Read by QxMD icon Read

Computational biology

Djordje Mirkovic, Phillip M Stepanian, Jeffrey F Kelly, Phillip B Chilson
The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes...
October 20, 2016: Scientific Reports
Alessandro Borri, Pasquale Palumbo, Abhyudai Singh
Synthetic biology combines different branches of biology and engineering aimed at designing synthetic biological circuits able to replicate emergent properties useful for the biotechnology industry, human health and environment. The role of negative feedback in noise propagation for a basic enzymatic reaction scheme is investigated. Two feedback control schemes on enzyme expression are considered: one from the final product of the pathway activity, the other from the enzyme accumulation. Both schemes are designed to provide the same steady-state average values of the involved players, in order to evaluate the feedback performances according to the same working mode...
October 2016: IET Systems Biology
V R Knight-Schrijver, V Chelliah, L Cucurull-Sanchez, N Le Novère
Recent growth in annual new therapeutic entity (NTE) approvals by the U.S. Food and Drug Administration (FDA) suggests a positive trend in current research and development (R&D) output. Prior to this, the cost of each NTE was considered to be rising exponentially, with compound failure occurring mainly in clinical phases. Quantitative systems pharmacology (QSP) modelling, as an additional tool in the drug discovery arsenal, aims to further reduce NTE costs and improve drug development success. Through in silico mathematical modelling, QSP can simulate drug activity as perturbations in biological systems and thus understand the fundamental interactions which drive disease pathology, compound pharmacology and patient response...
2016: Computational and Structural Biotechnology Journal
Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs), cellular growth factors and microRNAs. A subsystem's gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally-e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution...
October 2016: PLoS Computational Biology
Yoonsik Shim, Andrew Philippides, Kevin Staras, Phil Husbands
We propose a biologically plausible architecture for unsupervised ensemble learning in a population of spiking neural network classifiers. A mixture of experts type organisation is shown to be effective, with the individual classifier outputs combined via a gating network whose operation is driven by input timing dependent plasticity (ITDP). The ITDP gating mechanism is based on recent experimental findings. An abstract, analytically tractable model of the ITDP driven ensemble architecture is derived from a logical model based on the probabilities of neural firing events...
October 2016: PLoS Computational Biology
Jing-Min Liu, Yao-Yao Liu, Dong-Dong Zhang, Guozhen Fang, Shuo Wang
The rise of multimodal nanoprobes has promoted the development of new methods to explore multiple molecular targets simultaneously, or to combine various bioimaging tools in one assay to more clearly delineate localization and expression of bio-markers. Persistent luminescence nanophosphors (PLNPs) have been qualified as the promising contrast agent for in vivo imaging. The easy surface modification and proper nanostructure design strategy would favor the fabrication of PLNPs based multi-functional nanoprobes for biological application...
October 19, 2016: ACS Applied Materials & Interfaces
S P Pfeifer
Sequencing has revolutionized biology by permitting the analysis of genomic variation at an unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it accessible for a wide range of research topics. However, the produced data contain subtle but complex types of errors, biases and uncertainties that impose several statistical and computational challenges to the reliable detection of variants. To tap the full potential of high-throughput sequencing, a thorough understanding of the data produced as well as the available methodologies is required...
October 19, 2016: Heredity
Armando Lopes, Paulo Maló, Miguel de Araújo Nobre, Elena Sánchez-Fernández, Inês Gravito
BACKGROUND: There is a necessity of studies documenting the long-term outcome of full-arch flapless rehabilitations. PURPOSE: To evaluate the 7 years implant and prosthesis survival rate and 5-years marginal bone loss of full-arch fixed prosthetic rehabilitations supported by implants in immediate function with the All-on-4(®) treatment concept using a computer guided surgical protocol (NobelGuide(®) , Nobel Biocare). MATERIALS AND METHODS: This retrospective clinical study included 111 edentulous patients (n = 53 bruxers; n = 21 smokers; n = 59 systemically compromised), rehabilitated between February 2005 and November 2010 with 532 implants with the All-on-4(®) treatment concept using NobelGuide(®) ...
October 18, 2016: Clinical Implant Dentistry and related Research
Su Lui, Xiaohong Joe Zhou, John A Sweeney, Qiyong Gong
Unlike neurologic conditions, such as brain tumors, dementia, and stroke, the neural mechanisms for all psychiatric disorders remain unclear. A large body of research obtained with structural and functional magnetic resonance imaging, positron emission tomography/single photon emission computed tomography, and optical imaging has demonstrated regional and illness-specific brain changes at the onset of psychiatric disorders and in individuals at risk for such disorders. Many studies have shown that psychiatric medications induce specific measurable changes in brain anatomy and function that are related to clinical outcomes...
