bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA-induced allosteric coupling drives viral capsid assembly in bacteriophage MS2
Authors: Hamilton Sean , Modi Tushar , Šulc Petr , Ozkan Banu
Published: June 2023

Understanding the mechanisms by which single-stranded RNA viruses regulate capsid assembly around their RNA genomes has become increasingly important for the development of both antiviral treatments and drug delivery systems. Here, we investigate the effects of RNA-induced allostery in a single-stranded RNA virus —Levivirusbacteriophage MS2 — using the computational methods of the Dynamic Flexibility Index (DFI) and the Dynamic Coupling Index (DCI). We show that asymmetric binding of RNA to a symmetric MS2 coat protein dimer increases the flexibility of the distant FG-loop and induces a conformational change to an asymmetric dimer that is essential for proper capsid formation. We also show that a point mutation W82R in the FG-loop creates an assembly-deficient dimer in which RNA-binding has no significant effect on FG-loop flexibility. Lastly, we show that the highly flexible disordered FG-loop of the RNA bound asymmetric dimer not only becomes the controller of the rigid FG-loop but enhances its dynamic coupling with all the distal positions in the dimer. This strong dynamic coupling allows highly regulated communication and unidirectional signal transduction that drives the formation of the experimentally observed capsid intermediates.

Author summary

The final stage of an RNA virus’ life cycle is the assembly of a protein shell encapsulating the viral genome prior to release from the host organism. Despite rapid advancements in both experimental and theoretical biology since the mid-20th century, little is still known about the underlying mechanisms of viral capsid assembly. However, understanding the biophysical principles of viral capsid assembly would bring us one step closer to developing new biotechnologies such as antivirals that inhibit this critical stage of the life cycle or artificial capsids for targeted drug/vaccine delivery. Although we limit the present study to one simple RNA virus that infects bacteria, we propose that the physical implications can extend to other RNA viruses including the human coronavirus SARS-CoV-2. We also propose that the allosteric regulation by specific protein-RNA interactions might be a general mechanism exploited by many other ribonucleoprotein complexes, such as CRISPR-Cas9, spliceosome or ribosome.
Natural genetic variation underlying the negative effect of elevated CO2on ionome composition inArabidopsis thaliana
Authors: Cassan Océane , Pimparé Léa-Lou , Mozzanino Timothy , Fizames Cécile , Devidal Sébastien , Roux Fabrice , Milcu Alexandru , Lèbre Sophie , Gojon Alain , Martin Antoine
Published: June 2023

The elevation of atmospheric CO2leads to a decline in the plant mineral content, which might pose a significant threat to food security in the coming decades. To date, very few genes have been identified as having a role in the negative effect of elevated CO2on plant mineral composition. Yet, several studies have shown a certain degree of diversity in the ionome’s response to elevated CO2, associated with genotypic variation. This suggests the existence of genetic factors controlling the effect of CO2on ionome composition. However, no large-scale studies have been carried out to date to explore the genetic diversity of the ionome responses to elevated CO2. Here, we used six hundredArabidopsis thalianaaccessions, representing geographical distributions ranging from worldwide to regional and local environments, to analyze the natural genetic variation underlying the negative effect of elevated CO2on the ionome composition in plants. We show that the growth under elevated CO2leads to a global and important decrease of the ionome content whatever the geographic distribution of the population. We also observed a high range of genetic diversity in the response of the ionome composition to elevated CO2, and we identified sub-populations, showing effects on their ionome ranging from the most pronounced to resilience or even to a benefit in response to elevated CO2. Using genome-wide association mapping on the response of each mineral element to elevated CO2or on integrative traits, we identified a large set of QTLs and genes associated with the ionome response to elevated CO2. Finally, we demonstrate that the function of one of these genes is associated to the negative effect of elevated CO2on the plant mineral composition. This resource will contribute to understand the genetic mechanisms underlying the negative effect of elevated CO2on plant mineral nutrition, and could help towards the development of crops adapted to a high-CO2world.
Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps
Authors: Colinet Dominique , Cavigliasso Fanny , Leobold Matthieu , Pichon Appoline , Urbach Serge , Cazes Dominique , Poullet Marine , Belghazi Maya , Volkoff Anne-Nathalie , Drezen Jean-Michel , Gatti Jean-Luc , Poirié Marylène
Published: June 2023

