bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-specific eQTLs reveal causal genes underlying shared genetic architecture of critically ill COVID-19 and idiopathic pulmonary fibrosis
Authors: Dalapati Trisha , Wang Liuyang , Jones Angela G. , Cardwell Jonathan , Konigsberg Iain R. , Bossé Yohan , Sin Don D. , Timens Wim , Hao Ke , Yang Ivana , Ko Dennis C. 
Published: July 2024

SUMMARYMost genetic variants identified through genome-wide association studies (GWAS) are suspected to be regulatory in nature, but only a small fraction colocalize with expression quantitative trait loci (eQTLs, variants associated with expression of a gene). Therefore, it is hypothesized but largely untested that integration of disease GWAS with context-specific eQTLs will reveal the underlying genes driving disease associations. We used colocalization and transcriptomic analyses to identify shared genetic variants and likely causal genes associated with critically ill COVID-19 and idiopathic pulmonary fibrosis. We first identified five genome-wide significant variants associated with both diseases. Four of the variants did not demonstrate clear colocalization between GWAS and healthy lung eQTL signals. Instead, two of the four variants colocalized only in cell-type and disease-specific eQTL datasets. These analyses pointed to higherATP11Aexpression from the C allele of rs12585036, in monocytes and in lung tissue from primarily smokers, which increased risk of IPF and decreased risk of critically ill COVID-19. We also found lowerDPP9expression (and higher methylation at a specific CpG) from the G allele of rs12610495, acting in fibroblasts and in IPF lungs, and increased risk of IPF and critically ill COVID-19. We further found differential expression of the identified causal genes in diseased lungs when compared to non-diseased lungs, specifically in epithelial and immune cell types. These findings highlight the power of integrating GWAS, context-specific eQTLs, and transcriptomics of diseased tissue to harness human genetic variation to identify causal genes and where they function during multiple diseases.
Leukemogenesis in Acute Lymphoblastic Leukemia through the Lens of Developmental Dynamics of Lymphoid Progenitor Cells: a systematic review
Authors: Shafi Ovais , Rajpar Rahimeen , Kanwal Finza , Waqas Muhammad , Khan Osama Jawed , Raveena  , Kumar Ankash , Jabbar Abdul , Madhwani Manwar 
Published: July 2024

AbstractObjectiveThe objective of this study is to investigate how lymphoid progenitor mechanisms contribute to the leukemogenesis in Acute Lymphoblastic Leukemia.BackgroundAcute Lymphoblastic Leukemia (ALL), the leading childhood cancer, remains challenging despite treatment advances. ALL originates from aberrant clonal expansion of immature lymphoid progenitor cells (LPCs) due to genetic abnormalities. This study looks into LPC genetic dysregulations, aiming to identify therapeutic targets and enhance prognostic stratification. Understanding ALL pathogenesis not only improves outcomes but also informs broader cancer research, offering potential insights for hematologic malignancies and oncogenesis, promising advancements in clinical practice.MethodsDatabases, including PubMed, MEDLINE, Google Scholar, and open access/subscription-based journals were searched for published articles without any date restrictions, to investigate leukemogenesis in acute lymphoblastic leukemia and the impact of down syndrome through the developmental regulators of lymphoid progenitor cells. Based on the criteria mentioned in the methods section, studies were systematically reviewed to investigate ALL leukemogenesis. This study adheres to relevant PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses).ResultsAcute Lymphoblastic Leukemia (ALL) development is marked by dysregulations in key factors governing Lymphoid Progenitor Cells (LPCs) proliferation and differentiation. Dysregulations include upregulation of transcription factors Ikaros and PU.1, along with heightened expression of surface markers CD34 and CD38. Increased levels of signaling molecules IL-7, SCF, and FLT3 Ligand drive LPC proliferation, while alterations in epigenetic modifiers DNMTs, HDACs, and HATs further contribute to uncontrolled cell division. Dysregulated transcription factors Ikaros, PU.1, E2A (TCF3), EBF1, and Notch1 disrupt LPC differentiation pathways, alongside aberrant expression of surface markers CD10, CD7, and CD45RA. Dysregulated signaling through IL-7 and the Notch pathway, along with epigenetic modifications mediated by DNMTs, HDACs, and HATs, collectively create a conducive landscape for ALL development.ConclusionThis study into the origins of ALL investigates the roles of transcription factors, surface markers, signaling molecules, and epigenetic modifiers in LPC proliferation and differentiation. Dysregulation of these components, often due to mutations in genes like GATA1, CRLF2, JAK2, and RAS, disrupts normal hematopoietic development and leads to leukemic transformation.
Aberrant flexibility of dynamic brain network in patients with autism spectrum disorder
Authors: Zhang Hui , Peng Dehong , Tang Shixiong , Bi Anyao , Long Yicheng 
Published: July 2024