November 2016: Radiology
Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Blazewicz
Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins)...
October 19, 2016: Acta Biochimica Polonica
Jhih-Rong Lin, Ying Cai, Quanwei Zhang, Wen Zhang, Ruben Nogales, Zhengdong Zhang
Schizophrenia is a severe mental disorder with a large genetic component. Recent genome-wide association studies (GWAS) have identified many schizophrenia-associated common variants. For most of the reported associations, however, the underlying biological mechanisms are not clear. The critical first step for their elucidation is to identify the most likely disease genes as the source of the association signals. Here, we describe a general computational framework of post-GWAS analysis for complex disease gene prioritization...
October 17, 2016: Genetics
Jonathan Sandoval-Castillo, Catherine R M Attard, Shashikanth Marri, Chris J Brauer, Luciana M Möller, Luciano B Beheregaray
Captive breeding programs are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programs have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding...
October 18, 2016: Molecular Ecology Resources
Caterina Catalanotto, Carlo Cogoni, Giuseppe Zardo
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs...
October 13, 2016: International Journal of Molecular Sciences
Alberto Avolio
Blood vessels function as conduits for distribution of blood throughout the circulatory system. Large arteries, in addition to the essential conduit function, also serve to dampen the effect of pulsatile ventricular ejection that generates pulsatile pressure with each cardiac cycle; that is, they exhibit a 'cushion' function. The conduit function can be compromised by intimal effects that cause obstruction to flow, generally attributed to plaque formation due to intimal changes affected by atherosclerotic processes...
September 2016: Journal of Hypertension
Elsa Iannicelli, Francesco Carbonetti, Giulia Francesca Federici, Isabella Martini, Salvatore Caterino, Emanuela Pilozzi, Francesco Panzuto, Chiara Briani, Vincenzo David
OBJECTIVES: The aim of this study was to correlate computed tomography (CT) findings with pathology in gastrointestinal stromal tumors (GISTs). METHODS: A retrospective evaluation of CT images of 44 patients with GISTs was performed. Computed tomography findings analyzed were location, size, margins, degree and pattern of contrast enhancement, angiogenesis, necrosis, signs of invasion, peritoneal effusion, peritoneal implants, surface ulceration, and calcifications...
October 7, 2016: Journal of Computer Assisted Tomography
Qian Wang, Renato Polimanti, Henry R Kranzler, Lindsay A Farrer, Hongyu Zhao, Joel Gelernter
Schizophrenia (SZ) and HIV infection are serious disorders with a complex phenotypic relationship. Observational studies have described their comorbidity; their genetic correlation is not well studied. We performed extensive analysis in search of common genetic factors for SZ and HIV, and their relationship with risky sexual behavior (RSB). Summary statistics from genome-wide association studies of HIV infection and schizophrenia were obtained and 2379 European Americans were genotyped and assessed for RSB score...
October 17, 2016: Human Genetics
Jeganathan Manivannan, Manjunath Prashanth, Venkatesan Saravana Kumar, Manickaraj Shairam, Jayachandran Subburaj
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding...
October 18, 2016: Molecular BioSystems
Liu Chunbao, Li Li, Lei Yulong, Liu Changsuo, Zhang Yubo
Fish-like, dolphin-like, and bionic nonsmooth surfaces were employed in a hydraulic torque converter to achieve drag reduction and performance improvement, which were aimed at reducing profile loss, impacting loss and friction loss, respectively. YJSW335, a twin turbine torque converter, was bionically designed delicately. The biological characteristics consisted of fish-like blades in all four wheels, dolphin-like structure in the first turbine and the stator, and nonsmooth surfaces in the pump. The prediction performance of bionic YJSW335, obtained by computational fluid dynamics simulation, was improved compared with that of the original model, and then it could be proved that drag reduction had been achieved...
2016: Applied Bionics and Biomechanics
Efeturi Abraham Onoabedje, Akachukwu Ibezim, Sunday Nwankwor Okafor, Ufuoma Shalom Onoabedje, Uchechukwu Chris Okoro
Penicillin binding proteins (PBPs) are normal constituents of bacterial which are absent in mammalian cells. The theoretical binding modes of known oxazin-5-ones toward the protein were used as a guide to synthesis new inhibitors. Structural studies of protein-ligand complexes revealed that conformational discrepancies of the derivatives in the protein's binding site gave rise to the variation in their inhibition constant which ranged from 68.58 μM to 2.04 mM. Biological assay results further confirmed the antibiotic potencies of the studied compounds...
2016: PloS One
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1004884.].
October 2016: PLoS Computational Biology
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"