Animal venoms and other protein-based secretions that perform a variety of functions, from predation to defense, are highly complex cocktails of bioactive compounds. Gene duplication, accompanied by modification of the expression and/or function of one of the duplicates under the action of positive selection, followed by further duplication to produce multigene families of toxins is a well-documented process in venomous animals. This evolutionary model has been less described in parasitoid wasps, which use maternal fluids, including venom, to protect their eggs from encapsulation by the host immune system. Here, we evidence the convergent recruitment and accelerated evolution of two multigene families of RhoGAPs presumably involved in virulence in two unrelated parasitoid wasp species,Leptopilina boulardi(Figitidae) andVenturia canescens(Icheumonidae). In both species, these RhoGAPs are associated with vesicles that act as transport systems to deliver virulence factors, but are produced in different tissues: the venom gland inLeptopilinasp. and the ovarian calyx inV. canescens. We show that the gene encoding the cellular RacGAP1 is at the origin of the virulent RhoGAP families found inLeptopilinasp. andV. canescens. We also show that both RhoGAP families have undergone evolution under positive selection and that almost all of these RhoGAPs lost their GAP activity and GTPase binding ability due to substitutions in key amino acids. These results suggest an accelerated evolution and functional diversification of these vesicle-associated RhoGAPs in the two phylogenetically distant parasitoid species. The potential new function(s) and the exact mechanism of action of these proteins in host cells remain to be elucidated.
DiffSegR: An RNA-Seq data driven method for differential expression analysis using changepoint detection
Authors: Liehrmann Arnaud , Delannoy Etienne , Launay-Avon Alexandra , Gilbault Elodie , Loudet Olivier , Castandet Benoît , Rigaill Guillem
Published: June 2023

To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3’/5’)-degradation of rRNA, mRNA, and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available athttps://aliehrmann.github.io/DiffSegR/index.html.
The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)
Authors: Özkan Mustafa , Gürün Kanat , Yüncü Eren , Vural Kıvılcım Başak , Atağ Gözde , Akbaba Ali , Fidan Fatma Rabia , Sağlıcan Ekin , Altınışık N. Ezgi , Koptekin Dilek , Pawłowska Kamilla , Hodder Ian , Adcock Sarah E. , Arbuckle Benjamin S. , Steadman Sharon R. , McMahon Gregory , Erdal Yılmaz Selim , Bilgin C. Can , Geigl Eva-Maria , Götherstrom Anders , Grange Thierry , Togan İnci , Özer Füsun , Somel Mehmet
Published: June 2023

We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1stmillennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those ofEquus hydruntinus(orEquus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses representE.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest thatE.hydruntinuswas a sister clade to all ancient and present-dayE.hemionuslineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity reveal that the Anatolian wild ass population had severely lost genetic diversity by the mid-1stmillennium BCE, a likely omen of its eventual demise.
Multidimensional analysis of a social behavior identifies regression and phenotypic heterogeneity in a female mouse model for Rett syndrome
Authors: Mykins Michael , Bridges Benjamin , Jo Angela , Krishnan Keerthi
Published: June 2023

Regression is a key feature of neurodevelopmental disorders such as Autism Spectrum Disorder, Fragile X Syndrome and Rett syndrome (RTT). RTT is caused by mutations in the X-linked gene Methyl CpG-Binding Protein 2 (MECP2). It is characterized by an early period of typical development with subsequent regression of previously acquired motor and speech skills in girls. The syndromic phenotypes are individualistic and dynamic over time. Thus far, it has been difficult to capture these dynamics and syndromic heterogeneity in the preclinicalMecp2-heterozygous female mouse model (Het). The emergence of computational neuroethology tools allow for robust analysis of complex and dynamic behaviors to model endophenotypes in pre-clinical models. Towards this first step, we utilized DeepLabCut, a marker-less pose estimation software to quantify trajectory kinematics, and multidimensional analysis to characterize behavioral heterogeneity in Het over trials in the previously benchmarked, ethologically relevant social cognition task of pup retrieval. We report the identification of two distinct phenotypes of adult Het: Het that display a delay in efficiency in early days and then improve over days like wild-type mice, and Het that regress and perform worse in later days. Furthermore, regression is dependent on age, behavioral context, and is identifiable in early days of retrieval. Together, the novel identification of two populations of Het suggest differential effects on neural circuitry and opens new directions of exploration to investigate the underlying molecular and cellular mechanisms, and better design experimental therapeutics.
Phylogeogrphy reveals expansion of yellow fever virus genotypes in West and Central Africa
Authors: Motayo Babatunde Olanrewaju , Opayele Adewale , Akinduti Paul Akiniyi , Faneye Adedayo Omotayo , Omoregie Isibor Patrick , Oranusi Solomon Uche
Published: June 2023

