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Abstract Molecular dynamics (MD) is an indispensable atomistic-scale computational tool widely-used in various disciplines. In the past decades, nearly all ab initio MD and machine-learning MD have been based on the general-purpose central/graphics processing units (CPU/GPU), which are well-known to suffer from their intrinsic “memory wall” and “power wall” bottlenecks. Consequently, nowadays MD calculations with ab initio accuracy are extremely time-consuming and power-consuming, imposing serious restrictions on the MD simulation size and duration. To solve this problem, here we propose a special-purpose MD processing unit (MDPU), which could reduce MD time and power consumption by about 103 times (109 times) compared to state-of-the-art machine-learning MD (ab initio MD) based on CPU/GPU, while keeping ab initio accuracy. With significantly-enhanced performance, the proposed MDPU may pave a way for the accurate atomistic-scale analysis of large-size and/or long-duration problems which were impossible/impractical to compute before.

Abstract Background Phosphorus (P) plays a vital role in plant growth. The pqqC and phoD genes serve as molecular markers for inorganic and organic P breakdown, respectively. However, the understanding of how P-mobilizing bacteria in soil respond to long-term fertilization and rhizobium application is limited. Herein, soil that had been treated with fertilizer and rhizobium for 10 years was collected to investigate the characteristics of P-mobilizing bacterial communities. Five treatments were included: no fertilization (CK), phosphorus fertilizer (P), urea + potassium fertilizer (NK), NPK, and PK + Bradyrhizobium japonicum 5821 (PK + R). Results The soybean nodule dry weight was highest in the P treatment (1.93 g), while the soybean yield peaked in the PK + R treatment (3025.33 kg ha− 1). The abundance of the pqqC gene increased in the rhizosphere soil at the flowering-podding stage and in the bulk soil at the maturity stage under the P treatment, while its abundance increased in the bulk soil at the flowering-podding stage and in the rhizosphere soil at the maturity stage under the PK + R treatment. The abundance of the phoD gene was enhanced in the bulk soil at the flowering-podding stage under the PK + R treatment. The Shannon and Ace indexes of pqqC- and phoD-harboring bacteria were higher in the rhizosphere soil at maturity under the PK + R treatment compared to other treatments. Furthermore, a comprehensive analysis of the neutral community model and co-occurrence pattern demonstrated that the application of P fertilizer alone led to an increase in the distribution and dynamic movement of pqqC-harboring bacteria, but resulted in a decrease in complexity of network structure. On the other hand, rhizobium inoculation enhanced the distribution and dynamic movement of phoD-harboring bacteria, as well as the stability and complexity of the network structure. Pseudomonas and Nitrobacter, as well as Steptomyces, Stella, and Nonomuraea, may be crucial genera regulating the composition and function of pqqC- and phoD-harboring communities, respectively. Conclusions These findings affirm the crucial role of fertilization and rhizobium inoculation in regulating pqqC- and phoD-harboring bacterial communities, and highlight the significance of long-term phosphate-only fertilization and rhizobium inoculation in enhancing dissolved inorganic phosphorus and mineralized organophosphorus, respectively.

Forecasting typhoon waves during typhoons is crucial. In this paper, the numerical wave model SWAN was enhanced through integration with two machine learning methods: the Back Propagation Neural Network and Random Forest. This integration facilitated the development of two distinct models, namely SWAN-BP and SWAN-Tree. Through correlation analysis, key input features were identified for the machine learning models. The forecasts from the SWAN model were subsequently utilized as inputs to enhance further wave prediction. These hybrid models were validated using data from Typhoon Doksuri (2023) and Typhoon Nesat (2017). The results indicated significant improvements in predicting typhoon-induced wave heights with both the SWAN-BP and SWAN-Tree models compared to the original SWAN model. Specifically, the SWAN-BP model demonstrated a 33% improvement in accuracy for the Typhoon Doksuri, whereas the SWAN-Tree model exhibited a 24% improvement. For Typhoon Nesat, the accuracy improvements were 23% for the SWAN-BP model and 21% for the SWAN-Tree model. These findings demonstrate that integrating wave numerical models with machine learning techniques can significantly enhance the predictive accuracy of numerical models. This approach offers a cost-effective means to improve the existing wave forecasting database. Traditionally, the direct use of meteorological and oceanographic data for typhoon wave prediction might be compromised by biases inherent in the numerical wave models. However, the SWAN-BP and SWAN-Tree models effectively reduce these biases, thereby providing more accurate and robust predictions. In conclusion, this paper enhances the predictive accuracy of the SWAN model and establishes a crucial foundation for more precise typhoon wave forecasting through the application of machine learning techniques.

In order to limit the phenomenon that the global stability safety factor (GSF) of the diaphragm wall slurry trench calculated by the two-dimensional (2D) wedge method is too small, the 2D calculation model on global instability of trench wall is established by assuming the whole critical failure surface (CFS) is a quarter elliptic cylindrical surface, and the determination method of CFS is given too. In view of the successful application of the minimum potential energy principle in slope stability checking calculation and on the basis of the new model established, the 2D minimum potential energy method for calculating the GSF is proposed according to the minimum potential energy principle. The correctness of the 2D calculation model built and the rationality of the 2D calculation method proposed are verified based on ten engineering cases, and the sensitivity of the GSF to various parameters is analyzed on the basis of six design examples. Finally, the new calculation method is applied to the global stability checking calculation of trench wall in practical engineering, and the result shows the new calculation method given in this paper is still conservative, so the result calculated by the new calculation method is advised to be multiplied by a modification factor of 1.67 in practical application.

