bluuebunny/crossref_metadata_2025_split huggingface dataset:
UMI-Reducer: Collapsing duplicate sequencing reads via Unique Molecular Identifiers
Authors: Mangul Serghei , Driesche Sarah Van , Martin Lana S. , Martin Kelsey C. , Eskin Eleazar 
Published: January 2017

Short Structured AbstractSummaryEvery sequencing library contains duplicate reads. While many duplicates arise during polymerase chain reaction (PCR), some duplicates derive from multiple identical fragments of mRNA present in the original lysate (termed “biological duplicates”). Unique Molecular Identifiers (UMIs) are random oligonucleotide sequences that allow differentiation between technical and biological duplicates. Here we report the development of UMI-Reducer, a new computational tool for processing and differentiating PCR duplicates from biological duplicates. UMI-Reducer uses UMIs and the mapping position of the read to identify and collapse reads that are technical duplicates. Remaining true biological reads are further used for bias-free estimate of mRNA abundance in the original lysate. This strategy is of particular use for libraries made from low amounts of starting material, which typically require additional cycles of PCR and therefore are most prone to PCR duplicate bias.Availability and ImplementationThe UMI-Reducer is an open source Python software and is freely available for non-commercial use (GPL-3.0) athttps://sergheimangul.wordpress.com/umi-reducer/. Documentation and tutorials are available athttps://github.com/smangul1/UMI-Reducer/wiki/.Contactsmangul@ucla.edu,SVanDriesche@mednet.ucla.eduSupplementary informationFlowchart of Library Construction
New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins involved in Iron Sulfur Cluster Biogenesis
Authors: Fantini Marco , Malinverni Duccio , De Los Rios Paolo , Pastore Annalisa 
Published: January 2017

ABSTRACTDirect coupling analysis (DCA) is a powerful tool based on protein evolution and introduced to predict protein fold and protein-protein interactions which has been applied also to the prediction of entire interactomes. We have used DCA to analyse three proteins of the iron-sulfur biogenesis machine, an essential metabolic pathway conserved in all organisms. We show that, although based on a relatively small number of sequences due to its distribution in genomes, we can correctly recapitulate all the features of the fold of the CyaY/frataxin family, a protein involved in the human disease Friedreich’s ataxia. This result gave us confidence in the use of this tool. Application of DCA to the iron-sulfur cluster scaffold protein IscU, which has been suggested to function both as an ordered and a disordered form, allows us to clearly distinguish evolutionary traces of the structured species, suggesting that, if present in the cell, the disordered form has not left any evolutionary imprinting. We observe instead, for the first time, direct indications of how the protein can dimerize head-to-head and bind 4Fe4S clusters. Analysis of the alternative scaffold protein IscA provides strong support to a coordination of the cluster mediated by a dimeric rather than a tetrameric form as previously suggested. Our analysis also suggests the presence in solution of a mixture of monomeric and dimeric species and guide us to the prevalent one. Finally, we used DCA to analyse protein-protein interactions between some of these proteins and discuss the potentialities and the limitations of the method.
A research and industry perspective on automotive logistics performance measurement
Authors: Dörnhöfer Martin , Günthner Willibald A. 
Published: January 2017

PurposeThe purpose of this paper is to assess the current state of performance measurement (PM) in academic literature and in the automotive supply chain (SC). The research question is to what extent PM systems (PMS) in academic literature and in industry are applicable in automotive logistics.Design/methodology/approachThe authors use a combination of a systematic literature review (SLR) and an industry survey. The SLR is used to identify literature on design aspects for PMS and current PMS reported in academic literature. The survey adds an industry perspective and is used to validate the design aspects found in literature. The synthesis aims to deliver both, current research gaps and needs in industry.FindingsThe findings from SLR indicate, there is a broad base of literature regarding design aspects for PMS. Literature on PMS in context of automotive logistics is nevertheless rare. The industry survey leads to the conclusion that conformity with design aspects from literature increases added value of PMS. Nevertheless, current PMS show improvement needs in automotive context. Academic literature lacks detailed process orientation, transparency and is seen as too high level to be helpful for practitioners. For systems in industry, the SC perspective can be improved. In addition, applicability for continuous improvement is identified as research need in industry and literature.Research limitations/implicationsDue to the selected survey approach, additional research is required to obtain more generalizable results. To increase reliability and validity, a selection of the findings should be further analyzed, e.g. by focusing on regions outside Western Europe or a more in depth analysis of selected aspects. In addition insights into selected research topics highlighted in the paper should be assessed in detail by applying different methodologies (e.g. case studies) to validate the findings.Originality/valueThe findings add to the research on PMS. Latest academic literature is reviewed. The findings are combined with an industry perspective. The combination of SLR and a broad survey enables us to draw conclusions which are relevant for researchers and practitioners alike. Where academic research should focus more on the practical applicability, industry can benefit from the findings by integrating a more holistic perspective into their PMS, especially with a SC wide evaluation.
Logistics management research collaboration in Asia
Authors: Wu Yen-Chun , Goh Mark , Yuan Chih-Hung , Huang Shan-Huen 
Published: January 2017

