bluuebunny/crossref_metadata_2025 huggingface dataset:
Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic
Authors: Silva Kalinga Pavan T. , Sundar Ganesh , Khare Anupama
Published: December 2022

The rise of antimicrobial resistance has motivated the development of antibiotics that have multiple cellular targets, to theoretically reduce the frequency of resistance evolution, but adaptive trajectories and genetic determinants of resistance against such antibiotics are understudied. Here we investigate these in methicillin resistantStaphylococcus aureus(MRSA) using experimental evolution of ten independent populations in the presence of delafloxacin (DLX), a novel fluoroquinolone that targets both DNA gyrase and topoisomerase IV. We show that coding sequence mutations and genomic amplifications of the gene encoding a poorly characterized efflux pump, SdrM, lead to the evolution of high DLX resistance, circumventing the requirement for mutations in the target enzymes. Almost all of our evolved populations had one of two SdrM coding sequence mutations, which led to moderate DLX resistance. Additionally, these populations had 13 distinct genomic amplifications, each containingsdrMand two adjacent genes encoding efflux pumps, which resulted in up to 100-fold higher DLX resistance. While increasedsdrMexpression provided the selective advantage of the amplification in the DLX evolution, the adjacent efflux pumps hitchhiking in the genomic amplification contributed to cross-resistance against the aminoglycoside streptomycin. Finally, lack ofsdrMnecessitated mutations in both DNA gyrase and topoisomerase IV to evolve DLX resistance, and the presence ofsdrMthus increased the frequency of resistance evolution. Our study highlights that instead of reduced rates of resistance, evolution of resistance to antibiotics with multiple cellular targets can involve alternate high-frequency evolutionary paths such as genomic amplifications of efflux pumps, that may cause unexpected alterations of the fitness landscape, including antibiotic cross-resistance.
A regulatory toolkit of arabinose-inducible artificial transcription factors for Gram-negative bacteria
Authors: Naseri Gita , Raasch Hannah , Charpentier Emmanuelle , Erhardt Marc
Published: December 2022

The Gram-negative bacteriaSalmonellaTyphimurium andEscherichia coliare important model organisms, powerful prokaryotic expression platforms for biotechnological applications, and pathogenic strains constitute major public health threats. To facilitate new approaches for research, biomedicine, and biotechnological applications, we developed a set of arabinose-inducible artificial transcription factors (ATFs) using CRISPR/dCas9 andArabidopsis-derivedDNA-binding proteins, allowing to control gene expression inE. coliandSalmonellaover a wide inducer concentration range. As a proof-of-concept, we employed the developed ATFs to engineer aSalmonellabiosensorstrain, SALSOR 0.2 (SALmonella biosenSOR 0.2), which responds to the presence of alkaloid drugs with quantifiable fluorescent output. We demonstrated that SALSOR 0.2 was able to detect the presence of the antitussive noscapine alkaloid with ~2.3-fold increased fluorescent signal over background noise compared to a previously described biosensor. Moreover, we used plant-derived ATFs to control β-carotene biosynthesis inE. coli, which resulted in ~1.6-fold higher β-carotene production compared to expression of the biosynthesis pathway using a strong constitutive promoter. The arabinose-inducible ATFs reported here thus enhance the synthetic biology repertoire of transcriptional regulatory modules that allow tuning protein expression in the Gram-negative model organismsSalmonellaandE. coli.
Different low-complexity regions of SFPQ play distinct roles in the formation of biomolecular condensates
Authors: Marshall Andrew C. , Cummins Jerry , Kobelke Simon , Zhu Tianyi , Widagdo Jocelyn , Anggono Victor , Hyman Anthony , Fox Archa H. , Bond Charles S. , Lee Mihwa
Published: December 2022

Demixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism governing the organisation of molecules within the cell. Long disordered low complexity regions (LCRs) are a common feature of proteins that form biomolecular condensates. RNA-binding proteins with prion-like composition have been highlighted as drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQin vitroand in the cell. In contrast, we find that, unexpectedly, the longer N-terminal prion-like LCR of SFPQ attenuates condensation, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. Our data add nuance to the emerging understanding of biomolecular condensate formation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation.

