Computational analysis of genetic loci required for amphid structure and functions and their possibly corresponding microRNAs in C. elegans

Objective To examine the important roles of microRNAs （miRNAs） in regulating amphid structure and function, we performed a computational analysis for the genetic loci required for the sensory perception and their possibly corresponding miRNAs in C. elegans. Methods Total 55 genetic loci required for the amphid structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 30 genes among the 55 genetic loci selected have their possible corresponding regulatory miRNA（s）, and identified genes participate in the regulation of almost all aspects of amphid structure and function. In addition, our data suggest that both the amphid structure and the amphid functions might be regulated by a series of network signaling pathways. Moreover, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 30 genes exhibits different patterns. Conclusion We present the possible miRNA-mediated signaling pathways involved in the regulation of chemosensation and thermosensation by controlling the corresponding sensory neuron and interneuron functions. Our work will be useful for better understanding of the miRNA-mediated control of the chemotaxis and thermotaxis in C. elegans.

Computational analysis of genetic loci required for synapse structure and function and their corresponding microRNAs in C. elegans

Objective To elucidate the important functions of microRNAs （miRNAs） in regulating synaptic assembly and function, we performed a computational analysis for the genetic loci required for the synaptic structure and function and their corresponding miRNAs in C. elegans. Methods Total 198 genetic loci required for the synaptic structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 163 genes among the 198 genetic loci selected have their possibly corresponding regulatory miRNA （s）, which covered most of the important genetic loci required for the synaptic structure and function. Moreover, only 22 genes among the analyzed 38 genetic loci encoding synaptic proteins have more possibility to under the control of non-coding RNA genes. In addition, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 22 genes exhibits different patterns. Condusion Here we provide the computational screen and analysis results for the genetic loci required for synaptic structure and function and their possible corresponding miRNAs. These data will be useful for the further attempt to systematically determine the roles of miRNAs in synaptic assembly and function regulation in worms.

Analysis of behaviour of computational model to evaluate performance of heat pipe containing nanofluids

Application of nanofluids in heat pipes usually presents satisfactory experimental results regarding a thermal resistance reduction of the heat pipe.However,the existing computational studies connecting heat pipes and nanofluids lack a deeper discussion regarding the validity of the models currently used for representing the behaviour of a nanofluid in a heat pipe,particularly for unusual base fluids and nanoparticles such as carbon nanotubes or ethylene glycol.Thus,this comparative study presents the results of a set of computational simulations using pre-established equations for modelling a nanofluid in a heat pipe with experimental data from the literature.The results show agreement with the expected behaviour qualitatively and the presented maximum variations between 1.5% and 23.9% in comparison to the experimentally measured average temperatures.Also,the experimentally obtained temperature distribution of a heat pipe could not be reached numerically only with the use of adequate thermal properties,indicating that the boiling phenomenon is more complex than the current model used for computational simulations.Moreover,the existence of an optimal particle volume fraction for using nanofluids in this application could be observed by combining different properties models.

Computational analysis of fluid-structure interaction in case of fish swimming in the vortex street

The fluid-structure interaction (FSI) in case of fish swimming in the vortex street is investigated by numerical simulations. The vortex street is generated by a D-section cylinder. A 2-D fish model is placed on the downstream centerline of the bluff cylinder at a distance of 4 diameters away from the center of the cylinder. To simulate the fish body undulation and movement, the moving mesh is generated by a coupling approach based on the radial basis function and the overset grid technology. The Navier-Stokes equation in the arbitrary Lagrangian-Eulerian form is solved by coupling with the kinematics equation. Three cases are investigated: in a stationary position without deformation, a passive locomotion without deformation, and an active deformation based on the Kármán gait model. The results indicate that the fish body is acted by an alternating force and moment when it is located in the centerline of the vortex street. Furthermore, the fish could extract sufficient kinetic energy to overcome the drag under suitable conditions even when it keeps rigid and out of the suction zone. When the fish body undulates based on the Kármán gait model, the interaction is evidently shown between the fish body and the vortices. The theoretical analysis demonstrates that the lateral force and the moment acting on the fish body vary in a cosine formula, with the lateral translation and the body rotation as a result. This study focuses on the behavior of the fish body in the bluff cylinder wake and reproduces some phenomena observed in the experiments. Besides, the Kármán gait model is also theoretically analyzed, for the further exploration of the FSI mechanism in case of fish swimming.

