Search

Development of protein 3-D structural comparison methods is important in understanding protein functions. At the same time, developing such a method is very challenging. In the last 40 years, ever since the development of the first automated structural method, ~200 papers were published using different representations of structures. The existing methods can be divided into five categories: sequence-, distance-, secondary structure-, geometry-based, and network-based structural comparisons. Each has its uniqueness, but also limitations. We have developed a novel method where the 3-D structure of a protein is modeled using the concept of Triangular Spatial Relationship (TSR), where triangles are constructed with the Cα atoms of a protein as vertices. Every triangle is represented using an integer, which we denote as “key,” A key is computed using the length, angle, and vertex labels based on a rule-based formula, which ensures assignment of the same key to identical TSRs across proteins. A structure is thereby represented by a vector of integers. Our method is able to accurately quantify similarity of structure or substructure by matching numbers of identical keys between two proteins. The uniqueness of our method includes: (i) a unique way to represent structures to avoid performing structural superimposition; (ii) use of triangles to represent substructures as it is the simplest primitive to capture shape; (iii) complex structure comparison is achieved by matching integers corresponding to multiple TSRs. Every substructure of one protein is compared to every other substructure in a different protein. The method is used in the studies of proteases and kinases because they play essential roles in cell signaling, and a majority of these constitute drug targets. The new motifs or substructures we identified specifically for proteases and kinases provide a deeper insight into their structural relations. Furthermore, the method provides a unique way to study protein conformational changes. In addition, the results from CATH and SCOP data sets clearly demonstrate that our method can distinguish alpha helices from beta pleated sheets and vice versa. Our method has the potential to be developed into a powerful tool for efficient structure-BLAST search and comparison, just as BLAST is for sequence search and alignment.

Composites are widely used in aircraft structures that have free edges and are vulnerable to impact events during manufacturing and maintenance. On-edge impact may have a great contribution in terms of the compression strength loss of composites, but the influence remains unclear. This paper presents experiments and simulations of carbon-fiber-reinforced plastic (CFRP) materials with on-edge impact and compression after edge impact (CAEI). On-edge impact damage was introduced to the composite laminates through the drop weight method with 4, 6, 8 and 10 J impact energies, respectively. A special guide-rail-type fixture was used in the compression tests in which strain–force and load–displacement relationships were obtained. A continuous-step finite element model was proposed to simulate impact and compression. Continuum shell elements and Hashin failure criteria were used to simulate in-ply damage, and interlaminar damage was modelled by cohesive elements. The model was validated by correlating the experimental and numerical results. The investigation results revealed the relationships of the damage size and residual strength with the different impact energies. The crack length and delaminated area grow with the increase in impact energy. The residual compressive strength follows a downward trend with increasing impact energy.

Lithium (Li)-rich manganese (Mn)-rich oxide (LMR) cathode materials, despite of the high specific capacity up to 250 mAh g−1 suffer from instability of cathode/electrolyte interfacial layer at high working voltages, causing continuous voltage decay and capacity fading, especially at elevated temperatures. In various battery systems, localized high-concentration electrolytes (LHCEs) have been widely reported as a promising candidate to form effective electrode/electrolyte interphases. Here, an optimized LHCE is studied in graphite (Gr)-based full cells containing LMR cathode, being cycled at 25, 45 and 60 °C with the reference of a conventional LiPF6-based electrolyte. It is revealed that the LHCE can effectively suppress continuous electrolyte decompositions and mitigate the dissolution of Mn ions due to the formation of more protective electrode/electrolyte interphases on both anode and cathode, which, in turn, lead to significantly improved cycling stability and enhanced rate capability under the selected temperatures. The mechanistic understanding on the failure of the conventional LiPF6-containing electrolyte and the function of the LHCE in Gr||LMR cells under high temperatures provides valuable perspectives of electrolyte development for practical applications of LMR cathodes in high energy density batteries over a wide temperature range.

Long non-coding RNAs (lncRNAs) are key regulators of a range of human diseases, including various cancers, with multiple previous studies having explored lncRNA dysregulation in the context of gastric cancer (GC). The present study sought to expand upon these previous results by downloading lncRNA, mRNA, and microRNA (miRNA) expression profiles derived from 180 GC tissues and 24 normal control tissues within the Cancer Genome Atlas (TCGA) database. These datasets were then interrogated to identify GC-related differentially expressed (DE) RNAs (|fold change| ≥ 2, FDR< 0.01), leading to the identification of 1946 DE lncRNAs, 123 DE miRNAs, and 3159 DE mRNAs. These results were then used to generate a putative GC-related competitive endogenous RNA (ceRNA) network composed of 131 lncRNAs, 9 miRNAs, and 78 mRNAs. Subsequent survival analyses based upon this network revealed 17 of these lncRNAs to be significantly associated with GC patient survival (P < 0.05). Further multivariable Cox regression and lasso analyses allowed for the construction of an 8-lncRNA risk score that was able to effectively predict GC patient survival with good discriminative ability. The Kaplan-Meier Plotter database further confirmed that network hub genes that were related to these 8 lncRNAs were associated with GC patient prognosis (P < 0.05). As the ceRNA network in the present study was constructed with a focus on both disease stage and differential gene expression, it represents a key resource that will offer valuable insights into the mechanistic roles of ceRNA pathways in GC development and progression.

