bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enrichment of anchoring sites by introducing supramolecular halogen bonds for the efficient perovskite nanocrystal LEDs
Authors: Lu Po , Li Ting , Lu Min , Ruan Cheng , Sun Siqi , Wu Zhennan , Zhong Yuan , Zhang Fujun , Gao Yanbo , Huang Yaowei , Wang Yang , Hu Junhua , Yan Fengping , Zhang Yu 
Published: September 2023

AbstractConsidering the multi-functionalization of ligands, it is crucial for ligand molecular design to reveal the landscape of anchoring sites. Here, a typical triphenylphosphine (TPP) ligand was employed to explore its effect on the surface of CsPbI3 perovskite nanocrystals (PNCs). Except for the conventionally considered P-Pb coordination, an P-I supramolecular halogen bonding was also found on the NC surface. The coexistence of the above two types of bonding significantly increased the formation energy of iodine vacancy defects and improved the photoluminescence quantum yield of PNCs up to 93%. Meanwhile, the direct interaction of P and I enhanced the stability of the Pb-I octahedra and dramatically inhibited the migration of I ions. Furthermore, the introduction of additional benzene rings (2-(Diphenylphosphino)-biphenyl (DPB)) increased the delocalized properties of the PNC surface and significantly improved the charge transport of the PNCs. As a result, the DPB passivated CsPbI3 NCs based top-emitting LEDs exhibite a peak external quantum efficiency (EQE) of 22.8%, a maximum luminance of 15, 204 cd m−2, and an extremely low-efficiency roll-off of 2.6% at the current density of 500 mA cm−2.
Impact of transient acquired hypermutability on the inter- and intra-species competitiveness of Pseudomonas aeruginosa
Authors: On Yue Yuan , Figueroa Wendy , Fan Catherine , Ho Pok-Man , Bényei Éva Bernadett , Weimann Aaron , Ruis Christopher , Floto Andres R , Welch Martin 
Published: September 2023

Abstract
Once acquired, hypermutation is unrelenting, and in the long-term, leads to impaired fitness due to its cumulative impact on the genome. This raises the question of why hypermutators arise so frequently in microbial ecosystems. In this work, we explore this problem by examining how the transient acquisition of hypermutability affects inter- and intra-species competitiveness, and the response to environmental insults such as antibiotic challenge. We do this by engineering Pseudomonas aeruginosa to allow the expression of an important mismatch repair gene, mutS, to be experimentally controlled over a wide dynamic range. We show that high levels of mutS expression induce genomic stasis (hypomutation), whereas lower levels of induction lead to progressively higher rates of mutation. Whole-genome sequence analyses confirmed that the mutational spectrum of the inducible hypermutator is similar to the distinctive profile associated with mutS mutants obtained from the airways of people with cystic fibrosis (CF). The acquisition of hypermutability conferred a distinct temporal fitness advantage over the wild-type P. aeruginosa progenitor strain, in both the presence and the absence of an antibiotic selection pressure. However, over a similar time-scale, acquisition of hypermutability had little impact on the population dynamics of P. aeruginosa when grown in the presence of a competing species (Staphylococcus aureus). These data indicate that in the short term, acquired hypermutability primarily confers a competitive intra-species fitness advantage.
A systematic review of dentists' psychological wellbeing during the COVID-19 pandemic
Authors: Lefkowitz Brett , Houdmont Jonathan , Knight Alec 
Published: September 2023

AbstractBackgroundThe COVID-19 pandemic presented significant challenges to healthcare workers worldwide, including the effect on the psychological wellbeing of dentists.AimsTo evaluate the impact of the early phases of the pandemic on the psychological health, long-term wellbeing and clinical service provision of dentists, as well as the identification of the key risk and protective factors for adverse mental health outcomes (MHOs) in this group.MethodsA systematic review of cross-sectional studies (n = 53) from public and private dentistry sectors was employed to delineate the risk and protective factors for adverse MHOs.ResultsSelf-reports from these studies (1 December 2019 to 31 December 2021), involving 45,671 dentists worldwide were analysed. Study findings were classified according to their psychological impact (as risk or protective factors), categorised as 'operational' or 'organisational' and subdivided into 'psychosocial', 'occupational', 'sociodemographic' and 'environmental' elements. A GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) certainty of evidence score was calculated for all the identified factors.ConclusionsThis review confirmed the negative impact of the pandemic on the MHOs of dentists worldwide. Pivotal risk factors included fear of infection, transmission to families, lack of personal protective equipment and possible direct contact with infected patients. Enhanced infection control protocols, individual resilience and organisational support were identified as important protective factors.
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex
Authors: Dong Shuqi , Li Huadong , Wang Meilin , Rasheed Nadia , Zou Binqian , Gao Xijie , Guan Jiali , Li Weijie , Zhang Jiale , Wang Chi , Zhou Ningkun , Shi Xue , Li Mei , Zhou Min , Huang Junfeng , Li He , Zhang Ying , Wong Koon Ho , Zhang Xiaofei , Chao William Chong Hang , He Jun 
Published: September 2023

