bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biased activation of the vasopressin V2 receptor probed by NMR, paramagnetic ligands, and molecular dynamics simulations
Authors: Gaibelet Gérald , Fouillen Aurélien , Riché Stéphanie , Orcel Hélène , Mendre Christiane , Kanso Ali , Lanotte Romain , Nguyen Julie , Dimon Juliette , Urbach Serge , Sounier Rémy , Granier Sébastien , Bonnet Dominique , Cong Xiaojing , Mouillac Bernard , Déméné Hélène 
Published: June 2023

AbstractG protein-coupled receptors (GPCRs) control critical intercellular communications by responding to extracellular stimuli and undertaking conformational changes to convey signals to intracellular effectors. We combined NMR, molecular pharmacology, and molecular dynamics (MD) simulations to study the conformational diversity of the vasopressin V2 GPCR subtype (V2R) bound to different types of ligands: the antagonist tolvaptan, the endogenous unbiased agonist arginine-vasopressin, and MCF14, a Gs-protein biased agonist. We developed a double-labeling NMR scheme to study the conformational dynamics: V2R was subjected to lysine13CH3methylation, whereas the agonists were tagged with a paramagnetic probe. Paramagnetic relaxation enhancements were used to validate the ligand binding poses in the MD simulations. We found that the bias for the Gs protein over the β-arrestin pathway involves interactions between the conserved NPxxY motif in the transmembrane helix (TM) 7 and a central hydrophobic patch in TM3, which constrains TM7 and likely inhibits β-arrestin signaling. A similar mechanism was observed for the pathogenic mutation, I1303.43N, which constitutively activates the Gs protein without concomitant β-arrestin recruitment. This mechanism resembles to opioid receptors findings indicating common patterns in class A GPCRs.
An R package for ensemble learning stacking
Authors: Nukui Taichi , Onogi Akio 
Published: June 2023

AbstractSummaryWe developed an R package for stacking, which is an ensemble approach to supervised learning. Using this package, training and prediction of stacking can be conducted using one-row scripts.Availability and implementationThe R package stacking is available at the GitHub (https://github.com/Onogi/stacking).Contactonogiakio@gmail.comSupplementary informationThis manuscript has no supplementary information.
Identification of disulfidptosis-related-ferroptosis associated lncRNAs signature as a novel prognosis model for kidney renal clear cell carcinoma
Authors: Xu Zihan 
Published: June 2023

AbstractBackground:Clear cell renal cell carcinoma (ccRCC) represents 80% of all kidney cancers and has a poor prognosis. Newly discovered types of programmed cell death, ferroptosis and disulfidptosis, could have a direct impact on the outcome of KIRC cancer. Long non-coding RNAs (lncRNAs), which possess stable structures, can influence cancer prognosis and might be potential prognostic prediction factors for KIRC cancer. This study aims to investigate the correlation between disulfidptosis-related ferroptosis-related lncRNA and ccRCC in terms of immunity and prognosis.Methods:Coexpression analysis was employed to identify disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs). Differential expression analysis of DRFRLs was conducted using the ‘limma’ package in R software, and the ‘ConsensusClusterPlus’ package was utilized to identify molecular subtypes. Prognostic DRFRLs were identified via univariate Cox analysis, and a prognostic model based on eight DRFRLs was constructed through Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) algorithm. Kaplan-Meier (K-M) survival curve analysis and receiver operating characteristic (ROC) curve analysis were utilized to evaluate the prognostic power of this model. Additionally, differences in biological function were investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), while immunotherapy response was measured by utilizing tumor mutational burden (TMB) and tumor immune dysfunction and rejection (TIDE) scores. Single-cell analysis from the Tumor Immune Single Cell Center (TISCH) was employed to investigate cells with specific expression of the eight identified lncRNAs.Results:Two clusters (A and B) of disulfidptosis-related ferroptosis-related long non-coding RNAs (DRFRLs) were identified. Survival analysis revealed that patients with subtype A had a higher probability of survival compared to those in subtype B, suggesting that subtype A predicts better survival. An eight-lncRNA signature was established through LASSO-Cox regression, and Kaplan-Meier curves validated the accuracy of prognostic features prediction (P < 0.001). This signature demonstrated excellent prognostic performance, with an area under the curve (AUC) of 0.762, 0.761, and 0.749 at 1, 3, and 5 years in the training set and 0.790, 0.739, and 0.726 in the testing set, respectively. In the single-cell dataset, LINC01534, FOXD2-AS1, AC002070.1, and AL158212.3 were found to be expressed, with FOXD2-AS1 and AC002070.1 specifically expressing in the KC tumor immune microenvironment.Conclusions:The proposed signature of eight lncRNAs is a promising biomarker for predicting clinical outcomes and therapeutic responses in patients with ccRCC.
Molecular architecture and conservation of an immature human endogenous retrovirus
Authors: Krebs Anna-Sophia , Liu Hsuan-Fu , Zhou Ye , Rey Juan S. , Levintov Lev , Shen Juan , Howe Andrew , Perilla Juan R. , Bartesaghi Alberto , Zhang Peijun 
Published: June 2023

