bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of lactate metabolism-related LncRNAs in the prognosis, mutation, and tumor microenvironment of papillary thyroid cancer
Authors: Xia Minqi , Wang Shuo , Wang Li , Mei Yingna , Tu Yi , Gao Ling 
Published: March 2023

BackgroundLactate, a byproduct of glucose metabolism, is primarily utilized for gluconeogenesis and numerous cellular and organismal life processes. Interestingly, many studies have demonstrated a correlation between lactate metabolism and tumor development. However, the relationship between long non-coding RNAs (lncRNAs) and lactate metabolism in papillary thyroid cancer (PTC) remains to be explored.MethodsLactate metabolism-related lncRNAs (LRLs) were obtained by differential expression and correlation analyses, and the risk model was further constructed by least absolute shrinkage and selection operator analysis (Lasso) and Cox analysis. Clinical, immune, tumor mutation, and enrichment analyses were performed based on the risk model. The expression level of six LRLs was tested using RT-PCR.ResultsThis study found several lncRNAs linked to lactate metabolism in both The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) datasets. Using Cox regression analysis, 303 lactate LRLs were found to be substantially associated with prognosis. Lasso was done on the TCGA cohort. Six LRLs were identified as independent predictive indicators for the development of a PTC prognostic risk model. The cohort was separated into two groups based on the median risk score (0.39717 -0.39771). Subsequently, Kaplan-Meier survival analysis and multivariate Cox regression analysis revealed that the high-risk group had a lower survival probability and that the risk score was an independent predictive factor of prognosis. In addition, a nomogram that can easily predict the 1-, 3-, and 5-year survival rates of PTC patients was established. Furthermore, the association between PTC prognostic factors and tumor microenvironment (TME), immune escape, as well as tumor somatic mutation status was investigated in high- and low-risk groups. Lastly, gene expression analysis was used to confirm the differential expression levels of the six LRLs.ConclusionIn conclusion, we have constructed a prognostic model that can predict the prognosis, mutation status, and TME of PTC patients. The model may have great clinical significance in the comprehensive evaluation of PTC patients.
Genetic causal relationship between age at menarche and benign oesophageal neoplasia identified by a Mendelian randomization study
Authors: Su Yani , Hu Yunfeng , Xu Yiwei , Yang Mingyi , Wu Fangcai , Peng Yuhui 
Published: March 2023

ObjectiveThe occurrence and development of oesophageal neoplasia (ON) is closely related to hormone changes. The aim of this study was to investigate the causal relationships between age at menarche (AAMA) or age at menopause (AAMO) and benign oesophageal neoplasia (BON) or malignant oesophageal neoplasia (MON) from a genetic perspective.MethodsGenome-wide association study (GWAS) summary data of exposures (AAMA and AAMO) and outcomes (BON and MON) were obtained from the IEU OpenGWAS database. We performed a two-sample Mendelian randomization (MR) study between them. The inverse variance weighted (IVW) was used as the main analysis method, while the MR Egger, weighted median, simple mode, and weighted mode were supplementary methods. The maximum likelihood, penalized weighted median, and IVW (fixed effects) were validation methods. We used Cochran’s Q statistic and Rucker’s Q statistic to detect heterogeneity. The intercept test of the MR Egger and global test of MR pleiotropy residual sum and outlier (MR-PRESSO) were used to detect horizontal pleiotropy, and the distortion test of the MR-PRESSO analysis was used to detect outliers. The leave-one-out analysis was used to detect whether the MR analysis was affected by single nucleotide polymorphisms (SNPs). In addition, the MR robust adjusted profile score (MR-RAPS) method was used to assess the robustness of MR analysis.ResultsThe random-effects IVW results showed that AAMA had a negative genetic causal relationship with BON (odds ratio [OR] = 0.285 [95% confidence interval [CI]: 0.130-0.623], P = 0.002). The weighted median, maximum likelihood, penalized weighted median, and IVW (fixed effects) were consistent with random-effects IVW (P &lt; 0.05). The MR Egger, simple mode and weighted mode results showed that AAMA had no genetic causal relationship with BON (P &gt; 0.05). However, there were no causal genetic relationships between AAMA and MON (OR = 1.132 [95%CI: 0.621-2.063], P = 0.685), AAMO and BON (OR = 0.989 [95%CI: 0.755-1.296], P = 0.935), or AAMO and MON (OR = 1.129 [95%CI: 0.938-1.359], P = 0.200). The MR Egger, weighted median, simple mode, weighted mode, maximum likelihood, penalized weighted median, and IVW (fixed effects) were consistent with a random-effects IVW (P &gt; 0.05). MR analysis results showed no heterogeneity, the horizontal pleiotropy and outliers (P &gt; 0.05). They were not driven by a single SNP, and were normally distributed (P &gt; 0.05).ConclusionOnly AAMA has a negative genetic causal relationship with BON, and no genetic causal relationships exist between AAMA and MON, AAMO and BON, or AAMO and MON. However, it cannot be ruled out that they are related at other levels besides genetics.
Single-cell mapping of N6-methyladenosine in esophageal squamous cell carcinoma and exploration of the risk model for immune infiltration
Authors: Nie Yuanliu , Yao Guangyue , Xu Xiaoying , Liu Yi , Yin Ke , Lai Jingjiang , Li Qiang , Zhou Fengge , Yang Zhe 
Published: March 2023

