bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SONATA Data Format for Efficient Description of Large-Scale Network Models
Authors: Dai Kael , Hernando Juan , Billeh Yazan N. , Gratiy Sergey L. , Planas Judit , Davison Andrew P. , Dura-Bernal Salvador , Gleeson Padraig , Devresse Adrien , Dichter Benjamin K. , Gevaert Michael , King James G. , Van Geit Werner A. H. , Povolotsky Arseny V. , Muller Eilif , Courcol Jean-Denis , Arkhipov Anton 
Published: May 2019

AbstractIncreasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility.
Humans exploit robust locomotion by improving the stability of control signals
Authors: Santuz Alessandro , Brüll Leon , Ekizos Antonis , Schroll Arno , Eckardt Nils , Kibele Armin , Schwenk Michael , Arampatzis Adamantios 
Published: May 2019

AbstractIs the control of movement less stable when we walk or run in challenging settings? One might intuitively answer affirmatively, given that adding constraints to locomotion (e.g. rough terrain, age-related impairments, etc.) imply less stable movements. We investigated how young and old humans synergistically activate muscles during locomotion, when different perturbation levels are introduced. Of these control signals, called muscle synergies, we then analyzed the stability over time. Surprisingly, we found that perturbations and older age force the central nervous system to produce more stable signals. These outcomes show that robust locomotion in challenging settings is achieved by increasing the stability of control signals, whereas easier tasks allow for more unstable control.
cohorts: A Python package for clinical ‘omics data management
Authors: Giangreco Nicholas P. , Fine Barry , Tatonetti Nicholas P. 
Published: May 2019

AbstractSummaryPrecision medicine uses patient clinical and molecular characteristics to personalize diagnosis and treatment. This emerging discipline integrates multi-modal data into large-scale studies of human disease to make accurate individual-level predictions. The success of these studies will depend on the generalizability of the results, the ability of other researchers and clinicians to replicate studies, and the understandability of the methods used. Tools for data management and standardization are needed to promote flexible, transparent, and reproducible analyses. Here we present cohorts, a python package facilitating clinical and biomarker data management to enhance standardization and reproducibility of clinical findings.AvailabilityThe python package cohorts is available at http://www.github.com/ngiangre/cohorts.CONTACTNPT2105@CUMC.COLUMBIA.EDU
Experimental evidence of invasion facilitation in the zebra mussel-killer shrimp system
Authors: Rolla Matteo , Consuegra Sofia , Carrington Ellie , Hall David , Garcia de Leaniz Carlos 
Published: May 2019

AbstractInvasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical facilitation is not an acquired or learned trait. Our results have implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because invasion facilitation could significantly increase establishment success. Failure to consider invasion facilitation may underestimate the risk of establishment and likely impact of some aquatic invaders.
Intersection of motor volumes predicts the outcome of ambush predation of larval zebrafish
Authors: Bhattacharyya Kiran , McLean David L. , MacIver Malcolm A. 
Published: May 2019

AbstractThe escape maneuvers of animals are key determinants of their survival. Consequently these maneuvers are under intense selection pressure. Current work indicates that a number of escape maneuver parameters contribute to survival including response latency, escape speed, and direction. This work has found that the relative importance of these parameters is context dependent, suggesting that interactions between escape maneuver parameters and the predatory context together determine the likelihood of escape success. However, it is unclear how escape maneuver parameters interact to contribute to escape success across different predatory contexts. To clarify these issues, we investigated the determinants of successful escape maneuvers by analyzing the responses of larval zebrafish to the attacks of dragonfly nymphs. We found that the strongest predictor of the outcome was the time needed for the nymph to reach the fish’s initial position at the onset of the attack, measured from the time that the fish initiates its escape response. We show how this result is related to the intersection of the swept volume of the nymph’s grasping organs with the volume containing all possible escape trajectories of the fish. By analyzing the intersection of these volumes, we compute the survival benefit of recruiting the Mauthner cell, a neuron in anamniotes devoted to producing escapes. We discuss how escape maneuver parameters interact in determining escape response. The intersection of motor volume approach provides a framework that unifies the influence of many escape maneuver parameters on the likelihood of survival.
3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples
Authors: Lin Ruisheng , Clowsley Alexander H. , Lutz Tobias , Baddeley David , Soeller Christian 
Published: May 2019

AbstractAssessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time-and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.
Vascular endothelial growth factor (VEGF) expression and neuroinflammation is increased in the frontopolar cortex of individuals with autism spectrum disorder
Authors: Gnanasekaran Aswini , Kelchen Megan N. , Brogden Nicole K. , Smith Ryan M. 
Published: May 2019

AbstractAutism spectrum disorder (ASD) etiology is a complex mixture of genetic and environmental factors, the relative contributions of which varies across patients. Despite complex etiology, researchers observe consistent neurodevelopmental features in ASD patients, notably atypical forebrain cortical development. Growth factors, cytokines, and chemokines are important mediators of forebrain cortical development, but have not been thoroughly examined in brain tissues from individuals with autism. Here, we performed an integrative analysis of RNA and protein expression using frontopolar cortex tissues dissected from individuals with ASD and controls, hypothesizing that ASD patients will exhibit aberrant expression of growth factors, cytokines, and chemokines critical for neurodevelopment. We performed group-wise comparisons of RNA expression via RNA-Seq and growth factor, cytokine, and chemokine expression via multiplex enzyme-linked immunosorbent assay (ELISA). We also analyzed single cell sequencing data from the frontopolar cortex of typically developed individuals to identify cell types that express the growth factors we found differentially expressed in ASD. Our RNA-Seq analysis revealed 11 differentially expressed genes in ASD versus control brains, the most significant of which encodes for vascular endothelial growth factor (VEGF-A). Both RNA and protein levels of VEGF-A were upregulated in ASD brains. Our single cell analysis revealed that VEGF is expressed primarily by non-neuronal cells. We also found that the differentially expressed genes from our RNA-Seq analysis are enriched in microglia. The increased VEGF-A expression we observed in ASD, coupled with the enrichment of differentially expressed genes in microglia, begs the question of the role VEGF-A is playing in ASD. Microglia activation, as indicated by our RNA-Seq results, and the VEGF-A isoform expression we see in the ASD cortex, leads us to conclude that VEGF-A is playing a pro-inflammatory role, perhaps with unwanted long-term consequences for neurodevelopment.
Surprise response as a probe for compressed memory states
Authors: Levi-Aharoni Hadar , Shriki Oren , Tishby Naftali 
Published: May 2019

AbstractThe limited capacity of recent memory inevitably leads to partial memory of past stimuli. There is also evidence that behavioral and neural responses to novel or rare stimuli are dependent on one’s memory of past stimuli. Thus, these responses may serve as a probe of different individuals’ remembering and forgetting characteristics. Here, we utilize two lossy compression models of stimulus sequences that inherently involve forgetting, which in addition to being a necessity under many conditions, also has theoretical and behavioral advantages. One model is based on a simple stimulus counter and the other on the Information Bottleneck (IB) framework. These models are applied to analyze a novelty-detection event-related potential commonly known as the P300. The trial-by-trial variations of the P300 response, recorded in an auditory oddball paradigm, were subjected to each model to extract two stimulus-compression parameters for each subject: memory length and representation accuracy. These parameters were then utilized to estimate the subjects’ recent memory capacity limit under the task conditions. The results, along with recently published findings on single neurons on the IB model, underscore how a lossy compression framework can be utilized to account for trial-by-trial variability of neural responses at different spatial scales and in different individuals, while at the same time providing estimates of individual memory characteristics at different levels of representation using a theoretically-based parsimonious model.Author summarySurprise responses reflect expectations based on preceding stimuli representations, and hence can be used to infer the characteristics of memory utilized for a task. We suggest a quantitative method for extracting an individual estimate of effective memory capacity dedicated for a task based on the correspondence between a theoretical surprise model and electrophysiological single-trial surprise responses. We demonstrate this method on EEG responses recorded while participants were performing a simple auditory task; we show the correspondence between the theoretical and physiological surprise, and calculate an estimate of the utilized memory. The generality of this framework allows it to be applied to different EEG features that reflect different modes and levels of the processing hierarchy, as well as other physiological measures of surprise responses. Future studies may use this framework to construct a handy diagnostic tool for a quantitative, individualized characterization of memory-related disorders.
Governance and transparency of the Chinese charity foundations
Authors: Xue Qingmei , Niu Yuning 
Published: May 2019

