bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural organisation of perisomatic inhibition in the mouse medial prefrontal cortex
Authors: Nagy-Pál Petra , Veres Judit M. , Fekete Zsuzsanna , Karlócai Mária R. , Weisz Filippo , Barabás Bence , Reéb Zsófia , Hájos Norbert 
Published: June 2023

AbstractPerisomatic inhibition profoundly controls neural function. However, the structural organisation of inhibitory circuits giving rise to the perisomatic inhibition in the higher-order cortices is not completely known. Here, we performed a comprehensive analysis of those GABAergic cells in the medial prefrontal cortex (mPFC) that provide inputs onto the somata and proximal dendrites of pyramidal neurons. Our results show that most GABAergic axonal varicosities contacting the perisomatic region of superficial (layer 2/3) and deep (layer 5) pyramidal cells express parvalbumin (PV) or cannabinoid receptor type 1 (CB1). Further, we found that the ratio of PV/CB1 GABAergic inputs is larger on the somatic membrane surface of pyramidal tract neurons in comparison to those projecting to the contralateral hemisphere. Our morphological analysis of in vitro labelled PV+ basket cells (PVBC) and CCK/CB1+ basket cells (CCKBC) revealed differences in many features. PVBC dendrites and axons arborized preferentially within the layer where their soma was located. In contrast, the axons of CCKBCs expanded throughout layers, though their dendrites were found preferentially either in superficial or deep layers. Finally, using anterograde trans-synaptic tracing we observed that PVBCs are preferentially innervated by thalamic and basal amygdala afferents in layer 5a and 5b, respectively. Thus, our results suggest that PVBCs can control the local circuit operation in a layer-specific manner via their characteristic arborization, while CCKBCs rather provide cross-layer inhibition in the mPFC.Significance StatementInhibitory cells in cortical circuits are crucial for the precise control of local network activity. Nevertheless, in higher-order cortical areas that are involved in cognitive functions like decision making, working memory and cognitive flexibility, the structural organisation of inhibitory cell circuits is not completely understood. In this study we show that perisomatic inhibitory control of excitatory cells in the medial prefrontal cortex is performed by two types of basket cells endowed with different morphological properties that provide inhibitory inputs with distinct layer specificity on cells projecting to disparate areas. Revealing this difference in innervation strategy of the two basket cell types is a key step towards understanding how they fulfil their distinct roles in cortical network operations.
The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems
Authors: Wang Xiaopei , Ruan Yongsen , Zhang Lingjie , Chen Xiangnyu , Shi Zongkun , Wang Haiyu , Chen Bingjie , Tracy Miles , Huang Liying , Wu Chung-I , Wen Haijun 
Published: June 2023

ABSTRACTMulti-copy gene systems that evolve within, as well as between, individuals are common. They include viruses, mitochondrial DNAs, multi-gene families etc. The paradox is that neutral evolution in two stages should be far slower than single-copy systems but the opposite is often true, thus leading to the suggestion of natural selection. We now apply the new Generalized Haldane (GH) model to quantify genetic drift in the mammalian ribosomal RNA genes (or rDNAs). On average, rDNAs haveC∼ 150 - 300 copies. A neutral mutation in rDNA should take 4NC*generations to become fixed (N, the population size;C*, the effective copy number). WhileC>C*>> 1 is expected, the observed fixation time in mouse and human is < 4N, hence the paradox ofC*< 1. Genetic drift thus appears as much as 100 times stronger for rRNA genes as for single-copy genes. The large increases in genetic drift are driven by a host of molecular mechanisms such as gene conversion and unequal crossover. Although each mechanism of drift has been extremely difficult to quantify, the GH model permits the estimation of their total effects on genetic drift. In conclusion, the GH model can be generally applicable to multi-copy gene systems without being burdened by tracking the diverse molecular mechanisms individually.
Universal Dynamic Fitting of Magnetic Resonance Spectroscopy
Authors: Clarke William T , Ligneul Clémence , Cottaar Michiel , Ip I Betina , Jbabdi Saad 
Published: June 2023

