bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma neurofilament light protein provides evidence of accelerated brain ageing in treatment-resistant schizophrenia
Authors: Wannan Cassandra M. J. , Eratne Dhamidhu , Santillo Alexander F. , Malpas Charles , Cilia Brandon , Dean Olivia M. , Walker Adam , Berk Michael , Bousman Chad , Everall Ian , Velakoulis Dennis , Pantelis Christos ,   The MiND Study Group
Published: November 2023

AbstractBackgroundAccelerated brain aging has been observed across multiple psychiatric disorders. Blood markers of neuronal injury such as Neurofilament Light (NfL) protein may therefore represent biomarkers of accelerated brain aging in these disorders. The current study aimed to examine whether relationships between age and plasma NfL were increased in individuals with primary psychiatric disorders compared to healthy individuals.MethodsPlasma NfL was analysed in major depressive disorder (MDD, n = 42), bipolar affective disorder (BPAD, n = 121), treatment-resistant schizophrenia (TRS, n = 82), a large reference normative healthy control (HC) group (n= 1,926) and a locally-acquired HC sample (n = 59). A general linear model (GLM) was used to examine diagnosis by age interactions on NfL z-scores using the large normative HC sample as a reference group. Significant results were then validated using the locally-acquired HC sample.Resultsa GLM identified a significant age by diagnosis interaction for TRS vs HCs and BPAD vs HCs. Post hoc analyses revealed a positive correlation between NfL levels and age among individuals with TRS, whereas a negative correlation was found among individuals with BPAD. However, only the TRS findings were replicated using the locally-acquired HC sample. Post hoc analyses revealed that individuals with TRS aged <40 had lower NfL levels compared to same-age HCs, whereas individuals with TRS aged >40 had higher NfL levels compared to same-age HCs.ConclusionsThese findings add to the growing literature supporting the notion of accelerated brain ageing in schizophrenia-spectrum disorders.
Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species
Authors: Mazzamurro Fanny , Chirakadavil Jason Baby , Durieux Isabelle , Poiré Ludovic , Plantade Julie , Ginevra Christophe , Jarraud Sophie , Wilharm Gottfried , Charpentier Xavier , Rocha Eduardo P. C. 
Published: November 2023

AbstractNatural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 1282 strains of the human pathogensLegionella pneumophila(Lp) andAcinetobacter baumannii(Ab) and found that transformation rates evolve by large quick changes as a jump process across six orders of magnitude. Close to half of the strains are non-transformable in standard conditions. Transitions to non-transformability were frequent and recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which often accelerates adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs. Defense systems against the latter are associated with lower transformation except the adaptive CRISPR-Cas systems which show the inverse trend. The two species have different lifestyles and gene repertoires, but they exhibit very similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria.
Global analysis of the heparin-enriched plasma proteome captures matrisome-associated proteins in Alzheimer’s disease
Authors: Guo Qi , Ping Lingyan , Dammer Eric B. , Duong Duc M. , Yin Luming , Xu Kaiming , Shantaraman Ananth , Fox Edward J. , Johnson Erik C.B. , Roberts Blaine R. , Lah James J. , Levey Allan I. , Seyfried Nicholas T. 
Published: November 2023

AbstractMatrisome-associated heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology in Alzheimer’s disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry (MS)-based proteomic approaches. Here we utilized heparin affinity chromatography for the capture and enrichment of HBPs in plasma from healthy control and individuals with AD. This method was highly reproducible and effectively enriched well-known HBPs like APOE and thrombin, while also efficiently depleting high-abundance proteins such as albumin. To increase the depth of our analysis of the heparin-enriched plasma proteome and compare differences in disease we applied off-line fractionation and tandem mass tag mass spectrometry (TMT-MS) to compare the proteomic profiles between AD and control individuals across two datasets (n= 121 total samples). This led to the identification of 2865 proteins, spanning 10 orders of magnitude in protein abundance within the plasma. Notably, HBPs were some of the most increased proteins in AD plasma compared to controls. This included members of the matrisome-associated module in brain, SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB and the ɛ4 isoform of APOE. Heparin-enriched plasma proteins also exhibited strong correlations to conventional AD biomarkers including CSF Aβ, total tau (tTau), and phosphorylated tau (pTau) as well as plasma pTau supporting their role as potential surrogate markers of underlying brain pathology. Utilizing a consensus AD brain protein co-expression network, we assessed relationship between the plasma and brain proteomes and observed that specific plasma proteins exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes, further highlighting the complex interplay between the two compartments. In summary, these findings provide support for the integration of a heparin enrichment method with MS-based proteomics for identifying a wide spectrum of plasma biomarkers that mirror pathological changes in the AD brain.
DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+T cells
Authors: Yu Zheng , Sasidharan-Nair Varun , Bonifacius Agnes , Khan Fawad , Buchta Thalea , Beckstette Michael , Niemz Jana , Hilgendorf Philipp , Pietzsch Beate , Mausberg Philip , Keller Andreas , Falk Christine , Busch Dirk , Brinkmann Melanie M. , Schober Kilian , Cicin-Sain Luka , Müller Fabian , Eiz-Vesper Britta , Floess Stefan , Huehn Jochen 
Published: November 2023

