bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepRF: Ultrafast population receptive field mapping with deep learning
Authors: Thielen Jordy , Güçlü Umut , Güçlütürk Yagmur , Ambrogioni Luca , Bosch Sander E. , van Gerven Marcel A. J. 
Published: August 2019

AbstractPopulation receptive field (pRF) mapping is an important asset for cognitive neuroscience. The pRF model is used for estimating retinotopy, defining functional localizers and to study a vast amount of cognitive tasks. In a classic pRF, the cartesian location and receptive field size are modeled as a 2D Gaussian kernel in visual space and are estimated by optimizing the fit between observed responses and predicted responses. In the standard framework this is achieved using an iterative gradient descent algorithm. This optimization is time consuming because the number of pRFs to fit (e.g., fMRI voxels) is typically large. This computation time increases further with the complexity of the pRF model (e.g., adding HRF parameters, surround suppression and uncertainty measures). Here, we introduce DeepRF, which uses deep convolutional neural networks to estimate pRFs. We compare the performance of DeepRF with that of the conventional method using a synthetic dataset for which the ground truth is known and an empirical dataset. We show that DeepRF achieves state-of-the-art performance while being more than 3 orders of magnitude faster than the conventional method. This enables easier and faster modeling of more complex pRF models, resolving an important limitation of the conventional approach.
Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination
Authors: Sarkar Sukanta , Sinha Sudipta Kumar , Levine Herbert , Jolly Mohit Kumar , Dutta Partha Sharathi 
Published: August 2019

AbstractIn the vicinity of a tipping point, critical transitions occur when small changes in an input condition causes sudden, large and often irreversible changes in the state of a system. Many natural systems ranging from ecosystems to molecular biosystems are known to exhibit critical transitions in their response to stochastic perturbations. In diseases, an early prediction of upcoming critical transitions from a healthy to a disease state by using early warning signals is of prime interest due to potential application in forecasting disease onset. Here, we analyze cell-fate transitions between different phenotypes (epithelial, hybrid epithelial/mesenchymal (E/M) and mesenchymal states) that are implicated in cancer metastasis and chemoresistance. These transitions are mediated by a mutually inhibitory feedback loop microRNA-200/ZEB driven by the levels of transcription factor SNAIL. We find that the proximity to tipping points enabling these transitions among different phenotypes can be captured by critical slowing down based early warning signals, calculated from the trajectory of ZEB mRNA level. Further, the basin stability analysis reveals the unexpectedly large basin of attraction for a hybrid E/M phenotype. Finally, we identified mechanisms that can potentially elude the transition to a hybrid E/M phenotype. Overall, our results unravel the early warning signals that can be used to anticipate upcoming epithelial-hybrid-mesenchymal transitions. With the emerging evidence about the hybrid E/M phenotype being a key driver of metastasis, drug resistance, and tumor relapse; our results suggest ways to potentially evade these transitions, reducing the fitness of cancer cells and restricting tumor aggressiveness.Significance StatementEpithelial-hybrid-mesenchymal transitions play critical roles in cancer metastasis, drug resistance, and tumor relapse. Recent studies have proposed that cells in a hybrid epithelial/mesenchymal phenotype may be more aggressive than those on either end of the spectrum. However, no biomarker to predict upcoming transitions has been identified. Here, we show that critical slowing down based early warning signals can detect sudden transitions among epithelial, hybrid E/M, and mesenchymal phenotypes. Importantly, our results highlight how stable a hybrid E/M phenotype can be, and how can a transition to this state be avoided. Thus, our study provides valuable insights into restricting cellular plasticity en route metastasis.
Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal
Authors: Kaya Koray D. , Chen Holly Y. , Brooks Matthew J. , Kelley Ryan A. , Shimada Hiroko , Nagashima Kunio , de Val Natalia , Drinnan Charles T. , Gieser Linn , Kruczek Kamil , Erceg Slaven , Li Tiansen , Lukovic Dunja , Adlakha Yogita K. , Welby Emily , Swaroop Anand 
Published: August 2019

