bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders
Authors: Chiocchio Andrea , de Rysky Erica , Carere Claudio , Nascetti Giuseppe , Bisconti Roberta , Canestrelli Daniele
Published: December 2024

Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances having been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander
Salamandra salamandra
in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a ‘slow-thorough’ dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.
Meira qingyuanensis sp. nov., an anamorphic yeast species isolated from plant leaves
Authors: Cai Dan-Yang , Liu Shan , Hui Feng-Li
Published: December 2024

Two yeast strains, NYNU 224191 and NYNU 22411, were isolated from plant leaves of Cyclobalanopsis jenseniana and Schisandra sp. harvested from Qingyuan Mountain, Quanzhou City, Fujian Province, southeast China. Molecular phylogenetic analyses demonstrated that these two strains represent a novel species in the genus Meira. They are more closely related to M. marina, M. nashicola, M. plantarum and M. pileae than other Meira species based on phylogenetic analysis of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit (LSU) rRNA gene. The novel species differed from its closest relatives, M. marina, M. nashicola, M. plantarum and M. pileae, by 1.8–2% sequence divergence (11–12 substitutions and 1–2 gaps) in the D1/D2 domain and over 6.7% sequence divergence (40–60 substitutions and 53–77 gaps) in the ITS region, respectively. We propose the name Meira qingyuanensis sp. nov. (Holotype CICC 33567; Mycobank MB 855328) for the new species, which differs phenotypically from M. marina, M. plantarum and M. pileae in its ability to assimilate methyl-α-d-glucoside and the inability to assimilate salicin, and from M. nashicola in its ability to assimilate nitrate and nitrite and grow at 30 °C.
SOX2-induced IL1α-mediated immune suppression drives epithelial dysplasia malignant transformation
Authors: Taner Hülya F. , Gong Wang , Fitzsimonds Zackary R. , Li Zaiye , Wu Yuesong , He Yumin , Okuyama Kohei , Cheng Wanqing , Kuczura Jung , Rajesh Sashider , Manousidaki Andriana , Feng Shuo , Lee Miki , Nör Felipe , Lanzel Emily , Demehri Shadmehr , Polverini Peter J. , Nör Jacques E. , Wang Thomas D. , Que Jianwen , Wen Haitao , Xie Yuying , Moon James J. , Lei Yu Leo
Published: December 2024

Squamous cell carcinomas (SCC) are often preceded by potentially malignant precursor lesions, most of which remain benign. The terminal exhaustion phenotypes of effector T-cells and the accumulation of myeloid-derived suppressor cells (MDSC) have been thoroughly characterized in established SCC. However, it is unclear what precancerous lesions harbor a bona fide high risk for malignant transformation and how precancerous epithelial dysplasia drives the immune system to the point of no return. Here we show that expression of SRY-box transcription factor 2 (SOX2) in precancerous lesions imparts an irreversible risk that recruits suppressive myeloid cells by promoting the release of CCL2. We developed a unique genetically engineered mouse model (GEMM) to recapitulate the malignant transformation of epithelial dysplasia to SCC in the oral mucosa with high histologic and phenotypic fidelity. Using a combination of longitudinal human specimens and the Sox2-GEMM, we found that the myeloid cells in precancerous epithelial dysplasia exhibit a distinctive dichotomous profile featuring high levels of IL-1α-SLC2A1 and low levels of type-I interferon (IFN-I) signatures, which occurs before SCC emerges histologically. Brief priming of myeloid cells with IL-1α desensitizes them to IFN-I agonists and makes myeloid-derived suppressor cells (MDSC) even more suppressive of T-cell activation. Mechanistically, IL-1 activation represses the expression of DHHC3/7 enzymes, which are responsible for the palmitoylation of stimulator of interferon genes (STING). Early blockade of IL1 signaling using pharmacologic and genetic approaches similarly reduces MDSC and SLC2A1highmyeloid cells, suppresses epithelial dysplasia transformation, and extends survival. This work establishes a previously unrecognized SOX2-CCL2-IL1 pathway that leads to irreversible immune escape when precancerous epithelial lesions transform.
Scalable DNA Feature Generation and Transcription Factor Binding Prediction via Deep Surrogate Models
Authors: Kabir Anowarul , Inan Toki Tahmid , Rasmussen Kim , Shehu Amarda , Usheva Anny , Bishop Alan , Alexandrov Boian , Bhattarai Manish
Published: December 2024

