bluuebunny/crossref_metadata_2025_split huggingface dataset:
gencore: An Efficient Tool to Generate Consensus Reads for Error Suppressing and Duplicate Removing of NGS data
Authors: Chen Shifu , Zhou Yanqing , Chen Yaru , Huang Tanxiao , Liao Wenting , Xu Yun , Li Zhicheng , Gu Jia 
Published: December 2018

AbstractBackgroundRemoving duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, as NGS technology gains more recognition in clinical applications (i.e. cancer testing), researchers start to pay more attention to its sequencing errors, and prefer to remove these errors while performing deduplication operations. Recently, a new technology called unique molecular identifier (UMI) has been developed to better identify sequencing reads derived from different DNA fragments. Most existing duplicate removing tools cannot handle the UMI-integrated data. Some modern tools can work with UMIs, but are usually slow and use too much memory, making them not suitable for cloud-based deployment. Furthermore, existing tools rarely report rich statistical results, which are very important for quality control and downstream analysis. These unmet requirements drove us to develop an ultra-fast, simple, little-weighted but powerful tool for duplicate removing and sequence error suppressing, with features of handling UMIs and reporting informative results.ResultsThis paper presents an efficient tool gencore for duplicate removing and sequence error suppressing of NGS data. This tool clusters the mapped sequencing reads and merges reads in each cluster to generate one single consensus read. While the consensus read is generated, the random errors introduced by library construction and sequencing can be removed. This error-suppressing feature makes gencore very suitable for the application of detecting ultra-low frequency mutations from deep sequencing data. When unique molecular identifier (UMI) technology is applied, gencore can use them to identify the reads derived from same original DNA fragment. gencore reports statistical results in both HTML and JSON formats. The HTML format report contains many interactive figures plotting statistical coverage and duplication information. The JSON format report contains all the statistical results, and is interpretable for downstream programs.ConclusionsComparing to the conventional tools like Picard and SAMtools, gencore greatly reduces the output data’s mapping mismatches, which are mostly caused by errors. Comparing to some new tools like UMI-Reducer and UMI-tools, gencore runs much faster, uses less memory, generates better consensus reads and provides simpler interfaces. To our best knowledge, gencore is the only duplicate removing tool that generates both informative HTML and JSON reports. This tool is available at: https://github.com/OpenGene/gencore
High temperature corrosion behaviour of aluminised FC 25 cast iron using pack cementation
Authors: Chandra-Ambhorn Somrerk , Krasaelom Neramit , Thublaor Tummaporn , Leelachao Sirichai 
Published: December 2018

Purpose
This study aims to apply the pack cementation to develop the Fe-Al layers on the surface of FC 25 cast iron in order to increase the high-temperature corrosion resistance of the alloy.

Design/methodology/approach
Pack cementation was applied on the surface of FC 25 cast iron at 1,050°C. The bare and aluminised alloys were subjected to the oxidation test in 20 per cent O2-N2 at 850 °C. Scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy and X-ray diffraction (XRD) were used for characterisation.

Findings
The layers of pack cementation consisted of Fe2Al5, FeAl2 and FeAl, and solid solution alloyed with Al. The oxidation kinetics of the bare cast iron was parabolic. Mass gain of the aluminised cast iron was significantly decreased compared with that of the bare cast iron. This was because of the protective alumina formation on the aluminised alloy surface. Al in the Fe–Al layer also tended to be homogenised during oxidation.

Originality/value
Even though the aluminising of alloys was extensively studied, the application of that process to the FC 25 cast iron grade was originally developed in this work. The significantly reduced mass gain of the aluminised FC 25 cast iron makes the studied alloy be promising for the use as a valve seat insert in an agricultural single-cylinder four-stroke engine, which might be run by using a relatively cheaper fuel, i.e. LPG, but as a consequence requires the higher oxidation resistance of the engine parts.
4D-trajectory time windows: definition and uncertainty management
Authors: Rodríguez-Sanz Álvaro , Gómez Comendador Fernando , Arnaldo Valdés Rosa M. , Pérez-Castán Javier A. , González García Pablo , Najar Godoy Mar Najar Godoy 
Published: December 2018