Purpose
The purpose of this paper is to investigate the relation between various governance mechanisms and the transparency level by using a sample of the top 200 Chinese charity foundations on net assets.

Design/methodology/approach
Three types of governance forces are examined, including the board, the management and the capital providers. The Foundation Transparency Index (FTI), published by Chinese Foundation Center, is used as a proxy for the transparency level.

Findings
The evidences show that for the public foundations that can elicit fund from the public, providing compensation to the foundation managers could encourage them to increase the transparency level. Furthermore, the sophisticated donors also represent a useful governance force. For the non-public foundations that can only seek donors through private contacts, getting more members in their supervisory board and having more government grants are helpful in improving their transparency. The results are robust even after controlling for lagged FTI and other characteristics of foundations. And the transparency level is positively associated with the international connections for both types of foundations.

Research limitations/implications
This research is based on a limited sample. The results can hardly generalize to the other smaller foundations. However, the results are still meaningful for to the legislators, regulators and managers of Chinese charity foundations. Because the result implies that the overseas donors are effective monitors that could improve the foundation transparency, the newly published law may weaken this governance force.

Originality/value
This is the first paper that studies the governance of Chinese charity foundations. By using a third-party index to proxy for the transparency, the results complement existing literature.
Coerced CSR: lessons from consumer values and purchasing behavior
Authors: Ijabadeniyi Abosede , Govender Jeevarathnam Parthasarathy 
Published: May 2019

PurposeThe purpose of this paper is to investigate the underlying corporate social responsibility (CSR) factors which trigger consumers’ scrutiny of corporate behavior in the purchasing experience. There is more focus on how the direct effects of CSR can predict consumer behavior than the expression of value-based purchasing habits, especially in relation to how the multidimensionality of consumers’ expectations of CSR indirectly informs such behavior.Design/methodology/approachMall-intercept survey interviews were conducted with 411 shoppers across five shopping malls in South Africa. Data were based on the emotional, social and functional values consumers derive from the purchasing experiencevis-à-viseconomic, legal, ethical and philanthropic expectations of CSR and analyzed using the path analysis technique of structural equation modeling.FindingsIt was found that the relationship between consumers’ sense of value and purchasing behavior is mediated by perceived fulfillment of legal expectations of CSR (a primary redressing tool). Conversely, the fulfillment of ethical and economic CSR expectations (secondary redressing tools) serves as moderators of the relationship.Research limitations/implicationsThe benefit of approaching corporate communication from a value-based perspective is a proactive risk mitigation strategy. Consumers’ sense of value in the purchasing experience is triggered by companies’ adherence to institutionalized law on corporate behavior and reinforced by compliance to code of ethics and financial viability.Practical implicationsThis study offers insights for understanding how consumers redress corporate misconduct during crisis through the buying experience and explains how such understanding can be used to better predict and manage crisis communication.Social implicationsThe findings of this study suggest that CSR and corporate communication practices should be informed by the taken-for-granted assumptions which underpin espoused consumer values, where negligence of unspoken patterns of CSR-based consumer behavior could signal a crisis risk.Originality/valueThis study offers a model which demonstrates for the first time that consumers implicitly utilize CSR to redress corporate misconduct in the purchasing experience.
Inclusiveness and effectiveness of agricultural cooperatives: recent evidence from Ethiopia
Authors: Wassie Solomon Bizuayehu , Kusakari Hitoshi , Masahiro Sumimoto 
Published: May 2019

Purpose
Using a recent rural farm household survey, the purpose of this paper is to investigate inclusiveness and effectiveness of agricultural cooperatives in Ethiopia.

