bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo whole-genome assembly and annotation of a high-quality coffee variety from the primary origin of coffee,Coffea arabicavar. Geisha
Authors: Medrano Juan F. , Cantu Dario , Minio Andrea , Dreischer Christian , Gibbons Theodore , Chin Jason , Chen Shiyu , Van Deynze Allen , Hulse-Kemp Amanda M 
Published: June 2024

AbstractGeisha coffee is recognized for its unique aromas and flavors and accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly ofCoffea arabicavar. Geisha, considered an Ethiopian landrace thatrepresents germplasm from the Ethiopian center of origin of coffee. We used a hybridde novoassembly approach combining two long-reads single molecule sequencing technologies, Oxford Nanopore and Pacific Biosciences, together with scaffolding with Hi-C libraries. The final assembly is 1.03GB in size with BUSCO assessment of the assembly completeness of 97.7% of single-copy orthologs clusters. RNAseq and IsoSeq data were used as transcriptional experimental evidence for annotation and gene prediction revealing the presence of 47,062 gene loci encompassing 53,273 protein-coding transcripts. Comparison of the assembly to the progenitor subgenomes, separated the set of chromosome sequences inherited fromC. canephorafrom those ofC. eugenioides., Corresponding orthologs between Geisha and Red Bourbon had a 99.67% median identity, higher than what we observe with the progenitor assemblies (median 97.28%). Both, Geisha and Red Bourbon contain an inversion on Chromosome 10 relative to the pseudomolecules of the genetic material inherited from the two progenitors that must have happened before the separation in the geographical migration of the two varieties. Lending support of a single allopolyploidization event that gave origin toC. arabicaafter the hybridization event with the two progenitor lines. Broadening the availability of high-quality genome assemblies ofCoffea arabicavarieties, paves the way for understanding the evolution and domestication of coffee, as well as the genetic basis and environmental interactions of why a variety like Geisha is capable of producing beans with such exceptional and unique high-quality.
Forelimb motor recovery by modulating extrinsic and intrinsic signaling as well as neuronal activity after the cervical spinal cord injury
Authors: Takatani Hirohide , Fujita Naoki , Imai Fumiyasu , Yoshida Yutaka 
Published: June 2024

SUMMARYSingular strategies for promoting axon regeneration and motor recovery after spinal cord injury (SCI) have been attempted with limited success. Here, we propose the combinatorial approach of deleting extrinsic and intrinsic factors paired with neural stimulation, will enhance adaptive axonal growth and motor recovery after SCI. We previously showed the deletion ofRhoAandPtenin corticospinal neurons inhibits axon dieback and promotes axon sprouting after lumbar SCI. Here, we examined the effects ofRhoA;Ptendeletion coupled with neural stimulation after cervical SCI. This combinatorial approach promoted more boutons on injured corticospinal neurons in the spinal cord compared to soleRhoA;Ptendeletion. AlthoughRhoA;Ptendeletion does not promote motor recovery in the forelimb after SCI, stimulating corticospinal neurons in those mice results in partial motor recovery. These results demonstrate that a combinatorial approach that pairs genetic modifications with neuronal stimulation can promote axon sprouting and motor recovery following SCI.
The importance of mistakes: Variation in spores reveals trade-offs for range expansion in the xeric-adapted Australasian speciesCheilanthes distans(Pteridaceae)
Authors: Sosa Karla 
Published: June 2024