By conducting a two-dimensional experimental study, this paper aims to enhance the understanding of the mechanism of sand convective motions in the vicinity of a wall subjected to long-term cyclic lateral loadings. The experimental tests were conducted in a rectangular sandbox with a transparent front-wall, through which the process of sand particle motions could be recorded by using a high-resolution digital camera. The images were processed with a high time-resolved PIV (Particle Image Velocimetry) system. Based on the experimental data, this work (1) presents the sand flow field in the convective zones; (2) provides means to describe the convection mechanism; (3) proposes the relationships between the loading conditions and dimensions of the region with intense sand movement; and (4) elaborates the similarity of the sand flow velocity structure within the sand convective zones.

Because the soft weak soil layer rich in confined groundwater is prone to local instability and failure in the construction of diaphragm wall trenches, in order to check the local slurry wall stability in the construction of diaphragm wall trenches, a new three-dimensional (3D) calculation method on the local stability safety factor (LSF) of slurry walls is proposed based on the minimum potential energy principle. After the new method is applied to two engineering cases, the value of the LSF solved is 0.82 for engineering case 1, and the values of the LSF solved are 0.84 and 1.05 when the phreatic water levels are 2 and 4.5 m, respectively, for engineering case 2. These results are very close to the calculation results in the existing references, so the rationality of the new method is verified. Then the sensitivity of the LSFs obtained from the new method to various parameters has been analyzed and clarified on the basis of ten design examples. Finally, the new method is used to check the local slurry wall stability in the construction of diaphragm wall trenches for a practical project, and the obtained values of the LSF for three concerned weak soil layers are 1.37, 1.19, and 0.82, respectively. These results are in agreement with the actual situation in the construction site. This reveals that both the 3D model established and the 3D calculation method proposed in this paper are suitable for application in practical projects.

To synthesize new superheavy elements, the accurate prediction of nuclear masses of superheavy nuclei is essential for calculations of reaction Q values, neutron separation energies and α-decay energies, which are important for estimating beam energies, survival probabilities and also for identifications. In this work, we include existing α-decay energies of superheavy nuclei in the fitting procedure of extended Skyrme density functionals as corresponding nuclear masses are not available. Systematic α-decay energies are well reproduced with a standard deviation of 0.24 MeV. The high quality α-decay energies make it feasible for direct identification of new elements and new isotopes. The resulting binding energies in the heaviest region are surprisingly close to the inferences by AME2020. Our work should be useful for guiding experimental synthesis of new elements 119 and 120.

Circular RNAs (circRNAs) have been shown to be pivotal regulators in various human diseases by participating in gene splicing, acting as microRNA (miRNA) sponges, interacting with RNA-binding proteins (RBPs), and translating into short peptides. As the back-splicing products of pre-mRNAs, many circRNAs can modulate the expression of their host genes through transcriptional, post-transcriptional, translational, and post-translational control via interaction with other molecules. This review provides a detailed summary of these regulatory mechanisms based on the class of molecules that they interact with, which encompass DNA, mRNA, miRNA, and RBPs. The co-expression of circRNAs with their parental gene productions (including linear counterparts and proteins) provides potential diagnostic biomarkers for multiple diseases. Meanwhile, the different regulatory mechanisms by which circRNAs act on their host genes via interaction with other molecules constitute complex regulatory networks, which also provide noticeable clues for therapeutic strategies against diseases. Future research should explore whether these proven mechanisms can play a similar role in other types of disease and clarify further details about the cross-talk between circRNAs and host genes. In addition, the regulatory relationship between circRNAs and their host genes in circRNA circularization, degradation, and cellular localization should receive further attention.

In recent years, jacket foundations have been increasingly employed in offshore wind farms. Their complex design comprising piles and trusses poses challenges for conducting comprehensive flow field measurements using physical experiments. Consequently, the influence of the flow field on local scour around these foundations remains unclear. Therefore, numerical simulation methods are essential to depict the surrounding flow characteristics. This study utilizes large eddy simulation (LES) turbulence models within OpenFOAM to simulate the flow field around jacket foundations on flat-bed and equilibrium scour bathymetry. A flume experiment was conducted for numerical model establishment and validation. The close agreement between experimental and numerical results indicates that the LES model accurately reflects the flow patterns around the jacket foundation. Time-averaged and instantaneous flow characteristics, average kinetic energy (AKE), turbulence structure, and bed shear stress were analyzed. The results indicate that flow intensity is reduced due to the shielding effect and energy dissipation by the truss structure of the jacket foundation. Furthermore, the AKE of the flow upstream of the rear piles decreases by 18.9% in the flat-bed state and 28.0% in the equilibrium state, indicating more energy dissipation and less scour at the rear piles in the equilibrium state. The research findings offer valuable insights into the design and scour protection strategies for jacket foundations.

Abstract Ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) are important intermediate links in the nitrogen cycle. Apart from the AOA and AOB communities in soil, we further investigated co-occurrence patterns and microbial assembly processes subjected to inorganic and organic fertilizer treatments for over 35 years. The amoA copy numbers and AOA and AOB communities were found to be similar for the CK and organic fertilizer treatments. Inorganic fertilizers decreased the AOA gene copy numbers by 0.75–0.93-fold and increased the AOB gene copy numbers by 1.89–3.32-fold compared to those of the CK treatment. The inorganic fertilizer increased Nitrososphaera and Nitrosospira. The predominant bacteria in organic fertilizer was Nitrosomonadales. Furthermore, the inorganic fertilizer increased the complexity of the co-occurrence pattern of AOA and decreased the complexity pattern of AOB comparing with organic fertilizer. Different fertilizer had an insignificant effect on the microbial assembly process of AOA. However, great difference exists in the AOB community assembly process: deterministic process dominated in organic fertilizer treatment and stochastic processes dominated in inorganic fertilizer treatment, respectively. Redundancy analysis indicated that the soil pH, NO3 −N, and available phosphorus contents were the main factors affecting the changes in the AOA and AOB communities. Overall, this findings expanded our knowledge concerning AOA and AOB, and ammonia‐oxidizing microorganisms were more disturbed by inorganic fertilizers than organic fertilizers.

