bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic alterations drive inflammatory phenotypes in CHIP-associated heart failure
Authors: Mansouri Siavash , Hemmerling Inga , Hesami Golnaz , Cremer Sebastian , Kirschbaum Klara , Klatt Stephan , Behjati Fatemeh , Schulz Marcel H. , Li Xue , Scheller Marina , Müller-Tidow Carsten , Arndt Philipp Friedrich , Günther Stefan , Padmasekar Manju , Looso Mario , Rieger Michael A. , Kuhnert Stefan , Vogelmeier Claus F. , Bals Robert , Fleming Ingrid , Zeiher Andreas , Seeger Werner , Leuschner Florian , Savai Rajkumar , Dimmeler Stefanie , Pullamsetti Soni S 
Published: July 2024

SummaryMutations in DNA methyltransferase 3 alpha(DNMT3A)are the most frequent driver of clonal hematopoiesis of indeterminate potential (CHIP), and associated with higher risk of cardiovascular disease and pro-inflammatory activation of immune cells. Here, we investigated the mechanisms underlying DNMT3A CHIP-associated inflammatory phenotypes in macrophages. We show that monocytes ofDNMT3ACHIP-driver mutation carriers are associated with DNA hypomethylation of succinate dehydrogenase A (SDHA) and an altered tricarboxylic acid cycle metabolite profile. Silencing of DNMT3A in monocytes increased SDHA and elevated mitochondria complex II activity. The secreted complex II product, malate, further increased inflammatory activation in wild type monocytes to further augment inflammation in a paracrine manner. Pharmacological inhibition of SDHA (using dimethyl malonate) in mice harboringDNMT3Amutations in hematopoietic stem cells ameliorated the inflammatory response and improved cardiac function after myocardial infarction. Thus, interfering with the altered metabolic state may provide a new therapeutic option to dampen inflammatory activation in DNMT3A CHIP carrying patients.
Harnessing Community Science and Open Research-based Data to Track Distributions of Invasive Species in Japan
Authors: Sakai Shoko , Atsumi Keisuke , Genroku Takanori , Goka Koichi , Fujiki Shogoro 
Published: July 2024

AbstractAt the forefront of invasive alien species (IAS) control, information gaps about the latest IAS distribution can hinder the required actions of local governments. In Japan, many prefectural governments still lack a list of invasive species despite the request stipulated in the Invasive Alien Species Management Action Plan enacted in 2015. Here, we examined to what extent open research-based data deposited by museums and herbaria (ORD) and community science data deposited by volunteers (CSD) can fill the gaps. We focused on 145 plant and 38 insect invasive species, and updated their distribution maps using ORD and CSD. We found complementarity as well as common limitations between ORD and CSD. While taxonomic biases were weaker in ORD, CSD had better prefectural coverage. In addition, some important taxa have rarely been captured by CSD or ORD. Mixed strategies of facilitating community science, supporting local museums, and taxon-specific monitoring by experts are necessary.
Effects of selection for early dispersal on the ambrosia beetleXyleborinus saxeseniiand its fungal symbionts
Authors: Melet Antoine , Biedermann Peter 
Published: July 2024

AbstractOverlapping generations is a defining characteristic of advanced social life. In cooperative breeding societies, for example, temporary groups of mature offspring are formed that assist in the rearing of additional brood before the offspring disperse and reproduce independently. It is hypothesized that the number of helpers and their delayed dispersal period will determine the number of siblings that can be reared, thus resulting in an indirect fitness gain. The objective of this study, was to investigate the effect of artificial selection for early dispersal of mature offspring on the life history, behaviour and fungal symbionts in the cooperatively breeding ambrosia beetleXyleborinus saxesenii. Two lineages of beetles were bred in the laboratory for five successive generations. In one group, dispersing females were selected at random to initiate the next generation, while in the other group, only early dispersers were selected. A number of life-history traits exhibited a pronounced response in the initial generation, subsequently recuperating to levels approximating those observed at the outset of the experiment. The laboratory rearing resulted in an increasing proportion of successful nests in both lineages. Additionally, the control lineage exhibited a reduction in lifespan and in productivity. Furthermore, significant differences were observed in the fungal communities from the third generation onwards. The results suggest thatX. saxeseniihas limited potential to respond to this selection pressure, potentially due to sibmating and resulting low genetic variability. Furthermore, the correlation between nest lifespan and productivity is a crucial factor in explaining philopatry and altruism in this species.
Creation of a novel zebrafish model with low DHA status to study the role of maternal nutrition during neurodevelopment
Authors: Ranard Katherine M. , Appel Bruce 
Published: July 2024