Simulating DNA breathing dynamics, for instance Extended Peyrard-Bishop-Dauxois (EPBD) model, across the entire human genome using traditional biophysical methods like pyDNA-EPBD is computationally prohibitive due to intensive techniques such as Markov Chain Monte Carlo (MCMC) and Langevin dynamics. To overcome this limitation, we propose a deep surrogate generative model utilizing a conditional Denoising Diffusion Probabilistic Model (DDPM) trained on DNA sequence-EPBD feature pairs. This surrogate model efficiently generates high-fidelity DNA breathing features conditioned on DNA sequences, reducing computational time from months to hours–a speedup of over 1000 times. By integrating these features into the EPBDxDNABERT-2 model, we enhance the accuracy of transcription factor (TF) binding site predictions. Experiments demonstrate that the surrogate-generated features perform comparably to those obtained from the original EPBD framework, validating the model’s efficacy and fidelity. This advancement enables real-time, genome-wide analyses, significantly accelerating genomic research and offering powerful tools for disease understanding and therapeutic development.
DemoTape: Computational demultiplexing of targeted single-cell sequencing data
Authors: Borgsmüller Nico , Kuipers Jack , Gawron Johannes , Roncador Marco , Pohly Marcel , Acar Erkin , Do Thi Huong Lan , Reisenauer Stefanie , Feldkamp Mirjam Judith , Beisel Christian , Zenz Thorsten , Moor Andreas , Beerenwinkel Niko
Published: December 2024

Background

Single-cell sequencing can provide novel insights into the understanding and treatment of diseases. In cancer, for example, intratumor heterogeneity is a major cause of treatment resistance and relapse. Although technological progress has substantially increased the throughput of sequenced cells, single-cell sequencing remains cost and labor-intensive. Multiplexing, i.e., the pooling and subsequent joint preparation and sequencing of samples, followed by a demultiplexing step, is a common practice to reduce expenses and confounding batch effects, especially in single-cell RNA sequencing.

Results

Here, we introducedemoTape, a computational demultiplexing method for targeted single-cell DNA sequencing (scDNA-seq) data based on a distance metric between individual cells at single-nucleotide polymorphisms loci. To validatedemoTape, we sequence three B-cell lymphoma patients separately and multiplexed on the Tapestri platform. We find similar genotypes, clones, and evolutionary histories in all three samples when comparing the individual with the demultiplexed samples. Using the three individually sequenced samples, we simulate multiplexed ground truth data and show thatdemoTapeoutperforms state-of-the-art demultiplexing methods designed for RNA sequencing data. Additionally, we demonstrate through downsampling that the inferred clonal composition remained largely stable for samples with fewer cells despite the inevitable loss in resolution of low-frequency clones.

Conclusions

Multiplexing and subsequent genotype-based demultiplexing of scDNA-seq will reduce costs and workload, eventually allowing the sequencing of more samples. This will open new possibilities and accelerate the investigation of biological questions where cellular heterogeneity on the genomic level plays a crucial role.
Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs
Authors: Dubois Siegfried , Zytnicki Matthias , Lemaitre Claire , Faraut Thomas
Published: December 2024

Motivation

Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability.

Results

We aim to characterize the differences between variation graphs derived from the same set of genomes with a metric which expresses and pinpoint differences. We designed a pairwise variation graph comparison algorithm, which establishes an edit distance between variation graphs, threading the genomes through both graphs. We applied our method to pangenome graphs built from yeast and human chromosome collections, and demonstrate that our method effectively characterizes discordances between pangenome graph construction methods and scales to real datasets.

Availability

pancat compareis published as free Rust software under the AGPL3.0 open source license. Source code and documentation are available athttps://github.com/dubssieg/rs-pancat-compare.

Contact

siegfried.dubois@inria.fr

Supplementary information

Supplementary data are available online athttps://doi.org/10.5281/zenodo.10932490. Code to replicate figures and analysis is available online athttps://github.com/dubssieg/pancat_paper.
A decision-theoretic model of multistability: perceptual switches as internal actions
Authors: Safavi Shervin , Dayan Peter
Published: December 2024

Perceptual multistability has been studied for centuries using a diverse collection of approaches. Insights derived from this phenomenon range from core principles of information processing, such as perceptual inference, to high-level concerns, such as visual awareness. The dominant computational explanations of perceptual multistability are based on the Helmholtzian view of perception as inverse inference. However, these approaches struggle to account for the crucial role played by value, e.g., with percepts paired with reward dominating for longer periods than unpaired ones. In this study, we formulate perceptual multistability in terms of dynamic, value-based, choice, employing the formalism of a partially observable Markov decision process (POMDP). We use binocular rivalry as an example, considering different explicit and implicit sources of reward (and punishment) for each percept. The resulting values are time-dependent and influenced by novelty as a form of exploration. The solution of the POMDP is the optimal perceptual policy, and we show that this can replicate and explain several characteristics of binocular rivalry, ranging from classic hallmarks such as apparently spontaneous random switches with approximately gamma-distributed dominance periods to more subtle aspects such as the rich temporal dynamics of perceptual switching rates. Overall, our decision-theoretic perspective on perceptual multistability not only accounts for a wealth of unexplained data, but also opens up modern conceptions of internal reinforcement learning in service of understanding perceptual phenomena, and sensory processing more generally.
N1-methylpseudouridine mRNA modification enhances efficiency and specificity of gene overexpression by preventing Prkra-mediated global translation repression
Authors: Lu Tong , Chen Aijun , Wang Sen , Zhang Yizhuang , Yang Boya , Wang Jiasheng , Fang Hailing , Gong Qianqian , Li Ang , Liu Xiangguo , Ma Pengcheng , Mao Bingyu , Shi De-Li , Shao Ming
Published: December 2024