Yellow Fever virus remains the most medically significant Arbovirus in Africa, with the occurrence of large outbreaks with human fatalities in recent years in Africa. Molecular epidemiology has shown the presence of 4 genotypes circulating across Africa; however, paucity of data still exists regarding directional spread and phylogeography of the African Yellow fever genotypes. The need to fill this gap with information from spatiotemporal data from continuous occurrence of YF outbreaks in Africa conceptualized this study; which aims to investigate the most recent transmission events and directional spread of YF virus using updated genomic sequence data. Archived Yellow Fever sequence data was utilized along with epidemiologic data from outbreaks in Africa, to analyze the case/fatality distribution. Phylogeograhic analysis was also utilized to demonstrate the ancestral introduction and geographic clustering of YF genotypes in Africa. Directional spread and geographic transmission of YF was also investigated. African YF genotypes were found to be geographical distinct, circulating within distinct geographical boundaries. Spatiotemporal spread however revealed an eastward spread of the West African genotypes over time, and recent northward movement of the East African genotype. We conclude by recommending expanded human/ vectoral surveillance of YF and other Arboviruses of public health importance, and upscaling sequencing capabilities of new and existing public health labs in Africa to help in the defense against public health threats.
The Neonatal Gyrencephalic Cortex Maintains Regionally Distinct Streams of Neuroblasts
Authors: Kim JaeYeon , Sandoval Kadellyn , Poddar Aunoy , Chu Julia , Horton Emma , Cui Di , Nakamura Keira , Bartels Theresa , Wood Christian , Rowitch David H. , Kim Hosung , Sherwood Chet C. , Kramer Boris W , Roberts Angela C. , Ross Pablo J. , Xu Duan , Robertson Nicola J. , Ji Peng , Maga Elizabeth A. , Paredes Mercedes F.
Published: June 2023

Neurodevelopmental mechanisms have evolved to support the formation of diverse brain structures, such as in humans, during the perinatal period. Here, we demonstrate that neonatal gyrencephalic brains harbor an expanded subventricular zone, termed the Arc, defined by tiered arrangement of doublecortin (DCX)-expressing neuroblasts and vascular enrichment at the ventricular wall. The Arc is the origin of dorsal and ventral populations of migratory neuroblasts that target multiple regions involved in higher cognitive functions. Arc-derived migratory streams, primarily from the caudal ganglionic eminence, are composed of diverse neuronal subtypes with distinct spatial and migratory-receptor profiles. Our findings indicate the Arc is a structure present in phylogenetically divergent species that supports the expansion of postnatal neuronal migration, contributing to a protracted formation of cortical circuits in gyrencephalic brains.

One-Sentence Summary

The ventricular cytoarchitecture of gyrencephalic brains supports an ongoing supply of migratory neurons to the neonatal cortex.
AutoMacq: an automatic pipeline to analyse macaque structural MRI data
Authors: Kindred Nathan , Carella Susanna , van den Heuvel Martijn P , Balezeau Fabien , Wang Yujiang , Poirier Colline
Published: June 2023

MRI scanning of rhesus macaques is a growing field due to their evolutionary proximity and similar neuroanatomy to humans. As such, there is a need for automatic macaque MRI processing pipelines. AutoMacq is a pipeline capable of processing rhesus macaque MRI data to produce both voxel-based and surface-based metrics. It involves minimal manual intervention and can be carried out without expert knowledge of macaque neuroanatomy. To test the quality of the pipeline, scans from 74 subjects across 8 different sites were processed. Results indicate that over 87% of tissue segmentations and surfaces were of satisfactory quality to not require additional manual correction. Hemispheric comparisons and analyses of scan-rescan data showed strong reliability of the volumetric and surface-based outputs. Finally, to illustrate potential applications of AutoMacq, the change in grey matter volume with ageing was investigated cross-sectionally using subjects aged 3-15 years (corresponding to adolescence until mid-adulthood). The analysis revealed a linear decrease in grey matter volume with age similar to what has been found in humans, reinforcing the value of rhesus macaques as a model of healthy human ageing.
Visual activity enhances neuronal excitability in thalamic relay neurons
Authors: Duménieu Maël , Fronzaroli-Molinieres Laure , Iborra-Bonnaure Cécile , Wakade Anushka , Zanin Emilie , Aziz Aurore , Ankri Norbert , Incontro Salvatore , Denis Danièle , Brette Romain , Marquèze-Pouey Béatrice , Debanne Dominique , Russier Michael
Published: June 2023

The dorsal lateral geniculate nucleus (dLGN) has long been held to act as a basic relay for visual information travelling from the retina to cortical areas, but recent findings suggest a largely underestimated functional plasticity of dLGN neurons. However, the cellular mechanisms supporting this functional plasticity have not been yet explored. In particular, it remains to elucidate whether intrinsic neuronal excitability change upon visual stimuli. We show here that monocular deprivation for 10 days reduces the intrinsic excitability of dorsal LGN relay cells. Furthermore, dLGN neurons exhibit long-term potentiation of their intrinsic excitability (LTP-IE) when suprathreshold afferent retinal inputs are stimulated at 40 Hz or when spikes are induced with direct somatic current injection to reproduce patterns of retinal activity. LTP-IE is observed after eye opening and requires calcium influx mediated by L-type calcium channels. It involves activation of PKA and is expressed through the down-regulation of Kv1 potassium channels. In conclusion, our study provides the first evidence for intrinsic plasticity in dLGN relay cells, thus further pointing the role of thalamic neurons in activity-dependent visual plasticity and amblyopia.
Autism- and epilepsy-associatedEEF1A2mutations lead to translational dysfunction and altered actin bundling
Authors: Mohamed Muhaned S. , Klann Eric
Published: June 2023

