bluuebunny/crossref_metadata_2025_split huggingface dataset:
SeeCiTe: a method to assess CNV calls from SNP arrays using trio data
Authors: Lavrichenko Ksenia , Helgeland Øyvind , Njølstad Pål R , Jonassen Inge , Johansson Stefan 
Published: September 2020

AbstractMotivationSingle nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling.ResultsWe developed SeeCiTe (Seeing Cnvs in Trios), a novel CNV quality control tool that post-processes output from current CNV calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father, and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge it is the first tool that utilizes probe-level CNV data in trios to systematically highlight potential artefacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies.Availability and ImplementationThe software is implemented in R with the source code freely available athttps://github.com/aksenia/SeeCiTe.ContactKsenia.Lavrichenko@mpi.nl,Stefan.Johansson@uib.noorInge.Jonassen@uib.no
Transcriptomic analysis ofLentinus squarrosulusprovide insights into its biodegradation ability
Authors: Ravichandran Aarthi , Kolte Atul P , Dhali Arindham , Gopinath S. Maheswarappa , Sridhar Manpal 
Published: September 2020

AbstractBasidiomycetes are of special interest in biotechnological research for their versatile potential in degradation of lignocellulosic biomass. This study accordingly reports analysis of transcriptome of a white-rot BasidiomyceteL.squarrosulusgrown in simple potato dextrose broth supplemented with aromatic compound, reactive black dye to gain an insight into the degradation ability of the fungus. RNA was sequenced using Illumina NextSeq 500 to obtain 6,679,162 high quality paired end reads that were assembledde novousing CLC assembly cell to generate 25,244 contigs.Putative functions were assigned for the 10,494 transcripts based on sequence similarities through BLAST2GO 5.2 and Function annotator. Functional assignments revealed enhanced oxidoreductase activity through the expression of diverse biomass degrading enzymes and their corresponding co-regulators. CAZyme analysis through dbCAN and CUPP revealed the presence of 6 families of polysaccharide lyases, 51 families of glycoside hydrolases, 23 families of glycoside transferases, 7 families of carbohydrate esterases and 10 families of Auxiliary activities.Genes encoding the ligninolytic enzymes and auxiliary activities among the transcript sequences were identified through gene prediction by AUGUSTUS and FGENESH. Biochemical analysis of a couple of biomass degrading enzymes substantiated the functional predictions. In essence,L.squarrosulusgrown in a simple medium devoid of lignocellulosic substrate demonstrated presence of a repertoire of lignocellulose degrading enzymesimplying that source of lignocellulose is not required for expression of these biomass degrading enzymes. The study hereby underlines the significance ofL.squarrosulusin biomass degradation and its future functional exploitation in biomass conversion applications.
Accessory genome dynamics and structural variation ofShigellafrom persistent infections
Authors: Bengtsson Rebecca J. , Dallman Timothy J. , Jenkins Claire , Allen Hester , De Silva P. Malaka , Stenhouse George , Pulford Caisey V. , Bennett Rebecca J. , Baker Kate S. 
Published: September 2020

AbstractShigellosis is a diarrhoeal disease caused mainly byShigella flexneriandShigella sonnei. Infection fromShigellais thought to be largely self-limiting, with short- to medium- term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM) associated shigellosis have been reported whereShigellaof the same serotype were serially sampled from individuals between 1 to 1862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM associatedS. flexneriandS. sonneiisolates serially sampled from individual patients at various days apart. We find that pairs likely associated with persistent carriage infection and with smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection and with greater SNP-distance. We also observed evidence of antimicrobial resistance (AMR) acquisition during persistentShigellainfection, specifically the gain of extended spectrum beta-lactamase genes in two pairs associated with persistent carriage. Finally, we explored chromosomal structural variations and rearrangements in seven (5 chronic and 2 reinfection associated) pairs ofS. flexneri3a isolates from a MSM-associated epidemic sublineage, which revealed variations at several common regions across pairs. These variations were mediated by insertion sequence (IS) elements which facilitated plasticity of genetic material with a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes inShigelladuring persistent infection.ImportanceShigellaspp are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrhoeal illness globally, particularly among children under the age of 5 in low-income countries. In high-income countries, an alternative transmission pathway of sexually transmissible disease among men who have sex with men (MSM) is emerging as the dominant presentation of the disease. Within MSM we have captured prolonged infection and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short-lived, and confers homologous serotypic immunity. Using this recently-emerged transmission scenario we comprehensively characterise the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genome regions in these globally important pathogens.
CiliaQ – a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images
Authors: Hansen Jan Niklas , Rassmann Sebastian , Stüven Birthe , Jurisch-Yaksi Nathalie , Wachten Dagmar 
Published: September 2020

AbstractCilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfilling sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely-available, and easy-to-use ImageJ plugins. CiliaQ allows high throughput analysis of 2D and 3D, static or time-lapse images from fluorescence microscopy of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease.
Correspondence-aware manifold learning for microscopic and spatial omics imaging: a novel data fusion method bringing MSI to a cellular resolution
Authors: Smets Tina , De Keyser Tom , Tousseyn Thomas , Waelkens Etienne , De Moor Bart 
Published: September 2020

AbstractHigh-dimensional molecular measurements are transforming the field of pathology into a data-driven discipline. While H&E stainings are still the gold standard to diagnose disease, the integration of microscopic and molecular information is becoming crucial to advance our understanding of tissue heterogeneity. To this end, we propose a data fusion method that integrates spatial omics and microscopic data obtained from the same tissue slide. Through correspondence-aware manifold learning, we can visualise the biological trends observed in the high-dimensional omics data at microscopic resolution. While data fusion enables the detection of elements that would not be detected taking into account the separate data modalities individually, out-of-sample prediction makes it possible to predict molecular trends outside of the measured tissue area. The proposed dimensionality reduction-based data fusion paradigm will therefore be helpful in deciphering molecular heterogeneity by bringing molecular measurements such as MSI to the cellular resolution.
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2
Authors: Ghorbani Mahdi , Brooks Bernard R. , Klauda Jeffery B. 
Published: September 2020

AbstractThe ongoing pandemic caused by coronavirus SARS-COV-2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long MD simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. Role of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, where the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intra-communication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.
Skeletal Phenotype and Mechanisms of Bone Loss inWinnieMice as a Model for Inflammatory Bowel Disease
Authors: Saedi Ahmed Al , Sharma Shilpa , Hassan Ebrahim Bani , Chen Lulu , Ghasem-Zadeh Ali , Hassanzadeganroudsari Majid , Gooi Jonathan H , Stavely Rhian , Eri Rajaraman , Miao Dengshun , Nurgali Kulmira , Duque Gustavo 
Published: September 2020

