bluuebunny/crossref_metadata_2025 huggingface dataset:
Proximity Biotin Labeling Reveals KSHV Interferon Regulatory Factor Networks
Authors: Kumar Ashish , Salemi Michelle , Bhullar Resham , Guevara-Plunkett Sara , Lyu Yuanzhi , Wang Kang-Hsin , Izumiya Chie , Campbell Mel , Nakajima Ken-ichi , Izumiya Yoshihiro
Published: October 2020

Studies on “HIT&RUN” effects by viral protein are difficult when using traditional affinity precipitation-based techniques under dynamic conditions, because only proteins interacting at a specific instance in time can be precipitated by affinity purification. Recent advances in proximity labeling (PL) have enabled study of both static and dynamic protein-protein interactions. Here we applied PL method with recombinant Kaposi’s sarcoma-associated herpesvirus (KSHV). KSHV, a gamma-herpesvirus, uniquely encodes four interferon regulatory factors (IRFs 1-4) in the genome, and we identified KSHV vIRF-1 and vIRF-4 interacting proteins during reactivation. Fusion of mini-TurboID with vIRF-1 or vIRF-4 did not interfere with KSHV gene expression, DNA replication, orde novoinfections. PL identified 213 and 70 proteins for vIRF-1 and vIRF-4 respectively, which possibly interact during KSHV reactivation, and 47 of those were shared between the two vIRFs; the list also includes three viral proteins, ORF17, thymidine kinase, and vIRF-4. Functional annotation of respective interacting proteins showed highly overlapping biological functions such as mRNA processing and transcriptional regulation by TP53. Involvement of commonly interacting 44 cellular proteins in innate immune regulation were examined by siRNAs, and we identified that splicing factor 3B (SF3B) family proteins were clearly involved in interferons transcription and suppressed KSHV reactivation. We propose that recombinant TurboID-KSHV is a powerful tool to probe key cellular proteins that play a role in KSHV replication, and selective splicing factors may have a function beyond connecting two exon sequences to regulate innate immune responses.

Importance

Viral protein interaction with a host protein shows at least two sides: (i) taking host protein functions for its own benefit and (ii) disruption of existing host protein complex formation to inhibit undesirable host responses. Due to use of affinity-precipitation approaches, the majority of our studies focused on how the virus takes advantage of the newly-formed protein interactions for its own replication. Proximity labeling (PL) however, can also highlight the transient and negative effects – those interactions which lead to dissociation from the existing protein complex. Here we highlight the power of PL in combination with recombinant KSHV to study viral host interactions.
Dissecting Mammalian Spermatogenesis Using Spatial Transcriptomics
Authors: Chen Haiqi , Murray Evan , Laumas Anisha , Li Jilong , Nie Xichen , Hotaling Jim , Guo Jingtao , Cairns Bradley R. , Macosko Evan Z. , Cheng C. Yan , Chen Fei
Published: October 2020

Single-cell RNA sequencing has revealed extensive molecular diversity in gene programs governing mammalian spermatogenesis but fails to delineate their dynamics in the native context of seminiferous tubules — the spatially-confined functional units of spermatogenesis. Here, we use Slide-seq, a novel spatial transcriptomics technology, to generate a comprehensive spatial atlas that captures the spatial gene expression patterns at near single-cell resolution in the mouse and human testis. By using Slide-seq data, we devise a computational framework that accurately localizes testicular cell types in individual seminiferous tubules. Unbiased spatial transcriptome analysis systematically identifies spatially patterned genes and gene programs, nominating genes with previously underappreciated but important functions in spermatogenesis. Using the human testicular spatial atlas, we identify two spatially segregated spermatogonial populations composed of stem cells at distinct transcriptional states. Finally, a comparison of the spatial atlas generated from the wild type and diabetic mouse testis reveals a disruption in the spatial cellular organization in diabetic seminiferous tubules.
Performance of three freely available methods for extracting white matter hyperintensities: FreeSurfer, UBO Detector and BIANCA
Authors: Hotz Isabel , Deschwanden Pascal Frédéric , Liem Franziskus , Mérillat Susan , Kollias Spyridon , Jäncke Lutz
Published: October 2020

