bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing and evaluation program of lab. scale hybrid propulsion system
Authors: Makled Ah. EL-S
Published: October 2019

The objective of the present paper is to prove the validity design and fully automatically operation of HPS, seeking to achieve its safety, low cost, and flexibility. In the stage of preliminary design, a coupling between experimental and theoretical work has been done, making use of available laboratory facilities and software packages (thermo-chemical calculation), to fully demonstrate all operating conditions. The HPS design includes the solid fuel grain configuration, essential operating parameters, oxidizer feed through control devices, measuring tools with calibration system, data recording and operating system. Commercial fuel materials as Polymethyl methacrylate (PMMA) and Polyethylene (PE) are used during experimental work to represent conventional generation fuel. Furthermore, new generation fuels as paraffin, beeswax, and paraffin with energetic additive metal (AL powder) are used. Gaseous oxygen is used as oxidizer. That may guide to design and fabricate high performance real rocket weapon or space propulsion system, targeting longer term storage and a propulsion system with available technology. The objective is extended to select appropriate ignition system (NiCr coil igniter) for laboratory firing of small-scale engine. One of the main problems (price, safety, available technology) of propulsion system today has been tackled. To that end, analysis has been established, to investigate the regression rate, solid fuel mass flow rate and combustion efficiency for each fuel grain group types.
Numerical performance investigation of a thrust-optimized nozzle at different altitudes
Authors: AbuElkhier M. G. , Shaaban S. , Ahmed Mahmoud Y. M.
Published: October 2019

One of the major design aspects of jet propulsion engines is the nozzle design. The value of thrust generated by the nozzle is dependent on both the nozzle design and the flight altitude. The present paper is intended to shed more light on the jet flow structure and its evolution with flight altitude. In addition, the variation of thrust generated by the nozzle with flight altitude is addressed. A well-defined nozzle profile is adopted as a case study and numerical simulation using a commercial CFD tool is conducted. The solution method is validated by reproducing the experiments conducted on the case study nozzle.
Wi-Fi based indoor localization using trilateration and fingerprinting methods
Authors: El Ashry Abd Elgwad M. , Sheta Bassem I.
Published: October 2019

Nowadays, mobile devices such as personal computers and smartphones are emerging as a major key in today’s computing platforms for indoor object localization systems due to the object localization in indoor areas strongly suffers from limitation of using GNSS (Global navigation satellite system) systems due to low satellite availability and high signal attenuation. During the last decade, many researchers have developed indoor localization systems which are the process of obtaining user or device location through mobile devices using Wireless Fidelity (Wi-Fi) network signals with promising results and acceptable performance. In these Wi-Fi based localization systems, indoor positioning relies on different types of measurements including Time-Of-Arrival (TOA), Time-Difference-Of-Arrival (TDOA), Angle-Of-Arrival (AOA), and Received Signal Strength (RSS) of Wi-Fi signal.

In this paper, the techniques and algorithms that used for the RSS-based localization such as Trilateration and Fingerprinting which depend on the RSS from the access point (WI-FI). Using Received Signal Strength Ranging approach in the Trilateration method which depends on database that contains path-loss-exponent and shadowing parameter that differ according to the environment, solving the equation using different Access Points (APs) at least 3 APs, the no of the APs and there locations were varied to get the best accuracy which depends on the horizontal dilution of position (HDOP). At the Fingerprinting method depends on matching the recorded offline RSS from nearby access points (AP) to the online RSS received by the user on the move is reviewed. A comparison of location fingerprinting methods involving deterministic method (k-nearest neighbor method and weighted k-nearest neighbor method), probabilistic methods by estimation of likelihood functions with several approaches (non-parametric and parametric)are also explained. The performance parameters of this study include the two-dimensional root mean square error (2D-rms) which measures the localization accuracy. Moreover, the effect of increasing/decreasing the number of APs on the system accuracy is also discussed. The aim of this paper is to announce which method can provide better performance than the others and under what conditions.
A finite element solution of Bergan-Wang plate model
Authors: Hassan Kamal , Ali Ehab , Tawfik Mohammad
Published: October 2019

Bergan-Wang approach has led to a formulation of the strain energy of a plate bending deflection as function of only the transversal deflection of the plate. In this paper, two rectangular plate bending finite elements are introduced, using new degrees of freedom based on Bergan-Wang approach for analysis of thin, moderately thick plates, in terms of this unique variable. The first element has four nodes with 24 DOF while the second has 36 DOF. These two elements are conforming in case of thin plates. Adopting the usual 3 boundary conditions of Reissner-Mindlin theory, variety of examples have been analysed for thin and moderately thick plate bending problems with plurality of finite element meshes and a variety of thickness to plate length ratios with different boundary conditions on sides. As typical characteristics of Bergan-Wang approach, there is no locking as the thickness decreases and convergence to the classical thin plate solution is achieved. Comparison with Reissner-Mindlin and 3D solutions supports the study.
Aircraft protection for complex threat platforms through integrated EWOS application
Authors: Rudd-Orthner R , Mihaylova L S
Published: October 2019