Graphical Abstract
The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence
Authors: Lee UnJin , Arsala Deanna , Xia Shengqian , Li Cong , Ali Mujahid , Svetec Nicolas , Langer Christopher B , Sobreira Débora R. , Eres Ittai , Sosa Dylan , Chen Jianhai , Zhang Li , Reilly Patrick , Guzzetta Alexander , Emerson J.J. , Andolfatto Peter , Zhou Qi , Zhao Li , Long Manyuan
Published: December 2022

Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment of distally duplicated genes (enhancer capture) is an efficient mechanism for modulating tissue-specific production of pre-existing proteins. By leveraging genomic asymmetries in synteny and function that distinguish new genes evolving under enhancer capture-divergence (ECD) from those evolving under previous models, we performed a co-expression analysis onDrosophila melanogastertissue data to show the generality of ECD as a significant evolutionary driver of asymmetric, distally duplicated genes. We use the recently evolved geneHP6/Umbrea, which duplicated <15 million years ago (mya), as an example of the ECD process. By assaying genome-wide chromosomal conformations in multipleDrosophilaspecies, we show thatHP6/Umbreawas inserted into a pre-existing, evolutionarily stable 3D genomic structure spanning over 125kb. We then utilize this data to identify a newly discovered enhancer (FLEE1), buried within the coding region of the highly conserved, essential geneMFS18, that likely neo-functionalizedHP6/Umbrea, thereby driving the new duplicate gene copy to fixation. Finally, we demonstrate ancestral transcriptional co-regulation ofHP6/Umbrea’s future insertion site using single-cell transcriptomics, illustrating how enhancer capture provides a highly evolvable, one-step solution to Ohno’s Dilemma. The intuitive molecular mechanism underpinning the ECD model unveils a novel and robust framework to understand the fixation and neofunctionalization of distally duplicated genes.
Regulation of replicative histone RNA metabolism by the histone chaperone ASF1
Authors: Mendiratta Shweta , Ray-Gallet Dominique , Gatto Alberto , Lemaire Sébastien , Kerlin Maciej A. , Coulon Antoine , Almouzni Geneviève
Published: December 2022

In S phase, duplication and assembly of the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored a potential role of histone chaperones in this process thereby linking chromatin assembly with histone production in human cells. Depletion of the ASF1 chaperone specifically decreased the pool of replicative histones both at the levels of soluble protein and total RNA, while depletion of CAF-1 did not. Most replicative histone genes decreased in their overall expression as revealed by total RNA-seq. In contrast, both their newly synthesized RNAs and nascent RNAs at transcription sites increased as shown by 4sU-labeled RNA-seq and single-molecule RNA FISH, respectively. Further inspection of the sequences corresponding to replicative histone RNAs showed a 3’ processing defect, leading to unprocessed transcripts usually targeted for degradation. We discuss how this regulation of replicative histone RNA metabolism by ASF1 fine-tunes the histone dosage to avoid unbalanced situations deleterious for cell survival.
Divergent and diversified proteome content across a serially acquired plastid lineage
Authors: Novák Vanclová Anna M. G. , Nef Charlotte , Vancl Adél , Liu Fuhai , Füssy Zoltán , Bowler Chris , Dorrell Richard G.
Published: December 2022

Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes, prone to the loss and replacement of their plastids via serial endosymbiosis. One such replacement took place in the ancestors of the Kareniaceae, which harbor haptophyte-derived plastids containing the pigment fucoxanthin, instead of the ancestral peridinin dinoflagellate plastid. The metabolic functions of the fucoxanthin plastid are performed by a diverse range of nucleus-encoded and plastid-targeted proteins, which may originate from the haptophyte ancestor of the fucoxanthin plastid, the peridinin-containing ancestor of the dinoflagellate host, and/or from lateral gene transfers. However, the evolutionary composition of fucoxanthin plastid proteomes across the diversity of kareniacean dinoflagellates remains poorly understood. Here, we determine the total composition of the plastid proteomes of seven distantly-related kareniacean dinoflagellates, including newly-sequenced members of three genera (Karenia, Karlodinium, andTakayama). Using a custom plastid-targeting predictor, automatic single-gene tree building and phylogenetic sorting of plastid-targeted proteins, we project relatively limited (~10%) and functionally distinctive contributions of the haptophyte endosymbiont to the fucoxanthin plastid proteome, in comparison to plastid-targeted proteins of dinoflagellate host origin. Considering a concatenated multigene phylogeny of haptophyte-derived plastid proteins, we show that the haptophyte order Chrysochromulinales is the closest living relative of the fucoxanthin plastid donor. We additionally perform detailed analyses of the N-terminal targeting sequences of kareniacean plastid signal peptides, reporting a surprisingly high sequence conservation. Finally, considering planetary-scale distributions of key kareniacean genera and haptophyte orders fromTaraOceans, we suggest ecological and mechanistic factors accompanying the endosymbiotic acquisition of the fucoxanthin plastid.
Effectiveness ofPseudomonas aeruginosatype VI secretion system relies on toxin potency and type IV pili-dependent interaction
Authors: Rudzite Marta , Endres Robert G. , Filloux Alain
Published: December 2022