AbstractIn Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.
CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data
Authors: Puccio Simone , Grillo Giorgio , Alvisi Giorgia , Scirgolea Caterina , Galletti Giovanni , Mazza Emilia Maria Cristina , Consiglio Arianna , De Simone Gabriele , Licciulli Flavio , Lugli Enrico 
Published: September 2023

AbstractFlow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/.
Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths
Authors: Baillie Vicky L. , Madhi Shabir A. , Ahyong Vida , Olwagen Courtney P. 
Published: September 2023

AbstractPostmortem minimally invasive tissue sampling together with the detailed review of clinical records has been shown to be highly successful in determining the cause of neonatal deaths. However, conventional tests including traditional culture methods and nucleic acid amplification tests have periodically proven to be insufficient to detect the causative agent in the infectious deaths. In this study, metagenomic next generation sequencing was used to explore for putative pathogens associated with neonatal deaths in post-mortem blood and lung tissue samples, in Soweto, South Africa. Here we show that the metagenomic sequencing results corroborate the findings using conventional methods of culture and nucleic acid amplifications tests on post-mortem samples in detecting the pathogens attributed in the causal pathway of death in 90% (18/20) of the decedents. Furthermore, metagenomic sequencing detected a putative pathogen, including Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Serratia marcescens, in a further nine of 11 (81%) cases where no causative pathogen was identified. The antimicrobial susceptibility profile was also determined by the metagenomic sequencing for all pathogens with numerous multi drug resistant organism identified. In conclusion, metagenomic sequencing is able to successfully identify pathogens contributing to infection associated deaths on postmortem blood and tissue samples.
The Oncology Biomarker Discovery framework reveals cetuximab and bevacizumab response patterns in metastatic colorectal cancer
Authors: Ohnmacht Alexander J. , Stahler Arndt , Stintzing Sebastian , Modest Dominik P. , Holch Julian W. , Westphalen C. Benedikt , Hölzel Linus , Schübel Marisa K. , Galhoz Ana , Farnoud Ali , Ud-Dean Minhaz , Vehling-Kaiser Ursula , Decker Thomas , Moehler Markus , Heinig Matthias , Heinemann Volker , Menden Michael P. 
Published: September 2023

AbstractPrecision medicine has revolutionised cancer treatments; however, actionable biomarkers remain scarce. To address this, we develop the Oncology Biomarker Discovery (OncoBird) framework for analysing the molecular and biomarker landscape of randomised controlled clinical trials. OncoBird identifies biomarkers based on single genes or mutually exclusive genetic alterations in isolation or in the context of tumour subtypes, and finally, assesses predictive components by their treatment interactions. Here, we utilise the open-label, randomised phase III trial (FIRE-3, AIO KRK-0306) in metastatic colorectal carcinoma patients, who received either cetuximab or bevacizumab in combination with 5-fluorouracil, folinic acid and irinotecan (FOLFIRI). We systematically identify five biomarkers with predictive components, e.g., patients with tumours that carry chr20q amplifications or lack mutually exclusive ERK signalling mutations benefited from cetuximab compared to bevacizumab. In summary, OncoBird characterises the molecular landscape and outlines actionable biomarkers, which generalises to any molecularly characterised randomised controlled trial.
Dopamine regulates decision thresholds in human reinforcement learning in males
Authors: Chakroun Karima , Wiehler Antonius , Wagner Ben , Mathar David , Ganzer Florian , van Eimeren Thilo , Sommer Tobias , Peters Jan 
Published: September 2023

