AttCON: With better MSAs and attention mechanism for accurate protein contact map prediction.

Protein contact map prediction is a critical and vital step in protein structure prediction, and its accuracy is highly contingent upon the feature representations of protein sequence information and the efficacy of deep learning models. In this paper, we propose an algorithm, DeepMSA+, to generate protein multiple sequence alignments (MSAs) and to construct feature representations based on co-evolutionary information and sequence information derived from MSAs. We also propose an improved deep learning model, AttCON, for training input features to predict protein contact map. The model incorporates an attention module, and by comparing different attention modules, we find a parameter-free attention module suitable for contact map prediction. Additionally, we use the Focal Loss function to better address the data imbalance issue in protein contact map. We also developed a weighted evaluation index (W score) for model evaluation, which takes into account a wide range of metrics. W score is comprehensive in its scope, with a particular focus on the precision of predictions for medium-range and long-range contacts. Experimental results show that AttCON achieves good precision results on datasets from CASP11 to CASP15. Compared to some state-of-the-art methods, it achieves an average improvement of over 5% in both medium-range and long-range predictions, and W score is improved by an average of 2 points.

Correction to "Review of Advances in the Utilization of Biochar-Derived Catalysts for Biodiesel Production".

[This corrects the article DOI: 10.1021/acsomega.2c07909.].

Review of Advances in the Utilization of Biochar-Derived Catalysts for Biodiesel Production.

Biochar, obtained from the thermal decomposition of different biomass sources, can be used in various scientific technologies by virtue of its distinguishing performance. Recent developments in advanced biochar synthesis methods have led to continuous growth in the literature related to bulk biochar products and synthesized biochar substrates. This review specifically summarizes the current advanced methods for the synthesis of functional biochar catalysts and applications in (trans)esterification. Herein, first the method and design of synthesized biochar substrate catalysts are briefly introduced. Second, the applications of these synthesized biochar substrate catalysts upon (trans)esterification are comprehensively discussed. Finally, the current research status and the future perspectives of the synthesized biochar substrate catalyst are presented. It is expected that this summary will provide perspectives and instructions for future work on synthesized biochar catalysts for biodiesel products.

Exploiting the Waste Biomass of Durian Shell as a Heterogeneous Catalyst for Biodiesel Production at Room Temperature.

Durian shell, a biomass waste, was simply burned and then could serve as a heterogeneous catalyst for the transesterification reaction of palm oil with methanol at room temperature. The chemical composition, structure, and morphology of the catalyst were well-characterized by XRD, BET, SEM, TEM, EDS, TGA, FT-IR, and XPS measurement. With the preparation temperature rising to 350 °C, the maximum yield of the biodiesel could reach 94.1% at room temperature, and the optimum reaction conditions were 8 wt.% catalyst, 8:1 methanol/oil molar ratio, ad 2.5 h reaction time. The characterizations results indicated that K2O and K2CO3 existed on the surface of catalyst, and a moderate amount of carbon, which acts as a carrier, attributed to the activity of the catalyst. After repeating five times, the catalyst prepared at 350 °C showed better stability than other catalysts. This might be because the incomplete combustion of the remaining carbon slowed down the loss of K to some extent.

Protein sensors combining both on-and-off model for antibody homogeneous assay.

Protein sensors based on allosteric enzymes responding to target binding with rapid changes in enzymatic activity are potential tools for homogeneous assays. However, a high signal-to-noise ratio (S/N) is difficult to achieve in their construction. A high S/N is critical to discriminate signals from the background, a phenomenon that might largely vary among serum samples from different individuals. Herein, based on the modularized luciferase NanoLuc, we designed a novel biosensor called NanoSwitch. This sensor allows direct detection of antibodies in 1 µl serum in 45 min without washing steps. In the detection of Flag and HA antibodies, NanoSwitches respond to antibodies with S/N ratios of 33-fold and 42-fold, respectively. Further, we constructed a NanoSwitch for detecting SARS-CoV-2-specific antibodies, which showed over 200-fold S/N in serum samples. High S/N was achieved by a new working model, combining the turn-off of the sensor with human serum albumin and turn-on with a specific antibody. Also, we constructed NanoSwitches for detecting antibodies against the core protein of hepatitis C virus (HCV) and gp41 of the human immunodeficiency virus (HIV). Interestingly, these sensors demonstrated a high S/N and good performance in the assays of clinical samples; this was partly attributed to the combination of off-and-on models. In summary, we provide a novel type of protein sensor and a working model that potentially guides new sensor design with better performance.

Fast Gelation of Poly(ionic liquid)-Based Injectable Antibacterial Hydrogels.