In vitro transcribed messenger RNA (IVT mRNA) has emerged as a pivotal tool in mRNA-based therapies and has been extensively employed in gene function studies and genetic tool applications. However, the IVT process generates double-stranded RNA (dsRNA) by-products that are recognized by dsRNA sensors, triggering innate immune responses. In this study, we comprehensively analyzed the detrimental effects of dsRNA by-products on early zebrafish embryos, revealing that these by-products induce cell necrosis and delay maternal-zygotic transition by reducing global translation efficiency via Prkra, a recently identified dsRNA sensor in pluripotent cells. Importantly, we demonstrate that N1-methylpseudouridine (m1φ) modification of IVT mRNAs effectively mitigates these adverse effects, as m1φ-modified dsRNAs exhibit significantly lower binding affinity to the Prkra dimer. Our findings underscore a previously overlooked challenge in the use of IVT mRNA in early embryos and offer a robust solution to enhance the fidelity of mRNA applications. Furthermore, we elucidate that m1φ modification minimizes the dsRNA-induced stress response in pluripotent cells through a distinct mechanism.
Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction
Authors: Gómez-Pérez Daniel , Keller Alexander
Published: December 2024

Understanding microbial phenotypes from genomic data is crucial in areas of research including co-evolution, ecology and pathology. This study proposes a new approach to integrate literature-derived information with genomic data to study microbial traits, combining natural language processing (NLP) with functional genome analysis. We applied this methodology to publicly available data to overcome current limitations and provide novel insights into microbial phenotype prediction.

We fine-tuned specialized transformer-based large language models to analyze 3.3 million open-access scientific articles, extracting a network of phenotypic information linked to bacterial strains. The network maps relationships between bacterial strains and traits such as pathogenicity, metabolic capacity, and host and biome preference. By functionally annotating reference genome assemblies for strains in the phenotypic network, we were able to predict key genes influencing phenotypes.

Our findings align with known phenotypes and reveal novel correlations, leading to the identification of microbial genes relevant in particular disease and host-association phenotypes. The interconnectivity of strains within the network provided further understanding of microbial community interactions, leading to the identification of hub species by inferring trophic connections—insights challenging to extract by means of experimental work.

This study demonstrates the potential of machine learning methods to uncover cross-species patterns in microbial gene-phenotype correlations. As the number of sequenced strains and literature descriptions grows exponentially, such methods become crucial for extracting meaningful information and advancing microbiology research.
Adapting COVID-19 research infrastructure to capture influenza and respiratory syncytial virus alongside SARS-CoV-2 in UK healthcare workers winter 2022/23: Results of a pilot study in the SIREN cohort
Authors: Foulkes Sarah , Munro Katie , Sparkes Dominic , Broad Jonathan , Platt Naomi , Howells Anna , Akinbami Omolola , Khawam Jameel , Joshi Palak , Russell Sophie , Norman Chris , Price Lesley , Corrigan Diane , Cole Michelle , Timelin Jean , Forster Louise , Slater Katrina , Watson Conall H , Andrews Nick , Charlett Andre ,   SIREN study group, Atti Ana , Islam Jasmin , Brown Colin S , Turner Jonathan , Hopkins Susan , Hall Victoria
Published: December 2024

Introduction

The combination of patient illness and staff absence driven by seasonal viruses culminates in annual “winter pressures” on UK healthcare systems and has been exacerbated by COVID-19. In winter 2022/23 we ran a pilot study aiming to introduce multiplex testing to determine the incidence and burden of SARS-CoV-2, influenza and respiratory syncytial virus (RSV) in our cohort of UK healthcare workers (HCWs).

Methods

The pilot study was conducted from 28/11/2022-31/03/2023 within the SIREN prospective cohort study. Participants completed fortnightly questionnaires, capturing symptoms and sick leave, and multiplex PCR testing for SARS-CoV-2, influenza and RSV, regardless of symptoms. PCR-positivity rates by virus were calculated over time, and viruses were compared by symptoms and severity. Self-reported symptoms and associated sick leave were described. Sick leave rates were compared by vaccination status and demographics.

