bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis, Biological Activity of Trimethoprim derivative and the Complexes
Authors: Albahadly Hassan H , Al-Haidery Nahed H , Al-Salami Bushra K
Published: November 2021

This study demonstrates the synthesis of new ligands derived from trimethoprim with their Iron(III) and copper (ll) complexes. At the beginning, preparing new ligands, the first namly N, N’-(5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diyl)bis(3,4,5-trihydroxy benza mide)and the Ligand second namly N, N’-(((5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diyl) bis(azanediyl))bis(carbonthioyl) bis(3,4,5-trihydroxybenzamide) which prepared by nucleophilic addition of trimethoprim to Gallic chloride and prepared also by nucleophilic addition of trimethoprim to the Solution of Ammonium thiocyanate and Gallic chloride. Ferric Ion (III) and Copperic Ion (ll) complexes have been prepared with molar ratio [1:2]. The synthesis ligands have been characterized by Uv-Visible, FT-IR, 1HNMR, 13CNMR and EI-mass, while the complexes have been characterized by elemental analysis, Uv-Visible, FT-IR, Conductivity measurements and thermogravemtric (TgA) analysis. The ligands acts as multiple sites coordinating with ferric ion and copper ion, Via lone pair of nitrogen atom of NHC= and phenolic oxygen. In Vitro, the ligands and complexes have been tested for their growth Inhibitory activity against Gram negative bacteria Salmonella Spp and Gram Positive Staphylococcus Spp. The results of the test indicate that the synthesized compounds possessed a high inhibition effectiveness comparative with trimethoprim.
Allocation of Relief Centre for Flood Victims Using Location Set Covering Problem (LSCP)
Authors: Hashim Nur Idayu Mah , Sarifah Radiah Shariff S , Deni Sayang Mohd
Published: November 2021

The frequency of natural disaster has been increasing over the years, resulting in loss of life, damage to properties and destruction of the environment. Compared to other natural disaster, floods are the most significant natural hazard in Malaysia that affect thousands of people. It becomes of great concern especially, during these recent floods, several relief centers were experiencing problems when most of the flood’s victims needed to move to the other relief centers after the existing shelters were also affected by flood water. Furthermore, the relief centers were congested due to the large number of flood evacuees that were over the capacity provided. This study attempts to adapt an advance mathematical location-allocation models in making decision to locate and allocate flood victims during flood event. The Location Set Covering Problem (LSCP), with capacitated constraint is considered and solved using Excel Solver. The determination of safe locations for relief centres with respect to prone area is proposed by adding three new constraints which are the distance from river, elevation from sea level and rainfall amount. A flood case of Kuala Kuantan, Pahang in 2013 was used as the main study area for the analysis as well as the whole Kuantan district. Two scenarios of split and non-split allowed were tested for allocation process and result showed that the percentage allocation and number of relief centers involved increases when the distance increases accordingly. Hence, the model can be considered for better evacuation plan.
Research on Control Strategy of Manipulator Based on Simulation
Authors: Su JiaLei
Published: November 2021

The force supple control method of robotic arm has been widely researched internationally for many years, and its specific use varies according to the structure of the robotic arm, the location of the sensor, the working space environment, and other factors. Based on the force control principle and control method of the space robot arm, this paper adopts the position-based Cartesian spatial impedance control and proposes an effective forcesmoothing control method after pre-processing the feedback signal of the six-dimensional force sensor installed at the end of the space robot arm with the coordinate system conversion. In addition, the proposed position-based Cartesian spatial impedance control method is modeled and simulated to analyze the effect of each control element on the force-following control effect, to find out the control conditions that can optimize the force-position control effect, and finally to optimize the impedance parameters. This study aims to promote the rapid development of the field of robotic arm control.
Study on the Influence of Inserting Clearance on the Voltage Standing Wave Ratio in RF Connector
Authors: Li Xiang , Tong Lijun , Cai Libing , Xie Qian , Xu Jinling , Zhao Min , Shi Guangqin
Published: November 2021

RF (Radio Frequency) connector has been extensively applied in the field of communication for it is a key device of transmitting microwave signals. If he RF connector end is designed improperly in dimension, a clearance will be observed after inserting, resulting in an abnormal phenomenon in the voltage standing wave ratio (VSWR) of the RF connector. This paper studied the influence of the inserting clearance of RF connector on the voltage standing wave ratio through theoretical analysis and performance simulation. Moreover, the solution to the abnormal voltage standing wave ratio was also proposed. At last, the abnormal phenomenon of voltage standing wave ratio of the connector in the inserting process was handled by means of carrying out optimization design and test validation on the RF connector.
UAV detection algorithm based on the difference of power dispersion
Authors: Yuan Cheng , Jia Long-fei , Cheng Hong-li
Published: November 2021

