bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single‐cell profiling reveals the metastasis‐associated immune signature of hepatocellular carcinoma
Authors: Zhong Deyuan , Shi Ying , Ma Wenzhe , Liang Yuxin , Liu Hanjie , Qin Yingying , Zhang Lu , Yang Qinyan , Huang Xiaolun , Lu Yuanjun , Shang Jin 
Published: May 2024

AbstractAimMetastasis is the leading cause of mortality in hepatocellular carcinoma (HCC). The metastasis‐associated immune signature in HCC is worth exploring.MethodsBioinformatic analysis was conducted based on the single‐cell transcriptome data derived from HCC patients in different stages. Cellular composition, pseudotime state transition, and cell–cell interaction were further analyzed and verified.ResultsGenerally, HCC with metastasis exhibited suppressive immune microenvironment, while HCC without metastasis exhibited active immune microenvironment. Concretely, effector regulatory T cells (eTregs) were found to be enriched in HCC with metastasis. PHLDA1 was identified as one of exhaustion‐specific genes and verified to be associated with worse prognosis in HCC patients. Moreover, A novel cluster of CCR7+ dendritic cells (DCs) was identified with high expression of maturation and migration marker genes. Pseudotime analysis showed that inhibition of differentiation occurred in CCR7+ DCs rather than cDC1 in HCC with metastasis. Furthermore, interaction analysis showed that the reduction of CCR7+ DCs lead to impaired CCR7/CCL19 interaction in HCC with metastasis.ConclusionsHCC with metastasis exhibited upregulation of exhaustion‐specific genes of eTregs and inhibition of CCL signal of a novel DC cluster, which added new dimensions to the immune landscape and provided new immune therapeutic targets in advanced HCC.
Bioinformatics investigation of adaptive immune‐related genes in peri‐implantitis and periodontitis: Characteristics and diagnostic values
Authors: Yin Jingju , Fang Youran , Liao Yunyang , Chen Zhe , Liu Shaofeng , Zhu Hanghang , Song Kun , Shi Bin 
Published: May 2024

AbstractBackgroundPeri‐implantitis and periodontitis have similar immunological bioprocesses and inflammatory phenotypes. In the inflammatory process, the adaptive immune cells can drive the development of disease. This research investigated the differences and diagnostic significance of peri‐implantitis and periodontitis in adaptive immune responses.MethodsWe acquired four GEO datasets of gene expressions in surrounding tissues in healthy person, healthy implant, periodontitis, and peri‐implantitis patients. The structural characteristics and enrichment analyses of differential expression genes were examined. The adaptive immune landscapes in peri‐implantitis and periodontitis were then evaluated using single sample gene set enrichment analysis. The STRING database and Cytoscape were used to identify adaptive hub genes, and the ROC curve was used to verify them. Finally, qRT‐PCR method was used to verify the expression level of Hub gene in activated T cells on the titanium‐containing or titanium‐free culture plates.ResultsAt the transcriptome level, the data of healthy implant, peri‐implantitis and periodontitis were highly dissimilar. The peri‐implantitis and periodontitis both exhibited adaptive immune response. Except for the activated CD4+T cells, there was no significant difference in other adaptive immune cells between peri‐implantitis and periodontitis. In addition, correlation analysis showed that CD53, CYBB, and PLEK were significantly positively linked with activated CD4+T cells in the immune microenvironment of peri‐implantitis, making them effective biomarkers to differentiate it from periodontitis.ConclusionsPeri‐implantitis has a uniquely immunogenomic landscape that differs from periodontitis. This study provides new insights and ideas into the activated CD4+T cells and hub genes that underpin the immunological bioprocess of peri‐implantitis.
The development of anticyclic citrullinated peptide (anti‐CCP) antibody following severe COVID‐19
Authors: Roghani Seyed Askar , Dastbaz Mohammad , Lotfi Ramin , Shamsi Afsaneh , Abdan Zahra , Rostampour Rezvan , Soleymani Bijan , Zamanian Mohammad Hossein , Soufivand Parviz , Pournazari Mehran , Taghadosi Mahdi 
Published: May 2024

