bluuebunny/crossref_metadata_2025_split huggingface dataset:
Personalized genome assembly for accurate cancer somatic mutation discovery using cancer-normal paired reference samples
Authors: Xiao Chunlin , Chen Zhong , Chen Wanqiu , Padilla Cory , Fang Li-Tai , Liu Tiantian , Schneider Valerie , Wang Charles , Xiao Wenming 
Published: April 2021

AbstractThe use of personalized genome assembly as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but never been systematically investigated. Here we address the critical need of assessing the accuracy of somatic mutation detection using personalized genome assembly versus the standard human reference assembly (i.e. GRCh38). We first obtained massive whole genome sequencing data using multiple sequencing technologies, and then performedde novoassembly of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same donor with triple negative breast cancer. Compared to standard human reference assembly, the haplotype phased chromosomal-scale personalized genome was best demonstrated with individual specific haplotypes for some complex regions and medical relevant genes. We then used this well-assembled personalized genome as a reference for read mapping and somatic variant discovery. We showed that the personalized genome assembly results in better alignments of sequencing reads and more accurate somatic mutation calls. Direct comparison of mitochondrial genomes led to discovery of unreported nonsynonymous somatic mutations. Our findings provided a unique resource and proved the necessity of personalized genome assembly as a reference in improving somatic mutation detection at personal genome level not only for breast cancer reference samples, but also potentially for other cancers.
Establishment of the family Zarkiaceae (Oscillatoriales, Cyanobacteria) and description of the new marine generaZarkia(Zarkiaceae, Oscillatoriales) andRomeriopsis(Leptolyngbyaceae, Synechococcales), from northern Portugal
Authors: Hentschke Guilherme S. , Pinheiro Ângela , Ramos Vitor , Barreiro Aldo , Costa M. Sofia , Brule Sébastien , Vasconcelos Vitor M. , Leão Pedro N. 
Published: April 2021

ABSTRACTAbstract FigureThe morphology, 16S rRNA gene phylogeny and the 16S-23S rRNA gene ITS secondary structures of three strains of marine Cyanobacteria, isolated from inter- and subtidal environments from north Portugal were studied, resulting in the description ofZarkia subtidalensisgen. et. sp. nov. (Zarkiaceae fam. nov.) andRomeriopsis marinagen. et. sp. nov (Leptolyngbyaceae). No diacritical morphological characters were found either for the new family or for the new genera. The 16S rRNA gene Maximum Likelihood and Bayesian phylogenies supported thatZarkiaand Zarkiaceae are members of the Oscillatoriales, positioned close to Microcoleaceae genera, but distant fromMicrocoleus. Romeriopsisis positioned within the Leptolyngbyaceae and is closely related toAlkalinema. The secondary structures of the D1-D1’, Box B, V2 and V3 helices corroborate with the phylogenetic results. Furthermore, our study supports previous observations of polyphyletic Oscillatoriales families and reinforces the need for their taxonomical revision.
Evaluation of endogenous miRNA reference genes across different zebrafish strains, developmental stages and kidney disease models
Authors: Siegerist Florian , Lange Tim , Iervolino Anna , Koppe Thor Magnus , Zhou Weibin , Capasso Giovambattista , Endlich Karlhans , Endlich Nicole 
Published: April 2021

AbstractThe majority of kidney diseases arise from the loss of podocytes and from morphological changes of their highly complex foot process architecture, which inevitably leads to a reduced kidney filtration and total loss of kidney function. It could have been shown that microRNAs (miRs) play a pivotal role in the pathogenesis of podocyte-associated kidney diseases. Due to their fully functioning pronephric kidney, larval zebrafish have become a popular vertebrate model, to study kidney diseasesin vivo. Unfortunately, there is no consensus about a proper normalization strategy of RT-qPCR-based miRNA expression data in zebrafish. In this study we analyzed 9 preselected candidates dre-miR-92a-3p, dre-miR-206-3p, dre-miR-99-1, dre-miR-92b-3p, dre-miR-363-3p, dre-let-7e, dre-miR-454a, dre-miR-30c-5p, dre-miR-126a-5p for their capability as endogenous reference genes in zebrafish experiments.Expression levels of potential candidates were measured in 3 different zebrafish strains, different developmental stages, and in different kidney disease models by RT-qPCR. Expression values were analyzed with NormFinder, BestKeeper, GeNorm, and DeltaCt and were tested for inter-group differences.All candidates show an abundant expression throughout all samples and relatively high stability. The most stable candidate without significant inter-group differences was dre-miR-92b-3p making it a suitable endogenous reference gene for RT-qPCR-based miR expression zebrafish studies.
P53 TAD2 Domain (38-61) Forms Amyloid-like Aggregates in Isolation
Authors: Gadhave Kundlik , Kapuganti Shivani K , Mishra Pushpendra Mani , Giri Rajanish 
Published: April 2021