With the development and popularization of UAVs, illegal UAV accidents occur frequently. The complex signal environment in the city brings difficulties to detect UAV signal. In order to detect the UAV signal in the complex environment, this paper proposes a UAV detection algorithm based on the difference of power dispersion in time. Firstly, the algorithm performs short-time Fourier transform on the signal to obtain the time-frequency matrix. Secondly, The fixed frequency interference in the matrix is filtered by the local adaptive threshold. Finally, the UAV image transmission signal is detected by the discrete difference in time between image transmission signal and WiFi. Simulation results show that the algorithm can detect UAV signal under constant frequency interference and WiFi interference.
Stiffness Evaluation and fast matching method of mechanical composite structure
Authors: Lv Jishuang
Published: November 2021

Stiffness evaluation can improve the reliability and safety of combined machinery, which is often used to evaluate the performance of combined machinery. In order to study the stiffness evaluation method and rapid matching of mechanical composite structure, the composite machinery composed of high-power diesel is taken as the research object. The results show that the error between test mode and calculation mode is no more than 10%, indicating the reliability of finite element simulation model; two characterization methods of static stiffness and dynamic stiffness are determined, and the analysis methods of two characterization methods of combined machinery are discussed one by one. Taking the combined machinery of body, main bearing cap and oil pan as the research object, the overall stiffness characterization data of three parts are obtained one by one; finally, the principles of mechanical combination Stiffness Evaluation and rapid matching are summarized. This study provides a reference for Stiffness Evaluation and rapid matching of combined mechanical structures.
Research on Nano Refrigerant and Nano Lubricant to Improve Energy Saving of Refrigeration System
Authors: Kong Dexia , Wei Na , Dong Min
Published: November 2021

In order to improve the performance of the refrigeration system, researchers have introduced nano-refrigerant and nano-lubricating oil into the latest development of airconditioning system. However, explaining the role of nano-particles based on the physical phenomena affecting the vapor compression refrigeration system (VCRS) has been limited in experiments. Therefore, this paper reviews the mechanism of using nano-refrigerant and nano-lubricating oil to improve the performance of VCRS, discusses the compression work of the refrigeration system using nano-refrigerant and nano-lubricating oil and VCRS performance parameters such as COP and COF, and relates them to the overall performance of the system. The results show that the main factors affecting the performance of VCRS are heat transfer enhancement, refinement of the characteristics of cold oil mixture and improvement of tribological properties. The influence of nano-refrigerant and nano-lubricating oil on heat transfer, cold oil mixture and tribological properties of VCRS improves the overall performance of VCRS. Therefore, nano-refrigerant and nano-lubricant are expected to be the best choice to improve the efficiency of VCRS.
An improved simulated load test system
Authors: Hua Liang , Qi Jiaen , Huang Wei , Zhang Sijiang , Gao Feng , Peng Shengjiang
Published: November 2021

A miniaturized analog load-checking relay protection test device is developed in this paper, in which a high-precision wireless phase volt-ampere test device is configured. This device, characterized by intelligence and ease of operation, realizes the detection of the transformation ratio, polarity, phase, etc. of the secondary wiring of the transformer in the smart substation merging unit and the conventional substation. It meets the testing requirements of smart substations, and can test bus differential protection, line protection, and various protections such as main transformer differential.
Research on CNN-based intelligent recognition method for negative images of weld defects
Authors: HUANG Jiawei , BI Caixia , LIU Jiayue , DONG Shaohua
Published: November 2021

The existing technology of automatic classification and recognition of welding negative images by computer is difficult to achieve a multiple classification defect recognition while maintaining a high recognition accuracy, and the developed automatic recognition model of negative image defect cannot meet the actual needs of the field. Therefore, the convolutional neural network (CNN)-based intelligent recognition algorithm for negative image of weld defects is proposed, and a B/S (Browser/Server) architecture of weld defect feature image database combined with CNN is established subsequently, which converted from the existing CNN by the migration learning method. It makes full use of the negative big data and simplifies the algorithm development process, so that the recognition algorithm has a better generalization ability and the training algorithm accuracy of 97.18% achieved after training. The results of the comparison experiments with traditional recognition algorithms show that the CNN-based intelligent recognition algorithm for defective weld negatives has an accuracy of 92.31% for dichotomous defects, which is significantly better than the traditional recognition algorithm, the established recognition algorithm effectively improving the recognition accuracy and achieving multi-category defect recognition. At the same time, the CNN-based defect recognition method was established by combining the image segmentation algorithm and the defect intelligent recognition algorithm, which was applied to the actual negative images in the field with good results, further verifying the feasibility of CNN-based intelligent recognition algorithm in the field of defect recognition of welding negative images.
A packet replication algorithm for delay tolerant networks based on multi-metric
Authors: Liu Yongguang
Published: November 2021

