bluuebunny/crossref_metadata_2025 huggingface dataset:
Aerodynamic Performance Improvement by Streamlining The Front Fairing of a Racing Vehicle
Authors: Ferdaus F , Raghukiran N , Vijaykumar  , Karthikeyan
Published: April 2021

The paper helps to explore and demonstrate the weight reduction of a component with the help of efficient aerodynamics. This can help to reduce fuel consumption and improve the performance of a racing vehicle. The vehicle used is a KTM RC200 2015 which was tested on various factors such as aerodynamics, weight, fuel consumption, and performance. The results were eventually validated with appropriate simulation and experimental trials. To improve and sustain the performance of the engine, it is necessary to explore various factors such as weight reduction through material selection and aerodynamically streamlining the vehicle design. The main component that was tested is the front fairing of the bike. The front fairing plays a very important role in a bike’s performance. Therefore, the stock front fairing component is to be replaced with a modified component which also needs to meet all the regulatory safety standards. In the present work, two different front fairing components were used and one of them is made up of plastic representing the stock component while the second one is the customized and improved component made up of glass fiber reinforced epoxy. The results had shown promising improvements to the performance of the vehicle and it was observed that the material density and strength played a factor in the bike’s performance and fuel efficiency.
Failure Analysis of Drive Axle Shaft failed under Torsional Stress
Authors: Maurya P , Mulani N , Michael C , Jebaseelan D
Published: April 2021

Drive axles are an essential component for power transmission in any automobile. It transfers the power from the differential to the hub of the wheels which drives the vehicle. The axles are subjected to torsional stresses due to the torque from the differential and the resisting torque present due to the frictional resistance from the ground on the wheels. Hence, they are prone to torsional failures under fatigue with and without shock loading. In this paper, a comprehensive engineering failure analysis of the failed drive axle shaft of material EN 24-T, custom designed for a 200kg BAJA SAE all-terrain vehicle was performed. Destructive, non-destructive testing and material analysis along with finite element simulations using Ansys were carried out to better understand the nature and cause of the failure. Failure analysis data hints at the flaws in design considerations and scanning electron microscopy (SEM) images reveal the formation of bainitic microstructures within the component due to improper heat treatment which lowers the ultimate tensile strength of the material.
Design study of electric vehicle roll-cage obtained using modal analysis
Authors: Katait Shubham Arunrao , Dorlikar Pankaj
Published: April 2021

Understanding the dynamic behaviour of structures has become increasingly essential in the design process of any mechanical system. Modal factors like natural frequencies and mode shapes characterize the dynamic response of the structure and can be used for determination of the possible bending and torsion phenomenon. The Computer-Aided Drafting (CAD) model plays an important role in the design and development phases of an electric vehicle. For doing Finite Element Analysis (FEA) using software CAD model has to be imported so that after conversion Finite Element (FE) model can be solved. In the present case the CAD model is imported in HyperMesh. The FE model is generated and solved by using OptiStruct. Ignoring the first six natural frequencies and mode shapes due to its association with six degrees of freedom, subsequent six natural frequencies and mode shapes are proposed for an electric vehicle roll-cage. We can learn even more from CAD geometry and mode shapes in every direction about its stiffness and weight. Once we know our design baseline, we can use a software simulation to use a design study and improve its performance. We have considered the pipe diameter, thickness, tube width and height as main design parameters which needs to be optimized. In this paper, we optimized all these design parameters to make driver comfortable during driving by increasing natural frequency of the roll-cage structure by 3.34 times the human body threshold.
Significance of Taguchi Design compared to Response Surface Methodology in predicting optimal machining conditions for PCM process
Authors: Uday Kiran K A V , Vigneshwar N , Solomon Darius Gnanaraj , Arulraj Joseph Jeyapaul
Published: April 2021

Photochemical Machining (PCM) is a non-conventional machining process which produces stress free complex flat metal components. Optimization of process parameters for Photochemical machining of SS316L steel is done using Taguchi method and the results are compared with results obtained through Response surface methodology (RSM) available in literature. The objective of this work is to predict the optimal machining conditions of PCM to achieve minimum undercut for SS316L steel. The Factors affecting the response of the model are: Etching Time (Ti), Temperature (T) and Etchant Concentration (C) in PCM. This work shows that Taguchi method is faster compared to RSM in predicting the optimal conditions for minimizing defects in PCM process. Taguchi method requires only 9 experiments for finding optimal conditions whereas RSM requires 20 experiments saving about 55% of time and effort.
Effect of porosity and profile axial loading on elastic buckling and free vibration of functionally graded porous beam.
Authors: Harsha B P , Jeyaraj P , Lenin B M C
Published: April 2021

