Predicting potential SARS-CoV-2 spillover and spillback in animals.

BACKGROUND: The COVID-19 pandemic is spreading rapidly around the world, causing countries to impose lockdowns and efforts to develop vaccines on a global scale. However, human-to-animal and animal-to-human transmission cannot be ignored, as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread rapidly in farmed and wild animals. This could create a worrying cycle of SARS-CoV-2 spillover from humans to animals and spillback of new strains back into humans, rendering vaccines ineffective. METHOD: This study provides a key indicator of animals that may be potential susceptible hosts for SARS-CoV-2 and coronavirus infections by analysing the phylogenetic distance between host angiotensin-converting enzyme 2 and the coronavirus spike protein. Crucially, our analysis identifies animals that are at elevated risk from a spillover and spillback incident. RESULTS: One group of animals has been identified as potentially susceptible to SARS-CoV-2 by harbouring a parasitic coronavirus spike protein similar to the SARS-CoV-2 spike protein. These animals may serve as amplification hosts in spillover events from zoonotic reservoirs. This group consists of a mixture of animals infected internally and naturally: minks, dogs, cats, tigers. Additionally, no internal or natural infections have been found in masked palm civet. CONCLUSION: Tracing interspecies transmission in multi-host environments based solely on in vitro and in vivo examinations of animal susceptibility or serology is a time-consuming task. This approach allows rapid identification of high-risk animals to prioritize research and assessment of the risk of zoonotic disease transmission in the environment. It is a tool to rapidly identify zoonotic species that may cause outbreaks or participate in expansion cycles of coexistence with their hosts. This prevents the spread of coronavirus infections between species, preventing spillover and spillback incidents from occurring.

Programmable Biomolecule-Mediated Processors.

Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.

Evolution of Viral Pathogens Follows a Linear Order.

Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], SARS-CoV, MERS-CoV, human coronavirus-HKU1 [HCoV-HKU1], HCoV-OC43, HCoV-NL63, and HCoV-229E), influenza A (H1N1 and H3N2), flavivirus (dengue virus serotypes 1 to 4 and Zika) and ebolavirus (Zaire, Sudan, and Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak. IMPORTANCE This study reports a comparative analysis of amino acid usage within several key viral genera that are prone to triggering outbreaks. Interestingly, there is evidence that the amino acid usage within the viral genomes is not random but in a linear order.

Slip of fluid molecules on solid surfaces by surface diffusion.

The mechanism of fluid slip on a solid surface has been linked to surface diffusion, by which mobile adsorbed fluid molecules perform hops between adsorption sites. However, slip velocity arising from this surface hopping mechanism has been estimated to be significantly lower than that observed experimentally. In this paper, we propose a re-adsorption mechanism for fluid slip. Slip velocity predictions via this mechanism show the improved agreement with experimental measurements.

Fourier-based classification of protein secondary structures.

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices.

A new integrated symmetrical table for genetic codes.

Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature's coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes, which is presented in this paper. It could be very useful to understand the Nobel laureate Crick's wobble hypothesis - how one transfer ribonucleic acid can recognize two or more synonymous codons, which is an unsolved fundamental question in biological science.

A new model for fluid velocity slip on a solid surface.

A general adsorption model is developed to describe the interactions between near-wall fluid molecules and solid surfaces. This model serves as a framework for the theoretical modelling of boundary slip phenomena. Based on this adsorption model, a new general model for the slip velocity of fluids on solid surfaces is introduced. The slip boundary condition at a fluid-solid interface has hitherto been considered separately for gases and liquids. In this paper, we show that the slip velocity in both gases and liquids may originate from dynamical adsorption processes at the interface. A unified analytical model that is valid for both gas-solid and liquid-solid slip boundary conditions is proposed based on surface science theory. The corroboration with the experimental data extracted from the literature shows that the proposed model provides an improved prediction compared to existing analytical models for gases at higher shear rates and close agreement for liquid-solid interfaces in general.