AbstractIntroductionAutism spectrum disorder (ASD) is a collection of neurodevelopmental disorders whose pathobiology remains elusive. This study aimed to investigate the possible neural mechanisms underlying ASD using a dynamic brain network model and a relatively large-sample, multi-site dataset.MethodsResting-state functional magnetic resonance imaging data were acquired from 208 ASD patients and 227 typical development (TD) controls, who were drawn from the multi-site Autism Brain Imaging Data Exchange (ABIDE)-Preproceesed database. Brain network flexibilities were estimated and compared between the ASD and TD groups at both global and local levels, after adjusting for sex, age, head motion, and site effects. Correlations between the Autism Diagnostic Observation Schedule (ADOS) total score and brain network measures were also investigated after adjusting for the same above covariates.ResultsSignificantly increased brain network flexibilities (indicating a decreased stability) at the global level, as well as at the local level within the default-mode and sensorimotor areas were found in ASD patients than TD participants. Additionally, significant ASD-related decreases in flexibilities (indicating excessively increased stability) were also observed in several occipital regions at the nodal level. Most of these changes were significantly correlated with the ADOS total score in the entire sample.ConclusionThe results in this study suggested that ASD is characterized by significant changes in temporal stabilities of functional brain network. Our results also pointed to ASD-related dysfunctions in the default-mode, sensorimotor, and occipital systems from a perspective of brain network stability, which can further strengthen our understanding of the pathobiology of ASD.
Altered spike IgG Fc N-linked glycans are associated with hyperinflammatory state in adult COVID and Multisystem Inflammatory Syndrome in Children
Authors: Sherman Jacob D. , Karmali Vinit , Kumar Bhoj , Simon Trevor W. , Bechnak Sarah , Panjwani Anusha , Ciric Caroline R. , Wang Dongli , Huerta Chris , Johnson Brandi , Anderson Evan J. , Rouphael Nadine , Collins Matthew H. , Rostad Christina A. , Azadi Parastoo , Scherer Erin M. 
Published: July 2024

AbstractBackgroundSevere COVID and multisystem inflammatory syndrome (MIS-C) are characterized by excessive inflammatory cytokines/chemokines. In adults, disease severity is associated with SARS-CoV-2-specific IgG Fc afucosylation, which induces pro-inflammatory cytokine secretion from innate immune cells. This study aimed to define spike IgG Fc glycosylation following SARS-CoV-2 infection in adults and children and following SARS-CoV-2 vaccination in adults and the relationships between glycan modifications and cytokine/chemokine levels.MethodsWe analyzed longitudinal (n=146) and cross-sectional (n=49) serum/plasma samples from adult and pediatric COVID patients, MIS-C patients, adult vaccinees, and adult and pediatric healthy controls. We developed methods for characterizing bulk and spike IgG Fc glycosylation by capillary electrophoresis (CE) and measured levels of ten inflammatory cytokines/chemokines by multiplexed ELISA.ResultsSpike IgG were more afucosylated than bulk IgG during acute adult COVID and MIS-C. We observed an opposite trend following vaccination, but it was not significant. Spike IgG were more galactosylated and sialylated and less bisected than bulk IgG during adult COVID, with similar trends observed during pediatric COVID/MIS-C and following SARS-CoV-2 vaccination. Spike IgG glycosylation changed with time following adult COVID or vaccination. Afucosylated spike IgG exhibited inverse and positive correlations with inflammatory markers in MIS-C and following vaccination, respectively; galactosylated and sialylated spike IgG inversely correlated with pro-inflammatory cytokines in adult COVID and MIS-C; and bisected spike IgG positively correlated with inflammatory cytokines/chemokines in multiple groups.ConclusionsWe identified previously undescribed relationships between spike IgG glycan modifications and inflammatory cytokines/chemokines that expand our understanding of IgG glycosylation changes that may impact COVID and MIS-C immunopathology.
The S-ligninO-demethylase SyoA: Structural insights into a new class of heme peroxygenase enzymes
Authors: Harlington Alix C. , Das Tuhin , Shearwin Keith E. , Bell Stephen G. , Whelan Fiona 
Published: July 2024

