bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of SUMO-specific protease 2 causes isolated glucocorticoid deficiency by blocking adrenal cortex zonal transdifferentiation in mice
Authors: Dufour Damien , Dumontet Typhanie , Sahut-Barnola Isabelle , Carusi Aude , Onzon Méline , Pussard Eric , Wilmouth James Jr , Olabe Julie , Lucas Cécily , Levasseur Adrien , Damon-Soubeyrand Christelle , Pointud Jean-Christophe , Roucher-Boulez Florence , Tauveron Igor , Bossis Guillaume , Yeh Edward T. , Breault David T. , Val Pierre , Lefrançois-Martinez Anne-Marie , Martinez Antoine 
Published: December 2022

AbstractSUMOylation is a dynamic posttranslational modification, that provides fine-tuning of protein function involved in the cellular response to stress, differentiation, and tissue development. In the adrenal cortex, an emblematic endocrine organ that mediates adaptation to physiological demands, the SUMOylation gradient is inversely correlated with the gradient of cellular differentiation raising important questions about its role in functional zonation and the response to stress. Considering that SUMO-specific protease 2 (SENP2), a deSUMOylating enzyme, is upregulated by Adrenocorticotropic Hormone (ACTH)/cAMP-dependent Protein Kinase (PKA) signalling within the zonafasciculata, we generated mice with adrenal-specific Senp2 loss to address these questions. Disruption of SENP2 activity in steroidogenic cells leads to specific hypoplasia of the zona fasciculata, a blunted reponse to ACTH and isolated glucocorticoid deficiency. Mechanistically, overSUMOylation resulting from SENP2 loss shifts the balance between ACTH/PKA and WNT/β-catenin signalling leading to repression of PKA activity and ectopic activation of β-catenin. At the cellular level, this blocks transdifferentiation of β-catenin-positive zona glomerulosa cells into fasciculata cells and sensitises them to premature apoptosis. Our findings indicate that the SUMO pathway is critical for adrenal homeostasis and stress responsiveness.
Ampere-level current density ammonia electrochemical synthesis using CuCo nanosheets simulating nitrite reductase bifunctional nature
Authors: Fang Jia-Yi , Zheng Qi-Zheng , Lou Yao-Yin , Zhao Kuang-Min , Hu Sheng-Nan , Li Guang , Akdim Ouardia , Huang Xiao-Yang , Sun Shi-Gang 
Published: December 2022

AbstractThe development of electrocatalysts capable of efficient reduction of nitrate (NO3−) to ammonia (NH3) is drawing increasing interest for the sake of low carbon emission and environmental protection. Herein, we present a CuCo bimetallic catalyst able to imitate the bifunctional nature of copper-type nitrite reductase, which could easily remove NO2−via the collaboration of two active centers. Indeed, Co acts as an electron/proton donating center, while Cu facilitates NOx−adsorption/association. The bio-inspired CuCo nanosheet electrocatalyst delivers a 100 ± 1% Faradaic efficiency at an ampere-level current density of 1035 mA cm−2at −0.2 Vvs. Reversible Hydrogen Electrode. The NH3production rate reaches a high activity of 4.8 mmol cm−2h−1(960 mmol gcat−1h−1). A mechanistic study, using electrochemical in situ Fourier transform infrared spectroscopy and shell-isolated nanoparticle enhanced Raman spectroscopy, reveals a strong synergy between Cu and Co, with Co sites promoting the hydrogenation of NO3−to NH3via adsorbed *H species. The well-modulated coverage of adsorbed *H and *NO3led simultaneously to high NH3selectivity and yield.
Clay hydroxyl isotopes show an enhanced hydrologic cycle during the Paleocene-Eocene Thermal Maximum
Authors: Walters Gregory L. , Kemp Simon J. , Hemingway Jordon D. , Johnston David T. , Hodell David A. 
Published: December 2022

