bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using normative models pre-trained on cross-sectional data to evaluate intra-individual longitudinal changes in neuroimaging data
Authors: Rehák Bučková Barbora , Fraza Charlotte , Rehák Rastislav , Kolenič Marián , Beckmann Christian , Španiel Filip , Marquand Andre , Hlinka Jaroslav 
Published: June 2023

AbstractLongitudinal neuroimaging studies offer valuable insight into intricate dynamics of brain development, ageing, and disease progression over time. However, prevailing analytical approaches rooted in our understanding of population variation are primarily tailored for cross-sectional studies. To fully harness the potential of longitudinal neuroimaging data, we have to develop and refine methodologies that are adapted to longitudinal designs, considering the complex interplay between population variation and individual dynamics.We build on normative modelling framework, which enables the evaluation of an individual’s position compared to a population standard. We extend this framework to evaluate an individual’s longitudinalchangecompared to the longitudinal change reflected by the (population) standard dynamics. Thus, we exploit the existing normative models pre-trained on over 58,000 individuals and adapt the framework so that they can also be used in the evaluation of longitudinal studies. Specifically, we introduce a quantitative metric termed“z-diff”score, which serves as an indicator of a temporal change of an individual compared to a population standard. Notably, our framework offers advantages such as flexibility in dataset size and ease of implementation.To illustrate our approach, we applied it to a longitudinal dataset of 98 patients diagnosed with early-stage schizophrenia who underwent MRI examinations shortly after diagnosis and one year later.Compared to cross-sectional analyses, which showed global thinning of grey matter at the first visit, our method revealed a significant normalisation of grey matter thickness in the frontal lobe over time. Furthermore, this result was not observed when using more traditional methods of longitudinal analysis, making our approach more sensitive to temporal changes.Overall, our framework presents a flexible and effective methodology for analysing longitudinal neuroimaging data, providing insights into the progression of a disease that would otherwise be missed when using more traditional approaches.
Structural Basis of σ54Displacement and Promoter Escape in Bacterial Transcription
Authors: Gao Forson , Ye Fuzhou , Zhang Bowen , Cronin Nora , Buck Martin , Zhang Xiaodong 
Published: June 2023

AbstractGene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated and in bacteria, transcription initiation is mediated by σ factors, which recruit RNA polymerase (RNAP) to the promoter DNA region and facilitate open complex formation, where double stranded DNA is opening up into a transcription bubble and template strand DNA is in position for initial RNA synthesis. During initial transcription, DNA downstream of the transcription start site is fed into the active site of RNAP, whilst the upstream promoter DNA remains tethered to the RNAP via the σ factor, resulting in a build-up of tension. In order to progress to the processive elongation state, RNAP must escape from the promoter, and displace or dissociate the σ factor. Bacteria s factors can be broadly separated into two classes with the majority belong to the s70 class, represented by the σ70that regulate housekeeping genes. σ54forms a class on its own and regulate stress response genes. Extensive studies on σ70have revealed the molecular mechanisms of σ70promoter escape while how σ54transitions from initial transcription to elongation is unknown. Here we present a series of cryo electron microscopy structures of the σ54factor with progressively longer RNA, revealing the molecular mechanism of σ54displacement and promoter escape. Our data show that the initial instability is driven by DNA scrunching, and the final displacement steps are driven by both RNA extension and DNA scrunching.
Optimisation of sample preparation from primary mouse tissue to maintain RNA integrity for methods examining translational control
Authors: Munro June , Gillen Sarah L. , Mitchell Louise , Laing Sarah , Karim Saadia A. , Rink Curtis , Waldron Joseph A. , Bushell Martin 
Published: June 2023

AbstractProtein output of different mRNAs can vary by two orders of magnitude therefore it is critical to understand the processes that control gene expression that operate at the level of translation. Translatome-wide techniques such as polysome profiling and ribosome profiling are key methods for determining translations rates occurring on specific mRNAs. These techniques are now widely used in cell lines; however, they are underutilised in tissues and cancer models. Ribonuclease (RNase) expression is often found to be higher in complex primary tissues in comparison to cell lines. Methods used to preserve RNA during lysis often use denaturing conditions which needs to be avoided when requiring to maintain the interaction and position of the ribosome with the mRNA. Here we detail the cell lysis conditions that produce high quality RNA from several different tissues covering a range of endogenous RNase expression levels. We highlight the importance of RNA integrity for accurate determination of the global translation status of the cell as determined by polysome gradients and discuss key aspects to optimise for accurate assessment of the translatome from primary mouse tissue.
Low-troposphere microbial communities differ between dry-air and rainfall but do not show strong seasonal patterns in Metro Atlanta, Southeast USA
Authors: Davila-Santiago Lizbeth , Erb Casey , Yang Laura Hyesung , Hall Johanna , Negron Arnaldo , D’amico Isabelle , Hatt Janet K. , Konstantinidis Konstantinos T. 
Published: June 2023