AbstractDocosahexaenoic acid (DHA), a dietary omega-3 fatty acid, is a major building block of brain cell membranes. Offspring rely on maternal DHA transfer to meet their neurodevelopmental needs, but DHA sources are lacking in the American diet. Low DHA status is linked to altered immune responses, white matter defects, impaired vision, and an increased risk of psychiatric disorders during development. However, the underlying cellular mechanisms involved are largely unknown, and advancements in the field have been limited by the existing tools and animal models. Zebrafish are an excellent model for studying neurodevelopmental mechanisms. Embryos undergo rapid external development and are optically transparent, enabling direct observation of individual cells and dynamic cell-cell interactions in a way that is not possible in rodents. Here, we create a novel DHA-deficient zebrafish model by 1) disruptingelovl2,a key gene in the DHA biosynthesis pathway, via CRISPR-Cas9 genome editing, and 2) feeding mothers a DHA-deficient diet. We show that low DHA status during development is associated with a small eye morphological phenotype and demonstrate that even the morphologically normal siblings exhibit dysregulated gene pathways related to vision and stress response. Future work using our zebrafish model could reveal the cellular and molecular mechanisms by which low DHA status leads to neurodevelopmental abnormalities and provide insight into maternal nutritional strategies that optimize infant brain health.
A laboratory method for simulating the effects of subsequent fires on pyrogenic organic matter at different exposure depths in a sand matrix
Authors: Luo Mengmeng , Yedinak Kara , Bourne Keith , Whitman Thea 
Published: July 2024

AbstractBackgroundAcross a variety of anthropogenic and natural contexts, fire can reoccur in a previously burned location. However, effects of subsequent fire on preexisting pyrogenic organic matter (PyOM) stocks are difficult to discern. Laboratory experiments offer a powerful approach to investigating how subsequent fire impacts the preexisting PyOM.AimsWe aimed to design a highly repeatable laboratory method to effectively measure the impacts of subsequent fires on PyOM at different soil depths while addressing key limitations of previous methods.MethodsJack pine (Pinus banksianaLamb.) log burns were used to parameterize realistic heat flux profiles. Using a cone calorimeter, these profiles were applied to buried jack pine PyOM to simulate variable reburn fire intensities.Key resultsIn general, higher heat flux and shallower depths led to more mass loss of PyOM from combustion and more heat exposure.ConclusionsOur reburn method offers a highly replicable way to simulate specific fire scenarios. Conditions that result in more heat exposure (higher heat fluxes, shallower depths) are likely to lead to more loss of PyOM in subsequent fires.ImplicationsThe customizable method could simulate different fire scenarios to investigate spatial variability within a given fire event, or to study the effects of fire on different types of biomass or organisms, such as microbes.Summary textOur paper illustrates a laboratory method to better quantify loss of preexisting PyOM in soil after a fire.
An effective model for community-based conservation around authorized fishing settlements inside a devolved Wildlife Management Area in southern Tanzania
Authors: Duggan Lily M , Tarimo Lucia J , Walsh Katrina A , Kavishe Deogratius Roman , Crego Ramiro D , Elisa Manase , Mombo Felister , Butler Fidelma , Killeen Gerry 
Published: July 2024

