bluuebunny/crossref_metadata_2025_split huggingface dataset:
A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax
Authors: Trimarsanto Hidayat , Amato Roberto , Pearson Richard D , Sutanto Edwin , Noviyanti Rintis , Trianty Leily , Marfurt Jutta , Pava Zuleima , Echeverry Diego F , Lopera-Mesa Tatiana M , Montenegro Lidia Madeline , Tobón-Castaño Alberto , Grigg Matthew J , Barber Bridget , William Timothy , Anstey Nicholas M , Getachew Sisay , Petros Beyene , Aseffa Abraham , Assefa Ashenafi , Rahim Awab Ghulam , Chau Nguyen Hoang , Hien Tran Tinh , Alam Mohammad Shafiul , Khan Wasif A , Ley Benedikt , Thriemer Kamala , Wangchuck Sonam , Hamedi Yaghoob , Adam Ishag , Liu Yaobao , Gao Qi , Sriprawat Kanlaya , Ferreira Marcelo U , Barry Alyssa , Mueller Ivo , Drury Eleanor , Goncalves Sonia , Simpson Victoria , Miotto Olivo , Miles Alistair , White Nicholas J , Nosten Francois , Kwiatkowski Dominic P , Price Ric N , Auburn Sarah 
Published: September 2019

AbstractImported cases present a considerable challenge to the elimination of malaria. Traditionally, patient travel history has been used to identify imported cases, but the long-latency liver stages confound this approach in Plasmodium vivax. Molecular tools to identify and map imported cases offer a more robust approach, that can be combined with drug resistance and other surveillance markers in high-throughput, population-based genotyping frameworks. Using a machine learning approach incorporating hierarchical FST (HFST) and decision tree (DT) analysis applied to 831 P. vivax genomes from 20 countries, we identified a 28-Single Nucleotide Polymorphism (SNP) barcode with high capacity to predict the country of origin. The Matthews correlation coefficient (MCC), which provides a measure of the quality of the classifications, ranging from −1 (total disagreement) to 1 (perfect prediction), exceeded 0.9 in 15 countries in cross-validation evaluations. When combined with an existing 37-SNP P. vivax barcode, the 65-SNP panel exhibits MCC scores exceeding 0.9 in 17 countries with up to 30% missing data. As a secondary objective, several genes were identified with moderate MCC scores (median MCC range from 0.54-0.68), amenable as markers for rapid testing using low-throughput genotyping approaches. A likelihood-based classifier framework was established, that supports analysis of missing data and polyclonal infections. To facilitate investigator-lead analyses, the likelihood framework is provided as a web-based, open-access platform (vivaxGEN-geo) to support the analysis and interpretation of data produced either at the 28-SNP core or full 65-SNP barcode. These tools can be used by malaria control programs to identify the main reservoirs of infection so that resources can be focused to where they are needed most.
Ago2-seq identifies new microRNA targets for seizure control
Authors: Venø Morten T. , Reschke Cristina R. , Morris Gareth , Connolly Niamh M. C. , Su Junyi , Yan Yan , Engel Tobias , Jimenez-Mateos Eva M. , Harder Lea M. , Pultz Dennis , Haunsberger Stefan J. , Pal Ajay , Norwood Braxton A. , Costard Lara S. , Neubert Valentin , Gallo Federico Del , Salvetti Beatrice , Vangoor Vamshidhar R. , Rodriguez Amaya Sanz , Muilu Juha , Fabene Paolo F. , Pasterkamp R. Jeroen , Prehn Jochen H.M. , Schorge Stephanie , Andersen Jens S. , Rosenow Felix , Bauer Sebastian , Kjems Jørgen , Henshall David C. 
Published: September 2019

AbstractMicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in the hippocampus of three different animal models at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures. The commonly upregulated miRNAs were selected for a functionalin vivoscreen using oligonucleotide inhibitors. This revealed anti-seizure phenotypes upon inhibition of miR-10a-5p, miR-21a-5p and miR-142a-5p as well as neuroprotection-only effects for inhibition of miR-27a-3p and miR-431-5p. Proteomic data and pathway analysis on predicted and validated targets of these miRNAs indicated a role for TGFβ signaling in a shared seizure-modifying mechanism. Together, these results identify functional miRNAs in the hippocampus and a pipeline of new targets for seizure control in epilepsy.
Human Visual Search Follows Suboptimal Bayesian Strategy Revealed by a Spatiotemporal Computational Model
Authors: Zhou Yunhui , Yu Yuguo 
Published: September 2019

AbstractHumans perform sequences of eye movements to search for a target in complex environment, but the efficiency of human search strategy is still controversial. Previous studies showed that humans can optimally integrate information across fixations and determine the next fixation location. However, their models ignored the temporal control of eye movement, ignored the limited human memory capacity, and the model prediction did not agree with details of human eye movement metrics well. Here, we measured the temporal course of human visibility map and recorded the eye movements of human subjects performing a visual search task. We further built a continuous-time eye movement model which considered saccadic inaccuracy, saccadic bias, and memory constraints in the visual system. This model agreed with many spatial and temporal properties of human eye movements, and showed several similar statistical dependencies between successive eye movements. In addition, our model also predicted that the human saccade decision is shaped by a memory capacity of around 8 recent fixations. These results suggest that human visual search strategy is not strictly optimal in the sense of fully utilizing the visibility map, but instead tries to balance between search performance and the costs to perform the task.Author SummaryDuring visual search, how do humans determine when and where to make eye movement is an important unsolved issue. Previous studies suggested that human can optimally use the visibility map to determine fixation locations, but we found that such model didn’t agree with details of human eye movement metrics because it ignored several realistic biological limitations of human brain functions, and couldn’t explain the temporal control of eye movements. Instead, we showed that considering the temporal course of visual processing and several constrains of the visual system could greatly improve the prediction on the spatiotemporal properties of human eye movement while only slightly affected the search performance in terms of median fixation numbers. Therefore, humans may not use the visibility map in a strictly optimal sense, but tried to balance between search performance and the costs to perform the task.
Custom built scanner and simple image processing pipeline enables low-cost, high-throughput phenotyping of maize ears
Authors: Warman Cedar , Fowler John E 
Published: September 2019

AbstractHigh-throughput phenotyping systems are becoming increasingly powerful, dramatically changing our ability to document, measure, and detect phenomena. Unfortunately, taking advantage of these trends can be difficult for scientists with few resources, particularly when studying nonstandard biological systems. Here, we describe a powerful, cost-effective combination of a custom-built imaging platform and open-source image processing pipeline. Our maize ear scanner was built with off-the-shelf parts for <$80. When combined with a cellphone or digital camera, videos of rotating maize ears were captured and digitally flattened into projections covering the entire surface of the ear. Segregating GFP and anthocyanin seed markers were clearly distinguishable in ear projections, allowing manual annotation using ImageJ. Using this method, statistically powerful transmission data can be collected for hundreds of maize ears, accelerating the phenotyping process.
Cep55 overexpression promotes genomic instability and tumorigenesis in mice
Authors: Sinha Debottam , Nag Purba , Nanayakkara Devathri , Duijf Pascal H.G. , Burgess Andrew , Raninga Prahlad , Smits Veronique A.J. , Bain Amanda L. , Subramanian Goutham , Wall Meaghan , Finnie John. W. , Kalimutho Murugan , Khanna Kum Kum 
Published: September 2019

