bluuebunny/crossref_metadata_2025 huggingface dataset:
Biocontrol potential of grapevine endophytes against grapevine trunk pathogens
Authors: Silva-Valderrama Isidora , Toapanta Diana , Miccono Maria de los Angeles , Lolas Mauricio , Díaz Gonzalo A. , Cantu Dario , Castro Alvaro
Published: September 2020

Grapevine Trunk Diseases (GTDs) are a major challenge to the grape industry worldwide. GTDs are responsible for considerable loss of quality, production, and vineyard longevity. Seventy five percent of Chilean vineyards are estimated to be affected by GTDs. GTDs are complex diseases caused by several species of fungi, includingNeofusicoccum parvum, Diplodia seriata, andPhaeomoniella chlamydospora. In this study, we report the isolation of 169 endophytic and 209 epiphytic fungi from grapevines grown under organic and conventional farming in Chile. Multiple isolates ofClonostachys rosea, Trichodermasp.,Purpureocillium lilacium, Epiccocum nigrum, Cladosporiumsp., andChaetomiumsp. were evaluated for their potential of biocontrol activity against fungal trunk pathogens. Tests were carried out using two dual-culture-plate methods with multiple media types, including agar containing grapevine wood extract to simulate in planta nutrient conditions. Significant pathogen growth inhibition was observed by all isolates tested.C. roseashowed 98.2% inhibition of all pathogens in presence of grapevine wood extract. We observed 100% pathogen growth inhibition when autoclaved lignified grapevine shoots were pre-inoculated with eitherC. roseastrains orTrichodermasp.. Overall these results show thatC. roseastrains isolated from grapevines are promising biocontrol agents against GTDs.
Meta-analysis of genome-wide DNA methylation and integrative OMICs in human skeletal muscle
Authors: Voisin S , Jacques M , Landen S , Harvey NR , Haupt LM , Griffiths LR , Gancheva S , Ouni M , Jähnert M , Ashton KJ , Coffey VG , Thompson JM , Doering TM , Gabory A , Junien C , Caiazzo R , Verkindt H , Raverdy V , Pattou F , Froguel P , Craig JM , Blocquiaux S , Thomis M , Sharples AP , Schürmann A , Roden M , Horvath S , Eynon N
Published: September 2020

Knowledge of age-related DNA methylation changes in skeletal muscle is limited, yet this tissue is severely affected by aging in humans. Using a large-scale epigenome-wide association study (EWAS) meta-analysis of age in human skeletal muscle from 10 studies (total n = 908 human muscle methylomes), we identified 9,986 differentially methylated regions at a stringent false discovery rate < 0.005, spanning 8,748 unique genes, many of which related to skeletal muscle structure and development. We then integrated the DNA methylation results with known transcriptomic and proteomic age-related changes in skeletal muscle, and found that even though most differentially methylated genes are not altered at the mRNA or protein level, they are nonetheless strongly enriched for genes showing age-related differential expression. We provide here the most comprehensive picture of DNA methylation aging in human skeletal muscle, and have made our results available as an open-access, user-friendly, web-based tool calledMetaMeth(https://sarah-voisin.shinyapps.io/MetaMeth/).
Identification of TMEM106B as proviral host factor for SARS-CoV-2
Authors: Baggen Jim , Persoons Leentje , Jansen Sander , Vanstreels Els , Jacquemyn Maarten , Jochmans Dirk , Neyts Johan , Dallmeier Kai , Maes Piet , Daelemans Dirk
Published: September 2020

The ongoing COVID-19 pandemic is responsible for worldwide economic damage and nearly one million deaths. Potent drugs for the treatment of severe SARS-CoV-2 infections are not yet available. To identify host factors that support coronavirus infection, we performed genome-wide functional genetic screens with SARS-CoV-2 and the common cold virus HCoV-229E in non-transgenic human cells. These screens identified PI3K type 3 as a potential drug target against multiple coronaviruses. We discovered that the lysosomal protein TMEM106B is an important host factor for SARS-CoV-2 infection. Furthermore, we show that TMEM106B is required for replication in multiple human cell lines derived from liver and lung and is expressed in relevant cell types in the human airways. Our results identify new coronavirus host factors that may potentially serve as drug targets against SARS-CoV-2 or to quickly combat future zoonotic coronavirus outbreaks.
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

Motivation

Single 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.