AbstractDopamine fundamentally contributes to reinforcement learning, but recent accounts also suggest a contribution to specific action selection mechanisms and the regulation of response vigour. Here, we examine dopaminergic mechanisms underlying human reinforcement learning and action selection via a combined pharmacological neuroimaging approach in male human volunteers (n = 31, within-subjects; Placebo, 150 mg of the dopamine precursor L-dopa, 2 mg of the D2 receptor antagonist Haloperidol). We found little credible evidence for previously reported beneficial effects of L-dopa vs. Haloperidol on learning from gains and altered neural prediction error signals, which may be partly due to differences experimental design and/or drug dosages. Reinforcement learning drift diffusion models account for learning-related changes in accuracy and response times, and reveal consistent decision threshold reductions under both drugs, in line with the idea that lower dosages of D2 receptor antagonists increase striatal DA release via an autoreceptor-mediated feedback mechanism. These results are in line with the idea that dopamine regulates decision thresholds during reinforcement learning, and may help to bridge action selection and response vigor accounts of dopamine.
PO2/TransformON, an ontology for data integration on food, feed, bioproducts and biowaste engineering
Authors: Weber Magalie , Buche Patrice , Ibanescu Liliana , Dervaux Stéphane , Guillemin Hervé , Cufi Julien , Visalli Michel , Guichard Elisabeth , Pénicaud Caroline 
Published: September 2023

AbstractWe are witnessing an acceleration of the global drive to converge consumption and production patterns towards a more circular and sustainable approach to the food system. To address the challenge of reconnecting agriculture, environment, food and health, collections of large datasets must be exploited. However, building high-capacity data-sharing networks means unlocking the information silos that are caused by a multiplicity of local data dictionaries. To solve the data harmonization problem, we proposed an ontology on food, feed, bioproducts, and biowastes engineering for data integration in a circular bioeconomy and nexus-oriented approach. This ontology is based on a core model representing a generic process, the Process and Observation Ontology (PO2), which has been specialized to provide the vocabulary necessary to describe any biomass transformation process and to characterize the food, bioproducts, and wastes derived from these processes. Much of this vocabulary comes from transforming authoritative references such as the European food classification system (FoodEx2), the European Waste Catalogue, and other international nomenclatures into a semantic, world wide web consortium (W3C) format that provides system interoperability and software-driven intelligence. We showed the relevance of this new domain ontology PO2/TransformON through several concrete use cases in the fields of process engineering, bio-based composite making, food ecodesign, and relations with consumer’s perception and preferences. Further works will aim to align with other ontologies to create an ontology network for bridging the gap between upstream and downstream processes in the food system.
Shared and distinct neural correlates of first and second language morphological processing in bilingual brain
Authors: Gao Fei , Hua Lin , Armada-da-Silva Paulo , Zhang Juan , Li Defeng , Chen Zhiyi , Wang Chengwen , Du Meng , Yuan Zhen 
Published: September 2023

AbstractWhile morphology constitutes a crucial component of the human language system, the neural bases of morphological processing in the human brain remains to be elucidated. The current study aims at exploring the extent to which the second language (L2) morphological processing would resemble or differ from that of their first language (L1) in adult Chinese-English bilinguals. Bilingual participants were asked to complete a morphological priming lexical decision task drawing on derivational morphology, which is present for both Chinese and English, when their electrophysiological and optical responses were recorded concurrently. Functional near-infrared spectroscopy (fNIRS) revealed a neural dissociation between morphological and semantic priming effects in the left fronto-temporal network, while L1 Chinese engaged enhanced activation in the left prefrontal cortex for morphological parsing relative to L2 English. In the early stage of lexical processing, cross-language morphological processing manifested a difference in degree, not in kind, as revealed by the early left anterior negativity (ELAN) effect. In addition, L1 and L2 shared both early and late structural parsing processes (P250 and 300 ~ 500 ms negativity, respectively). Therefore, the current results support a unified competition model for bilingual development, where bilinguals would primarily employ L1 neural resources for L2 morphological representation and processing.
Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity
Authors: Wenger Alice , Biran Alva , Alcaraz Nicolas , Redó-Riveiro Alba , Sell Annika Charlotte , Krautz Robert , Flury Valentin , Reverón-Gómez Nazaret , Solis-Mezarino Victor , Völker-Albert Moritz , Imhof Axel , Andersson Robin , Brickman Joshua M. , Groth Anja 
Published: September 2023