BackgroundN6-methyladenosine (m6A) modification is the most common RNA modification, but its potential role in the development of esophageal cancer and its specific mechanisms still need to be further investigated.MethodsBulk RNA-seq of 174 patients with esophageal squamous carcinoma from the TCGA-ESCC cohort, GSE53625, and single-cell sequencing data from patients with esophageal squamous carcinoma from GSE188900 were included in this study. Single-cell analysis of scRNA-seq data from GSE188900 of 4 esophageal squamous carcinoma samples and calculation of PROGENy scores. Demonstrate the scoring of tumor-associated pathways for different cell populations. Cell Chat was calculated for cell populations. thereafter, m6A-related differential genes were sought and risk models were constructed to analyze the relevant biological functions and impact pathways of potential m6A genes and their impact on immune infiltration and tumor treatment sensitivity in ESCC was investigated.ResultsBy umap downscaling analysis, ESCC single-cell data were labelled into clusters of seven immune cell classes. Cellchat analysis showed that the network interactions of four signaling pathways, MIF, AFF, FN1 and CD99, all showed different cell type interactions. The prognostic risk model constructed by screening for m6A-related differential genes was of significant value in the prognostic stratification of ESCC patients and had a significant impact on immune infiltration and chemotherapy sensitivity in ESCC patients.ConclusionIn our study, we explored a blueprint for the distribution of single cells in ESCC based on m6A methylation and constructed a risk model for immune infiltration analysis and tumor efficacy stratification in ESCC on this basis. This may provide important potential guidance for revealing the role of m6A in immune escape and treatment resistance in esophageal cancer.
Experimental investigation on microlayer behavior and bubble growth based on laser interferometric method
Authors: Wang Ji , Wang Hongbin , Xiong Jinbiao 
Published: March 2023

High-speed laser interferometry is synchronized with a high-speed camera to visualize the dynamic microlayer behavior during bubble growth in a pool boiling under pressures from 0.1 to 0.3 MPa. An Indium–Tin-Oxide (ITO) film coated on sapphire is employed as the heating unit to provide the nominal surface heat fluxes in the range from 90 to 150 kW/m2. Based on the instantaneous microlayer thickness and photographed bubble images, microlayer formation and depletion and their relationship with bubble growth are analyzed. Appreciable effects of pressure on microlayer dynamics and bubble growth have been observed. At higher pressure, the microlayer existence time decreases and consequently, the contribution of the microlayer evaporation becomes less important. At elevated pressure, the effects of liquid subcooling and surface heat flux on bubble growth become more pronounced. The dimensionless instantaneous maximum microlayer thickness, δmax/√vt, shows exponential dependence on the ratio rd/rb,1 which increases linearly with time before the microlayer depletion. A correlation is proposed to predict the instantaneous maximum microlayer thickness synthesizing the two relations. The local heat flux will be overestimated and the wall temperature profile is contrary to the experimental observation when the flow inside the microlayer is negligible. During the bubble growth period, only part of the microlayer is evaporated and the internal flow inside cannot be neglected.
Activation of peroxymonosulfate by cow manure biochar@1T-MoS2 for enhancing degradation of dimethyl phthalate: Performance and mechanism
Authors: He Yutian , Wang Xinzhi , Ke Yuhan , Qiu Yiquan , Zhou Qiao , Shen Zheyu , Xie Han , Li Yingqiang , Huang Mingzhi 
Published: March 2023