Utility function of packet is often used to decide how to replicate packet in DTN networks. But this method has more uncertainty and relies on a single performance metric. For this problem, in order to reduce the impact of a single metric uncertainty, multiple utility metrics are introduced in the new algorithm. A packet replication probability calculation method based on entropy weight is designed. By calculating the entropy weight of each metric, the algorithm obtains the replication probability of each packet and takes the probability as the priority of packet replication. Because of considering the two metrics of packet expected transmission delay and node encounter possibility, the algorithm effectively reduces the influence of encounter time distribution problem and direction prediction problem in the original algorithm, and reduces the uncertainty of utility function. Simulation results show that the algorithm reduces the packet replication number and the average delay, improves the successful packet delivery rate. The overall performance of the network is further improved.
Spectral Analysis of (Multi-) Pulse-Position Modulation
Authors: Gu Silyu , Liang Chunliang , Zhang Jiaxu
Published: November 2021

Nowadays, laser communication has received great achievements owing to its advantages, e.g., large channel capacity, easy miniaturization of communication system and strong anti-interference ability in different conditions. Pulse position modulation (PPM), as an important modulation technology in laser communication system that transmit signal with lower power, is attracting much attention. However, the performance of the modulation scheme highly depends on the bandwidth of transmission. To remedy this defect of PPM, the multipulse position modulation (MPPM) scheme is proposed to increase the accuracy and bandwidth limit. This modulation scheme has stronger anti-interference ability than PPM. Therefore, there has been rising interest in studying the characteristics of the multi-PPM. In this article, we developed an appropriate mathematical model to represent a PPM transmission, analyzed the spectrum of the transmission and characterized the bandwidth of this transmission. Compared with benchmarks of MPPM scheme, its performance has been discussed. According to the analysis, MPPM strongly increases band-utilization efficiency, however PPM has a better bit error rate (BER) performance than MPPM.
Research on temperature acquisition system of printing machine oven based on wireless Sensor network
Authors: WU Rui , WANG Yi-ming , WANG Yu-hu
Published: November 2021

Aiming at the problems such as limited transmission distance of traditional temperature data, complex wiring and aging line, ZigBee wireless network is introduced into the temperature acquisition system of the intaglio printing machine oven, which makes the whole system easy to operate and simple, and greatly improves the transmission distance of temperature signal. The composition of the temperature monitoring system and the hardware circuit of the ZigBee master node are described, including DC 5 V power supply circuit and USB interface power supply circuit, the connection circuit between the RADIO frequency board and the backboard, to realize the construction of the network and the wireless reception of temperature data. To realize the construction of the network and wireless reception of temperature data. It combines ZigBee wireless communication technology to complete real-time transmission of multi-point temperature data, realize real-time LCD display of multi-point temperature data collected by DS18B20, and realize ZigBee networking function based on ZigBee protocol stack.
Design of Digital Pulse-Position Modulation System
Authors: Yu Nanjun , Wang Pengzhao , Zhuang Zhiyi
Published: November 2021

Pulse-Position Modulation (PPM) is a modulation method that only makes every pulse in the carrier pulse sequence change with time but without changing the shape and amplitude of the pulse signal. In this paper, a PPM system is designed. Firstly, an appropriate mathematical model is established to represent PPM transmission, and the shape of the pulse signal is designed. After that, we write the code and add a white Gaussian noise channel. Then the transmission process is simulated and visualized. At last, the error rate of the scheme is analyzed and discussed through MATLAB simulation then compared with other modulation methods. The goal of this paper is to study PPM by designing a PPM system fully. Besides, our method is compared with other modulation methods to understand the advantages and disadvantages of PPM. This may help other scholars to design and research the PPM system.
Testability Analysis Method of Radar Equipment Based on Dependency Model
Authors: Du Xiaoshuai , Hu Bing , Qin Jian
Published: November 2021

In order to improve the testability design level of radar equipment, achieve rapid detection and isolation of faults, and reduce the life cycle cost of the system, a testability analysis method of radar equipment based on correlation model is proposed. The basic process of correlation model modeling is introduced. On this basis, the optimization method of test points for fault detection and isolation and the generation method of fault diagnosis strategy are analyzed. The effectiveness of the proposed method is verified by applying it to radar transmitting subsystem.
Research on Comparison of LiDAR and Camera in Autonomous Driving
Authors: Wang Peide
Published: November 2021

With the improvement of vehicles automation, autonomous vehicles become one of the research hotspots. Key technologies of autonomous vehicles mainly include perception, decision-making, and control. Among them, the environmental perception system, which can convert the physical world’s information collection into digital signals, is the basis of the hardware architecture of autonomous vehicles. At present, there are two major schools in the field of environmental perception: camera which is dominated by computer vision and LiDAR. This paper analyzes and compares the two majors schools in the field of environmental perception and concludes that multi-sensor fusion is the solution for future autonomous driving.
Study on Influencing Factors and Laws of Fuel Injection Consistency of Common Rail Injector
Authors: Zhang Ziwei , Xu Chunlong
Published: November 2021