Computational Analysis of the Transcriptional Regulation of the Actin Family

Transcriptional regulation is a very important regulatory step in the regulation of gene expression. Transcription factors (TFs) play an important role in controlling the temporal special specificity of gene expression. The regulation area of actin genes was analyzed statistically to predict the transcription factor binding sites in the regulatory area. A group of transcription factors located in most of the sequences is believed to play an important role in co-regulating the expression of actin genes.

Computational analysis of vibration modes of disk-shaped piezoelectric traveling wave motors

According to Kirchhoff-Love's assumptions, this paper establishes linear system of equations for solving eigen frequency constant and corresponding mode shape. Using engineer-ing and numerical analysis software Matlab5.2 and method of coefficient determinant searching arithmetic, eigen frequency constant and mode shape of the stator with i.d./ o.d. ratio of 0.1, 0.3, 0.35, 0.6 and different vibration modes are accurately solved and analyzed. By means of Newton interpolation method, contributions of transverse deflection amplitude and vibration energy corresponding to various modes are determined. This paper offers a valid theoretical foundation for the optimum design of the stator of disk-shaped ultrasonic motors. Furthermore, according to results of numerical analysis, several choosing principles of vibration modes are summarized.

Computational mission analysis and conceptual system design for super low altitude satellite

This paper deals with system engineering and design methodology for super low altitude satel ites in the view of the com-putational mission analysis. Due to the slight advance of imaging instruments, such as the focus of camera and the image element of charge coupled device （CCD）, it is an innovative and economical way to improve the camera’s resolution to enforce the satel ite to fly on the lower altitude orbit. DFH-3, the mature satel ite bus de-veloped by Chinese Academy of Space Technology, is employed to define the mass and power budgets for the computational mis-sion analysis and the detailed engineering design for super low altitude satel ites. An effective iterative algorithm is proposed to solve the ergodic representation of feasible mass and power bud-gets at the flight altitude under constraints. Besides, boundaries of mass or power exist for every altitude, where the upper boundary is derived from the maximum power, while the minimum thrust force holds the lower boundary before the power reaching the initial value. What’s more, an analytical algorithm is employed to numerical y investigate the coverage percentage over the altitude, so that the nominal altitude could be selected from al the feasi-ble altitudes based on both the mass and power budgets and the repetitive ground traces. The local time at the descending node is chosen for the nominal sun-synchronous orbit based on the average evaluation function. After determining the key orbital ele-ments based on the computational mission analysis, the detailed engineering design on the configuration and other subsystems, like power, telemetry telecontrol and communication （TT＆amp;C）, and attitude determination and control system （ADCS）, is performed based on the benchmark bus, besides, some improvements to the bus are also implemented to accommodate the flight at a super low altitude. Two operation strategies, drag-free closed-loop mode and on/off open-loop mode, are presented to maintain the satel-lite’s altitude. Final y, a flight planning schedule for the satel ite is demonstrated from its launch into the initial altitude at the very beginning to its decay to death in the end.

Experimental and computational analysis of the coolant distribution considering the viscosity of the cutting fluid during machining with helical deep hole drills

An experimental analysis regarding the distribution of the cutting fluid is very difficult due to the inaccessibility of the contact zone within the bore hole.Therefore,suitable simulation models are necessary to evaluate new tool designs and optimize drilling processes.In this paper the coolant distribution during helical deep hole drilling is analyzed with high-speed microscopy.Micro particles are added to the cutting fluid circuit bya developed high-pressure mixing vessel.After the evaluation of suitable particle size,particle concentration and coolant pressure,a computational fluid dynamics(CFD)simulation is validated with the experimental results.The comparison shows a very good model quality with a marginal difference for the flow velocity of 1.57%between simulation and experiment.The simulation considers the kinematic viscosity of the fluid.The results show that the fluid velocity in the chip flutes is low compared to the fluid velocity at the exit of the coolant channels of the tool and drops even further between theguidechamfers.Theflow velocity and the flow pressure directly at the cutting edge decrease to such an extent that the fluid cannot generate a sufficient cooling or lubrication.With the CFD simulation a deeper understanding of the behavior and interactions of the cutting fluid is achieved.Based on these results further research activities to improve the coolant supply can be carried out with great potential to evaluate new tool geometries and optimize the machining process.

