bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene regulatory effects of a large chromosomal inversion in highland maize
Authors: Crow Taylor , Ta James , Nojoomi Saghi , Aguilar-Rangel M. Rocío , Rodríguez Jorge Vladimir Torres , Gates Daniel , Rellan-Alvarez Ruben , Sawers Ruairidh , Runcie Daniel 
Published: December 2019

AbstractChromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms that underlie an inversion’s role in adaption. In this study, we explore how large-scale transcriptomic data can be used to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. First, using a large publicly available association mapping panel, we confirmed that Inv4m is associated with locally adaptive agronomic phenotypes, but only in highland fields. Second, we created two families segregating for standard and inverted haplotypess of Inv4m in a isogenic B73 background, and measured gene expression variation association with Inv4m across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m, and speculate that the genetic basis of its effects on adaptive traits is distributed across many separate functional variants.Author SummaryChromosomal inversions are an important type of genomic structural variant. However, mapping causal alleles within their boundaries is difficult because inversions suppress recombination between homologous chromosomes. This means that inversions, regardless of their size, are inherited as a unit. We leveraged the high-dimensional phenotype of gene expression as a tool to study the genetics of a large chromosomal inversion found in highland maize populations in Mexico - Inv4m. We grew plants carrying multiple versions of Inv4m in a common genetic background, and quantified the transcriptional reprogramming induced by alternative alleles at the locus. Inv4m has been shown in previous studies to have a large effect on flowering, but we show that the functional variation within Inv4m affects many developmental and physiological processes.Author ContributionsT. Crow, R. Rellan-Alvarez, R. Sawers and D. Runcie conceived and designed the experiment. M. Aguilar-Rangel, J. Rodrǵuez, R. Rellan-Alvarez and R. Sawers generated the segregating families. T. Crow, J. Ta, S. Nojoomi, M. Aguilar-Rangel, J. Rodrǵuez D. Gates, D. Runcie performed the experiment. T. Crow, D. Gates, D. Runcie analyzed the data. T. Crow, D. Runcie wrote the original manuscript, and R. Rellan-Alvarez and R. Sawers provided review and editing.
Development of a highly effective African swine fever virus vaccine by deletion of the I177L gene results in sterile immunity against the current epidemic Eurasia strain
Authors: Borca Manuel V. , Medina Elizabeth Ramirez , Silva Ediane , Vuono Elizabeth , Rai Ayushi , Pruitt Sarah , Holinka Lauren G. , Salinas Lauro Velazquez , Zhu James , Gladue Douglas P. 
Published: December 2019

AbstractAfrican swine fever virus (ASFV) is the etiological agent of a contagious and often lethal disease of domestic pigs that has significant economic consequences for the swine industry. The disease is devastating the swine industry in Central Europe and East Asia, with current outbreaks caused by circulating strains of ASFV derived from the 2007 Georgia isolate (ASFV-G), a genotype II ASFV. In the absence of any available vaccines, African Swine Fever (ASF) outbreak containment relies on control and culling of infected animals. Limited cross protection studies suggest that in order to ensure a vaccine is effective it must be derived from the current outbreak strain or at the very least from an isolate with the same genotype. Here we report the discovery that deletion of a previously uncharacterized gene, I177L, from the highly virulent ASFV-G produces complete virus attenuation in swine. Animals inoculated intramuscularly with the virus lacking the I177L gene, ASFV-G-ΔI177L, in a dose range of 102to 106HAD50remained clinically normal during the 28 day observational period. All ASFV-G-ΔI177L-infected animals had low viremia titers, showed no virus shedding, developed a strong virus-specific antibody response and, importantly, they were protected when challenged with the virulent parental strain ASFV-G. ASFV-G-ΔI177L is one of the few experimental vaccine candidate virus strains reported to be able to induce protection against the ASFV Georgia isolate, and the first vaccine capable of inducing sterile immunity against the current ASFV strain responsible for recent outbreaks.ImportanceCurrently there is no commercially available vaccine against African swine fever. Outbreaks of this disease are devastating the swine industry from Central Europe to East Asia, and they are being caused by circulating strains of African swine fever virus derived from the Georgia2007 isolate. Here we report the discovery of a previously uncharacterized virus gene, which when deleted completely attenuates the Georgia isolate. Importantly, animals infected with this genetically modified virus were protected from developing ASF after challenge with the virulent parental virus. Interestingly, ASFV-G-ΔI177L confers protection even at low doses (102HAD50) and remains completely attenuated when inoculated at high doses (106HAD50), demonstrating its potential as a safe vaccine candidate. At medium doses (104HAD50) sterile immunity is achieved. Therefore, ASFV-G-ΔI177L is a novel efficacious experimental ASF vaccine protecting pigs from the epidemiologically relevant ASFV Georgia isolate.
Is the replication crisis a problem for biologists? A geometric morphometric approach
Authors: Vrdoljak Juan , Sanchez Kevin Imanol , Arreola-Ramos Roberto , Diaz Huesa Emilce Guadalupe , Villagra Alejandro , Avila Luciano Javier , Morando Mariana 
Published: December 2019