A New Model for Temperature Jump at a Fluid-Solid Interface.

The problem presented involves the development of a new analytical model for the general fluid-solid temperature jump. To the best of our knowledge, there are no analytical models that provide the accurate predictions of the temperature jump for both gas and liquid systems. In this paper, a unified model for the fluid-solid temperature jump has been developed based on our adsorption model of the interfacial interactions. Results obtained from this model are validated with available results from the literature.

Magnetic Fields Facilitate DNA-Mediated Charge Transport.

Exaggerated radical-induced DNA damage under magnetic fields is of great concern to medical biosafety and biomolecular electronic devices. In this report, the effects of an external magnetic field (MF) on DNA electronic conductivity were investigated by studying the efficiencies of photoinduced DNA-mediated charge transport (CT) via guanine damage. Under a static MF of 300 mT, positive enhancements in the decomposition of 8-cyclopropyldeoxyguanosine ((8CP)G) were observed at both the proximal and distal guanine doublets, indicating a more efficient propagation of radical cations and higher electronic conductivity of duplex DNA. MF-assisted CT has shown sensitivity to magnetic field strength, duplex structures, and the integrity of base pair stacking. Spin evolution of charge injection and the alignment of base pairs to the CT-active conformation during radical propagation were proposed to be the two major factors that MF contributes to facilitate DNA-mediated CT. Herein, MF-assisted CT may offer a new avenue for designing DNA-based electronic devices and unraveling MF effects on redox and radical relevant biological processes.

Programmable DNA-Mediated Multitasking Processor.

Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.

Beyond Parrondo's paradox.

The Parrondo's paradox is a counterintuitive phenomenon where individually-losing strategies can be combined in producing a winning expectation. In this paper, the issues surrounding the Parrondo's paradox are investigated. The focus is lying on testifying whether the same paradoxical effect can be reproduced by using a simple capital dependent game. The paradoxical effect generated by the Parrondo's paradox can be explained by placing all the parameters in one probability space. Based on this framework, it is able to generate other possible paradoxical effects by manipulating the parameters in the probability space.

A statistical thin-tail test of predicting regulatory regions in the Drosophila genome.

BACKGROUND: The identification of transcription factor binding sites (TFBSs) and cis-regulatory modules (CRMs) is a crucial step in studying gene expression, but the computational method attempting to distinguish CRMs from NCNRs still remains a challenging problem due to the limited knowledge of specific interactions involved. METHODS: The statistical properties of cis-regulatory modules (CRMs) are explored by estimating the similar-word set distribution with overrepresentation (Z-score). It is observed that CRMs tend to have a thin-tail Z-score distribution. A new statistical thin-tail test with two thinness coefficients is proposed to distinguish CRMs from non-coding non-regulatory regions (NCNRs). RESULTS: As compared with the existing fluffy-tail test, the first thinness coefficient is designed to reduce computational time, making the novel thin-tail test very suitable for long sequences and large database analysis in the post-genome time and the second one to improve the separation accuracy between CRMs and NCNRs. These two thinness coefficients may serve as valuable filtering indexes to predict CRMs experimentally. CONCLUSIONS: The novel thin-tail test provides an efficient and effective means for distinguishing CRMs from NCNRs based on the specific statistical properties of CRMs and can guide future experiments aimed at finding new CRMs in the post-genome time.

A statistical fat-tail test of predicting regulatory regions in the Drosophila genome.

A statistical study of cis-regulatory modules (CRMs) is presented based on the estimation of similar-word set distribution. It is observed that CRMs tend to have a fat-tail distribution. A new statistical fat-tail test with two kurtosis-based fatness coefficients is proposed to distinguish CRMs from non-CRMs. As compared with the existing fluffy-tail test, the first fatness coefficient is designed to reduce computational time, making the novel fat-tail test very suitable for long sequences and large database analysis in the post-genome time and the second one to improve separation accuracy between CRMs and non-CRMs. These two fatness coefficients may serve as valuable filtering indexes to predict CRMs experimentally.