The type VI secretion system (T6SS) is an antibacterial weapon that is used by numerous Gram-negative bacteria to gain competitive advantage by injecting toxins into adjacent prey cells. Predicting the outcome of a T6SS-dependent competition is not only reliant on presence-absence of the system but instead involves a multiplicity of factors.Pseudomonas aeruginosapossesses 3 distinct T6SSs and a set of more than 20 toxic effectors with diverse functions including disruption of cell wall integrity, degradation of nucleic acids or metabolic impairment. We generated a comprehensive collection of mutants with various degrees of T6SS activity and/or sensitivity to each individual T6SS toxin. By imaging whole mixed bacterial macrocolonies, we then investigated how theseP. aeruginosastrains gain a competitive edge in multiple attacker/prey combinations. We observed that the potency of single T6SS toxin varies significantly from one another as measured by monitoring the community structure, with some toxins acting better in synergy or requiring a higher payload. Remarkably the degree of intermixing between preys and attackers is also key to the competition outcome and is driven by the frequency of contact as well as the ability of the prey to move away from the attacker using type IV pili-dependent twitching motility. Finally, we implemented a computational model to better understand how changes in T6SS firing behaviours or cell-cell contacts lead to population level competitive advantages, thus providing conceptual insight applicable to all types of contact-based competition.
Regulation of pSYSA defense plasmid copy number inSynechocystisthrough RNase E and a highly transcribed asRNA
Authors: Kaltenbrunner Alena , Reimann Viktoria , Hoffmann Ute A. , Aoyagi Tomohiro , Sakata Minori , Nimura-Matsune Kaori , Watanabe Satoru , Steglich Claudia , Wilde Annegret , Hess Wolfgang R.
Published: December 2022

Synthetic biology approaches toward the development of cyanobacterial producer strains require the availability of appropriate sets of plasmid vectors. A factor for the industrial usefulness of such strains is their robustness against pathogens, such as bacteriophages infecting cyanobacteria. Therefore, it is of great interest to understand the native plasmid replication systems and the CRISPR-Cas based defense mechanisms already present in cyanobacteria. In the model cyanobacteriumSynechocystissp. PCC 6803, four large and three smaller plasmids exist. The ∼100 kb plasmid pSYSA is specialized in defense functions by encoding all three CRISPR-Cas systems and several toxin-antitoxin systems. The expression of genes located on pSYSA depends on the plasmid copy number in the cell. The pSYSA copy number is positively correlated with the expression level of the endoribonuclease E. As molecular basis for this correlation we identified the RNase E-mediated cleavage within the pSYSA-encodedssr7036transcript. Together with a cis-located abundant antisense RNA (asRNA1), this mechanism resembles the control of ColE1-type plasmid replication by two overlapping RNAs, RNA I and II. In the ColE1 mechanism, two non-coding RNAs interact, supported by the small protein Rop, which is encoded separately. In contrast, in pSYSA the similar-sized protein Ssr7036 is encoded within one of the interacting RNAs and it is this mRNA that likely primes pSYSA replication. Essential for plasmid replication is furthermore the downstream encoded protein Slr7037 featuring primase and helicase domains. Deletion ofslr7037led to the integration of pSYSA into the chromosome or the other large plasmid pSYSX. Moreover, the presence ofslr7037was required for successful replication of a pSYSA-derived vector in another model cyanobacterium,Synechococcus elongatusPCC 7942. Therefore, we annotated the protein encoded byslr7037as Cyanobacterial Rep protein A1 (CyRepA1). Our findings open new perspectives on the development of shuttle vectors for genetic engineering of cyanobacteria and of modulating the activity of the entire CRISPR-Cas apparatus inSynechocystissp. PCC 6803.
A putative design for electromagnetic activation of split proteins for molecular and cellular manipulation
Authors: Grady Connor J. , Schossau Jory , Ashbaugh Ryan C. , Pelled Galit , Gilad Assaf A.
Published: December 2022