In order to study the influence of parameters of common rail injector internal components on cycle injection consistency, its simulation model is established by AMESim, and the model is validated by the experimental injection rate data. The effects of solenoid valve spring preload, gag bit lift, fuel discharge hole diameter, fuel inlet hole diameter, needle valve lift, needle valve preload and nozzle diameter on the change of injection quantity under different operating conditions are studied by simulation method, and the impact weight of each parameter on fuel injection consistency is analyzed. The results show that the preload of solenoid valve, fuel discharge hole diameter, oil inlet hole diameter, needle valve lift and nozzle diameter are the main parameters affecting the consistency of cycle injection. The percentages of five parameters influencing on the consistency of cyclic injection are 8.68-16.84%, 11.41-23.68%, 17.2086-37.74%, 12.772-18.34% and 9.69-37.27% respectively.
Numerical Simulation on Gas-Solid Two-Phase Flow in Horizontal Pneumatic Conveying Pipe Based on DPM Model
Authors: Guo Zihan , Zhang Jun , Huang Jinman
Published: November 2021

The determination of pipe deposition and optimum conveying velocity in pneumatic conveying has an important impact on conveying efficiency. The Euler-Lagrange method DPM model is used to analyse five different particle sizes and densities of small particles, and the flow pattern in the horizontal pipeline at different particle sizes and densities is derived from the graphs of the maximum discrete phase concentration, particle trajectory and discrete phase concentration distribution for each working condition. The simulation results show that the deposition increases with particle size and density, the optimum conveying speed increases with particle size and density, the larger the deposition, the larger the required conveying velocity. The velocity of 2 m/s can make the particles below 20μm suspended transport, the velocity of 4 m/s allows particles with a particle size of 30μm and a density of 1000 kg/m3 or less to be transported in suspension and 6 m/s allows particles with a density of 2000 kg/m3 or less to be transported in suspension. The aim is to provide a reference for the design of pneumatic conveying systems and the selection of the optimum conveying velocity.
Experimental Study on the Effect of Locally Convergent Configurations on the Flow Pattern in PMMA Microchips
Authors: Zhang Jinsong , Liu Zhongxin , Wang Chao , Wang Zhiliang
Published: November 2021

The geometries of micro-channel play a key role in forming of digital droplets, and can be real-time or effective controlling methodologies. Local convergence regions are designed in the rectangular cross-section channels on PMMA microchips, in which two-phase coaxial jets are introduced by inserting a syringe needle. The two-phase flow (lubricating oil (continuous phase, flow rate Q
c)/deionized water (dispersed phase, flow rate Q
d)) is considered. Two geometric control variables, the relative position (needle displacement x) and tapering characteristics (convergence angle α), are naturally adopted to discribe such geometry configurations. The micro-flow under the change of these two parameters is mainly studied in this paper. Four kinds of characteristic flow patterns, namely, sausages, slug, dripping and jetting, are found in the experiment, and their occurring parameters and developing dynamic characteristics are discussed. The experiment shows that the increase of inner needle displacement x can produce higher frequency and finer droplets, which is in consistent with our previous results obtained in round tube experiments and simulations. While increasing the convergence angle α, contrarily, takes opposite effects.
Study on the Expansion of Primary Flow for the Mixing Uniformity in the Two-Phase Ejector
Authors: Zheng Lixing , Hu Hongwei , Mi Changning
Published: November 2021

The expansion of primary flow in the suction chamber of the CO2 two-phase ejector is investigated and its influences on the mixing characteristics are analyzed. An ejector model is developed, by constructing differential equations for mass, momentum and energy then get the governing equation. In the suction chamber, the expansion of primary flow and the compression of secondary flow are modeled along the flow path. Based on the constant-pressure mixing theory, the pressure equilibrium positions of two stream (namely at the inlet and inside of mixing chamber, respectively) are considered. The mass and energy transfer in the mixing chamber were analyzed by using the double-flow model formulation. The ejector performance parameters are obtained for the different operation conditions, and the distributions of temperature and velocity of two streams in the mixing chamber are presented. The simulation results showed the influence of primary flow expansion on the pressure lift ratio was relatively obvious, and the larger expansion distance was helpful to improve the mixing efficiency and decrease the thermodynamic entropy change during the mixing. Moreover, the temperature of secondary flow for lower primary flow pressure presented larger descent rates at the initial of mixing. This work is helpful for the improvement of ejector theoretical model and the optimization design.
Analysis of Characteristics of Damping Valve Based on High-Order Discrete Scheme
Authors: Pan Shichao , Li Weimin
Published: November 2021

In this paper, based on the high-order discrete scheme, a two-way fluid-solid coupling numerical simulation is for the damping valve plate. According to the discrete method, the governing equations of fluid structure coupling of damping valve plate are studied, including the basic conservation laws; Meanwhile, it analyzes the discretization of the control equation, including the discretization method and the high-order discretization format when the finite volume method is adopted. And based on this discrete format, a numerical simulation was performed on the damping valve, the oil flow condition is analyzed, and the velocity of the throttling hole at different time points and the throttling pressure are analyzed.
Feasibility of Boosting Low-Energy-Quality Steam by Using Wave Rotor
Authors: Dai Yuqiang , Tang Zhipeng , Li Mohan , Hao Gang , Zhang Luwei , Wu Jintao
Published: November 2021