White matter hyperintensities (WMH) of presumed vascular origin are frequently found in MRIs of healthy older adults. WMH are also associated with aging and cognitive decline. Here, we compared and validated three freely available algorithms for WMH extraction: FreeSurfer, UBO Detector, and BIANCA (Brain Intensity AbNormality Classification Algorithm) using a longitudinal dataset comprising MRI data of cognitively healthy older adults (baselineN= 231, age range 64–87 years). As reference we manually segmented WMH in T1w, 3D FLAIR, 2D FLAIR images. These manual segmentations were then used to assess the segmentation accuracy of the different automated algorithms. Further, we assessed the relationships of WMH volume estimates provided by the algorithms with Fazekas scores and age. FreeSurfer underestimated the WMH volumes and scored worst in Dice Similarity Coefficient (DSC = 0.434) but its WMH volumes strongly correlated with the Fazekas scores (rs= 0.73). BIANCA accomplished the highest DCS (0.602) with 3D FLAIR images. However, the relations with the Fazekas scores were only moderate, especially in the 2D FLAIR images (rs= 0.41), and many outlier WMH volumes were detected when exploring within-person trajectories (2D FLAIR: ~30%). UBO Detector performed similarly to BIANCA in DSC with both modalities and reached the best DSC in 2D FLAIR (0.531) without requiring a tailored training dataset. In addition, it achieved very high associations with the Fazekas scores (2D FLAIR:rs= 0.80).

In summary, our results emphasize the importance of carefully contemplating the choice of the WMH segmentation algorithm and MR-modality.
Diluvial nation: building imperial Japan through floods
Authors: Yoshikawa Lisa
Published: October 2020

Purpose

This article assesses the development of flood relief and recovery, and their narratives, as political sites for the central and local governments to negotiate each other's standing and role in imperial Japan.

Design/methodology/approach

The article examines local flood narratives, most prominently from Okayama, to assess how imperial Japan's central government intruded into the periphery through disaster relief, and how the localities negotiated and challenged Tokyo's political agenda on the ground and through these narratives.

Findings

The above sources reveal that the national government attempted to use flood experiences to unite the pluralizing society by three main means: building meteorological stations, relief laws, and through the imperial being. The process was systematized gradually, and local prefectures aided and challenged Tokyo's attempts. The prefectures also used disasters to try to bring unity within their community.

Originality/value

Historical flood narratives are often used to mine data from which future preventative and management measures are constructed. The article suggests the narratives' political nature, and hence the nuances that must be considered in these efforts.
A critical analysis of safety performance indicators in construction
Authors: Shaikh Aziz Yousif , Osei‐Kyei Robert , Hardie Mary
Published: October 2020

Purpose

Safety performance indicators are a major research concern globally in the construction sector, so this study aims to systematically analyse construction safety performance indicators from some top research publications from 2000 to 2019.

Design/methodology/approach

Systematic review was performed using Scopus search engine and relevant publications were compiled. Visual and far reaching search in all publications were performed. Final analysis was done to evaluate selected attributes.

Findings

The outcome of the analysis showed growing interest in research on construction safety performance indicators since 2000. From the review, 48 safety performance indicators are identified from 41 selected publications. The most reported safety performance indicators were safety climate, safety orientation, management commitment to safety, near-miss and job site audits. It was noted further that USA, Australia, Canada and China have been international locations of attention for most research on construction safety performance indicators. The 48 safety indicators are classified into six categories, namely people indicators, culture indicators, processes indicators, infrastructure indicators, metrics indicators and technology indicators

Practical implications

The findings identified provide researchers and practitioners a summary of the safety indicators in the construction sector through a vision to streamline future applications and increase the safety performance in the construction sector.

Originality/value

A safety performance indicators' list has been established for the adoption of future empirical research. The findings will make a significant contribution to current but limited knowledge on safety performance indicators in construction industry.
Design principles for creating digital badges to support learning
Authors: Horstman Theresa , Tierney Gavin , Tzou Carrie
Published: October 2020

Purpose

This paper aims to focus on two areas of digital badge design that impact learner experience: the value and meaning of badges outside of their original context and badge function and platform functionality that impact learner experience.

Design/methodology/approach

This research uses a design-based research approach. For this paper, components of badge systems were analyzed to identify the characteristics of learning experiences in each program.

Findings

Findings in this paper are from a National Science Foundation-funded project where digital badge systems were co-designed to connect informal science learning with college credit. The badge design principles presented to address the value of badges and badge function and platform functionality, as well as making program design more systematic and using badge design as a conceptual, organizing design framework for improved educational programs.

Research limitations/implications

Though this research is limited in the number of programs examined, the findings provide a framework for the language and standards to discuss and implement digitals badges.

Practical implications

This paper will be of use to programing developers seeking to integrate badges into their educational programs or simply reexamine their educational goals and opportunities for learners.

Originality/value

This paper challenges the conventional use of badges for simply increasing learner engagement by illustrating that the badge design and development process can improve program design and subsequent learner experience rather than serving purely as a learner motivational tool.
Does multitasking computer self-efficacy mitigate the impact of social media affordances on overload and fatigue among professionals?
Authors: Islam A.K.M. Najmul , Whelan Eoin , Brooks Stoney
Published: October 2020

Purpose

This paper investigates the moderating role of multitasking computer self-efficacy on the relationship between social media affordances and social media overload as well as its moderation between social media overload and social media fatigue.

