RM-structure alignment based statistical machine translation model

A novel model based on structure alignments is proposed for statistical machine translation in this paper. Meta-structure and sequence of meta-structure for a parse tree are defined. During the translation process, a parse tree is decomposed to deal with the structure divergence and the alignments can be constructed at different levels of recombination of meta-structure （RM）. This method can perform the structure mapping across the sub-tree structure between languages. As a result, we get not only the translation for the target language, but sequence of meta-stmctu .re of its parse tree at the same time. Experiments show that the model in the framework of log-linear model has better generative ability and significantly outperforms Pharaoh, a phrase-based system.

Biofabrication of aligned structures that guide cell orientation and applications in tissue engineering

The organized alignment of cells in various tissues plays a significant role in the maintenance of specific functions.To induce such an alignment,ideal scaffolds should simulate the characteristics and morphologies of natural tissues.Aligned structures that guide cell orientation are used to facilitate tissue regeneration and repair.We here review how various aligned structures are fabricated,including aligned electrospun nanofibers,aligned porous or channeled structures,micropatterns and combinations thereof,and their application in nerve,skeletal muscle,tendon,and tubular dentin regeneration.The future use of aligned structures in tissue engineering is also discussed.

CORE:Common Region Extension Based Multiple Protein Structure Alignment for Producing Multiple Solution

Over the past several decades, biologists have conducted numerous studies examining both general and specific functions of proteins. Generally, if similarities in either the structure or sequence of amino acids exist for two proteins, then a common biological function is expected. Protein function is determined primarily based on the structure rather than the sequence of amino acids. The algorithm for protein structure alignment is an essential tool for the research. The quality of the algorithm depends on the quality of the similarity measure that is used, and the similarity measure is an objective function used to determine the best alignment because of their individual strength and weakness However, none of existing similarity measures became golden standard They require excessive filtering to find a single alignment. In this paper, we introduce a new strategy that finds not a single alignment, but multiple alignments with different lengths. This method has obvious benefits of high quality alignment. However, this novel method leads to a new problem that the running time for this method is considerably longer than that for methods that find only a single alignment. To address this problem~ we propose algorithms that can locate a common region （CORE） of multiple alignment candidates, and can then extend the CORE into multiple alignments. Because the CORE can be defined from a final alignment, we introduce CORE＊ that is similar to CORE and propose an algorithm to identify the CORE＊. By adopting CORE＊ and dynamic programming, our proposed method produces multiple alignments of various lengths with higher accuracy than previous methods. In the experiments, the alignments identified by our algorithm are longer than those obtained by TM-align by 17% and 15.48%, on average, when the comparison is conducted at the level of super-family and fold, respectively.

MODIS captures large-scale atmospheric gravity waves over the Atlantic Ocean

On April 27,2016,a striking true-color satellite image acquired by the Moderate Resolution Imaging Spectroradiometer（MODIS）onboard National Aeronautics and Space Administration’s（NASA’s）Aqua satellite showed several groups of very well structured arc cloud patterns（Fig.1）,which are associaed with atmospheric gravity waves,aligned in the middle of the Atlantic Ocean between

FP-Zernike:An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval

The release of AlphaFold2 has sparked a rapid expansion in protein model databases.Efficient protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural retrieval.Although existing structure alignment algorithms can address this challenge,they are often time-consuming.Currently,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean distance.However,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom datasets.To overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature points.Users simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized datasets.FP-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark datasets.In addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested readers.Our demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a retrieval.The experiments confirmed that it achieved the state-of-the-art accuracy level.FP-Zernike is an open-source toolkit,with the source code and related data accessible at https://ngdc.cncb.ac.cn/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://www.structbioinfo.cn/.