AbstractObjectiveWe aimed to investigate the skeletal phenotype ofWinniemouse model of spontaneous chronic colitis, which carries a mutation in theMuc2gene and closely replicates IBD symptoms and pathophysiology. These mice have a high level of gut-derived serotonin (GDS), a potent osteoblastogenesis inhibitor. We explored the underlying mechanisms of bone loss associated with chronic intestinal inflammation.DesignWinniemale and female mice prior to colitis onset (6 weeks old) and progression (14 and 24 weeks) were compared to age- and sex-matched C57BL/6 controls. We assessed bone quality (static and dynamic histomorphometry, micro-CT, 3-point bending), intestinal inflammation (lipocalin-2), GDS levels, serum levels of calcium, phosphorus and vitamin D,ex vivobone marrow analysis and molecular mechanisms inhibiting osteoblastogenesis.ResultsSignificant deterioration in trabecular and cortical microarchitecture, reductions in bone formation, mineral apposition rate, bone volume, osteoid volume and bone strength were observed inWinniemice compared to C57BL/6 controls. Decreased osteoblast and increased osteoclast numbers were prominent inWinniemice. We report for the first time that elevated GDS cross-talks with molecular pathways to inhibit bone formation inWinniemice. Increased expression of 5-HTR1B and FOXO1 mRNAs, dissociation of FOXO1/CREB1 complex and association of FOXO1 with ATF4, promoting the transcriptional activity of FOXO1, results in suppression of osteoblast proliferation inWinniemice compared to controls.ConclusionThese findings open avenues for the development of targeted therapies for IBD-related bone loss.Significance of this studyWhat is already known on this subject?- Osteoporosis is a common extraintestinal manifestation of inflammatory bowel disease (IBD).- Currently available treatments are not effective for IBD-associated bone loss.- The mechanisms of bone loss are poorly understood. A major limitation has been the lack of an appropriate animal model for IBD-associated bone loss.What are the new findings?- We report for the first-time the skeletal phenotype inWinniemouse model of IBD- This study presents a novel mechanism of IBD-associated bone loss, involving elevated gut-derived serotonin crosstalk with molecular pathways inhibiting bone formation.How might it impact on clinical practice in the foreseeable future- These findings open avenues for the development of targeted therapies for IBD-related bone loss.
The influence of the Chinese government's political ideology in the field of corporate environmental reporting
Authors: Situ Hui , Tilt Carol , Seet Pi-Shen 
Published: September 2020

PurposeIn a state capitalist country such as China, an important influence on company reporting is the government, which can influence company decision-making. The nature and impact of how the Chinese government uses its symbolic power to promote corporate environmental reporting (CER) have been under-studied, and therefore, this paper aims to address this gap in the literature by investigating the various strategies the Chinese government uses to influence CER and how political ideology plays a key role.Design/methodology/approachThis study uses discourse analysis to examine the annual reports and corporate social responsibility (CSR) reports from seven Chinese companies between 2007 and 2011. And the data analysis presented is informed by Bourdieu's conceptualisation of symbolic power.FindingsThe Chinese government, through exercising the symbolic power, manages to build consensus, so that the Chinese government's political ideology becomes the habitus which is deeply embedded in the companies' perception of practices. In China, the government dominates the field and owns the economic capital. In order to accumulate symbolic capital, companies must adhere to political ideology, which helps them maintain and improve their social position and ultimately reward them with more economic capital. The findings show that the CER provided by Chinese companies is a symbolic product of this process.Originality/valueThe paper provides contributions around the themes of symbolic power wielded by the government that influence not only state-owned enterprises (SOEs) but also firms in the private sector. This paper also provides an important contribution to understanding, in the context of a strong ideologically based political system (such as China), how political ideology influences companies' decision-making in the field of CER.
A cartography of delay risks in the Australian construction industry: impact, correlations and timing
Authors: Derakhshanfar Hossein , Ochoa J. Jorge , Kirytopoulos Konstantinos , Mayer Wolfgang , Langston Craig 
Published: September 2020

PurposeThe purpose of this research is to identify the most impactful delay risks in Australian construction projects, including the associations amongst those risks as well as the project phases in which they are most likely present. The correlation between project and organisational characteristics with the impact of delay risks was also studied.Design/methodology/approachA questionnaire survey was used to collect data from 118 delayed construction projects in Australia. Data were analysed to rank the most impactful delay risks, their correlation to project and organisational characteristics and project phases where those risks are likely to emerge. Association rule learning was used to capture associations between the delay risks.FindingsThe top five most impactful delay risks in Australia were changes by the owner, slow decisions by the owner, preparation and approval of design drawings, underestimation of project complexity and unrealistic duration imposed to the project, respectively. There is a set of delay risks that are mutually associated with project complexity. In addition, while delay risks associated with resources most likely arise in the execution phase, stakeholder and process-related risks are more smoothly distributed along all the project phases.Originality/valueThis research for the first time investigated the impact of delay risks, associations amongst them and project phases in which they are likely to happen in the Australian context. Also, this research for the first time sheds light on the project phases for the individual project delay risks which aids the project managers to understand where to focus on during each phase of the project.
Moving ridge neuronal espionage network simulation for reticulum invasion sensing
Authors: Sreeram G. , Pradeep S. , Rao K. Sreenivasa , Raju B. Deevana , Nikhat Parveen 
Published: September 2020

Purpose
The paper aims to precise and fast categorization on to transaction evolves into indispensible. The effective capacity difficulty of all the IDS simulates today at below discovery amount of fewer regular barrage associations and therefore the next warning rate.