Protein synthesis is a fundamental cellular process in neurons that is essential for synaptic plasticity and memory consolidation. Here, we describe our investigations of a neuron- and muscle-specific translation factor,eukaryoticElongationFactor1a2(eEF1A2), which when mutated in patients results in autism, epilepsy, and intellectual disability. We characterize three most commonEEF1A2patient mutations, G70S, E122K, and D252H, and demonstrate that all three mutations decreasede novoprotein synthesis and elongation rates in HEK293 cells. In mouse cortical neurons, theEEF1A2mutations not only decreasede novoprotein synthesis, but also alter neuronal morphology, regardless of endogenous levels of eEF1A2, indicating that the mutations act via a toxic gain of function. We also show that eEF1A2 mutant proteins display increased tRNA binding and decreased actin bundling activity, suggesting that these mutations disrupt neuronal function by decreasing tRNA availability and altering the actin cytoskeleton. More broadly, our findings are consistent with the idea that eEF1A2 acts as a bridge between translation and the actin skeleton, which is essential for proper neuron development and function.

Significance Statement

EukaryoticElongationFactor 1A2 (eEF1A2) is a muscle- and neuron-specific translation factor responsible for bringing charge tRNAs to the elongating ribosome. Why neurons express this unique translation factor is unclear; however, it is known that mutations inEEF1A2cause severe drug-resistant epilepsy, autism and neurodevelopmental delay. Here, we characterize the impact of three common disease-causing mutations inEEF1A2and demonstrate that they cause decreased protein synthesis via reduced translation elongation, increased tRNA binding, decreased actin bundling activity, as well as altered neuronal morphology. We posit that eEF1A2 serves as a bridge between translation and the actin cytoskeleton, linking these two processes that are essential for neuronal function and plasticity.
Mechanisms of dual modulatory effects of spermine on the mitochondrial calcium uniporter complex
Authors: Tu Yung-Chi , Chao Fan-Yi , Tsai Ming-Feng
Published: June 2023

The mitochondrial Ca2+uniporter mediates the crucial cellular process of mitochondrial Ca2+uptake, which regulates cell bioenergetics, intracellular Ca2+signaling, and cell death initiation. The uniporter contains the pore-forming MCU subunit, an EMRE protein that binds to MCU, and the regulatory MICU1 subunit, which can dimerize with MICU1 or MICU2 and under resting cellular [Ca2+] occludes the MCU pore. It has been known for decades that spermine, which is ubiquitously present in animal cells, can enhance mitochondrial Ca2+uptake, but the underlying mechanisms remain unclear. Here, we show that spermine exerts dual modulatory effects on the uniporter. In physiological concentrations of spermine, it enhances uniporter activity by breaking the physical interactions between MCU and the MICU1-containing dimers to allow the uniporter to constitutively take up Ca2+even in low [Ca2+] conditions. This potentiation effect does not require MICU2 or the EF-hand motifs in MICU1. When [spermine] rises to millimolar levels, it inhibits the uniporter by targeting the pore region in a MICU-independent manner. The MICU1-dependent spermine potentiation mechanism proposed here, along with our previous finding that cardiac mitochondria have very low MICU1, can explain the puzzling observation in the literature that mitochondria in the heart show no response to spermine.
Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex
Authors: Deng Sunbin , Cai Jiaxi , Harrison Stephen C. , Zhou Huilin , Hinshaw Stephen M.
Published: June 2023

Successful mitosis depends on the timely establishment of correct chromosomal attachments to microtubules. The kinetochore, a modular multiprotein complex, mediates this connection by recognizing specialized chromatin containing a histone H3 variant called Cse4 in budding yeast and CENP-A in vertebrates. Structural features of the kinetochore that enable discrimination between Cse4/CENP-A and H3 have been identified in several species. How and when these contribute to centromere recognition and how they relate to the overall structure of the inner kinetochore are unsettled questions. We have determined the crystal structure of a Cse4 peptide bound to the essential inner kinetochore Okp1-Ame1 heterodimer from budding yeast. The structure and related experiments show in detail an essential point of Cse4 contact and provide information about the arrangement of the inner kinetochore.
The white-footed deermouse, an infection-tolerant reservoir for several zoonotic agents, tempers interferon responses to endotoxin in comparison to the mouse and rat
Authors: Milovic Ana , Duong Jonathan V. , Barbour Alan G.
Published: June 2023

