Fast Accumulation Research Articles

Faster accumulation and greater contribution of glomalin to the soil organic carbon pool than amino sugars do under tropical coastal forest restoration.

Microbial metabolic products play a vital role in maintaining ecosystem multifunctionality, such as soil physical structure and soil organic carbon (SOC) preservation. Afforestation is an effective strategy to restore degraded land. Glomalin-related soil proteins (GRSP) and amino sugars are regarded as stable microbial-derived C, and their distribution within soil aggregates affects soil structure stability and SOC sequestration. However, the information about how afforestation affects the microbial contribution to SOC pools within aggregates is poorly understood. We assessed the accumulation and contribution of GRSP and amino sugars within soil aggregates along a restoration chronosequence (Bare land, Eucalyptus exserta plantation, native species mixed forest, and native forest) in tropical coastal terraces. Amino sugars and GRSP concentrations increased, whereas their contributions to the SOC pool decreased along the restoration chronosequence. Although microaggregates harbored greater microbial abundances, amino sugars and GRSP concentrations were not significantly affected by aggregate sizes. Interestingly, the contributions of amino sugars and GRSP to SOC pools decreased with decreasing aggregate size which might be associated with increased accumulation of plant-derived C. However, the relative change rate of GRSP was consistently greater in all restoration chronosequences than that of amino sugars. The accumulation of GRSP and amino sugars in SOC pools was closely associated with the dynamics of soil fertility and the microbial community. Our findings suggest that GRSP accumulates faster and contributes more to SOC pools during restoration than amino sugars did which was greatly affected by aggregate sizes. Afforestation substantially enhanced soil quality with native forest comprising species sequestering more SOC than the monoculture plantation did. Such information is invaluable for improving our mechanistic understanding of microbial control over SOC preservation during degraded ecosystem restoration. Our findings also show that plantations using arbuscular mycorrhizal plants can be an effective practice to sequester more soil carbon during restoration.

Maintenance of tRNA and elongation factors supports T3SS proteins translational elongations in pathogenic bacteria during nutrient starvation

BackgroundSufficient nutrition contributes to rapid translational elongation and protein synthesis in eukaryotic cells and prokaryotic bacteria. Fast synthesis and accumulation of type III secretion system (T3SS) proteins conduce to the invasion of pathogenic bacteria into the host cells. However, the translational elongation patterns of T3SS proteins in pathogenic bacteria under T3SS-inducing conditions remain unclear. Here, we report a mechanism of translational elongation of T3SS regulators, effectors and structural protein in four model pathogenic bacteria (Pseudomonas syringae, Pseudomonas aeruginosa, Xanthomonas oryzae and Ralstonia solanacearum) and a clinical isolate (Pseudomonas aeruginosa UCBPP-PA14) under nutrient-limiting conditions. We proposed a luminescence reporter system to quantitatively determine the translational elongation rates (ERs) of T3SS regulators, effectors and structural protein under different nutrient-limiting conditions and culture durations.ResultsThe translational ERs of T3SS regulators, effectors and structural protein in these pathogenic bacteria were negatively regulated by the nutrient concentration and culture duration. The translational ERs in 0.5× T3SS-inducing medium were the highest of all tested media. In 1× T3SS-inducing medium, the translational ERs were highest at 0 min and then rapidly decreased. The translational ERs of T3SS regulators, effectors and structural protein were inhibited by tRNA degradation and by reduced levels of elongation factors (EFs).ConclusionsRapid translational ER and synthesis of T3SS protein need adequate tRNAs and EFs in nutrient-limiting conditions. Numeric presentation of T3SS translation visually indicates the invasion of bacteria and provides new insights into T3SS expression that can be applied to other pathogenic bacteria.

Cadophora species from marine glaciers in the Qinghai-Tibet Plateau: an example of unsuspected hidden biodiversity