The ability to manipulate cellular function using an external stimulus is a powerful strategy for studying complex biological phenomena. One approach to modulate the function of the cellular environment is split proteins. In this method, a biologically active protein or an enzyme is fragmented so that it reassembles only upon a specific stimulus. While there are many tools available to induce these systems, nature has provided other mechanisms that can be utilized to expand the split protein toolbox. Here we show a novel method for reconstituting split proteins using magnetic stimulation. We have found that the Electromagnetic Perceptive Gene (EPG) changes conformation due to magnetic fields stimulation. By fusing split fragments of a certain protein to both termini of the EPG, the fragments can be reassembled into a functional protein under magnetic stimulation due to conformational change. We show this effect with three separate split proteins; NanoLuc, APEX2, and Herpes Simplex Virus Type-1 Thymidine Kinase. Our results show for the first time, that reconstitution of split proteins can be achieved only with magnetic fields. We anticipate that this study will be a starting point for future magnetically inducible split protein designs for cellular perturbation and manipulation. With this technology, we can help to expand the toolbox of the split protein platform and allow better elucidation of complex biological systems.
Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies
Authors: Stamp Julian , DenAdel Alan , Weinreich Daniel , Crawford Lorin
Published: December 2022

Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this study, we present the “multivariate MArginal ePIstasis Test” (mvMAPIT) — a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detectmarginal epistasisor the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact — thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search-based methods. Our proposed mvMAPIT builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate mvMAPIT as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference andP-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized GWA studies. With simulations, we illustrate the benefits of mvMAPIT over univariate (or single-trait) epistatic mapping strategies. We also apply mvMAPIT framework to protein sequence data from two broadly neutralizing anti-influenza antibodies and approximately 2,000 heterogenous stock of mice from the Wellcome Trust Centre for Human Genetics. The mvMAPIT R package can be downloaded athttps://github.com/lcrawlab/mvMAPIT.
Ultra-long-range interactions between active regulatory elements
Authors: Friman Elias T. , Flyamer Ilya M. , Boyle Shelagh , Bickmore Wendy A.
Published: December 2022

Contacts between enhancers and promoters are thought to relate to their ability to activate transcription. Investigating mechanisms that drive such chromatin interactions is therefore important for understanding gene regulation. Here, we have determined contact frequencies between millions of pairs of cis-regulatory elements from chromosome conformation capture datasets and analysed a collection of hundreds of DNA-binding factors for binding at regions of enriched contacts. This analysis revealed enriched contacts at sites bound by many factors associated with active transcription. We show that active regulatory elements, independent of cohesin and polycomb, interact with each other across distances of 10s of megabases in vertebrate and invertebrate genomes and that interactions correlate and change with activity. However, these ultra-long-range interactions are not dependent on RNA polymerase II transcription or several transcription cofactors. We propose that long-range interactions between cis-regulatory elements are driven by three distinct mechanisms – cohesin-mediated loop extrusion, polycomb contacts, and association between active regions.
Differential sensing by theC. albicansGpr1 receptor results in morphogenesis, β-glucan masking and survival in macrophages
Authors: Van Genechten Wouter , Wijnants Stefanie , Vreys Jolien , Van Dijck Patrick
Published: December 2022

The human fungal pathogen,Candida albicans, is very proficient at several classical virulence factors such as morphogenesis, adhesion, biofilm formation and immune evasion through β-glucan masking. The protein kinase A (PKA) pathway is involved in both morphogenesis and β-glucan masking. Several signals converge onto the PKA pathway, but it contains only a single upstream G-protein coupled receptor, Gpr1. We identified specific residues within the N-terminal tail of Gpr1 that are required for methionine-induced morphogenesis through Tpk2. Furthermore, we observe that Gpr1-Gpa2 has an active role in exposing glucans. Even though Gpr1 is required for survival whenC. albicansis challenged with macrophages, specifically disrupting morphogenesis did not attenuate this survival. Additionally, constitutive β-glucan masking did not improveC. albicanssurvival rates in the macrophage assay. Taken together, this indicates that Gpr1 may regulate additional mechanisms, possibly through glutamine 461, which are crucial in a macrophage context.

Significance Statement

Candida albicansis a human fungal pathogen mostly present as a commensal in the gastrointestinal tract. It can rapidly adapt to its everchanging environment through continuous monitoring of extracellular signals. These extracellular signals include methionine and lactate which induce respectively morphogenesis and β-glucan masking through the G-protein coupled receptor, Gpr1. Through a mutagenic approach we different amino acids of the receptor sense methionine and/or lactate but we show that Gpr1 may have an additional ligand that affect its survival in macrophages.
Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas’s cat,Otocolobus manul
Authors: Flack Nicole , Drown Melissa , Walls Carrie , Pratte Jay , McLain Adam , Faulk Christopher
Published: December 2022