Results

5,863 participants were included, 84.6% female, 70.3% ≥45-years, and 33.4% were nurses. PCR-positivity peaked in early December for all three viruses (4.6 positives per 100 tests (95%CI 3.5, 5.7) SARS-CoV-2, 3.9 (95%CI 2.2, 5.6) influenza, 1.4 (95%CI 0.4, 2.4) RSV), declining to <0.3/100 tests after January for influenza/RSV, and around 2.5/100 tests for SARS-CoV-2. Over one-third of all infections were asymptomatic, and symptoms were similar for all viruses. 1,368 (23.3%) participants reported taking sick leave, median 4 days (range 1-59). Rates of sick leave were higher in participants with co-morbidities, working in clinical settings, and who had not been vaccinated (COVID-19 booster or seasonal influenza vaccine) versus those who had received neither vaccine (2.04 vs 1.41 sick days/100 days, adjusted Incidence Rate Ratio 1.47 (95%CI 1.38, 1.56).

Conclusion

This pilot demonstrated the use of multiplex testing allowed better understanding of the impact of seasonal respiratory viruses and respective vaccines on the HCW workforce. This highlights the important information on asymptomatic infection and persisting levels of SARS-CoV-2 infection.
Exploring genetic risk factors for pneumonia using biobank resources - Insights across subpopulations
Authors: Heikkilä Anni , Sliz Eeva , Väyrynen Sara , Reis Kadri , Elnahas Abdelrahman G. , Reigo Anu , Esko Tõnu ,   Estonian Biobank Research Team,   FinnGen, Kettunen Johannes , Hautala Timo
Published: December 2024

Background

Pneumonia risk is influenced by demographics, chronic disease burden, lifestyle, and environmental factors. Despite genome-wide association studies (GWAS), the role of host genetics in pneumonia is still not fully understood, especially in certain subgroups.

Methods

We conducted a GWAS for pneumonia across FinnGen and Estonian Biobank (EstBB) (91,062 cases and 520,119 controls) populations. Cases with at least one pneumonia episode and subgroups based on the age at first pneumonia diagnosis, recurrent pneumonia, and asthma status were considered. We further estimated genetic correlations and causal relationships between pneumonia and other traits using linkage disequilibrium score regression and Mendelian randomization.

Results

We identified 13 loci including 5 replicated (PTGER4, TNFRSF1A, CHRNA5, MUC5A, HLA) and 8 novel associations (PTPN22, CRP, APOE, FHIT, MAPKAPK2, TNFSF15, HNF1A, RIN3) mainly harboring genes regulating immunity or lung health associated with pneumonia across subgroups. Interestingly, novel associations included theAPOElocus with the ε4 allele having a protective effect on pneumonia. Additionally, we report genetic correlations between pneumonia and 204 other traits, and nine traits potentially causal to pneumonia risk.

Conclusions

Loci associated with pneumonia harbour genes mainly related to acute inflammation, T cell development, antigen presentation and lung health. The stratified analyses demonstrate differences in genetic risk factors contributing to development of pneumonia in different patient subgroups. In summary, the findings of our study highlight the importance of immunological mechanisms at early life and in adults as well as significance of lifestyle and lung health among the elderly.
Integrative scRNA-seq and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis
Authors: Kulzhanova Gulzada , Klee Alexis , Botros Mina , Hansen Victoria L. , Reuter John , Tashbib Eliya Tazreena , Fadial Eloise , Ricciardi Benjamin F. , Giordano Brian , Wu Chia-Lung
Published: December 2024

Femoroacetabular impingement (FAI) and synovitis have been recognized as essential factors for developing osteoarthritis (OA) in the hip joints. However, little is known about altered synovial cellular compositions, their associated transcriptomic profiles, and cell-cell interactions between patients with FAI and hip OA. In the current study, by using integrative single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (Spatial-seq), we identified the molecular mechanisms by which synovial cells promote hip OA pathogenesis from FAI. Compared to FAI synovium, epiregulin (EREG)-enriched lining fibroblast-like synoviocytes (FLS) were significantly increased in the hip OA synovium. TheseEREG+FLS are pro-inflammatory due to their high expression ofCXCL1,IL8 (CXCL8), andMMPs. Furthermore, pseudotime analysis predicts thatEREG+FLS are potentially derived fromDPP4+PI16+sublining FLS. Importantly, analysis of cell-cell interactions indicates that fibroblast growth factor 2 (FGF2) secreted fromCOL1A1+IGFBP5+fibrotic macrophages may signal through syndecan 4 (SDC4) expressed byEREG+lining FLS, inducing the expression of IL6, IL8, MMP1, and PTGS2. The GO term analysis of activated genes downstream of FGF2-SDC4 signaling revealed that biological processes associated with inflammation and angiogenesis were upregulated in hip OA, while mechanical stimulus and skeletal muscle differentiation were dominant in FAI. Moreover, we also found thatEREG+CCL20+MMP3hilining FLS as well as most MΦ and monocyte populations are unique to hip OA patients when compared to knee OA and RA patients. The findings of this study offer a groundwork in tailoring novel targets and therapies for FAI and hip OA patients.
Accelerated amyloid deposition in SARS-CoV-2 infected mouse models of Alzheimer’s disease
Authors: Parekh Parag , Badachhape Andrew A. , Redd JeAnna R. , Bonilla Lauren J. , Bhandari Prajwal , Kneubehl Alexander R. , Bhavane Rohan , Clinton Jennifer L.S. , Admane Prasad , Menon Renuka , Srivastava Mayank , Sun Xianwei , Narang Saphal , Tanifum Eric , Ghaghada Ketan B. , Ronca Shannon E. , Annapragada Ananth V.
Published: December 2024

