bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interhemispheric CA1 projections support spatial cognition and are affected in a mouse model of the 22q11.2 deletion syndrome
Authors: de León Reyes Noelia S. , Bortolozzo-Gleich Maria Helena , Nomura Yuki , García Fregola Cristina , Nieto Marta , Gogos Joseph A. , Leroy Félix 
Published: September 2024

AbstractUntangling the hippocampus connectivity is critical for understanding the mechanisms supporting learning and memory. However, the function of interhemispheric connections between hippocampal formations is still poorly understood. So far, two major hippocampal commissural projections have been characterized in rodents. Mossy cells from the hilus of the dentate gyrus project to the inner molecular layer of the contralateral dentate gyrus and CA3 and CA2 pyramidal neuron axonal collaterals to contralateral CA3, CA2 and CA1. In contrary, little is known about commissural projection from the CA1 region. Here, we show that CA1 pyramidal neurons from the dorsal hippocampus project to contralateral dorsal CA1 as well as dorsal subiculum. We further demonstrate that the interhemispheric projection from CA1 to dorsal subiculum supports spatial memory and spatial working memory in WT mice, two cognitive functions impaired in male mice from theDf16(A)+/-model of 22q11.2 deletion syndrome (22q11.2DS) associated with schizophrenia. Investigation of the CA1 interhemispheric projections inDf16(A)+/-mice revealed that these projections are disrupted with male mutants showing stronger anatomical defects compared to females. Overall, our results characterize a novel interhemispheric projection from dCA1 to dorsal subiculum and suggest that dysregulation of this projection may contribute to the cognitive deficits associated with the 22q11.2DS.
Characterization of tumor heterogeneity through segmentation-free representation learning
Authors: Tan Jimin , Le Hortense , Deng Jiehui , Liu Yingzhuo , Hao Yuan , Hollenberg Michelle , Liu Wenke , Wang Joshua M. , Xia Bo , Ramaswami Sitharam , Mezzano Valeria , Loomis Cynthia , Murrell Nina , Moreira Andre L. , Cho Kyunghyun , Pass Harvey , Wong Kwok-Kin , Ban Yi , Neel Benjamin G. , Tsirigos Aristotelis , Fenyö David 
Published: September 2024

AbstractThe interaction between tumors and their microenvironment is complex and heterogeneous. Recent developments in high-dimensional multiplexed imaging have revealed the spatial organization of tumor tissues at the molecular level. However, the discovery and thorough characterization of the tumor microenvironment (TME) remains challenging due to the scale and complexity of the images. Here, we propose a self-supervised representation learning framework, CANVAS, that enables discovery of novel types of TMEs. CANVAS is a vision transformer that directly takes high-dimensional multiplexed images and is trained using self-supervised masked image modeling. In contrast to traditional spatial analysis approaches which rely on cell segmentations, CANVAS is segmentation-free, utilizes pixel-level information, and retains local morphology and biomarker distribution information. This approach allows the model to distinguish subtle morphological differences, leading to precise separation and characterization of distinct TME signatures. We applied CANVAS to a lung tumor dataset and identified and validated a monocytic signature that is associated with poor prognosis.
PIP2 promotes the incorporation of CD43, PSGL-1 and CD44 into nascent HIV-1 particles
Authors: Cardoso Ricardo de Souza , Murakami Tomoyuki , Jacobovitz Binyamin , Veatch Sarah L. , Ono Akira 
Published: September 2024

AbstractDeterminants regulating sorting of host transmembrane proteins at sites of enveloped virus assembly on the plasma membrane (PM) remain poorly understood. Here, we demonstrate for the first time that PM acidic phospholipid PIP2 regulates such sorting into an enveloped virus, HIV-1. Incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles is known to have profound effects on viral spread; however, the mechanisms promoting their incorporation were unknown. We found that depletion of cellular PIP2 blocks the incorporation of CD43, PSGL-1, and CD44 into HIV-1 particles. Expansion microscopy revealed that PIP2 depletion diminishes nanoscale co-clustering between viral structural protein Gag and the three transmembrane proteins at PM and that Gag induces PIP2 enrichment around itself. CD43, PSGL-1, and CD44 also increased local PIP2 density, revealing their PIP2 affinity. Altogether, these results support a new mechanism where local enrichment of an acidic phospholipid drives co-clustering between viral structural and cellular transmembrane proteins, thereby modulating the content, and hence the fate, of progeny virus particles.
SARS-CoV-2 Nsp15 antagonizes the cGAS-STING-mediated antiviral innate immune responses
Authors: Chiu Hsin-Ping , Yeo Yao Yu , Lai Tsoi Ying , Hung Chuan-Tien , Kowdle Shreyas , Haas Griffin D , Jiang Sizun , Sun Weina , Lee Benhur 
Published: September 2024