3D vertically aligned microchannel structure to enhance piezoelectric energy harvesting performance of PZT/PVDF&CNTs piezoelectric composites

Piezoelectric energy harvesters(PEHs)have attracted significant attention with the ability of converting mechanical energy into electrical energy and power the self-powered microelectronic components.Generally,material's superior energy harvesting performance is closely related to its high transduction coefficient(d_(33)×g_(33)),which is dependent on higher piezoelectric coefficient d33 and lower dielectric constantεr of materials.However,the high d33 and lowεr are difficult to be simultaneously achieved in piezoelectric ceramics.Herein,lead zirconate titanate(PZT)based piezoelectric composites with vertically aligned microchannel structure are constructed by phase-inversion method.The polyvinylidene fluoride(PVDF)and carbon nanotubes(CNTs)are mixed as fillers to fabricate PZT/PVDF&CNTs composites.The unique structure and uniformly distributed CNTs network enhance the polarization and thus improve the d33.The PVDF filler effectively reduce theεr.As a consequence,the excellent piezoelectric coefficient(d_(33)=595 pC/N)and relatively low dielectric constant(ε_(r)=1,603)were obtained in PZT/PVDF&CNTs composites,which generated an ultra-high d_(33)×g_(33) of 24,942×10^(−15) m^(2)/N.Therefore,the PZT/PVDF&CNTs piezoelectric composites achieve excellent energy harvesting performance(output voltage:66 V,short current:39.22μA,and power density:1.25μW/mm^(2)).Our strategy effectively boosts the performance of piezoelectric-polymer composites,which has certain guiding significance for design of energy harvesters.

Lithiophilic hyperbranched Cu nanostructure for stable Li metal anodes

Porous copper(Cu)current collectors are regarded as a promising host for stabilizing lithium(Li)metal anodes but suffer from uncontrollable Li metal deposition due to the intrinsic lithiophobic nature of Cu.This study proposes a vertically aligned Cu host with hyperbranched CuxO nanostructure to provide lithiophilic nucleation sites for homogeneous Li metal deposition.Specifically,the vertically aligned Cu nanostructure dramatically reduces the local current density and brings homogeneous Li‐ion flux.The lithiophilic hyperbranched CuxO nanostructure with a low nucleation barrier could induce homogeneous Li nucleation and growth.As a result,the Cu@CuxO nanostructured host exhibits a low nucleation overpotential of 44.3 mV and achieves highly electrochemical reversibility with high Coulombic efficiency of 98.33%in a half‐cell.The Cu@CuxO nanostructured electrode is capable of working under different current densities varying from 0.5 to 5 mA/cm2 in a symmetric cell.The assembled full cell coupling of the Li/Cu@CuxO composite anode with the LiFePO4 cathode manifests stable long‐term cycling life at 1 C.This study elaborates on the synergistic effect of electrode structure design and interfacial chemistry modification to regulate the Li deposition/dissolution behavior,thus exhibiting remarkable electrochemical performances for next‐generation Li‐metal batteries.

Electrically tunable generation of vectorial vortex beams with micro-patterned liquid crystal structures

We develop a new method for smooth and continuous space-variant alignment of the liquid crystal medium in micro-patterned structures, which is based on a radial micro-structured pattern of polymeric ribbons exhibiting out-of-plane orientation with respect to the ITO-coated glass plates. Thanks to the broad range of electrical tunability of the optical retardation for the micro-patterned liquid crystal structures, transformation of the fundamental Gaussian beam into different types of specific beams, including generalized cylindrical vector beams, vortex beams, and vectorial vortex beams, is efficiently demonstrated.

Oil-Water Separation Performance of Electrospray Reduced Graphene Oxide Microspheres with a Local Radially Aligned and Porous Structure

Micro-size oil adsorbents are effective for the rapid remediation of special oil spills.Here,N-doped reduced graphene oxide(RGO)microspheres(ca.150µm in diameter)with a local radially aligned and porous structure are fabricated by combining electrospray-freeze-drying with thermal treatment for rapid separation of oil-water.Owing to its hydrophobic/oleophilic properties and oriented structure,the N-doped RGO microspheres achieve high capacities and fast adsorption rates for a variety of oils and organic solvents.Furthermore,excellent oil-water separation performance on floating oil/oil-water emulsions and stable cyclic adsorption capacities are obtained for the local radially aligned and porous microsphere.Therefore,N-doped RGO microspheres with the unique porous structure have the potential for the remediation of oily sewage and oil spills.

