bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking the genetic structure of neuroanatomical phenotypes with psychiatric disorders
Authors: Auvergne Antoine , Traut Nicolas , Henches Léo , Troubat Lucie , Frouin Arthur , Boetto Christophe , Kazem Sayeh , Julienne Hanna , Toro Roberto , Aschard Hugues 
Published: November 2023

AbstractThere is increasing evidence of shared genetic factors between psychiatric disorders and brain magnetic resonance imaging (MRI) phenotypes. However, deciphering the joint genetic architecture of these outcomes has proven challenging, and new approaches are needed to infer potential genetic structure underlying those phenotypes. Here, we demonstrate how multivariate analyses can help reveal links between MRI phenotypes and psychiatric disorders missed by univariate approaches. We first conducted univariate and multivariate genome-wide association studies (GWAS) for eight MRI-derived brain volume phenotypes in 20K UK Biobank participants. We performed various enrichment analyses to assess whether and how univariate and multitrait approaches can distinguish disorder-associated and non-disorder-associated variants from six psychiatric disorders: bipolarity, attention-deficit/hyperactivity disorder (ADHD), autism, schizophrenia, obsessive-compulsive disorder, and major depressive disorder. Univariate MRI GWAS displayed only negligible genetic correlation with psychiatric disorders at all the levels we investigated. Multitrait GWAS identified multiple new associations and showed significant enrichment for variants related to both ADHD and schizophrenia. We further clustered top associated variants based on their MRI multitrait association using an optimizedk-medoids approach and detected two clusters displaying not only enrichment for association with ADHD and schizophrenia, but also consistent direction of effects. Functional annotation analyses pointed to multiple potential mechanisms, suggesting in particular a role of neurotrophin pathways on both MRI and schizophrenia. Altogether our results show that multitrait association signature can be used to infer genetically-driven latent MRI variables associated with psychiatric disorders, opening paths for future biomarker development.
High-resolution comparative atomic structures of two Giardiavirus prototypes infectingG. duodenalisparasite
Authors: Wang Han , Gianluca Marucci , Munke Anna , Hassan Mohammad Maruf , Lalle Marco , Okamoto Kenta 
Published: November 2023

AbstractGiardia lamblia virus(GLV) is a non-enveloped icosahedral dsRNA virus and an endosymbiont virus infecting the zoonotic protozoan parasiteGiardia duodenalis(syn.G. lamblia, G. intestinalis), a pathogen of mammals, including humans. Elucidating the transmission mechanism of GLV is crucial to an in-depth understanding of the virulence of the virus inG. duodenalis. GLV belongs to the familyTotiviridae,which infects yeast and protozoa intracellularly; however, it also transmits extracellularly, similar to phylogenetically distantly related toti-like viruses that infect multicellular hosts. The GLV capsid structure is extensively involved in the longstanding discussion concerning the acquisition of extracellular transmission inTotiviridaeand toti-like viruses. Hence, this study constructed the first high-resolution comparative atomic models of two GLV strains, namely GLV-HP and GLV-CAT, which showed different intracellular localization and virulence phenotypes, using cryo-EM single-particle analysis. The atomic models of the GLV capsids presented swapped C-terminal extensions, extra surface loops, and a lack of cap-snatching pockets, similar to those of toti-like viruses. However, their open pores and lack of the extra crown protein (CrP) resemble those of other yeast and protozoanTotiviridaeviruses, demonstrating the essential structures for acquiring extracellular cell-to-cell transmission. The intensive structural comparison between GLV-HP and GLV-CAT indicates the first evidence of critical structural motifs for the transmission and virulence of GLV inG. duodenalis.
The shared genetic architecture and evolution of human language and musical rhythm
Authors: Alagöz Gökberk , Eising Else , Mekki Yasmina , Bignardi Giacomo , Fontanillas Pierre ,   23andMe Research Team, Nivard Michel G. , Luciano Michelle , Cox Nancy J. , Fisher Simon E. , Gordon Reyna L. 
Published: November 2023