Results

We 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 Implementation

The software is implemented in R with the source code freely available athttps://github.com/aksenia/SeeCiTe.

Contact

Ksenia.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

Basidiomycetes 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

Shigellosis 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.

Importance

Shigellaspp 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.
Non-Equilibrium Living Polymers
Authors: Michieletto D.
Published: September 2020

Systems of “living” polymers are ubiquitous in industry and are traditionally realised using surfactants. Here I review the state-of-the-art of living polymers and discuss non-equilibrium extensions that may be realised with advanced synthetic chemistry or DNA functionalised by proteins. These systems are not only interesting in order to realise novel “living” soft matter but can also shed insight into how genomes are (topologically) regulated in vivo.
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

Cilia 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

High-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

The 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

Objective

We 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.

Design

Winniemale 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.

Results

Significant 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.

Conclusion

These findings open avenues for the development of targeted therapies for IBD-related bone loss.

Significance of this study

What 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

Purpose

In 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/approach

This 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.

Findings

The 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/value

The 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

Purpose

The 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/approach

A 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.

Findings

The 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/value

This 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.
The accounting, budgeting and fiscal impact of COVID-19 on the United Kingdom
Authors: Heald David , Hodges Ron
Published: September 2020

Purpose

This paper analyses the nature and impact of budgetary responses to the pandemic in the context of the strengths and weaknesses of UK public sector financial management.

Design/methodology/approach

The analysis is developed through consideration of four modes of government accounting. Data are drawn from multiple official sources, which report actual and forecast government receipts and expenditures as the crisis unfolds.

Findings

There have been dramatic effects on UK government finances. Government receipts have fallen by 12% and expenditures have increased by 36% in the first three months of the crisis (April–June 2020), compared to the previous year. Government debt increased to £1,984bn (99.6% of GDP), the highest percentage since March 1961 (ONS, 2020c). The pandemic will have the greatest impact on UK public finances in 2020–21, with a record budget deficit which, under the OBR (2020c) central scenario, may approach £322bn and increase public sector net debt to £2,205bn (104.1% of GDP).

Research limitations/implications

The research is necessarily limited by the impact of the pandemic and the government's responses in a rapidly changing social, economic and fiscal environment.

Practical implications

Statistical accounting and budgeting dominate attention because of reporting speed and issues of international comparability. The pandemic has emphasised the importance of timeliness. Government financial reporting is marginalised, though this should not be permanent if the pandemic retreats. Fiscal sustainability analysis will warn that UK public finances are even more unsustainable than before the pandemic.

Social implications

The interaction of higher levels of debt and future increases in interest rates might result in a new era of austerity and further centralisation of public power and economic decision-making in one of the world's most centralised democracies.

Originality/value

The paper provides an early, structured analysis of the impact of the COVID-19 emergency on UK government finances.
PROMES: An ontology‐based messaging service for semantically interoperable information exchange during disaster response
Authors: Elmhadhbi Linda , Karray Mohamed‐Hedi , Archimède Bernard , Otte J. Neil , Smith Barry
Published: September 2020

