bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stenotrophomonas maltophilianatural history and evolution in the airways of adults with cystic fibrosis
Authors: Izydorczyk Conrad , Waddell Barbara J. , Thornton Christina S. , Conly John M. , Rabin Harvey R. , Somayaji Ranjani , Surette Michael G. , Church Deirdre L. , Parkins Michael D. 
Published: March 2023

ABSTRACTStenotrophomonas maltophiliais an opportunistic pathogen infecting person with cystic fibrosis (pwCF) and portends a worse prognosis. Studies ofS. maltophiliainfection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution ofS. maltophiliain a large Canadian cohort of pwCF over a thirty-seven year period.S. maltophiliawas recovered at least once in 25.5% of the cohort. Yearly isolates from 74 pwCF (23%) were typed by pulsed-field gel electrophoresis, and shared pulsotypes underwent whole-genome sequencing. Most pwCF were infected by unique strains, but serial infections with different strains, and strains shared between patients, were observed. In chronic carriage, longer time periods between positive collection dates increased the likelihood that subsequent isolates were unrelated. Isolates from individual pwCF were largely clonal, with genetic diversity driven by gene content differences. Disproportionate progression of CF lung disease was not observed amongst those infected with multiple strains over time (versus a single) or amongst those with shared clones (versus strains only infecting one patient). We did not observe evidence of patient-to-patient transmission despite relatedness between isolates. Instead, genomic analyses suggested common, indirect sources as their origins. Sixteen multi-mutated genes were identified as having a potential role in adaptation ofS. maltophiliato CF, including in a regulator of an efflux pump and in an iron acquisition gene cluster. The information derived from a genomics-based understanding of the natural history ofS. maltophiliainfection within CF provides unique insight into its potential for in-host evolution.IMPORTANCEIn this largest and longest single center study ofS. maltophiliacausing infections in persons with cystic fibrosis, we concluded that patient-to-patient infection transmission had not occurred. We determined that infection by a newS. maltophiliastrain was more likely the longer the time between its recovery in sputum, suggesting infection by individual strains is generally short-lived. Amongst bacterial isolates belonging to the same clonal complex, isolates could be better differentiated by their gene content than mutations, suggesting gene gain/loss may contribute more to the genetic diversity of these strains than mutation. Infection by multiple strains, or a shared strain found in at least one other person, was not associated with progression to end-stage lung disease.
Impact of magnetite nanowires orientation on morphology and activity ofin vitrohippocampal neural networks
Authors: Cortés-Llanos Belén , Rauti Rossana , Ayuso-Sacido Ángel , Pérez Lucas , Ballerini Laura 
Published: March 2023

AbstractNanomaterials design, synthesis and characterization are ever-expanding approaches towards developing biodevices or neural interfaces to treat neurological diseases. The ability of nanomaterials features, to tune neuronal networks morphology or functionality is still under study. In this work, we unveil how, when interfacing mammalian brain cultured neurons, iron oxide nanowires (NWs) orientation affects neuronal and glial densities, and network activity. Iron oxide NWs were synthesized by electrodeposition, fixing the diameter to 100 nm and the length to 1 μm. Scanning electron microscopy, Raman and contact angle measurements were performed to characterize the NWs morphology, chemical composition and hydrophilicity. Hippocampal cultures were seeded on NWs devices and after 14 days the cell morphology was studied by immunocytochemistry and confocal microscopy. Live calcium imaging was performed to study neuronal activity. Using random (R-NWs) a higher neuronal and glial cell densities were obtained compared with the control and vertical (V-NWs), while using V-NWs more stellate glial cells were found. R-NWs produced a reduction in neuronal activity while V-NWs increased the neuronal network activity, possibly due to higher neuronal maturity and a lower number of GABAergic neurons, respectively. These results highlight the potential of NWs manipulations to design ad hoc regenerative interfaces.
Leptospiratranscriptome sequencing using long-read technology reveals unannotated transcripts and potential polyadenylation of mRNA molecules
Authors: Xu Ruijie , Prakoso Dhani , Salvador Liliana C. M. , Rajeev Sreekumari 
Published: March 2023

