bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonisation lags predict sympatric diversity in birds
Authors: Reijenga Bouwe R. , Etienne Rampal S. , Murrell David J. , Pigot Alex L. 
Published: August 2024

AbstractEcological communities are assembled over time, suggesting a crucial role for evolutionary history in determining the diversity of species assemblages. Indeed, differences in the build-up of sympatric diversity across space, time and clades may reflect variation in the historical patterns of speciation and thus time available for colonisation. However, quantifying the role of evolutionary history is challenging and thus its potential effects have received far less attention than the effects of ecological limits to diversity. Here we use a dynamic model of assembly by allopatric speciation, colonisation, and local extinction to test how evolutionary history predicts variation in sympatric diversity across clades of passerine birds. We show that the clade-specific history of speciation strongly impacts the build-up of sympatry over time, and that phylogenetic tree shape statistics are key predictors of differences in sympatric diversity between clades. Within clades the proportion of species that are sympatric is highest in old, species-poor, and phylogenetically balanced clades. These historical factors all promote the average age of extant species, providing more time for species to expand their geographic distributions and colonise communities. We further show that phylogenetic patterns in community structure frequently interpreted as evidence that community assembly is limited by the saturation of ecological niche space can be explained simply by the lag-time to colonisation following speciation. Our results show that the macroevolutionary history of speciation and assembly time is essential in explaining variation in the structure and diversity of ecological communities.
Genetic suppression interactions are highly conserved across genetic backgrounds
Authors: Paltenghi Claire , van Leeuwen Jolanda 
Published: August 2024

ABSTRACTGenetic suppression occurs when the phenotypic defects caused by a deleterious mutation are rescued by another mutation. Suppression interactions are of particular interest for genetic diseases, as they identify ways to reduce disease severity, thereby potentially highlighting avenues for therapeutic intervention. To what extent suppression interactions are influenced by the genetic background in which they operate remains largely unknown. However, a high degree of suppression conservation would be crucial for developing therapeutic strategies that target suppressors. To gain an understanding of the effect of the genetic context on suppression, we isolated spontaneous suppressor mutations of temperature sensitive alleles ofSEC17, TAO3, andGLN1in three genetically diverse natural isolates of the budding yeastSaccharomyces cerevisiae. After identifying and validating the genomic variants responsible for suppression, we introduced the suppressors in all three genetic backgrounds, as well as in a laboratory strain, to assess their specificity. Ten out of eleven tested suppression interactions were conserved in the four yeast strains, although the extent to which a suppressor could rescue the temperature sensitive mutant varied across genetic backgrounds. These results suggest that suppression mechanisms are highly conserved across genetic contexts, a finding that is potentially reassuring for the development of therapeutics that mimic genetic suppressors.
Inhibition of IAPs induces programmed cell death and inflammatory signaling in patient-derived metastatic breast cancer organoids
Authors: Wächtershäuser Kaja Nicole , Schneider Jana V. , Gessner Alec , Andrieux Geoffroy , Kur Ivan , Duschek Nadine , Weigert Andreas , Boerries Melanie , Rieger Michael A. , Stelzer Ernst H.K. , Pampaloni Francesco , van Wijk Sjoerd J.L. 
Published: August 2024

AbstractBreast cancer (BC) is the most common type of cancer among women worldwide and underlies relapse, disease progression and metastasis. Resistance to chemotherapy and programmed cell death (PCD), including apoptosis, strongly affects therapy success and remains a major challenge. Representative and translational models to understand, manipulate and cultivate advanced BC and to model PCD resistance are therefore urgently required. Smac mimetics are promising compounds to circumvent apoptosis resistance and are able to induce caspase-independent necroptosis, a lytic and inflammatory mode of PCD. Here, we apply primary, patient-derived human mammary organoids (hMOs) to investigate alternative forms of PCD to overcome apoptosis resistance. Using time lapse brightfield with immunofluorescent confocal microscopy, biochemistry and gene expression analysis, we demonstrate that Smac mimetics induce apoptosis in primary hMOs. By mimicking apoptosis resistance via caspase inhibition, hMOs undergo necroptosis, associated with expression and secretion of inflammatory mediators. Inhibition of linear ubiquitination by the LUBAC inhibitor HOIPIN-8 prevents necroptosis, as well as the expression and release of inflammatory mediators in hMOs. Our findings demonstrate that primary hMOs are effective models to model, study and manipulate PCD responses and inflammation in in primary BC organoids and open new therapeutic screening options for chemotherapy-resistant BC.
Comprehensive Database of Circular Permutations: Systematic Detection and Analysis Using Deep Learning
Authors: Hu Yue , Huang Bin 
Published: August 2024