AbstractThe composition and seasonal patterns of airborne bacterial and fungal communities and how these are affected by atmospheric conditions (e.g., dry vs. rain), origin of air masses, and presence of air pollutants remain understudied, despite their obvious importance for public health. To provide insights into these questions, monthly dry air and rain samples were collected at the Environmental Science and Technology building rooftop on Georgia Tech’s campus (Metro Atlanta) between June 2017 and November 2019. The sampling included the remnants of Hurricane Irma and a Saharan dust event in 2020. Amplicon sequencing of the V4 region of the 16S rRNA gene and the fungal nuclear ribosomal internal transcribed spacer (ITS) region showed that spore-forming bacteria and widespread fungi were enriched in dry samples, while photosynthetic bacteria and wood-decaying fungi were more abundant in rain samples, demonstrating the effect of sample type on bioaerosol composition. Further, higher relative abundance of fungal human pathogens and allergens were identified in the dry-air and Saharan dust samples, includingAlternaria alternataandCladosporium cladosporioides. Bacterial and fungal species richness and composition appeared to be relatively consistent between seasons for both sample types. Accordingly, sample type and seasonality explained ∼14% and ∼8.5% of the microbial diversity between samples, respectively, while presence of air pollutants and three-day back trajectory data were not significant. Collectively, our data indicates that dry air might represent a higher public health risk and provides a reference point for the long-term monitoring of airborne microbial communities in an urban Southeast US setting.ImportanceIn the atmosphere, or in the air we breathe, bioaerosols are always present. Bioaerosols are biological particles (alive or dead) suspended in the air, being bacteria and fungi the most abundant. In addition, bioaerosols can potentially contribute to weather/climate patterns. Although and unfortunately, a clear biodiversity pattern from different atmospheric events (air, rain, snow, etc.) remains to be discovered, especially in urban areas, where bioaerosols can also have implications for public health. The role of airborne microbes and their diversity patterns in the atmosphere constitutes a significant gap in our understanding of their interactions with health, climate, and other ecosystems compared to other environments. Our research provides the first reference point for long-term monitoring of airborne microbial communities in an urban Southeast US setting. This research contributes novel knowledge about public health and insights for integrating biological information into weather and climate prediction models.
A novel platform for metabolomics using barcoded structure-switching aptamers
Authors: Tan June H. , Mercado Maria P. , Fraser Andrew G. 
Published: June 2023

AbstractSmall organic molecules like metabolites and drugs are critical for diagnostics, treatment, and synthetic biology. Measuring them presents two key challenges however: they are biochemically highly diverse and there is no method to amplify them. Mass spectrometry has been the workhorse of metabolomics for decades but is costly and slow and single-cell metabolomics remains very challenging. Here we describe an alternative platform for metabolomics based on structure-switching aptamers (SSAs). SSAs are short nucleic acid molecules that each recognise a specific target ligand and undergo a major conformational change on ligand binding. This conformational change can drive detection such as fluorescence allowing SSAs to be used as sensors. We adapted conventional SSAs to a novel readout: barcode release. Each SSA recognises a unique ligand and each SSA releases a unique barcode allowing many ligands to be detected in parallel. We show that these barcode SSAs (bSSAs) can be multiplexed and act as independent sensors and that barcode release can be massively amplified to allow high sensitivity. Finally, we establish methods for the generation of large collections of bSSAs where barcode-SSA matching is completely directed. We believe that this novel platform which converts metabolite detection into barcode sequencing will allow the deep multiplexed detection of metabolites and drugs down to the scale of single cells.
Structural Characterization of the Full-length Hantaan Virus Polymerase
Authors: Keown Jeremy R. , Carrique Loïc , Nilsson-Payant Benjamin , Fodor Ervin , Grimes Jonathan M. 
Published: June 2023

