bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics
Authors: Hotaling Scott , Wilcox Edward R. , Heckenhauer Jacqueline , Stewart Russell J. , Frandsen Paul B. 
Published: July 2022

AbstractBackgroundGenerating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly,Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6,750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata.ResultsHiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ∼20 KbH-fibroingene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size.ConclusionsHighly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.
The selective autophagy receptor p62 and the heat shock protein HSP27 facilitate lysophagy via the formation of phase-separated condensates
Authors: Gallagher Elizabeth R. , Holzbaur Erika L.F. 
Published: July 2022

SummaryLysosomes are membrane-bound organelles that regulate cellular proteostasis. Loss of lysosomal integrity initiates cell death pathways. Thus, cells must rely on quality control mechanisms for protection, including the selective isolation and degradation of damaged lysosomes by lysophagy. Here, we report that the selective autophagy receptor SQSTM1/p62 is an essential lysophagy receptor recruited to damaged lysosomes in both HeLa cells and neurons. p62 oligomers form liquid-like condensates that are critical in lysophagy. These condensates are regulated by the small heat shock protein HSP27, which binds p62 to prevent p62 aggregation and facilitate autophagosome formation. Mutations in p62 are implicated in Amyotrophic Lateral Sclerosis (ALS), and expression of ALS-associated mutations in p62 impair lysophagy, suggesting that deficits in this pathway may contribute to the cellular pathogenesis of ALS. Thus, p62 oligomers cooperate with HSP27 to promote lysophagy by forming a platform for autophagosome biogenesis at damaged lysosomes.
Temporal single cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury
Authors: Benhar Inbal , Ding Jiarui , Yan Wenjun , Whitney Irene E. , Jacobi Anne , Sud Malika , Burgin Grace , Shekhar Karthik , Tran Nicholas M. , Wang Chen , He Zhigang , Sanes Joshua R. , Regev Aviv 
Published: July 2022

AbstractNon-neuronal cells play key roles in the complex cellular interplay that follows central nervous system (CNS) insult. To understand this interplay at a tissue level, we generated a single-cell atlas of immune, glial and retinal pigment epithelial cells from adult mouse retina before and at multiple time points after axonal transection (optic nerve crush; ONC), identifying rare and undescribed subsets, and delineating changes in cell composition, expression programs, and interactions. Computational analysis charted an inflammatory cascade after injury with three phases. The early phase consisted of reactivation of retinal macroglia and microglia, providing chemotactic signals for immune infiltration, concurrent with infiltration of CCR2+monocytes from the circulation. In the second phase, these differentiated to macrophage subsets resembling resident border-associated macrophages. In parallel, a multicellular interferon program, likely driven by microglia-derived type-I interferon, was synchronously activated across resident glia, expanding beyond rare interferon-responding subsets of glia unexpectedly present in the naïve retina. Our findings provide insights regarding post-injury CNS tissue dynamics and a framework to decipher cellular circuitry, spatial relationships and molecular interactions following tissue injury.
Parsimonious EBM: generalising the event-based model of disease progression for simultaneous events
Authors: Parker CS , Oxtoby NP , Young AL ,   Alzheimer’s Disease Neuroimaging Initiative, Alexander DC , Zhang H 
Published: July 2022

AbstractThis study introduces the parsimonious event-based model of disease progression (P-EBM). The P-EBM generalises the event-based model of disease progression (EBM) to allow inference of fewer disease progression stages than the number of input biomarkers. The original EBM is designed to estimate a single distinct biomarker abnormality, termed an event, at each model stage. By allowing multiple events within a common stage, the P-EBM prevents redundant complexity to permit discovery of parsimonious sequences of disease progression - those that contain purely serial events, as in the original EBM, as well as those containing one or more sets of simultaneous events. This study describes P-EBM theory, evaluates its sequence estimation and staging performance and demonstrates its application to derive a parsimonious sequence of disease progression in sporadic Alzheimer’s disease (AD). Results show that the P-EBM can accurately recover a wider range of sequences than EBM under a range of realistic experimental scenarios, including different numbers of simultaneous events, biomarker disease signals and dataset sizes. The P-EBM sequence successfully highlights redundant biomarkers and stages subjects using fewer biomarkers. In sporadic AD, the P-EBM estimates a shorter sequence than the EBM with substantially higher likelihood which plausibly suggests that some biomarker events appear simultaneously. The P-EBM has potential application for generating new insights into disease evolution and for suggesting efficient biomarker collection strategies for patient staging.
Dynamic changes in the mouse hepatic lipidome following warm ischemia reperfusion injury
Authors: Liss Kim H.H. , Mousa Muhammad , Bucha Shria , Lutkewitte Andrew , Allegood Jeremy , Cowart L. Ashley , Finck Brian N. 
Published: July 2022