Design/methodology/approach

The authors hypothesize that social media affordances will have a positive impact on social media overload (i.e. information and communication overload). They also hypothesize that social media overload will affect social media fatigue. In addition, they hypothesize that multitasking computer self-efficacy will attenuate the effect of social media affordances on both information overload and communication overload. Similarly, they also hypothesize that multitasking computer self-efficacy will attenuate the effects of both information overload and communication overload on fatigue. The authors test this model by collecting two-wave data from 220 professionals using PLS techniques.

Findings

Social media affordances have significant impacts on information overload, but not on communication overload. In turn, information overload and communication overload significantly affect social media fatigue. Multitasking computer self-efficacy was found to attenuate the effect of social media affordances on both information overload and communication overload. Furthermore, the study results suggest that multitasking computer self-efficacy attenuates the effect of information overload and reinforces the effect of communication overload on social media fatigue.

Originality/value

Most prior literature focused on students rather than on professionals. There is a lack of research that investigates how the affordances of social media relate to social media overload and fatigue. Furthermore, research that investigates mitigating mechanisms of social media fatigue has been rare. This paper fills these important research gaps.
Corporate social responsibility and institutional investors: the intervening effect of financial performance
Authors: Maqbool Shafat , Zamir Nasir
Published: October 2020

Purpose

The research on the role of corporate social responsibility in investors' decision process has proliferated over the past few decades. This paper aims to explore the mediating role of financial performance in the relationship between corporate social responsibility and institutional investors.

Design/methodology/approach

Panel regression was performed on a sample of 29 commercial banks nine years from 2009 to 2017.

Findings

The initial findings of the study show that that corporate social responsibility has a positive and significant impact on institutional investors. However, when the interaction term (financial performance) was incorporated, the relationship between CSR and institutional turns out to be neutral. The study concludes that financial performance plays a pivotal role in the selection of investment avenues.

Originality/value

In Indian context, there is a dearth of research work which studies the impact of sustainable practices on investors' decision process. This topic has received wider attention but lacks insights from developing countries, like India. This article presents a new approach to verify the relationship through the mediating variable (financial performance).
Toward new strategies of Islamic financial products development
Authors: Mansour Walid
Published: October 2020

Purpose

This paper aims to propose a conceptual framework for the assessment of Islamic financial products’ development.

Design/methodology/approach

A coordinate grid with two perpendicular axes (profitability and compliance to Shari’ah) is developed and used to produce a nine-zone matrix. The research design is further developed by using a linear, composite index to assess product development feasibility and specifications. Subsequently, three strategic paths are identified: profitability-led strategic path, compliance-led strategic path and intermediate strategic path.

Findings

The findings indicate that the ideal strategic behavior the Islamic financial institutions have to borrow corresponds to the intermediate strategic path because it optimizes the trade-off between the two attributes under consideration. A proper development strategy of Islamic financial products should not ignore the compliance to the substance of Shari’ah and combine it simultaneously with profitability.

Originality/value

The paper’s originality consists in the identification of the portfolio of Islamic financial products’ strategic positioning in the nine-zone matrix and the determination of the most suitable product development strategy.
Enhancing student empathy through the taxonomy of significant learning
Authors: Billiot Theresa , Forbes Lukas P.
Published: October 2020

Purpose

The purpose of this paper is to use Fink’s (2013) taxonomy of significant learning in a retail marketing class to help rural, price-sensitive students develop empathy toward high-end urban customers while becoming self-directed learners.

Design/methodology/approach

Using a 16-week pilot course, students developed a gaming prototype and learned about the challenges of targeting those from a higher socioeconomic status.

Findings

Results indicate that educators using Fisk’s taxonomy of significant learning might be able to positively influence the empathy that individuals on the lower end of the socioeconomic spectrum might feel toward higher-end customers. In addition, qualitative data reflects how a majority of students acknowledged empathy as their weakness but data also reveals how students plan to become continuous learners to improve their empathy in the future.

Originality/value

This paper has two key contributions. First, it shows how using a creative style of teaching within a marketing classroom can influence a key characteristic that buyers would need to successfully engage with higher-end clients. Second, it uses a new technique (gaming) in which to do so.
Enabling knowledge sharing through psychological safety in inter-organisational arrangements
Authors: Rivera Angel Eustorgio , Rodríguez-Aceves Lucía , Mojarro-Duran Barbara I.
Published: October 2020

Purpose

This study aims to generate additional insights into the relationship between knowledge sharing (KS) and psychological safety (PS) in an inter-organisational arrangement through the lens of the knowledge-based view and PS theory.

Design/methodology/approach

A relational data survey was designed to collect systematic information from key actors in two manufacturing organisations. The questionnaire assessed KS as the dependent variable and four independent variables – three behavioural (respect, tolerance, trust) and one contextual (suitable working environment) – as proxies of PS. The multiple regression quadratic assignment procedure was used to analyse the effect of PS on KS.

