bluuebunny/crossref_metadata_2025_split huggingface dataset:
AncFlow: An Ancestral Sequence Reconstruction Approach for Determining Novel Protein Structural
Authors: Rouzbehani Ryin , Kelley Scott T. 
Published: July 2024

ABSTRACTThe rapid growth of sequence data from high-throughput sequencing technologies has unveiled a vast number of previously unknown proteins, presenting a significant challenge in their functional characterization. Ancestral sequence reconstruction (ASR) has emerged as a powerful tool to elucidate the evolutionary history of protein families and identify sequence determinants of protein function. Here, we present AncFlow, an automated software pipeline that integrates phylogenetic analysis, subfamily identification, and ASR to generate ancestral protein sequences for structural prediction using state-of-the-art tools like AlphaFold. AncFlow streamlines the process of ASR by combining multiple sequence alignment, phylogenetic tree inference, subfamily identification, and ancestral sequence reconstruction from unaligned protein sequences. The reconstructed ancestral sequences are then subjected to structural prediction using AlphaFold, enabling the investigation of the structural basis of functional divergence within protein families. We validated AncFlow using two well-characterized protein families: acyltransferases and dehydrogenases. The pipeline successfully reconstructed ancestral sequences for multiple internal nodes of the phylogenetic trees, and their predicted structures were compared with those of extant proteins. By analyzing the structural similarities and differences between ancestral and extant proteins, we gained insights into the evolutionary mechanisms underpinning the functional diversification within these families. AncFlow demonstrates the potential of integrating ASR and structural prediction to unravel the structural basis of functional divergence in protein families. The insights gained from this approach can guide protein engineering efforts, facilitating the design of proteins with desired functions. As the amount of sequence data continues to grow, AncFlow provides a valuable tool for exploring the evolutionary landscape of proteins and accelerating the discovery of novel protein functions.
MRI signatures of cortical microstructure in human development align with oligodendrocyte cell-type expression
Authors: Genc Sila , Ball Gareth , Chamberland Maxime , Raven Erika P , Tax Chantal MW , Ward Isobel , Yang Joseph Yuan-Mou , Palombo Marco , Jones Derek K 
Published: July 2024

AbstractNeuroanatomical changes to the cortex during adolescence have been well documented using MRI, revealing ongoing cortical thinning and volume loss with age. However, the underlying cellular mechanisms remain elusive with conventional neuroimaging. Recent advances in MRI hardware and new biophysical models of tissue informed by diffusion MRI data hold promise for identifying the cellular changes driving these morphological observations. This study used ultra-strong gradient MRI to obtain high-resolution, in vivo estimates of cortical neurite and soma microstructure in sample of typically developing children and adolescents. Cortical neurite signal fraction, attributed to neuronal and glial processes, increased with age (mean R2fneurite=.53, p<3.3e-11, 11.91% increase over age), while apparent soma radius decreased (mean R2Rsoma=.48, p<4.4e-10, 1% decrease over age) across domain-specific networks. To complement these findings, developmental patterns of cortical gene expression in two independent post-mortem databases were analysed. This revealed increased expression of genes expressed in oligodendrocytes, and excitatory neurons, alongside a relative decrease in expression of genes expressed in astrocyte, microglia and endothelial cell-types. Age-related genes were significantly enriched in cortical oligodendrocytes, oligodendrocyte progenitors and Layer 5-6 neurons (pFDR<.001) and prominently expressed in adolescence and young adulthood. The spatial and temporal alignment of oligodendrocyte cell-type gene expression with neurite and soma microstructural changes suggest that ongoing cortical myelination processes contribute to adolescent cortical development. These findings highlight the role of intra-cortical myelination in cortical maturation during adolescence and into adulthood.
Temperature drives seagrass recovery across the Western North Atlantic
Authors: Smulders Fee O. H. , Campbell Justin E. , Altieri Andrew H. , Armitage Anna R. , Bakker Elisabeth S. , Barry Savanna C. , Becker S. Tatiana , Bethel Enrique , Douglass James G. , van Duijnhoven Hannah J. , de Fouw Jimmy , Frazer Thomas K. , Glazner Rachael , Goeke Janelle A. , Gort Gerrit , Heck Kenneth L. , Kramer Olivier A. A. , van de Leemput Ingrid A. , Manuel Sarah A. , Martin Charles W. , Martinez López Isis G. , McDonald Ashley M. , Munson Calvin J. , O’Shea Owen R. , Paul Valerie J. , Reynolds Laura K. , Rhoades O. Kennedy , Rodriguez Bravo Lucia M. , Sang Amanda , Sawall Yvonne , Smith Khalil , Thompson Jamie E. , van Tussenbroek Brigitta , Wied William L. , Christianen Marjolijn J. A. 
Published: July 2024

