bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular vesicles and co-isolated endogenous retroviruses differently affect dendritic cells
Authors: Cocozza Federico , Martin-Jaular Lorena , Lippens Lien , Di Cicco Aurelie , Arribas Yago A , Dingli Florent , Richard Michael , Merle Louise , Poullet Patrick , Loew Damarys , Lévy Daniel , Hendrix An , Kassiotis George , Joliot Alain , Tkach Mercedes , Théry Clotilde
Published: January 2023

Cells secrete membrane-enclosed extracellular vesicles (EVs) and non-vesicular nanoparticles (ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed either to induce immune priming of antigen presenting cells, or, to be immuno-suppressive agents promoting tumor immune escape. We suspect that such disparate functions are due to variable composition in EV subtypes and ENPs of the analyzed EV preparations. We aimed to exhaustively characterize the array of secreted EVs and ENPs of murine tumor cell lines. Unexpectedly, we identified virus-like particles (VLPs) from endogenous murine leukemia virus in preparations of EVs produced by tumor cells. We established a robust protocol to separate small (s)EVs from VLPs and ENPs. We compared their protein composition and analyzed their functional interaction with target dendritic cells (DCs). ENPs were poorly captured and did not affect DCs. sEVs specifically induced DC death. A mixed EV/VLP preparation was the most efficient to induce DC maturation and antigen presentation. Our results call for systematic re-evaluation of the respective proportions and functions of non-viral EVs and VLPs produced by tumors and their contribution to anti-tumor immune responses and to tumor progression.
Nanopore-based direct RNA sequencing of theTrypanosoma bruceitranscriptome identifies novel lncRNAs
Authors: Kruse Elisabeth , Göringer H. Ulrich
Published: January 2023

Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression posttranscriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example, by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized today. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known because of the inherent cDNA recoding and DNA amplification limitations of short-read RNA sequencing. Here we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosomeT. bruceiwith a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 109 of which are stage-specifically expressed. We also present insights into the complexity of theT. bruceitranscriptome, including alternative transcriptional start and stop sites and potential transcript isoforms to provide a bias-free understanding of the intricate RNA landscape inT. brucei.
Cryo-EM structure of the polyphosphate polymerase VTC: Coupling polymer synthesis to membrane transit
Authors: Liu Wei , Wang Jiening , Comte-Miserez Véronique , Zhang Mengyu , Yu Xuejing , Chen Qingfeng , Mayer Andreas , Wu Shan , Ye Sheng
Published: January 2023

The eukaryotic polyphosphate (polyP) polymerase VTC complex synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the vacuolar membrane to maintain an intracellular phosphate (Pi) homeostasis. To discover how VTC complex solves this fundamental aspect, we determined a cryo-electron microscopy structure of an endogenous VTC complex (Vtc4/Vtc3/Vtc1) fromSaccharomyces cerevisiaeat 3.1 Å resolution. The structure reveals a heteropentameric architecture of one Vtc4, one Vtc3 and three Vtc1 subunits. The transmembrane region forms a polyP selective channel, probably adopting a resting state conformation, in which a latch-like, horizonal helix of Vtc4 limits the entrance. The catalytic Vtc4 central domain locates on top of the pseudo-symmetric polyP channel, creating a strongly electropositive pathway for nascent polyP that can couple synthesis to translocation. The SPX domain of Vtc4 positively regulates polyP synthesis and regulation of VTC complex. The non-catalytic Vtc3 regulates VTC through a phoshorylatable loop. Our findings, along with the functional data, allow us to propose a mechanism of polyP channel gating and VTC complex activation.
Counterintuitive Binding of Phosphorylated DEP Domain from Dishevelled Protein to Negatively Charged Membranes
Authors: Falginella Francesco L. , Drabinová Martina , Bryja Vítezslav , Vácha Robert
Published: January 2023

To accomplish its role of signaling hub in all Wnt signaling pathways, Dishevelled (DVL) protein needs to dynamically relocalize to the inner leaflet of the cellular plasma membrane (PM). Combined experimental and computational evidence showed that the binding of DVL to the PM is mainly driven by the electrostatic attraction between a stretch of positively charged amino acids located on the C-terminal DEP domain of DVL and anionic phospholipid species, with a striking preference for phosphatidic acid (PA). Here, by means of computational simulations and QCM-D experiments, we demonstrate that four recently identified phosphorylation sites on DEP domain, alter the electrostatic potential of the membrane binding interface, but do not prevent the recruitment to anionic membranes. On the contrary, the phosphorylated residues are involved in hydrogen bond and ion-mediated interactions with the lipid headgroup of PA. Our results suggest that the effect of phosphorylation on protein-membrane association could be counterintuitive and sensitive to changes in the local environment including specific lipids, salts, and pH.

