bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of community-associated methicillin-resistant Staphylococcus aureus ΨUSA300 among Japanese people with HIV, resulted from stepwise mutations in 2010s
Authors: Shinohara Koh , Uehara Yuki , Teruya Katsuji , Sasaki Takashi , Baba Tadashi , Nakaminami Hidemasa , Kananizadeh Pegah , Morimoto Yuh , Kikuchi Yoshimi , Oka Shinichi 
Published: May 2023

AbstractAlthough infection with the methicillin-resistant Staphylococcus aureus (MRSA) clone USA300 is extremely rare in Japan, the uniquely evolved clone ΨUSA300 has been reported in Japan. An outbreak of a distinct USA300 clone was recently reported in an HIV/AIDS referral hospital in Tokyo. The present study investigated the evolutionary origin and genetic diversity of USA300-related clones causing regional outbreaks among people living with HIV (PLWHIV) in Tokyo. MRSA isolates collected from PLWHIV in an HIV/AIDS referral center in Tokyo were subjected to whole-genome sequencing and their genetic features were compared with those of previously described USA300 MRSA genomes. Of the 28 MRSAs isolated in 2016–2019, 23 (82.1%) were identified as USA300, with 22 (95.6%) of the latter identified as ΨUSA300. Although the genomic structure of ΨUSA300 was identical to the structures of reference USA300 strains, one clade (cluster A) was found to have acquired 29 previously identified lineage-specific mutations in a stepwise manner. The estimated divergence dates of ΨUSA300 and Cluster A were 2009 and 2012, respectively. These findings suggested that the ΨUSA300 clone had spread among PLWHIVs in Tokyo in the early 2010s, with stepwise acquisition of lineage-specific nonsynonymous mutations.
Establishment of a novel model of endometriosis-associated ovarian cancer by transplanting uterine tissue from Arid1a/Pten knockout mice
Authors: Ono Motoki , Miyamoto Tsutomu , Asaka Ryoichi , Uchikawa Junko , Ando Hirofumi , Tanaka Yasuhiro , Shinagawa Manaka , Yokokawa Yusuke , Asaka Shiho , Wang Tian-Li , Shih Ie-Ming , Shiozawa Tanri 
Published: May 2023

AbstractAlthough endometriosis is primarily benign, it has been identified as a risk factor for endometriosis-associated ovarian cancer (EAOC). Genetic alterations in ARID1A, PTEN, and PIK3CA have been reported in EAOC; however, an appropriate EAOC animal model has yet to be established. Therefore, the present study aimed to create an EAOC mouse model by transplanting uterine pieces from donor mice, in which Arid1a and/or Pten was conditionally knocked out (KO) in Pax8-expressing endometrial cells by the administration of doxycycline (DOX), onto the ovarian surface or peritoneum of recipient mice. Two weeks after transplantation, gene KO was induced by DOX and endometriotic lesions were thereafter removed. The induction of only Arid1a KO did not cause any histological changes in the endometriotic cysts of recipients. In contrast, the induction of only Pten KO evoked a stratified architecture and nuclear atypia in the epithelial lining of all endometriotic cysts, histologically corresponding to atypical endometriosis. The induction of Arid1a; Pten double-KO evoked papillary and cribriform structures with nuclear atypia in the lining of 42 and 50% of peritoneal and ovarian endometriotic cysts, respectively, which were histologically similar to EAOC. These results indicate that this mouse model is useful for investigating the mechanisms underlying the development of EAOC and the related microenvironment.
Research on the isolation and identification of black spot disease of Rosa chinensis in Kunming, China
Authors: Li Yanjie , Pu Meiying , Cui Yusi , Gu Ju , Chen Xi , Wang Louqin , Wu Hongzhi , Yang Yuyong , Wang Chao 
Published: May 2023

