Differential word expression analyses highlight plague dynamics during the second pandemic

Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools routinely used in biology, we developed a quantitative lexicography of 32 texts describing two major plague outbreaks, using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome, comprising overrepresented terms in plague-related texts, indicated that ‘buboes' and ‘carbuncles' are words that were significantly associated with the plague and signalled an ectoparasite-borne plague. Moreover, plague-related words were associated with the terms ‘merchandise’, ‘movable’, ‘tatters', ‘bed’ and ‘clothes'. Analysing ancient texts using the method reported in this paper can certify plague-related historical records and indicate the particularities of each plague outbreak, which can inform on the potential sources for the causative Yersinia pestis .

Design of a custom-made device for real-time optical measurement of differential mineral concentrations in three-dimensional scaffolds for bone tissue engineering

Monitoring bone tissue engineered (TEed) constructs during their maturation is important to ensure the quality of applied protocols. Several destructive, mainly histochemical, methods are conventionally used to this aim, requiring the sacrifice of the investigated samples. This implies (i) to plan several scaffold replicates, (ii) expensive and time consuming procedures and (iii) to infer the maturity level of a given tissue construct from a cognate replica. To solve these issues, non-destructive techniques such as light spectroscopy-based methods have been reported to be useful. Here, a miniaturized and inexpensive custom-made spectrometer device is proposed to enable the non-destructive analysis of hydrogel scaffolds. Testing involved samples with a differential amount of calcium salt. When compared to a reference standard device, this custom-made spectrometer demonstrates the ability to perform measurements without requiring elaborate sample preparation and/or a complex instrumentation. This preliminary study shows the feasibility of light spectroscopy-based methods as useful for the non-destructive analysis of TEed constructs. Based on these results, this custom-made spectrometer device appears as a useful option to perform real-time/in-line analysis. Finally, this device can be considered as a component that can be easily integrated on board of recently prototyped bioreactor systems, for the monitoring of TEed constructs during their conditioning.

Physico-chemical and spectroscopic investigation of flavonoid dispersed C n TAB micelles

In this study, kaempferol (0.2 m/mmol kg −1 ) dispersed cationic surfactant micelles were prepared as a function of alkyltrimethylammonium bromide (C n TAB) hydrophobicity (C = 12 to C = 16). The dispersion study of kaempferol in different C n TAB, i.e. dodecyltrimethylammonium bromide (C = 12), tetradecyltrimethylammonium bromide (C = 14) and hexadecyltrimethylammonium bromide (C = 16), was conducted with the physico-chemical properties of density, sound velocity, viscosity, surface tension, isentropic compressibility, acoustic impedance, surface excess concentration and area occupied per molecule and thermodynamic parameters Gibbs free energy, enthalpy and activation energy measured at 298.15 K. These properties were measured with varying concentration of C n TAB from 0.0260 to 0.0305 mol kg −1 in a 10% (w/w) aqueous dimethyl sulfoxide solvent system. The variations in these measured properties have been used to infer the kaempferol dispersion stability via hydrophobic–hydrophilic, hydrophilic–hydrophilic, van der Waals, hydrogen bonding and other non-covalent interactions.

Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod

Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda , species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda . Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus , but confirm the presence of two asymmetrical sites recently reported in two other isopod species.

Numerical biomechanics modelling of indirect mitral annuloplasty treatments for functional mitral regurgitation

Mitral valve regurgitation (MR) is a common valvular heart disease where an improper closure leads to leakage from the left ventricle into the left atrium. There is a need for less-invasive treatments such as percutaneous repairs for a large inoperable patient population. The aim of this study is to compare several indirect mitral annuloplasty (IMA) percutaneous repair techniques by finite-element analyses. Two types of generic IMA devices were considered, based on coronary sinus vein shortening (IMA-CS) to reduce the annulus perimeter and based on shortening of the anterior–posterior diameter (IMA-AP). The disease, its treatments, and the heart function post-repair were modelled by modifying the living heart human model (Dassault Systèmes). A functional MR pathology that represents ischaemic MR was generated and the IMA treatments were simulated in it, followed by heart function simulations with the devices and leakage quantification from blood flow simulations. All treatments were able to reduce leakage, the IMA-AP device achieved better sealing, and there was a correlation between the IMA-CS device length and the reduction in leakage. The results of this study can help in bringing IMA-AP to market, expanding the use of IMA devices, and optimizing future designs of such devices.