Computational Geometric Analysis for <i>C. elegans</i>Trajectories on Thermal and Salinity Gradient

Elegans are one of the best model organisms in neural researches, and tropism movement is a typical learning and memorizing activity. Based on one imaging technique called Fast Track-Capturing Microscope (FTCM), we investigated the movement regulation. Two movement patterns are extracted from various trajectories through analysis on turning angle. Then we applied this classification on trajectory regulation on the compound gradient field, and theoretical results corresponded with experiments well, which can initially verify the conclusion. Our breakthrough is performed computational geometric analysis on trajectories. Several independent features were combined to describe movement properties by principal composition analysis (PCA) and support vector machine (SVM). After normalizing all data sets, no-supervising machine learning was processed along with some training under certain supervision. The final classification results performed perfectly, which indicates the further application of such computational analysis in biology researches combining with machine learning.

Impact analysis of casting parts considering shrinkage cavity defect

Shrinkage cavity may be detrimental to mechanical performances of casting parts.As a consequence,design engineers often use overly large safety factors in many designs due to insufficient understanding of quantitative effects of shrinkage cavity defects.In this paper,process of Al alloy wheel impact test was computationally analyzed for both the wheel models with and without shrinkage cavity defects.Based on shrinkage cavity data obtained from industrial CT (Computerized Tomography),the shrinkage cavity defects were modeled with SSM (Shape Simplification Method),which reconstructs shrinkage cavity defects to hollow spheroid primitives.After the impact simulation was conducted,the results show that under impact test condition,the wheel considering shrinkage cavity defects may fracture while the sound-assumed wheel may not.

Analysis of a New Composite Material for Watercraft Manufacturing

In this paper, we investigate the properties of an alternative material for use in marine engineering, namely a rigid and light sandwich-structured composite made of expanded polystyrene and fiberglass. Not only does this material have an improved section modulus, but it is also inexpensive, light, easy to manipulate, and commercially available in various sizes. Using a computer program based on the finite element method, we calculated the hogging and sagging stresses and strains acting on a prismatic boat model composed of this material, and determined the minimum sizes and maximum permissible stresses to avoid deformation. Finally, we calculated the structural weight of the resulting vessel for comparison with another structure of comparable dimensions constructed from the commonly used core material Divinycell.

3D FEM analysis for layered rock considering anisotropy of shear strength

An empirical expression of cohesion （C） and friction angle （Ф） for layered rock was suggested. This expression was compared with a test result made by the former researchers. The constitutive relationship of a transversely isotropic medium and Mohr-Coulomb criterion in which C and Ф vary with directions were employed, and a relative 3D elasto-plastic FEM code was developed, in which the important thing was to adopt a search-trial method to find the orientation angle （p） of shear failure plane （or weakest shear plane） with respect to the major principal stress as well as the corresponding C and Ф Taking an underground opening as the calculation object, the numerical analyses were carried out by using the FEM code for two cases of transversely isotropic rock and isotropic rock, respectively, and the computation results were compared. The results show that when the rock is a transversely isotropic one, the distributions of displacements, plastic zones and stress contours in the surrounding rock will be non-axisymmetric along the tunnel＇s vertical axis, which is very different from that of isotropic rock. The stability of the tunnel in transversely isotropic rock is relatively low.

Can the computed tomography texture analysis of colorectal liver metastases predict the response to first-line cytotoxic chemotherapy?

BACKGROUND Artificial intelligence in radiology has the potential to assist with the diagnosis,prognostication and therapeutic response prediction of various cancers.A few studies have reported that texture analysis can be helpful in predicting the response to chemotherapy for colorectal liver metastases,however,the results have varied.Necrotic metastases were not clearly excluded in these studies and in most studies the full range of texture analysis features were not evaluated.This study was designed to determine if the computed tomography(CT)texture analysis results of non-necrotic colorectal liver metastases differ from previous reports.A larger range of texture features were also evaluated to identify potential new biomarkers.AIM To identify potential new imaging biomarkers with CT texture analysis which can predict the response to first-line cytotoxic chemotherapy in non-necrotic colorectal liver metastases(CRLMs).METHODS Patients who presented with CRLMs from 2012 to 2020 were retrospectively selected on the institutional radiology information system of our private radiology practice.The inclusion criteria were non-necrotic CRLMs with a minimum size of 10 mm(diagnosed on archived 1.25 mm portal venous phase CT(FOLFOX,FOLFIRI,FOLFOXIRI,CAPE-OX,CAPE-IRI or capecitabine).The final study cohort consisted of 29 patients.The treatment response of the CRLMs was classified according to the RECIST 1.1 criteria.By means of CT texture analysis,various first and second order texture features were extracted from a single nonnecrotic target CRLM in each responding and non-responding patient.Associations between features and response to chemotherapy were assessed by logistic regression models.The prognostic accuracy of selected features was evaluated by using the area under the curve.RESULTS There were 15 responders(partial response)and 14 non-responders(7 stable and 7 with progressive disease).The responders presented with a higher number of CRLMs(P=0.05).In univariable analysis,eight texture features of the responding CRLMs were associated with treatment response,but due to strong correlations among some of the features,only two features,namely minimum histogram gradient intensity and long run low grey level emphasis,were included in the multiple analysis.The area under the receiver operating characteristic curve of the multiple model was 0.80(95%CI:0.64 to 0.96),with a sensitivity of 0.73(95%CI:0.48 to 0.89)and a specificity of 0.79(95%CI:0.52 to 0.92).CONCLUSION Eight first and second order texture features,but particularly minimum histogram gradient intensity and long run low grey level emphasis are significantly correlated with treatment response in non-necrotic CRLMs.

