bluuebunny/crossref_metadata_2025 huggingface dataset:
An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques
Authors: Madden Patrick J. , Thomas Yanique , Blair Robert V. , Samer Sadia , Doyle Mark , Midkiff Cecily C. , Doyle-Meyers Lara A. , Becker Mark E. , Arif Muhammad S. , McRaven Michael D. , Simons Lacy M. , Carias Ann M. , Martinelli Elena , Lorenzo-Redondo Ramon , Hultquist Judd F , Villinger Francois J. , Veazey Ronald S. , Hope Thomas J.
Published: March 2022

The systemic nature of SARS-CoV-2 infection is highly recognized, but poorly characterized. A non-invasive and unbiased method is needed to clarify whole body spatiotemporal dynamics of SARS-CoV-2 infection after transmission. We recently developed a probe based on the anti-SARS-CoV-2 spike antibody CR3022 to study SARS-CoV-2 pathogenesis in vivo. Herein, we describe its use in immunoPET to investigate SARS-CoV-2 infection of three rhesus macaques. Using PET/CT imaging of macaques at different times post-SARS-CoV-2 inoculation, we track the 64Cu-labelled CR3022-F(ab’)2 probe targeting the spike protein of SARS-CoV-2 to study the dynamics of infection within the respiratory tract and uncover novel sites of infection. Using this method, we uncovered differences in lung pathology between infection with the WA1 isolate and the delta variant, which were readily corroborated through computed tomography scans. The 64Cu-CR3022-probe also demonstrated dynamic changes occurring between 1- and 2-weeks post-infection. Remarkably, a robust signal was seen in the male genital tract (MGT) of all three animals studied. Infection of the MGT was validated by immunofluorescence imaging of infected cells in the testicular and penile tissue and severe pathology was observed in the testes of one animal at 2-weeks post-infection. The results presented here underscore the utility of using immunoPET to study the dynamics of SARS-CoV-2 infection to understand its pathogenicity and discover new anatomical sites of viral replication. We provide direct evidence for SARS-CoV-2 infection of the MGT in rhesus macaques revealing the possible pathologic outcomes of viral replication at these sites.

Graphic Abstract

PET/CT detected SARS-CoV-2 infection of 4 different tissues in the male genital tract illuminates the cause of COVID-19 clinical sequalae of male sexual health and fertility
Figure 1.

Diagram shows schematic illustration of the male genital tract of the rhesus macaque. Virus icon shows sites of SARS-CoV-2 PET signal. Text highlighting the clinical sequalae associated with each sight of infection is shown in text adjacent to each infection site.
Automated, Reproducible Investigation of gene set Differential Enrichment via the AUTO-go framework
Authors: Sperandio Eleonora , Grassucci Isabella , D’Ambrosio Lorenzo , Pallocca Matteo
Published: March 2022

Reproducibility in Life Sciences is challenged in the analysis of large multi-omics datasets. One of the final steps of said processes is Gene Set enrichment, where web tools represent a valuable resource but not a reliable surrogate for standardized, high-quality visualizations. The AUTO-go framework proposes standardization of the Gene Functional Enrichment process along with an R framework able to produce high-quality visualization in an automated manner, improving the reproducibility of the whole analytical process. We present three use cases in Cancer Transcriptomics and Epigenomics datasets as a proof-of-concept to visualize Multiple Differential Expression and Single Sample Gene Set Enrichment Analysis.

Author Summary

Bioinformatics and Data Science are routinely challenged to distill intelligible results from huge amounts of data. These results, in turn, are conveyed through plots and visualizations that should be easily reproducible for scientific soundness and ethical reasons. A specific area in which these analyses are of critical importance is Genomics, where Genes functions need to be enriched when comparing pathological states or treatments. Here we present a software framework that aims at standardizing said differential analyses and visualizations when dealing with genomics data. Finally, we show how it can be employed to shear light on publicly available datasets, even in small casuistry of Rare Cancers.
Metabolomic profiles of chronic distress predict future cardiovascular disease risk
Authors: Balasubramanian Raji , Shutta Katherine H. , Guasch-Ferre Marta , Huang Tianyi , Jha Shaili C. , Zhu Yiwen , Shadyab Aladdin H. , Manson JoAnn E. , Hu Frank , Rexrode Kathryn M. , Clish Clary B. , Hankinson Susan E. , Kubzansky Laura D.
Published: March 2022

Background

Chronic psychological distress has been associated with increased risk of cardiovascular disease (CVD). However, mechanistic evidence explaining the observed associations remains limited and, with data are particularly sparse among women. This study examined if a metabolite profile linked with distress would be associated with increased risk of CVD.