Findings

This paper strengthens the findings of previous studies that identify PS as a relevant antecedent of KS in organisations. Additionally, the paper also suggests that a relational approach is more relevant to understand PS as a group concept measured through networks of respect, tolerance, trust and suitable working environments.

Practical implications

This study may help managers identify ways in which they can strengthen the work-related relationships when such behavioural and contextual variables occur in inter-organisational arrangements, and thus obtaining additional relational rents based on an increase in KS.

Originality/value

This study contributes to the literature on how KS in organisations is driven by behavioural and contextual variables that can be operationalised as PS. Moreover, this study expands the understanding of previous research on PS by taking a relational approach to its conceptualisation and measurement within a Latin American context.
Heritage-based value of a corporate brand: antecedents and effects on the firm’s financial value
Authors: Paek Wonsun , Ryu Hyerin , Jun Sunkyu
Published: October 2020

Purpose

The purpose of this study is to show that a corporate brand with a long history coupled with relevance to the present obtains heritage-based value in society and the second aim is to examine a boundary condition in which the heritage-based value of a corporate brand increases the firm’s financial value.

Design/methodology/approach

A survey was conducted to investigate when and how a corporate brand obtains its heritage-based value in society and archival analysis was conducted to analyze the relationship between the heritage-based value of a corporate brand and the firm’s financial value.

Findings

The longevity of a corporate brand increased its heritage-based value, particularly when the brand was perceived to be temporally continuous, through the enhancement of authenticity perception and the heritage-based value had a positive effect on the firm’s financial value for younger firms.

Research limitations/implications

This study extends the benefits of the heritage association of a corporate brand to the firm level but has a limitation in its cross-sectional method.

Practical implications

The study results justify monetary costs incurred in the course of developing and cultivating a brand’s heritage association.

Originality/value

It is believed that this study is the first quantitative research examining the relationship between the heritage-based value of corporate brands and firms’ financial value.
Drivers of emerging market professional service firm success: the role of internal firm competencies and capabilities
Authors: Mathew Nicholas , Javalgi Rajshekhar (Raj) , Dixit Ashutosh , Gross Andrew
Published: October 2020

Purpose

The purpose of this study is to investigate the effects of emerging market professional service small and medium-sized enterprises’ (PSF SME) internal competencies and capabilities on their ability to establish relationship value among clients and achieve superior financial performance. This study addresses the paucity of research on emerging market PSF SMEs and their ability to build value for their clients.

Design/methodology/approach

Data were collected from 251 senior managers or owners of PSF SMEs who were from an emerging market economy but had operations in various foreign markets. The two-step structural equation modeling procedure was used to analyze the data and investigate the hypothesized relationships.

Findings

The results show the positive impacts of the PSF SME’s human capital on innovativeness, service capabilities and relationship value. Human capital also had indirect positive impacts on relationship value and financial performance. Service capabilities were found to have a positive impact on relationship value and financial performance. In addition, innovativeness was found to have a positive impact on financial performance.

Practical implications

Emerging market PSF SMEs can gain competitive advantages and build solid long-term relationships with clients in the global marketplace when they focus on strengthening their human capital resources and successfully leveraging their innovativeness and service capabilities.

Originality/value

The study fills a gap in international business and management literature by offering guidance on how emerging market PSF SMEs can effectively use their internal resources and capabilities to build solid relationships with clients, deliver superior services and achieve global marketplace success.
Rainfall pulses mediate long‐term plant community compositional dynamics in a semi‐arid rangeland
Authors: Liang Maowei , Feng Xiao , Gornish Elise S.
Published: October 2020

Semi‐arid rangelands, comprising more than 40% of the Earth's land surface, provide critical ecosystem services. Worldwide, these ecosystems are experiencing rapid degradation due to overgrazing and precipitation changes. However, how plants respond to these interacting factors remains relatively unexplored, and precisely which and how rainfall factors determine plant community dynamics in rangelands has not been well developed.

We used a long‐term (1953‒2018) dataset from semi‐arid rangeland to investigate coupled effects of grazing intensity and rainfall intensity (the total amount of precipitation) on different groups of plant cover (herbaceous, woody and cacti plants) using linear mixed‐effects models, redundancy analysis and structural equation models. We examined how rainfall intensity influenced plant cover dynamics according to pulse size (intensity over time) categories, which we analysed at three scales: yearly, within the wet season only (June–September) and within the dry season only (October–May).