AbstractLiver failure secondary to nonalcoholic fatty liver disease (NAFLD) has become the most common cause for liver transplantation in many parts of the world. Moreover, the prevalence of NAFLD not only increases the demand for liver transplantation, but also limits the supply of suitable donor organs because steatosis predisposes grafts to ischemia-reperfusion injury (IRI). There are currently no pharmacological interventions to limit hepatic IR injury because the mechanisms by which steatosis leads to increased injury are unclear. To identify potential novel mediators of IR injury, we used liquid chromatography and mass spectrometry to assess temporal changes in the hepatic lipidome in steatotic and non-steatotic livers after warm IRI in mice. Our untargeted analyses revealed distinct differences between the steatotic and non-steatotic response to IRI and highlighted dynamic changes in lipid composition with marked changes in glycerolipids and glycerophospholipids. These findings enhance our knowledge of the lipidomic changes that occur following IRI and provide a foundation for future mechanistic studies. A better understanding of the mechanisms underlying such changes will lead to novel therapeutic strategies to combat IR injury.
Integrated rational and evolutionary engineering of genome-reducedPseudomonas putidastrains empowers synthetic formate assimilation
Authors: Turlin Justine , Dronsella Beau , Maria Alberto De , Lindner Steffen N. , Nikel Pablo I. 
Published: July 2022

AbstractFormate is a promising, water-soluble C1 feedstock for biotechnology since it can be efficiently produced from CO2—but very few industrially-relevant hosts have been engineered towards formatotrophy. Here, the non-pathogenic soil bacteriumPseudomonas putidawas adopted as a platform for synthetic formate assimilation. The metabolism of genome-reduced variants ofP. putidawas rewired to establish synthetic auxotrophies that could be functionally complemented by expressing components of the reductive glycine (rGly) pathway. The rGly pathway mediates the formate → glycine → serine transformations that yield pyruvate, ultimately assimilated into biomass. We adopted a modular engineering approach, dividing C1 assimilation in segments composed of both heterologous activities (sourced fromMethylorubrum extorquens) and native reactions. Promoter engineering of chromosomally-encoded functions coupled to modular expression of rGly pathway elements enabled growth on formate as carbon source and acetate for energy supply. Adaptive laboratory evolution of two lineages of engineeredP.putidaformatotrophs significantly reduced doubling times to ca. 15 h. During evolution, two catabolic regimes became predominant in independently evolved clones, eitherviaglycine hydroxymethylation (GlyA) or oxidation (ThiO). Taken together, our results expand the landscape of microbial platforms for C1-based biotechnological production towards supporting a formate bioeconomy.GraphicalAbstract
Impact of pregravid obesity on anti-microbial fetal monocyte response
Authors: Sureshchandra Suhas , Doratt Brianna M. , Mendoza Norma , Varlamov Oleg , Rincon Monica , Marshall Nicole E. , Messaoudi Ilhem 
Published: July 2022

ABSTRACTMaternal pre-pregnancy (pregravid) obesity is associated with adverse outcomes for both mother and offspring. Amongst the complications for the offspring is increased susceptibility and severity of neonatal infections necessitating admission to the intensive care unit, notably bacterial sepsis and enterocolitis. Previous studies have reported aberrant responses to LPS and polyclonal stimulation by umbilical cord blood monocytes that were mediated by alterations in the epigenome. In this study, we show that pregravid obesity dysregulates umbilical cord blood monocyte responses to bacterial and viral pathogens. Specifically, interferon-stimulated gene expression and inflammatory responses to E. coli and respiratory syncytial virus (RSV) were significantly dampened. Although upstream signaling events were comparable, translocation of the key transcription factor NF-κB and chromatin accessibility at pro- inflammatory gene promoters following TLR stimulation was significantly attenuated. Using a rhesus macaque model of western style diet induced obesity, we further demonstrate that this defect is detected in fetal peripheral monocytes and tissue-resident macrophages during gestation. Collectively, these data indicate that maternal obesity and high-fat diet present metabolic, signaling, and epigenetic impediments to pathogen recognition in fetal innate immune cells that result in a state of immune paralysis during gestation and at birth.
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
Authors: Luo Shitong , Su Yufeng , Peng Xingang , Wang Sheng , Peng Jian , Ma Jianzhu 
Published: July 2022