AbstractClimate-driven shifts in herbivores, temperature and nutrient runoff threaten coastal ecosystem resilience. However, our understanding of ecological resilience, particularly for foundation species, remains limited due to a rarity of field experiments that are conducted across appropriate spatial and temporal scales and that investigate multiple stressors. This study aimed to evaluate the resilience of a widespread tropical marine plant (turtlegrass) to disturbances across its geographic range and how this is impacted by environmental gradients in (a)biotic factors. We assessed the resilience (i.e. recovery) of turtlegrass to a simulated disturbance (complete above- and belowground biomass removal) over a year. Contrary to temperate studies, higher temperature generally enhanced seagrass recovery. While nutrients and light availability had minimal impact, combined high levels of nutrients and herbivore grazing (meso and megaherbivore) reduced aboveground recovery. Our results suggest that the resilience of some tropical species, especially in cooler subtropical waters, may initially increase with warming.
A lipid nanoparticle-mRNA vaccine provides potent immunogenicity and protection againstMycobacterium tuberculosis
Authors: Lukeman Hannah , Al-Wassiti Hareth , Fabb Stewart A. , Lim Leonard , Wang Trixie , Britton Warwick J. , Steain Megan , Pouton Colin W. , Triccas James A. , Counoupas Claudio 
Published: July 2024

AbstractMycobacterium tuberculosisremains the largest infectious cause of mortality worldwide, even with over a century of widespread administration of the only licensed tuberculosis (TB) vaccine, Bacillus Calmette-Guérin (BCG). mRNA technology remains an underexplored approach for combating chronic bacterial infections such as TB. We have developed a lipid nanoparticle (LNP)-mRNA vaccine encoding for a fusion protein of two immunogenic TB antigens, termed mRNACV2. In C57BL/6 mice intramuscularly vaccinated with mRNACV2, high frequencies of polyfunctional, antigen-specific Th1 CD4+T cells were observed in the blood and lungs, which was associated with the rapid recruitment of both innate and adaptive immune cells to lymph nodes draining the site of immunisation. mRNACV2vaccination provided significant pulmonary protection inM. tuberculosis-infected mice, reducing bacterial load and inflammatory infiltration in the lungs. As BCG is widely administered in infants in TB endemic countries, new TB vaccines should be able to boost the effects of BCG. Importantly, mRNACV2enhanced immune responses and long-term protection when used to boost BCG-primed mice. These findings, which provide the first report of a highly protective LNP-mRNA vaccine for TB, highlight the potential of the LNP-mRNA platform for TB control and support further research to facilitate translation to humans.
Development of an Organ-on-a-Chip for Correlative Microscopy: Visualizing Early Osteogenesis in 3D with High Resolution
Authors: Schaart Judith M. , Wasserberg Dorothee , Eufrásio Cruz Marcos A. , Lindert Mariska Kea-te , van der Meijden Robin H.M. , Roverts Rona , Debera Nataliya D. , Lu Minh Phu , Rouwkema Jeroen , Nijhuis Wouter H. , van der Meer Andries D. , Jonkheijm Pascal , Sommerdijk Nico , Akiva Anat 
Published: July 2024

