bluuebunny/crossref_metadata_2025_split huggingface dataset:
Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle
Authors: Ding Xiongqi , Robbe-Masselot Catherine , Fu Xiali , Léonard Renaud , Marsac Benjamin , Dauriat Charlene J. G. , Lepissier Agathe , Rytter Héloïse , Ramond Elodie , Dupuis Marion , Euphrasie Daniel , Dubail Iharilalao , Schimmich Cécile , Qin Xiaoquan , Parraga Jessica , Leite-de-Moraes Maria , Ferroni Agnes , Chassaing Benoit , Sermet-Gaudelus Isabelle , Charbit Alain , Coureuil Mathieu , Jamet Anne 
Published: December 2023

AbstractStaphylococcus aureus is a predominant cause of chronic lung infections. While the airway environment is rich in highly sialylated mucins, the interaction of S. aureus with sialic acid is poorly characterized. Using S. aureus USA300 as well as clinical isolates, we demonstrate that quorum-sensing dysfunction, a hallmark of S. aureus adaptation, correlates with a greater ability to consume free sialic acid, providing a growth advantage in an air-liquid interface model and in vivo. Furthermore, RNA-seq experiment reveals that free sialic acid triggers transcriptional reprogramming promoting S. aureus chronic lifestyle. To support the clinical relevance of our results, we show the co-occurrence of S. aureus, sialidase-producing microbiota and free sialic acid in the airway of patients with cystic fibrosis. Our findings suggest a dual role for sialic acid in S. aureus airway infection, triggering virulence reprogramming and driving S. aureus adaptive strategies through the selection of quorum-sensing dysfunctional strains.
Delineating the early dissemination mechanisms of acral melanoma by integrating single-cell and spatial transcriptomic analyses
Authors: Wei Chuanyuan , Sun Wei , Shen Kangjie , Zhong Jingqin , Liu Wanlin , Gao Zixu , Xu Yu , Wang Lu , Hu Tu , Ren Ming , Li Yinlam , Zhu Yu , Zheng Shaoluan , Zhu Ming , Luo Rongkui , Yang Yanwen , Hou Yingyong , Qi Fazhi , Zhou Yuhong , Chen Yong , Gu Jianying 
Published: December 2023

AbstractAcral melanoma (AM) is a rare subtype of melanoma characterized by a high incidence of lymph node (LN) metastasis, a critical factor in tumor dissemination and therapeutic decision-making. Here, we employ single-cell and spatial transcriptomic analyses to investigate the dynamic evolution of early AM dissemination. Our findings reveal substantial inter- and intra-tumor heterogeneity in AM, alongside a highly immunosuppressive tumor microenvironment and complex intercellular communication networks, particularly in patients with LN metastasis. Notably, we identify a strong association between MYC+ Melanoma (MYC+MEL) and FGFBP2+NKT cells with LN metastasis. Furthermore, we demonstrate that LN metastasis requires a metabolic shift towards fatty acid oxidation (FAO) induced by MITF in MYC+MEL cells. Etomoxir, a clinically approved FAO inhibitor, can effectively suppress MITF-mediated LN metastasis. This comprehensive dataset enhances our understanding of LN metastasis in AM, and provides insights into the potential therapeutic targeting for the management of early AM dissemination.
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment
Authors: Roslan Muhamad Aidilfitri Mohamad , Omar Mohd Norfikri , Sharif Nur Azlina Mohd , Raston Nurul Hanun Ahmad , Arzmi Mohd Hafiz , Neoh Hui-Min , Ramzi Ahmad Bazli 
Published: December 2023

AbstractThe human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.
Effects of independent versus dependent stressful life events on major symptom domains of schizophrenia
Authors: Ma Yizhou , Chiappelli Joshua , Kvarta Mark D. , Bruce Heather , van der Vaart Andrew , Goldwaser Eric L. , Du Xiaoming , Sampath Hemalatha , Lightner Samantha , Endres Jane , Yusuf Akram , Yuen Alexa , Narvaez Samantha , Campos-Saravia Danny , Kochunov Peter , Hong L. Elliot 
Published: December 2023