AbstractWildlife Management Areas (WMAs) represent a relatively new institutional model for devolved, locally-led conservation in Tanzania, in which local villages set aside part of their land for wildlife conservation and manage that resource collectively, so that their stakeholder communities can collectively leverage economic and social benefits from income-generating activities like tourism. This study examines the relationship between community-defined land use plans andde factoland use practices, and the influence of the latter on the relative abundance and distribution of large wild mammals in a across the Ifakara-Lupiro-Mangula (ILUMA) WMA, which acts as a key buffer zone between Nyerere National Park (NNP) to the east and adjacent stakeholder villages to the north and west. All observed signs of wildlife and human activity were recorded across 32 locations inside ILUMA and in the permanent settlements and national park that respectively border it to the west and east. Across much of ILUMA WMA, in areas where agreed land use plans were not adhered to, rampant cattle herding and land clearing for agriculture were associated with reductions in wildlife richness and biodiversity, as well as overall ecosystem integrity. Although human settlement was also generally associated with reduced natural ecosystem integrity, some important exceptions to this rule illustrate how sustainable livelihoods for local people that are based on well-managed natural resource harvesting practices may actually enhance conservation effectiveness: Three authorised human settlements within the WMA, where fishing was the primary permitted livelihood and local communities collaborated with the WMA management, were surrounded by pristine land cover with thriving terrestrial wildlife populations. Correspondingly, the best conserved parts of the WMA not only included those closest to the boundary with the national park to the east, but also these fishing villages along the riverbank to the north, where compliance with agreed land use plans was most rigorous. Overall, this study documents a useful example of how a devolved conservation area may conditionally host resident local communities undertaking selective natural resource extraction activities and collaborate with them to achieve effectivede factoconservation practices.
CRISPR-mediated chromosome deletion facilitates genetic mapping of Vip3Aa resistance gene within complex genomic region in an invasive global pest
Authors: Jin Minghui , Shan Yinxue , Peng Yan , Chen Senlin , Zhou Xuanhe , Liu Kaiyu , Xiao Yutao 
Published: July 2024

AbstractConnecting genetic variation to phenotypes and understanding the underlying biological mechanisms has been a fundamental goal of biological genetics. Here, we used the association analysis to identify a Vip3Aa resistance-associated genomic region in a strain of fall armyworm, JC-R, which exhibits >5000-fold resistance to the Bt toxin Vip3Aa. However, through various analytical approaches and fine-scale mapping across different populations, we demonstrated that this genomic region exhibits strong genetic linkage. The chromosome-level genome of JC-R and its parent strain JC-S were assembled, and extensive structural variations in the linkage regions were identified, which could be responsible for maintaining the linkage. To identify the causal variation within this linked region, a chromosome fragment stepwise knockout strategy based on CRISPR/Cas9 was developed. By crossing with the resistant strain and phenotyping segregating offspring on Vip3Aa-containing diet, we identified a chromosomal segment, KO8, containing the resistant gene. Subsequently, we conducted a comprehensive analysis of the variations in the KO8 region using multi-omics approaches, including genomic data, RNA-seq, proteomic, PacBio long read Iso-seq, and phosphoproteomic data. This analysis identified multiple variations in the chitin synthase geneCHS2, including amino acid substitution, alternative splicing, and changes in phosphorylation sites. After knocking out theCHS2, larvae exhibited over 6777-fold resistance to Vip3Aa. These results demonstrate that the chromosome fragment stepwise knockout strategy is a viable approach for studying complex genomic regions, and highlight the value of comprehensive analysis of genetic variations using multi-omics data. The identified candidate gene could potentially advance monitoring and management of pest resistance to Vip3Aa.
A Bayesian Hierarchical Model of Trial-To-Trial Fluctuations in Decision Criterion
Authors: Vloeberghs Robin , Urai Anne E. , Desender Kobe , Linderman Scott W. 
Published: July 2024

AbstractClassical decision models assume that the parameters giving rise to choice behavior are stable, yet emerging research suggests these parameters may fluctuate over time. Such fluctuations, observed in neural activity and behavioral strategies, have significant implications for understanding decision-making processes. However, empirical studies on fluctuating human decision-making strategies have been limited due to the extensive data requirements for estimating these fluctuations. Here, we introduce hMFC (Hierarchical Model for Fluctuations in Criterion), a Bayesian framework designed to estimate slow fluctuations in the decision criterion from limited data. We first showcase the importance of considering fluctuations in decision criterion: incorrectly assuming a stable criterion gives rise to apparent history effects and underestimates perceptual sensitivity. We then present a hierarchical estimation procedure capable of reliably recovering the underlying state of the fluctuating decision criterion with as few as 500 trials per participant, offering a robust tool for researchers with typical human datasets. Critically, hMFC does not only accurately recover the state of the underlying decision criterion, it also effectively deals with the confounds caused by criterion fluctuations. Lastly, we provide code and a comprehensive demo atwww.github.com/robinvloeberghs/hMFCto enable widespread application of hMFC in decision-making research.
A novel and potent MICA/B antibody is therapeutically effective inKRAS LKB1mutant lung cancer models
Authors: Kowash Ryan R , Sabnani Manoj , Gray Laura T , Deng Qing , Girard Luc , Naito Yujiro , Masuhiro Kentaro , Minna John D , Gerber David E , Koyama Shohei , Liu Zhiqian Lucy , Baruah Hemanta , Akbay Esra A 
Published: July 2024

