bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overlapping clustering of gene expression data using penalized weighted normalized cut
Authors: Teran Hidalgo Sebastian J. , Zhu Tingyu , Wu Mengyun , Ma Shuangge 
Published: October 2018

AbstractClustering has been widely conducted in the analysis of gene expression data. For complex diseases, it has played an important role in identifying unknown functions of genes, serving as the basis of other analysis, and others. A common limitation of most existing clustering approaches is to assume that genes are separated into disjoint clusters. As genes often have multiple functions and thus can belong to more than one functional cluster, the disjoint clustering results can be unsatisfactory. In addition, due to the small sample sizes of genetic profiling studies and other factors, there may not be sufficient evidence to confirm the specific functions of some genes and cluster them definitively into disjoint clusters. In this study, we develop an effective overlapping clustering approach, which takes account into the multiplicity of gene functions and lack of certainty in practical analysis. A penalized weighted normalized cut (PWNCut) criterion is proposed based on the NCut technique and an norm constraint. It outperforms multiple competitors in simulation. The analysis of the cancer genome atlas (TCGA) data on breast cancer and cervical cancer leads to biologically sensible findings which differ from those using the alternatives. To facilitate implementation, we develop the function
pwncut in the
R package
NCutYX.
Explaining steam‐enhanced carbonation of CaO based on first principles
Authors: Yang Peng , Duan Lunbo , Tang Hongjian , Cai Tianyi , Sun Zhao 
Published: October 2018

AbstractCalcium‐based sorbents have been regarded as effective agents for capturing CO2 from industrial flue gas. Recent studies have shown that steam can enhance the carbonation performance of calcium‐based sorbents. In this paper, a CaO (001) surface was made to investigate the micro‐level mechanism of steam‐enhanced carbonation based on first principles calculations. Charge transfer and bond population were calculated to evaluate an interaction effect between adsorbates and the CaO (001) surface. Individual adsorption of CO2 and H2O was compared with binary adsorption and co‐adsorption of the two molecules on the CaO (001) surface, based on dispersion‐corrected density functional theory (DFT‐D) calculations. First, the predicted adsorption energies suggest the O‐top site is the best site. It forms carbonate‐like structure and hydroxyl‐like structure for the individual adsorption of CO2 and H2O. Binary adsorption calculations indicate that H2O is more easily adsorbed by the CaO (001) surface than CO2. The adsorption of H2O and CO2 adsorption are promoted in comparison with their individual adsorption on the CaO (001) surface. Moreover, the analysis of adsorption energies and partial density of states (PDOS) suggests that a H2O‐CaO (001) surface (CaO (001) surface that has already adsorbed H2O) is more reactive than the clean CaO (001) surface for CO2 adsorption, which further supports the idea that the steam‐enhanced mechanism is an Eley–Rideal (E–R) mechanism, which means H2O is adsorbed on the CaO surface, and then CO2 is adsorbed. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd.
Overexpression of cysteine‐glutamate transporter and CD44 for prediction of recurrence and survival in patients with oral cavity squamous cell carcinoma
Authors: Lee Jae Ryung , Roh Jong‐Lyel , Lee Sun Mi , Park Yangsoon , Cho Kyung‐Ja , Choi Seung‐Ho , Nam Soon Yuhl , Kim Sang Yoon 
Published: October 2018

AbstractBackgroundThis study analyzed the expression of CD44 and cystine‐glutamate transporter SLC7A11 (xCT) in primary oral cavity squamous cell carcinoma (SCC) and the relationships of expression to tumor recurrence and patient survival.MethodsAssociations between CD44 and xCT expression and clinicopathologic results were analyzed in 231 patients with oral cavity SCC. Cox proportional hazard analyses were used to identify factors associated with recurrence‐free survival (RFS), disease‐specific survival (DSS), and overall survival (OS).ResultsOverexpression of CD44 and/or xCT was associated with advanced T classification, perineural invasion, and lymphovascular invasion (P < .05 each). High expression of xCT was also associated with nodal metastasis and depth of invasion (P < .01 each). Multivariate analysis indicated that high expression of xCT and both xCT and CD44 were independent predictors of poor RFS, DSS, and OS (P < .05 each).ConclusionOverexpression of xCT or xCT plus CD44 may predict posttreatment recurrence and survival in patients with oral cavity SCC.
Transoral surgery using the Flex Robotic System: Initial experience in the United States
Authors: Persky Michael J. , Issa Mohamad , Bonfili Jennifer R. , Goyal Neerav , Goldenberg David , Duvvuri Umamaheswar 
Published: October 2018