BackgroundTraumatic brain injury (TBI) increases the risk of mental disorders and neurodegenerative diseases in the chronic phase. However, there is limited neuropathological or molecular data on the long-term neural dysfunction and its potential mechanism following adolescent TBI.MethodsA total of 160 male mice aged 8 weeks were used to mimic moderate TBI by controlled cortical impact. At 1, 3, 6 and 12 months post-injury (mpi), different neurological functions were evaluated by elevated plus maze, forced swimming test, sucrose preference test and Morris water maze. The levels of oxidative stress, antioxidant response, reactive astrocytes and microglia, and expression of inflammatory cytokines were subsequently assessed in the ipsilateral hippocampus, followed by neuronal apoptosis detection. Additionally, the morphological complexity of hippocampal astrocytes was evaluated by Sholl analysis.ResultsThe adolescent mice exhibited persistent and incremental deficits in memory and anxiety-like behavior after TBI, which were sharply exacerbated at 12 mpi. Depression-like behaviors were observed in TBI mice at 6 mpi and 12 mpi. Compared with the age-matched control mice, apoptotic neurons were observed in the ipsilateral hippocampus during the chronic phase of TBI, which were accompanied by enhanced oxidative stress, and expression of inflammatory cytokines (IL-1β and TNF-α). Moreover, the reactive astrogliosis and microgliosis in the ipsilateral hippocampus were observed in the late phase of TBI, especially at 12 mpi.ConclusionAdolescent TBI leads to incremental cognitive dysfunction, and depression- and anxiety-like behaviors in middle-aged mice. The chronic persistent neuroinflammation and oxidative stress account for the neuronal loss and neural dysfunction in the ipsilateral hippocampus. Our results provide evidence for the pathogenesis of chronic neural damage following TBI and shed new light on the treatment of TBI-induced late-phase neurological dysfunction.

The semi-circular breakwater (SBW) has been implemented at numerous global locations due to its outstanding wave dissipation effectiveness and high structural performance. This study extends prior research by investigating the seabed dynamic response and hydrodynamic response characteristics around perforated SBWs. A coupled numerical model is developed to integrate waves, a semi-circular breakwater, and a sandy seabed. Wave behavior is simulated using Reynolds-averaged Navier–Stokes equations with a k-ε turbulence closure scheme, and the seabed response is numerically simulated using Biot’s full-dynamic (u-w) equations. After verifying computational accuracy, a series of tests is conducted to explore the effects of marine environments and SBW characteristics. Test results reveal a positive correlation between seabed response and wave height, wave period, and perforation number, while showing a negative correlation between seabed response and water depth and perforation rate. The basic perforation type is more effective than front and rear perforation types in maintaining a stable flow field and seabed response. These findings provide insights for designing SBWs for effective wave dissipation and seabed stability in complex marine environments, offering valuable recommendations for future designs.

Microbial diversity is an important indicator of soil fertility and plays an indispensable role in farmland ecosystem sustainability. The short-term effects of fertilization and rhizobium inoculation on soil microbial diversity and community structure have been explored extensively; however, few studies have evaluated their long-term effects. Here, we applied quantitative polymerase chain reaction (qPCR) and amplicon sequencing to characterize the effect of 10-year fertilizer and rhizobium inoculation on bacterial communities in soybean bulk and rhizosphere soils at the flowering–podding and maturity stages. Four treatments were examined: non-fertilization control (CK), phosphorus and potassium fertilization (PK), nitrogen and PK fertilization (PK + N), and PK fertilization and Bradyrhizobium japonicum 5821 (PK + R). Long-term co-application of rhizobium and PK promoted soybean nodule dry weight by 33.94% compared with PK + N, and increased soybean yield by average of 32.25%, 5.90%, and 5.00% compared with CK, PK, and PK + N, respectively. The pH of PK + R was significantly higher than that of PK and PK + N at the flowering–podding stage. The bacterial abundance at the flowering–podding stage was positively correlated with soybean yield, but not at the maturity stage. The significant different class Gemmatimonadetes, and the genera Gemmatimonas, and Ellin6067 in soil at the flowering–podding stage were negatively correlated with soybean yield. However, the bacterial community at class and genus levels at maturity had no significant effect on soybean yield. The key bacterial communities that determine soybean yield were concentrated in the flowering–podding stage, not at maturity stage. Rhizosphere effect, growth period, and treatment synergies resulted in significant differences in soil bacterial community composition. Soil organic matter (OM), total nitrogen (TN), pH, and available phosphorus (AP) were the main variables affecting bacterial community structure. Overall, long-term co-application of rhizobium and fertilizer not only increased soybean yield, but also altered soil bacterial community structure through niche reconstruction and microbial interaction. Rhizobium inoculation plays key role in reducing nitrogen fertilizer application and promoting sustainable agriculture practices.