The advancement of threats is focusing commanders to consider how to combat these complex threats throughout the kill chain including prior to launch and Anti-Access Area Denial (A2AD). To match this technology race, modern platforms have been designed with integrated command and control systems and automated Defensive Aids Suites built on modular open system architectures incorporating less diverse but more complex software driven systems. The successful operation of these combat systems is reliant upon the availability of accurate, configured, harmonised and “time sensitive” mission data without which the systems may be ineffective. This paper explores the use of threat analysis diagramming techniques, and open architectures tightly integrated with a EWOS life-cycle; to develop countermeasures with a measured response beyond the traditional self-protection kill chain stages of self-protection. It introduces how threat analysis prepares understanding for simulation and how a countermeasure description language can be used to store and exchange countermeasures in a structured form. This level of intelligence data support and analysis coordinated and synchronised across multiple platforms thereby facilitating the complexities of force protection higher up the kill chain into an onion of protection mapped to a Venn diagram of countermeasure types (design intentions) with differing data needs.
Waste reduction by linear programing optimizing
Authors: Salah Eldein Sameh A , Sobhi Nahed
Published: October 2019

The global economic crisis forces many industrial companies to be more concerned in reducing unnecessary cost, and eliminating all possible wastes inside the production lines. So that, most of companies focused on adopting the lean production tools [1]. The core idea of lean manufacturing is actually quite simple; relentlessly work on eliminating wastes from the manufacturing process. These wastes have a direct impact on costs, and profit [2]. Real-life problems can be modelled as linear programs. Linear programming is a problem-solving approach developed for situations involving maximizing or minimizing a linear function subject to linear constraints that, limit the degree to which the objective can be pursued. The objectives of this paper are to develop methods to reduce the waste in the different manufacturing processes in a technical support unit of Airplanes. This paper focuses on developing a linear programming approach in order to reduce the waste of material used in the production line. Single Minute Exchange of Die methodology (SMED) was implemented in order to reduce the changeover time. The achieved results showed that the linear programming is an effective and cheapest tool in optimizing the waste in the production lines. By using linear programming, the organization can reduce the wasted materials from 15.1% to 6.6%, with annual costs saving 288,480 Egyptian pounds (EGP). The achieved results from implementing a simple lean production tool such as, SMED helps the organization to reduce the changeover time by 44%, with annual costs saving 29,440 EGP.
Modelling and simulation of 3DOF parallel manipulator using artificial neural network
Authors: Youssef Abdelrahman , Bayoumy Amgad M , Rostom Mostafa , Tolbah Farid A
Published: October 2019

Parallel Robot (PR) has shown its ability to be precise in its movement. Actuators move simultaneously to achieve the required target, on top of that its payload is much greater than what a serial robot can withstand. To determine workspace of the robot with known angles Forward kinematics has to be introduced which, bring a lot of difficulty as it requires the solution of multiple coupled nonlinear algebraic equations. Those equations bring multiple valid solutions. Those solutions could lead to different locations. As it is not going to make the pick and place for PR will be easier. This paper will discuss a numerical method that calculates the Forward Kinematics for PR. This method uses Artificial Neural Network which relay on training with a certain number of iterations. The set of data to be used in the training can be obtained from PR simulation. This method will serve to know workspace around PR as it will help it to pick the target object.
Numerical simulation of the stochastic Burgers’ equation using MLMC and CBC algorithm
Authors: Nagy Shady A , El-Beltagy Mohamed A
Published: October 2019

Burgers turbulence is a model for developing tools to study the Navier-Stokes turbulence, many hydrodynamical problemsin the theory related to random Lagrangian systems. Many questions that are generally asked in Navier-Stokes turbulence can be answered using Burgers turbulence. The aim of the present paper is to apply Multi-level Monte Carlo (MLMC) on stochastic Burgers’ equation by using component-by-component algorithm (CBC). CBC algorithm is developed by the concept of circulant matrix that reduces the cost as a Quasi Monte Carlo technique from O(s n) to O(s n log n) where s is the dimension of integral with equi-distributed points. In this paper, Burgers’ equation is discretized using the finite-volume technique, the MLMC with different random samples is applied and the stability is tested. The results show that MLMC is suitable only for some cases of stochastic differential equations (SDEs) when using pseudo random generator, which is Monte Carlo with high cost than using CBC.
LTE Wide Band Metamaterial Antenna
Authors: Ezzat M.A.M.K. , Allam A.M. , Fawzy D.E.
Published: October 2019

