bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary glioblastoma transcriptome data analysis for screening survival‐related genes
Authors: Yang Ying , Yan Ranran , Zhang Liwen , Meng Xiangli , Sun Wen 
Published: October 2019

AbstractPurposeThe aim of this study was to screen survival‐related genes for glioblastoma (GBM).MethodsGSE53733 was downloaded from Gene Expression Omnibus (GEO) database, including 16 short‐term (ST), 31 intermediate (IM), and 23 long‐term (LT) survivors. Analysis of variance was used to analyze the expression in three groups. The genes with P < .01 were screened as differentially expressed genes (DEGs). Soft clustering was performed using Mfuzz to mine the expression patterns of differential genes in three groups of overall survival (OS) classification. The cytoscape plugin clueGO was used for functional enrichment analysis. The protein interaction between differential genes was extracted from the STRING V10 database, and the protein‐protein interaction (PPI) network was constructed and displayed with cytoscape. The hub genes were verified by quantitative reverse‐transcription polymerase chain reaction.ResultsTotal 662 DEGs were obtained among three groups and enriched in 12 clusters. The overlap analysis between clusters could classify these 12 clusters Cluster A and B. Total 264 OS.DEGs were contained in Cluter A and Cluster B, and enriched in 28 Gene Ontology terms, such as trophoblast giant cell differentiation (P value = 6.18E−04), muscle fiber development (P value = 9.09E−04), and negative regulation of stem cell differentiation (P value = 1.76E−03). The top five nodes with highest degree in OS.PPI were HDAC1, DECR1, RASL11A, PDIA3, and POLR2F. The expression of DECR1 and POLR2F was significantly lower, while the levels of HDAC1 and PDIA3 were highly expressed in GBM tissues.ConclusionDECR1, POLR2F, HDAC1, and PDIA3 might be potential key genes affected the overall survival time of patients with GBM.
Retracted: Negative feedback of NF‐κB signaling by long noncoding RNA MALAT1 controls lipopolysaccharide‐induced inflammation injury in human lung fibroblasts WI‐38
Authors: Zhu Wei , Men Xuelin 
Published: October 2019

AbstractThe study was designed to elucidate the regulatory mechanism of long noncoding RNA human metastasis associated lung adenocarcinoma transcript 1 (MALAT1) in lipopolysaccharides (LPS)‐caused inflammation injury in human lung fibroblasts WI‐38. WI‐38 cells were stimulated with LPS to construct acute pneumonia cell model. MALAT1 in LPS‐stimulated WI‐38 cells was examined. LPS‐induced inflammation injury was estimated using viability, apoptosis, and cytokine secretion including interleukin‐1β (IL‐1β) and IL‐6. Furthermore, the modulatory relations of MALAT1 and nuclear factor‐kappa B (NF‐κB) signaling were explored. We found that the sensitivity of WI‐38 cells to apoptosis was enhanced by LPS‐caused inflammation. Moreover, LPS promoted MALAT1 expression which was found to alleviate LPS‐caused damages. Besides, NF‐κB p65 overexpression resulted in an increased expression of MALAT1, and MALAT1 was identified as a target gene of p65. Furthermore, overexpression of MALAT1 reduced NF‐κB activation. Pulldown assay showed that MALAT1 could directly interact with p65. Taken together, our findings revealed that MALAT1 was upregulated in LPS‐stimulated WI‐38 cells. Through directly interacting with p65, MALAT1 blocked LPS‐caused activation of NF‐κB and repressed LPS‐induced inflammation injury. MALAT1 may serve as a potential diagnostic indicator or therapeutic target for pneumonia.
MicroRNA‐1296‐5p suppresses the proliferation, migration, and invasion of human osteosarcoma cells by targeting NOTCH2
Authors: Wang Lei , Hu Kejun , Chao Yu , Wang Xueli 
Published: October 2019

