bluuebunny/crossref_metadata_2025_split huggingface dataset:
An epigenome atlas of neural progenitors within the embryonic mouse forebrain
Authors: Rhodes Christopher T. , Thompson Joyce J. , Mitra Apratim , Asokumar Dhanya , Lee Dongjin R. , Lee Daniel J. , Zhang Yajun , Jason Eva , Dale Ryan K. , Rocha Pedro P. , Petros Timothy J. 
Published: March 2021

ABSTRACTA comprehensive characterization of epigemonic organization in the embryonic mouse forebrain will enhance our understanding of neurodevelopment and provide insight into mechanisms of neurological disease. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters with associated transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.
SPART, a versatile and standardized data exchange format for species partition information
Authors: Miralles Aurélien , Ducasse Jacques , Brouillet Sophie , Flouri Tomas , Fujisawa Tomochika , Kapli Paschalia , Knowles L. Lacey , Kumari Sangeeta , Stamatakis Alexandros , Sukumaran Jeet , Lutteropp Sarah , Vences Miguel , Puillandre Nicolas 
Published: March 2021

AbstractA wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of SD under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the “inferred species”. The syntax also allows to optionally report support values, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
Evolution of MEG: a first MEG-feasible fluxgate magnetometer
Authors: Koshev N. , Butorina A. , Skidchenko E. , Kuzmichev A. , Ossadtchi A. , Ostras M. , Fedorov M. , Vetoshko P. 
Published: March 2021

AbstractIn the current article we present a first solid-state sensor feasible for magnetoencephalography (MEG), and working at room temperature. The sensor is a fluxgate magnetometer based on yttrium-iron garnet films (YIGM). In this feasibility study we prove the concept of usage the YIGM in terms of MEG by registering a simple brain induced field: the human alpha rhythm1. All the experiments and results are validated with usage of another kind of high-sensitive magnetometers - optically pumped magnetometer (OPM), which currently appears to be well-established in terms of MEG.
Replicative senescence dictates the emergence of disease-associated microglia and contributes to Aβ pathology
Authors: Hu Yanling , Fryatt Gemma L. , Ghorbani Mohammadmersad , Obst Juliane , Menassa David A. , Martin-Estebane Maria , Muntslag Tim A. O. , Olmos-Alonso Adrian , Guerrero-Carrasco Monica , Thomas Daniel , Cragg Mark S. , Gomez-Nicola Diego 
Published: March 2021

ABSTRACTThe sustained proliferation of microglia is a key hallmark of Alzheimer’s disease (AD), accelerating its progression. Here, we sought to understand the long-term impact of the early and prolonged microglial proliferation observed in AD, hypothesising that extensive and repeated cycling would engender a distinct transcriptional and phenotypic trajectory. We found that the early and sustained microglial proliferation seen in an AD-like model promotes replicative senescence, characterised by increased βgal activity, a senescence-associated transcriptional signature and telomere shortening, correlating with the appearance of disease-associated microglia (DAM) and senescent microglial profiles in human post-mortem AD cases. Prevention of early microglial proliferation hindered the development of senescence and DAM, impairing the accumulation of Aβ and associated neuritic damage. Overall, our results support that excessive microglial proliferation leads to the generation of senescent DAM, which contribute to early Aβ pathology in AD.
Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases
Authors: Kubota Naoto , Suyama Mikita 
Published: March 2021