Forensic microbiology has been widely used in the diagnosis of causes and manner of death, identification of individuals, detection of crime locations, and estimation of postmortem interval. However, the traditional method, microbial culture, has low efficiency, high consumption, and a low degree of quantitative analysis. With the development of high-throughput sequencing technology, advanced bioinformatics, and fast-evolving artificial intelligence, numerous machine learning models, such as RF, SVM, ANN, DNN, regression, PLS, ANOSIM, and ANOVA, have been established with the advancement of the microbiome and metagenomic studies. Recently, deep learning models, including the convolutional neural network (CNN) model and CNN-derived models, improve the accuracy of forensic prognosis using object detection techniques in microorganism image analysis. This review summarizes the application and development of forensic microbiology, as well as the research progress of machine learning (ML) and deep learning (DL) based on microbial genome sequencing and microbial images, and provided a future outlook on forensic microbiology.

Microbial community succession during decomposition has been proven to be a useful tool for postmortem interval (PMI) estimation. Numerous studies have shown that the intestinal microbial community presented chronological changes after death and was stable in terrestrial corpses with different causes of death. However, the postmortem pattern of intestinal microbial community succession in cadavers retrieved from water remains unclear. For immersed corpses, the postmortem submersion interval (PMSI) is a useful indicator of PMI. To provide reliable estimates of PMSI in forensic investigations, we investigated the gut microbial community succession of corpses submersed in freshwater and explored its potential application in forensic investigation. In this study, the intestinal microbial community of mouse submersed in freshwater that died of drowning or CO2 asphyxia (i.e., postmortem submersion) were characterized by 16S rDNA amplification and high-throughput sequencing, followed by bioinformatic analyses. The results demonstrated that the chronological changes in intestinal bacterial communities were not different between the drowning and postmortem submersion groups. α-diversity decreased significantly within 14 days of decomposition in both groups, and the β-diversity bacterial community structure ordinated chronologically, inferring the functional pathway and phenotype. To estimate PMSI, a regression model was established by random forest (RF) algorithm based on the succession of postmortem microbiota. Furthermore, 15 genera, including Proteus, Enterococcus, and others, were selected as candidate biomarkers to set up a concise predicted model, which provided a prediction of PMSI [MAE (± SE) = 0.818 (± 0.165) d]. Overall, our present study provides evidence that intestinal microbial community succession would be a valuable marker to estimate the PMSI of corpses submerged in an aquatic habitat.

IntroductionBodies recovered from water, especially in the late phase of decomposition, pose difficulties to the investigating authorities. Various methods have been proposed for postmortem submersion interval (PMSI) estimation and drowning identification, but some limitations remain. Many recent studies have proved the value of microbiota succession in viscera for postmortem interval estimation. Nevertheless, the visceral microbiota succession and its application for PMSI estimation and drowning identification require further investigation.MethodsIn the current study, mouse drowning and CO2 asphyxia models were developed, and cadavers were immersed in freshwater for 0 to 14 days. Microbial communities in the liver and brain were characterized via 16S rDNA high-throughput sequencing.ResultsOnly livers and brains collected from 5 to 14 days postmortem were qualified for sequencing. There was significant variation between microbiota from liver and brain. Differences in microbiota between the cadavers of mice that had drowned and those only subjected to postmortem submersion decreased over the PMSI. Significant successions in microbial communities were observed among the different subgroups within the late phase of the PMSI in livers and brains. Eighteen taxa in the liver which were mainly related to Clostridium_sensu_stricto and Aeromonas, and 26 taxa in the brain which were mainly belonged to Clostridium_sensu_stricto, Acetobacteroides, and Limnochorda, were selected as potential biomarkers for PMSI estimation based on a random forest algorithm. The PMSI estimation models established yielded accurate prediction results with mean absolute errors ± the standard error of 1.282 ± 0.189 d for the liver and 0.989 ± 0.237 d for the brain.ConclusionsThe present study provides novel information on visceral postmortem microbiota succession in corpses submerged in freshwater which sheds new light on PMSI estimation based on the liver and brain in forensic practice.

Postmortem interval (PMI) estimation has always been a major challenge in forensic science. Conventional methods for predicting PMI are based on postmortem phenomena, metabolite or biochemical changes, and insect succession. Because postmortem microbial succession follows a certain temporal regularity, the microbiome has been shown to be a potentially effective tool for PMI estimation in the last decade. Recently, artificial intelligence (AI) technologies shed new lights on forensic medicine through analyzing big data, establishing prediction models, assisting in decision-making, etc. With the application of next-generation sequencing (NGS) and AI techniques, it is possible for forensic practitioners to improve the dataset of microbial communities and obtain detailed information on the inventory of specific ecosystems, quantifications of community diversity, descriptions of their ecological function, and even their application in legal medicine. This review describes the postmortem succession of the microbiome in cadavers and their surroundings, and summarizes the application, advantages, problems, and future strategies of AI-based microbiome analysis for PMI estimation.

Wenzheng Guan and Maosheng Xia et al. use a combination of pharmacological, genetic, and calcium imaging approaches to describe two mechanisms of iron-induced astrocytic calcium signaling. Altogether, these results suggest that astrocytes may act as a barrier to excessive iron in the brain, thereby improving our understanding of the role of astrocytes in normal neurodevelopment.