AbstractOsteosarcoma (OS) is a highly aggressive bone tumor with a poor prognosis. MicroRNAs are revealed to exerts essential roles in the carcinogenesis and tumor invasion of OS. But, the function of miR‐1296‐5p and its related mechanism in OS progression have not yet been studied. This study discovered the levels of miR‐1296‐5p in OS and corresponding noncancerous tissues, and we demonstrated that miR‐1296‐5p level was markedly downregulated in tumor specimens as compared with nontumor tissues. In addition, we discovered that miR‐1296‐5p was also underexpressed in OS cells compared with the hFOB1.19 osteoblast cells. Interestingly, the reduced expression of miR‐1296‐5p was confirmed to associated with large tumor size, advanced tumor stages, and distance metastasis, respectively. Patients with OS low‐expressing miR‐1296‐5p showed a prominent shorter survival. In addition, gain‐of‐function assays verified that miR‐1296‐5p overexpression remarkably repressed OS cell proliferation, migration, and invasion. Conversely, depletion of miR‐1296‐5p facilitated the growth and mobility of OS cells. Notably, miR‐1296‐5p inversely modulated notch receptor 2 (NOTCH2) in OS cells. The level of NOTCH2 messenger RNA was negatively correlated with miR‐1296‐5p level in OS samples. NOTCH2 knockdown markedly suppressed the abilities of MG‐63 cell proliferation and mobility. More importantly, the restoration of NOTCH2 prominently rescued miR‐1296‐5p‐induced tumor‐suppressive effects on MG‐63 cells. In conclusion, our study identified the reduced expression of miR‐1296‐5p, which contributed to OS progression. miR‐1296‐5p might be a promising prognostic marker and therapeutic target in OS.
Vascular endothelial growth factor enhances tendon‐bone healing by activating Yes‐associated protein for angiogenesis induction and rotator cuff reconstruction in rats
Authors: Huang Yao , Pan Min , Shu Hao , He Bing , Zhang Fucheng , Sun Luning 
Published: October 2019

AbstractLocal angiogenesis following rotator cuff reconstruction is crucial for tendon‐bone healing. The current research on the mechanism underlying angiogenesis that promotes tendon‐bone healing is scarce. This study investigates the mechanism underlying vascular endothelial growth factor (VEGF)‐Hippo signaling pathway's involvement in tendon‐bone healing following rotator cuff reconstruction. Verteporfin, the inhibitor of the Yes‐associated protein (YAP), was used to mechanically test and analyze two groups of tensile‐failure loads following rotator cuff reconstruction and to detect collagen and angiogenesis‐related marker expressions in the tendon. The interaction mechanism of the VEGF‐Hippo signaling pathway was assessed using human umbilical vein endothelial cells (HUVECs). The diameter of the supraspinatus tendon reduced following verteporfin treatment. Mechanical tests revealed that verteporfin significantly reduces the tensile‐failure load of the supraspinatus tendon. Verteporfin significantly reduces collagen 1 (Col 1), Col 3, Angiopoietin 2, CD31, Von Willebrand factor, CTGF, and CYR61 expressions. In HUVECs, VEGF activates VEGF receptors and inhibits LATS and YAP phosphorylation. YAP is then transferred to the nucleus to further activate downstream pathways. Therefore, verteporfin can inhibit VEGF‐induced YAP pathway activation by inhibiting YAP activity. Angiogenesis in tendon‐bone healing following rotator cuff reconstruction requires VEGF‐Hippo signaling pathway synergy.
Shape from focus based on 3D structure tensor using optical microscopy
Authors: Mahmood Muhammad T. , Lee Ik H. 
Published: October 2019

AbstractShape from focus (SFF) is a widely used passive optical method for 3D shape reconstruction. In SFF, a focus measure, which is used to estimate the relative focus level, plays a critical role in depth estimation. In this article, we present a new focus measure for accurate 3D shape estimation in optical microscopy based on the analysis of 3D structure tensor. First, the 3D tensors are computed from the input image sequence for each pixel. Then, each tensor is decomposed into point, curve, and surface tensors by decomposing tensors into eigenvalues and eigenvectors. Finally, the surfaceness is used to measure the quality of sharpness. The proposed focus measure provides accurate focus values and better resistance against noise. The proposed measure is evaluated by conducting experiments using image sequences of simulated and microscopic real objects. The comparative analysis demonstrates the effectiveness of the proposed focus measure in recovering 3D shape.
Uncountable dichromatic number without short directed cycles
Authors: Joó Attila 
Published: October 2019

AbstractHajnal and Erdős proved that a graph with uncountable chromatic number cannot avoid short cycles, it must contain, for example, (among other obligatory subgraphs). It was shown recently by Soukup that, in contrast of the undirected case, it is consistent that for any there exists an uncountably dichromatic digraph without directed cycles shorter than . He asked if it is provable already in ZFC (i.e., Zermelo ‐Fraenkel set theory with the Axiom of choice). We answer his question positively by constructing for every infinite cardinal and a digraph of size with dichromatic number at least without directed cycles of length less than .
Who are the missing men? Characterising men who never tested for HIV from population‐based surveys in six sub‐Saharan African countries
Authors: Quinn Caitlin , Kadengye Damazo T , Johnson Cheryl C , Baggaley Rachel , Dalal Shona 
Published: October 2019