AbstractAntibodies are immune system proteins that protect the host by binding to specific antigens such as viruses and bacteria. The binding between antibodies and antigens is mainly determined by the complementarity-determining regions (CDR) of the antibodies. In this work, we develop a deep generative model that jointly models sequences and structures of CDRs based on diffusion probabilistic models and equivariant neural networks. Our method is the first deep learning-based method that generates antibodies explicitly targeting specific antigen structures and is one of the earliest diffusion probabilistic models for protein structures. The model is a “Swiss Army Knife” capable of sequence-structure co-design, sequence design for given backbone structures, and antibody optimization. We conduct extensive experiments to evaluate the quality of both sequences and structures of designed antibodies. We find that our model could yield competitive results in binding affinity measured by biophysical energy functions and other protein design metrics.
Bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir treatment inhibits cancer metastasis
Authors: Wang Changdong , Shen Yanxi , Xu Jie , Ma Yongping 
Published: July 2022

AbstractPrevious studies have found thatBifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir (BF-TK/GCV) reduces the expression of VEGF and CD146 which implies tumor metastasis inhibition. However, the mechanism of BF-TK/GCV inhibits tumor metastasis is still not fully studied. Here, we comprehensively identified and quantified protein expression profiling for the first time in gastric cancer (GC) cells MKN-45 upon BF-TK/GCV treatment using quantitative proteomics. A total of 159 and 72 differential expression proteins (DEPs) were significantly changed in BF-TK/GCV / BF-TK and BF-TK/GCV / BF/GCV groups. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed some enriched metastasis-related pathways such as gap junction and cell adhesion molecules pathways. Moreover, transwell assay proved that BF-TK/GCV inhibited the invasion and migration of tumor cells. Furthermore, immunohistochemistry (IHC) demonstrated that BF-TK/GCV reduced the expression of HIF-1A, MTOR, NF-κB1-p105, VCAM1, CEBPB and CXCL12, which were associated with tumor metastasis.In summary, besides apoptosis, BF-TK/GCV also inhibited tumor metastasis, which deepened and expanded the understanding of BF-TK/GCV anti-tumor mechanisms.
Germline protein, Cup, non-cell autonomously limits migratory cell fate in Drosophila oogenesis
Authors: Saha Banhisikha , Acharjee Sayan , Ghosh Gaurab , Dasgupta Purbasa , Prasad Mohit 
Published: July 2022

AbstractAttaining migratory fate from a stationary cell population is complex and indispensable both for the multicellular organism development as well for the pathological condition like tumor metastasis. Though widely prevalent in the metazoans, the molecular understanding of this phenomenon remains elusive. Specification of migratory border cells from the follicular epithelium during Drosophila oogenesis has emerged as one of the excellent model systems to study how motile cell are specified. JAK-STAT activation in 6-10 anterior most follicle cells of the Drosophila egg chamber transforms them to a migratory cluster called the border cells. We show that a nurse cell protein, Cup, non-cell autonomously restricts the domain of JAK-STAT activation in the anterior follicle cells. Further examination suggests that Cup functions through Rab11GTPase to regulate Delta trafficking in the nurse cells potentiating Notch activation in the anterior follicle cells. Since Notch activity in the follicle cells modulates the JAK-STAT, any perturbation in Notch activation affects the border cell fate. Altogether, we propose that germline Cup affects the border cell fate through appropriate activation of Notch and JAK-STAT signaling in the follicle cells.
Blockchain in accounting, accountability and assurance: an overview
Authors: Spanò Rosanna , Massaro Maurizio , Ferri Luca , Dumay John , Schmitz Jana 
Published: July 2022

PurposeThis study aims to present an overview of topics addressed in the papers appearing in this AAAJ special issue: Blockchain in accounting, accountability and assurance.Design/methodology/approachThe authors present a review focussing on the papers published in this special issue. The authors imported the eight accepted papers into NVivo, coding them according to the research topics posed in the call for papers. Then, the authors conducted an in vivo coding for the emerging themes found in the papers.FindingsBlockchain is a multifaced topic with multiple implications for accounting, auditing and accountability, the accounting professions, and governance. However, blockchain is still a developing topic. Blockchain research traditionally has four stages. More recently, a new research stage deserving more investigation is emerging based on the interaction of blockchain with other technological developments such as virtual reality and the metaverse.Originality/valueThe review not only uncovers and systematises the multiple implications of blockchain for accounting research. It also unveils the dark side of blockchain, focusing on the technology's negative environmental and social implications. Last, the authors highlight why accounting research should more extensively examine contemporary issues.
The contagion effect of decreasing audit's quality on financial statement audit engagement: the Indonesian case
Authors: Budisantoso Totok , Kurniawan Heni 
Published: July 2022

