bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncertainty propagation of storage reliability evaluation using two-level MCS/NIPC
Authors: Suo Bin , Li Shun , Zhou Jie 
Published: February 2021

Abstract
In order to solve the problem of limited sample size and life data in the storage reliability evaluation of high-value weapons, the storage reliability evaluation method of electronic product based on storage performance modeling and simulation was studied. The problem of epistemic-aleatory mixed uncertainty propagation in product storage performance model with time degradation factor was discussed emphatically. The calculation method of two-level Monte Carlo simulation and non-intrusive polynomial chaos is proposed, which solved the problem that the computational capacity of storage performance simulation would increase explosivelly when the number of uncertainty parameters is large. Finally, the effectiveness of the method is verified by an example of circuit storage reliability evaluation, and the calculation efficiency is about 100 times higher than that of the two-lever MCS method.
Reliability Analysis Deflector of Underwater Wall Detection Device Based on Finite Element and Response Surface Methodology
Authors: Yang S Q , Yang H L , Bai S L , Xu G H 
Published: February 2021

Abstract
Before the diversion plugging in hydropower project, underwater wall detection device can complete the probe of visual detection and obstacle clearing in high-velocity flow. Deflector which can provide a stronger compress diversion tunnel sluice gate power is the most important part in underwater wall detection device, but the mechanical and uncertainty analysis aren’t enough. In this paper, Finite Element Method and Response Surface Methodology are used to analyze strength and deformation of the deflector, meanwhile, the limit state functions about the maximal bending stress and maximal deformation are developed. Then, though comparing the data with experimental data and the value computed by user formula, the error is less than 2% and the error is allowable in engineering design. Finally, reliability analysis the deflector is achieved with the First-Order Reliability Method. In a word, form the calculating results and engineering operation, we know that the propose method in this paper using finite element method and response surface methodology to develop the function related to the limit functions of deflector under uncertainty is practical and feasible.
Abnormal identification of lubricating oil parameters and evaluation of physical and chemical properties based on machine learning
Authors: Yang Kun , Wang Xia 
Published: February 2021

Abstract
This paper firstly proposes an abnormality identification model for online oil monitoring parameters. The SVR model was established to predict the output power, and the information entropy of the deviation between the predicted value of the regression model and the actual monitoring value was used to identify the abnormal parameters of the oil. The physical and chemical properties of the oil was evaluated and predicted comprehensively. Principal component analysis (PCA) was used to eliminate the correlation between parameters, and then the deviation degree of each principal component is calculated after feature transformation. After adding the deviation degrees of each principal component according to their weights, the performance evaluation index of the oil is obtained. At the same time, a prediction model of oil performance trend based on Gated Recurrent Unit is proposed. The feasibility and applicability of this model are verified by comparing with the results of LSTM neural network and ARIMA model. The evaluation of the physical and chemical properties of the oil can detect the deterioration of the oil condition at the early stage, avoiding or reducing accidents, so as to ensure the safe and reliable operation of the unit.
Effects of load and rotational speed on the friction and wear properties of PTFE composites
Authors: Guaii Tao , Liu Yunsheng , Shou Haiming , Li Feng 
Published: February 2021

Abstract
PTFE composites has a lower hardness and shear strength than steel. Therefore, wear mainly occurs in PTFE composites itself when rubs with steel. For studying the friction and wear properties of PTFE composites, a series of experimental tests were conducted under different sliding velocities and load pressures using block-on-ring testing machine. Through weighting PTFE composites specimens before and after the experiment, we can get the wear mass losses of specimens, then the wear rate of PTFE composites is obtained by combining material density, loading pressure and wear length. At the same time, the friction coefficient is recorded in real time by the monitoring system of the testing machine The analysis results are as follows: at constant sliding velocities, the wear rate of PTFE composites gradually decreases with the increase of loading pressure; at constant loading pressure, the wear rate of PFTE composites decreases gradually with the increase of sliding speed. This leads to further conclusions that motor should not run in low speed range for a long time when PTFE composites is used as motor bearing material.
A PDEM-COM framework for uncertainty quantification of backward issues involving both aleatory and epistemic uncertainties
Authors: Wan Z Q , Chen J B , Beer M 
Published: February 2021

