bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered DNA methylation in ion transport and immune signalling genes is associated with severity in Pancreatic Ductal Adenocarcinoma
Authors: Chatterjee Ankita , Bararia Akash , Ganguly Debopriyo , Roy Paromita , Banerjee Sudeep , Ghosh Shibajyoti , Gulati Sumit , Ghatak Supriyo , Chattopadhay Bitan Kumar , Maitra Arindam , Basu Priyadarshi , Chatterjee Aniruddha , Sikdar Nilabja 
Published: June 2021

AbstractBackgroundPancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a relative five-year survival rate of only 8.5%. In this study we investigated epigenetic marksassociated with PDAC severity and prognosis, through studying alterations in DNA methylation patterns.MethodsDNA methylome for tumor and adjacent normal tissue samples from PDAC patients (n=7) were generated using Illumina 450K bead chips. Differentially methylated positions (DMPs) were identified with |delta beta| > 0.2 and p-value<0.01 by comparing tumors with the adjacent normal tissues. Validation of differential methylation and associated gene expression at selected genes was carried out in an independent cohort PDAC patient.ResultsWe identified 76 DMPs in PDAC patients that mapped to 43 genes. Among them, 44.7% (n=34) were hypo-methylated and 55.3% (n=42) were hyper-methylated DMPs in cancer samples. The trends of change in methylation at these 76 DMPs from well to moderate were like that from moderate to poorly differentiated cancer samples. The gradual trend in differential methylation was observed both in our cohort and the TCGA-PAAD cohort, suggesting methylation marks can serve as early indicators of disease pathology. Altered promoter methylation, which may affect gene expression, was observed for transcription regulators (BHLHE23, GSC2, FOXE1 and TWIST1), gated ion channels (KCNA6, and CACNB2), tumor suppressors (RASSF1, SPRED2, and NPY) and genes functioning in interferon signalling (SIGIRR, MX2, and OAS2). We also have compared the TCGA-PAAD dataset with normal pancreatic tissue data from GTEx V8 dataset leading to a confluent observation.ConclusionsWe reported the first study on methylome in PDAC tumors from patients in India. We identified altered DNA methylation associated with increasing severity in PDAC among some genes like SIGIRR, MX2 along with other previously reported loci. We also concluded a confluence in our observation when comparing the TCGA-PAAD dataset with GTEx V8 dataset.
A high-throughput multiplexing and selection strategy to complete bacterial genomes
Authors: Arredondo-Alonso Sergio , Pöntinen Anna K. , Cléon François , Gladstone Rebecca A. , Schürch Anita C. , Johnsen Pål J , Samuelsen Ørjan , Corander Jukka 
Published: June 2021

AbstractBackgroundBacterial whole-genome sequencing based on short-read sequencing data often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits to unambiguously bridge those contiguous sequences into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced.Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose a long-read isolate selection strategy that optimizes a representative selection of isolates from large-scale bacterial collections.ResultsDespite an uneven distribution of long-reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98) which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable: (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library.ConclusionsThe proposed long-read isolate selection ensures completing bacterial genomes of isolates that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance
Authors: Dorel Mathurin , Klinger Bertram , Mari Tommaso , Toedling Joern , Blanc Eric , Messerschmidt Clemens , Nadler-Holly Michal , Ziehm Matthias , Sieber Anja , Hertwig Falk , Beule Dieter , Eggert Angelika , Schulte Johannes H. , Selbach Matthias , Blüthgen Nils 
Published: June 2021

AbstractVery high risk neuroblastoma is characterised by increased MAPK signalling, and targeting MAPK signalling is a promising therapeutic strategy. We used a deeply characterised panel of neuroblastoma cell lines and found that the sensitivity to MEK inhibitors varied drastically between these cell lines. By generating quantitative perturbation data and mathematical modelling, we determined potential resistance mechanisms. We found that negative feedbacks within MAPK signalling and to the IGF receptor mediate re-activation of MAPK signalling upon treatment in resistant cell lines. By using cell-line specific models, we predict that combinations of MEK inhibitors with RAF or IGFR inhibitors can overcome resistance, and tested these predictions experimentally. In addition, phospo-proteomics profiles confirm the cell-specific feedback effects and synergy of MEK and IGFR targeted treatements. Our study shows that a quantitative understanding of signalling and feedback mechanisms facilitated by models can help to develop and optimise therapeutic strategies, and our findings should be considered for the planning of future clinical trials introducing MEKi in the treatment of neuroblastoma.
Unexpected gene activation following CRISPR-Cas9-mediated genome editing
Authors: Manjón Anna G , Teunissen Hans , de Wit Elzo , Medema René H 
Published: June 2021

