bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of candidate genes for cleft lip ± cleft palate using murine single-cell expression data
Authors: Siewert Anna , Reiz Benedikt , Krug Carina , Heggemann Julia , Mangold Elisabeth , Dickten Henning , Ludwig Kerstin U. 
Published: April 2023

Introduction: Cleft lip ± cleft palate (CL/P) is one of the most common birth defects. Although research has identified multiple genetic risk loci for different types of CL/P (i.e., syndromic or non-syndromic forms), determining the respective causal genes and understanding the relevant functional networks remain challenging. The recent introduction of single-cell RNA sequencing (scRNA-seq) has provided novel opportunities to study gene expression patterns at cellular resolution. The aims of our study were to: (i) aggregate available scRNA-seq data from embryonic mice and provide this as a resource for the craniofacial community; and (ii) demonstrate the value of these data in terms of the investigation of the gene expression patterns of CL/P candidate genes.Methods and Results: First, two published scRNA-seq data sets from embryonic mice were re-processed, i.e., data representing the murine time period of craniofacial development: (i) facial data from embryonic day (E) E11.5; and (ii) whole embryo data from E9.5–E13.5 from the Mouse Organogenesis Cell Atlas (MOCA). Marker gene expression analyses demonstrated that at E11.5, the facial data were a high-resolution representation of the MOCA data. Using CL/P candidate gene lists, distinct groups of genes with specific expression patterns were identified. Among others we identified that a co-expression network including Irf6, Grhl3 and Tfap2a in the periderm, while it was limited to Irf6 and Tfap2a in palatal epithelia, cells of the ectodermal surface, and basal cells at the fusion zone. The analyses also demonstrated that additional CL/P candidate genes (e.g., Tpm1, Arid3b, Ctnnd1, and Wnt3) were exclusively expressed in Irf6+ facial epithelial cells (i.e., as opposed to Irf6- epithelial cells). The MOCA data set was finally used to investigate differences in expression profiles for candidate genes underlying different types of CL/P. These analyses showed that syndromic CL/P genes (syCL/P) were expressed in significantly more cell types than non-syndromic CL/P candidate genes (nsCL/P).Discussion: The present study illustrates how scRNA-seq data can empower research on craniofacial development and disease.
Correction method by introducing cloud cover forecast factor in model temperature forecast
Authors: Mei Han , Qishu Wu , Huijun Liu , Siyu Yin , Guofei Wei 
Published: April 2023

Objective temperature forecast products can achieve better forecast quality by using one-dimensional regression correction directly based on the present model temperature forecast product, and the forecast accuracy can be further improved by adding appropriate auxiliary factors. In this paper, ECMWF forecast products and ground observation data from Fujian are used to revise the surface temperature at 2 m by introducing a cloud cover forecast factor based on the model temperature forecast correction method. Analysis shows that the forecast deviation of daily maximum and minimum temperature after the revision of a single-factor forecast is obviously correlated with cloud cover. A variety of prediction schemes are designed, and the final scheme is determined through comparative testing. The following conclusions are drawn: all schemes based on cloud cover grouping can improve forecast performance, and the total cloud cover scheme is generally better than the low cloud cover scheme. There is a good positive correlation between the forecast deviation of maximum temperature and the mean total cloud cover; that is, the more cloud cover, the bigger the deviation. The minimum temperature is negatively correlated with cloud cover when the cloud cover is less than 40% and positively correlated for the rest. The absolute forecast deviations of the maximum and minimum temperatures are larger when the total cloud cover is less. Whether for Tmax or Tmin forecast, the binary regression scheme after grouping consistently showed the best performance, with the lowest MAE. The final scheme was used to forecast the maximum and minimum temperature in 2021, and most verification indicators showed improvement in most forecast periods. The forecast accuracy for the 36-h daily maximum and minimum temperature is 81.312% and 91.480%, respectively, which is 2.4%–2.6% higher than the single-factor regression scheme. The forecast skill scores (FSS) reach 0.065 and 0.086, indicating that the method can effectively improve forecast quality in a stable manner and can be used for practical forecasting.
Preferential flow in the understory soil of Hippophae rhamnoides at different stump heights
Authors: Liu Lu , Liu Xiaoyu , Yao Yunfeng , Qi Wei , Guo Yuefeng 
Published: April 2023