PurposeThe purpose of this paper is to investigate the state of logistics management research in Asia. The study focuses on the research agenda, the topics of interest, and the extent of research collaboration in logistics theory building and knowledge specific to Asia.Design/methodology/approachThis study uses a mixed methods approach namely, content analysis drawn from the articles found in six well-recognized peer-reviewed logistics management related journals from 2003 to 2013, followed by social network analysis which is applied on the selected articles to provide a structure of the collaboration relationship.FindingsInitial findings suggest that there are some scholars in Asia who are instrumental in research collaboration and in building a body of knowledge on logistics management focused on Asia. More co-production of knowledge from deeper and tightly knit industry-academic collaboration is needed to progress this domain. Most of the published work use an empirical instrument drawn from the resource-based view to explore firm level supply chain collaboration and strategy. This suggests a positivist research tradition within logistics. There is a shortage of studies conducted on the supply chain as a network of enterprises.Research limitations/implicationsThe review of the articles is limited to six logistics specific journals and the authors only concentrate on logistics management research focused on Asia. The contributions from the other journals may have been missed. More collaboration at the institutional, national, and international levels is called for especially on cross-collaboration between practice and theory.Practical implicationsThough the analysis is restricted to 260 articles found in six journals, this paper can shed light on the research needs from different perspectives and facilitate the progress of logistics management research in Asia.Originality/valueThis is the first paper to discuss the state of logistics management research collaboration in Asia, and provides an overview of the research issues, topics, and approaches undertaken thus far. Through this work, this study hopes that it will encourage greater research collaboration between industry and academia, and academics themselves.
Analysis of enterprise supply chain communication networks in engineering product development
Authors: Addo-Tenkorang Richard , Helo Petri T. 
Published: January 2017

Purpose
For decades now, industrial manufacturers’ complex product development (CPD) activities have seen various improvement approaches as well as product development (PD) support processes all in the quest to achieve shorter PD lead-times and higher return on investments. CPD process improvements, in terms of complex engineering design and delivery, still lack a lot more variance to be addressed on the “better, faster and cheaper” paradigm for efficient communication and information exchange flow processes. The paper aims to discuss these issues.

Design/methodology/approach
This paper presents employing social network theory analysis and statistical Pearson (r) correlation analysis in a triangulation approach to a proposed optimum conceptual information technology systems’ architecture and a “best practice” information flow process toward enhancing an industrial sustainable competitive advantage. Closed-end questionnaires were used to collect data for the scale or level of communication network from a sample size of eight Ship Power supply chain network complex engineering design and delivery systems-design teams with at least five members from each team.

Findings
Two extremely interesting findings and observations were identified from the analysis carried out (isolates and close-harmonic analysis) as well as the findings from the hypotheses’ testing. These essential analyses of the engineering systems-design teams were conducted by using the triangulation or mixed-method described in the abstract methodology identified above.

Originality/value
Effective and efficient real-time communication is seen as the vehicle for effective organization management. Although there may be some studies on effective technical communication in organizational and enterprise supply chain management settings, this research identifies a new robust and extensive analysis and feasible solutions to most of the communication bottlenecks and inefficient socio-industrial information flow processes, which need enhancement for industrial competitive advantage. Furthermore, the contribution of this paper further enhances the level 4 implementation aspect of the supply chain operation reference model in a replicable industry-specific perspective.
Autonomous obstacle avoidance of an unmanned surface vehicle based on cooperative manoeuvring
Authors: Wu Peng , Xie Shaorong , Liu Hengli , Li Ming , Li Hengyu , Peng Yan , Li Xiaomao , Luo Jun 
Published: January 2017

Purpose
Autonomous obstacle avoidance is important in unmanned surface vehicle (USV) navigation. Although the result of obstacle detection is often inaccurate because of the inherent errors of LIDAR, conventional methods typically emphasize on a single obstacle-avoidance algorithm and neglect the limitation of sensors and safety in a local region. Conventional methods also fail in seamlessly integrating local and global obstacle avoidance algorithms. This paper aims to present a cooperative manoeuvring approach including both local and global obstacle avoidance.

Design/methodology/approach
The global algorithm used in our USV is the Artificial Potential Field-Ant Colony Optimization (APF-ACO) obstacle-avoidance algorithm, which plans a relative optimal path on the specified electronic map before the cruise of USV. The local algorithm is a multi-layer obstacle-avoidance framework based on a single LIDAR to present an efficient solution to USV path planning in the case of sensor errors and collision risks. When obstacles are within a layer, the USV uses a corresponding obstacle-avoidance algorithm. Then the USV moves towards the global direction according to fuzzy rules in the fuzzy layer.