The white-footed deermousePeromyscus leucopus, a long-lived rodent, is a key reservoir for agents of several zoonoses, including Lyme disease. While persistently infected, this deermouse is without apparent disability or diminished fitness. For a model for inflammation elicited by various pathogens, the endotoxin lipopolysaccharide (LPS) was used to compare genome-wide transcription in blood byP. leucopus,Mus musculusandRattus norvegicusand adjusted for white cell concentrations. Deermice were distinguished from the mice and rats by LPS response profiles consistent with non-classical monocytes and alternatively-activated macrophages. LPS-treatedP. leucopus, in contrast to mice and rats, also displayed little transcription of interferon-gamma and lower magnitude fold-changes in type 1 interferon-stimulated genes. This was associated with comparatively reduced transcription of endogenous retrovirus sequences and cytoplasmic pattern recognition receptors in the deermice. The results reveal a mechanism for infection tolerance in this species and perhaps other animal reservoirs for agents of human disease.
The double-edged role of FASII regulator FabT inStreptococcus pyogenesinfection
Authors: Lambert Clara , Gaillard Marine , Wongdontree Paprapach , Bachmann Caroline , Hautcoeur Antoine , Gloux Karine , Guilbert Thomas , Méhats Celine , Prost Bastien , Solgadi Audrey , Abreu Sonia , Andrieu Muriel , Poyart Claire , Gruss Alexandra , Fouet Agnes
Published: June 2023

InStreptococcus pyogenes, the type II fatty acid (FA) synthesis pathway FASII is feedback- controlled by the FabT repressor bound to an acyl-Acyl carrier protein. Despite FabT defects being linked to reduced virulence in animal models, spontaneousfabTmutants arisein vivo. To resolve this paradox, we characterized the conditions and mechanisms that require FabT activity, and those that promotefabTmutant emergence. The primaryfabTmutant defect is energy dissipation: specific nutrients are consumed, but the mutant fails to grow on human tissue, cells, or cell filtrates where nutrients are limited. These features explain the FabT requirement during infection. Conversely,fabTmutants exhibited a marked growth advantage over the wild-type in biotopes rich in saturated FAs.fabTmutants emerge in this context, where continued FASII activity prevented environmental FA incorporation. Anex vivomuscle model demonstrated that wild-typeS. pyogeneswas inhibited, whilefabTmutant growth was stimulated, but conditional to FASII activity. Our findings elucidate the rationale for emergingfabTmutants that improve survival in lipid-rich biotopes, but lead to a genetic impasse for infection.
Differential activity patterns in the upper and lower blade of the dentate gyrus
Authors: Fredes Felipe , Masaracchia Laura , Capogna Marco , Vidaurre Diego
Published: June 2023

The dentate gyrus is considered the first stage in the trisynaptic circuit of the hippocampus. Granule cells of the dentate gyrus fire very sparsely with a low probability of overlapping patterns of active neurons. This characteristic supports the most prevalent view of the dentate gyrus function as that of a pattern separator: to generate dissimilar neuronal representations from overlapping input states that represent similar but not identical environments. However, there are two distinct granule cell blades that have been shown to have different activity patterns: the upper blade and the lower blade. These may support different purposes, but their differential function is not well understood. Here we have recorded calcium imaging data from both the upper and the lower blade of the dentate gyrus from two mice (the upper blade from one, the lower blade from the other), while they perform a simple decision-making task. We found that only the lower blade encodes subjective emotional response while the upper blade preferentially encodes the actual response. Importantly, we found that correlations between cells carried more information about these two behavioural variables than individual firings, suggesting that neuron correlations encode here important information above and beyond individual unit activity.
Implementing circular economy principles in infrastructure procurement to support circular supply chains
Authors: Karlovsek Jurij , Meath Cristyn , Miles-Mwangangi Lawrence , MacDonald Charles , Brockmann Alfredo
Published: June 2023

Purpose

The aim of this paper is to study the procurement of infrastructure through the lens of circular economy (CE) principles to achieve contractual delivery methods which promote circular supply chains.

Design/methodology/approach

This paper provides an analysis of the key concepts related to the research topic based on a review of recent academic literature. Moreover, based on the empirical and academic experience of the authors in the infrastructure industry, there are multiple actionable discussion points which are raised. However, the research for this paper was undertaken with a focus on literature rather than direct observations and empirical research, which may limit discussion to scholarly rather than practical applications.

Findings

The paper finds that CE principles can be leveraged to capture additional economic benefit in the infrastructure industry. In addition, there are specific project delivery methods which may act as workable practices towards more circular supply chains.

Originality/value

The value of this paper is in the CE-related suggestions the paper provides to procurement practitioners. This work also attempts to link contractual procurement with tangible outcomes across the project lifecycle, including operation and end of life (EOL) of the infrastructure asset.
DeLone and McLean’s reformulated information systems success model: a systematic review of available literature in public sector (2011-2022)
Authors: Iqbal Memoona , Rafiq Muhammad
Published: June 2023

Purpose

DeLone and McLean (D&M) has been amongst the most widely used models to assess the success elements of information systems (IS) since 1992. A decade later in 2003, D&M proposed a revised design that included several components which have been left out of original proposed model. This study aims to rely on the review of a number of papers casing the era 2011–2022 that satisfies a specific set of requirements to identify the research gaps in this area and to prepare a future research agenda.

Design/methodology/approach

This study is a systematic review: a technique that identifies and evaluates pertinent research. This gathers and analyses data from selected studies with objective to catalogue all empirical research studies, which responds to a certain study topic or hypothesis to meets predetermined inclusion criteria. Data collection method was divided into four stages, and selection details are determined through flow chart.