AbstractIn many cases, when cellular machinery is unable to restore changed protein conformations, they start sticking through exposed hydrophobic patches and form aggregates. A strong association between protein aggregation and Human diseases (such as Alzheimer’s, Parkinson’s, and Huntington’s disease) is well proven. p53 is a transcription factor that is also known as the guardian of the genome associated with cellular processes such as DNA repair, apoptosis, senescence, control of cell cycle, stress signaling and cellular homeostasis. The loss of function mutations in p53 have been implicated in several cancers. Experimental evidences have proposed a possible link between cancer and protein aggregation in evidence of the implication of amyloidogenic mutant proteins in ten different types of cancer. Aggregation studies focusing on different P53 domains, mostly, the central core domain and its mutants under the influence of various environmental conditions and P53 TAD domain (1-63) have been reported. P53 TADs interact with diverse cellular factors to modulate the function of P53 and elicit appropriate cellular response under different stress conditions. In this study, the aggregation of P53 TAD2 domain (38-61) have been studied in isolation. The aggregates were generated in-vitro in acidic pH conditions after in-silico scoring for amyloidogenic propensity and characterized using dye-based assays (ThT and bis-ANS fluorescence), CD spectroscopy, and microscopy (SEM, TEM and AFM). It was observed that P53 TAD2 follows nucleation-dependent kinetics and forms amyloid-like aggregates. On reductionists approach, this study highlights the nature of P53 TAD2 domain (amino acids 38-61) aggregation.
High-quality reference genome ofFasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions
Authors: Luo Xier , Cui Kuiqing , Wang Zhiqiang , Yin Lijuan , Li Zhipeng , Wu Zhengjiao , Feng Tong , Wang Xiaobo , Jin Weikun , Di Wenda , Wang Dongying , ur Rehman Saif , Huang Weiyi , Zhu Xingquan , Zhang Weiyu , Ruan Jue , Liu Qingyou 
Published: April 2021

AbstractFasciola giganticaandFasciola hepaticaare causative pathogens offascioliasis, with the widest latitudinal, longitudinal, and altitudinal distribution; however, among parasites, they have the largest sequenced genomes, hindering genomic research. In the present study, we used various sequencing and assembly technologies to generate a new high-qualityFasciola giganticareference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation between Fasciola and Fasciolopsis during the Cretaceous-Paleogene boundary mass extinction, and (2) the habitat switch to the liver during the Paleocene-Eocene Thermal Maximum, accompanied by gene length increment. Long interspersed element (LINE) duplication contributed to the second transposon-mediated alteration, showing an obvious trend of insertion into gene regions, regardless of strong purifying selection. Gene ontology analysis of genes with long LINE insertions identified membrane-associated and vesicle secretion process proteins, further implicating the functional alteration of the gene network. We identified 852 excretory/secretory proteins and 3300 protein-protein interactions betweenFasciola giganticaand its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy number variations, might play a central role in the phase I detoxification process. Analysis of 559 single-copy orthologs suggested thatFasciola giganticaandFasciola hepaticadiverged at 11.8 Ma near the Middle and Late Miocene Epoch boundary. We identified 98 rapidly evolving gene families, including actin and aquaporin, which might explain the large body size and the parasitic adaptive character resulting in these liver flukes becoming epidemic in tropical and subtropical regions.
SVhound: Detection of future Structural Variation hotspots
Authors: Paulin Luis F , Raveendran Muthuswamy , Harris R. Alan , Rogers Jeffrey , von Haeseler Arndt , Sedlazeck Fritz J 
Published: April 2021