AbstractWe evaluated two models to link stressful life events (SLEs) with the psychopathology of schizophrenia spectrum disorders (SSD). We separated SLEs into independent (iSLEs, unlikely influenced by one’s behavior) and dependent (dSLEs, likely influenced by one’s behavior). Stress-diathesis and stress generation models were evaluated for the relationship between total, i- and d- SLEs and the severity of positive, negative, and depressive symptoms in participants with SSD. Participants with SSD (n = 286; 196 males; age = 37.5 ± 13.5 years) and community controls (n = 121; 83 males; 35.4 ± 13.9 years) completed self-report of lifetime negative total, i- and d- SLEs. Participants with SSD reported a significantly higher number of total SLEs compared to controls (B = 1.11, p = 6.4 × 10–6). Positive symptom severity was positively associated with the total number of SLEs (β = 0.20, p = 0.001). iSLEs (β = 0.11, p = 0.09) and dSLEs (β = 0.21, p = 0.0006) showed similar association with positive symptoms (p = 0.16) suggesting stress-diathesis effects. Negative symptom severity was negatively associated with the number of SLEs (β = –0.19, p = 0.003) and dSLEs (β = −0.20, p = 0.001) but not iSLEs (β = –0.04, p = 0.52), suggesting stress generation effects. Depressive symptom severity was positively associated with SLEs (β = 0.34, p = 1.0 × 10–8), and the association was not statistically stronger for dSLEs (β = 0.33, p = 2.7 × 10–8) than iSLEs (β = 0.21, p = 0.0006), p = 0.085, suggesting stress-diathesis effects. The SLE – symptom relationships in SSD may be attributed to stress generation or stress-diathesis, depending on symptom domain. Findings call for a domain-specific approach to clinical intervention for SLEs in SSD.
Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean
Authors: Lee Young Ho , Abueg Linelle , Kim Jin-Koo , Kim Young Wook , Fedrigo Olivier , Balacco Jennifer , Formenti Giulio , Howe Kerstin , Tracey Alan , Wood Jonathan , Thibaud-Nissen Françoise , Nam Bo Hye , No Eun Soo , Kim Hye Ran , Lee Chul , Jarvis Erich D. , Kim Heebal 
Published: December 2023

AbstractChub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, nearly all containing telomeric repeats at their ends. We annotated 31,656 genes and discovered that approximately 2.19% of the genome contained DNA transposon elements repressed within duplicated genes. Analyzing 5-methylcytosine (5mC) modifications using HiFi reads, we observed open/close chromatin patterns at gene promoters, including the FADS2 gene involved in Omega-3 production. This chromosome-level reference genome provides unprecedented opportunities for advancing our knowledge of chub mackerels in biology, industry, and conservation.
Morpho-chemical characterization of individual ancient starches retrieved on ground stone tools from Palaeolithic sites in the Pontic steppe
Authors: Birarda G. , Badetti E. , Cagnato C. , Sorrentino G. , Pantyukhina I. , Stani C. , Dal Zilio S. , Khlopachev G. , Covalenco S. , Obada T. , Skakun N. , Sinitsyn A. , Terekhina V. , Marcomini A. , Lubritto C. , Cefarin N. , Vaccari L. , Longo L. 
Published: December 2023

AbstractDespite the extensive literature on the retrieval of digestible starches from archaeological contexts, there are still significant concerns regarding their genuine origin and durability. Here, we propose a multi-analytical strategy to identify the authenticity of ancient starches retrieved from macrolithic tools excavated at Upper Paleolithic sites in the Pontic steppe. This strategy integrates the morphological discrimination of starches through optical microscopy and scanning electron microscopy with single starch chemo-profiling using Fourier transform infrared imaging and microscopy. We obtained evidence of aging and biomineralization in the use-related starches from Palaeolithic sites, providing a methodology to establish their ancient origin, assess their preservation status, and attempt their identification. The pivotal application of this multidisciplinar approach demonstrates that the macrolithic tools, from which starches were dislodged, were used for food-processing across the Pontic Steppe around 40,000 years ago during the earliest colonization of Eurasia by Homo sapiens.
Circadian rhythm and circulating cell-free DNA release on healthy subjects
Authors: Poulet Geoffroy , Hulot Jean-Sébastien , Blanchard Anne , Bergerot Damien , Xiao Wenjin , Ginot Frederic , Boutonnet-Rodat Audrey , Justine Abdelli , Beinse Guillaume , Geromel Vanna , Pellegrina Laurence , Azizi Michel , Laurent-Puig Pierre , Benhaim Leonor , Taly Valerie 
Published: December 2023