Plant community cover showed a humpbacked trend in the last six decades, mostly through changes in woody plants. Although both grazing intensity and rainfall presented similar humpbacked trends with plant community cover, our models demonstrated that the reduction of plant cover from the 1990s has been mainly caused by a decrease of rainfall rather than grazing intensity, particularly due to profound reductions of the intensity of relatively small rainfall pulses (e.g. 5.1–15 mm/day) during the dry season. Specifically, these small rainfall pulses can increase plant cover of all subgroups of woody and herbaceous species, thereby increasing plant community cover. Moreover, rainfall pulses during the wet season had negative effects on herbaceous species and positive effects on woody plants. These results suggest a phenological niche partitioning between woody plants and herbaceous in subtropical rangelands.

Synthesis and applications. Our results show how critical seasonal rainfall pulses are for regulating plant community compositional dynamics, which has significant implications for rangeland management and our ability to adapt and mitigate amplified climate influences in semi‐arid ecosystems.
Grazing and climate change have site‐dependent interactive effects on vegetation in Asian montane rangelands
Authors: Kohli Mayank , Mijiddorj Tserennadmid Nadia , Suryawanshi Kulbhushansingh Ramesh , Mishra Charudutt , Boldgiv Bazartseren , Sankaran Mahesh
Published: October 2020

Climate over Asian montane rangelands is changing faster than the global average, posing serious threats to the future of the region's livestock‐based economies and cultures. Effects of climate change on rangeland vegetation likely depend on grazing by herbivores but the potential responses of vegetation to such changes in climate and grazing regimes remain unclear.

We examined vegetation responses to experimentally simulated climate change (warming, drought and increased rainfall) and grazing (clipping vegetation) between 2015 and 2018 at two mountain rangeland sites: Spiti valley, in the Indian Trans‐Himalaya and Tost, in the Gobi‐Altai Mountains in Mongolia.

Clipping and climate change manipulations interactively reduced vegetation cover and biomass but did not affect species richness. Treatment effects and their interactions varied between sites. In ungrazed plots, vegetation cover and biomass declined sharply in response to warming (18%–35%) and drought (20%–50%) at the two sites, and, surprisingly also declined slightly in response to increased rainfall (20%) at Tost. While the effects of climate treatments were largely similar in the grazed and ungrazed plots in Tost, they were larger in the ungrazed plots in Spiti. The decline in vegetation cover was driven by a decline in the cover of both forbs and grasses.

In combination, grazing and warming (Tost) or drought (Spiti) had sub‐additive effects, that is, the decrease in vegetation cover in response to grazing and warming/drought was less than the sum of their independent effects but greater than the effect of either manipulation alone. Of the two, warming had a greater effect than drought at the more arid site (Tost), whereas drought had a larger effect at the more mesic site (Spiti).

Synthesis and applications. Our findings show that future changes in climate, including just over 1°C of warming, could undermine the sustainability of pastoral economies and the persistence of wildlife across Asian montane rangelands. Furthermore, grazing by herbivores will play an important role in mediating rangeland responses to climate change; thus, pasture management in concert with local pastoralists will be crucial in mitigating the adverse effects of climate change on rangelands, pastoral livelihoods and wildlife populations.
Explaining the immigration policy mix: Countries' relative openness to asylum and labour migration
Authors: SCHULTZ CAROLINE , LUTZ PHILIPP , SIMON STEPHAN
Published: October 2020

Western democracies have developed complex policies to manage migration flows. Much of the scholarly literature and political discourse assume that countries have become increasingly selective and that they prioritise economic intakes. Despite clear efforts by policymakers to distinguish between refugees and migrant workers, we know surprisingly little about how countries combine different policy dimensions and which factors shape their relative openness to different target groups. In this article, we shed light on how countries combine two of the main admission channels, asylum and labour migration, by introducing the concept of the ‘immigration policy mix’. A comparative analysis of 33 OECD countries between 1980 and 2010 examines the pattern and drivers behind their immigration policy mix: Does the policy mix follow a pattern of convergence, is it subject to political dynamics or is it path dependent? The results reveal that despite a shift in political sympathies from asylum to labour migration, countries' immigration policy mixes have strongly converged into more liberal policies overall. The immigration policy mix primarily reflects governments’ limited room to manoeuvre due to competing political pressures. These insights demonstrate that the immigration policy mix serves to enhance our understanding of countries’ complex regulation of immigration.
Plasma‐activated water: Physicochemical properties, microbial inactivation mechanisms, factors influencing antimicrobial effectiveness, and applications in the food industry
Authors: Zhao Yi‐Ming , Patange Apurva , Sun Da‐Wen , Tiwari Brijesh
Published: October 2020

