bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families
Authors: Zhong Yichen , Sani Hakimeh Moghaddas , Paudel Bishnu Prasad , Low Jason K. K. , Silva Ana P. G. , Mueller Stefan , Deshpande Chandrika , Panjikar Santosh , Reid Xavier J. , Bedward Max J. , van Oijen Antoine M. , Mackay Joel P. 
Published: June 2022

SummaryCHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ∼150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.
Dominant constraints on the evolution of rhythmic gene expression
Authors: Cheng Yang , Chi Yuhao , Sun Linying , Wang Guang-Zhong 
Published: June 2022

AbstractAlthough the individual transcriptional regulators of the core circadian clock are distinct amongst different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, whether analogous design principles govern the gene expression output of circadian clocks is unknown. Herein, we performed a comparative analysis of rhythmic gene expression in eight diverse species and captured four common distribution patterns of cycling gene expression across these species. We hypothesized that maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the late- and early-phase peaks of rhythmic expression have been subjected to this type of selective pressure. Therefore, energetic costs have constricted the cycling transcriptome throughout evolutionary history.
Investigating interspecific quorum sensing influence on cocoa fermentation quality through defined microbial cocktails
Authors: Almeida O.G.G. , Pereira M. G. , Bighetti-Trevisan R. L. , Santos E.S. , De Campos E. G. , Felis G.E. , Guimarães L.H.S. , Polizeli M.L.T.M , De Martinis B. S. , De Martinis E.C.P. 
Published: June 2022

AbstractThe fermentation of cocoa beans is a key process to supply high quality ingredients for the chocolate industry. In spite of several attempts to obtain standardised microbial cultures for cocoa fermentation, it is still a spontaneous process. It has been suggested lactobacilli present potential for quorum sensing (QS) regulation in cocoa fermentation, and in the present research, laboratory scale fermentations were carried out to further elucidate possible QS influence on microbial shifts and fermented seeds quality. The experimental design comprised the 96 hours-fermentations designated as F0 (control), F1 (yeasts, lactic acid bacteria, and acetic acid bacteria), F2 (yeasts and acetic acid bacteria), F3 (yeasts only), with evaluation of the microbial succession by plate counting, determination of enzymatic activities by classical methods and qualitative evaluation of flavour compounds by gas-chromatography (GC-MS) with headspace sampling. Besides, QS was estimated by quantification of the expression of luxS genes by Reverse Transcriptase Real Time PCR analysis using selected primers. The results demonstrated that microbial successions were displayed in lab conditions, but no statistical difference in terms of microbial enumeration and α-diversity metrics were observed among the experimental and control fermentations. Moreover, enzymatic activities were not correlated to the total microbiota, indicating the seeds’ endogenous hydrolases protagonist enzymes secretion and activity. Regarding luxS genes measuring for the species Lactiplantibacillus plantarum and Limosilactobacillus fermentum, genes were active in fermentation in the start to the end phase and to the beginning to the middle phase of fermentation, respectively. Correlation analysis among luxS expression and volatile metabolites evidenced Lp. plantarum association with detrimental compounds for fermentation quality. This data contributes to our previous research which monitored fermentations to survey enzymatic changes and QS potential along the process and sheds light of QS-related strategies of lactobacilli dominance in cocoa fermentations.
E-cadherin in developing murine T cells controls spindle alignment and differentiation during β-selection
Authors: Charnley Mirren , Allam Amr H , Newton Lucas M , Humbert Patrick O , Russell Sarah M 
Published: June 2022

AbstractA critical stage of T cell development is β-selection; at this stage the TCRβ chain is generated and the developing T cell starts to acquire antigenic specificity. Progression through β-selection is assisted by a low affinity interaction between the nascent TCRβ chain and peptide presented on stromal MHC and external cues provided by the niche, including Notch and CXCR4. In this study, we reveal the importance of a new cue within the murine developing T cell niche which is critical for T cell development. E-cadherin mediates cell-cell interactions and influences cell fate in many developmental systems. In developing T cells E-cadherin contributed to the formation of an immunological synapse and the alignment of the mitotic spindle with the polarity axis during division, which facilitated subsequent T cell development. Collectively, these data highlight a new aspect of the developing T cell niche and provide insights into the role of E-cadherin in the β-selection stage of T cell development.
Oxysterols drive inflammation via GPR183 during influenza virus and SARS-CoV-2 infection
Authors: Foo Cheng Xiang , Bartlett Stacey , Chew Keng Yih , Ngo Minh Dao , Bielefeldt-Ohmann Helle , Arachchige Buddhika Jayakody , Matthews Benjamin , Reed Sarah , Wang Ran , Sweet Matthew J. , Burr Lucy , Sinclair Jane E. , Parry Rhys , Khromykh Alexander , Short Kirsty R. , Rosenkilde Mette Marie , Ronacher Katharina 
Published: June 2022