How disease risk awareness modulates transmission: coupling infectious disease models with behavioural dynamics

Epidemiological models often assume that individuals do not change their behaviour or that those aspects are implicitly incorporated in parameters in the models. Typically, these assumptions are included in the contact rate between infectious and susceptible individuals. However, adaptive behaviours are expected to emerge and play an important role in the transmission dynamics across populations. Here, we propose a theoretical framework to couple transmission dynamics with behavioural dynamics due to infection awareness. We modelled the dynamics of social behaviour using a game theory framework, which is then coupled with an epidemiological model that captures the disease dynamics by assuming that individuals are aware of the actual epidemiological state to reduce their contacts. Results from the mechanistic model show that as individuals increase their awareness, the steady-state value of the final fraction of infected individuals in a susceptible-infected-susceptible (SIS) model decreases. We also incorporate theoretical contact networks, having the awareness parameter dependent on global or local contacts. Results show that even when individuals increase their awareness of the disease, the spatial structure itself defines the steady state.

Porosity of the porous carbonate rocks in the Jingfengqiao–Baidiao area based on finite automata

This study is based on the processing of computed microtomography images of rock samples. In this study, a finite automation is constructed using the grey value, red-green-blue (RGB) value and Euler number of polarized images of carbonate rocks from the Jingfengqiao–Baidiao area. The finite automaton is used to perform black and white binary processing of the polarized images of the carbonate rocks. The porosity of the carbonate rock is calculated based on the black and white binarization processing results of the polarized images of the carbonate rocks. The obtained porosity is compared with the carbonate porosity obtained by use of the traditional carbonate research method. When the two porosities are close, the image processing threshold of the finite automata is considered to be credible. Based on the finite automata established using the image processing threshold, the black and white binary images of the polarized images of the carbonate rocks are used to establish a rock pore image using I mage J2X. The polarized images of the carbonate rocks are classified according to their RGB values using the finite automata for the porosity classification, and the obtained images are used as textures to paste onto a cube to construct a three-dimensional data model of the carbonate rocks. This study also uses 16S rDNA analysis to verify the formation mechanism of the carbonate pores in the Jingfengqiao–Baidiao area. The results of the 16S rDNA analysis show that the pores in the carbonate rocks in the Jingfengqiao–Baidiao area are closely related to microorganisms, represented by denitrifying bacteria.

Quantifying transmissibility of SARS-CoV-2 and impact of intervention within long-term healthcare facilities

Estimates of the basic reproduction number ( R 0 ) for COVID-19 are particularly variable in the context of transmission within locations such as long-term healthcare (LTHC) facilities. We sought to characterize the heterogeneity of R 0 across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that occurred within LTHC facilities in British Columbia, Canada as of 21 September 2020. We estimated R 0 in 18 LTHC outbreaks with a novel Bayesian hierarchical dynamic model of susceptible, exposed, infected and recovered individuals, incorporating heterogeneity of R 0 between facilities. We further compared these estimates to those obtained with standard methods that use the exponential growth rate and maximum likelihood. The total size of outbreaks varied dramatically, with range of attack rates 2%–86%. The Bayesian analysis provided an overall estimate of R 0 = 2.51 (90% credible interval 0.47–9.0), with individual facility estimates ranging between 0.56 and 9.17. Uncertainty in these estimates was more constrained than standard methods, particularly for smaller outbreaks informed by the population-level model. We further estimated that intervention led to 61% (52%–69%) of all potential cases being averted within the LTHC facilities, or 75% (68%–79%) when using a model with multi-level intervention effect. Understanding of transmission risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.

Exposure to the COVID-19 pandemic environment and generosity

We report data from an online experiment which allows us to study how generosity changed over a 6-day period during the initial explosive growth of the COVID-19 pandemic in Andalusia, Spain, while the country was under a strict lockdown. Participants ( n = 969) could donate a fraction of a €100 prize to an unknown charity. Our data are particularly rich in the age distribution and we complement them with daily public information about COVID-19-related deaths, infections and hospital admissions. We find correlational evidence that donations decreased in the period under study, particularly among older individuals. Our analysis of the mechanisms behind the detected decrease in generosity suggests that expectations about others' behaviour, perceived mortality risk and (alarming) information play a key—but independent—role for behavioural adaptation. These results indicate that social behaviour is quickly adjusted in response to the pandemic environment, possibly reflecting some form of selective prosociality.

Oxidase enzymes as sustainable oxidation catalysts

Oxidation is one of the most important processes used by the chemical industry. However, many of the methods that are used pose significant sustainability and environmental issues. Biocatalytic oxidation offers an alternative to these methods, with a now significant enzymatic oxidation toolbox on offer to chemists. Oxidases are one of these options, and as they only depend on molecular oxygen as a terminal oxidant offer perfect atom economy alongside the selectivity benefits afforded by enzymes. This review will focus on examples of oxidase biocatalysts that have been used for the sustainable production of important molecules and highlight some important processes that have been significantly improved through the use of oxidases. It will also consider emerging classes of oxidases, and how they might fit in a future biorefinery approach for the sustainable production of important chemicals.