Hierarchical Visual Analysis and Steering Framework for Astrophysical Simulations

A framework for accelerating modern long-running astrophysical simulations is presented, which is based on a hierarchical architecture where computational steering in the high-resolution run is performed under the guide of knowledge obtained in the gradually refined ensemble analyses. Several visualization schemes for facilitating ensemble management, error analysis, parameter grouping and tuning are also integrated owing to the pluggable modular design. The proposed approach is prototyped based on the Flash code, and it can be extended by introducing userdefined visualization for specific requirements. Two real-world simulations, i.e., stellar wind and supernova remnant, are carried out to verify the proposed approach.

A new computational approach for modeling diffusion tractography in the brain

Computational models provide additional tools for studying the brain,however,many techniques are currently disconnected from each other.There is a need for new computational approaches that span the range of physics operating in the brain.In this review paper,we offer some new perspectives on how the embedded element method can fill this gap and has the potential to connect a myriad of modeling genre.The embedded element method is a mesh superposition technique used within finite element analysis.This method allows for the incorporation of axonal fiber tracts to be explicitly represented.Here,we explore the use of the approach beyond its original goal of predicting axonal strain in brain injury.We explore the potential application of the embedded element method in areas of electrophysiology,neurodegeneration,neuropharmacology and mechanobiology.We conclude that this method has the potential to provide us with an integrated computational framework that can assist in developing improved diagnostic tools and regeneration technologies.

A Putative Protein with No Known Function in Arabidopsis thaliana Harbors a Domain with Adenylyl Cyclase Activity

Adenylyl cyclases (ACs) are a special group of enzymes that catalyze formation of the second messenger molecule, 3',5'-cyclic adenosine monophosphate (cAMP) from 5'-adenosine triphosphate (ATP). Apparently, even though cAMP is increasingly becoming an important signaling molecule in higher plants, the identification of plant ACs has somewhat remained slow. Here we report the recombinant cloning, partial expression and affinity purification of the truncated version (AtAC261-388) of a putative Arabidopsis thaliana protein (AtAC: At3g21465) followed by a demonstration of its inherent enzymatic activity as an AC. Currently, AtAC is not assigned any particular function in A. thaliana but simply annotated as an AC-like protein and, therefore, we targeted it for our study to establish if it is indeed a bona fide AC molecule. From our work, we firstly, show through enzyme immunoassaying and mass spectrometry that the recombinant AtAC261-388 can generate cAMP from ATP in vitro in a manganese-dependent manner that is activated by calcium and hydrogen carbonate. Secondly, we reveal through computational analysis that the AC center of AtAC is solvent-exposed, and amenable to the unhindered access of ATP as a substrate for catalysis. Lastly, we show that the recombinant AtAC261-388 can complement AC-deficiency (cyaA mutation) in SP850 cells when expressed in this mutant Escherichia coli strain.