Methods

A plasma metabolite-based distress score (MDS) of twenty metabolites was derived in a cross-sectional, 1:1 matched case-control dataset (n=558 women) in the Nurses’ Health Study (NHS). We then calculated this score in two other cohorts, the Women’s Health Initiative Observational Cohort (WHI-OS) and the Prevención con Dieta Mediterránea (PREDIMED) trial, and tested association with risk of developing adjudicated measures of CVD in each cohort. We considered incident coronary heart disease (CHD) in the WHI-OS dataset which included 944 postmenopausal women (472 CHD cases; mean time to event of 5.8 years), and incident CVD (including stroke, myocardial infarction, CVD death) in the PREDIMED dataset which included 980 men and women (224 CVD cases, mean time to event of 3.1 years).

Results

In the WHI-OS, a 1-SD increase in the plasma MDS was associated with a 14% increased risk of incident CHD (odds ratio [OR]=1.14, 95% CI: 1.03 – 1.26), adjusting for known CVD risk factors excluding total and HDL cholesterol. This association was attenuated after including total and HDL cholesterol (OR=1.09; 95% CI: 0.98 – 1.21). Of the component metabolites in the MDS, tryptophan and threonine were inversely associated with incident CHD risk. In PREDIMED, each one SD increase in the MDS was associated with a 17% increased incident CVD risk (OR=1.17, 95% CI: 1.00 – 1.38), after adjusting for risk factors including total and HDL cholesterol. Similar associations were observed in men and women. Four individual metabolites in the MDS were associated with incident CVD risk in fully adjusted models in PREDIMED. Biliverdin and C36:5 PC plasmalogen had inverse associations, whereas C16:0 ceramide and C18:0 LPE each had positive associations with CVD risk.

Conclusions

Our study sheds light on the key molecular alterations that characterize chronic distress and are predictive of subsequent CVD risk in men and women. These findings provide additional evidence for the role of distress in CVD development.
Human MAIT cells show clonal diversity but transcriptional and functional homogeneity
Authors: Garner Lucy C. , Amini Ali , FitzPatrick Michael E.B. , Provine Nicholas M. , Klenerman Paul
Published: March 2022

Mucosal-associated invariant T (MAIT) cells are considered to have limited clonal diversity. In contrast, recent studies suggest the presence of functionally distinct subsets. We investigated this model through single-cell analysis of the MAIT cell TCR repertoire and transcriptional profile in human blood and liver. Further, we developed functional RNA-sequencing (fRNA-seq), an approach to integrate cellular function and TCR clonotype at a single-cell level following differential stimulation. MAIT cells showed surprising clonal diversity, with TCR repertoires shared across tissues but unique to individuals. Functional diversity within resting MAIT cells was low and largely related to tissue site. MAIT cells displayed distinct transcriptional responses to in vitro TCR and cytokine stimulation, with cells positioned along gradients of activation. Clonal origin influenced both resting and activated transcriptional profiles. Overall, MAIT cells exhibit diverse donor-specific TCR repertoires which, along with tissue and activation context, influence their phenotype and function.
Early Childhood Reading for Pleasure: Evidence from the ABCD Study for Benefits to Cognitive Performance and Mental Health and Associated Changes in Brain Structure
Authors: Sun Yunjun , Sahakian Barbara J. , Langley Christelle , Yang Anyi , Jiang Yuchao , Zhao Xingming , Li Chunhe , Cheng Wei , Feng Jianfeng
Published: March 2022

BACKGROUND

Early childhood has increasingly been recognized as an important neurodevelopmental period. However, the links between specific forms of early educational activities and cognition and mental health remain unclear.

METHODS

A large-scale analysis on the attainments of childhood Reading for Pleasure (early RfP) and its relationship with young adolescent measures of cognition, mental health and brain structure was conducted, using linear mixed-effects model, structural equation and mediation analyses. Participants were from the Adolescent Brain and Cognitive Development (ABCD) study, a USA national cohort (n=11,878). A two-sample Mendelian randomization (MR) analysis using genetic instruments from two independent genome-wide association studies (GWAS) based on ABCD and GWAS meta-analyses including UK-biobank datasets were conducted to assess potential causal inference.

RESULTS

Early RfP was positively associated with cognitive assessments, which in contrast, was negatively associated with dimensional psychiatric problems in young adolescents. MR analysis revealed a beneficial relationship between early RfP and later-life cognitive performance, and a trend towards a protective relationship between early RfP and later-life attention disorder. Brain regions in which larger cortical areas were positively associated with early RfP included the superior temporal, prefrontal, left angular, parahippocampal, right anterior cingulate (ACC), occipital, supramarginal and orbital regions and subcortical ventral diencephalon (DC), thalamus, and brainstem volumes. Mediation analysis indicated that the brain regions significantly mediated the effects of early RfP with better cognitive performance and lower psychiatric problems.