Owing to the difficult utilization of the low-pressure level in the process industry, the low-energy-quality steam is often condensed to recover the demineralized water or just discharged directly, causing a huge waste of thermal energy. A novel technology of enhancing the steam’s energy quality by using the wave rotor based on the principle of moving shockwave compression is proposed. The supercharging ability of 3-port wave rotor is studied by meaning of 1-dimension unsteady theory and computational fluid dynamic. A practical thermodynamic flowsheet of boosting the low-pressure steam driven by high-pressure steam is also proposed and analysed in detail. As an example, to boost the saturated steam of pressure 1.0 MPa to 1.953 MPa, a three-stage wave rotor solution is proposed and is verified its feasibility. The high supercharging ratio and entrainment ratio of the wave rotor are much higher than the traditional steam ejector shows the feasibility of enhancing energy-quality of low-pressure steam.
A Quantitative Study of Carmine Aqueous Solution Based on Drop-Coating Deposition Micro-Raman Spectroscopy (DCDR)
Authors: Huang Wei
Published: November 2021

Carmine is a kind of colorant which is widely used in food, beverage, medicine, cosmetics and tobacco industry. However, excessive use of carmine may lead to the risks of carcinogenic, teratogenic and mutagenic, which seriously threaten the health and safety of consumers. In this paper, DCDR technology is utilized to develop a quantitative method for the detection of carmine, which requires only a small volume deposition of analyte solution (several μL) on a suitable hydrophobic substrate. The conventional Raman spectrum of carmine aqueous solution and corresponding Raman spectrum using DCDR method were compared, illustrating a much higher sensitivity for DCDR method. The Raman spectra of carmine aqueous solution with different concentrations of 100, 50, 10, 8, 4 and 2μg/mL are acquired from the spots on the “coffee-ring” with DCDR method. Using DCDR method, a good linear relationship has been observed between the intensities of the two characteristic peaks, 1364cm−1 as well as 1572cm−1, and the concentrations of the solution, with the linear correlation coefficient of R2>0.99. The results illustrate that DCDR method has a good potential in the quantitative analysis of colorant like carmine, providing a promising technique for a rapid detection for food additives.
Progress of Development and Application of Drag Reduction Agents for Slick-Water Fracturing
Authors: Xu Ke , Lu Yongjun , Chang Jin , Weng Dingwei , Li Yang
Published: November 2021

Fracturing technology is the key technology of shale oil and gas exploitation in the United States. The key of hydraulic fracturing lies in the formulation of fracturing fluid, which can improve the permeability of shale gas layer, reduce pumping resistance, optimize production conditions, reduce strata damage and other purposes. Slick-water is widely used in water-based fracturing for unconventional oil and gas exploitation, which can reduce the friction resistance. As the core of the slickwater fracturing fluid, the friction reducer determine the fluid’s performances. Combining with the related literature at home and abroad, this paper analyzes the mechanism of friction reducer, introduces the research and application progress of natural polysaccharide, surfactant and polyacrylamide. It is considered that both the instant powder polymer and W/W dispersion polymer have great application potential. The friction reducer with high-efficiency sand-carrying and salt resistance is the focus of future research.
Numerical Simulation of Adsorption and Heat Transfer in Porous Media Using Lattice Boltzmann Method
Authors: Wang Jianhu , Duan Zhongdi , Cheng Cheng , Tang Wenyong
Published: November 2021

An adsorption model for fluid flow, heat, and mass transfer of the adsorbent bed was established. Based on the single relaxation time lattice Boltzmann method, a dual-distributed lattice Boltzmann model of density and concentration was established to solve the fluid flow and mass transfer process in the surface area of the adsorbent bed. The adsorption and heat transfer process on the surface of the adsorbent bed was incorporated into the dual-distributed lattice Boltzmann model by the fourth-order Runge-Kutta finite difference method. The multiphysics fields under Poiseuille flow were simulated by the presented model, and the adsorption capacity and temperature distribution during the adsorption process were investigated.
Focusing of Brownian Particles in a Fluid Induced by the Temperature Difference
Authors: Ying Yuxiang , Zheng Kaixuan , Nie Deming
Published: November 2021

In this work the Brownian motion of particles in a two-dimensional channel was numerically studied through a fluctuating-lattice Boltzmann method. The effects of the fluid temperature difference on the biased Brownian motion of particles were examined. It is shown that the particles are likely to move towards and stay at the low temperature zone. More importantly, the focusing of Brownian particles may be realized if the temperature difference is large enough. This paper also provides a quantitative analysis on this issue.
Atmospheric turbulence characterization using a neuromorphic camera-based imaging sensor
Authors: Polnau Ernst , Vorontsov Mikhail A
Published: November 2021

New capabilities for atmospheric turbulence spatio-temporal dynamics characterization and refractive index structure parameter (