AbstractLeptospirosis caused by the spirochete bacteriaLeptospirais an emerging zoonosis that causes life-threatening disease in humans and animals. However, a detailed understanding ofLeptospira’sRNA profiles is limited. In this study, we sequenced and analyzed the transcriptome of multipleLeptospiraserovars using Oxford Nanopore Technologies’ direct cDNA and direct RNA sequencing methods. We identified several operon transcriptional units, novel RNA coding regions, and evidence of potential posttranscriptional polyadenylation in theLeptospiratranscriptome. Some coding regions of multiple RNA molecules that have not been previously annotated could be potential sRNA or ncRNA molecules that support gene expression regulation purposes inLeptospira. Many of the relative positions of these unannotated RNA coding regions were consistent in their neighboring coding regions across the reference genomes of two pathogenicLeptospiraanalyzed in this study. Besides, the majority of the unannotated coding regions and operon transcriptional units were not detected in the nonpathogenicLeptospira, suggesting potential virulence-related functions for these RNA molecules coding regions. Overall, our study confirms the utility of ONT’s sequencing in studying prokaryotic transcriptome profiles and offers a tool to improve our understanding of the structural composition of RNA molecules and prokaryotic polyadenylation. However, the findings from our study also warrant that the presence of homopolymers of adenine bases in the transcripts may interfere with the interpretation of bacterial transcriptome profiles. Carefully designed experiments are needed to unravel the role of the features described in this study inLeptospiravirulence and pathogenesis.Author SummaryLeptospirosis caused by the spirochete bacteria,Leptospira,is recognized as one of the most widespread zoonotic diseases. Leptospirosis is a neglected disease and has been estimated to cause over one million annual human clinical cases and over 60,000 deaths.Leptospiraare maintained in the renal tubules of asymptomatic animal reservoirs, and in contaminated environments, such as soil and water. Studying gene expression profiles is an important component of bacterial pathogenesis studies, and a number of methods are available to do it. Our study compared various transcriptome sequencing methods using one of the latest next generation sequencing tools (Oxford Nanopore Technologies) and evaluated the compositions of RNA in differentLeptospira’stranscriptomes. We identified many previously undescribed and potentially significant features within theLeptospiratranscriptome that may contribute to the virulence and pathogenesis ofLeptospira sp. Our findings lead to new opportunities for researchers to sequence prokaryotic RNA molecules and to unravel many regulatory mechanisms.
Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer
Authors: Hosseini Amir , Lindholm Håvard T. , Chen Raymond , Mehdipour Parinaz , Marhon Sajid A. , Ishak Charles A. , De Carvalho Daniel D. 
Published: March 2023

AbstractViral mimicry describes the immune response induced by endogenous stimuli such as dsRNA formed by endogenous retroelements. Activation of viral mimicry has the potential to kill cancer cells or augment anti-tumor immune response. Paradoxically, cancer cells frequently present a dysregulated epigenome, leading to increased expression of retroelements. We previously found that ADAR1 p150 upregulation is an adaptation mechanism to tolerate high retroelement-derived dsRNA levels, leading to a druggable dependency. Here, we systematically identified novel mechanisms of viral mimicry adaptation associated with cancer cell dependencies. We correlated the gene knockout sensitivity from the DepMap dataset and interferon stimulated gene (ISG) expression in the Cancer Cell Line Encyclopedia (CCLE) dataset of 1005 human cell lines and identified pathways such as RNA modification and nucleic acid metabolism. Among the top hits was the RNA decay protein XRN1 as an essential gene for the survival of a subset of cancer cell lines. XRN1-sensitive cancer cell lines have a high level of cytosolic dsRNA and high ISG expression. Furthermore, sensitivity to XRN1 knockout was mediated by MAVS and PKR activation, indicating that the cells die due to XRN1-dependent induction of viral mimicry. XRN1-resistant cell lines had low basal dsRNA levels, but became synthetically dependent on XRN1 upon treatment with viral mimicry inducing drugs such as 5-AZA-CdR or palbociclib. Finally, XRN1-dependency is partly independent of ADAR1 activity. These results confirm the potential for our ISG correlation analysis to discover novel regulators of viral mimicry and show that XRN1 activation is an adaptive mechanism to control high dsRNA stress induced by dysregulated retroelements in cancer cells and creates a dependency that can be explored for novel cancer therapies.
Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally-mixed coastal temperate habitat
Authors: Brunet Maéva , Duff Nolwen Le , Rigaut-Jalabert Fabienne , Romac Sarah , Barbeyron Tristan , Thomas François 
Published: March 2023

AbstractCoastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonization by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate thein situabundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally-mixed coastal habitat of the Western English Channel. We show that members of the genusZobelliaare a stable, low-abundance component of healthy macroalgal microbiota and can also colonize particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables.Zobelliacan become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimatedin situgrowth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling.Originality-significance statementGlycan-degrading bacteria play a crucial role in marine habitats to remineralize organic carbon sequestered in algal biomass. Yet, resolving what factors regulate thein situabundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we investigate the seasonal dynamics of abundance and activity of an environmentally relevant glycan-degrading bacterial genus in two constrasted compartments of the same coastal habitat, i.e. the surface of diverse macroalgae and the water column. These results provide insights into the recurring temporal patterns and environmental constraints driving natural populations of alga-degrading bacteria that influence ocean carbon cycling.
Bacterial defences interact synergistically by disrupting phage cooperation
Authors: Maestri Alice , Pursey Elizabeth , Chong Charlotte , Pons Benoit J. , Gandon Sylvain , Custodio Rafael , Chisnall Matthew , Grasso Anita , Paterson Steve , Baker Kate , Houte Stineke van , Chevallereau Anne , Westra Edze R. 
Published: March 2023

SummaryThe constant arms race between bacteria and their phages has resulted in a large diversity of bacterial defence systems1,2, with many bacteria carrying several systems3,4. In response, phages often carry counter-defence genes5–9. If and how bacterial defence mechanisms interact to protect against phages with counter-defence genes remains unclear. Here, we report the existence of a novel defence system, coined MADS (Methylation Associated Defence System), which is located in a strongly conserved genomic defence hotspot inPseudomonas aeruginosaand distributed across Gram-positive and Gram-negative bacteria. We find that the natural co-existence of MADS and a Type IE CRISPR-Cas adaptive immune system in the genome ofP. aeruginosaSMC4386 provides synergistic levels of protection against phage DMS3, which carries an anti-CRISPR (acr) gene. Previous work has demonstrated that Acr-phages need to cooperate to overcome CRISPR immunity, with a first sacrificial phage causing host immunosuppression to enable successful secondary phage infections10,11. Modelling and experiments show that the co-existence of MADS and CRISPR-Cas provides strong and durable protection against Acr-phages by disrupting their cooperation and limiting the spread of mutants that overcome MADS. These data reveal that combining bacterial defences can robustly neutralise phage with counter-defence genes, even if each defence on its own can be readily by-passed, which is key to understanding how selection acts on defence combinations and their coevolutionary consequences.
Natural constraints explain working memory capacity limitations in sensory-cognitive models
Authors: Xie Yudi , Duan Yu , Cheng Aohua , Jiang Pengcen , Cueva Christopher J. , Yang Guangyu Robert 
Published: March 2023

AbstractThe limited capacity of the brain to retain information in working memory has been well-known and studied for decades, yet the root of this limitation remains unclear. Here we built sensory-cognitive neural network models of working memory that perform tasks using raw visual stimuli. Contrary to intuitions that working memory capacity limitation stems from memory or cognitive constraints, we found that pre-training the sensory region of our models with natural images imposes sufficient constraints on models to exhibit a wide range of human-like behaviors in visual working memory tasks designed to probe capacity. Examining the neural mechanisms in our model reveals that capacity limitation mainly arises in a bottom-up manner. Our models offer a principled and functionally grounded explanation for the working memory capacity limitation without parameter fitting to behavioral data or much hyperparameter tuning. This work highlights the importance of developing models with realistic sensory processing even when investigating memory and other high-level cognitive phenomena.
Exploring the effects of director network on open innovation: the moderating role of CEO short-sightedness
Authors: Xu Chaohui , Xu Yingjie 
Published: March 2023

PurposeThis paper aims to explore the effects of director network on open innovation. As an informal institutional arrangement, the director network is an important source for the enterprise to obtain external information, which provide resource basis for open innovation. Chief Executive Officer (CEO) as the top of management team could make short-sighted decisions for personal interests; this paper also investigates the moderating role of CEO short-sightedness between director network and open innovation.Design/methodology/approachThis paper takes 4,102 Chinese listed companies from 2007 to 2020 as the research sample. By introducing network centrality and structural hole to measure director network and using data mining to extract key words related to CEO short-sightedness from annual reports, this paper constructs several multiple linear regression models to analyze the impact of director network on open innovation and the moderating role of CEO short-sightedness.FindingsThe analysis finds that director network can facilitate corporate open innovation. Enterprises can acquire more external resources in high centrality and structural hole of director network and promote ability for corporate open innovation. The relationship between director network and open innovation is negatively moderated by CEO short-sightedness. When the level of corporate governance and analyst attention is high, the negative effect of CEO short-sightedness on the innovation effect of directors’ networks is suppressed.Originality/valueThis is the first empirical paper to investigate the promotion effect of director network on open innovation as well as the negative moderating role of CEO short-sightedness. The findings bring new perspectives to the open innovation and enlightenments for practical activities from social relationship aspect.
Impact of circular economy network building: resilience strategy to climate action
Authors: Lin Chun-Chien , Chang Yu-Chen 
Published: March 2023

Purpose
This study aims to examine how external and internal conditions drive the impact of circular economy mechanism by decomposing into three policy networks in terms of reduce, reuse and recycle, to better understand the contingency model of climate change and effect of firm size on subsequent performance.

