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Endemic to the upper and middle reaches of the Yangtze River in China, elongate loach (Leptobotia elongata) has become a vulnerable species mainly due to overfishing and habitat destruction. Thus far, no genome data of this species are reported. As a result, lacking of such genomic information has restricted practical conservation and utilization of this economic fish. Here, we constructed chromosome-level genome assemblies for both male and female elongate loach by integration of MGI, PacBio HiFi and Hi-C sequencing technologies. Two primary genome assemblies (586-Mb and 589-Mb) were obtained for female and male fishes, respectively. Indeed, 98.22% and 98.61% of the contig sequences were anchored onto 25 chromosomes, with identification of 26.22% and 25.92% repeat contents in both assembled genomes. Meanwhile, a total of 25,215 and 25,253 protein-coding genes were annotated, of which 97.41% and 98.8% could be predicted with functions. Taken together, our genome data presented here provide a valuable genomic resource for in-depth evolutionary and functional research, as well as molecular breeding and conservation of this economic fish species.
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Cromosomas , Cipriniformes , Genoma , Animales , Femenino , Masculino , Cipriniformes/genética , ChinaRESUMEN
In silicon carbide processing, the surface and subsurface damage caused by fixed abrasive grinding significantly affects the allowance of the next polishing process. A novel grinding wheel with a soft and hard composite structure was fabricated for the ultra-precision processing of SiC substrates, and the grinding performance of the grinding wheel was assessed in this study. Different types of gels, heating temperatures, and composition ratios were used to fabricate the grinding wheel. The grinding performance of the grinding wheel was investigated based on the surface integrity and subsurface damage of SiC substrates. The results showed that the grinding wheel with a soft and hard composite structure was successfully fabricated using freeze-dried gel with a heating temperature of 110 °C, and the component ratio of resin to gel was 4:6. A smooth SiC substrate surface with almost no cracks was obtained after processing with the grinding wheel. The abrasive exposure height was controlled by manipulating the type and ratio of the gel. Furthermore, the cutting depth in nanoscale could be achieved by controlling the abrasive exposure height. Therefore, the fabrication and application of the grinding wheels with soft and hard composite structures is important for the ultra-precision processing of large-size SiC substrates.
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Antigen presentation on MHC class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an anti-drug response. Significant progress has been made in pMHCII presentation modeling due to the collection of large-scale pMHC mass spectrometry datasets (ligandomes) and advances in machine learning. Here, we develop graph-pMHC, a graph neural network approach to predict pMHCII presentation. We derive adjacency matrices for pMHCII using Alphafold2-multimer and address the peptide-MHC binding groove alignment problem with a simple graph enumeration strategy. We demonstrate that graph-pMHC dramatically outperforms methods with suboptimal inductive biases, such as the multilayer-perceptron-based NetMHCIIpan-4.0 (+20.17% absolute average precision). Finally, we create an antibody drug immunogenicity dataset from clinical trial data and develop a method for measuring anti-antibody immunogenicity risk using pMHCII presentation models. Our model increases receiver operating characteristic curve (ROC)-area under the ROC curve (AUC) by 2.57% compared to just filtering peptides by hits in OASis alone for predicting antibody drug immunogenicity.
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Antígenos de Histocompatibilidad Clase II , Péptidos , Presentación de Antígeno , Antígenos de Histocompatibilidad Clase II/química , Redes Neurales de la Computación , Péptidos/química , HumanosRESUMEN
Objective: We aimed to determine the reliability of using the Fibrosis-4 (FIB-4) index in COVID-19 patients without underlying liver illness. Method: We employed multivariate logistic regression to identify variables that exhibited statistically significant influence on the ultimate outcome. Multilayer perceptron analysis was employed to develop a prediction model for the FIB-4 index concerning ICU admission and intubation rates. However, the scarcity of cases rendered the assessment of the mortality rate unfeasible. We plotted ROC curves to analyze the predictive strength of the FIB-4 index across various age groups. Result: In univariate logistic regression, only the FIB-4 index and respiratory rate demonstrated statistical significance on all poor outcomes. The FIB-4 index for mortality prediction had an ROC and AUC of 0.863 (95% CI: 0.781-0.9444). It demonstrates predictive power across age groups, particularly for age ≥65 (AUC: 0.812, 95% CI: 0.6571-0.9673) and age <65 (AUC: 0.878, 95% CI: 0.8012-0.9558). Its sensitivity for intubation and ICU admission prediction is suboptimal. Conclusion: FIB-4 index had promising power in prediction of mortality rate in all age groups.