AbstractRationaleSevere viral respiratory infections are often characterized by extensive myeloid cell infiltration and activation and persistent lung tissue injury. However, the immunological mechanisms driving excessive inflammation in the lung remain elusive.ObjectivesTo identify the mechanisms that drive immune cell recruitment in the lung during viral respiratory infections and identify novel drug targets to reduce inflammation and disease severity.MethodsPreclinical murine models of influenza virus and SARS-CoV-2 infection.ResultsOxidized cholesterols and the oxysterol-sensing receptor GPR183 were identified as drivers of monocyte-macrophage infiltration to the lung during influenza virus (IAV) and SARS-CoV-2 infections. Both IAV and SARS-CoV-2 infections upregulated the enzymes cholesterol 25-hydroxylase (CH25H) and cytochrome P450 family 7 subfamily member B1 (CYP7B1) in the lung, resulting in local production of the oxidized cholesterols 25-hydroxycholesterol and 7α,25-dihydroxycholesterol (7α,25-OHC). Loss-of-function mutation of GPR183, or treatment with a GPR183 antagonist, reduced macrophage infiltration and inflammatory cytokine production in the lungs of IAV- or SARS-CoV-2-infected mice. The GPR183 antagonist also significantly attenuated the severity of SARS-CoV-2 infection by reducing weight loss and viral loads.ConclusionThis study demonstrates that oxysterols drive inflammation in the lung and provides the first preclinical evidence for therapeutic benefit of targeting GPR183 during severe viral respiratory infections.Author SummaryViral infections trigger oxysterol production in the lung, attracting macrophages via GPR183. Blocking GPR183 reduced inflammation and disease severity in SARS-CoV-2 infection, making GPR183 a putative target for therapeutic intervention.
Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease
Authors: Leibold Josef , Amor Corina , Tsanov Kaloyan M. , Ho Yu-Jui , Sánchez-Rivera Francisco J. , Feucht Judith , Baslan Timour , Chen Hsuan-An , Tian Sha , Simon Janelle , Wuest Alexandra , Wilkinson John E. , Lowe Scott W. 
Published: June 2022

ABSTRACTMetastatic gastric carcinoma is a highly lethal cancer that responds poorly to conventional and molecularly targeted therapies. Despite its clinical relevance, the mechanisms underlying the behavior and therapeutic response of this disease are poorly understood owing, in part, to a paucity of tractable models that faithfully recapitulate different subtypes of the human disease. To close this gap, we developed methods to somatically introduce different oncogenic lesions directly into the stomach epithelium and show that genotypic configurations observed in patients produce metastatic gastric cancers that recapitulate the histological, molecular, and clinical features of all non-viral molecular subtypes of the human disease. Applying this platform to both wild-type and immune-deficient mice revealed previously unappreciated links between the genotype, organotropism and immune surveillance of metastatic cells that produced distinct patterns of metastasis that were mirrored in patients. Our results establish and credential a highly portable platform for producing autochthonous cancer models with flexible genotypes and host backgrounds, which can unravel mechanisms of gastric tumorigenesis or test new therapeutic concepts aimed at improving outcomes in gastric cancer patients.
Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography
Authors: Hernandez Pichardo Alejandra , Littlewood James , Taylor Arthur , Wilm Bettina , Lévy Raphaël , Murray Patricia 
Published: June 2022

AbstractElucidating the mechanisms of action and long-term safety of cell therapies is necessary for their clinical translation. Non-invasive imaging technologies such as bioluminescence imaging (BLI), computed tomography (CT) and multispectral optoacoustic tomography (MSOT) have been proposed as tools for longitudinal cell monitoring but their performances have not been compared. Here, we evaluate combinations of these modalities to track the in vivo distribution of gold-labelled mesenchymal stromal cells (MSCs). We found that injected MSCs labelled with gold nanoparticles and expressing the reporter gene firefly luciferase could be detected with BLI and MSOT but not CT. We conclude that the MSCs did not carry enough contrast agent to be tracked by CT, demonstrating that CT tracking of gold-labelled cells is not a practical approach as high amounts of gold, which might impair cell viability, are necessary.
Patterns of sexual variation in hominoid mandibular morphology: a framework for interpreting the hominin fossil record
Authors: Nadal Lucía , Lahr Marta Mirazón 
Published: June 2022

