bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward automatic prediction of EGFR mutation status in pulmonary adenocarcinoma with 3D deep learning
Authors: Zhao Wei , Yang Jiancheng , Ni Bingbing , Bi Dexi , Sun Yingli , Xu Mengdi , Zhu Xiaoxia , Li Cheng , Jin Liang , Gao Pan , Wang Peijun , Hua Yanqing , Li Ming 
Published: May 2019

AbstractTo develop a deep learning system based on 3D convolutional neural networks (CNNs), and to automatically predict EGFR‐mutant pulmonary adenocarcinoma in CT images. A dataset of 579 nodules with EGFR mutation status labels of mutant (Mut) or wild‐type (WT) was retrospectively analyzed. A deep learning system, namely 3D DenseNets, was developed to process 3D patches of nodules from CT data, and learn strong representations with supervised end‐to‐end training. The 3D DenseNets were trained with a training subset of 348 nodules and tuned with a development subset of 116 nodules. A strong data augmentation technique, mixup, was used for better generalization. We evaluated our model on a holdout subset of 115 nodules. An independent public dataset of 37 nodules from the cancer imaging archive (TCIA) was also used to test the generalization of our method. Conventional radiomics analysis was also performed for comparison. Our method achieved promising performance on predicting EGFR mutation status, with AUCs of 75.8% and 75.0% for our holdout test set and public test set, respectively. Moreover, strong relations were found between deep learning feature and conventional radiomics, while deep learning worked through an enhanced radiomics manner, that is, deep learned radiomics (DLR), in terms of robustness, compactness and expressiveness. The proposed deep learning system predicts EGFR‐mutant of lung adenocarcinomas in CT images noninvasively and automatically, indicating its potential to help clinical decision‐making by identifying eligible patients of pulmonary adenocarcinoma for EGFR‐targeted therapy.
Prognosis of three histological subtypes of colorectal adenocarcinoma: A retrospective analysis of 8005 Chinese patients
Authors: Li Chao , Zheng Hongtu , Jia Huixun , Huang Dan , Gu Weilie , Cai Sanjun , Zhu Ji 
Published: May 2019

AbstractBackground and objectivesTo evaluate the effect of the varied histological subtypes on clinical outcomes and to determine the prognostic implications of mucinous adenocarcinomas (MAC) and signet ring cell carcinomas (SRCC) compared with classic adenocarcinomas (AC).MethodsA total of 8005 patients, including 7502 AC, 428 MAC and 75 SRCC, who underwent definitive surgery between 2007 and 2015 at Fudan University Shanghai Cancer Center were remained for analysis in this study.ResultsMAC and SRCC were more common in right‐sided colon cancer, in males and in young patients, compared to AC; moreover, MAC and SRCC led to a higher probability to develop lymph node metastasis, lymphovascular invasion and perineural invasion. For survival outcomes, we found that the 5‐year overall survival (OS) of SRCC was significantly lower than that of MAC and AC, while the 5‐year OS of MAC is much lower than that of AC. However, in multivariable analysis, the difference in survival between SRCC, MAC and AC was no longer significant, especially when stratified by N stage.ConclusionsMAC and SRCC are rare subtypes of colorectal cancer with a higher T stage, N stage as well as higher incidence of lymphovascular and nerve invasion. However, neither MAC nor SRCC was an independent predictor of decreased survival in multivariate analysis.
Cerebral Embolism due to a Large Papillary Fibroelastoma arising from the Coumadin Ridge
Authors: Kamimura Teppei , Tanaka Kanta , Yamagami Hiroshi , Koga Masatoshi 
Published: May 2019

AbstractA 70‐year‐old woman developed acute cerebral infarction. Transthoracic echocardiography showed a large mobile mass in the left atrium, suggesting cardiac myxoma as the most likely diagnosis. Surgical exploration revealed a papillary fibroelastoma originating from the coumadin ridge, which is fairly rare but important as a source of cerebral embolization.
New Size‐Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application
Authors: Hirashima Shingo , Han Ji Hoon , Tsuno Hitomi , Tanigaki Yusuke , Park Soyoung , Sugiyama Hiroshi 
Published: May 2019