AbstractIntroductionWe sought to characterize men who had never tested for HIV, understand factors associated with not testing, and measure survey HIV test uptake among never testers. We analysed nationally representative Demographic and Health Surveys of six African countries from 2013 to 2016: Ethiopia, Malawi, Zimbabwe, Rwanda, Lesotho and Zambia.MethodsEligible men were household residents or overnight visitors aged 15 to 59 years. We analysed questionnaire responses on HIV testing, known behavioural risk factors, and corresponding HIV laboratory results. We used survey‐weighted logistic regression to identify factors associated with never testing for HIV.ResultsApproximately double the proportion of men had never tested for HIV compared to women (Malawi: 30% vs. 17%, p < 0.0001; Zimbabwe: 35% vs. 19%, p < 0.0001; Lesotho: 34% vs. 15%, p < 0.0001; Zambia: 36% vs. 20%, p < 0.0001); although, less of a differential existed in Ethiopia (54% vs. 56%, p = 0.12) and Rwanda (19% vs. 14%, p < 0.0001). When offered a test during the survey, 85% to 99% of sexually active men who reported never previously testing, accepted testing. HIV positivity ranged from <0.05% to 14% for never tested men. After adjusting for age, factors associated with never having tested for HIV were never being married (aOR range: 1.46 to 10.39), not having children (aOR: 1.36 to 3.59) and lower education (less than primary education aOR: 2.77 to 5.59).ConclusionsAlthough higher proportions of men than women had never tested for HIV, 85% to 99% of men did accept a test when offered. Finding opportunities to offer HIV testing to single men without children, older men who have never tested, and those disadvantaged with less schooling and employment, alongside other facility and community‐based services, will be important in identifying those living with undiagnosed HIV and improving men's health.
Randomized, Controlled Early Intervention of Dynamic Mode Fractional Ablative CO2 Laser on Acute Burn Injuries for Prevention of Pathological Scarring
Authors: Waibel Jill S. , Gianatasio Chloe , Rudnick Ashley 
Published: October 2019

Background and ObjectivesThis study challenges the currently accepted treatment parameters of waiting 1 year following burn injury to treat the resultant scarring. It assesses the impact of treating burn and trauma wounds at less than 3 months of injury on scar formation, providing a new temporal paradigm to patients in the prevention and minimization of scar formation.Study Design/Materials and MethodsThis randomized clinical trial included 19 patients with moderate‐to‐severe acute burn injuries less than 3 months from injury. The treatment areas underwent three fractional ablative CO2 laser treatments at 8‐week intervals. The primary outcomes were improvement in the Manchester Scar Scale (MSS) and photography. Secondary outcomes were optical coherence tomography (OCT), treatment time, immediate post‐treatment response, and histology.ResultsUpon blinded evaluation, 100% of treatment areas were correctly identified when compared with control. MSS scores before and after treatment were totaled with an averaged sum of 13.33 per scar at baseline to 8.39 after treatment, a 63% average improvement versus control (P < 0.001). Histology and OCT demonstrated a re‐organization of the underlying skin structure. The average treatment time was 18 minutes. Immediate post‐treatment responses were limited to mild‐to‐moderate erythema.ConclusionsEarly intervention with ablative fractional laser on acute traumatic wounds resulted in significant decrease of scar formation compared with untreated areas on the same wounds, providing an impactful new time course to treat severe burn and trauma injuries. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.
dPGS Regulates the Phenotype of Macrophages via Metabolic Switching
Authors: Wu Hao , Reimann Sabine , Siddiqui Sophiya , Haag Rainer , Siegmund Britta , Dernedde Jens , Glauben Rainer 
Published: October 2019