ABSTRACTEpigenetic mechanisms stabilize gene expression patterns during CD8+T cell differentiation. However, although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions when compared to bulk memory CD8+T cells. Among them wasTBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+T cells.TBKBP1demethylation in terminal effector CD8+T cells correlated withTBKBP1expression and was stable upon long-termin vitroculture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.
Inference of Locus-Specific Population Mixtures From Linked Genome-Wide Allele Frequencies
Authors: Reyna-Blanco Carlos S. , Caduff Madleina , Galimberti Marco , Leuenberger Christoph , Wegmann Daniel 
Published: November 2023

1AbstractAdmixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rates for the entire genome and do not explicitly account for linkage. Here, we introduceTreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred.TreeSwirlbuilds uponTreeMixthat uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast toTreeMix, our model infers locus-specific mixture proportions employing a Hidden Markov Model that accounts for linkage. Through simulated data, we demonstrate thatTreeSwirlcan accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
PLK4 homodimerization is required for CEP152 centrosome localization and spindle organization
Authors: Kasera Harshita , Singh Priyanka 
Published: November 2023

ABSTRACTPolo-Like Kinase 4 (PLK4) is a unique serine/threonine kinase family member that homodimerizes using its cryptic polo-box (CPB) region. Homodimerization of PLK4 causes transphosphorylation, which activates its ubiquitin-mediated degradation. Interestingly, CPB is also involved in interaction with the upstream centrosome recruiters, CEP152 and CEP192 in human cells. However, the effect of PLK4 homodimerization on the CEP192-CEP152 network remains unexplored. In this work, we identified a frequently occurring cancerous PLK4 variant (E774*), which truncated the protein at the 774 position. The truncated PLK4 is unable to homodimerize and interact with CEP152 and CEP192. During the S-phase progression, we show that CEP152 recruits PLK4 to centrosomes. The homodimerization of PLK4, in turn, is needed for maintaining CEP152 centrosome levels. CEP152 levels correlate to pericentrin at S-phase centrosomes, which generate focused spindles by the M-phase. The homodimerization mutant exhibits reduced levels of CEP152 and pericentrin at S-phase centrosomes, which causes unfocused spindles at the M-phase and reduces cell viability. This work shows the requirement of PLK4 homodimerization for proper centrosome and spindle organization, which is disrupted in cancer.
The Arabidopsis Information Resource in 2024
Authors: Reiser Leonore , Bakker Erica , Subramaniam Sabarinath , Chen Xingguo , Sawant Swapnil , Khosa Kartik , Prithvi Trilok , Berardini Tanya Z. 
Published: November 2023