Traditional antibacterial hydrogels have a broad-spectrum bactericidal effect and are widely used as wound dressings. However, the biological toxicity and drug resistance of these antibacterial hydrogels cannot meet the requirements of long-term clinical application. Imidazolium poly(ionic liquids) (PILs) are polymeric antibacterial agents exhibiting strong antibacterial properties, as they contain a strong positive charge. In this study, two imidazolium PILs, namely poly(N-butylimidazolium propiolic acid sodium) (PBP) and poly(N-(3,6-dioxaoctane) imidazolium propiolic acid sodium) (PDP), as high efficiency antibacterial agents, were synthesized by polycondensation reaction. Then, the PILs were compounded with polyethylene glycol (PEG) by a thiol-yne click reaction to prepare injectable antibacterial hydrogels. An in vitro assay showed that the injectable antibacterial hydrogels could not only quickly kill Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), but also had low toxicity for human skin fibroblasts cells (HSFs) and human umbilical vein endothelial cells (HUVECs), respectively. Additionally, the lipopolysaccharide (LPS) inflammation model revealed that the injectable antibacterial hydrogels also had anti-inflammatory effects, which would be advantageous to accelerate wound healing.

Biomimetic Nonuniform, Dual-Stimuli Self-Morphing Enabled by Gradient Four-Dimensional Printing.

Programmable nonuniform deformation is of great significance for self-shape-morphing systems that are commonly seen in biological systems and also has practical applications in drug delivery, biomedical devices and robotics, etc. Here, we present a novel gradient four-dimensional (4D) printing method toward biomimetic nonuniform, dual-stimuli self-morphing. By modeling and printing graded active materials with water swelling properties, we can configure continuously smooth gradients of volume fraction of the active material in bilayer structures. The variation of swelling ratio mismatch between the two layers can be delicately regulated, which results in the programmable nonuniform shape transformation. The shape-shifting results can be predicted by the established mathematical model and computational simulations. Furthermore, we demonstrate dual-stimuli self-morphing structures by printing the graded water-responsive elastomer materials onto a heat-shrinkable shape memory polymer, which could produce different shape changes in response to humidity and different temperatures. This method pioneers a versatile approach to broaden the design space for 4D printing and will be compatible with a wide range of active materials meeting various requirements in diverse potential applications.

A study on the tubular composite with tunable compression mechanical behavior inspired by wood cell.

Biological materials have fascinating mechanical properties built up from simple basic material blocks. It is worthwhile to learn how biological materials are constructed, and to apply the knowledge in advanced manufacturing, and to realize new materials by design. In this study, we chose the tubular cell in the soft wood as a biological prototype, and tried to mimic its intelligent construction principle to regulate the compression mechanical behavior through the helical structure. First, by using the multi-material three-dimensional printing technology, we fabricated a series of tubular composites with the helix fibers of a rigid plastic embedded into an elastomeric matrix. Then, through the uniaxial compression tests, we characterized the mechanical behavior of the specimens, having different fiber angle from 0 to 50 deg at constant volume fraction. The results showed that both stiffness and fracture toughness of the printed composite could be regulated effectively by adjusting the fiber angle of the helical structure. Moreover, the helical structure with high fiber angle is able to improve the compression stability of the tubular composite with big lumen. In addition, for the biomimetic composites, the volume fraction of the reinforcements should exceed 40%. Finally, we proposed a new structural design method by combining the reinforcements of different architectures into a double-layered configuration. The intelligent strategy is proven to balance the conflict between the stiffness and toughness of the composites to some extent, and without changing in the building constituents.

Demonstration of a thermo-optic phase shifter by utilizing high-Q resonance in high-index-contrast grating.

A thermo-optic phase shifter is proposed and demonstrated by utilizing the high-Q resonance in high-index-contrast grating (HCG). The Q-factor up to ∼12000 is measured in a footprint of 110 µm×300 µm. By heating the HCG with paired metal strip micro-heaters, the optical resonance shifts, which induces phase modulation. A phase shift of ∼1.2π under heating power of ∼32 mW is directly observed and demodulated from the fringes shifting in a Michelson interferometer. The proposed configuration can also be extended to realize high-speed phase shift by adopting electro-optical modulation.

Blueprint for Large-Scale Silicon Optical Phased Array Using Electro-Optical Micro-Ring Pixels.