INTERPRETATION

Our results highlight the importance of encouraging RfP in young children during the critical early childhood stage, as it was associated with beneficial outcomes for cognition, mental health, and brain structure later in life.
ARID1A maintains transcriptionally repressive H3.3 associated with CHD4-ZMYND8 chromatin interactions
Authors: Reske Jake J. , Wilson Mike R. , Armistead Brooke , Perez Cristina , Hrit Joel , Adams Marie , Rothbart Scott B. , Missmer Stacey A. , Fazleabas Asgerally T. , Chandler Ronald L.
Published: March 2022

ARID1A is a signature subunit of the mammalian SWI/SNF (BAF) chromatin remodeling complex and is mutated at a high rate in malignancies and benign diseases originating from the uterine endometrium. Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements. ARID1A loss leads to H3.3 depletion at ARID1A bound active regulatory elements and a concomitant redistribution of H3.3 towards genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3-containing chromatin regulation. ZMYND8, the CHD4-interacting acetyl-histone H4 reader, specifies ARID1A-CHD4-H3.3 target regulatory activity towards histone H4 lysine 16 acetylation (H4K16ac) to repress super-enhancers. ARID1A, H3.3, CHD4, and ZMYND8 co-repress the expression of genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. Altogether, these studies demonstrate that cooperation among a histone reader and different types of chromatin remodelers safeguards the endometrium through transcriptionally repressive H3.3.
An Open-source, Cost-Efficient Excitation Module for Single-molecule Microscopy
Authors: George Dylan R. , Ambrose Benjamin , Cadby Ashley J. , Craggs Timothy D.
Published: March 2022

In fluorescence microscopy, scientific-grade laser diodes are key components and contribute a considerable expense to the total cost of the microscope setup. Existing open-source laser excitation modules are mainly designed for super-resolution imaging and have not been fully characterised to meet the requirements of single-molecule spectroscopy measurements. In this paper we introduce an open-source, cost-efficient excitation module that can be used for confocal, accurate single-molecule FRET, fluorescence correlation spectroscopy (FCS) and low-power super-resolution techniques. The module delivers two diode lasers (520 nm and 638 nm) via a single-mode fibre, with stable power output (<1% deviation), which can be modulated on the microsecond timescale. Here, we benchmark these lasers against smFRET standards, and recover consistent diffusion coefficients from FCS measurements, thereby demonstrating their suitability for a range of single-molecule spectroscopic experiments, whilst reducing the overall costs of our open-source smFRET instrument (the smfBox) by ~50%, making these types of experiments even more accessible to the widest possible userbase.
Improvements on Sample Preparation and Peptide Separation for Reduced Peptide Mapping Based Multi-Attribute Method analysis of Therapeutic Monoclonal Antibodies Using Lys-C Digestion
Authors: Li Xuanwen , Rawal Baibhav , Rivera Shannon , Letarte Simon , Richardson Douglas D.
Published: March 2022

The mass spectrometry based multi-attribute method (MAM) has gained popularity in the field of biopharmaceutical analysis as it promises a single method for comprehensive monitoring of multiple product quality attributes (PQAs) and product purity. Sample preparation for protein digestion and peptide separation are critical considerations for a reduced peptide mapping-based MAM. To avoid desalting steps required in tryptic protein digestion and in order to improve peptide separation for hydrophilic peptides, we developed an improved robust sample preparation using Lys-C protease for high-throughput MAM testing. Additionally, this method optimizes the peptide retention and separation of a stability-indicating VSNK peptide using a HSS T3 column for comprehensive PQA monitoring. A fully automated sample preparation had similar assay variations for PQAs monitoring compared to manual sample preparation. To the best of our knowledge, this is the first report of a high-resolution MS-based MAM using Lys-C digestion with enhanced PQA monitoring for hydrophilic peptides. The improved, robust MAM workflow for protein digestion and peptide separation will pave the way for broader MAM qualification and its applications for the characterization and quality control of therapeutic monoclonal antibodies.
Levels of p53 expression determine the competitive ability of embryonic stem cells during the onset of differentiation
Authors: Montero Salvador Perez , Bowling Sarah , Pérez-Carrasco Rubén , Rodriguez Tristan A.
Published: March 2022

During development, the rate of tissue growth is determined by the relative balance of cell division and cell death. Cell competition is a fitness quality control mechanism that contributes to this balance by eliminating viable cells that are less-fit than their neighbours. What mutations confer cells with a competitive advantage or the dynamics of the interactions between winner and loser cells are not well understood. Here, we show that embryonic cells lacking the tumour suppressor p53 are super-competitors that eliminate their wild-type neighbours through the direct induction of apoptosis. This elimination is context dependant, as does not occur when cells are pluripotent and is triggered by the onset of differentiation. Furthermore, by combining mathematical modelling and cell-based assays we show that the elimination of wild-type cells is not through a competition for space or nutrients, but instead is mediated by short range interactions that are dependent on the local cell neighbourhood. This highlights the importance of the local cell neighbourhood and the competitive interactions within this neighbourhood for the regulation of proliferation during early embryonic development.
Acentrosomal spindles assemble from branching microtubule nucleation near chromosomes
Authors: Gouveia Bernardo , Setru Sagar U. , King Matthew R. , Stone Howard A. , Shaevitz Joshua W. , Petry Sabine
Published: March 2022