AbstractA significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
Metabolic regulation in erythroid differentiation by systemic ketogenesis in fasted mice
Authors: Ma Wenjuan , Arima Yuichiro , Umemoto Terumasa , Yokomizo Tomomasa , Xu Yuqing , Miharada Kenichi , Tanaka Yosuke , Suda Toshio 
Published: June 2023

SummarySystemic ketogenesis affects murine erythroid differentiation under fasting condition, while less ketone body β OHB boosts fatty acid synthesis and mevalonate pathway along with decreased levels of histone acetylation, which are beneficial for erythroid differentiation and maturation undergoing stressed erythropoiesis.AbstractErythroid terminal differentiation and maturation depends on enormous energy supply. During periods of fasting, ketone bodies from the liver are transported into circulation and utilized as crucial fuel for peripheral tissues. However, the effects of fasting or ketogenesis on erythroid behavior remain unknown. Here, we generated a mouse model with insufficient ketogenesis by conditionally knocking out the gene encoding the hepatocyte-specific ketogenic enzyme hydroxymethylglutary-CoA synthase 2 (Hmgcs2KO). Intriguingly, erythroid maturation was enhanced with boosted fatty acid synthesis in bone marrow of hepaticHmgcs2KO mouse under fasting condition, suggesting that systemic ketogenesis has a profound effect on erythropoiesis. Moreover, we observed significantly activated fatty acids synthesis and mevalonate pathway along with reduced histone acetylation in immature erythrocytes under less systemic ketogenesis condition. Our findings revealed an innovative insight to erythroid differentiation, in which metabolic homeostasis and histone acetylation mediated by ketone bodies are essential factors in adaptation towards nutrient deprivation and stressed erythropoiesis.
Microbiome time series data reveal predictable patterns of change
Authors: Karwowska Zuzanna , Szczerbiak Paweł , Kosciolek Tomasz 
Published: June 2023

ABSTRACTBackgroundThe gut microbiome is crucial for human health and disease. Longitudinal studies are gaining importance in understanding its dynamics over time, compared to cross-sectional approaches. Investigating the temporal dynamics of the microbiome, including individual bacterial species and clusters, is essential for comprehending its functionality and impact on health. This knowledge has implications for targeted therapeutic strategies, such as personalized diets and probiotic therapy.ResultsHere, by adopting a rigorous statistical approach, we aim to shed light on the temporal changes in the gut microbiome and unravel its intricate behavior over time. We leveraged four long and dense time series of the gut microbiome in generally healthy individuals examining how its composition evolves as a community and how individual bacterial species behave over time. We also explore whether specific clusters of bacteria exhibit similar fluctuations, which could provide insights into potential functional relationships and interactions within the microbiome Our study reveals that despite its high volatility, the human gut microbiome is stable in time and can be predicted based solely on its previous states. We characterize the unique temporal behavior of individual bacterial species and identify distinct longitudinal regimes in which bacteria exhibit specific patterns of behavior. Finally, through cluster analysis, we identify groups of bacteria that exhibit coordinated fluctuations over time.ConclusionsOur findings contribute to our understanding of the dynamic nature of the gut microbiome and its potential implications for human health. The provided guidelines support scientists studying gut microbiome complex dynamics, promoting further research and advancements in microbiome analysis.
Epistolizing accountability: a critical exploration of INGO annual report leaders' letters
Authors: Abnett Helen 
Published: June 2023