AbstractHantaviridaeare a family of segmented negative-sense RNA viruses that contains important human and animal pathogens including Andes orthohantavirus and Hantaan orthohantavirus.Hantaviridaecontain a viral RNA-dependent RNA polymerase that replicates and transcribes the viral genome in the cytoplasm of infected cells. Here we establish the expression and purification of the polymerase from the Old World Hantaan orthohantavirus and characterise the structure using single particle cryo electron microscopy. We determine a series of structures at resolutions between 2.7 and 3.3 Å of RNA free polymerase comprising the core, core and endonuclease, and a full-length polymerase. The full-length polymerase structure depicts the location of the cap binding and C-terminal domains which are arranged in a conformation that is incompatible with transcription and in a novel conformation not observed in previous conformations of cap-snatching viral polymerase. We further describe structures with 5′ vRNA promoter in the presence and absence of a nucleotide triphosphate. The nucleotide bound structure mimics a replication pre-initiation complex and the nucleotide stabilises the motif E in a conformation distinct from those previously observed. We observe motif E in four distinct conformations including β-sheet, two helical arrangements, and an ordered loop. The insights gained here form a starting point for future detailed mechanistic studies of both the transcription and replication activities of the hantavirus polymerase and for the development of therapeutic targets.
Addiction recovery stories: Rebecca Kippax in conversation with Lisa Ogilvie
Authors: Kippax Rebecca , Ogilvie Lisa 
Published: June 2023

Purpose
The purpose of this paper is to examine recovery through lived experience. It is part of a series that explores candid accounts of addiction and recovery to identify the important components in the recovery process.

Design/methodology/approach
The G-CHIME model comprises six elements important to addiction recovery (Growth, Connectedness, Hope, Identity, Meaning in life and Empowerment). It provides a standard against which to consider addiction recovery, having been used in this series, as well as in the design of interventions that improve well-being and strengthen recovery. In this paper, a first-hand account is presented, followed by a semi-structured e-interview with the author of the account. Narrative analysis is used to explore the account and interview through the G-CHIME model.

Findings
This paper shows that addiction recovery is a remarkable process that can be effectively explained using the G-CHIME model. The significance of each component in the model is apparent from the account and e-interview presented.

Originality/value
To the best of the authors’ knowledge, each account of recovery in this series is unique, and as yet, untold.
Decolonizing international business
Authors: Boussebaa Mehdi 
Published: June 2023

Purpose
The purpose of this paper is to encourage scholars of international business (IB) to engage with the “decolonizing the university” project and reflect on what decolonizing might mean for IB research and education. The paper also argues that it is particularly important for IB scholars to join the decolonizing project given that the field’s main object of study – the multinational enterprise – has been central to colonialism.

Design/methodology/approach
An essay style is adopted to introduce the decolonizing project to IB and to explain why and how this scholarly field might benefit from engaging with it. As part of that, the paper calls upon IB scholars to work on decolonizing the field and to do so by not only interrogating its knowledge claims but also broadening the scope of its research so it can address the theme of neo-colonialism.

Findings
The paper reveals the conspicuous absence of IB scholars from the decolonizing project and situates such absence within a long-standing indifference within IB to the issue of colonialism.

Social implications
In learning about and engaging with the decolonizing project, IB scholars will be able to not only enrich IB theory and education but also help to tackle one of the grand challenges facing the modern world society, namely, social inequality and injustice rooted in colonialism.

Originality/value
It is hoped that this paper will stimulate reflection on IB’s absence from the decolonizing project and assist scholars in developing an understanding of the project’s rationale and underlying literature. It is also hoped that the paper will open dialogue within IB about how this field might be decolonized and help scholars engage meaningfully with other disciplines as they do so.
What a legacy: a call to action to facilitate entry into the licensed cannabis market in Canada
Authors: Wright-Brown Tanisha , Brennan Sandy , Blackwood Michael , Donnan Jennifer 
Published: June 2023

Purpose
Almost five years after legalization, the unlicensed cannabis market is still thriving in Canada, and legacy cannabis retailers continue to face barriers to legal market entry. This study aims to shed light on these challenges and offer policy recommendations supporting legacy retailers and the government’s goals of enhancing public safety and displacing the unlicensed market.

Design/methodology/approach
This study reviewed online sources, including the media, gray literature, government, and other policy and legal websites, to identify legacy retailers’ challenges to entering the Canadian ecosystem since legalization and policy approaches of legalized jurisdictions with similar issues.

Findings
Legacy retailers face financial, legal and social barriers to entering the legal market. The Canadian government should focus on lowering and eliminating these barriers by developing programs that reduce financial risks and required capital, facilitate partnership programs and accelerators, provide innovative options that reduce overhead expenses, encourage pooled ownership to support small businesses, prioritize market entry for equity-deserving individuals and enable automatic expungement. A description of programs that have been implemented in other jurisdictions to address similar barriers is provided.

Practical implications
The policy recommendations in this paper would enable increased entrepreneurship and employment in a growing sector. While the tax revenue earned from the new market entrants may not be enough to support all the recommended policy initiatives, it could be reinvested to fund some of them creating sustainable growth opportunities.