AbstractIn the last decade, clinical studies have investigated the clinical relevance of circulating cell-free-DNA (ccfDNA) as a diagnostic and prognosis tool in various diseases including cancers. However, limited knowledge on ccfDNA biology restrains its full development in the clinical practice. To improve our understanding, we evaluated the impact of the circadian rhythm on ccfDNA release in healthy subjects over a 24-h period. 10 healthy female subjects underwent blood sampling at 8am and 20 healthy male subjects underwent serial blood sampling (8:00 AM, 9:00 AM, 12:00 PM, 4:00 PM, 8:00 PM, 12:00 AM, 4 AM (+ 1 Day) and 8 AM (+ 1 Day)). We performed digital droplet-based PCR (ddPCR) assays to target 2 DNA fragments (69 & 243 bp) located in the KRAS gene to determine the ccfDNA concentration and fragmentation profile. As control, half of the samples were re-analyzed by capillary miniaturized electrophoresis (BIAbooster system). Overall, we did not detect any influence of the circadian rhythm on ccfDNA release. Instead, we observed a decrease in the ccfDNA concentration after meal ingestion, suggesting either a post-prandial effect or a technical detection bias due to a higher plasma load in lipids and triglycerides. We also noticed a potential effect of gender, weight and creatinine levels on ccfDNA concentration.
Prognostic factors of resected pathological stage I lung adenocarcinoma: evaluating subtypes and PD-L1/CD155 expression
Authors: Nishizawa Natsumasa , Shimajiri Shohei , Oyama Rintaro , Manabe Takehiko , Nemoto Yukiko , Matsumiya Hiroki , Honda Yohei , Taira Akihiro , Takenaka Masaru , Kuroda Koji , Tanaka Fumihiro 
Published: December 2023

AbstractWe aimed to compare the prognostic impacts of adenocarcinoma subtypes, programmed death-ligand I (PD-L1), and CD155 expression on patients with resected pathological stage (p-stage) I lung adenocarcinoma. In total, 353 patients with completely resected p-stage I lung adenocarcinomas were retrospectively reviewed. The expression levels of PD-L1 and CD155 in tumour cells from each adenocarcinoma subtype were evaluated using several clinicopathological and histological features, such as the presence of a micropapillary pattern. A total of 52 patients (14.7%) had PD-L1-positive tumours, whereas 128 patients (36.3%) had CD155-positive tumours, with a tumour proportion score of 5% for both PD-L1 and CD155 expression. Compared with patients with other adenocarcinoma subtypes, those with solid-predominant adenocarcinomas were significantly more positive for PD-L1 and CD155. Multivariate analysis showed that PD-L1 expression status was significantly associated with progression-free survival and overall survival, whereas CD155 expression and the presence of a micropapillary pattern were not significantly associated with either parameter. Patients with PD-L1-positive tumours had poorer prognoses than those with CD155-positive tumours. Moreover, PD-L1 and CD155 were significantly expressed in solid-predominant adenocarcinomas. The results of this study suggest that immune checkpoint inhibitors can be used as adjuvants in the treatment of patients with p-stage I adenocarcinoma.
Identification of CT-based non-invasive radiomic biomarkers for overall survival prediction in oral cavity squamous cell carcinoma
Authors: Ling Xiao , Alexander Gregory S. , Molitoris Jason , Choi Jinhyuk , Schumaker Lisa , Mehra Ranee , Gaykalova Daria A. , Ren Lei 
Published: December 2023