Microtubules are generated at centrosomes, chromosomes, and within spindles during cell division. Whereas microtubule nucleation at the centrosome is well characterized, much remains unknown about where, when, and how microtubules are nucleated at chromosomes. To address these questions, we reconstituted microtubule nucleation from purified chromosomes in meiotic Xenopus egg extract and found that chromosomes alone can form spindles. We visualized microtubule nucleation at chromosomes using total internal reflection fluorescence microscopy to find that this occurs through branching microtubule nucleation. The initial branches nucleate near and towards kinetochores, helping explain how kinetochores might be efficiently captured. By depleting molecular motors, we find that the organization of the resultant polar branched networks is consistent with a theoretical model where the effectors for branching nucleation are released by chromosomes, forming a concentration gradient around them that spatially biases branching nucleation. In the presence of motors, these branched networks are organized into multipolar spindles.
Alternative splicing downstream of EMT enhances phenotypic plasticity and malignant behavior in colon cancer
Authors: Xu Tong , Verhagen Mathijs , Joosten Rosalie , Sun Wenjie , Sacchetti Andrea , Sagredo Leonel Munoz , Orian-Rousseau Véronique , Fodde Riccardo
Published: March 2022

Phenotypic plasticity allows carcinoma cells to transiently acquire the quasi-mesenchymal features necessary to detach from the primary mass and proceed along the invasion-metastasis cascade. A broad spectrum of epigenetic mechanisms is likely to cause the epithelial–to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) transitions necessary to allow local dissemination and distant metastasis. Here, we report on the role played by alternative splicing (AS) in eliciting phenotypic plasticity in colon cancer.

By taking advantage of the identification of a subpopulation of quasi-mesenchymal and highly metastatic EpCAMlo colon cancer cells, we here show that the differential expression of ESRP1 and other RNA-binding proteins (RBPs) downstream of the EMT master regulator ZEB1, alters the AS pattern of a broad spectrum of targets including CD44 and NUMB, thus resulting in the generation of specific isoforms functionally associated with increased invasion and metastasis. Additional functional and validation studies indicate that both the newly identified RBPs and the CD44s and NUMB2/4 splicing isoforms promote local invasion and distant metastasis and are associated with poor survival.

The systematic elucidation of the spectrum of EMT-related RBPs and AS targets in colon cancer and in other malignancies, apart from the insights in the mechanisms underlying phenotypic plasticity, will lead to the identification of novel and tumor-specific therapeutic targets.
Four novel, immortal cell lines derived from embryos of Xenopus tropicalis
Authors: Gorbsky Gary J. , Daum John R. , Sapkota Hem , Summala Katja , Yoshida Hitoshi , Georgescu Constantin , Wren Jonathan D. , Peshkin Leonid , Horb Marko E.
Published: March 2022

The diploid anuran, Xenopus tropicalis, has emerged as a key research model in cell and developmental biology. To enhance the usefulness of this species, we developed methods for generating immortal cell lines from Nigerian strain (NXR_1018, RRID:SCR_013731) X. tropicalis embryos. We generated 14 cell lines that were propagated for several months. We selected four morphologically distinct lines, XTN-6, XTN-8, XTN-10, and XTN-12 for further characterization. Karyotype analysis revealed that three of the lines, XTN-8, XTN-10, and XTN-12 were primarily diploid. XTN-6 cultures showed a consistent mixed population of diploid cells, cells with chromosome 8 trisomy, and cells containing a tetraploid content of chromosomes. The lines were propagated using conventional culture methods as adherent cultures at 30°C in a simple, diluted L-15 medium containing fetal bovine serum without use of a high CO2 incubator. Transcriptome analysis indicated that the four lines were distinct lineages. These methods will be useful in the generation of cell lines from normal and mutant strains of X. tropicalis as well as other species of Xenopus.
Conformity by information or relation? An exploration of investors' response in equity crowdfunding
Authors: Li Yaokuang , Ling Li , Wu Juan , Zhang Daru , Fu Weizhong
Published: March 2022

Purpose

This paper aims to investigate the role of informational and relational mechanisms on equity crowdfunding investors' conformity behaviors by focusing on a relational culture of China.

Design/methodology/approach

The data of 108 financing projects and 7,688 investment records from a union of Chinese equity crowdfunding platforms are gathered. Lead investors' response to a campaign and follow-investors’ former links explain investors' conformity by social network analysis (SNA) and ordinary least squares (OLS) analysis.

Findings

The results show that informational and relational influences drive conformity in Chinese equity crowdfunding. Moreover, the informational influence weakens in a highly centralized structure of linked investors.

Research limitations/implications

The results add new knowledge to follow-investors’ conformity behaviors in equity crowdfunding and enrich the literature on conformity theory by finding the contextual effect of information-influenced conformity and the adaption of conformity theory to cultural uniqueness. Besides, this preliminary work also suggests opportunities for future research.

Practical implications

The paper inspires new consideration on a strategical use of follow-investors’ conformity mentality to promote successfully financing and reminds platform managers to be alert to the interference of small groups formed based on informal relationships to the normal financing order.