PurposeThe use of the 4D trajectory operational concept in the future air traffic management (ATM) system will require the aircraft to meet very accurately an arrival time over a designated checkpoint. To do this, time intervals known as time windows (TW) are defined. The purpose of this paper is to develop a methodology to characterise these TWs and to manage the uncertainty associated with the evolution of 4D trajectories.Design/methodology/approach4D trajectories are modelled using a point mass model and EUROCONTROL’s BADA methodology. The authors stochastically evaluate the variability of the parameters that influence 4D trajectories using Monte Carlo simulation. This enables the authors to delimit TWs for several checkpoints. Finally, the authors set out a causal model, based on a Bayesian network approach, to evaluate the impact of variations in fundamental parameters at the chosen checkpoints.FindingsThe initial results show that the proposed TW model limits the deviation in time to less than 27 s at the checkpoints of an en-route segment (300 NM).Practical implicationsThe objective of new trajectory-based operations is to efficiently and strategically manage the expected increase in air traffic volumes and to apply tactical interventions as a last resort only. We need new tools to support 4D trajectory management functions such as strategic and collaborative planning. The authors propose a novel approach for to ensure aircraft punctuality.Originality/valueThe main contribution of the paper is the development of a model to deal with uncertainty and to increase predictability in 4D trajectories, which are key elements of the future airspace operational environment.
A novel improvement of Kriging surrogate model
Authors: He Wei , Xu Yuanming , Zhou Yaoming , Li Qiuyue 
Published: December 2018

Purpose
This paper aims to introduce a method based on the optimizer of the particle swarm optimization (PSO) algorithm to improve the efficiency of a Kriging surrogate model.

Design/methodology/approach
PSO was first used to identify the best group of trend functions and to optimize the correlation parameter thereafter.

Findings
The Kriging surrogate model was used to resolve the fuselage optimization of an unmanned helicopter.

Practical implications
The optimization results indicated that an appropriate PSO scheme can improve the efficiency of the Kriging surrogate model.

Originality/value
Both the STANDARD PSO and the original PSO algorithms were chosen to show the effect of PSO on a Kriging surrogate model.
Data flows and the digital economy: information as a mobile factor of production
Authors: Mueller Milton , Grindal Karl 
Published: December 2018

Purpose
This paper aims to analyze the direction and balance of transnational information flows and look at how nonpriced digital information exchanges related to international trade in goods and services.

Design/methodology/approach
The authors obtained quantitative data about Web-related data flows between countries and regions using Telegeography data on “Server Location as a Percentage of Top Websites.” They then explore how those flows are correlated to trade in goods.

Findings
Web traffic is highly transnational. More than half of the top 100 websites in 9 of the world’s 13 sub-regions are hosted in the USA. More than 15 per cent of the top 100 websites in 9 of the 13 subregions are hosted in Western Europe. East Asia has the largest negative balance in the relationship between incoming and outgoing Web requests. The authors found a very strong negative correlation (−0.878) between Web traffic balances and the balance of trade in goods across all subregions. A similarly strong positive correlation was found with services trade; however, the incompleteness of the data does not allow for strong conclusions yet.

Research limitations/implications
Further research is needed to correlate Web traffic flows with capital flows. The authors also do not have a well-developed theory to explain the strong negative correlation between information flows and goods trade.

Practical implications
The data and analysis have useful implications for digital economy policy. It indicates that digital protectionism of the sort practice by China may succeed in increasing domestic producers’ share of Web requests, but does not make them globally competitive. The strong negative correlation between the balance of unpriced Web information and the balance of trade in goods indicates interdependence rather than domination, challenging narratives that information flow imbalances are caused by market power of the big platforms.

Social implications
The paper demonstrates the degree to which unpriced digital exchanges are transnational and how various countries are more or less globally competitive in the supply of information that the rest of the world finds attractive.

Originality/value
No other published papers have used the data on website traffic data, and previous research has not explored empirically the correlation between information flows and goods trade.
Heat transfer in a porous cavity in presence of square solid block
Authors: Nandalur Ameer Ahamad , Kamangar Sarfaraz , Badruddin Irfan Anjum 
Published: December 2018

Purpose
The purpose of this study was to analyze the heat transfer in a square porous cavity that has a solid block placed at its center. The prime focus of this study is to investigate the effect of size of the square solid block and other physical parameters on the heat transfer rate from the hot surface into the porous medium. The left vertical surface of cavity is maintained at a hot temperature and the right vertical surface at a cool temperature, Tc. The finite element method is used to simplify the governing equations and is solved iteratively. It is noted that the size of the solid block plays a vital role in dictating the heat transfer from the hot surface to porous medium.

Design/methodology/approach
The current work is based on finite element formulation of a square porous cavity that has a solid square block placed at its center. Governing equations were solved iteratively.

Findings
The size of the solid block has a pronounced effect on the heat transfer behavior inside the porous cavity.