AbstractFor many species, sexual dimorphism is one of the major sources of intraspecific variation. This is the case in some extant great apes, such as gorillas and orangutans, and to a lesser degree in humans, chimpanzees and bonobos. This variation has been well documented in various aspects of these species skeletal anatomy, including differences in the size and shape of the body, cranium, canines, and cresting of males and females, but less is known about sexually dimorphic variation of great ape mandibles. This is particularly important for building robust analog models to interpreting variation in the early hominin fossil record which preserves a large proportion of isolated mandibles and partial mandibles. Here we describe the phenotypical expression of sexual dimorphism in the mandible of six extant hominoid species, including humans, using geometric morphometrics. Our analyses show that the extent of sexual dimorphism in mandibular size and shape amongst the species studied is not the same, as well as the presence of significant differences in the degree of sexual dimorphism being expressed at different sections of the mandible. Furthermore, we find significant differences in how sexual dimorphism is expressed phenotypically even amongst closely related species with small divergence times. We discuss the potential pathways leading to such variation and the implications for extinct hominin variability.
Management accounting knowledge, limited managerial discretion and the use of management accounting: evidence from Japanese public hospitals
Authors: Shirinashihama Yoshitaka 
Published: June 2022

PurposeThis study examines whether management accounting knowledge and limited managerial discretion encourage and/or hinder the use of management accounting.Design/methodology/approachBased on the data obtained from public hospitals in Japan, this study tests whether top managers with more management accounting knowledge use management accounting more. Additionally, the study verifies whether lower managerial discretion leads to the use of less management accounting and conducts hierarchical multiple regression analysis.FindingsThe results show that the higher management accounting knowledge is, the more likely management accounting is to be used. By contrast, the more limited management discretion is, the less likely management accounting is to be used.Originality/valueThe author's management accounting research based on the upper echelon theory has shown that characteristics such as the education and experience of top managers affect the use of management accounting systems. However, the impact of management accounting knowledge and managerial discretion, which is one of the important characteristics of top managers, on management accounting has rarely been studied.
Modeling the determinants of BIM-enabled integration and collaboration
Authors: Olugboyega Oluseye , Windapo Abimbola 
Published: June 2022

PurposeBIM research to date has in general zeroed in on featuring the significance of BIM-enabled integration and collaboration (BIMIC) rather than giving exact proof of its occurrence. Accordingly, this research quantitatively explored the determinants of BIMIC in South Africa.Design/methodology/approachThis research conceptualized a four-pillar model of BIM-enabled integration and collaboration. The speculations in the model were examined using SEM-MLE.FindingsThe aftereffects of the SEM-MLE demonstrated that network communication, knowledge sharing, and transfer, information sharing and exchange and trust-based relationships are critical determinants of BIMIC. The model's prescient power demonstrates an acceptable validity, and the boundary gauges showed that all the hypotheses were measurably huge.Research limitations/implicationsThis research gives a hypothetical premise for further investigation of BIMIC by supporting the postulations on the occurrence of collaboration and integrations among the BIM-SCM.Practical implicationsThe idea investigated involving SEM in this research gives a holistic view to the BIM managers in arranging BIM-based activities and overseeing BIM cycles and supply chain members. It likewise offers rules and structures for accomplishing and overseeing integration and collaboration among the BIM supply chain members.Originality/valueDespite 20 years of exploration on the BIM concept and adoption, no idea has been given to clarify the determinants of integration and collaboration as a BIM cycle. The four-pillar model of BIMIC created and tested in this research clarified BIMIC and contributed a new model to the current literature on the BIM process.
Effects of air-suction guide structures on the condensing zone of pneumatic compact spinning with perforated drum
Authors: Demir Murat 
Published: June 2022

PurposeThe purpose of this study is to investigate the effects of air-suction slots geometry on the condensing zone of pneumatic compact spinning.Design/methodology/approachThis paper investigated the condensing zone of pneumatic compact spinning with perforated drum for different structures of air-inlet slot geometry with computational fluid dynamics. For this purpose, three air-suction guides with different air-slots were designed. To create the condensing zone for the numerical simulation, a suction insert and the perforated drum were also designed. Flow velocity components on the X, Y, and Z axes, static pressure distribution and the streamline diagram were used for comparative analysis. Designed air-suction guides were produced with a 3D printer and used for yarn production.FindingsNumerical simulation results showed that condensing effects were provided for all three types of air-suction guides and approaching air-slots on the suction guides resulted in greater flow components but may cause fluctuations. Experimental results also showed that actual flow velocity components (Z-axis) are effective on hairiness (H) properties of the yarn while assisting flow-velocity components are more effective on the evenness and tenacity properties of the yarn.Originality/valueThis paper presents the numerical flow field simulation of compact spinning for different structures of air-suction guides with detailed measurements. To know the effects of air-suction guides on the condensing zone may be helpful to improve yarn properties. In addition, a 3D printer was used for the production of designed parts.
Co-movement and causal relationships between conventional and Islamic stock market returns under regime-switching framework
Authors: Mathlouthi Fatma , Bahloul Slah 
Published: June 2022