AbstractThis study addresses the limited non-invasive tools for Oral Cavity Squamous Cell Carcinoma (OSCC) survival prediction by identifying Computed Tomography (CT)-based biomarkers to improve prognosis prediction. A retrospective analysis was conducted on data from 149 OSCC patients, including CT radiomics and clinical information. An ensemble approach involving correlation analysis, score screening, and the Sparse-L1 algorithm was used to select functional features, which were then used to build Cox Proportional Hazards models (CPH). Our CPH achieved a 0.70 concordance index in testing. The model identified two CT-based radiomics features, Gradient-Neighboring-Gray-Tone-Difference-Matrix-Strength (GNS) and normalized-Wavelet-LLL-Gray-Level-Dependence-Matrix-Large-Dependence-High-Gray-Level-Emphasis (HLE), as well as stage and alcohol usage, as survival biomarkers. The GNS group with values above 14 showed a hazard ratio of 0.12 and a 3-year survival rate of about 90%. Conversely, the GNS group with values less than or equal to 14 had a 49% survival rate. For normalized HLE, the high-end group (HLE > − 0.415) had a hazard ratio of 2.41, resulting in a 3-year survival rate of 70%, while the low-end group (HLE ≤ − 0.415) had a 36% survival rate. These findings contribute to our knowledge of how radiomics can be used to predict the outcome so that treatment plans can be tailored for patients people with OSCC to improve their survival.
Testing a vaccine candidate against Hepatitis C virus designed by combinatorial optimization
Authors: Malaina Iker , Martinez Luis , Salcines-Cuevas David , Teran-Navarro Hector , Ocejo-Vinyals J. Gonzalo , Gonzalez-Lopez Elena , Soriano Vicente , Ubeda María , Perez Pinilla Martin-Blas , Martinez de la Fuente Ildefonso , Alvarez-Dominguez Carmen 
Published: December 2023

AbstractThis paper presents a new procedure for vaccine design against highly variable viruses such as Hepatitis C. The procedure uses an optimization algorithm to design vaccines that maximize the coverage of epitopes across different virus variants. Weighted epitopes based on the success ratio of immunological assays are used to prioritize the selection of epitopes for vaccine design. The procedure was successfully applied to design DC vaccines loaded with two HCV peptides, STG and DYP, which were shown to be safe, immunogenic, and able to induce significant levels of anti-viral cytokines, peptide-specific cellular immune responses and IgG antibodies. The procedure could potentially be applied to other highly variable viruses that currently lack effective vaccines.
Facile method for 3D printing conformally onto uneven surfaces and its application to face masks
Authors: Ji Zehao , Brion Douglas A. J. , Samson Kerr D. G. , Pattinson Sebastian W. 
Published: December 2023

AbstractConventional additive manufacturing processes, where parts are built through layer-wise deposition of material on a horizontal plane, can be limiting when a part must be printed or fit onto uneven surfaces. Such situations will arise with increasing frequency as additive manufacturing application areas such as construction and medical devices continue to grow. In this work, we develop a simple and practical approach to generate toolpaths to print 3D structures onto uneven surfaces conformally. The algorithm uses only conventional planar toolpaths of both the structure to be printed and the substrate to be printed on and converts these to non-planar toolpaths, allowing easy integration with existing additive manufacturing workflows. The technique is demonstrated by printing flexible seals onto bespoke rigid face mask frames conformally via a conventional single-material 3D printer using the generated conformal toolpath. A notable improvement in air seal performance was observed for customized face masks with conformal soft seals compared to conventionally 3D-printed fully rigid face masks. This also shows the potential of the developed toolpath generation method to aid in the prototyping and fabrication of conformal medical and other devices.
Arresting calcium-regulated sperm metabolic dynamics enables prolonged fertility in poultry liquid semen storage
Authors: Sushadi Pangda Sopha , Kuwabara Maiko , Maung Ei Ei Win , Mohamad Mohtar Mohamad Shuib , Sakamoto Kouyo , Selvaraj Vimal , Asano Atsushi 
Published: December 2023