Design/methodology/approach
The study employs a logit model to examine inclusiveness and an endogenous switching regression (ESR) model to evaluate the effectiveness of agricultural cooperatives.

Findings
The results show that agricultural cooperatives are less inclusive of land-poor and illiterate households. On the other hand, the estimated results indicate that cooperatives effectively improved agricultural performance and welfare of its member households – i.e. membership in cooperatives increases yield and income by 1.37 quintal/hectare and 1,804 birr, respectively. Moreover, the result shows that marketing cooperatives effectively increased marketed surplus of their members by 34 percent.

Research limitations/implications
The study has important implications regarding the ways to improve the effectiveness and/or inclusiveness of agricultural cooperatives.

Originality/value
While accounting for the collective behavior of cooperatives, this study uses multiple outcome variables in examining the effectiveness of cooperatives in Ethiopia. Furthermore, this paper employs the ESR model and accounts for potential problems in estimating impact using non-experimental data.
Employee social sustainability: prioritizing dimensions in the UAE’s airlines industry
Authors: Al Marzouqi Abdulla Hasan , Khan Mehmood , Hussain Matloub 
Published: May 2019

PurposeThis paper aims to identify and prioritize the dimensions that impact employee social sustainability in the airline industry in the United Arab Emirates (UAE).Design/methodology/approachThe five main criteria (employee well-being, communication, management support, reward and control system and training) and 18 sub-criteria were identified from the literature. The sample comprised four experts covering the HR, finance and training functions from a major UAE airline organization. Applying the analytical-hierarchy-process (AHP) methodology resulted in obtaining priority weights for the factors assigned to employee-social-sustainability implementation.FindingsManagement support was found to have the highest priority among the study dimensions impacting employee social sustainability. Surprisingly, reward system was found to be the least important dimension.Research limitations/implicationsThe study was carried out on a single airline organization, limiting the generalizability of the findings. Future studies should be extended to cater to different organizational contexts and varying operational conditions.Practical implicationsThe findings should be of value to human resource management and policymakers in developing countries, such as the UAE, where employee social sustainability should be sought as a means to develop an efficient and sustainable workforce in different industrial sectors.Originality/valueThis study is among the few pioneering studies that focus on employee social sustainability. The use of AHP to prioritize employee-social-sustainability dimensions is also considered pioneering within the field and is anticipated to support future studies, and a deeper understanding, of employee social sustainability.
Green cost calculus for corporate environmental responsibility
Authors: Ghosh Ray Kamal 
Published: May 2019

PurposeThe purpose of this study is to show that corporations may resort to legal compliance instead of acting voluntarily towards abatement of environmental damages as a strategy for improving their reputation.Design/methodology/approachBased on the natural philosophy and postulate of business, theoretical models have been developed to justify the purpose of this paper. Financial impacts of Indian revenue law on environmental damage prevention by the polluting firms have been gauged mathematically.FindingsCorporate environmental responsibilities have seemed to be more reputation-led than innovation-led or efficiency-led. Reputation-led environmental responsibilities can have ways to bypass innovations and some firms can simply comply with regulations at the society’s cost (may be to a sizeable extent). If penalty is imposed on companies in the form of taxation for damaging the environment, then companies get chances to pass the financial burden to the shareholders in the form of lower dividend pay-outs. Unless the capital market supports corporate green initiatives, there may be destruction of shareholder wealth.Research limitations/implicationsExtensive empirical analysis have not been conducted as the paper concentrates on developing theoretical understanding of the models of “green cost”.Practical implicationsThe exploration and outcomes of this paper can offer several directions to the government, business and social activists in articulating green economic policy for the benefits of all.Social implicationsThe civil society will understand better what the corporate environmental responsibility really means for them.Originality/valueThis paper has made a modest endeavour to develop theoretical models of both “green cost internalisation” and “green cost externalisation”. It has paved the path for further deliberations and research.