Originality/value

This is the first study that discovers the non-informational influence and the limited influence of information on equity crowdfunding conformity through contextual concerns.
The effect of toxic leadership on turnover intention and counterproductive work behaviour in Indonesia public organisations
Authors: Hattab Syahruddin , Wirawan Hillman , Salam Rudi , Daswati Daswati , Niswaty Risma
Published: March 2022

Purpose

Leadership has been known for its tremendous impact on employees' outcomes in any organisation. Constructive leadership positively impacts employees, while destructive leadership causes counterproductive work behaviours (CWB). This study aims to investigate the effect of toxic leadership on employees' CWB via the role of turnover intention by employing the psychological contract theory.

Design/methodology/approach

The participants were recruited using various recruitment methods such as online recruitment and alumni networks. After dropping some participants who failed to complete the three-wave data collection procedure, 457 responses were used for the final data analysis. The participants came from various public organisations in Indonesia (e.g. hospitals).

Findings

The results found that the effect of toxic leadership on employees' CWB was mediated by the role of turnover intention. Under a toxic leader, employees might intend to leave the organisations and commit CWB as the employees perceived the psychological contract breach.

Practical implications

Firstly, public organisations should implement some strategies to reduce the emergence of toxic behaviours. Secondly, public organisations should evaluate and examine how leadership is exercised within public organisations. Lastly, the organisations must ensure that their leaders do not breach employees' psychological contracts.

Originality/value

This study has highlighted the effect of toxic leadership on CWB in public service organisations by employing a psychological contract theory and a power distance perspective.
Using social learning theory in examining YouTube viewers’ desire to imitate travel vloggers
Authors: Le Linh Ha , Hancer Murat
Published: March 2022

Purpose

Applying social learning theory and the source credibility model, this study aims to investigate the impacts of perceived attractiveness, expertise and trustworthiness of YouTube travel vloggers on viewers’ wishful identification and behavioral intention. The study also aims to examine the effects of vlogger gender on viewers’ perception and on their wish to be like the vlogger.

Design/methodology/approach

With an online data collection from 402 YouTube travel vlog viewers, a moderated mediation model was tested using multiple linear regression and multivariate nested linear regression.

Findings

This study found that physical attractiveness, social attractiveness and credibility of travel vloggers positively affected audience wishful identification, among which credibility had the strongest impact. The effect of the travel vlogger’s social attractiveness on viewer wishful identification was even strengthened when the vlogger and the viewer were of different genders. Wishful identification partially mediated the relationship between vloggers’ attributes and viewers’ behavioral intention. Finally, the finding revealed female vloggers were perceived as more physically attractive than males, whereas male vloggers were assessed as more credible than their female counterparts.

Originality/value

Expanding upon the literature on mass media and social media, this study explains the mechanism of developing intention to imitate the travel vloggers of YouTube viewers. The findings provide tourism and hospitality managers with solution in choosing the most inspirational travel vlogger to influence consumer behavior.
Organizational justice perceptions and turnover intention: a meta-analytic review
Authors: Özkan Ahmet Hakan
Published: March 2022

Purpose

The aim of the study was to survey the relationships between organizational justice perceptions and turnover intention by using meta-analysis and to determine the possible moderators affecting these relationships.

Design/methodology/approach

In total, 83 correlation values were used. Comprehensive meta-analysis software (CMA) was used to analyze the collected studies. Heterogeneity and publication bias of each data set were tested.

Findings

Each data were heterogeneous and included no publication bias. The results suggested that the effect size of distributive justice on turnover intention is −0.396, interactional justice on turnover intention is −0.341, interpersonal justice on turnover intention is −0.361, informational justice on turnover intention is −0.358, procedural justice on turnover intention is −0.369 and overall organizational justice on turnover intention is −0.436. Region was a moderator for the relationship between distributive justice and turnover intention.

Originality/value

The results of the study can provide guidance to the future researchers. Moreover, the managers can use these results for the implementation of organizational strategies and policies.
Policing reforms in the 21st century: an examination of racial diversity post-executive order 13684
Authors: Yu Helen H.
Published: March 2022

Purpose

This study aims to examine minority representation amid the largest police departments in the USA that employ at least 500 sworn officers to determine whether the passage of Executive Order 13684 (2014)—a comprehensive criminal justice reform initiative to identify policing best practices and offer recommendations on how those practices can promote effective crime reduction while (re)building public trust—had any policy impact for increasing racial diversity in policing.

Design/methodology/approach

Survey responses on race and ethnicity are collected from 83 police departments across three cross-sectional points in time (2007–2013 and 2013–2016) to examine changes in racial diversity.

Findings

The findings suggest that nearly 20% of the police departments in this study had increases in racial diversity that could be attributed to Executive Order 13684 (2014).

Research limitations/implications

Insufficient time may have lapsed between the passage of Executive Order 13684 (2014) and the last survey collection period to generate meaningful change.