AbstractObjectivesThe dysregulated immune response is one of the cardinal features of severe coronavirus disease 2019 (COVID‐19). This study was conducted to clarify the occurrence of autoantibodies (AABs) associated with systemic autoimmune rheumatic diseases (SARDs) in hospitalized patients with a moderate, severe, and critical form of COVID‐19.MethodsThe serum samples obtained from 176 hospitalized COVID‐19 patients were investigated in this study, including patients with moderate (N = 90), severe (N = 50), and critical (N = 36) forms of COVID‐19. Also, the serum samples collected from healthy subjects before the COVID‐19 pandemic were used as controls (N = 176). The antinuclear antibodies (ANAs), antidouble‐stranded DNA (anti‐dsDNA), cytoplasmic‐anti neutrophil cytoplasmic antibody (c‐ANCA), perinuclear ANCA (p‐ANCA), antiphospholipid antibodies (aPLs), and anticyclic citrullinated peptide (anti‐CCP) occurrence was evaluated using a solid‐phase enzyme‐linked immunosorbent assay (ELISA).ResultsThe results showed that the occurrence of ANAs, anti‐dsDNA, anti‐CCP, c‐ANCA, and p‐ANCA was significantly higher in the COVID‐19 patients compared to serum obtained from healthy subjects (p < .0001, p < .0001, p < .0001, p < .05, and p < .001, respectively). The positive number of anti‐CCP tests increased significantly in severe COVID‐19 compared to the moderate group (p < .01).ConclusionOur study further supports the development of autoantibodies related to systemic autoimmune rheumatologic diseases. To the best of our knowledge, this is the first study with a large sample size that reported the occurrence of anti‐CCP in a severe form of COVID‐19.
Machine learning reveals ferroptosis features and a novel ferroptosis classifier in patients with sepsis
Authors: Chen Zhigang , Wei Shiyou , Yuan Zhize , Chang Rui , Chen Xue , Fu Yu , Wu Wei 
Published: May 2024

AbstractObjectiveSepsis is an organ malfunction disease that may become fatal and is commonly accompanied by severe complications such as multiorgan dysfunction. Patients who are already hospitalized have a high risk of death due to sepsis. Even though early diagnosis is very important, the technology and clinical approaches that are now available are inadequate. Hence, there is an immediate necessity to investigate biological markers that are sensitive, specific, and reliable for the prompt detection of sepsis to reduce mortality and improve patient prognosis. Mounting research data indicate that ferroptosis contributes to the occurrence, development, and prevention of sepsis. However, the specific regulatory mechanism of ferroptosis remains to be elucidated. This research evaluated the expression profiles of ferroptosis‐related genes (FRGs) and the diagnostic significance of the ferroptosis‐related classifiers in sepsis.Methods and ResultsWe collected three peripheral blood data sets from septic patients, integrated the clinical examination data and mRNA expression profile of these patients, and identified 13 FRGs in sepsis through a co‐expression network and differential analysis. Then, an optimal classifier tool for sepsis was constructed by integrating a variety of machine learning algorithms. Two key genes, ATG16L1 and SRC, were shown to be shared between the algorithms, and thus were identified as the FRG signature of classifier. The tool exhibited satisfactory diagnostic efficiency in the training data set (AUC = 0.711) and two external verification data sets (AUC = 0.961; AUC = 0.913). In the rat cecal ligation puncture sepsis model, in vivo experiments verified the involvement of ATG16L1 and SRC in the early sepsis process.ConclusionThese findings confirm that FRGs may participate in the development of sepsis, the ferroptosis related classifiers can provide a basis for the development of new strategies for the early diagnosis of sepsis and the discovery of new potential therapeutic targets for life‐threatening infections.
Differential expression of lymphocyte subpopulations in the peripheral blood of patients with COVID‐19: Implications for disease severity and prognosis
Authors: Xu XinQiang , Huang JunYuan , Zhang Haiqi , Lu Weiguo , Liu Jiduo 
Published: May 2024

