bluuebunny/crossref_metadata_2025_split huggingface dataset:
MEG/EEG group study with MNE: recommendations, quality assessments and best practices
Authors: Jas Mainak , Larson Eric , Engemann Denis , Leppäkangas Jaakko , Taulu Samu , Hämäläinen Matti , Gramfort Alexandre 
Published: December 2017

AbstractCognitive neuroscience questions are commonly tested with experiments that involve a cohort of subjects. The cohort can consist of a handful of subjects for small studies to hundreds or thousands of subjects in open datasets.While there exist various online resources to get started with the analysis of magnetoencephalography (MEG) or electroencephalography (EEG) data, such educational materials are usually restricted to the analysis of a single subject. This is in part because data from larger group studies are harder to share, but also analyses of such data are often require subject-specific decisions which are hard to document.This work presents the results obtained by the reanalysis of an open dataset from Wakeman and Henson (2015) using the MNE software package. The analysis covers preprocessing steps, quality assurance steps, sensor space analysis of evoked responses, source localization, and statistics in both sensor and source space. Results with possible alternative strategies are presented and discussed at different stages such as the use of high-pass filtering versus baseline correction, tSSS versus SSS, the use of a minimum norm inverse versus LCMV beamformer, and the use of univariate or multivariate statistics. This aims to provide a comparative study of different stages of M/EEG analysis pipeline on the same dataset, with open access to all of the scripts necessary to reproduce this analysis.
50 Hz volumetric functional imaging with continuously adjustable depth of focus
Authors: Lu Rongwen , Tanimoto Masashi , Koyama Minoru , Ji Na 
Published: December 2017

AbstractUnderstanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), which turns frame rate into volume rate by extending the excitation focus in axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the focal length. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 μm depth in larval zebrafish at 50 Hz volume rate with adjustable imaging thickness.
ClassificaIO: machine learning for classification graphical user interface
Authors: Roushangar Raeuf , Mias George I. 
Published: December 2017

AbstractMachine learning methods are being used routinely by scientists in many research areas, typically requiring significant statistical and programing knowledge. Here we present ClassificaIO, an open-source Python graphical user interface for machine learning classification for the scikit-learn Python library. ClassificaIO provides an interactive way to train, validate, and test data on a range of classification algorithms. The software enables fast comparisons within and across classifiers, and facilitates uploading and exporting of trained models, and both validation and testing data results. ClassificaIO aims to provide not only a research utility, but also an educational tool that can enable biomedical and other researchers with minimal machine learning background to apply machine learning algorithms to their research in an interactive point-and-click way. The ClassificaIO package is available for download and installation through the Python Package Index (PyPI) (http://pypi.python.org/pypi/ClassificaIO) and it can be deployed using the “import” function in Python once the package is installed. The application is distributed under an MIT license and the source code is publicly available for download (for Mac OS X, Linux and Microsoft Windows) through PyPI and GitHub (http://github.com/gmiaslab/ClassificaIO, andhttps://doi.org/10.5281/zenodo.1320465).
Juvenile honest food solicitation and parental investment as a life history strategy: a kin demographic selection model
Authors: Garay József , Csiszár Villő , Móri Tamás F. , Szilágyi András , Varga Zoltán , Számadó Szabolcs 
Published: December 2017

AbstractParent-offspring communication remains an unresolved challenge for biologist. The difficulty of the challenge comes from the fact that it is a multifaceted problem with connections to life-history evolution, parent-offspring conflict, kin selection and signalling. Previous efforts mainly focused on modelling resource allocation at the expense of the dynamic interaction during a reproductive season. Here we present a two-stage model of begging where the first stage models the interaction between nestlings and parents within a nest and the second stage models the life-history trade-offs. We show in an asexual population that honest begging results in decreased variance of collected food between siblings, which leads to mean number of surviving offspring. Thus, honest begging can be seen as a special bet-hedging against informational uncertainty, which not just decreases the variance of fitness but also increases the arithmetic mean.Author SummaryParent-offspring communication is a fascinating problem that captures the attention of scientist and layman alike. Parent-offspring interaction is the first interaction with non-self in the life of most young birds and mammals. The future life success of such young animals crucially depends on how successful they are in interacting and communicating with their parents. This communication has different functions: it is important for the offspring to solicit food from the parent and it is important for the parent to be informed about the state (hunger level) of the offspring. There is an optimization problem on top of this level: the parent has to ‘decide’ what part of the available resources should be allocated to the offspring and what part should she keep for herself. Here we show in a probabilistic model that the honest phenotype -where offspring beg only if they are hungry-has a greater growth rate than a selfish type - which begs regardless of its hunger level. This result holds in asexual populations; here honesty serves as a reduction uncertainty for the parents. The improved decision making of the parents -in turn-increases the survival of the offspring as well.
One problem, too many solutions: How costly is honest signalling of need?
Authors: Számadó Szabolcs , Czégel Dániel , Zachar István 
Published: December 2017