AbstractHigh expression of centrosomal protein CEP55 has been correlated with clinico-pathological parameters across multiple human cancers. Despite significantin vitrostudies and association of aberrantly overexpressed CEP55 with worse prognosis, its causal rolein vivotumorigenesis remains elusive. Here, using a ubiquitously overexpressing transgenic mouse model, we show thatCep55overexpression causes spontaneous tumorigenesis and acceleratesTrp53+/-induced tumoursin vivo. At the cellular level, using mouse embryonic fibroblasts (MEFs), we demonstrate thatCep55overexpression induces proliferation advantage by modulating multiple cellular signalling networks including the PI3K/AKT pathway. Notably, theCep55overexpressing MEFs demonstrate high level of mitotic chromosomal instability (CIN) due to stabilized microtubules. Interestingly,Cep55overexpressing MEFs have a compromised Chk1-dependent S-phase checkpoint, causing increased replication speed and DNA damage, resulting in a prolonged aberrant mitotic division. Importantly, this phenotype was rescued by pharmacological inhibition of Pi3k/Akt or expression of mutant Chk1 (S280A), that is insensitive to regulation by active AKT, inCep55overexpressing cell. Collectively, our data demonstrates causative effects of deregulated Cep55 on genome stability and tumorigenesis which have potential implications for tumour initiation and therapy.
APOBEC3B reporter myeloma cell lines identify DNA damage response pathways leading to APOBEC3B expression
Authors: Yamazaki Hiroyuki , Shirakawa Kotaro , Matsumoto Tadahiko , Kazuma Yasuhiro , Matsui Hiroyuki , Horisawa Yoshihito , Stanford Emani , Sarca Anamaria Daniela , Shirakawa Ryutaro , Shindo Keisuke , Takaori-Kondo Akifumi 
Published: September 2019

AbstractApolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminase 3B (A3B) is a DNA editing enzyme which induces genomic DNA mutations in multiple myeloma and various other cancers. APOBEC family proteins are highly homologous so it is especially difficult to investigate the biology of A3B alone in cancer cells. To investigate A3B function in myeloma cells easily and comprehensively, we used CRISPR/Cas9 to generate A3B reporter cells that contain 3×FLAG tag and IRES-EGFP sequences integrated at the end of the A3B gene. These reporter cells stably express 3xFLAG tagged A3B and the reporter EGFP and this expression is enhanced under known stimuli, such as PMA. Conversely, shRNA knockdown of A3B decreased EGFP fluorescence and 3xFLAG tagged A3B protein levels. We screened a series of anticancer treatments using these cell lines and identified that most conventional therapies, such as antimetabolites or radiation, exacerbated endogenous A3B expression, but recent molecular targeting drugs, including bortezomib, lenalidomide and elotuzumab, did not. Furthermore, chemical inhibition of ATM, ATR and DNA-PK suppressed the EGFP expression upon treatment with antimetabolites. These results suggest that DNA damage response triggers A3B expression through ATM, ATR and DNA-PK signaling.
Simultaneous development and periodic clustering of simple and complex cells in visual cortex
Authors: Kim Gwangsu , Jang Jaeson , Paik Se-Bum 
Published: September 2019

AbstractNeurons in the primary visual cortex (V1) are often classified as simple or complex cells, but it is debated whether they are discrete hierarchical classes of neurons developing sequentially, or if they represent a continuum of variation within a single class of cells developing simultaneously. Herein, we show that simple and complex cells may arise simultaneously from the universal process of retinal development. From analysis of the cortical receptive fields in cats, we show evidence that simple and complex cells originate from the periodic variation of ON-OFF segregation in the feedforward projection of retinal mosaics, by which they organize into periodic clusters in V1. Our key prediction that clusters of simple and complex cells correlate topographically with orientation maps was confirmed by data in cats. Our results suggest that simple and complex cells are not two distinct neural populations but arise from common retinal afferents, simultaneous with orientation tuning.HighlightsSimple and complex cells arise simultaneously from retinal afferents.Simple/complex cells are organized into periodic clusters across visual cortex.Simple/complex clusters are topographically correlated with orientation maps.Development of clustered cells in V1 is explained by the Paik-Ringach model.
Liverpool knowledge quarter sustainability network: case study
Authors: Stenton Ian , Hanmer-Dwight Rachael 
Published: September 2019

Purpose
This paper aims to study the development of the Liverpool Knowledge Quarter Sustainability Network (KQSN). It outlines the sectors included in the collaborative knowledge-sharing, the nature of the work it facilitates, and considers how the network can transform its existing objectives around the shared vision of the United Nations sustainable development goals (SDGs).