PurposeThis paper explores how INGOs communicate their activities and achievements. In doing so, the study seeks to increase our understanding of INGOs' accountability practices.Design/methodology/approachThis paper uses thematic analysis to analyse 90 ‘leaders’ letters' (the letters that many charities include at the beginning of their Annual Reports and Accounts), published by 39 INGOs between 2015 and 2018.FindingsThis paper argues that within the Annual Report letters under consideration, INGOs' accountability practices focus on quantitative, process-driven, output reporting. In doing so, it is the actions and agency of INGOs that are primarily emphasised. INGO constituents are largely excluded from representation. Donors are presented only as contributors of financial capital. Drawing on field theory, the paper argues that this representational practice means INGO constituents are almost irrelevant to INGOs' representational and accountability communication practices.Originality/valueThis paper is indebted to previous important work and, building on such scholarship, seeks to contribute to the ongoing conversation about INGO accountability. While reinforcing some prior knowledge, the findings here also differ in the understanding of how donors are portrayed. The paper extends previous analyses by using field theory to show that the INGO field as considered here is a space in which representations of accountability are based on organisational and transactional factors, and does not value the humanity of INGOs' constituents. This connects to operations of power, between donors, INGOs, and constituents, and reinforces inequitable power within the development system.
Drivers of liking and value perception for a new apple cultivar in Italy
Authors: Rivaroli Sergio , Spadoni Roberta , Tartarini Stefano , Gregori Roberto , Riedel Bettina , Draicchio Paola , Folini Luca , Altintzoglou Themistoklis , Canavari Maurizio 
Published: June 2023

PurposeCombining sensory evaluations and hypothetical valuation mechanisms, this study aims to investigate the impact of consumers' product sensory attributes on willingness to pay (WTP) and overall liking for a new apple cultivar.Design/methodology/approachA sample of non-expert participants (n = 122) evaluated the overall liking and just-about-right (JAR) attributes. A variable transformation approach was applied to make linear and interval regression models between the JAR attributes, overall liking scores and participants' WTP.FindingsThe study reveals the high consumer appreciation for the new apple in both hedonic and economic terms. After controlling the anchoring effect's bias, the predicted mean WTP for the new apple cultivar was €3.26 per kilogramme. Crunchiness and flavour significantly affect both participants' overall liking and WTP.Research limitations/implicationsThe main limitation is the non-probabilistic sampling procedure, which does not allow for the generalisation of the results. Penalty analysis for JAR attributes in monetary and hedonic terms is beneficial for optimising the product and evaluating its potential in the marketplace.Practical implicationsThe findings provide helpful directions for product optimisation in future breeding programmes to ensure the long-term sustainability of the new apple cultivars in the marketplace.Originality/valueThis study provides evidence of the beneficial synergy of mixing sensory-oriented research with the behavioural economics field of study.
A hybrid method to determine optimal design axial forces of servo steel struts in excavations with high deformation requirements
Authors: Di Honggui , Jin Yuyin , Zhou Shunhua , Wu Di 
Published: June 2023

PurposeThe application of servo steel struts enables the active control of the excavation-induced deformation in foundation pits. However, there is currently only one design axial force for each servo steel strut, which requires in-situ axial force adjustments based on the experience of site engineers. The purpose of this study is to develop a method for determining the design axial forces of servo steel struts at different excavation steps.Design/methodology/approachIn this study, a hybrid method for determining the design axial forces of servo steel struts in different excavation steps was established based on the combination of the elastic foundation beam model and nonlinear optimisation.FindingsThe hybrid method is capable of providing a better set of design axial forces than the original design method. The lateral wall displacement and bending moment could be better controlled. Ordinary steel struts should be prevented from being set between servo steel struts to avoid axial force losses.Practical implicationsThe axial forces of the servo steel struts at different excavation steps should be designed to achieve better deformation control effects. Moreover, a well-designed set of axial forces can also reduce the internal forces of the retaining structure.Originality/valueThe hybrid method enables the determination of the design axial forces of servo steel struts at different excavation steps, which can guide axial force adjustments in practical projects.
Shariah-compliant status and investors demand for IPOs: the moderating role of regulatory quality
Authors: Mehmood Waqas , Ali Anis , Mohd-Rashid Rasidah , Aman-Ullah Attia 
Published: June 2023

Purpose
The purpose of this study is to look at how Shariah-compliant status and Shariah regulation affect the demand for initial public offerings (IPOs) in Pakistan. The Shariah-compliant status, which is seen as a method that offers a credible signal to investors, may explain the anomaly in IPO demand.

Design/methodology/approach
This research used multivariate and quantile regression models to assess data from 85 IPOs issued on the Pakistan Stock Exchange between 2000 and 2019.

Findings
Shariah-compliant status has a considerable negative association with IPO demand. Nevertheless, there is a considerable positive association among Shariah regulation and IPO demand. Furthermore, the interaction among regulatory quality and Shariah-compliant status has a considerable strong influence on IPO demand. As a consequence, the findings show that Shariah-compliant firms might possibly attract the attention of investors. Investors were found to concur on the amicability of rigorous rules and permissible Shariah-compliance aspects.

Research limitations/implications
Future studies could analyse the financial ratio benchmark (cash and debt) to determine the Shariah-compliant status and Shariah regulation to better understand the problem of IPO demand in the context of Pakistan.