AbstractBackgroundThis multicenter, retrospective review documents the initial experience using the Flex system for transoral surgery in 2 United States academic centers.MethodsAll patients who underwent transoral robotic surgery using the Medrobotics Flex Robotic System (Raynham, MA) between September 2015 and May 2017 were reviewed. Rates of successful surgery and complications were evaluated.ResultsThirty‐six men and 32 women were enrolled in the study. The average age was 55.6 years (range 17‐82 years). The Flex system was used successfully in surgery of the tongue base, the palatine tonsils, the supraglottis, the glottis, the hypopharynx, the oral tongue, and the soft palate. Only 6 cases (7.6%) required readmission after discharge. There were no intraoperative or immediate postoperative complications, with no cases of intraoperative hemorrhage.ConclusionTo the best of our knowledge, this is the first study in the United States evaluating the use of the Flex system to safely resect lesions in the oral cavity, larynx, and pharynx.
Estimating dominant runoff modes across the conterminous United States
Authors: Buchanan Brian , Auerbach Daniel A. , Knighton James , Evensen Darrick , Fuka Daniel R. , Easton Zachary , Wieczorek Michael , Archibald Josephine A. , McWilliams Brandon , Walter Todd 
Published: October 2018

AbstractEffective natural resource planning depends on understanding the prevalence of runoff generating processes. Within a specific area of interest, this demands reproducible, straightforward information that can complement available local data and can orient and guide stakeholders with diverse training and backgrounds. To address this demand within the contiguous United States (CONUS), we characterized and mapped the predominance of two primary runoff generating processes: infiltration‐excess and saturation‐excess runoff (IE vs. SE, respectively). Specifically, we constructed a gap‐filled grid of surficial saturated hydraulic conductivity using the Soil Survey Geographic and State Soil Geographic soils databases. We then compared surficial saturated hydraulic conductivity values with 1‐hr rainfall‐frequency estimates across a range of return intervals derived from CONUS‐scale random forest models. This assessment of the prevalence of IE versus SE runoff also incorporated a simple uncertainty analysis, as well as a case study of how the approach could be used to evaluate future alterations in runoff processes resulting from climate change. We found a low likelihood of IE runoff on undisturbed soils over much of CONUS for 1‐hr storms with return intervals <5 years. Conversely, IE runoff is most likely in the Central United States (i.e., Texas, Louisiana, Kansas, Missouri, Iowa, Nebraska, and Western South Dakota), and the relative predominance of runoff types is highly sensitive to the accuracy of the estimated soil properties. Leveraging publicly available data sets and reproducible workflows, our approach offers greater understanding of predominant runoff generating processes over a continental extent and expands the technical resources available to environmental planners, regulators, and modellers.
3D‐printed polycaprolactone scaffold mixed with β‐tricalcium phosphate as a bone regenerative material in rabbit calvarial defects
Authors: Pae Hyung‐Chul , Kang Joo‐Hyun , Cha Jae‐Kook , Lee Jung‐Seok , Paik Jeong‐Won , Jung Ui‐Won , Kim Byung‐Hoon , Choi Seong‐Ho 
Published: October 2018

AbstractDefect‐specific bone regeneration using 3‐dimensional (3D) printing of block bone has been developed. Polycaprolactone (PCL) is biocompatible polymer that can be used as 3D scaffold. The aim of this study is to assess the biocompatibility and osteogenic efficacy of 3D printed PCL scaffold and to evaluate the effectiveness of β‐tricalcium phosphate (β‐TCP) addition in PCL scaffold. In this work, four circular defects (diameter: 8 mm) in rabbit calvarium were randomly assigned to (1) negative control (control), (2) PCL block (PCL), (3) PCL mixed with 10 wt% β‐TCP (PCL/β‐TCP), and (4) PCL/β‐TCP plus collagen membrane (PCL/β‐TCP + M). Animals were euthanized at 2 (n = 5) and 8 weeks (n = 5). Results indicated that in micro‐CT, PCL/β‐TCP + M showed the highest total augmented volume and new bone volume at 8 weeks, but there was no significant difference among four groups. Histomorphometrically, PCL, PCL/β‐TCP, and PCL/β‐TCP + M showed the significantly higher total augmented area compared to the control. PCL/β‐TCP + M showed the highest new bone area but not statistically higher than the control. New bone formation deep inside the scaffold was observed only in β‐TCP added scaffold. PCL showed high biocompatibility with great volume maintenance. Addition of β‐TCP to PCL seemed to increase hydrophilicity and osteoconductivity. Developments in 3D‐printed PCL material are expected. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B: 1254–1263, 2019.
Dysregulation of FTX/miR‐545 signaling pathway downregulates Tim‐3 and is responsible for the abnormal activation of macrophage in cirrhosis
Authors: Liu Xia , Li Cong , Zhu Jie , Li Wenshuai , Zhu Qiang 
Published: October 2018