AbstractThrough a survey of rose diseases in the South Tropical Garden in Kunming, China, it was found that black spot was the most common and serious disease of rose cultivated in the open air there, with an incidence of more than 90%. In this study, fungus isolation was performed on leaf samples of five black spot susceptible varieties of rose from the South Tropical Garden by tissue isolation. 18 strains of fungus were initially obtained, and seven of them were finally identified to cause black spot symptoms on healthy leaves of rose after verification by Koch's rule. By observing the morphology of colonies and spores, and constructing a phylogenetic tree by combining molecular biology and multiple genes, two pathogenic fungus were identified, namely, Alternariaalternata and Gnomoniopsisrosae.G.rosae was the first pathogenic fungi of rose black spot isolated and identified in this study. The results of this study can provide a reference base for further research and control of the black spot disease of rose in Kunming.
Bacteriophage-loaded functional nanofibers for treatment of P. aeruginosa and S. aureus wound infections
Authors: Kielholz Tobias , Rohde Felix , Jung Nathalie , Windbergs Maike 
Published: May 2023

AbstractThe increasing incidence of infected skin wounds poses a major challenge in clinical practice, especially when conventional antibiotic therapy fails. In this context, bacteriophages emerged as promising alternatives for the treatment of antibiotic-resistant bacteria. However, clinical implementation remains hampered by the lack of efficient delivery approaches to infected wound tissue. In this study, bacteriophage-loaded electrospun fiber mats were successfully developed as next-generation wound dressings for the treatment of infected wounds. We employed a coaxial electrospinning approach, creating fibers with a protective polymer shell, enveloping bacteriophages in the core while maintaining their antimicrobial activity. The novel fibers exhibited a reproducible fiber diameter range and morphology, while the mechanical fiber properties were ideal for application onto wounds. Further, immediate release kinetics for the phages were confirmed as well as the biocompatibility of the fibers with human skin cells. Antimicrobial activity was demonstrated against Staphylococcus aureus and Pseudomonas aeruginosa and the core/shell formulation maintained the bacteriophage activity for 4 weeks when stored at − 20 °C. Based on these promising characteristics, our approach holds great potential as a platform technology for the encapsulation of bioactive bacteriophages to enable the translation of phage therapy into clinical application.
PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum
Authors: Wu Yue , Chaumier Timothée , Manirakiza Eric , Veluchamy Alaguraj , Tirichine Leila 
Published: May 2023

AbstractRecent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView (https://PhaeoEpiView.univ-nantes.fr) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.
Predictors of postoperative pain six months after breast surgery
Authors: J. Ghadimi Delaram , Looha Mehdi Azizmohammad , Akbari Mohammad Esmaeil , Akbari Atieh 
Published: May 2023

AbstractBreast cancer, with a high prevalence and survival rate, leads to long-term complications. A major sequel is acute or chronic postoperative pain, and we investigated the possible relationship with clinical and psychological variables. Patients undergoing breast surgery filled out the loneliness (ULS-8) and depression (HADS) questionnaires. Patients rated their pain intensity with the Numerical Rating Scale (0–10, NRS) two days, seven days, and six months after surgery. Of 124 patients, the mean age was 45.86 years old, and the pain scores on the second and seventh postoperative days were 5.33 and 3.57, respectively. Sixth-month pain was significantly correlated with the acute scores with a mean of 3.27; and in the multivariate analysis, it was significantly associated with preoperative pain (p-value = 0.007), self-reported loneliness (p-value = 0.010), and adjuvant radiotherapy (p-value = 0.004). In conclusion, loneliness may be a risk factor for postoperative pain in breast surgery.
Spermidine improves angiogenic capacity of senescent endothelial cells, and enhances ischemia-induced neovascularization in aged mice
Authors: Ueno Daisuke , Ikeda Koji , Yamazaki Ekura , Katayama Akiko , Urata Ryota , Matoba Satoaki 
Published: May 2023

