism and G allele (OR= 1.92; 95% CI: 1.35- 2.73, p= 0.0002) of MTRR A66G gene polymorphism were significantly associated with prostate cancer susceptibility. Meta-analyses of MTHFR C677T and MTRR A66G gene polymorphisms showed no significant association between these polymorphisms and prostate cancer risk in overall or in subgroup meta-analysis stratified by ethnicity. Conclusion: MTHFR C677T and MTRR A66G gene polymorphisms seem to play a significant role in prostate cancer susceptibility in North Indian population, while results of meta-analysis revealed no association between MTHFR C677T and MTRR A66G gene polymorphisms and prostate cancer susceptibility.
Quantifying non-communicable diseases’ burden in Egypt using State-Space model

The study aimed to model and quantify the health burden induced by four non-communicable diseases in Egypt, the first to be conducted in the context of a less developing county. The study used the State-Space model and adopted two Bayesian methods: Particle Filter and Particle Independent Metropolis-Hastings to model and estimate the NCDs' health burden trajectories. We drew on time-series data of the International Health Metric Evaluation, CAPMAS's Annual Bulletin of Health Services Statistics, the World Bank, and WHO data. Both Bayesian methods showed that the burden trajectories are on the rise. Most of the findings agreed with our assumptions and are in line with the literature. Previous year burden strongly predicts the burden of the current year. High prevalence of the risk factors, disease prevalence, and the disease's severity level all increase illness burden. Years of life lost due to death has high loadings in most of the diseases. Contrary to the study assumption, results found a negative relationship between disease burden and health services utilization which can be attributed to the lack of full health insurance coverage and the pattern of health care seeking behavior in Egypt. Our study highlights that Particle Independent Metropolis-Hastings is sufficient in estimating the parameters of the study model, in the case of time-constant parameters. The study recommends using state Space models with Bayesian estimation approaches with time-series data in public health and epidemiology research.
Macromolecular room temperature crystallography

Abstract X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
The diffusing-velocity random walk: a spatial-Markov formulation of heterogeneous advection and diffusion

Abstract The spatial distribution of a scalar undergoing advection and diffusion is impacted by the velocity variability sampled by tracer particles. In spatially structured velocity fields, such as porous medium flows, Lagrangian velocities along streamlines are often characterized by a well-defined correlation length and can thus be described by spatial-Markov processes. Diffusion, on the other hand, is generally modelled as a temporal process, making it challenging to capture advective and diffusive dynamics in a single framework. We develop a description of transport based on a spatial-Markov velocity process along Lagrangian particle trajectories, incorporating the effect of diffusion as a local averaging process in velocity space. The impact of flow structure on this diffusive averaging is quantified through an effective shear rate. The latter is fully determined by the point statistics of velocity magnitudes together with characteristic longitudinal and transverse length scales associated with the flow field. For infinite longitudinal correlation length, our framework recovers Taylor dispersion, and in the absence of diffusion it reduces to a standard spatial-Markov velocity model. We derive dynamical equations governing the evolution of particle position and velocity and obtain scaling laws for the dependence of longitudinal dispersion on Péclet number. These results provide new insights into the role of shear and diffusion on dispersion processes in heterogeneous media.
Prevalence, risk factors and sources of anxiety among Emergency Department healthcare workers in Pakistan during COVID-19 pandemic: A single center survey

Summary COVID-19 has challenged the mental health of healthcare workers confronting it world-wide. Our study identifies the prevalence and risk of anxiety among emergency healthcare workers confronting COVID-19 in Pakistan. We conducted a cross-sectional survey in an Emergency Department using the Generalized Anxiety Scale (GAD-7), and questions about sources of anxiety. Of 107 participants, 61.7% were frontline workers. The prevalence of anxiety was 50.5%. Nonparametric tests determined that nurses, younger and inexperienced staff, developed significant anxiety. Multivariate ordinal regression determined independent risk factors for developing anxiety were younger age (OR 2.11, 95% CI 0.89–4.99) and frontline placement (OR 1.34, 95% CI 0.33–1.66). Significant sources of stress were fear of infecting family (P = 0.003), lack of social support when the health care providers were themselves unwell (P = 0.02) and feelings of inadequate work performance (P = 0.05). Our study finds that HCWs’ anxiety is considerable. Appropriate measures for its alleviation and prevention are required.
Thermal boundary layer structure in low-Prandtl-number turbulent convection