AbstractTheO-demethylation of lignin aromatics is a rate-limiting step in their bioconversion to high-value compounds. A recently discovered cytochrome P450 enzyme SyoA was found to demethylate the sinapyl alcohol-derived (S-lignin) aromatic syringol. In this work, we solved high-resolution X-ray crystal structures of SyoA in the substrate-free and substrate-bound states and evaluate the demethylation ofpara-substituted S-lignin aromatics via the monooxygenase pathway and peroxide shunt pathway. We found that SyoA demethylates S-lignin aromatics with the following activity: 4-methylsyringol > syringaldehyde > syringol exclusively using the peroxide shunt pathway. The atomic-resolution structure of SyoA reveals the position of the non-canonical residues in the I-helix (Gln252 and Glu253). Site-directed mutagenesis of this amide-acid pair of a homologous CYP255 enzyme GcoA, which can catalyze the O-demethylation of guaiacol using both monooxygenase and peroxygenase activity, showed the amide-acid pair is critical for both pathways. This work expands the enzymatic toolkit for improving the capacity to funnel lignin towards high-value compounds, and defines the new chemistry within the active site of the enzyme that enables efficient peroxygenase activity. These insights provide a framework for engineered peroxygenase activity in other cytochrome P450 enzymes, with the potential for more facile catalysis, relative to traditional P450 monooxygenases which require difficult to handle redox partners and expensive nicotinamide cofactors.
Connecting Cosmic Inflation to Particle Physics with LiteBIRD, CMB-S4, EUCLID, and SKA
Authors: Drewes Marco , Ming Lei 
Published: July 2024

We show that next generation Cosmic Microwave Background (CMB) experiments will be capable of the first ever measurement of the inflaton coupling to other particles, opening a new window to probe the connection between cosmic inflation and particle physics. This sensitivity is based on the impact that the reheating phase after cosmic inflation has on the redshifting of cosmic perturbations. For our analysis we introduce a simple analytic method to estimate the sensitivity of future CMB observations to the reheating temperature and the inflaton coupling. Applying our method to LiteBIRD and CMB-S4 we find that, within a given model of inflation, these missions have the potential to impose both an upper and a lower bound on the inflaton coupling. Further improvement can be achieved if CMB data are combined with optical and 21 cm surveys. Our results demonstrate the potential of future observations to constrain microphysical parameters that can provide an important clue to understand how a given model of inflation may be embedded in a more fundamental theory of nature.

Published by the American Physical Society
2024
Diversity, equity and inclusion work: a difference that makes a difference … ?
Authors: Armstrong Ann 
Published: July 2024

PurposeI examine if current diversity, equity and inclusion (DEI) initiatives can actually accomplish what they aim and claim to do. I argue that perforce they cannot, as they remain instruments of capitalist corporations and other similar structures.Design/methodology/approachI draw on a variety of literature, from poetry to theories and to empirical findings.FindingsDEI work so far does not live up to its hyped-up claims. It is time for scholars and practitioners to question the DEI industrial complex and its influence on organizational dynamics. It is not clear that justice can ever be achieved in a capitalist neoliberal economy.Research limitations/implicationsThe paper is not an empirical paper.Practical implicationsDEI work needs to be re-conceived so that it addresses power imbalances, rather serving as a tool to keep organizations comfortable in seeming to change.Social implicationsDEI practitioners will need to draw deeply on their courage so that they do not reinforce the existing systems of capitalist oppression through their well-intentioned work.Originality/valueThe paper argues that DEI work can accomplish little without a radical reconceptualization of its nature as a genuine tool for change, rather than simply window dressing.
Supply chain integration, competitive strategies and firm performance
Authors: Hendijani Rosa , Saeidi Saei Reza 
Published: July 2024