AbstractDynamic (2D) magnetic resonance spectroscopy is a collection of techniques where acquisitions of spectra are repeated under varying experimental or physiological conditions. Dynamic MRS comprises a rich set of contrasts, including diffusion-weighted, relaxation-weighted, functional, edited, or hyperpolarized spectroscopy, leading to quantitative insights into multiple physiological or microstructural processes. Conventional approaches to dynamic MRS analysis ignore the shared information between spectra, and instead proceed by independently fitting noisy individual spectra before modelling temporal changes in the parameters. Here we propose a universal dynamic MRS toolbox which allows simultaneous fitting of dynamic spectra of arbitrary type. A simple interface allows information to be shared and precisely modelled across spectra to make inferences on both spectral and dynamic processes. We demonstrate and thoroughly evaluate our approach in three types of dynamic MRS techniques. Simulations of functional and edited MRS are used to demonstrate the advantages of dynamic fitting. Analysis of synthetic functional 1H-MRS data shows a marked decrease in parameter uncertainty as predicted by prior work. Analysis with our tool replicates the results of two previously published studies using the original in vivo functional and diffusion-weighted data. Finally, joint spectral fitting with diffusion orientation models is demonstrated in synthetic data. The toolbox is shared as a fully open-source software with comprehensive documentation, example data, and tutorials.
Characterization of the genetic composition and establishment of a core collection for the INERA Robusta coffee (Coffea canephora) field genebank from the Democratic Republic of the Congo
Authors: Verleysen Lauren , Bollen Robrecht , Kambale Jean-Léon , Tshimi Ebele , Ntumba Katshela Benjamin , Depecker Jonas , Poncet Valérie , Assumani Dieu-Merci , Vandelook Filip , Stoffelen Piet , Honnay Olivier , Ruttink Tom 
Published: June 2023

ABSTRACTCultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope, but substantial effort must be made to improve its cupping quality and other agronomic traits. Robusta coffee genetic resources conserved in field genebanks can play an important role in this context, but many of them are limited and poorly characterized. In this study, we aimed to characterize the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (Democratic Republic of the Congo) and to propose a Robusta core collection. We combined genome-wide GBS marker sets with a novel versatile multiplex amplicon sequencing (HiPlex) screening assay, for the genetic screening of the INERA Coffee Collection and created tools for future genetic screening. A set of 730 coffee shrubs in the collection were genotyped at 86 HiPlex loci and 263 unique genetic fingerprints were identified. Representative fingerprints were compared to ‘Lula’ cultivars, ‘Luki’ cultivars, Congolese subgroup A, and wild genotypes growing in the rainforest of the Yangambi region. The majority of the unique genetic fingerprints were identified as ‘Lula’ cultivars but also four Congolese subgroup A and nine wild genotypes were found in the collection. Twenty-five percent of the unique genetic fingerprints had a hybrid identity which could result from seed-based propagation of the collection or natural cross-pollination. Moreover, eight unique genetic fingerprints were frequently identified as a parent and these may correspond to the ancient selected mother plants, or direct descendants thereof, of which seed material was widely distributed from 1930 to 1960 for the creation of coffee plantations. Finally, to delineate core collections we tested the maximization strategy and genetic distance method for the INERA Coffee Collection, and proposed i) a core collection conserving the loci diversity of the collection,i.e.100 accessions and ii) a core collection holding the highest genetic distances between the accessions,i.e.10 accessions. Our study provides a method for the genetic characterization of Robusta coffee collections in general and contributes to the revaluation and exploitation of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.
The structure of the OmpA/Pal protein ofAnaplasma phagocytophilum
Authors: Cadby I.T. 
Published: June 2023