Disaster response requires the cooperation of multiple emergency responder organizations (EROs). However, after‐action reports relating to large‐scale disasters identity communication difficulties among EROs as a major hindrance to collaboration. On the one hand, the use of two‐radio communication, based on multiple orthogonal frequencies and uneven coverage, has been shown to degrade inter‐organization communication. On the other hand, because they reflect different areas of expertise, EROs use differing terminologies, which are difficult to reconcile. These issues lead to ambiguities, misunderstandings, and inefficient exchange of data and information among those involved, which can impede the response process and slow decision making. We, therefore, hypothesize that promoting semantic interoperability across ERO information systems might improve information exchange among stakeholders and thereby allow a more coherent response to the disaster. We propose an ontology‐based messaging service on the basis of the Emergency Data Exchange Language (EDXL) standards. The parties involved will continue to use the terminologies to which they are accustomed, but the system will resolve inconsistencies and thereby enhance mutual understanding among EROs by ensuring semantic translation of the exchanged information. The evaluation of the semantic translation demonstrated the effectiveness and accuracy of the proposed service.
Statistics and The “Little Grey Cells”
Authors: Jackson James
Published: September 2020

Can statistical analysis compete with Hercule Poirot and Miss Marple when it comes to solving Agatha Christie's many murder mysteries? James Jackson investigates
What Does it Mean to Mislead?
Authors: Harkness Timandra
Published: September 2020

Philosopher Jennifer Mather Saul explains her work on misleadingness and lying, and its relevance to statistical communication. Interview by Timandra Harkness
Use of angiotensin converting enzyme inhibitors in patients receiving therapeutic plasma exchange with a centrifuge‐based apheresis system
Authors: Jang Soo Min , Bahjri Khaled , Lee Joanna , Nabavi Sanaz , Abdipour Amir
Published: September 2020

Angiotensin‐converting enzyme inhibitors (ACEi) are frequently used antihypertensive medications with additional advantages such as reducing proteinuria and cardiovascular events. ACEi are commonly held at least 24 hours before a therapeutic plasma exchange (TPE) to reduce possibility of adverse events (AEs) including adverse drug reactions (ADR). The objective of this study was to determine if ACEi use increases the risk of ADR in patients receiving TPE with a conventional centrifuge‐based apheresis system. This is a retrospective chart review study (n = 252; 52% male). Binary logistic regression was used to analyze the association of ACEi use and AEs. Of 171 patients who had AE during TPE, only 38 patients were taking ACEi. There was no significant association between ACEi use and AEs after adjustments (odds ratio = 0.885, 95% confidence interval: 0.468, 1.674). Our results suggest that risk of AEs is not higher in patients taking ACEi receiving TPE using a centrifuge‐based machine. Randomized controlled prospective trials may be needed to further investigate this matter.
Functional properties of gonad protein isolates from three species of sea urchin: a comparative study
Authors: Shang Wen‐Hui , Yan Jia‐Nan , Du Yi‐Nan , Cui Xiao‐Fan , Su Sheng‐Yi , Han Jia‐Run , Xu Yun‐Sheng , Xue Chang‐Feng , Zhang Tie‐Tao , Wu Hai‐Tao , Zhu Bei‐Wei
Published: September 2020

Sea urchin Mesocentrotus nudus, Glyptocidaris crenularis, and Strongylocentrotus intermedius gonad protein isolates (mnGPIs, gcGPIs, and siGPIs) were extracted by isoelectric solubilization/precipitation (ISP) from the defatted gonads, and their functional properties were compared. Sodium dodecyl sulfate polyacrylamide gel electrophoresis results showed the similar protein pattern between each protein isolate and defatted gonad, indicating the high efficiency of ISP processing for protein recovery. Amino acid profileconfirmed that the mnGPIs and siGPIs could be potential sources of essential amino acid in nature. As regard to functional properties, mnGPIs showed higher water‐ and oil‐ holding capacities followed bysiGPIs and gcGPIs and all protein isolates presented great foaming property. As for emulsifying activity index (EAI), mnGPIs, gcGPIs, and siGPIs showed the minimum solubility and EAI at pH 5, 3, and 4, respectively, and behaved a pH‐dependent manner. The gcGPIs revealed the highest EAI from pH 6 to 8 among the samples. In addition, circular dichroism showed increased content of β‐sheet at the expense of α‐helix and β‐turn, suggesting the structure denaturation of the protein isolates. Indeed, no statistical difference was observed between secondary structure of mnGPIs and siGPIs. Moreover, ISP processing increased free sulfhydryl content of sea urchin protein isolates, but no difference was observed among the samples. Furthermore, siGPIs revealed the highest amount of total sulfhydryl and disulfide bonds, whereas both defatted gonads and protein isolates from G. crenularis presented the maximum surface hydrophobicity. These results suggest that gonad protein isolates from three species of sea urchin possess various functionalities and therefore can be potentially applied in food system.