Thermally stable ionic liquid-based sol-gel coating for ultrasonic extraction-solid-phase microextraction-gas chromatography determination of phthalate esters in agricultural plastic films.

A novel sol-gel-coated ionic liquid-based ([AMIM][N(SO(2)CF(3))(2)]-OH-TSO) fiber was successfully applied for the determination of phthalate esters (PAEs) in agricultural plastic films by ultrasonic extraction (UE) combined with solid phase microextraction-gas chromatography (SPME-GC) due to its high thermal stability, specific selectivity and extraction efficiency. The extractant for UE and the adsorption time for SPME were optimized to achieve higher extraction efficiency. The desorption temperature and time were also optimized to avoid the carryover effect of previous extraction, and ultimately improve the precision and accuracy of the method. The [AMIM][N(SO(2)CF(3))(2)]-OH-TSO fiber showed comparable, or even higher response to most of the investigated PAEs than the commercial PDMS, PDMS-DVB and PA fibers. The carryover problem, often encountered when using commercial fibers, had been eliminated when desorption was performed at 360°C for 8 min. The proposed SPME-GC method showed good linearity over three to four orders of magnitude, and low limits of detection ranged from 0.003 to 0.063 µg L(-1). The relative standard deviation values obtained were below 10%, and the recoveries were in the ranges of 90.2-111.4%. Some of the PAEs studied were detected at very high concentration in these agricultural plastic film samples, resulting in a potential risk of crop damage, environmental contamination and human health exposure.

DNA-based computing of strategic assignment problems.

DNA-based computing is a novel technique to tackle computationally difficult problems, in which computing time grows exponentially corresponding to problematic size. A strategic assignment problem is a typical nondeterministic polynomial problem, which is often associated with strategy applications. In this Letter, a new approach dealing with strategic assignment problems is proposed based on manipulating DNA strands, which is believed to be better than the conventional silicon-based computing in solving the same problem.

Developing classification indices for Chinese pulse diagnosis.

AIM: To develop classification criteria for Chinese pulse diagnosis and to objectify the ancient diagnostic technique. METHODS: Chinese pulse curves are treated as wave signals. Multidimensional variable analysis is performed to provide the best curve fit between the recorded Chinese pulse waveforms and the collective Gamma density functions. RESULTS: Chinese pulses can be recognized quantitatively by the newly-developed four classification indices, that is, the wave length, the relative phase difference, the rate parameter, and the peak ratio. The new quantitative classification not only reduces the dependency of pulse diagnosis on Chinese physician's experience, but also is able to interpret pathological wrist-pulse waveforms more precisely. CONCLUSIONS: Traditionally, Chinese physicians use fingertips to feel the wrist-pulses of patients in order to determine their health conditions. The qualitative theory of the Chinese pulse diagnosis is based on the experience of Chinese physicians for thousands of years. However, there are no quantitative theories to relate these different wrist-pulse waveforms to the health conditions of patients. In this paper, new quantified classification indices have been introduced to interpret the Chinese pulse waveform patterns objectively.

Pairwise alignment of the DNA sequence using hypercomplex number representation.

A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex number representation of the DNA base-nucleic acid codes and incorporated with the method of dot matrix analysis and various algorithms of sequence alignment. The problem of DNA sequence alignment can be processed in a rather similar way to pairwise alignment of the protein sequence.

Slamming of a breaking wave on a wall.

This paper is intended to study impact forces of breaking waves on a rigid wall based on a nonlinear potential-flow theory. This is a model problem for some technologically important design issues such as the impact of breaking waves on ships, coastal and offshore structures. We are interested in the short-time successive triggering of nonlinear effects using a small-time expansion. The analytical solutions for the impact force on a rigid wall and the free-surface profile are derived.