PurposeThis paper aims at examining the co-movement dependent regime and causality relationships between conventional and Islamic returns for emerging, frontier and developed markets from November 2008 to August 2020.Design/methodology/approachFirst, the authors used the Markov-switching autoregression (MS–AR) model to capture the regime-switching behavior in the stock market returns. Second, the authors applied the Markov-switching regression and vector autoregression (MS-VAR) models in order to study, respectively, the co-movement and causality relationship between returns of conventional and Islamic indexes across market states.FindingsResults show the presence of two different regimes for the three studied markets, namely, stability and crisis periods. Also, the authors found evidence of a co-movement relationship between the conventional and Islamic indexes for the three studied markets whatever the regime. For the Granger causality, it is proved only for emerging and developed markets and only during the stability regime. Finally, the authors conclude that Islamic indexes can act as diversifiers, or safe-haven assets are not strongly supported.Originality/valueThis paper is the first study that examines the co-movement and the causal relationship between conventional and Islamic indexes not only across different financial markets' regimes but also during the COVID-19 period. The findings may help investors in making educated decisions about whether or not to add Islamic indexes to their portfolios especially during the recent outbreak.
Active regulation of ultraviolet light exposure overrides thermal preference behaviour in eastern fence lizards
Authors: Conley Dane A. , Lattanzio Matthew S. 
Published: June 2022

Abstract

Over a century of ecophysiological studies on lizards have perpetuated the assumption that basking and shuttling movements between sun and shade function solely for temperature regulation. However, these behaviours also modulate exposure to ultraviolet (UV) wavelengths that are essential for maintaining physiological homoeostasis as well as ensuring proper growth and development and enhancing long‐term fitness.

An alternative hypothesis is that lizards also actively regulate their UV exposure. In this scenario, UV needs may even override temperature needs (or vice versa), generating asymmetries in the ability of a lizard to regulate both conditions equally. We test this hypothesis using field and laboratory data collected on adult Sceloporus undulatus.

We found that S. undulatus actively regulate UV exposure and prioritize UV over temperature, favouring body temperatures much higher than preferred values to sustain preferred UV exposure. In stark contrast, temperature had no reciprocal impact on UV regulation behaviour. Our field data support these patterns, suggesting that lizards may even seek out hotter environments despite thermal costs to enhance UV exposure.

We conclude that S. undulatus actively regulate for UV as well as temperature. Unfortunately, outside of zoos and private hobbyists, appreciation of the importance of UV for ectotherm survival and reproductive success has been minimal. Addressing this deficit will therefore be vital to improve our understanding of the factors shaping the evolution of ectotherm photoregulation behaviour in nature.

Read the free Plain Language Summary for this article on the Journal blog.
Interaction fidelity is less common than expected in plant–pollinator communities
Authors: Parra Santiago A. , Thébault Elisa , Fontaine Colin , Dakos Vasilis 
Published: June 2022

Abstract

Pairs of plants and pollinators species sometimes consistently interact throughout time and across space. Such consistency can be interpreted as a sign of interaction fidelity, that is a consistent interaction between two species when they co‐occur in the same place. But how common interaction fidelity is and what determines interaction fidelity in plant–pollinator communities remain open questions.

We aim to assess how frequent is interaction fidelity between plants and their pollinators and what drives interaction fidelity across plant–pollinator communities.

Using a dataset of 141 networks around the world, we quantify whether the interaction between pairs of plant and pollinator species happens more (‘interaction fidelity’) or less (‘interaction avoidance’) often than expected by chance given the structure of the networks in which they co‐occur. We also explore the relationship between interaction fidelity and species' degree (i.e. number of interactions), and the taxonomy of the species involved in the interaction.

Our findings reveal that most plant–pollinator interactions do not differ from random expectations, in other words show neither fidelity nor avoidance. Out of the total 44,814 co‐occurring species pairs we found 7,877 unique pair interactions (18%). Only 551 (7%) of the 7,877 plant–pollinator interactions did show significant interaction fidelity, meaning that these pairs interact in a consistent and non‐random way across networks. We also find that 39 (0.09%) out of 44,814 plant–pollinator pairs showed significant interaction avoidance. Our results suggest that interactions involving specialist species have a high probability to show interaction fidelity and a low probability of interaction avoidance. In addition, we find that particular associations between plant and insect orders, as for example interactions between Hymenoptera and Fabales, showed high fidelity and low avoidance.

Although niche and neutral processes simultaneously influence patterns of interaction in ecological communities, our findings suggest that it is rather neutral processes that are shaping the patterns of interactions in plant–pollinator networks.