SIGNIFICANCE

Phosphorylation regulates the cellular activity and localization of many peripheral proteins by, among others, decreasing the affinity for negatively charged membranes. Here, we report how phosphorylation affects the membrane interaction of DEP domain from Dishevelled protein, the intracellular signaling hub in Wnt pathways. We found that despite the negative charge induced by phosphorylation, DEP domain was steadily adsorbed to the surface of negatively charged PA-rich membranes, due to a dense network of cation-mediated interactions and hydrogen bonds.
Carotenoid retention during post-harvest storage ofCapsicum annuum: the role of the fruit surface structure
Authors: Holden Alexandra C. , Cohen Hagai , Daniel V. Rickett , Aharoni Asaph , Fraser Paul D.
Published: January 2023

Degradation of carotenoids in food crops during post-harvest storage results in major economic and nutritional losses. In this study, a pepper (Capsicum annuum) panel for post-harvest carotenoid retention was studied to elucidate underlying mechanisms associated with this commercial trait of interest. Quantitative determination of carotenoid pigments and concurrent cellular analysis indicated that those pepper fruit with thicker lipid exocarp layers and smooth surfaces, following post-harvest drying and storage, possessed increased carotenoid retention. Total cutin monomer content increased in high carotenoid retention fruits and sub-epidermal cutin deposits were responsible for the difference in exocarp thickness. Cutin biosynthesis and cuticle precursor transport genes were differentially expressed between high and low carotenoid retention genotypes, and this supports the finding that fruit cuticle biosynthesis is associated with carotenoid retention. Carotenoids were located within cells embedded within the sub-epidermal cutin layer, and these carotenoids were protected from degradation due to the lack of permeability of the fruit surface to reactive oxygen species, and their precursors. The identification of a novel role for the pepper fruit surface in protecting against carotenoid degradation serves as an important discovery for the function of the fruit cuticle and provides an exploitable resource to enhance fruit quality.

Highlight statement

Carotenoid pigments in Chilli pepper confer post-harvest colour and nutritional quality. Analysis of diverse commercial genotypes indicates the involvement of the fruit surface in carotenoid retention
The Autophagy Receptor NBR1 Directs the Clearance of Photodamaged Chloroplasts
Authors: Lee Han Nim , Chacko Jenu Varghese , Solís Ariadna Gonzalez , Chen Kuo-En , Barros Jessica , Signorelli Santiago , Harvey Millar A. , Vierstra Richard D. , Eliceiri Kevin W. , Otegui Marisa S.
Published: January 2023

The ubiquitin-binding NBR1 autophagy receptor plays a prominent role in recognizing ubiquitylated protein aggregates for vacuolar degradation by macroautophagy. Here, we show that upon exposing Arabidopsis plants to intense light, NBR1 associates with photodamaged chloroplasts independently of ATG7, a core component of the canonical autophagy machinery. NBR1 coats both the surface and interior of chloroplasts, which is then followed by direct engulfment of the organelles into the central vacuole via a microautophagy-type process. The relocalization of NBR1 into chloroplasts does not require the chloroplast translocon complexes embedded in the envelope but is instead greatly enhanced by removing the self-oligomerization mPB1 domain of NBR1. The delivery of NBR1-decorated chloroplasts into vacuoles depends on the ubiquitin-binding UBA2 domain of NBR1 but is independent of the ubiquitin E3 ligases SP1 and PUB4, known to direct the ubiquitylation of chloroplast surface proteins. Compared to wild-type plants,nbr1mutants have altered levels of a subset of chloroplast proteins and display abnormal chloroplast density and sizes upon high light exposure. We postulate that, as photodamaged chloroplasts lose envelope integrity, cytosolic ligases reach the chloroplast interior to ubiquitylate thylakoid and stroma proteins which are then recognized by NBR1 for autophagic clearance. This study uncovers a new function of NBR1 in the degradation of damaged chloroplasts by microautophagy.
Engineered Antiviral Sensor Targets Infected Mosquitoes
Authors: Dalla Benetta Elena , López-Denman Adam J. , Li Hsing-Han , Masri Reem A. , Brogan Daniel J. , Bui Michelle , Yang Ting , Li Ming , Dunn Michael , Klein Melissa J. , Jackson Sarah , Catalan Kyle , Blasdell Kim R. , Tng Priscilla , Antoshechkin Igor , Alphey Luke S. , Paradkar Prasad N. , Akbari Omar S.
Published: January 2023

Escalating vector disease burdens pose significant global health risks, so innovative tools for targeting mosquitoes are critical. We engineered an antiviral strategy termed REAPER (vRNAExpressionActivatesPoisonousEffectorRibonuclease) that leverages the programmable RNA-targeting capabilities of CRISPR Cas13 and its potent collateral activity. Akin to a stealthy Trojan Horse hiding in stealth awaiting the presence of its enemy, REAPER remains concealed within the mosquito until an infectious blood meal is up taken. Upon target viral RNA infection, REAPER activates, triggering programmed destruction of its target arbovirus such as chikungunya. Consequently, Cas13 mediated RNA targeting significantly reduces viral replication and its promiscuous collateral activity can even kill infected mosquitoes. This innovative REAPER technology adds to an arsenal of effective molecular genetic tools to combat mosquito virus transmission.