ABSTRACTRetinal organoids generated from human pluripotent stem cells exhibit considerable variability in temporal dynamics of differentiation. To assess the maturity of neural retina in vitro, we performed transcriptome analyses of developing organoids from human embryonic and induced pluripotent stem cell lines. We show that the developmental variability in organoids was reflected in gene expression profiles and could be evaluated by molecular staging with the human fetal and adult retinal transcriptome data. We also demonstrated that addition of 9-cis retinal, instead of widely-used all-trans retinoic acid, accelerated rod photoreceptor differentiation in organoid cultures, with higher rhodopsin expression and more mature mitochondrial morphology evident by day 120. Our studies thus provide an objective transcriptome-based modality for determining the differentiation state of retinal organoids, which should facilitate disease modeling and evaluation of therapies in vitro.Summary StatementThree-dimensional organoids derived from human pluripotent stem cells have been extensively applied for investigating organogenesis, modeling diseases and development of therapies. However, substantial variations within organoids pose challenges for comparison among different cultures and studies. We generated transcriptomes of multiple distinct retinal organoids and compared these to human fetal and adult retina gene profiles for molecular staging of differentiation state of the cultures. Our analysis revealed the advantage of using 9-cis retinal, instead of the widely-used all-trans retinoic acid, in facilitating rod photoreceptor differentiation. Thus, a transcriptome-based comparison can provide an objective method to uncover the maturity of organoid cultures across different lines and in various study platforms.
Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing
Authors: Kleftogiannis Dimitrios , Ho Danliang , Liew Jun Xian , Poon Polly , Gan Anna , Ng Raymond Chee-Hui , Tan Benita Kiat-Tee , Tay Kiang Hiong , Lim Swee-Ho , Tan Gek San , Shih Chih Chuan , Lim Tony , Lee Ann Siew-Gek , Tan Iain , Yap Yoon-Sim , Ng Sarah 
Published: August 2019

AbstractAnalysis of circulating cell-free DNA (cfDNA) data has opened new opportunities for characterizing tumour mutational landscapes with many applications in genomic-driven oncology. We developed a customized targeted cfDNA sequencing approach for breast cancer (BC) using unique molecular identifiers (UMIs) for error correction. Our assay, spanning a 284.5 kb target region, is combined with freely-available bioinformatics pipelines that provide ultra-sensitive detection of single nucleotide variants (SNVs), and reliable identification of copy number variations (CNVs) directly from plasma DNA. In a cohort of 35 BC patients, our approach detected actionable driver and clonal SNVs at low (~0.5%) frequency levels in cfDNA that were concordant (83.3%) with sequencing of primary and/or metastatic solid tumour sites. We also detectedERRB2gene CNVs used for HER2 subtype classification with 80% precision compared to immunohistochemistry. Further, we evaluated fragmentation profiles of cfDNA in BC and observed distinct differences compared to data from healthy individuals. Our results show that the developed assay addresses the majority of tumour associated aberrations directly from plasma DNA, and thus may be used to elucidate genomic alterations in liquid biopsy studies.
Cerebral Dopamine Neurotrophic Factor regulates multiple neuronal subtypes and behavior
Authors: Chen Yu-Chia , Baronio Diego , Semenova Svetlana , Abdurakhmanova Shamsiiat , Panula Pertti 
Published: August 2019

AbstractCerebral Dopamine Neurotrophic Factor (CDNF) protects dopaminergic neurons against toxic damage in the rodent brain, and is in clinical trials to treat Parkinson’s disease patients. Yet the underlying mechanism is poorly understood. To examine its mode of action and significance, we examined the development of neurotransmitter systems from larval to adult mutant zebrafish lacking cdnf. Although a lack of cdnf did not affect overall brain dopamine levels, dopaminergic neuronal clusters showed significant abnormalities. The number of histamine neurons that surround the dopaminergic neurons was significantly reduced. Expression of tyrosine hydroxylase 2 in the brain was elevated in cdnf mutants throughout their lifespan. There were abnormally few GABA neurons in the hypothalamus in the mutant larvae, and expression of glutamate decarboxylase was reduced throughout the brain. cdnf mutant adults showed a range of behavioral phenotypes, including increased sensitivity to pentylenetetrazole-induced seizures. Shoaling behavior of mutant adults was abnormal, and they did not display social attraction to conspecifics. CDNF plays a profound role in shaping the neurotransmitter circuit structure, seizure susceptibility, and complex behaviors in zebrafish. These findings are informative for dissecting the diverse functions of this poorly understood factor in human conditions related to Parkinson’s disease and complex behaviors
Variations in Brain Morphometry Among Healthy Preschoolers Born Very Preterm
Authors: Hasler Holly M. , Brown Timothy T. , Akshoomoff Natacha 
Published: August 2019

