bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key molecules associated with thyroid carcinoma prognosis: A study based on transcriptome sequencing and GEO datasets
Authors: Bai Miaoyu , Ke Shanjia , Yu Hongjun , Xu Yanan , Yu Yue , Lu Shounan , Wang Chaoqun , Huang Jingjing , Ma Yong , Dai Wenjie , Wu Yaohua 
Published: August 2022

BackgroundThyroid carcinoma (THCA) has a low mortality rate, but its incidence has been rising over the years. We need to pay attention to its progression and prognosis. In this study, a transcriptome sequencing analysis and bioinformatics methods were used to screen key genes associated with THCA development and analyse their clinical significance and diagnostic value.MethodsWe collected 10 pairs of THCA tissues and noncancerous tissues, these samples were used for transcriptome sequencing to identify disordered genes. The gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database. Comprehensive analysis of thyroid clinicopathological data using The Cancer Genome Atlas (TCGA). R software was used to carry out background correction, normalization and log2 conversion. We used quantitative real-time PCR (qRT–PCR) and Western blot to determine differentially expressed genes (DEGs) expression in samples. We integrated the DEGs expression, clinical features and progression-free interval (PFI). The related functions and immune infiltration degree were established by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and single-sample Gene Set Enrichment Analysis (ssGSEA). The UALCAN database was used to analyse the methylation level.ResultsWe evaluated DEGs between normal tissue and cancer. Three genes were identified: regulator of G protein signaling 8 (RGS8), diacylglycerol kinase iota (DGKI) and oculocutaneous albinism II (OCA2). The mRNA and protein expression levels of RGS8, DGKI and OCA2 in normal tissues were higher than those in THCA tissues. Better survival outcomes were associated with higher expression of RGS8 (HR=0.38, P=0.001), DGKI (HR=0.52, P=0.022), and OCA2 (HR=0.41, P=0.003). The GO analysis, KEGG analysis and GSEA proved that the coexpressed genes of RGS8, DGKI and OCA2 were related to thyroid hormone production and peripheral downstream signal transduction effects. The expression levels of RGS8, DGKI and OCA2 were linked to the infiltration of immune cells such as DC cells. The DNA methylation level of OCA2 in cancer tissues was higher than that in the normal samples.ConclusionsRGS8, DGKI and OCA2 might be promising prognostic molecular markers in patients with THCA and reveal the clinical significance of RGS8, DGKI and OCA2 in THCA.
The gene expression profile of the glucocorticoid receptor 1 (gr1) but not gr2 is modulated in mucosal tissues of gilthead sea bream (Sparus aurata) exposed to acute air-exposure stress
Authors: Vallejos-Vidal Eva , Sanz-Milián Beatriz , Teles Mariana , Reyes-Cerpa Sebastián , Mancera Juan Miguel , Tort Lluis , Reyes-López Felipe E. 
Published: August 2022

The perception of an acute stressor (short-duration; high-intensity) induces a physiological response that activates the hypothalamic-pituitary-interrenal (HPI) axis and the subsequent release of cortisol. Cortisol carries out its effect at the molecular level through its recognition by the mineralocorticoid receptor (MR) and the glucocorticoid receptor (GR). Recently, we unveiled the nucleotide sequence of the glucocorticoid receptor 1 (gr1) and gr2 in gilthead sea bream (Sparus aurata). Importantly, GR1 and GR2 respond to different levels of cortisol concentration in fish and, consequently, play a differential role in the stress response. To date, and despite their relevance, no data describes the modulation of these receptors in response to an acute stressor in gilthead sea bream (S. aurata). In this study, we evaluated the kinetics of modulation of cortisol receptors expression (gr1, gr2, mr), and its similarity with the expression pattern of selected genes associated with stress (hsp70; enolase) and immune response (lysozyme; c3; il-1β; tnf-α; il-10; tgf-β1) in gilthead sea bream mucosal tissues (skin; gills; anterior gut). To do it, fish were acutely stressed by three-minute air exposure, and the expression profile was evaluated at zero, 1 h, 6 h, and 24 h post-stress (hps). The cortisol level in plasma and skin mucus peaked at 1 hps. All the mucosal tissues showed a time-dependent and tissue-specific upregulation of gr1 and mr. The immune-related genes showed the upregulation of il-1β at 6 hps (gills; anterior gut), and tnf-α and c3 at 24 hps (anterior gut). Taking together, our study concludes that fish subjected to three-minute air exposure modulated the expression of gr1 but not gr2 in mucosal tissues (skin; gills; anterior gut). Furthermore, our data reinforce the idea of a stimulatory effect induced in genes associated with the innate immune response after acute stress but focused at the mucosal level and in a time- and tissue-dependent manner.
Response of soil carbon fractions and enzyme activities to mowing management on in a coastal wetland of the yellow river delta
Authors: Cui Qian , Yang Hongjun , Wang Guangmei , Ma Jinzhao , Feng Lu , Liu Jingtao 
Published: August 2022