Findings
The presented method offers a solution for obstacle avoidance in a complex environment. The USV follows the global trajectory planed by the APF-ACO algorithm. While, the USV can bypass current obstacle in the local region based on the multi-layer method effectively. This fact was validated by simulations and field trials.

Originality/value
The method presented in this paper takes advantage of algorithm integration that remedies errors of obstacle detection. Simulation and experiments were also conducted for performance evaluation.
Design and realization of a novel magnetic nutation drive for industry robotic wrist reducer
Authors: Huang Ding-jian , Yao Li-gang , Li Wen-jian , Zhang Jun 
Published: January 2017

PurposeThe purpose of this research is to achieve a novel magnetic nutation drive for an industry robotic wrist reducer.Design/methodology/approachA novel magnetic nutation drive is proposed, and the structure and principle of the designed magnetic nutation drive are described in this study. Three-dimensional finite element analysis is used to compute the magnetic and torque of the magnetic nutation drive. Furthermore, a prototype of this novel magnetic nutation drive device is developed with 3D printing technology and tested to verify the feasibility of the proposed structure and principle.FindingsThe simulation and experimental results indicated that the proposed magnetic nutation drive device could meet the desired specifications, and that this novel magnetic nutation drive device successfully realized the non-contact transmission ratio of 105:1 required for a robotic wrist reducer.Practical implicationsThis novel magnetic nutation drive is low-cost and easy to make and use, and which provides the non-contact transmission ratio of 105:1 required for a robotic wrist reducer.Originality/valueFor the first time, this research applies the permanent magnet drive technology to nutation drive and puts forward a new non-contact nutation drive mode. The novel drive mode can solve some problems of the traditional mechanical contact nutation drive, such as vibration, friction loss, mechanical fatigue and necessity of lubrication. The proposed non-contact nutation drive device can achieve a high reduction ratio with compact structure and can be suitable for industry application.
An agile assistant robot integrating operation and rolling locomotion
Authors: Li Yezhuo , Yao Yan-An , Cheng Junlin , Tian Yaobin , Liu Ran 
Published: January 2017

Purpose
The purpose of this paper is to propose an agile assistant robot to be used as a mobile partner with two rotational motions and one translational motion. This robot possesses the rolling function and three operating abilities to assistant human beings in the industrial environment.

Design/methodology/approach
The main body of the robot is a typical 4-RSR (where R denotes a revolute joint and S denotes a spherical joint) parallel mechanism. The mechanism can reach any position on the ground by two rolling modes (the equivalent Watt linkage rolling mode and the equivalent 6R linkage rolling mode), and the robot can work as a spotlight or a worktable in operating modes at the target location. The mobility, rolling modes, operating modes and kinematics are analyzed.

Findings
Based on the results of kinematics of this assistant robot, the upper platform of the 4-RSR rolling mechanism has two rotational motions and one translational motion which can be used in the industry. The proposed concept is verified by experiments on a physical prototype.

Practical implications
This paper also discusses the application to industrial cases where cooperation between workers and robots is required.

Originality/value
The work presented in this paper is a novel exploration to apply parallel mechanisms to the field of assistant rolling robots. It is also a new attempt to use the rolling mechanism in the field of mobile operating robots for industry tasks.
Pylon-Climber: a novel climbing assistive robot for pylon maintenance
Authors: Lu Xiaolong , Zhao Shiping , Yu Deping , Liu Xiaoyu 
Published: January 2017

Purpose
The purpose of this paper is to describe the design and development of “Pylon-Climber”, a pole climbing robot (PCR) for climbing along the corner columns of electricity pylon and assisting the electricians to complete maintenance tasks.

Design/methodology/approach
Introduces a PCR that is composed of a simple climbing mechanism and two novel grippers. The gripper consists of two angle-fixed V-blocks, and the size of V-block is variable. The clamping method of the angle bar meets the requirement of the force closure theorem. The whole design adopts symmetrical design ideas.

Findings
The developed prototype proved possibility of application of PCRs for inspection and maintenance of pylon. The novel gripper can provide enough adhesion force for climbing robot.

Practical implications
The robot is successfully tested on a test tower composed of different specification steel angles, oblique ledges and overlapping steel struts.