AbstractOrgans-on-a-chip are of increasing interest for studying tissue development in health and disease. In the past years, platforms have been developed to analyze developmental biological processes by light microscopy and biochemical assays. While these show great potential for pharmaceutical applications, retrieving ultrastructural information about microtissues remains challenging. In this study, an organ-on-a-chip is presented that is suitable for analysis by correlative light and electron microscopy. Using osteogenic cultures in which the cells and deposited collagen matrix align between pillars, the applicability of this platform for high-resolution, longitudinal monitoring of the microtissue development during multiple weeks with 3D live fluorescence microscopy is shown. The analysis of complete microtissues showed the development of two distinct actin patterns during differentiation. Furthermore, intact microtissues were extracted and cryo-fixed by high-pressure freezing, to enable processing for volume electron microscopy. The region of interest for electron microscopy was selected based on the fluorescence images and the resulting FIB/SEM image stack shows ultrastructural information about the cellular organization, collagen alignment, and mineralization in the cultures. The platform developed in this study shows great potential for increasing our understanding of processes underlying structural organization of tissues in health and disease, by allowing ultrastructural analysis of tissues during development.Table of ContentsAn organ-on-a-chip is presented that is suitable for high-resolution fluorescence microscopy over multiple weeks and from which intact samples can be extracted for analysis by volume electron microscopy. A case-study with osteogenically differentiated microtissues showed the development of two types of actin patterns during differentiation. Subsequent electron microscopy showed the presence of aligned cells and collagen, as well as mineral deposition.
Improvement of inert-gas distribution for fuel tanks with the objective of minimum bleed flowrate
Authors: Lin Xinyu , Liu Weihua 
Published: July 2024

Purpose
To ensure the safety of aircraft fuel tanks, the FAA issued an airworthiness clause (25.981(b)) suggesting that the risk of combustion and explosion be reduced by installing a Flammability Reduction Means or an Ignition Mitigation Means. The airflow distribution method has a significant effect on the inerting performance. Therefore, this study aims to determine an optimum airflow distribution method of the inerting system.

Design/methodology/approach
This paper establishes the calculation model of the oxygen concentration in the ullage of a multi-bay fuel tank, calculates the oxygen concentration in the ullage of an aircraft tank in single-flow and dual-flow modes under series and parallel ventilation methods and analyses the inerting performance of the tank under different airflow distribution methods.

Findings
The results show that: (1) the bleed flow rate required to achieve whole process inerting of multi-bay fuel tank in dual-flow mode is lower than that in single-flow mode; (2) under the parallel ventilation method, the decrease of oxygen concentration and the uniformity of each bay are better than that in the series ventilation method; (3) dual-flow mode staged ventilation method can be used to achieve the whole process inerting of the tanks under the minimum engine bleed consumption.

Originality/value
The novelty of this paper is to analyze and optimize the airflow distribution method of the inerting system under the whole flight envelope to minimize the engine bleed consumption.
A lightweight interactive approach for unstructured surface mesh generation
Authors: Liu Yang , Hu Yuefan , Xie Dongxiang , Zhang Yongjie , Chen Jianqiang 
Published: July 2024

PurposeThe paper aims to propose a generation approach for unstructured surface mesh to speed up mesh generation.Design/methodology/approachThe paper proposes a lightweight interactive generation approach for unstructured surface mesh and presents several key technologies to support this approach.FindingsThe experimental results show that the proposed approach is feasible for unstructured meshes and it can accelerate the mesh generation process.Research limitations/implicationsMore geometric defects should be covered, and more convenient and efficient interactive means need to be provided.Practical implicationsThe proposed approach and key technologies are implemented in NNW-GridStar.UG, which is the unstructured version of the mesh generation software of National Numerical Windtunnel (NNW).Originality/valueThis paper proposes a lightweight interactive approach for unstructured surface mesh generation, which can speed up mesh generation.
Clawback enforcement heterogeneity and the horizon of executive pay: empirical evidence
Authors: Remesal Alvaro 
Published: July 2024

Purpose
Clawback provisions entitle shareholders to recover previously awarded incentive compensation after the discovery of accounting manipulation or misconduct. The author evaluates the impact of clawback enforcement heterogeneity on the horizon of executive compensation.

Design/methodology/approach
The author provides empirical tests to evaluate the impact of clawback adoption decisions. The author deals with the endogeneity of clawback adoption decisions through an instrumental variables strategy that exploits the transmission of governance choices within firms’ networks.