Familial Alzheimer’s disease (AD) involving known AD causing genes accounts for a small fraction of cases, the vast majority are sporadic. Neuroinflammation, secondary to viral infection, has been suggested as an initiating or accelerating factor. In this work we tested the hypothesis that SARS-CoV-2 (SCV2) viral infection accelerates the development of AD pathology in mouse models of AD. We profiled transcriptomic changes using transgenic APP/PSEN1 and P301S mouse models that develop AD pathology and k18hACE2 mice that express the humanized ACE2 receptor used by SCV2 to enter cells. This study identified the interferon and chemokine responses constituting key shared pathways between SCV2 infection and the development of AD pathology. Two transgenic mouse models of AD: APP/PSEN1 (develops amyloid pathology) and 3xTg AD (develops both amyloid and tau pathology) were crossed with k18-hACE2 mice to generate hybrid hACE2-3xTg and hACE2-APP/PSEN1 mice. Neuroinflammation and amyloid deposition in the brain of infected mice were imagedin vivousing molecular MRI (mMRI) probes and confirmed postmortem by histopathology. Results show that 11-14-month-old SCV2 infected hACE2-3xTg mice exhibit neuroinflammation 10 days post infection and 4–5-month-old hACE2-APP/PS1 hybrid mice develop amyloid deposits, while age-matched uninfected mice exhibit neither phenotype. This suggests that SCV2 infection could induce or accelerate AD when risk factors are present.
SARITA: A Large Language Model for Generating the S1 Subunit of the SARS-CoV-2 Spike Protein
Authors: Rancati Simone , Nicora Giovanna , Bergomi Laura , Buonocore Tommaso Mario , Czyz Daniel M , Parimbelli Enea , Bellazzi Riccardo , Salemi Marco , Prosperi Mattia , Marini Simone
Published: December 2024

The COVID-19 pandemic has profoundly impacted global health, economics, and daily life, with over 776 million cases and 7 million deaths from December 2019 to November 2024. Since the original SARS-CoV-2 Wuhan strain emerged, the virus has evolved into variants such as Alpha, Beta, Gamma, Delta, and Omicron, all characterized by mutations in the Spike glycoprotein, critical for viral entry into human cells via its S1 and S2 subunits. The S1 subunit, binding to the ACE2 receptor and mutating frequently, affects infectivity and immune evasion; the more conserved S2, on the other hand, facilitates membrane fusion. Predicting future mutations is crucial for developing vaccines and treatments adaptable to emerging strains, enhancing preparedness and intervention design. Generative Large Language Models (LLMs) are becoming increasingly common in the field of genomics, given their ability to generate realistic synthetic biological sequences, including applications in protein design and engineering. Here we present SARITA, an LLM with up to 1.2 billion parameters, based on GPT-3 architecture, designed to generate high-quality synthetic SARS-CoV-2 Spike S1 sequences. SARITA is trained via continuous learning on the pre-existing protein model RITA. When trained on Alpha, Beta, and Gamma variants (data up to February 2021 included), SARITA correctly predicts the evolution of future S1 mutations, including characterized mutations of Delta, Omicron and Iota variants. Furthermore, we show how SARITA outperforms alternative approaches, including other LLMs, in terms of sequence quality, realism, and similarity with real-world S1 sequences. These results indicate the potential of SARITA to predict future SARS-CoV-2 S1 evolution, potentially aiding in the development of adaptable vaccines and treatments.
Mass generation in an Abelian gauge theory with multiple scalar fields and no tree-level dimensionful couplings
Authors: Romatschke Paul , Su Chun-Wei , Weller Ryan
Published: December 2024

We study the Abelian Higgs model with multiple scalar fields, but without mass terms. Solving the model nonperturbatively order-by-order in the number of scalar fields, we find that radiative corrections generate masses for the scalar and gauge boson, without spontaneous symmetry breaking. The mass scales are set by the Λ-parameter of the electroweak running coupling, thereby naturally avoiding the hierarchy problem. No part of our calculation employs a weak-coupling expansion, and we find that the perturbative vacuum is metastable, and hence must decay to the stable nonperturbative vacuum of the theory, which we identify. Although the field content of our Lagrangian is standard, our results predict the existence of two heavy scalar resonances in addition to the Higgs. We believe that these predicted resonances will ultimately allow experimentalists to discriminate between our method and standard solutions of the Higgs model.