Large numbers of marine glaciers in the Qinghai-Tibet Plateau are especially sensitive to changes of climate and surface conditions. They have suffered fast accumulation and melting and retreated quickly in recent years. In 2017, we surveyed the cold-adapted fungi in these unique habitats and obtained 1208 fungal strains. Based on preliminary analysis of ITS sequences, 41 isolates belonging to the genus Cadophora were detected. As one of the most frequently encountered genera, the Cadophora isolates were studied in detail. Two phylogenetic trees were constructed: one was based on the partial large subunit nrDNA (LSU) to infer taxonomic placement of our isolates and the other was based on multi-locus sequences of LSU, ITS, TUB and TEF-1α to investigate more exact phylogenetic relationships between Cadophora and allied genera. Combined with morphological characteristics, nine Cadophora species were determined, including seven new to science. Among the new species, only C. inflata produces holoblastic conidia and all the others express phialidic conidiogenesis. All isolates have optimum growth temperature at 20 °C or 25 °C. With more species involved, the currently circumscribed genus became obviously paraphyletic. All members are clustered into two main clades: one clade mainly includes most of the Cadophora species which have phialidic conidiogenesis and we refer to as ‘Cadophora s. str.’; the remaining Cadophora species have multiform conidiogenesis and are clustered in the second clade, with members of other genera in Ploettnerulaceae interspersed among the subclades. The results show a high diversity of Cadophora from marine glaciers in the Qinghai-Tibet Plateau and most of them are novel species.

Polymer-coated BiOCl nanosheets for safe and regioselective gastrointestinal X-ray imaging.

Bismuth-based compounds are considered to be the best candidates for computed tomography (CT) imaging of gastrointestinal (GI) tract due to high X-ray absorption. Here, we report the introduction of polymer-coated bismuth oxychloride (BiOCl) nanosheets for highly efficient CT imaging in healthy mice and animal with colitis. We demonstrate simple, low cost and fast aqueous synthesis protocol which provides gram-quantity yield of chemically stable BiOCl nanosheets. The developed contrast gives 2.55-fold better CT enhancement compared to conventional contrast with negligible in vivo toxicity. As a major finding we report a regioselective CT imaging of GI tract by using nanoparticles coated with differentially charged polymers. Coating of nanoparticles with a positively charged polymer leads to their fast accumulation in small intestine, while the coating with negatively charged polymers stimulates prolonged stomach retention. We propose that this effect may be explained by a pH-controlled aggregation of nanoparticles in stomach. This feature may become the basis for advancement in clinical diagnosis of entire GI tract.

Dynamic Changes in the Antioxidative Defense System in the Tea Plant Reveal the Photoprotection-Mediated Temporal Accumulation of Flavonoids under Full Sunlight Exposure.

To reveal the mechanisms underlying how light affects flavonoid metabolism and the potential role of flavonoids in protecting against photooxidative stress in tea leaves, tea plants adapted to low-light conditions were exposed to full sunlight over 48 h. There was an increase in the activities of catalase (CAT) and superoxide dismutase (SOD) as well as greater accumulation of reactive oxygen species, lutein, tocopherols, ascorbate and malondialdehyde, suggestive of a time-dependent response to photooxidative stress in tea leaves. Analysis of the time dependency of each element of the antioxidant system indicated that carotenoids and tocopherols exhibited the fastest response to light stress (within 3 h), followed by SOD, CAT and catechin, which peaked at 24 h. Meanwhile, flavonols, vitamin C and glutathione showed the slowest response. Subsequent identification of the main phytochemicals involved in protecting against oxidative stress using untargeted metabolomics revealed a fast and initial accumulation of nonesterified catechins that preceded the increase in flavonol glycosides and catechin esters. Gene expression analysis suggested that the light-induced accumulation of flavonoids was highly associated with the gene encoding flavonol synthase. Ultraviolet B (UV-B) irradiation further validated the time-dependent and collaborative effects of flavonoids in photoprotection in tea plants. Intriguingly, the dynamics of the metabolic response are highly distinct from those reported for Arabidopsis, suggesting that the response to light stress is not conserved across plants. This study additionally provides new insights into the functional role of flavonoids in preventing photooxidative stress and may contribute to further improving tea quality through the control of light intensity.

Вакцина на основе N-белка SARS-CoV-2 формирует выраженный Т-клеточный иммунитет на N-белок новых штаммов

The second generation COVID-19 vaccines should produce the long-term protective immune response to the existing and novel strains of SARS-CoV-2. The Convacell® vaccine was designed to produce such immune response by using N protein as an antigen. N-protein is not susceptible to fast accumulation of mutations and is highly homologous to nucleocapsid proteins of other β-coronaviruses. The study was aimed to perform in vitro assessment of the Convacell® vaccine ability to produce immune response to the Wuhan, Delta, and Omicron strains. Mononuclear cells of vaccinated volunteers and survivors were subjected to N protein stimulation. After that specific activation of the cells was assessed by flow cytometry. The results showed that a sibstantial percentage of CD4 and CD8 cells produced IFNγ and IL2 in response to stimulation. No significant reduction of the response to strains Delta and Omicron compared to the Wuhan strain was revealed. The findings support the direction of the N protein based vaccine design towards creation of the universal vaccine.