Elastic buckling and free vibration behaviour of porous functionally graded beam under profile axial mechanical loading is presented analytically. Symmetric and asymmetric porosity distribution with non linear material functional grading is presented. Buckling study is carried out first, then free vibration study under buckling loads is presented with profile loading. The effect of porosity, porosity pattern, slenderness ratio, boundary condition on critical buckling load and fundamental frequency is also studied. Ritz method with shear and normal deformable beam theory (SNDBT) is employed for formulation. It is observed that, with increase in porosity, buckling load decreases for both porosity distribution whereas, fundamental frequency increases for symmetric porosity distribution and is vice versa for asymmetric porosity distribution under all loading conditions.
Design of frontal longitudinal for enhancement in crashworthiness performance
Authors: Abdulqadir Samer Fakhri , Bassam Alaseel , Ansari M N M , Topa A
Published: April 2021

The increase in the number of vehicles due to increase in population leads to an increase in the number of accidents. To find a design that keeps occupants as safe as possible by enhancing the energy absorption capabilities and hence decreasing the number of fatalities is taking place. Non-linear finite element is used in this study to predict new design performance and to compare with other conventional S-shaped designs. It was shown that the proposed design increased the specific energy absorption (SEA) by 265% in comparison with the conventional S-Shaped frame design with octagonal geometries and increased in SEA 16% of the S-Shaped with foam filled-square cross-sectional. In this study, the specific energy absorption will take in consideration the energy absorber used is made of mild steel.
Water absorption of kenaf/glass/epoxy hybrid composites for insulator core
Authors: Ansari M N M , Bassam Alaseel , Nazim A R M , Nordin Noor Afeefah , Yahya Zainudin
Published: April 2021

Kenaf fibres have gained substantial attracted considerable attention due to their economic feasibility and environmental acceptability. Natural fibre (kenaf) has started in mechanical and electrical applications by hybridising synthetic (glass) fibres. In recent years, the hybrid composite has been employed in various functions in industrial engineering. The present study deals with water absorption of glass/kenaf/epoxy hybrid composite materials used in high voltage polymeric insulator rods. Kenaf fibres have substituted two proportions of glass fibres (20 vol% IR20EP and 30 vol% IR30EP) with modified 60% of epoxy resins to fabricate the kenaf/glass/epoxy hybrid composites. The water absorption test was carried out at room temperature, and the water absorption resistance for composites was calculated regarding the rate of water absorption. Remarkable variations in the characteristics of water soaking up of the hybrid composite were obtained demonstrating that the water absorption influence on the insulator rod properties relies on the arrangement profiles and volume fraction of kenaf fibre of composite used. Based on the finding, a minor impact of water absorption on the glass fibre (non-hybrid) composite was noticed. Adding kenaf fibres to the composite fibreglass rod increases the composite’s water absorption. Glass fibres around kenaf fibres have been shown to minimise water absorption. After 330 hours, all the composite specimens attained stability and ceased to soak up water.
Mechanical properties of Tungsten Tri-oxide (WO3) reinforced poly (lactic-acid) (PLA) nanocomposites
Authors: Shaath M.L.M. , Ansari M.N.M , Nordin Noor Afeefah , Al-Furjan M.S.H.
Published: April 2021

In this paper, Tungsten trioxide reinforced poly (lactic acid) (PLA) blend nanocomposites were prepared using twin screw extrusion and injection moulding with different nanofillers concentrations (0.5wt%, 1wt%, 3wt%, and 5wt%) together mixed into a PLA matrix. Mechanical properties such as tensile and flexural properties were investigated. The tensile and flexural results indicate a noticeable enhancement in the mechanical strength of the PLA material. The WO3/PLA nanocomposites were compared with neat PLA to identify the attributes and loading effects on the mechanical behaviour of the nanocomposites. A high content of tungsten led to a brittle, fragile, and inelastic composite, while a lower content resulted in a high elastic modulus and stiffness of the composite. The composites reinforced with 3wt% of WO3 has improved its tensile strength and flexural strength by 30.77% and 41.38% respectively. The extrusion stability and composite molten state were compromised in the presence of high concentration of tungsten while a lower percentage eased processing and injection.
Design and Vibration Analysis of Injection Moulding Machine Base Structure
Authors: Kesava Manikanta Kumar CH , Annamalai K , Vinoth kumar S , Ponraj A
Published: April 2021

In this study the dynamic behaviour and vibration parameters of Injection Moulding Machine Base Structure was performed by analysing the structure numerically as well as experimentally. Modal analysis and FRF analysis performed numerically to find the mode pattern, natural frequencies and critical points. Vibration parameters are measured by performing experimentation using FFT analyser and the data was taken by using BK (Bruel & kjaer) Connect software. The Fast Fourier Transform (FFT) analyzer is used to transform the continuous time domain data to continuous frequency domain data. The experimental results show that structure is vibrating high at clamping unit location along x-direction. Vibration level can be controlled at that particular location by increasing the stiffness of the structure.
Study of thermal behavior of Aluminium foams in batteries of electric vehicles
Authors: Harish S. , Jeyanthi S. , Abinash M. , Suresh Kumar R. , Agarwal Sahil , Venkatachalam G.
Published: April 2021

