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https://www.readbyqxmd.com/read/29152808/observational-safety-study-of-specific-outcomes-after-trivalent-cell-culture-seasonal-influenza-vaccination-optaflu-%C3%A2-among-adults-in-thin-database-of-electronic-uk-primary-healthcare-records
#1
Gillian C Hall, Paul T G Davies, M Yousuf Karim, Mendel D M Haag, Caroline O'Leary
PURPOSE: To investigate the safety of trivalent seasonal influenza vaccine (TIVc) (Optaflu(®) ), the first cell culture seasonal trivalent influenza vaccine available in Europe. METHODS: Codes and unstructured text in adult electronic healthcare records (The Health Improvement Network) were searched for a TIVc brand name or batch number and possible outcomes within a 3 month pre- to 6 month post-TIVc exposure study period (2012-2015). The outcomes were severe allergic reactions, Bell's palsy, convulsions, demyelination, paresthesia, noninfectious encephalitis, neuritis (optic and brachial), vasculitis, inflammatory bowel disease, and thrombocytopenia...
November 20, 2017: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/29151698/circulating-mirnas-as-biomarkers-for-severe-acute-pancreatitis-associated-with-acute-lung-injury
#2
Xiao-Guang Lu, Xin Kang, Li-Bin Zhan, Li-Min Kang, Zhi-Wei Fan, Li-Zhi Bai
AIM: To identify circulating micro (mi)RNAs as biological markers for prediction of severe acute pancreatitis (SAP) with acute lung injury (ALI). METHODS: Twenty-four serum samples were respectively collected and classified as SAP associated with ALI and SAP without ALI, and the miRNA expression profiles were determined by microarray analysis. These miRNAs were validated by quantitative reverse transcription-polymerase chain reaction, and their putative targets were predicted by the online software TargetScan, miRanda and PicTar database...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29147538/scaling-behaviour-and-rate-determining-steps-in-filamentous-self-assembly
#3
Georg Meisl, Luke Rajah, Samuel A I Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K Buell, Adriano Aguzzi, Sara Linse, Michele Vendruscolo, Christopher M Dobson, Tuomas P J Knowles
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29138860/an-rna%C3%A2-sequencing-study-identifies-candidate-genes-for-angiotensin-ii%C3%A2-induced-cardiac-remodeling
#4
Jin Shu, Zhanwen Liu, Li Jin, Haiya Wang
The present study aimed to reveal the underlying mechanism of angiotensin II (AngII)‑induced cardiac remodeling and to identify potential therapeutic targets for prevention. Rat cardiac fibroblasts (CFs) were cultured with 10 nM AngII for 12 h, and CFs without AngII were used as the control. Following RNA isolation from AngII treated and control CFs, RNA‑sequencing was performed to detect gene expression levels. Differentially‑expressed genes (DEGs) were identified using the linear models for microarray analysis package in R software, and their functions and pathways were examined via enrichment analysis...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29137180/metabolomic-modularity-analysis-mma-to-quantify-human-liver-perfusion-dynamics
#5
Gautham Vivek Sridharan, Bote Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L Yarmush, Korkut Uygun
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29133453/expanding-the-informational-chemistries-of-life-peptide-rna-networks
#6
REVIEW
Olga Taran, Chenrui Chen, Tolulope O Omosun, Ming-Chien Hsieh, Allisandra Rha, Jay T Goodwin, Anil K Mehta, Martha A Grover, David G Lynn
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29123999/inflammation-related-genes-are-upregulated-in-surgical-margins-of-advanced-stage-oral-squamous-cell-carcinoma
#7
Jaijam Suwanwela, Thanaphum Osathanon
Aims: Advanced stage of oral squamous cell carcinoma (OSCC) exhibits different properties compared with the early stage for example an invasion ability. The present study investigated a differential gene expression of surgical margin between advanced and early stage of OSCC. Methods: Gene Expression Omnibus dataset (GSE31056) was downloaded and re-analyzed. Surgical margin samples were categorized into 2 groups; early stage and late stage. Differential gene expression analysis was performed...
September 2017: Journal of Oral Biology and Craniofacial Research
https://www.readbyqxmd.com/read/29117534/building-predictive-models-of-genetic-circuits-using-the-principle-of-maximum-caliber
#8
Taylor Firman, Gábor Balázsi, Kingshuk Ghosh
Learning the underlying details of a gene network is a major challenge in cellular and synthetic biology. We address this challenge by building a chemical kinetic model that utilizes information encoded in the stochastic protein expression trajectories typically measured in experiments. The applicability of the proposed method is demonstrated in an auto-activating genetic circuit, a common motif in natural and synthetic gene networks. Our approach is based on the principle of maximum caliber (MaxCal)-a dynamical analog of the principle of maximum entropy-and builds a minimal model using only three constraints: 1) protein synthesis, 2) protein degradation, and 3) positive feedback...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29111050/xyloglucan-based-hydrogel-films-for-wound-dressing-structure-property-relationships
#9
Alessia Ajovalasit, Maria Antonietta Sabatino, Simona Todaro, Sabina Alessi, Daniela Giacomazza, Pasquale Picone, Marta Di Carlo, Clelia Dispenza
Thin xyloglucan-based hydrogel films have been synthetized and characterized in the prospect of producing wound dressings. Polyvinyl alcohol (PVA) and glycerol (Gro) were added to have an optimal combination of softness, conformability and resilience. Physical hydrogels have been transformed into permanent covalent hydrogels by reaction with glutaraldehyde (GA). Network structure-process-property relationships are discussed on the account of the results of several complementary characterizations: FTIR, rheology, thermal analysis, morphological analysis, moisture retention and swelling measurements...