Abstract We study the structure of the thermal boundary layer (BL) in Rayleigh–Bénard convection for Prandtl number ($Pr$) 0.021 by conducting direct numerical simulations in a two-dimensional square box for Rayleigh numbers ($Ra$) up to $10^9$. The large-scale circulation in the flow divides the horizontal plates into three distinct regions, and we observe that the local thermal BL thicknesses in the plume-ejection region are larger than those in the plume-impact and shear-dominated regions. Moreover, the local BL width decreases as $Ra^{-\beta (x)}$, with $\beta (x)$ depending on the position at the plate. We find that the values of $\beta (x)$ are nearly the same in the impact and shear regions, and are larger in the ejection region. Thus, the local BL width decreases faster in the ejection region than in the shear and impact regions, and we estimate that the thermal BL structure would be uniform throughout the horizontal plate for $Ra \geq 8 \times 10^{12}$ in our low-$Pr$ convection. We compare the thermal BL profiles measured at various positions at the plate with the Prandtl–Blasius–Pohlhausen (PBP) profile and find deviations everywhere for all the Rayleigh numbers. However, the dynamically rescaled profiles, as suggested by Zhou & Xia (Phys. Rev. Lett., vol. 104, 2010, 104301), agree well with the PBP profile in the shear and impact regions for all the Rayleigh numbers, whereas they still deviate in the ejection region. We also find that, despite the growing fluctuations with increasing $Ra$, thermal boundary layers in our low-$Pr$ convection are transitional and not yet fully turbulent.
Genome Sequence of Bifidobacterium breve INIA P734 (CECT 8178), a Strain Isolated from Human Breast Milk

The draft genome sequence of Bifidobacterium breve INIA P734, a strain shared by mother and child, is reported. It consists of 50 contigs, with 2,391,925 bp, 2,099 genes, and a G+C content of 58.8%. The genome analysis revealed the absence of antibiotic resistance and pathogenicity-related genes. ABSTRACT The draft genome sequence of Bifidobacterium breve INIA P734, a strain shared by mother and child, is reported. It consists of 50 contigs, with 2,391,925 bp, 2,099 genes, and a G+C content of 58.8%. The genome analysis revealed the absence of antibiotic resistance and pathogenicity-related genes.
Complete Genome Sequence of Mycobacterium orygis Strain 51145

We report the complete 4,352,172-bp genome sequence of Mycobacterium orygis strain 51145 assembled into a single circular chromosome. Comparative genomic analyses with other lineages of the Mycobacterium tuberculosis complex can provide insights into the biology, evolution, and epidemiology of this important group of pathogenic mycobacteria. ABSTRACT We report the complete 4,352,172-bp genome sequence of Mycobacterium orygis strain 51145 assembled into a single circular chromosome. Comparative genomic analyses with other lineages of the Mycobacterium tuberculosis complex can provide insights into the biology, evolution, and epidemiology of this important group of pathogenic mycobacteria.
Bacterial Diversity Profiling around the Orca Seamount in the Bransfield Strait, Antarctica, Based on 16S rRNA Gene Amplicon Sequences

Hydrothermal vent activity is often associated with submarine volcanism. Here, we investigated the presence of microorganisms related to hydrothermal activity in the Orca seamount. Data profiling of the 16S rRNA gene amplicon sequences revealed a diversity pattern dominated mainly by the phyla Proteobacteria, Acidobacteria, Planctomycetes, and Bacteroidetes. ABSTRACT Hydrothermal vent activity is often associated with submarine volcanism. Here, we investigated the presence of microorganisms related to hydrothermal activity in the Orca seamount. Data profiling of the 16S rRNA gene amplicon sequences revealed a diversity pattern dominated mainly by the phyla Proteobacteria, Acidobacteria, Planctomycetes, and Bacteroidetes.
Metabolic Profiling of Praziquantel-mediated Prevention of Opisthorchis viverrini-induced Cholangiocyte Transformation in the Hamster Model of Cholangiocarcinoma

Background: Opisthorchis viverrini (Ov) infection-induced cholangiocarcinoma (CCA) is a major public health problem in northeastern Thailand. Praziquantel was shown to prevent CCA development in an Ov-infected hamster model; however, the molecular mechanism remains unknown. Materials and Methods: In this study, we used a hamster model with Ov and N-nitrosodimethylamine-induced CCA to study the mechanisms of praziquantel action. The liver tissues from the hamsters with and without praziquantel treatment were analyzed using 1H nuclear magnetic resonance spectroscopy. Results: A total of 14 metabolites were found to be significantly different between the two groups. Furthermore, the combination of acetate, inosine and sarcosine was shown to exert an anti-inflammatory effect through interleukin-6 inhibition in a macrophage cell line, suggesting a mechanism by which praziquantel may prevent inflammation caused by Ov, cholangiocyte transformation and further CCA develpoment. Conclusion: These findings might avail the development of a preventive strategy for CCA in high-risk populations.
Survey of Maize Rhizosphere Microbiome Using Shotgun Metagenomics