Abstract
Uncertainties that exist in nature or due to lack of knowledge have been widely recognized by researchers and engineering practitioners throughout engineering design and analysis for decades. Though great efforts have been devoted to the issues of uncertainty quantification (UQ) in various aspects, the methodologies on the quantification of aleatory uncertainty and epistemic uncertainty are usually logically inconsistent. For instance, the aleatory uncertainty is usually quantified in the framework of probability theory, whereas the epistemic uncertainty is quantified mostly by non-probabilistic methods. In the present paper, a probabilistically consistent framework for the quantification of both aleatory and epistemic uncertainty by synthesizing the probability density evolution method (PDEM) and the change of probability measure (COM) is outlined. The framework is then applied to the backward issues of uncertainty quantification. In particular, the uncertainty model updating issue is discussed in this paper. A numerical example is presented, and the results indicate the flexibility and efficiency of the proposed PDEM-COM framework.
Research on Structural reliability and reliability sensitivity of EMU pantograph
Authors: Feng Zhou , Chang Wu , Zixu Zhang 
Published: February 2021

Abstract
Due to the uncertainty of the contact state between the pantograph and the power grid when the EMU is running at high speed, as well as the influence of road conditions and environment, the external load applied to the pantograph and the material properties of the pantograph have certain randomness, thus affecting the current collection quality of the pantograph and the service life of the carbon slide plate. Taking a certain type of EMU single arm pantograph as the research object, a three-dimensional model is established, ANSYS Workbench software is used to carry out the finite element analysis to determine the dangerous point and its stress response; the simulation samples of material properties and stress of dangerous points are obtained by using sampling method and test design method based on the principle of normal distribution; the reliability index and reliability of pantograph structure strength are analyzed, based on the random perturbation method and the first-order second- moment method, and using the simulation sample data extracted by Latin hypercube sampling, and the reliability accuracy is verified by Monte Carlo method. Based on the definition of reliability sensitivity, the influence degree of each input variable on the reliability change of pantograph structure is determined as follows: external load > Poisson’s ratio > material density > elastic modulus, which provides reference for improving the reliability, service life and structural optimization design of pantograph
The digital axiograph – a novel tool in bruxism prevention
Authors: Taneva I , Uzunov T , Apostolov N , Filev N 
Published: February 2021

Abstract
Digital (electronic) axiography is an applicable promising technology with proven accuracy that allows registering the spatial location of the mandible and all lower jaw movements: mouth opening and closing, protrusion, left and right laterotrusion, dynamic function. In spite of bruxism treatment still being a controversial topic, occlusal splint application is proven to be the most efficient way of prevention. The purpose of the study is to develop a protocol of planning and producing preventive occlusal splints for bruxism management by means of digital axiography. The implementation of digital technologies reveals new possibilities in diagnosing, treating and tracking bruxism. With great attention to the individual trajectories of the lower jaw movements, the effectiveness of the occlusal splint prophylaxis is no longer hypothetical.
Preparation of graphene oxide membrane-daptomycin/epidermal growth factor dressing and its effect on wound healing
Authors: Zhou Daijun , tian Peng , Li Dong , Li Jianjun , Zhang Tao 
Published: February 2021

Abstract
Herein, a series of environmentally friendly dressings were specially fabricated from graphene oxide (GO) membrane (a high quality substrate with antibacterial function) and Daptomycin (antibacterial function)/Epidermal growth factor (EGF, wound healing function) for the purpose of antibacterial applications. A performance comparison was designed by employing four dressing samples, including the neat GO membrane (Group A), GO membrane-Daptomycin (Group B), GO membrane-EGF (Group C), and GO membrane-Daptomycin/EGF (Group D). The results analyzed using Fourier transform infrared spectroscopy suggested that Daptomycin and EGF might be adhered to the GO membrane. The contact angle test showed that the hydrophilicity of material gradually increased from Group A to Group D. Groups B and D displayed similar in vitro antibacterial activities, better than those of Groups A and C (their antibacterial performances were similar to each other); all the four experimental groups outperformed the control group (P > 0.05). On the other hand, Groups C and D could promote the proliferation effectively within 1–7 days (P < 0.05), and they also showed similar activities in the cell migration, which were higher than those of Groups A and B (close to each other); all the experimental groups outdid the control group (P < 0.05). Moreover, by monitoring the expression levels of PCNA and CD31 , samples from Group D could promote both angiogenesis and cell reproduction when covering the skin defects (P < 0.05). At the seventh days after the injury, the control and experimental groups of A, B, C, and D displayed healing rates of 40.6%, 53.0%, 66.8%, 60.1%, and 68.3%, respectively. Based on a successful fabrication of GO membrane-Daptomycin/EGF dressings, antibacterial effects as well as growth-promoting performance were well realized by samples in Group D. This is benifitial for the wound healing to a great extent.
The effects of Mg2+ concentration, (NH4)2SO4 concentration and current density on electrolytic manganese process
Authors: Wang Hai-Feng , Qin Ji-Tao , Tian Jia-Yu , Wang Jia-Wei , Zhao Ping-Yuan , Lu Fang-hai 
Published: February 2021