PurposeThe main objective on this research is providing evidence of the contagion effect of decreasing audit's quality. Audit failure affects the quality of the financial analysis that has been carried out and has a big impact on the accuracy of decision making due to the material information bias. Findings of this research will urge the Public Accounting Firm (PAF) to design a quality control of the audit services. This action is taken with the consideration of maintaining the quality of audit services and the reputation of auditors.Design/methodology/approachUtilizing manufacturing data listed on Bursa Efek Indonesia (BEI), the researchers developed a model to explain the audit failure which is seen from restatement of financial statement in the subsequent period.FindingsThis research indicates that audit failure to detect the misstatement will decrease the audit's quality of other companies audited by the same auditor. There is also an insight that contagion effect of decreasing auditor quality was stronger for non-big four and non-industry specialist auditors.Research limitations/implicationsAudit failure still has the potential to occur. There is the potential that a failure in an audit of a particular client entity has an impact on defects of other clients served. If this allegation is proven, there are big challenges faced by the public accounting profession and PAF to pay special attention in order to maintain the professional reputation.Practical implicationsProfessional body and government need to develop a robust standard and operating procedures as well as quality control on audit engagement.Originality/valueDue to the intention of fraud occurred in Indonesia, namely SNP Finance and Garuda Indonesia case. It is important to learn from that cases. This research gives fruitful insights to prevent the same case in the future.
The CSR-performance nexus in the French tourism sector: do MCs matter?
Authors: Theiri Saliha , Alareeni Bahaaeddin Ahmed 
Published: July 2022

Purpose
The concept of corporate social responsibility (CSR) covers a wide range of actions toward sustainable development. While there are growing bodies of research examining the drivers of CSR, little has been done to examine the effect of the characteristics of the managerial team on CSR. This paper aims to investigate the interplay between managerial characteristics and CSR practices to discover how such a fit affects financial performance.

Design/methodology/approach
A partial least squares-path modeling approach was applied to a sample of 60 French companies in the tourism sector (hotels, restaurants, leisure and leisure equipment) from 2014 to 2019. This choice was triggered by the importance of this sector in job creation, which has been strongly impacted by the pandemic crisis.

Findings
The findings suggest the positive impact of the managerial characteristics on the practices of CSR activities under certain financial constraints related to the size and indebtedness level. Then, the authors clarify that the variable characteristics component of the managerial team is mainly the educational level, the managerial experience and the ethical behavior. However, no age effect is mentioned. Third, the authors show that the managerial team characteristics and the practices of CSR activities restore the financial tourism sector performance.

Research limitations/implications
This study has obviously certain limitations: first, the selected European sample can mark a big difference in the founding results because of the difference in civil rights. Second, the sample is more marked in the CSR activities. Third, this study did not take into consideration variables operationalizing ownership structure and board nature.

Originality/value
This study develops a model based on “managerial team” mechanisms in a sensitive area. This is a breakthrough in understanding the determinants of CSR strategies and their impact on performance while taking into account the management team’s personal characteristics.
Measuring the personal perspective on work engagement: An empirical exploration of the self-anchoring work engagement scale in Poland
Authors: Kulikowski Konrad 
Published: July 2022

PurposeWork engagement is among the most influential constructs in human resource management, but work engagement's current understanding overlooks what employees consider as engagement. The author aims to advance the human resources theory and practice by discussing the need for understanding engagement from the employee point of view, and the author explores the properties of a self-anchoring work engagement scale – the measure capturing the personal perspective on work engagement.Design/methodology/approachThe author has presented a conceptual discussion providing a rationale for capturing employee personal perspective on work engagement as supplementary to multi-item measures capturing researcher perspective. Based on empirical evidence, the author tests convergent and discriminant validity of self-anchoring work engagement in relation to job resources, job demands and burnout; the author confronts the nomological network of self-anchoring scale with previous work engagement meta-analysis.FindingsThe obtained results provided preliminary evidence supporting convergent and discriminant validity of self-anchoring work engagement. The analysis of the nomological network of self-anchoring work engagement in comparison to the previous meta-analysis revealed that self-anchoring work engagement might be more strongly related to challenging job demands than the multi-item researcher perspective work engagement.Research limitations/implicationsPractical implicationsSocial implicationsOriginality/valueThe author's findings provide a modicum of evidence that asking employees about self-assessment of employees' work engagement on a 0–10 scale provides researchers with access to a freely available measurement method of the personal perception on work engagement.Contribution to impact