Originality/value
Design and development of a novel climbing assistive robot for pylon maintenance. The robot is able to climb along the column of electricity pylon and pass all obstacles. The gripper can reliably grasp the angle bar with different specification and overlapping steel struts from multiple directions.
Stability analysis and control in the process of floating-target capture with hardware-in-the-loop system
Authors: Xie Zongwu , Zhao Xiaoyu , Zhang Yu , Zhang Qi , Yang Haitao , Sun Kui , Jin Minghe 
Published: January 2017

Purpose
The purpose of this paper is to develop an easily implemented and practical stabilizing strategy for the hardware-in-the-loop (HIL) system. As the status of HIL system in the ground verification experiment for space equipment keeps rising, the stability problems introduced by high stiffness of industrial robot and discretization of the system need to be solved ungently. Thus, the study of the system stability is essential and significant.

Design/methodology/approach
To study the system stability, a mathematical model is built on the basis of control circle. And root-locus and 3D root-locus method are applied to the model to figure out the relationship between system stability and system parameters.

Findings
The mathematical model works well in describing the HIL system in the process of capturing free-floating targets, and the stabilizing strategy can be adopted to improve the system dynamic characteristic which meets the needs of the practical application.

Originality/value
A method named 3D root-locus is extended from traditional root-locus method. And the improved method graphically displays the stability of the system under the influence of multivariable. And the strategy that stabilize the system with elastic component has a strong feasible and promotional value.
Cloud robotics: a review of technologies, developments and applications
Authors: Bogue Robert 
Published: January 2017

Purpose
This paper aims to provide an insight into the current state of cloud robotics developments, technology and applications.

Design/methodology/approach
Following a short introduction, this paper first considers the potential benefits of cloud robotics. It discusses cloud service providers and then considers a range of recent applications and developments involving humanoid, mobile and industrial robots. This is followed by details of some recent market entrants and their developments. Finally, brief concluding comments are drawn.

Findings
Cloud robotics is a rapidly developing technology made possible by the current ubiquitous internet connectivity and the growing number of powerful cloud computing services available. Benefits include access to big data sets, open-source algorithms, code and programmes, massively powerful parallel or grid computing and the sharing of information between robots. The technology has been applied successfully to humanoid, industrial, mobile and other classes of robots, often through direct collaborations between robot manufacturers and major IT companies. Several new companies have been established in very recent years to exploit the capabilities of cloud robotic technologies.

Originality/value
Cloud robotics is a highly topical and rapidly developing field, and this paper provides a detailed insight into recent developments and applications.
An integrated approach to grey relational analysis, analytic hierarchy process and data envelopment analysis
Authors: Pakkar Mohammad Sadegh 
Published: January 2017

Purpose
This paper aims to propose an integration of the analytic hierarchy process (AHP) and data envelopment analysis (DEA) methods in a multiattribute grey relational analysis (GRA) methodology in which the attribute weights are completely unknown and the attribute values take the form of fuzzy numbers.

Design/methodology/approach
This research has been organized to proceed along the following steps: computing the grey relational coefficients for alternatives with respect to each attribute using a fuzzy GRA methodology. Grey relational coefficients provide the required (output) data for additive DEA models; computing the priority weights of attributes using the AHP method to impose weight bounds on attribute weights in additive DEA models; computing grey relational grades using a pair of additive DEA models to assess the performance of each alternative from the optimistic and pessimistic perspectives; and combining the optimistic and pessimistic grey relational grades using a compromise grade to assess the overall performance of each alternative.

Findings
The proposed approach provides a more reasonable and encompassing measure of performance, based on which the overall ranking position of alternatives is obtained. An illustrated example of a nuclear waste dump site selection is used to highlight the usefulness of the proposed approach.

Originality/value
This research is a step forward to overcome the current shortcomings in the weighting schemes of attributes in a fuzzy multiattribute GRA methodology.
Social marketing and systems science: past, present and future
Authors: Brychkov Dmitry , Domegan Christine 
Published: January 2017

Purpose
The purpose of this paper is to present retrospective, current and prospective aspects of social marketing and systems science integration.

Design/methodology/approach
The paper uses a periodization methodology, based on turning points of conceptual integration between social marketing and systems science.

Findings
The paper identifies three periods of integration between social marketing and systems science: initialization of marketing and systems science integration; further conceptualization of the link between marketing and systems science, coupled by permeation of systems thinking into social marketing; and deep integration of social marketing with systems science. The latter period is ongoing and focuses on the origination of strategic systems-based theories and practices for sustainable social change.

Research limitations/implications
The use of a periodization methodology might be biased by subjectivity, as chronological sequences of conceptualization-related events can be hard to decipher and can be reluctant to structural analysis. The necessity to examine the link between marketing and systems science, in so far as social marketing draws upon marketing theory regarding integration with systems science, has social marketing overshadowed by marketing at some points in time.

Practical implications
Historical research of social marketing and systems science integration provides a robust platform for large-scale practical manifestation of system-based strategic projects in social marketing.

Originality/value
This paper demonstrates that the permeation of systems thinking into the social marketing paradigm is gaining momentum and describes the trends, prospects and complexities associated with the accelerating integration.