AbstractThe Paleocene-Eocene Thermal Maximum (PETM) was an abrupt global warming event associated with a large injection of carbon into the ocean-atmosphere system, as evidenced by a diagnostic carbon isotope excursion (CIE). Evidence also suggests substantial hydrologic perturbations, but details have been hampered by a lack of appropriate proxies. To address this shortcoming, here we isolate and measure the isotopic composition of hydroxyl groups (OH−) in clay minerals from a highly expanded PETM section in the North Sea Basin, together with their bulk oxygen isotope composition. At this location, we show that hydroxyl O- and H-isotopes are less influenced than bulk values by clay compositional changes due to mixing and/or inherited signals and thus better track hydrologic variability. We find that clay OH− hydrogen-isotope values (δ2HOH) decrease slowly prior to the PETM and then abruptly by ∼8‰ at the CIE onset. Coincident with an increase in relative kaolinite content, this indicates increased rainfall and weathering and implies an enhanced hydrologic cycle response to global warming, particularly during the early stages of the PETM. Subsequently, δ2HOH returns to pre-PETM values well before the end of the CIE, suggesting hydrologic changes in the North Sea were short-lived relative to carbon-cycle perturbations.
Memory for nonadjacent dependencies in the first year of life and its relation to sleep
Authors: Friedrich Manuela , Mölle Matthias , Born Jan , Friederici Angela D. 
Published: December 2022

AbstractGrammar learning requires memory for dependencies between nonadjacent elements in speech. Immediate learning of nonadjacent dependencies has been observed in very young infants, but their memory of such dependencies has remained unexplored. Here we used event-related potentials to investigate whether 6- to 8-month-olds retain nonadjacent dependencies and if sleep after learning affects this memory. Infants were familiarised with two rule-based morphosyntactic dependencies, presented in sentences of an unknown language. Brain responses after a retention period reveal memory of the nonadjacent dependencies, independent of whether infants napped or stayed awake. Napping, however, altered a specific processing stage, suggesting that memory evolves during sleep. Infants with high left frontal spindle activity show an additional brain response indicating memory of individual speech phrases. Results imply that infants as young as 6 months are equipped with memory mechanisms relevant to grammar learning. They also suggest that during sleep, consolidation of highly specific information can co-occur with changes in the nature of generalised memory.
Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach
Authors: Välikangas Tommi , Suomi Tomi , Chandler Courtney E. , Scott Alison J. , Tran Bao Q. , Ernst Robert K. , Goodlett David R. , Elo Laura L. 
Published: December 2022

AbstractQuantitative proteomics has matured into an established tool and longitudinal proteomics experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, and has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a Robust longitudinal Differential Expression (RolDE) approach. The methods are evaluated using over 3000 semi-simulated spike-in proteomics datasets and three large experimental datasets. In the comparisons, RolDE performs overall best; it is most tolerant to missing values, displays good reproducibility and is the top method in ranking the results in a biologically meaningful way. Furthermore, RolDE is suitable for different types of data with typically unknown patterns in longitudinal expression and can be applied by non-experienced users.
A conformation-specific nanobody targeting the nicotinamide mononucleotide-activated state of SARM1
Authors: Hou Yun Nan , Cai Yang , Li Wan Hua , He Wei Ming , Zhao Zhi Ying , Zhu Wen Jie , Wang Qiang , Mai Xinyi , Liu Jun , Lee Hon Cheung , Stjepanovic Goran , Zhang Hongmin , Zhao Yong Juan 
Published: December 2022

