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https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#1
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430345/healing-response-of-rat-pulp-treated-with-an-injectable-keratin-hydrogel
#2
Lavanya Ajay Sharma, Robert M Love, Mohammad A Ali, Ajay Sharma, Soraia Macari, Avadhoot Avadhani, George J Dias
BACKGROUND: Keratin has shown promising outcomes as a biomaterial due to its inherent bioactivity, biocompatibility and regenerative effects. The effect of keratin on repair and regeneration of dental tissues has never been studied before. Current therapies to treat pulp tissues involve its replacement with inert, synthetic materials that do not have a proper biological function, leading to failure and tooth loss. This study aimed to develop a biocompatible keratin hydrogel (KH) suitable for pulp therapies...
April 20, 2017: Journal of Applied Biomaterials & Functional Materials
https://www.readbyqxmd.com/read/28430005/issues-in-current-microrna-target-identification-methods
#3
Hervé Seitz
microRNAs are currently believed to control a large diversity of physiological processes, through the collective repression of thousands of target genes. Both experimental and computational analyses indeed suggest that each microRNA regulates tens or hundreds of genes. But some observations suggest that the phenotypic consequences of many published miRNA/mRNA interactions are dubious. For example, the reported amplitude of miRNA-guided repression is very small, while biological processes tend to be robust to small changes in gene expression...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28429146/clinical-validity-of-biochemical-and-molecular-analysis-in-diagnosing-leigh-syndrome-a-study-of-106-japanese-patients
#4
Erika Ogawa, Masaru Shimura, Takuya Fushimi, Makiko Tajika, Keiko Ichimoto, Ayako Matsunaga, Tomoko Tsuruoka, Mika Ishige, Tatsuo Fuchigami, Taro Yamazaki, Masato Mori, Masakazu Kohda, Yoshihito Kishita, Yasushi Okazaki, Shori Takahashi, Akira Ohtake, Kei Murayama
Leigh syndrome (LS) is a progressive neurodegenerative disorder of infancy and early childhood. It is clinically diagnosed by typical manifestations and characteristic computed tomography (CT) or magnetic resonance imaging (MRI) studies. Unravelling mitochondrial respiratory chain (MRC) dysfunction behind LS is essential for deeper understanding of the disease, which may lead to the development of new therapies and cure. The aim of this study was to evaluate the clinical validity of various diagnostic tools in confirming MRC disorder in LS and Leigh-like syndrome (LL)...
April 20, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28428762/gendered-pathways-how-mathematics-ability-beliefs-shape-secondary-and-postsecondary-course-and-degree-field-choices
#5
REVIEW
Lara Perez-Felkner, Samantha Nix, Kirby Thomas
Do mathematics ability beliefs explain gender gaps in the physical science, engineering, mathematics, and computer science fields (PEMC) and other science fields? We leverage U.S. nationally representative longitudinal data to estimate gendered differences in girls' and boys' perceptions of mathematics ability with the most difficult or challenging material. Our analyses examine the potentially interacting effects of gender and these ability beliefs on students' pathways to scientific careers. Specifically, we study how beliefs about ability with challenging mathematics influence girls' and boys' choices to pursue PEMC degrees, evaluating educational milestones over a 6-year period: advanced science course completion in secondary school and postsecondary major retention and selection...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28428742/a-set-based-mixed-effect-model-for-gene-environment-interaction-and-its-application-to-neuroimaging-phenotypes
#6
Changqing Wang, Jianping Sun, Bryan Guillaume, Tian Ge, Derrek P Hibar, Celia M T Greenwood, Anqi Qiu
Imaging genetics is an emerging field for the investigation of neuro-mechanisms linked to genetic variation. Although imaging genetics has recently shown great promise in understanding biological mechanisms for brain development and psychiatric disorders, studying the link between genetic variants and neuroimaging phenotypes remains statistically challenging due to the high-dimensionality of both genetic and neuroimaging data. This becomes even more challenging when studying gene-environment interaction (G×E) on neuroimaging phenotypes...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28428554/network-assisted-analysis-of-gwas-data-identifies-a-functionally-relevant-gene-module-for-childhood-onset-asthma
#7
Y Liu, M Brossard, C Sarnowski, A Vaysse, M Moffatt, P Margaritte-Jeannin, F Llinares-López, M H Dizier, M Lathrop, W Cookson, E Bouzigon, F Demenais
The number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28427670/estimation-of-the-distribution-of-low-intensity-ultrasound-mechanical-index-as-a-parameter-affecting-the-proliferation-of-spermatogonia-stem-cells-in-vitro
#8
Zeinab Hormozi Moghaddam, Manijhe Mokhtari-Dizaji, Mansoureh Movahedin, Mohammad Ehsan Ravari
Considering the use of physical and mechanical stimulation, such as low-intensity ultrasound for proliferation and differentiation of stem cells, it is essential to understand the physical and acoustical mechanisms of acoustic waves in vitro. Mechanical index is used for quantifying acoustic cavitation and the relationship between acoustic pressure and the frequency. In this study, modeling of the mechanical index was applied to provide treatment protocol and to understand the effective physical processes on reproducibility of stem cells...