This paper presents the effect of Metamaterials (MTMs) unit cells on the performance of LTE wide band antenna. It is a conventional rectangular patch antenna with dimension of 10 mm x 6 mm. It is implemented on FR-4 lossy substrate material with relative permittivity of εr = 4.4, thickness of 1.6 mm and loss tangent of 0.025. It is feed through a microstrip line with dimension of 22 mm x 3 mm. The overall dimension of the antenna is 35 mm x 35 mm x 1.6 mm. It operates over a frequency band from 2.1914 GHz to 2.6802 GHz with central frequency 2.4392 GHz and 4.831 GHz to 5.5642 GHz with central frequency 5.1573 GHz. The simulated gain at frequency 5.1573 is 3.834 dBi. MTMs cells are supporting the truncated ground layer as it widens the band and increases the gain. The antenna ground layer is replaced with different unit cell configurations, truncated ground with different array of patches, truncated ground with array of Ring Resonator (RR), truncated ground with different array of patches with vias, truncated ground with array of RR with vias, and truncated mushroom grounded. The antenna is supported with MTMs conducts gain 5.6 dBi. The design is implemented through CST microwave studio and measured through network analyzer.
Design of HHO cell as energy source for electric vehicles
Authors: Sayed Mahmoud M.A. , Shalaby Marwa S. , Rady Wafa , Hussien Wessam , Magdy Mohamed , El-Sabagh K. , Mohamed A. , Nour Eldin A. , Maher F. , Osama M.
Published: October 2019

Hydrogen has proven itself to be a great source of energy due to its physical characteristics and its high availability. One way to use the energy inside hydrogen is the fuel cell. But inside a moving car, hydrogen storage tank existence requires high precautions and present many increasing risks; so our idea takes the theory of HHO (hydrogen generator) to separate hydrogen and then utilize a fuel cell to produce clean source of energy. This produced electrical energy will be used in operating an electrically powered car, and in charging the HHO cell. Electrically powered cars as an aim draws us to this work, the first part for producing hydrogen gas from water, the design parameters of the electrochemical cell, and the reached findings will be presented. It was found that stainless steel 304 was more convenient for the electrode materials compared with other metals. The amount of hydrogen evolved was confirmed by pop-sound test. The fuel cells was settled to be the most effective way to handle this source of power as its efficiency is relatively high. The fuel cells are used to convert the power in the hydrogen atoms to electricity by combining them with oxygen atom forming water molecules.
Design, simulation and implementation of low cost microstrip array antenna for KU–band satellite system
Authors: Hassouna Mohamed H , Swelam W. , Mohamed Abdel Naser Fawzy , Abdel Azeem Mohamed H.
Published: October 2019

This paper present 32 Element microstrip rectangular patch array antenna for KU-Band. The aim of the design is to achieve low cost, low weight and high gain antenna for the transmissions frequency range of KU – Band satellite system. The paper also present 5 designs for array antenna 2, 4,8,16 and 32 elements and the results comparison between them. The substrate material is FR-4 with 1.58 mm thickens. The simulation made by CST Microwave studio 2017. The size of final design is 85×98.81 mm and the bandwidth is 1.489 GHz. The frequency range of design starting from 13.318 GHz to 14.842 GHz with maximum Gain 13.7 dB. The final design of 32 elements array antenna has been fabricated and compared with the simulation results, a good agreements were obtained and the difference between fabrication and measurements results was due to fabrication and measurements tools tolerance. The fabricated design has been measured using Vector network analyzer ROHDE & SCHWARZ ZVB20.
Development of Two-Fingered Underactuated Robot Gripper using 3D Printer
Authors: Sadun Amirul Syafiq , Jalani Jamaludin , Nasir Siti Hana , Roslan Mohd Nazrul , Hashim Hairulazwan , Anuar Syazwani Mohd
Published: October 2019

This research present the development of a two-fingered underactuated robot gripper by using 3D printed machine with a material of Polylactic acid or PLA. The gripper design consist of two individual servo motors that drives the finger movement to perform a certain amount of grasping force. The new design of the finger using Solidworks was inspired by several existing robot gripper however with a low cost approach to obtain a good finger tracking and angular control. The fully fabricated and assembled gripper was then tested to determine the operation results during basic grasping and ungrasping by connected to Arduino Mega and MATLAB software. The angular data during the operation shows that the gripper successfully perform a stable operations despite some minor disturbance due to the mechanical defect on the servo plate. Further analysis will be conducted in the future in order to identify the full capability of the gripper in real world application such as force control operations.
Redesigning of Agarwood Extracting Machine Applying DFMA Principle
Authors: Salim M S , Lajis M A , Ros Z C , Nawawi A , Shamsudin S , Yusuf N K
Published: October 2019

This paper presents the comparative study of design efficiency of two different designs of agarwood extracting oil machines by performing using the Design for Manufacturing and Assembly (DFMA) method. The DFMA method was used as it is a well-established technique for improving the efficiency of the product leading to minimizing production costs. It also shortens product development time by reducing the number of components in a product. The study used two different designs of agarwood extracting oil machines as a case study. The result shows that the percentage of the design efficiency of existing design model 1 is 9.25%, whereas it is 15% of redesign. Thus, the redesign model 2 is much better as compared to existing design model 1 in terms of its assembly operation and design efficiency. Therefore, the redesign model 2 is greener than existing design model 1. Therefore, the application of the DFMA method to enhance the development of a agarwood extracting product has been proven to be highly useful in the design work.
Stability and reinforcement analysis of weathering steel high voltage transmission tower
Authors: Yao YAO , Ling Xu Wang , You Jia Zhang
Published: October 2019