AbstractReplicability of findings is the key factor of scientific reliability. However, literature on this topic is scarce and apparently taboo for large scientific areas. Some authors named the failure to reproduce scientific findings ‘replication crisis’. Geometric morphometrics, a vastly used technique, is especially silent on replication crisis concern. Nevertheless, some works pointed out that sharing morphogeometric information is not a trivial fact, but need to be careful and meticulous. Here, we investigated the replicability of geometric morphometrics protocols on complex shapes and measurement error extension in three different types of taxa, as well as the potentiality of these protocols to discriminate among closely related species. We found a wide range of replication error that contributed from 19.5% to 60% of the total variation. Although, measurement error decreased with the complexity of the quantified shape, it often maintained high values. All protocols were able to discriminate between species, but more morphogeometric information does not imply better performance. We present evidence of replication crisis in life sciences and highlight the need to explore in deep different sources of variation that could lead to low replicability findings. Lastly, we enunciate some recommendations in order to improve the replicability and reliability of scientific findings.
Reticulocyte Infection Leads to Altered Behaviour, Drug Sensitivity and Host Cell Remodelling byPlasmodium falciparum
Authors: Naidu Renugah , Chu Trang TT , Tripathi Jaishree , Hu Yang , Subramanian Gowtham , Tong Jie Xin , Tripathi Pallavi , Fang Kong , Tan Kevin SW , Lim Chwee Teck , Chan Jerry K.Y. , Bozdech Zbynek , Chandramohanadas Rajesh 
Published: December 2019

AbstractPlasmodia are host-specific, both at the organism and cellular levels. During asexual development,Plasmodium spp.infect cells of erythroid lineage, with an overall propensity towards reticulocytes. This applies to evenPlasmodium (P.) falciparum, the most common causative agent of human malaria, implications of which remain unexplored. Herein, for the first time, we characterize the developmental stages and features ofP. falciparumculturedin vitroin young reticulocytes (CD71+) in comparison to standard normocyte (CD71-) cultures. We demonstrate that there are notable differences in the patterns of invasion, development and sensitivity to potent antimalarials (such as artemisinin and dihydroartemisinin) for parasites residing in CD71+reticulocytes. Through a transcriptomic approach, we report thatP. falciparumparasites are able to sense the host cell environment, and calibrate their metabolic and host cell remodelling pathways through differential gene expression. These results form an exciting avenue on which hitherto unexplored interactions betweenPlasmodium sppand different stages of host red blood cells could be investigated in the broader contexts of drug resistance, host tropism and zoonosis.Author SummaryParasites causing malaria infect red blood cells for development and proliferation during asexual development. This asexual erythrocytic stage determines higher parasite densities and eventual disease manifestation. Although the most virulent species of Plasmodium infecting humans known asPlasmodium falciparumis able to infect red blood cells of all ages, these parasites show a preference for younger blood cells. Of note, the biochemical and biophysical properties of young and adult red blood cells vary significantly. Herein, we undertook a comparative profiling of invasion process, parasite development and drug response ofPlasmoddium falciparumin two host cells: young red blood cells (reticulocytes) and mature red blood cells (normocytes). We demonstrate thatP. falciparuminfects human reticulocytes with higher affinity and demonstrate differential sensitivity to drugs such as artemisinin while they reside within reticulocytes. Furthermore, we show thatP. falciparumis able to detect differences in host environment and adapt to it by changing the expression of genes required for host cell remodelling.
Genomics of Human Respiratory Syncytial Virus Vaccine Attenuation
Authors: Junier Thomas , Kaiser Laurent , Chaturvedi Nimisha , Hartert Tina , Fellay Jacques 
Published: December 2019

ABSTRACTThe human orthopneumovirus (HRSV) is a major cause of lower respiratory tract infection in children worldwide. Despite decades of efforts, no vaccine is available. In this work, we report mutations that are frequent in vaccine candidates and rare in wild-type genomes, taking into account all the publicly available HRSV sequence data. These mutations are different from the ones already known to attenuate the virus, and thus may contribute to the effort towards producing a live attenuated vaccine against HRSV.
Vaping Perpetuates Cardiac Electrical Instability
Authors: Abouassali Obada , Chang Mengmeng , Reiser Michelle , Kanithi Manasa , Soni Ravi , Chidipi Bojjibabu , Noujaim Sami F. 
Published: December 2019