AbstractSince 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about theArabidopsis thalianagenome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a ‘gold standard’ functional annotation set that reflects the current state of knowledge about the Arabidopsis genome. At the same time, the resource serves as a nexus for community-based collaborations aimed at improving data quality, access and reuse. For the past decade, our work has been made possible by subscriptions from our global user base. This update covers our ongoing biocuration work, some of our modernization efforts that contribute to the first major infrastructure overhaul since 2011, the introduction of JBrowse2, and the resource’s role in community activities such as organizing the structural reannotation of the genome. For gene function assessment, we used Gene Ontology annotations as a metric to evaluate: (1) what is currently known about Arabidopsis gene function, and (2) the set of ‘unknown’ genes. Currently, 74% of the proteome has been annotated to at least one Gene Ontology term. Of those loci, half have experimental support for at least one of the following aspects: molecular function, biological process, or cellular component. Our work sheds light on the genes for which we have not yet identified any published experimental data and have no functional annotation. Drawing attention to these unknown genes highlights knowledge gaps and potential sources of novel discoveries.Article SummaryThe Arabidopsis Information Resource (TAIR,www.arabidopsis.org) is a comprehensive website aboutArabidopsis thaliana, a small plant that’s very easy to grow and analyze in the laboratory and is used to understand how many other plants function. We share our progress in data collection and organization, website and tool improvement, and our involvement in community projects.
Tissue-resident alveolar macrophages reduce O3-induced inflammation via MerTK mediated efferocytosis
Authors: Guttenberg M.A. , Vose A.T. , Birukova A. , Lewars K. , Cumming R.I. , Albright M.C. , Mark J.I. , Salazar C.J. , Swaminathan S. , Yu Z. , Sokolenko Yu. V. , Bunyan E. , Yaeger M.J. , Fessler M.B. , Que L.G. , Gowdy K.M. , Misharin A.V. , Tighe R.M. 
Published: November 2023

AbstractLung inflammation, caused by acute exposure to ozone (O3) – one of the six criteria air pollutants – is a significant source of morbidity in susceptible individuals. Alveolar macrophages (AMØs) are the most abundant immune cells in the normal lung and their number increases following O3exposure. However, the role of AMØs in promoting or limiting O3-induced lung inflammation has not been clearly defined. Here, we used a mouse model of acute O3exposure, lineage tracing, genetic knockouts, and data from O3-exposed human volunteers to define the role and ontogeny of AMØs during acute O3exposure. Lineage tracing experiments showed that 12, 24, and 72 h after exposure to O3(2 ppm) for 3h all AMØs were tissue-resident origin. Similarly, in humans exposed to FA and O3(200 ppb) for 135 minutes, we did not observe ∼21h post-exposure an increase in monocyte-derived AMØs by flow cytometry. Highlighting a role for tissue-resident AMØs, we demonstrate that depletion of tissue-resident AMØs with clodronate-loaded liposomes led to persistence of neutrophils in the alveolar space after O3exposure, suggesting that impaired neutrophil clearance (i.e., efferocytosis) leads to prolonged lung inflammation. Moreover, depletion of tissue-resident AMØ demonstrated reduced clearance of intratracheally instilled apoptotic Jurkat cells, consistent with reduced efferocytosis. Genetic ablation of MerTK – a key receptor involved in efferocytosis – also resulted in impaired clearance of apoptotic neutrophils followed O3exposure. Overall, these findings underscore the pivotal role of tissue-resident AMØs in resolving O3-induced inflammation via MerTK-mediated efferocytosis.
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
Authors: Mandlbauer Ariane , Sun Qiong , Popitsch Niko , Schwickert Tanja , Spanova Miroslava , Wang Jingkui , Ameres Stefan , Busslinger Meinrad , Cochella Luisa 
Published: November 2023

AbstractMany microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet most miRNA profiling efforts remain at the tissue and organ levels. To overcome challenges in accessing the microRNomes from tissue-embedded cells, we had previously developed mime-seq (miRNome bymethylation dependent sequencing), a technique in which cell-specific miRNA methylation inC. elegansandDrosophilaenabled chemo-selective sequencing without the need for cell sorting or biochemical purification. Here, we present mime-seq 2.0 for profiling miRNAs from specific mouse cell types. We engineered a chimeric RNA methyltransferase that is tethered to Argonaute and efficiently methylates miRNAs at their 3’-terminal 2’OH in mouse and human cell lines. We also generated a transgenic mouse for conditional expression of this methyltransferase, which can be used to direct methylation of miRNAs in a cell-type of choice. We validated the use of this mouse by profiling miRNAs from B cells and bone marrow plasma cells.
Reputational self-awareness: an innovative career development tool
Authors: Foster Jeff , Stone Thomas , Jawahar I.M. , Steinheider Brigitte , Gray Truit W. 
Published: November 2023