Originality/value
The paper provides practical, timely policy recommendations on expanding the legal cannabis market in Canada and addressing unintended negative consequences of current policies.
The effects of project uncertainty on guanxi governance and contractual governance
Authors: Lin Yi-Hsin , Niu Deshuang , Guo Yanzhe , Zeng Ningshuang 
Published: June 2023

PurposeThis study examines how project uncertainties (environmental uncertainty and participant uncertainty) affect guanxi and contractual governance and assesses the mediating role of guanxi governance between project uncertainty and contractual governance.Design/methodology/approachData were collected in two stages from Chinese contractors. First, in-depth interviews were conducted with nine construction engineering project practitioners in different contracts as a pilot for questionnaire designing. Second, a cross-sectional questionnaire survey was conducted with professionals and practitioners of construction enterprises to collect primary data. Partial least squares structural equation modeling (PLS-SEM) was used to test seven hypotheses based on data collected from 198 respondents.FindingsProject environmental uncertainty promotes the use of guanxi governance, while project participant uncertainty hinders it; the relationship between both types of uncertainty and contractual governance is the same as with guanxi governance. Furthermore, guanxi governance promotes contractual governance and partially mediates project environmental uncertainty and contractual governance and a complete mediating role between project participant uncertainty and contractual governance.Research limitations/implicationsAs the interviewed samples are mainly from China, the study should be replicated using large representative samples from East Asian countries, such as Japan and South Korea, to gain a more comprehensive understanding of the influence of guanxi governance. Further, while the internal consistency reliability and convergent validity of the questionnaire data in this study align with the standards, a larger sample size would improve the reliability and validity of the research results and better represent the overall work situation of contractors, owners and public policymakers.Originality/valueThe results provide insights into project governance research and have implications for construction practitioners in deploying governance-related resources.
The sexual identity disclosure dilemma for lesbian, gay, and bisexual employees in the Indian workplace
Authors: Lyndon Shiji , Rawat Preeti S. , Bhardwaj Ketan , Navare Ajinkya 
Published: June 2023

PurposeThe purpose of this paper is to extend the theoretical understanding of the disclosure dilemma experienced by lesbian, gay and bisexual (LGB) employees. The study focuses on examining the factors related to self-disclosure such as co-worker support and fear of disclosure. Further, the study also aims at testing the impact of coworker support on the psychological well-being of LGB employees.Design/methodology/approachThe study adopts a concurrent triangulation research design, which involves a simultaneous collection of quantitative and qualitative data. Using a survey questionnaire, data from 200 LGB employees were collected. Semi-structured interviews were carried out with 10 LGB employees. The qualitative findings were treated as complementary to the relationship tested through the quantitative method.FindingsQuantitative results reveal that co-worker support positively impacts self-disclosure by LGB employees. And the fear of disclosure mediates the relationship between coworker support and self-disclosure. Further, self-disclosure is positively related to psychological well-being. The qualitative study brings insights from the lived experiences around these factors. This research expands knowledge about the factors associated with the disclosure of LGB employees.Originality/valueThe study examines the factors related to the disclosure of sexual identity and the experiences of the dilemma of LGB employees in the workplace. Most of the studies in the context of LGB have adopted a quantitative research design. The current study adopts a mixed methods approach with a concurrent triangulation research design.
Integrating external stakeholders for improvement in green innovation performance: role of green knowledge integration capability and regulatory pressure
Authors: Ullah Sami , Ahmad Tooba , Lyu Bei , Sami Abdul , Kukreti Mohit , Yvaz A. 
Published: June 2023

Purpose
Green innovation, particularly in manufacturing firms, is one of the most advocated methods to curb the effects of climate change. This study aims to investigate the impact of the integration of green customers and suppliers on the green innovation performance of food manufacturing firms in Pakistan. The institutional and resource-based view theories determine the moderating role of regulatory pressure and the mediating role of green knowledge integration capability (GKIC).

Design/methodology/approach
Data was collected from 511 middle management-level employees of food manufacturing firms in Pakistan. The questionnaire was tested for reliability and validity. Hierarchical regression is used to test the proposed hypothesis.

Findings
A marginal improvement in integration with green customers can increase the green innovation performance (GIP) of a firm by 23.6%. Green supplier integration can improve the GIP by 14.2%, whereas the GKIC mediates the relationship between Green Customers Integration (GCI) and GIP but not for green suppliers integration (GSI). The moderating effect of regulatory pressure was significant for the relationship between GCI and GIP but insignificant for GSI.

Originality/value
Food manufacturing accounts for approximately 16% of global green house gases (GHG) emissions. Sustainable development goals (SDGs) cannot be achieved without a significant decrease in GHG emissions by food manufacturing companies. Therefore, it is crucial to investigate firms' green innovation performance in this sector. The findings of this study can help policymakers develop policies for achieving SDGs.