Novel nonthermal inactivation technologies have been increasingly popular over the traditional thermal food processing methods due to their capacity in maintaining microbial safety and other quality parameters. Plasma‐activated water (PAW) is a cutting‐edge technology developed around a decade ago, and it has attracted considerable attention as a potential washing disinfectant. This review aims to offer an overview of the fundamentals and potential applications of PAW in the agri‐food sector. A detailed description of the interactions between plasma and water can help to have a better understanding of PAW, hence the physicochemical properties of PAW are discussed. Further, this review elucidates the complex inactivation mechanisms of PAW, including oxidative stress and physical effect. In particular, the influencing factors on inactivation efficacy of PAW, including processing factors, characteristics of microorganisms, and background environment of water are extensively described. Finally, the potential applications of PAW in the food industry, such as surface decontamination for various food products, including fruits and vegetables, meat and seafood, and also the treatment on quality parameters are presented. Apart from decontamination, the applications of PAW for seed germination and plant growth, as well as meat curing are also summarized. In the end, the challenges and limitations of PAW for scale‐up implementation, and future research efforts are also discussed. This review demonstrates that PAW has the potential to be successfully used in the food industry.
Inhibitory effect of sweet whey fermented by Lactobacillus plantarum strains against fungal growth: A potential application as an antifungal agent
Authors: Izzo Luana , Luz Carlos , Ritieni Alberto , Quiles Beses Juanma , Mañes Jordi , Meca Giuseppe
Published: October 2020

The presence of mycotoxigenic fungi such as Aspergillus, Penicillium, and Fusarium genera represents a problem in food preservation and consequently, its spoilage. During the fermentation process with lactic acid bacteria, a range of secondary metabolites associated with beneficial health effects were released. In the present study, goat whey fermented by Lactobacillus plantarum (CECT 220, 221, 223, and 748) species has shown a satisfactory inhibitory effect against 28 fungi, showing for certain species of Fusarium genus and also, for Aspergillus steynii, a value of minimum inhibitory concentration until 1.95 g/L. In addition, phenyllactic acid was identified in each sample of fermented whey at a concentration ranged from 0.34 to 1.21 mg/L. These results suggest the possible use of fermented whey as a source of new preservatives of natural origin to incorporate in food matrices for the purpose of improving the shelf life.

Practical Application

Whey could be a good candidate for use as a natural antifungal agent to incorporate in food matrices. Whey could be used to prevent specific fungal growth that naturally occurs in food preparations. Consequentially, whey could enhance the shelf life of edible products.
N,N'‐Diphenylthiourea electrochemical sensor for the detection of l‐glutamate and Aspartate in beef
Authors: Wang Xiaodan , Hu Feng , Zhu Lingtao , Liu Dengyong , Dong Yanli , Wang Cuilian , Wu Duo
Published: October 2020

This study was conducted to design an electrochemical sensor for detection of l‐glutamate (L‐Glu) and Aspartate (Asp), which contribute largely to the umami taste of beef. Using N, N'‐diphenylthiourea (DPTU), polypyrrole (PPy), and polyvinyl chloride (PVC), a composite electrode (DPTU/PVC/PPy/Pt) was prepared for rapidly electrochemical detection of l‐Glu and Asp. The surface morphology of the synthesized functionalized electrode was characterized by Field Emission Scanning Electron Microscopy (FESEM). Potentials of umami amino acids accounted for 97.8%, while six interferential amino acids existed. The linear correlation between the content of l‐Glu and Asp in beef broth was studied under different treatment conditions. The sensor compared with an amino acid analyzer well detected the contents of l‐Glu and Asp in beef broths, with a coefficient of 0.991 in Pearson correlation analysis and an accuracy of 88.9%. The proposed electrochemical sensor showed good concurrence with previously reported methods and was effectively employed for the quantification of l‐ Glu and Asp in beef.

Practical Application

The sensor exhibits the good performance with high stability and high accuracy. And it is a potential sensing platform with good reproducibility, making the proposed method suitable and reliable for routine analysis of L‐Glu and Asp in beef. This method was proved promising for quantitative detecting amino acids in beef.
Co‐oxidation of Antarctic krill oil with whey protein and myofibrillar protein in oil‐in‐water emulsions
Authors: Wang Yuliu , Liu Yanzi , Ma Lei , Yang Lu , Cong Peixu , Lan Haohui , Xue Changhu , Xu Jie
Published: October 2020

Antarctic krill oil (AKO) is usually encapsulated by the protein materials, enhancing its oxidative stability. Proteins exhibit immense effect on lipid oxidation and induce protein–lipid co‐oxidation. This study aimed at elucidating the co‐oxidation mechanism of AKO and whey protein (WP) or myofibrillar protein (MP) in oil‐in‐water emulsions. The estimations of malondialdehyde (MDA) content, phospholipid molecular species, and pyrrole content resulted in increased and decreased oxidation rate of AKO (especially phosphatidylethanolamine) by WP and MP, respectively. Meanwhile, protein concentration, sulfhydryl content, the loss of tryptophan fluorescence intensity, and sodium dodecyl sulfate‐polyacrylamide gel electrophoresis results demonstrated that AKO promoted WP oxidation but inhibited MP oxidation. Further, the antioxidative abilities of seven common antioxidants were evaluated. Ascorbyl palmitate showed the most substantial antioxidative effect for both AKO and proteins (about 70% decrease of MDA content and 30% decrease of the decrease ratio of tryptophan fluorescence intensity). This finding supported that different proteins could exhibit different pro/anti‐oxidative effects on lipid oxidation, especially for marine lipids abundant in phospholipids and polyunsaturated fatty acids. Besides, MP could also act as antioxidant in MP AKO emulsions, further extending its application from traditional surfactants.