One-Sentence Summary

Engineered Cas13-based antiviral sensor kills infected mosquitoes upon activation from arbovirus infection.
Haploid androgenetic development in bovines reveals imbalanced WNT signaling and impaired cell fate differentiation
Authors: Aguila Luis M. , Nociti Ricardo P. , Sampaio Rafael V. , Therrien Jacinthe , Meirelles Flavio V. , Felmer Ricardo N. , Smith Lawrence C.
Published: January 2023

Haploid embryos have contributed significantly to our understanding of the role of parental genomes in development and can be applied to important biotechnology for human and animal species. However, development to the blastocyst stage is severely hindered in bovine haploid androgenetic embryos (hAE). To further our understanding of such developmental arrest, we performed a comprehensive comparison of the transcriptomic profile of morula-stage embryos, which were validated by qRT-PCR of transcripts associated with differentiation in haploid and biparental embryos. Among numerous disturbances, results showed that pluripotency pathways, especially the wingless-related integration site (WNT) signaling, were particularly unbalanced in hAE. Moreover, transcript levels ofKLF4, NANOG, POU5F1, SOX2, CDX2, CTNNBL1, AXIN2, andGSK3Bwere noticeably altered in hAE, suggesting disturbance of pluripotency and canonical WNT pathway. To evaluate the role of WNT on hAE competence, we exposed early day-5 morula stage embryos to theGSK3Binhibitor CHIR99021. Although no alterations were observed in pluripotency and WNT-related transcripts, exposure to CHIR99021 improved their ability to reach the blastocysts stage, confirming the importance of the WNT pathway in the developmental features of bovine hAE.

Summary statement

This study shows the importance of the WNT pathway on bovine haploid androgenetic development by walking through transcriptomics and pluripotency markers associated with cell fate determination during early development.
Dimerization mechanism of an inverted-topology ion channel in membranes
Authors: Ernst Melanie , Orabi Esam A. , Stockbridge Randy B. , Faraldo-Gómez José D. , Robertson Janice L.
Published: January 2023

Many ion channels are multi-subunit complexes with a polar permeation pathway at the oligomeric interface, but their mechanisms of assembly into functional, thermodynamically stable units within the membrane are largely unknown. Here we characterize the assembly of the inverted-topology, homodimeric fluoride channel Fluc, leveraging a known mutation, N43S, that weakens Na+binding to the dimer interface, thereby unlocking the complex. While single-channel recordings show Na+is required for activation, single-molecule photobleaching and bulk Förster Resonance Energy Transfer experiments in lipid bilayers demonstrate that N43S Fluc monomers and dimers exist in dynamic equilibrium, even without Na+. Molecular dynamics simulations indicate this equilibrium is dominated by a differential in the lipid-solvation energetics of monomer and dimer, which stems from hydrophobic exposure of the polar ion pathway in the monomer. These results suggest a model wherein membrane-associated forces induce channel assembly while subsequent factors, in this case Na+binding, result in channel activation.

Teaser

Membrane morphology energetics foster inverted-topology Fluc channels to form dimers, which then become active upon Na+binding.
Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments
Authors: Sriworarat Chaichontat , Nguyen Annie , Eagles Nicholas J. , Collado-Torres Leonardo , Martinowich Keri , Maynard Kristen R. , Hicks Stephanie C.
Published: January 2023

High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Samui, a performant and interactive image visualization tool that runs completely in the web browser. Samui is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Samui with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Samui along with example datasets is available athttps://samuibrowser.com.
Arrhythmia-associated Calmodulin Variants Interact with KCNQ1 to Confer Aberrant Membrane Trafficking and Function
Authors: Kang Po wei , Woodbury Lucy , Angsutararux Paweorn , Sambare Namit , Shi Jingyi , Marras Martina , Abella Carlota , Bedi Anish , Zinn DeShawn , Cui Jianmin , Silva Jonathan R.
Published: January 2023

Rationale

Missense variants in calmodulin (CaM) predispose patients to arrhythmias associated with high mortality rates. As CaM regulates several key cardiac ion channels, a mechanistic understanding of CaM variant-associated arrhythmias requires elucidating individual CaM variant effect on distinct channels. One key CaM regulatory target is the KCNQ1 (KV7.1) voltage-gated potassium channel that underlie the IKscurrent. Yet, relatively little is known as to how CaM variants interact with KCNQ1 or affect its function.

Objective

To observe how arrhythmia-associated CaM variants affect binding to KCNQ1, channel membrane trafficking, and KCNQ1 function.

Methods and Results

We combine a live-cell FRET binding assay, fluorescence trafficking assay, and functional electrophysiology to characterize >10 arrhythmia-associated CaM variants effect on KCNQ1. We identify one variant (G114W) that exhibits severely weakened binding to KCNQ1 but find that most other CaM variants interact with similar binding affinity to KCNQ1 when compared to CaM wild-type over physiological Ca2+ranges. We further identify several CaM variants that affect KCNQ1 and IKsmembrane trafficking and/or baseline current activation kinetics, thereby contextualizing KCNQ1 dysfunction in calmodulinopathy. Lastly, we delineate CaM variants with no effect on KCNQ1 function.