Findings
While the author finds that clawback adoption reduces the frequency of accounting manipulation, this reduction is accompanied by heterogeneous effects on the horizon of executive pay across firms. Clawback adopters with high director independence, high leverage, high managerial termination payments and low executive ownership tilt their compensation toward the short-term.

Practical implications
The results, robust to alternative specifications, suggest that clawbacks allow strong-enforcement firms to tilt compensation toward the short-term, offsetting some of the direct manipulation disincentives generated by the clawback. The stock market reacts positively to the adoption in firms with weak enforcement, suggesting that clawbacks significantly reduce the managers’ rent-extraction capacity.

Originality/value
Using a novel empirical and identification approach, the results suggest that clawbacks allow strong-enforcement firms to tilt compensation toward the short-term, offsetting some of the direct manipulation disincentives generated by the clawback.
The impact of earnings opacity on corporate social responsibility: insights from Vietnamese listed firms
Authors: Nguyen Ha Thi Thu , Nguyen Tri Tri , Nguyen Hien Thi Thu 
Published: July 2024

PurposeThis paper studies the association between earnings opacity and corporate social responsibility disclosures of firms listed on the Vietnamese Stock Exchange.Design/methodology/approachWe utilize a dataset comprising a sample of all listed Vietnamese firms for the period of 2014–2022. Data regarding corporate social responsibility information are gathered manually. Following Dechow et al. (1995), Kothari et al. (2005) and Bhattacharya et al. (2003), earnings opacity is measured by using three proxies, including abnormal accruals, earnings smoothing and loss avoidance. Our hypothesis was tested via ordinary least squares (OLS) regressions. To address endogeneity problems, we use the two-stage instrumental variable method (IV-2SLS) as well as the generalized method of moments (GMM) to ensure the robustness of our results.FindingsWe find that earnings opacity is positively related to corporate social responsibility disclosures. Cross-sectional analyses indicate that managers of firms disguise their opportunistic behaviour by disclosing more information about corporate social responsibility. The evidence also shows that firms experience long-run underperformance when having higher earnings opacity and greater sustainability disclosures. Our results remain robust even after correcting for endogeneity using the IV approach and the GMM method.Practical implicationsEvidence from this study can serve as a warning signal to the investment community, highlighting that some methods aimed at enhancing a firm’s corporate social responsibility disclosures might be used to obstruct other unethical activities. Moreover, the results of this study can help regulators gain a better comprehension of firms' reporting patterns concerning corporate social responsibility initiatives. It should not only reform the corporate social responsibility regulation but also impose stronger litigation for firms to enhance the quality of corporate social responsibility disclosures.Originality/valueWe are the first to present evidence regarding the relationship between earnings opacity and corporate social responsibility disclosure in Vietnam.
Enhancing user engagement and loyalty in online travel agents: a gamification approach
Authors: Choirisa Septi Fahmi , Waworuntu Alexander , Istiono Wirawan 
Published: July 2024

Purpose
This study aims to investigate the effects of gamification features on brand engagement dimensions in online travel agents (OTAs), specifically brand awareness and loyalty.

Design/methodology/approach
The proposed model is empirically evaluated through an online survey of 406 Indonesian OTA users. Partial least squares structural equation modeling analysis was used to assess the model.

Findings
The findings reveal that gamification boosts emotional and social brand engagement, while achievement improves cognitive brand engagement. Cognitive brand engagement only affects brand loyalty, excluding brand awareness; however, emotional and social brand engagement substantially impact brand awareness and loyalty.

Originality/value
This study addresses the gap in the limited empirical studies on gamification in the tourism and hospitality industries, with a particular focus on OTAs.
Based on the S–O–R theory adoption intention of blockchain technology in libraries: a two-stage analysis SEM–PLS and ANN
Authors: Khan Asad Ullah , Jan Saeed Ullah , Khan Muhammad Naeem , Aziz Fazeelat , Sohu Jan Muhammad , Ali Johar , Khan Maqbool , Chohan Sohail Raza 
Published: July 2024