January 1, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29110513/ankaferd-influences-mrna-expression-of-iron-regulated-genes-during-iron-deficiency-anemia
#10
Afife Gulec, Sukru Gulec
Ankaferd Blood Stopper (ABS) comprises a mixture of plants and stops bleeding via forming a protein network by erythroid aggregation. Bleeding causes reduction of iron levels in body. It has been indicated that ABS contains significant amount of iron. Thus, we investigated the biological activity of ABS-derived iron on iron-regulated genes during iron-deficiency anemia (IDA). IDA We selected Caco-2 and HepG2 cell lines as in vitro models of human intestine and liver, respectively. Iron deficiency anemia was induced by deferoxamine...
January 1, 2017: Clinical and Applied Thrombosis/hemostasis
https://www.readbyqxmd.com/read/29110175/optimization-and-verification-of-droplet-digital-pcr-even-specific-methods-for-the-quantification-of-gm-maize-das1507-and-nk603
#11
Katarzyna Grelewska-Nowotko, Magdalena Żurawska-Zajfert, Ewelina Żmijewska, Sławomir Sowa
In recent years, digital polymerase chain reaction (dPCR), a new molecular biology technique, has been gaining in popularity. Among many other applications, this technique can also be used for the detection and quantification of genetically modified organisms (GMOs) in food and feed. It might replace the currently widely used real-time PCR method (qPCR), by overcoming problems related to the PCR inhibition and the requirement of certified reference materials to be used as a calibrant. In theory, validated qPCR methods can be easily transferred to the dPCR platform...
November 6, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29099123/exploring-the-emergence-of-complexity-using-synthetic-replicators
#12
REVIEW
Tamara Kosikova, Douglas Philp
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks...
November 3, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/29097405/the-evolution-of-gene-specific-transcriptional-noise-is-driven-by-selection-at-the-pathway-level
#13
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
https://www.readbyqxmd.com/read/29095957/circular-rna-profile-of-infantile-hemangioma-by-microarray-analysis
#14
Cong Fu, Renrong Lv, Guangqi Xu, Linfeng Zhang, Jianhai Bi, Li Lin, Xiaowen Liu, Ran Huo
BACKGROUND: Circular RNAs (circRNAs) are a recently identified class of noncoding RNAs that participate in several physiological processes. However, the expression of circRNAs in infantile hemangioma (IH) remains unknown. METHODS: The profile of circRNAs was assessed by microarray in four pairs of IH and adjacent skin tissues. The expression of circRNAs was validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, circRNA-microRNAs (miRNA)-mRNA networks were constructed using bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/29080799/slow-update-stochastic-simulation-algorithms-for-modeling-complex-biochemical-networks
#15
Debraj Ghosh, Rajat K De
The stochastic simulation algorithm (SSA) based modeling is a well recognized approach to predict the stochastic behavior of biological networks. The stochastic simulation of large complex biochemical networks is a challenge as it takes a large amount of time for simulation due to high update cost. In order to reduce the propensity update cost, we proposed two algorithms: slow update exact stochastic simulation algorithm (SUESSA) and slow update exact sorting stochastic simulation algorithm (SUESSSA). We applied cache-based linear search (CBLS) in these two algorithms for improving the search operation for finding reactions to be executed...
October 30, 2017: Bio Systems
https://www.readbyqxmd.com/read/29077809/linking-metabolic-network-features-to-phenotypes-using-sparse-group-lasso
#16
Satya Swarup Samal, Ovidiu Radulescu, Andreas Weber, Holger Fröhlich
Motivation: Integration of metabolic networks with '-omics' data has been a subject of recent research in order to better understand the behaviour of such networks with respect to differences between biological and clinical phenotypes. Under the conditions of steady state of the reaction network and the non-negativity of fluxes, metabolic networks can be algebraically decomposed into a set of sub-pathways often referred to as extreme currents (ECs). Our objective is to find the statistical association of such sub-pathways with given clinical outcomes, resulting in a particular instance of a self-contained gene set analysis method...
November 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29064083/new-insights-into-flavivirus-biology-the-influence-of-ph-over-interactions-between-prm-and-e-proteins
#17
Edson R A Oliveira, Ricardo B de Alencastro, Bruno A C Horta
Diseases caused by flaviviruses, such as dengue and zika, are globally recognized as major threats. During infection, a critical point in their replicative cycle is the maturation step, which occurs throughout the cellular exocytic pathway. This step is a pH-dependent process that involves the modification of the viral envelope by converting prM (pre-membrane) into M (membrane) proteins with the release of a "pr peptide". After this reaction, the pr peptides remain bound to the viral envelope while the virions cross the acidic trans-Golgi network, and are released only at neutral pH after secretion of the virus particles...
October 24, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29058744/hybrid-deterministic-stochastic-simulation-of-complex-biochemical-systems
#18
Paola Lecca, Fabio Bagagiolo, Marina Scarpa
In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects...
October 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29040409/towards-dynamic-genome-scale-models
#19
David Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
The analysis of the dynamic behaviour of genome-scale models of metabolism (GEMs) currently presents considerable challenges because of the difficulties of simulating such large and complex networks. Bacterial GEMs can comprise about 5000 reactions and metabolites, and encode a huge variety of growth conditions; such models cannot be used without sophisticated tool support. This article is intended to aid modellers, both specialist and non-specialist in computerized methods, to identify and apply a suitable combination of tools for the dynamic behaviour analysis of large-scale metabolic designs...
October 13, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29038751/combining-graph-and-flux-based-structures-to-decipher-phenotypic-essential-metabolites-within-metabolic-networks
#20
Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, Maria-Paz Cortes, Jeanne Got, Camille Trottier, Damien Eveillard, Anne Siegel
BACKGROUND: The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions...
2017: PeerJ
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