AbstractBackgroundPreterm birth is associated with an increased risk of neonatal brain injury, which can lead to alterations in brain maturation. Advances in neonatal care have dramatically reduced the incidence of the most significant medical consequences of preterm birth. Relatively healthy preterm infants remain at increased risk for subtle injuries that impact future neurodevelopmental and functioning.AimsTo investigate the gray matter morphometry measures of cortical thickness, surface area, and sulcal depth in the brain using magnetic resonance imaging at 5 years of age in healthy children born very preterm.Study designCohort studySubjectsParticipants were 52 children born very preterm (VPT; less than 33 weeks gestational age) and 37 children born full term.Outcome measuresCortical segmentation and calculation of morphometry measures were completed using FreeSurfer version 5.3.0 and compared between groups using voxel-wise, surface-based analyses.ResultsThe VPT group had a significantly thinner cortex in temporal and parietal regions as well as thicker gray matter in the occipital and inferior frontal regions. Reduced surface area was found in the fusiform area in the VPT group. Sulcal depth was also lower in the VPT group within the posterior parietal and inferior temporal regions and greater sulcal depth was found in the middle temporal and medial parietal regions. Results in some of these regions were correlated with gestational age at birth in the VPT group.ConclusionsThe most widespread differences between the VPT and FT groups were found in cortical thickness. These findings may represent a combination of delayed maturation and permanent alterations caused by the perinatal processes associated with very preterm birth.
Pharmacological efficacy of a synergistic composition based on activators of cAMP accumulation as a wound healing agent
Authors: Martynov Artur , Bomko Tatyana , Nosalskaya Tatyana , Farber Boris , Brek Ostap 
Published: August 2019

AbstractIntroductionWound-healing dipyridamole- and papaverine-based aerosols (D1/D2) as activators of the accumulation of cyclic adenosine monophosphate are promising drugs that can accelerate wound healing in wound processes of various origins.Materials and methods128 rats were used in the study, including 38 in a pharmacological experiment on a model of stencil wounds and 90 in an experiment that studied the effect of spray on the number of CD34 cells in the blood of rats with chemically induced immunodeficiency. Immunodeficiency was caused by the fivefold administration of cyclophosphamide and prednisone. The expression level of CD34 was determined using flow cytofluorimeter.Results and discussionTopical application of D1/D2 aerosol samples on the skin of rats contributed to a statistically significant acceleration of regeneration processes. In terms of the appearance of granulations and epithelialization of wounds, D1/D2 aerosols were superior to dexpanthenol ointment. The maximum effect from the use of D1/D2 was observed on the 60th day, and restoration of the physiological level of pluripotent cells was observed as early as on the 10th day after the start of spray application. By accelerating wound healing, dipyridamole with papaverine probably stimulate the division of stem cells at the periphery without enhancing bone marrow function.
Career adaptability and the success of self-initiated expatriates in China
Authors: Jannesari Milad , Sullivan Sherry E. 
Published: August 2019

PurposeUsing a career lens, the purpose of this paper is to examine the psychological factors related to the career success (e.g. performance and adjustment) of self-initiated expatriates (SIEs).Design/methodology/approachThis research examines the previously unstudied relationship between career adaptability and career success. Data were collected by surveying 273 SIEs employed in professional jobs in China.FindingsAs hypothesized, career adaptability was positively related to performance as well as to adjustment. Psychological availability mediated the relationships of career adaptability with performance and with adjustment. Contrary to expectations, supportive supervision did not moderate the relationship between career adaptability and either performance or adjustment.Research limitations/implicationsBecause the data were collected in a single, self-report survey, future studies should collect longitudinal data so that the effects of changes in career adaptability on adjustment and performance can be determined. In addition, as all of the participants were professionals, future research should examine SIEs employed in blue-collar jobs.Originality/valueAs this is the first study to consider how career adaptability may influence SIEs’ performance and adjustment, it offers unique insights into the work experiences of SIEs. Additionally, this study examines the theoretical underpinnings of career construction theory, namely, the previously hypothesized but untested relationship between career adaptability and adjustment.
Digging deep into the enterprise innovation ecosystem
Authors: Sun Cong , Wei Jiang 
Published: August 2019

Purpose
The purpose of this paper is to explore how Chinese enterprises overcome their lack of resource and capabilities and eventually fulfill global resource accumulation, fast innovative commercialization and significant technological breakthrough by establishing and coordinating innovation ecosystem at firm level.

Design/methodology/approach
This paper first reviewed the literature on the structure and coordinating mechanism of enterprise innovation ecosystem and identified two important gaps on the characteristics of ecosystem actors and the logic of innovative coordination. Then, the paper adopted grounded analysis about the construction and evolution of Haier’s innovation ecosystem based on longitudinal case data. On the basis of the case study, the construct of firm-level innovation ecosystem and new logic of coordination are formed.

Findings
This paper found the emerging phenomenon of sub-organizational ecosystem actors and depicted that the establishing process of firm-level innovation ecosystem went through three majors stages, and the corresponding coordinating logic changed from proactive intervention to reactive self-evolution.