AbstractObjectiveTo investigate the expression patterns and clinical significance of specific lymphocyte subsets in the peripheral blood of patients with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection.MethodsBetween December 2022 and February 2023, a cohort of 165 patients from the First Affiliated Hospital of Guangzhou University of Chinese Medicine were analyzed. The participants represented various stages of coronavirus infection severity: mild, moderate, severe, and critical. Additionally, 40 healthy individuals constituted the control group. The FC 500MPL flow cytometer and associated reagents for flow cytometry.ResultsCompared with the healthy control group, activated B lymphocytes witnessed a pronounced increase (p < .05). A significant decrease was observed in the levels of Breg, Cytotoxic T cells or Suppressor T‐cell (Tc/s), late‐activated T, late‐activated Th, and late‐activated Tc/s lymphocytes (p < .05). Th, initial Th, initial Tc/s, total Treg, natural Treg, induced Treg, early activated T, and early activated Th lymphocyte levels showed no significant difference (p > .05). As the disease progressed, there was an uptick in midterm activated T lymphocytes (p < .05), while Breg, T, Tc/s, senescent Tc/s, and total senescent T levels dwindled (p < .05). Noteworthy patterns emerged across different groups for B1, T‐lymphocytes, Tc/s, B2, CD8+ Treg cells, and other subsets, highlighting variance in immune responses relative to disease severity. When juxtaposed, no significant difference was found in the expression levels of lymphocyte subsets between patients who died and those deemed critically ill (p > .05).ConclusionSubsets of Treg and B‐cells could act as yardsticks for the trajectory of SARS‐CoV‐2 infection and might have potential in forecasting patient trajectories. A comprehensive evaluation of lymphocyte subsets, especially in real‐time, holds the key to discerning the clinical severity in those with COVID‐19. This becomes instrumental in monitoring treatment outcomes, tracking disease evolution, and formulating prognostications. Moreover, the results provide a deeper understanding of the cellular immune defense mechanisms against the novel coronavirus infection.
Comparison of stimulation protocols for dose determination of gonadotropins: A systematic review and Bayesian network meta‐analysis based on randomized controlled trials
Authors: Peng Yangqin , Ma Shujuan , Hu Liang , Li Yuan , Wang Xiaojuan , Xiong Yiquan , Tan Jing , Gong Fei 
Published: May 2024

AbstractBackgroundTo date, evidence regarding the effectiveness and safety of individualized controlled ovarian stimulation (COS) compared with standard dose COS has been inadequate.ObjectivesTo evaluate the updated evidence from published randomized controlled trials (RCTs) about the efficacy and safety of individualized COS with different ovarian reserve test biomarkers or clinical experience versus standard dose COS.Search StrategyTerms and descriptors related to COS, individualized or standard, and RCT were combined to search, and only English language studies were included. Conference abstracts and comments were excluded.Selection CriteriaRCTs with comparison between different individualized COS strategies and standard starting dose strategy were included.Data Collection and AnalysisTwo reviews independently assessed the eligibility of retrieved citations in a predefined standardized manner. Relative risk (RRs) and the weighted mean difference (WMD) with 95% confidence intervals (CIs) were pooled using a random‐effects model on R software version 4.2.2.Main ResultsCompared with the standard dose COS strategy in pairwise meta‐analysis, the individualized COS strategy was associated with a notable lower risk of ovarian hyperstimulation syndrome (OHSS; 174/2384 [7.30%] vs 114/2412 [4.73%], RR 0.66, 95% CI: 0.47–0.93, I2 = 46%), a significantly lower risk of hyperresponse to stimulation (hyperresponse; 476/2402 [19.82%] vs 331/2437 [13.58%], RR 0.71, 95% CI: 0.57–0.90, I2 = 61%), and a slightly longer ovarian stimulation days (duration of stimulation; WMD 0.20, 95% CI: 0.01–0.40, I2 = 66%). Bayesian network meta‐analysis also found that biomarker‐tailored strategy had a significantly lower risk of OHSS than standard dose strategy (OHSS; RR 0.63, 95% CI: 0.41–0.97, I2 = 47.5%).ConclusionCompared with standard dose COS strategy, individualized COS strategy could significantly reduce the risks of OHSS and hyperresponse to stimulation, but the duration of stimulation was slightly longer.Trial RegistrationPROSPERO: CRD42023358439.
Evaluating the use of the AMBIANCE‐Brief measure in clinical settings: Assessing acceptability, feasibility, and utility of the AMBIANCE‐Brief
Authors: Eirich Rachel , Pador Paolo , Watt Julianna , Racine Nicole , Lyons‐Ruth Karlen , Madigan Sheri 
Published: May 2024

AbstractCommunity agencies and practitioners around the globe seek opportunities to learn various assessment tools and interventions rooted in attachment theory. However, information regarding the feasibility of implementation and sustainability of these tools once participants have been trained to use them, is limited. This study investigated the perceived acceptability, feasibility, utility, relevance, fidelity, and sustainability of the Atypical Maternal Behavior Instrument for Assessment and Classification‐Brief (AMBIANCE‐Brief) among practitioners who had taken a training. Practitioners (N = 59) who attended a virtual AMBIANCE‐Brief training originating from Canada between June 2020 and November 2021 completed an online follow‐up survey. Practitioners reported that they primarily used the AMBIANCE‐Brief for case conceptualization (68%). Additionally, 95% agreed that the AMBIANCE‐Brief was relevant to their clinical practice, 98% agreed it was useful for their clinical work, 76% agreed that it was feasible to implement into their clinical work, and 59% found it easy to incorporate into their treatment planning with clients. Findings suggest that the AMBIANCE‐Brief may be acceptable, feasible, and useful for practitioners. Avenues for continuing to evaluate the AMBIANCE‐Brief include cross‐cultural validity, coder drift, and booster sessions. Additional work clarifying how practitioners integrate the measure into practice would be valuable.
Teacher vulnerability as a pedagogical tool: A comparative case study in two literacy classrooms
Authors: Lai Yi , Pacheco Mark B. , McKee Jared 
Published: May 2024