AbstractThe synthetic compound dendritic polyglycerol sulfate (dPGS) is a pleiotropic acting molecule but shows a high binding affinity to immunological active molecules as L‐/P‐selectin or complement proteins leading to well described anti‐inflammatory properties in various mouse models. In order to make a comprehensive evaluation of the direct effect on the innate immune system, macrophage polarization is analyzed in the presence of dPGS on a phenotypic but also metabolic level. dPGS administered macrophages show a significant increase of MCP1 production paralleled by a reduction of IL‐10 secretion. Metabolic analysis reveals that dPGS could potently enhance the glycolysis and mitochondrial respiration in M0 macrophages as well as decrease the mitochondrial respiration of M2 macrophages. In summary the data indicate that dPGS polarizes macrophages into a pro‐inflammatory phenotype in a metabolic pathway‐dependent manner.
The CuAAC: Principles, Homogeneous and Heterogeneous Catalysts, and Novel Developments and Applications
Authors: Neumann Steve , Biewend Michel , Rana Sravendra , Binder Wolfgang H. 
Published: October 2019

AbstractThe copper‐catalyzed azide/alkyne cycloaddition reaction (CuAAC) has emerged as the most useful “click” chemistry. Polymer science has profited enormously from CuAAC by its simplicity, ease, scope, applicability and efficiency. Basic principles of the CuAAC are reviewed with a focus on homogeneous and heterogeneous catalysts, ligands, anchimeric assistance, and basic chemical principles. Recent developments of ligand design and acceleration are discussed.
Measurement of ester‐based transformer oil aging using tapered single mode‐multimode‐single mode fiber structure
Authors: Razzaq Alaa , Zainuddin Hidayat , Hanaffi Farhan , Chyad Radhi M. , Abdul Razak Hanim , Latiff Anas Abdul 
Published: October 2019

AbstractNowadays, ester‐based transformer oil has been an interest in high voltage transformers as an insulating and cooling medium. In‐service transformer oil is subjected to electrical and thermal stresses, leading to degradation process of the oil. In this work, a tapered single mode‐multimode‐single mode (SMS) optical fiber structure was used to detect transformer oil aging based on the change in oil refractive index (RI). An optical sensor was fabricated by splicing technique and chemical etching. For comparison, five samples of transformer ester oils were examined. The results show that high‐level‐aging transformer oil possesses a greater RI than fresh transformer oil. A correlation analysis was conducted among sensor output signal, oil absorption spectrum test, and breakdown voltage test. The performance of the sensor demonstrated good sensitivity and linearity of 20.41 nm/RIU and 95.95%, respectively. The single mode‐multimode‐single mode sensor was easily fabricated, low cost and could be used for real‐time high voltage transformer monitoring.
UWB antenna with sweeping dual notch based on metamaterial SRR fictive rotation
Authors: Fertas Khelil , Ghanem Farid , Azrar Arab , Aksas Rabia 
Published: October 2019

AbstractIn this article, a novel frequency switchable method for Ultra‐Wide‐Band (UWB) microstrip antenna with dual notches is presented and discussed. This method is based on hexagonal‐shaped Split Ring Resonator (SRR) metamaterial cells located close to the 50‐Ω feed line and ideal switches inserted at the inner and the outer SRR of each cell. The incorporation of these ideal switches helps in changing the location of the opening of the inner ring (inner ring fictive rotation) and in activating or deactivating the filtering introduced by the metamaterial cells. The resulting radiating structure has an impedance bandwidth extending from 2.8 GHz to more than 11GHz accompanied with dual notched bands characteristic. It offers several cases by opening or closing the ideal switches. The obtained simulation results agree well with measurements carried out on the fabricated prototypes.
MRI‐based transfer function determination through the transfer matrix by jointly fitting the incident and scattered field
Authors: Tokaya Janot P. , Raaijmakers Alexander J.E. , Luijten Peter R. , Sbrizzi Alessandro , van den Berg Cornelis A.T. 
Published: October 2019