Cohesive sediment is ubiquitous in aquatic systems, which often forms fractal aggregates due to cohesive and adhesive forces between particles and is generally eroded as aggregates at low bed shear stresses. The erosion of aggregates plays a significant role in cohesive sediment dynamics. However, the effects of fractal bed aggregation on the erosion threshold of sediment have not been well understood. The incipient motion condition of cohesive sediment is investigated, in which particle aggregation is taken into account by employing the fractal theory and the van der Waals force between particles. A formula for the critical shear stress for surface erosion of cohesive sediments composed of fractal aggregates is developed based on the balance analysis of momentums acting on an aggregate in the bed surface. The developed formula has been successfully applied to different kinds of cohesive sediment. The fractal dimension is found as a function of the solid volume fraction and the diameter of primary particles. The contribution rate of the effective weight of aggregate to the erosion threshold of cohesive sediment is quantified.

Excessive iron released by hemoglobin and necrotic tissues is the predominant factor that aggravates the outcome of traumatic brain injury (TBI). Regulating the levels of iron and its metabolism is a feasible way to alleviate damage due to TBI. However, the spatial-temporal iron metabolism and iron deposition in neurons and glial cells after TBI remains unclear. In our study, male C57BL/6 mice (8–12 weeks old, weighing 20–26 g) were conducted using controlled cortical impact (CCI) models, combined with treatment of iron chelator deferoxamine (DFO), followed by systematical evaluation on iron deposition, cell-specific expression of iron metabolic proteins and ferroptosis in ipsilateral cortex. Herein, ferroptosis manifest by iron overload and lipid peroxidation was noticed in ipsilateral cortex. Furthermore, iron deposition and cell-specific expression of iron metabolic proteins were observed in the ipsilateral cortical neurons at 1–3 days post-injury. However, iron overload was absent in astrocytes, even though they had intense TBI-induced oxidative stress. In addition, iron accumulation in oligodendrocytes was only observed at 7–14 days post-injury, which was in accordance with the corresponding interval of cellular repair. Microglia play significant roles in iron engulfment and metabolism after TBI, and excessive affects the transformation of M1 and M2 subtypes and activation of microglial cells. Our study revealed that TBI led to ferroptosis in ipsilateral cortex, iron deposition and metabolism exhibited cell-type-specific spatial-temporal changes in neurons and glial cells after TBI. The different effects and dynamic changes in iron deposition and iron metabolism in neurons and glial cells are conducive to providing new insights into the iron-metabolic mechanism and strategies for improving the treatment of TBI.

Abstract Fertilizer-induced changes in soil nutrients regulate nitrogen (N) fixation in the terrestrial biosphere, but the influences of N and phosphorus (P) fertilization on the diazotroph communities in successive crop seasons were unclear. In this study, we assessed the effects of N and P (high vs. low doses) on the abundance and structure of N2-fixation communities after wheat and soybean harvest in a long-term (34 and 35 years) fertilization experiment. In both seasons, long-term N addition significantly decreased the abundance of nifH genes and 16S rDNA; in addition, high doses of N and P fertilizer decreased the richness of diazotrophs, whereas low doses did not. The proportion of the dominant genus, Bradyrhizobium, in the soybean season (86.0%) was higher than that in the wheat season (47.9%). Fertilization decreased diazotroph diversity and the relative abundance of Bradyrhizobium in the wheat season, but had insignificant effects in the soybean season. The addition of N, but not P, significantly changed the communities of both diazotrophs (at the genus level) and rhizobia (at the species level) in the two seasons. Soil pH was positively associated with nifH abundance and diazotrophic richness; soil NO3 − content was negatively correlated with diazotrophic richness and positively correlated with diversity. Soil pH and NO3 − content were the two main drivers shaping the soil diazotrophic community. Overall, long-term inorganic N had a greater influence than P on both diazotrophic abundance and community composition, and diazotrophic diversity was more clearly affected by fertilization in the wheat season than in the soybean season.

Duchenne muscular dystrophy (DMD) is one of the most common and severest muscular dystrophies. Although it can be a cause of death when associated with cardiac muscle and/or respiratory muscles, no cases of sudden deaths in the setting of undiagnosed DMD with cardiac involvement have been reported in the literatures. Previous studies showed that N-terminal-proBNP (NT-proBNP) was a robust laboratory biomarker to diagnose and monitor cardiac failure in clinical situations, suggesting that it may be used as an auxiliary indicator for diagnosis on left ventricular dysfunction in sudden cardiac deaths in forensic settings. Here, we reported a case of 29-year-old man who died suddenly. Autopsy revealed that muscles of the body were almost replaced by fatty and fibrotic tissues. The heart was enlarged with disarray and degeneration of cardiomyocytes in cardiac muscle. Total absence of dystrophin was detected by immunohistochemical staining, which confirmed DMD. Postmortem biochemical test of pericardial fluid revealed a high level of NT-proBNP, indicating dysfunction of the left ventricle before death. The cause of death was certified as an early dilated cardiomyopathy (DCM)/dysfunction of the left ventricle secondary to DMD, suggesting that sudden cardiac death with cardiac dysfunction could be identified by immunohistochemical method in combination with pericardial fluid NT-proBNP determination after systemic autopsy.