Responsive Peptide Nanofibers with Theranostic and Prognostic Capacity.

Photodynamic therapy (PDT) is a highly promising therapeutic modality for cancer treatment. The development of stimuli‐responsive photosensitizer nanomaterials overcomes certain limitations in clinical PDT. Herein, we report the rational design of a highly sensitive PEGylated photosensitizer‐peptide nanofiber (termed PHHPEG6 NF) that selectively aggregates in the acidic tumor and lysosomal microenvironment. These nanofibers exhibit acid‐induced enhanced singlet oxygen generation, cellular uptake, and PDT efficacy in vitro, as well as fast tumor accumulation, long‐term tumor imaging capacity and effective PDT in vivo. Moreover, based on the prolonged presence of the fluorescent signal at the tumor site, we demonstrate that PHHPEG6 NFs can also be applied for prognostic monitoring of the efficacy of PDT in vivo, which would potentially guide cancer treatment. Therefore, these multifunctional PHHPEG6 NFs allow control over the entire PDT process, from visualization of photosensitizer accumulation, via actual PDT to the assessment of the efficacy of the treatment.

Responsive Peptide Nanofibers with Theranostic and Prognostic Capacity

AbstractPhotodynamic therapy (PDT) is a highly promising therapeutic modality for cancer treatment. The development of stimuli‐responsive photosensitizer nanomaterials overcomes certain limitations in clinical PDT. Herein, we report the rational design of a highly sensitive PEGylated photosensitizer‐peptide nanofiber (termed PHHPEG6 NF) that selectively aggregates in the acidic tumor and lysosomal microenvironment. These nanofibers exhibit acid‐induced enhanced singlet oxygen generation, cellular uptake, and PDT efficacy in vitro, as well as fast tumor accumulation, long‐term tumor imaging capacity and effective PDT in vivo. Moreover, based on the prolonged presence of the fluorescent signal at the tumor site, we demonstrate that PHHPEG6 NFs can also be applied for prognostic monitoring of the efficacy of PDT in vivo, which would potentially guide cancer treatment. Therefore, these multifunctional PHHPEG6 NFs allow control over the entire PDT process, from visualization of photosensitizer accumulation, via actual PDT to the assessment of the efficacy of the treatment.

Rediscovery of Hall-Petch strengthening in bulk ultrafine grained pure Mg at cryogenic temperature: A combined in-situ neutron diffraction and electron microscopy study

Grain refinement can lead to the strengthening of metallic materials according to the Hall-Petch relationship. However, our recent results suggested that grain boundary sliding is the dominant deformation mode in bulk ultrafine grained (UFG) pure Mg at room temperature, leading to softening. Here, for the first time, we report that the Hall-Petch strengthening can be regained in bulk UFG pure Mg at cryogenic temperature. At 77K, the UFG pure Mg with a mean grain size of 0.6 μm exhibited ultrahigh tensile yield strength and ultimate tensile strength of 309 MPa and 380 MPa, respectively. Combined in-situ neutron diffraction and electron microscopy investigation indicated that residual dislocation structures and deformation twins hardly formed in the UFG specimen during tensile test at 298K. In contrast, fast accumulation of lattice defects and remarkable reorientation were evident at 77K, suggesting that the grain-boundary-mediated process was suppressed and the plastic deformation was dominated by dislocation slip and deformation twinning. In addition, all the pure Mg specimens exhibited pronounced strain hardening at 77 K, which was mainly attributed to the suppressed grain boundary sliding and dynamic recovery. The mean dislocation density and relative fractions of dislocations with various Burgers vectors of the UFG specimen deformed at 77K were determined quantitatively from neutron diffraction data. Despite the strong strain hardening capacity, the UFG specimen fractured prematurely at an elongation of 5% at 77K. The significantly reduced ductility at 77K was possibly caused by its higher tensile strength, which generated high intergranular stress and resulted in intergranular fracture before reaching the point of plastic instability. Potential ways for improving the strength and ductility synergy of the UFG Mg at cryogenic temperature were proposed.

Anhydrous Fast Proton Transport Boosted by the Hydrogen Bond Network in a Dense Oxide-Ion Array of α-MoO3.

