Predicting types of human-related maritime accidents with explanations using selective ensemble learning and SHAP method.

Maritime accidents frequently lead to severe property damage and casualties, and an accurate and reliable risk prediction model is necessary to help maritime stakeholders assess the current risk situation. Therefore, the present study proposes a hybrid methodology to develop an explainable prediction model for maritime accident types. Based on the advantages of selective ensemble learning method, this study pioneers to introduce a two-stage model selection method, aiming to enhance the predictive accuracy and stability of the model. Then, SHAP (Shapley Additive Explanations) method is integrated to identify effective mapping associations of seafarers' unsafe acts and their risk factors with the prediction results. The results demonstrate that the model developed achieves good prediction performance with an accuracy of 87.50 % and an F1-score of 84.98 %, which benefits stakeholders in assessing the type of maritime accident in advance, so as to make proactive intervention measures.

Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM.

The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.

Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT.

The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length ß-tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases.

Investigation of electrochemical properties, leachate purification, organic matter characteristics, and microbial diversity in a sludge treatment wetland- microbial fuel cell.

Sludge treatment wetland-microbial fuel cell (STW-MFC) is a unique sludge treatment process that produces bioelectricity, but its technology is still in its infancy. This study investigated the electrochemical properties, organic matter characteristics, leachate purification, and microbial community structure of STW-MFCs as affected by electrode location. When electrodes were placed in the filler layer, the STW-MFC system presented a higher power generation capacity (maximum output power density: 0.498 W/m3; peak cell voltage: 0.879 V) and organic matter degradation efficiency. The hydrophilic fraction was the main dissolved organic carbon fraction in sludge extracellular biological organic matter (EBOM) and leachate dissolved organic matter (DOM). Aromatics were mainly concentrated in the hydrophobic acid fraction. The UV-254 content of sludge EBOM decreased mainly in the hydrophilic and transphilic acid fractions. The excitation-emission matrix analysis showed that tryptophan-like protein was more easily eliminated than tyrosine-like protein. In addition, there was a strong correlation between voltage and NH4+ removal efficiency; a negative correlation between total chemical oxygen demand (TCOD), total nitrogen (TN), and total phosphorus (TP) removal efficiency, and a negative correlation between pH and TN, TP, and NH4+ removal efficiencies. High-throughput sequencing showed that the system was most abundant in Thermomonas, Geothrix and Geobacter when the electrodes were placed in the filled layer, while the levels of genes for membrane transport, carbohydrate metabolism and energy metabolism functions were higher than in other systems. This work will support STW- MFC widespread implementation by illuminating the underlying mechanics of different anode positions.

Effects of substrate type on variation of sludge organic compounds, bioelectric production and microbial community structure in bioelectrochemically-assisted sludge treatment wetland.

A bioelectrochemical assisted sludge treatment wetland (BE-STW) is a promising technology used in the elimination of organic compounds and recovery of bio-energy. In this study, four BE-STW systems were constructed to investigate the effects of some substrates (i.e. graphite particles, zeolite, ceramsite, and gravel) on organic compounds biodegradation and transformation, electricity production, and anodic bacterial community. The maximum output voltages were 0.939, 0.870, 0.741 and 0.835 V, and the maximum power densities were 0.467, 0.143, 0.110, and 0.131 W/m3 for the graphite particles (BS-GP), zeolite (BS-Z), ceramsite (BS-C), and gravel (BS-G) systems, respectively. Also, the dissolved organic carbon (DOC) removal rates were 61.84%, 28.54%, 25.56%, and 18.34% in BS-GP, BS-G, BS-Z, and BS-C, respectively. The degradation of aromatic compounds in sludge extracellular biological organic matter (EBOM) was mainly due to the decrease of hydrophilic fraction (HPI) and transphilic acid fraction (TPI-A) contents. Moreover, aromatic proteins were preferentially removed in BS-Z. For BS-C, the tyrosine-like proteins and humic acid-like substances in TPI-A were totally removed. An excitation-emission matrix (EEM) analysis showed that the fluorescent intensity of the humic acid-like substances was the lowest in BS-GP, and no fluorescence peaks of fulvic acid-like substances were observed. Finally, at the genus level, Longilinea, Terrimonas, Ottowia, and Saccharibacteria_genera_incertae_sedis were the dominant bacteria in BE-STW, and Methylophilus was also only detected in BS-GP. These results confirmed that substrate materials have a significant impact on the preferentially degraded organic matter in BE-STWs, which can provide a theoretical basis for the practical application of STW in the future.