Practical Application

AKO is usually encapsulated by the protein materials, enhancing its oxidative stability. The results demonstrated MP could inhibit AKO oxidation, and vice versa, especially when ascorbyl palmitate was added at the same time. As a result, this finding explored a new potential wall material with antioxidative ability for the encapsulated products of AKO.
Biomolecular composition of capping layer and stability of biogenic selenium nanoparticles synthesized by five bacterial species
Authors: Bulgarini Alessandra , Lampis Silvia , Turner Raymond J. , Vallini Giovanni
Published: October 2020

Biogenic metal/metalloid nanoparticles of microbial origin retain a functional biomolecular capping layer that confers structural stability. Little is known about the composition of such capping material. In this study, selenium nanoparticles (SeNPs) synthesized by five different bacterial strains underwent comparative analysis with newly proposed protocols for quantifying the concentration of carbohydrates, proteins and lipids present in capping layers. SeNPs were therefore treated with two different detergents to remove portions of the surrounding caps in order to assess the resulting effects. Capping material quantification was carried out along with the measure of parameters such as hydrodynamic diameter, polydispersity and surface charge. SeNPs from the five strains showed differences in their distinct biomolecule ratios. On the other hand, structural changes in the nanoparticles induced by detergents did not correlate with the amounts of capping matrix removed. Thus, the present investigation suggests a hypothesis to describe capping layer composition of the bacterial SeNPs: some biomolecules are bound more strongly than others to the core metalloid matrix, so that the diverse capping layer components differentially contribute to the overall structural characteristics of the nanoparticles. Furthermore, the application of the approach here in combining quantification of cap‐associated biomolecules with the measurement of structural integrity‐related parameters can give the biogenic nanomaterial field useful information to construct a data bank on biogenically synthesized nanostructures.
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
Authors: Edler Daniel , Klein Johannes , Antonelli Alexandre , Silvestro Daniele
Published: October 2020

raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood.

Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front‐end to setup and run phylogenetic analyses.

Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built‐in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one‐click model testing to select the best substitution models using ModelTest‐NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML‐NG, which provides new functionality and higher performance on large datasets.

raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.
Hierarchical computing for hierarchical models in ecology
Authors: McCaslin Hanna M. , Feuka Abigail B. , Hooten Mevin B.
Published: October 2020

Bayesian hierarchical models allow ecologists to account for uncertainty and make inference at multiple scales. However, hierarchical models are often computationally intensive to fit, especially with large datasets, and researchers face trade‐offs between capturing ecological complexity in statistical models and implementing these models.

We present a recursive Bayesian computing (RB) method that can be used to fit Bayesian models efficiently in sequential MCMC stages to ease computation and streamline hierarchical inference. We also introduce transformation‐assisted RB (TARB) to create unsupervised MCMC algorithms and improve interpretability of parameters. We demonstrate TARB by fitting a hierarchical animal movement model to obtain inference about individual‐ and population‐level migratory characteristics.

Our recursive procedure reduced computation time for fitting our hierarchical movement model by half compared to fitting the model with a single MCMC algorithm. We obtained the same inference fitting our model using TARB as we obtained fitting the model with a single algorithm.

For complex ecological statistical models, like those for animal movement, multi‐species systems, or large spatial and temporal scales, the computational demands of fitting models with conventional computing techniques can limit model specification, thus hindering scientific discovery. Transformation‐assisted RB is one of the most accessible methods for reducing these limitations, enabling us to implement new statistical models and advance our understanding of complex ecological phenomena.
Targeting miR‐124/Ferroportin signaling ameliorated neuronal cell death through inhibiting apoptosis and ferroptosis in aged intracerebral hemorrhage murine model
Authors: Bao Wen‐Dai , Zhou Xiao‐Ting , Zhou Lan‐Ting , Wang Fudi , Yin Xiaoping , Lu Youming , Zhu Ling‐Qiang , Liu Dan
Published: October 2020