Developing high-power battery chemistry is an urgent task to buffer fluctuating renewable energies and achieve a sustainable and flexible power supply. Owing to the small size of the proton and its ultrahigh mobility in water via the Grotthuss mechanism, aqueous proton batteries are an attractive candidate for high-power energy storage devices. Grotthuss proton transfer is ultrafast owing to the hydrogen-bonded networks of water molecules. In this work, similar continuous hydrogen bond networks in a dense oxide-ion array of solid α-MoO3 are discovered, which facilitate the anhydrous proton transport even without structural water. The fast proton transfer and accumulation that occurs during (de)intercalation in α-MoO3 is unveiled using both experiments and first-principles calculations. Coupled with a zinc anode and a superconcentrated Zn2+ /H+ electrolyte, the proton-transport mechanism in anhydrous hydrogen-bonded networks realizes an aqueous MoO3 -Zn battery with large capacity, long life, and fast charge-discharge abilities.

NPP Krško 3 inch Cold Leg Break LOCA Calculation using RELAP5/MOD 3.3 and MELCOR 1.8.6 Codes

NPP Krško input deck developed at Faculty of Electrical Engineering and Computing (FER) Zagreb, for severe accident code MELCOR 1.8.6 is currently being tested. MELCOR is primarily used for the analyses of severe accidents including in-vessel and ex-vessel core melt progression as well as containment response under severe accident conditions. Accurate modelling of the plant thermal-hydraulic behaviour as well as engineering safety features, e.g., Emergency Core Cooling System, Auxiliary feedwater system and various containment systems (e.g., Passive Autocatalytic Recombiners, Fan Coolers and Containment spray) is necessary to correctly predict the plant response and operator actions. For MELCOR input data verification, the comparison of the results for small break (3 inch) cold leg Loss of Coolant Accident (LOCA) for NPP Krško using MELCOR 1.8.6 and RELAP5/MOD 3.3 was performed. A detailed RELAP5/MOD 3.3 model for NPP Krško has been developed at FER and it has been extensively used for accident and transient analyses. The RELAP5 model has been upgraded and improved along with the plant modernization in the year 2000. and after more recent plant modifications. The results of the steady state calculation (first 1000 seconds) for both MELCOR and RELAP5 were assessed against the referent plant data. In order to test all thermal-hydraulic aspects of developed MELCOR 1.8.6 model the accident was analysed, and comparison to the existing RELAP5 model was performed, with all engineering safety features available. After initial fast pressure drop and accumulator injection for both codes stable conditions were established with heat removal through the break and core inventory maintained by safety injection. Transient was simulated for 10000 seconds and overall good agreement between results obtained with both codes was found.

Nitrogen burial characteristics of Quaternary sediments and its controls on high ammonium groundwater in the Central Yangtze River Basin

As the strata sedimentary process proceeds, considerable amounts of nitrogen (N) is buried in sediments, which controls the sources and fate of N in the “groundwater-sediment” system. However, there is little concern regarding N burial characteristics in continuous sediment profiles from surface layer to deep aquifer thus far. In this study, lithology, grain size, geochronology, exchangeable N contents and geochemical proxies of sediments were analyzed to reveal the controlling mechanisms of N burial characteristics in Quaternary sediments and to interpret the enrichment of N in groundwater of central Yangtze River Basin. The results demonstrated a similar distribution trend for buried N in two sedimentary cores, which were high in the surface layer and decreased to stable in the deep aquifer. Excessive exchangeable N (EX-N) contents in sediments were mainly attributed to geologic origin. The N burial characteristics were controlled by the evolution of depositional environment: sedimentary facies determined the concentrations of total organic nitrogen (TON), further affecting the mineralization capacity of sediments; while paleoclimate regulated the intensity of the N transformation processes, ultimately influencing the actual concentrations of EX-N in sediments. In addition, due to the fast accumulation of alluvial deposits after Last Glacial Maximum and rapid development of Jianghan Lake Groups during Holocene, abundant organic matter (with high TON contents) was buried in sediments, which were still able to produce more ammonium or nitrate, and further posing continuous threats to groundwater quality. This study provided a new interpretation for the formation of high-ammonium aquifer in terms of depositional evolution.