The local instability of weathering steel transmission towers is an important reason for the collapse of transmission towers.In this paper, the wind speed is converted into wind pressure and applied to ANSYS finite element model established according to the actual equal proportion, and the influence of secondary stress and the orientation of Angle steel are considered.The stability of transmission tower is analyzed according to buckling coefficient.The results show that the buckling coefficient and the buckling position increase with the reinforcement degree of the main material of the weathering steel transmission tower.After the reinforcement of the first and second sections of the main transmission material is completed, the buckling position moves up to the web bar of the transverse arm.The buckling coefficient of T type is about 39% and 25% higher than that of the cross type and Z type respectively, which can effectively improve the safe operation ability of the line.
Application of new automatic welding equipment and welding technology in the future construction machinery field
Authors: Yan Zhang , Fei Zhang
Published: October 2019

The production efficiency of machinery manufacturing industry is affected by the automatic welding equipments and technologies directly. Through introducing the working principle and applicable working conditions of new automatic welding equipments and welding technologies, the writer uses laser tracking equipment and welding deformation technology to analyze the possibility of application of automatic welding technology in the field of construction machinery, so as to provide useful reference for improving the quality of mechanical welding, reducing production costs and strengthening brand effect.
Practical Research on Welding Simulation of Q345 Steel
Authors: Wang Zhi-ling
Published: October 2019

In this paper, we use TCL/TK integrated language analysis software and semi-ellipsoid heat source model and life-death element method to simulate the butt welding process of Q345 steel plate with thickness of 10 mm. We simulated and analyzed the temperature field, stress field and welding deformation of multi-layer welding. Through welding simulation analysis, we extracted the distribution of welding residual stress and welding deformation of butt joint, and obtained the transverse and longitudinal shrinkage of butt plate and the main reasons. The results show that the multi-layer butt welding seam and its adjacent area are under tension, and the numerical value generally reaches the yield strength, and the two sides are under compression. The tensile stress in the middle of the weld bead is the largest and decreases gradually toward both ends. The cross-sectional area of single-sided multi-layer welding seam is larger and asymmetric along the thickness of the plate. After welding, the transverse shrinkage and angular deformation of the welded parts are larger. At the same time, the accuracy of the simulation results is verified by actual welding and testing.
Ball on the plate balancing control system
Authors: Kopichev Michael M , Putov Anton V , Pashenko Anastasia N
Published: October 2019

The problem of balancing is a continuous study challenge for application in many spheres of interest from education to transportation. Two-degree of freedom ball balancing laboratory test bench is an important plant for control systems understanding. This paper focuses on the mechanical design and control algorithm of balancing a ball on a plate. The plant was equipped with resistive touch screen for ball position data acquisition, stepper motors with position sensors for platform inclination angle feedback data and AVR microcontroller-based two-loop subordinate control system with PID controllers for ball position maintaining. The laboratory bench was designed and assembled in Saint Petersburg Electrotechnical University “LETI” at the Automatic control systems department.
A Position Synchronization Control for Dual Redundant Electro-mechanical Actuation in Flight Control System
Authors: Wang D Y , Li D Q , Chen J , Zheng S C
Published: October 2019

The paper develops a position synchronization controller for a new active/active dual redundant electro-mechanical actuation system and designs a test platform to validate the performance of the controller. The mathematic models of the position synchronization system are firstly built based on the schematic of the active/active dual redundant electro-mechanical actuation system. The position controller for DEMA and GEMA of is developed based on the velocity and acceleration feed forward and traditional PID theory. A series of motion experiments are carried out to verify the effectiveness of the controller design for active/active dual redundant electro-mechanical actuation system. The experiments results show that the position controllers designed for either DEMA or GEMA are satisfied, the biggest following error is not more than 0.1mm. And the synchronous motion tests show that the PI plus Output Saturation feedback position synchronization control can reduce more than 30 percent synchronous position errors. Furthermore, the tests of position synchronization show that EMA stiffness has a big influence on the synchronous precision. The new position synchronization controller designed based on the accurate system model and actual system parameters can better achieve the position synchronization requirements of the dual redundant EMA system, which makes good sense for redundant systems.
Evaluation of the Slow Release Oxygen Properties and pH Control Ability of Oxygen Slow-releasing Materials
Authors: Chen Zehao , Guo Pengfei , Tian Hailong , Wang Ying , Feng Chenghong
Published: October 2019

In this study, an oxygen slow-releasing materials (OSRM) was developed by simple one-step synthesis. The composition of OSRM included calcium peroxide, bentonite or carclazyte, cement, potassium dihydrogen phosphate (KH2PO4) and ammonium sulphate((NH4)2SO4). The OSRM was natural and non-toxic. The slow release oxygen properties and pH control ability of OSRM were evaluated. Results showed that the oxygen concentration increased and kept stable in a week after the addition of OSRM. The OSRM added with KH2PO4 and (NH4)2SO4 was better than The OSRM doped with carclazyte in controling the pH approaching to neutralization. Besides, The OSRM doped with carclazyte instead of bentonite led to the oxygen release slowly. In stimulated sediment environment, the pH value in water was stable at about 7.6 after 4 g/L of OSRM added. This phenomenon may be due to functional groups with buffer capacity occurred in sediment.
Optimization of Process Parameters for Closed-die Forging Based on Finite Element Simulation
Authors: Guo Wei , Zou Jin
Published: October 2019