C
n

2

) sensing via white light imaging of remotely located non-cooperative targets using an optical system with a neuromorphic (event) based sensor are demonstrated through a set of experimental trials conducted over a 7 km imaging path and proposed event data processing technique.
Occupational Exposure Assessment Tools in Europe: A Comprehensive Inventory Overview
Authors: Peters Susan , Vienneau Danielle , Sampri Alexia , Turner Michelle C , Castaño-Vinyals Gemma , Bugge Merete , Vermeulen Roel
Published: November 2021

Objectives

The Network on the Coordination and Harmonisation of European Occupational Cohorts (OMEGA-NET) was set up to enable optimization of the use of industrial and general population cohorts across Europe to advance aetiological research. High-quality harmonized exposure assessment is crucial to derive comparable results and to enable pooled analyses. To facilitate a harmonized research strategy, a concerted effort is needed to catalogue available occupational exposure information. We here aim to provide a first comprehensive overview of exposure assessment tools that could be used for occupational epidemiological studies.

Methods

An online inventory was set up to collect meta-data on exposure assessment tools. Occupational health researchers were invited via newsletters, editorials, and individual e-mails to provide details of job-exposure matrices (JEMs), exposure databases, and occupational coding systems and their associated crosswalks to translate codes between different systems, with a focus on Europe.

Results

Meta-data on 36 general population JEMs, 11 exposure databases, and 29 occupational coding systems from more than 10 countries have been collected up to August 2021. A wide variety of exposures were covered in the JEMs on which data were entered, with dusts and fibres (in 14 JEMs) being the most common types. Fewer JEMs covered organization of work (5) and biological factors (4). Dusts and fibres were also the most common exposures included in the databases (7 out of 11), followed by solvents and pesticides (both in 6 databases).

Conclusions

This inventory forms the basis for a searchable web-based database of meta-data on existing occupational exposure information, to support researchers in finding the available tools for assessing occupational exposures in their cohorts, and future efforts for harmonization of exposure assessment. This inventory remains open for further additions, to enlarge its coverage and include newly developed tools.
A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape
Authors: Zhang Yongqing , Wang Zixuan , Zeng Yuanqi , Liu Yuhang , Xiong Shuwen , Wang Maocheng , Zhou Jiliu , Zou Quan
Published: November 2021

The discovery of putative transcription factor binding sites (TFBSs) is important for understanding the underlying binding mechanism and cellular functions. Recently, many computational methods have been proposed to jointly account for DNA sequence and shape properties in TFBSs prediction. However, these methods fail to fully utilize the latent features derived from both sequence and shape profiles and have limitation in interpretability and knowledge discovery. To this end, we present a novel Deep Convolution Attention network combining Sequence and Shape, dubbed as D-SSCA, for precisely predicting putative TFBSs. Experiments conducted on 165 ENCODE ChIP-seq datasets reveal that D-SSCA significantly outperforms several state-of-the-art methods in predicting TFBSs, and justify the utility of channel attention module for feature refinements. Besides, the thorough analysis about the contribution of five shapes to TFBSs prediction demonstrates that shape features can improve the predictive power for transcription factors-DNA binding. Furthermore, D-SSCA can realize the cross-cell line prediction of TFBSs, indicating the occupancy of common interplay patterns concerning both sequence and shape across various cell lines. The source code of D-SSCA can be found at https://github.com/MoonLord0525/.
Light attention predicts protein location from the language of life
Authors: Stärk Hannes , Dallago Christian , Heinzinger Michael , Rost Burkhard
Published: November 2021

Although knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expert-designed input features leveraging information from multiple sequence alignments (MSAs) that is resource expensive to generate. Here, we showcased using embeddings from protein language models for competitive localization prediction without MSAs. Our lightweight deep neural network architecture used a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention. The method significantly outperformed the state-of-the-art (SOTA) for 10 localization classes by about 8 percentage points (Q10). So far, this might be the highest improvement of just embeddings over MSAs. Our new test set highlighted the limits of standard static datasets: while inviting new models, they might not suffice to claim improvements over the SOTA.

Availability and implementation

The novel models are available as a web-service at http://embed.protein.properties. Code needed to reproduce results is provided at https://github.com/HannesStark/protein-localization. Predictions for the human proteome are available at https://zenodo.org/record/5047020.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores
Authors: Warmerdam Robert , Lanting Pauline ,   Lifelines Cohort Study, Deelen Patrick , Franke Lude
Published: November 2021

Motivation

Identifying sample mix-ups in biobanks is essential to allow the repurposing of genetic data for clinical pharmacogenetics. Pharmacogenetic advice based on the genetic information of another individual is potentially harmful. Existing methods for identifying mix-ups are limited to datasets in which additional omics data (e.g. gene expression) is available. Cohorts lacking such data can only use sex, which can reveal only half of the mix-ups. Here, we describe Idéfix, a method for the identification of accidental sample mix-ups in biobanks using polygenic scores.