Practical Application

Sea urchin M. nudus, G. crenularis, and S. intermedius gonads are edible, whereas the functional properties of protein isolates from sea urchin gonad remain unknown. In this case, the extraction and comparison of three species of sea urchin gonad protein isolates will not only confirm functional properties but also screen food ingredients with suitable functions. In this study, functionalities of protein isolates derived from M. nudus, G. crenularis, and S. intermedius gonads would provide potential application in bakery food and meat products or as emulsifier candidates in food system.
Tendon function after replantation of complete thumb avulsion amputations
Authors: Yuan Chaoqun , Liu Hongjun , Zhang Hanyu , Wang Tianliang , Gu Jiaxiang
Published: September 2020

Background

Tendon avulsion at the musculotendinous junction caused by digit avulsion amputation is still a challenging problem. We aimed to compare the tendon functional outcomes of two repair methods for tendon avulsion rupture at the musculotendinous junction in patients with complete thumb avulsion amputations.

Methods

A retrospective study was performed to evaluate patients with complete thumb avulsion amputations whose tendons were repaired through reattachment to muscle (group I) or tendon transfer (group II) between July 2008 and October 2019. Outcomes of total range of motion, pinch strength, grip strength and reoperation rate were included.

Results

A total of 23 patients met the inclusion criteria, with a mean follow‐up of 16.6 ± 4.2 months. Total active range of motion was comparable between groups I and II (P = 0.095). Pinch strength of group I was lower than group II (P = 0.001). The result of grip strength was found to be similar (P = 0.075). In addition, there was no significant difference in reoperation rate (P > 0.05).

Conclusion

Tendon transfer can attain higher pinch strength for replantation of thumb avulsion amputations. It is recommended for patients with jobs that demand higher strength.
Perampanel reduces paroxysmal depolarizing shift and inhibitory synaptic input in excitatory neurons to inhibit epileptic network oscillations
Authors: Yang Ya‐Chin , Wang Guan‐Hsun , Chuang Ai‐Yu , Hsueh Shu‐Wei
Published: September 2020

Background and Purpose

Perampanel is a newly approved anticonvulsant uniquely targeting AMPA receptors, which mediate the most abundant form of excitatory synaptic transmission in the brain. However, the network mechanism underlying the anti‐epileptic effect of the AMPAergic inhibition remains to be explored.

Experimental Approach

The mechanism of perampanel action was studied with the basolateral amygdala network containing pyramidal–inhibitory neuronal resonators in seizure models of 4‐aminopyridine (4‐AP) and electrical kindling.

Key Results

Application of either 4‐AP or electrical kindling to the basolateral amygdala readily induces AMPAergic transmission‐dependent reverberating activities between pyramidal–inhibitory neuronal resonators, which are chiefly characterized by burst discharges in inhibitory neurons and corresponding recurrent inhibitory postsynaptic potentials in pyramidal neurons. Perampanel reduces post‐kindling “paroxysmal depolarizing shift” especially in pyramidal neurons and, counterintuitively, eliminates burst activities in inhibitory neurons and inhibitory synaptic inputs onto excitatory pyramidal neurons to result in prevention of epileptiform discharges and seizure behaviours. Intriguingly, similar effects can be obtained with not only the AMPA receptor antagonist CNQX but also the GABAA receptor antagonist bicuculline, which is usually considered as a proconvulsant.