Coastal wetlands are considered as important “blue carbon” sink, and mowing management induced by anthropogenic activities is anticipated to profoundly affect soil carbon stocks in coastal wetlands. However, the impacts of mowing management on soil organic carbon (SOC) and enzyme activities and the mechanisms responsible for associated changes in Phragmites australis wetland remain uncertain. We conducted a field mowing manipulation experiment [control (CK), mowing and returning straw in December (12MS), mowing and removing straw in December (12MR), mowing and returning straw in March (3MS), and mowing and removing straw in March (3MR)] in P. australis wetland of the Yellow River Delta and quantified their impacts on soil quality, SOC, SOC fractions, and enzyme activities. Results showed that mowing treatments led to overall increases in soil nutrients [total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+, and NO3−] and decreases in soil C/N ratio. The effects of mowing treatments on soil nutrient content were pronounced on topsoil than deep soil, and the maximum value of TC, TN, and TP reached in the 12MR treatment. Compared with CK, the 12MS, 12MR, 3MS, and 3MR treatments at 0–10 cm depth significantly enhanced SOC content by 8.78%, 32.9%, 16.5%, and 30.1%, respectively, but only the 3MS treatment enhanced SOC by 16.5% at 10–20 cm depth. Mowing treatments increased dissolved organic carbon (DOC), microbial biomass carbon (MBC), particulate organic carbon (POC), and labile organic carbon (LOC) and the contents of DOC, MBC, POC, and LOC decreased with soil depth. Mowing treatments stimulated the activities of sucrase and urease in topsoil, but only the 3MR treatment improved alkaline phosphatase activity in topsoil. Path analysis indicated that mowing management dominantly modulates SOC by changing sucrase activity, alkaline phosphatase activity, TN, TP, NH4+, NO3−, DOC, and LOC in 0–10 cm depth. However, SOC was significantly controlled by sucrase activity, urease activity, TC, TN, TP, LOC, and POC in 10–20 cm depth. Collectively, our results indicate that the continuous mowing management is beneficial to enhance soil quality and carbon storage capacity of P. australis wetlands, which will contribute to enhance carbon sequestration and sink capacity of coastal wetlands.
Safety and anterior chamber structure of evolution implantable Collamer lens implantation with short white-to-white corneal diameters
Authors: Chen Xun , Chen Fang , Wang Xuanqi , Xu Yilin , Cheng Mingrui , Han Tian , Wang Xiaoying , Zhou Xingtao 
Published: August 2022

IntroductionTo evaluate the safety and anterior chamber structure of implantation of the Evolution (EVO) implantable Collamer lens (EVO-ICL) in patients with short white-to-white (WTW) corneal diameters.Materials and methodsThe study population was divided into two groups: the experimental group (34 eyes of 34 patients) with WTW corneal diameters of ≤10.6 mm and the control group (59 eyes of 59 patients) with WTW corneal diameters of &gt;10.6 mm. The outcome measures included uncorrected distance visual acuity, corrected distance visual acuity, refractive power, intraocular pressure (IOP), anterior chamber angle, depth, volume, and vault.ResultsThe safety indices of the experimental and control groups were 1.17 ± 0.30 and 1.12 ± 0.14, respectively (P &gt; 0.05); the effectiveness indices were 1.16 ± 0.31 and 1.07 ± 0.17, respectively (P &gt; 0.05). The simulation curves of the expected and actual corrections in the experimental and control groups were y = 0.9876x – 0.0927 and y = 0.9799x + 0.0343, respectively. There were no significant differences between the IOPs and anterior chamber structures of the two groups (P &gt; 0.05). The average vaults of the experimental and control groups were 395.76 ± 155.32 and 389.49 ± 135.01 μm, respectively (P &gt; 0.05).ConclusionEVO-ICL implantation in patients with short WTW corneal diameters (≤ 10.6 mm) was determined to be a safe, effective, and predictable method for correcting myopia. The changes in the anterior chamber structure were still within normal limits after the surgery, the IOP remained stable, and the ideal vault was achieved after the surgery.
Point-of-care application of diaphragmatic ultrasonography in the emergency department for the prediction of development of respiratory failure in community-acquired pneumonia: A pilot study
Authors: Chu Sheng-En , Lu Jian-Xun , Chang Shi-Chuan , Hsu Kuang-Hung , Goh Zhong Ning Leonard , Seak Chen-Ken , Seak Joanna Chen-Yeen , Ng Chip-Jin , Seak Chen-June 
Published: August 2022