AbstractThis study presents a comprehensive approach to detect circular permutations in Protein Data Bank up to date (PDB, 287081 proteins which sequence length is under 800 up to 20240101). We systematically analyzed the Protein Data Bank (PDB) to identify circular permutations, leveraging FoldSeek and MMseqs2 for structural and sequence similarity searches. The 143756535 candidate pairs were filtered by some threshold for corresponding analysis. TM-align, icarus or plmCP was used to align protein structures and refine detection accuracy, while facilitated the precise identification of circular permutations. Finally, we got 20801 candidate circular permutation pairs and 3351 circular permutation proteins(https://github.com/YueHuLab/Circular-permutation-in-PDB). Our methodology provides a robust framework for uncovering circular permutations in protein databases, enhancing our understanding of protein structural variations and evolutionary adaptations.
RNA order regulates its interactions with zwitterionic lipid bilayers
Authors: Singh Akhil Pratap , Prabhu Janak , Vanni Stefano 
Published: August 2024

AbstractRNA-lipid interactions directly influence RNA activity, which plays a crucial role in developing new applications in medicine and biotechnology. However, while specific preferential behaviors between RNA and lipid bilayers have been identified experimentally, their molecular origin remains unexplored. Here we use molecular dynamics simulations to investigate the interaction between RNA and membranes composed of zwitterionic lipids at the atomistic level. Our data reproduce and rationalize previous experimental observations, including that short-chain RNAs rich in guanine have higher affinity for gel-phase membranes compared to RNA sequences rich in other nucleotides and that RNA prefers gel-phase membranes to fluid bilayers. Our simulations reveal that RNA order is a key molecular determinant of RNA-zwitterionic phospholipid interactions. Our data provides a wealth of information at the atomic level that will help accelerating research on RNA-lipid assemblies for task-specific applications such as designing lipid-based nanocarriers for RNA delivery.
Gaze reflects confidence in explicit decisions while relying on a distinct computational mechanism
Authors: Stern Yonatan , Netzer Ophir , Koren Danny , Zvilichovsky Yair , Hertz Uri , Salomon Roy 
Published: August 2024

AbstractThe eyes are considered a ‘window’ into the mind, shedding light on the cognitive processes leading to explicit decisions. Yet, eye movements are also a distinct oculomotor decision that is the outcome of an independent cognitive system. When exploring novel environments, the convergence and divergence of gaze and explicit decisions highlights the eyes’ dual role. However, the computational mechanisms underlying this interplay and its contribution to adaptative behavior remains unclear. Combining virtual reality based associative learning paradigms with computational modeling across one exploratory and two pre-registered experiments (Total N = 115), we examine learning as multi-system process encompassing explicit decisions and ocular expectations. The two exhibited a partial overlap in their learning. On the one hand, participants’ explicit predictions about target location and their subsequent anticipatory gaze direction robustly converged, and gaze reveals the latent probability of the explicit choice. Moreover, gaze exhibited computational hallmarks of confidence, reflecting an oculomotor assessment of the explicit prediction. On the other hand, ocular and explicit decisions consistently diverged indicating an independent computation reflected in gaze. Although the two systems learn and ascribe value similarly, they utilize different decision mechanisms. Oculomotor decisions were less driven by choice consistency across trials enabling increased exploration. Under uncertainty explicit and oculomotor decisions tended to diverge, enabling a hedging of one’s decision. These findings highlight how together, explicit and oculomotor systems’ learning enables adaptive embodied behavior.Significance StatementThe eyes often reveal additional information beyond one’s explicit decision, offering a ‘window into the mind’ (e.g., leading poker players to wear sunglasses). Yet, eye movements are the product of a distinct system, occasionally diverging from explicit decisions. However, what additional information is conveyed by gaze, and what leads to its occasional divergence remain unclear. Using virtual reality and computational modeling, this study demonstrates a partial overlap between the two. Generally, they robustly converge, and gaze reflects a confidence-like assessment of explicit decisions. Yet they also diverge due to distinct decision mechanisms. Their divergence enables a ‘hedging’ of one’s decision under uncertainty. This demonstrates a multimodal decision process, where different action systems make overlapping but independent choices.
Repeated Sub-anaesthetic dose of Ketamine Elevates Superoxide Dismutase in Pharmacological Model of Schizophrenia-Like Phenotypes in Mice
Authors: Yusuf Usman , Adegbuyi Aderibigbe Oladele , Adewale Fehintola Fatai 
Published: August 2024