July 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28427316/a-multiscale-modelling-approach-to-understand-atherosclerosis-formation-a-patient-specific-case-study-in-the-aortic-bifurcation
#9
Mona Alimohammadi, Cesar Pichardo-Almarza, Obiekezie Agu, Vanessa Díaz-Zuccarini
Atherogenesis, the formation of plaques in the wall of blood vessels, starts as a result of lipid accumulation (low-density lipoprotein cholesterol) in the vessel wall. Such accumulation is related to the site of endothelial mechanotransduction, the endothelial response to mechanical stimuli and haemodynamics, which determines biochemical processes regulating the vessel wall permeability. This interaction between biomechanical and biochemical phenomena is complex, spanning different biological scales and is patient-specific, requiring tools able to capture such mathematical and biological complexity in a unified framework...
May 2017: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28427314/capturing-complexity-in-pulmonary-system-modelling
#10
Alys R Clark, Haribalan Kumar, Kelly Burrowes
Respiratory disease is a significant problem worldwide, and it is a problem with increasing prevalence. Pathology in the upper airways and lung is very difficult to diagnose and treat, as response to disease is often heterogeneous across patients. Computational models have long been used to help understand respiratory function, and these models have evolved alongside increases in the resolution of medical imaging and increased capability of functional imaging, advances in biological knowledge, mathematical techniques and computational power...
May 2017: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28426839/medical-history-in-the-hellenic-journal-of-nuclear-medicine
#11
EDITORIAL
Andreas Otte, Byeong Cheol Ahn
The Hellenic Journal of Nuclear Medicine is about to celebrate its 20th anniversary end of 2017. On board of the editorial team since 2003, this journal has influenced me like a good friend over the many past years. From time to time, the journal has published interesting and valuable historical notes. They show that nuclear medicine has a history and that medicine is its basis. They also teach us today, and some of the ancient perspectives and approaches are still valid. The reader of HJNM may be interested in these historical contributions, as they are timeless...
January 2017: Hellenic Journal of Nuclear Medicine
https://www.readbyqxmd.com/read/28426095/models-of-global-gene-expression-define-major-domains-of-cell-type-and-tissue-identity
#12
Andrew P Hutchins, Zhongzhou Yang, Yuhao Li, Fangfang He, Xiuling Fu, Xiaoshan Wang, Dongwei Li, Kairong Liu, Jiangping He, Yong Wang, Jiekai Chen, Miguel A Esteban, Duanqing Pei
The current classification of cells in an organism is largely based on their anatomic and developmental origin. Cells types and tissues are traditionally classified into those that arise from the three embryonic germ layers, the ectoderm, mesoderm and endoderm, but this model does not take into account the organization of cell type-specific patterns of gene expression. Here, we present computational models for cell type and tissue specification derived from a collection of 921 RNA-sequencing samples from 272 distinct mouse cell types or tissues...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28425476/lncrnas2pathways-identifying-the-pathways-influenced-by-a-set-of-lncrnas-of-interest-based-on-a-global-network-propagation-method
#13
Junwei Han, Siyao Liu, Zeguo Sun, Yunpeng Zhang, Fan Zhang, Chunlong Zhang, Desi Shang, Haixiu Yang, Fei Su, Yanjun Xu, Chunquan Li, Huan Ren, Xia Li
Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, we have developed a novel computational method, LncRNAs2Pathways, to identify the functional pathways influenced by the combinatorial effects of a set of lncRNAs of interest based on a global network propagation algorithm...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424560/an-exploratory-study-of-host-polymorphisms-in-genes-that-clinically-characterize-breast-cancer-tumors-and-pretreatment-cognitive-performance-in-breast-cancer-survivors