AbstractCoronavirus (CoV) Nsp15 is a viral endoribonuclease (EndoU) with a preference for uridine residues. CoV Nsp15 is an innate immune antagonist which prevents dsRNA sensor recognition and stress granule formation by targeting viral and host RNAs. SARS-CoV-2 restricts and delays the host antiviral innate immune responses through multiple viral proteins, but the role of SARS-CoV-2 Nsp15 in innate immune evasion is not completely understood. Here, we generate an EndoU activity knockout rSARS-CoV-2Nsp15-H234Ato elucidate the biological functions of Nsp15. Relative to wild-type rSARS-CoV-2, replication of rSARS-CoV-2Nsp15-H234Awas significantly decreased in IFN-responsive A549-ACE2 cells but not in its STAT1 knockout counterpart. Transcriptomic analysis revealed upregulation of innate immune response genes in cells infected with rSARS-CoV-2Nsp15-H234Arelative to wild-type virus, including cGAS-STING, cytosolic DNA sensors activated by both DNA and RNA viruses. Treatment with STING inhibitors H-151 and SN-011 rescued the attenuated phenotype of rSARS-CoV-2Nsp15-H234A. SARS-CoV-2 Nsp15 inhibited cGAS-STING-mediated IFN-β promoter and NF-κB reporter activity, as well as facilitated the replication of EV-D68 and NDV by diminishing cGAS and STING expression and downstream innate immune responses. Notably, the decline in cGAS and STING was also apparent during SARS-CoV-2 infection. The EndoU activity was essential for SARS-CoV-2 Nsp15-mediated cGAS and STING downregulation, but not all HCoV Nsp15 share the consistent substrate selectivity. In the hamster model, rSARS-CoV-2Nsp15-H234Areplicated to lower titers in the nasal turbinates and lungs and induced higher innate immune responses. Collectively, our findings exhibit that SARS-CoV-2 Nsp15 serves as a host innate immune antagonist by targeting host cGAS and STING.Significance statementHost innate immune system serves as the primary defense against pathogens, including SARS-CoV-2. Co-evolving with the hosts, viruses develop multiple approaches to escape the host surveillance. SARS-CoV-2 silences and dysregulates innate immune responses, and the chaos of antiviral IFN responses highly correlates to COVID-19 disease severity. Nsp15 is a conventional innate immune antagonist across coronaviruses, but the biological impact about SARS-CoV-2 Nsp15 is still unclear. Here, we provide a novel insight that SARS-CoV-2 Nsp15 hampers the expression of innate immune regulator – cGAS and STING via its endoribonuclease activity, then further ameliorates virus replication.
A genome assembly and annotation for the Australian alpine skinkBassiana duperreyiusing long-read technologies
Authors: Hanrahan Benjamin J. , Alreja Kirat , Reis Andre L. M. , Chang J King , Dissanayake Duminda S.B. , Edwards Richard J. , Bertozzi Terry , Hammond Jillian M. , O’Meally Denis , Deveson Ira W. , Georges Arthur , Waters Paul , Patel Hardip R. 
Published: September 2024

AbstractThe eastern three-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southwest of the continent including Tasmania. It is an oviparous species that is distinctive because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of aBassiana duperreyiXY male individual, constructed using a combination of PacBio HiFi and ONT long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mbp, N90 of 26 Mbp, 200 gaps and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n=11>1 Mbp) were identified using Y-specific contigs generated by genome subtraction. We identified two novel alpha-satellite repeats of 187 bp and 199 bp in the putative centromeres that did not form higher order repeats. The genome assembly exceeds the standard recommended by the Earth Biogenome Project; 0.02% false expansions, 99.63% kmer completeness, 94.66% complete single copy BUSCO genes and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. TheB. duperreyigenome assembly has one of the highest completeness levels for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity, and for other comparative genomics studies of the Scincidae.Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Scincidae; Lygosominae; Eugongylini;Bassiana(=Acritoscincus);Bassiana duperreyi(Gray, 1838) (NCBI: txid316450).
Nanomotion technology for testing azithromycin susceptibility ofSalmonella enterica
Authors: Hinnu Mariliis , Mets Toomas , Kerkez Ivana , Putrinš Marta , Kaldalu Niilo , Cathomen Gino , Verge Marta Pla , Cichocka Danuta , Sturm Alexander , Tenson Tanel ,   ERADIAMR consortium
Published: September 2024

ABSTRACTAzithromycin is used to treat invasive salmonellosis, despite conflicting effective concentrationsin vitroandin vivo. Resistance ofSalmonella entericato azithromycin is increasing. We demonstrate that nanomotion technology can be used for rapid phenotypic testing ofSalmonella’s susceptibility to azithromycin. Nanomotion changes under various culture conditions correlated with susceptibility measured by MIC determination, CFU counting, and fluorescent reporter-based estimates of intrabacterial azithromycin accumulation.
Motor learning is regulated by GDNF levels in postnatal cerebellar Purkinje cells
Authors: Nagaeva Elina , Turconi Giorgio , Mätlik Kärt , Segerstråle Mikael , Olfat Soophie , Iivanainen Vilma , Taira Tomi , Andressoo Jaan-Olle 
Published: September 2024