AbstractRhythm and language-related traits are phenotypically correlated, but their genetic overlap is largely unknown. Here, we leveraged two large-scale genome-wide association studies performed to shed light on the shared genetics of rhythm (N=606,825) and dyslexia (N=1,138,870). Our results reveal an intricate shared genetic and neurobiological architecture, and lay groundwork for resolving longstanding debates about the potential co-evolution of human language and musical traits.
Incorporation of 5 methylcytidine alleviates innate immune response to self-amplifying RNA vaccine
Authors: Komori Mai , Morey Amber L. , Quiñones-Molina Andrés A. , Fofana Josiane , Romero Luis , Peters Elizabeth , Matsuda Kenta , Gummuluru Suryaram , Smith Jonathan F. , Akahata Wataru , Akiyama Hisashi 
Published: November 2023

AbstractIn order to improve vaccine effectiveness and safety profile of existing synthetic RNA-based vaccines, we have developed a self-amplifying RNA (saRNA)-based vaccine expressing membrane-anchored receptor binding domain (RBD) of SARS-CoV-2 S protein (S-RBD) and have demonstrated that a minimal dose of this saRNA vaccine elicits robust immune responses. Results from a recent clinical trial with 5-methylcytidine (5mC) incorporating saRNA vaccine demonstrated reduced vaccine-induced adverse effects while maintaining robust humoral responses. In this study, we investigate the mechanisms accounting for induction of efficient innate and adaptive immune responses and attenuated adverse effects induced by the 5mC-incorporated saRNA. We show that the 5mC-incorporating saRNA platform leads to prolonged and robust expression of antigen, while induction of type-I interferon (IFN-I), a key driver of reactogenicity, is attenuated in peripheral blood mononuclear cells (PBMCs), but not in macrophages and dendritic cells. Interestingly, we find that the major cellular source of IFN-I production in PBMCs is plasmacytoid dendritic cells (pDCs), which is attenuated upon 5mC incorporation in saRNA. In addition, we demonstrate that monocytes also play an important role in amplifying proinflammatory responses. Furthermore, we show that the detection of saRNA is mediated by a host cytosolic RNA sensor, RIG-I. Importantly, 5mC-incorporating saRNA vaccine candidate produced robust IgG responses against S-RBD upon injection in mice, thus providing strong support for the potential clinical use of 5mC-incorporating saRNA vaccines.
Characterisation of ligand gating, ion conduction and the ion selectivity mechanism in the endo-lysosomal ion channel hTPC2
Authors: Şahin Alp Tegin , Zachariae Ulrich 
Published: November 2023

AbstractTwo pore channels (TPCs) are two-fold symmetric endo-lysosomal cation channels forming important drug targets especially for antiviral drugs. They are activated by calcium, ligand binding, and membrane voltage, and to date, are the only ion channels shown to alter their ion selectivity depending on the type of bound ligand. However, despite their importance in the field, ligand activation of TPCs and the molecular mechanisms underlying their ion selectivity are still poorly understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PI(3,5)P2. We performed all-atom in silico electrophysiology simulations to study Na+and Ca2+permeation across hTPC2 in real-time and to investigate the conformational changes induced by the presence or absence of bound PI(3,5)P2. Our findings reveal that hTPC2 adopts distinct structures depending on the presence of PI(3,5)P2and elucidate the conformational transition pathways between these structures. Additionally, we examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. Our simulations reproduce the experimental observation that hTPC2 is more selective for Na+over Ca2+ions in the presence of PI(3,5)P2and explain the mechanism of this ion selectivity. They highlight the importance of specific ion binding sites at the luminal channel entrance, the selectivity filter, and the central channel cavity for ion conduction, enabling a distant knock-on mechanism for efficient permeation of Na+ions.
A whole-body micro-CT scan library that captures the skeletal diversity of Lake Malawi cichlid fishes
Authors: Bucklow Callum V. , Genner Martin J. , Turner George F. , Maclaine James , Benson Roger , Verd Berta 
Published: November 2023