Conclusions

This study provides comprehensive functional data that reveal how CaM variants contribute to creating a pro-arrhythmic substrate by causing abnormal KCNQ1 membrane trafficking and current conduction. We find that CaM variant regulation of KCNQ1 is not uniform with effects varying from benign to significant loss of function. This study provides a new approach to collecting details of CaM binding that are key for understanding how CaM variants predispose patients to arrhythmia via the dysregulation of multiple cardiac ion channels.
Staphylococcalsecreted cytotoxins are competition sensing signals forPseudomonas aeruginosa
Authors: Wang Grace Z. , Warren Elizabeth A. , Haas Allison L. , Peña Andrea Sánchez , Kiedrowski Megan R. , Lomenick Brett , Chou Tsui-Fen , Bomberger Jennifer M. , Tirrell David A. , Limoli Dominique H.
Published: January 2023

Coinfection with two notorious opportunistic pathogens, the Gram-negativePseudomonas aeruginosaand Gram-positiveStaphylococcus aureus, dominates chronic pulmonary infections. While coinfection is associated with poor patient outcomes, the interspecies interactions responsible for such decline remain unknown. Here, we dissected molecular mechanisms of interspecies sensing betweenP. aeruginosaandS. aureus. We discovered thatP. aeruginosasensesS. aureussecreted peptides and, counterintuitively, moves towards these toxins.P. aeruginosatolerates such a strategy through “competition sensing”, whereby it preempts imminent danger/competition by arming cells with type six secretion (T6S) and iron acquisition systems. Intriguingly, while T6S is predominantly described as weaponry targeting Gram-negative and eukaryotic cells, we find that T6S is essential for fullP. aeruginosacompetition withS. aureus, a previously undescribed role for T6S. Importantly, competition sensing was activated during coinfection of bronchial epithelia, including T6S islands targeting human cells. This study reveals critical insight into both interspecies competition and how antagonism may cause collateral damage to the host environment.
Modelling the adoption of Internet of things (IoT) for sustainable construction in a developing economy
Authors: Dosumu Oluwaseun Sunday , Uwayo Seth Moise
Published: January 2023

Purpose

The need to improve sustainable construction with the appropriate technology adoption in the fourth and fifth industrial revolutions cannot be overemphasized. This study modelled the adoption of Internet of things (IoT) technologies in the construction industry to improve sustainable construction. Consequently, the study would assist construction stakeholders and policymakers in achieving sustainable construction through concerted efforts toward improving IoT adoption.

Design/methodology/approach

The study obtained the IoT technologies and the challenges of IoT adoption in the construction industry through a literature review. Subsequently, the awareness (knowledge of the existence and uses) of IoT technologies, the significance of the challenges and the level of adoption of the IoT technologies were tested on construction stakeholders in Kigali with a structured questionnaire. Consequently, a structural equation model of IoT adoption was developed.

Findings

The structural equation model indicates the relationship between the awareness, challenges and adoption of IoT technologies. It equally describes the effect sizes of the awareness and challenges of IoT on the adoption of IoT technologies.

Research limitations/implications

This study is beneficial to construction stakeholders as it portrays the exclusive impacts of the awareness and the challenges of IoT technologies on the adoption of IoT. The study also benefits the government and policymakers as it provides a basis for intensifying efforts to create awareness and mitigate the challenges of IoT adoption for sustainable construction. The study also provides a basis for future studies on IoT adoption in the construction industry.

Originality/value

There are several studies on the adoption of IoT. There is however scarcity of studies on how the awareness and the challenges of IoT technologies impact the adoption of IoT in the construction industry. Thus, this study bridges the gap by modelling the adoption of IoT technologies for improved sustainable construction.
Protecting workers' well-being in times of crisis: the first wave of COVID-19 in an Australian healthcare setting in 2020
Authors: Achat Helen M. , Stubbs Joanne M. , Mittal Rakhi , Schindeler Suzanne , Gilroy Nicole
Published: January 2023

Purpose

The COVID-19 pandemic continues to challenge healthcare systems worldwide. The authors examined the lived experiences and perceptions of healthcare workers (HCWs) in managerial and senior positions to explore the pandemic's effects on well-being and valued organisational responses.

Design/methodology/approach

Using purposive sampling, the authors conducted 39 semi-structured interviews with senior staff including health service administrators, heads of department and senior clinicians at a designated COVID-19 facility in New South Wales, Australia. Interviews were conducted from November 2020 to February 2021 to reflect on experiences during the height of the pandemic in 2020 (mid-March to the end of May 2020).

Findings

Workplace experiences affecting HCWs' well-being included being shunned by others, fear of infecting family, fear of the unknown, concerns about personal protective equipment, lack of direction from above and increased workload. Organisational interventions to protect the health and safety of HCWs and their patients included redeployment, improved communication, effective management committees, education and mental health supports.

Practical implications

Organisations can minimise worker-identified factors threatening their well-being during a health crisis by applying broad-ranging initiatives including inclusive and open communication, promoting flexible work practices, providing up-to-date guidelines and policies and fostering camaraderie between workers.