AbstractBiological trade-offs present a central issue for evolutionary biology: it has been a fundamental understanding within the field that limits exist on the phenotypic traits a species is able to exhibit in part due to trade-offs. Reproduction—with its myriad forms—has been studied extensively in the context of these dynamics. And while considerable literature has explored trade-offs between seed size and number and their associated environmental conditions, none has looked at spore size trade-offs in ferns. We can hypothesise potential trade-offs in spore size: smaller spores should be able to disperse farther, but may not have sufficient provisions to survive in environments that require them to remain at the gametophyte stage for longer periods if their germination cues are mismatched. Reproductive mode (sexual vs. asexual) and ploidy may also be playing a role. In order to study trade-offs related to spore size, I focus on the Australasian fern speciesCheilanthes distans(Pteridaceae), which is most often found in xeric environments, growing in crevices or on top of rocks which are haphazardly scattered across their range. Apomictic diplospores in this species are formed through first division restitution, a meiotic pathway particularly prone to mistakes in chromosome pairing and cell division (as compared to premeiotic endomitosis). Rather than being problematic, these mistakes ultimately lead to considerable additional variation in spore size, spore products (through a range of aneuploid spores), and spore ploidy. In this study, I explore trade-offs between spore size, dispersal, and germination, taking into account effects from reproductive mode and ploidy. I carried out an extensive survey ofC. distansspecimens to establish the prevalence of sexual vs. apomictic (asexual) specimens, and to describe in greater depth the variation in ploidy across the species. I also collected data on spore size and sporogenesis forms. With these data I then asked: is spore size correlated with range area or with germination? And does spore form correlate with either spore size or germination? Ultimately, I find that variations in sporogenesis may be leading to large variation in spore sizes—especially since spores traditionally considered abortive are in fact viable—and that this variation may provide abundant fodder for evolution to act through trade-offs between dispersal into large ranges and germination leading to establishment. Especially in light of the fact that many spores that were historically considered abortive are fully viable and likely shaping evolution in important ways, it is worth remarking on what these results illustrate more broadly: the way in which we have constructed ‘disability’ ultimately affects how we perceive so-called ‘genetic errors’—both in humans and in other species—and thus limits what we allow ourselves to imagine ‘disabled’ beings are capable of.
Short steps can take you far: Phylogenetic analysis of AustralasianCheilanthes distansreveals frequent shorter-range dispersal
Authors: Sosa Karla 
Published: June 2024

AbstractBiologists have long pondered species’ geographical distributions and sought to understand what factors drive dispersal and determine species ranges. In considering plant species with large ranges, a question that has remained underexplored is whether large ranges are attained primarily through many instances of short scale dispersal or whether instead widespread ranges are attained by propagules with increased dispersal distances. Ferns provide an ideal system to explore this question as their propagules are very small spores, which have been theorised can be carried by wind to essentially anywhere on the planet. Unfortunately, population-level genetic data in ferns is relatively uncommon, limiting our ability to answer this and related questions. For this work, I focus onCheilanthes distans(Pteridaceae) as a study system, a widespread fern with extensive spore variation that occurs over Australia and into New Zealand/Aotearoa, New Caledonia, and other Pacific islands. I sampled widely across the species’ range, in addition to across AustralasianCheilanthes(as a robust tree for the genus does not exist), ultimately building a phylogeny based on the GoFlag 451 bait set. With these data, we can investigate additional questions, including whether reproductive mode, polyploidy, or lineage influence dispersal, as well as whether movement is occurring randomly or is instead asymmetrical. I explored the relationships between sexual and apomictic specimens to understand whether the former are the parental lineages to apomictic plants and whether we find evidence for apomictic plants dispersing out of a small parental range. I investigated how many times polyploid lineages have arisen inC. distansand whether they are each limited geographically, perhaps forming isolated ranges that collectively result inC. distans’larger range. Additionally, I generated estimates for ancestral ranges and dispersal between populations to understand whether certain lineages are limited to particular geographic regions, to explore the directionality of dispersal, and to assess whether most movement is happening over short or long distances. Particularly interestingly, I find that most dispersal in this species appears to occur over smaller steps rather than longer jumps, underscoring how short movement can nevertheless allow for establishment of large ranges; this dispersal is not limited phylogenetically and seems to occur equally for all lineages. What is more, I find evidence for asymmetrical dispersal directionality, apparently most frequently tracking trade winds. These findings demonstrate the importance of population-level data, and provide concrete results that add nuance to long-standing dispersibility hypotheses in the fern community that have, until now, lacked empirical data.
Structure-guided design of aPlasmodium vivaxDuffy binding protein-based vaccine immunogen
Authors: Barber Natalie M. , Pholcharee Tossapol , Lias Amelia M , Quinkert Doris , Nugent James , King Lloyd D. W. , Draper Simon J. , Higgins Matthew K. 
Published: June 2024