AbstractModified parental histones are segregated symmetrically to daughter DNA strands during replication and can be inherited through mitosis. How this may sustain the epigenome and cell identity remains unknown. Here we show that transmission of histone-based information during DNA replication maintains epigenome fidelity and embryonic stem cell plasticity. Asymmetric segregation of parental histones H3–H4 in MCM2-2A mutants compromised mitotic inheritance of histone modifications and globally altered the epigenome. This included widespread spurious deposition of repressive modifications, suggesting elevated epigenetic noise. Moreover, H3K9me3 loss at repeats caused derepression and H3K27me3 redistribution across bivalent promoters correlated with misexpression of developmental genes. MCM2-2A mutation challenged dynamic transitions in cellular states across the cell cycle, enhancing naïve pluripotency and reducing lineage priming in G1. Furthermore, developmental competence was diminished, correlating with impaired exit from pluripotency. Collectively, this argues that epigenetic inheritance of histone modifications maintains a correctly balanced and dynamic chromatin landscape able to support mammalian cell differentiation.
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation
Authors: Jiang Huanyu , Zhou Rui , An Liping , Guo Junfeng , Hou Xinhui , Tang Jiao , Wang Fei , Du Quanyu 
Published: September 2023

AbstractIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic disease with an unclear etiology and no effective treatment. This study aims to elucidate the pathogenic mechanism networks involving multiple targets and pathways in IPF. Extracts and metabolites of Astragalus membranaceus (AM) and Radix paeoniae rubra (RPR), two well-known traditional Chinese medicines, have demonstrated therapeutic effects on IPF. However, the underlying mechanisms of AM and RPR remain unclear. Utilizing network pharmacology analysis, differentially expressed genes (DEGs) associated with IPF were obtained from the GEO database. Targets of AM and RPR were identified using the TCM Systems Pharmacology Database and Analysis Platform and SwissTargetPrediction. A protein–protein interaction (PPI) network was subsequently constructed and analyzed using the STRING database and Cytoscape software. Gene ontology enrichment analysis and kyoto encyclopedia of genes and genomes analysis were conducted using Metascape. Additionally, a component-target-pathway network and a Sankey diagram were employed to identify the main active components, and molecular docking was performed between these components and proteins encoded by key targets. Finally, in vivo studies were conducted based on network pharmacology. A total of 117 common targets between DEGs of IPF and drug targets were identified and included in the PPI network, in which AKT1, MAPK3, HSP90AA1, VEGFA, CASP3, JUN, HIF1A, CCND1, PTGS2, and MDM2 were predicted as key targets. These 117 targets were enriched in the PI3K-AKT pathway, HIF-1 signaling pathway, apoptosis, and microRNAs in cancer. Astragaloside III, (R)-Isomucronulatol, Astragaloside I, Paeoniflorin, and β-sitosterol were selected as the main active components. Docking scores ranged from − 4.7 to − 10.7 kcal/mol, indicating a strong binding affinity between the main active compounds and key targets. In vivo studies have indeed shown that AM and RPR can alleviate the pathological lung fibrotic damage caused by bleomycin treatment. The treatment with AM and RPR resulted in a reduction of mRNA levels for key targets AKT1, HSP90AA1, CASP3, MAPK3, and VEGFA. Additionally, the protein expression levels of AKT1, HSP90AA1, and VEGFA were also reduced. These results support the therapeutic potential of AM and RPR in ameliorating pulmonary fibrosis and provide insight into the molecular mechanisms involved in their therapeutic effects.
Increased temporal binding during voluntary motor task under local anesthesia
Authors: Driller Karina Kirk , Fradet Camille , Mathijssen Nina , Kraan Gerald , Goossens Richard , Hayward Vincent , Hartcher-O’Brien Jess 
Published: September 2023

AbstractTemporal binding refers to a systemic bias in the perceived time interval between two related events, most frequently voluntary motor actions and a subsequent sensory effect. An inevitable component of most instrumental motor actions is tactile feedback. Yet, the role of tactile feedback within this phenomenon remains largely unexplored. Here, we used local anesthesia of the index finger to temporarily inhibit incoming sensory input from the finger itself, while participants performed an interval-estimation task in which they estimated the delay between a voluntary motor action (button press) and a second sensory event (click sound). Results were compared to a control condition with intact sensation. While clear binding was present in both conditions, the effect was significantly enhanced when tactile feedback was temporarily removed via local anesthesia. The results are discussed in light of current debates surrounding the underlying mechanisms and function of this temporal bias.