AbstractGenome-wide association studies (GWAS) have been performed to identify thousands of variants in the human genome as disease risk markers, but functional variants that actually affect gene regulation and their genomic features remain largely unknown. Here we performed a comprehensive survey of functional variants in the regulatory elements of the human genome. We integrated hematopoietic transcription factor (TF) footprints datasets generated by ENCODE project with multiple quantitative trait locus (QTL) datasets (eQTL, caQTL, bQTL, and hQTL) and investigated the associations of functional variants and immune system disease risk. We identified candidate regulatory variants highly linked with GWAS lead variants and found that they were strongly enriched in active enhancers in hematopoietic cells, emphasizing the clinical relevance of enhancers in disease risk. Moreover, we found some strong relationships between traits and hematopoietic cell types or TFs. We highlighted some credible regulatory variants and found that a variant, rs2291668, which potentially functions in the molecular pathogenesis of multiple sclerosis, is located within a TF footprint present in a protein-coding exon of theTNFSF14gene, indicating that protein-coding exons as well as noncoding regions can possess clinically relevant regulatory elements. Collectively, our results shed light on the molecular pathogenesis of immune system diseases. The methods described in this study can readily be applied to the study of the risk factors of other diseases.
Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of theCoronaviridae
Authors: Miller Allison K. , Mifsud Jonathon C.O. , Costa Vincenzo A. , Grimwood Rebecca M. , Kitson Jane , Baker Cindy , Brosnahan Cara L. , Pande Anjali , Holmes Edward C. , Gemmell Neil J. , Geoghegan Jemma L. 
Published: March 2021

AbstractTheNidoviralescomprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to theCoronaviridae, in a range of aquatic hosts including fish, amphibians and reptiles. We sought to identify additional members of theCoronaviridaein both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data, and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within theLetovirinaesubfamily of theCoronaviridae, including those in a jawless fish – the pouched lamprey. By mining fish transcriptome data we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across theCoronaviridae, but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationships of viruses within theLetovirinaedoes not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
Accurate and efficient time-domain classification with adaptive spiking recurrent neural networks
Authors: Yin Bojian , Corradi Federico , Bohté Sander M. 
Published: March 2021

ABSTRACTInspired by more detailed modeling of biological neurons, Spiking neural networks (SNNs) have been investigated both as more biologically plausible and potentially more powerful models of neural computation, and also with the aim of extracting biological neurons’ energy efficiency; the performance of such networks however has remained lacking compared to classical artificial neural networks (ANNs). Here, we demonstrate how a novel surrogate gradient combined with recurrent networks of tunable and adaptive spiking neurons yields state-of-the-art for SNNs on challenging benchmarks in the time-domain, like speech and gesture recognition. This also exceeds the performance of standard classical recurrent neural networks (RNNs) and approaches that of the best modern ANNs. As these SNNs exhibit sparse spiking, we show that they theoretically are one to three orders of magnitude more computationally efficient compared to RNNs with comparable performance. Together, this positions SNNs as an attractive solution for AI hardware implementations.
Novelty-related engagement of VTA and anterior hippocampus propagate changes in cortical network plasticity at different scales
Authors: Cowan Emily T. , Fain Matthew , O’Shea Ian , Ellman Lauren M. , Murty Vishnu P. 
Published: March 2021

AbstractThe detection of novelty indicates changes in the environment and the need to update existing representations. In response to novelty, interactions across the ventral tegmental area (VTA)-hippocampal circuit support experience-dependent plasticity in the hippocampus. While theories have broadly suggested plasticity-related changes are also instantiated in the cortex, research has also shown evidence for functional heterogeneity in cortical networks. It therefore remains unclear how the hippocampal-VTA circuit engages cortical networks, and whether novelty targets specific cortical regions or diffuse, large-scale cortical networks. To adjudicate the role of the VTA and hippocampus in cortical network plasticity, we used human functional magnetic resonance imaging (fMRI) to compare resting state functional coupling before and following exposure to novel scene images. Functional coupling between right anterior hippocampus and VTA was enhanced following novelty exposure. However, we also found evidence for a double dissociation, with anterior hippocampus and VTA showing distinct patterns of post-novelty functional coupling enhancements, targeting task-relevant regions versus large-scale networks, respectively. Further, significant correlations between these networks and the novelty-related plasticity in the anterior hippocampal-VTA functional network suggest the central hippocampal-VTA network may facilitate the interactions with the cortex. These findings support an extended model of novelty-induced plasticity, in which novelty elicits plasticity-related changes in both local and global cortical networks.Significance StatementNovelty detection is critical for adaptive behavior, signaling the need to update existing representations. By engaging the bi-directional hippocampal-VTA circuit, novelty has been shown to induce plasticity-related changes in the hippocampus. However, it remains an open question how novelty targets such plasticity-related changes in cortical networks. We show that anterior hippocampus and VTA target cortical networks at different spatial scales, with respective enhancements in post-novelty functional coupling with a task-relevant cortical region and a large-scale memory network. The results presented here support an extended model of novelty-related plasticity, in which engaging the anterior hippocampal-VTA circuit through novelty exposure propagates cortical plasticity through hippocampal and VTA functional pathways at distinct scales, targeting specific or diffuse cortical networks.
Influence of individual characteristics, training design and environmental factors on training transfer: a study using hierarchical regression
Authors: Kodwani Amitabh Deo , Prashar Sanjeev 
Published: March 2021