The temperature of batteries in electric vehicles increases with time due to internal chemical reactions. This temperature rise is undesirable because it promotes corrosion and affects the battery life and thus a coolant can be used to prevent the temperature rise. The use of lightweight material and thermal management properties have a huge impact when designing a battery, especially, when using Aluminium foams it gives an exceptional advantage ranging from lightness, ductility to excellent absorption and conductivity making it a great deal for the future-oriented development of electric vehicles and market acceptance. The current research work tries to prove that Al foam can be used as a coolant in batteries of electric vehicles because of its porosity and density. The battery and Al foam are modelled in SOLIDWORKS and simulations are conducted in CFD and transient thermal to observe the heat transfer, flow characteristics and cooling effect on foam surface. The pores in Al foam are placed in three different patterns and two sizes (3mm and 5 mm) while modelling and hence six distinct models of Al foam are taken into study. The results from the simulations are compared and the Al foam that reduces maximum temperature at the outlet is chosen as the best coolant.
A Finite Element Analysis Based Study on Effects of Polyurea Coating for Blast Mitigation
Authors: Dinesh R , Vasundra P , Davidson Jebaseelan D
Published: April 2021

One of main threats for Armoured fighting vehicles (AFVs) is anti-tank mines. Future war scenario insists on light tanks that can withstand land mines with higher order destruction. Hence a non-classical approach for blast mitigating structures has dealt with. In this sequence, there are two kinds of approach, one is to redesign the bottom plate structure and second is using special materials for coating. This work investigates the effect of special material Viz., Polyurea coating on the bottom structure of the AFV hull. Polyurea coating added to the Steel plate (considered as localized AFV vehicle hull structure) in such a way that the coating thickness is lesser than the thickness of base material. Explicit dynamic Finite Element (FE) based numerical simulations were performed using ANSYS AUTODYN. In this setup, coating is introduced to the Steel plate in two variations, namely, on non-blast face (opposite to the blast load) and blast face. The simulation is carried out with varying coating thickness (6mm, 8mm, 10mm 14mm) and with varying blast charges of TNT (2kg, 5kg, 7kg, and 12kg) in the stand-off distance (distance from the center of the explosive to the plate) of 450mm. The peak deformation of the plate caused by the blast load on the coated and uncoated homogenous plate is compared for their relative performances.
Analysis of Forces generated in Human Body segments for Real time Space flight
Authors: Uday Kiran K A V , Raghuraman D R S
Published: April 2021

Human body modelling for a space travel is a significant task to be considered for analyzing the forces generated on the human body segments. During the flight from earths atmosphere due to high escape velocity and acceleration, huge reaction forces will be generated on body segments which are beyond human capacitance. Recent studies evaluated the forces generated in various body segments by equipping external sensor vest or strips around the body parts where the application is limited for several on ground operations like hopping, sitting etc. and few studies analyzed the theoretical forces by modelling the human body as a second order spring mass damper system. The main objective of this work is to analyze the forces experienced by the human body segments for like Head, Neck, Upper Torso, Central Torso and Lower Torso for real time space flight data. The analysis is done on the anthropometric data of 50th percentile male US citizens available in literature by considering the human body as a second order spring mass damper system and the real time space flight parameters are taken from STS-121 space shuttle launched from Kennedy Space centre on July 4th 2006. The obtained resultant forces are plotted against the time of flight and it is observed that high forces are generated on Central Torso compared to remaining body parts and are varying with altitude of the vehicle.
CT Guided Diagnosis: Cascaded U-Net for 3D Segmentation of Liver and Tumor
Authors: Mourya G K , Bhatia D , Gogoi M , Handique A
Published: April 2021

Volumetric estimation of the liver tumor is the first step to identifying the livers critical disorder. The liver and its tumor ratio prerequisite measures to select the therapeutic procedure. 3D printing and virtual reality platform require a segmented liver entity mask to evaluate the pre and post-treatment analysis. A cascaded U-Net model is proposed for automatic segmentation of liver and tumor in CT images. LiTS CT data set utilized for this study. The images were pre-processed using the windowing technique for contrast enhancement. Two U-Net models were modified for liver and tumor segmentation, respectively and connected in a cascaded manner. U-Net decoder end was modified in comparison to the original U-Net. The probability map of the first U-Net fed to the second U-Net and the input image to segment out the liver tumor. Eight subject volumetric CT datasets were utilized to test the cascaded U-Net performance and achieved average Dice coefficient for liver and tumor 0.95 and 0.69, respectively. Liver tumor diagnosis and treatment accuracy depend upon the precision of segmentation algorithms. Designed model segmented liver almost accurately and tumor segmented with limited accuracy. A further modification is required for the tumor segmentation cause of the occurrence of false negative.
Petrographical characteristics as an indicator of physico-mechanical properties of concrete aggregate
Authors: Bianco L , Micallef G
Published: April 2021

