bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)
Authors: Nieuwenhuis Ronald , Hesselink Thamara , van den Broeck Hetty C. , Cordewener Jan , Schijlen Elio , Bakker Linda , Trivino Sara Diaz , Struss Darush , de Hoop Simon-Jan , de Jong Hans , Peters Sander A. 
Published: November 2021

AbstractWe present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations as well as k-mer clustering analysis pointed to the presence of at least 2 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation, using gene models derived from mapped IsoSeq transcriptome data, generated over 130,000 putative genes. Mapped transcriptome data from public okra accessions of Asian origin confirmed the predicted genes, showing limited genetic diversity of 1SNP/2.1kb. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.
Profile of the in silico secretome of the palm dieback pathogen, a fungus that puts natural oases at risk
Authors: Rafiqi Maryam , Jelonek Lukas , Diouf Aliou M. , Mbaye AbdouLahat , Rep Martijn , Diarra Alhousseine 
Published: November 2021

AbstractUnderstanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that causes dieback disease on date palms, a tree that provides several critical ecosystem services in natural oases; and consequently, of major importance in this vulnerable habitat. Here, we assess the current state of global pathogen spread, we annotate the genome of a sequenced pathogen strain isolated from the native range and we analyse its in silico secretome. The palm dieback pathogen secretes a large arsenal of effector candidates including a variety of toxins, a distinguished profile of secreted in xylem proteins (SIX) as well as an expanded protein family with an N-terminal conserved motif [SG]PC[KR]P that could be involved in interactions with host membranes. Using agrobiodiversity as a strategy to decrease pathogen infectivity, while providing short term resilient solutions, seems to be widely overcome by the pathogen. Hence, the urgent need for future mechanistic research on the palm dieback disease and a better understanding of pathogen genetic diversity.
A method to quantitate maternal transcripts localized in sea urchin egg cortex by RT-qPCR with accurate normalization
Authors: Kipryushina Yulia O. , Maiorova Mariia A. , Yakovlev Konstantin V. 
Published: November 2021

AbstractThe sea urchin egg cortex is a peripheral region of eggs consisting of cell membrane and adjacent cytoplasm, which contains actin and tubulin cytoskeleton, cortical granules and some proteins required for early development. Method for isolation of cortices from sea urchin eggs and early embryos has been developed in 70s of 20th Century. Since that time this method has been reliable tool to study protein localization and cytoskeletal organization in cortex of unfertilized eggs and embryos during first cleavages. This study is an estimation of reliability of RT-qPCR to analyze levels of maternal transcripts that are localized in egg cortex. Firstly, we selected seven potential reference genes, 28S, Cycb, Ebr1, GAPDH, Hmg1, Smtnl1 and Ubb, which transcripts are maternally deposited in sea urchin eggs. The candidate reference genes were ranked by five different algorithms (BestKeeper, CV, ΔCt, geNorm and NormFinder) upon calculated level stability in both eggs and isolated cortices. Our results show that gene ranking differs in total RNA and mRNA samples, though Ubb is most suitable reference gene in both cases. To validate feasibility of comparative analysis of eggs and isolated egg cortices by RT-qPCR, we selected Daglb-2 as a gene of interest, which transcripts potentially localized in cortex, and found increased level of Daglb-2 in egg cortices. This suggests that proposed RNA isolation method with subsequent quantitative RT-qPCR analysis can be used to approve cortical association of transcripts in sea urchin eggs.
Causal effect of adiposity on the risk of 19 gastrointestinal diseases: a Mendelian randomization study
Authors: Kim Min Seo , Song Minku , Kim Soyeon , Kim Beomsu , Kang Wonseok , Kim Jong Yeob , Myung Woojae , Lee Inhyeok , Do Ron , Khera Amit V , Won Hong-Hee 
Published: November 2021