Published by the American Physical Society
2024
Influence of center vortex interactions on the static potentials
Authors: Hosseini Nejad Seyed Mohsen
Published: December 2024

We analyze the static potentials induced by vacuum domains for various representations in SU(4) Yang-Mills theory within the framework of the domain structure model. By studying the interactions within the vacuum domains, we can uncover fundamental properties of the static potentials. It appears that attractions within the vacuum domains strongly adhere to Casimir scaling at intermediate distances. Conversely, the repulsions within the vacuum domains may decompose them into center vortices with the lowest magnitude of center vortex fluxes, thereby exhibiting N-ality at asymptotic distances.

Published by the American Physical Society
2024
Determination of scales and measures for assessing social sustainability practices in construction projects
Authors: Kordi Nurul Elma , Belayutham Sheila , Che Ibrahim Che Khairil Izam
Published: December 2024

Purpose

This paper addresses the scarcity of research on social sustainability (SS) in sustainable construction (SC) by establishing indicators and descriptors for SS throughout the construction project life cycle. The objective is to provide an objective assessment and improve SS practices.

Design/methodology/approach

The study employs a comprehensive methodology involving literature review, semi-structured interviews, focus group discussions and structured interviews. A total of 42 indicators were identified from the literature and presented to 20 expert panels, resulting in the addition of seven indicators. A refined set of 49 indicators was then presented to 25 experts via focus group discussions, and structured interviews were conducted to determine suitable descriptors and scales for each indicator.

Findings

The study identified 19 indicators for the pre-construction phase, 25 for the construction phase and 4 for the post-construction phase. These findings offer an objective assessment of SS practices across the construction project life cycle. The indicators and descriptors serve as a valuable tool for industry practitioners to monitor and improve social aspects, fostering SC.

Research limitations/implications

The study’s limitations include the context-specific nature of the findings and the potential subjectivity introduced through the selection of expert panels.

Practical implications

The identified indicators and descriptors have practical implications for industry practitioners, providing guidelines to enhance social sustainability practices throughout the project life cycle.

Originality/value

This study fills a research gap by focussing on SS in construction. The comprehensive methodology contributes to theory development and provides practical tools for practitioners to advance social sustainability practices.
A measurement model of trust in construction projects
Authors: Wu Hongyue , Chen Yunfeng , Cox Robert F. , Jin Ruoyu
Published: December 2024

Purpose

Lack of trust in construction projects will lead to poor project performance or project failure, indicating the importance of trust-building. Existing studies have developed various trust models, while most studies covered limited trust factors, failed to clarify their meanings and relationships or lacked qualitative or quantitative evidence. Thus, this study aims to develop a measurement model of trust in construction projects with theoretical justification as well as qualitative and quantitative data.

Design/methodology/approach

A literature review was conducted to identify conceptual types, factors and indicators of trust. Individual interviews and focus groups were performed to test the proposed framework with qualitative data. A survey and confirmatory factor analysis (CFA) method were utilized to build the measurement model of trust using quantitative data in BIM-assisted projects.

Findings

The proposed trust framework covered the four conceptual types, four factors (integrity, competency, benevolence and commitment) and 13 indicators, supported by the results of interviews and focus groups. The measurement model of trust from CFA results supported the significant, positive, and one-to-one relationships between 13 indicators and four factors of trust in BIM-assisted projects.

Originality/value

Theoretically, the study provides new insights into the multi-dimensional nature of trust. In practice, the findings could facilitate trustors and trustees to better understand, build, measure and enhance trust in construction projects.
Many hands make light work: the cross-level influence of top management team behavioral integration on group ambidextrous innovation
Authors: Xia Yuhuan , Gai Mingzhe , Han Changlin , Liu Xiyao , Liu Zhen , Xu Lei
Published: December 2024

Purpose

This study aims to explore the cross-level effect of the top management team (TMT) on group ambidextrous innovation and to analyze the mediating role of group behavioral integration and the moderating effect of group expertise heterogeneity.

Design/methodology/approach

We conducted a multi-source and multi-stage survey. We collected valid data from 43 companies in China, resulting in 141 samples from 43 TMTs and 462 valid responses from 111 organizational groups. The proposed theoretical model and hypotheses were tested using structural equation modeling.

Findings

The study findings demonstrated that TMT behavioral integration was positively related to group behavioral integration. Group behavioral integration mediates the relationship between TMT behavioral integration and these two types of innovations. Furthermore, we found that group expertise heterogeneity magnified the positive effect of group behavioral integration on exploratory innovation.

Originality/value

This study reveals the cross-level effects of TMT behavioral integration on other organizational groups and enriches the existing literature on TMT behavioral integration and ambidextrous innovation.
Does employee innovation matter in the UK hotel industry? The mediating role of psychological safety
Authors: Alzyoud Sultan , Partington Shobana Nair , Dandis Ala' Omar
Published: December 2024

Purpose

In the current turbulent and highly competitive environment, hotels’ management is under pressure to be innovative and improve their products and services continuously to meet and exceed guests’ expectations. Therefore, the primary objective of this study is to develop and test a framework of the factors that can promote employee psychological safety and help drive employee innovation in hotels in the UK.