AbstractSterile alpha (SAM) and Toll/interleukin-1 receptor (TIR) motif containing 1 (SARM1) is an autoinhibitory NAD-consuming enzyme that is activated by the accumulation of nicotinamide mononucleotide (NMN) during axonal injury. Its activation mechanism is not fully understood. Here, we generate a nanobody, Nb-C6, that specifically recognizes NMN-activated SARM1. Nb-C6 stains only the activated SARM1 in cells stimulated with CZ-48, a permeant mimetic of NMN, and partially activates SARM1 in vitro and in cells. Cryo-EM of NMN/SARM1/Nb-C6 complex shows an octameric structure with ARM domains bending significantly inward and swinging out together with TIR domains. Nb-C6 binds to SAM domain of the activated SARM1 and stabilized its ARM domain. Mass spectrometry analyses indicate that the activated SARM1 in solution is highly dynamic and that the neighboring TIRs form transient dimers via the surface close to one BB loop. We show that Nb-C6 is a valuable tool for studies of SARM1 activation.
Simultaneous capturing phonon and electron dynamics in MXenes
Authors: Zhang Qi , Li Jiebo , Wen Jiao , Li Wei , Chen Xin , Zhang Yifan , Sun Jingyong , Yan Xin , Hu Mingjun , Wu Guorong , Yuan Kaijun , Guo Hongbo , Yang Xueming 
Published: December 2022

AbstractPlasmonic MXenes are of particular interest, because of their unique electron and phonon structures and multiple surface plasmon effects, which are different from traditional plasmonic materials. However, to date, how electronic energy damp to lattice vibrations (phonons) in MXenes has not been unraveled. Here, we employed ultrafast broadband impulsive vibrational spectroscopy to identify the energy damping channels in MXenes (Ti3C2Tx and Mo2CTx). Distinctive from the well-known damping pathways, our results demonstrate a different energy damping channel, in which the Ti3C2Tx plasmonic electron energy transfers to coherent phonons by nonthermal electron mediation after Landau damping, without involving electron-electron scattering. Moreover, electrons are observed to strongly couple with A1g mode (~60 fs, 85–100%) and weakly couple with Eg mode (1–2 ps, 0–15%). Our results provide new insight into the electron-phonon interaction in MXenes, which allows the design of materials enabling efficient manipulation of electron transport and energy conversion.
Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon
Authors: Vaughn Justin N. , Branham Sandra E. , Abernathy Brian , Hulse-Kemp Amanda M. , Rivers Adam R. , Levi Amnon , Wechter William P. 
Published: December 2022

AbstractThe genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. Here, we examine the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon (Cucumis melo). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations.
Genetically engineered mesenchymal stem cells with dopamine synthesis for Parkinson’s disease in animal models
Authors: Li Jun , Li Nan , Wei Jingkuan , Feng Chun , Chen Yanying , Chen Tingwei , Ai Zongyong , Zhu Xiaoqing , Ji Weizhi , Li Tianqing 
Published: December 2022

AbstractAlthough striatal delivery of three critical genes for dopamine synthesis by viruses is a potential clinical approach for treating Parkinson’s disease (PD), the approach makes it difficult to finely control dopamine secretion amounts and brings safety concerns. Here, we generate genetically engineered mesenchymal stem cells encoding three critical genes for dopamine synthesis (DOPA-MSCs). DOPA-MSCs retain their MSC identity and stable ability to secrete dopamine during passaging. Following transplantation, DOPA-MSCs reinstate striatal dopamine levels and correct motor function in PD rats. Importantly, after grafting into the caudate and putamen, DOPA-MSCs provide homotopic reconstruction of midbrain dopamine pathways by restoring striatal dopamine levels, and safely and long-term (up to 51 months) correct motor disorders and nonmotor deficits in acute and chronic PD rhesus monkey models of PD even with advanced PD symptoms. The long-term benefits and safety results support the idea that the development of dopamine-synthesized engineered cell transplantation is an important strategy for treating PD.
Qualitative study of user perspectives and experiences of digital inhaler technology
Authors: Adejumo Ireti , Patel Mitesh , McKeever Tricia M. , Shaw Dominick E. , Bains Manpreet 
Published: December 2022