AbstractObjectiveThe study evaluated behavioural phenotypes and the level of Superioxde Dismutase activity in repeated sub-anaesthetic dose of ketamine administered to model schizophrenia in animal study.MethodAnimals were divided into groups (n=6), control group received distilled water (10mL/kg) as vehicle (VEH), Ketamine treated group (KET) received sub-anaesthetic dose of ketamine (20mg/kg) for 14 days consecutively. Animals in risperidone treated group (KET+RISP) were pre-treated with sub-anaesthetic dose of ketamine (20mg/kg) alone for 7 consecutive days, and from day 8-14, risperidone (0.5mg/kg) was administered 1 hour post-ketamine treatment. All treatment were administered intraperitoneally (i.p). Twenty-four (24) hours after the last treatment, Behavioural phenotypes (locomotor activity and cognition) were assessed in locomotor activity cage and elevated maze plus. Thereafter level of superioxde dismutase (SOD) activity was evaluated in homogenized brain tissue of each mouse using spectrophotometric analysis.ResultKET group showed significant (p<0.05) increase in movement counts and number of rearing events in locomotor activity test, also prolonged latency to enter the open arms in cognitive assessment compared to animals that received distilled water (10mg/kg), and risperidone (0.5mg/kg) treatment. The level of Superioxide Dismutase (SOD) activity was significantly elevated in KET group compare with vehicle control and risperidone treated animals.ConclusionRepeated dose of ketamine may pose differential effect on endogenous antioxidant system which may elevate superioxide dismutase activity in ketamine induced schizophrenic rodent as positive control mechanism.
Genotoxicity of Prenatal and Early Childhood Exposure to Pesticides: A Protocol and Pilot Study of a Systematic Review and Meta-Analysis
Authors: Sherif Moustafa , Darwish Aya , Ádám Balázs 
Published: August 2024

1.AbstractObjectivesTo systematically review and meta-analyse the genotoxic impact of prenatal and early childhood pesticide exposure, investigating prevalence, specific pesticides, effect size, mechanisms, genetic susceptibility, and vulnerable periods.Study DesignA protocol for systematic review and meta-analysis. A pilot study was also conducted to develop appropriate extraction and risk of bias tool.MethodsAdhering to 2020 PRISMA guidelines, the review will explore genotoxic impact of prenatal and early childhood pesticide exposure in children up to 5 years. The protocol had been registered in the International Prospective Register of Systematic Reviews (PROSPERO) database (CRD42024510877). Searches was done across PubMed, EMBASE, Web of Science, and Scopus use keywords ‘prenatal or childhood’, ‘pesticides’, and ‘genotoxicity’. Manual reference screening supplements searches. Eligible observational studies (cross-sectional, case-control, cohort designs) in English will be included, while excluding case reports and in vitro studies, using Covidence screening tool. Two independent reviewers will use Newcastle-Ottawa Scale and novel tool for cross-sectional studies for screening, data extraction, and risk of bias assessment. Findings will be synthesized narratively, with potential meta-analysis of genotoxicity outcomes. GRADE approach will assess the evidence quality.ResultsA pilot test screened 1,405 studies, resulting in 21 eligible for full-text screening. Twelve were excluded. Data extraction and risk of bias assessment followed pre-defined protocols. Findings informed the refinement of study procedures.ConclusionsThe protocol outlines a comprehensive approach to systematically review the genotoxic impact of prenatal and early childhood pesticide exposure, aiming to provide necessary insights to a better understanding of this environmental risk.
Structural analysis of a ligand-triggered intermolecular disulfide switch in a major latex protein from opium poppy
Authors: Carr Samuel C. , Facchini Peter J. , Ng Kenneth K. S. 
Published: August 2024

