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Network analysis

Yanwei Xing, Zhiwei Zhao, Yuekun Zhu, Liangliang Zhao, Anlong Zhu, Daxun Piao
The objective of this study was to identify potentially significant genes and long non-coding RNAs (lncRNAs) in colon cancer for a panel of lncRNA signatures that could be used as prognostic markers for colon adenocarcinoma (COAD) based on the data from The Cancer Genome Atlas (TCGA). RNA-seq V2 exon data of COAD were downloaded from the TCGA data portal for 285 tumor samples and 41 normal tissue samples adjacent to tumors. Differentially expressed mRNAs and lncRNAs were identified. A functional enrichment analysis of differentially expressed mRNAs was performed, followed by protein-protein interaction (PPI) network construction and significant module selection...
May 2018: Oncology Reports
Jing Lin, Jianling Zuo, Yong Cui, Chaoli Song, Xiaojun Wu, Huaizhi Feng, Jian Li, Shuo Li, Qinian Xu, Wenxin Wei, Guanzhong Qiu, Hua He
Acquired chemoresistance refers to tumor cells gradually losing their sensitivity to anticancer drugs during the course of treatment, resulting in tumor progression or recurrence. This phenomenon, which has deleterious outcomes for the patient, has long been observed in patients with glioblastoma receiving temozolomide (TMZ)-based radiochemotherapy. Currently, the mechanisms for acquired TMZ chemoresistance are not fully understood. In the present study, a TMZ-resistant cell line U251R with a 4-fold 50% inhibition concentration compared with its TMZ-sensitive parent cell line was isolated by incremental long-time TMZ treatment in the human glioblastoma cell line U251...
May 2018: Oncology Reports
Juanjuan Gao, Qi Tang, Xiaohui Zhu, Shihua Wang, Yongli Zhang, Wenbin Liu, Zhiqiang Gao, Hua Yang
Cholesteatoma is a pathologically benign but clinically destructive middle ear disease, which is caused by excessive epidermal migration and uncontrolled hyperproliferation of keratinocytes of squamous epithelium, leading to various clinical manifestations and serious complications, such as hearing loss, dizziness, facial paralysis, meningitis, and hydrocephalus. However, the pathogenesis of cholesteatoma is still not fully understood. Herein, we performed microarray analysis to identify the differentially expressed patterns of lncRNAs in cholesteatoma for the first time...
May 2018: Oncology Reports
Mahesh Rangu, Zhujia Ye, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, Theodore W Thannhauser
In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 μM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis...
March 22, 2018: Proteomes
Rosario Pignatello, Tiziana M G Pecora, Giuseppa G Cutuli, Alfio Catalfo, Guido De Guidi, Barbara Ruozi, Giovanni Tosi, Simona Cianciolo, Teresa Musumeci
Trans-resveratrol (RSV) was microencapsulated in Eudragit® RS100 and RL100 resin blends. Lyophilized microspheres were characterized in the solid state for their micromeritic properties and drug loading. FT-IR, PXRD and DSC analyses suggested that RSV formed an intimate microcrystalline dispersion within the polymer network, also confirmed by SEM analysis. This produced a reduced degradation of RSV after storage at 40°C, compared to the neat drug, and a protection of the drug from UV light-induced trans-cis isomerization (60% intact drug was found after 60 sec irradiation at 350 nm, compared to 37% for the pure drug)...
March 22, 2018: Pharmaceutical Development and Technology
Yu-Yan Li, Guang Zheng, Liang Liu
OBJECTIVE: To decipher the possible mechanisms of Sinomenium Acutum (SA) in treating diseases by a bioinformatics method. METHODS: SA ingredients were searched according to Chinese Pharmacopoeia, Chinese Medicine Dictionary and Traditional Chinese Medicines Database (TCMD). Active compounds and target proteins of SA were acquired through the Pubchem platform. Pathway, network and function analyses of SA were performed with ingenuity pathway analysis (IPA), a bioinformatics analysis platform...
March 21, 2018: Chinese Journal of Integrative Medicine
Aaron B Simmons, Peter G Fuerst
The retina is a highly organized neural tissue consisting of three neural layers and two synaptic layers. Blood vessels that nourish the mouse and human neural retina mirror this organization consisting of three plexus layers, or plexuses, that run parallel within the retina, connected by interplexus vessels to create a closed vascular network. Here, we describe a methodology to describe this organization that can be used to interrogate factors mediating retinal vessel patterning including: coverage of the vascular plexuses, branching and orientation of the interplexus connections, and digital reconstruction of the retinal vasculature to measure vessel length and density...