The physical and mechanical properties of concrete designed to a C40 mix using 6.5 mm and 10.0 mm aggregate from Montenegro and Malta respectively were investigated. Ultrasonic pulse velocity (UPV) and compressive strength (CS) tests corroborated findings in the literature. The coarseness of aggregate was found to be of primary technological importance: CS increased with increasing aggregate size. Although UPV in all the tests was between 3.5 km/s and 4.5 km/s – that is the concrete quality was of good grade – the CS of the control cubes for the 6.5mm and 10.0mm coarse aggregate mixtures was 27 N/mm2 and 39 N/mm2 respectively. The homogeneity of the concrete was affected by the physical and mechanical properties of the aggregate, including its size, but its petrological texture was also a significant parameter. The petrological characteristics of the aggregate severely affected the load-bearing capacity of the concrete. These characteristics had a significant bearing on the physico-mechanical properties of the hardened concrete.
Influence of urban development on change in microclimatic parameters of urbanized area
Authors: Bulgakov A , Skobeleva E
Published: April 2021

The expediency of quantitative analysis of safety and comfort of the spatial environment when creating master plans of cities was shown by the authors. Predictable thermal comfort should be considered here as one of the significant indicators of the environmental safety of the routes from places of residence to socially significant facilities and recreational zones. It is suggested to use thermal indexes adapted for the conditions of open urban spaces to consider the influence of climatic variables totality on the person’s thermal sensation. The physiologically effective temperature (PET) is one such index. This model takes visceral temperature, perspiration rate, the moisture of the skin, and on the other hand the meteorological parameters, including the influence of urban area conditions on them. Criteria values of PET for the middle zone of Russia are determined on the basis of bioclimatic estimation of the territory according to air temperature, cloudiness and wind speed. The authors determined experimentally the parameters of the urban microclimate.
Exploring the potential for organic and more environmentally friendly plastics in the building industry
Authors: Chitonu G C , Cazacu C E
Published: April 2021

Modern building techniques, materials and methods open possibilities for rediscovery and new applications of organic and more environmentally friendly solutions in multiple sectors of the building industry. As more scientists and engineers are looking at sustainable resources, the possibilities for managing the potential weaknesses of making more environmentally friendly building and product materials are bringing new materials and methods to the market at a rapid pace. The new biodegradable solutions are looking into natural fibres, or crops and wood. Hemp-based materials are already well re-established in multiple environmentally friendly products in the building industry. Hemp-lime, hemp insulation or hemp plastics are materials with low carbon footprint which are successfully being used in construction, replacing successfully non-renewable building materials. In cars, the BMW i3 has for several years featured hemp and kenaf, and Hunton Nativo wood fibre insulation is another example from the building industry of how renewable climate friendly materials can easily replace non-renewable materials. This article aims to highlight some existing solutions, and possible improvements to products in the building industry.
Aspects regarding the extension and consolidation of a house located on a sloping plot of land
Authors: Deaconu O
Published: April 2021

When the land available for a construction is in slope, with a high degree, there can be a series of problems related to geotechnical data and execution difficulties, considering the foundations and the structure itself. The grade of difficulty is considerably increased when an extension or attic is intended to be design and build. The paper is presenting some considerations to this problem, taken into account a study case – extension of an existing structure for a family house.
Influence of the input frequency for soundness evaluation of concrete structure based on waveform analysis
Authors: Ikebata K , Kobayashi Y , Oda K , Nakamura K
Published: April 2021

In the soundness evaluation method based on waveform analysis in time domain, the response waveforms that are measured while the target is in sound condition is indispensable. Therefore, it is expected that this method is for the evaluation of precast concrete products because the state of the products is almost identical and it is able to measure the response waveforms before using the products. On the other hand, although there are difficulties to apply this method for the evaluation of the existing structures because the response waveform is not measured before using, it is expected that this method can be applied to the evaluation of the existing structures by making the response waveform on the basis of the numerical simulation. The computational conditions should be set properly based on the actual measurement conditions for the numerical simulation. Among the computational conditions, the input frequency is determined based on the diameter of the steel ball and contact time if the excitation is given by making an impact with the steel ball by using the theory proposed by Sansalone et al. However, Kubo et al. reported that the measured contact time is different from the theoretical value and the difference reaches maximum twice. The influence of the difference would not be negligible for the soundness evaluation and should be considered carefully to perform the soundness evaluation accurately. Therefore, in this study, the response waveforms are computed on a numerical model with excitations of various input frequencies, and the influence of the input frequency to the response waveform is discussed by comparing the computed response waveforms.
The study on stability of composite panel structure under axial compression load
Authors: Jiang J , Chen C , Zhang X , Yang Z
Published: April 2021

The axial compressive load test and finite element simulation are made to study the mechanical properties of aircraft stiffened composite panel. Firstly, the numerical simulation model of composite stiffened panel structure is constructed, the accuracy and feasibility of the simulation model are verified by calculating the value of MAC (Modal Assurance Criterion) between the computational free modal and experimental free modal. Then, the nonlinear post-buckling numerical simulation is carried out to extract the buckling load, the post-buckling load path and the failure load. Then, the axial compression test of the panel structure is carried out by the testing machine, and the load-displacement curve and the load-strain curve of the loading position are obtained. Finally, the correctness of the analysis method is proved by comparing the numerical simulation value with the experimental analysis value. The experimental research method of the mechanical properties of the composite stiffened panel under axial load is explored, which can be used as a reference for the study of the bearing capacity of the stiffened panel.
Evaluation of the quality of the road infrastructure with the photogrammetry technique
Authors: Popa V , Năstase G , Dragomir G , Brezeanu A , Şerban A
Published: April 2021