AbstractObjectivesWe applied Mendelian randomization (MR) to investigate the causal associations of body mass index (BMI) and waist circumference (WC) with 19 gastrointestinal (GI) disorders.DesignMR study.SettingThe UK Biobank, Genetic Investigation of Anthropometric Traits (GIANT) Consortium, FinnGen consortium, and genome-wide association studies.ParticipantsOverall, >400,000 UK Biobank participants, >170,000 participants of Finnish descent, and numerous consortia participants with predominantly European ancestry.InterventionsSingle-nucleotide polymorphisms associated with BMI and WC were used as instrumental variables to estimate the causal associations with the GI conditions.Main outcome measuresRisk of developing 19 GI diseasesResultsAfter correction for multiple testing (Bonferroni-corrected threshold of P<0.05/19) and testing for consistencies using several MR methods with varying assumptions (inverse variance weighted, weighted median, MR-Egger, and MR-PRESSO), genetically predicted BMI was associated with increased risks of non-alcoholic fatty liver disease (NAFLD), cholecystitis, cholelithiasis, and primary biliary cholangitis. The odds ratio (OR) per one standard deviation (SD) increased in genetically predicted BMI (4.77 kg/m2) from 1.22 (95% confidence interval [CI] 1.12–1.34; P<0.0001) for NAFLD to 1.65 (95% CI 1.31–2.06; P<0.0001) for cholecystitis. Genetically predicted WC was associated with increased risks of NAFLD, alcoholic liver disease (ALD), cholecystitis, cholelithiasis, colon cancer, and gastric cancer. ALD was associated with WC even after adjustment for alcohol consumption in multivariable MR analysis. The OR per 1 SD increased in genetically predicted WC (12.52 cm) from 1.41 (95% CI 1.17–1.70; P=0.0015) for gastric cancer to 1.74 (95% CI 1.21–1.78; P<0.0001) for cholelithiasis.ConclusionsHigher BMI and WC are causally associated with an increased risk of GI abnormalities, particularly of hepatobiliary organs (liver, biliary tract, and gallbladder) that are functionally related to fat metabolism. Abdominal obesity measured by WC might be more influential and relevant with a diverse span of GI diseases than BMI, highlighting a possible pathophysiological role of visceral abdominal fats in the development of GI disorders and cancers.Graphical Abstract
The role of extra-curricular activities in increasing student engagement
Authors: Munir Saba , Zaheer Muhammad 
Published: November 2021

PurposeThe first objective of this study is to review the mechanism of conducting extra-curricular activities (ECAs) in the open and distance learning (ODL) setting. To achieve this objective, the procedure of ECAs at the Virtual University of Pakistan has been studied. The second objective of this study is to find the impact of ECAs on student engagement.Design/methodology/approachThis is a cross-sectional quantitative study. The questionnaire has been used to collect the data. The purposive sampling technique has been used, while this study's sample size is 970. An independent sample t-test has been used to find the difference between the groups.FindingsThis study shows a significant difference between the engagement levels of students who have been part of any ECA at university compared to the students who never participated in any ECA.Research limitations/implicationsThe results have been derived from the data gathered from one university only that might hinder the generalizability of the findings. The same study can be conducted in other ODL institutions to authenticate the findings.Practical implicationsThis study will help in realizing the policymakers of ODL about the importance of ECCAs. This study has also discussed an existing system of conducting ECCAs in an ODL setting that can be generalized and implemented across all the ODL universities to enhance student engagement.Originality/valueThis study has highlighted the importance of ECAs in ODL institutions that have been neglected since forever. This study is novel because it has highlighted the importance of social interaction of students in ODL and its relation with student engagement that has not been highlighted by any study so far.
Assessment and treatment of anxiety in children and adolescents with ASD: a systematic review
Authors: Perihan Celal , Burke Mack D. , Bowman-Perrott Lisa , Bocanegra Joel 
Published: November 2021

Purpose
The purpose of this study was to investigate the quality of current studies that assess and treat anxiety symptoms in children with autism spectrum disorder (ASD). More specifically the study aimed to answer the following questions: What are the qualities of the current studies using cognitive behavioral therapies (CBTs) to treat anxiety symptoms in children with ASD? Did studies make necessary modifications and adaptations to CBTs according to the evidence-based strategies and implement these versions of CBTs with precise fidelity? Were the selected measurements appropriate for assessing the anxiety symptoms in children with ASD?