This study aimed to clarify the effects of stumping on preferential flow in the understory soils of Hippophae rhamnoides and to assess appropriate stumping height for optimization of preferential flow. Root properties, soil properties, and preferential flow for different H. rhamnoides stump heights (0, 10, 15, 20 cm, and no-stumping, labeled conditions S1, S2, S3, S4, and CK, respectively) were studied using in situ dye-tracing and laboratory analysis. The results showed that stumping significantly increased preferential flow development. This effect was maximized in condition S3, with dye-tracing coverage (DC) of 36.77%, maximum dye depth (MaxD) of 40.02 cm, uniform infiltration depth (Unifr) of 14.28 cm, preferential flow ratio (PFfr) of 23.85%, and length index (LI) of 96.72%. In terms of root length density (RLD), root mass density (RMD), root surface area density (RSAD), soil water content (SWC), soil total porosity (TP), mean weight diameter (MWD), and soil organic matter (SOM), the conditions were ranked S3&gt;S2&gt;S1&gt;S3&gt;CK; for root average diameter (RAD), they were ranked S3&lt;S2&lt;S1&lt;S4&lt;CK. Structural equation modeling showed that DC was affected directly by TP, MWD, and SWC and indirectly by RAD, RLD, RMD, RSAD, and SOM, explaining up to 89.1% of the variance. Thus, stumping of H. rhamnoides affected soil properties through the mechanism of root development, thereby improving preferential flow development in the soil and soil infiltration. The optimal stump height was 15 cm. These findings are critical for vegetation recovery and for prevention and control of soil erosion in feldspathic sandstone areas.
Impact of digital technology on carbon emissions: Evidence from Chinese cities
Authors: Shen Yang , Yang Zhihong , Zhang Xiuwu 
Published: April 2023

IntroductionPromoting the development of digital technology is an important step in meeting the challenge of global climate change and achieving carbon peaking and carbon neutrality goals.MethodsBased on panel data of Chinese cities from 2006 to 2020, this paper used econometrics to investigate the impact and mechanism of digital technology on carbon emissions.ResultsThe results showed that digital technology can significantly reduce carbon emission intensity and improve carbon emission efficiency. These results remained robust after changing the estimation method, adding policy omission variables, replacing core variables, and solving the endogeneity problem. Digital technology can indirectly reduce carbon emissions by promoting green technological innovation and reducing energy intensity, and it plays a significant role in the carbon emission reduction practices of carbon emission trading policies and comprehensive national big data pilot zones. The replicability, non-exclusivity, and high mobility of digital technology help to accelerate the spread of knowledge and information between different cities, which leads to a spillover effect on carbon emission reductions. Our unconditional quantile regression model results showed that digital technology’s carbon emission reduction effect continuously decreases with increases in carbon dioxide emissions.DiscussionThe results of this paper provide evidence for the potential use of digital technology in achieving the goal of carbon neutrality, which is of great significance for achieving high-quality innovation and promoting the green transformation of the economy and society.
Inflammasome signaling proteins as biomarkers of COVID-19
Authors: Hadad Roey , Keane Robert W. , de Rivero Vaccari Juan Pablo 
Published: April 2023

IntroductionOne of the main characteristics of COVID-19 is an exacerbated inflammatory response that results in cardiometabolic complications and dysfunction in the nervous system. Moreover, these complications may extend beyond the period of active SARS-CoV2 infection and even extend over a year. Thus, it is important to better understand the contribution of the inflammatory responses in COVID-19 patients, not just in the acute phase but also after the infection has subsided.MethodsWe measured the protein levels of inflammasome signaling proteins using Simple Plex microfluidics technology in patients with an active SARS-CoV2 infection and in recovered patients to determine their potential use as biomarkers of COVID-19. We carried out statistical analyses to identify which proteins were increased in COVID-19 patients with active infection and in recovered patients. The receiver operating characteristics (ROC) were calculated for each analyte to determine their potential fit as biomarkers.ResultsThe inflammasome proteins caspase-1, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), interleukin (IL)-1β and IL-18 were elevated in the plasma of patients with active infection and remained elevated after the infection was resolved for approximately 2 months after. Levels of caspase-1 and ASC continued to increase long after patients had recovered from the infection. Furthermore, when measuring biomarkers of inflammation during active infection, analyses with area under the curve (AUC) values above 0.75 indicated that caspase-1, ASC, IL-1β and IL-18 are reliable biomarkers of the inflammatory response during active COVID-19 infection. Moreover, when measuring biomarkers of inflammation after recovery from active infection, caspase-1 and ASC presented AUC values above 0.9.DiscussionThese findings indicate that inflammasome signaling proteins can be used to reliably monitor the inflammatory innate immune response in COVID-19 patients.
Combination of machine learning-based bulk and single-cell genomics reveals necroptosis-related molecular subtypes and immunological features in autism spectrum disorder
Authors: Liu Lichun , Fu Qingxian , Ding Huaili , Jiang Hua , Zhan Zhidong , Lai Yongxing 
Published: April 2023