Several proteins from plant pathogenesis-related family 10 (PR10) are highly abundant in the latex of opium poppy and have recently been shown to play diverse and important roles in the biosynthesis of benzylisoquinoline alkaloids (BIAs). The recent determination of the first crystal structures of PR10-10 showed how large conformational changes in a surface loop and adjacent β-strand are coupled to the binding of BIA compounds to the central hydrophobic binding pocket. A more detailed analysis of these conformational changes is now reported to further clarify how ligand binding is coupled to the formation and cleavage of an intermolecular disulfide bond that is only sterically allowed when the BIA binding pocket is empty. To decouple ligand binding from disulfide-bond formation, each of the two highly conserved cysteine residues (Cys59 and Cys155) in PR10-10 was replaced with serine using site-directed mutagenesis. Crystal structures of the Cys59Ser mutant were determined in the presence of papaverine and in the absence of exogenous BIA compounds. A crystal structure of the Cys155Ser mutant was also determined in the absence of exogenous BIA compounds. All three of these crystal structures reveal conformations similar to that of wild-type PR10-10 with bound BIA compounds. In the absence of exogenous BIA compounds, the Cys59Ser and Cys155Ser mutants appear to bind an unidentified ligand or mixture of ligands that was presumably introduced during expression of the proteins in Escherichia coli. The analysis of conformational changes triggered by the binding of BIA compounds suggests a molecular mechanism coupling ligand binding to the disruption of an intermolecular disulfide bond. This mechanism may be involved in the regulation of biosynthetic reactions in plants and possibly other organisms.
Exploring consumer perceptions and adoption intention of home meal kit services
Authors: Maneerat Nitjaree , Byrd Karen , Behnke Carl , Nelson Douglas , Almanza Barbara 
Published: August 2024

PurposeThis study aimed to determine the factors affecting consumers’ perceptions and intention to purchase home meal kit services (HMK), a convenient home-cooked meal option, considering the moderating effects of monetary restriction, through the lens of the theory of planned behaviour (TPB).Design/methodology/approachThis cross-sectional study used an online, self-administered survey to collect data from 374 US adults. Results were tested for variable associations via multiple linear regression and moderation analyses.FindingsHMK adoption intention was positively associated with attitude and subjective norms but negatively associated with perceived behavioural control. Consumers’ HMK attitude demonstrated a significant positive relationship with food safety concerns and perceived time constraints. Income and financial constraints were significant moderators of the associations between TPB determinants and HMK intention. The findings emphasised the possibility of using HMK as a foodservice option for time-challenged consumers with food safety concerns.Originality/valueThis study addressed the limited research on HMK, a competitive meal option that foodservice businesses could implement to boost revenue. The study establishes the contribution in understanding the motivators and barriers that potentially affect consumers’ HMK behaviour through the lens of TPB. The results expand the scope of the TPB application in food-related research, providing a deeper understanding of antecedents and other factors on consumers’ HMK behavioural attitudes. Understanding this information will enable practitioners to develop strategies that meet consumers’ concerns when embracing this service to promote HMK.
Airbnb customer experience in long-term stays: a structural topic model and ChatGPT-driven analysis of the reviews of remote workers
Authors: Ramos-Henriquez Jose M. , Morini-Marrero Sandra 
Published: August 2024

Purpose
This study aims to characterize remote workers’ Airbnb experiences through the cognitive outcomes of their experiences and to consider the differences between long and short stays.