PurposeThe authors introduce a new construct, reputational self-awareness (RSA). RSA represents the congruence between how individuals think they are viewed by others (i.e. metaperceptions) versus how they are actually viewed (i.e. other ratings). The authors sought to demonstrate that RSA is a superior predictor of performance indices.Design/methodology/approachPersonality self-ratings from 381 business students and their ratings by 966 others were collected via online surveys. Other raters rated self-raters' personalities as well as their task performance, organizational citizenship behaviors (OCBs) and counterproductive work behaviors (CWBs).FindingsResults indicate that RSA predicts variance in performance above and beyond self-report ratings, and performance is highest when metaperceptions and other ratings of performance are aligned. These results support the use of a multi-perspective approach to personality assessment as a useful tool for coaching and career development.Research limitations/implicationsThe authors' results support the use of a multi-perspective approach to personality assessment as a useful tool for coaching and career development. A cross-sectional design was used in which personality and performance data were gathered from respondents, and the P 720 is a relatively new personality instrument.Practical implicationsRSA is a valuable tool for employee development, coaching and counseling because, as extant research and the authors' findings demonstrate, awareness of how others view and judge one, one's reputation is essential information to guide work behaviors and career success. Therefore, a key career-development goal for trainers and counselors should be to use a multi-perspective approach to maximize clients' RSA.Social implicationsUse of other ratings as opposed to traditional self-rating of personality provides superior prediction of behavior and is more useful for career development.Originality/valueThis is the first study to demonstrate utility of RSA, i.e. that individuals who more accurately assess their personality are rated as performing better by others. The authors' results offer new insights for personality research and career development and support the use of personality assessment from multiple perspectives, thus enabling the exploration of potentially insightful research questions that cannot be examined by assessing personality from a single perspective.
Who is successful in career development? A person-centered approach to the study of career orientation profiles
Authors: Bazine Nicolas , Chénard-Poirier Léandre Alexis , Battistelli Adalgisa , Lagabrielle Marie-Christine 
Published: November 2023

PurposeThis research examined the presence of career orientation profiles by investigating how young workers combined protean career orientation attitudes, motivation to learn to develop one's career and an optimistic future perspective on their career. It explored how a differentiated endorsement of these attitudes and motivation (i.e. career orientation profiles) were associated with the adoption of multiple career-enhancing behaviors, namely proactive career behaviors (i.e. career planning, networking and skill development) and learning behaviors with technologies.Design/methodology/approachLatent profile analysis was conducted among young individuals starting their career (N = 767) and found four distinct profiles.FindingsThe first profile revealed that 17.2% of workers in this sample were displaying low levels in protean career orientation, motivation to learn and optimistic future time perspective (profile 1). Two differentiated profiles showed either low levels of protean career orientation and high levels of motivation to learn (profile 2) or high levels of protean career attitudes and low levels of motivation to learn (profile 3). These profiles presented an average level of future time perspective and represented 13.8 and 40.6% of the sample. Finally, 28.4% of the sample showed high levels on all these variables (profile 4).Originality/valueOnly young workers who showed high levels on all these indicators also presented high levels of proactive behaviors and learning with technologies. The other three profiles were associated with suboptimal levels on these outcomes. Taken together, these results offer new insights into the psychological state of mind of workers most adapted to succeed in a modern career.
Understanding the key risks in circular construction projects: from systematic review to conceptual framework
Authors: Wuni Ibrahim Yahaya , Abankwa Derek Asante 
Published: November 2023

Purpose
Circular construction offers sustainable solutions and opportunities to disentangle a project’s life cycle, including demolition, deconstruction and repurposing of architectural, civil engineering and infrastructure projects from the extraction of natural resources and their wasteful usage. However, it introduces additional layers of novel risks and uncertainties in the delivery of projects. The purpose of this study is to review the relevant literature to discover, classify and theorize the critical risk factors for circular construction projects.

Design/methodology/approach
The paper conducted a systematic literature review to investigate the risks of circular construction projects. It deployed a multistage approach, including literature search and assessment, metadata extraction, citation frequency analysis, Pareto analysis and total interpretive structural modeling.

Findings
Sixty-eight critical risk factors were identified and categorized into nine broad taxonomies: material risks, organizational risks, supply chain risks, technological risks, financial risks, design risks, health and safety risks, regulatory risks and stakeholder risks. Using the Pareto analysis, a conceptual map of 47 key critical risk factors was generated for circular construction projects. A hierarchical model was further developed to hypothesize the multiple possible connections and interdependencies of the taxonomies, leading to chain reactions and push effects of the key risks impacting circular construction projects.

Originality/value
This study constitutes the first systematic review of the literature, consolidating and theorizing the chain reactions of the critical risk factors for circular construction projects. Thus, it provides a better understanding of risks in circular construction projects.