Design/methodology/approach
The reticulum perception is that the methods which examine and determine the scheme of contact on unearths toward number of dangerous and perchance fateful interchanges occurring toward the system. Within character of guaran-teeing the slumberous, opening and uprightness count of to socialize for professional. The precise and fast categorization on to transaction evolves into indispensible. The effective capacity difficulty of all the intrusion detection simulation (IDS) simulates today at below discovery amount of fewer regular barrage associations and therefore the next warning rate. The container with systems of connections are reproduction everything beacon subject to the series of actions to achieve results accepts exists a contemporary well-known method. At the indicated motivation a hybrid methodology supported pairing distinct ripple transformation and human intelligence artificial neural network (ANN) for IDS is projected. The lack of balance of the situation traversing the space beyond information range was eliminated through synthetic minority oversampling technique-based oversampling have low regular object and irregular below examine of the dominant object. We are binding with three layer ANN is being used for classification, and thus the experimental results on knowledge discovery databases are being used for the facts in occurrence of accuracy rate and disclosure estimation toward identical period. True and false made up accepted.

Findings
At the indicated motivation a hybrid methodology supported pairing distinct ripple transformation and human intelligence ANN for IDS is projected. The lack of balance of the situation traversing the space beyond information range was eliminated through synthetic minority oversampling technique-based oversampling have low regular object and irregular below examine of the dominant object.

Originality/value
Chain interruption discovery is the series of actions for the results knowing the familiarity opening and honor number associate order, the scientific categorization undertaking become necessary. The capacity issues of invasion discovery is the order to determine and examine. The arrangement of simulations at the occasion under discovery estimation for low regular aggression associations and above made up feeling sudden panic amount.
Attaining digital advocacy behaviour through destination image and satisfaction
Authors: Saini Shefali , Arasanmi Chris Niyi 
Published: September 2020

Purpose
This study aims to examine the consequences of tourism destination image and satisfaction on digital advocacy in a touristic environment. The study also tested the mediation role of satisfaction in the relationship between the tourism destination image and tourists’ advocacy.

Design/methodology/approach
This study adopts a quantitative research design, suing the intercept survey method to collect data from 185 international tourists in New Zealand. The process macro regression method was used to analyse the collected data.

Findings
The findings from this study are: firstly, the study demonstrates that tourism destination image influenced tourists’ digital advocacy behaviour. Secondly, tourists’ satisfaction significantly changed tourists’ advocacy behaviour. Thirdly, tourists’ satisfaction mediates the relationship between the tourism destination image and tourists’ advocacy behaviour in this study.

Research limitations/implications
This study examined tourism destination image and satisfaction as predictors of tourist digital advocacy behaviour; the findings have some valuable impacts for organisations, especially the destination marketing organisation’s tourism strategies. The result also implies that customer satisfaction is a predictor of advocacy behaviours; and the need to focus on increasing tourist satisfaction by putting in place well-crafted tourism products and services.

Practical implications
The finding also implies that customer satisfaction is an important antecedent of advocacy behaviours; and the need to focus on increasing tourist satisfaction by putting in place well-crafted tourism-based strategies.

Originality/value
This study is one of the few investigations on tourists’ digital advocacy behaviour. The study also assessed the mediating impact of customer satisfaction in the relationship between tourism destination image and tourists’ advocacy behaviour, an area, which suffers from a languor of research.