Rhizosphere microbial communities are vital for plant growth and soil sustainability; however, the composition of rhizobacterial communities, especially the assembly process and co-occurrence pattern among microbiota after the inoculation of some beneficial bacteria, remains considerably unclear. In this study, we investigated the structure of rhizomicrobial communities, their assembly process, and interactions contrasting when Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 are co-inoculated or Bradyrhizobium japonicum 5038 mono-inoculated in black and cinnamon soils of soybean fields. The obtained results indicated that the Chao and Shannon indices were all higher in cinnamon soil than that in black soil. In black soil, the co-inoculation increased the Shannon indices of bacteria comparing with that of the mono-inoculation. In cinnamon soil, the co-inoculation decreased the Chao indices of fungi comparing with that of mono-inoculation. Compared with the mono-inoculation, the interactions of microorganisms of co-inoculation in the co-occurrence pattern increased in complexity, and the nodes and edges of co-inoculation increased by 10.94, 40.18 and 4.82, 16.91% for bacteria and fungi, respectively. The co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 increased the contribution of stochastic processes comparing with Bradyrhizobium japonicum 5038 inoculation in the assembly process of soil microorganisms, and owing to the limitation of species diffusion might restrict the direction of pathogenic microorganism movement. These findings support the feasibility of rebuilding the rhizosphere microbial system via specific microbial strain inoculation and provide evidence that the co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 can be adopted as an excellent compound rhizobia agent resource for the sustainable development of agriculture.

Ferroptosis and iron-related redox imbalance aggravate traumatic brain injury (TBI) outcomes. NRF2 is the predominant transcription factor regulating oxidative stress and neuroinflammation in TBI, but its role in iron-induced post-TBI damage is unclear. We investigated ferroptotic neuronal damage in the injured cortex and observed neurological deficits post-TBI. These were ameliorated by the iron chelator deferoxamine (DFO) in wild-type mice. In Nrf2-knockout (Nrf2−/−) mice, more sever ferroptosis and neurological deficits were detected. Dimethyl fumarate (DMF)-mediated NRF2 activation alleviated neural dysfunction in TBI mice, partly due to TBI-induced ferroptosis mitigation. Additionally, FTH-FTL and FSP1 protein levels, associated with iron metabolism and the ferroptotic redox balance, were highly NRF2-dependent post-TBI. Thus, NRF2 is neuroprotective against TBI-induced ferroptosis through both the xCT-GPX4- and FTH-FTL-determined free iron level and the FSP1-regulated redox status. This yields insights into the neuroprotective role of NRF2 in TBI-induced neuronal damage and its potential use in TBI treatment.

The erosion threshold of sand-mud mixtures is investigated by analyzing the momentum balance of a sand particle or a mud parcel in the mixture bed surface, and a formula for the critical shear stress of sand-mud mixtures is developed, which also applies for pure sand and mud. The developed formula suggests that the variation of the critical shear stress of sand-mud mixtures over mud content is mainly caused by the varying dry bulk density of the mud component in the mixture. The developed formula reproduces well the variation of the critical shear stress of sand-mud mixtures over mud content and can predict the critical shear stress of both sand-mud mixtures and pure mud in the process of consolidation. The developed formula promises to be convenient for application by relating the critical shear stress to mud content and the dry bulk density of sediment.

Autopsy is of great significance for elucidating the pathological changes, pathogenesis and cause of death of Coronavirus Disease 2019 (COVID-19) and can provide a theoretical basis for scientific and accurate prevention and control of its outbreak. Based on related laws and regulations, such as the Law of the People’s Republic of China on Prevention and Control of Infectious Diseases, clinical manifestations and epidemiological characteristics of COVID-19 and guidelines on the prevention and control of this epidemic, combined with the practical work of forensic pathology examinations, we developed the Guide to Forensic Pathology Practice for Death Cases Related to Coronavirus Disease 2019 (COVID-19) (Trial Draft). This guide describes the background investigation of the death cases, autopsy room requirements, personal prevention and protections, external examinations, autopsy practices and auxiliary examinations, and thus offers a reference for forensic and pathological examination institutions and staff.

Increased inorganic nitrogen (N) and phosphorus (P) additions expected in the future will endanger the biodiversity and stability of agricultural ecosystems. In this context, a long-term fertilizer experiment (37 years) was set up in the black soil of northeast China. We examined interaction impacts of elevated fertilizer and host selection processes on arbuscular mycorrhizal fungi (AMF) communities in wheat rhizosphere soil using the Illumina MiSeq platform. The soil samples were subjected to five fertilization regimes: no fertilizer (CK) and low N (N1), low N plus low P (N1P1), high N (N2), and high N plus high P (N2P2) fertilizer. Long-term fertilization resulted in a significant shift in rhizosphere soil nutrient concentrations. The N fertilization (N1 and N2) did not significantly change rhizosphere AMF species diversity, but N plus P fertilization (N1P1 and N2P2) decreased it compared with CK. Non-metric multidimensional scaling showed that the rhizosphere AMF communities in CK, N1, N2, N1P1 and N2P2 treatments were distinct from each other. The AMF communities were predominantly composed of Glomeraceae, accounting for 30.0–39.1% of the sequences, and the relative abundance of family Glomeraceae was more abundance in fertilized soils, while family Paraglomeraceae were increased in N1 and N2 compared with CK. Analysis shown that AMF diversity was directly affected by soil C:P ratio but indirectly affected by plant under long-term fertilization. Overall, the results indicated that long-term N and P fertilization regimes changed rhizosphere AMF diversity and community composition, and rhizosphere AMF diversity was both affected by soil C:P ratio and plant.

Translating high-resolution imaging methods to the curved organic surface of a nanoparticle has been challenging. Here, the authors are able to spatially resolve the sub-molecular surface details of a silver nanocluster by comparing scanning tunneling microscopy images and simulated topography data through a pattern recognition algorithm.