In this study, finite element software was used to simulate and optimize the process parameters including billet thickness, forging speed, and friction coefficient during closed-die forging. The results show that the mean equivalent strain of the billet gradually increases as the thickness reduces. However, the corners of the billet show certain arcs and the materials are insufficiently filled when the thickness is too small. The higher the die-forging speed is, the more significantly the temperature rises and the more non-uniformly the temperature distributes in the billet. In addition, the mean equivalent strain shows little change when the friction coefficient increased from 0.1 to 0.3, but the strain distribution became more inhomogeneous.
Analysis of optimal profile modification amount of spur gear under disturbance of backlash and center distance
Authors: Shen Enen , Hu Yumei , He Zao , Zhang Huan , Min Yanghan
Published: October 2019

Under high temperature conditions, backlash and center distance of gear pair deviate from the preset value, which makes original modification amount deviate from the optimal value. The Finite Element Method was used to verify the deviation of the optimal modification amount under the disturbance of backlash and center distance. Taking the backlash, center distance variation and modification amount as independent variables and the transmission error fluctuation as dependent variables, the mapping relationship between the four factors was established by the Kriging model, Then, the law of the influence of the three variables on the transmission error fluctuation was analyzed, and the optimal modification amount after the backlash and center distance disturbance was obtained. The results showed that when the resistance moment is constant, the increase of modification amount and backlash value leads to the increase of transmission error fluctuation, while the increase of center distance reduces the transmission error fluctuation. Among the three variables, the transmission error fluctuation is the most sensitive to backlash, followed by modification amount and the change of center distance. The modified modification amount reduces the transmission error fluctuation by 2.4% and the contact force fluctuation by 14.9%.
Effect of Ru on the concentration distribution of elements and creep properties of nickel-based superalloy
Authors: Liang Shuang , Liu Zhixin
Published: October 2019

The effects of Ru on creep properties, microstructure and elemental concentration distribution of nickel..based single crystal superalloy containing without Ru and 2% Ru are studied by means of creep tests under high temperature, morphology observation after heat treatment and determination of elemental concentration distribution by atomic probe. The results show that Ru can inhibit the precipitation of TCP phase and improve the solid solubility of W element in the alloy and the creep life of the alloy at high temperature. At the same time, the addition of element Ru can make the alloy to produce “reverse distribution” effect, improve the alloying degree of γ’S phase and the effect of solution strength, which final significantly improve the high temperature creep rupture properties of the alloy containing Ru.
Optical memory architectures for fast routing address look-up (AL) table operation
Authors: Vagionas Christos , Tsakyridis Apostolos , Mourgias-Alexandris George , Pitris Stelios , Maniotis Pavlos , Pleros Nikos , Alexoudi Theoni
Published: October 2019

Today, the increasing demand for fast routing processes has turned the address look-up (AL) operation into one of the main critical performance operations in modern optical networks, since it conventionally relies on slow-performing AL tables. Specifically, AL memory tables are comprised of content addressable memories (CAMs) for storing a known route of the forwarding information base of the router, and random access memories (RAMs) for storing the respective output port for this route. They thus allow for a one-cycle search operation of a packet’s destination address, yet they typically operate at speeds well below 1 GHz, in contrast with the vastly increasing optical line rates. In this paper, we present our overall vision towards light-based optical AL memory functionalities that may facilitate faster router AL operations, as the means to replace slow-performing electronic counterparts. In order to achieve this, we report on the development of a novel optical RAM cell architecture that performs for the first time with a speed of up to 10 Gb s−1, as well as our latest works on multi-bit 10 Gb s−1 optical CAM cell architectures. Specifically, the proposed optical RAM cell exploits a semiconductor optical amplifier-Mach–Zehnder interferometer in a push-pull configuration and deep saturation regime, doubling the speed of prior optical RAM cell configurations. Error-free write/read operation is demonstrated with a peak power penalty of 6.2 dB and 0.4 dB, respectively. Next, we present the recent progress on optical CAM cell architectures, starting with an experimental demonstration of a 2-bit optical CAM match-line architecture that achieves an exact bitwise search operation of an incoming 2-bit destination address at 10 Gb s−1, while the analysis is also extended to a numerical evaluation of a multi-cell 4-bit CAM-based row architecture with wavelength division multiplexed outputs for fast parallel memory operations at speeds of up to 4 × 20 Gb s−1. Finally, we present a comparative study between electronic and optical RAMs and CAMs in terms of energy and speed and discuss the further challenges towards our vision.
Premenopausal Use of Progestogens and Cutaneous Melanoma Risk: A French Prospective Cohort Study
Authors: Cervenka Iris , Al Rahmoun Marie , Mahamat-Saleh Yahya , Boutron-Ruault Marie-Christine , Fournier Agnès , Kvaskoff Marina
Published: October 2019