To develop an efficient and green method to recycling lead slag, a novel strategy to fabricate nano-lead dioxide from lead slag was applied by the hydro-electrometallurgy. In leaching system, the optimum condition of leaching time 100 min, 80 °C, stirring rate 500 rpm, liquid/solid ratio 20 and 1 mol/L methanesulfonic acid resulted in lead recovery of 89% and residue obtained without toxicity. The kinetic study revealed that the methanesulfonic acid leaching of lead slag shows good agreement with a diffusion-controlled shrinking-particle model. Additionally, the apparent activation energy of MSA leaching of lead slag was determined using Arrhenius model as 13.621 kJ/mol. Furthermore, Nano-PbO2 recovered from waste lead paste was prepared for the electrolysis of water to produce ozone. The experimental results showed that the ozone production of nano-PbO2 recovered from waste lead slag was not significantly different from the nano-PbO2 prepared by pure reagents. In conclusion, waste lead slag can be recycled for the fabrication of nano-PbO2, which has a significant advantage on realizing the recycling of lead resources.

The electrodes were fabricated in double-titanium cyclic voltametric electrodeposition system, corresponding to the anode and cathode of the system. For further study the practicality of this mode, the performance of the resulting electrodes was investigated. Through a series of physical and electrochemical characterization, it is concluded that the IrOx electrode corresponding to the anode of the system has a flat and uniform deposit layer, and shows better electrolytic durability (its actual working life is more than 3072 h), while the cathode electrode has better performance in electrocatalytic activity.

The reliability of MyotonPRO that can monitor the mechanical properties of tissues is still unclear. This study aimed to analyze the within-day inter-operator and between-day intra-operator reliability of MyotonPRO for assessing tone and stiffness of quadriceps femoris and patellar tendon at different knee angles. The tone and stiffness of healthy participants (15 males and 15 females, aged 24.7±1.6 years) in the supine and resting position were measured using the MyotonPRO device. The measurements were quantified at 0°, 30°, 60°, and 90° of knee flexion. The intraclass correlation coefficient (ICC), standard error of measurement (SEM), and minimal detectable change (MDC) were calculated and a Bland-Altman analysis was conducted to estimate reliability. The results indicated excellent inter-operator reliability (ICC > 0.78) and good to excellent intra-operator reliability (ICC > 0.41). The inter-operator SEM measurements ranged between 0.1-0.9 Hz and 3.8-37.9 N/m, and intra-operator SEM ranged between 0.5-1.3 Hz and 7.9-52.0 N/m. The inter-operator MDC ranged between 0.3-2.5 Hz and 10.5-105.1 N/m, and intra-operator SEM ranged between 1.1-3.3 Hz and 21.9-144.1 N/m. The agreement of inter-operator was better than that of intra-operator. The study concluded that MyotonPRO is a reliable device to detect the tone and stiffness of quadriceps femoris and patellar tendon.

In view of the fact that China’s power dispatching agencies and trading centers are relatively independent, but the medium and long-term power transactions need physical execution, which leads to higher requirements for transaction security boundary, this paper proposes a calculation method of available transmission capacity for medium and long-term power transactions, which calculates the available transmission capacity of transmission channels through probabilistic method to improve the enforceability of transaction results. Numerical simulation results also verify the effectiveness of the algorithm.

Beam-column joints which shoulders high-level and vertical shearing effect that maintains balance of beam and column end is the major component influencing the performance of the whole framework. Post earthquake investigation suggests that collapse of frame structure is induced by failure of joints in most cases. Thus, beam-column joints must have strong bearing capacity and good ductility, and reinforced concrete structure just meets the above requirement. But corrosion caused by long time use of reinforced concrete framework will lead to degeneration of mechanical performance of joints. To find out the rule of effect of steel reinforcement with different corrosion rate on degeneration of bearing capacity of reinforced concrete framework joints, this study made a nonlinear numerical analysis on fifteen models without stirrup in the core area of reinforced concrete frame joints using displacement method considering axial load ratio of column end and constraint condition. This work aims to find out the key factor that influences mechanical performance of joints, thus to provide a basis for repair and reinforcement of degenerated framework joints.

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo.

Posterior dislocation of the shoulder (PSD) is a rare injury; the diagnosis is often missed on initial examination. We present a systematic review of the current literature and discuss the key of the diagnosis of PSD. We searched the MEDLINE, PubMed, EMBASE, MD Consult, and the Cochrane Controlled Trial Register databases for the articles according to our eligibility criteria. Finally, 53 articles were included in our systematic review. There were 242 shoulders in 205 patients. In total, in the initial assessment with anteroposterior radiographs in 166 cases, only 19 (11.4%) cases confirmed the right diagnosis. When anteroposterior combined with axillary or Y view radiographs or computed tomography were present as the initial assessments in 36 cases, the diagnoses were made correctly and timely (100%). When axillary or Y view radiographs or computed tomography were taken subsequently, the diagnosis was confirmed in all 205 patients.