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INTRODUCTION: Mudskippers are a large group of amphibious fishes that have developed many morphological and physiological capacities to live on land. Genomics comparisons of chromosome-level genome assemblies of three representative mudskippers, Boleophthalmus pectinirostris (BP), Periophthalmus magnuspinnatus (PM) and P. modestus (PMO), may be able to provide novel insights into the water-to-land evolution and adaptation. METHODS: Two chromosome-level genome assemblies for BP and PM were respectively sequenced by an integration of PacBio, Nanopore and Hi-C sequencing. A series of standard assembly and annotation pipelines were subsequently performed for both mudskippers. We also re-annotated the PMO genome, downloaded from NCBI, to obtain a redundancy-reduced annotation. Three-way comparative analyses of the three mudskipper genomes in a large scale were carried out to discover detailed genomic differences, such as different gene sizes, and potential chromosomal fission and fusion events. Comparisons of several representative gene families among the three amphibious mudskippers and some other teleosts were also performed to find some molecular clues for terrestrial adaptation. RESULTS: We obtained two high-quality haplotype genome assemblies with 23 and 25 chromosomes for BP and PM respectively. We also found two specific chromosome fission events in PM. Ancestor chromosome analysis has discovered a common fusion event in mudskipper ancestor. This fusion was then retained in all the three mudskipper species. A loss of some SCPP (secretory calcium-binding phosphoprotein) genes were identified in the three mudskipper genomes, which could lead to reduction of scales for a part-time terrestrial residence. The loss of aanat1a gene, encoding an important enzyme (arylalkylamine N-acetyltransferase 1a, AANAT1a) for dopamine metabolism and melatonin biosynthesis, was confirmed in PM but not in PMO (as previously reported existence in BP), suggesting a better air vision of PM than both PMO and BP. Such a tiny variation within the genus Periophthalmus exemplifies to prove a step-by-step evolution for the mudskippers' water-to-land adaptation. CONCLUSION: These high-quality mudskipper genome assemblies will become valuable genetic resources for in-depth discovery of genomic evolution for the terrestrial adaptation of amphibious fishes.
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Perciformes , Agua , Animales , Genómica , Peces/genética , Perciformes/genética , CromosomasRESUMEN
For NiTi alloys prepared by the Laser Powder Bed Fusion (LPBF), changes in the building directions will directly change the preferred orientation and thus directly affect the smart properties, such as superelasticity, as well as change the distribution state of defects and impurity elements to affect the phase transformation behaviour, which in turn affects the smart properties at different temperatures. In this study, the relationship between impurity elements, the building directions, and functional properties; the effects of building directions on the crystallographic anisotropy; phase composition; superelastic properties; microhardness; geometrically necessary dislocation (GND) density; and impurity element content of NiTi SMAs fabricated by LPBF were systematically studied. Three building directions measured from the substrate, namely, 0°, 45° and 90°, were selected, and three sets of cylindrical samples were fabricated with the same process parameters. Along the building direction, a strong <100>//vertical direction (VD) texture was formed for all the samples. Because of the difference in transformation temperature, when tested at 15 °C, the sample with the 45° orientation possessed the highest strain recovery of 3.2%. When tested at the austenite phase transformation finish temperature (Af)+10 °C, the 90° sample had the highest strain recovery of 5.83% and a strain recovery rate of 83.3%. The sample with the 90° orientation presented the highest microhardness, which was attributed to its high dislocation density. Meanwhile, different building directions had an effect on the contents of O, C, and N impurity elements, which affected the transformation temperature by changing the Ni/Ti ratio. This study innovatively studied the impurity element content and GND densities of compressive samples with three building directions, providing theoretical guidance for LPBFed NiTi SMA structural parts.
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Wood has a rich three-dimensional pore structure and many bottom-up nanochannels. However, the structure of wood itself has limited ability to adsorb dyes, so the effective combination of the unique structure of wood and Pd NPs was studied to achieve efficient degradation of dyes. First, the three-dimensional structure of natural wood is optimized by combining the complex pore structure of wood with Pd NPs to improve the contact process between the dye and Pd NPs. Then, Pd (II) ion can be well reduced to Pd NPs by wood lignin. In addition, Pd NPs can be fixed by hydroxyl groups on cellulose in wood. The flow state inside Pd NPs/wood film and the contact area between catalyst and dye were discussed in detail by hydrodynamic simulation, which filled the gap. It provides reference for composite structure. When Pd NPs/wood membrane was used to treat methylene blue (MB), the degradation efficiency was up to 96.7%, which was 90% higher than that of natural wood. Its TOF value was 1.82 molMB molPd-1min-1, which was higher than that in the previous literature. Therefore, the novelty of this study is that the mechanism of catalytic degradation of MB by Pd nanoparticles/wood composites is reported for the first time. The internal flow mode and contact condition of the new material are understood, which has a good application prospect.