Synthesis and Crystal Structure of Novel Mixed-metal Alkoxide Clusters of Ytterbium and Sodium: Yb_4O_4(O^iPr)_(16)Na_(12)

The mixed-metal cluster Yb4O4（OiPr）16Na12 has been synthesized and structurally determined by IR, elemental analysis, and single-crystal X-ray diffraction. The crystal belongs to the cubic system, space group P23 with a = b = c = 13.9788（3）A, V = 2731.55（10）A3, Z = 1, Dc = 1.202 g/cm3, Mr = 1977.42,/J = 3.480 mm-1, F（000） = 972, the final R = 0.0288 and wR = 0.1511 for 1677 observed reflections with I 〉 2σ（I）. X-ray analysis reveals that Yb4O4（Oipr）16Na12 is centrosym- metric and the structure contains four ytterbium metals and twelve sodium metals, and each ytterbium atom is coordinated by six oxygen atoms. In addition, an ancillary computational analysis of the optimized molecular unit was provided. The large energy gap （3,31 eV） between HOMO and LUMO indicates that the structure framework is particularly stable.

Combining CUBIC Optical Clearing and Thy1-YFP-16 Mice to Observe Morphological Axon Changes During Wallerian Degeneration

Objective:Wallerian degeneration is a pathological process closely related to peripheral nerve regeneration following injury,and includes the disintegration and phagocytosis of peripheral nervous system cells.Traditionally,morphological changes are observed by performing immunofluorescence staining after sectioning,which results in the loss of some histological information.The purpose of this study was to explore a new,nondestmetive,and systematic method for observing axonal histological changes during Wallerian degeneration.Methods:Thirty male Thy1-YFP-16 mice(SPF grade,6 weeks old,20±5 g)were randomly selected and divided into clear,unobstructed brain imaging cocktails and computational analysis(CUBIC)optical clearing(n=15)and traditional method groups(n=15).Five mice in each group were sacrificed at 1st,3rd,and 5th day following a crush operation.The histological axon changes were observed by CUBIC light optical clearing treatment,direct tissue section imaging,and HE staining.Results:The results revealed that,compared with traditional imaging methods,there was no physical damage to the samples,which allowed for three-dimensional and deep-seated tissue imaging through CUBIC.Local image information could be nicely obtained by direct fluorescence imaging and HE staining,but it was difficult to obtain image information of the entire sample.At the same time,the image information obtained by fluorescence imaging and HE staining was partially lost.Conclusion:The combining of CUBIC and Thy1-YFP transgenic mice allowed for a clear and comprehensive observation of histological changes of axons in Wallerian degeneration.

Estimation of Geodetic Parameters with VLBI Data of Last 5 Years

The meaning to research the potential of VLBI for geodetic applications is summarized. And the observation models and their related parameters of geodetic interest are investigated. Then, the principle and method of using the random model in VLBI data processing are investigated. With the world wide VLBI data from 2000-2004, the conditions to compute the parameters of geodetic interest are introduced, and so are the computing methods and processes. And the computed resuits of the parameters of geodetic interest are analyzed.

Differentiation of pyogenic hepatic abscesses from malignant mimickers using multislice-based texture acquired from contrast-enhanced computed tomography

BACKGROUND： Pyogenic hepatic abscess may mimic primary or secondary carcinoma of the liver on contrast-enhanced computed tomography（CECT）. The present study was to explore the usefulness of the analysis of multislice-based texture acquired from CECT in the differentiation between pyogenic hepatic abscesses and malignant mimickers.METHODS： This retrospective study included 25 abscesses in 20 patients and 33 tumors in 26 subjects who underwent CECT. To make comparison, we also enrolled 19 patients with hepatic single simple cyst. The images from CECT were analyzed using a Laplacian of Gaussian band-pass filter（5 filter levels with sigma weighting ranging from 1.0 to 2.5）. We also quantified the uniformity, entropy, kurtosis and skewness of the multislice-based texture at different sigma weightings. Statistical significance for these parameters was tested with oneway ANOVA followed by Tukey honestly significant difference（HSD） test. Diagnostic performance was evaluated using the receiver operating characteristic（ROC） curve analysis.RESULTS： There were significant differences in entropy and uniformity at all sigma weightings（P〈0.001） among hepatic abscesses, malignant mimickers and simple cysts. The significant difference in kurtosis and skewness was shown at sigma 1.8 and 2.0 weightings（P=0.002-0.006）. Tukey HSD testshowed that the abscesses had a significantly higher entropy and lower uniformity compared with malignant mimickers（P=0.000-0.004）. Entropy（at a sigma 2.0 weighting） had the largest area under the ROC curve（0.888） in differentiating abscesses from malignant mimickers, with a sensitivity of 81.8% and a specificity of 88.0% when the cutoff value was set to 3.64.CONCLUSION： Multislice-based texture analysis may be useful for differentiating pyogenic hepatic abscesses from malignant mimickers.