MINIMUM HAUSDORFF DISTANCE UNDER RIGID MOTIONS AND COMPARISON OF PROTEIN STRUCTURES

Hausdorff distance between two compact sets, defined as the maximum distance from a point of one set to another set, has many application in computer science. It is a good measure for the similarity of two sets. This paper proves that the shape distance between two compact sets in R^n defined by nfinimum Hausdorff distance under rigid motions is a distance. The authors introduce similarity comparison problems in protein science, and propose that this measure may have good application to comparison of protein structure as well. For calculation of this distance, the authors give one dimensional formulas for problems （2, n）, （3, 3）, and （3, 4）. These formulas can reduce time needed for solving these problems. The authors did some data, this formula can reduce time needed to one As n increases, it would save more time. numerical experiments for （2, n）. On these sets of fifteenth of the best algorithms known on average.

RECOGNITION OF STRUCTURE SIMILARITIES IN PROTEINS

Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function, so calculating the similarity of protein structures is a fundamental problem in structural biology and plays a key role in protein fold classification, fold function inference, and protein structure prediction. Large progress has been made in recent years in this field and many methods for considering structural similarity have been proposed, including methods for protein structure comparison, retrieval of protein structures from databases, and ligand binding site comparison. Most of those methods can be available on the World Wide Web, but evaluation of all the methods is still a hard problem. This paper summarizes some popular methods and latest methods for structure similarities, including structure alignment, protein structure retrieval, and ligand binding site alignment.

Corrugated Graphene Paper Reinforced Silicone Resin Composite for Efficient Interface Thermal Management

With the rapid development of high-power-density electronic devices,interface thermal resistance has become a critical barrier for effective heat management in high-performance electronic products.Therefore,there is an urgent demand for advanced thermal interface materials(TIMs)with high cross-plane thermal conductivity and excellent compressibility to withstand increasingly complex operating conditions.To achieve this aim,a promising strategy involves vertically arranging highly thermoconductive graphene on polymers.However,with the currently available methods,achieving a balance between low interfacial thermal resistance,bidirectional high thermal conductivity,and large-scale production is challenging.Herein,we prepared a graphene framework with continuous filler structures in in-plane and cross-plane directions by bonding corrugated graphene to planar graphene paper.The interface interaction between the graphene paper framework and polymer matrix was enhanced via surface functionalization to reduce the interface thermal resistance.The resulting three-dimensional thermal framework endows the polymer composite material with a cross-plane thermal conductivity of 14.4 W·m^(-1)·K^(-1)and in-plane thermal conductivity of 130W·m^(-1)·K^(-1)when the thermal filler loading is 10.1 wt%,with a thermal conductivity enhancement per 1 wt%filler loading of 831%,outperforming various graphene structures as fillers.Given its high thermal conductivity,low contact thermal resistance,and low compressive modulus,the developed highly thermoconductive composite material demonstrates superior performance in TIM testing compared with TFLEX-700,an advanced commercial TIM,effectively solving the interfacial heat transfer issues in electronic systems.This novel filler structure framework also provides a solution for achieving a balance between efficient thermal management and ease of processing.

Bidirectionally aligned MXene hybrid aerogels assembled with MXene nanosheets and microgels for supercapacitors

MXene nanomaterials are one of the most promising electrode material candidates for supercapacitors owing to their high conductivity,abundant surface functional groups and large surface area.However,electrodes based on MXene may result in low ion-accessible surface area and blocked ion transport pathways because of the self-restacking of MXene nanosheets.It is essential to suppress the self-res tacking of nanosheets and increase the electrochemical active sites in order to optimize the electrode.In this work,bidirectionally aligned MXene hybrid aerogel(A-MHA)assembled with MXene nanosheets and microgels is prepared using a facile bidirectional freeze casting and freeze-drying method.The bidirectionally aligned structure together with the three-dimensional structured microgels in the A-MHAs,can improve the ionaccessible surface area and provide more barrier-free channels by exposing more active sites and ensuring electrolyte transport freely.The A-MHA with MXene microgels content of 40 wt%exhibits a high specific capacitance of 760 F·g^(-1)at 1 A·g^(-1)and a remarkable cyclic performance of 97%after 10,000 cycles at100 mV·s^(-1)in 1 mol·L^(-1)H_(2)SO_(4)electrolyte.A-MHAs show remarkable electrochemical properties and are of potential application in energy storage.