BackgroundNecroptosis is a novel form of controlled cell death that contributes to the progression of various illnesses. Nonetheless, the function and significance of necroptosis in autism spectrum disorders (ASD) remain unknown and require further investigation.MethodsWe utilized single-nucleus RNA sequencing (snRNA-seq) data to assess the expression patterns of necroptosis in children with autism spectrum disorder (ASD) based on 159 necroptosis-related genes. We identified differentially expressed NRGs and used an unsupervised clustering approach to divide ASD children into distinct molecular subgroups. We also evaluated immunological infiltrations and immune checkpoints using the CIBERSORT algorithm. Characteristic NRGs, identified by the LASSO, RF, and SVM-RFE algorithms, were utilized to construct a risk model. Moreover, functional enrichment, immune infiltration, and CMap analysis were further explored. Additionally, external validation was performed using RT-PCR analysis.ResultsBoth snRNA-seq and bulk transcriptome data demonstrated a greater necroptosis score in ASD children. Among these cell subtypes, excitatory neurons, inhibitory neurons, and endothelials displayed the highest activity of necroptosis. Children with ASD were categorized into two subtypes of necroptosis, and subtype2 exhibited higher immune activity. Four characteristic NRGs (TICAM1, CASP1, CAPN1, and CHMP4A) identified using three machine learning algorithms could predict the onset of ASD. Nomograms, calibration curves, and decision curve analysis (DCA) based on 3-NRG have been shown to have clinical benefit in children with ASD. Furthermore, necroptosis-based riskScore was found to be positively associated with immune activation. Finally, RT-PCR demonstrated differentially expressed of these four NRGs in human peripheral blood samples.ConclusionA comprehensive identification of necroptosis may shed light on the underlying pathogenic process driving ASD onset. The classification of necroptosis subtypes and construction of a necroptosis-related risk model may yield significant insights for the individualized treatment of children with ASD.
Quantifying connectivity between mesophotic and shallow coral larvae in Okinawa Island, Japan: a quadruple nested high-resolution modeling study
Authors: Takeyasu Kimika , Uchiyama Yusuke , Mitarai Satoshi 
Published: April 2023

Coral bleaching has recently been occurring extensively across the world’s oceans, primarily because of high water temperatures. Mesophotic corals that inhabit depths of approximately 30–150 m are expected to survive bleaching events and reseed shallow water corals afterward. In Okinawa, Japan, mesophotic coral ecosystems have been reported to serve as a refuge for preserving the genotypic diversity of bleaching-sensitive corals. The connectivity of larval populations among different habitats is a key element that determines the area to be conserved in desirable coral ecosystems. Because coral larvae are largely transported passively by ambient oceanic currents, particularly in the horizontal direction, numerical ocean circulation models greatly help to quantify connectivity with detailed spatiotemporal network structures. The present study aimed to quantify the short-distance connectivity of shallow and mesophotic coral larvae in reef areas on the northwest coast of Okinawa Island. To this end, a quadruple nested high-resolution synoptic ocean model at a lateral spatial grid resolution of 50 m was developed, which was capable of realizing detailed coastal currents influenced by complex nearshore topography, and coupled with an offline 3-D Lagrangian particle-tracking model. After validating the developed model, short-distance horizontal coral connectivity across reef areas on the northwest coast was successfully evaluated. The alongshore lateral connectivity had apparent asymmetry caused by depth-dependent horizontal currents, whereas the larvae spawned at shallow and mesophotic depths were reachable to each other. Such across-depth larval dispersal was attributable to the mixed-layer depth in the spawning period, viz., the boreal spring, which approximately coincides with the boundary between shallow and mesophotic coral, leading to the intensive vertical exchange of virtual larvae.
Case report: A comatose patient with pregabalin overdose successfully treated with continuous renal replacement therapy
Authors: Nielsen Visti Torbjørn , Wijayasinghe Nelun , Høgberg Lotte Christine Groth , Bøgevig Søren 
Published: April 2023

