(information technology) articles in PubMed
- Bioinspired decision architectures containing host and microbiome processing units. [Journal Article]
- Bioinspir Biomim 2016; 11(5):056017BB
- Biomimetic robots have been used to explore and explain natural phenomena ranging from the coordination of ants to the locomotion of lizards. Here, we developed a series of decision architectures ins...
Biomimetic robots have been used to explore and explain natural phenomena ranging from the coordination of ants to the locomotion of lizards. Here, we developed a series of decision architectures inspired by the information exchange between a host organism and its microbiome. We first modeled the biochemical exchanges of a population of synthetically engineered E. coli. We then built a physical, differential drive robot that contained an integrated, onboard computer vision system. A relay was established between the simulated population of cells and the robot's microcontroller. By placing the robot within a target-containing a two-dimensional arena, we explored how different aspects of the simulated cells and the robot's microcontroller could be integrated to form hybrid decision architectures. We found that distinct decision architectures allow for us to develop models of computation with specific strengths such as runtime efficiency or minimal memory allocation. Taken together, our hybrid decision architectures provide a new strategy for developing bioinspired control systems that integrate both living and nonliving components.
- Effects of in vitro and in vivo avermectin exposure on alpha synuclein expression and proteasomal activity in pigeons. [Journal Article]
- Ecotoxicol Environ Saf 2016 Sep 24; 135:24-31EE
- Avermectins (AVMs) are used worldwide in agriculture and veterinary medicine. Residues of avermectin drugs, causing toxicological effects on non-target organisms, have raised great concern. The aim o...
Avermectins (AVMs) are used worldwide in agriculture and veterinary medicine. Residues of avermectin drugs, causing toxicological effects on non-target organisms, have raised great concern. The aim of this study was to investigate the effects of AVM on the expression levels of alpha synuclein (α-Syn) and proteasomal activity in pigeon (Columba livia) neurons both in vivo and in vitro. The results showed that, the mRNA and protein levels of α-Syn increased in AVM treated groups relative to control groups in the cerebrum, cerebellum and optic lobe in vivo. Dose-dependent decreases in the proteasomal activity (i.e., chymotrypsin-like, trypsin-like and peptidylglutamyl peptidehydrolase) were observed both in vivo and in vitro. The results suggested that AVM could induce the expression levels of α-Syn and inhibit the normal physiological function of proteasome in brain tissues and neurons. The information presented in this study is helpful to understand the mechanism of AVM-induced neurotoxicology in birds.
- The pathological behaviors and prognostic factors of Chinese and Japanese colorectal cancers from general hospitals: a comparative study of the inpatients with surgical operation. [Journal Article]
- Oncotarget 2016 Sep 24O
- Here, we collected the information of 17304 and 2014 inpatients with colorectal cancer (CRC) from general hospitals of China and Japan respectively, and analyzed microscopic and macroscopic aspects, ...
Here, we collected the information of 17304 and 2014 inpatients with colorectal cancer (CRC) from general hospitals of China and Japan respectively, and analyzed microscopic and macroscopic aspects, even stratified by the age and gender. It was found that Chinese CRC patients showed younger prone, more rectal and ascending cancers, less sigmoid and transverse cancers, larger size, less invasion into lymphatic system or metastasis into lymph node, and poorer differentiation than Japanese ones (p < 0.05). TNM staging was employed as an independent factor for the prognosis of the CRC patients regardless of the country (p < 0.05). Female patients showed larger tumor size, easier invasion and metastasis into lymphatic system, and worse differentiation than males (p < 0.05). The younger patients displayed frequent invasion and metastasis into lymphatic system, and poor differentiation in comparison to elder ones (p < 0.05). These findings demonstrated that Japanese patients seemed to have more invasion and metastasis due to standard and precise operation and pathological diagnosis accuracy. Actually, Chinese patients had more aggressive pathological characteristics and a poorer prognosis. Therefore, it is essential to establish a routine screening methodology, a standard treatment system and postoperative diagnosis protocol for the prevention and therapeutics of Chinese CRC patients, especially for female and young patients.
- Building a 'Repository of Science': The importance of integrating biobanks within molecular pathology programmes. [Review]
- Eur J Cancer 2016 Sep 23; 67:191-199EJ
- Repositories containing high quality human biospecimens linked with robust and relevant clinical and pathological information are required for the discovery and validation of biomarkers for disease d...
Repositories containing high quality human biospecimens linked with robust and relevant clinical and pathological information are required for the discovery and validation of biomarkers for disease diagnosis, progression and response to treatment. Current molecular based discovery projects using either low or high throughput technologies rely heavily on ready access to such sample collections. It is imperative that modern biobanks align with molecular diagnostic pathology practices not only to provide the type of samples needed for discovery projects but also to ensure requirements for ongoing sample collections and the future needs of researchers are adequately addressed. Biobanks within comprehensive molecular pathology programmes are perfectly positioned to offer more than just tumour derived biospecimens; for example, they have the ability to facilitate researchers gaining access to sample metadata such as digitised scans of tissue samples annotated prior to macrodissection for molecular diagnostics or pseudoanonymised clinical outcome data or research results retrieved from other users utilising the same or overlapping cohorts of samples. Furthermore, biobanks can work with molecular diagnostic laboratories to develop standardised methodologies for the acquisition and storage of samples required for new approaches to research such as 'liquid biopsies' which will ultimately feed into the test validations required in large prospective clinical studies in order to implement liquid biopsy approaches for routine clinical practice. We draw on our experience in Northern Ireland to discuss how this harmonised approach of biobanks working synergistically with molecular pathology programmes is a key for the future success of precision medicine.