PurposeThe purpose of this paper is to explore and provide empirical evidence for the combined effects of individual characteristics, training design factors as well as environmental factors (as pre-training factors) on training transfer.Design/methodology/approachPrimary data were collected from 235 managerial-level full-time employees in two phases with a temporal gap of two months. Both procedural and statistical measures were used to minimize the common method variance problem. Hierarchical regression analysis was conducted to analyze the data.FindingsThe results of this study clearly point out that all four predictor variables (voluntary participation, prior training information, training needs identification and training evaluation) positively and significantly influence training transfer.Research limitations/implicationsThe study contributes to the training transfer literature in three ways. One, the authors have shown the positive influence of pre-training factors (together as well as independently) on training transfer. The study is grounded in a strong theoretical framework, thus fulfilling the previous gap. This study brings more clarity to those variables (such as voluntary training) which are having contradicting views in the extant literature.Practical implicationsThe study has significant findings for the organizations operating in the current business scenario in their endeavor to enhance learning transfer, which is very low and a major cause of concern for every organization. If management is aware of the success factors of training transfer, they can ensure a better training transfer.Originality/valueThe training transfer literature showcases two significant gaps; first of all, it lacks in using appropriate motivational theories, and second, there is variability in the results. This paper bridges both the gaps and attempts to advance our understanding of training transfer grounded in the theoretical framework by focusing on the role of individual, motivational and situational factors of training transfer to understand better which predictor variables can improve training transfer.
Up-fuse transforming plastic waste into innovative products: the case study of a sustainable Egyptian start-up
Authors: Abdelnaeim Shrouk Mahmoud , El-Bassiouny Noha M. , Paul Pallab 
Published: March 2021

Learning outcomes
Understand the implementation phase of sustainable start-ups. Identifying the 4 Ps of sustainable start-ups. Understand the different types of challenges faced by Up-Fuse regarding their target customers and their value proposition. Highlighting the important strategic decisions that sustainable start-ups have to consider in their business cycle. Analyzing the differences between the market conditions globally and in the Middle East and North Africa (MENA) region.

Case overview/synopsis
Sustainable entrepreneurship is the type of entrepreneurship that is market-oriented and creative while at the same time putting the environment, society and economy into consideration. Sustainable entrepreneurs offer value through their goods and services that are beneficial or at least do not harm the environment or the society. The case provides background information and facts about doing business in the MENA region and Egypt specifically. Afterward, the case study emphasizes the challenges that are faced by sustainable entrepreneurs in Egypt through analyzing the case of a sustainable Egyptian start-up. The case study is on Up-Fuse, one of the sustainable start-ups in Egypt that produce backpacks, shoulder and waist bags, laptop sleeves, cases and pouches. This case study aims at describing the different challenges and strategic decisions that sustainable start-ups go through in Egypt.

Complexity academic level
This case targets undergraduate management students, marketing students, master of business administration students, entrepreneurship students and entrepreneurs. This case can be taught in courses with marketing, entrepreneurship and sustainability focus.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship.
Internal workforce, symbolism and licensed products: 17th Asian Games
Authors: Lee Hyun-Woo , Hussain Umer , Park Shawn Saeyeul , Shin Sunyun , Shim Woo Taek 
Published: March 2021

Learning outcomes
The questions raised in the case study could escort a classroom or online discussion for understanding licensed product consumption motives among the internal workforce.