We investigated the influence of premenopausal use of progestogens on melanoma using data from E3N (Etude Epidémiologique Auprès de Femmes de l’Education Nationale), a prospective cohort of 98,995 French women, aged 40–65 years at inclusion. We used Cox models to adjust for age and melanoma risk factors. Over 1992–2008, 540 melanoma cases were ascertained among 79,558 women. We found a modest association between self-reported progestogen use and melanoma risk (hazard ratio (HR) = 1.23, 95% confidence interval (CI) = 1.02, 1.47), which was reduced after adjustment for melanoma risk factors (HR = 1.15, 95% CI: 0.95, 1.39). There was no heterogeneity across types of progestogens (P = 0.22), and use of multiple progestogens was positively associated with melanoma risk (HR = 1.33, 95% CI: 1.04, 1.70). Among users, we found no relationship with duration of progestogen use, age at start and last use, and time since first and last use. Although our results did not show evidence of a confounding effect of sun exposure, progestogen users had lower levels of residential sun exposure and were more likely to report sunscreen use, suggesting specific sun exposure profiles in users. Our findings do not support a strong influence of progestogens on melanoma risk. Further research is needed to confirm these results.
Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data
Authors: Lafontaine Adam T , Mayer Bruce J , Machida Kazuya
Published: October 2019

Current web-based sequence logo analyses for studying domain–peptide interactions are often conducted only on high affinity binders due to conservative data thresholding. We have developed Dynalogo, a combination of threshold varying tool and sequence logo generator written in the R statistical programming language, which allows on-the-fly visualization of binding specificity over a wide range of affinity interactions. Hence researchers can easily explore their dataset without the constraint of an arbitrary threshold. After importing quantitative data files, there are various data filtering and visualizing features available. Using a threshold control, users can easily track the dynamic change of enrichment and depletion of amino acid characters in the sequence logo panel. The built-in export function allows downloading filtered data and graphical outputs for further analyses. Dynalogo is optimized for analysis of modular domain–peptide binding experiments but the platform offers a broader application including quantitative proteomics.

Availability and implementation

Dynalogo application, user manual and sample data files are available at https://dynalogo.cam.uchc.edu. The source code is available at https://github.com/lafontaine-uchc/dynalogo.

Supplementary information

Supplementary data are available at Bioinformatics online.
An improved encoding of genetic variation in a Burrows–Wheeler transform
Authors: Büchler Thomas , Ohlebusch Enno
Published: October 2019

Motivation

In resequencing experiments, a high-throughput sequencer produces DNA-fragments (called reads) and each read is then mapped to the locus in a reference genome at which it fits best. Currently dominant read mappers are based on the Burrows–Wheeler transform (BWT). A read can be mapped correctly if it is similar enough to a substring of the reference genome. However, since the reference genome does not represent all known variations, read mapping tends to be biased towards the reference and mapping errors may thus occur. To cope with this problem, Huang et al. encoded single nucleotide polymorphisms (SNPs) in a BWT by the International Union of Pure and Applied Chemistry (IUPAC) nucleotide code. In a different approach, Maciuca et al. provided a ‘natural encoding’ of SNPs and other genetic variations in a BWT. However, their encoding resulted in a significantly increased alphabet size (the modified alphabet can have millions of new symbols, which usually implies a loss of efficiency). Moreover, the two approaches do not handle all known kinds of variation.

Results

In this article, we propose a method that is able to encode many kinds of genetic variation (SNPs, multi-nucleotide polymorphisms, insertions or deletions, duplications, transpositions, inversions and copy-number variation) in a BWT. It takes the best of both worlds: SNPs are encoded by the IUPAC nucleotide code as in Huang et al. (2013, Short read alignment with populations of genomes. Bioinformatics, 29, i361–i370) and the encoding of the other kinds of genetic variation relies on the idea introduced in Maciuca et al. (2016, A natural encoding of genetic variation in a Burrows-Wheeler transform to enable mapping and genome inference. In: Proceedings of the 16th International Workshop on Algorithms in Bioinformatics, Volume 9838 of Lecture Notes in Computer Science, pp. 222–233. Springer). In contrast to Maciuca et al., however, we use only one additional symbol. This symbol marks variant sites in a chromosome and delimits multiple variants, which are added at the end of the ‘marked chromosome’. We show how the backward search algorithm, which is used in BWT-based read mappers, can be modified in such a way that it can cope with the genetic variation encoded in the BWT. We implemented our method and compared it with BWBBLE and gramtools.