ABSTRACTHere we describe a dataset of freely available, readily processed, whole-bodyμCT-scans of 56 species (116 specimens) of Lake Malawi cichlid fishes that captures a considerable majority of the morphological variation present in this remarkable adaptive radiation. We contextualise the scanned specimens within a discussion of their respective ecomorphological groupings and suggest possible macroevolutionary studies that could be conducted with these data. We also describe a methodology to efficientlyμCT-scan (on average) 23 specimens per hour, limiting scanning time and alleviating the financial cost whilst maintaining high resolution. We demonstrate the utility of this method by reconstructing 3D models of multiple bones from multiple specimens within the dataset. We hope this dataset will enable further morphological study of this fascinating system and permit wider-scale comparisons with other cichlid adaptive radiations.
Diversity of arbuscular mycorrhizal fungi under the rhizosphere soil of different cropping systems surrounding Hawassa town, South Ethiopia
Authors: Zeleke Girma , Dobo Beyene , Asefa Fassil 
Published: November 2023

ABSTRACTThis research was conducted to study the diversity of Arbuscular Mycorrhizal Fungi (AMF) in the rhizosphere of different plants at the vicinity of Hawassa city, Southern Ethiopia. The rate of root colonisation and diversity of AMF in the rhizosphere soils of permanent crops, major annual crops, forest areas, and open grazing fields were investigated. It discovered 928 spores of 23 distinct AMF morpho-species in 12 AMF genera and 12 annual and perennial crops. The AMF genera identified were: Acaulospora, Cetraspora, Claroideoglomus, Dentiscutata, Diversispora, Funneliformis, Gigaspora, Glomus, Racocetra, Rhizophagus, Sclerocystis, and Scutellospora. In tomatoes grown inorganically, a compromised species richness may result from the extensive use of agrochemicals. Further research into the effects of agricultural inputs on the subsurface microbial population may be necessary, as this is outside the purview of this publication. When compared to all other land uses, the AMF beneath the rhizosphere soil of Eucalyptus trees has the largest biomass, with spore density of 1907.4±0.404 spores 100g-1 of dry soil. The lowest AMF biomass has been recorded in the rhizosphere soil of Mango tree, with spore density of 260.1±0.121 spores 100g-1dry soil. The results of this study show that the mycorrhizal colonisation and spore density of the plants under investigation are decreased by monocropping, intense agricultural practises, and the application of inorganic fertilisers. Thus, it is thought that conservation agriculture, together with the development of plant species consortiums in agricultural polts, will preserve the biological diversity of Arbuscular mycorrhizal fungi and the integrity of the environment.Significance of the study to the field- plant species diversity is dependent on arbuscular mycorrhizal fungi diversity and density- AMF Favours environmental resilience, carbon sequestration, and improves soil structure- Application of inorganic agricultural inputs decrease, AMF diversity- AMF diversity is affected by land use change, environmental pollution and climate change
Fine-tuning of Fgf8 morphogen gradient by heparan sulfate proteoglycans in the extracellular matrix
Authors: Gupta Mansi , Kurth Thomas , Heinemann Fabian , Schwille Petra , Keil Sebastian , Knopf Franziska , Brand Michael 
Published: November 2023

AbstractEmbryonic development is orchestrated by the action of morphogens, which spread out from a local source and activate, in a field of target cells, different cellular programs based on their concentration gradient. Fibroblast growth factor 8 (Fgf8) is a morphogen with important functions in embryonic organizing centers. It forms a gradient in the extracellular space by free diffusion, interaction with the extracellular matrix (ECM) and receptor-mediated endocytosis. However, morphogen gradient regulation by ECM is still poorly understood. Here we show that specific Heparan Sulfate Proteoglycans (HSPGs) bind Fgf8 directly in the ECM of living zebrafish embryos, thus affecting its diffusion and signaling. Using single-molecule Fluorescence Correlation Spectroscopy, we quantify this bindingin vivo, and find two different modes of interaction. First, reducing or increasing the concentration of specific HSPGs in the extracellular space alters Fgf8 diffusion, and thus, its gradient shape. Second, ternary complex formation of Fgf8 ligand with Fgf-receptors and HSPGs at the cell surface requires HSPG attachment to the cell membrane. Together, our results show that graded Fgf8 morphogen distribution is achieved by constraining free Fgf8 diffusion through successive interactions with HSPGs at the cell surface and in ECM space.Statement of significanceFgf8 is a secreted morphogen signaling molecule that instrúcts neighboring arrays of undifferentiated cells about their position and cellular identity in tissue. Fgf8 and other morphogens are often distributed in a graded fashion, and can typically work at very low concentrations. To reproducibly generate information in developing tissue, mechanisms have evolved to carefully control distribution and concentration of Fgf8 morphogen. We show that freely diffusing Fgf8 morphogen moves through interstitial cell spaces on its way to target cells, and while doing so, interacts with ECM molecules in these spaces and at cell surfaces via low affinity, reversible binding. These interactions are important tuning mechanisms that contribute to forming the Fgf8 morphogen gradient and to cell surface receptor binding, and thus, to controlling cell type identity.Abstract FigureGraphical abstractTo generate a gradient, the morphogen Fgf8 shuttles between fast free diffusion through extracellular space (i), slow diffusion or immobility (ii, iii) when bound to Heparan Sulfate Proteoglycans (HSPGs), in the extracellular matrix (ECM) and at cell surface receptors (iv), as revealed by single molecule studies in living zebrafish embryos.
Managing risks in IPD-ish projects: experience from Hong Kong
Authors: Ma Qiuwen , Cheung Sai On , Li Shan 
Published: November 2023