Conclusion and Implications

Ictogenesis depends on the AMPA receptor‐dependent recruitment of pyramidal–inhibitory neuronal network oscillations tuned by dynamic glutamatergic and GABAergic transmission. The anticonvulsant effect of perampanel then stems from disruption of the coordinated network activities rather than simply decreased neuronal excitability or excitatory transmission. Positive or negative modulation of epileptic network reverberations may be pro‐ictogenic or anti‐ictogenic, respectively, constituting a more applicable rationale for the therapy against seizures.
Applying expert elicitation of viability and persistence to a lynx species status assessment
Authors: Cummings Jonathan W. , Parkin Mary , Zelenak Jim , Bell Heather , Broderdorp Kurt , Holt Bryon , McCollough Mark , Smith Tamara
Published: September 2020

In 2015, the United States Fish and Wildlife Service initiated a review of the status of Canada lynx (Lynx canadensis) in the contiguous United States. Available research and monitoring, while substantial, lacked information on the demographic rates, abundance, and trends necessary to complete a full viability assessment. Therefore, alternative sources of information were needed to inform the species status assessment. We designed and conducted an expert elicitation to capture the knowledge, professional judgments, and opinions of lynx experts to assess the status of, and the drivers influencing, these lynx populations. We elicited the likelihood and level of uncertainty regarding future persistence over several time frames (at years 2025, 2050, and 2100). The elicitation revealed experts' concerns that expected climate‐driven losses in habitat quality, quantity, and related factors will likely result in declines. Experts expect resident populations of lynx will persist in all five currently occupied geographic units in 2025; in 4 or 5 of the units at 2050; and in 2 or 3 units at 2100. Experts expressed a high level of uncertainty regarding the rate and extent of decline due to projected climate warming and corresponding effects to these lynx populations. In the absence of adequate monitoring data, this type of expert elicitation is a useful method to aid classification decisions, such as providing the scientific information the Service relied upon to complete the November 5, 2017 5‐year review which recommended that the lynx distinct population segment be removed from the list of threatened and endangered species.
The context dependence of non‐consumptive predator effects
Authors: Wirsing Aaron J. , Heithaus Michael R. , Brown Joel S. , Kotler Burt P. , Schmitz Oswald J.
Published: September 2020

Non‐consumptive predator effects (NCEs) are now widely recognised for their capacity to shape ecosystem structure and function. Yet, forecasting the propagation of these predator‐induced trait changes through particular communities remains a challenge. Accordingly, focusing on plasticity in prey anti‐predator behaviours, we conceptualise the multi‐stage process by which predators trigger direct and indirect NCEs, review and distil potential drivers of contingencies into three key categories (properties of the prey, predator and setting), and then provide a general framework for predicting both the nature and strength of direct NCEs. Our review underscores the myriad factors that can generate NCE contingencies while guiding how research might better anticipate and account for them. Moreover, our synthesis highlights the value of mapping both habitat domains and prey‐specific patterns of evasion success (‘evasion landscapes’) as the basis for predicting how direct NCEs are likely to manifest in any particular community. Looking ahead, we highlight two key knowledge gaps that continue to impede a comprehensive understanding of non‐consumptive predator–prey interactions and their ecosystem consequences; namely, insufficient empirical exploration of (1) context‐dependent indirect NCEs and (2) the ways in which direct and indirect NCEs are shaped interactively by multiple drivers of context dependence.
Notq Arrives at the Clinic: How Druze Therapists Deal with the Cultural Phenomenon of Remembering and Talking about Previous Incarnation Among the Druze in Israel
Authors: Natoor Maha , Shoshana Avihu
Published: September 2020

