bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interaction between microbiota and immune in intestinal inflammatory diseases: Global research status and trends
Authors: Liu Chuan , Su Wenhao , Tan Zongbiao , Zhang Jixiang , Dong Weiguo 
Published: February 2023

AimsThis study aimed to conduct a bibliometric analysis of the relevant literature on the interaction between microbiota and immune in intestinal inflammatory diseases, and show its current status, hotspots, and development trends.MethodsThe related literature was acquired from the Web of Science Core Collection on October 12, 2022. Co-occurrence and cooperation relationship analysis of authors, institutions, countries, references, and keywords in the literature were carried out through CiteSpace 6.1.R3 software and the Online Analysis platform of Literature Metrology. At the same time, the relevant knowledge maps were drawn, and the keywords cluster analysis and emergence analysis were performed.Results3,608 related publications were included, showing that the number of articles in this field is increasing year by year. The results showed that Gasbarrini A and Sokol H were the authors with the highest cumulative number of articles with 25, and the institution with the most articles was Harvard University with 142 articles. The USA was far ahead in the article output, with 1,131 articles, and had a dominant role, followed by China with 707 articles. The journal Frontiers in Immunology contributed the most to this research field with 213 articles. In the cooperation network analysis, the USA, Harvard University, and Xavier RJ were the most widely collaborated country, institution, and author, respectively, which implied a high level of influence. Keywords analysis showed that there were 770 keywords, which were mainly classified as internal related diseases, such as “inflammatory bowel disease”, “irritable bowel syndrome”, “colorectal cancer”, and the mechanism of interaction of microbiota and immune, such as “intestinal microbiota”, “commensal microbiota”, “regulatory T cell”, “dendritic cell”, “barrier function”, “activation”, “anti-inflammatory properties”, “intestinal epithelium”, and “diversity”. Emerging analysis showed that future research hotspots and trends might be the short-chain fatty acid, gut dysbiosis, gut-liver axis, and fusobacterium nucleatum.ConclusionThis research was the first bibliometric analysis of publications in the field of interaction between microbiota and immune in intestinal inflammatory diseases using visualization software and data information mining, and obtained the current status, hotspots, and development of this field, which provides a theoretical basis for its scientific research.
Ox-LDL induced profound changes of small non-coding RNA in rat endothelial cells
Authors: Wang Yu , Liu Tianhua , Xiao Wenying , Bai Yanyan , Yue Dandan , Feng Liuliu 
Published: February 2023

IntroductionAtherosclerosis (AS) is a common cardiovascular disease with a high incidence rate and mortality. Endothelial cell injury and dysfunction are early markers of AS. Oxidative low-density lipoprotein (Ox-LDL) is a key risk factor for the development of AS. Ox-LDL promotes endothelial cell apoptosis and induces inflammation and oxidative stress in endothelial cells. Small non-coding RNAs (sncRNAs) mainly include Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), microRNAs (miRNAs) and repeat-associated RNAs. Studies have shown that small non-coding RNAs play an increasingly important role in diseases.MethodsWe used ox-LDL to treat rat endothelial cells to simulate endothelial cell injury. The expression changes of sncRNA were analyzed by small RNA high-throughput sequencing, and the expression changes of piRNA, snoRNA, snRNA, miRNA and repeat-associated RNA were verified by quantitative polymerase chain reaction (qPCR).ResultsSmall RNA sequencing showed that 42 piRNAs were upregulated and 38 piRNAs were downregulated in endothelial cells treated with ox-LDL. PiRNA DQ614630 promoted the apoptosis of endothelial cells. The snoRNA analysis results showed that 80 snoRNAs were upregulated and 68 snoRNAs were downregulated in endothelial cells with ox-LDL treatment, and snoRNA ENSRNOT00000079032.1 inhibited the apoptosis of endothelial cells. For snRNA, we found that 20 snRNAs were upregulated and 26 snRNAs were downregulated in endothelial cells with ox-LDL treatment, and snRNA ENSRNOT00000081005.1 increased the apoptosis of endothelial cells. Analysis of miRNAs indicated that 106 miRNAs were upregulated and 91 miRNAs were downregulated in endothelial cells with ox-LDL treatment, and miRNA rno-novel-136-mature promoted the apoptosis of endothelial cells. The repeat RNA analysis results showed that 4 repeat RNAs were upregulated and 6 repeat RNAs were downregulated in endothelial cells treated with ox-LDL.DiscussionThis study first reported the expression changes of sncRNAs in endothelial cells with ox-LDL treatment, which provided new markers for the diagnosis and treatment of endothelial cell injury.
The association between self-monitoring of blood glucose and HbA1c in type 2 diabetes
Authors: Yuan Yanping , Zhou Xianghai , Jia Weiping , Zhou Jian , Zhang Fan , Du Jianling , Ji Linong 
Published: February 2023

