bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of t-SNE to Human Genetic Data
Authors: Li Wentian , Cerise Jane E , Yang Yaning , Han Henry 
Published: March 2017

AbstractThe t-SNE (t-distributed stochastic neighbor embedding) is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot. We conclude that the ability for t-SNE to reveal population stratification at different scales could be useful for human genetic association studies.
Extensive hidden genetic variation shapes the structure of functional elements in Drosophila
Authors: Chakraborty Mahul , Zhao Roy , Zhang Xinwen , Kalsow Shannon , Emerson J.J. 
Published: March 2017

AbstractMutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, though the fragmented nature of most contemporary assemblies obscure them. To discover such mutations, we assembled the first reference quality genome of Drosophila melanogaster since its initial sequencing. By comparing this genome to the existing D. melanogaster assembly, we create a structural variant map of unprecedented resolution, revealing extensive genetic variation that has remained hidden until now. Many of these variants constitute strong candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that dramatically amplifies the expression of detoxification genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high quality references are to deciphering phenotypes.
So many genes, so little time: a practical approach to divergence-time estimation in the genomic era
Authors: Smith Stephen A. , Brown Joseph W. , Walker Joseph F. 
Published: March 2017

AbstractPhylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. “Gene shopping”, wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available inSortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated lognormal (UCLN) models. However, this overlap was often due to imprecise estimates from the UCLN model. We find that “gene shopping” can be an efficient approach to divergence-time inference for phylogenomic datasets that may otherwise be characterized by extensive gene tree heterogeneity.
Tagger: BeCalm API for rapid named entity recognition
Authors: Jensen Lars Juhl 
Published: March 2017

AbstractMost BioCreative tasks to date have focused on assessing the quality of text-mining annotations in terms of precision of recall. Interoperability, speed, and stability are, however, other important factors to consider for practical applications of text mining. The new BioCreative/BeCalm TIPS task focuses purely on these. To participate in this task, I implemented a BeCalm API within the real-time tagging server also used by the Reflect and EXTRACT tools. In addition to retrieval of patent abstracts, PubMed abstracts, and Pub-Med Central open-access articles as required in the TIPS task, the BeCalm API implementation facilitates retrieval of documents from other sources specified as custom request parameters. As in earlier tests, the tagger proved to be both highly efficient and stable, being able to consistently process requests of 5000 abstracts in less than half a minute including retrieval of the document text.
How ecosystems recover from pulse perturbations: A theory of short- to long-term responses
Authors: Arnoldi J.-F. , Bideault A. , Loreau M. , Haegeman B. 
Published: March 2017

AbstractQuantifying stability properties of ecosystems is an important problem in ecology. A common approach is based on the recovery from pulse perturbations, and posits that the faster ecosystems return to their pre-perturbation state, the more stable they are. In theoretical studies the recovery dynamics are often collapsed into a single quantity: the long-term rate of return, called asymptotic resilience. However, empirical studies typically measure the recovery dynamics at much shorter time scales. In this paper we explain why asymptotic resilience is rarely representative of the short-term recovery. First, we show that, in contrast to asymptotic resilience, short-term return rates depend on features of the perturbation, in particular on the way its intensity is distributed over species. We argue that empirically relevant predictions can be obtained by considering the median response over a set of perturbations, for which we provide explicit formulas. Next, we show that the recovery dynamics are controlled through time by different species: abundant species tend to govern the short-term recovery, while rare species often dominate the long-term recovery. This shift from abundant to rare species typically causes short-term return rates to be unrelated to asymptotic resilience. Finally, we discuss how these findings might help to better connect empirical observations and theoretical predictions.
A study of the structural properties of sites modified by theO-linked 6-N-acetylglucosamine transferase
Authors: Britto-Borges Thiago , Barton Geoffrey J. 
Published: March 2017