Practical implications

This study responds to the call by the President’s Task Force on 21st Century Policing (2015) to highlight those successful police departments, as well as those less successful police departments, for improving diversity in the police force.

Originality/value

To the best of the author’s knowledge, the findings from this study provide one of the first attempts to examine how federal recommendations impact local policing practices.
Stem traits, compartments and tree species affect fungal communities on decaying wood
Authors: Yang Shanshan , Poorter Lourens , Kuramae Eiko E. , Sass‐Klaassen Ute , Leite Marcio F. A. , Costa Ohana Y. A. , Kowalchuk George A. , Cornelissen Johannes H. C. , van Hal Jurgen , Goudzwaard Leo , Hefting Mariet M. , van Logtestijn Richard S. P. , Sterck Frank J.
Published: March 2022

Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.
‘The King's Other Islands of the Sea’: The Channel Islands in the Plantagenet Realm, 1254–1341
Authors: Kelleher Alexander
Published: March 2022

This article examines the relationship between the Plantagenet kings of England and the Channel Islands from 1254–1341. Notwithstanding a rich volume of accessible record material to consult, the history of the Channel Islands has been omitted from studies of the Plantagenet kings of England and in comparative studies of their wider ‘dominions’ on account of the Islands complex political status and cultural differences. It is argued here that the Islands, rather than being dismissed as political anomalies, were viewed by the kings of England as an integral entity and make an important contribution to understanding the larger construct of the Plantagenet realm. The first half of this article explores the maintenance of Plantagenet control in the Islands following the loss of Normandy and the significance of their inclusion in Henry III’s 1254 appanage to his eldest son Edward. The second half of the article surveys the position of the Islands in the context of the Anglo‐French relations between the Treaty of Paris and the Hundred Years’ War. Paradoxically, strategic location was the key reason for the rights and privileges granted to the Islands which went well beyond what otherwise insignificant territories could have reasonably achieved but was also the cause of its long‐term militarisation and subjection to periodic attacks and counter attacks by the kingdom of France.
Extracellular vesicle formation in Lactococcus lactis is stimulated by prophage‐encoded holin–lysin system
Authors: Liu Yue , Tempelaars Marcel H. , Boeren Sjef , Alexeeva Svetlana , Smid Eddy J. , Abee Tjakko
Published: March 2022

Gram‐positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how EVs are released through the cell walls in Gram‐positive bacteria. In this study, we characterized underlying mechanisms of EV production and provide evidence for a role of prophage activation in EV release using the Gram‐positive bacterium Lactococcus lactis as a model. By applying a standard EV isolation procedure, we observed the presence of EVs in the culture supernatant of a lysogenic L. lactis strain FM‐YL11, for which the prophage‐inducing condition led to an over 10‐fold increase in EV production in comparison with the non‐inducing condition. In contrast, the prophage‐encoded holin–lysin knockout mutant YL11ΔHLH and the prophage‐cured mutant FM‐YL12 produced constantly low levels of EVs. Under the prophage‐inducing condition, FM‐YL11 did not show massive cell lysis. Defective phage particles were found to be released in and associated with holin–lysin‐induced EVs from FM‐YL11, as demonstrated by transmission electron microscopic images, flow cytometry and proteomics analysis. Findings from this study further generalized the EV‐producing phenotype to Gram‐positive L. lactis, and provide additional insights into the EV production mechanism involving prophage‐encoded holin–lysin system. The knowledge on bacterial EV production can be applied to all Gram‐positive bacteria and other lactic acid bacteria with important roles in fermentations and probiotic formulations, to enable desired release and delivery of cellular components with nutritional values or probiotic effects.
A novel risk calculator predicting surgical site infection after spinal surgery in patients with cerebral palsy
Authors: Matsumoto Hiroko , Franzone Jeanne M. , Sinha Rishi , Roye Benjamin D. , Glotzbeker Michael P. , Skaggs David L. , Flynn John M. , Lenke Lawrence G. , Sponseller Paul D. , Vitale Michael G.
Published: March 2022

Aim

To develop and validate a risk calculator based on preoperative factors to predict the probability of surgical site infection (SSI) in patients with cerebral palsy (CP) undergoing spinal surgery.

Method

This was a multicenter retrospective cohort study of pediatric patients with CP who underwent spinal fusion. In the development stage, preoperative known factors were collected, and a risk calculator was developed by comparing multiple models and choosing the model with the highest discrimination and calibration abilities. This model was then tested with a separate population in the validation stage.

Results

Among the 255 patients in the development stage, risk of SSI was 11%. A final prediction model included non‐ambulatory status (odds ratio [OR] 4.0), diaper dependence (OR 2.5), age younger than 12 years (OR 2.5), major coronal curve magnitude greater than 90° (OR 1.3), behavioral disorder/delay (OR 1.3), and revision surgery (OR 1.3) as risk factors. This model had a predictive ability of 73.4% for SSI, along with excellent calibration ability (p = 0.878). Among the 390 patients in the validation stage, risk of SSI was 8.2%. The discrimination of the model in the validation phase was 0.743 and calibration was p = 0.435, indicating 74.3% predictive ability and no difference between predicted and observed values.