AbstractThe “cost of begging” is a prominent prediction of costly signalling theory, suggesting that offspring begging has to be costly in order to be honest. More specifically, it predicts that there is a single cost function for the offspring (depending on e.g. offspring quality) that maintains honesty and it must be proportional to parent’s fitness loss. Here we show another interpretation of the cost. We demonstrate that cost, proportional to the fitness gain of the offspring, also results in honest signalling. Since the loss of the parent does not necessarily coincide with the gain of the offspring, it is provable that any linear combination of the two cost functions (one proportional to parent’s loss, one to offspring’s gain) also leads to honest signalling. Our results, applied for a specific model, support the previous general conclusion that signalling games have different cost functions for different equilibria. Consequently, costly signalling theory cannot predict a unique equilibrium cost in signalling games especially in case of parent-offspring conflicts. As an important consequence, any measured equilibrium cost in real cases has to be compared both to the parent’s fitness loss and to the offspring’s fitness gain in order to provide meaningfully interpretation.
Short-term hyperglycaemia induces motor defects in C. elegans
Authors: Shirdhankar Runita , Sorathia Nabila , Rajyadhyaksha Medha 
Published: December 2017

AbstractHyperglycaemia causes various intracellular changes resulting in oxidative stress leading to loss of integrity and cell death. While cellular effects of hyperglycaemia have been reported extensively there is no clarity on whether the cellular changes translate into alterations in behaviour. Study of behavioural alterations also provides a sublime top-down approach to dapple the putative systems affected due to hyperglycaemic stress. Hence, this aspect of effect of hyperglycaemia deserves attention as it could be an early indicator of neurodegenerative changes. Caenorhabditis elegans is an excellent model to address these questions since it has a simple nervous system and the ability to respond to various cues.We have investigated alteration in behaviour which involves various motor and sensory function of the C. elegans nervous system under hyperglycaemia. Exposure of C. elegans to 400 mM glucose for 4hr did not kill the worm but gave rise to decreased number of progeny, exhibiting other aberrant behaviours. This dosage was considered to cause hyperglycaemic stress and used further in the studies. Various assays that quantified behaviour, such as feeding (pharyngeal pumping/min), locomotion (distance travelled by the worms/min), olfactory response towards Butanol (response index) and gustatory response NaCl (response index) were conducted under both normal and hyperglycaemic conditions. The behavioural alterations were validated by scrutinizing changes in level of Acetylchloine which regulates motor behaviour and morphology of chemosensory neurons. Our results indicate that hyperglycaemia alters motor behaviour of the worm which was validated by a reduction in ACh levels. However, chemosensory systems were robust enough to resist reduction in neuronal integrity due to hyperglycaemic assault.
Dynamic Optimization with Particle Swarms (DOPS): A meta-heuristic for parameter estimation in biochemical models
Authors: Sagar Adithya , LeCover Rachel , Shoemaker Christine , Varner Jeffrey 
Published: December 2017

AbstractBackgroundMathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Parameter estimation typically involves expensive function evaluations and noisy data, making it difficult to quickly obtain optimal solutions. Further, biochemical models often have many local extrema which further complicates parameter estimation. Toward these challenges, we developed Dynamic Optimization with Particle Swarms (DOPS), a novel hybrid meta-heuristic that combined multi-swarm particle swarm optimization with dynamically dimensioned search (DDS). DOPS uses a multi-swarm particle swarm optimization technique to generate candidate solution vectors, the best of which is then greedily updated using dynamically dimensioned search.ResultsWe tested DOPS using classic optimization test functions, biochemical benchmark problems and real-world biochemical models. We performed trials with function evaluations per trial, and compared the performance of DOPS with other commonly used meta-heuristics such as differential evolution (DE), simulated annealing (SA) and dynamically dimensioned search (DDS). On average, DOPS outperformed other common meta-heuristics on the optimization test functions, benchmark problems and a real-world model of the human coagulation cascade.ConclusionsDOPS is a promising meta-heuristic approach for the estimation of biochemical model parameters in relatively few function evaluations. DOPS source code is available for download under a MIT license at http://www.varnerlab.org.
The Tandem Duplicator Phenotype is a prevalent genome-wide cancer configuration driven by distinct gene mutations
Authors: Menghi Francesca , Barthel Floris P , Yadav Vinod , Tang Ming , Ji Bo , Tang Zhonghui , Carter Gregory W. , Ruan Yijun , Scully Ralph , Verhaak Roel G. W. , Jonkers Jos , Liu Edison T. 
Published: December 2017