Several processes which occur in the rhizosphere make it a vital region in plant development. However, studies that examine the rhizosphere microbiome and their functional potentials remain scarce. Shotgun metagenomics was employed here to evaluate the functional potentials of the maize rhizosphere microbiome of farms in two South African provinces. ABSTRACT Several processes which occur in the rhizosphere make it a vital region in plant development. However, studies that examine rhizosphere microbiomes and their functional potentials remain scarce. Shotgun metagenomics was employed here to evaluate the functional potentials of the maize rhizosphere microbiome of farms in two South African provinces.
SARS-CoV-2 spillover events

Spillover from mink to humans highlights SARS-CoV-2 transmission routes from animals Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and COVID-19 all broke out in recent decades and are caused by different strains of coronavirus (CoV). These viruses are considered to originate from bats and to have been transmitted to humans through intermediate hosts. SARS-CoV was identified in palm civets in wildlife markets and MERS-CoV in dromedary camels (1), but the direct source of the COVID-19 causative agent, SARS-CoV-2, is still undetermined. On page 172 of this issue, Oude Munnink et al. (2) report an in-depth investigation of SARS-CoV-2 infections in animals and humans working or living in 16 mink farms in the Netherlands. SARS-CoV-2 infections were detected in 66 out of 97 (68%) of the owners, workers, and their close contacts. Some people were infected with viral strains with an animal sequence signature, providing evidence of SARS-CoV-2 spillover back and forth between animals and humans within mink farms.
Complete Genome Sequence of Streptomyces Phage Shaeky

Here, we present the genome of siphophage Shaeky, infecting the Gram-positive bacterium Streptomyces sp. strain Mg1. Shaeky has very low sequence identity to other phages, with phage phiC31 being the most closely related in the NCBI database. The Shaeky genome is 45,617 bp with 77 protein-coding genes and 16 tRNAs. ABSTRACT Here, we present the genome of siphophage Shaeky, infecting the Gram-positive bacterium Streptomyces sp. strain Mg1. Shaeky has very low sequence identity to other phages, with phage phiC31 being the most closely related in the NCBI database. The Shaeky genome is 45,617 bp with 77 protein-coding genes and 16 tRNAs.
Complete Genome Sequence of Streptomyces Phage Shady

Streptomyces spp. are saprophytic soil bacteria that produce secondary metabolites with therapeutic potential. This announcement describes the isolation and genome annotation of Streptomyces sp. strain Mg1 siphophage Shady. Learning more about Shady’s novel 45-kb genome, containing 76 predicted protein-coding genes, could be industrially advantageous when using streptomycetes for their products. ABSTRACT Streptomyces spp. are saprophytic soil bacteria that produce secondary metabolites with therapeutic potential. This announcement describes the isolation and genome annotation of Streptomyces sp. strain Mg1 siphophage Shady. Learning more about Shady’s novel 45-kb genome, containing 76 predicted protein-coding genes, could be industrially advantageous when using streptomycetes for their products.
Draft Genome Sequences of Four Citrobacter Isolates Recovered from Wild Australian Shorebirds

Citrobacter is a ubiquitous bacterial genus whose members inhabit a variety of niches. Some species are clinically important for both antimicrobial resistance (AMR) carriage and as the cause of nosocomial infections. Surveillance of Citrobacter species in the environment can provide indicators of the spread of AMR genes outside clinical spaces. In this study, we present draft genome sequences of four Citrobacter isolates obtained from three species of wild Australian shorebirds. ABSTRACT Citrobacter is a ubiquitous bacterial genus whose members inhabit a variety of niches. Some species are clinically important for both antimicrobial resistance (AMR) carriage and as the cause of nosocomial infections. Surveillance of Citrobacter species in the environment can provide indicators of the spread of AMR genes outside clinical spaces. In this study, we present draft genome sequences of four Citrobacter isolates obtained from three species of wild Australian shorebirds.
Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates

We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame. ABSTRACT We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.