AbstractHere, the synthesis, photophysical characterization, and application of a new size‐expanded thymine nucleoside, dioxT, is described. dioxT has desirable qualities as a T surrogate, including excellent quantum yield (0.36) and high environmental sensitivity. When incorporated into single‐ and double‐stranded DNA, dioxT showed excellent photophysical characteristics including a high quantum yield (average 0.20), and unlike BgQ, demonstrated dependence on neighboring bases without significant destabilization of the duplex. Interestingly, the matched base pair of adenine (A) and dioxT has the unique property that it exhibits higher fluorescence than mismatched base pairs, and dioxT has self‐quenching effects. As one example of the possible applications of these promising features, single nucleoside polymorphism typing is demonstrated for discrimination of A by using dioxT. The results suggest that dioxT can be used for a broad range of applications in chemical biology.
Fluorescent Nitric Oxide Photodonors Based on BODIPY and Rhodamine Antennae
Authors: Parisi Cristina , Failla Mariacristina , Fraix Aurore , Rolando Barbara , Gianquinto Eleonora , Spyrakis Francesca , Gazzano Elena , Riganti Chiara , Lazzarato Loretta , Fruttero Roberta , Gasco Alberto , Sortino Salvatore 
Published: May 2019

AbstractTwo novel NO photodonors (NOPDs) based on BODIPY and Rhodamine antennae activatable with the highly biocompatible green light are reported. Both NOPDs exhibit considerable fluorescence emission and release NO with remarkable quantum efficiencies. The combination of the photoreleasing and emissive performance for both compounds is superior to those exhibited by other NOPDs based on similar light‐harvesting centres, making them very intriguing for image‐guided phototherapeutic applications. Preliminary biological data prove their easy visualization in cell environment due to the intense green and orange‐red fluorescence and their photodynamic action on cancer cells due to the NO photo‐liberated.
Presence of Streptococcus dentisani in the dental plaque of children from different Colombian cities
Authors: Angarita‐Díaz María P. , Díaz Jaime A. , Tupaz Herlinto A. , López‐López Arantxa , Forero Diana , Mira Alex , Dávila Fernando , Cerón Ximena A. , Ochoa‐Acosta Emilia M. , Goméz Olga L. , Gonzalez Gladys 
Published: May 2019

AbstractStreptococcus dentisani has been identified as an oral cavity probiotic due to its beneficial characteristics. One of its beneficial features is the production of bacteriocins, which inhibit the growth of cariogenic bacteria, and another is its buffering capacity through the production of ammonium from arginine. The purpose of this study was to determine the presence of S. dentisani in the dental plaque of Colombian children and whether the presence of this bacterium is related to oral health and other conditions. Dental plaque and information on diet and oral hygiene habits were collected from children between 6 and 12 years of age from four Colombian cities, divided into caries‐free children (International Caries Detection and Assessment System [ICDAS] 0, Decayed Missing Filled Teeth index [DMFT] 0), children with ICDAS 1 and 2, and children with ICDAS >3. Plaque DNA was extracted and quantified, and real‐time polymerase chain reaction was performed using specific primers. This bacterium was identified in all samples, with a median of 0.46 cells/ng DNA (interquartile range [IQR] 0.13–1.02), without finding significant differences between the groups (P > 0.05). In caries‐free children, a median of 0.45 cells/ng DNA (IQR 0.14–1.23) was found. In children with ICDAS 1 and 2, the median was 0.49 cells/ng DNA (IQR 0.11–0.97), and in children with ICDAS >3, the median was 0.35 cells/ng DNA (IQR 0.12–1.07). However, statistically significant differences were found in the origin of children (P < 0.01), the use of fluoride‐containing products (P < 0.01), and the frequency of food intake (P < 0.05). In conclusion, the presence of S. dentisani was quantified in children from four Colombian cities, without finding significant differences in oral health status. Nevertheless, three conditions showed a possible relationship with S. dentisani.
Conscious sedation in Spanish dental schools: Current situation
Authors: Vela María Inmaculada , Arregui María , Giner Lluis , Jiménez Esther 
Published: May 2019

AbstractThe current Spanish curricula for degrees in dentistry include conscious sedation (CS) as a basic training competency. However, is the CS training delivered by Spanish dental schools a consensus‐based educational framework enabling students to use this anesthetic technique after graduation? To answer this research question, a study was designed aiming to identify the strategies used to teach this competency in Spanish dental schools and the characteristics of teaching. The authors reviewed legislation concerning officially established requirements for a degree in dentistry as well as curricula currently taught in Spain. Our analysis identified clear discrepancies among the schools of dentistry studied. The only overlap was observed in reference to the level of proficiency imparted, which prevents Spanish dentistry students from using this anesthetic technique after graduation. Specific features of the normative framework and of the Spanish legislative system underlying the design of the present curricula of degrees in dentistry would explain the discrepancies in CS competencies taught at our schools of dentistry. Almost 10 years since its implementation and in light of the new demands of the complex society in which we live, Spanish universities must unify their educational criteria regarding CS training to ensure the appropriate qualification of our new dentists in this technique.
Design of band elimination filter for PMSM vector control operable in overmodulation region of inverter
Authors: Nakayama Yosuke , Doki Shinji 
Published: May 2019