AbstractConcurrentKRAS LKB1(STK11, KL) mutant Non-Small Cell Lung Cancers (NSCLC) is particularly difficult to treat and does not respond well to current immune checkpoint blockade (ICB) therapies. This is due to numerous mechanisms including low antigen presentation limiting T cell mediated killing. To activate anti-tumor immunity, we targeted tumor cell – natural killer (NK) cell interactions. We tested whether a novel antibody based therapeutic strategy that predominantly activates natural killer (NK) cells demonstrates efficacy in pre-clinical mouse models of KL NSCLC. NK cells rely on binding of ligands, such as Major Histocompatibility Complex (MHC) class I-related chain A or B (MICA/B), to the activating receptor NKG2D. Importantly MICA and MICB are widely expressed in elevated levels across NSCLC subtypes including KL lung cancers. Proteases with the tumor microenvironment (TME) can cleave these proteins rendering tumor cells less visible to NK cells. We therefore developed a MICA monoclonal antibody, AHA-1031, which utilizes two NK cell activating receptors. AHA1031 prevents ligand shedding without interfering with binding to NKG2D while targeting cancer cells to antibody mediated cell dependent cytotoxicity (ADCC). Our therapeutic novel antibody has significant monotherapy activity in KL cancer models including xenografts of human cell lines and patient derived xenografts. Activating NK cells through MICA/B stabilization and inducing ADCC offers an alternative and potent therapy option in KL tumors. MICA/B are shed across different tumors making this therapeutic strategy universally applicable.
Origin and development of uniparental and polyploid blastomeres
Authors: Zhao Yan , Fernández-Montoro Andrea , Peeters Greet , Jatsenko Tatjana , De Coster Tine , Angel-Velez Daniel , Lefevre Thomas , Voet Thierry , Tšuiko Olga , Kurg Ants , Smits Katrien , Van Soom Ann , Vermeesch Joris Robert 
Published: July 2024

AbstractWhole-genome (WG) abnormalities, such as uniparental diploidy and triploidy, cause fetal death. Occasionally, they coexist with biparental diploid cells in live births. Understanding the origin and early development of WG abnormal blastomeres is crucial for explaining the formation of androgenotes, gynogenotes, triploidy, chimerism, and mixoploidy. By haplotyping 118 blastomeres from first cleavages, we identified various mechanisms of heterogoneic divisions that lead to WG abnormal blastomeres or their coexistence with normal blastomeres in both multipolar and bipolar cleaving zygotes. After culturing the totipotent blastomeres to three preimplantation stages and performing transcriptome profiling on over 600 cells, we discovered that stress responses contribute to developmental impairment in WG abnormal cells, resulting in either cell arrest or blastocyst formation. Some first-cleavage-derived WG abnormal blastomeres can survive early development and progress to blastocysts. Their potential dominance in preimplantation embryos represents an overlooked cause of abnormal development. Haplotype based screening could further increase pregnancy rates.
The integrated stress response regulates 18S nonfunctional rRNA decay in mammals
Authors: Coria Aaztli R. , Shah Akruti , Shafieinouri Mohammad , Taylor Sarah J. , Guiblet Wilfried , Miller Jennifer T. , Mani Sharma Indra , Wu Colin Chih-Chien 
Published: July 2024