Solutions that are integrating different modern techniques related to a new or an existing road, using non-destructive test brings several advantages which the content of the article highlights. Comparing the current method used in the road technique AND 540 and the aerial scanning techniques, the main element that stands out is the speed of accomplishing an ample work which consists in the 3D processing much faster and more accurately. The article presents a short current stage of these applications in the field of civil engineering. Creating 3D surfaces that it compares with what it was initially and also processing registered the deformations and displacements. A case study of a road sector is also presented to highlight everything that this technique brings.
Reactive power compensation in the railway electrical traction system, using synchronous machines controlled by SCADA
Authors: Popov A F , Fratu M
Published: April 2021

This article brings forward a solution for compensating the reactive power of the railway electrical traction system. Using the V-characteristics of the synchronous machine, reactive power can be produced or absorbed from the power supply network, keeping the power factor at a value as close to 1 as possible. Given that the load consumed by the railway electrical traction system is variable, it is necessary to be able to promptly correct the power factor. The SCADA system will change the synchronous machine’s operating characteristics relative as a function of the angle between the voltage and the current that are set at a given time by the consumers (electrical locomotives) passing through the railway section. By compensating the reactive power, the amount of active power supplied to the electrical network of the railway traction system is increased, without the need to modify the cross-section of the electrical conductors.
Reasons for the collapse of ceilings during the construction of monolithic buildings
Authors: Tomakov M V , Pykhtin A I , Tomakov V I , Tomakova I A
Published: April 2021

Construction works, as a rule, differ in complexity and hazards of works. Nowadays, cases of collapses of a formwork of the cast concrete section of a building under construction in the course of concreting became frequent. Accidents entail death of people and significant material losses. Purpose of the research: the purpose of the research is to study accidents occurred during installation of in-situ concrete floors of buildings and to reveal the typical causes of a formwork system collapse. The initial materials were the data on the causes of accidents at construction sites obtained on the basis of the analysis of statistical materials on injuries, as well as data on the identified violations of the requirements for safe work practices in capital construction and reconstruction of buildings and structures. A total of 148 accidents at construction sites from 1997 to 2019 were considered. The paper systematizes some main errors and violations of technologies committed in the course of in-situ concrete works. Typical causes common for all formwork collapses during concrete works for in-situ floor slabs installation are revealed. Among the objective causes of accidents and high injury rate in this type of construction works the following should be highlighted: the lack of method statements and construction plans; lack of supervision of the correct and safe execution of works; shortcomings in the organization of training and testing of labor protection knowledge; violation of technological regulations and safety rules.
The impact of the decreasing number of users on the evolution of a centralized heating system
Authors: Vitan E , Rus T , Hotupan A , Cilibiu C
Published: April 2021

The paper presents an analysis of a centralized heating system located in a city in the west-central part in Romania. We examined the last 15 years of functioning of the system from a technical and economic point of view. One of the main factors that led to the inefficiency of this system, and in the end to collapse, was the reduction of the system’s thermal efficiency due to the decrease of customers over time. In conclusion, we highlighted the necessity of a periodic diagnosis of system’s efficiency and a risk analysis to avoid economic problems and collapse.
Titanium Dioxide Incorporated Polyamide Thin Film Composite Photocatalytic Membrane for Bisphenol A Removal
Authors: Syahida Mat Anan Noor , Jaafar Juhana , Sato Shuichi , Mohamud Rohimah
Published: April 2021

Polyamide thin film composite immobilized with TiO2 is prepared using M-phenylene diamine and Trimesoyl chloride via interfacial polymerization. To determine the characteristics and performance of the membranes, effect of TiO2 loading is studied. 2 (w/v) % of MPD solution and 0.2 (w/v) % of TMC/n-hexane solution were used to prepare PA TFC membrane with different amount of TiO2 loading (0 wt. %, 0.1 wt. %, 0.2 wt. %, 0.3 wt. %, 0.4 wt. % and 0.5 wt. %).PA/TiO2 composite membranes are characterized by FESEM, EDX, FTIR and water contact angle. The properties of the membranes have improved upon TiO2 loading. With over 90% of BPA rejection exhibited by all the fabricated membranes, it is proved that the membranes especially PA/TiO2 TFC membrane with 0.4 wt. % TiO2 (with the highest rejection and degradation value of 99.9% and 14% respectively) are potentially employed as the hybrid photocatalytic membrane for BPA removal.
Retraction: Reconstruction of Cyber and Physical Software Using Novel Spread Method (IOP Conf. Ser.: Mater. Sci. Eng.
322 052010)
Authors: Ma Wubin , Deng Su , Huang Hongbin
Published: April 2021

IOP Publishing Limited ("IOPP") is retracting this paper following an investigation which revealed that sections of the manuscript are computer generated. IOP Publishing is investigating why this was not identified during the submission and peer review process by the conference. As a member of the Committee for Publication Ethics (COPE) this has been investigated in accordance with COPE guidelines and it was agreed the article should be retracted.