Results

In the Lifelines population-based biobank, we calculated polygenic scores (PGSs) for 25 traits for 32 786 participants. We then applied Idéfix to compare the actual phenotypes to PGSs, and to use the relative discordance that is expected for mix-ups, compared to correct samples. In a simulation, using induced mix-ups, Idéfix reaches an AUC of 0.90 using 25 polygenic scores and sex. This is a substantial improvement over using only sex, which has an AUC of 0.75. Subsequent simulations present Idéfix’s potential in varying datasets with more powerful PGSs. This suggests its performance will likely improve when more highly powered GWASs for commonly measured traits will become available. Idéfix can be used to identify a set of high-quality participants for whom it is very unlikely that they reflect sample mix-ups, and for these participants we can use genetic data for clinical purposes, such as pharmacogenetic profiles. For instance, in Lifelines, we can select 34.4% of participants, reducing the sample mix-up rate from 0.15% to 0.01%.

Availabilityand implementation

Idéfix is freely available at https://github.com/molgenis/systemsgenetics/wiki/Idefix. The individual-level data that support the findings were obtained from the Lifelines biobank under project application number ov16_0365. Data is made available upon reasonable request submitted to the LifeLines Research office (research@lifelines.nl, https://www.lifelines.nl/researcher/how-to-apply/apply-here).

Supplementary information

Supplementary data are available at Bioinformatics online.
GNN-based embedding for clustering scRNA-seq data
Authors: Ciortan Madalina , Defrance Matthieu
Published: November 2021

Motivation

Single-cell RNA sequencing (scRNA-seq) provides transcriptomic profiling for individual cells, allowing researchers to study the heterogeneity of tissues, recognize rare cell identities and discover new cellular subtypes. Clustering analysis is usually used to predict cell class assignments and infer cell identities. However, the high sparsity of scRNA-seq data, accentuated by dropout events generates challenges that have motivated the development of numerous dedicated clustering methods. Nevertheless, there is still no consensus on the best performing method.

Results

graph-sc is a new method leveraging a graph autoencoder network to create embeddings for scRNA-seq cell data. While this work analyzes the performance of clustering the embeddings with various clustering algorithms, other downstream tasks can also be performed. A broad experimental study has been performed on both simulated and scRNA-seq datasets. The results indicate that although there is no consistently best method across all the analyzed datasets, graph-sc compares favorably to competing techniques across all types of datasets. Furthermore, the proposed method is stable across consecutive runs, robust to input down-sampling, generally insensitive to changes in the network architecture or training parameters and more computationally efficient than other competing methods based on neural networks. Modeling the data as a graph provides increased flexibility to define custom features characterizing the genes, the cells and their interactions. Moreover, external data (e.g. gene network) can easily be integrated into the graph and used seamlessly under the same optimization task.

Availability and implementation

https://github.com/ciortanmadalina/graph-sc.

Supplementary information

Supplementary data are available at Bioinformatics online.
Induction of mismatch repair deficiency, compromised DNA damage signaling and compound hypermutagenesis by a dietary mutagen in a cell-based model for Lynch syndrome
Authors: Ijsselsteijn Robbert , van Hees Sandrine , Drost Mark , Jansen Jacob G , de Wind Niels
Published: November 2021

The prevalent cancer predisposition Lynch syndrome (LS, OMIM #120435) is caused by an inherited heterozygous defect in any of the four core DNA mismatch repair (MMR) genes MSH2, MSH6, MLH1 or PMS2. MMR repairs errors by the replicative DNA polymerases in all proliferating tissues. Its deficiency, following somatic loss of the wild-type copy, results in a spontaneous mutator phenotype that underlies the rapid development of, predominantly, colorectal cancer (CRC) in LS. Here, we have addressed the hypothesis that aberrant responses of intestinal stem cells to diet-derived mutagens may be causally involved in the restricted cancer tropism of LS. To test this we have generated a panel of isogenic mouse embryonic stem (mES) cells with heterozygous or homozygous disruption of multiple MMR genes and investigated their responses to the common dietary mutagen and carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Our data reveal that PhIP can inactivate the wild-type allele of heterozygous mES cells via the induction of either loss of heterozygosity (LOH) or intragenic mutations. Moreover, while protective DNA damage signaling (DDS) is compromised, PhIP induces more mutations in Msh2, Mlh1, Msh6 or Pms2-deficient mES cells than in wild-type cells. Combined with their spontaneous mutator phenotypes, this results in a compound hypermutator phenotype. Together, these results indicate that dietary mutagens may promote CRC development in LS at multiple levels, providing a rationale for dietary modifications in the management of LS.
Prenatal gyrification pattern affects age at onset in frontotemporal dementia
Authors: Harper Luke , Lindberg Olof , Bocchetta Martina , Todd Emily G , Strandberg Olof , van Westen Danielle , Stomrud Erik , Landqvist Waldö Maria , Wahlund Lars-Olof , Hansson Oskar , Rohrer Jonathan D , Santillo Alexander
Published: November 2021