AbstractViewing teacher vulnerability as a pedagogical tool, this comparative case study examined two secondary literacy teachers' use of vulnerability in relation to various instructional goals. Through the analysis of eight video‐recorded lessons, we found that teachers demonstrated vulnerability through multiple ways within their literacy instruction through modeling ways of connecting personal experiences to texts, and establishing classroom norms that welcome difficult emotions and experiences. However, we also found that teacher vulnerability can sometimes lead to uncertainty, and even constrain student participation. We argue that teacher vulnerability helps establish a humanizing pedagogy, and offer possible strategies for teachers who are vulnerable within literacy instruction. We conclude with a discussion of different levels of appropriating vulnerability as a pedagogical tool.
Mechanistic evaluation of myristicin on apoptosis and cell cycle regulation in breast cancer cells
Authors: Sufina Nazar Sudhina , Ayyappan Janeesh Plakkal 
Published: May 2024

AbstractThe current study was focused on the anticancer activity of myristicin against MCF‐7 human breast cancer (BC) cells. BC is the most common and leading malignant disease in women worldwide. Now‐a‐days, various conventional therapies are used against BC and still represent a chief challenge because those treatments fail to differentiate normal cells from malignant cells, and they have severe side effects also. So, there is a need develop new therapies to decrease BC‐related morbidity and mortality. Myristicin, a 1‑allyl‑5‑methoxy‑3, 4‑methylenedioxybenzene, is a main active aromatic compound present in various spices, such as nutmeg, mace, carrot, cinnamon, parsely and some essential oils. Myristicin has a wide range of effects, including antitumor, antioxidative and antimicrobial activity. Nevertheless, the effects of myristicin on human BC cells remain largely unrevealed. The cytotoxicity effect of myristicin on MCF‑7 cells was increased dose dependently detected by (4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide and Lactate Dehydrogenase assays. Myristicin was found to be significantly inducing the cell apoptosis, as compared to control, using acridine orange/ethidium bromide, Hoechst stain and annexin V. Moreover, it activates cell antimigration, intracellular reactive oxygen species generation and cell cycle arrest in the G1/S phase. In addition, myristicin induces the expression of apoptosis and cell cycle genes (Caspases8, Bax, Bid, Bcl2, PARP, p53, and Cdk1) was demonstrated by quantitative polymerase chain reaction and apoptosis proteins (c‐PARP, Caspase 9, Cytochrome C, PDI) expression was also analyzed with western blot. Overall, we illustrated that myristicin could regulate apoptosis signaling pathways in MCF‐7 BC cells.
A self‐determination theory perspective on the relationship between emotion regulation styles, mindfulness facets, and well‐being in adults with self‐injury
Authors: Petrovic Julia , Mills Devin J. , Heath Nancy L. 
Published: May 2024

AbstractBackgroundThe relevance of emotion regulation (ER) difficulties to nonsuicidal self‐injury (NSSI; the deliberate destruction of one's bodily tissue without suicidal intent) has been repeatedly documented. Recently, specific mindfulness facets (i.e., awareness, nonjudging, describing) have been proposed as mechanisms that explain this relationship. The present study sought to extend this line of inquiry by exploring the mediating role of mindfulness facets in the relation between self‐determination theory‐based ER styles (i.e., integrative ER, suppressive ER, emotion dysregulation) and indices of positive and negative well‐being (i.e., subjective vitality, NSSI difficulties), while controlling for gender, in adults with recent NSSI engagement.MethodsUS adults with a history of more than one occurrence of NSSI within the last year (n = 222) completed online measures of ER styles, mindfulness facets, subjective vitality, and NSSI difficulties.ResultsA mediation model indicated that the effects of ER styles on positive and negative well‐being were explained by specific mindfulness facets (i.e., awareness, nonjudging, nonreactivity, describing).ConclusionsThe present study provides preliminary evidence that facets of dispositional mindfulness may be mechanisms through which ER styles impact positive and negative indices of well‐being in adults with lived experience of NSSI.
Phylogenetics, subspecies, and conservation of the eastern pinesnake
Authors: Krohn Alexander R. , Apodaca Joseph J. , Collins Louisa , Hudson Bryan D. , Barrett Kyle 
Published: May 2024