IOPP expresses its thanks to the independent advisors who have shared their thoughts regarding this paper during the course of the investigation.

The authors disagree with this retraction.

Retraction published: 27 April 2021
Retraction: An Novel Architecture of Large-scale Communication in IOT (IOP Conf. Ser.: Mater. Sci. Eng.
322 052057)
Authors: Ma Wubin , Deng Su , Huang Hongbin
Published: April 2021

IOP Publishing Limited ("IOPP") is retracting this paper following an investigation which revealed that sections of the manuscript are computer generated. IOP Publishing is investigating why this was not identified during the submission and peer review process by the conference. As a member of the Committee for Publication Ethics (COPE) this has been investigated in accordance with COPE guidelines and it was agreed the article should be retracted.

IOPP expresses its thanks to the independent advisors who have shared their thoughts regarding this paper during the course of the investigation.

The authors disagree with this retraction.

Retraction published: 27 April 2021
The hybrid topological longitudinal transmon qubit
Authors: Dinerstein Alec , Gorham Caroline S , Dumitrescu Eugene F
Published: April 2021

We introduce a new hybrid qubit consisting of a Majorana qubit interacting with a transmon longitudinally coupled to a resonator. To do so, we equip the longitudinal transmon qubit with topological quasiparticles, supported by an array of heterostructure nanowires, and derive charge- and phase-based interactions between the Majorana qubit and the resonator and transmon degrees of freedom. Inspecting the charge coupling, we demonstrate that the Majorana self-charging can be eliminated by a judicious choice of charge offset, thereby maintaining the Majorana degeneracy regardless of the quasiparticles spatial arrangement and parity configuration. We perform analytic and numerical calculations to derive the effective qubit–qubit interaction elements and discuss their potential utility for state readout and quantum error correction. Further, we find that select interactions depend strongly on the overall superconducting parity, which may provide a direct mechanism to characterize deleterious quasiparticle poisoning processes.
Finite dimensional semigroups of unitary endomorphisms of standard subspaces
Authors: Neeb Karl-H.
Published: April 2021

LetV\mathtt {V}be a standard subspace in the complex Hilbert spaceH\mathcal {H}andGGbe a finite dimensional Lie group of unitary and antiunitary operators onH\mathcal {H}containing the modular group(ΔVit)t∈R(\Delta _{\mathtt {V}}^{it})_{t \in \mathbb {R}}ofV\mathtt {V}and the corresponding modular conjugation JVJ_{\mathtt {V}}. We study the semigroup\[SV={g∈G∩U⁡(H):gV⊆V}S_{\mathtt {V}} = \{ g\in G \cap \operatorname {U}(\mathcal {H})\colon g\mathtt {V} \subseteq \mathtt {V}\}\]and determine its Lie wedge<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="bold upper L of left-parenthesis upper S Subscript monospace upper V Baseline right-parenthesis equals StartSet x element-of German g colon exp left-parenthesis double-struck upper R Subscript plus Baseline x right-parenthesis subset-of-or-equal-to upper S Subscript monospace upper V Baseline EndSet">L⁡(SV)={x∈g:exp⁡(R+x)⊆SV}\operatorname {\textbf {L}}(S_{\mathtt {V}}) = \{ x \in \mathfrak {g} \colon \exp (\mathbb {R}_+ x) \subseteq S_{\mathtt {V}}\}, i.e., the generators of its one-parameter subsemigroups in the Lie algebrag\mathfrak {g}of GG. The semigroupSVS_{\mathtt {V}}is analyzed in terms of antiunitary representations and their analytic extension to semigroups of the formGexp⁡(iC)G \exp (iC), whereC⊆gC \subseteq \mathfrak {g}is anAd⁡(G)\operatorname {Ad}(G)-invariant closed convex cone.

Our main results assert that the Lie wedgeL⁡(SV)\operatorname {\textbf {L}}(S_{\mathtt {V}})spans a33-graded Lie subalgebra in which it can be described explicitly in terms of the involutionτ\tauofg\mathfrak {g}induced byJVJ_{\mathtt {V}}, the generatorh∈gτh \in \mathfrak {g}^\tauof the modular group, and the positive cone of the corresponding representation. We also derive some global information on the semigroupSVS_{\mathtt {V}}itself.
Enhanced bioproduction of fucosylated oligosaccharide 3-fucosyllactose in engineered Escherichia coli with an improved de novo pathway
Authors: Ni Zhijian , Wu Jinyong , Li Zhongkui , Yuan Lixia , Wang Yu , Chen Xiangsong , Yao Jianming
Published: April 2021