AbstractThe discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) and its development as a genome editing tool has revolutionized the field of molecular biology. In the DNA damage field, CRISPR has brought an alternative to induce endogenous double-strand breaks (DSB) at desired genomic locations and study the DNA damage response and its consequences. Many systems for sgRNA delivery have been reported in order to efficiency generate this DSB, including lentiviral vectors. However, some of the consequences of these systems are yet not well understood. Here we report that lentiviral-based sgRNA vectors can integrate into the endogenous genomic target location, leading to undesired activation of the target gene. By generating a DSB in the regulatory region of the ABCB1 gene using a lentiviral sgRNA vector, we can induce the formation of taxol-resistant colonies. We show that these colonies upregulated ABCB1 via integration of the EEF1A1 and the U6 promoters from the sgRNA vector. We believe that this is an unreported CRISPR/Cas9 artefact that researchers need to be aware of when using lentiviral vectors for genome editing.
Bacteriophage T4 Vaccine Platform for Next-generation Influenza Vaccine Development
Authors: Li Mengling , Guo Pengju , Chen Cen , Feng Helong , Zhang Wanpo , Gu Changqin , Wen Guoyuan , Rao Venigalla B. , Tao Pan 
Published: June 2021

AbstractDeveloping influenza vaccines that protect against a broad range of viruses is a public health priority, and several conserved viral proteins or domains have been identified as promising targets for such vaccine development. However, none of the targets is immunogenic, and vaccine platforms that can incorporate multiple antigens with enhanced immunogenicity are desperately needed. In this study, we provided proof-of-concept for the development of next-generation influenza vaccine using T4 phage virus-like particle (VLP) platform. With extracellular domain of influenza matrix protein 2 (M2e) as a readout, we showed that more than 1,280 M2e molecules can be assembled on a 120×90 nanometer phage capsid to form T4-M2e VLPs, which are highly immunogenic and induced complete protection against influenza virus challenge without any addition adjuvant. Potentially, additional conserved antigens or molecular adjuvants could be incorporated into the T4-M2e VLPs to customize influenza vaccines to address different issues. All the components of T4 VLP vaccines can be mass-produced in E. coli in a short time, therefore, providing a rapid approach to deal with the potential influenza pandemic.
Optimal resource management and allocation for autonomous-vehicle-infrastructure cooperation under mobile edge computing
Authors: Zhou Shengpei , Chang Zhenting , Song Haina , Su Yuejiang , Liu Xiaosong , Yang Jingfeng 
Published: June 2021

Purpose
With the continuous technological development of automated driving and expansion of its application scope, the types of on-board equipment continue to be enriched and the computing capabilities of on-board equipment continue to increase and corresponding applications become more diverse. As the applications need to run on on-board equipment, the requirements for the computing capabilities of on-board equipment become higher. Mobile edge computing is one of the effective methods to solve practical application problems in automated driving.

Design/methodology/approach
In this study, in accordance with practical requirements, this paper proposed an optimal resource management allocation method of autonomous-vehicle-infrastructure cooperation in a mobile edge computing environment and conducted an experiment in practical application.

Findings
The design of the road-side unit module and its corresponding real-time operating system task coordination in edge computing are proposed in the study, as well as the method for edge computing load integration and heterogeneous computing. Then, the real-time scheduling of highly concurrent computation tasks, adaptive computation task migration method and edge server collaborative resource allocation method is proposed. Test results indicate that the method proposed in this study can greatly reduce the task computing delay, and the power consumption generally increases with the increase of task size and task complexity.

Originality/value
The results showed that the proposed method can achieve lower power consumption and lower computational overhead while ensuring the quality of service for users, indicating a great application prospect of the method.
Online monitoring experiments of turbo-shaft engine based on electrostatic sensor
Authors: Guo Jiachen , Jiang Heng , Zhong Zhirong , Zuo Hongfu , Zhang Huan 
Published: June 2021

Purpose
Electrostatic monitoring technology is a useful tool for monitoring and detecting component faults and degradation, which is necessary for engine health management. This paper aims to carry out online monitoring experiments of turbo-shaft engine to contribute to the practical application of electrostatic sensor in aero-engine.

Design/methodology/approach
Combined with the time and frequency domain methods of signal processing, the authors analyze the electrostatic signal from the short timescale and the long timescale.

Findings
The short timescale analysis verifies that electrostatic sensor is sensitive to the additional increased charged particles caused by abnormal conditions, which makes this technology to monitor typical failures in aero-engine gas path. The long scale analysis verifies the electrostatic sensor has the ability to monitor the degradation of the engine gas path performance, and water washing has a great impact on the electrostatic signal. The spectrum of the electrostatic signal contains not only the motion information of the charged particles but also the rotating speed information of the free turbine.