AbstractRecent population studies are ever growing in size of samples to investigate the diversity of a given population or species. These studies reveal ever new polymorphism that lead to important insights into the mechanisms of evolution, but are also important for the interpretation of these variations. Nevertheless, while the full catalog of variations across entire species remains unknown, we can predict which regions harbor additional variations that remain hidden and investigate their properties, thereby enhancing the analysis for potentially missed variants.To achieve this we implemented SVhound (https://github.com/lfpaulin/SVhound), which based on a population level SVs dataset can predict regions that harbor novel SV alleles. We tested SVhound using subsets of the 1000 genomes project data and showed that its correlation (average correlation of 2,800 tests r=0.7136) is high to the full data set. Next, we utilized SVhound to investigate potentially missed or understudied regions across 1KGP and CCDG that included multiple genes. Lastly we show the applicability for SVhound also on a small and novel SV call set for rhesus macaque (Macaca mulatta) and discuss the impact and choice of parameters for SVhound. Overall SVhound is a unique method to identify potential regions that harbor hidden diversity in model and non model organisms and can also be potentially used to ensure high quality of SV call sets.
Relationships between research supervisors and students from coursework-based master’s degrees: information usage under social media
Authors: Dong Gunnan , Chiu Dickson K.W. , Huang Po-Sen , Ho Kevin K.W. , Lung Mavis Man-wai , Geng Ying 
Published: April 2021

Purpose
Existing studies reflect that traditional teaching–learning relationships between supervisors and graduate students have become disjointed with actuality seriously. In particular, there are practical difficulties in handling many students from coursework-based postgraduate degrees under current university curricula. Therefore, this study aims to explore the relationship between research supervisors and graduate students on social media, which is popular among students.

Design/methodology/approach
This study surveyed 109 graduate students from two majors (population around 100 each) of a university in Hong Kong to explore their information usage for research on social media, related attitudes and their perceived supervisor relationships. The differences between the two majors were also compared.

Findings
The authors’ findings indicated that graduate students were active on social media, and social media has successfully provided effective alternate ways for students to communicate with their research supervisors. Social media could improve relationships between supervisors and research students and among fellow students. Besides education purposes, students also discussed their personal affairs on social media with supervisors, demonstrating enhanced trusted relationships. Graduate students also showed confidence in the further application of social media in higher education. Some differences between respondents from the two programs were also found in terms of communication contents, strengths, personal preferences and purposes for using social media.

Originality/value
Scant studies focus on the relationship between supervisors and graduate students under the current social media environment, especially for students from coursework-based postgraduate degrees. At a deeper level, for the widespread use of social media in the information age, this study explores the specific changes brought about by social media. Therefore, this study is of great theoretical and practical value to graduate education under the current social media environment.
System dynamics modelling of fixed and dynamic Kanban controlled production systems: a supply chain perspective
Authors: K. Jagan Mohan Reddy , A. Neelakanteswara Rao , Lanka Krishnanand , Gopal PRC 
Published: April 2021

Purpose
Pull production systems have received much attention in the supply chain management environment. The number of Kanbans is a key decision variable in the pull production system as it affects the finished goods inventory (FGI) and backorders of the system. The purpose of this study is to compare the performance of the fixed and dynamic Kanban systems in terms of operational metrics (FGI and backorders) under the demand uncertainty.

Design/methodology/approach
In this paper, the system dynamics (SD) approach was used to model the performance of fixed and dynamic Kanban based production systems. SD approach has enabled the feedback mechanism and is an appropriate tool to incorporate the dynamic control during the simulation. Initially, a simple Kanban based production system was developed and then compared the performance of production systems with fixed and dynamic controlled Kanbans at the various demand scenarios.

Findings
From the present study, it is observed that the dynamic Kanban system has advantages over the fixed Kanban system and also observed that the variation in the backorders with respect to the demand uncertainty under the dynamic Kanban system is negligible.

Research limitations/implications
In a just-in-time production system, the number of Kanbans is a key decision variable. The number of Kanbans is mainly depended on the demand, cycle time, safety stock factor (SSF) and container size. However, this study considered only demand uncertainty to compare the fixed and dynamic Kanban systems. This paper further recommends researchers to consider other control variables which may influence the number of Kanbans such as cycle time, SSF and container size.

Originality/value
This study will be useful to decision-makers and production managers in the selection of the Kanban systems in uncertain demand applications.
How to overcome online banner blindness? A study on the effects of creativity
Authors: Yang Qiang , Zhou Yuanjian , Jiang Yushi , Huo Jiale 
Published: April 2021

Purpose
This study aims to explore whether creativity can overcome banner blindness in the viewing of web pages and demonstrate how visual saliency and banner-page congruity constitute the boundary conditions for creativity to improve memory for banner ads.

Design/methodology/approach
Three studies were conducted to understand the influence of advertising creativity and banner blindness on recognition of banner ads, which were assessed using questionnaires and bias adjustment. The roles of online user tasks (goal-directed vs free-viewing), visual saliency (high vs low) and banner-page congruity (congruent vs incongruent) were considered.