AimsFasting capillary blood glucose (FCG) and postprandial capillary blood glucose (PCG) both contribute to HbA1c in diabetes. Due to the collinearity between FCG and PCG, the HbA1c prediction model could not be developed with both FCG and PCG by linear regression. The study aimed to develop an HbA1c prediction model with both FCG and PCG to estimate HbA1c in type 2 diabetes.MethodsA total of 1,642 patients with type 2 diabetes who had at least three FCG and three PCG measurements in the past 3 months were enrolled in the study. The mean of FCG (MEANFCG) and PCG (MEANPCG) were calculated for each patient. The patients were randomized into exploratory and validation groups. The former was used for developing HbA1c prediction models and the latter for performance evaluation.ResultsThe new HbA1c prediction model using ridge regression expressed as HbA1c (%) = 0.320×MEANFCG (mmol/L) + 0.187×MEANPCG (mmol/L) + 2.979, R2 = 0.668. Compared to linear regression models developed with FCG, PCG, fasting plasma glucose (FPG), and 2-hour postprandial plasma glucose (2-h PPG), respectively, the new HbA1c prediction model showed the smallest mean square error, root mean square error, mean absolute error. The concordance correlation coefficient of the new HbA1c prediction model and the linear regression models with MEANFCG, MEANPCG, FPG or 2-h PPG were 0.810,0.773,0.749,0.715,0.672.ConclusionWe have developed a new HbA1c prediction model with both FCG and PCG, which showed better prediction ability and good agreement.
White blood cells and coronary heart disease: A mendelian randomization study
Authors: Zhao Qiuping , Liu Rongmei , Chen Hui , Yang Xiaomo , Dong Jiajia , Bai Minfu 
Published: February 2023

Background: The causal direction and magnitude of the associations between blood cell count and coronary heart disease (CHD) remain uncertain due to susceptibility of reverse causation and confounding. This study aimed to investigate the associations between blood cell count and CHD using Mendelian randomization (MR).Methods: In this two-sample MR study, we identified independent blood cell count associated genetic variants from a genome-wide association studies (GWAS) among European ancestry individuals. Summary level data of CHD was obtained from a GWAS consisting of 547261 subjects. Methods of inverse variance weighted (IVW), Mendelian Randomization-Egger (MR-Egger), weighted median, and outlier test (MR-PRESSO) were conducted to investigate the associations between blood cell and CHD.Results: Among all cardiovascular outcomes of interest, blood cell counts were only associated with CHD. Our findings indicated that white blood cell count and neutrophil cell count were significantly associated with increased risk of CHD [odds ratio (OR) = 1.07, 95% confidence interval (CI), 1.01–1.14; OR = 1.09, 1.02–1.16). However, there was no significant association between monocyte cell count, basophil cell count, lymphocyte cell count, eosinophil cell count, and CHD (p &gt; 0.05). The results after excluding outliers were consistent with main results and the sensitivity analyses showed no evidence of pleiotropy (MR-Egger intercept, p &gt; 0.05).Conclusion: Our MR study suggested that greater white blood cell count and neutrophil cell count were associated with a higher risk of CHD. Future studies are still warranted to validate the results and investigate the mechanisms underlying these associations.
iPoLNG—An unsupervised model for the integrative analysis of single-cell multiomics data
Authors: Zhang Wenyu , Lin Zhixiang 
Published: February 2023