The new inspiration from the theoretical re-exploration of traditional autoxidation pathways leading to sulfate formation in the haze episode

The high concentration and fast accumulation of sulfate have been identified in most of the haze episodes’ events. It is well known that the autoxidation process is one of the most common and essential routes for sulfate formation. However, the detailed mechanism underlying sulfate formation, especially that from oxygen (O2) involved autoxidation process, has not been fully established since there is no direct experimental proof available till now. In this work, we thoroughly explored the possible sulfate formation pathways involving O2 through high-level quantum chemical calculation investigation. It is revealed that in the autoxidation process, the reaction of SO3− with O2 will occur on the doublet potential energy surface to form SO5−. We further proposed a pH dependent reaction mechanism in which SO5− will react with different forms of SO2 (HOSO2−, SO32−) through four different pathways to produce sulfate. More importantly, by calculating the branching ratios for different pathways, we found the most dominant path involving O2 in sulfate formation in almost all the atmospherically relevant pH during pollution period. In this path, SO5− react with SO32− through two steps: a O atom transfer process and a subsequent single electron transfer (SET) process. Detailed calculation results emphasize the importance of autoxidation mechanism in explaining sulfate formation during pollution period, and therefore provide some important and detailed information for understanding the possible reason of haze episode.

Trabecular-like Ti–6Al–4V scaffold for bone repair: A diversified mechanical stimulation environment for bone regeneration

A bionic scaffold with ideal osteoconductive and osteoinductive characteristics is in urgent demand. The trabecular-like scaffold and corresponding regular scaffold with cubic cells were designed through Voronoi diagram and fabricated using L-PBF process. High-cycle fatigue test, fluid simulation, bone regeneration model prediction, and in vivo experiments were conducted. The research results revealed that the irregular structure significantly weakened the fatigue property of the trabecular-like scaffold, embodied by fast ratcheting strain accumulation and premature appearance of damage strain. The trabecular-like scaffold showed similar fluid behaviors to the CT-reconstructed cancellous bone, including permeation rate, pressure, velocity, and shear rate. It could be roughly concluded that there was a diversified mechanical stimulation environment formed in irregular structure, involving micro deformation, mass transportation, fluid shear stress and pressure, biological factor diffusion, better matching the demand for osteogenic mechanical stimulation, consequently making the implanted trabecular-like scaffold show better osteogenic ability than the regular scaffold.

When terminology hinders research: the colloquialisms of transitions of control in automated driving

During the last 20 years, technological advancement and economic interests have motivated research on automated driving and its impact on drivers’ behaviour, especially after transitions of control. Indeed, once the Automated Driving System (ADS) reaches its operational limits, it is forced to request human intervention. However, the fast accumulation and massive quantity of produced studies and the gaps left behind by standards have led to an imprecise and colloquial use of terms which, as technology and research interest evolve, creates confusion. The goal of this survey is to compare how different taxonomies describe transitions of control, address the current use of widely adopted terms in the field of transitions of control and explain how their use should be standardized to enhance future research. The first outcome of this analysis is a schematic representation of the correspondence among the elements of the reviewed taxonomies. Then, the definitions of “takeover” and “handover” are clarified as two parallel processes occurring in every transition of control. A second set of qualifiers, which are necessary to unequivocally define a transition of control and identify the agent requesting the transition and the agent receiving the request (ADS or the driver), is provided. The “initiator” is defined as the agent requesting the transition to take place, and the “receiver” is defined as the agent receiving that request.

Damage State Assessment of Metal Pipes of a Power Plant, Subjected to Thermal Stresses

During the operating of industrial equipment and installations, elastoplastic deformations may occur over time in their most demanding areas due to thermal stresses, mechanical stresses (due to internal pressure, weight, inertial forces) or thermomechanical stresses resulting from their combination. Thermal stresses are cause by the non-uniformity of the expansions produced by the temperature differences, by the non-uniformity of the coefficients of linear thermal expansion of the materials used in isothermal or non-isothermal operating conditions. Increasing the temperature reduces the material strength by creating elastoplastic deformations and thus, to the loss of available plasticity of the material. The sudden change in operating regimes and the increase in the number of these regime changes at high temperatures, is one of the main causes of the faster accumulation of degradation, and the reduction of components remaining life. On the other hand, environmental factors have an important influence on the operating behaviour of equipment, since they favour the induction of corrosion or erosion-corrosion phenomena due to the flow of fluid circulated through installations at high temperatures. The complexity of the thermomechanical stresses, to which materials are subjected during operation, leads to the need for periodic assess of their characteristics through specific tests and analyses. Paper presents the results of analyses and tests performed to assess the damage state of pipes from a thermal power plant system, results that allow to estimate the service remaining life of the pipeline system for a proper operating in safe conditions.