PurposeThis study aims to examine the interaction between different types of supply chain integration (SCI) and competitive strategies on firm performance.Design/methodology/approachThe research method is quantitative. The study develops a structured model and a set of hypotheses based on the related theories. Empirical data is collected in a cross-sectional manner using an online survey to test the model and its hypotheses. The survey comprised standard scales to measure study variables. The scales had high reliability and validity and were commonly used in the literature. The study was conducted on Iranian firms working in steel and auto parts industries. Based on official reports, a total of 305 active companies were found in these two industries. Due to the small population size, all companies in the two industries were contacted for participation. Overall, 84 firms completed the survey. To test the research hypotheses, the authors used hierarchical regression analyses using SPSS 27 software.FindingsResults showed that internal integration improves financial performance when firms follow a cost leadership strategy. Differentiation strategy and process integration interact positively and improve operational performance. Type of industry had no significant effect. The results add to the SCI literature by showing that a match between competitive strategy and integration type can influence both operational and financial performance. In total, firms should focus on the appropriate dimension of SCI based on their competitive strategy to improve the performance of the firm.Originality/valueThe impact of competitive strategy as a moderator on the SCI-performance relationship has not been widely addressed in the literature. In one study, Huoet al.(2014) investigated this relationship using data from 604 manufacturing companies in China. The results provided support for financial performance but not for operational performance. However, the influence of competitive strategies on the SCI performance may vary in different countries and contexts with dissimilar environmental, social and cultural characteristics. As several supply chain scholars have argued, understanding contextual conditions that influence the effect of best practices such as SCI on performance are critical
Exploring integrated reporting's influence on international firms' value relevance
Authors: Hichri Abir , Alqatan Ahmad 
Published: July 2024

Purpose
Analyzing the impact of integrated reporting (IR) on international firms' value relevance, considering diverse information such as income, cash flows, risks, uncertainties and various capitals.

Design/methodology/approach
This paper used a sample of 300 international companies between 2010 and 2019. This paper collected the data from the Thomson Reuters Eikon database. Quantitative methods were used to test the hypotheses. Furthermore, the feasible generalized least squares (FGLS) method was performed to test the hypotheses.

Findings
The results suggest that IR and value relevance positively correlate, confirming the hypothesis. Moreover, this paper verified these results by conducting robustness tests on the contribution of the framework and guidelines prepared by the International Integrated Reporting Council (IIRC) in 2013.

Practical implications
This study enables users to evaluate company transparency and the relevance of disclosed nonfinancial information, providing valuable insights for report preparers and investors seeking profitable opportunities.

Originality/value
The interest in this research was motivated by the authors’ research field, which is innovative, as few studies have been conducted to explain the relationship between IR and value relevance. Similarly, this paper incorporated into their analysis the importance of the framework created by the IIRC in 2013 in preparing and presenting an integrated report. This paper considered the contribution of this framework to the creation of information content. This design has been overlooked in previous studies. However, this paper mobilized the FGLS method, which has been little used in previous studies.
Innovators and Transformers Revisiting the gap between academia and practice: insights from the green logistics phenomenon
Authors: Jazairy Amer , Pohjosenperä Timo , Prataviera Lorenzo Bruno , Juntunen Jouni 
Published: July 2024