Originality/value
This study highlights the heat transfer due to a conducting square solid block at mid of porous cavity.
Positivity at the workplace
Authors: Shahid Sehrish , Muchiri Michael K. 
Published: December 2018

Purpose
Recognising the value of positive organisational behaviour at the workplace, this paper aims to provide a major review of the current state of research on positivity, and subsequently proposes new pathways for more theory building relating to important constructs conceptually related to positivity. Following the integration of emerging but disparate research on workplace positivity and related concepts, the paper develops a conceptual framework depicting the relationships amongst authentic leader behaviours, organisational virtuousness, psychological capital, thriving and job performance.

Design/methodology/approach
The paper offers a systematic critical review of published studies representing the literature addressing authentic leadership, organisational virtuousness, thriving, psychological capital and job performance. The paper relied on computerised keyword searches in the main business source databases of Emerald, ProQuest, ScienceDirect, EBSCOhost and SpringerLink.

Findings
This paper leads to a conceptual framework proposing direct relationships between authentic leadership, psychological capital, organisational virtuousness and job performance. Further, authentic leadership is proposed to potentially nurture organisational virtuousness, psychological capital, employee thriving and job performance, given the theoretical linkages between these conceptually relevant variables related to positivity. Additionally, organisational virtuousness and psychological capital are projected to mediate the relationship between authentic leadership and employee thriving. Finally, organisational virtuousness, psychological capital and employee thriving are designated as mediators of the relationship between authentic leadership and job performance.

Research limitations/implications
This paper proposes a conceptual framework focusing on one form of positive leader behaviour and also assumes specific causal pathways using a positivistic research approach to understanding the leadership–performance relationship. The paper did not examine all possible antecedents of positivity at the workplace.

Practical implications
The proposed conceptual framework should form the basis of many organisational interventions, especially in relation to boosting authentic leadership, organisational virtuousness, psychological capital, employee thriving and job performance. By suggesting the association between authentic leadership, psychological capital and organisational virtuousness, this paper highlights potential benefits from effective leaders’ commitment to enhancing psychological capital and organisational virtuousness and engendering thriving behaviour and job performance.

Originality/value
This novel paper has the potential to stimulate the empirical studies on workplace positivity through the association of authentic leadership, psychological capital, organisational virtuousness and thriving.
The impact of 360 feedback appraisal system on organizational justice and sustainability
Authors: El Haddad Rania , Karkoulian Silva , Nehme Rabih 
Published: December 2018

Purpose
This paper aims to extend previous results demonstrating a statistically significant causal relationship between the implementation of 360-degree feedback in an organization and employees’ perceptions of organizational justice. It explores the sustainability of this justice, ultimately making it an integral part of the organizational culture. The paper examines whether the previous model (based on relationships among 360-degree feedback, organizational justice and sustainability of organizational justice) is invariant across different levels of management (i.e. operational and top/middle managers) and across a group of female versus male employees.

Design/methodology/approach
Structural equation modeling multigroup analysis and invariance tests were conducted with a cross-sectional sample of 400 employees in various positions in home appliances and electronics organizations.

Findings
The results further sustain/contest previous findings on the relationships among appraisal, organizational justice and sustainability among respondents of different genders and at different managerial levels. The results also provide significant practical implications. Top managers and supervisors can incorporate gender and managerial level differences identified in this study to modify their management styles and appraisal techniques to install high levels of organizational justice and achieve a competitive edge through the sustained levels of this organizational justice.

Originality/value
This study is the first to explore the impact of implementing a 360-degree appraisal system on employees’ perceptions of justice, while taking into consideration gender differences, i.e. whether males or females tend to perceive different types of justice within the organization and whether they differ in the way that they react to the appraisal system being implemented within the workplace. Given all the positive traits associated with a 360-feedback appraisal system, the way that this feedback is viewed and interpreted by employees can differ according to the employee’s rank within the organization, i.e. whether he/she belongs to top/middle management team or the operational/front-line management team.
The relationship between tax avoidance and firm value with income smoothing
Authors: Akbari Farzana , Salehi Mahdi , Bagherpour Vlashani Mohammad Ali 
Published: December 2018

Purpose
The purpose of this paper is to investigate the relationship between tax avoidance, firm value and managerial ability in Tehran Stock Exchange and Over the Counter (OTC), according to the related theoretical foundations.

Design/methodology/approach
To calculate the managerial ability in this study, DEA is used based on the accounting data, company profile and industry and the hypotheses are estimated in a period of 12 years during 2004 to 2015 in TSE and OTC. Within the previous studies, to test the hypotheses, only the classical regression method is usually used and most of the times the effect of macroeconomic variables is not considered. In this study, in a new act for testing the hypotheses, three statistical methods are used, that is, classical regression models, mixed effects multilevel models and Bayesian multilevel models. Also in this study, the test of structural change is used to control the effects of macroeconomic variables, like inflation and other economic and political influence, on the results.