Design/methodology/approach
The structural topic model methodology was used to identify relevant topics. Data were collected from InsideAirbnb for Lisbon, Portugal and Austin, Texas, USA, for 2022 and early 2023, focusing on reviews that mentioned remote work.

Findings
The Airbnb experiences of remote workers and digital nomads are characterized as professionals who express mostly affective outcomes, but also have behavioral and nonaffective outcomes during their stay. In addition, the findings support the moderating role of length of stay and city.

Research limitations/implications
This paper contributes to the literature by exploring how length of stay affects the priorities of remote workers on Airbnb, highlighting the different needs of long-term and short-term stays, and helping to consolidate and clarify the scattered research on customers’ long-term experiences in tourism and hospitality.

Practical implications
The Airbnb experience of remote workers is the highly valued as evidenced by the high rate of commending reviews indicating a willingness to stay there again. It is suggested that Airbnb hosts continue their helpful role and ensuring the functionality and availability of essential facilities and emphasizing neighborhood amenities specific to long and short stays. ChatGPT4 was found to be valuable for extracting data and assigning topic labels.

Originality/value
This study uses a novel structural topic model, augmented with ChatGPT4, to analyze Airbnb customer reviews that mention remote work, thereby improving inferences about the characterization of remote workers.
Data-driven sensegiving and sensemaking: a phenomenological investigation
Authors: Namvar Morteza , Im Ghiyoung P. , Li Jingqi (Celeste) , Chung Claris 
Published: August 2024

PurposeBusiness analytics (BA) is a new frontier of technology development and has enormous potential for value creation. Information systems research shows ample evidence of its positive business impacts and organizational performance. However, there is limited understanding of how decision-makers or users of BA outcomes actually engage with data analysts in the process of data-driven insight generation and how they improve their understanding of business environments using BA outcomes. To aid this engagement and understanding, this study investigates the interaction between decision-makers and data analysts when they attempt to uncover data capacities and business needs and acquire business insights from BA tools.Design/methodology/approachThis study employs an interpretive field study with thematic analysis. The authors conducted interviews with 31 participants who all relied on BA in their daily decisions. The study participants were engaged in different BA roles, including data analysts and decision-makers. They validated the applicability and usefulness of our findings through a focus group with eight practitioners, including decision-makers and data analysts from the same companies.FindingsThis study proposes a process model of data-driven sensemaking and sensegiving based on Weick’s sensemaking framework. The findings exhibit that decision-makers are engaged in sensemaking by identifying areas of focus, determining BA scope, evaluating generated insights and turning BA into action. The findings also show that data analysts engage in sensemaking by consolidating data, data understanding, preparing preliminary outcomes and generating actionable reports. This study shows how sensemaking processes and sensegiving activities work together over time through immediate enactment, selection and decision cycles.Originality/valueThis study is a first attempt to understand interactions in the context of BA using the perspective of sensemaking and sensegiving.
EU membership and income inequality: escaping the single and binary treatment approach
Authors: Serwach Tomasz 
Published: August 2024

PurposeIn this paper, the impact of the 2004 European Union accession on income inequalities within New Member States is analyzed.Design/methodology/approachAn empirical analysis is conducted with nine New Member States over the period 1991–2015, with 55 economies serving as a control group. The newly introduced (by de Chaisemartin and D’Haultfœuille, 2023) method belonging to the family of difference-in-differences (DID) estimators is applied to allow for multiple non-binary treatments.FindingsWhile accession to the European Union had a positive and significant impact on the market and net Gini coefficients in the treated countries, no evidence of the impact of accession on redistribution was found. Single-unit estimates signal that income inequalities rose due to EU membership in some member countries; the most convincing evidence shows that income distribution in Latvia was especially affected.Originality/valueThe author applied the method which addresses the presence of multiple non-binary treatments. Full-fledged membership was preceded by association status, and accession to the EU was accompanied or followed by engagement in other layers of integration (European Monetary Union and Schengen Area). Controlling for these features, the author was able to assess whether the pure EU effect contributed to increases in income inequalities.