Interpretation

This study provides a risk calculator to identify the risk of SSI after spine surgery for patients with CP. This will allow us to enhance decision‐making and patient care while providing valid hospital comparisons, public reporting mechanisms, and reimbursement determinations.
Reopening of a school of dentistry in the era of COVID‐19 pandemic, “Step‐by‐step” approach
Authors: Hasanzade Mahya , Aminishakib Pouyan , Mortaz Hejri Sara , Kharazifard Mohamma Javad , Siadat Hakimeh
Published: March 2022

Introduction

The COVID‐19 pandemic has a great impact on all aspects of higher education worldwide. In Iran, after several months of lockdown, all dental schools coped with the challenge of “reopening.” School of Dentistry of Tehran University of Medical Sciences (TUMS) planned to facilitate the process of reopening using a “step‐by‐step” approach. The aim of this study was sharing our experiences of reopening of the school during the pandemic.

Methods

TUMS School of Dentistry planned a “step‐by‐step” approach of reopening of school to both provide infrastructure of online education for theoretical credits and reassure all staff and students about infection control for practical courses. Also, a two‐section survey on students’ satisfaction with a variety of aspects of reopening process and the clinical performance of students in different clinical courses was conducted.

Results

Findings showed 65.1% of the students, attended the survey, were satisfied with reopening of the school. Also, 86.4% were satisfied with the new online method of education for theoretical courses. Regarding personal protective equipment (PPE) provided for the students, 22.9% and 56.5% of them were satisfied and moderately satisfied, respectively. Additionally, 78.2% of the students were satisfied with the newly developed online assessment method.

Conclusion

Although reopening of schools during COVID‐19 pandemic seems enigmatic for all authorities and students, the “step‐by‐step” plan designed by TUMS School of dentistry including emotional and infrastructural prerequisites might be a reliable method for all people, who are in charge of management of dental school in uncertain crisis.
Long‐maintained social–ecological systems and genetic diversity in coexisting insects: A case of the straw‐thatched roof nesting solitary wasp Symmorphus apiciornatus (Hymenoptera: Vespidae: Eumeninae)
Authors: Sato Goshi , Kojima Jun‐ichi , Horikoshi Hinako , Saito‐Morooka Fuki
Published: March 2022

Thatched roofs are artificial environments that serve as nesting sites for a variety of insects, including tube‐nesting wasps, but they have been declining drastically in recent years. In this study, we investigated the nesting habits of a eumenine wasp, Symmorphus apiciornatus, nesting in a group at thatched roofs in a northern part of Ibaraki Prefecture, central Japan. Genetic diversity and genetic structure in the area were also investigated. Sex ratios at most study sites were not biased. Males emerged first and waited for females to mate around the natal nests, suggesting a high possibility of breeding between the wasps having emerged at a given thatched roof under the recent situation where there has been a drastic reduction in the number of houses with a thatched roof. Nevertheless, the genetic diversity in a given local population or a thatched roof was relatively high and significant genetic differentiation among thatched roofs was not detected.
Yellow–green color polymorphism in males of a pea aphid clone and its genetic pattern
Authors: Li Yang , Akimoto Shin‐ichi
Published: March 2022

Although most aphid species living on leaves have a green body color, little is known regarding the biosynthetic pathways of green pigments. We found that a clone of the pea aphid, Acyrthosiphon pisum (Harris) produced both green‐ and yellow‐colored males. The females of this clone were green in color, while 8.4% of the males produced were yellow. To date, yellow body color has been reported only in a single mutant clone in A. pisum. To explore the genetic pattern of yellow body color, green or yellow males were mated with green females of the same clone. The hatchability of the eggs sired by yellow males (26.2%) was less than half that of the eggs sired by green males (79.0%). The hatched foundresses of both groups were all green, with no yellow foundresses. Because aphids have an XX‐XO sex determination system, color polymorphism in males suggests that male body color may be governed by an X‐linked locus. If females possess heterozygosity at the putative locus, they can produce alternative phenotypes in males. The small proportion of yellow males and absence of yellow foundresses imply that the allele responsible for yellow body color has a deleterious effect. The present study suggests that this clone could be used to elucidate the biosynthetic pathways and underlying genetics of green pigments in aphids.
Development of a Quantitative Framework for Evaluating Natural Attenuation of 1,1,1‐TCA, 1,1‐DCA, 1,1‐DCE, and 1,4‐Dioxanein Groundwater
Authors: Adamson David T. , Wilson John T. , Newell Charles J. , Strasert Brian A. , de Blanc Phillip C. , Freedman David L. , Lebrón Carmen , Danko Anthony
Published: March 2022