AbstractPlasmodium vivaxremains one of the major causative agents of human malaria and a vaccine is urgently required. It is an obligate intracellular parasites and replication within red blood cells is essential for development of disease and for transmission. The interaction between PvDBP on the parasite surface and the DARC receptor on human reticulocytes is essential for aPlasmodium vivaxblood stage infection. Human vaccination with the RII region of PvDBP slowed parasite replication, showing that PvDBP is a promising vaccine candidate. However, it did not induce sterile protection, and further development is required to generate a vaccine which protects from clinical malaria. In this study, we develop a vaccine immunogen containing a region of PvDBP-RII, known as subdomain 3, which contains the epitope for a broadly-reactive growth-inhibitory antibody, DB9. We used structure-guided approaches to resurface subdomain 3 such that it folds as an isolated molecule. We show that this engineered subdomain 3 is more stable and more easily produced than PvDBP-RII and induces a more effective growth-inhibitory antibody response. We therefore present an improved PvDBP-based immunogen for use in blood stage vaccines to prevent malaria due toPlasmodium vivax.One sentence summaryStructure-guided design leads to a more effective Duffy-binding protein-based vaccine immunogen to preventPlasmodium vivax.
Reduced accrual of mineral-associated organic matter after two years of enhanced rock weathering in cropland soils, though no net losses of soil organic carbon
Authors: Sokol Noah W. , Sohng Jaeeun , Moreland Kimber , Slessarev Eric , Goertzen Heath , Schmidt Radomir , Samaddar Sandipan , Holzer Iris , Almaraz Maya , Geoghegan Emily , Houlton Benjamin , Montañez Isabel , Pett-Ridge Jennifer , Scow Kate 
Published: June 2024

AbstractEnhanced rock weathering (ERW), the application of crushed silicate rock to soil, can remove atmospheric carbon dioxide by converting it to (bi)carbonate ions or solid carbonate minerals. However, few field studies have empirically evaluated ERW in field settings. A critical question remains as to whether additions of crushed rock might positively or negatively affect soil organic matter (SOM) – Earth’s largest terrestrial organic carbon (C) pool and a massive reservoir of organic nitrogen (N). Here, in three irrigated cropland sites in California, USA, we investigated the effect of crushed meta-basalt rock additions on different pools of soil organic carbon and nitrogen (i.e., mineral-associated organic matter and particulate organic matter), active microbial biomass, and microbial community composition. After two years of crushed rock additions, mineral-associated organic matter (MAOM) stocks were lower in the upper surface soil (0-10 cm) compared to unamended controls. At the two sites where baseline pre-treatment data were available, neither total SOC nor SON decreased over the two years of study in crushed rock or unamended control plots. However, the accrual rate of MAOM-C and MAOM-N at 0-10 cm was lower in plots with crushed rock vs. unamended controls. Before ERW is deployed at large scales, our results suggest that field trials should assess the effects of crushed rock on SOM pools, especially over multi-year time scales, to accurately assess changes in net C and understand the mechanisms driving interactions between ERW and SOM cycling.
Integrated single-cell RNA-seq analysis revealed PTN secreted by fibroblasts acting on itself and macrophages via SDC4 ligand in myocardial hypertrophy
Authors: Sheng Ke , Ran Yuqing , Guan Yuting , Tan Pingping , Zhang Rongrong , Qian Songwei , Lin Hongzhou , Wu Huilan , Peng Yongmiao , Huang Yuqing , Zhao Zhiguang , Zhu Guanghui , Ji Weiping , Guo Xiaoling 
Published: June 2024