Pallas’s cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined withO. manul’s zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17,097 bp mitogenome forO. manul. The primary nuclear assembly had 56x sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score forCarnivora-specific genes. High genome collinearity withinFelidaepermitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; sixty-one differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance betweenFelinaenuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
Virulence Differences of Monkeypox Virus Clades 1, 2a and 2b.1 in a Small Animal Model
Authors: Americo Jeffrey L. , Earl Patricia L. , Moss Bernard
Published: December 2022

Human monkeypox, a disease with similarities to smallpox, is endemic in Africa where it has persisted as a zoonosis with limited human-to-human spread. Unexpectedly, the disease expanded globally in 2022 driven by human-to-human transmission outside of Africa. It is not yet known whether the latter is due solely to behavioral and environmental factors or whether the monkeypox virus is adapting to a new host. Genome sequencing has revealed differences between the current outbreak strains, classified as clade 2b, and the prior clade 2a and clade 1 viruses but whether these differences contribute to virulence or transmission has not been determined. We demonstrate that the wild-derived inbred CAST/EiJ mouse provides an exceptional animal model for investigating clade differences in monkeypox virus virulence and show that the order is clade 1 > clade 2a > clade 2b.1. The greatly reduced replication of the clade 2b.1 major outbreak strain in mice and absence of lethality at 100-times the lethal dose of a closely related clade 2a virus, despite similar multiplication in cell culture, suggest that clade 2b is evolving diminished virulence or adapting to other species.

SIGNIFICANCE

Three clades of monkeypox virus are recognized: clade 1 is present in the Congo Basin, causes 10% human mortality and is transmitted by rodents with little human-to-human spread; clade 2a exists in West Africa, has a low mortality and is also a zoonosis; clade 2b is currently spreading globally by human transmission. The genetic basis for differences in virulence and transmission have not been determined. A major roadblock is the need for a small animal model that can be studied under the stringent safety conditions required. Here we demonstrate that the three clades exhibit highly significant differences in CAST/EiJ mice in the order clade 1 > clade 2a > clade 2b, similar to the severity of clinical disease.
Crystal structure of a covalently linked Aurora-A–MYCN complex
Authors: Diebold Mathias , Schönemann Lars , Eilers Martin , Sotriffer Christoph , Schindelin Hermann
Published: December 2022

Formation of the Aurora-A–MYCN complex increases levels of the oncogenic transcription factor MYCN in neuroblastoma cells by abrogating its degradation through the ubiquitin proteasome system. While some small-molecule inhibitors of Aurora-A were shown to destabilize MYCN, clinical trials have not been satisfactory to date. MYCN itself is considered to be `undruggable' due to its large intrinsically disordered regions. Targeting the Aurora-A–MYCN complex rather than Aurora-A or MYCN alone will open new possibilities for drug development and screening campaigns. To overcome the challenges that a ternary system composed of Aurora-A, MYCN and a small molecule entails, a covalently cross-linked construct of the Aurora-A–MYCN complex was designed, expressed and characterized, thus enabling screening and design campaigns to identify selective binders.
Lean construction and resilience while coping with the COVID-19 pandemic: an analysis of construction companies in Brazil
Authors: Simeão Isaías , Ferreira Karine Araujo
Published: December 2022

Purpose

Despite the benefits provided by the implementation of the lean philosophy, the most recent research discusses whether the high degrees of efficiency obtained with the implementation this philosophy could contribute positively or negatively in current pandemic scenario. This study aims to analyze how resilient construction industry companies in Brazil were in the face of the COVID-19 pandemic, comparing the performance of construction companies with different implementation levels of lean construction.

Design/methodology/approach

Three case studies were carried out in construction companies in Brazil with different application levels of the lean philosophy.

Findings

Among the results obtained, greater resilience to face COVID-19 was verified in those with a higher implementation level of the lean philosophy. Additionally, it was found that the larger the size of the companies surveyed, the greater the level of implementation of the lean philosophy.

Research limitations/implications

Due to the state of pandemic, and the work carried out in the home office, contact with companies was restricted. In addition, few companies actually adopt the lean philosophy in the construction sector in Brazil. Most of companies use only a few lean construction tools in specific sectors. For the few others who actually implement the philosophy, the acceptance to participate in the research was low.

Originality/value

The lean construction is something very new and innovative for the construction sector in Brazil, and there is little evidence of its use. Few companies adopt the philosophy in the country, and many of them also did not experience such an impactful moment in their entire existence. Thus, the analysis of the relationship between lean construction and resilience in the civil construction sector in Brazil is something innovative.
A bibliometric analysis of IJQRM journal (2002–2022)
Authors: Singh Navjit , Gupta Akriti , Kapur Bharti
Published: December 2022

Purpose

The purpose of this study is to explore the trends in publications made to International Journal of Quality and Reliability Management (IJQRM) for time period ranging from 2002–2022. In this study authors performed bibliometric analysis on the publications extracted from Scopus database using citations, authors, keywords and bibliographic coupling methods. The analysis helped authors highlighting the achievements of the journal towards the development of field of “quality” and “reliability” management and explore future avenues to be researched upon in the domain.