ABSTRACTPurkinje cells, the sole output neurons of the cerebellar cortex, are crucial for cerebellum-dependent motor learning. Previously we demonstrated that a ubiquitous 2-3-fold increase of endogenous glial cell line-derived neurotrophic factor (GDNF) improves motor learning. However, GDNF impacts many organ systems and cell types throughout the body leaving the underlying mechanism elusive. Here, we utilize an innovative conditional GDNF Hypermorphic mouse model to show that a 2-fold increase in endogenous GDNF specifically in postnatal Purkinje cells (PCs) is sufficient to enhance motor learning in adult animals. We demonstrate that improved motor learning is associated with increased glutamatergic input to PCs and elevated spontaneous firing rate of these cells, opposite to cerebellar ataxia where reduction in motor function and learning associates with decreased spontaneous activity of PCs. Notably, the GDNF expression levels variation range studied in our mouse model’s cerebellum falls within the normal range of variation observed in healthy human cerebellums. Our findings uncover a molecular pathway and a specific cell type that regulate motor learning, potentially explaining some individual differences in human motor skill acquisition.
Identifying barriers in constructing green buildings in Oman: a study on project contractors’ experience
Authors: Zainul Abidin Nazirah , Powmya Ayishathul 
Published: September 2024

PurposeOman commitment for Sustainable Development Goals 2030 pushes green building at the forefront of construction industry. However, its green building progress is slower than other Gulf Cooperation Council countries, and only a handful of local contractors have been involved in green project development. Understanding the barriers to green project delivery will open avenues for better project planning and preparation. This research aims to identify the barriers experienced by the contractors when constructing green buildings in Oman.Design/methodology/approachQualitative research, via a semi-structured interview process, explores the barriers experienced by 14 contractors when constructing Leadership in Energy and Environmental Design (LEED) green building projects in Oman. Using NVivo 12 software, thematic analysis was conducted through the generation of coding and themes which enable the identification of the relevant barriers.FindingsThe research uncovered 10 barriers and grouped them into five categories. The five categories are as follows: (1) insufficient skills development, (2) lack of government support and regulatory adjustment, (3) limitation in materials procurement, (4) documentation and coordination limitation and (5) difficulty in green rating compliance.Originality/valueThe research identified 10 barriers of constructing green buildings in Oman. These barriers gravitated on 4 issues: knowledge and competency, green rating requirements, government involvement and materials procurement. It streamlined clusters of the potential research area for more effective green building action plans in the future. Two barriers are deemed uniquely applied to Oman, namely “lack of needed regulatory adjustment” and “absence of local rating tools”. This insight can serve as a valuable steppingstone to push more green buildings for the country.
Unveiling the inhibitors to CPS adoption in freight logistics: a TOE-based perspective
Authors: Rawat Umabharati , Anbanandam Ramesh 
Published: September 2024

PurposeThe digital evolution of production and logistics systems requires seamless integration of various functions. Cyber-physical systems (CPS) can streamline operations, reduce costs and optimise freight transport dynamics. Therefore, CPS adoption is essential to transform existing logistics infrastructure by connecting logistical equipment to cyberspace. This research addresses the critical issue of low CPS adoption in logistics. By analysing the barriers, the study proposes effective strategies to increase CPS integration significantly.Design/methodology/approachThis study used the technology-organisation-environment (TOE) framework and identified 18 barriers to CPS adoption in freight logistics. The barriers were then analysed using the fuzzy data-driven multi-criteria decision-making (MCDM) method, i.e. fuzzy-based decision-making trial and evaluation laboratory (Fuzzy-DEMATEL).FindingsThe computational analysis of the proposed framework shows that “the complexity of CPS and lagged data-driven logistics infrastructure” (T1) is a major technological inhibitor to CPS adoption. The “high cost of CPS technology” (O8) and a “lack of top management support” (O3) are the top causal inhibitors at the organisational level. “Lack of data governance and regulatory framework” (E2) is the main environmental inhibitor.Practical implicationsThe causal mapping of the TOE-based barriers helps policymakers and logisticians to develop strategies or follow recommended adoption strategies to improve CPS adoption in logistics.Originality/valueThis study is a pioneering effort to unveil the adoption barriers of CPS in the freight logistics industry and suggest strategies for fostering adoption. This research could provide valuable insights for logistics organisations to support CPS-driven logistics modernisation.
A comprehensive review on survivor syndrome in the workplace
Authors: George Tijo , Maheshwari Bhawana 
Published: September 2024