AbstractElectronic monitoring devices (EMDs) have been trialled in interventions to improve inhaled corticosteroid adherence and clinical outcomes. This study sought to understand the perceptions and experiences of EMD end-users. Participants recruited into a six-month EMD study were invited to a semi-structured interview. Interviews were audio-recorded, transcribed verbatim and analysed using the framework approach. Twenty-eight participants (68% female, median age 47) were interviewed. Individuals described feeling responsible for their asthma control. Recent attacks motivated a desire to maintain control. Study participation led to increased awareness of asthma status and medication use. Several individuals were open to integrating digital monitoring data with other mHealth inputs, perceiving the potential to enhance communication with clinicians and empower self-management. Openness to data sharing was tied to expectations of transparent data use. Data supported integrating beliefs and habit formation to achieve behaviour change. There was a willingness for an integrated, platform-based approach to digital self-management.
Preparation of metrological states in dipolar-interacting spin systems
Authors: Zheng Tian-Xing , Li Anran , Rosen Jude , Zhou Sisi , Koppenhöfer Martin , Ma Ziqi , Chong Frederic T. , Clerk Aashish A. , Jiang Liang , Maurer Peter C. 
Published: December 2022

AbstractSpin systems are an attractive candidate for quantum-enhanced metrology. Here we develop a variational method to generate metrological states in small dipolar-interacting spin ensembles with limited qubit control. For both regular and disordered spatial spin configurations the generated states enable sensing beyond the standard quantum limit (SQL) and, for small spin numbers, approach the Heisenberg limit (HL). Depending on the circuit depth and the level of readout noise, the resulting states resemble Greenberger-Horne-Zeilinger (GHZ) states or Spin Squeezed States (SSS). Sensing beyond the SQL holds in the presence of finite spin polarization and a non-Markovian noise environment. The developed black-box optimization techniques for small spin numbers (N ≤ 10) are directly applicable to diamond-based nanoscale field sensing, where the sensor size limits N and conventional squeezing approaches fail.
Recovery from microplastic-induced marine deoxygenation may take centuries
Authors: Kvale Karin , Oschlies Andreas 
Published: December 2022

AbstractClimate change and plastics pollution are dual threats to marine environments. Here we use biogeochemical and microplastic modelling to show that even if there is complete removal of microplastics and cessation of deposition in the oceans in 2022, regional recovery from microplastic-induced remineralization and water column deoxygenation could take hundreds of years for coastal upwelling zones, the North Pacific and Southern Ocean. Surface stratification and reduced sea ice cover further impede regional recovery, highlighting the importance of aggressive mitigation of plastic pollution.
Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration
Authors: Moiseeva Victoria , Cisneros Andrés , Sica Valentina , Deryagin Oleg , Lai Yiwei , Jung Sascha , Andrés Eva , An Juan , Segalés Jessica , Ortet Laura , Lukesova Vera , Volpe Giacomo , Benguria Alberto , Dopazo Ana , Benitah Salvador Aznar , Urano Yasuteru , del Sol Antonio , Esteban Miguel A. , Ohkawa Yasuyuki , Serrano Antonio L. , Perdiguero Eusebio , Muñoz-Cánoves Pura 
Published: December 2022

AbstractTissue regeneration requires coordination between resident stem cells and local niche cells1,2. Here we identify that senescent cells are integral components of the skeletal muscle regenerative niche that repress regeneration at all stages of life. The technical limitation of senescent-cell scarcity3was overcome by combining single-cell transcriptomics and a senescent-cell enrichment sorting protocol. We identified and isolated different senescent cell types from damaged muscles of young and old mice. Deeper transcriptome, chromatin and pathway analyses revealed conservation of cell identity traits as well as two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time and ageing. Senescent cells create an aged-like inflamed niche that mirrors inflammation associated with ageing (inflammageing4) and arrests stem cell proliferation and regeneration. Reducing the burden of senescent cells, or reducing their inflammatory secretome through CD36 neutralization, accelerates regeneration in young and old mice. By contrast, transplantation of senescent cells delays regeneration. Our results provide a technique for isolating in vivo senescent cells, define a senescence blueprint for muscle, and uncover unproductive functional interactions between senescent cells and stem cells in regenerative niches that can be overcome. As senescent cells also accumulate in human muscles, our findings open potential paths for improving muscle repair throughout life.
Longitudinal data collection to follow social network and language development dynamics at preschool
Authors: Dai Sicheng , Bouchet Hélène , Karsai Márton , Chevrot Jean-Pierre , Fleury Eric , Nardy Aurélie 
Published: December 2022