Availability and implementation

https://www.uni-ulm.de/in/theo/research/seqana/.
Ophthalmological findings in facioscapulohumeral dystrophy
Authors: Goselink Rianne J M , Schreur Vivian , van Kernebeek Caroline R , Padberg George W , van der Maarel Silvère M , van Engelen Baziel G M , Erasmus Corrie E , Theelen Thomas
Published: October 2019

Ophthalmological abnormalities in facioscapulohumeral dystrophy may lead to treatable vision loss, facilitate diagnostics, could help unravelling the pathophysiology and serve as biomarkers. In this study, we provide a detailed description of the ophthalmological findings in a well-defined cohort of patients with facioscapulohumeral dystrophy using state of the art retina imaging techniques. Thirty-three genetically confirmed patients (aged 7–80 years) and 24 unrelated healthy controls (aged 6–68 years) underwent clinical ophthalmological examination, fundus photography, optical coherence tomography/angiography, genotyping and neurological examination. All patients had normal corrected visual acuity and normal intraocular pressure. In 27 of the 33 patients, weakness of the orbicularis oculi was observed. Central retinal pathology, only seen in patients and not in healthy controls, included twisting (tortuosity) of the retinal arteries in 25 of the 33 patients and retinal pigment epithelium defects in 4 of the 33 patients. Asymmetrical foveal hypoplasia was present in three patients, and exudative abnormalities were observed in one patient. There was a correlation between the severity of retinal tortuosity and the D4Z4 repeat array size (R2 = 0.44, P < 0.005). Follow-up examination in a subgroup of six patients did not show any changes after 2 years. To conclude, retinal abnormalities were frequent but almost always subclinical in patients with facioscapulohumeral dystrophy and consisted primarily of arterial tortuosity and foveal abnormalities. Retinal tortuosity was seen in the retinal arterioles and correlated with the D4Z4 repeat array size, thereby providing clinical evidence for an underlying genetic linkage between the retina and facioscapulohumeral dystrophy.
Sperm allocation strategies in a sperm heteromorphic insect
Authors: Esfandi Kambiz , He Xiong Z , Wang Qiao
Published: October 2019

Theories predict that in polyandrous species, the focal male should increase sperm allocation per mate in the presence of rivals to gain greater share of paternity, but in the presence of additional mates, he should reduce sperm allocation per mate to save sperm for insemination of more mates. However, empirical findings are often inconsistent and reasons behind are unclear. Furthermore, many studies use copulation duration as an estimate of the number of sperm transferred. Yet, empirical evidence for such assumption is largely lacking. Here, we used a sperm heteromorphic insect Ephestia kuehniella whose males produce two types of sperm, eupyrenes (fertile) and apyrenes (nonfertile), to test these postulations. We allowed focal males to detect chemical and acoustic but no tactile cues from rivals or additional mates both before and during mating and measured copulation duration and sperm allocation in successive copulations. We demonstrate that males transfer significantly more eupyrenes per mate in the presence of rivals and that the sperm allocation pattern persists in successive copulations under this condition. However, males do not adjust apyrene allocation in response to rivals probably because apyrenes play a relatively minor role in male reproductive success. Contrary to a previous study, focal males do not respond to additional mates most likely due to the lack of tactile cues in the present study. We reveal that sperm allocation is not a function of copulation duration in this insect for spermatophore formation and delivery occupy most of copulation duration and sperm transfer is complete near the end of copulation.
Correlation between specific groups of heterotrophic bacteria and microcystin biodegradation in freshwater bodies of central Europe
Authors: Dziga Dariusz , Kokociński Mikołaj , Barylski Jakub , Nowicki Grzegorz , Maksylewicz Anna , Antosiak Adam , Banaś Agnieszka Katarzyna , Strzałka Wojciech
Published: October 2019

Microcystins produced by several toxic cyanobacterial strains constitute an important problem for public health. Bacterial degradation of these hepatotoxins may play an important role in natural ecosystems, however the nature of the process is very poorly understood. The aim of our study was to investigate the possible interactions between cyanotoxin producers and degraders. Samples collected from 24 water bodies in western Poland were analysed to determine the chemo-physical parameters, phytoplankton content, bacterial community structure and microcystin-biodegradation potency. A redundancy analysis identified a positive correlation between the capacity of a community to degrade microcystin LR (MC-LR) and temperature, pH, chlorophyll a concentration and the abundance of MC-producers. The relative abundance of classes F38, TM7-3 and the order WCHB1-81c (Actinobacteria) was significantly higher in the lakes with MC-biodegradation potency. Some specific bacterial genera belonging to Acidobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes and TM7 were closely correlated with the occurrence of Microcystis spp. Furthermore, the MC biodegradation process was connected with the same bacterial groups. Thus, our approach allowed us to provide a broader picture of some specific relations between microcystin producers and potential microcystin degraders. A more comprehensive analysis of the existing correlations may be helpful in our understanding of natural mechanisms of MC elimination using bacteria such as MC-degraders.
Effect of a fungus, Hypoxylon spp., on endophytes in the roots of Asparagus
Authors: Huang Guoshuai , Jin Qunying , Peng Huazheng , Zhu Tangjun , Ye Hualin
Published: October 2019