ABSTRACTBackgroundTobacco cigarette smoking is on the decline, but the usage of electronic nicotine delivery systems (ENDS) is gaining popularity, specifically in the teen and young adult age groups. While the cardiac toxicity of tobacco cigarette smoking has been widely studied and is well established, the possible cardiac toxicity of ENDS products and their design characteristics, such as added flavorings, are largely underexplored. Vaping, a form of electronic nicotine delivery, uses “e-liquid” to generate “e-vapor”, a smoke-like aerosolized mixture of nicotine and flavors. Here, we tested the hypothesis that vaping results in cardiac electrophysiological instability and arrhythmogenesis. We thus investigated how e-liquids with different flavors affect cardiac in-vitro and in-vivo toxicity, in cell culture and in animals.MethodsThree e-liquids with vanilla, cinnamon or fruit flavors were studied. We quantified apoptosis and oxygen consumption rate in HL-1 cells cultured with e-vapors extracts. In human iPSC derived ventricular cardiomyocytes (hiPSC-CM) cultured with e-vapor extract, beating frequency and repolarization duration were measured using multiple electrode arrays (MEA). Mass spectrometry (GC-MS) was used to analyze the composition of the e-vapors. Telemetric ECGs were obtained in freely moving C57BL/6J mice exposed to vanilla flavored e-vapor for 10 weeks and heart rate variability was analyzed (HRV). In-vivo inducibility of ventricular tachycardia as well as optical mapping of voltage in isolated Langendorff-perfused hearts were also carried out.ResultsE-vapor caused a dose dependent increase in toxicity in Hl-1 myocytes and e-vapors containing vanilla and cinnamon flavorings, as indicated by GC-MS, were more toxic, and inhibited cellular respiration more than the fruit flavored e-vapor. In hiPSC-CM cultured with 25% cinnamon flavored e-vapor for 24 hours, beating frequency increased, and the field potential duration significantly increased compared to air control. Inhalation exposure to vanilla flavored e-vapor for 10 weeks caused significant effects on HRV. Additionally, inducible VT was significantly longer, and in optical mapping, the magnitude of ventricular action potential duration alternans was significantly larger in the exposed mice compared to controlConclusionThe widely popular flavored ENDS are not harm free, and they show potential toxicity to the heart, in-vitro, and in vivo. Further studies are needed to further assess their cardiac safety profile, and long-term health effects.
Differential response trajectories to acute exercise in blood and muscle
Authors: Amar David , Lindholm Malene E. , Norrbom Jessica , Wheeler Matthew T. , Rivas Manuel A. , Ashley Euan A. 
Published: December 2019

AbstractA physically active lifestyle is essential for maintaining health, and is a powerful way to prevent chronic disease. However, the molecular mechanisms that drive exercise adaptation and transduce its beneficial effects, are incompletely understood. Here, we combined data from 49 studies that measured the whole transcriptome in humans before and after exercise to provide the power to draw novel observations not seen in any individual study alone. The resulting curated and standardized resource includes samples from skeletal muscle (n=1,260) and blood (n=726) in response to endurance or resistance exercise and training. Using a linear mixed effects meta-regression model selection strategy, we detected specific time patterns and novel regulatory modulators of the acute exercise response. Acute and long term responses to exercise were transcriptionally distinct. Exercise induced a more pronounced inflammatory response in skeletal muscle of older individuals. We identified multiple sex-specific response genes, where MTMR3 is a novel exercise-regulated gene. These results deepen our understanding of the transcriptional responses to exercise and provide a powerful resource for future research efforts in exercise physiology and medicine.
Comparative analysis on Chinese and foreign innovation performance research—based on Bibliometrics and science mapping analysis
Authors: Fang Xiaochen , Zhu Jinwei 
Published: December 2019

Purpose
This paper aims to present a systematic review of the literature concerning major aspects of innovation performance and compare the research hotspots of innovation performance in the twenty-first century with three primary purposes: first, to view the trend of Chinese and English literature on innovation performance research; second, to summarize the research streams in innovation performance; and third, to predict possible directions for future innovation performance research.

Design/methodology/approach
The authors first introduce a framework of innovation performance research developments. Then they construct a representative data set of bibliographic records, obtaining 1,768 articles in the SSCI citation index database and 1,431 articles in the CSSCI database. The authors then make a comparative analysis from two aspects: research themes and development of academic communities. The research objects are keywords and references so that co-word and co-cited reference networks are established. Finally, the authors combine the direction of research streams about “innovation performance” to summarize 28 questions in three research fields that can be studied in the future.