PurposeA purely experimental method for MRI‐based transfer function (TF) determination is presented. A TF characterizes the potential for radiofrequency heating of a linear implant by relating the incident tangential electric field to a scattered electric field at its tip. We utilize the previously introduced transfer matrix (TM) to determine transfer functions solely from the MR measurable quantities, that is, the and transceive phase distributions. This technique can extend the current practice of phantom‐based TF assessment with dedicated experimental setup toward MR‐based methods that have the potential to assess the TF in more realistic situations.Theory and MethodsAn analytical description of the magnitude and transceive phase distribution around a wire‐like implant was derived based on the TM. In this model, the background field is described using a superposition of spherical and cylindrical harmonics while the transfer matrix is parameterized using a previously introduced attenuated wave model. This analytical description can be used to estimate the transfer matrix and transfer function based on the measured distribution.ResultsThe TF was successfully determined for 2 mock‐up implants: a 20‐cm bare copper wire and a 20‐cm insulated copper wire with 10 mm of insulation stripped at both endings in respectively 4 and 3 different trajectories. The measured TFs show a strong correlation with a reference determined from simulations and between the separate experiments with correlation coefficients above 0.96 between all TFs. Compared to the simulated TF, the maximum deviation in the estimated tip field is 9.4% and 12.2% for the bare and insulated wire, respectively.ConclusionsA method has been developed to measure the TF of medical implants using MRI experiments. Jointly fitting the incident and scattered distributions with an analytical description based on the transfer matrix enables accurate determination of the TF of 2 test implants. The presented method no longer needs input from simulated data and can therefore, in principle, be used to measure TF's in test animals or corpses.
Portable and platform‐independent MR pulse sequence programs
Authors: Cordes Cristoffer , Konstandin Simon , Porter David , Günther Matthias 
Published: October 2019

PurposeTo introduce a new sequence description format for vendor‐independent MR sequences that include all calculation logic portably. To introduce a new MRI sequence development approach which utilizes flexibly reusable modules.MethodsThe proposed sequence description contains a sequence module hierarchy for loop and group logic, which is enhanced by a novel strategy for performing efficient parameter and pulse shape calculation. These calculations are powered by a flow graph structure. By using the flow graph, all calculations are performed with no redundancy and without requiring preprocessing. The generation of this interpretable structure is a separate step that combines MRI techniques while actively considering their context. The driver interface is slim and highly flexible through scripting support. The sequences do not require any vendor‐specific compiling or processing step. A vendor‐independent frontend for sequence configuration can be used. Tests that ensure physical feasibility of the sequence are integrated into the calculation logic.ResultsThe framework was used to define a set of standard sequences. Resulting images were compared to respective images acquired with sequences provided by the device manufacturer. Images were acquired using a standard commercial MRI system.ConclusionsThe approach produces configurable, vendor‐independent sequences, whose configurability enables rapid prototyping. The transparent data structure simplifies the process of sharing reproducible sequences, modules, and techniques.
3D Whole‐heart free‐breathing qBOOST‐T2 mapping
Authors: Milotta Giorgia , Ginami Giulia , Bustin Aurelien , Neji Radhouene , Prieto Claudia , Botnar René M. 
Published: October 2019

PurposeTo develop an accelerated motion corrected 3D whole‐heart imaging approach (qBOOST‐T2) for simultaneous high‐resolution bright‐ and black‐blood cardiac MR imaging and quantitative myocardial T2 characterization.MethodsThree undersampled interleaved balanced steady‐state free precession cardiac MR volumes were acquired with a variable density Cartesian trajectory and different magnetization preparations: (1) T2‐prepared inversion recovery (T2prep‐IR), (2) T2‐preparation, and (3) no preparation. Image navigators were acquired prior the acquisition to correct for 2D translational respiratory motion. Each 3D volume was reconstructed with a low‐rank patch‐based reconstruction. The T2prep‐IR volume provides bright‐blood anatomy visualization, the black‐blood volume is obtained by means of phase sensitive reconstruction between first and third datasets, and T2 maps are generated by matching the signal evolution to a simulated dictionary. The proposed sequence has been evaluated in simulations, phantom experiments, 11 healthy subjects and compared with 3D bright‐blood cardiac MR and standard 2D breath‐hold balanced steady‐state free precession T2 mapping. The feasibility of the proposed approach was tested on 4 patients with suspected cardiovascular disease.ResultsHigh linear correlation (y = 1.09 × −0.83, R2 = 0.99) was found between the proposed qBOOST‐T2 and T2 spin echo measurements in phantom experiment. Good image quality was observed in vivo with the proposed 4x undersampled qBOOST‐T2. Mean T2 values of 53.1 ± 2.1 ms and 55.8 ± 2.7 ms were measured in vivo for 2D balanced steady‐state free precession T2 mapping and qBOOST‐T2, respectively, with linear correlation of y = 1.02x+1.46 (R2 = 0.61) and T2 bias = 2.7 ms.ConclusionThe proposed qBOOST‐T2 sequence allows the acquisition of 3D high‐resolution co‐registered bright‐ and black‐blood volumes and T2 maps in a single scan of ~11 min, showing promising results in terms of T2 quantification.