AbstractThis paper proposes a filter design for improving the control performance of the current control system of permanent magnet synchronous motors (PMSMs) using the overmodulation region of an inverter. The control performance of a vector control system for PMSMs using the overmodulation region of an inverter can be improved by suppressing harmonic components that are generated in this region. This paper utilizes band elimination filter (BEF) to eliminate harmonic components; however, unsuitable BEF setting leads to generation of large current oscillation at the resonant frequency of current feedback loop with BEF. In order to deal with these problems, the proposed filter design focuses on gain setting at the cutoff frequency of BEF. The proposed filter design can prevent the generation of current oscillation at the resonant frequency of the system, and can improve current control performance without complex adjustments. Simulations and experiments are carried out to show the effectiveness of the proposed BEF setting.
Two sequential layers of antibody‐mediated control of Legionella pneumophila infection
Authors: Weber Stefan S. , Stoycheva Diana , Nimmerjahn Falk , Oxenius Annette 
Published: May 2019

AbstractProtective immunity against intracellular pathogens, including bacteria, usually relies on cellular immunity. However, antibodies are also implicated in mediating protection against intracellular bacteria. In case of airway infection with Legionella pneumophila (Lpn), the causative agent of Legionnaires' disease, pre‐existing Lpn‐specific antibodies were shown to afford protection within two days of infection. Here we dissected the early kinetics of Ab‐mediated protection against airway Lpn infection and observed two kinetically and mechanistically distinct phases of protection by passively administered antibodies. Within the first hour of infection, Lpn‐opsonizing antibodies provided almost 10‐fold protection in an antibody Fc‐dependent, but FcR‐independent manner. Later on, by two days post infection, Lpn‐specific Ab‐mediated protection strictly involved FcγR, Syk kinase activity in alveolar macrophages and induction of reactive oxygen species (ROS). The findings presented here contribute to the understanding of the mechanisms of Ab‐mediated control of Lpn infection in actively or passively immunized individuals.
IT for the informal sector in developing countries: A broader perspective
Authors: Seetharaman Priya , Cunha Maria Alexandra , Effah John 
Published: May 2019

AbstractAlthough the informal sector's presence in the developed world is by no means meagre, the themes and issues related to information technology (IT) for this sector in the developing country contexts seem stark and deeply contrasted with those relating to the informal sector in developed countries. Solutions which attempt to exploit the potential of IT for the informal sector have thus far been either knee‐jerk, ad‐hoc, or have mimicked those targeted at the formal sector. However, technology tools available today can accelerate, catalyze, and go beyond the conventional straight‐jacketed technology, economic, and policy solutions for the informal sector. The papers in this special issue reflect this theme and attempt to present a glimpse of the possibilities for achieving and the challenges in effecting such solutions.
Nonalcoholic Fatty Liver Disease in The Rotterdam Study: About Muscle Mass, Sarcopenia, Fat Mass, and Fat Distribution
Authors: Alferink Louise Johanna Maria , Trajanoska Katerina , Erler Nicole Stephanie , Schoufour Josje Dorothea , de Knegt Robert Jacobus , Ikram M. Arfan , Janssen Harry Leonardus Antonius , Franco Oscar H. , Metselaar Herold J. , Rivadeneira Fernando , Darwish Murad Sarwa 
Published: May 2019