Design/methodology/approach

In this paper outputs derived through VoS viewer and bibliographic data of Scopus were used to examine various tabular and pictorial aspects of the authors, sources, documents, countries and keywords analysis.

Findings

The analysis results revealed that International Journal of Quality and Reliability Management (IJQRM) has got incredible 33,344 citations since 2002 with average citation count per document at 22.69. Sohal A.S. from Monash University, Australia has topped the list of most influential authors in terms of citations per document (107.20 citations/doc) published with IJQRM. However, Antony J. with massive 39 publications in total with 2074 citations is the most prominent contributor for the journal. The author has gained 6% of the total journal citations. The contributions from India, United Kingdom (UK), United States of America (USA), Iran, Australia, Portugal, Brazil, Spain, Sweden, Malaysia and Saudi Arabia are more noteworthy.

Research limitations/implications

The study has implications for future researchers and journal editorial team to explore possibilities in tapping various uncovered and upcoming research areas related to the scope of journal. The findings of the study may prompt research initiatives linked to diverse fields in sync with changes happening across globe such as: Artificial Intelligence, Robotics, Data Science etc.

Originality/value

The study is an attempt to investigate the long standing heritage offered by IJQRM to the world of quality and reliability management. The authors tried to unearth some hidden facts about the IJQRM and attempted to showcase the past and explore future directions to the researchers and editorial team.
Collegiate social class and connectedness: class in a transitional period of life
Authors: Grabsch Dustin K. , Jennings-Rentz Alexander , Kunovich Robert M. , Hinduja Sakshi , Chinnam Dedeepya
Published: December 2022

Purpose

This research study set out to answer the following question: How does social class relate to social connectedness in college?

Design/methodology/approach

The authors operationalized a nonexperimental, cross-sectional and analytical study design to analyze 271 survey responses.

Findings

This study illustrates that discretionary income has the most dramatic practical significance on the social connectedness of undergraduate students at the research site. As the body of knowledge regarding effective measures of social class for collegians increases, institutions should consider more innovative measures like discretionary spending, perceived social class and others during this unique transitional period of life.

Originality/value

A widened perspective of social class in college could aid in supporting the university and college goals of student success and social well-being.
The global foreign direct investment network: evolution and influencing factors
Authors: Li Bing , Shi Zhihui , Guo Wei
Published: December 2022

Purpose

As foreign direct investment (FDI) plays an important role in economic globalization. This paper examines the structural features of the global FDI network based on FDI flows data and changes in the position of countries within the network.

Design/methodology/approach

In order to study the structural characteristics of the global FDI network and the status and changes of countries in the global FDI network, the authors build the investment network and apply the QAP (Quadratic Assignment Procedure) analysis to examine the evolutionary characteristics of the network and its influencing factors.

Findings

The global FDI network becomes more interconnected and has a clear “core-periphery” structure. The network connections and volumes have increased dramatically and most countries spread their assets across multiple countries, while only a handful of countries have concentrated investments. The topological structure of the global FDI network has changed noticeably, although this process has been slow and stable and countries in the core position have remained largely intact. The authors find that trade relations between countries, geographic distance and differences in economic size, income levels and institutional environments all have a significant impact on the global FDI network.

Research limitations/implications

Although we find some valuable results, some aspects need further investigation. For example, how a country uses the investment network to boost its economy and how the different industries in the investment network change over time. It is important to get the industry-level details to understand the impact of the global investment network from a government's perspective.

Practical implications

FDI affects the distribution of international capital and contributes to the development of the global economy. Therefore, it is important to study the characteristics of the global FDI network and its development patterns. With more understanding about the network as well as its evolutionary pattern, the government can possibly carry out some policies to promote direct investments as well as economic development.

Social implications

All countries should actively engage in international direct investments and strengthen their economic ties. At the same time, they can put more emphasis on inward or outward FDI based on their own level of economic development to better establish the circulation channel for domestic and international capital.