3-fucosyllactose (3-FL) and 2'-fucosyllactose (2'-FL), are two important fucosylated oligosaccharides in human milk. Extensive studies on 2'-FL enabled its official approval for use in infant formula. However, development of 3-FL has been somewhat sluggish due to its low content in human milk and poor yield in enlarged production. Here, an α-1,3-fucosyltransferase mutant was introduced into an engineered Escherichia coli (E. coli) capable of producing GDP-L-fucose, leading to a promising 3-FL titer in a 5.0-L bioreactor. To increase the availability of cofactors (NADPH and GTP) for optimized 3-FL production, zwf, pntAB, and gsk genes were successively overexpressed, finally resulting in a higher 3-FL level with a titer of 35.72 g/L and a yield of 0.82 mol 3-FL/mol lactose. Unexpectedly, the deletion of pfkA gene led to a much lower performance of 3-FL production than the control strain. Still, our strategy achieved the highest 3-FL level in E. coli to date.
JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites
Authors: Jiang Jyun-Yu , Ju Chelsea J -T , Hao Junheng , Chen Muhao , Wang Wei
Published: April 2021

Motivation

Circular RNA (circRNA) is a novel class of long non-coding RNAs that have been broadly discovered in the eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backspliced to an upstream acceptor site. These circRNA sequences are conserved across species. More importantly, rising evidence suggests their vital roles in gene regulation and association with diseases. As the fundamental effort toward elucidating their functions and mechanisms, several computational methods have been proposed to predict the circular structure from the primary sequence. Recently, advanced computational methods leverage deep learning to capture the relevant patterns from RNA sequences and model their interactions to facilitate the prediction. However, these methods fail to fully explore positional information of splice junctions and their deep interaction.

Results

We present a robust end-to-end framework, Junction Encoder with Deep Interaction (JEDI), for circRNA prediction using only nucleotide sequences. JEDI first leverages the attention mechanism to encode each junction site based on deep bidirectional recurrent neural networks and then presents the novel cross-attention layer to model deep interaction among these sites for backsplicing. Finally, JEDI can not only predict circRNAs but also interpret relationships among splice sites to discover backsplicing hotspots within a gene region. Experiments demonstrate JEDI significantly outperforms state-of-the-art approaches in circRNA prediction on both isoform level and gene level. Moreover, JEDI also shows promising results on zero-shot backsplicing discovery, where none of the existing approaches can achieve.

Availability and implementation

The implementation of our framework is available at https://github.com/hallogameboy/JEDI.

Supplementary information

Supplementary data are available at Bioinformatics online.
‘Single-subject studies’-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases
Authors: Aberasturi Dillon , Pouladi Nima , Zaim Samir Rachid , Kenost Colleen , Berghout Joanne , Piegorsch Walter W , Lussier Yves A
Published: April 2021

Motivation

Identifying altered transcripts between very small human cohorts is particularly challenging and is compounded by the low accrual rate of human subjects in rare diseases or sub-stratified common disorders. Yet, single-subject studies (S3) can compare paired transcriptome samples drawn from the same patient under two conditions (e.g. treated versus pre-treatment) and suggest patient-specific responsive biomechanisms based on the overrepresentation of functionally defined gene sets. These improve statistical power by: (i) reducing the total features tested and (ii) relaxing the requirement of within-cohort uniformity at the transcript level. We propose Inter-N-of-1, a novel method, to identify meaningful differences between very small cohorts by using the effect size of ‘single-subject-study’-derived responsive biological mechanisms.

Results

In each subject, Inter-N-of-1 requires applying previously published S3-type N-of-1-pathways MixEnrich to two paired samples (e.g. diseased versus unaffected tissues) for determining patient-specific enriched genes sets: Odds Ratios (S3-OR) and S3-variance using Gene Ontology Biological Processes. To evaluate small cohorts, we calculated the precision and recall of Inter-N-of-1 and that of a control method (GLM+EGS) when comparing two cohorts of decreasing sizes (from 20 versus 20 to 2 versus 2) in a comprehensive six-parameter simulation and in a proof-of-concept clinical dataset. In simulations, the Inter-N-of-1 median precision and recall are > 90% and >75% in cohorts of 3 versus 3 distinct subjects (regardless of the parameter values), whereas conventional methods outperform Inter-N-of-1 at sample sizes 9 versus 9 and larger. Similar results were obtained in the clinical proof-of-concept dataset.

Availability and implementation

R software is available at Lussierlab.net/BSSD.
Predicting MHC-peptide binding affinity by differential boundary tree
Authors: Feng Peiyuan , Zeng Jianyang , Ma Jianzhu
Published: April 2021

Motivation

The prediction of the binding between peptides and major histocompatibility complex (MHC) molecules plays an important role in neoantigen identification. Although a large number of computational methods have been developed to address this problem, they produce high false-positive rates in practical applications, since in most cases, a single residue mutation may largely alter the binding affinity of a peptide binding to MHC which cannot be identified by conventional deep learning methods.