Introduction: Dimethyl phthalate (DMP) which has been widely detected in water is neurotoxic to humans and should be effectively eliminated. Persulfate-based advanced oxidation processes are considered to be reliable methods aiming at emerging contaminants degradation, while an efficient catalyst is urgently needed for the activation of the reaction. As a typical 2D material, 1T-MoS2 is expected to be applied to the activation of persulfate owing to its abundant active sites and excellent electrical conductivity. In practical applications, 1T-MoS2 has the phenomenon of reunion which affects the exposure of its catalytic sites.Methods: Therefore, in this study, we used waste cow manure as a raw material to prepare biochar and achieved high exposure of 1T-MoS2 activation sites by loading 1T-MoS2 onto the surface of cow manure biochar through hydrothermal synthesis. The prepared composite catalytic material CMB@1T-MoS2 was used to activate PMS for the degradation of DMP.Results: It was found that CMB@1T-MoS2 has better effect than CMB or 1T-MoS2 alone for the degradation of DMP, reaching 77.65% at pH = 3. Under alkaline conditions, the degradation rate of DMP was reduced due to the inhibition of the catalytic process. Among the different coexisting anions, HCO-3 interfered and inhibited the degradation process the most, leading to the lowest degradation rate of DMP with 42.45%.Discussion: The quenching experiments and EPR analysis showed that SO-4• and •OH were the main ROS in the CMB@1T-MoS2/PMS process. This study promotes the resourceful use of cow manure and is expected to provide a novel persulfate-based advanced oxidation process catalyzed by CMB@1T-MoS2 for the elimination of DMP in an aqueous environment.
Combination of ozone-based advanced oxidation process and nanobubbles generation toward textile wastewater recovery
Authors: Hutagalung Sutrisno Salomo , Rafryanto Ande Fudja , Sun Wei , Juliasih Nurochma , Aditia Sri , Jiang Jizhou , Arramel  , Dipojono Hermawan Kresno , Suhardi Sri Harjati , Rochman Nurul Taufiqu , Kurniadi Deddy 
Published: March 2023

The intricate nature of various textile manufacturing processes introduces colored dyes, surfactants, and toxic chemicals that have been harmful to ecosystems in recent years. Here, a combination ozone-based advanced oxidation process (AOP) is coupled with a nanobubbles generator for the generation of ozone nanobubbles (NB) utilized the same to treat the primary effluent acquired from textile wastewaters. Here we find several key parameters such as chemical oxygen demand ammonia content (NH3), and total suspended solids indicating a substantial recovery in which the respective percentages of 81.1%, 30.81%, and 41.98%, upon 300 min residence time are achieved. On the other hand, the pH is shifted from 7.93 to 7.46, indicating the generation of hydrogen peroxide (H2O2) due to the termination reaction and the self-reaction of reactive oxygen species (ROS). We propose that the reactive oxygen species can be identified from the negative zeta potential measurement (−22.43 ± 0.34 mV) collected in the final state of treatment. The combined method has successfully generated ozone nanobubbles with 99.94% of size distributed in 216.9 nm. This highlights that enhancement of ozone’s reactivity plays a crucial role in improving the water quality of textile wastewater towards being technologically efficient to date.
Characterizing a rare neurogenetic disease, SLC13A5 citrate transporter disorder, utilizing clinical data in a cloud-based medical record collection system
Authors: Spelbrink Emily M. , Brown Tanya L. , Brimble Elise , Blanco Kirsten A. , Nye Kimberly L. , Porter Brenda E. 
Published: March 2023