A series of quantitative decision frameworks were developed to aid in the evaluation of Monitored Natural Attenuation (MNA) as a remedy for 1,4‐dioxane, chlorinated ethanes, and chlorinated ethenes. The end product is an updated version of BioPIC, a successful, existing decision framework for MNA of chlorinated ethenes. In evaluating MNA, the goal is to follow existing protocols but also incorporate more recent insights that have increased the potential viability of this technology for a wider number of contaminants. This includes data supporting the first line of evidence for MNA (decreasing concentration trends over time at appropriate sampling locations), as well as data that will serve as secondary and tertiary lines of evidence for MNA. For the BioPIC update, a similar lines of evidence approach was developed, using information from literature and project‐specific data to identify the relevant lines of evidence. As part of the update, a model for predicting contaminant trends over time and distance, including a method to estimate site‐specific biodegradation rate constants for chlorinated ethenes, chlorinated ethanes, and 1,4‐dioxane, has been included within BioPIC. The quantitative software tool provides step‐by‐step technical guidance for collecting and evaluating other lines of evidence, including data associated with targeted14C assays, isotope fractionation, biomarkers for degradation, geochemical parameters, and co‐contaminant concentrations, to improve the MNA evaluation process.
Risk Management Failures: What Are They and When Do They Happen?
Authors: Stulz René M.
Published: March 2022

The losses experienced by financial institutions during the Global Financial Crisis convinced many observers that current corporate risk management practices are deeply flawed, and that such flaws contributed greatly to the crisis. The author challenges this view by calling for and demonstrating the need to distinguish between flawed assessments by risk managers and corporate risk‐taking decisions that, although resulting in losses, were reasonable at the time they were made.

In making this distinction, the author also identifies a number of different ways that risk management can fail. In addition to choosing the wrong risk metrics and misidentifying or mismeasuring risks, risk managers can fail to communicate their risk assessments and provide effective guidance to top management and boards. And once top management has used that information to help determine the firm's risk appetite and strategy, the risk management function can also fail to monitor risks appropriately and maintain the firm's targeted risk positions.

But if risk management has been mistakenly identified as the culprit in many cases, current risk management practice can be improved by taking into account the lessons from financial crises past and present. In particular, such crises have occurred with enough frequency that crisis conditions can be modeled, at least to some extent. And when models reach their limits of usefulness, companies should consider using scenario planning that aims to reveal the implications of crises for their financial health and survival. Instead of relying on past data, scenario planning uses forward‐looking economic analysis to evaluate the expected impact of sudden illiquidity and the associated feedback effects that are common in financial crises.
How Companies Can Use Hedging to Create Shareholder Value
Authors: Stulz René M.
Published: March 2022

Assessing the performance of a corporate risk management program, and how it is expected to increase the value of the enterprise, is a difficult undertaking mainly because the costs of risk management tend to be much easier to quantify—indeed, they often appear directly on the firm's bottom line—than the expected benefits. This article provides a framework for designing and evaluating corporate risk management and hedging programs.

The author begins by discussing how to evaluate the benefits and costs of a risk management program in general terms, and then focuses more directly on the assessment of corporate hedging programs, which are generally conducted with derivatives. In practice, there are many obstacles to designing and carrying out a successful hedging program. But one of the most common has been the tendency of top managements to insist that hedging programs be “costless.” The author argues that just as the purchase of fire insurance is not viewed as a waste of funds or “bad investment” if the insured house does not burn down, the use of derivatives in a well‐designed hedge should not be viewed as a mistake if the deriv ative position produces losses.

To guard against this mistake, the people who design and implement risk management strategies must ensure that their CEOs and boards understand the possible outcomes of the strategy—including losses on derivatives position—and how the strategy itself increases the (expected) value of the firm. Further, management should attempt to communicate the principles underlying its risk management program and the value created by its hedging strategy to the investment community.
FinTech, BigTech, and the Future of Banks
Authors: Stulz René M.
Published: March 2022

Banks are unique financial institutions in that they combine the production of liquid claims—that is, demand deposits—with loans. Though banks can replicate most of what FinTech firms can do, FinTech firms benefit from an uneven playing field in that they are less regulated than banks. The uneven playing field enables nonbank FinTech firms to challenge banks in specific product areas where success is not tied to what makes banks unique—namely, their deposit‐gathering abilities and the potential for synergies with borrowers provided by deposits. And although banks’ responses to FinTech have also been hampered by their legacy IT systems and by the internal frictions inherent in large diversified firms, FinTech's narrow product offerings and lack of established “franchises” appear to put clear limits on FinTech's ability to displace banks.

Unlike FinTech, however, BigTech firms have some advantages that banks will find it harder to replicate, and so they present a much stronger challenge to established banks in two main areas: consumer finance and loans to small firms. And FinTech as well as BigTech are contributing to a trend in which banks are losing a comparative advantage that has derived from having more immediate access to information about parties seeking credit. The extent to which banks succeed in warding off such threats will depend on their ability (1) to make effective—possibly even better—use of the same information technology now being used by its new competitors and (2) to achieve economies of scale and scope their nonbank competitors will find hard to match.