Originality/value

This paper examines foreign direct investments through the lens of a global network. In contrast to traditional bilateral studies, this paper focuses on the network structure and evolution, reflecting the dynamics of the entire direct investment system as well as the changing positions of participating countries.
Blockchain empowers supply chains: challenges, opportunities and prospects
Authors: Li Yongjian , Chen Ting
Published: December 2022

Purpose

The advantages of blockchain technology are being widely discussed by academics, the business community and government, because blockchain can promote data sharing, optimise business processes, reduce operation costs, improve collaborative efficiency and build credible systems. The supply chain is becoming a key area for the application of blockchain technology. However, few studies have discussed the effect of such emerging technologies on the supply chain in depth. Therefore, this paper aims to analyse how blockchain empowers supply chain and promotes supply chain management.

Design/methodology/approach

Based on a review of relevant literature and blockchain applications in practice, this paper analyses the development and research status of blockchain technologies. In addition, considering the different operational processes within the supply chain, the authors discuss the opportunities and challenges of blockchain technologies, such as the transparency of supply, intelligent manufacturing, the security of logistics, the platformisation of sales and the ecology of governance.

Findings

The authors find that information sharing, information traceability and trust establishment are the key categories of research achievements and applications of supply chain management. The central issues for blockchain researchers are the authenticity of transaction data, the traceability of long supply chains and the establishment of trust for all participants.

Originality/value

From the practical and theoretical perspectives, this paper shows the development of blockchain technologies to clarify the challenges, opportunities and prospects. This paper elucidates and facilitates the development of emerging interdisciplinary research and the practice of supply chain.
Talent designation as a mixed blessing: Short‐ and long‐term employee reactions to talent status
Authors: Tyskbo Daniel , Wikhamn Wajda
Published: December 2022

Talent management (TM) continues to attract considerable attention from both practitioners and academics. Existing research investigating employee reactions to being awarded talent status has not elucidated the processual nature of such reactions. This study extends TM research by providing a nuanced understanding of how employees react to talent designation over time and why. Specifically, it distinguishes between short‐ and long‐term reactions and uses the lenses of psychological contract (PC) theory and social identity theory (SIT) to unpack mechanisms underlying immediate positive, and delayed negative, employee reactions to talent designation. Results from qualitative analysis of interviews with talents in three organizations show how—as time elapsed and no identity‐relevant events occurred—perceptions of “talent emptiness” and “indeterminacy” developed. The study unfolds the complex interaction between SIT and PC (including breach and violation) to explain talents’ evolving reactions over time. As such, it contributes to TM literature by providing a nuanced understanding of the processes underlying employee reactions in exchanges involving socioemotional resources.
Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons
Authors: Flamio Richard , Swift Dominic G. , Portnoy David S. , Chojnacki Kimberly A. , DeLonay Aaron J. , Powell Jeffrey , Braaten Patrick J. , Heist Edward J.
Published: December 2022

Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon (Scaphirhynchus albus) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon (S. platorynchus) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site‐associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced‐representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.
Incidental diagnosis of pulmonary cryptococcosis by rebiopsy for epidermal growth factor receptor T790M mutation: A case report
Authors: Kobe Hiroshi , Yokoe Shinya , Ishida Tadashi
Published: December 2022

Cryptococcosis is an invasive fungal infection that can occur in cancer patients. A case of pulmonary cryptococcosis in a patient treated with erlotinib + ramucirumab for epidermal growth factor receptor (EGFR) L858R point mutation‐positive non‐small cell lung cancer is presented. During chemotherapy, a new pulmonary nodule was found and considered progressive disease. Examination of the biopsy specimen taken to identify EGFR T790M mutation incidentally led to the diagnosis of pulmonary cryptococcosis. Three months after taking fluconazole, chest computed tomography showed that the pulmonary nodule had shrunk. New pulmonary nodules during lung cancer treatment require careful attention, not only because of disease progression, but also because of the possibility of infection in an immunocompromised host.
Lipid emulsion for xenobiotic overdose: PRO
Authors: Fettiplace Michael R. , Weinberg Guy
Published: December 2022