Abstract Arbuscular mycorrhizal fungi (AMF) play vital roles in sustaining soil productivity and plant communities. However, adaption and differentiation of AMF in response to commonly used fertilization remain poorly understood. In this study, we showed that the AMF community composition was primarily driven by soil physiochemical changes associated with chronic inorganic and organic fertilization of 37 years in Mollisols. High-throughput sequencing indicated that inorganic fertilizer negatively affected AMF diversity and richness, implying a reduction of mutualism in plant–AMF symbiosis; however, a reverse trend was observed for the application of inorganic fertilizer combined with manure. With regards to AMF community composition, order Glomerales was dominant, but varied significantly among different fertilization treatments. All fertilization treatments decreased family Glomeraceae and genus Funneliformis, while Rhizophagus abundance increased. Plant-growth-promoting-microorganisms of family Claroideoglomeraceae and genus Claroideoglomus were stimulated by manure application, and likely benefited pathogen suppression and phosphorus (P) acquisition. Family Gigasporaceae and genus Gigaspora were negatively correlated with available P in soil. Additionally, redundancy analysis further suggested that soil available P, organic matter and pH were the most important factors in shaping AMF community composition. These results provide strong evidence for niche differentiation of phylogenetically distinct AMF populations under different fertilization regimes. Manure likely contributes to restoration and maintenance of plant–AMF symbiosis, and the balanced fertilization would favor the growth of beneficial AMF communities as one optimized management in support of sustainable agriculture in Mollisols.

Horizontal-axis tidal turbines (HATTs) have an acknowledged potential to extract a considerable amount of clean renewable energy from ocean tides. Among these, bidirectional HATTs (BHATTs) with bidirectional hydrofoils are thought to have higher economy than general HATTs. To improve the BHATTs, this study systemically investigated the influence of swept blades on the performance and hydrodynamics of the BHATT. A three-dimensional (3D) numerical model based on OpenFOAM was adopted to simulate a full-scale BHATT. The numerical framework was validated using two well-known experiments, and the mesh convergence was taken into consideration. The results indicate that the forward and backward swept blades have a limited impact on the performance and hydrodynamics of the BHATT. The upstream swept blade leads to a 4.3% decrease in the load on the rotor at design tip speed ratio (TSR) with a 2.0% decrease in the power. The BHATT with a downstream swept blade can produce 3.2% more energy at TSR = 6. Moreover, the swept blades have the opposite effect on the power of the BHATT at TSR = 6 and TSR = 9.

Abstract Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.

Abstract Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Chronic alcohol consumption leads to myocardial injury, ventricle dilation, and cardiac dysfunction, which is defined as alcoholic cardiomyopathy (ACM). To explore the induced myocardial injury and underlying mechanism of ACM, the Liber-DeCarli liquid diet was used to establish an animal model of ACM and histopathology, echocardiography, molecular biology, and metabolomics were employed. Hematoxylin-eosin and Masson’s trichrome staining revealed disordered myocardial structure and local fibrosis in the ACM group. Echocardiography revealed thinning wall and dilation of the left ventricle and decreased cardiac function in the ACM group, with increased serum levels of brain natriuretic peptide (BNP) and expression of myocardial BNP mRNA measured through enzyme-linked immunosorbent assay and real-time quantitative polymerase chain reaction (PCR), respectively. Through metabolomic analysis of myocardium specimens, 297 differentially expressed metabolites were identified which were involved in KEGG pathways related to the biosynthesis of unsaturated fatty acids, vitamin digestion and absorption, oxidative phosphorylation, pentose phosphate, and purine and pyrimidine metabolism. The present study demonstrated chronic alcohol consumption caused disordered cardiomyocyte structure, thinning and dilation of the left ventricle, and decreased cardiac function. Metabolomic analysis of myocardium specimens and KEGG enrichment analysis further demonstrated that several differentially expressed metabolites and pathways were involved in the ACM group, which suggests potential causes of myocardial injury due to chronic alcohol exposure and provides insight for further research elucidating the underlying mechanisms of ACM.

The Asian musk shrew (shrew) is a new reservoir of a rat hepatitis E virus (HEV) that has been classified into genotype HEV-C1 in the species Orthohepevirus C. However, there is no information regarding classification of the new rat HEV based on the entire genome sequences, and it remains unclear whether rat HEV transmits from shrews to humans. We herein inoculated nude rats (Long-Evans rnu/rnu) with a serum sample from a shrew trapped in China, which was positive for rat HEV RNA, to isolate and characterize the rat HEV distributed in shrews. A rat HEV strain, S1129, was recovered from feces of the infected nude rat, indicating that rat HEV was capable of replicating in rats. S1129 adapted and grew well in PLC/PRF/5 cells, and the recovered virus (S1129c1) infected Wistar rats. The entire genomes of S1129 and S1129c1 contain four open reading frames and share 78.3–81.8% of the nucleotide sequence identities with known rat HEV isolates, demonstrating that rat HEVs are genetically diverse. We proposed that genotype HEV-C1 be further classified into subtypes HEV-C1a to HEV-C1d and that the S1129 strain circulating in the shrew belonged to the new subtype HEV-C1d. Further studies should focus on whether the S1129 strain infects humans.

Influenza A(H7N9) virus emerged in eastern China in February 2013 and continues to circulate in this region, but its ecology is poorly understood. In April 2013, the Guangdong Provincial Center for Disease Control and Prevention (CDC) implemented environmental and human syndromic surveillance for the virus. Environmental samples from poultry markets in 21 city CDCs (n = 8,942) and respiratory samples from persons with influenza-like illness or pneumonia (n = 32,342) were tested; viruses isolated from 6 environmental samples and 16 patients were sequenced. Sequence analysis showed co-circulation of 4 influenza A(H7N9) virus strains that evolved by reassortment with avian influenza A(H9N2) viruses circulating in this region. In addition, an increase in human cases starting in late 2013 coincided with an increase in influenza A H7 virus isolates detected by environmental surveillance. Co-circulation of multiple avian influenza viruses that can infect humans highlights the need for increased surveillance of poultry and potential environmental sources.