BackgroundEarly recognition of patients with community-acquired pneumonia (CAP) at risk of poor outcomes is crucial. However, there is no effective assessment tool for predicting the development of respiratory failure in patients with CAP. Diaphragmatic ultrasonography (DUS) is a novel technique developed for evaluating diaphragmatic functionviameasurements of the diaphragm thickening fraction (DTF) and diaphragm excursion (DE). This study evaluated the accuracy of DUS in predicting the development of respiratory failure in patients with CAP, as well as the feasibility of its use in the emergency department (ED) setting.Materials and methodsThis was a single-center prospective cohort study. We invited all patients with ED aged ≥ 20 years who were diagnosed with CAP of pneumonia severity index (PSI) SIe diagnosed with CAP of pneumonia severe with respiratory failure or septic shock were excluded. Two emergency physicians performed DUS to obtain DTF and DE measurements. Data were collected to calculate PSI, CURB-65 score, and Infectious Diseases Society of America/American Thoracic Society severity criteria. Study endpoints were taken at the development of respiratory failure or 30 days post-ED presentation. Continuous variables were analyzed usingT-tests, while categorical variables were analyzed using chi-square tests. Further logistic regression and receiver operating characteristic curve analyses were performed to examine the ability to predict the development of respiratory failure. Intra- and inter-rater reliability was examined with intraclass correlation coefficients (ICCs).ResultsIn this study, 13 of 50 patients with CAP enrolled developed respiratory failure. DTF was found to be an independent predictor (OR: 0.939,p= 0.0416). At the optimal cut-off point of 23.95%, DTF had 69.23% of sensitivity, 83.78% of specificity, 88.57% of negative predictive value, and 80% of accuracy. Intra- and inter-rater analysis demonstrated good consistency (intra-rater ICC 0.817, 0.789; inter-rater ICC 0.774, 0.781).ConclusionDUS assessment of DTF may reliably predict the development of respiratory failure in patients with CAP presenting to the ED. Patients with DTF &gt; 23.95% may be considered for outpatient management.
Acute decompensation events differentially impact the risk of nosocomial infections and short-term outcomes in patients with cirrhosis
Authors: Xu Xianbin , Yu Xia , Gong Kai , Tu Huilan , Yao Junjie , Lan Yan , Ye Shaoheng , Weng Haoda , Shi Yu , Sheng Jifang 
Published: August 2022

AimsThis research aimed to evaluate the influence of acute decompensation (AD) events upon admission on the subsequent risk of nosocomial infections (NIs) and the synergy between AD and the following NIs on the short-term outcome.MethodsA total of 419 hospitalized individuals with cirrhosis and AD participated in the current study. Various AD events at admission and outcomes in patients with or without NIs were compared. The logistic regression and Cox proportional hazards models were designed for NIs development and liver transplant (LT)-free mortality at 28 and 90 days, respectively.ResultsDuring hospitalization, 91 patients developed NIs. Notably, a higher proportion of patients with NIs had jaundice (52.7 vs. 30.5%; p &lt; 0.001) and bacterial infections (37.4 vs. 20.7%; p = 0.001) at admission compared to patients without NIs, while a lower proportion suffered gastrointestinal hemorrhage (16.5 vs. 36.6%; p &lt; 0.001). Multivariate analysis revealed that jaundice was independently linked with the development of NIs (OR, 2.732; 95% CI: 1.104–6.762). The 28-day (16.5 vs. 7.3%; p = 0.008) and 90-day (27.5 vs. 15.9%; p = 0.011) LT-free mortality rates of patients with NIs were significantly higher than those without NIs. According to the Cox proportional hazards model, jaundice remained an independent risk factor for 90-day death (HR, 5.775; 95% CI: 1.217–27.397). The connection between total bilirubin and 90-day mortality was nonlinear, and a 6 mg/mL threshold was proposed.ConclusionThe types of AD events differentially predispose to risk of NIs. Presenting jaundice at admission is independently associated with NIs occurrence and increased 90-day mortality of patients with NIs. Antibiotic prophylaxis may benefit this specific subset of patients.
In silico analysis reveals the co-existence of CRISPR-Cas type I-F1 and type I-F2 systems and its association with restricted phage invasion in Acinetobacter baumannii
Authors: Yadav Gulshan , Singh Ruchi 
Published: August 2022