Pregabalin (PB) overdose causes mild symptoms and coma is rarely seen unless the patient has also ingested sedatives and/or has preexisting renal disease. We present a case report of a suicide attempt with PB where the patient presented in a comatose state that was successfully treated with continuous renal replacement therapy (CRRT). Treatment of PB overdose is usually supportive.However, previous reports of PB overdose have been treated with intermittent hemodialysis (IHD) in patients with preexisting renal disease. The problem with IHD is that it is only available in specialist centers and unsuitable for unstable patients. In the following case report, the patient presented to the emergency department (ED) unconscious and hypotensive. It was thought that the patient tried to commit suicide by taking an overdose of zopiclone tablets, as empty packets of zopiclone tablets were found beside the patient. There was no effect with flumazenil treatment, so the patient was intubated, mechanically ventilated, and admitted to the intensive care unit (ICU) where inotropic support was started. Despite supportive therapy, there was no improvement in the patient’s condition. Further investigation into the patient’s medical records uncovered prescriptions of PB. Based on this finding, plasma PB levels were measured and found to be 20 times the upper limit of the therapeutic reference range. CRRT was instituted and after 6 h of treatment the patient woke up. Hospitals with ICUs often have CRRT available in their units whereas IHD is less readily available. This case report demonstrates that CRRT is an effective method for treating PB overdose in an unconscious unstable patient that was unsuitable for transfer to another hospital.
Staphylococcus aureus increases Prostaglandin E2 secretion in cow neutrophils by activating TLR2, TLR4, and NLRP3 inflammasome signaling pathways
Authors: Zhang Kai , Jia Yan , Qian Yinghong , Jiang Xueying , Zhang Shuangyi , Liu Bo , Cao Jinshan , Song Yongli , Mao Wei 
Published: April 2023

IntroductionIn clinical settings, dairy cows are often attacked by pathogenic bacteria after delivery, especially Staphylococcus aureus (S. aureus). Neutrophils have long been regarded as essential for host defense against S. aureus. Prostaglandin E2 (PGE2) can additionally be used as an inflammatory mediator in pathological conditions to promote the repair of inflammatory injuries. However, whether S. aureus can promote the accumulation of PGE2 after the infection of neutrophils in cows and its mechanism remain unclear. Lipoprotein is an important immune bioactive ingredient of S. aureus.MethodsIn this study, the changes in neutrophils were monitored in dairy cows infected with wild-type S. aureus (SA113) and an S. aureus lipoprotein-deficient strain (Δlgt); meanwhile, we established whether pattern recognition receptors mediate this process and whether S. aureus lipoproteins are necessary for causing the release of PGE2 from cow neutrophils.ResultsThe results showed that Δlgt was less effective than SA113 in inducing the production of IL-1β, IL-6, IL-8, IL-10, and PGE2 within neutrophils; furthermore, TLR2, TLR4, and NLRP3 receptors were found to mediate the inducible effect of lipoprotein on the above inflammation mediators and cytokines, which depended on MAPK and Caspase-1 signaling pathways. In addition, TLR2, TLR4, and NLRP3 inhibitors significantly inhibited PGE2 and cytokine secretion, and PGE2 was involved in the interaction of S. aureus and neutrophils in dairy cows, which could be regulated by TLR2, TLR4, and NLRP3 receptors. We also found that S. aureus was more likely to be killed by neutrophils when it lacked lipoprotein and TLR2, TLR4, and NLRP3 were involved, but PGE2 seemed to have no effect.DiscussionTaken together, these results suggest that lipoprotein is a crucial component of S. aureus in inducing cytokine secretion by neutrophils as well as killing within neutrophils, which could be accomplished by the accumulation of PGE2 by activating MAPK and the Caspase-1 signaling pathways through TLR2, TLR4, and NLRP3 receptors. These results will contribute to a better understanding of the interaction between S. aureus and host immune cells in dairy cows.
LTF induces senescence and degeneration in the meniscus via the NF-κB signaling pathway: A study based on integrated bioinformatics analysis and experimental validation
Authors: Zhang Jun , Zhu Jiayong , Zhao Boming , Nie Daibang , Wang Wang , Qi Yongjian , Chen Liaobin , Li Bin , Chen Biao 
Published: April 2023