Findings
The findings suggest that creativity alone is not sufficient to overcome the banner blindness phenomenon. Specifically, in goal-directed tasks, the effect of creativity on recognition of banner ads is dependent on banner ads’ visual saliency and banner-page congruity. Creative banners are high on visual saliency, and banner-page congruity yields higher recognition rates.

Practical implications
Creativity matters for attracting consumer attention. And in a web page context, where banner blindness prevails, the design of banners becomes even more important in this respect. Given the prominence of banners in online marketing, it is also necessary to tap the potential of creativity of banner ads.

Originality/value
First, focusing on how creativity influences memory for banner ads across distinct online user tasks not just provides promising theoretical insight on the tackling of banner blindness but also enriches research on advertising creativity. Second, contrary to the popular belief of extant literature, the findings suggest that, in a web page context, improvement in memory for banner ads via creativity is subject to certain boundary conditions. Third, a computational neuroscience software program was used in this study to assess the visual saliency of banner ads, whereas signal detection theory was used for adjustment of recognition scores. This interdisciplinary examination combining the two perspectives sheds new light on online advertising research.
Strategic planning, strategy map and management control: a case study
Authors: Li Hezun , An Na , Liu Junyong 
Published: April 2021

Purpose
This paper aims to explore the relationship between the components of the management control system (MCS) based on the reform process of the management system of China Resources Group and the influence of these components on the implementation effect of MCS.

Design/methodology/approach
This study uses an exploratory research method and an open-ended grounded theory approach to conduct six formal investigations and several in-depth interviews with employees and senior management in China Resources Group. This paper supplements these data by performing a documentary analysis of the internal documents of China Resources Group such as the statistical yearbook, business plan and meeting records.

Findings
This study puts forward four propositions. The formal strategic planning process creates an application environment for the strategy map and balanced scorecard (BSC), making it easier for an enterprise to adopt these tools. The combination of the strategy map and formal strategic planning helps to build the logical relationship between strategic goals and budget goals and strengthens the correlation between budget and strategy. In diversified organizations applying MCS, the strategy map and BSC facilitate the implementation of the strategy for specialized business units, while the financial measure system facilitates the implementation of the strategy for diversified business units. Strategic boundaries based on financial measures in the MCS help organizations determine the scope of strategic choices before implementing strategies.

Research limitations/implications
Because of the chosen research approach, the research results may lack generalizability and the influence of the strategic planning process on budget participation, budget slack and other budget behaviors has not been fully discussed. Therefore, future studies are expected to provide more evidence regarding strategic planning and budget behaviors.

Practical implications
Before establishing a strategy map and BSC, the enterprise should consider the application environment to ensure their feasibility and legitimacy and construct the BSC system under appropriate conditions. A formal strategic planning process should be formed within the enterprise; that is, a set of detailed management methods should be adopted and clear rules should be used to support the enterprise management control process. The enterprise should add strategic boundaries to the MCS to determine the scope of strategic choices and the budgeting bottom line.

Originality/value
This paper sheds light on the impact of the formal strategic planning process on the organization and contributes new evidence on the key success factors for implementing the strategy map and BSC, enriching the researchers’ understanding of the applicability of the BSC.
A systematic review of consumer information search in online and offline environments
Authors: C. Haridasan Anu , Fernando Angeline Gautami , Saju B. 
Published: April 2021

Purpose
The purpose of this study is to identify major themes and potential research opportunities in online and offline consumer search.

Design/methodology/approach
A systematic review was conducted based on 118 articles identified from prevalent journal databases. Keywords frequency analysis was carried out to identify the major themes. An inductive thematic analysis was carried out to verify the generated themes.

Findings
Results show that uncertainty, knowledge, perceived risk, price, experience and involvement are the major themes associated with consumer information search. Uncertainty, one of the major themes of offline search, has not been studied in the online search context. Similarly, the previous experience needs to be explored in the context of the offline search. Finally, potential research opportunities for future research has been summarized based on the retrieved themes.

Research limitations/implications
The systematic review provides an in-depth understanding on the current research on information search literature with future research directions.

Practical implications
This study helps retailers to understand the key elements that motivate consumers to perform external information searches from online and offline sources and to curate targeted information provision strategies to influence purchase decisions.

Social implications
Consumers with limited internet availability may access channels prior to decision-making. The themes identified in this study can aid policymakers to design affordable access to these channels.

Originality/value
This study adds to the sparse literature on systematic reviews on consumer search for online and offline channels.