IntroductionAcinetobacter baumannii, an opportunistic pathogen, rapidly acquires antibiotic resistance, thus compelling researchers to develop alternative treatments at utmost priority. Phage-based therapies are of appreciable benefit; however, CRISPR-Cas systems are a major constraint in this approach. Hence for effective implementation and a promising future of phage-based therapies, a multifaceted understanding of the CRISPR-Cas systems is necessary.MethodsThis study investigated 4,977 RefSeq genomes of A. baumannii from the NCBI database to comprehend the distribution and association of CRISPR-Cas systems with genomic determinants.ResultsApproximately 13.84% (n = 689/4,977) isolates were found to carry the CRSIPR-Cas system, and a small fraction of isolates, 1.49% (n = 74/4,977), exhibited degenerated CRISPR-Cas systems. Of these CRISPR-Cas positive (+) isolates, 67.48% (465/689) isolates harbored type I-F1, 28.59% (197/689) had type I-F2, and 3.7% (26/689) had co-existence of both type I-F1 and type I-F2 systems. Co-existing type I-F1 and type I-F2 systems are located distantly (∼1.733 Mb). We found a strong association of CRISPR-Cas systems within STs for type I-F1 and type I-F2, whereas the type I-F1 + F2 was not confined to any particular ST. Isolates with type I-F1 + F2 exhibited a significantly high number of mean spacers (n = 164.58 ± 46.41) per isolate as compared to isolates with type I-F2 (n = 82.87 ± 36.14) and type I-F1 (n = 54.51 ± 26.27) with majority targeting the phages. Isolates with type I-F1 (p &lt; 0.0001) and type I-F2 (p &lt; 0.0115) displayed significantly larger genome sizes than type I-F1 + F2. A significantly reduced number of integrated phages in isolates with co-existence of type I-F1 + F2 compared with other counterparts was observed (p = 0.0041). In addition, the isolates carrying type I-F1 + F2 did not exhibit reduced resistance and virulence genes compared to CRISPR-Cas(–) and CRISPR-Cas (+) type I-F1 and type I-F2, except for bap, abaI, and abaR.ConclusionOur observation suggests that the co-existence of type I-F1 and F2 is more effective in constraining the horizontal gene transfer and phage invasion in A. baumannii than the isolates exhibiting only type I-F1 and only type I-F2 systems.
Antibacterial properties of lactoferrin: A bibliometric analysis from 2000 to early 2022
Authors: Xu Yunling , Wang Yuji , He Jiaolong , Zhu Wanping 
Published: August 2022

BackgroundHere, a bibliometric and knowledge map analysis are used to analyze the research hot spots and development trends regarding the antibacterial effect of lactoferrin (LF). By looking for research hot spots and new topics, we provide new clues and research directions for future research.MethodsArticles and reviews regarding the antibacterial effect of LF were retrieved and from the Web of Science Core Collection (WoSCC) on 25 June 2022. CiteSpace and VOSviewer were used to conduct the bibliometric and knowledge map analysis.ResultsIn total, 8,292 authors at 2,151 institutions from 86 countries published 1,923 articles in 770 academic journals. The United States was the leader regarding research on the antibacterial effects of LF, while the Netherlands was a pioneer in conducting research in this field. The University of California system contributed the most publications. Bolscher JGM published most articles, while Wayne Bellamy had most cocitations. However, there was insufficient cooperation among the various institutions and authors. BioMetals published most LF-antibacterial activity-related articles, whereas Infection and Immunity was most commonly cocited journal. The most influential research hot spots about the antibacterial effect of LF focused on antimicrobial peptides, casein, human milk, expression, and Escherichia coli-related research. The latest hot spots and research frontier included COVID-19, antibiofilm activity, and immune defense.ConclusionsLF is a multifunctional protein with a broad spectrum of antimicrobial activities. The related field of antibacterial properties of LF will remain a research hot spot in future.
Gut microbiota and short-chain fatty acids may be new biomarkers for predicting neonatal necrotizing enterocolitis: A pilot study
Authors: Liu Xiao-Chen , Du Ting-Ting , Gao Xiong , Zhao Wen-Jing , Wang Zheng-Li , He Yu , Bao Lei , Li Lu-Quan 
Published: August 2022