SUMMARYThe tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 Kb, 231 Kb, and 1.7 Mb. TDPs with prominent ~11 Kb TDs feature the conjoint loss of TP53 and BRCA1. TDPs with ~231 Kb and ~1.7 Mb TDs associate with CCNE1 pathway activation or CDK12 disruptions, in conjunction with TP53 mutations. We prove the driver role of TP53 and BRCA1 abrogation for TDP induction by generating short-span TDP mammary tumors in genetically modified mouse models harboring deleterious mutations in only these two genes. Lastly, heterogeneous combinations of mutations mediated by TDs are selected for and contribute to the oncogenic burden of TDP tumors.
Newly independent nations and large engineering projects: the case of the Volta River Project
Authors: Amankwah-Amoah Joseph , Osabutey Ellis L.C. 
Published: December 2017

PurposeThe purpose of this paper is to explicate how newly independent nations combined local and international resources to plan and build large engineering projects aimed at enhancing economic development. It discusses the key factors and issues related to the planning and building of the Akosombo Dam and related townships from 1962 to 1967.Design/methodology/approachThe assessment is based on the archival information from the Volta River Authority together with other archival government data and interview transcripts before, during and after the completion (from the 1950s to the 1960s) of the Volta River Project (VRP).FindingsThe paper presents insights from the VRP in newly independent Ghana and demonstrates how multiple international firms combine with host country stakeholders to usher in one of the most important engineering projects in post-colonial Africa. It also highlights how poor bargaining power and weak integration of the project outcome to future development objectives, with negligence by succeeding political actors, could inhibit the full achievement of intended long-term project outcomes.Research limitations/implicationsMost of the conclusions are drawn from a single project within one country and would need to be supported by additional multi-country research. The study also presents an opportunity to explore how lessons learnt could influence policymaking in new, large and complex infrastructure projects.Originality/valueThe paper reviews antecedents, processes and outcomes of a major post-independence infrastructure project in a sub-Saharan African country.
Human-computer interaction and value co-creation in electronic service
Authors: Li Lei , Huang Qingyun , Yeung KwanHo , Jian Zhaoquan 
Published: December 2017

Purpose
The purpose of this paper is to investigate the effect of human-computer interaction (HCI) on customers’ perceived electronic service (e-service) value and the mediating role of task-technology fit (TTF) in that effect.

Design/methodology/approach
This paper develops a model based on service-dominant logic (SDL) and TTF theory, and validates it using a hierarchical regression with the data collected from 634 online banking customers in Guangdong Province and Guangxi Zhuang Autonomous Region in China.

Findings
The findings reveal that HCI in e-service contexts comprises five components. Three fundamental components (i.e. technology functionality, customer technology readiness and task routine) contribute to value co-creation. Two core components (i.e. interaction between customer technology readiness and technology functionality, and interaction between task routine and technology functionality) are inhibitors, but the inhibitory effect of the former is only significant in the Guangdong sample. TTF takes a mediating role in these relationships, but the mediating effect of the former core component is only significant in the Guangdong sample.

Originality/value
This paper explains two basic questions about the trigger points of value co-creation in e-service contexts (i.e. what their operational definitions are and how to measure them) and unlocks the “black box” of value co-creation by taking TTF as a mediator. SDL and TTF theory are extended. The paper provides suggestions for how practitioners can efficiently advance value co-creation with customers.
Optimising quantity of manufacturing and remanufacturing in an electric vehicle battery closed-loop supply chain
Authors: Gu Xiaoyu , Ieromonachou Petros , Zhou Li , Tseng Ming-Lang 
Published: December 2017