AbstractProtein O-GlcNAcylation (O-GlcNAc) is an essential post-translational modification (PTM) in higher eukaryotes. The O-linked β-N-acetylglucosamine transferase (OGT), targets specific Serines and Threonines (S/T) in intracellular proteins. However, unlike phosphorylation, fewer than 25% of known O-GlcNAc sites match a clear sequence pattern. Accordingly, the three dimensional structures of O-GlcNAc sites were characterised to investigate the role of structure in molecular recognition. Of the 143/1,584 O-GlcNAc sites in 620 proteins were mapped to protein X-ray structures. The modified S/T were 1.7x more likely to be annotated in the REM465 field which defines missing residues in a protein structure, while 7 O-GlcNAc sites were solvent inaccessible and unlikely to be targeted by OGT. The 132/143 sites with complete backbone atoms clustered into 10 groups, but these were indistinguishable from clusters from unmodified S/T. This suggests there is no prevalent three-dimensional motif for OGT recognition. Predicted features from the 620 proteins were compared to unmodified S/T in O-GlcNAcylated proteins and globular proteins. The Jpred4 predicted secondary structure shows that modified S/T were more likely to be coils. 5/6 methods to predict intrinsic disorder indicated O-GlcNAcylated S/T to be significantly more disordered than unmodified S/T. Although the analysis did not find a pattern in the site three-dimensional structure, it revealed the residues around the modification site are likely to be disordered and suggests a potential role of secondary structure elements in OGT site recognition.
Traversing the fantasy of the heroic entrepreneur
Authors: Johnsen Christian Garmann , Sørensen Bent Meier 
Published: March 2017

PurposeWhile considerable critical energy has been devoted to unmasking the figure of the heroic entrepreneur, the idea that entrepreneurs are unique individuals with special abilities continues to be widespread in scholarly research, social media and popular culture. The purpose of this paper is to traverse the fantasy of the heroic entrepreneur by offering a reading of Richard Branson’s autobiography,Losing My Virginity.Design/methodology/approachThe theoretical approach of this paper is informed by Slavoj Žižek’s concept of fantasy and his critical analytical strategy of “traversing the fantasy”. Žižek offers a theoretical framework that allows us to understand how narratives of famous entrepreneurs create paradoxical fantasies that produce desire.FindingsBy offering a reading of Richard Branson’s autobiography,Losing My Virginity, this paper serves to illustrate how the fantasy of the heroic entrepreneur creates the injunction to overcome oneself and become true to oneself, but also how this figure is ridden with contradictions and impossibilities. Branson’s book will eventually be shown to be a religious narrative, where the entrepreneur is responsible for redeeming the crises not only of the economy, but of being as such.Originality/valueRather than striving towards a processual approach that lays emphasis on the collective effort involved in entrepreneurship, this paper critically engages directly with the heroic entrepreneur by exploring how this figure is a fantasy that structures desire. This paper shows how critical entrepreneurship studies could benefit from an approach that analyses how the cultural representation of business celebrates the heroic entrepreneur as a source of value creation. The authors further argue that it is the contradictions and impossibilities embodied in the figure of the heroic entrepreneur that carry its far-reaching appeal.
Come on out of the ghetto, please! – Building the future of entrepreneurship research
Authors: Baker Ted , Welter Friederike 
Published: March 2017

PurposeThe purpose of this paper is to make the argument that previously marginalized but now flourishing subfields of entrepreneurship research continue to provide insights that can form the basis for future entrepreneurship research that is more broadly practical and critical. What is currently core or “mainstream” in entrepreneurship research would then be seen as an important but rare special case.Design/methodology/approachThe essay briefly explores a number of illustrative themes that have emerged and become important in women’s entrepreneurship research (acknowledging that some similar themes have emerged in other subfields). These themes are used to suggest how broader application of such insights to theory-building about entrepreneurship in general – rather than “just” to “women’s entrepreneurship” – might greatly enrich the field.FindingsThe authors’ arguments suggest that research focused on ghettoized subfields such as women’s entrepreneurship challenge the assumptions of what entrepreneurship is and what it contributes. For example the richer perspective on motivations, goals, and outcomes and on the possibilities of emancipation that currently animate research on women’s entrepreneurship can improve the understanding of all entrepreneurship.Originality/valueToo much of current entrepreneurship research is both of limited practical value for “practitioners” and of little “critical value” for scholars interested in how things might work better. The authors argue that by broadening the set of goals, motivations, contexts and accomplishments that are taken as legitimate targets of study, entrepreneurship research can become both more practical and more critical and thus more broadly useful and legitimate.
Adaptive neural network visual servoing of dual-arm robot for cyclic motion
Authors: Qu Jiadi , Zhang Fuhai , Fu Yili , Li Guozhi , Guo Shuxiang 
Published: March 2017

Purpose
The purpose of this paper is to develop a vision-based dual-arm cyclic motion method, focusing on solving the problems of an uncertain grasp position of the object and the dual-arm joint-angle-drift phenomenon.