AbstractDyLNet is a large-scale longitudinal social experiment designed to observe the relations between child socialisation and oral language learning at preschool. During three years, a complete preschool in France was followed to record proximity interactions of about 200 children and adults every 5 seconds using autonomous Radio Frequency Identification Wireless Proximity Sensors. Data was collected monthly with one week-long deployments. In parallel, survey campaigns were carried out to record the socio-demographic and language background of children and their families, and to monitor the linguistic skills of the pupils at regular intervals. From data we inferred real social interactions and distinguished inter- and intra-class interactions in different settings. We share ten weeks of cleaned, pre-processed and reconstructed interaction data recorded over a complete school year, together with two sets of survey data providing details about the pupils’ socio-demographic profile and language development level at the beginning and end of this period. Our dataset may stimulate researchers from several fields to study the simultaneous development of language and social interactions of children.
Depersonalization disorder as a systematic downregulation of interoceptive signals
Authors: Saini Fedal , Ponzo Sonia , Silvestrin Francesco , Fotopoulou Aikaterini , David Anthony S. 
Published: December 2022

AbstractDepersonalisation disorder (DPD) is a psychopathological condition characterised by a feeling of detachment from one's own body and surrounding, and it is understood as emerging from the downregulation of interoceptive afferents. However, the precise mechanisms that drive this ‘interoceptive silencing’ are yet to be clarified. Here we present a computational and neurobiologically plausible model of DPD within the active inference framework. Specifically, we describe DPD as arising from disrupted interoceptive processing at higher levels of the cortical hierarchy where the interoceptive and exteroceptive streams are integrated. We simulated the behaviour of an agent subjected to a situation of high interoceptive activation despite the absence of a perceivable threat in the external environment. The simulation showed how a similar condition, if perceived as inescapable, would result in a downregulation of interoceptive signals, whilst leaving the exteroceptive ones unaffected. Such interoceptive silencing would force the agent to over-rely on exteroceptive information and would ultimately lead to the DPD phenomenology. Finally, our simulation shows that repeated exposure to similar situations over time will lead the agent to increasingly disengage from bodily responses even in the face of a less triggering situation, explaining how a single episode of depersonalization can lead to chronic DPD.
Multi-agent simulation model updating and forecasting for the evaluation of COVID-19 transmission
Authors: Castro Brenno Moura , Reis Marcelo de Miranda , Salles Ronaldo Moreira 
Published: December 2022

AbstractAgent-based models have been an emerging approach in epidemiological modelling, specifically in investigating the COVID-19 virus. However, there are challenges to its validation due to the absence of real data on specific socio-economic and cognitive aspects. Therefore, this work aims to present a strategy for updating, verifying and validating these models based on applying the particle swarm optimization algorithm to better model a real case. For such application, this work also presents a new framework based on multi-agents, whose significant contribution consists of forecasting needed hospital resources, population adaptative immunization and reports concerning demographic density, including physical and socio-economic aspects of a real society in the modelling task. Evaluation metrics such as the data’s Shape Factor (SF), Mean Square Error (RMSE), and statistical and sensitivity analyses of the responses obtained were applied for comparison with the real data. The Brazilian municipality of Passa Vinte, located in the State of Minas Gerais (MG), was used as a case study. The model was updated in cumulative cases until the 365th day of the pandemic. The statistical and sensitivity analysis results showed similar patterns around the actual data up to the 500th day of the pandemic. Their mean values of SF and RMSE were 0.96 and 7.22, respectively, showing good predictability and consistency, serving as an adequate tool for decision-making in health policies.