Design/methodology/approach
A systematic review protocol was developed from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (Moher et al., 2009). A rubric was adapted based on the CEC (Council for Exceptional Children; Cook, 2014) group comparison studies standards and the Evaluative Method for Determining EBP in Autism (Reichow et al., 2007). The 3-point Likert Scale (Chard et al., 2009) was adapted to score each study based on the rubric.

Findings
CBT is a first-line treatment with significant mixed results. Current studies use adapted versions of existing CBTs for children with ASD without reporting empirical evidence to these adaptations and changes. Reporting of the implementation fidelity is still an issue in the treatment of anxiety. Anxiety measurements that were designed for typically developing children failure to detect unusual anxiety symptoms in children with ASD.

Research limitations/implications
The first limitation of this study was including a variety of studies across CBT programs and types of anxiety symptoms. Types of anxiety and CBT treatments may require separate analyses with specific indicators. Due to the limited studies, reviews could not be analyzed across types of CBT programs. The second limitation was the types of studies. Most of the studies were pilot studies. Pilot studies might use various instruments and CBTs components for making selections to produce the best effects and results. The final limitation was the lack of examination of the data analysis process.

Originality/value
These findings are important because due to the variety of changes or adaptation to CBTs, inappropriate implementations and failure to detect unusual anxiety symptoms of children with ASD may cause significant differences in treatment responses and outcomes. The study demonstrated that the majority of the studies used adapted versions of existing CBTs without reporting empirical evidence for these adaptations and changes. The findings have shown that reporting of the implementation fidelity is still an issue. Moreover, the majority of studies had used anxiety measurements that were designed for typically developing children, not for children with ASD.
Who killed food tourism? Unaware cannibalism in online conversations about traveling in Italy
Authors: Bigi Alessandro , Cassia Fabio , Ugolini Marta Maria 
Published: November 2021

PurposeA food tourism destination can fully exploit its competitiveness if food-related attributes are consistently highlighted both in its promotion and in user-generated content. However, in the context of food tourism research, a possible image incongruence has not yet been studied. Tourism destination image incongruence occurs when different travel information sources reflect inconsistent representations of a destination's attributes. This study addresses this gap, focusing on Italian food and wine as drivers to attract visitors. This study examines whether food-related attributes are present in online travel-related conversations and are perceived differently by people with and without knowledge about the destination.Design/methodology/approachContent analysis based on a Bayesian machine-learning technique utilizing Leximancer software was applied to analyze questions and answers posted on TripAdvisor forums by potential and past visitors of four destinations in Italy (Naples, Florence, Parma and Ferrara). Questions and answers expressed by people with different knowledge in Italian and English were analyzed separately to gain deeper understanding.FindingsContrary to expectations, food-related themes were almost completely absent in the conversations analyzed, with only a few exceptions in Italian question sections. This situation depicts a sort of “cannibalism”, in the sense that the centrality of food-related attributes is engulfed by other, less sensorial, enjoyable and memorable aspects of the travel experience.Research limitations/implicationsAnalysis suggests that hype may exist in food tourism promotion related to destination image incongruence. However, while based on a large volume of conversations, the analysis covers only four Italian cities.Practical implicationsDestination management organizations (DMOs) should develop their strategy and communication considering internal and external elements: their marketing targets on one side and the local culture and attractions' perceptions on the other. Standard marketing processes (segmenting, targeting, positioning) and theories should be put in place. The application of standard marketing dynamics and studies should push the DMOs to understand that the internally perceived cultural values of the touristic destinations could not be known or joint univocally by the global external customers and that a local promotional activity should start with branding and not commercial activities.Originality/valueThis is the first study to suggest the existence of hype in food tourism promotion of Italian destinations and to provide evidence supporting this argument.
Is the future of internships online? An examination of stakeholder attitudes towards online internships
Authors: Irwin Amy , Perkins Joy , Hillari Leah Luise , Wischerath Darja 
Published: November 2021