AbstractBackgroundAccumulating evidence has suggested the involvement of miR‐545 and long noncoding RNA (lncRNA) FTX in a wide range of diseases. Therefore, this study aimed to investigate the molecular mechanism underlying the function of miR‐545 and lncRNA FTX in hepatitis B virus (HBV)‐related cirrhosis.MethodThe level of Tim‐3, TLR‐4, and endotoxin was detected in CD14+, CD14
+CD16
+, and CD14
+CD16
− monocytes isolated from both patients with cirrhosis and healthy controls. ELISA assays were performed to detect the effect of Lipopolysaccharide (LPS) or FTX on the expression of tumor necrosis factor alpha (TNF‐a), interleukin‐6 (IL‐6), IL‐1β, and Nuclear factor kB (NF‐kB). In‐silico analysis, luciferase assay, real‐time polymerase chain reaction (PCR), and Western blot analysis were utilized to determine the regulatory relationship between miR‐545 and Tim‐3.ResultsThe levels of Tim‐3, Tim‐3 MIF and endotoxin were reduced in the CD14+ monocytes isolated from patients with cirrhosis. In addition, the level of Tim‐3 was also decreased in the CD14
+CD16
− monocytes isolated from patients with cirrhosis, whereas the level of Tim‐3 in CD14
+CD16
+ monocytes showed no evident difference between healthy controls and patients with cirrhosis. Furthermore, TLR‐4 was highly expressed in CD14
+CD16
+ monocytes isolated from patients with cirrhosis, whereas Tim‐3 was negatively regulated by endotoxin and the correlation coefficient was ‐0.5287. After the LPS stimulation, although the level of TNF‐a, IL‐6, IL‐1β, and NF‐kB was higher in both patients with cirrhosis and healthy controls, the effect of LPS in patients with cirrhosis was much more significant. In addition, the cirrhosis group showed a lower level of FTX and Tim‐3, but a higher level of miR‐545. Moreover, miR‐545 directly bound to the 3′untranslated region (3′UTR) of Tim‐3 and inhibited the luciferase activity of cells cotransfected with miR‐545 mimics and wild‐type 3′UTR of Tim‐3. Furthermore, FTX downregulated the expression of miR‐545, TNF‐a, IL‐6, IL‐1β, and NF‐kB, but upregulated the expression of Tim‐3.ConclusionThe results of this study confirmed the effect of FTX, miR‐545, and Tim‐3 on the expression of inflammatory cytokines, the lymphocyte/monocyte ratio, and the severity and prognosis of HBV‐related cirrhosis.
Total flavonoids from Smilax glabra Roxb blocks epithelial‐mesenchymal transition and inhibits renal interstitial fibrosis by targeting miR‐21/PTEN signaling
Authors: Luo Qihan , Cai Zhaowei , Tu Jue , Ling Yun , Wang Dejun , Cai Yueqin 
Published: October 2018