A new hope: Mitochondria, a critical factor in the war against prions

Prion diseases encompass a group of incurable neurodegenerative disorders that occur due to the misfolding and aggregation of infectious proteins. The most well-known prion diseases are Creutzfeldt-Jakob disease (CJD), bovine spongiform encephalopathy (also known as mad cow disease), and kuru. It is estimated that around 1–2 persons per million worldwide are affected annually by prion disorders. Infectious prion proteins propagate in the brain, clustering in the cells and rapidly inducing tissue degeneration and death. Prion disease alters cell metabolism and energy production damaging mitochondrial function and dynamics leading to a fast accumulation of damage. Dysfunction of mitochondria could be considered as an early precursor and central element in the pathogenesis of prion diseases such as in sporadic CJD. Preserving mitochondria function may help to resist the rapid spread and damage of prion proteins and even clearance. In the war against prions and other degenerative diseases, studying how to preserve the function of mitochondria by using antioxidants and even replacing them with artificial mitochondrial transfer/transplant (AMT/T) may bring a new hope and lead to an increase in patients' survival. In this perspective review, we provide key insights about the relationship between the progression of prion disease and mitochondria, in which understanding how protecting mitochondria function and viability by using antioxidants or AMT/T may help to develop novel therapeutic interventions.

CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model.

Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Thus, there is a need for computational host prediction. Despite some promising results, computational host prediction remains a challenge because of the limited known interactions and the sheer amount of sequenced phages by high-throughput sequencing technologies. The state-of-the-art methods can only achieve 43% accuracy at the species level. In this work, we formulate host prediction as link prediction in a knowledge graph that integrates multiple protein and DNA-based sequence features. Our implementation named CHERRY can be applied to predict hosts for newly discovered viruses and to identify viruses infecting targeted bacteria. We demonstrated the utility of CHERRY for both applications and compared its performance with 11 popular host prediction methods. To our best knowledge, CHERRY has the highest accuracy in identifying virus–prokaryote interactions. It outperforms all the existing methods at the species level with an accuracy increase of 37%. In addition, CHERRY’s performance on short contigs is more stable than other tools.

Experimental and numerical modeling on liquefaction resistance of geotextile reinforced sand

Historical cases show that the liquefaction of sand is an important cause of earthquake disasters. Geosynthetics are widely used to improve the performance of sand deposit. However, limited studies have been conducted on the effect of geosynthetics on mitigation of sand liquefaction. In this study, the liquefaction resistance performance of geotextile reinforced sand is discussed by a series of strain-controlled cyclic triaxial tests with different cyclic strain amplitudes and layer numbers of geotextile. The influence of geotextile layout and cyclic strain amplitude on the liquefaction behavior of saturated sand is studied. Experimental results show that the liquefaction resistance of saturated sand increases with the increase of layer number of geotextiles and decreases with the increase of cyclic strain amplitude. The increased cyclic strain amplitude leads to fast accumulation of pore water pressure. Furthermore, a single element numerical model is created based on the finished cyclic triaxial test, and parameter calibration is carried out for reinforced sand by matching the excess pore water pressure. Numerical simulation results show that the computed responses with calibrated parameters are in good agreement with the experimental ones. This will provide a valuable reference for numerical modeling and engineering application of geotextile reinforced sand.

Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution.

Early identification of adaptive mutations could provide timely help for the control and prevention of the COVID-19 pandemic. The fast accumulation of SARS-CoV-2 sequencing data provides important support, while also raising a great challenge for the recognition of adaptive mutations. Here, we proposed a computational strategy to detect potentially adaptive mutations from their fixed and parallel patterns in the phylogenetic trajectory. We found that the biological meanings of fixed substitution and parallel mutation are highly complementary, and can reasonably be integrated as a fixed and parallel (paraFix) mutation, to identify potentially adaptive mutations. Tracking the dynamic evolution of SARS-CoV-2, 37 sites in spike protein were identified as having experienced paraFix mutations. Interestingly, 70% (26/37) of them have already been experimentally confirmed as adaptive mutations. Moreover, most of the mutations could be inferred as paraFix mutations one month earlier than when they became regionally dominant. Overall, we believe that the concept of paraFix mutations will help researchers to identify potentially adaptive mutations quickly and accurately, which will provide invaluable clues for disease control and prevention.