We propose a modularized architecture of a large-scale optical phased array (OPA) on a silicon on insulator (SOI) platform, using electro-optical (EO) pixels. Each pixel contains a directional coupler, a micro-ring phase shifter, and a grating optical antenna, on a compact configuration of area 50 µm × 50 µm, with optical and electrical interconnections. Moreover, we present an exemplary blueprint of an OPA consisting of 32 × 32 EO pixels, which sets the width of the main lobe as 0.04° × 0.04° and the field of view as 1.78°. By applying an over-coupled condition, the modulation efficiency and the accompanying intensity modulation are balanced, thus, the OPA performance is not severely degraded. The discussion on the fabrication tolerance shows that the proposed architecture is robust and feasible regarding the state-of-the-art fabrication process, and the performance of the main lobe width and field of view can be further optimized by a larger system size and smaller pixel size. Furthermore, the complexity of interconnections linearly depends on the number of rows and columns, making it highly scalable.

Process Parameter Optimization of Extrusion-Based 3D Metal Printing Utilizing PW-LDPE-SA Binder System.

Recently, with a broadening range of available materials and alteration of feeding processes, several extrusion-based 3D printing processes for metal materials have been developed. An emerging process is applicable for the fabrication of metal parts into electronics and composites. In this paper, some critical parameters of extrusion-based 3D printing processes were optimized by a series of experiments with a melting extrusion printer. The raw materials were copper powder and a thermoplastic organic binder system and the system included paraffin wax, low density polyethylene, and stearic acid (PW-LDPE-SA). The homogeneity and rheological behaviour of the raw materials, the strength of the green samples, and the hardness of the sintered samples were investigated. Moreover, the printing and sintering parameters were optimized with an orthogonal design method. The influence factors in regard to the ultimate tensile strength of the green samples can be described as follows: infill degree > raster angle > layer thickness. As for the sintering process, the major factor on hardness is sintering temperature, followed by holding time and heating rate. The highest hardness of the sintered samples was very close to the average hardness of commercially pure copper material. Generally, the extrusion-based printing process for producing metal materials is a promising strategy because it has some advantages over traditional approaches for cost, efficiency, and simplicity.

Morphological and confocal laser scanning microscopic investigations of the adductor muscle-shell interface in scallop.

The challenge of joining dissimilar advanced materials has led researchers around the world to search for new and more efficient solutions. This way, we can highlight the muscle-shell attachment in mollusk, which possessed high strength and toughness. In order to make clear how this "bi-material interface" derives its superior mechanical properties, the morphological features of the adductor muscle scar in Patinopecten yessoensis was investigated by means of confocal laser scanning microscopy (CLSM). This scar area was found to consist of a myostracum with many evenly distributed pit structures and a fracture section with a parallel arranged prism-like structure. The measured values of the distribution density, diameter, and depth of those pit structures were 24 ± 4/49,152 µm2, 7.36 ± 2.47 µm, and 1 ± 0.31 µm respectively. Profile of each pit wall was arc curve without closed angle. Furthermore, CLSM micrographs showed that considerable micro pits (0.1-0.9 µm in diameter) distribute round the pit wall and on the pit bottom. This special micromorphology is the first report on the adductor muscle scar in scallop. In addition, the mineral state and mechanical property of the scar surface was analyzed by XRD and nanoindentation test respectively. In general, the study results presented in this work elucidated that the adductor muscle of P. yessoensis was attached to the shell by insertion of collagen fibers and fibril bundles branched from themselves into pits on the myostracum. This specific connection mechanism can increase the strength of the interface without compromising its ductility and toughness.

Functional analysis of ß-amyrin synthase gene in ginsenoside biosynthesis by RNA interference.

KEY MESSAGE: Down-regulation of ß-amyrin synthase gene expression by RNA interference led to reduced levels of ß-amyrin and oleanane-type ginsenoside as well as up-regulation of dammarane-type ginsenoside level. In the biosynthetic pathway of ginsenosides, ß-amyrin synthase catalyzes the reaction from oxidosqualene to ß-amyrin, the proposed aglycone of oleanane-type saponins. Here, RNAi was employed to evaluate the role of this gene in ginsenoside biosynthesis of Panax ginseng hairy roots. The results showed that RNAi-mediated down-regulation of this gene led to reduced levels of ß-amyrin and oleanane-type ginsenoside Ro as well as increased level of total ginsenosides, indicating an important role of this gene in biosynthesis of ginsenoside. Expression of key genes involved in dammarane-type ginsenoside including genes of dammarenediol synthase and protopanaxadiol and protopanaxatriol synthases were up-regulated in RNAi lines. While expression of squalene synthase genes was not significantly changed, ß-amyrin oxidase gene was down-regulated. This work will be helpful for further understanding ginsenoside biosynthesis pathway.