Design/methodology/approach
A novel cascade control structure is proposed which associates an adaptive neural network with kinematics redundancy optimization. A radial basis function (RBF) neural network in conjunction with a conventional proportional–integral (PI) controller is applied to compensate for the uncertainty of the image Jacobian matrix which includes the estimated grasp position. To avoid the joint-angle-drift phenomenon, a dual neural network (DNN) solver in conjunction with a PI controller and dual-arm-coordinated constraints is applied to optimize the closed-chain kinematics redundancy.

Findings
The proposed method was implemented on an industrial robotic MOTOMAN with two 7-degrees of freedom robotic arms. Two experiments of carrying a tray repeatedly and turning a steering wheel were carried out, and the results indicate that the closed-trajectories tracking is achieved successfully both in the image plane and the joint spaces with the uncertain grasp position, which validates the accuracy and realizability of the proposed PI-RBF-DNN control strategy.

Originality/value
The adaptive neural network visual servoing method is applied to the dual-arm cyclic motion with the uncertain grasp position of the object. The proposed method enhances the environmental adaptability of a dual-arm robot in a practical manipulation task.
Seamless autonomous navigation based on the motion constraint of the mobile robot
Authors: Chen Weina , Zeng Qinghua , Liu Jianye , Wang Huizhe 
Published: March 2017

Purpose
The purpose of this paper is to propose a seamless autonomous navigation method based on the motion constraint of the mobile robot, which is able to meet the practical need of maintaining the navigation accuracy during global positioning system (GPS) outages.

Design/methodology/approach
The seamless method uses the motion constraint of the mobile robot to establish the filter model of the system, in which the virtual observation about the speed is used to overcome the shortage of the navigation accuracy during GPS outages. The corresponding motion constraint model of the mobile robot is established. The proposed seamless navigation scheme includes two parts: the micro inertial navigation system (MINS)/GPS-integrated filter model and the motion constraint filter model. When the satellite signals are good, the system works on the MINS/GPS-integrated mode. If some obstacles block the GPS signals, the motion constraint measurement equation will be effective so as to improve the navigation accuracy of the mobile robot.

Findings
Three different vehicle tests of the mobile robot show that the seamless navigation method can overcome the shortage of the navigation accuracy during GPS outages, so as to improve the navigation performance in practical applications.

Originality/value
A seamless navigation system based on the motion constraint of the mobile robot is proposed to overcome the shortage of the navigation accuracy during GPS outages, thus improving the adaptability of the robot navigation.
Tele-operated propeller-type climbing robot for inspection of petrochemical vessels
Authors: Alkalla Mohamed Gouda , Fanni Mohamed A. , Mohamed Abdelfatah M. , Hashimoto Shuji 
Published: March 2017

Purpose
The purpose of this paper is to propose a new propeller-type climbing robot called EJBot for climbing various types of structures that include significant obstacles, besides inspection of industrial vessels made of various materials, including non-ferromagnetic material. The inspection includes capturing images for important spots and measuring the wall thickness.

Design/methodology/approach
The design mainly consists of two coaxial upturned propellers mounted on a mobile robot with four standard wheels. A new hybrid actuation system that consists of propeller thrust forces and standard wheel torques is considered as the adhesion system for this climbing robot. This system generates the required adhesion force to support the robot on the climbed surfaces. Dynamic simulation using ADAMS is performed and ensures the success of this idea.

Findings
Experimental tests to check the EJBot’s capabilities of climbing different surfaces, such as smooth, rough, flat and cylindrical surfaces like the real vessel, are successfully carried out. In addition, the robot stops accurately on the climbed surface at any desired location for inspection purposes, and it overcomes significant obstacles up to 40 mm.

Practical implications
This proposed climbing robot is needed for petrochemical and liquid gas vessels, where a regular inspection of the welds and the wall thickness is required. The interaction between the human and these vessels is dangerous and not healthy due to the harmful environment inside these vessels.