Incidence of intracerebral hemorrhage (ICH) and brain iron accumulation increases with age. Excess iron accumulation in brain tissues post‐ICH induces oxidative stress and neuronal damage. However, the mechanisms underlying iron deregulation in ICH, especially in the aged ICH model have not been well elucidated. Ferroportin1 (Fpn) is the only identified nonheme iron exporter in mammals to date. In our study, we reported that Fpn was significantly upregulated in perihematomal brain tissues of both aged ICH patients and mouse model. Fpn deficiency induced by injecting an adeno‐associated virus (AAV) overexpressing cre recombinase into aged Fpn‐floxed mice significantly worsened the symptoms post‐ICH, including hematoma volume, cell apoptosis, iron accumulation, and neurologic dysfunction. Meanwhile, aged mice pretreated with a virus overexpressing Fpn showed significant improvement of these symptoms. Additionally, based on prediction of website tools, expression level of potential miRNAs in ICH tissues and results of luciferase reporter assays, miR‐124 was identified to regulate Fpn expression post‐ICH. Higher serum miR‐124 levels were correlated with poor neurologic scores of aged ICH patients. Administration of miR‐124 antagomir enhanced Fpn expression and attenuated iron accumulation in aged mice model. Both apoptosis and ferroptosis, but not necroptosis, were regulated by miR‐124/Fpn signaling manipulation. Our study demonstrated the critical role of miR‐124/Fpn signaling in iron metabolism and neuronal death post‐ICH in aged murine model. Thus, Fpn upregulation or miR‐124 inhibition might be promising therapeutic approachs for this disease.
Sulforaphane prevents age‐associated cardiac and muscular dysfunction through Nrf2 signaling
Authors: Bose Chhanda , Alves Ines , Singh Preeti , Palade Philip T. , Carvalho Eugenia , Børsheim Elisabet , Jun Se‐Ran , Cheema Amrita , Boerma Marjan , Awasthi Sanjay , Singh Sharda P.
Published: October 2020

Age‐associated mitochondrial dysfunction and oxidative damage are primary causes for multiple health problems including sarcopenia and cardiovascular disease (CVD). Though the role of Nrf2, a transcription factor that regulates cytoprotective gene expression, in myopathy remains poorly defined, it has shown beneficial properties in both sarcopenia and CVD. Sulforaphane (SFN), a natural compound Nrf2‐related activator of cytoprotective genes, provides protection in several disease states including CVD and is in various stages of clinical trials, from cancer prevention to reducing insulin resistance. This study aimed to determine whether SFN may prevent age‐related loss of function in the heart and skeletal muscle. Cohorts of 2‐month‐old and 21‐ to 22‐month‐old mice were administered regular rodent diet or diet supplemented with SFN for 12 weeks. At the completion of the study, skeletal muscle and heart function, mitochondrial function, and Nrf2 activity were measured. Our studies revealed a significant drop in Nrf2 activity and mitochondrial functions, together with a loss of skeletal muscle and cardiac function in the old control mice compared to the younger age group. In the old mice, SFN restored Nrf2 activity, mitochondrial function, cardiac function, exercise capacity, glucose tolerance, and activation/differentiation of skeletal muscle satellite cells. Our results suggest that the age‐associated decline in Nrf2 signaling activity and the associated mitochondrial dysfunction might be implicated in the development of age‐related disease processes. Therefore, the restoration of Nrf2 activity and endogenous cytoprotective mechanisms by SFN may be a safe and effective strategy to protect against muscle and heart dysfunction due to aging.
Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence
Authors: Drake John , McMichael Gowon O. , Vornholt Eric Sean , Cresswell Kellen , Williamson Vernell , Chatzinakos Chris , Mamdani Mohammed , Hariharan Siddharth , Kendler Kenneth S. , Kalsi Gursharan , Riley Brien P. , Dozmorov Mikhail , Miles Michael F. , Bacanu Silviu‐Alin , Vladimirov Vladimir I.
Published: October 2020

Background

Long noncoding RNA (lncRNA) have been implicated in the etiology of alcohol use. Since lncRNA provide another layer of complexity to the transcriptome, assessing their expression in the brain is the first critical step toward understanding lncRNA functions in alcohol use and addiction. Thus, we sought to profile lncRNA expression in the nucleus accumbens (NAc) in a large postmortem alcohol brain sample.

Methods

LncRNA and protein‐coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL).

Results

At Bonferroni adj. p‐value ≤ 0.05, we identified 19 lncRNA and 5 PCG significant modules, which were enriched for neuronal and immune‐related processes. In these modules, we further identified 86 and 315 PCG and lncRNA hubs, respectively. At false discovery rate (FDR) of 10%, the correlation analyses between the lncRNA and PCG hubs revealed 3,125 positive and 1,860 negative correlations. Integration of hubs with genotype data identified 243 eQTLs affecting the expression of 39 and 204 PCG and lncRNA hubs, respectively.

Conclusions

Our study identified lncRNA and gene networks significantly associated with AD in the NAc, coordinated lncRNA and mRNA coexpression changes, highlighting potentially regulatory functions for the lncRNA, and our genetic (cis‐eQTL) analysis provides novel insights into the etiological mechanisms of AD.