Originality/value

The voices of senior clinical and managerial staff have been largely unheard during the COVID-19 pandemic. The authors addressed this deficit by describing their experiences and insights regarding the pandemic's impact on well-being and the organisation's responses to simultaneously safeguarding its staff and providing quality patient care.
Tribological properties of trimethylolpropane oleate synthesized through esterification reaction with nano-MoS2 catalysts of different shapes
Authors: Li Zhixiang , Han Shuo , Wang Lei , Hu Kunhong
Published: January 2023

Purpose

This study aims to investigate the catalytic performance and tribological properties of MoS2 powder.

Design/methodology/approach

In this work, the authors attempted to use MoS2 nanoparticles (nano-MoS2) as a catalyst to synthesize trimethylolpropane oleate (TMPTO) by esterification of trimethylolpropane and oleic acid. The small amount of highly dispersed nano-MoS2 catalyst remaining in TMPTO needed not to be separated and could be used as a lubricant modifier directly to achieve the purpose of improving the lubricity performance of TMPTO.

Findings

The results demonstrated that nano-MoS2 had good catalytic esterification ability and achieved in situ dispersion of about 0.191% nano-MoS2 in TMPTO while catalyzing the synthesis of base oil. After high-speed centrifugal sedimentation treatment, the product TMPTO still retained about 0.008% of nano-MoS2. The above-synthesized TMPTO has significantly better lubricity performance than commercially available TMPTO, in which the friction coefficient and wear rate could be reduced by 75%.

Originality/value

The results of this study provide an idea for the design of catalysts for ester oil synthesis.
How can we encourage mindful consumption? Insights from mindfulness and religious faith
Authors: Gupta Sharad , Lim Weng Marc , Verma Harsh V. , Polonsky Michael
Published: January 2023

Purpose

Mindful consumption is a popular concept that is often associated with mindfulness and religious faith, but nonetheless, its empirical associations to these remain relatively underexplored. Clarifying the impact of mindfulness and religious faith on mindful consumption is important to delineate their effectiveness in influencing consumers to reconsider consumption decisions (e.g. the need for additional products) given the detrimental effects of mindless consumption (e.g. financial debt, environmental degradation and materialistic culture). The concern about mindfulness potentially being a religious matter can also be resolved through empirical validation. Hence, the purpose of this research is to advance the empirical understanding of how mindfulness and religious faith impact on mindful consumption and whether mindfulness and religious faith are interrelated.

Design/methodology/approach

The authors adopt a multistudy approach to scaffold the exploration of mindfulness and religious faith as precursors of mindful consumption.

Findings

Study 1 carries out an experiment with undergraduates and demonstrates that mindfulness encourages mindful consumption. Study 2 conducts an offline survey with undergraduates and provides evidence that mindfulness and religious faith independently (i.e. without interacting with each other) encourage mindful consumption. Study 3 uses an online survey of consumers for conceptual replication and reaffirms the findings of Studies 1 and 2 across gender, occupations and household incomes (except middle-income households).

Research limitations/implications

The implications of these findings are discussed, wherein mindfulness and religious faith are earmarked as viable avenues for promoting mindful consumption.

Originality/value

This seminal attempt uses multiple studies to empirically validate the nature and generalizability of relationships between mindfulness, religious faith and mindful consumption.
Unsilencing colonial archives via automated entity recognition
Authors: Luthra Mrinalini , Todorov Konstantin , Jeurgens Charles , Colavizza Giovanni
Published: January 2023

Purpose

This paper aims to expand the scope and mitigate the biases of extant archival indexes.

Design/methodology/approach

The authors use automatic entity recognition on the archives of the Dutch East India Company to extract mentions of underrepresented people.

Findings

The authors release an annotated corpus and baselines for a shared task and show that the proposed goal is feasible.

Originality/value

Colonial archives are increasingly a focus of attention for historians and the public, broadening access to them is a pressing need for archives.
Positive ageing in institutional homes: towards a de-stigmatization process
Authors: Gupta Satish Kr , Mukherjee Anirban
Published: January 2023

Purpose

This qualitative research examines the varied reasons for relocation to old age homes (OAHs) in contemporary India. The purpose of this study investigates the acceptance of institutional living in Lucknow (a Tier II city of India) and whether migration to OAHs is a voluntary decision. This study also examines the lifeworld of the older adult in these OAHs in an attempt to find out whether OAHs are conducive to positive ageing. Derivatively, the authors study their engagement/time use pattern and social networking patterns in the OAHs. Finally, the research seeks to learn whether OAHs are slowly substituting older adult care given within the family by offering the best of the facilities and services.

Design/methodology/approach

This qualitative research was conducted in two private OAHs in Lucknow, India. The findings of the study are based on 28 qualitative interviews conducted with the inmates, administrative staff and caretakers. The interviews were unstructured and open-ended and were supported by observations. The observation was not only made of the social setting but also the reaction of the participants. The idea was to develop an emic view of the subject by exploring valid narratives. Pseudonyms were used to report the finding so as to maintain the confidentiality of the research subjects.

Findings

This research moves beyond the traditional wisdom that people move to OAH because of the push factors within the family. OAHs in India have evolved over the years and high-end OAHs are equipped with modern amenities to cater to the upper class in their twilight years. Residents were found to lead active lives in OAHs and their common habitus and bonding capital helped them to face the vagaries of old age more confidently. Their active life and membership in various civic organizations challenge the contention of the role theory that the aged are more prone to lose rather than gain roles.