Design/methodology/approach

A survey questionnaire was constructed and distributed to employees in four- and five-star hotels in the UK. Non-probability convenience sampling was performed in this study. Structural equation modeling (SEM) was used to test the research’s model and hypotheses.

Findings

The findings revealed a positive and significant association between psychological safety and employee innovation. Furthermore, psychological safety was found to fully mediate the influence of leader inclusiveness, respectful relationships at work and autonomy on employee innovation. Also, leader inclusiveness and role clarity were discovered to be associated with autonomy, whereas proactive personality was found to be related to employee innovation directly. The outcomes also showed that a proactive personality fully mediates the impact of autonomy and respectful relationships on employee innovation.

Originality/value

This study presents an original chain-mediation model that illustrates the mechanism of how employee innovative behavior can be encouraged by focusing on the mediation of psychological safety. To the best of the authors’ knowledge, this study is among the first attempts to shed light on the role of psychological safety in promoting employee innovation in the hotel sector.
Impact of corporate governance structure on performance of listed firms: empirical evidence from Palestine
Authors: Talalwa Mohammad , Magableh Fu’ad , Badwan Nemer
Published: December 2024

Purpose

The purpose of this study is to investigate the influence of corporate governance structure corporate governance on a firm’s performance in the Palestinian business environment between 2016 and 2023. The specific environment of the developing Palestinian economy is the main motivation and emphasis of this investigation.

Design/methodology/approach

Data were gathered from 49 financial and non-financial firms listed on the Palestine Stock Exchange between 2016 and 2023. While the random and fixed effects estimates were utilized to be the most suitable for this particular investigation, they were used to undertake the data analysis procedure. The study employed two-stage least squares (2SLS) to assess the robustness and correctness of data to bolster the findings and subsequent implications.

Findings

The findings show that the return on equity, a measure of corporate performance, was positively but not significantly impacted by the presence of women on the executive boards of Palestinian companies. This suggests that the variable in question had no bearing on the success of the firms. In terms of moderating influence, corporate governance structure had no bearing on the link between dual chief executives, institution ownership, government ownership, independent directors and firm performance. Family ownership and board size had negative, significant impacts on performance.

Research limitations/implications

The research limitations of this study are that it focuses exclusively on manufacturing firms listed on the Palestine Exchange (PEX) over a seven-year period, which limits its generalizability to other industries and regions. Furthermore, due to a lack of data, the model did not account for global diversity on boards of directors.

Practical implications

The findings of this research help managers understand how management structures impact business success and provide regulatory authorities with insights into gender diversity and corporate governance legislation in Palestine. It suggests enhancing company performance, competitiveness and capital acquisition by improving governance information quality, building investor confidence, raising standards and reforming governance systems.

Originality/value

This study contributes to the literature by enhancing the understanding of how corporate governance and gender diversity affect the financial performance of listed firms, addressing a research gap in the Palestinian market. It is one of the few studies examining company performance during political turmoil, specifically focusing on the increased role of women on Palestinian boards.
Nurturing sustainability practices: a qualitative inquiry into environmental innovations as a catalyst in manufacturing enterprises in an emerging economy
Authors: Alinda Kassim
Published: December 2024

Purpose

This study explores how medium and large manufacturing firms integrate environmental innovations to foster sustainability practices. It seeks to uncover the specific challenges these firms face and the strategies they employ to effectively implement sustainable initiatives in response to growing environmental pressures.

Design/methodology/approach

Using a qualitative phenomenological approach, the study analyzes twelve detailed case studies, engaging in conversational interviews to capture the lived experiences of key stakeholders. Through direct quotations and thematic analysis, the research offers in-depth insights into the practical implementation of sustainability practices driven by environmental innovations.

Findings

The study identifies those environmental innovations – both in products and processes – are critical drivers for addressing specific sustainability challenges. Firms that successfully implement these innovations do so by leveraging internal resources and external collaborations, which enable them to navigate environmental regulations, reduce waste and enhance operational efficiency. However, the findings also highlight significant barriers such as financial constraints and resistance to change within traditional manufacturing systems.

Research limitations/implications

The study is limited by the use of a convenience sampling method and potential biases in interview responses. Future research should adopt more robust sampling techniques and explore longitudinal impacts to mitigate subjectivity and enhance generalizability.

Practical implications

The findings offer practical insights for manufacturing firms seeking to implement sustainability practices. By understanding the mechanisms through which environmental innovations can be integrated into their operations, firms can develop more effective strategies for enhancing environmental performance.

Originality/value

This study contributes original insights into the strategic application of environmental innovations within the manufacturing sub-sector. It highlights the role of innovations in overcoming sustainability challenges, offering a nuanced understanding of how firms can align operational goals with environmental imperatives.
Quality in qualitative research: a relational process
Authors: Timonen Virpi , Foley Geraldine , Conlon Catherine
Published: December 2024

Purpose

Demonstrating quality in qualitative research is challenging. Excessive reliance on checklists can lead to poor quality qualitative research masquerading as high quality. We seek to equip readers with foundational understanding of how to ensure quality of their qualitative research by emphasizing a relational approach to research.