Findings

This research discovered D&M 2003 model use in many contexts, countries and cultures to better comprehend the topic and addresses its gaps, particularly with regard to public sector and its particularities. Publications have frequently emphasized the significance of this idea while studying public sector information systems by using associated variables-related items. Findings also include a summary of key components and dimensions used in reviewed studies in relation to each of the seven variables, and associated particularities in government sector over the world.

Originality/value

To the best of the authors’ knowledge, this is the first ever effort in this developing country in discipline of Information Management to execute such kind of study to review D&M ISS model in detail at this stage to evaluate nonacademic public sector information systems around the world.
The cost-effectiveness of resilient healthcare
Authors: Saurin Tarcisio Abreu , Wiig Siri , Patriarca Riccardo , Grotan Tor Olav
Published: June 2023

Purpose

The purpose of this conceptual paper is to develop a model of the hypothesized relationships between investments and outcomes of resilient health care (RHC).

Design/methodology/approach

Based on the extant literature, the aforementioned model is described along with proxy measures of its composing variables and a matrix for assessing the cost-effectiveness of RHC instantiations. Additional possible relationships are set out in two propositions for theory testing.

Findings

The model conveys that RHC gives rise to both desired and undesired outcomes. Investments moderate the relationships between RHC and its outcomes. Both investments and outcomes can be broadly categorized as either human or technical. Moreover, the propositions refer to what type and how much investment is necessary to perform in a resilient manner, what are the intended or desired outcomes of RHC, for how long and who is affected by these outcomes.

Originality/value

The cost-effectiveness perspective of RHC is new and the proposed model opens opportunities for empirical and theoretical research.
Mediating effect of industry dynamics, absorptive capacity and resource commitment in new digital technology adoption and effective implementation processes
Authors: Rauniar Rupak , Rawski Greg , Cao Qing Ray , Shah Samhita
Published: June 2023

Purpose

Drawing upon a systematic literature review in new technology, innovation transfer and diffusion theories, and from interviews with technology leaders in digital transformation programs in the US Oil & Gas (O&G) industry, the authors explore the relationships among O&G industry dynamics, organization's absorptive capacity and resource commitment for new digital technology adoption-implementation process.

Design/methodology/approach

The authors employed the empirical survey method to gather the data (a sample size of 172) in the US O&G industry and used structural equation modeling (SEM) to test the measurement model for validity and reliability and the conceptual model for hypothesized structural relationships.

Findings

The results provide support for the study’s causal model of adoption and implementation with positive and direct relationships between the initiation and trial stages, between the trial stages and the evaluation of effective outcomes and between the effective outcomes and the effective implementation stages of digital technologies. The results also reveal partial mediating relationships of industry dynamics, absorptive capacity and resource commitment between respective stages.

Practical implications

Based on the current study's findings, managers are recommended to pay attention to the evolving industry dynamics during the initiation stage of new digital technology adoption, to utilize the organization's knowledge-based absorptive capacity during digital technology trial and selection stages and to support the digital technology implementation project when the adoption decision of a particular digital technology has been made.

Originality/value

The empirical research contributes literature on digital technology adoption and implementation by identifying and demonstrating the importance of industry dynamics, absorptive capacity and resource commitment factors as mediating variables at various stages of the adoption-implementation process and empirically validating a process-based causal model of digital technology adoption and a successful implementation project that has been missing in the current body of literature on digital transformation.
Socially sustainable smart cities: mapping the research trends by co-word analysis
Authors: Ebrahiem Samia , El-Kholei Ahmed O. , Yassein Ghada
Published: June 2023

Purpose

The article attempts to shed light on the social aspects of research that deal with Sustainable Development Goals (SDGs) and sustainable cities. The aim is to offer a global view of these facets' evolution and to provide information on people-centered smart cities.

Design/methodology/approach

The research is qualitative. A systematic bibliometric approach is a framework for the research. The unit of analysis is publications on SDGs and Smart Cities (SCs) indexed in Scopus. The authors used VOSviewer text mining functionality to construct co-occurrence networks of socially related critical terms extracted from textual data. The co-occurrence of keywords presents a valuable method and process for attaining in-depth analysis and fast comprehension of trends and linkages in articles from a holistic approach.

Findings

Social media, social sustainability and social capital are the three multifaceted social keywords that co-occur in SDGs and SCs. The paper provides a brief compendium of resources and frameworks to build a socially sustainable smart city.

Research limitations/implications

The retrieval date was on 15 August 2019. The authors used the same search query for new papers released in 2019 and afterwards to update their findings. The authors collected 657 documents on SCs, compared to 2,975 documents about SDGs demonstrating that their findings are still trending in the same direction, emphasizing the importance of the research topic. SCs' social aspects are still chartered areas that require the attention to future research.

