keyword
MENU ▼
Read by QxMD icon Read
search

Computational biology

keyword
https://www.readbyqxmd.com/read/28823079/mechanobiological-model-of-arterial-growth-and-remodeling
#1
Maziyar Keshavarzian, Clark A Meyer, Heather N Hayenga
A coupled agent-based model (ABM) and finite element analysis (FEA) computational framework is developed to study the interplay of bio-chemo-mechanical factors in blood vessels and their role in maintaining homeostasis. The agent-based model implements the power of REPAST Simphony libraries and adapts its environment for biological simulations. Coupling a continuum-level model (FEA) to a cellular-level model (ABM) has enabled this computational framework to capture the response of blood vessels to increased or decreased levels of growth factors, proteases and other signaling molecules (on the micro scale) as well as altered blood pressure...
August 19, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28822696/influence-of-surgical-decompression-on-the-expression-of-inflammatory-and-tissue-repair-biomarkers-in-periapical-cysts
#2
Janderson Teixeira Rodrigues, Henrique Dos Santos Antunes, Luciana Armada, Fábio Ramôa Pires
OBJECTIVE: The biologic effects of surgical decompression on the epithelium and connective tissues of periapical cysts are not fully understood. The aim of this study was to evaluate the expression of tissue repair and inflammatory biomarkers in periapical cysts before and after surgical decompression. STUDY DESIGN: Nine specimens of periapical cysts treated with decompression before undergoing complete enucleation were immunohistochemically analyzed to investigate the expression of interleukin-1β, tumor necrosis factor-α, transforming growth factor-β1, matrix metalloproteinase-9, Ki-67, and epidermal growth factor receptor...
July 5, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/28821595/a-computational-model-of-1-5-ag-dynamics-during-pregnancy
#3
Seyedeh M Zekavat, Slava Butkovich, Grace J Young, David M Nathan, Danny Petrasek
The importance of 1,5-anhydroglucitol (1,5-AG) as an intermediate biomarker for diabetic pregnancy is multi-fold: (1) it serves as a reliable indicator of moderate-level glycemic control, especially during early gestation; (2) it has been associated with increased risk of diabetes, independent of HbA1c and fasting glucose; and (3) it is an independent risk factor for the development of eclampsia during pregnancy. However, the clinical use of this biomarker during pregnancy has been underutilized due to physiological changes in glomerular filtration rate, plasma volume, and other hemodynamic parameters which have been hypothesized to bias gestational serum 1,5-AG concentrations...
August 2017: Physiological Reports
https://www.readbyqxmd.com/read/28821273/a-practical-guide-to-single-cell-rna-sequencing-for-biomedical-research-and-clinical-applications
#4
REVIEW
Ashraful Haque, Jessica Engel, Sarah A Teichmann, Tapio Lönnberg
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation...
August 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28820886/circulating-mirnas-in-sepsis-a-network-under-attack-an-in-silico-prediction-of-the-potential-existence-of-mirna-sponges-in-sepsis
#5
Catalin Vasilescu, Mihnea Dragomir, Mihai Tanase, Dana Giza, Raluca Purnichescu-Purtan, Meng Chen, Sai-Ching Jim Yeung, George A Calin
Biomarkers based on the molecular mechanism of sepsis are important for timely diagnosis and treatment. A large panel of small non-coding microRNAs was reported to modulate the immune response in sepsis but have not been tested in clinical practice. Large-scale identification of microRNA networks in sepsis might reveal a new biological mechanism that can be also targeted by gene therapy. Therefore, the main objective of this study is to perform a comparison of the miRNA network between septic patients and healthy controls...
2017: PloS One
https://www.readbyqxmd.com/read/28820673/asymmetric-compression-of-representational-space-for-object-animacy-categorization-under-degraded-viewing-conditions
#6
Tijl Grootswagers, J Brendan Ritchie, Susan G Wardle, Andrew Heathcote, Thomas A Carlson
Animacy is a robust organizing principle among object category representations in the human brain. Using multivariate pattern analysis methods, it has been shown that distance to the decision boundary of a classifier trained to discriminate neural activation patterns for animate and inanimate objects correlates with observer RTs for the same animacy categorization task [Ritchie, J. B., Tovar, D. A., & Carlson, T. A. Emerging object representations in the visual system predict reaction times for categorization...
August 18, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/28820140/clarity-of-objectives-and-working-principles-enhances-the-success-of-biomimetic-programs
#7
Jonas Wolff, David Wells, Chris Reid, Sean John Blamires
Biomimetics, the transfer of functional principles from living systems into product designs, is increasingly being utilized by engineers. Nevertheless, recurring problems must be overcome if it is to avoid becoming a short-lived fad. Here we assess the efficiency and suitability of methods typically employed by examining three flagship examples of biomimetic design approaches from different disciplines: (1) the creation of gecko-inspired adhesives; (2) the synthesis of spider silk, and (3) the derivation of computer algorithms from natural self-organizing systems...