- Investigating neovascularization in rat decellularized intestine - an in vitro platform for studying angiogenesis. [Journal Article]
- Tissue Eng Part A 2016 Sep 27TE
- One of the main challenges currently faced by tissue engineers is the loss of tissues post implantation due to delayed neovascularization. Several strategies are under investigation to create vascula...
One of the main challenges currently faced by tissue engineers is the loss of tissues post implantation due to delayed neovascularization. Several strategies are under investigation to create vascularized tissue but none have yet overcome this problem. In this study we produced a decellularized natural vascular scaffold from rat intestine to use as an in vitro platform for neovascularization studies for tissue engineered constructs. Decellularization resulted in almost complete (97%) removal of nuclei and DNA, while collagen, glycosaminoglycans and laminin content was preserved. Decellularization did, however, result in the loss of elastin and fibronectin. Some pro-angiogenic factors were retained, as fragments of decellularized intestine were able to stimulate angiogenesis in the chick chorioallantoic membrane assay. We demonstrated that decellularization left perfusable vascular channels intact, and these could be re-populated with human dermal microvascular endothelial cells. Optimization of re-endothelialisation of the vascular channels showed this was improved by continuous perfusion of the vasculature and further improved by infusion of human dermal fibroblasts into the intestinal lumen, from where they invaded into the decellularized tissue. Finally we explored the ability of the perfused cells to form new vessels. In the absence of exogenous angiogenic stimuli, Dll4, a marker of endothelial capillary-tip cell activation during sprouting angiogenesis was absent, indicating the reformed vasculature was largely quiescent. However, after addition of VEGFA, Dll4 positive endothelial cells could be detected, demonstrating this engineered vascular construct maintained its capacity for neovascularization. In summary we have demonstrated how a natural xenobiotic vasculature can be used as an in vitro model platform to study neovascularization and provide information on factors that are critical for efficient re-endothelialisation of decellularized tissue.
- Using Bayesian hierarchical models to better understand nitrate sources and sinks in agricultural watersheds. [Journal Article]
- Water Res 2016 Sep 20; 105:527-539WR
- Export coefficient models (ECMs) are often used to predict nutrient sources and sinks in watersheds because ECMs can flexibly incorporate processes and have minimal data requirements. However, ECMs d...
Export coefficient models (ECMs) are often used to predict nutrient sources and sinks in watersheds because ECMs can flexibly incorporate processes and have minimal data requirements. However, ECMs do not quantify uncertainties in model structure, parameters, or predictions; nor do they account for spatial and temporal variability in land characteristics, weather, and management practices. We applied Bayesian hierarchical methods to address these problems in ECMs used to predict nitrate concentration in streams. We compared four model formulations, a basic ECM and three models with additional terms to represent competing hypotheses about the sources of error in ECMs and about spatial and temporal variability of coefficients: an ADditive Error Model (ADEM), a SpatioTemporal Parameter Model (STPM), and a Dynamic Parameter Model (DPM). The DPM incorporates a first-order random walk to represent spatial correlation among parameters and a dynamic linear model to accommodate temporal correlation. We tested the modeling approach in a proof of concept using watershed characteristics and nitrate export measurements from watersheds in the Coastal Plain physiographic province of the Chesapeake Bay drainage. Among the four models, the DPM was the best--it had the lowest mean error, explained the most variability (R(2) = 0.99), had the narrowest prediction intervals, and provided the most effective tradeoff between fit complexity (its deviance information criterion, DIC, was 45.6 units lower than any other model, indicating overwhelming support for the DPM). The superiority of the DPM supports its underlying hypothesis that the main source of error in ECMs is their failure to account for parameter variability rather than structural error. Analysis of the fitted DPM coefficients for cropland export and instream retention revealed some of the factors controlling nitrate concentration: cropland nitrate exports were positively related to stream flow and watershed average slope, while instream nitrate retention was positively correlated with nitrate concentration. By quantifying spatial and temporal variability in sources and sinks, the DPM provides new information to better target management actions to the most effective times and places. Given the wide use of ECMs as research and management tools, our approach can be broadly applied in other watersheds and to other materials.
- Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information. [Journal Article]
- PLoS One 2016; 11(9):e0163628Plos
- A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell f...
A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.
- A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. [Journal Article]
- PLoS Pathog 2016; 12(9):e1005883PP
- The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversi...
The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3'-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.
- Respiratory Signal Prediction Based on Adaptive Boosting and Multilayer Perceptron Neural Network. [Journal Article]
- Int J Radiat Oncol Biol Phys 2016 Oct 1; 96(2S):E702IJ
New Search Next
- A Feasible Small Footprint Bunker Concept for Real-Time Magnetic Resonance Imaging-Guided Proton Beam Therapy. [Journal Article]
- Int J Radiat Oncol Biol Phys 2016 Oct 1; 96(2S):E602IJ