Results

We developed a differential boundary tree-based model, named DBTpred, to address this problem. We demonstrated that DBTpred can accurately predict MHC class I binding affinity compared to the state-of-art deep learning methods. We also presented a parallel training algorithm to accelerate the training and inference process which enables DBTpred to be applied to large datasets. By investigating the statistical properties of differential boundary trees and the prediction paths to test samples, we revealed that DBTpred can provide an intuitive interpretation and possible hints in detecting important residue mutations that can largely influence binding affinity.

Availability and implementation

The DBTpred package is implemented in Python and freely available at: https://github.com/fpy94/DBT.

Supplementary information

Supplementary data are available at Bioinformatics online.
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
Authors: Ragueneau Eliot , Shrivastava Anjali , Morris John H , del-Toro Noemi , Hermjakob Henning , Porras Pablo
Published: April 2021

IntAct App is a Cytoscape 3 application that grants in-depth access to IntAct’s molecular interaction data. It build networks where nodes are interacting molecules (mainly proteins, but also genes, RNA, chemicals…) and edges represent evidence of interaction. Users can query a network by providing its molecules, identified by different fields and optionally include all their interacting partners in the resulting network. The app offers three visualizations: one only displaying interactions, another representing every evidence and the last one emphasizing evidence where mutated versions of proteins were used. Users can also filter networks and click on nodes and edges to access all their related details. Finally, the application supports automation of its main features via Cytoscape commands.

Availability and implementation

Implementation available at https://apps.cytoscape.org/apps/intactapp, while the source code is available at https://github.com/EBI-IntAct/IntactApp.
Reactome and the Gene Ontology: digital convergence of data resources
Authors: Good Benjamin M , Van Auken Kimberly , Hill David P , Mi Huaiyu , Carbon Seth , Balhoff James P , Albou Laurent-Philippe , Thomas Paul D , Mungall Christopher J , Blake Judith A , D’Eustachio Peter
Published: April 2021

Motivation

Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions.

Results

To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community.

Supplementary information

Supplementary data are available at Bioinformatics online.
Analysis of Dynamic Network Reconfiguration in Adults with Attention-Deficit/Hyperactivity Disorder Based Multilayer Network
Authors: Cui Xiaohong , Ding Congli , Wei Jing , Xue Jiayue , Wang Xiaoyue , Wang Bin , Xiang Jie
Published: April 2021

Attention-deficit/hyperactivity disorder (ADHD) has been reported exist abnormal topology structure in the brain network. However, these studies often treated the brain as a static monolithic structure, and dynamic characteristics were ignored. Here, we investigated how the dynamic network reconfiguration in ADHD patients differs from that in healthy people. Specifically, we acquired resting-state functional magnetic resonance imaging data from a public dataset including 40 ADHD patients and 50 healthy people. A novel model of a “time-varying multilayer network” and metrics of recruitment and integration were applied to describe group differences. The results showed that the integration scores of ADHD patients were significantly lower than those of controls at every level. The recruitment scores were lower than healthy people except for the whole-brain level. It is worth noting that the subcortical network and the thalamus in ADHD patients exhibited reduced alliance preference both within and between functional networks. In addition, we also found that recruitment and integration coefficients showed a significant correlation with symptom severity in some regions. Our results demonstrate that the capability to communicate within or between some functional networks is impaired in ADHD patients. These evidences provide a new opportunity for studying the characteristics of ADHD brain networks.
Focal Subcortical White Matter Lesions Disrupt Resting State Cortical Interhemispheric Functional Connectivity in Mice
Authors: Aykan Sanem A , Xie Hongyu , Lai James Han , Zheng Yi , Chung David Y , Kura Sreekanth , Anzabi Maryam , Sugimoto Kazutaka , McAllister Lauren M , Yaseen M Abbas , Boas David A , Whalen Michael J , Sakadzic Sava , Ayata Cenk
Published: April 2021

The corpus callosum is the largest white matter tract and critical for interhemispheric connectivity. Unfortunately, neurocognitive deficits after experimental white matter lesions are subtle and variable, limiting their translational utility. We examined resting state functional connectivity (RSFC) as a surrogate after a focal lesion in the lateral corpus callosum induced by stereotaxic injection of L-NIO in mice. RSFC was performed via optical intrinsic signal imaging through intact skull before and on days 1 and 14 after injection, using interhemispheric homotopic and seed-based temporal correlation maps. We measured the lesion volumes at 1 month in the same cohort. L-NIO induced focal lesions in the corpus callosum. Interhemispheric homotopic connectivity decreased by up to 50% 24 h after L-NIO, partially sparing the visual cortex. All seeds showed loss of connectivity to the contralateral hemisphere. Moreover, ipsilesional motor and visual cortices lost connectivity within the same hemisphere. Sham-operated mice did not show any lesion or connectivity changes. RSFC imaging reliably detects acute disruption of long interhemispheric and intrahemispheric connectivity after a corpus callosum lesion in mice. This noninvasive method can be a functional surrogate to complement neurocognitive testing in both therapeutic and recovery studies after white matter injury.