Infusion of lipid emulsion for drug overdose arose as a treatment for local anaesthetic systemic toxicity (LAST) initially based on laboratory results in animal models with the subsequent support of favourable case reports. Following successful translation to the clinic, practitioners also incorporated lipid emulsion as a treatment for non‐local anaesthetic toxicities but without formal clinical trials. Recent clinical trials demonstrate a benefit of lipid emulsion in antipsychotic, pesticide, metoprolol and tramadol overdoses. Formal trials of lipid emulsion in LAST may never occur, but alternative analytic tools indicate strong support for its efficacy in this indication; for example, lipid emulsion has obviated the need for cardiopulmonary bypass in most cases of LAST. Herein, we describe the pre‐clinical support for lipid emulsion, evaluate the most recent clinical studies of lipid emulsion for toxicity, identify a possible dose‐based requirement for efficacy and discuss the limitations to uncontrolled studies in the field.
Burkitt lymphoma after solid‐organ transplant: Treatment and outcomes in the paediatric PTLD collaborative
Authors: Afify Zeinab , Orjuela‐Grimm Manuela , Smith Christine Moore , Dalal Mansi , Ford James B. , Pillai Pallavi , Robles Joanna M. , Reddy Sonika , McCormack Sarah , Ehrhardt Matthew J. , Ureda Tonya , Alperstein Warren , Edington Holly , Miller Tamara P. , Rubinstein Jeremy D. , Kavanaugh Madison , Bukowinski Andrew J. , Friehling Erika , Rivers Julie M. , Chisholm Karen M. , Marks Lianna J. , Mason Clinton C.
Published: December 2022

Burkitt lymphoma arising in paediatric post‐solid‐organ transplantation‐Burkitt lymphoma (PSOT‐BL) is a clinically aggressive malignancy and a rare form of post‐transplant lymphoproliferative disorder (PTLD). We evaluated 35 patients diagnosed with PSOT‐BL at 14 paediatric medical centres in the United States. Median age at organ transplantation was 2.0 years (range: 0.1–14) and age at PSOT‐BL diagnosis was 8.0 years (range: 1–17). All but one patient had late onset of PSOT‐BL (≥2 years post‐transplant), with a median interval from transplant to PSOT‐BL diagnosis of 4.0 years (range: 0.4–12). Heart (n = 18 [51.4%]) and liver (n = 13 [37.1%]) were the most frequently transplanted organs. No patients had loss of graft or treatment‐related mortality. A variety of treatment regimens were used, led by intensive Burkitt lymphoma‐specific French–American–British/Lymphomes Malins B (FAB/LMB), n = 13 (37.1%), and a low‐intensity regimen consisting of cyclophosphamide, prednisone and rituximab (CPR) n = 12 (34.3%). Median follow‐up was 6.7 years (range: 0.5–17). Three‐year event‐free and overall survival were 66.2% and 88.0%, respectively. Outcomes of PSOT‐BL patients receiving BL‐specific intensive regimens are comparable to reported BL outcomes in immunocompetent children. Multi‐institutional collaboration is feasible and provides the basis of prospective data collection to determine the optimal treatment regimen for PSOT‐BL.
Trajectories of cough without a cold in early childhood and associations with atopic diseases
Authors: Divaret‐Chauveau Amandine , Mauny Frederic , Hose Alexander , Depner Martin , Dalphin Marie‐Laure , Kaulek Vincent , Barnig Cindy , Schaub Bianca , Schmausser‐Hechfellner Elisabeth , Renz Harald , Riedler Josef , Pekkanen Juha , Karvonen Anne M. , Täubel Martin , Lauener Roger , Roduit Caroline , Vuitton Dominique Angèle , von Mutius Erika , Demoulin‐Alexikova Silvia ,   the PASTURE study group
Published: December 2022

Background

Although children can frequently experience a cough that affects their quality of life, few epidemiological studies have explored cough without a cold during childhood.

Objectives

The objective of the study was to describe the latent class trajectories of cough from one to 10 years old and analyse their association with wheezing, atopy and allergic diseases.

Methods

Questions about cough, wheeze and allergic diseases were asked at 1, 1.5, 2, 3, 4, 5, 6 and 10 years of age in the European prospective cohort of Protection against Allergy: STUdy in Rural Environment (PASTURE). Specific IgE assays were performed at 10 years of age. Questions regarding a cough without a cold were used to build a latent class model of cough over time.

Results

Among the 961 children included in the study, apart from the never/infrequent trajectory (59.9%), eight trajectories of cough without a cold were identified: five grouped acute transient classes (24.1%), moderate transient (6.8%), late persistent (4.8%) and early persistent (4.4%). Compared with the never/infrequent trajectory, the other trajectories were significantly associated with wheezing, asthma and allergic rhinitis. For asthma, the strongest association was with the early persistent trajectory (ORa = 31.00 [14.03–68.51]), which was inversely associated with farm environment (ORa = 0.39 [0.19–0.77]) and had a high prevalence of cough triggers and unremitting wheeze. Late and early persistent trajectories were also associated with food allergy. Atopic sensitization was only associated with the late persistent trajectory.

Conclusion

Late and early persistent coughs without a cold are positively associated with atopic respiratory diseases and food allergy. Children having recurrent cough without a cold with night cough and triggers would benefit from an asthma and allergy assessment. Growing up on a farm is associated with reduced early persistent cough.