2018: Methods in Molecular Biology
Shatakshee Chatterjee, Rohan Chaubal, Arindam Maitra, Nilesh Gardi, Amit Dutt, Sudeep Gupta, Rajendra A Badwe, Partha P Majumder, Priyanka Pandey
PURPOSE: We have reported a survival benefit of single injection of hydroxyprogesterone prior to surgery for primary tumour in patients with node-positive operable breast cancer. Hydroxyprogesterone was meant to recapitulate the luteal phase of menstrual cycle in these women. We wanted to understand the molecular basis of action of hydroxyprogesterone on primary breast tumours in a peri-operative setting. METHODS: We performed whole transcriptome sequencing (RNA-Seq) of primary breast tumour samples collected from patients before and after hydroxyprogesterone exposure and controls...
March 21, 2018: Breast Cancer Research and Treatment
James Deraeve, William H Alexander
Multi-voxel pattern analysis often necessitates feature selection due to the high dimensional nature of neuroimaging data. In this context, feature selection techniques serve the dual purpose of potentially increasing classification accuracy and revealing sets of features that best discriminate between classes. However, feature selection techniques in current, widespread use in the literature suffer from a number of deficits, including the need for extended computational time, lack of consistency in selecting features relevant to classification, and only marginal increases in classifier accuracy...
March 21, 2018: Neuroinformatics
Fabienne D Simonis, Carmen S V Barbas, Antonio Artigas-Raventós, Jaume Canet, Rogier M Determann, James Anstey, Goran Hedenstierna, Sabrine N T Hemmes, Greet Hermans, Michael Hiesmayr, Markus W Hollmann, Samir Jaber, Ignacio Martin-Loeches, Gary H Mills, Rupert M Pearse, Christian Putensen, Werner Schmid, Paolo Severgnini, Roger Smith, Tanja A Treschan, Edda M Tschernko, Marcos F Vidal Melo, Hermann Wrigge, Marcelo Gama de Abreu, Paolo Pelosi, Marcus J Schultz, Ary Serpa Neto
BACKGROUND: The majority of critically ill patients do not suffer from acute respiratory distress syndrome (ARDS). To improve the treatment of these patients, we aimed to identify potentially modifiable factors associated with outcome of these patients. METHODS: The PRoVENT was an international, multicenter, prospective cohort study of consecutive patients under invasive mechanical ventilatory support. A predefined secondary analysis was to examine factors associated with mortality...
March 21, 2018: Annals of Intensive Care
Suying Bao, Lilong Jia, Xueya Zhou, Zhi-Gang Zhang, Hazel Wai Lan Wu, Zhe Yu, Gordon Ng, Yanhui Fan, Dana S M Wong, Shishu Huang, Kelvin Kai Wang To, Kwok-Yung Yuen, Man Lung Yeung, You-Qiang Song
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection...
March 21, 2018: Functional & Integrative Genomics
I Gnass, S Krutter, N Nestler
BACKGROUND: People with cancer are increasingly supported by home care services. Pain is a relevant symptom of these diseases and nurses of home care services are involved in the treatment. The German National Expert Standard "Pain management in nursing" includes evidence-based recommendations for the implementation of adequate pain management. Considering the given structural conditions of home care services, nurses describe both barriers and challenges with the implementation...
March 21, 2018: Der Schmerz
Azadeh Ahmadi, Zahra Fatemi, Sara Nazari
Using the multivariate statistical methods, this study interprets a set of data containing 23 water quality parameters from 10 quality monitoring stations in Karkheh River located in southwest of Iran over 5 years. According to cluster analysis, the stations are classified into three classes of quality, and the most important factors on the whole set of parameters and each class are determined by the help of factor analysis. The results indicate the effects of natural factors, soil weathering and erosion, urban and human wastewater, agricultural and industrial wastewater on water quality at different levels and any location...