The paracingulate sulcus is a tertiary sulcus formed during the third trimester. In healthy individuals paracingulate sulcation is more prevalent in the left hemisphere. The anterior cingulate and paracingulate gyri are focal points of neurodegeneration in behavioral variant frontotemporal dementia (bvFTD). This study aims to determine the prevalence and impact of paracingulate sulcation in bvFTD. Structural magnetic resonance images of individuals with bvFTD (n = 105, mean age 66.9 years), Alzheimer’s disease (n = 92, 73.3), and healthy controls (n = 110, 62.4) were evaluated using standard protocol for hemispheric paracingulate sulcal presence. No difference in left hemisphere paracingulate sulcal frequency was observed between groups; 0.72, 0.79, and 0.70, respectively, in the bvFTD, Alzheimer’s disease, and healthy control groups, (P = 0.3). A significant impact of right (but not left) hemispheric paracingulate sulcation on age at disease onset was identified in bvFTD (mean 60.4 years where absent vs. 63.8 where present [P = 0.04, Cohen’s d = 0.42]). This relationship was not observed in Alzheimer’s disease. These findings demonstrate a relationship between prenatal neuronal development and the expression of a neurodegenerative disease providing a gross morphological example of brain reserve.
Modes of the bioprosthetic valve failure of the porcine and pericardial valves in the mitral position
Authors: Uchino Gaku , Murakami Hirohisa , Mukohara Nobuhiko , Tanaka Hiroshi , Nomura Yoshikatsu , Miyahara Syunsuke , Kawashima Motoharu , Fujisue Jun , Tonoki Shuto
Published: November 2021

OBJECTIVES

This study was conducted to examine the incidence and modes of the bioprosthetic valve failure of the porcine valve in the mitral position and compare them with those of the pericardial valve.

METHODS

This study included 240 patients (116 men [48.3%]; mean age, 74.87 ± 6.61 years) who underwent mitral valve replacement using the St. Jude Medical Epic bioprosthesis (Epic) (N = 125) or Carpentier–Edwards Perimount (CEP) pericardial valve (N = 115) from January 2000 to December 2020.

RESULTS

The median clinical follow-up durations in the Epic and CEP groups were 54.5 months (range, 0–111 months) and 81.5 months (range, 0–194 months), respectively. Structural valve degeneration (SVD) was observed in 9 patients (7.2%) in the Epic group and 11 patients (9.6%) in the CEP group. The rates of freedom from SVD at 3, 5 and 7 years were 97.7%, 90.5% and 75.5% in the Epic group and 100.0%, 96.1% and 90.0% in the CEP group, respectively. SVD reoperation was performed for 7 patients (5.6%) in the Epic group and 6 patients (5.2%) in the CEP group. The rates of freedom from SVD reoperation at 3, 5 and 7 years were 97.7%, 90.5% and 75.5% in the Epic group and 100%, 96.1% and 90.0% in the CEP group, respectively. Epic SVD was predominantly due to leaflet tearing, whereas CEP SVD was predominantly due to leaflet calcification and adhesion to the subvalvular apparatus.

CONCLUSIONS

SVD of the porcine valve was predominantly due to leaflet tearing. The rate of reoperation for SVD was slightly higher for the porcine valve in the mitral position than for the pericardial valve at adjusted survival analysis.
Predictors of mortality in patients with acute small-bowel perforation transferred to ICU after emergency surgery: a single-centre retrospective cohort study
Authors: Wu Jianzhang , Shu Ping , He Hongyong , Li Haojie , Tang Zhaoqing , Sun Yihong , Liu Fenglin
Published: November 2021

Background

Although small-bowel perforation is a life-threatening emergency even after immediate surgical intervention, studies have rarely investigated surgical outcomes due to its relatively low incidence. This study aimed to investigate the outcomes of emergency surgery for patients with small-bowel perforation transferred to the intensive care unit (ICU) and the risk factors for mortality.

Methods

Consecutive patients with small-bowel perforation who were confirmed via emergency surgery and transferred to the ICU in Zhongshan Hospital, Fudan University (Shanghai, China) between February 2011 and May 2020 were retrospectively analysed. Medical records were reviewed to determine clinical features, laboratory indicators, surgical findings, and pathology.

Results

A total of 104 patients were included in this study, among whom 18 (17.3%), 59 (56.7%), and 27 (26.0%) underwent perforation repair, segmental resection with primary anastomosis, and small-bowel ostomy, respectively. Malignant tumours were the leading cause of perforation in these patients (40.4%, 42/104). The overall post-operative complication rate and mortality rates were 74.0% (77/104) and 19.2% (20/104), respectively. Malignant tumour-related perforation (odds ratio [OR], 4.659; 95% confidence interval [CI], 1.269–17.105; P = 0.020) and high post-operative arterial blood-lactate level (OR, 1.479; 95% CI, 1.027–2.131; P = 0.036) were identified as independent risk factors for post-operative mortality in patients with small-bowel perforation transferred to the ICU.

Conclusions

Patients with small-bowel perforation who are transferred to the ICU after emergency surgery face a high risk of post-operative complications and mortality. Moreover, those patients with malignant tumour-related perforation and higher post-operative blood-lactate levels have poor prognosis.