Originality/value

The authors’ decision to use two separate data sets for SCs and SDGs data files helps to provide a more comprehensive picture of the research landscape. It may identify areas where research is lacking or needs future research. The authors present an integrative agenda for a smart city to be socially sustainable. Innovative approaches to urban planning are required to empower the place and context and improve the users' satisfaction, where innovative solutions enable smart, sustainable and inclusive societies. Infrastructure governance is a critical keystone. It could guarantee that public investments contribute to sustainable urban development while enhancing city resilience, particularly in facing climate change and inclusive growth challenges.
How do consumers evaluate products in virtual reality? A literature review for a research agenda
Authors: Branca Generoso , Marino Vittoria , Resciniti Riccardo
Published: June 2023

Purpose

This paper aims to review the existing literature about consumers’ evaluation of products in virtual reality (VR), provide an accurate overview of this field, systematise the knowledge developed so far, identify the research gaps and propose a future research agenda.

Design/methodology/approach

A systematic literature review was performed on Scopus and Web of Science, resulting in a final pool of 31 articles.

Findings

Four main themes were identified, and a detailed research agenda is proposed based on the findings and following the theory, context, characteristics, methodology framework.

Research limitations/implications

The provision of formal inclusion and exclusion criteria may have resulted in additional potentially relevant articles not indexed in the data set under consideration.

Originality/value

The paper highlights how products are perceived in VR, the consumers’ responses, the peculiarities of VR compared to other conditions and VR as a product test environment. To the best of the authors’ knowledge, this paper seems to represent the first systemic review that focusses solely on how consumers assess products in VR. The results lead to a broad proposal of directions for future research that can expand knowledge on VR in marketing. Practical implications concern the use of VR to design product strategies and as a testing and prototyping environment.
Occurrence of extended‐spectrum β‐lactamases‐producing Escherichia coli isolates over gradient pollution in an urban tropical estuary
Authors: Costa Wellington Felipe , Paranhos Rodolfo , Mello Marianne Pataro , Picão Renata Cristina , Laport Marinella Silva
Published: June 2023

Bacterial resistance to antimicrobials is a global public health problem that surpasses the human context and can be increased by pollution. However, the lack of systematic monitoring of resistance in some aquatic matrices, such as tropical estuaries, makes it unknown whether its occurrence is associated with anthropogenic pollution in these environments. Therefore, we investigated the occurrence of extended‐spectrum beta‐lactamases (ESBLs) producing Escherichia coli as a resistance indicator for 12 consecutive months at three representative points of a pollution gradient in Guanabara Bay (GB), Brazil. Sixty‐six E. coli strains were selected from 72 samples of GB waters in the presence of ceftriaxone (8 μg mL−1) and identified by MALDI‐TOF MS. Of the 66, 55 (83.3%) strains were ESBL producers. They carried beta‐lactamase/ESBL genes, with the predominance of blaCTX‐M (54, 98.2%), especially the blaCTX‐M‐1,2 allele (49.1%). These strains were detected frequently (81.8%) from the point with the highest pollution levels. Furthermore, the marker for Class 1 integron, intI1 gene, was detected in 54.5% of ESBL producers. These data suggest an association between antimicrobial‐resistant E. coli and sewage pollution in aquatic environments raising concerns about the possible risks of human exposure to these waters and fish consumption.
GC–MS analysis of eight aminoindanes using three derivatization reagents
Authors: Rose Amber R. , Joshi Monica , Staretz Marianne E. , Wood Matthew , Brettell Thomas A.
Published: June 2023

Aminoindanes are a class of novel psychoactive substances (NPSs) that have become more prevalent over the past decade. GC–MS is often utilized for identifying seized drugs and is well regarded for its ability to separate mixtures. However, certain aminoindanes have similar mass spectral data and require specific gas chromatographic stationary phases for separation. Derivatization is an alternative method that can be applied to GC–MS to enhance chromatographic results, providing more selective analysis in seized‐drug identification. This study investigates derivatization techniques to provide options for forensic science laboratories in accurately identifying aminoindanes. Three derivatization reagents, N‐methyl‐bis(trifluoroacetamide) (MBTFA), heptafluorobutyric anhydride (HFBA), and ethyl chloroformate (ECF) were evaluated for the analysis of eight aminoindanes by GC–MS using two common gas chromatographic stationary phases, Rxi®‐5Sil MS and Rxi®‐1Sil MS. All three derivatization methods successfully isolated eight aminoindanes, including the isomers 4,5‐methylenedioxy‐2‐aminoindane (4,5‐MDAI), and 5,6‐methylenedioxy‐2‐aminoindane (5,6‐MDAI) that could not be differentiated prior to derivatization. Reduced peak tailing and increased abundance were observed after derivatization for all the compounds, and mass spectra of the derivatives contained individualizing fragment ions that allowed for further characterization of the aminoindanes. This excluded 4,5‐MDAI and 5,6‐MDAI as they shared the same characteristic ions and were only distinguishable by their retention times. All three derivatization techniques used in this study allow for successful characterization of the aminoindanes and give forensic science laboratories flexibility in their analysis approach when they encounter these compounds.
Nutritional, biological, and structural properties of bioactive peptides from bellflower, Persian‐willow, and bitter‐orange pollens
Authors: Sarabandi Khashayar , Dashipour Alireaza , Izadi Zahra , Akbarbaglu Zahra , Katouzian Iman , Jafari Seid Mahdi
Published: June 2023