AbstractWhether or where to draw subspecies' taxonomic boundaries is much more than an esoteric argument. Subspecific taxonomies and associated geographic ranges have important conservation and management implications because the Endangered Species Act (ESA) protects distinct populations segments below the species level. Genomic data can help resolve taxonomic disputes and assist with conservation policy; however, because subspecific lineages often exhibit gene flow, genomic lineages for subspecific taxa are rarely distinct. We used genomic data from the eastern pinesnake (Pituophis melanoleucus) to determine the geographic range of the morphologically variable Florida pinesnake (P. m. mugitus), which is petitioned for listing under the ESA. The overall genomic pattern of the eastern pinesnake is one of admixture, and there are gradual differences over the wide range of the species. But there still are discernable areas of genetic differentiation that correspond to the morphologically defined Florida pinesnake, and other subspecies. This pattern of admixture should be expected for subspecies. We propose that boundaries for the Florida pinesnake should maximize the species redundancy, resilience, and representation based on genomic data. We also propose best practices for managers and policymakers interpreting genomic data of subspecies, given that the genomic cutoffs will rarely be truly distinct.
Unveiling differential thermal sensitivities in marine phytoplankton within the China Seas
Authors: Wang Changyun , Cai Shujie , Tong Zhuyin , Chen Jixin , Lin Lizhen , Xiao Wupeng , Liu Xin , Huang Bangqin 
Published: May 2024

AbstractIn this study, we explored the realized thermal sensitivities of various phytoplankton groups in natural seawater, a crucial aspect for understanding the dynamics of marine ecosystems under climate change. Utilizing a decadal pigment dataset (2002–2015) from China Seas and employing generalized additive mixed models coupled with maximum entropy modeling, we discerned thermal sensitivity differentiations among nine phytoplankton groups, encompassing the full‐size spectrum. Our findings revealed that cryptophytes were exceptionally thermally sensitive, with a strong correlation between temperature changes and biomass variance. Characterized by a preference for cooler waters, cryptophytes had a low mean temperature niche and a narrow niche breadth. Notably, they exhibited the lowest temperature tipping point, highlighting their heightened vulnerability to warming trends. These findings underscored the significance of cryptophytes, an often‐overlooked group, in understanding ecosystem responses to climate shifts, and emphasized their potential role as key indicators in marine ecological studies under global warming.
Enhanced Spontaneous Emission through High‐k Modes in CsPbBr3 Perovskite Hyperbolic Metamaterials
Authors: Caligiuri Vincenzo , Siprova Svetlana , Godbert Nicolas , Moccia Massimo , Biffi Giulia , Termine Roberto , Balestra Gianluca , Cuscunà Massimo , Amoruso Maria Laura , Scuderi Mario , Galdi Vincenzo , Golemme Attilio , Aiello Iolinda , De Luca Antonio 
Published: May 2024

AbstractNovel optical sources require fast decay rates, making hyperbolic metamaterials (HMMs) an increasingly attractive option. HMMs are well‐known for their remarkable anisotropy, and leverage hyperbolic dispersion to enhance the decay rate of a fluorophore placed on top of them. This study tackles the complex task of embedding a fluorophore into an HMM, successfully overcoming challenges related to surface roughness, thickness imperfections, and layer washing effects. Specifically, CsPbBr3 perovskite nanocrystals (NCs)‐based HMM are fabricated, by alternating silver/nanocrystals (Ag/NCs) layers. Through a systematic investigation of the photophysical response following the deposition of each bilayer, compelling evidence of the achievement of hyperbolic dispersion is provided. Specifically, the impact of “high‐k” modes is isolated, which is distinctive to the HMM architecture. Therefore, the longstanding debate regarding the number of bilayers needed to achieve hyperbolic dispersion is conclusively resolved. The research demonstrates a nearly twofold increase in the decay rate and a threefold enhancement in photoluminescence intensity. These findings are further supported by theoretical Purcell factor calculations. This study marks a pioneering advancement in the field of bulk dye‐embedded HMMs, laying the groundwork for the development of advanced optical sources such as “resonant gain HMMs”.