Originality/value
This paper tried to make contributions to the studies of structure and coordinating mechanism of enterprise innovation ecosystem, and proposed the enterprise itself could build firm-level ecosystem within its organizational boundary and interact with external ecosystem. The findings enlightened the nested structure of ecosystem, opened the black box of organizational boundary and broke the limitation that existing researches only analyse innovation ecosystem at system level and regard firms as basic analytical unit. Besides, this paper proposed that the coordination of innovation ecosystem can be passively fulfilled by network effect and ecological evolution, where previous studies mainly focused on proactive institutional intervention and resource investment. This point could provide Chinese enterprises with good references.
Clustering of host countries to facilitate learning between similar international construction markets
Authors: Ozyurt Beste , Dikmen Irem , Birgonul M. Talat 
Published: August 2019

Purpose
In the global construction industry, experience gained in various countries is a major source of competitive advantage. By transferring the knowledge gained in previous projects using an effective knowledge management strategy, they can increase their competitiveness by adopting best practices and by not repeating the same mistakes under similar conditions. The purpose of this paper is to demonstrate how similar countries can be clustered to facilitate learning in global markets.

Design/methodology/approach
Initially, country factors that can affect success in international projects and can be used to assess the similarity of markets were identified by an extensive literature review and prioritised by a web-based questionnaire. A country evaluation form was prepared to collect country-specific data to be used in the cluster analysis of 39 countries where the Turkish contractors have been frequently working since the last 45 years. Cluster analysis was performed with SPSS 23.0.

Findings
Three country clusters were obtained and validated. Ultimately, how obtained country clusters may be used to facilitate learning from international construction projects was demonstrated by using an illustrative example.

Research limitations/implications
The findings depend on the experience and perspective of Turkish contractors doing business abroad. Thus, the identified clusters are not generic. Moreover, country clusters were not identified considering only the country factors such as economy, culture, politics, etc.; thus, countries in the same cluster do not necessarily represent “similar” countries in terms of macro-factors. Clusters were identified so that the lessons learned can be effectively transferred within the same cluster considering construction and project-related factors as well as country-related factors. Although the findings cannot be generalised and clusters are not static, it is believed that the methodology used in this research is repeatable for different countries considering different timeframes.

Originality/value
Theoretical contributions include the identification of factors that can be used for similarity assessment of countries for transferring lessons learned as well as a methodology for clustering. Findings may also have a practical value for the Turkish contractors.
The influence of KIBS-client interactions on absorptive capacity-building for environmental innovation
Authors: Pace Lisa A. , Miles Ian 
Published: August 2019

Purpose
Firms need to develop absorptive capacities to effectively source and exploit knowledge relevant to environmental behaviour for their own innovation activity. Business-to-business interactions can represent a significant route through which knowledge and resources about environmental innovations are transferred along the supply chain. The purpose of this paper is to explore how firms exploit business partnerships in order to build capacity for environmental innovation. In order to do so, it investigates two elements of B2B interactions – partner alignment and compatibility – and their influence on absorptive capacity-building.

Design/methodology/approach
This paper is based on a qualitative interview study of knowledge intensive business services (KIBS) operating in the environmental goods and services sector and their clients involved in adopting environmental innovations. Matched pairs of engineering consulting firms and their clients – tourism accommodation establishments – were selected as a sampling frame in order to study the influence of partner alignment and compatibility on the exchange of environmentally relevant knowledge and competencies.

Findings
The findings show that the synergistic attributes of business partners influence absorptive capacity-building and give rise to different patterns of interaction of KIBS with their client. The B2B interactions investigated are characterised by alignment along multiple objectives about the relevance of environmental behaviour. Furthermore, the compatibility of the partners’ competences is a key determinant of environmental innovation outcome.

Practical implications
The study highlights the role of managers in identifying and selecting those business partnerships that accrue greater potential benefit for accessing resources and competencies for eco-innovation.

Originality/value
The study contributes to the literature on absorptive capacity and innovation by demonstrating how B2B interactions – in this study, the interaction of KIBS with their clients – influence the capacity of firms to adopt environmental innovations which is an area of study that deserves further attention.
Women’s health: a benefit of education in Australia
Authors: Tran Dai Binh , Thi My Tran Hanh 
Published: August 2019

Purpose
The purpose of this paper is to examine the relationship between education and health amongst Australian women.

Design/methodology/approach
This study uses the Household, Income and Labour Dynamics in Australia data set. Spouse’s education is employed as an instrument to solve the potential endogeneity of educational attainment.

Findings
The results indicate that an additional year of schooling can lead to an increase in self-reported health, physical health, mental health and a reduced likelihood of having long-term health conditions. Women who are not in the labour force are likely to enjoy higher benefits of education compared to their employed counterparts. The findings also suggest that the relationship between education and health can be explained by the extent of positive health behaviours and social capital as mediators.

Research limitations/implications
The conclusion from the results might be different in the case of men, reducing the generalisability of the results. Several objective health variables should be used to provide further aspects of health on which education has an impact.

Practical implications
As the positive effect of education on women’s health is empirically found, investment in women’s education should be seriously considered and reevaluated.

Originality/value
This paper focuses on Australian women which not only reduces the heterogeneity between genders but also adds to the rare number of studies on this topic in Australia. This paper also employs a formal mediation analysis to examine what are the mechanisms explaining the relationship between education and health.