A disease outbreak with dengue-like symptoms was reported in Guangdong Province, China, in October 2010. Testing results confirmed that the pathogen causing the outbreak was chikungunya virus. Phylogenic analysis indicated that this virus was a member of the Indian Ocean clade of the East/Center/South African subgroup of chikungunya virus.

BACKGROUND: Human Enterovirus 71 and Coxsackie A16 have caused many outbreaks in the last decade in mainland China, resulting in thousands of fatal cases. Seroepidemiology which provides important information to document population immunity is rare in China. METHODOLOGY/PRINCIPAL FINDINGS: A cross sectional study of Enterovirus 71 (EV71) and Coxsackie A16 (CA16) seroprevalence was carried out in Guangdong, China, pre- and post- the 2010 hand, foot and mouth disease (HFMD) epidemic period. The levels of EV71 and CA16 specific antibodies were evaluated by a microneutralization test and the geometric mean titer (GMT) was calculated and compared. Our results indicated frequent infection by EV71 and CA16 in Guangdong before the 2010 epidemic. Only EV71 neutralizing antibody but not CA16 seroprevalence was significantly increased after the 2010 HFMD epidemic. Children less than 3 years old especially those aged 2 years showed the lowest positive rates for EV71 and CA16 NA before epidemic and the most significantly increased EV71 seroprevalence after epidemic. CA16 GMT values declined after the 2010 epidemic. CONCLUSIONS: These results indicate EV71 was the major pathogen of HFMD in Guangdong during the 2010 epidemic. The infection occurs largely in children less than 3 years, who should have first priority to receive an EV71 vaccine.

BACKGROUND: Since 1997, several countries within the Asian Pacific region have been affected by one or more massive outbreaks of Hand Foot and Mouth Disease (HFMD). Virus typing experiments revealed that these outbreaks were caused by strains of human enterovirus 71 (EV71) belonging to several different, recently emerged subgenogroups. In mainland China, a different situation was observed. The first outbreak, localized in Shangdong Province, was reported in 2007, and was followed by a wide-spread outbreak in mainland China in 2008. Since then, numbers of reported HFMD cases have been persistently high. METHODOLOGY/PRINCIPAL FINDINGS: To gain insight in the epidemiological behavior of EV71 in China, we studied genetic diversity and EV71 population dynamics to address whether the increase in number of reported EV71 infections reflects a real increase in viral spread or is just the result of increased awareness and surveillance. We used systematically collected VP1 gene sequences of 257 EV71 strains collected in Guangdong province from 2008 to 2010 as part of HFMD surveillance activities, and supplemented them with 305 GenBank EV71 reference stains collected in China from 1998 to 2010. All isolates from Guangdong Province belonged to subgenogroup C4. Viral population dynamics indicated that the increased reporting of HFMD in China since 2007 reflects a real increase in viral spread and continued replacement of viral lineages through time. Amino acid sequence comparisons revealed substitution of amino acid in residues 22, 145 and 289 through time regularly with the VP1 gene of EV71 strains isolated in mainland China from 1998 to 2010. CONCLUSIONS: EV71 strains isolated in mainland China mainly belonged to subgenogroup C4. There was exponential growth of the EV71 virus population in 2007 and 2008. There was amino acid substitution through time regularly with the VP1 gene which possibly increased viral spread and/or ability of the virus to circulate persistently among the Chinese population.

Background: Traumatic brain injury (TBI) increases the risk of mental disorders and neurodegenerative diseases in the chronic phase. However, there is limited neuropathological or molecular data on the long-term neural dysfunction and its potential mechanism following adolescent TBI. Methods: A total of 160 male mice aged 8 weeks were used to mimic moderate TBI by controlled cortical impact. At 1, 3, 6 and 12 months post-injury (mpi), different neurological functions were evaluated by elevated plus maze, forced swimming test, sucrose preference test and Morris water maze. The levels of oxidative stress, antioxidant response, reactive astrocytes and microglia, and expression of inflammatory cytokines were subsequently assessed in the ipsilateral hippocampus, followed by neuronal apoptosis detection. Additionally, the morphological complexity of hippocampal astrocytes was evaluated by Sholl analysis. Results: The adolescent mice exhibited persistent and incremental deficits in memory and anxiety-like behavior after TBI, which were sharply exacerbated at 12 mpi. Depression-like behaviors were observed in TBI mice at 6 mpi and 12 mpi. Compared with the age-matched control mice, apoptotic neurons were observed in the ipsilateral hippocampus during the chronic phase of TBI, which were accompanied by enhanced oxidative stress, and expression of inflammatory cytokines (IL-1ß and TNF-a). Moreover, the reactive astrogliosis and microgliosis in the ipsilateral hippocampus were observed in the late phase of TBI, especially at 12 mpi. Conclusion: Adolescent TBI leads to incremental cognitive dysfunction, and depression- and anxiety-like behaviors in middle-aged mice. The chronic persistent neuroinflammation and oxidative stress account for the neuronal loss and neural dysfunction in the ipsilateral hippocampus. Our results provide evidence for the pathogenesis of chronic neural damage following TBI and shed new light on the treatment of TBI-induced late-phase neurological dysfunction. [ABSTRACT FROM AUTHOR]