Holey aligned electrodes through in-situ ZIF-8-assisted-etching for high-performance aqueous redox flow batteries

Fabricating electrodes with large specific surface area(SSA)and high permeability has been the longstanding target in redox flow batteries(RFBs).In this work,we propose a novel ZIF-8-assisted etching approach to form holey fibers in the electrospinning process of aligned electrode structures.The etching approach allows the formation of holey fibers with small pores of~50 nm,offering large active surface areas for redox reactions,while the aligned macrostructure with the holey fibers of 3–5 lm in diameter ensures a high permeability along the fiber direction.The application of the prepared electrodes to a vanadium redox flow battery(VRFB)enables an energy efficiency(EE)of 87.2%at the current density of 200 m A cm^(-2),which is 13.3%higher than that with conventional electrospun carbon electrodes.Even at high current densities of 300 and 400 m A cm^(-2),the battery still maintains energy efficiencies of 83.3%and 79.3%.More excitingly,the prepared electrode yields a high limiting current density of4500 m A cm^(-2) and a peak power density of 1.6 W cm^(-2).It is anticipated that the present electrospinning method combining the ZIF-8-assisted etching approach with a way to form ordered fiber structures will allow even more high-performance electrodes for RFBs in the future.

Highly aligned lithiophilic electrospun nanofiber membrane for the multiscale suppression of Li dendrite growth

Using inorganic fibrous membranes as protective layers has yielded success in suppressing dendrite growth.However,conventional fibrous membranes usually have large voids and low affinity for Li,promoting inhomogeneous charge distribution and allowing some dendrites to grow.Herein,we introduce a highly aligned TiO_(2)/SiO_(2)(A-TS)electrospun nanofiber membrane as a protective layer for the Li metal anode.The A-TS membrane is fabricated by a custom-made electrospinning system with an automatic fiber alignment collector that allows control of the fibers’orientation.At the scale of the individual fibers,their high binding energies with Li can attract more“dead”Li by reacting with the SiO_(2) component of the composite,avoiding uncontrollable deposition on the metal anode.At the membrane scale,these highly ordered structures achieve homogeneous contact and charge distribution on the Li metal surface,leaving no vulnerable areas to nucleate dendrite formation.Additionally,the excellent mechanical and thermal stability properties of the A-TS membrane prevent any potential puncturing by dendrites or thermal runaway in a battery.Hence,an A-TS@Li anode exhibits stable cycling performance when used in both Li-S and Li-NCM811 batteries,highlighting significant reference values for the future design and development of high-energy-density metal-based battery systems.

Computational Biology Study of S100 Family with Suggestions for Crystallization

The S100 family is a class of calcium regulated proteins with EF hand. They are widely distributed and are implicated in diverse intracellular and extracellular physiological processes. A study of the S100 family using computational biology methods such as multiple sequence alignment, structural alignment and the construction of an evolutionary tree will promote understanding of S100 protein structures and their function, and could provide suggestions for crystallization.

Probe Staurosporine Drug Binding Site on Protein Kinase by PFSC

We used a new approach,protein folding shape code（PFSC）,to predict the potential staurosporine binding sites in protein kinases.Firstly,all available three dimensioned（3D） structures of protein kinases in protein databank（PDB） were converted into one-dimensional PFSC description,based on which a PFSC-kinome library was constructed.Secondly,a set of protein kinase-staurosporine complexes were analyzed to define the common structural features of the binding sites.Thirdly,the structural features of the staurosporine binding sites were used to virtually screen the PFSC-kinome library to predict multiple protein receptors that have potential binding capacity for staurosporine.Collectively,the development of the similar method for predicting drug binding site demonstrates that virtual screening protein database can provide valuable information on drug discovery and understanding of pharmacological pathways.