Practical implications
The findings in this article prove the effectiveness of electrostatic monitoring and contribute to the application of this technology to aero-engine.

Originality/value
The research in this paper would be the foundation to achieve the application of the technology in aero-engine.
Ghana’s ICT4AD policy: between policy and reality
Authors: Kubuga Kennedy Kumangkem , Ayoung Daniel Azerikatoa , Bekoe Stephen 
Published: June 2021

PurposeNearly at the end of its lifespan, the Ghana ICT4AD policy is in a position for a holistic view, especially through the eyes of the intended beneficiaries. This paper aims to fill that gap. The paper measures the gap between what was intended and what has been realised and, based on that, makes recommendations for stakeholders.Design/methodology/approachThe research used the design reality gap analysis approach to numerically examine the deviation or otherwise of the ideals of the Ghana ICT4AD policy from or to the reality on the ground. It required the breaking down of the problem into dimensions and subdimensions and involved interviewing office holders, academics, practitioners and students over a three-year period. The recommendations include a review of the policy before it expires and an explicit designation of an agency responsible for coordination, monitoring and evaluation of the various stages of the policy.FindingsThe chief finding is that Ghana’s ICT4AD policy might miss the targets totally, or might well be a partial failure unless action is taken to close the design–reality gaps identified by the research. As the policy is almost at the end of its lifespan, recommendations are even more useful when the recommended revision takes place.Research limitations/implicationsThe major limitation of the is that it looks only at the implementation success or failure without a probe into the causal factors and/or the impact on society.Practical implicationsThe policy runs full term at end 2022, with large gaps between the plans of the framers and the reality on the ground. An immediate revision of the policy is most recommended.Originality/valueBesides this study, the authors have not come across any such comprehensive study of the Ghana ICT4AD policy, especially with the amount of data now available after two decades. There is a similarity with a Pakistani study, which has been acknowledged in this study, but the two works differ greatly in methodology, context and style.
Predicting agricultural and livestock products purchases using the Internet search index and data mining techniques
Authors: Rho Hoyoung , Choi Keunho , Yoo Donghee 
Published: June 2021

PurposeThis study identifies whether the Internet search index can be used as effective enough data to identify agricultural and livestock product demand and compare the accuracy of the prediction of major agricultural and livestock products purchases between these prediction models using artificial neural network, linear regression and a decision tree.Design/methodology/approachArtificial neural network, linear regression and decision tree algorithms were used in this study to compare the accuracy of the prediction of major agricultural and livestock products purchases. The analysis data were studied using 10-fold cross validation.FindingsFirst, the importance of the Internet search index among the 20 explanatory variables was found to be high for most items, so the Internet search index can be used as a variable to explain agricultural and livestock products purchases. Second, as a result of comparing the accuracy of the prediction of six agricultural and livestock purchases using three models, beef was the most predictable, followed by radishes, chicken, Chinese cabbage, garlic and dried peppers, and by model, a decision tree shows the highest accuracy of prediction, followed by linear regression and an artificial neural network.Originality/valueThis study is meaningful in that it analyzes the purchase of agricultural and livestock products using data from actual consumers' purchases of agricultural and livestock products. In addition, the use of data mining techniques and Internet search index in the analysis of agricultural and livestock purchases contributes to improving the accuracy and efficiency of agricultural and livestock purchase predictions.
The effect of COVID-19 prevention methods training given through distance learning on state anxiety level: the case of private sector
Authors: Ucuk Sultan , Yildirim Gulay 
Published: June 2021