Single-cell multiomics technologies, where the transcriptomic and epigenomic profiles are simultaneously measured in the same set of single cells, pose significant challenges for effective integrative analysis. Here, we propose an unsupervised generative model, iPoLNG, for the effective and scalable integration of single-cell multiomics data. iPoLNG reconstructs low-dimensional representations of the cells and features using computationally efficient stochastic variational inference by modelling the discrete counts in single-cell multiomics data with latent factors. The low-dimensional representation of cells enables the identification of distinct cell types, and the feature by factor loading matrices help characterize cell-type specific markers and provide rich biological insights on the functional pathway enrichment analysis. iPoLNG is also able to handle the setting of partial information where certain modality of the cells is missing. Taking advantage of GPU and probabilistic programming, iPoLNG is scalable to large datasets and it takes less than 15 min to implement on datasets with 20,000 cells.
Immunogenicity of SARS-CoV-2 mRNA intramuscular vaccination in patients with muscular disorders
Authors: Kasai Ryousuke , Funato Michinori , Maruta Kanako , Yasuda Kunihiko , Minatsu Hiroshi , Ito Junji , Takahashi Kazuhiro 
Published: February 2023

BackgroundsLittle clinical data is available on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with muscular disorders (MDs). The immunogenicity of SARS-CoV-2 vaccines against MDs, in particular, remains unknown. Thus, this study aimed to confirm the immunogenicity and safety of the SARS-CoV-2 vaccine against MDs.MethodsAll participants were vaccinated with two doses of mRNA vaccines (BNT162b2, Pfizer-BioNTech). The serum samples were collected from each patient on the day of second dose of vaccination, and then, consecutively, after one month, three months, and six months. Anti-SARS-CoV-2 IgG levels were determined using the Abbott SARS-CoV-2 IgG II Quant assay.ResultsWe evaluated 75 individuals, including 42 patients with MDs and 33 patients with non-muscular disorders (non-MDs). Non-MD patients primarily include those with severe motor and intellectual disabilities. The median age of the patients was 32 years (range 12–64 years). After one and three months following the second immunization, patients with MDs had lower antibody responses. Furthermore, three months following the second immunization, the proportion of high responders among patients with MDs decreased significantly compared to that among patients without MDs (p-value of less than 0.01). No serious adverse events were observed in patients with or without MDs.ConclusionIntensity and latency of antibody response were suppressed in patients with MDs. Although MDs may be a key contributor in predicting the antibody response to SARS-CoV-2 vaccination, SARS-CoV-2 immunization in MDs needs extensive research.
Murine scald models characterize the role of neutrophils and neutrophil extracellular traps in severe burns
Authors: Elrod Julia , Lenz Moritz , Kiwit Antonia , Armbrust Lina , Schönfeld Lavinia , Reinshagen Konrad , Pagerols Raluy Laia , Mohr Christoph , Saygi Ceren , Alawi Malik , Rohde Holger , Herrmann Martin , Boettcher Michael 
Published: February 2023

IntroductionSevere burns cause unique pathophysiological alterations especially on the immune system. A murine scald model was optimized as a basis for the understanding of immunological reactions in response to heat induced injury. The understanding of the roles of neutrophil extracellular traps (NETs) and DNases will support the development of new surgical or pharmacological strategies for the therapy of severe burns.MethodsWe studied C57BL/6 mice (n=30) and employed four scalding protocols with varying exposure times to hot water. An additional scald group with a shorter observational time was generated to reduce mortality and study the very early phase of pathophysiology. At 24h or 72h, blood was drawn and tissue (wound, liver, lung, spleen) was analyzed for the presence of NETs, oxidative stress, apoptosis, bacterial translocation, and extracellular matrix re-organization. In addition, we analyzed the transcriptome from lung and liver tissues.ResultsExposure to hot water for 7s led to significant systemic and local effects and caused considerable late mortality. Therefore, we used an observation time of 24h in this groups. To study later phases of burns (72h) an exposure time of 6s is optimal. Both conditions led to significant disorganization of collagen, increased oxidative stress, NET formation (by immunodetection of H3cit, NE, MPO), apoptosis (cC3) and alterations of the levels of DNase1 and DNase1L3. Transcriptome analysis revealed remarkable alterations in genes involved in acute phase signaling, cell cohesion, extracellular matrix organization, and immune response.ConclusionWe identified two scald models that allow the analysis of early (24h) or late (72h) severe burn effects, thereby generating reproducible and standardized scald injuries. The study elucidated the important involvement of neutrophil activity and the role of NETs in burns. Extensive transcriptome analysis characterized the acute phase and tissue remodeling pathways involved in the process of healing and may serve as crucial basis for future in-depth studies.
Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis
Authors: Zhang Le , Badai Jiayidaer , Wang Guan , Ru Xufang , Song Wenkai , You Yujie , He Jiaojiao , Huang Suna , Feng Hua , Chen Runsheng , Zhao Yi , Chen Yujie 
Published: February 2023