The fungal isolate Hypoxylon spp. (Sj18) was isolated from the root of pecan. It might have effects on the plant's stress tolerance and endophytic community. Inoculation experiments were carried out on the roots of Asparagus with normal and inactivated Sj18, and the diversity and community structure of endophytes in the root of inoculated Asparagus were studied. It was found that Sj18 fungi affected the endophytic community of Asparagus roots. From being a low-abundance genus, the salt-tolerant bacterium Halomonas became the dominant genus. In order to verify that Sj18 can improve salt tolerance, Arabidopsis thaliana was inoculated with Sj18 in a salt tolerance test. The result showed that A. thaliana grew better in a high salt environment after inoculation with Sj18. Sj18 changed the microbe diversity, community composition and structure of endophytes in the roots of Asparagus, which increased the bacterial diversity. A total of 16 phyla and 184 genera of bacteria were detected. However, the diversity of fungi decreased.
Genetically Increased Telomere Length and Aging-Related Traits in the U.K. Biobank
Authors: Demanelis Kathryn , Tong Lin , Pierce Brandon L
Published: October 2019

Telomere length (TL) shortens over time in most human cell types and is a potential biomarker of aging. However, the causal association of TL on physical and cognitive traits that decline with age has not been extensively examined in middle-aged adults. Using a Mendelian randomization (MR) approach, we utilized genetically increased TL (GI-TL) to estimate the impact of TL on aging-related traits among U.K. Biobank (UKB) participants (age 40–69 years). We manually curated 53 aging-related traits from the UKB and restricted to unrelated participants of British ancestry (n = 337,522). We estimated GI-TL as a linear combination of nine TL-associated single nucleotide polymorphisms (SNPs), each weighted by its previously-reported association with leukocyte TL. Regression models were used to assess the associations between GI-TL and each trait. We obtained MR estimates using the two-sample inverse variance weighted (IVW) approach. We identified six age-related traits associated with GI-TL (Bonferroni-corrected threshold p < .001): pulse pressure (PP) (p = 5.2 × 10-14), systolic blood pressure (SBP) (p = 2.9 × 10-15), diastolic blood pressure (DBP) (p = 5.5 × 10-6), hypertension (p = 5.5 × 10-11), forced expiratory volume (FEV1) (p = .0001), and forced vital capacity (FVC) (p = 3.8 × 10-6). Under MR assumptions, one standard deviation increase in TL (~1,200 base pairs) increased PP, SBP, and DBP by 1.5, 2.3, and 0.8 mmHg, respectively, while FEV1 and FVC increased by 34.7 and 52.2 mL, respectively. The observed associations appear unlikely to be due to selection bias based on analyses including inverse probability weights and analyses of simulated data. These findings suggest that longer TL increases pulmonary function and blood pressure traits among middle-aged UKB participants.
Innovative recruitment strategies for a comprehensive worksite wellness initiative
Authors: Ablah Elizabeth , Umansky Emily , Wilcox Elizabeth A , Usher Jeff , Church Jennifer , Barnes Virginia
Published: October 2019

Recruiting for wellness initiatives is challenging. WorkWell KS, a statewide worksite wellness initiative, offers unique worksite recruitment strategies that may serve as lessons. From 2012 to 2018, WorkWell KS utilized champions, well-connected local leaders, to recruit worksites. A total of 784 worksites were recruited for at least one WorkWell KS workshop. A survey of champions requested identification of strategies, barriers and facilitators for successful recruitment and continued engagement. Forty-three champions reported on recruitment experiences. Sixty-three percent of respondents attributed recruitment success to having funding to complete their work. Face-to-face meetings was the most commonly reported successful strategy. Eighty-six percent of respondents reported that improving employee health was motivation for worksites to participate. Champions with a significant funding incentive for worksites commonly indicated that funding was a motivating factor. The most commonly selected factor for continued engagement was having a worksite staff member with wellness in their job description (67% of respondents). Forty-nine percent of respondents reported worksites’ lack of time as a barrier to participation. The WorkWell KS initiative has implemented innovative recruitment methods that leverage well-connected leaders to recruit worksites to participate in a comprehensive worksite wellness initiative. Future worksite-based initiatives may benefit from adopting recruitment strategies presented here.
Within family Mendelian randomization studies
Authors: Davies Neil M , Howe Laurence J , Brumpton Ben , Havdahl Alexandra , Evans David M , Davey Smith George
Published: October 2019

Mendelian randomization (MR) is increasingly used to make causal inferences in a wide range of fields, from drug development to etiologic studies. Causal inference in MR is possible because of the process of genetic inheritance from parents to offspring. Specifically, at gamete formation and conception, meiosis ensures random allocation to the offspring of one allele from each parent at each locus, and these are unrelated to most of the other inherited genetic variants. To date, most MR studies have used data from unrelated individuals. These studies assume that genotypes are independent of the environment across a sample of unrelated individuals, conditional on covariates. Here we describe potential sources of bias, such as transmission ratio distortion, selection bias, population stratification, dynastic effects and assortative mating that can induce spurious or biased SNP–phenotype associations. We explain how studies of related individuals such as sibling pairs or parent–offspring trios can be used to overcome some of these sources of bias, to provide potentially more reliable evidence regarding causal processes. The increasing availability of data from related individuals in large cohort studies presents an opportunity to both overcome some of these biases and also to evaluate familial environmental effects.