Case overview/synopsis
Despite the Asiad (an abbreviation of Asian Games) being organized in the most populous continent, its financial profitability is minimal compared with the summer Olympic Games and other major sporting events. Thereby, Asiad board members are seeking to understand how they can target the right segment via licensed products. This will ultimately increase licensed product sales. On July 1, 2017, a board meeting was held in which the licensing product manager, Young Lee, proposed to target the internal workforce via licensed products based on 17th Asiad’s data and previous literature. Lee analyzed the attributes of licensed products sold at 17th Asiad and its psychological connection with the internal workforce. Hence, the purpose of this case study was to decipher the internal workforce feasibility as the right segment to target via licensed products for Asiad's management. The case study’s primary data was collected via IB worldwide (now Galaxia SM CO, Ltd), one of the leading sport marketing organizations in South Korea. The IB worldwide (now Galaxia SM CO, Ltd) signed an exclusive product license agreement with the Incheon Asian Games Organizing Committee jointly and individually with the Olympic Council of Asia to produce licensed products (e.g. Mascot dolls). This realistic case study should be understood through the lens of symbolic interactionism. Finally, this study is important to consider because the internal workforce licensed products consumption has gained little attention in sports marketing literature.

Complexity Academic Level
The case can be taught in marketing research and consumer behavior courses.

Subject code
CSS 8: Marketing.

Supplementary materials
Teaching notes are available for educators only.
Assessing the effectiveness of vocational training programs in Pakistan: an experimental study
Authors: Chamadia Sumaira , Mubarik Muhammad Shujaat 
Published: March 2021

PurposeThe major objective of this study is to examine the efficacy of the technical and vocational training courses imparted to generate employment or enhance the productivity of participants.Design/methodology/approachThe study was conducted in the province of Sindh, Pakistan by adopting a quasi-experimental approach. The experiment was conducted on 105 individuals—with the age group of 20–25—distributed between the treatment group and the control group. The data collected through the experiment were analyzed by applying a paired-sample t-test, independent sample t-test and one-way between-group analysis of variance (ANOVA).FindingsThe findings of this study show statistically significant higher monthly earnings of Rs14, 223 after the training intervention program. Findings also exhibit a significant difference in monthly earnings between the control and the treatment groups.Practical implicationsThe findings of the study can provide useful input to policymakers while devising the policies regarding technical education and vocational training (TVET) and to the international donors in assessing the impact of the training initiatives.Originality/valueThis study presents experimental-driven evidence on the role of technical education and vocational training in improving the labor market outcomes.
Identifying and measuring the impact of cultural events on hotels’ performance
Authors: Piga Claudio , Melis Giuseppe 
Published: March 2021

Purpose
Focusing on two beer festivals held in Nottingham, England, this study aims to evaluate their indirect impact on the performance of city hotels. This study builds on theoretical insights from the revenue management literature to shed empirical light on the potentially beneficial effects of events on the hotels’ performance. This study investigates the impact of the differential support offered by the destination management organisation (DMO) over two years.

Design/methodology/approach
Using online prices posted in advance of the events on an online travel agent, the authors assess hotel performance for each day of the events relative to the same day of the week in a week with no event. A similar comparison is made to assess the impact across two different years. In both cases, an ordinary least squares methodology was used.

Findings
Both events appear not to have had a strong impact on hotel prices and occupancy in 2016, i.e. when the DMO’s promotional effort was more proactive. Instead, in 2017, one event registered higher hotel prices and occupancy both relative to the year before and to the “business as usual” week.

Practical implications
The study identifies the existence of an indirect positive economic impact of the events on the hospitality sector.

Originality/value
The investigation adopts a more naturalistic experimental design to collect the data, which allows the authors to control for both the impact on prices and occupancy at the level of the single hotel. The evidence is therefore micro-founded. Moreover, results shed light on the role played by the DMO.