ABSTRACTPeptidoglycan associated lipoprotein (Pal) and Outer Membrane Protein A (OmpA), interact with the outer membrane and peptidoglycan in Gram-negative bacteria, conferring structural integrity to the bacterial cell and functioning in cell division. Both OmpA and Pal proteins have moonlighting roles as virulence factors, facilitating infection and host-pathogen interactions in a range of bacteria. The OmpA-like protein ofAnaplasma phagocytophilum, a tick-borne pathogen that infects a wide range of hosts, seems to function primarily as a virulence factor, since this bacterium lacks a peptidoglycan cell wall. Here we present crystal structures of the OmpA-like protein ofA. phagocytophilum, demonstrating that this protein has amino acid insertions that confer flexibility. This insertion is also found in the OmpA-like proteins of other pathogens, related toA. phagocytophilum. Whether this flexibility is reflective of any adaptations for host-pathogen interactions remains to be determined but, since the OmpA-like proteins ofAnaplasmaspecies are current targets for vaccine development, might have importance for these efforts.
Molecular basis of Progressive Familial Intrahepatic Cholestasis 3. A proteomics study
Authors: Guerrero Laura , Carmona-Rodríguez Lorena , Santos Fátima Millhano , Ciordia Sergio , Stark Luiz , Hierro Loreto , Vicent David , Corrales Fernando J. 
Published: June 2023

AbstractBackground and aimsProgressive familiar intrahepatic cholestasis type 3 (PFIC3) is a severe rare liver disease which affects between 1/50,000 to 1/100,000 children. In physiological conditions, bile is produced by the liver and stored in the gallbladder, then it flows to the small intestine to play its role in fat digestion. To prevent tissue damage, bile acids are kept into phospholipid micelles. Mutations in phosphatidyl choline transporter ABCB4 (MDR3) lead to intrahepatic accumulation of free bile acids that results in liver damage. PFIC3 onset occurs usually at early ages, progress rapidly and the prognosis is poor. Currently, besides the palliative use of ursodeoxycholate, the only available treatment for this disease is liver transplantation, which is really challenging for short-aged patients.MethodsTo gain insight into the pathogenesis of PFIC3 we have performed an integrated proteomics and phosphoproteomics study in human liver samples to then validate the emerging functional hypotheses in a PFIC3 murine model.ResultsWe identified 6,246 protein groups, 324 proteins among them showing differential expression between control and PFIC3. The phosphoproteomic analysis allowed the identification of 5,090 phosphopeptides, from which 215 corresponding to 157 protein groups, were differentially phosphorylated in PFIC3, including MDR3. Regulation of essential cellular processes and structures, such as inflammation, metabolic reprograming, cytoskeleton and extracellular matrix remodeling and cell proliferation were identified as main drivers of the disease.ConclusionOur results provide a strong molecular background that significantly contributes to a better understanding of PFIC3 and provides new concepts that might prove useful in the clinical management of patients.Lay Summary/Key PointsPFIC3 is a rare disease that affect 1/50,000 to 1/100,000 children that present severe symptoms in the first years of life and have scarce therapeutic options. We identified a panel of proteins that recapitulate some of the main cellular processes associated to the progression of liver injury in PFIC3 patients and suggest alternative treatment options.
Comparative analysis of PDZ-binding motifs in the diacylglycerol kinase family
Authors: Zambo Boglarka , Gogl Gergo , Morlet Bastien , Eberling Pascal , Negroni Luc , Moine Hervé , Travé Gilles 
Published: June 2023