AbstractAging is closely associated with the increased morbidity and mortality of ischemic cardiovascular disease, at least partially through impaired angiogenic capacity. Endothelial cells (ECs) play a crucial role in angiogenesis, and their angiogenic capacity declines during aging. Spermidine is a naturally occurring polyamine, and its dietary supplementation has exhibited distinct anti-aging and healthy lifespan-extending effects in various species such as yeast, worms, flies, and mice. Here, we explore the effects of spermidine supplementation on the age-related decline in angiogenesis both in vitro and in vivo. Intracellular polyamine contents were reduced in replicative senescent ECs, which were subsequently recovered by spermidine supplementation. Our findings reveal that spermidine supplementation improved the declined angiogenic capacity of senescent ECs, including migration and tube-formation, without affecting the senescence phenotypes. Mechanistically, spermidine enhanced both autophagy and mitophagy, and improved mitochondrial quality in senescent ECs. Ischemia-induced neovascularization was assessed using the hind-limb ischemia model in mice. Limb blood flow recovery and neovascularization in the ischemic muscle were considerably impaired in aged mice compared to young ones. Of note, dietary spermidine significantly enhanced ischemia-induced angiogenesis, and improved the blood flow recovery in the ischemic limb, especially in aged mice. Our results reveal novel proangiogenic functions of spermidine, suggesting its therapeutic potential against ischemic disease.
Single-cell transcriptional profiling of hearts during cardiac hypertrophy reveals the role of MAMs in cardiomyocyte subtype switching
Authors: Luan Yi , Guo Guangyu , Luan Ying , Yang Yang , Yuan Ruixia 
Published: May 2023

AbstractPathological cardiac hypertrophy is the main predecessor of heart failure. Its pathology is sophisticated, and its progression is associated with multiple cellular processes. To explore new therapeutic approaches, more precise examination of cardiomyocyte subtypes and involved biological processes is required in response to hypertrophic stimuli. Mitochondria and the endoplasmic reticulum (ER) are two crucial organelles associated with the progression of cardiac hypertrophy and are connected through junctions known as mitochondria-associated endoplasmic reticulum membranes (MAMs). Although MAM genes are altered in cardiac hypertrophy, the importance of MAMs in cardiac hypertrophy and the expression pattern of MAMs in certain cardiac cell types require a comprehensive analysis. In this study, we analyzed the temporal expression of MAM proteins in the process of cardiac hypertrophy and observed that MAM-related proteins preferentially accumulated in cardiomyocytes at the initial stage of cardiac hypertrophy and underwent a gradual decline, which was synchronized with the proportion of two cardiomyocyte subtypes (CM2 and CM3). Meanwhile, these subtypes went through a functional switch during cardiac hypertrophy. Trajectory analysis suggested that there was a differentiation trajectory of cardiomyocyte subtypes from high to low MAM protein expression. Distinct regulon modules across different cardiomyocyte cell types were revealed by transcriptional regulatory network analysis. Furthermore, scWGCNA revealed that MAM-related genes were clustered into a module that correlated with diabetic cardiomyopathy. Altogether, we identified cardiomyocyte subtype transformation and the potential critical transcription factors involved, which may serve as therapeutic targets in combating cardiac hypertrophy.
An automated image-based workflow for detecting megabenthic fauna in optical images with examples from the Clarion–Clipperton Zone
Authors: Mbani Benson , Buck Valentin , Greinert Jens 
Published: May 2023