AbstractThe preservation of liquid semen is pivotal for both industrial livestock production and genetic management/conservation of species with sperm that are not highly cryo-tolerant. Nevertheless, with regard to poultry semen, even brief in vitro storage periods can lead to a notable decline in fertility, despite the in vivo capacity to maintain fertility for several weeks when within the hen’s sperm storage tubules. For fertility in sperm, intracellular calcium ions ([Ca2+]i) play a key role in signaling towards modifying energy metabolism. While reducing [Ca2+]i has been found to enhance the preservation of sperm fertility in some mammals, the connection between semen fertility and calcium availability in avian sperm has received limited attention. In this study, we demonstrate that the use of extracellular and intracellular calcium chelators in liquid semen extenders, specifically EGTA and EGTA-AM, has distinct effects on prolonging the fertility of chicken sperm. These results were validated through in vivo fertility tests. Mechanistically, the effects observed were linked to coordination of mitochondrial metabolism and ATP catabolism. Despite both calcium chelators inducing hypoxia, they differentially regulated mitochondrial respiration and ATP accumulation. This regulation was closely linked to a bimodal control of dynein ATPase activity; a direct initial activation with reduction in [Ca2+]i, and subsequent suppression by cytoplasmic acidification caused by lactic acid. These findings not only contribute to advancing poultry liquid semen preservation techniques, but also elucidates biologically relevant mechanisms that may underlie storage within the female reproductive tract in birds.
Automatic GAN-based MRI volume synthesis from US volumes: a proof of concept investigation
Authors: Vukovic Damjan , Ruvinov Igor , Antico Maria , Steffens Marian , Fontanarosa Davide 
Published: December 2023

AbstractUsually, a baseline image, either through magnetic resonance imaging (MRI) or computed tomography (CT), is captured as a reference before medical procedures such as respiratory interventions like Thoracentesis. In these procedures, ultrasound (US) imaging is often employed for guiding needle placement during Thoracentesis or providing image guidance in MISS procedures within the thoracic region. Following the procedure, a post-procedure image is acquired to monitor and evaluate the patient’s progress. Currently, there are no real-time guidance and tracking capabilities that allow a surgeon to perform their procedure using the familiarity of the reference imaging modality. In this work, we propose a real-time volumetric indirect registration using a deep learning approach where the fusion of multi-imaging modalities will allow for guidance and tracking of surgical procedures using US while displaying the resultant changes in a clinically friendly reference imaging modality (MRI). The deep learning method employs a series of generative adversarial networks (GANs), specifically CycleGAN, to conduct an unsupervised image-to-image translation. This process produces spatially aligned US and MRI volumes corresponding to their respective input volumes (MRI and US) of the thoracic spine anatomical region. In this preliminary proof-of-concept study, the focus was on the T9 vertebrae. A clinical expert performs anatomical validation of randomly selected real and generated volumes of the T9 thoracic vertebrae and gives a score of 0 (conclusive anatomical structures present) or 1 (inconclusive anatomical structures present) to each volume to check if the volumes are anatomically accurate. The Dice and Overlap metrics show how accurate the shape of T9 is when compared to real volumes and how consistent the shape of T9 is when compared to other generated volumes. The average Dice, Overlap and Accuracy to clearly label all the anatomical structures of the T9 vertebrae are approximately 80% across the board.
Inflammatory burden, lifestyle and atherosclerotic cardiovascular disease: insights from a population based cohort study
Authors: Bay Benjamin , Blaum Christopher , Kellner Caroline , Bei der Kellen Ramona , Ojeda Francisco , Waibel Julia , Arnold Natalie , Behrendt Christian-A. , Rimmele David L. , Thomalla Goetz , Twerenbold Raphael , Blankenberg Stefan , Zyriax Birgit , Brunner Fabian J. , Waldeyer Christoph 
Published: December 2023

AbstractThe inflammatory burden as measured by high-sensitivity C-reactive Protein (hsCRP) is recognized as a cardiovascular risk factor, which can however be affected by lifestyle-related risk factors (LRF). Up-to-date the interplay between hsCRP, LRF and presence and extent of atherosclerotic disease is still largely unknown, which we therefore sought to investigate in a contemporary population-based cohort. We included participants from the cross-sectional population-based Hamburg City Health Study. Affected vascular beds were defined as coronary, peripheral, and cerebrovascular arteries. LRF considered were lack of physical activity, overweight, active smoking and poor adherence to a Mediterranean diet. We computed multivariable analyses with hsCRP as the dependent variable and LRF as covariates according to the number of vascular beds affected. In the 6765 individuals available for analysis, we found a stepwise increase of hsCRP concentration both according to the number of LRF present as well as the number of vascular beds affected. Adjusted regression analyses showed an independent association between increasing numbers of LRF with hsCRP levels across the extent of atherosclerosis. We demonstrate increasing hsCRP concentrations according to both the number of LRF as well as the extent of atherosclerosis, emphasizing the necessity of lifestyle-related risk factor optimization.