AbstractBackgroundHypertrophic cardiomyopathy (HCM) is characterized by massive myocardial hypertrophy, which is the most frequent cause of sudden death and can lead to heart failure (HF) or stroke. The objective of this study was to explore the communication network among various cells in the heart of pathological HCM derived from transverse aortic constriction (TAC) mouse model, and investigate the potential mechanism through data mining, biological informatics analysis, and experimental validation.Methods and ResultsThe integrated analyses including CellChat, Seurat, gene ontology (GO), pseudo-time trajectory analysis, and weighted gene co-expression network analysis (WGCNA) were performed based on the single-cell RNA-seq data (scRNA-seq). In vitrotests were conducted to verify bioinformatic analysis findings through enzyme-linked immunosorbent assay (ELISA), real-time quantitative PCR (RT-qPCR), Edu staining, and transwell assay.In vivotests were also performed to further verify bioinformatic analysis findings by western blot and immunofluorescence assays based on our established TAC mouse model with myocardial hypertrophy. Our results showed that in the heart of TAC mouse, the interaction between cardiac fibroblasts and macrophages was most common, and the increasing pleiotrophin (PTN) secreted by cardiac fibroblasts could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines, such as TNF-α, IL-6, Cox-2, Cd83, Egr2, and IL-10 through acting on its ligand recombinant Syndecan 4 (SDC4), which may affect cardiomyocyte normal function and eventually cause HCM. This study first demonstrated that PTN derived from cardiac fibroblasts may act on SDC4 to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM.ConclusionsIn this study, the complex interaction network between cardiac fibroblasts and macrophages of TAC mice based on the scRNA-seq data was investigated, and we found that the increasing PTN secreted by cardiac fibroblasts under cardiac pressure overload could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines through acting on SDC4 ligand, which may affect cardiomyocyte normal function and eventually cause HCM. In addition, our study suggested that PTN derived from cardiac fibroblasts may act on SDC4 ligand to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM.
‘Vivaldi’: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2’
Authors: McClure C. Patrick , Tsoleridis Theocharis , Holmes Nadine , Chappell Joseph G. , Byaruhanga Timothy , Duncan Joshua , Tofan Miruna , Khater Abdul , Berry Louise , Clark Gemma , Irving William L. , Tarr Alexander W. , Ball Jonathan K. , Astbury Stuart , Loose Matt 
Published: June 2024

AbstractPrior to the emergence of SARS-CoV-2 in 2019, Alphacoronaviruses 229E and NL63 and Betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbidity and mortality and potential to inform the future trajectory of SARS-CoV-2 endemicity, they are infrequently sequenced. We therefore developed a 1200bp amplicon-based whole genome sequencing scheme targeting all four seasonal coronaviruses and SARS-CoV-2.The ‘Vivaldi’ method was applied retrospectively and prospectively using Oxford Nanopore Technology to approximately 400 seasonal coronavirus infections diagnosed in Nottingham, UK, from February 2016 to July 2023. We demonstrate that the amplicon multiplex strategy can be applied agnostically to determine complete genomes of five different species from two coronaviral genera. 304 unique seasonal coronavirus genomes of greater than 95% coverage were achieved: 64 for 229E, 85 for NL63, 128 for OC43 and 27 for HKU1. They collectively indicated a dynamic seasonal coronavirus genomic landscape, with co-circulation of multiple variants emerging and declining over the UK winter respiratory infection season, with further geographical distinction when compared to a global dataset. Prolonged infection with concomitant intra-host evolution was also observed for both Alpha-(NL63) and Betacoronaviruses (OC43).This data represents the largest single cohort of seasonal coronavirus genomes to date and also a novel amplicon scheme for their future global surveillance suitable for widespread and easy adoption in the post-SARS-CoV-2 era of viral genomics.
Defining the disturbance in cortical glutamate and GABA function in psychosis and its origins and consequences
Authors: Deakin Bill , Liddle Elizabeth , Rathnaiah Mohanbabu , Gregory Cathy , Katshu Mohammad , Williams Gemma , Conen Silke , Smallman Richard , Koelewijn Loes C. , Anton Adriana , Kumar Jyothika , Gasgoyne Lauren E. , Chen Chen , Nikkheslat Naghmeh , Evans John , Lanz Bernard , Walters James , Talbot Peter , Palaniyappan Lena , Singh Krish D. , Morris Peter , Williams Steven R. , Liddle Peter F. 
Published: June 2024