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Nanopartículas del Metal , Azul de Metileno , Azul de Metileno/química , Madera , Colorantes/química , Lignina , Nanopartículas del Metal/químicaRESUMEN
Developing wide spectra-responsive photocatalysts has attracted considerable attention in the photocatalytic technology to achieve excellent catalytic activity. Ag3PO4, with strong response to light spectra shorter than 530 nm, shows extremely outstanding photocatalytic oxidation ability. Unfortunately, the photocorrosion of Ag3PO4 is still the biggest obstacle to its application. Herein, the La2Ti2O7 nanorod was used to anchor Ag3PO4 nanoparticles in this study, and a novel Z-Scheme La2Ti2O7/Ag3PO4 heterostructure composite was constructed. Remarkably, the composite showed strong responsive to most of the spectra in natural sunlight. The Ag0 formed in-situ acted as the recombination center of photogenerated carriers, which promoted their efficient separation and contributed to the improved photocatalytic performance of the heterostructure. When the mass ratio of Ag3PO4 in the La2Ti2O7/Ag3PO4 catalyst was 50%, the degradation rate constant of Rhodamine B (RhB), methyl orange (MO), chloroquine phosphate (CQ), tetracycline (TC), and phenol under natural sunlight irradiation were 0.5923, 0.4463, 0.1399, 0.0493, and 0.0096 min-1, respectively. Furthermore, the photocorrosion of the composite was greatly inhibited, 76.49% of CQ and 83.96% of RhB were still degraded after four cycles. Besides, the holes and O2â¢- played a significant role in RhB degradation, and it included multiple mechanisms of deethylation, deamination, decarboxylation, and cleavage of ring-structures. Moreover, the treated solution can also show safety to the water receiving environment. Overall, the synthesized Z-Scheme La2Ti2O7/Ag3PO4 composite exhibited immense potential for removing various organic pollutants through photocatalytic technology under natural sunlight irradiation.
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Nanotubos , Luz Solar , Titanio , Fosfatos/química , Compuestos de PlataRESUMEN
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as "MNË® and "LAË® respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.
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Ecocardiografía , Ventrículos Cardíacos , Humanos , Femenino , Ventrículos Cardíacos/diagnóstico por imagen , TóraxRESUMEN
For NiTi alloys, different additive manufacturing processes may have different compressive recovery capabilities. In particular, there are relatively few studies on the compressive recovery ability of NiTi alloys by the laser-directed energy deposition (LDED) process. In this paper, the compression recovery properties of NiTi alloys with the LDED process were investigated quasi-in-situ by means of transmission electron microscopy, an electron backscatter diffractometer, and focused ion beam-fixed-point sample preparation. The results showed that the material can be completely recovered under 4% deformation and the B19' martensite phase content and dislocation density are basically unchanged. However, the recovery rate was only 90% and the unrecoverable strain was 0.86% at 8% deformation. Meanwhile, the B19' martensite phase content and dislocation density of the material increased. Furthermore, with the increase in deformation, the relative dislocation pinning effect of the Ti2Ni precipitated phase in the alloy was enhanced, which reduced the compressive strain recovery to a certain extent.
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The motility ability of intestinal lipopolysaccharide (LPS)-producing bacteria determines their translocation to the enterohepatic circulation and works as an infectious complication. In this study, the health effects of Cordyceps militaris polysaccharides (CMPs) were re-evaluated based on whether these polysaccharides could affect the motility of gut commensal LPS-producing bacteria and impede their translocation. The results showed that CMP-m fermentation in the gut could change the chemical environment, leading to a decrease in velocity and a shift in the motility pattern. Further study suggested that detachment/fragmentation of flagella, decreased motor forces, and changed chemical conditions might account for this weakened motility. The adhesion and invasion abilities of gut bacteria were also reduced, with lower expression of virulence-related genes. These results indicated that the health regulation effects of CMP-m might be through decreasing the motility of LPS-producing bacteria, hindering their translocation and therefore reducing the LPS level in the enterohepatic circulation.
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Cordyceps , Microbioma Gastrointestinal , Bacterias/metabolismo , Cordyceps/metabolismo , Fermentación , Lipopolisacáridos/metabolismo , Polisacáridos/farmacología , Polisacáridos/metabolismoRESUMEN
Large amount of municipal sludge is difficult to handle; its resource utilization is an effective measure. In this study, the municipal sludge from sewage treatment plant was pyrolyzed without gas protection at different temperatures and potassium hydroxide (KOH) concentrations for activation. The pyrolysis products, named biomass ash, with higher surface area and enriched pore structures could be obtained at the pyrolysis temperature of 773 K. Moreover, the KOH activation for raw municipal sludge could further increase the surface area of the pyrolysis biomass ash. The maximum specific surface area was 44.71 m2/g, which was obtained under 2 mol/L KOH activation before pyrolysis at 773 K. And in this situation, the obtained pyrolysis biomass ash as adsorbent showed the maximum adsorption capacity of 50.75 mg/g toward tetracycline (TC). Moreover, the TC adsorption onto pyrolysis biomass ash obtained under various conditions followed the pseudo-second-order kinetic model. Adsorption thermodynamics analysis suggested the TC adsorption onto the pyrolysis biomass ash with no pre-activation was mainly due to the multi-molecule heterogeneous adsorption, while the TC adsorption onto pyrolysis biomass ash pretreated through the activation of KOH followed the monomer adsorption mechanism. This different adsorption mechanism was largely related to the pore structure, polarity, and aromaticity of the adsorbent.