August 18, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28819656/simulating-the-reactions-of-substituted-pyridinio-n-phosphonates-with-pyridine-as-a-model-for-biological-phosphoryl-transfer
#8
Anna Pabis, Nicholas H Williams, Shina C L Kamerlin
Phosphoryl transfer reactions can proceed through several plausible mechanisms, and the potential for both solvent and substrate-assisted pathways (involving proton transfer to the phosphoryl oxygens) complicates both experimental and computational interpretations. To avoid this problem, we have used electronic structure calculations to probe the mechanisms of the reactions of pyridinio-N-phosphonates with pyridine. These compounds avoid the additional complexity introduced by proton transfer between the nucleophile and the leaving group, while also serving as a valuable model for biological P-N cleavage...
August 18, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28819560/a-novel-peptide-blocking-cancer-cell-invasion-by-structure-based-drug-design
#9
Yuki Yamada, Seiji Kanayama, Fuminori Ito, Noriyuki Kurita, Hiroshi Kobayashi
The receptor for the urokinase-type plasminogen activator (uPA), uPAR, facilitates tumor cell invasion and metastasis by focusing on several ligands, including uPA, integrins and vitronectin. With computational prediction algorithms and structure-based drug design, we identified peptides containing the Gly-Lys-Gly-Glu-Gly-Glu-Gly-Lys-Gly sequence (peptide H1), which strongly interacts with uPAR. The aim of the present study was to investigate the effect of allosteric inhibition at the uPAR interface using a novel synthetic peptide and its function on ovarian cancer cell invasion...
September 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28819307/crispr-cas9-editing-reveals-novel-mechanisms-of-clustered-microrna-regulation-and-function
#10
Lazaros Lataniotis, Andreas Albrecht, Fatma O Kok, Clinton A L Monfries, Lorena Benedetti, Nathan D Lawson, Simon M Hughes, Kathleen Steinhofel, Manuel Mayr, Anna Zampetaki
MicroRNAs (miRNAs) are important regulators of diverse physiological and pathophysiological processes. MiRNA families and clusters are two key features in miRNA biology. Here we explore the use of CRISPR/Cas9 as a powerful tool to delineate the function and regulation of miRNA families and clusters. We focused on four miRNA clusters composed of miRNA members of the same family, homo-clusters or different families, hetero-clusters. Our results highlight different regulatory mechanisms in miRNA cluster expression...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818579/developing-integrated-pbpk-pd-coupled-mechanistic-pathway-model-mirna-bdnf-an-approach-towards-system-toxicology
#11
Raju Prasad Sharma, Marta Schuhmacher, Vikas Kumar
Integration of a dynamic signal transduction pathway into the tissue dosimetry model is a major advancement in the area of computational toxicology. This paper illustrates the ways to incorporate the use of existing system biological model in the field of toxicology via its coupling to the Physiological based Pharmacokinetics and Pharmacodynamics (PBPK/PD) model.This expansion framework of integrated PBPK/PD coupled mechanistic system pathway model can be called as system toxicology that describes the kinetics of both -the chemicals and -biomolecules, help us to understand the dynamic and steady-state behaviors of molecular pathways under perturbed condition...
August 14, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28818495/direct-in-silico-visualization-of-ligands-channelling-through-proteins-the-next-generation-frontier-of-computational-biology-comment-on-ligand-diffusion-via-enhanced-sampling-molecular-dynamics-by-jakub-rydzewski-and-wieslaw-nowak
#12
https://www.readbyqxmd.com/read/28818005/computational-biology-future-challenges-for-the-patenting-of-repurposed-drugs
#13
Bruce Bloom
No abstract text is available yet for this article.
August 18, 2017: Pharmaceutical Patent Analyst
https://www.readbyqxmd.com/read/28817636/uncovering-robust-patterns-of-microrna-co-expression-across-cancers-using-bayesian-relevance-networks
#14
Parameswaran Ramachandran, Daniel Sánchez-Taltavull, Theodore J Perkins
Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths...
2017: PloS One
https://www.readbyqxmd.com/read/28817608/data-driven-coarse-graining-of-large-biomolecular-structures
#15
Yi-Ling Chen, Michael Habeck
Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements...