Introduction: SLC13A5 citrate transporter disorder is a rare autosomal recessive genetic disease that has a constellation of neurologic symptoms. To better characterize the neurologic and clinical laboratory phenotype, we utilized patient medical records collected by Ciitizen, an Invitae company, with support from the TESS Research Foundation.Methods: Medical records for 15 patients with a suspected genetic and clinical diagnosis of SLC13A5 citrate transporter disorder were collected by Ciitizen, an Invitae company. Genotype, clinical phenotypes, and laboratory data were extracted and analyzed.Results: The 15 patients reported all had epilepsy and global developmental delay. Patients continued to attain motor milestones, though much later than their typically developing peers. Clinical diagnoses support abnormalities in communication, and low or mixed tone with several movement disorders, including, ataxia and dystonia. Serum citrate was elevated in the 3 patients in whom it was measured; other routine laboratory studies assessing renal, liver and blood function had normal values or no consistent abnormalities. Many electroencephalograms (EEGs) were performed (1 to 35 per patient), and most but not all were abnormal, with slowing and/or epileptiform activity. Fourteen of the patients had one or more brain magnetic resonance imaging (MRI) reports: 7 patients had at least one normal brain MRI, but not with any consistent findings except white matter signal changes.Discussion: These results show that in addition to the epilepsy phenotype, SLC13A5 citrate transporter disorder impacts global development, with marked abnormalities in motor abilities, tone, coordination, and communication skills. Further, utilizing cloud-based medical records allows industry, academic, and patient advocacy group collaboration to provide preliminary characterization of a rare genetic disorder. Additional characterization of the neurologic phenotype will be critical to future study and developing treatment for this and related rare genetic disorders.
Case report: Gene mutation analysis and skin imaging of isolated café-au-lait macules
Authors: Zhong Zhenyu , Yang Tianhui , Liu Siqi , Wang Shan , Zhou Shan , Du Shuli , Zheng Liyun , Wang Xiuli , Wang Hui , Wang Yifan , Gao Min 
Published: March 2023

Background: Café-au-lait macules (CALMs) are common birthmarks associated with several genetic syndromes, such as neurofibromatosis type 1 (NF1). Isolated CALMs are defined as multiple café-au-lait macules in patients without any other sign of NF1. Typical CALMs can have predictive significance for NF1, and non-invasive techniques can provide more accurate results for judging whether café-au-lait spots are typical.Objectives: The study aimed to investigate gene mutations in six Chinese Han pedigrees of isolated CALMs and summarize the characteristics of CALMs under dermoscopy and reflectance confocal microscopy (RCM).Methods: In this study, we used Sanger sequencing to test for genetic mutations in six families and whole exome sequencing (WES) in two families. We used dermoscopy and RCM to describe the imaging characteristics of CALMs.Results: In this study, we tested six families for genetic mutations, and two mutations were identified as novel mutations. The first family identified [NC_000017.11(NM_001042492.2):c.7355G&gt;A]. The second family identified [NC_000017.11(NM_001042492.2):c.2739_2740del]. According to genotype-phenotype correlation analyses, proband with frameshift mutation tended to have a larger number of CALMs and a higher rate of having atypical CALMs. Dermoscopy showed uniform and consistent tan-pigmented network patches with poorly defined margins with a lighter color around the hair follicles. Under RCM, the appearance of NF1 comprised the increased pigment granules in the basal layer and significantly increased refraction.Conclusion: A new heterozygous mutation and a new frameshift mutation of NF1 were reported. This article can assist in summarizing the properties of dermoscopy and RCM with CALMs.
SOCS3 as a potential driver of lung metastasis in colon cancer patients
Authors: Li Xuejie , Yang Zuyi , Chen Bi , Gu Lei , Tian Guoyan , Sui Xinbing 
Published: March 2023