Design/methodology/approach
Drawing on circular economy network and resource-based view (RBV)-network-resilience strategy framework, a pooled longitudinal cross-sectional data model is developed using a sample of 4,050 Taiwanese manufacturing multinational corporations (MNCs) making foreign direct investment between 2013 and 2018. Structural equation modeling analysis is used to comprehensively examine and investigate each circular economy policy network in the context of climate change and firm size. Post hoc multigroup analysis (MGA) is also conducted.

Findings
MGA shows that the reduce policy network is positively and negatively related to manufacturing know-how and production size, respectively. The impact of reuse policy network can enhance the competence of large firms. The recycle policy network is more prominent in terms of competence enhancement of climate change.

Practical implications
MNCs are seeking to build circular economy policy networks to a greater extent, given climate change pressure and guidelines.

Originality/value
This study adds to the circular economy and RBV-network-related literature on climate change and interactions to enhance performance, echoing the recent call on the sustainability of the circular economy of MNCs.
Evaluation and adoption of artificial intelligence in the retail industry
Authors: Fu Hsin-Pin , Chang Tien-Hsiang , Lin Sheng-Wei , Teng Ying-Hua , Huang Ying-Zi 
Published: March 2023

PurposeThe introduction of artificial intelligence (AI) technology has had a substantial influence on the retail industry. However, AI adoption entails considerable responsibilities and risks for senior managers. In this study, the authors developed an evaluation and selection mechanism for successful AI technology adoption in the retail industry. The multifaceted measurement and identification of critical factors (CFs) can enable retailers to adopt AI technology effectively and maintain a sustainable competitive advantage.Design/methodology/approachThe evaluation and adoption of organisational AI technology involve multifaceted decision-making for management. Therefore, the authors used the analytic network process to develop an AI evaluation framework for calculating the weight and importance of each consideration. An expert questionnaire survey was distributed to senior retail managers and 17 valid responses were obtained. Finally, the Vlse Kriterijumska Optimizacija Kompromisno Resenje (VIKOR) method was used to identify CFs for AI adoption.FindingsThe results revealed five CFs for AI adoption in the retail industry. The findings indicated that after AI adoption, top retail management is most concerned with factors pertaining to business performance and minor concerned about the internal system's functional efficiency. Retailers pay more attention to technology and organisation context, which are matters under the retailers' control, than to external uncontrollable environmental factors.Originality/valueThe authors developed an evaluation framework and identified CFs for AI technology adoption in the retail industry. In terms of practical application, the results of this study can help AI service providers understand the CFs of retailers when adopting AI. Moreover, retailers can use the proposed multifaceted evaluation framework to guide their adoption of AI technology.
Asymmetric effects of climate variability on food security in Morocco: evidence from the nonlinear ARDL model
Authors: Soumbara Sid'Ahmed , El Ghini Ahmed 
Published: March 2023

PurposeThis study aims to examine the asymmetric effects of average temperature (TP) and rainfall (RF) on the Moroccan food security, measured by the food production index (FPI), using annual data from 1961 to 2020.Design/methodology/approachThe study uses the Climate Change and Food Security Framework (CCFS) developed by the Food and Agriculture Organization (FAO) and employs the nonlinear auto-regressive distributed lag (NARDL) model and various econometric techniques to show the effects of climate variability in the short and long-term. It also examines if the impacts on Moroccan food security are asymmetric by analyzing the positive and negative partial sums of mean temperature and rainfall.FindingsThe study shows that RF has a long-term relationship with FPI, with increased RF leading to increased FPI and decreased RF leading to decreased FPI. FPI responds more strongly and persistently to a positive shock in RF than to an adverse shock. The study also identifies an asymmetric relationship between FPI and RF, with increased TP enhancing food output in the long run and a decrease reducing food production in the long run.Research limitations/implicationsThe current study could have some limitations. For instance, there are several other non-climate factors that might potentially impact food security. In particular, CO2 emissions which from the literature is a key variable that represent climate change impact on food security, was not included. The present research has not included those factors mainly because adding more variables to the model reduces the degree of freedom available to estimate the parameters, resulting in inaccurate results.Originality/valueThis paper contributes to the food security literature by utilizing the latest asymmetry methodology to decompose climate changes into their positive and negative trends and examining the contrasting impacts food production.