Abstract
In this paper, the effects of Mg2+ concentration, (NH4)2SO4 concentration and current density on the current efficiency, cell voltage and morphology of electrolytic manganese metal were studied. The current efficiency of electrolytic manganese decreased with the increase of Mg2+ concentration in the electrolyte; Increasing the concentration of (NH4)2SO4 , the current efficiency of electrolytic manganese showed a gradually increasing trend. By changing the current density, the current efficiency of electrolytic manganese increased first and then decreased. When the current density was 400 A·m−2, the current efficiency was the highest, it was about 66.63%. The cell voltage in the process of manganese electrolysis was independent of Mg2+ concentration and (NH4)2SO4 concentration, but only positively related to current density. Through the macroscopic analysis of the cathode plate, the greater the current efficiency was, the brighter the color of the metal manganese sheet was, it shew a silver white, and the dendritic growth of metal manganese was less. From the microscopic morphology of the manganese metal sheet, the electrolytic manganese metal was formed by stacking metal manganese sheets, each metal manganese sheet exhibited a regular hexagonal structure, the shape was similar to a ‘pyramid’, it had a better compactness, in which the better the current efficiency was, the better the compactness of the electrolytic manganese metal was. Under different experimental conditions, crystal plane (330,411) was the strongest and best orientation for the growth of electrolytic manganese. Cyclic voltammetry experiments showed that Mg2+ was not beneficial to electrodeposition of manganese, the increase of (NH4)2SO4 was beneficial to improve the current efficiency, and it was consistent with the conclusion of electrolysis experiment.
Green synthesis, characterization and antibacterial study on the catechin-functionalized ZnO nanoclusters
Authors: Zhao Baihan , Deng Shixian , Li Jingchao , Sun Congcong , Fu Yujie , Liu Zhiguo 
Published: February 2021

Abstract
Green synthesis of zinc oxide nanomaterials has received recent attention due to the potential application of these nanomaterials as biocidal agents to combat antibiotic resistant organisms. In this paper, we provide a facile, one-step hydrothermal approach to prepare catechin-functionalized ZnO nanoclusters in aqueous solution. The obtained ZnO nanoclusters were characterized by UV spectroscopy (UV), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), atomic force microscopy (AFM), x-ray diffraction (XRD) and x-ray photoelectron spectroscopy (XPS). The results of FTIR indicated that the catechin molecules were adsorbed on the surface of ZnO nanoclusters. TEM determination revealed that small ZnO nanoparticles tend to aggregate and form nanocluster structures. Antibacterial activity was tested by paper disk diffusion and the catechin-functionalized ZnO nanoclusters showed high biocidal activity against gram-positive bacteria, gram-negative bacteria and fungi.
Ultrahigh resolution integrated optic short range surface plasmon-polariton based sensor for aqueous environment
Authors: Sharma Vinod K 
Published: February 2021

Abstract
We propose a short length plasmonic integrated optic sensor with ultrahigh sensitivity and resolution for aqueous environment. The sensor section is a simple multilayer structure consisting of a dielectric planar waveguide separated from a thin metal film by a low index buffer layer. The sensor is based on the hybrid coupling between the guided mode and the short range plasmonic mode supported by the thin metal film. Periodic coupling between these modes takes place along the length of the sensor. For optimized layer thicknesses, resonant peak appears at very short length of sensing section. The spectral position of resonant peak is strongly dependent on the analyte index. We show theoretically that a spectral sensitivity of 3.2 × 104 nm RIU−1 with FWHM of 2 nm and resolution of 6.2 × 10–8 RIU can be achieved for aqueous environment.
The three-dimensional genome in zebrafish development
Authors: Labudina Anastasia , Horsfield Julia A 
Published: February 2021

Abstract
In recent years, remarkable progress has been made toward understanding the three-dimensional (3D) organisation of genomes and the influence of genome organisation on gene regulation. Although 3D genome organisation probably plays a crucial role in embryo development, animal studies addressing the developmental roles of chromosome topology are only just starting to emerge. Zebrafish, an important model system for early development, have already contributed important advances in understanding the developmental consequences of perturbation in 3D genome organisation. Zebrafish have been used to determine the effects of mutations in proteins responsible for 3D genome organisation: cohesin and CTCF. In this review, we highlight research to date from zebrafish that has provided insight into how 3D genome organisation contributes to tissue-specific gene regulation and embryo development.
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Authors: Ji Yanrong , Zhou Zhihan , Liu Han , Davuluri Ramana V 
Published: February 2021

Abstract

Motivation
Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios.