ABSTRACT
Nonalcoholic fatty liver disease (NAFLD) is the most prevalent liver disease worldwide. Obesity is a major risk factor for NAFLD and recently, low skeletal muscle mass emerged as additional risk factor for NAFLD. However, the different contributions of body mass index (BMI) to the risk of NAFLD are not yet well-known. We therefore studied body composition and muscle function with NAFLD in an elderly population-based study. Participants of European descent underwent dual-energy X-ray absorptiometry (DXA) and hepatic ultrasonography. NAFLD was defined as liver steatosis in absence of secondary causes for steatosis. Skeletal muscle index (SMI) was defined as appendicular lean mass/height2 and (pre)sarcopenia was defined using the European Working Group on Sarcopenia in Older People (EWGSOP) consensus guidelines. All analyses were stratified by sex and BMI (cut point: 25 kg/m2) and adjusted for age, weight, height, homeostasis model assessment of insulin resistance (HOMA-IR), triglycerides, and android-fat-to-gynoid-fat ratio (AGR). We included 4609 participants, of whom 1623 had NAFLD (n = 161 normal-weight and n = 1462 overweight). Presarcopenia and sarcopenia prevalence was low (5.9% and 4.5%, respectively) and both were not associated with NAFLD. SMI was associated with less NAFLD in normal-weight women (OR, 0.48; 95% CI, 0.29 to 0.80). A similar association for SMI and NAFLD was seen in normal-weight men, but significance dissipated after adjustment for AGR (OR, 0.63; 95% CI, 0.39 to 1.02). Generally, fat mass was a better predictor for NAFLD than lean mass. In particular, android fat mass was associated with all NAFLD subgroups (OR from 1.77 in overweight men to 8.34 in normal-weight women, pmax = 0.001), whereas substitution of gynoid fat mass for other body components had a significant protective association with NAFLD in every subgroup, but normal-weight men. Likewise, AGR was the best performing predictor for NAFLD prevalence (OR from 1.97 in normal-weight men to 4.81 in normal-weight women, pmax &lt; 0.001). In conclusion, both high fat mass and low SMI were associated with normal-weight NAFLD. However, fat distribution (as assessed by AGR) could best predict NAFLD prevalence. © 2019 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc.
Circular RNA rno_circ_0004002 regulates cell proliferation, apoptosis, and epithelial‐mesenchymal transition through targeting miR‐342‐5p and Wnt3a in anorectal malformations
Authors: Qu Yuan , Liu Dan , Jia Huimin , Yang Zhonghua 
Published: May 2019

AbstractCircular RNAs (circRNAs) are a novel class of noncoding RNAs that have regulatory functions in varieties of diseases. The purpose of this study was to investigate the potential role of circRNAs in anorectal malformations (ARM). With sequencing analysis, 78 circRNAs were identified to be differentially expressed on gestational day (GD) 19 in ARM and normal anorectal tissues, including 41 upregulated and 37 downregulated circRNAs. Among the downregulated circRNAs, rno_circ_0004002 was selected as the candidate circRNA. Functionally, silencing of rno_circ_0004002 was correlated with suppression of proliferation, and promotion of apoptosis and epithelial‐mesenchymal transition (EMT) in anorectal development. For the mechanism investigation, bioinformatic prediction and luciferase reporter assay revealed that rno_circ_0004002 was proved to be a sponge of miR‐342‐5p, and miR‐342‐5p could target 3'‐UTR of Wnt3a to negatively regulate its expression. The quantitative reverse transcription polymerase chain reaction (qRT‐PCR) results showed that the expression of miR‐342‐5p was significantly increased in ARM anorectal tissues compared with normal tissues on GD19 and GD21, and the expression of Wnt3a demonstrated the opposite on GD21. In addition, rescue assays disclosed that miR‐342‐5p inhibitor could reverse the role of rno_circ_0004002 knockdown on the repression of anorectal development. In summary, our study shed light on the regulatory mechanism of rno_circ_0004002 in cell proliferation, apoptosis, and EMT via sponging miR‐342‐5p, which downregulated the Wnt3a expression in anorectal development. We also suggested that GD19 and GD21 was the crucial time in the progression of ARM, and rno_circ_0004002/miR‐342‐5p/Wnt3a might serve as potential therapeutic targets for ARM.
Gene expression profile of the hippocampus of rats subjected to traumatic brain injury
Authors: Huang Guo‐Hui , Cao Xiang‐Yuan , Li Yuan‐Yuan , Zhou Cheng‐Cheng , Li Lei , Wang Ke , Li Hong , Yu Peng , Jin Yi , Gao Liang 
Published: May 2019