AbstractDiacylglycerol kinases (DGKs) control local and temporal amounts of diacylglycerol (DAG) and phosphatidic acid (PA) by converting DAG to PA through phosphorylation in cells. Certain DGK enzymes possess C-terminal sequences that encode potential PDZ-binding motifs (PBMs), which could be involved in their recruitment into supramolecular signaling complexes. In this study, we used two different interactomic approaches, quantitative native holdup (nHU) and qualitative affinity purification (AP), both coupled to mass spectrometry (MS) to investigate the PDZ partners associated with the potential PBMs of DGKs. Complementing these results with site-specific affinity interactomic data measured on isolated PDZ domain fragments and PBM motifs, as well as evolutionary conservation analysis of the PBMs of DGKs, we explored functional differences within different DGK groups. All our results indicate that putative PBM sequences of type II enzymes are likely to be nonfunctional. In contrast, type IV enzymes possess highly promiscuous PBMs that interact with a set of PDZ proteins with very similar affinity interactomes. The combination of various interactomic assays and evolutionary analyses provides a useful strategy for identifying functional domains and motifs within diverse enzyme families.
Incorporating strontium enriched amorphous calcium phosphate granules in collagen/collagen-magnesium-hydroxyapatite osteochondral scaffold improves subchondral bone repair
Authors: Xu Jietao , Vecstaudža Jana , Wesdorp Marinus A. , Labberté Margot , Kops Nicole , Salerno Manuela , Kok Joeri , Simon Marina , Harmand Marie-Françoise , Vancíková Karin , van Rietbergen Bert , Misciagna Massimiliano Maraglino , Dolcini Laura , Filardo Giuseppe , Farrell Eric , van Osch Gerjo J.V.M. , Ločs Jānis , Brama Pieter A.J. 
Published: June 2023

AbstractTo date, osteochondral defect repair with a collagen/collagen-magnesium-hydroxyapatite (Col/Col-Mg-HAp) scaffold has demonstrated good clinical results. However, subchondral bone repair has been suboptimal, potentially leading to damage to the regenerated overlying neocartilage. This study aimed at improving the bone repair potential of this scaffold by incorporating strontium (Sr) ion enriched amorphous calcium phosphate (Sr-ACP) granules (100-150 µm). Sr concentration of Sr-ACP was determined with ICP-MS at 2.49 ± 0.04 wt.%. Then 30 wt.% ACP or Sr-ACP granules were integrated into the scaffold prototypes. The ACP or Sr-ACP granules were well distributed and embedded in the collagenic matrix demonstrated by micro-CT and scanning electron microscopy/energy dispersive x-ray spectrometry. Good cytocompatibility of ACP/Sr-ACP granules and ACP/Sr-ACP enriched scaffolds was confirmed inin vitrocytotoxicity assays. An overall promising early tissue response and good biocompatibility of both ACP and Sr-ACP enriched scaffolds were demonstrated in a subcutaneous mouse model. In a goat osteochondral defect model, significantly more bone observed at 6 months with the treatment of Sr-ACP enriched scaffolds compared to scaffold only in particular in the weight-bearing femoral condyle subchondral bone defect. Overall, the incorporation of osteogenic Sr-ACP granules in Col/Col-Mg-HAp scaffolds showed to be a feasible and promising strategy to improve subchondral bone repair.
TCRpcDist: Estimating TCR physico-chemical similarity to analyze repertoires and predict specificities
Authors: Perez Marta A. S. , Chiffelle Johanna , Bobisse Sara , Mayol-Rullan Francesca , Arnaud Marion , Sauvage Christophe , Coukos George , Harari Alexandre , Zoete Vincent 
Published: June 2023

AbstractApproaches to analyse and cluster TCR repertoires to reflect antigen specificity are critical for the diagnosis and prognosis of immune-related diseases and the development of personalized therapies. Sequence-based approaches showed success but remain restrictive, especially when the amount of experimental data used for the training is scarce. Structure-based approaches which represent powerful alternatives, notably to optimize TCRs affinity towards specific epitopes, show limitations for large scale predictions. To handle these challenges, we present TCRpcDist, a 3D-based approach that calculates similarities between TCRs using a metric related to the physico-chemical properties of the loop residues predicted to interact with the epitope. By exploiting private and public datasets and comparing TCRpcDist with competing approaches, we demonstrate that TCRpcDist can accurately identify groups of TCRs that are likely to bind the same or similar epitopes. Additionally, we experimentally validated the ability of TCRpcDist to predict antigen-specificities of tumor-infiltrating lymphocytes orphan TCRs obtained from four cancer patients. TCRpcDist is a promising approach to support TCR repertoire analysis and cancer immunotherapies.One Sentence SummaryWe present a new approach for TCR clustering which allows TCR deorphanization for the first time.
What makes experimental research publishable in leading hospitality and tourism journals? Perspectives of editorial board members
Authors: Leung Xi Yu , Fong Lawrence Hoc Nang , Xue Xunyue (Joanne) , Mattila Anna S. 
Published: June 2023

Purpose
Hospitality and tourism research lags in using experimental designs. This study aims to reveal prestigious scholars’ opinions and suggestions on how to effectively design and execute experimental research.