Findings
The results of these three methods show that the effect of income smoothing and earnings quality on the relationship between tax avoidance and firm value are significant.

Originality/value
Although several studies are conducted so far on the subject of the study, the current study is the first project which combined Bayesian econometrics. Therefore, the results are quite noble.
Team psychological safety and team performance
Authors: Jha Sumi 
Published: December 2018

PurposeThe purpose of this paper is to examine the relationships between team psychological safety and team performance and to test the mediating effect of learning orientation and moderating effect of psychological empowerment on that relationship.Design/methodology/approachData were collected from 50 teams and 345 team members from 20 different organizations. The moderated mediation analysis of psychological empowerment was tested using hierarchical regression analysis (PROCESS Macro) in SPSS.FindingsThe results show that higher the psychological empowerment, higher is the effect of psychological safety and learning orientation on team performance. Results supported the moderated mediation analysis of psychological empowerment.Practical implicationsGiven that psychological empowerment and learning orientation of team members will effect team performance, organizational efforts to foster psychological empowerment should be rewarding. Focusing on channelizing team psychological safety to improve team members’ relationship, openness and comfort with each other will increase team performance.Originality/valueThe study incorporated learning orientation and psychological empowerment to redefine the relationship between psychological safety and team performance.
Erosion studies of cermet-coated ASTM A36 steel
Authors: Shibe Vineet , Chawla Vikas 
Published: December 2018

PurposeThis paper aims to perform the solid particle erosion studies in simulated coal-fired boiler conditions with a view to compare the erosion behavior of two different types of detonation gun (D-Gun) sprayed cermet coating powders, that is, WC-12%Co and Cr3C2-25%NiCr on ASTM A36 steel and bare (uncoated) ASTM A36 steel.Design/methodology/approachErosion studies were performed using an air jet erosion test rig at impingement angles of 45°, 60° and 90°. During the erosion studies weight loss, erosion rates in terms of volume loss (mm3/g) and measurement of erosion profiles were determined using optical profilometer.FindingsBoth cermet coatings had successfully protected the ASTM A36 steel from erosion at impingement angles of 45°, 60° and 90°. In the case of bare ASTM A36 steel, the erosion rates were maximal at an impingement angle of 45° and minimal at an impingement angle of 90°, thus depicting the peculiar erosion behavior of ductile materials. WC-12%Co coated specimens exhibited erosion behavior that is closer to the behavior of ductile materials. Cr3C2-25%NiCr coated specimens exhibited the maximum erosion rate at an impingement angle of 90° and minimum at an impingement angle of 45°, hence depicting the typical behavior of brittle materials.Practical implicationsIt is expected that these results will contribute to the improvement of erosion resistance of induced draft fans, by the application of D-Gun sprayed WC-12%Co and Cr3C2-25%NiCr cermet coatings.Originality/valueThis paper evaluates the solid particle erosion behavior of bare and cermet-coated ASTM A36 steel which will be helpful in choosing the suitable cermet coating for induced draft fan applications.
The investigation of tribological behavior of carbon fiber-reinforced composite materials
Authors: Kaya İsmail , Parlar Zeynep 
Published: December 2018

Purpose
The tribological behavior of composites varies on matrices materials, the reinforcement material and the direction of reinforcement materials. The purpose of this study is to examine the effects of fiber orientation on the tribological properties of carbon fiber–reinforced epoxy composite.

Design/methodology/approach
The experiments were carried out with a pin-on-ring tribometer. The tests were executed according to three different parameters: load, sliding velocity and direction of reinforcement. Loads measuring 92 N and 150 N were applied at sliding velocities of 1 and 2 m/s, in parallel, antiparallel and normal directions of fiber reinforcements. The frictional force was read every 500 m of sliding distance. To calculate specific wear rate, the mass of the samples was measured before and after each experiment. Moreover, temperature was measured every 1000 m of sliding distance via three-point infrared thermometer, to examine the effect of temperature variations. The sample surfaces were also examined in optic microscope after the experiments. Higher friction coefficient values were obtained in the normal direction-oriented carbon fiber specimen.

Findings
Comparing the friction coefficient values, antiparallel and parallel direction-oriented carbon fiber specimens gave lower friction coefficient values. The increase of sliding velocity and normal load resulted in the increase of surface temperature and this lead to the increase of friction coefficient.

Originality/value
This study shows the effects of fiber orientation on the tribological behavior of carbon fiber–reinforced epoxy composite. According to fiber orientations, relatively moving counter surfaces of this material shows different tribological behaviors.