Originality/value

The originality of the research lies in the fact that the authors are extending the arguments made by the role theory of social ageing. The theory proposes that aged people are more likely to lose out roles rather than gain new ones. This study finds that the elderly tend to live a very active life in OAHs and engaged various civic organizations. Although they may lose/voluntarily give up the roles like the head of the household, spouse, etc., they acquire new roles in the context of OAHs.
Maternal and host effects mediate the adaptive expansion and contraction of the microbiome during ontogeny in a holometabolous, polyphagous insect
Authors: Jose Polpass Arul , Yuval Boaz , Jurkevitch Edouard
Published: January 2023

Polyphagous, holometabolous insects adapt to rapid diet shifts imposed by their ecology and their life cycle. One shift is linked to development, as larvae and adults usually dwell and feed in different environments, using different resources. The second is caused by changes in larval hosts, often occurring at each generation. Studies show that the insect's microbiome also changes in relation to development and larval host. However, parental and larval host contributions to its structure and trans‐generational dynamics remain uncharted.

We investigated the sources of variation of the microbiome of the highly polyphagous Mediterranean fruit fly by tracking microbiome structure and its potential functional impact in fly lineages over generations and fruit host shifts, using 16S rRNA gene amplicon single variant analysis.

Bacterial community alpha‐diversity expanded and contracted cyclically in a life stage‐dependent manner with the mothers' microbiome community ‘resetting’ to the same structure across generations. Expansion occurred at the larval stage, while alpha‐diversity decreased in tenerals, and significantly in mothers. In contrast, richness was highest in mothers, with rare taxa expanding in larvae depending upon fruit type.

Metabolic predictions using PICRUSt pointed to increased metabolism of vitamins in mothers, and of aromatic compouds in larvae and tenerals, while indicator species analysis suggested fruit host composition‐dependent potential functional adaptations.

Our data indicate lineage, fruit host and their interactions as the main sources of microbiome variation and provide examples of possible metabolic developmental and ecological adaptations. Taken together, these data support the hypothesis that microbiome diversity and microbiome‐driven local adaptations act as a mechanism sustaining polyphagy.

Read the free Plain Language Summary for this article on the Journal blog.
Shell disease syndromes of decapod crustaceans
Authors: Rowley Andrew F. , Coates Christopher J.
Published: January 2023

The term shell disease subsumes a number of debilitating conditions affecting the outer integument (the carapace) of decapod crustaceans, such as lobsters and crabs. Herein, we seek to find commonality in the aetiology and pathology of such conditions, and those cases that result in the progressive erosion of the cuticle through to the visceral tissues by a cocktail of microbial‐derived enzymes including lipases, proteases and chitinases. Aquimarina spp. are involved in shell disease in many different crustaceans across a wide geographical area, but the overall view is that the condition is polymicrobial in nature leading to dysbiosis within the microbial consortium of the damaged cuticle. The role of environment, decapod behaviour and physiology in triggering this disease is also reviewed. Finally, we provide a conceptual model for disease aetiology and suggest several avenues for future research that could improve our understanding of how such factors trigger, or exacerbate, this condition.
itsdm: Isolation forest‐based presence‐only species distribution modelling and explanation in r
Authors: Song Lei , Estes Lyndon
Published: January 2023

Multiple statistical algorithms have been used for species distribution modelling (SDM). Due to shortcomings in species occurrence datasets, presence‐only methods (such as MaxEnt) have become increasingly widely used. However, sampling bias remains a challenging issue, particularly for density‐based approaches. The Isolation Forest (iForest) algorithm is a presence‐only method less sensitive to sampling patterns and over‐fitting because it fits the model by describing the unsuitable instead of suitable conditions.

Here, we present the itsdm package for species distribution modelling with iForest, which provides a workflow wrapper for the algorithms in iForest family and convenient tools for model diagnostic and post‐modelling analysis.

itsdm allows users to fit and evaluate an iForest SDM using presence‐only occurrence data. It also helps the users to understand relationships between species and the living environment using Shapley values, a suggested technique in explainable artificial intelligence (xAI). Additionally, itsdm can make spatial response maps that indicate how species respond to environmental variables across space and detect areas potentially affected by a changing environment.

We demonstrated the usage of the itsdm package and compared iForest with other mainstream SDMs using virtual species. The results enlightened that iForest is an advantageous presence‐only SDM when the actual distribution range is unclear.
Subjective and objective evaluation of corneal haze after accelerated corneal crosslinking for corneal ectasias
Authors: Stein Rebecca , Ong Tone Stephan , Lebovic Gerald , Singal Neera , Hatch Wendy
Published: January 2023

Purpose

To evaluate the relationship between subjective (slit lamp examination [SLE]) and objective (densitometry) measurements of corneal haze after accelerated corneal crosslinking (aCXL), assess the relationship between densitometry and corrected distance visual acuity (CDVA), and determine the effect of baseline characteristics on densitometry after aCXL in eyes with progressive keratoconus and other ectasias.