#14
Theresa A Koleck, Catherine M Bender, Beth Z Clark, Christopher M Ryan, Puja Ghotkar, Adam Brufsky, Priscilla F McAuliffe, Priya Rastogi, Susan M Sereika, Yvette P Conley
PURPOSE: Inspired by the hypothesis that heterogeneity in the biology of breast cancers at the cellular level may account for cognitive dysfunction symptom variability in survivors, the current study explored relationships between host single-nucleotide polymorphisms (SNPs) in 25 breast cancer-related candidate genes (AURKA, BAG1, BCL2, BIRC5, CCNB1, CD68, CENPA, CMC2, CTSL2, DIAPH3, ERBB2, ESR1, GRB7, GSTM1, MELK, MKI67, MMP11, MYBL2, NDC80, ORC6, PGR, RACGAP1, RFC4, RRM2, and SCUBE2), identified from clinically relevant prognostic multigene-expression profiles for breast cancer, and pretreatment cognitive performance...
2017: Breast Cancer: Targets and Therapy
https://www.readbyqxmd.com/read/28424527/unified-alignment-of-protein-protein-interaction-networks
#15
Noël Malod-Dognin, Kristina Ban, Nataša Pržulj
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424087/heroes-of-peer-review-robert-lowe
#16
Robert Lowe
In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biology.
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28423900/methodology-for-the-simulation-of-molecular-motors-at-different-scales
#17
Abhishek Singharoy, Christophe Chipot
Millisecond-scale conformational transitions represent a seminal challenge for traditional molecular dynamics simulations, even with the help of high-end supercomputer architectures. Such events are particularly relevant to the study of molecular motors-proteins or abiological constructs that convert chemical energy into mechanical work. Here, we present a hybrid-simulation scheme combining an array of methods including elastic network models, transition path sampling, and advanced free-energy methods, possibly in conjunction with generalized-ensemble schemes to deliver a viable option for capturing the millisecond-scale motor steps of biological motors...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28423569/accurate-prediction-of-protein-protein-interactions-by-integrating-potential-evolutionary-information-embedded-in-pssm-profile-and-discriminative-vector-machine-classifier
#18
Zheng-Wei Li, Zhu-Hong You, Xing Chen, Li-Ping Li, De-Shuang Huang, Gui-Ying Yan, Ru Nie, Yu-An Huang
Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423538/gene-regulatory-pattern-analysis-reveals-essential-role-of-core-transcriptional-factors-activation-in-triple-negative-breast-cancer
#19
Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo-Cheng Yuan, Chengchao Shou
BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype. Genome-scale molecular characteristics and regulatory mechanisms that distinguish TNBC from other subtypes remain incompletely characterized. RESULTS: By combining gene expression analysis and PANDA network, we defined three different TF regulatory patterns. A core TNBC-Specific TF Activation Driven Pattern (TNBCac) was specifically identified in TNBC by computational analysis...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423275/single-or-multiple-access-channels-to-the-cyp450s-active-site-an-answer-from-free-energy-simulations-of-the-human-aromatase-enzyme
#20
Alessandra Magistrato, Jacopo Sgrignani, Rolf Krause, Andrea Cavalli
Cytochromes P450 (CYP450), in particular CYP19A1 and CYP17A1, are key clinical targets of breast and prostate anticancer therapies, critical players in drug metabolism and their overexpression in tumours is associated with drug resistance. In these enzymes ligands (substrates, drugs) metabolism occurs in deeply buried active sites accessible only via several gruelling channels, whose exact biological role remains unclear. Gaining direct insights on the mechanism by which ligands travel in and out, is becoming increasingly important given that channels are involved in the modulation of binding/dissociation kinetics and the specificity of ligands toward a CYP450...
April 19, 2017: Journal of Physical Chemistry Letters
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