Design/methodology/approach
The authors conducted an open-ended survey on 187 editors and editorial board members from 22 top hospitality and tourism journals. Their answers were coded following an inductive method of coding, and a list of themes and categories was synthesized.

Findings
The results summarize common problems of this method and indicate significant barriers to making experimental studies publishable. The review criteria for experimental studies are presented from four aspects: overall design, stimuli and manipulations, data collection and reporting results.

Research limitations/implications
The results provide valuable suggestions for researchers interested in experimental design in the hospitality and tourism field. The study contributes to a shift toward well-designed and well-executed experimental research in hospitality and tourism.

Originality/value
To the best of the authors’ knowledge, the study is the first to survey editorial board members of impactful hospitality and tourism journals to reveal their insights into the experimental methodology. The study makes significant theoretical and methodological contributions by addressing calls to understand common problems and barriers to experimental research in our field.
Determinants of debunking information sharing behaviour in social media users: perspective of persuasive cues
Authors: Chao Fan , Wang Xin , Yu Guang 
Published: June 2023

PurposeSharing and disseminating debunking information are critical to correcting rumours and controlling disease when dealing with public health crises. This study investigates the factors that influence social media users' debunking information sharing behaviour from the perspective of persuasion. The authors examined the effects of argument adequacy, emotional polarity, and debunker's identity on debunking information sharing behaviour and investigated the moderating effects of rumour content and target.Design/methodology/approachThe model was tested using 150 COVID-19-related rumours and 2,349 original debunking posts on Sina Weibo.FindingsFirst, debunking information that contains adequate arguments is more likely to be reposted only when the uncertainty of the rumour content is high. Second, using neutral sentiment as a reference, debunking information containing negative sentiment is shared more often regardless of whether the government is the rumour target, and information containing positive sentiment is more likely to be shared only when the rumour target is the government. Finally, debunking information published by government-type accounts is reposted more often and is enhanced when the rumour target is the government.Originality/valueThe study provides a systematic framework for analysing the behaviour of sharing debunking information among social media users. Specifically, it expands the understanding of the factors that influence debunking information sharing behaviour by examining the effects of persuasive cues on debunking information sharing behaviour and the heterogeneity of these effects across various rumour contexts.
Norms or fun? The influence of ethical concerns and perceived enjoyment on the regulation of deepfake information
Authors: Li Minghui , Wan Yan 
Published: June 2023

PurposeDeepfake information poses more ethical risks than traditional disinformation in terms of fraud, slander, rumors and other malicious uses. However, owing to its high entertainment value, deepfake information with ethical risks has become popular. This study aims to understand the role of ethics and entertainment in the acceptance and regulation of deepfake information.Design/methodology/approachMixed methods were used to qualitatively identify ethical concerns and quantitatively evaluate the influence of ethical concerns and perceived enjoyment on the ethical acceptability and social acceptance of deepfake information.FindingsThe authors confirmed that informed consent, privacy protection, traceability and non-deception had a significantly positive impact on ethical acceptability and indirectly influenced social acceptance, with privacy protection being the most sensitive. Perceived enjoyment impacts the social acceptance of deepfake information and significantly weakens the effect of ethical acceptability on social acceptance.Originality/valueThe ethical concerns affecting acceptance behavior identified in this study provide an entry point for the ethical regulation of deepfake information. The weakening effect of perceived enjoyment on ethics serves as a wake-up call for regulators to guard against pan-entertainment deepfake information.