In this study, the composition of amino acids, nutritional characteristics, degree of hydrolysis (DH), antioxidant properties, and antibacterial activity of proteins and hydrolysates of bellflower (Campanula latifolia), Persian willow (Salix aegyptiaca), and bitter orange (Citrus aurantium L.) were investigated under the influence of different proteases (Alcalase: Al, trypsin: Tr, pancreatin: Pa, and pepsin: Pe). Evaluation of the structural features of the proteins showed amide regions (amide A, B, I‐III) and secondary structures. Hydrophobic amino acids (∼38%), antioxidants (∼21%), and essential types (∼46%) form a significant part of the structure of flower pollen. The digestibility and nutritional quality (PER) of the hydrolyzed samples (CP: 1.67; CA: 1.89, and PW: 1.93) were more than the original protein. Among proteins and peptides, the highest degree of hydrolysis (34.6%: Al‐PWH), inhibition of free radicals DPPH (84.2%: Al‐CPH), ABTS (95.2%: Pa‐CPH), OH (86.7%: Tr‐CAH), NO (57.8%: Al‐CPH), reducing power (1.31: Pa‐CPH), total antioxidant activity (1.46: Pa‐CPH), and chelation of iron ions (80%: Al‐CPH and Al‐CAH) and copper (50.3%: Pa‐CAH) were affected by protein type, enzyme type, and amino acid composition. Also, the highest inhibition of the growth of Escherichia coli (25 mm) and Bacillus cereus (24 mm) were related to CP and PW hydrolysates, respectively. The results of this research showed that hydrolyzed flower pollens can be used as a rich source of essential amino acids as well as natural antioxidants and antibacterial in food and dietary products.

Practical Application

Enzymatic hydrolysis of Campanula latifolia, Persian willow, and Citrus aurantium pollen proteins was performed. The hydrolyzed ones had high nutritional quality and digestibility (essential amino acids and PER index). Antioxidant properties and chelation of metal ions of peptides were affected by the type of protein and enzyme. The hydrolysates showed inhibitory activity against the growth of Esherichia coli and Bacillus cereus.
Numerical Simulation of Thermo‐Hydro‐Mechanical‐Chemical Response Caused by CO2Injection into Saline Geological Formations: A Case Study from the Ordos Project, China
Authors: FAN Zejin , XU Tianfu , YANG Bo , ZHANG Hui , ZHU Huixing
Published: June 2023

Thermo‐hydro‐mechanical‐chemical (THMC) interactions are prevalent during CO2geological sequestration (CGS). In this study, a sequential coupling THMC numerical simulation program was constructed, which can be used to explore the following issues of CGS: fluid and heat flow, solute transport; stresses, displacements and rock failures related to geo‐mechanical effects; equilibrium and kinetic chemical reactions; chemical damage to mechanical properties of the rock. Then, the coupling program was applied to the Ordos CGS Project to study the formation response under the multi‐field interaction caused by CO2injection. The simulation results show that the mechanical process dominates the short CO2injection period. Specifically, the formation's permeability near the injection well increases by 43%, due to the reduction of effective stress, which significantly promotes the lateral migration of CO2. When the injection rate exceeds 0.15 million tons per year, the cohesion of the reservoir rock is not enough to resist the shear force inside the rock and rock failure may occur. During the subsequent long‐term sequestration period (200 years), the influence of mineral reactions gradually increases. Due to calcite dissolution, the shear modulus of caprock is predicted to decrease by 7.6%, which will to some extent increase the risk of rock failure.
orchaRd 2.0: An R package for visualising meta‐analyses with orchard plots
Authors: Nakagawa Shinichi , Lagisz Malgorzata , O'Dea Rose E. , Pottier Patrice , Rutkowska Joanna , Senior Alistair M. , Yang Yefeng , Noble Daniel W. A.
Published: June 2023

Although meta‐analysis has become an essential tool in ecology and evolution, reporting of meta‐analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and individual effect sizes.

Here, we have added significant enhancements by integrating many new functionalities intoorchaRd 2.0. This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators.

orchaRd 2.0has additional functions which calculate key statistics from multilevel meta‐analytic models such asI2andR2. Importantly,orchaRd 2.0contributes to better reporting by complying with PRISMA‐EcoEvo (preferred reporting items for systematic reviews and meta‐analyses in ecology and evolution). Taken together,orchaRd 2.0can improve the presentation of meta‐analytic results and facilitate the exploration of previously neglected patterns.

In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for example, by citations in a figure legend, acknowledging the use of relevant packages.