IntroductionCentral nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important, yet challenging to study due to disease lesion locations and other complexities.MethodsUtilizing the powerful method of spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular hemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications.ResultsOur data identified three main 3D global pseudospace-time trajectory bundles that represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex affected by experimental IVH stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH stimulation.DiscussionThese results are informative for understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injury, strategizing more effective clinical management regimens, and developing novel bioinformatics strategies for the study of other CNS diseases. The algorithm strategies used in this study are searchable via a web service (www.combio-lezhang.online/3dstivh/home).
Heat shock protein 90 inhibitor RGRN-305 potently attenuates skin inflammation
Authors: Ben Abdallah Hakim , Seeler Sabine , Bregnhøj Anne , Ghatnekar Gautam , Kristensen Lasse S. , Iversen Lars , Johansen Claus 
Published: February 2023

IntroductionChronic inflammatory skin diseases may have a profound negative impact on the quality of life. Current treatment options may be inadequate, offering an unsatisfactory response or side effects. Therefore, ongoing efforts exist to identify novel effective and safe treatments. Heat shock protein (HSP) 90 is a chaperone that promotes the activity of a wide range of client proteins including key proinflammatory molecules involved in aberrant inflammation. Recently, a proof-of-concept clinical trial of 13 patients suggested that RGRN-305 (an HSP90 inhibitor) may be an oral treatment for psoriasis. However, HSP90 inhibition may be a novel therapeutic approach extending beyond psoriasis to include multiple immune-mediated inflammatory skin diseases.MethodsThis study aimed to investigate (i) the anti-inflammatory effects and mechanisms of HSP90 inhibition and (ii) the feasibility of topical RGRN-305 administration (new route of administration) in models of inflammation elicited by 12-O-tetradecanoylphorbol-13-acetate (TPA) in primary human keratinocytes and mice (irritative dermatitis murine model).Results/DiscussionIn primary human keratinocytes stimulated with TPA, a Nanostring® nCounter gene expression assay demonstrated that HSP90 inhibition with RGRN-305 suppressed many proinflammatory genes. Furthermore, when measured by quantitative real-time polymerase chain reaction (RT-qPCR), RGRN-305 significantly reduced the gene expression of TNF, IL1B, IL6 and CXCL8. We next demonstrated that topical RGRN-305 application significantly ameliorated TPA-induced skin inflammation in mice. The increase in ear thickness (a marker of inflammation) was significantly reduced (up to 89% inhibition). In accordance, RT-qPCR of the ear tissue demonstrated that RGRN-305 robustly reduced the gene expression of proinflammatory markers (Tnf, Il1b, Il6, Il17A and Defb4). Moreover, RNA sequencing revealed that RGRN-305 mitigated TPA-induced alterations in gene expression and suppressed genes implicated in inflammation. Lastly, we discovered that the anti-inflammatory effects were mediated, at least partly, by suppressing the activity of NF-κB, ERK1/2, p38 MAPK and c-Jun signaling pathways, which are consistent with previous findings in other experimental models beyond skin inflammation. In summary, HSP90 inhibition robustly suppressed TPA-induced inflammation by targeting key proinflammatory cytokines and signaling pathways. Our findings suggest that HSP90 inhibition may be a novel mechanism of action for treating immune-mediated skin disease beyond psoriasis, and it may be a topical treatment option.
Species distribution models describe spatial variability in mesopelagic fish abundance in the Southern Ocean
Authors: Woods Briannyn L. , Van de Putte Anton P. , Hindell Mark A. , Raymond Ben , Saunders Ryan A. , Walters Andrea , Trebilco Rowan 
Published: February 2023