PurposeBlockchain, a groundbreaking technology that recently surfaced, is under thorough scrutiny due to its prospective utility across different sectors. This research aims to delve into and assess the cognitive elements that impact the integration of blockchain technology (BT) within library environments.Design/methodology/approachUtilizing the Stimulus–Organism–Response (SOR) theory, this research aims to facilitate the implementation of BT within academic institution libraries and provide valuable insights for managerial decision-making. A two-staged deep learning structural equation modelling artificial neural network (ANN) analysis was conducted on 583 computer experts affiliated with academic institutions across various countries to gather relevant information.FindingsThe research model can correspondingly expound 71% and 60% of the variance in trust and adoption intention of BT in libraries, where ANN results indicate that perceived possession is the primary predictor, with a technical capability factor that has a normalized significance of 84%. The study successfully identified the relationship of each variable of our conceptual model.Originality/valueUnlike the SOR theory framework that uses a linear model and theoretically assumes that all relationships are significant, to the best of the authors’ knowledge, it is the first study to validate ANN and SEM in a library context successfully. The results of the two-step PLS–SEM and ANN technique demonstrate that the usage of ANN validates the PLS–SEM analysis. ANN can represent complicated linear and nonlinear connections with higher prediction accuracy than SEM approaches. Also, an importance-performance Map analysis of the PLS–SEM data offers a more detailed insight into each factor's significance and performance.
Real asset liquidity and accounting conservatism: evidence from asset redeployability
Authors: Huang Wei , Zhang Rui-Zhong (R.Z.) 
Published: July 2024

PurposeThis study examines the implications of real asset liquidity for accounting conservatism. We investigate whether the liquidity of a firm’s physical assets mitigates lenders’ demand for conservatism by increasing the amount lenders can recover if the firm is liquidated, a theoretical prediction in Göx and Wagenhofer (2009).Design/methodology/approachWe use an asset redeployability index as a proxy for firm-level real (physical) asset liquidity and adopt ordinary least squares (OLS) regressions in the test. We also investigate the differential impact of real asset liquidity on conservatism in two unique settings where lenders’ demand for accounting conservatism varies (loan initiation and bank deregulation).FindingsWe find that accounting conservatism decreases as real asset liquidity increases. The negative effect of real asset liquidity on conservatism increases as the quantity of the firm’s real assets increases, and the negative association is strengthened when firms face high financing constraints and have access to public debt markets. The moderating effect of real asset liquidity on lenders’ demand for conservatism increases (decreases) when real asset liquidity is more (less) important to lenders.Originality/valueThis study provides direct empirical evidence for the theoretical prediction in Göx and Wagenhofer (2009). Prior research shows that real asset liquidity impacts a firm’s capital structure and investment decisions (Campello and Giambona, 2013; Kim and Kung, 2017; Ortiz-Molina and Phillips, 2014; Williamson, 1988). We complement this literature by providing evidence that real asset liquidity also plays a role in financial reporting by reducing accounting conservatism.
Transient, context‐dependent fitness costs accompanying viral resistance in isolates of the marine microalga Micromonas sp. (class Mamiellophyceae)
Authors: Bedi de Silva Anamica , Polson Shawn W. , Schvarcz Christopher R. , Steward Grieg F. , Edwards Kyle F. 
Published: July 2024

AbstractMarine microbes are important in biogeochemical cycling, but the nature and magnitude of their contributions are influenced by their associated viruses. In the presence of a lytic virus, cells that have evolved resistance to infection have an obvious fitness advantage over relatives that remain susceptible. However, susceptible cells remain extant in the wild, implying that the evolution of a fitness advantage in one dimension (virus resistance) must be accompanied by a fitness cost in another dimension. Identifying costs of resistance is challenging because fitness is context‐dependent. We examined the context dependence of fitness costs in isolates of the picophytoplankton genus Micromonas and their co‐occurring dsDNA viruses using experimental evolution. After generating 88 resistant lineages from two ancestral Micromonas strains, each challenged with one of four distinct viral strains, we found resistance led to a 46% decrease in mean growth rate under high irradiance and a 19% decrease under low. After a year in culture, the experimentally selected lines remained resistant, but fitness costs had attenuated. Our results suggest that the cost of resistance in Micromonas is dependent on environmental conditions and the duration of population adaptation, illustrating the dynamic nature of fitness costs of viral resistance among marine protists.