PurposeIntegrated project delivery (IPD) project that does not use multiparty agreement is identified as IPD-ish. The use of IPD-ish arrangement by incorporating integration practices in conventional contract can be viewed as the part of the adoption process of IPD. Moreover, inappropriate integration practices invite new forms of risks and the absence of multiparty agreement adds to the challenges of risk management in IPD-ish projects. This study discusses such challenges and proposes the use of joint risk management to address the potential pitfalls in IPD-ish arrangement.Design/methodology/approachA mixed research method was applied. First, the criticality of IPD-ish general and integration-specific risks was examined through a survey. Second, a real IPD-ish project was used to exemplify the use of joint risk management (JRM) to manage IPD-ish risks.FindingsTwo types of risks, namely integration risks (IRs) and general risks (GRs), are identified in IPD-ish projects. Two major findings for the IRs: (1) the most critical IRs are related to unbalanced incentivization and inefficient multidisciplinary teams; and (2) only team formation related pre-contract JRM strategies affect IRs. As for the GRs, the most critical ones are associated with design issues and can be effectively mitigated by post-contract JRM.Originality/valueUsing IPD-ish arrangement is an inevitable part of implementation of full IPD. This happens as many change-averse owners would like to test the integration principles using a conventional contract that they are familiar with. In fact, success in IPD-ish would pave the path for further adoption of IPD. This study offers insight into categorization of risks in IPD-ish projects. Appropriate use of post-contract and organization related pre-contract JRM would improve the chance of teasing out the values of IPD through IPD-ish arrangements. Care should be taken to introduce some contracting integration initiatives, such as risk/reward sharing incentive.
Perceptions of Airbnb’s impact beyond the tourist bubbles of Cusco, Peru: an exploration of resident irritability
Authors: Arevalo Mildred , Day Jonathon , Sotomayor Sandra , Guillen Nancy Karen 
Published: November 2023

Purpose
Specifically, this study aims to examine residents’ perceptions regarding the following: the sociocultural, environmental and economic impacts generated by the presence of Airbnb and the irritability caused by the presence of Airbnb based on Doxey’s Doxey (1975) irritation index (i.e. index).

Design/methodology/approach
Twenty-one semistructured in-depth interviews were conducted between February and March 2021 with residents of three condominiums in the Huancaro residential complex. Data were analyzed using the qualitative data analysis software ATLAS.ti 8.

Findings
Results showed that participants perceived negative economic impacts regarding investments, jobs, real estate prices and overall cost of living; negative sociocultural impacts regarding criminality, social conflicts and cultural exchange; and negative environmental impacts regarding sanitation in the context of the pandemic and the state of the Airbnb apartments. Further, it was found that participants related to the following three of the four stages of irritability: euphoria, apathy and annoyance.

Research limitations/implications
It is necessary to complement the information with the perceptions of the residents about the city’s authorities and managers in the hotel business before the stage of the COVID-19 pandemic and the current stage.