AbstractIt is widely thought that the onset of psychotic symptoms in schizophrenia may arise from an early neurotoxic phase, possibly related to oxidative stress or inflammation, and a late residual damage phase associated with persistent negative symptoms. We tested this hypothesis in a 3-centre study using magnetic resonance spectroscopy (MRS) to determine whether abnormalities in glutamate, glutamine and GABA content in anterior cingulate cortex (ACC) differed between people with minimally treated ‘Recent’ onset schizophrenia and an ‘Established’ group with > 10 years of treatment. We tested whether neurochemical abnormalities were i) mediated by raised circulating inflammatory cytokine concentrations, c-reactive protein (CRP) and interleukin-6 (IL-6), or depletion of glutathione and ii) associated with ratings of positive and negative symptoms. Relative to age-matched controls, the Established group showed significantly greater reduction in ACC glutamate than the Recent group, which did not differ from controls. This effect was not attributable to antipsychotic drug exposure. Patient ACC glutathione was negatively correlated with age. IL-6 was increased in both clinical groups, while increases in CRP were greater in the Established than Recent group. Elevated CRP was entirely accounted for by greater antipsychotic drug exposure and BMI, while residual elevation in IL-6 in the Established group did not account for their lower ACC glutamate. GABA was reduced relative to controls across ACC and occipital voxels. This reduction was not associated with drug treatment, BMI or cytokine levels. Only ACC GABA content correlated significantly with symptoms, lower content with greater positive and negative symptoms across both groups.
The Lived Experience of Mothers of Children with Cancer
Authors: Seyoum Lidya K. , Berhane Adugnaw , Girma Eshetu 
Published: June 2024

AbstractBackgroundThus, the path of mothers with cancer children is intricate and severe. Several studies have addressed this topic. Most have considered the long-term effects of the children’s cancer diagnosis on the mother from a mental health perspective. The experience of living with cancer children as mothers reveals the urgent need to pay attention to the mother’s emotional, psychological, and social factors shaping caregiving.ObjectiveThis study aimed to look further into the lived experiences of Ethiopian mothers with children suffering from childhood cancer.MethodInterpretive phenomenological approach of qualitative study conducted at the pediatric oncology unit of Tikur Anbessa Specialized Hospital and Tesfa Addis Parents Childhood Organization. Study participants were selected using the snowball purposive sampling technique. Data were collected using semi-structured interviews. A total of 12 mothers were interviewed. Interpretative phenomenological analysis was employed and Open Code 4.3 software was used for data management and used thematic analysis.ResultWhen raising a child with childhood cancer, mothers encounter a wide range of issues in the context of childhood cancer care, including fatigue, poor access to high-quality medical care, divorce, parenting withdrawal, excessive medical expenses, lack of sufficient and accurate information, anxiety, impatience, forgetfulness, regret, and spiritual struggles. To overcome such difficulties, mothers employ loans, financial aid, and the sale of their homes and other assets to reduce their financial burden. Mothers’ other coping method was to accept many sorts of support from family, friends, strangers, and organizations. The assistance received helped mothers gain resilience.ConclusionThe study provides crucial insights into the experiences of mothers of children with childhood cancer. The diagnosis of childhood cancer has a profound impact on mothers, and it elicits various reactions from them. Investigate the emotional, mental, and social drivers of caregiving, emphasizing important factors such as financial pressure, insufficient quality medical treatment, emotional disturbances, and strategies of coping with their children by the mothers. Establish counseling and support schemes for mothers to cope with cancer therapy for their child. Organize community awareness campaigns to increase understanding, reduce stigma, and promote early treatment.