Background: The functional integrity of the meniscus continually decreases with age, leading to meniscal degeneration and gradually developing into osteoarthritis (OA). In this study, we identified diagnostic markers and potential mechanisms of action in aging-related meniscal degeneration through bioinformatics and experimental verification.Methods: Based on the GSE98918 dataset, common differentially expressed genes (co-DEGs) were screened using differential expression analysis and the WGCNA algorithm, and enrichment analyses based on Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were further performed. Next, the co-DEGs were imported into the STRING database and Cytoscape to construct a protein‒protein interaction (PPI) network and further validated by three algorithms in cytoHubba, receiver operating characteristic (ROC) curve analysis and the external GSE45233 dataset. Moreover, the diagnostic marker lactotransferrin (LTF) was verified in rat models of senescence and replicative cellular senescence via RT‒qPCR, WB, immunohistochemistry and immunofluorescence, and then the potential molecular mechanism was explored by loss of function and overexpression of LTF.Results: According to the analysis of the GSE98918 dataset, we identified 52 co-DEGs (42 upregulated genes and 10 downregulated genes) in the OA meniscus. LTF, screened out by Cytoscape, ROC curve analysis in the GSE98918 dataset and another external GSE45233 dataset, might have good predictive power in meniscal degeneration. Our experimental results showed that LTF expression was statistically increased in the meniscal tissue of aged rats (24 months) and senescent passage 5th (P5) meniscal cells. In P5 meniscal cells, LTF knockdown inhibited the NF-κB signaling pathway and alleviated senescence. LTF overexpression in passage 0 (P0) meniscal cells increased the expression of senescence-associated secretory phenotype (SASP) and induced senescence by activating the NF-κB signaling pathway. However, the senescence phenomenon caused by LTF overexpression could be reversed by the NF-κB inhibitor pyrrolidine dithiocarbamate (PDTC).Conclusion: For the first time, we found that increased expression of LTF was observed in the aging meniscus and could induce meniscal senescence and degeneration by activating the NF-κB signaling pathway. These results revealed that LTF could be a potential diagnostic marker and therapeutic target for age-related meniscal degeneration.
The “chameleon” sellar lesions: a case report of unexpected sellar lesions
Authors: Bove Ilaria , Franca Raduan Ahmed , Ugga Lorenzo , Solari Domenico , Elefante Andrea , De Caro Maria Laura Del Basso , Cavallo Luigi Maria 
Published: April 2023

IntroductionThe sellar region and its boundaries represent a challenging area, harboring a variety of tissues of different linings. Therefore, a variety of diseases can arise or involve in this area (i.e., neoplastic or not). A total of three challenging cases of “chameleon” sellar lesions treated via EEA were described, and the lesions mimicked radiological features of common sellar masses such as craniopharyngiomas and/or pituitary adenomas, and we also report a literature review of similar cases.MethodsA retrospective analysis of three primary cases was conducted at the Università degli Studi di Napoli Federico II, Naples, Italy. Clinical information, radiological examinations, and pathology reports were illustrated.ResultsA total of three cases of so-called “chameleon” sellar lesions comprising two men and one woman were reported. Based on the intraoperative finding and pathological examination, we noticed that case 1 had suprasellar glioblastoma, case 2 had a primary neuroendocrine tumor, and case 3 had cavernous malformation.ConclusionNeurosurgeons should consider “unexpected” lesions of the sellar/suprasellar region in the preoperative differential diagnosis. A multidisciplinary approach with the collaboration of neurosurgeons, neuroradiologists, and pathologists plays a fundamental role. The recognition of unusual sellar lesions can help surgeons with better preoperative planning; so an endoscopic endonasal approach may represent a valid surgical technique to obtain decompression of the optic apparatus and vascular structures and finally a pathological diagnosis.