AbstractBackgroundSmilax glabra Roxb, a traditional Chinese herb, has been widely used in folk medicine. The current study was performed to investigate the protective effect of
S. glabra Roxb extract, pure total flavonoids from
Smilax glabra Roxb (PTFS), on renal interstitial fibrosis (RIF) and its underlying mechanism.MethodsFirst, a surgical model of unilateral ureteral obstruction was established in rats to induce RIF. Then, rats were grouped and treated with PTFS at different concentration. Second, HK‐2 cells underwent an epithelial‐mesenchymal transition (EMT) by the addition of transforming growth factor‐β1 (TGF‐β1). Additionally, HK‐2 cells after inducing for EMT were transfected with microRNA‐21 (miR‐21) mimic or inhibitor. These HK‐2 cells were grouped and treated with PTFS at different concentration. Finally, real‐time polymerase chain reaction and Western blot analysis were performed to detect the expression of possible signaling factor involved in RIF in renal tissues or HK‐2 cells after PTFS treatment.ResultsIn vivo and in vitro experiments indicated that PTFS treatment could decrease the expression of α‐smooth muscle actin (α‐SMA; mesenchymal marker) and increase the expression of E‐cadherin (epithelial marker) in both messenger RNA and protein level. Moreover, PTFS also attenuated the expression of TGF‐β1/Smad signaling in both renal tissues and HK‐2 cells that underwent EMT. Overexpression or inhibition of miR‐21 in HK‐2 cells activated or blocked the PI3K/Akt signaling via targeting phosphatase and tension homolog (PTEN), and then promoted or suppressed the progress of TGF‐β1‐induced EMT by regulating the expression of α‐SMA and E‐cadherin. Furthermore, PTFS treatment inhibited TGF‐β1‐induced EMT progress by blocking miR‐21/PTEN/PI3K/Akt signaling.ConclusionPTFS has strong anti‐EMT and antifibrosis effects both in vitro and in vivo. The mechanism underlying these effects may be related to inhibition of TGF‐β1/Smad, and their downstream miR‐21/PTEN signaling, leading to blocks of EMT process during RIF.
Ablation alleviates atrial fibrillation by regulating the signaling pathways of endothelial nitric oxide synthase/nitric oxide via miR‐155‐5p and miR‐24‐3p
Authors: Wang Maojing , Sun Libo , Ding Wei , Cai Shanglang , Zhao Qing 
Published: October 2018

AbstractBackgroundThis study aimed to identify the microRNAs implicated in atrial fibrillation (AF) to investigate the molecular mechanisms underlying the role of microRNAs in ablation‐based AF treatment.MethodsReal‐time polymerase chain reaction (PCR) and microRNA microarrays were utilized to measure the profiles of microRNA expression in AF to identify differentially expressed microRNAs. Enzyme‐linked immunosorbent assay, real‐time PCR, Western blot analysis, and immunohistochemistry assays were also performed to investigate the regulatory relationships among various factors implicated in AF. Finally, bioinformatic tools and luciferase assays were used to confirm the roles of miR‐155‐5p, miR‐24‐3p, endothelial nitric oxide synthase (eNOS), and nitric oxide (NO) in the pathogenesis of AF.ResultsWe demonstrated that the levels of miR‐155‐5p and miR‐24‐3p were greatly reduced in postablation AF patients compared with those AF patients not treated by ablation. Furthermore, the NO level in the AF+ group was much lower than that of the AF− group. Finally, in a swine model of AF, evident upregulation of miR‐155‐5p and miR‐24‐3p was found in AF pigs, whereas the ablation treatment reduced the levels of miR‐155‐5p and miR‐24‐3p in AF pigs. On contrary, as targets of miR‐155‐5p and miR‐24‐3p, the levels of eNOS and NO increased when the expression of miR‐155‐5p and miR‐24‐3p decreased.ConclusionMiR‐155‐5p and miR‐24‐3p are involved in the pathogenesis of AF via regulating the expression of eNOS and the production of NO. In addition, ablation treatment helps the recovery from AF by reducing the expression of miR‐155‐5p and miR‐24‐3p.
Regulation of miR‐125a expression by rs12976445 single‐nucleotide polymorphism is associated with radiotherapy‐induced pneumonitis in lung carcinoma patients
Authors: Huang Xuan , Zhang Tianze , Li Guanghua , Guo Xiaona , Liu Xuesong 
Published: October 2018

AbstractBackgroundThe expression of miR‐125 is regulated by an single‐nucleotide polymorphism (SNP), rs12976445, which may be involved in the risk of pneumonitis among non–small‐cell lung carcinoma patients undergoing the radiotherapy. We investigated this hypothesis via clinical data analysis and in vitro experiments.MethodsAn online microRNA (miRNA) database (www.mirdb.org) and luciferase reporter assays were used to confirm the role of transforming growth factor‐β1 (TGFB1) as a target gene of miR‐125a. Quantification by real‐time PCR and Western blot analysis were used to measure the expression of miRNA‐125a and TGFB1 among different groups (carrying CC, CT, and TT genotypes of rs12976445) or cells transfected with a scramble control, miR‐125a mimics, TGFB1 siRNA, or miR‐125a inhibitors.ResultsWe evaluated 699 NSCLC patients and found that the patients carrying the TT or CT genotype of rs12976445 had a higher risk of radiotherapy‐induced pneumonitis. Computational analysis and luciferase assays validated that TGFB1 is a target gene of miR‐125a. The expression level of miR‐125a mRNA was significantly downregulated in the CT and TT groups, while the expression levels of TGFB1 and SMAD2 were significantly upregulated in the CC group. The expression of TGFB1 and SMAD2 was regulated by miR‐125a in A549 cells.ConclusionThe rs12976445 SNP in miR‐125a is associated with the risk of pneumonitis after in lung cancer patients undergoing the radiotherapy by regulating the expression of miR‐125a and TGFB1.
Identification of surrogate prognostic biomarkers for allergic asthma in nasal epithelial brushing samples by WGCNA
Authors: Liu Zhaoyu , Li Ming , Fang Xiangming , Shen Lu , Yao Wenxia , Fang Zhiyuan , Chen Jitao , Feng Xiao , Hu La , Zeng Zicheng , Lin Chunyi , Weng Jinsheng , Lai Yuxiong , Yi Gao 
Published: October 2018