ABSTRACT18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive. NRD was originally identified and has exclusively been studied inSaccharomyces cerevisiae.Here, we show that 18S NRD is conserved in mammals. Using genome-wide CRISPR genetic interaction screens, we find that mammalian NRD acts through the integrated stress response (ISR) via GCN2 and ribosomal protein ubiquitination by RNF10. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translational arrest at start sites. Indeed, biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Overall, the ISR promotes nonfunctional 18S rRNA and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10 axis surveils ribosome functionality at translation initiation.
Loss ofRREB1reduces adipogenesis and improves insulin sensitivity in mouse and human adipocytes
Authors: Yu Grace Z. , Krentz Nicole A. J. , Bentley Liz , Zhao Meng , Paphiti Keanu , Sun Han , Honecker Julius , Nygård Marcus , Dashti Hesam , Bai Ying , Reid Madeleine , Thaman Swaraj , Wabitsch Martin , Rajesh Varsha , Yang Jing , Mattis Katia K , Abaitua Fernando , Casero Ramon , Hauner Hans , Knowles Joshua W , Wu Joy Y , Mandrup Susanne , Claussnitzer Melina , Svensson Katrin J , Cox Roger D. , Gloyn Anna L. 
Published: July 2024

AbstractThere are multiple independent genetic signals at theRas-responsive element binding protein 1(RREB1) locus associated with type 2 diabetes risk, fasting glucose, ectopic fat, height, and bone mineral density. We have previously shown that loss ofRREB1in pancreatic beta cells reduces insulin content and impairs islet cell development and function. However, RREB1 is a widely expressed transcription factor and the metabolic impact of RREB1 lossin vivoremains unknown. Here, we show that male and female global heterozygous knockout (Rreb1+/-) mice have reduced body length, weight, and fat mass on high-fat diet.Rreb1+/-mice have sex- and diet-specific decreases in adipose tissue and adipocyte size; male mice on high-fat diet had larger gonadal adipocytes, while males on standard chow and females on high-fat diet had smaller, more insulin sensitive subcutaneous adipocytes. Mouse and human precursor cells lacking RREB1 have decreased adipogenic gene expression and activated transcription of genes associated with osteoblast differentiation, which was associated withRreb1+/-mice having increased bone mineral densityin vivo. Finally, human carriers ofRREB1T2D protective alleles have smaller adipocytes, consistent with RREB1 loss-of-function reducing diabetes risk.
ERGA-BGE genome ofValencia hispanica(Valenciennes, 1826): a critically endangered Iberian toothcarp
Authors: Ventura Marc , Franch Nati , Fernández Rosa , Palma-Guerrero Javier , Böhne Astrid , Monteiro Rita , Aguilera Laura , Gut Marta , Alioto Tyler S. , Câmara Ferreira Francisco , Cruz Fernando , Gómez-Garrido Jèssica , Haggerty Leanne , Martin Fergal , Brown Thomas 
Published: July 2024

AbstractThe reference genome ofValencia hispanica, a critically endangered actinopterygian species endemic to the Iberian Peninsula, is key to unravelling its genetic architecture and adaptation to freshwater ecosystems. This genomic resource will enable targeted conservation efforts and shed light on the species’ essential role in ecological dynamics, including its contributions to algal biomass regulation and role in the aquatic food web while also highlighting the challenges it faces from habitat degradation and invasive species. Furthermore, it offers opportunities to gain valuable insights into the evolutionary paths within the Valenciidae family, significantly advancing our comprehension of genetic diversity and adaptability in aquatic ecosystems. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.29Gb, composed of 99 contigs and 28 scaffolds, with contig and scaffold N50 values of 38.3Mb and 56.9Mb, respectively.
Fixed-time fault-tolerant attitude tracking control for UAV based on fixed-time extended state observer
Authors: Wu Qilong , Zhu Qidan 
Published: July 2024

Purpose
To improve the robustness of carrier-based unmanned aerial vehicle (UAV) with actuator faults attitude tracking control system, this paper aims to propose a fixed-time backstepping (FXTBSC) fault-tolerant control based on a fixed-time extended state observer.

Design/methodology/approach
A fixed-time extended state observer (FXTESO) is designed to estimate the total disturbance including nonlinear, coupling, actuator faults and external disturbances. The integration of backstepping control and fixed-time technology ensures fixed-time convergence.

Findings
The simulation results of tracking the desired attitude angle show that the anti-interference, fault tolerance and tracking accuracy of FXTBSC-FXTESO are better than the BSC-ESO control method.

Originality/value
Different from the traditional BSC-ESO, the convergence speed and convergence accuracy of FXTBSC-FXTESO proposed in this paper are better than conventional extended state observer. And the fixed time controller has the advantages of high tracking accuracy, fault tolerance and anti-interference ability.