Design/methodology/approach
The KQSN operates in a collaborative cross-sectoral forum to support, facilitate or coordinate projects around sustainability, with core leads sitting in higher education and health care.

Findings
The KQSN supports projects through collaborative activity and enables members to access specialist advice available through the network. Through its membership, the KQSN is primed to develop metrics for demonstrating Knowledge Quarter SDG-aligned activity. The KQSN has scope to increase its level of implementation arising from its shared values, with a renewed focus around the SDGs.

Practical implications
This paper contributes to the 2018 EAUC Annual Conference theme of “Collaborations for Change” and the need for transformative partnerships that are prepared to align their mission to the SDGs.

Originality/value
Unlike discipline- or sector-specific networks, the KQSN has an inclusive membership, making it an original multi-disciplinary sustainability platform for neighbouring organisations in and around Liverpool's Knowledge Quarter. This case study can support other knowledge cluster communities to replicate its model. This case study also presents a diverse range of small projects, which are easily replicable and hopefully will inspire others to do something similar.
Gamification in e-learning
Authors: Poondej Chanut , Lerdpornkulrat Thanita 
Published: September 2019

Purpose
This study aims to deploy game elements in an e-learning course on the Moodle platform. One of the greatest challenges of e-learning can be motivating and engaging students in learning. Gamification has been attracting increasing attention as a key underlying aspect of pedagogy that can be used to increase student engagement and motivation in learning.

Design/methodology/approach
To investigate student satisfaction and engagement with an e-learning course, here an Information Literacy Skills course, the authors collected data from 104 undergraduate students enrolled on the course in Thailand. In addition, the authors used student interaction data obtained from Moodle to examine whether there were any differences in the frequency of online interaction with the course between the students who performed at an above-average level and those who were below average.

Findings
The findings indicated that the students were highly satisfied with the gamification tools in Moodle and they were engaged in the gamified e-learning course. The authors found a significant difference in the frequency of online interaction with the course between the group who performed at an above-average level and the group who were below average.

Practical implications
The findings have important implications for the development of gamification in e-learning.

Originality/value
This paper fulfills an identified need to study how gamification idea can be implemented in e-learning.
Measuring the flexibility index for a supply chain using graph theory matrix approach
Authors: Singh Rajesh Kumar , Kumar Pravin 
Published: September 2019

Purpose
In complex business environment of today, organizations are trying to be flexible and agile for meeting dynamic demands of customers in terms of product variety, cost cutting and decreasing product life cycle. The main purpose of this paper is to identify different attributes of flexibility and to propose an approach for evaluating flexibility index of a supply chain.

Design/methodology/approach
Total 33 factors are identified from the literature and further clustered into six major groups. They are top management commitment, organizational factors, mutual understanding, flow of information, relationship and decision-making and responsiveness. On the basis of these factors, an index has been developed by using graph theory matrix approach to evaluate the flexibility intensity of the supply chain for the firm in consideration.

Findings
The proposed approach has been illustrated in context to an Indian automobile organization, and value of the flexibility index has been evaluated. Framework proposed will help the supply chain managers to evaluate the flexibility index of their respective organizations.

Research limitations/implications
As values taken for different flexibility sub-factors are based on inputs given by managers of case organization, chances of bias may be there. Therefore, a study may be validated with more case studies to validate the proposed framework. Based on the flexibility index, organizations can find their strong and weak areas for strategy development.

Originality/value
A firm can also compare the flexibility index of its own supply chain with other’s supply chain or with the best in the industry for benchmarking purpose. Benchmarking of flexibility will help organizations in developing strategies to compete in dynamic market scenario.
Innovation drivers in Ecuadorian manufacturing
Authors: Rochina-Barrachina María Engracia , Rodríguez Jorge Antonio 
Published: September 2019

Purpose
The purpose of this paper is to study which are the drivers of different types of innovations for manufacturing firms. The considered innovation types are product, process, organizational and marketing innovations. In addition, this study also aims to understand why most types of innovation (with the exception of organizational innovation) have decreased over time.