AbstractBackgroundAllergic asthma is a lower respiratory tract disease of Th2 inflammation with multiple molecular mechanisms. The upper and lower airways can be unified by the concept of a united airway and, as such, gene expression studies of upper epithelial cells may provide effective surrogate biomarkers for the prognostic study of allergic asthma.ObjectiveTo identify surrogate biomarkers in upper airway epithelial cells for the prognostic study of allergic asthma.MethodsNasal epithelial cell gene expression in 40 asthmatic and 17 healthy control subjects were analyzed by weighted gene coexpression network analysis (WGCNA) to identify gene network modules and profiles in allergic asthma. Functional enrichment analysis was performed on the coexpression genes in certain highlighted modules.ResultsA total of 13 coexpression modules were constructed by WGCNA from 2804 genes in nasal epithelial brushing samples of the 40 asthmatic and 17 healthy subjects. The number of genes in these modules ranged from 1086 (Turquoise module) to 45 (Salmon). Eight coexpression modules were found to be significantly correlated (P < 0.05) with two clinic traits, namely disease status, and severity. Four modules were positively correlated (
P < 0.05) with the traits and these, therefore, contained genes that are mostly overexpressed in asthma. Contrastingly, the four other modules were found to be negatively correlated with the clinic traits. Functional enrichment analysis of the positively correlated modules showed that one (Magenta) was mainly enriched in mast cell activation and degranulation; another (Pink) was largely involved in immune cell response; the third (Yellow) was predominantly enriched in transmembrane signal pathways; and the last (Blue) was mainly enriched in substructure components of the cells. The hub genes in the modules were
KIT,
KITLG,
GATA2,
CD44,
PTPRC, and
CFTR, and these were confirmed as having significantly higher expression in the nasal epithelial cells. Combining the six hub genes enabled a relatively high capacity for discrimination between asthmatics and healthy subjects with an area under the receiver operating characteristic (ROC) curve of 0.924.ConclusionsOur findings provide a framework of coexpression gene modules from nasal epithelial brushing samples that could be used for the prognostic study of allergic asthma.
Microporous cellulosic scaffold as a spheroid culture system modulates chemotherapeutic responses and stemness in hepatocellular carcinoma
Authors: Wu Guoyi , Zhan Shanshan , Rui Chen , Sho Eiketsu , Shi Xiaolei , Ding Yitao 
Published: October 2018

AbstractHepatocellular carcinoma (HCC) treatments are evaluated by two‐dimensional (2D) in vitro culture systems, despite their limited ability to predict drug efficacy. The three‐dimensional (3D) microporous scaffold provides the possibility of generating more reliable preclinical models to increase the efficacy of cancer treatments. The physical properties of a microporous cellulosic scaffold were evaluated. The cellulosic scaffold was biocompatible and had a highly porous network with appropriate pore size, swelling rate, and stiffness of cancer cell cultures. Cellulosic scaffolds were compared with 2D polystyrene for the culture of HepG2 and Huh7 human HCC cells. Cellulosic scaffolds promoted tumor spheroid formation. Cells cultured on scaffolds were more resistant to chemotherapy drugs and showed upregulation of EpCAM and Oct4. The migration ability of HCC cells cultured on scaffolds was significantly greater than that of cells grown in 2D cultures as evidenced by the downregulation of E‐cadherin. In addition, the proportion of CD44+/CD133+ HCC cancer stem cells (CSCs) was significantly greater in cells cultured on scaffolds than in those grown in 2D cultures. These findings suggest that cellulosic scaffolds effectively mimic the in vivo tumor behavior and may serve as a platform for the study of anticancer therapeutics and liver CSCs.