Results
To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks.

Availability and implementation
The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT).

Supplementary information
Supplementary data are available at Bioinformatics online.
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer
Authors: Kim So Yeon , Choe Eun Kyung , Shivakumar Manu , Kim Dokyoon , Sohn Kyung-Ah 
Published: February 2021

Abstract

Motivation
To better understand the molecular features of cancers, a comprehensive analysis using multi-omics data has been conducted. In addition, a pathway activity inference method has been developed to facilitate the integrative effects of multiple genes. In this respect, we have recently proposed a novel integrative pathway activity inference approach, iDRW and demonstrated the effectiveness of the method with respect to dichotomizing two survival groups. However, there were several limitations, such as a lack of generality. In this study, we designed a directed gene–gene graph using pathway information by assigning interactions between genes in multiple layers of networks.

Results
As a proof-of-concept study, it was evaluated using three genomic profiles of urologic cancer patients. The proposed integrative approach achieved improved outcome prediction performances compared with a single genomic profile alone and other existing pathway activity inference methods. The integrative approach also identified common/cancer-specific candidate driver pathways as predictive prognostic features in urologic cancers. Furthermore, it provides better biological insights into the prioritized pathways and genes in an integrated view using a multi-layered gene–gene network. Our framework is not specifically designed for urologic cancers and can be generally applicable for various datasets.

Availability and implementation
iDRW is implemented as the R software package. The source codes are available at https://github.com/sykim122/iDRW.

Supplementary information
Supplementary data are available at Bioinformatics online.
Crypt4GH: a file format standard enabling native access to encrypted data
Authors: Senf Alexander , Davies Robert , Haziza Frédéric , Marshall John , Troncoso-Pastoriza Juan , Hofmann Oliver , Keane Thomas M. 
Published: February 2021

Abstract

Motivation
The majority of genome analysis tools and pipelines require data to be decrypted for access. This potentially leaves sensitive genetic data exposed, either because the unencrypted data is not removed after analysis, or because the data leaves traces on the permanent storage medium.

Results
: We defined a file container specification enabling direct byte-level compatible random access to encrypted genetic data stored in community standards such as SAM/BAM/CRAM/VCF/BCF. By standardizing this format, we show how it can be added as a native file format to genomic libraries, enabling direct analysis of encrypted data without the need to create a decrypted copy.

Availability and implementation
The Crypt4GH specification can be found at: http://samtools.github.io/hts-specs/crypt4gh.pdf.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prophylactic sublay non-absorbable mesh positioning following midline laparotomy in a clean-contaminated field: randomized clinical trial (PROMETHEUS)
Authors: Pizza F , D’Antonio D , Ronchi A , Lucido F S , Brusciano L , Marvaso A , Dell’Isola C , Gambardella C 
Published: February 2021

Abstract

Background
Incisional hernia is a frequent postoperative complication after midline laparotomy. Prophylactic mesh augmentation in abdominal wall closure after elective surgery is recommended, but its role in emergency surgery is less well defined.

Methods
This prospective randomized trial evaluated the incidence of incisional hernia in patients undergoing urgent midline laparotomy for clean-contaminated surgery. Closure using a slowly absorbable running suture was compared with closure using an additional sublay mesh (Parietex ProGrip™). Patients were randomized just before abdominal wall closure using computer-generated permuted blocks. Patients, care providers, staff collecting data, and those assessing the endpoints were all blinded to the group allocation. Patients were followed up for 24 months by means of clinical and ultrasonographic evaluations.

Results
From January 2015 to June 2018, 200 patients were randomized: 100 to primary closure (control group) and 100 to Parietex ProGrip™ mesh-supported closure (mesh group). Eight patients in the control group and six in the mesh group were lost to follow-up. By 24 months after surgery, 21 patients in the control group and six in the mesh group had developed incisional hernia (P = 0.002). There was no difference between groups in the incidence of haematoma (2 versus 5; P = 0.248) and superficial wound infection (4 versus 5; P = 0.733). Multivariable analysis confirmed the role of mesh in preventing incisional hernia (odds ratio 0.11, 95 per cent c.i. 0.03 to 0.37; P  &lt; 0.001). One patient in the mesh group required mesh removal because of deep infection.

Conclusion
Prophylactic mesh-augmented abdominal wall closure after urgent laparotomy in clean-contaminated wounds is safe and effective in reducing the incidence of incisional hernia. Registration number: NCT04436887 (http://www.clinicaltrials.gov).