BackgroundThe suppressor of cytokine signaling 3 (SOCS3) is the negative feedback regulator of the JAK-STAT signaling pathway. The purpose of our study was to investigate the SOCS3 status in colon primary tumor and lung metastasis and its relationship with macrophages.MethodsThe SOCS3 expression pattern and its relationship with the immune response in pan-cancer was investigated using multiple methods. Samples and corresponding clinical information of 32 colon cancer patients with lung metastasis were collected, and the CD68, CD163, and SOCS3 status were conducted using immunohistochemistry (IHC). The relationship between SOCS3 status and macrophage markers was analyzed. Besides, we explored the molecular mechanisms of SOCS3 in lung metastasis via the TCGA database.ResultsHigh SOCS3 expression was more inclined to poor prognosis and was positively correlated with main immune cell infiltration in almost each cancer type, especially in colon cancer. Compared with the colon primary tumor, lung metastasis harbored higher CD163 and SOCS3 expression, and high SOCS3 expression was more likely to be associated with high CD163 expression in lung metastasis. Besides, the exceptional differentially expressed genes in lung metastasis significantly enriched in immune responses and regulations.ConclusionsSOCS3 possessed value as a prognostic marker and target for immunotherapeutic intervention in different tumors and might be a potential target of tumor progression and tumor immunotherapy in colon cancer.
Active regression model for clinical grading of COVID-19
Authors: Sh Yuan , Dong Jierong , Chen Zhongqing , Yuan Meiqing , Lyu Lingna , Zhang Xiuli 
Published: March 2023

BackgroundIn the therapeutic process of COVID-19, the majority of indicators that physicians have for assisting treatment have come from clinical tests represented by proteins, metabolites, and immune levels in patients’ blood. Therefore, this study constructs an individualized treatment model based on deep learning methods, aiming to realize timely intervention based on clinical test indicator data of COVID-19 patients and provide an important theoretical basis for optimizing medical resource allocation.MethodsThis study collected clinical data from a total of 1,799 individuals, including 560 controls for non-respiratory infectious diseases (Negative), 681 controls for other respiratory virus infections (Other), and 558 coronavirus infections (Positive) for COVID-19. We first used the Student T-test to screen for statistically significant differences (Pvalue&lt;0.05); we then used the Adaptive-Lasso method stepwise regression to screen the characteristic variables and filter the features with low importance; we then used analysis of covariance to calculate the correlation between variables and filter the highly correlated features; and finally, we analyzed the feature contribution and screened the best combination of features.ResultsFeature engineering reduced the feature set to 13 feature combinations. The correlation coefficient between the projected results of the artificial intelligence-based individualized diagnostic model and the fitted curve of the actual values in the test group was 0.9449 which could be applied to the clinical prognosis of COVID-19. In addition, the depletion of platelets in patients with COVID-19 is an important factor affecting their severe deterioration. With the progression of COVID-19, there is a slight decrease in the total number of platelets in the patient’s body, particularly as the volume of larger platelets sharply decreases. The importance of plateletCV (count*mean platelet volume) in evaluating the severity of COVID-19 patients is higher than the count of platelets and mean platelet volume.ConclusionIn general, we found that for patients with COVID-19, the increase in mean platelet volume was a predictor for SARS-Cov-2. The rapid decrease of platelet volume and the decrease of total platelet volume are dangerous signals for the aggravation of SARS-Cov-2 infection. The analysis and modeling results of this study provide a new perspective for individualized accurate diagnosis and treatment of clinical COVID-19 patients.
Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio
Authors: Deblais Loic , Jang Hyein , Kauffman Mike , Gangiredla Jayanthi , Sawyer Marianne , Basa Saritha , Poelstra Jelmer W. , Babu Uma S. , Harrison Lisa M. , Hiett Kelli L. , Balan Kannan V. , Rajashekara Gireesh 
Published: March 2023

IntroductionWith more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States.MethodsThe goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020.ResultsA total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3’-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%).Discussion/ConclusionOur study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.