PurposeThe world of work is becoming digital, a process accelerated by the recent COVID-19 pandemic and resultant remote working guidelines. Online internships have become more popular in this context, and yet there remains a lack of research investigating how these internships are perceived across stakeholders. The purpose of this paper was to begin to address this research gap by exploring academic, student and employer perceptions of online internships with a focus on employability.Design/methodology/approachThe research explored 156 stakeholders (53 students, 50 academics and, 53 employer/professionals) perceptions via a mixed-methods online study encompassing quantitative responses to internship vignettes, alongside open-ended questions designed to explore stakeholder attitudes in more depth.FindingsStakeholder groups reported similar attitudes towards online internships. Overall, online internships were viewed as valid, flexible, work experience, linked to skill development and likely to enhance student employability. However, concerns were raised regarding communication protocols and development, intern isolation and a lack of organisational immersion.Practical implicationsBased on the research, the authors make three recommendations to continue to enhance and develop the online internship experience: ensure multiple methods of regular communication between student and organisation, attempt virtual immersion in the organisation and assign each intern additional support beyond their immediate supervisor.Originality/valueBased on a holistic and novel analysis of key stakeholders' viewpoints, this paper provides much needed insights and evidence on how to design and quality assure effective online internship practice.
A new model of fuel spray shape at early stage of injection in a marine diesel engine
Authors: Grochowalska Joanna , Jaworski Piotr , Kapusta Łukasz Jan , Kowalski Jerzy 
Published: November 2021

Purpose
In the cylinders of a marine diesel engine, self-ignition occurs in a very short time after the fuel injection into the combustion chamber. Therefore, this paper aims to develop a model of diesel fuel spray for the early stage of fuel spray in the marine diesel engine. The main technical aspects such as nozzle diameter of the marine engine injector and backpressure in the combustion chamber were taken into consideration.

Design/methodology/approach
In this paper, laboratory experimental studies were carried out to determine parameters of fuel spray in an early stage of injection in the marine diesel engine. The optical measuring Mie scattering technique was used to record the fuel injection process. The working space was a constant volume chamber. The backpressure parameters in the constant volume chamber were the same as during the operation of the marine diesel engine. Based on the experimental studies and important Hiroyasu and Arai models of fuel spray presented in literature was proposed new model of fuel spray parameters for marine diesel injectors.

Findings
In this paper, the proposed new model of the two main parameters described fuel spray evolution”: new model of spray tip penetration (STP) and spray cone angle (SCA). New model propagation of fuel STP in time was included the influence of nozzle diameter and backpressure. The proposed model has a lower error, about 15%–34%, than the model of Hiroyasu and Arai. Moreover, a new model of the evolution over time of the SCA is developed.

Research limitations/implications
In the future research of fuel spray process must be taken influence of the fuel temperature. Diesel fuel has a different density and viscosity in dependence of fuel temperature. Therefore are predicted of the expansion about influence of fuel temperature, new model of fuel spray for a marine diesel engine. The main limitations occurring in the research are not possible to carry out the research while real operation marine diesel engine.

Originality/value
An experimental test was carried out for a real fuel injector of a marine diesel engine. Design parameters and fuel injection parameters were selected on the basis of the actual one. In the literature, SCA is defined as a constant parameter for the specific preliminary data. A new model for the early stage of fuel spray of SCA propagation in time has been proposed. The early stage of fuel spray is especially important, because in this time comes in there to fuel self-ignition.
Finnish architects' attitudes towards multi-storey timber-residential buildings
Authors: Ilgın Hüseyin Emre , Karjalainen Markku , Pelsmakers Sofie 
Published: November 2021

PurposeThe paper aims to understand Finnish architects' attitudes towards the use of timber as a structural material in multi-storey (over two--storeys high) residential construction.Design/methodology/approachThe study was conducted through a literature survey mainly including international peer-reviewed journals and similar research projects. Furthermore, the literature survey informed the generation of the web-based survey questionnaire design to gather information on architects' perceptions, attitudes and interest in the use of wood in multi-storey (over two-storeys high) residential buildings.FindingsThe paper's findings are as follows: (1) respondents perceived the most important advantages of wood as a lightweight, local and ecological material; (2) wood construction (compared to concrete) included perceived concerns about it being more costly and needing more complex engineering and (3) respondents had a favourable overall attitude towards the use of wood particularly in low-rise residential construction, whilst their perception of tall housing, including timber ones, was mostly negative.Originality/valueNo studies have evaluated the use of wood in tall residential buildings and architects' perceptions in Finland.