Originality/value
This robot utilizes propeller thrusts and wheel torques simultaneously to generate adhesion and traction forces. Therefore, a versatile robot able to climb different kinds of structures is obtained.
Design of an electromagnetic prismatic joint with variable stiffness
Authors: Zhao Yong , Yu Jue , Wang Hao , Chen Genliang , Lai Xinmin 
Published: March 2017

Purpose
This paper aims to propose an electromagnetic prismatic joint with variable stiffness. The joint can absorb the sudden shocks and improve the natural dynamics of robotics. The ability of regulating the output stiffness can also be used for force control in industrial applications.

Design/methodology/approach
Unlike some existing designs of variable stiffness joints (VSJs) in which the stiffness regulation is implemented using the stiffness adjustment motor and mechanisms, the main structure of the electromagnetic VSJ is a permanent magnet (PM) arranged inside coaxial cylinder coils. The adjustment of input current can cause the change of magnetic force between the PM and the cylinder coils, and thus leads to the variation of output stiffness.

Findings
According to the theoretical model, the output stiffness of the electromagnetic VSJ is linearly proportional to the input current. The experiments further indicate that the current-controlled stiffness can make the stiffness variation response of this VSJ more rapid for practical applications. Due to the large damping introduced by the copper-based self-lubrication bearings, the VSJ shows good properties in motion positioning and trajectory tracking.

Originality/value
In summary, the electromagnetic VSJ is compact in size and light in weight. It is possible to realize the online adaptability to work conditions with dynamic load by using this VSJ.
The value of textual haptic information in online clothing shopping
Authors: Rodrigues Tomé , Silva Susana C. , Duarte Paulo 
Published: March 2017

PurposeThe purpose of this paper is to evaluate the potential of textual haptic information to minimize the effects of need for touch (NFT) in global online environments by testing the effect of hands on description on consumer perception and intention to purchase.Design/methodology/approachThe study was developed in three stages. A total of 140 valid responses were obtained in stage three. Multiple linear regression models and paired-samples t-test were applied to test the hypotheses.FindingsThe results show that textual haptic information has a positive impact on consumers’ perception and on the intention to purchasing.Practical implicationsTo improve online sales firms should minimize the drawback of the inability of touching the product by providing textual haptic information.Originality/valueThe findings are especially valuable since the number of studies assessing NFT in online apparel commerce is currently very limited. Thus, this study adds new empirical evidences to existent body of knowledge and could assist the development of global marketing strategies for increasing online fashion sales.
Women’s activewear trends and drivers: a systematic review
Authors: O’Sullivan Grant Anthony , Hanlon Clare , Spaaij Ramon , Westerbeek Hans 
Published: March 2017

Purpose
The activewear industry would benefit from an evidence-based understanding of how activewear is incorporated into women’s lives and their changing participation in physical activity. Activewear brands may be missing the trend of women moving from organised sport to non-organised and individualised sport and recreation. The purpose of this paper is to explore the degree to which academic and industry research understood patterns and influences on female’s activewear consumption and identified what significant gaps are evident in understanding the drivers and industry trends that pertain to female consumers of activewear.

Design/methodology/approach
The systematic literature review sought academic and industry research papers. Articles were selected if they included female participants; and/or addressed consumer related information; and focussed on active wear. Article findings were thematically analysed.

Findings
Most literature exploring activewear consumption fails to take gender into consideration or explore unique female consumer profiles. Females are bringing activewear into other parts of their wardrobe and place more value on fashion, even for sports attire. Research identified the need for activewear brands to consider lifestyle, emotional and personality elements of consumer behaviour. However a specific focus on women’s branding was absent. Women’s age and generation influenced their activewear consumption. Although some industry reports discussed the shift in use of activewear, no studies explored the impact of the critical shift in women’s physical activity patterns on the activewear industry.

Originality/value
This review identifies the gap in knowledge regarding women’s activewear consumption patterns and needs, and the importance of reflecting the changes in female physical activity participation. It also links marketing and design of women’s activewear to the needs of female consumers based on their actual patterns and trends in physical activity. The findings are relevant to activewear researchers, brands, marketers and producers.