Insight into the organic matter degradation enhancement in the bioelectrochemically-assisted sludge treatment wetland: Transformation of the organic matter and microbial community evolution.

Sludge treatment wetland (STW) has been widely used to dewater and mineralize the various sludge, but the low degradation ability of organic matter can limit its application. Bioelectrochemistry has been proven to accelerate the degradation of organic compounds and recover bioenergy from the sludge. In this study, a bioelectrochemical-assisted sludge treatment wetland (BE-STW) system was constructed to determine the most common types of degraded organic matter and the functional bacterial community. It was found that the bioelectrochemistry process contributed to a further removal of the total chemical oxygen demand (TCOD) by 19% (±0.6) and the additional soluble chemical oxygen demand (SCOD) value was 64.10% (±0.63), with a voltage output of 0.961 V and a power density of 0.351 W/m3. The hydrophilic and hydrophobic acid fractions of the sludge were preferentially removed in BE-STW. The tryptophan-like protein and fulvic acid-like substances were totally removed, whereas, the hydrolysis of aromatic organic compounds in the neutral and hydrophobic acid fractions was enhanced. Also, the enrichment of Longilinea and Methylophilus improved the hydrolysis of organic matter. Moreover, the high relative abundance of Thauera, Dechloromonas, and Syntrophorhabdus could accelerate the degradation of aromatic compounds in the BE-STW system. The bacteria from the genus Geobacter was predominantly detected (2.48%) in the anodic biofilm on BE-STW. The results showed that bioelectrochemistry could improve the sludge stabilization degree in STW, accelerate the organic matter degradation and hydrolysis efficiency, and harvest bioelectricity, simultaneously. This technology can provide a new pathway to increase the efficiency of the traditional STW systems.

Cryo-EM of mammalian PA28αß-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αß.

The proteasome activator PA28αß affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αß-iCP structure, how PA28αß regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αß-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αß and iCP through XL-MS. Our structures reveal a slight leaning of PA28αß towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αß is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αß-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.

Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections.

The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for drug development for treating COVID-19. Here, we report the identification and characterization of two groups of mouse neutralizing monoclonal antibodies (MAbs) targeting the receptor-binding domain (RBD) on the SARS-CoV-2 spike (S) protein. MAbs 2H2 and 3C1, representing the two antibody groups, respectively, bind distinct epitopes and are compatible in formulating a noncompeting antibody cocktail. A humanized version of the 2H2/3C1 cocktail is found to potently neutralize authentic SARS-CoV-2 infection in vitro with half inhibitory concentration (IC50) of 12 ng/mL and effectively treat SARS-CoV-2-infected mice even when administered at as late as 24 h post-infection. We determine an ensemble of cryo-EM structures of 2H2 or 3C1 Fab in complex with the S trimer up to 3.8 Å resolution, revealing the conformational space of the antigen-antibody complexes and MAb-triggered stepwise allosteric rearrangements of the S trimer, delineating a previously uncharacterized dynamic process of coordinated binding of neutralizing antibodies to the trimeric S protein. Our findings provide important information for the development of MAb-based drugs for preventing and treating SARS-CoV-2 infections.

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM.

The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.

pH-Sensitive Nanoparticles Codelivering Docetaxel and Dihydroartemisinin Effectively Treat Breast Cancer by Enhancing Reactive Oxidative Species-Mediated Mitochondrial Apoptosis.

Tumor growth and metastasis are the major causes of high mortality in breast cancer. We previously constructed pH-sensitive nanoparticles (D/D NPs) for the codelivery of docetaxel (DTX) and dihydroartemisinin (DHA) and demonstrated that D/D NPs showed anticancer activity in breast cancer cells in vitro. The present study further investigated the therapeutic effect of D/D NPs on orthotopic breast cancer in vivo and examined the antitumor mechanism of D/D NPs. D/D NPs significantly increased the apoptosis of 4T1 cells with a synergistic effect of DTX and DHA. D/D NPs increased reactive oxygen species, reduced mitochondrial membrane potential, increased the expression of p53, and induced cytochrome c release into the cytoplasm to activate caspase-3. In an orthotopic metastatic breast cancer mouse model derived from 4T1 cells, D/D NPs inhibited tumor growth and prevented lung metastasis due to the synergistic effect of DTX and DHA. No distinct changes were observed in the histology of major organs. These results indicate that pH-sensitive D/D NP-based combination therapy may be a promising strategy for the treatment of metastatic breast cancers via the ROS-mediated mitochondrial apoptosis pathway.