BackgroundDysbacteriosis is thought to play an important role in the pathogenesis of necrotizing enterocolitis (NEC). We aimed to identify new biomarkers among gut microbiota and short-chain fatty acids (SCFAs) for the early prediction of NEC.Materials and methodsThirty-four preterm infants with gestational ages of ≤ 34 weeks who developed gastrointestinal symptoms were divided into the NEC group (n = 17) and non-NEC group (n = 17). In the NEC group, the gut microbiota and SCFAs in feces were assessed when the infants were enrolled (Group P) and when they were diagnosed with NEC (Group N). In the non-NEC group, samples were assessed when the infants were enrolled (Group C).ResultsThe Ace and Chao1 indices were higher in Group P than in Group C (P &lt; 0.05), and there was no difference between Groups C and N or between Groups P and N (P &gt; 0.05). There was no significant difference in the Simpson and Shannon indices among Groups C, P and N (P &gt; 0.05). The four main phyla showed no differences (P &gt; 0.05) in composition, while at the genus level, compared with Group C, in Group P, Clostridioides, Blautia and Clostridium_sensu_stricto_1 were increased, while Lactobacillus and Bifidobacterium were decreased (P &lt; 0.05). At the species level, Streptococcus salivarius and Rothia mucilaginosa increased, while Bifidobacterium animals subsp. lactis decreased (P &lt; 0.05). In Group N, at the genus level, Stenotrophomonas, Streptococcus and Prevotella increased (P &lt; 0.05). Compared with those in Group C, the levels of acetic acid, propanoic acid and butyric acid decreased significantly in Groups P and N (P &lt; 0.05), and the areas under the curves (AUCs) of these three SCFAs between groups C and P were 0.73, 0.70, and 0.68, respectively.ConclusionThe increase in Streptococcus salivarius and Rothia mucilaginosa and decrease in Bifidobacterium_animals_subsp._lactis, as well as the decrease in acetic, propionic and butyric acids, may help in the early prediction of NEC.
Body mass index related to executive function and hippocampal subregion volume in subjective cognitive decline
Authors: Chen Ruilin , Cai Guiyan , Xu Shurui , Sun Qianqian , Luo Jia , Wang Yajun , Li Ming , Lin Hui , Liu Jiao 
Published: August 2022

ObjectiveThis study aims to explore whether body mass index (BMI) level affects the executive function and hippocampal subregion volume of subjective cognitive decline (SCD).Materials and methodsA total of 111 participants were included in the analysis, including SCD (38 of normal BMI, 27 of overweight and obesity) and normal cognitive control (NC) (29 of normal BMI, 17 of overweight and obesity). All subjects underwent the Chinese version of the Stroop Color-Word Test (SCWT) to measure the executive function and a high-resolution 3D T1 structural image acquisition. Two-way ANOVA was used to examine the differences in executive function and gray matter volume in hippocampal subregions under different BMI levels between the SCD and NC.ResultThe subdimensions of executive function in which different BMI levels interact with SCD and NC include inhibition control function [SCWT C-B reaction time(s): F(1,104) = 5.732, p = 0.018], and the hippocampal subregion volume of CA1 [F(1,99) = 8.607, p = 0.004], hippocampal tail [F(1,99) = 4.077, p = 0.046], and molecular layer [F(1,99) = 6.309, p = 0.014]. After correction by Bonferroni method, the population × BMI interaction only had a significant effect on the CA1 (p = 0.004). Further analysis found that the SCWT C-B reaction time of SCD was significantly longer than NC no matter whether it is at the normal BMI level [F(1,104) = 4.325, p = 0.040] or the high BMI level [F(1,104) = 21.530, p &lt; 0.001], and the inhibitory control function of SCD was worse than that of NC. In the normal BMI group, gray matter volume in the hippocampal subregion (CA1) of SCD was significantly smaller than that of NC [F(1,99) = 4.938, p = 0.029]. For patients with SCD, the high BMI group had worse inhibitory control function [F(1,104) = 13.499, p &lt; 0.001] and greater CA1 volume compared with the normal BMI group [F(1,99) = 7.619, p = 0.007].ConclusionThe BMI level is related to the inhibition control function and the gray matter volume of CA1 subregion in SCD. Overweight seems to increase the gray matter volume of CA1 in the elderly with SCD, but it is not enough to compensate for the damage to executive function caused by the disease. These data provide new insights into the relationship between BMI level and executive function of SCD from the perspective of imaging.