AbstractTraumatic brain injury (TBI) is a serious public health problem as well as a leading cause of severe posttraumatic disability. Numerous studies indicate that the differentially expressed genes (DEGs) of neural signaling pathways are strongly correlated with brain injury. To further analyze the roles of the DGEs in the central nervous system, here we systematically investigated TBI on the hippocampus and its injury mechanism at the whole genome level. On the basis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Analyses, we revealed that the DEGs were involved in many signaling pathways related to the nervous system, especially neuronal survival‐related pathways. Finally, we verified the microarray results and detected the gene expression of neuronal survival‐related genes in the hippocampus by using real‐time quantitative polymerase chain reaction. With Western blot and axon growth assay, the expression of P2rx3 was upregulated in rats subjected to TBI, and overexpression of P2rx3 promoted neurite growth of NG108 cells. Our results suggested that the DEGs (especially P2rx3) and several signaling pathways might play a pivotal role in TBI. We also provided several targeted genes related to TBI for future investigation.
Quantitative assessment of the association between TAP2 rs241447 polymorphism and cancer risk
Authors: Liu Rongzeng , Ma Yan , Chen Xiafei 
Published: May 2019

AbstractThe findings regarding the relation of transporter associated with antigen processing (TAP) to cancer risk have been inconsistent. The aim of this study was to comprehensively evaluate the association between TAP2 rs241447 polymorphism and cancer susceptibility. A meta‐analysis of nine investigations with 2800 cases and 1620 controls was conducted to gain a better understanding of the effect of TAP2 rs241447 polymorphism on cancer risk. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the strength of the correlation between TAP2 gene polymorphism and cancer susceptibility. The pooled results from TAP2 rs241447 polymorphism showed a decreased risk of cancer in two dominant genetic models (GG + AG vs AA: OR = 0.86, 95% CI, 0.75‐0.99; AG vs AA: OR = 0.85, 95% CI, 0.73‐0.99). From the subgroup analysis, decreased cancer susceptibility was found in Caucasians (GG + AG vs AA: OR = 0.82, 95% CI, 0.68‐0.99), especially among the subgroup of cervical carcinoma (GG + AG vs AA: OR = 0.82, 95% CI, 0.69‐0.96; AG vs AA: OR = 0.83, 95% CI, 0.70‐0.99). Overall, the results suggest that TAP2 rs241447 polymorphism contributes to decreased cancer susceptibility.
miRNA expression profiling uncovers a role of miR‐302b‐3p in regulating skin fibroblasts senescence
Authors: Tan Jingyong , Hu Longyuan , Yang Xin , Zhang Xin , Wei Canshen , Lu Qing , Chen Zhilin , Li Jing 
Published: May 2019

AbstractNumbers of emerging evidence suggest that variable microRNA (miRNA) expression facilitates the aging process. In this study, we distinguished aberrant miRNA expression in aged skin and explored the biological functions and potential mechanism of upregulated miR‐302b‐3p. At first, miRNA microarray analysis was examined to explore miRNA expression profiling in the skin of aging mice model by D‐galactose (d‐gal) injection. We identified 29 aberrant miRNAs in aged mice skin. Next, KEGG enrichment analysis was conducted with DIANA‐miPath v3.0, which was revealed that enrichment pathways involved in such processes as extracellular matrix‐receptor interaction, MAPK signaling pathway, and mammalian target of rapamycin (mTOR) signaling pathway. The target genes of deregulated miRNAs were predicted from four bioinformatic algorithms (miRDB, Targetscan, miRwalk, and Tarbase). The interaction network of miRNAs and their targets were visualized using Cytoscape software. As a result, we found that some hub genes (including JNK2, AKT1/2/3, PAK7, TRPS1, BCL2L11, and IKZF2) were targeted by 12 potential miRNAs (including miR‐302b‐3p, miR‐291a‐5p, miR‐139‐3p, miR‐467c‐3p, miR‐186‐3p, etc.). Subsequently, we identified five upregulated miRNA via quantitative polymerase chain reaction and all of them were confirmed increased significantly in aged skin tissues compared with young control tissues. Among them, high expression of miR‐302b‐3p was verified in both aged skin tissues and senescence fibroblasts. Furthermore, miR‐302b‐3p mimic accelerated skin fibroblast senescence and suppressed the longevity‐associated gene Sirtuin 1(Sirt1) expression, whereas miR‐302b‐3p inhibitor could delay skin fibroblast senescence and contribute Sirt1 expression. In addition, we demonstrated that c‐Jun N‐terminal kinase 2(JNK2) is a direct target of miR‐302b‐3p by a luciferase reporter assay. An inverse correlation was verified in fibroblasts between miR‐302b‐3p and JNK2. Most importantly, siRNA JNK2 confirmed that low expression of JNK2 could accelerate fibroblasts senescence. In conclusion, our results indicated that overexpressed miR‐302b‐3p plays an important biological role in accelerating skin aging process via directly targeting JNK2 gene.