Findings
The momentum of the literature in English on innovation performance is increasing, whereas the Chinese literature has declined in recent years. The direction of research streams in Chinese and English literature is the same: they are the “innovation system/elements” research stream, the “innovation activity/ability” research stream and the “innovation network/social capital” research stream. Although the directions are the same, the specific contents of the research are different. The direction of future development of innovation performance research can be undertaken in three aspects: follow research into expanding hot topics, mine the research of typical academic circles and develop research into exploring more fields. Combined with the direction of research streams, 28 questions in three research fields are summarized.

Originality/value
Based on the background of “mass entrepreneurship and innovation” in China, the research on enterprise “innovation performance” is becoming more and more important. The findings help us summarize the research streams related to innovation performance research, better understand the themes that point to directions for future development of innovation performance research and summarize 28 questions.
The impact of information technology investment on enterprise financial performance in China
Authors: Ji Peinan , Yan Xiangbin , Yu Guang 
Published: December 2019

Purpose
This paper aims to examine the influence of information technology (IT) investment, including innovative IT investment and non-innovative IT investment, on comprehensive enterprise financial performance in a developing country, China.

Design/methodology/approach
This paper applies the method proposed by Barber and Lyon to construct the control group to study the impact of IT investment on financial performance of enterprises, using a sample of 229 IT investment announcement data of Chinese listed companies between 2011 and 2015.

Findings
The analysis of the financial benefits of these IT implementations yields mixed results. The results show that companies investing in IT can significantly improve profitability both the implementation and post-implementation periods for the full sample, improve the solvency only during the implementation phase, improve the growth ability after implementation time and cannot reduce business costs in all periods. At the same time, the authors find that, compared with non-innovative IT investment, the innovative samples do not achieve better financial performance, except the profitability financial indicator.

Research limitations/implications
There are several limitations in this research. First, there is no large sample about the IT investment information data set in China, so this study was compelled to use limited sample data from China; hence, this could lead to errors of too early generalization. Second, the firms in the sample are all in China’s listed companies, so this may either not accurately or possibly could reflect the entire environment of developing countries.

Originality/value
First, it extends the scope of the established literature by examining the influence of IT investment with China’s public firms data and IT investment to see if such spending has had an influence on corporate financial performance. Second, there is a lack of research on the impact of IT investment on comprehensive financial performance of an enterprise, compared with the previous one-sided financial performance, such as profitability or financial cost. Third, as far as the authors are aware, there are no studies on the impact of IT investment on firm financial performance based on innovative and non-innovative classification.
A blockchain-based trusted security zone architecture
Authors: Jo Jeong Hoon , Rathore Shailendra , Loia Vincenzo , Park Jong Hyuk 
Published: December 2019

Purpose
The purpose of this paper is to propose a trusted security zone architecture that uses a blockchain technology to provide secure sharing of data in the security zone while maintaining the integrity, confidentiality and availability of data. The blockchain uses a distributed network to ensure data availability and uses public ledgers to ensure the integrity and confidentiality of data.

Design/methodology/approach
The proposed architecture uses a blockchain technology to provide secure sharing of data in the security zone while maintaining the integrity, confidentiality and availability of data. The blockchain uses a distributed network to ensure data availability and uses public ledgers to ensure the integrity and confidentiality of data.

Findings
Analysis of the proposed architecture with a use case scenario demonstrates that it provides a robust security measure against unauthorized network intrusions.

Originality/value
Unlike the existing security zone, this paper adopts a method of storing data by using blockchain. It meets the need to study integrated authentication management methods of future research.
International competitiveness of China’s biomass products: a CMS and RCA analysis
Authors: Shuai Jing , Huang Fubin , Leng Zhihui , Cheng Xin 
Published: December 2019

Purpose
This paper aims to estimate the international competitiveness of China’s biomass energy products during 2007-2016 in the context of the Belt and Road Initiative.

Design/methodology/approach
In this paper, the authors used the constant market share model and the revealed comparative advantage index to analyze the evolution trend of China’s biomass products’ international competitiveness during the past decade from 2007 to 2016 based on the market structure of the Belt and Road Initiative.

Findings
The results show that: China’s major biomass energy products have no comparative advantages in the world market, nevertheless, their international competitiveness is on the rise; China’s biomass energy products have been agglomerated to the regional markets where the market demand growth is fast in the Belt and Road countries; and the unreasonable structure is an important factor influencing the international competitiveness of China’s biomass exports.

Originality/value
The authors analyzed the international competitiveness of China’s biomass energy products based on the “Belt and Road Initiative” with all the trading items, in an effort to propose policy implications for enhancing the comparative advantages of China’s biomass products in the international market especially in the Belt and Road regions.