Setting

Kensington Eye Institute and Bochner Eye Institute, Toronto, Canada.

Design

Retrospective analysis of a prospective interventional cohort study.

Methods

Scheimpflug‐derived corneal densitometry, CDVA, maximum keratometry (Kmax), and central corneal thickness were measured preoperatively and up to 1 year after aCXL, and post‐operative haze was estimated with SLE (n = 483 eyes). A random effect model was used to examine the relationship between post‐operative subjective haze with SLE and densitometry. Linear mixed models were used to examine the relationship between densitometry, pre‐operative baseline characteristics, and CDVA.

Results

There was a significant association between subjective haze with SLE and densitometry (p < 0.001). There was a significant relationship between CDVA and densitometry: for every 10 GSUs of increased densitometry in the 0–2 mm zone, CDVA worsened by approximately half a Snellen line (p < 0.001). Age and pre‐operative Kmax were significant predictors of densitometry. For every 10 years of age, densitometry increased by 0.68 GSUs (95% CI [0.27 to 1.07], p < 0.001). For every 10 D of increased preoperative Kmax, densitometry increased by 0.69 GSUs (95% CI [0.41 to 0.98], p < 0.001).

Conclusions

Subjective haze after aCXL estimated with SLE, is significantly associated with densitometry. Increased densitometry after aCXL is associated with a reduction in CDVA.
Method considerations and study protocol for a Nordic multi‐centre prospective study on outcomes in rare paediatric epilepsy surgery subgroups
Authors: Reinholdson Jesper , Malmgren Kristina , Chaplin John , Olsson Ingrid , Hallböök Tove
Published: January 2023

Epilepsy surgery is a therapeutic option for selected children with drug‐resistant epilepsy. Children who are surgical candidates have a high prevalence of neurodevelopmental comorbidities. There is a lack of adequately sized prospective studies in a number of rare surgical subgroups, especially of outcome domains such as cognitive level and health‐related quality‐of‐life. In this article, we describe method considerations and a study protocol for a Nordic population‐based multi‐centre follow‐up programme covering seizure as well as non‐seizure outcomes in children aged <4 years undergoing resective epilepsy surgery and children aged ≤18 years undergoing hemispherotomy, callosotomy or surgery for hypothalamic hamartoma.
A discussion among deans on advancing community engaged research
Authors: Sprague Martinez Linda , Chassler Deborah , Lobb Rebecca , Hakim Dema , Pamphile Jennifer , Battaglia Tracy A.
Published: January 2023

The benefits of community‐engaged research (CEnR) have been documented in the literature. However, the adoption of community engaged (CE) and participatory approaches among health researchers remains limited. The Boston University (BU) Clinical Translational Science Institute's community engagement program initiated a discussion among five BU Deans to explore their approaches to support the practice of CEnR among faculty in their schools. The discussion was recorded and the transcript analyzed to identify and explore themes that emerged. Most strategies discussed by the Deans were not focused on changing institutional systems to advance CEnR. Instead, the analyses showed that institutional CE efforts highlighted by the Deans were focused on “responsibility centered on one person” or “research mentors.” Approaches to developing a culture of CEnR that centers responsibility for promoting it on a few people in a university may place significant burden on leadership and researchers and is not an effective way to promote culture change. Systems change is needed to support CEnR, improve accountability, and realize successful partnerships between academic institutions and communities. The dialogue among Deans focused on the topic of CEnR provided an effective method to catalyze discussion and over time may help to strengthen a culture of CEnR research.
Prediction of cervical cancer precursor lesions by quantitative methylation specific PCR: A retrospective study
Authors: Al Roomy Moody , Chehadeh Wassim , Al Awadhi Rana
Published: January 2023

Objective

This study was undertaken to evaluate the performance of FAM19A4 and hsa‐mir‐124‐2 hypermethylation as a triage tool for women who are at risk of developing cervical cancer or high‐grade cervical cancer precursor lesions by taking into consideration the cytology report, histology diagnosis, and human papillomavirus (HPV) status.

Methods

A total of 330 cervical ThinPrep samples were retrospectively collected and used for DNA isolation. HPV DNA was detected by real‐time polymerase chain reaction (PCR), and HPV genotypes were identified by Sanger‐based sequencing. DNA extracts were bisulphite‐treated, and hypermethylation of FAM19A4 and hsa‐mir‐124‐2 genes was detected by a quantitative methylation‐specific PCR (qMSP) test using the QIAsure Methylation assay.

Results

Hypermethylated genes were detected in 27 (9.6%) cervical samples, mostly found in women diagnosed with high‐grade squamous intraepithelial legions (77.8%) or cervical intraepithelial neoplasia grade 3 (CIN3) (72.7%). The sensitivity and the specificity of the qMSP test for predicting CIN3 lesions among women with high‐risk HPV was 75% and 91%, respectively.