IntroductionMesopelagic fishes play a central role in the transfer of energy through open-ocean food webs, particularly in the Southern Ocean where they are both important predators of zooplankton and a key prey group for many higher predators. However, they are notoriously difficult to sample, which has limited our understanding of the bio-physical predictors of their abundance and spatiotemporal variability. Species distribution models can be used to help understand species’ ecological requirements by relating records of their presence or abundance to environmental data.MethodsHere, we used data from Myctobase – a new circumpolar database of mesopelagic fishes – to model patterns in abundance of eight key myctophid species (family Myctophidae) and the genus Bathylagus in the Southern Ocean south of 45°S. We developed species-specific boosted regression tree models to obtain circumpolar predictions of abundance. Average daytime and night-time summer predictions for the period 1997 to 2011 at 0 to 200m depths were generated for each species.ResultsDepth and solar position were important predictors and species were stratified in their depth distribution. For all species, except for G. nicholsi, there was an interaction between depth of capture and solar position, reflecting diel vertical migration. Other important variables included sea surface temperature, dissolved oxygen at 200 m, chlorophyll a, and sea surface height, indicating an association with water mass properties. Circumpolar patterns of abundance varied between species with some displaying affinities for oceanic regions at Antarctic latitudes (e.g., E. antarctica and Bathylagus spp.) or sub-Antarctic latitudes (e.g., K. anderssoni and P. tenisoni); and affinities for shelf regions (e.g., P. boliniand G. nicholsi).DiscussionOur findings suggest that the abundance of mesopelagic fish is influenced by diel vertical migration and meso- and sub-mesoscale oceanographic features, with the Polar Front being a major delimiting feature. Our study showed contrasting patterns in community composition with higher species diversity north of the Polar Front that might be indicative of latitudinal variability in food web structure. Our spatial analysis is an important step toward resolving what determines important habitat for mesopelagic fishes, providing foundational information for understanding shifting food web dynamics into the future.
Where does Arctic beach debris come from? Analyzing debris composition and provenance on Svalbard aided by citizen scientists
Authors: Meyer Anna Natalie , Lutz Birgit , Bergmann Melanie 
Published: February 2023

Plastic debris is ubiquitous in all ecosystems and has even reached locations that humans will hardly reach such as the deep ocean floor and the atmosphere. Research has highlighted that plastic debris is now pervasive even in remote Arctic regions. While modeling projections indicated local sources and long-distance transport as causes, empirical data about its origin and sources are scarce. Data collected by citizen scientists can increase the scale of observations, especially in such remote regions. Here, we report abundance and composition data of marine debris collected by citizen scientists on 14 remote Arctic beaches on the Spitsbergen archipelago. In addition, citizen scientists collected three large, industrial sized canvas bags (hereafter: big packs), filled with beached debris, of which composition, sources and origin were determined. A total debris mass of 1,620 kg was collected on about 38,000 m2 (total mean = 41.83 g m-2, SEM = ± 31.62). In terms of abundance, 23,000 pieces of debris were collected on 25,500 m2 (total mean = 0.37 items of debris m-2, SEM = ± 0.17). Although most items were plastic in both abundance and mass, fisheries waste, such as nets, rope, and large containers, dominated in mass (87%), and general plastics, such as packaging and plastic articles, dominated in abundance (80%). Fisheries-related debris points to local sea-based sources from vessels operating in the Arctic and nearby. General plastics could point to both land- and ship based sources, as household items are also used on ships and debris can be transported to the north via the oceans current. Overall, 1% of the items (206 out of 14,707 pieces) collected in two big packs (2017 and 2021), bore imprints or labels allowing an analysis of their origin. If the categories ‘global’ and ‘English language’ were excluded, most of identifiable items originated from Arctic states (65%), especially from Russia (32%) and Norway (16%). But almost a third of the items (30%) was of European provenance, especially from Germany (8%). Five percent originated from more distant sources (e.g. USA, China, Korea, Brazil). Global measures such as an efficient and legally binding plastic treaty with improved upstream measures and waste management are urgently needed, to lower the amount of plastic entering our environments and in turn lifting the pressure on the Arctic region and its sensitive biota.