2017: PloS One
https://www.readbyqxmd.com/read/28817585/selecting-targets-for-the-diagnosis-of-schistosoma-mansoni-infection-an-integrative-approach-using-multi-omic-and-immunoinformatics-data
#16
Gardenia B F Carvalho, Daniela M Resende, Liliane M V Siqueira, Marcelo D Lopes, Débora O Lopes, Paulo Marcos Z Coelho, Andréa Teixeira-Carvalho, Jeronimo C Ruiz, Cristina T Fonseca
In order to effectively control and monitor schistosomiasis, new diagnostic methods are essential. Taking advantage of computational approaches provided by immunoinformatics and considering the availability of Schistosoma mansoni predicted proteome information, candidate antigens of schistosomiasis were selected and used in immunodiagnosis tests based on Enzime-linked Immunosorbent Assay (ELISA). The computational selection strategy was based on signal peptide prediction; low similarity to human proteins; B- and T-cell epitope prediction; location and expression in different parasite life stages within definitive host...
2017: PloS One
https://www.readbyqxmd.com/read/28817244/key-developments-that-impacted-the-field-of-mechanobiology-and-mechanotransduction
#17
Michelle Wall, David Butler, Alicia El Haj, Josephine C Bodle, Elizabeth G Loboa, Albert J Banes
Advances in mechanobiology have evolved through insights from multiple disciplines including structural engineering, biomechanics, vascular biology, and orthopaedics. In this paper, we reviewed the impact of key reports related to the study of applied loads on tissues and cells and the resulting signal transduction pathways. We addressed how technology has helped advance the burgeoning field of mechanobiology (over 33,600 publications from 1970-2016). We analyzed the impact of critical ideas and then determined how these concepts influenced the mechanobiology field by looking at the citation frequency of these reports as well as tracking how the overall number of citations within the field changed over time...
August 17, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28817145/coherent-electronic-and-nuclear-dynamics-in-a-rhodamine-heterodimer-dna-supramolecular-complex
#18
M Cipolloni, B Fresch, I Occhiuto, P Rukin, K G Komarova, A Cecconello, I Willner, R D Levine, F Remacle, E Collini
Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because of the decisive implications for understanding the biological processes and engineering artificial materials for solar energy harvesting. A supramolecular rhodamine heterodimer on a DNA scaffold was suitably engineered to mimic the basic donor-acceptor unit of light-harvesting antennas. Ultrafast 2D electronic spectroscopic measurements allowed identifying clear features attributable to a coherent superposition of dimer electronic and vibrational states contributing to the coherent electronic charge beating between the donor and the acceptor...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28816826/tissue-engineered-bone-differentiated-from-human-adipose-derived-stem-cells-inhibit-posterolateral-fusion-in-an-athymic-rat-model
#19
Comron Saifi, Jonahtan Bernhard, Jamal N Shillingford, Petros Petridis, Samuel Robinson, X Edward Guo, Mark Weidenbaum, Ronald A Lehman, Howard S An, Lawrence G Lenke, Gordana Vunjak-Novakovic, Joseph L Laratta
STUDY DESIGN: Biological augmentation spinal arthrodesis trial in athymic rats OBJECTIVE.: To assess the efficacy of tissue-engineered bone to promote L4-L5 intertransverse process fusion in an athymic rat model. SUMMARY OF BACKGROUND DATA: Each year in the United States, over 400,000 spinal fusion surgeries are performed requiring bone graft. The current gold standard for posterolateral lumbar fusion is autogenous iliac crest bone graft (ICBG), but the harvesting of ICBG is associated with increased operative time and significant complications...
August 14, 2017: Spine
https://www.readbyqxmd.com/read/28816149/a-multi-institution-retrospective-analysis-of-cervix-intracavitary-brachytherapy-treatments-part-1-is-eqd2-good-enough-for-reporting-radiobiological-effects
#20
Emma C Fields, Rakhi Melvani, George Hajdok, David D'Souza, Bernard Jones, Kelly Stuhr, Quentin Diot, Christine M Fisher, Nitai Mukhopadhyay, Dorin Todor
PURPOSE: When brachytherapy doses are reported or added, biologically effective dose (BED) minimum dose covering 90% of the volume (D90) is used as if dose is delivered uniformly to the target. Unlike BED(D90), equivalent uniform BED (EUBED) and generalized biologically equivalent uniform dose (gBEUD) are quantities that integrate dose inhomogeneity. Here we compared BED(D90) and equivalent uniform BED (EUBED)/gBEUD in 3 settings: (1) 2 sites using tandem and ovoid (T&O) but different styles of implants; (2) 2 sites using different devices-T&O and tandem and ring (T&R)-and different styles; and (3) the same site using T&O and T&R with the same style...
September 1, 2017: International Journal of Radiation Oncology, Biology, Physics
keyword
keyword
20301
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"