Discussion/Conclusion

There was a significant correlation between high‐grade cervical cancer precursor lesions and detection of hypermethylated genes in samples positive for high‐risk HPV. Our results suggest that the QIAsure Methylation test can be used as a triage tool to identify women at risk for cervical cancer progression.
Dating business cycles in the United Kingdom, 1700–2010
Authors: Broadberry Stephen , Chadha Jagjit S. , Lennard Jason , Thomas Ryland
Published: January 2023

This paper constructs a new chronology of the business cycle in the United Kingdom from 1700 on an annual basis and from 1920 on a quarterly basis to 2010. The new chronology points to several observations about the business cycle. First, the cycle has significantly increased in duration and amplitude over time. Second, contractions have become less frequent but are as persistent and costly as at other times in history. Third, the typical recession has been tick‐shaped with a short contraction and longer recovery. Finally, the major causes of downturns have been sectoral shocks, financial crises, and wars.
Iron chelation therapy
Authors: Bruzzese Antonella , Martino Enrica Antonia , Mendicino Francesco , Lucia Eugenio , Olivito Virginia , Bova Carlo , Filippelli Gianfranco , Capodanno Isabella , Neri Antonino , Morabito Fortunato , Gentile Massimo , Vigna Ernesto
Published: January 2023

Iron overload is a pathological condition resulting from a congenital impairment of its regulation, increased intestinal iron absorption secondary to bone marrow erythroid hyperplasia, or a chronic transfusional regimen. In normal conditions, intracellular and systemic mechanisms contribute to maintaining iron balance. When this complex homeostatic mechanism fails, an iron overload could be present. Detecting an iron overload is not easy. The gold standard remains the liver biopsy, even if it is invasive and dangerous. Identifying iron using noninvasive techniques allowed a better understanding of the rate of iron overload in different organs, with a low risk for the patient. Estimating serum ferritin (mg/L) is the easiest and, consequently, the most employed diagnostic tool for assessing body iron stores, even if it could be a not specific method. The most common hematological causes of iron overload are myelodysplastic syndromes, sickle cell disease, and thalassemia. In all of these conditions, three drugs have been approved for the treatment of iron overload: deferiprone, deferoxamine, and deferasirox. These chelators have been demonstrated to help lower tissue iron levels and prevent iron overload complications, improving event‐free survival (EFS). Nowadays, the decision to start chelation and which chelator to choose remains the joint decision of the clinician and patient.
Rapid bluing and slow browning: reversible body color change according to ambient temperature in damselfly Indolestes peregrinus (Ris, 1916)
Authors: Hasebe Yuki , Nagano Yuta , Yokoi Tomoyuki
Published: January 2023

Variation in body color occurs in many animals, and its function differs by species. Some species use multiple colors to create different effects. Most dragonflies change their body color unilaterally with maturation, whereas in a few species these changes are reversible. Both sexes of the damselfly Indolestes peregrinus show temperature‐dependent reversible body color changes, with a brown color when the ambient temperature decreases and a blue color when the temperature increases. To elucidate the temperature range at which this color change occurs and the exact elapsed time for the color change, laboratory experiments were conducted to determine whether the time required for body color change was related to ambient temperature and whether sex differences affected this duration. The body color and time required for the change were recorded under four temperature conditions. Bluing was completed in a few minutes, whereas browning took several hours. Moreover, sexual differences were observed, whereby males showed a more rapid transformation to blue than that of females. Our results suggest that the rapid bluing has some importance in this species, especially in males.
Fertilization alters the abundance but not the diversity of soil fauna: A meta‐analysis
Authors: Zhu Yan , Bian Haixue , Ju Chenghui , Xu Chonghua , Zhou Yan , Zhang Huiguang , Xu Xia
Published: January 2023

Aim

Soil fauna, a functionally important group of soil organisms, are greatly affected by fertilization. However, it is still debated whether and how fertilization affects the soil faunal community. Here, we aimed to synthesize the global patterns of soil fauna communities in response to fertilization in terrestrial ecosystems.

Location

Global.

Time period

1997–2021.

Major taxa studied

Soil fauna.

Methods

We examined the effects of fertilization on the abundance, number of groups and Shannon diversity of soil fauna by synthesizing 1218 observations based on 39 published studies. We also explored the associations between fertilization‐induced changes in the soil faunal community and changes in soil and microbial properties.

Results

Fertilization increased the abundance of soil fauna by 56.3%, without significantly affecting the number of groups and the Shannon index. The type of fertilizer affected the responses of soil faunal abundance, and the effects of fertilizer type were altered by climate zones, ecosystem types and soil depths. Both organic and organic–mineral fertilizer treatments significantly increased the abundance of soil fauna in most climate zones, ecosystem types and soil depths, whereas mineral fertilizer treatment had no such effect. Additionally, we found inconsistent responses of soil fauna to fertilization among different taxonomic groups, not only at the order level but also at the class level, providing evidence for the idiosyncratic nature of the effects of fertilization on soil fauna. Furthermore, our regression analysis showed that changes in food resources, including soil nutrients and microbes, were crucial controls for the response of soil faunal abundance to fertilization.

Main conclusions

Fertilization generally increased soil faunal abundance at the global scale by affecting food resources, and the effects of fertilization were dependent on the specific soil fauna and type of fertilizer. We suggest the use of organic or organic–mineral fertilizers, rather than mineral fertilizers, to increase the benefits on specific soil fauna.