Design/methodology/approach

We outline existing paradigm-specific and cross-paradigm accounts of the constituents of quality in qualitative research and identify credibility and relevance as the shared criteria. We define quality in qualitative research as a relational process wherein the relations constitutive of credibility and relevance are actively constructed throughout the research process.

Findings

Quality cannot be ensured with the help of checklists alone. Quality arises from formulating a research question that is relevant; sampling for (or accessing) data through a credible process pertaining to the relevant concern; engaging analysis in a credible manner and doing justice to the data while continuing to remain relevant to the studied concern. Quality in qualitative research is a set of relationships, threaded through the entire research process, between the researcher and the researched concern, participants, data, data analysis and audience. The foundations of qualitative inquiry, across all paradigms, demand an engaged, committed researcher attending iteratively and with care – relationally – to every stage of the research process in pursuit of quality.

Originality/value

We elaborate parsimonious quality criteria that are specific to qualitative research. Adopting a relational ethic of commitment to quality at each stage of the research process is conducive towards high-quality qualitative research.
Do private equity investors value ESG and SDGs? Evidence from Tunisia
Authors: Ben Noamene Tarek
Published: December 2024

Purpose

This study aims to explore the perceptions of Environmental, Social and Governance (ESG) principles by private equity investors in Tunisia and evaluate how these perceptions are aligned with the United Nations Sustainable Development Goals (SDGs).

Design/methodology/approach

Semi-structured interviews were conducted with private equity investors operating in Tunisia to assess their level of understanding and awareness of ESG concepts and their expectations regarding the adoption of ESG criteria in their investment decisions.

Findings

This study reveals that while private equity (PE) investors in Tunisia are familiar with sustainability principles, their knowledge of ESG concepts is limited. ESG criteria are generally not incorporated into investment decisions unless mandated by foreign partners. The findings of this study also indicate that most Tunisian PE investors emphasize the importance of aligning ESG principles with the Sustainable Development Goals (SDGs) to meet international standards and remain competitive in raising global funds and forming partnerships with foreign partners.

Research limitations/implications

Despite the insightful findings, this study has limitations primarily because of its qualitative nature and relatively small sample size. Conducting extensive quantitative research involving a broader range from the PE ecosystem would provide deeper insights into the integration of ESG principles in Tunisia.

Originality/value

This study provides valuable insights into ESG perceptions within a specific investor niche – the PE industry – and contributes to the limited body of literature on ESG, particularly in emerging markets like Tunisia.
Tax Subsidy Disclosure and Local Economic Effects
Authors: DE SIMONE LISA , LESTER REBECCA , RAGHUNANDAN ANEESH
Published: December 2024

We examine if the effectiveness of business tax subsidies varies based on state disclosure laws. The prior accounting literature on government disclosure documents substantial variation in the quality of such disclosures, raising questions about their effectiveness for monitoring. State and local business subsidies for investment and employment have tripled in size over the past 30 years, but transparency problems inhibit clear assessments of whether subsidies achieve their intended outcomes. We examine both internal disclosure laws, which mandate subsidy reporting by the granting state agency to other state oversight agencies, and external disclosure laws, which mandate reporting to the public. We find positive effects of subsidies on local employment when subsidies are subject to internal disclosure laws; by implementing such regimes, governments could forego 1.2–1.7 subsequent subsidies per county, saving $419.0–$593.5 million in aggregate. In contrast, we observe little effect of external disclosure, which we show is due to governments either substituting to other types of incentives or posting stale information that impedes public monitoring. We contribute to the government disclosure literature by demonstrating the real employment effects of internal government disclosures, and we provide policy‐relevant evidence about the conditions under which external disclosure regimes facilitate public monitoring.
Imperative for a health‐centred focus on climate change in radiology
Authors: Taboun Omar , DesRoche Chloe , Hanneman Kate
Published: December 2024

Climate change negatively impacts individual and population‐level health through multiple pathways, including poor air quality, extreme heat and changes in infectious disease. These health effects will lead to higher health system and medical imaging utilisation. At the same time, the delivery of radiology services generates substantial greenhouse gas emissions. Mitigation strategies to reduce the environmental impact of medical imaging and adaptation strategies to build resiliency to current and future impacts of climate change in radiology should be centred on human health. A health‐centred response in radiology reinforces the role of radiologists as physicians and emphasises the opportunity for medical imaging to promote health and advance our understanding of climate‐related health effects. This review discusses the need for a health‐centred focus on climate change in radiology, including the effects of climate change on human health and health systems, intersection of climate change with health equity, health benefits of climate action and opportunities to leverage medical imaging to improve human health.