AbstractRecent advances in optical underwater imaging technologies enable the acquisition of huge numbers of high-resolution seafloor images during scientific expeditions. While these images contain valuable information for non-invasive monitoring of megabenthic fauna, flora and the marine ecosystem, traditional labor-intensive manual approaches for analyzing them are neither feasible nor scalable. Therefore, machine learning has been proposed as a solution, but training the respective models still requires substantial manual annotation. Here, we present an automated image-based workflow for Megabenthic Fauna Detection with Faster R-CNN (FaunD-Fast). The workflow significantly reduces the required annotation effort by automating the detection of anomalous superpixels, which are regions in underwater images that have unusual properties relative to the background seafloor. The bounding box coordinates of the detected anomalous superpixels are proposed as a set of weak annotations, which are then assigned semantic morphotype labels and used to train a Faster R-CNN object detection model. We applied this workflow to example underwater images recorded during cruise SO268 to the German and Belgian contract areas for Manganese-nodule exploration, within the Clarion–Clipperton Zone (CCZ). A performance assessment of our FaunD-Fast model showed a mean average precision of 78.1% at an intersection-over-union threshold of 0.5, which is on a par with competing models that use costly-to-acquire annotations. In more detail, the analysis of the megafauna detection results revealed that ophiuroids and xenophyophores were among the most abundant morphotypes, accounting for 62% of all the detections within the surveyed area. Investigating the regional differences between the two contract areas further revealed that both megafaunal abundance and diversity was higher in the shallower German area, which might be explainable by the higher food availability in form of sinking organic material that decreases from east-to-west across the CCZ. Since these findings are consistent with studies based on conventional image-based methods, we conclude that our automated workflow significantly reduces the required human effort, while still providing accurate estimates of megafaunal abundance and their spatial distribution. The workflow is thus useful for a quick but objective generation of baseline information to enable monitoring of remote benthic ecosystems.
Extensive cytokine biomarker analysis in serum of Guillain-Barré syndrome patients
Authors: Li Xiaocong , Yang Liping , Wang Guowei , Yuan Yanping , Wei Na , Yang Wanqiu , Wang Xiaoli , Wang Zhenhai 
Published: May 2023

AbstractGuillain-Barré syndrome (GBS) is an acute idiopathic polyneuropathy which is related to infection and immune mechanism. The exact pathogenesis of the disease is unknown and treatment is limited. Thus, the purpose of the study is to identify biomarkers of GBS serum and elucidate their involvement in the underlying pathogenesis of GBS that could help to treat GBS more accurately. Antibody array technology was used to detect the expression levels of 440 proteins in serum of 5 GBS group and 5 healthy control group. Sixty-seven differentially expressed proteins (DEPs) were identified by antibody array, among which FoLR1, Legumain, ErbB4, IL-1α, MIP-1α and IGF-2 were down-regulated, while 61 proteins were up-regulated. Bioinformatics analysis indicated that most DEPs were associated with leukocytes, among which IL-1α, SDF-1b, B7-1, CD40, CTLA4, IL-9, MIP-1α and CD40L were in the center of protein–protein interaction (PPI) network. Subsequently, the ability of these DEPs to distinguish GBS from healthy control was further evaluated. CD23 was identified by means of Random Forests Analysis (RFA) and verified by enzyme-linked immunosorbent assay (ELISA). The ROC curve result of CD23 respectively displayed that its sensitivity, specificity and AUC were 0.818, 0.800 and 0.824. We speculate that activation of leukocyte proliferation and migration in circulating blood might be associated with inflammatory recruitment of peripheral nerves, leading to the occurrence and development of GBS, but this conclusion still requires deeper confirmation. More importantly, central proteins may play a pivotal role in the pathogenesis of GBS. In addition, we detected IL-1α, IL-9, and CD23 in the serum of GBS patients for the first time, which may be promising biomarkers for the treatment of GBS.
Exploring the effects of habituation and scent in first-person 360-degree videos on consumption behavior
Authors: Li Benjamin J. , Lee Hui Min 
Published: May 2023