Practical implications
The study identifies improve Airbnb operations like establishing health paraments and defining cohabitation rules at the condominiums.

Social implications
The residents consider that visitors’ returns produce positive and negative impacts on the quality of life being important for understanding their perceptions.

Originality/value
Short-term rental companies, such as Airbnb, generate a range of impacts on urban residents, particularly when travelers encroach on areas of the city beyond the traditional “tourist bubbles.” This study explored the perceptions of Airbnb’s impacts on activities among residents of Huancaro, a residential section of Cusco-Peru, in the context of tourism reopening after a year of an almost complete halt in tourism activities because of the COVID-19 pandemic. The study also highlighted the heterogenetic responses to Airbnb within the community.
Mataram mosques management: intention to place mosque funds in Islamic banks
Authors: Adriansyah Lalu Rizky , As-Salafiyah Aisyah 
Published: November 2023

Purpose
This study aims to examine idle funds in mosques in Mataram City and analyze the intentions of the mosque chairman to place mosque funds in Sharia banks. Six variables are used to analyze the intention; attitudes, subjective norms, behavioral control, sharia financial literacy, sharia banking knowledge and the responsibility of the management for the trust of the society.

Design/methodology/approach
This research consists of two studies; descriptive research examining idle funds of mosques and correlational research analyzing the intentions of mosque directors to place mosque funds in Sharia banks. Intentions will be analyzed using the theory of planned behavior approach, developed through the PLS-SEM method, and the data obtained from questionnaires through surveys were processed using the SmartPLS 3 application.

Findings
This study found that the average surplus between income and expenditure reaches IDR2.7m monthly. Also, 75% of mosques have placed their funds in Islamic banks. This study shows a positive relationship between the level of Islamic financial literacy, knowledge of Islamic banking, responsibility for public trust, attitudes toward Islamic banking, subjective norms and behavioral control in influencing the intentions to place mosque funds in Islamic banks. However, only behavioral control is accepted as it significantly influences intentions. Behavioral control means that to maximize intentions, Islamic banks need to make it easier for mosque administrators to place funds.

Originality/value
This research signifies a pioneering effort in examining idle funds within mosques, particularly those equipped with comprehensive financial reports within Mataram City. Furthermore, it spearheads an inquiry into the intentions of mosques to channel their funds into Sharia banks, underpinned by rigorous quantitative methodologies.
A spatio-temporal framework to assess urban heat island effect on Yeni Mamak urban transformation zone (Ankara, Türkiye)
Authors: Baş Bütüner Funda , Cakmakli Aysem Berrin , Karakadilar Ahmet Can , Deniz Esra 
Published: November 2023

PurposeThis article explores the impacts of the changing land-use on urban heat island (UHI) in an urban transformation zone in Ankara (Türkiye). Identifying a characteristic rural landscape until the 1950s, the study area experienced a drastic land-use change by razing the fertile landscape of the city and replacing it with a sealed surface. Development of the squatter houses after the 1960s and, subsequently, the implementation of a new housing morphology have introduced new sceneries, scales and surface conditions that make the study area a noteworthy case to analyze.Design/methodology/approachRegarding the drastic spatio-temporal change of the study area, this research assesses the impacts of the changing land-use on UHI based on three periods. Using 1957, 1991 and 2021 aerial imaginaries and maps, it analyzes the temperature alteration caused by the changing land-use. To do so, different surface types, green patterns and built-up areas have been modeled using Ankara climatic data and transferred to ENVI-Met to calculate the Universal Thermal Climate Index (UTCI) values.FindingsThe calculation has been developed over a transect covering an area of 40 m × 170 m, which includes diversity in terms of architecture, landscape and open space elements. To encourage future design strategies, the research findings deliberate into three extents that discuss the lacking climate knowledge in the ongoing urban transformation projects: impervious surface ratio and regional albedo variation, changing aspect ratio and temperature variation at the pedestrian level.Originality/valueUrban transformation projects, being countrywide operations in Türkiye, need to cover climate-informed design strategies. Herein, the article underlines the critical position of design decisions in forming a climate-informed urban environment. Dwelling on a typical model of housing transformation in Türkiye, the research could trigger climate-informed urban development strategies in the country.