Design/methodology/approach
The two non-overlapping waves of the Ecuadorian National Innovation Activities Survey 2013 and 2015 (NIAS) are used. To identify the determinants of the different types of innovations and to check whether the decisions to innovate are correlated, a tetravariate probit model is used.

Findings
The results obtained point to some relevant differences in terms of the drivers of the different types of innovation. In addition, it is also evident that with the passage of time, certain problems that may be reducing the incentives to innovate have become more acute.

Originality/value
The study adds new empirical evidence to the literature on the role of investments in incorporated technology in innovation in developing countries. In particular, for Ecuadorian firms, the acquisition of incorporated technology in capital goods seems to be very relevant. This highlights the existence of a supply-driven innovation strategy. However, there is also room for innovation strategies driven by demand conditions.
Views on aging in selection: HR implications
Authors: Jeske Debora , Setti Annalisa , Gibbons Daisy Beth 
Published: September 2019

Purpose
It is well-known that stereotypes on aging and perceptions about the suitability of certain jobs for certain age groups can influence performance ratings. However, it is unclear whether and how subjective views on aging are associated with judgment on someone else’s performance. The purpose of this study is to explore the role of aging perceptions and images of aging on performance ratings for a fictitious set of male candidates with different age and job profiles. Ratings of interest were job suitability, developmental potential, interpersonal skills and performance capacity.

Design/methodology/approach
Using an online survey format, data was collected from 203 Irish and UK employees to assess how they evaluated different fictitious candidates for a local development committee. The age and mentorship status of the candidates were also manipulated.

Findings
The age or mentoring status of the candidate did not play a significant role in how they were rated. Multiple regression analyses indicated, however, that participants’ aging perceptions and aging images had a significantly positive influence on how they rated the fictitious candidates (after controlling for participant variables such as age and experience). However, positive images of aging and aging perceptions on the part of the participants predicted more positive overall job suitability ratings, developmental potential, interpersonal skills and performance capacity. When the participants had more negative views on aging, they would also allocate lower ratings.

Originality/value
The results indicate that employee attitudes about aging play a role in how they will rate others. Given the importance of potential rating bias, the authors propose a number of training interventions that human resource professionals may be able to carry out to positively shape the informational basis for more negative aging attitudes.
Probing crustal anisotropy by receiver functions at the deep continental drilling site KTB in Southern Germany
Authors: Bianchi Irene , Bokelmann Götz 
Published: September 2019

ABSTRACTSeismic anisotropy is a unique observational tool for remotely studying deformation and stress within the Earth. Effects of anisotropy can be seen in seismic data; they are due to mineral alignment, fractures or layering. Seismic anisotropy is linked to local stress and strain, allowing modern geophysics to derive geomechanical properties from seismic data for supporting well planning and fracking. For unravelling anisotropic properties of the crust, the teleseismic receiver functions methodology has started to be widely applied recently due to its ability in retrieving the three‐dimensional characteristics of the media sampled by the waves. The applicability of this technique is tested here by a field test carried out around the Kontinental Tiefbohrung site in southeastern Germany. We compare our results to previous investigations of the metamorphic rock pile of the Zone Erbendorf‐Vohenstrauss, drilled down to 9 km depth, which sampled an alternating sequence of paragneiss and amphibolite, in which a strong foliation has been produced by ductile deformation. The application of the receiver functions reveals the presence of two distinct anisotropic layers within the metamorphic rock pile at 0–4 km and below 6 km depth, with up to 8% anisotropy; the depth of these two layers corresponds to the location of mica‐rich paragneiss which show intense foliation, and finally proves the relation between the signal in the receiver functions, rock texture and presence of cracks. We have now the capability of providing insights from passive seismic data on geomechanical properties of the rocks, useful for geological exploration and engineering purposes, which will help influencing expensive drilling decisions thanks to future application of this seismic technique.