Practical implications
The outcomes of this research are useful for issuers and underwriters in comprehending the characteristics that influence high and early IPO success. Such knowledge may assist issuers and underwriters in responsibly planning and managing the IPO process.

Social implications
The results may be useful to investors looking for critical information in prospectuses to make the best choice when subscribing to IPOs in Pakistan.

Originality/value
This is one of the first studies to provide empirical data on the links among Shariah-compliant status, Shariah regulation and IPO demand in Pakistan. Furthermore, this research demonstrates the interaction impact of regulatory quality and Shariah-compliant status on IPO demand.
A diversity of endosymbionts across Australian aphids and their persistence in aphid cultures
Authors: Yang Qiong , Gill Alex , Robinson Katie L. , Umina Paul A. , Ross Perran A. , Zhan Dongwu , Brown Courtney , Bell Nicholas , MacMahon Ashley , Hoffmann Ary A. 
Published: June 2023

AbstractThere is increasing interest in the use of endosymbionts in pest control, which will benefit from the identification of endosymbionts from potential donor species for transfer to pest species. Here, we screened for endosymbionts in 123 Australian aphid samples across 32 species using 16S DNA metabarcoding. We then developed a qPCR method to validate the metabarcoding data set and to monitor endosymbiont persistence in aphid cultures. Pea aphids (Acyrthosiphon pisum) were frequently coinfected with Rickettsiella and Serratia, and glasshouse potato aphids (Aulacorthum solani) were coinfected with Regiella and Spiroplasma; other secondary endosymbionts detected in samples occurred by themselves. Hamiltonella, Rickettsia and Wolbachia were restricted to a single aphid species, whereas Regiella was found in multiple species. Rickettsiella, Hamiltonella and Serratia were stably maintained in laboratory cultures, although others were lost rapidly. The overall incidence of secondary endosymbionts in Australian samples tended to be lower than recorded from aphids overseas. These results indicate that aphid endosymbionts probably exhibit different levels of infectivity and vertical transmission efficiency across hosts, which may contribute to natural infection patterns. The rapid loss of some endosymbionts in cultures raises questions about factors that maintain them under field conditions, while endosymbionts that persisted in laboratory culture provide candidates for interspecific transfers.
How does economic complexity influence environmental degradation? New insights from African countries
Authors: Ntang Philemon Bonaventure , Baida Louise Angèle , Abba Yadou Barnabe 
Published: June 2023

AbstractThis paper seeks to investigate the effect of economic complexity on environmental degradation in 20 selected African countries over the period 1991–2014. The Feasible Generalized Least Square (FGLS), and Driscoll‐Kraay estimators (DK) are used to capture the objectives of the study. The results suggest that economic complexity and economic growth enhance environmental degradation. Also, natural resources rents and globalization improve environmental quality. Furthermore, the findings reject the U‐shaped relationship between economic complexity and environmental degradation. In addition, the Dumitrescu‐Hurlin panel causality test shows a bidirectional causal relation between economic complexity and environmental degradation. Taking into account the ecological deficit or ecological reserve status of country, it is shown that while the natural resource rents reduce environmental degradation in ecological reserve countries, they increase environmental degradation in ecological deficit countries. The results are robust when an alternative measure of economic complexity is used. Based on these findings, the paper suggests that the governments of African countries should take into account economic complexity when designing their environmental protection policies.
Colonization of diatoms in and on porcine bone substrate and considerations of diatom ecology for forensic science
Authors: Marshall Michelle , Chraïbi Victoria , Morgan Ryan 
Published: June 2023

AbstractThe presence of diatom algae in bone marrow has been used as forensic evidence of drowning for several decades; however, these studies are based on known or suspected recent drowning events. This study addresses the potential for diatoms to enter the bone marrow of skeletal remains, that is, de‐fleshed long bones post‐mortem. In laboratory and field experiments, bones were either inflicted with two access points by a cut and acid pitting or left intact. The bones were submerged in water for at least 1 week and up to 3 months. Samples of the bone surface and marrow were inspected for diatoms. The analysis considered the time required for diatoms to enter marrow and whether genus characteristics like size or mobility affect entry. The presence of an access point influenced diatom entry in that bones without an introduced access point had zero to one diatom present in the marrow, whereas a bone with an access point had >150 diatoms present in the marrow. The results of both laboratory and field phases suggest that diatoms will reliably colonize bone in as quickly as 1 week, establishing and maintaining communities for at least 3 months. However, the bone surface assemblages differ from the source community. Bone marrow displayed even more restrictive access to diatom colonization, resulting in communities dominated by small raphid diatoms. Based on these findings, we suggest some caveats on the use of diatoms as trace evidence in forensic science with recommendations for future avenues of research.