This article deals with the cultural idiom Notq—the remembering and talking about a previous incarnation among the Druze. The study focuses on the interface between the dominant Western psychological perspective and the Druze ethnopsychology. Sixteen Druze therapists including social workers and psychologists were interviewed about the Notq and how it arises in the clinic. The research shows that while the therapists understand and respect Notq, they mostly suspend it and only some work with it. The findings reveal that the Druze therapists are confronted with a complex conflict: they have no internal‐cultural legitimacy to reject Notq, and they have no external‐professional basis for accepting it. This study, in using the example of the Notq, illustrates important issues that are addressed by transcultural psychologists and psychological anthropologists; cultural idioms; minority therapists; the dominance of Western psychological knowledge; and the interface between psychology and religion.
Patient experiences of the urgent cancer referral pathway—Can the NHS do better? Semi‐structured interviews with patients with upper gastrointestinal cancer
Authors: Haste Anna , Lambert Mark , Sharp Linda , Thomson Richard , Sowden Sarah
Published: September 2020

Background

Timeliness is viewed as a key feature of health‐care quality. Internationally, this is challenging. In England, cancer waiting time targets are currently not being met. For example, between 2015 and 2018 only 71% of patients with upper gastrointestinal (UGI) cancer started treatment within the recommended 62 days of referral.

Objective

We explored patients’ experiences to identify areas for service improvement.

Design

Semi‐structured interviews were conducted.

Setting and participants

Twenty patients who were referred through the urgent (two‐week) GP referral route and were within six months of receiving first treatment were recruited.

Data analysis

Data from the interviews were analysed thematically.

Results

Four themes were developed: organization of care; diagnosis; support; and views and expectations of the NHS. Patients described cross‐cutting issues such as complex and varied pathways and uncertainty about what would happen next. They felt daunted by the intensity and speed of investigations. They were presented with a recommended course of action rather than options and had little involvement in decision making. They were grateful for care, reluctant to complain and resigned to the status quo.

Discussion and conclusions

In order to meet patient needs, the NHS needs to improve communication and streamline pathways. Future cancer pathways also need to be designed to support shared decision making, be truly person‐centred and informed by patient experience.
The synergy of germline C634Y and V292M RET mutations in a northern Chinese family with multiple endocrine neoplasia type 2A
Authors: Yang Zheng , Qi Xinmeng , Gross Neil , Kou Xiujuan , Bai Yunlong , Feng Yaru , Wang Bochun , Zafereo Mark E. , Li Guojun , Sun Chuanzheng , Li Huihui , Chen Xiaohong , Huang Zhigang
Published: September 2020

Genetic analysis for germline mutations of RET proto‐oncogene has provided a basis for individual management of medullary thyroid carcinoma (MTC) and pheochromocytoma. Most of compound mutations have more aggressive phenotypes than single point mutations, but the compound C634Y/V292M variant in MTC has never been reported. Thus, we retrospectively investigated synergistic effect of C634Y and V292M RET germline mutations in family members with multiple endocrine neoplasia type 2A. Nine of 14 family members in a northern Chinese family underwent RET mutation screening using next‐generation sequencing and PCR followed by direct bidirectional DNA sequencing. Clinical features of nine individuals were retrospectively carefully reviewed. In vitro, the scratch‐wound assay was used to investigate the difference between the cells carrying different mutations. We find no patients died of MTC. All 3 carriers of the V292M variant were asymptomatic and did not have biochemical or structural evidence of disease (age: 82, 62 and 58). Among 4 C634Y mutation carriers, 2 patients had elevated calcitonin with the highest (156 pg/mL) in an 87‐year‐old male. Two carriers of compound C634Y/V292M trans variant had bilateral MTC with pheochromocytoma or lymph node metastasis (age: 54 and 41 years, respectively). Further, the compound C634Y/V292M variant had a faster migration rate than either single point mutation in vitro (P < .05). In conclusion, the V292M RET variant could be classified as ‘likely benign’ according to ACMG (2015). The compound variant V292M/C634Y was associated with both more aggressive clinical phenotype and faster cell growth in vitro than was either single mutation.