PurposeLogistics and supply chain management (L&SCM) scholars and practitioners have devoted extensive efforts to advancing green logistics practices (GLPs), yet the intersection between the two domains in relation to the topic remains underexplored. To accelerate GLPs’ development amid the escalating climate crisis, this research examines this intersection by comparing the responsiveness of academia and practice to the call for green logistics over time.Design/methodology/approachTo compare between academia and practice, we combined a systematic literature review on the development of GLPs in L&SCM journals (N = 122) with a content analysis of annual and sustainability reports published by the four major global logistics service providers (LSPs: DHL, DB Schenker, UPS and FedEx; N = 156) over the past three decades.FindingsThis research reveals that all the GLPs covered in the L&SCM literature have already been applied and reported by practitioners, both consistently and over a significant period of time. Academic progress, in turn, is delayed by slow-paced empirical methods, elevated research quality standards, prolonged funding and recruitment processes, and extended peer-review intervals. Further, a tendency toward reactive knowledge creation rather than proactive knowledge transfer is evident, obscuring the role of L&SCM scholars in steering the industry’s green advancement.Practical implicationsRecommendations are offered to L&SCM authors, editors, reviewers and university departments to advance pracademic endeavors in green logistics research and increase its responsiveness to global events.Originality/valueThis is one of the first studies to scrutinize the intersection between academia and practice on the evolution of GLPs. The revealed gaps prompted us to suggest a transformative paradigm for academia-practice collaborations targeting the L&SCM discipline at large, combining a bold proactive research stream aimed at knowledge transfer with a more traditional reactive stream aimed at knowledge creation.
Analysis of green supply chains under fairness concern and differential power structure
Authors: Ghosh Soumita , Chakraborty Abhishek , Raj Alok 
Published: July 2024

Purpose
This study aims to examine how fairness concerns and power structure in dyadic green supply chains impact retail price, supply chain profits and greening level decisions.

Design/methodology/approach
This study develops game-theoretic models considering fairness concerns and asymmetric power structures under an iso-elastic demand setting. The research paper employs the Stackelberg game approach, taking into consideration the fairness concern of the channel leader.

Findings
The findings indicate that under fairness, there is an increase in both wholesale and retail prices, as well as greening expenditures. Notably, when comparing the two models (manufacturer Stackelberg and retailer Stackelberg), double marginalization is more pronounced in the retailer Stackelberg setup than in the manufacturer Stackelberg setup. In a traditional supply chain with iso-elastic demand, the follower typically extracts higher profit compared to the leader; however, our results show that, under fairness conditions, the leader achieves higher profit than the follower. Additionally, our study suggests that supply chain coordination is unattainable in a fairness setup. This paper provides insights for managers on the optimal supply chain structure and the level of fairness to maximize profit.

Originality/value
This paper investigates the impact of a leader's fairness on the optimal decisions within a green supply chain, an area that has received limited attention previously. Additionally, the study investigates how fairness concerns manifest in distinct power dynamics, specifically, in the contexts of manufacturer Stackelberg and retailer Stackelberg.
Learn bamboo from bamboo: a kinaesthetic communication approach to curating cultures, crafts, and construction for higher education
Authors: Subasinghe Chamila 
Published: July 2024

Purpose
Beyond symptomatic communication barriers between designers and communities, glocal resiliency building (GRB) by intercultural groups often challenges traditional service-learning trajectories. Without ambitious performance hurdles, two higher education institutions from Australia and Thailand built rapport via their shared love for Bamboo to level hierarchies between groups: architects, both social and professional.

Design/methodology/approach
The author used Basho’s “self” – object nexus, as depicted in “Learn Bamboo from Bamboo” Haiku, as a methodology to structure our observations of stakeholders (Haas, 1994). This reflective account, narrated through a tabulated account of iterative engagements among various stakeholders, narrates the metacognitive process of GRB.

Findings
Amidst intercultural communication tensions that could have alienated efforts, Bamboo’s resourcefulness prompted positive stakeholder interactions. Interculturally relatable Bamboo culture could become an effective mode of communication via a synthesis of craft and construction to cultivate culturally intelligent behaviours.

Research limitations/implications
Bamboo was a technology of community that overcame cultural tensions by completing an architectural product.

Originality/value
Despite different languages, work ethics and uneasiness, this activism project sensitised differentiating perspectives to transform traditional knowledge hierarchies to negotiate local know-how. Hence, it highlights activism as a methodology for figuring out the unknown layered in spatial and aspatial attributes of material cultures.