PurposeThe aim of this study was to determine the effect of coronavirus disease 2019 (COVID-19) prevention methods training given by distance learning technique on the state anxiety level of the workers of a company serving in the communication sector.Design/methodology/approachThe sample of this experimental and cross-sectional study consisted of 52 people working in the communication sector. Data were collected using a questionnaire and the state anxiety inventory. Data were analyzed using descriptive statistics, t-test, variance analysis, Kruskal–Wallis, Mann–Whitney U and Tukey’s test.FindingsWhile the state anxiety scores of the workers working in the communication sector were 47.94 ± 4.90 before the training, they were found to be 43.98 ± 5.20 after the training.Research limitations/implicationsAs in every study, this study has some limitations. Although a homogeneous sample is tried to be formed since it only covers this group, it should be considered that there is a limitation in terms of generalizability. In addition, the fact that the knowledge score is not measured and the relationship between the knowledge score and the anxiety score is not evaluated should be considered as a limitation. Finally, it is also a limitation that the questionnaire form, which includes measurement tools, is applied online. It is thought that measuring errors can be minimized if questionnaires are applied face to face.Practical implicationsThe results of the study showed that the training given to the workers in the communication sector contributed positively to the reduction of anxiety levels. It is important to provide training and support to those with high anxiety levels. After providing effective protection for nurses/midwives under pandemic conditions and preventing their uncertainties, they can contribute to the reduction of anxiety levels by providing training to individuals who serve the society. It is recommended to plan health trainings for the anxiety of other sector workers serving the society and to focus on these groups. Thus, the effective protection of individuals and their service quality will increase and their anxiety may decrease.Originality/valueInformative support from nurses/midwives can make it easier to control anxiety arising from the COVID-19 pandemic. The results are important in order to draw attention to the anxiety of other sector workers serving the society and the importance of informative roles of nurses. In order to reduce the anxiety levels of workers in different sectors, it is recommended to conduct more supportive training activities and to draw attention to the workers serving the society.
A comprehensive survey on utilization of hybrid nanofluid in plate heat exchanger with various number of plates
Authors: Afshari Faraz , Tuncer Azim Doğuş , Sözen Adnan , Variyenli Halil Ibrahim , Khanlari Ataollah , Gürbüz Emine Yağız 
Published: June 2021

Purpose
Using suspended nanoparticles in the base fluid is known as one of the most efficient ways for heat transfer augmentation and improving the thermal efficiency of various heat exchangers. Different types of nanofluids are available and used in different applications. The main purpose of this study is to investigate the effects of using hybrid nanofluid and number of plates on the performance of plate heat exchanger. In this study, TiO2/water single nanofluid and TiO2-Al2O3/water hybrid nanofluid with 1% particle weight ratio have been used to prepare hybrid nanofluid to use in plate type heat exchangers with three various number of plates including 8, 12 and 16.

Design/methodology/approach
The experiments have been conducted with the aim of examining the impact of plates number and used nanofluids on heat transfer enhancement. The performance tests have been done at 40°C, 45°C, 50°C and 55°C set outlet temperatures and in five various Reynolds numbers between 1,600 and 3,800. Also, numerical simulation has been applied to verify the heat and flow behavior inside the heat exchangers.

Findings
The results indicated that using both nanofluids raised the thermal performance of all tested exchangers which have a various number of plates. While the major outcomes of this study showed that TiO2-Al2O3/water hybrid nanofluid has priority when compared to TiO2/water single type nanofluid. Utilization of TiO2-Al2O3/water nanofluid led to obtaining an average improvement of 7.5%, 9.6% and 12.3% in heat transfer of heat exchangers with 8, 12 and 16 plates, respectively.

Originality/value
In the present work, experimental and numerical analyzes have been conducted to investigate the influence of using TiO2-Al2O3/water hybrid nanofluid in various plate heat exchangers. The attained findings showed successful utilization of TiO2-Al2O3/water nanofluid. Based on the obtained results increasing the number of plates in the heat exchanger caused to obtain more increment by using both types of nanofluids.
Role of digital economy and technology adoption for financial inclusion in India
Authors: Vyas Vishal , Jain Priyanka 
Published: June 2021

Purpose
The study aims to explore the role of digital economy and technology adoption for financial inclusion in the Indian context.

Design/methodology/approach
A conceptual framework was developed and hypotheses were tested through a survey conducted on 433 educated adults (males and females) residing in different districts of Rajasthan (India). Data was collected through a structured questionnaire and was subjected to confirmatory factor analysis. Structural equation modeling (second-order) was used to validate the measurement model and to test the mediating effect.

Findings
The measurement model is a confirmatory factor analysis and measures the reliability of the observed variables in relation to the latent constructs and indices shows the overall model fit. Structural model results indicate a complete mediation and a reflective impact (R2 = 0.28) of the extended technology acceptance model on digital economy and financial inclusion relationship.

Research limitations/implications
The study has taken into account only the perception of educated adults residing more specifically in one geographical area of a country. Thus, it limits the generalization of results in terms of implications to other regions and countries.

Practical implications
The proposed framework and implications are quite significant for policymakers and service providers to understand the nexus and strategic choices involved in this area. Moreover, understanding of user’s frame dependence would help in the development of digital assistive models that would perhaps mitigate the gap from participation (digital economy) to acceptance (financial inclusion).

Originality/value
Present study proposed a three-dimensional hypothetical model and conceptualized the digital economy (independent variable) as participation, behavioral intentions measured through the extended technology acceptance model (mediating variable) as adoption and financial inclusion (dependent variable) as acceptance to better understand the nexus. It represents the foremost step and a unique effort in this area. Moreover, the study was empirical and has wider applications both from the perspectives of end-users and service providers.