March 22, 2018: Environmental Monitoring and Assessment
U Hassan, R Zhu, R Bashir
Sepsis, as a leading cause of death worldwide, relies on systemic inflammatory response syndrome (SIRS) criteria for its diagnosis. SIRS is highly non-specific as it relies on monitoring of patients' vitals for sepsis diagnosis, which are known to change with many confounding factors. Changes in leukocyte counts and CD64 expression levels are known specific biomarkers of pro-inflammatory host response at the onset of sepsis. Recently, we have developed a biosensor chip that can enumerate the leukocyte counts and quantify the neutrophil CD64 expression levels from a drop of blood...
March 22, 2018: Lab on a Chip
Elisabeth Wittenberg, Andreas Meyer, Steffen Eggers, Volker Abetz
Styrene-butadiene copolymers are modified with varying fractions of benzoic acid moieties being able to perform hydrogen bonding. This is done by using a simple synthetic approach which utilizes click chemistry. Temperature-dependent dynamic mechanical properties are studied, and it turns out that even the apparently rather simple hydrogen bonding motif has a marked impact on the material properties due to the fact that it facilitates the formation of a supramolecular polymer network. Besides a glass transition, the investigated functionalized copolymers exhibit a second endothermic transition, known as a quasi-melting...
March 22, 2018: Soft Matter
Reza Karbalaei, Marzieh Allahyari, Mostafa Rezaei-Tavirani, Hamid Asadzadeh-Aghdaei, Mohammad Reza Zali
Aim: Analysis reconstruction networks from two diseases, NAFLD and Alzheimer`s diseases and their relationship based on systems biology methods. Background: NAFLD and Alzheimer`s diseases are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on relation and same spreading pathways of these two diseases. In addition, they have some similar risk factors, exclusively lifestyle such as feeding, exercises and so on...
2018: Gastroenterology and Hepatology From Bed to Bench
Zohaib Khan, Vahid Rahimi-Eichi, Stephan Haefele, Trevor Garnett, Stanley J Miklavcic
Background: Unmanned aerial vehicles offer the opportunity for precision agriculture to efficiently monitor agricultural land. A vegetation index (VI) derived from an aerially observed multispectral image (MSI) can quantify crop health, moisture and nutrient content. However, due to the high cost of multispectral sensors, alternate, low-cost solutions have lately received great interest. We present a novel method for model-based estimation of a VI using RGB color images. The non-linear spatio-spectral relationship between the RGB image of vegetation and the index computed by its corresponding MSI is learned through deep neural networks...
2018: Plant Methods
Tatiana V Karpinets, Vancheswaran Gopalakrishnan, Jennifer Wargo, Andrew P Futreal, Christopher W Schadt, Jianhua Zhang
Studies of microbial communities by targeted sequencing of rRNA genes lead to recovering numerous rare low-abundance taxa with unknown biological roles. We propose to study associations of such rare organisms with their environments by a computational framework based on transformation of the data into qualitative variables. Namely, we analyze the sparse table of putative species or OTUs (operational taxonomic units) and samples generated in such studies, also known as an OTU table, by collecting statistics on co-occurrences of the species and on shared species richness across samples...
2018: Frontiers in Microbiology
Daihong Liu, Shanshan Duan, Chaoyang Zhou, Ping Wei, Lihua Chen, Xuntao Yin, Jiuquan Zhang, Jian Wang
Type 2 diabetes mellitus (T2DM) affects a vast population and is closely associated with cognitive impairment. However, the mechanisms of cognitive impairment in T2DM patients have not been unraveled. Research on the basic units (nodes or hubs and edges) of the brain functional network on the basis of neuroimaging may advance our understanding of the network change pattern in T2DM patients. This study investigated the change patterns of brain functional hubs using degree centrality (DC) analysis and the connectivity among these hubs using functional connectivity and Granger causality analysis...
2018: Frontiers in Aging Neuroscience
Shengbing Wang, Vidya Venkatraman, Erin L Crowgey, Ting Liu, Zongming Fu, Ronald J Holewinski, Mark J J Ranek, David A Kass, Brian O'Rourke, Jennifer E Van Eyk
<u>Rationale:</u> Glycogen synthase kinase 3β (GSK3β) is a multifunctional and constitutively active kinase known to regulate a myriad of cellular processes. The primary mechanism to regulate its function is through phosphorylation-dependent inhibition at serine-9 residue. Emerging evidence indicates that there may be alternative mechanisms that control GSK3β for certain functions. <u>Objective:</u> Here we sought to understand the role of protein S-nitrosylation (SNO) on the function of GSK3β...
March 21, 2018: Circulation Research
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