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Pirólisis , Aguas del Alcantarillado , Aguas del Alcantarillado/química , Adsorción , Temperatura , Biomasa , Carbón Orgánico/química , Tetraciclina/química , AntibacterianosRESUMEN
The municipal sludge activated by FeCl3 solution was pyrolyzed at 500 °C without gas protection, and the pyrolysis products, named as biomass ash, could effectively adsorb tetracycline (TC) from aqueous solution. Different FeCl3 concentrations could directly affect the physicochemical properties of the biomass ash, so that the biomass ash as adsorbent showed different adsorption efficiency toward TC. The activation of FeCl3 increased the oxygen-containing functional groups and surface polarities of the biomass ash. When the concentration of FeCl3 solution was 0.5 mol/L, the biomass ash behaved the maximum specific surface area (37.74 m2/g) and the best adsorption efficiency. The pseudo-second-order kinetics model and the Freundlich multi-molecule model could fully explain the TC adsorption process by the biomass ash pyrolyzed from municipal sludge activated by FeCl3. Moreover, the adsorption mechanism was mainly attributed to the chemical adsorption.
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Pirólisis , Contaminantes Químicos del Agua , Adsorción , Antibacterianos , Biomasa , Carbón Orgánico/química , Cinética , Oxígeno , Aguas del Alcantarillado/química , Tetraciclina/química , Contaminantes Químicos del Agua/análisisRESUMEN
Semiconductor photocatalysis technology has shown great potential in the field of organic pollutant removal, as it can use clean and pollution-free solar energy as driving force. The discovery of silver phosphate (Ag3PO4) is a major breakthrough in the field of visible light responsive semiconductor photocatalysis due to its robust capacity to absorb visible light < 520 nm. Furthermore, the holes produced in Ag3PO4 under light excitation possess a strong oxidation ability. However, the strong oxidation activity of Ag3PO4 is only achieved in the presence of electron sacrifice agents. Otherwise, photocorrosion would greatly reduce the reuse efficiency of Ag3PO4. This review thus focuses on the structural characteristics and preparation methods of Ag3PO4. Particularly, the recent advances in noble metal deposition, ion doping, and semiconductor coupling, as well as methods of magnetic composite modification for the improvement of catalytic activity and recycling efficiency of Ag3PO4-based catalysts, were also discussed, and all of these measures could enhance the catalytic performance of Ag3PO4 toward organic pollutants degradation. Additionally, some potential modification methods for Ag3PO4 were also proposed. This review thus provides insights into the advantages and disadvantages of the application of Ag3PO4 in the field of photocatalysis, clarifies the photocorrosion essence of Ag3PO4, and reveals the means to improve photocatalytic activity and stability of Ag3PO4. Furthermore, it provides a theoretical and methodological basis for studying Ag3PO4-based photocatalyst and also compiles valuable information regarding the photocatalytic treatment of organic polluted wastewater.
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Purificación del Agua , Catálisis , Luz , Magnetismo , Luz SolarRESUMEN
The semiconductor photocatalytic technology has been considerably studied due to its excellent catalytic performance in water pollution control. Herein, in this study, novel SrCoO3/Ag3PO4 composite materials with different SrCoO3 content were synthesized via a simple hydrothermal synthesis method. The characteristics of the as-prepared samples were detected through SEM/HRTEM, XRD, UV-vis DRS, PL, ESR, FT-IR, and XPS techniques, and then, the photocatalytic performance of SrCoO3/Ag3PO4 toward the degradation of tetracycline was investigated. When the mass ratio of SrCoO3 and Ag3PO4 in the composite was 1:1.5, the degradation rate constant of tetracycline in SrCoO3/Ag3PO4 (1:1.5) system is 0.0102 min-1, which is 1.7 times that of the Ag3PO4, and 3.78 times that of the SrCoO3. In addition, reactive species were also analyzed through the free radical trapping experiment and DMPO spin-trapping ESR spectra analysis, showing that OHâ¢, h+, and O2â¢-participated in the catalytic degradation process of tetracycline to varying degrees. Finally, the photocatalytic mechanism of SrCoO3/Ag3PO4 was also proposed.
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Fosfatos , Compuestos de Plata , Luz , Espectroscopía Infrarroja por Transformada de Fourier , TetraciclinaRESUMEN
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5â¯Mb, a scaffold N50 of 29.5â¯Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.