AbstractAlthough immersive virtual environments can influence food-related thoughts, emotions and behavior, the influence of repeated exposure to food cues in such environments has rarely been explored. This study seeks to understand if habituation, a decrease in one’s physiological and behavioral response that results from repeated simulation, can take place while repeatedly watching 360-degrees of food being consumed. The influence of scent as an olfactory cue is further explored, based on past research on embodied cognition. In Study One (n = 42), participants who viewed 30 repetitions of someone eating an M&M ate significantly fewer M&Ms than those who viewed three repetitions. Study Two (n = 114) used a 2 (behavior: eating M&M/inserting a coin) × 2 (repetitions: 3/30) between-subjects experiment to confirm that results from Study One were due to habituation of the consumption video, finding that there were only significant differences between repetitions in the M&M condition. Finally, Study Three (n = 161) comprised a 2 (repetition: 3/30) × 2 (scent: present/absent) between-subjects experiment. Participants in the 30-repetition condition and those in the scent-present condition ate significantly fewer M&Ms respectively, but no interaction effects were found. The theoretical and practical implications of these findings are discussed.
Divergent effectiveness of irrigation in enhancing food security in droughts under future climates with various emission scenarios
Authors: Zhang Qiang , Yu Huiqian , Li Jianfeng , Clothier Brent , Singh Vijay P. , Shen Zexi 
Published: May 2023

AbstractFood security is a key target in the UN Sustainable Development Goals (SDGs) and is also one of the biggest challenges for China, the largest developing country in population in the world. Massive attention has been directed to the future impacts of hydrometeorological extremes on crop yield. However, knowledge gaps still stand concerning the effectiveness of irrigation, as the largest water consumption sector, on agricultural production under different climate scenarios. Here we showed the drought based on the modified Palmer Drought Severity Index and analyzed the drought-induced wheat yield losses in irrigated and non-irrigated agriculture across China according to three methods including the Multiple Linear Regression method, Deep Learning algorithm, and Erosion-Productivity Impact Calculator model. We found that the droughts become more intensive in the future, and drought-induced wheat yield loss under RCP8.5 scenario was expected to reach 32–49%. Intercomparison of drought-induced wheat yield changes between irrigated and non-irrigated agriculture indicated significantly less drought-induced crop-yield losses given sufficient irrigation under the RCP2.6 and RCP6.0 scenarios. However, our results under RCP8.5 suggested that the effectiveness of irrigation in enhancing food security is minor under this high-emission future climate scenario. These findings allowed us to revisit the effectiveness of irrigation in a warming climate and highlighted the importance of climate change mitigation in food security.
Synergistic combination of information from ground observations, geostationary satellite, and air quality modeling towards improved PM2.5 predictability
Authors: Yu Jinhyeok , Song Chul H. , Lee Dogyeong , Lee Sojin , Kim Hyun S. , Han Kyung M. , Park Seohui , Im Jungho , Park Soon-Young , Jeon Moongu , Peuch Vincent-Henri , Saide Pablo E. , Carmichael Gregory R. , Kim Jeeho , Kim Jhoon , Song Chang-Keun , Woo Jung-Hun , Ryu Seong-Hyun 
Published: May 2023

AbstractConcentrations of ambient particulate matter (such as PM2.5 and PM10) have come to represent a serious environmental problem worldwide, causing many deaths and economic losses. Because of the detrimental effects of PM2.5 on human health, many countries and international organizations have developed and operated regional and global short-term PM2.5 prediction systems. The short-term predictability of PM2.5 (and PM10) is determined by two main factors: the performance of the air quality model and the precision of the initial states. While specifically focusing on the latter factor, this study attempts to demonstrate how information from classical ground observation networks, a state-of-the-art geostationary (GEO) satellite sensor, and an advanced air quality modeling system can be synergistically combined to improve short-term PM2.5 predictability over South Korea. Such a synergistic combination of information can effectively overcome the major obstacle of scarcity of information, which frequently occurs in PM2.5 prediction systems using low Earth orbit (LEO) satellite-borne observations. This study first presents that the scarcity of information is mainly associated with cloud masking, sun-glint effect, and ill-location of satellite-borne data, and it then demonstrates that an advanced air quality modeling system equipped with synergistically-combined information can achieve substantially improved performances, producing enhancements of approximately 10%, 19%, 29%, and 10% in the predictability of PM2.5 over South Korea in terms of index of agreement (IOA), correlation coefficient (R), mean biases (MB), and hit rate (HR), respectively, compared to PM2.5 prediction systems using only LEO satellite-derived observations.