PurposeBatteries installed on electric vehicles (EVs) should normally be removed when their capacity falls to 70-80 per cent, but they are still usable for other purposes, such as energy storage. This paper studies an EV battery closed-loop supply chain (CLSC) consisting of a battery manufacturer and a remanufacturer. The manufacturer produces new batteries by using natural resources, while the remanufacturer collects returned batteries and makes decisions based on the return quality, that is, to reuse or recycle. The purpose of this paper is to maximise the individual profits through optimising the amount of manufacturing and remanufacturing, respectively, and optimising the purchase price of returned batteries.Design/methodology/approachBased on the Nash equilibrium, this paper develops a three-period model in the CLSC. In period 1, batteries are made from raw materials; in period 2, returned batteries from period 1 are sorted into low quality and high quality. Some high-quality returns can be reused for other purposes while those non-reusable returns are recycled into materials. In period 3, all the returns are recycled into materials. The analytical results are derived.FindingsThe result of the analyses suggest that first, among the variables that affect the (re-)manufacturing decision, the purchase price for returned batteries plays a critical role. In particular, the price of low-quality returns has more influence than the price of high quality returns. Second, the higher purchase price for re-usable returns does not necessarily lead to a higher return rate of reusable returns. Third, the manufacturer’s profit is normally higher than the remanufacturer’s. This suggests the need to design incentives to promote the remanufacturing sector. And finaly, although it is appreciated that maximising the utilisation of batteries over the life-cycle would benefit the environment, the economic benefit needs further investigation.Originality/valueAlthough the CLSC has been widely studied, studies on the EV battery CLSC are scarce. The EV battery CLSC is particularly challenging in terms of the reusability of returns because used EV batteries cannot be reused for the original purpose, which complicates CLSC operations. This paper explores the interrelationship between manufacturer and remanufacturer, explaining the reasons why recycling is still underdeveloped, and suggests the possibility of enhancing remanufacturing profitability.
Understanding consumers’ continuance intention to contribute online reviews
Authors: Xiang Li , Zheng Xiabing , Zhang Kem Z.K. , Lee Matthew K.O. 
Published: December 2017

PurposeThe purpose of this paper is to integrate broaden theoretical perspectives in the investigation of the key antecedents of consumers’ continuous review contribution behavior on restaurant guide online opinion platforms (OOPs). Integrating both rational and relational theoretical perspectives with an extension of the investment model, a research model was proposed to explain what factors influence consumers’ intention to continuously contribute electronic WOM (eWOM) on OOPs.Design/methodology/approachThe research model was empirically tested with an online survey study of 438 eWOM contributors from a leading Chinese restaurant guide OOP, Dianping.com.FindingsThe results indicated that satisfaction, affective commitment, and continuance commitment were key determinants of consumers’ continuance intention to contribute eWOM on the platform. Satisfaction was driven by concern for other consumers, social benefits, platform assistance, and venting negative feelings. Quality of alternatives and investment size significantly affected continuance commitment.Research limitations/implicationsThe selection of respondents is bound to the China area within a particular OOP, although the chosen OOP is a leading one in China. In addition, this study focuses on the perspective of commitment, but some social factors are neglected.Originality/valueThis paper provides an integrated theoretical framework to explore the factors determining consumers’ continuance intention to contribute restaurant reviews on OOPs. From both rational and relational theoretical perspectives, the proposed model reveals the factors that encourage consumers to continue contributing eWOM on OOPs.
IoT-based production logistics and supply chain system – Part 2
Authors: Tu Mengru , K. Lim Ming , Yang Ming-Fang 
Published: December 2017

Purpose
The purpose of this paper is threefold: to present internet of things (IoT)-based cyber-physical system (CPS) architecture framework to facilitate the integration of IoT and CPS; to implement an IoT-based CPS prototype based on the architecture framework for a PL application scenario of in a case study; and to devise evaluation methods and conduct experimental evaluations on an IoT-based CPS prototype.

Design/methodology/approach
The design research method, case study, emulation experiment method, and cost-benefit analysis are applied in this research. An IoT-based CPS architecture framework is proposed, and followed by the development of prototype system and testbed platform. Then, the emulation and experimental evaluation of IoT-based CPS are conducted on the testbed, and the experimental results are analyzed.

Findings
The emulation experiment results show that the proposed IoT-based CPS outperforms current barcode-based system regarding labor cost, efficiency, and operational adaptiveness. The evaluation of the IoT-based CPS prototype indicates significant improvements in PL tasks and reduced part inventory under a dynamic changing shop-floor environment.

Practical implications
The case study shows that the proposed architecture framework and prototype system can be applied to many discrete manufacturing industries, such as automobile, airplane, bicycle, home appliance, and electronics.

Originality/value
The proposed IoT-based CPS is among the first to address the need to integrate IoT and CPS for PL applications, and to conduct experimental evaluations and cost-benefit analysis of adopting IoT-based CPS for PL. This paper also contributes to the IoT research by using diverse research methods to offer broader insights into understanding IoT and CPS.