PurposeThis study explores the concept of “workplace survivor syndrome” (WSS) using bibliometric analysis and literature review, thereby identifying the avenues for future research in business management.Design/methodology/approachThe study adopted a methodological combination of bibliometric analysis and literature review. The methodological order is as follows: using the Scopus database and identifying 118 articles from ABDC listed journals, performance analysis by VOS viewer (citation analysis), science mapping analysis by Biblioshiny (visualisation and graphical presentation), and finally, the content analysis of the best 40 articles with a minimum of 50 citations and without any year restriction.FindingsThe bibliometric analysis reveals the most influential authors, articles, journals, countries, publication trends, impactful articles, and impactful authors of workplace survivor syndrome research, along with popular keywords used in this area. The content analysis identified three themes: emotional, cognitive, and behavioural syndrome. The content analysis reported the central mechanism adopted in 40 articles, including theories, methodologies, variables, sample size, etc. Additionally, the study explored the positive reviews on WSS.Research limitations/implicationsThe study considered only the articles from the ABDC journal quality list for the review.Originality/valueThe article is persuasively the first research to provide the intellectual structure and comprehensive bibliometric analysis of workplace survivor syndrome.
Construction and application of a novel grey relational analysis model considering factor coupling relationship
Authors: Hu Aqin , Xie Naiming 
Published: September 2024

PurposeThe purpose of this paper is to explore a new grey relational analysis model to measure the coupling relationship between the indicators for the water environment status assessment. Meanwhile, the model deals with the problem that the changing of indicator order may result in the changing of the degree of grey relation.Design/methodology/approachThe binary index submatrix of the sample matrix is given first. Then the product of the matrix and its own transpose is used to measure the characteristics of the index and the coupling relationship between the indicators. Thirdly, the grey relational coefficient is defined based on the matrix norm, and a grey coupling relational analysis model is proposed.FindingsThe paper provides a novel grey relational analysis model based on the norm of matrix. The properties, normalization, symmetry, relational order invariance to the multiplicative, are studied. The paper also shows that the model performs very well on the water environment status assessment in the eight cities along the Yangtze River.Originality/valueThe model in this paper has supplemented and improved the grey relational analysis theory for panel data.
Investigating supply chain resilience in digital car sharing enterprises: a case study from Turkey
Authors: Karadayi-Usta Saliha , Kadaifci Cigdem 
Published: September 2024

PurposeThe purpose of this study is to extract factors enabling the digital car sharing enterprises' supply chain resilience (SCR), to interpret different factor prioritizations in terms of industry representatives’ assessments and specialties, and to discuss the results by applying and comparing different ranking techniques.Design/methodology/approachTo achieve the purpose, the factors were identified via an in-depth systematic literature review, and next, these factors were examined by industry representatives to gather the decision matrices, then analytic hierarchy process (AHP) and measuring attractiveness by a categorical based evaluation technique (MACBETH) were applied separately to model the decision problem, and finally the findings were interpreted with different participants’ perspectives.FindingsThe findings revealed that the AHP and MACBETH provide nearly identical rankings in terms of main factors by implying the significance of the triple bottom line of sustainability. Therefore, the economic, social, and environmental dimensions of sustainability should be accomplished to obtain a resilient digital car sharing enterprise supply chain. In addition, readiness and agility are the other important factors affecting the enterprises’ resilience, and finally, although digitalization seemed to be the least important one, its sub-factor emerged at the top of the ranking list.Originality/valueUp to the authors’ knowledge, this is the first study in the literature that focuses on the SCR of car sharing companies, a particular type of digital enterprise, and uses AHP and MACBETH to examine the important factors that might affect the SCR of these companies. Practitioners should take the findings of both methods into account when evaluating the results and determine the short- and long-term strategies accordingly.
The influence of foreignness on CEO pay
Authors: Rivas Jose Luis , Lopez-Iturriaga Felix , Semadeni Mathew 
Published: September 2024

Purpose
This study aims to explore the relationship between foreignness and CEO pay.

Design/methodology/approach
This study combines cross-sectional and time series observations analyzed with panel data methodology in a sample of 59 firms listed in the Spanish IBEX-35 index between 2006 and 2020.

Findings
International ownership influences CEO underpayment and foreign sales influence CEO overpayment.

Practical implications
CEO pay is susceptible to being influenced by foreign non-American variables. An appropriate understanding of these factors can contribute to discussing policies that balance the level of CEO payment in large public firms.

Originality/value
Research on internationalization and CEO pay is scarce. A handful of studies confirm the link between Americanization and executive compensation in Europe. However, the authors still do not know if the level of CEO pay is influenced by non-American exposure. To do this, the authors test the effect of firm – ownership, sales, board – and individual – CEO – exposure to international, non-US environments on the level of over/underpayment of CEOs in a sample of Spanish firms.