Using a kernel density estimation based classifier to predict species-specific microRNA precursors

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are short non-coding RNA molecules participating in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years. Recently, <it>ab initio </it>approaches obtain more attention because that they can discover species-specific pre-miRNAs. Most <it>ab initio </it>approaches proposed novel features to characterize RNA molecules. However, there were fewer discussions on the associated classification mechanism in a miRNA predictor.</p> <p>Results</p> <p>This study focuses on the classification algorithm for miRNA prediction. We develop a novel <it>ab initio </it>method, miR-KDE, in which most of the features are collected from previous works. The classification mechanism in miR-KDE is the relaxed variable kernel density estimator (RVKDE) that we have recently proposed. When compared to the famous support vector machine (SVM), RVKDE exploits more local information of the training dataset. MiR-KDE is evaluated using a training set consisted of only human pre-miRNAs to predict a benchmark collected from 40 species. The experimental results show that miR-KDE delivers favorable performance in predicting human pre-miRNAs and has advantages for pre-miRNAs from the genera taxonomically distant to humans.</p> <p>Conclusion</p> <p>We use a novel classifier of which the characteristic of exploiting local information is particularly suitable to predict species-specific pre-miRNAs. This study also provides a comprehensive analysis from the view of classification mechanism. The good performance of miR-KDE encourages more efforts on the classification methodology as well as the feature extraction in miRNA prediction.</p

A study on the flexibility of enzyme active sites

<p>Abstract</p> <p>Background</p> <p>A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted.</p> <p>Results</p> <p>Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites.</p> <p>Conclusions</p> <p>This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites.</p

Lasing on nonlinear localized waves in curved geometry

The use of geometrical constraints opens many new perspectives in photonics and in fundamental studies of nonlinear waves. By implementing surface structures in vertical cavity surface emitting lasers as manifolds for curved space, we experimentally study the impacts of geometrical constraints on nonlinear wave localization. We observe localized waves pinned to the maximal curvature in an elliptical-ring, and confirm the reduction in the localization length of waves by measuring near and far field patterns, as well as the corresponding dispersion relation. Theoretically, analyses based on a dissipative model with a parabola curve give good agreement remarkably to experimental measurement on the transition from delocalized to localized waves. The introduction of curved geometry allows to control and design lasing modes in the nonlinear regime.Comment: 6 pages, 6 figure

Prevention and early management of carotid blowout syndrome for patients receiving head and neck salvage boron neutron capture therapy (BNCT)

Background/purpose The incidence rate of oral and pharyngeal cancers in Taiwan has increased gradually over the past few decades. The standard treatment strategy for oral and pharyngeal cancers includes surgery or radiotherapy, with concurrent chemotherapy in certain types of tumors. Unfortunately, in-field recurrence is sometimes inexorable. Furthermore, re-irradiation of the recurrence site may cause severe complications due to the tolerance of normal tissue to radiation therapy. One fatal complication is carotid blowout syndrome (CBS). Boron neutron capture therapy (BNCT) is a new modality of radiation therapy, which is also mentioned as targeted radiotherapy. It is a feasible treatment that has the potential to spare normal tissue from being damaged by irradiation while simultaneously treating the primary tumor. In this presentation, we will share our experience with BNCT in treating recurrent head and neck cancers, as well as the prevention and management of CBS. Materials and methods We evaluated 4 patients with head and neck cancers treated by BNCT in Taiwan. All patients had undergone surgery previously and had received postoperative concurrent chemoradiotherapy. Results The 4 patients in this study were diagnosed with head and neck malignancies. The median follow-up period after the first course of BNCT was 15.1 months. After BNCT, 2 patients developed impending CBS, and 1 of them died. The remaining 3 patients survived until the last date of follow-up. Conclusion Pre-BNCT carotid artery evaluation through computed tomography angiography and early intervention if necessary is crucial when treating patients with recurrent head and neck cancers by BNCT

Integrin-mediated membrane blebbing is dependent on the NHE1 and NCX1 activities.

Integrin-mediated signal transduction and membrane blebbing have been well studied to modulate cell adhesion, spreading and migration^1-6^. However, the relationship between membrane blebbing and integrin signaling has not been explored. Here we show that integrin-ligand interaction induces membrane blebbing and membrane permeability change. We found that sodium-proton exchanger 1 (NHE1) and sodium-calcium exchanger 1 (NCX1) are located in the membrane blebbing sites and inhibition of NHE1 disrupts membrane blebbing and decreases membrane permeability change. However, inhibition of NCX1 enhances cell blebbing to cause cell swelling which is correlated with an intracellular sodium accumulation induced by NHE17. These data suggest that sodium influx induced by NHE1 is a driving force for membrane blebbing growth, while sodium efflux induced by NCX1 in a reverse mode causes membrane blebbing retraction. Together, these data reveal a novel function of NHE1 and NCX1 in membrane permeability change and blebbing and provide the link for integrin signaling and membrane blebbing

Scutellaria baicalensis decreases ritonavir-induced nausea

BACKGROUND: Protease inhibitors, particularly ritonavir, causes significant gastrointestinal disturbances such as nausea, even at low doses. This ritonavir-induced nausea could be related to its oxidative stress in the gut. Alleviation of drug-induced nausea is important in effectively increasing patients' compliance and improving their quality of life. Conventional anti-emetic drugs can only partially abate the symptoms in these patients, and their cost has also been a concern. Rats respond to nausea-producing emetic stimuli by increasing consumption of non-nutritive substances like kaolin or clay, a phenomenon known as pica. In this study, we used this rat pica model to evaluate the effects of Scutellaria baicalensis, a commonly used oriental herbal medicine, on ritonavir-induced nausea. RESULTS: Rats treated with 20 mg/kg ritonavir significant caused increases of kaolin consumption at 24 to 48 hr (P < 0.01). Pretreatment with 0.3 and 3 mg/kg Scutellaria baicalensis extract significantly decreased ritonavir-induced kaolin intake in a dose-related manner (P < 0.01). Compared to vehicle treatment, the extract completely prevented ritonavir-induced kaolin consumption at dose 3 mg/kg. The area under the curves (AUC) for kaolin intake from time 0 to 120 hr for vehicle only, ritonavir only, SbE 0.3 mg/kg plus ritonavir, and SbE 3 mg/kg plus ritonavir were 27.3 g•hr, 146.7 g•hr, 123.2 g•hr, and 32.7 g•hr, respectively. The reduction in area under the curves of kaolin intake from time 0 to 120 hr between ritonavir only and SbE 0.3 mg/kg plus ritonavir, ritonavir only and SbE 3 mg/kg plus ritonavir were 16.0% and 77.7%, respectively. CONCLUSION: Scutellaria baicalensis significantly attenuated ritonavir-induced pica, and demonstrated a potential in treating ritonavir-induced nausea

The nexus between military expenditures and economic growth in the BRICS and the US : an empirical note

This empirical note re-examines the causal linkages between military expenditures and economic growth for the BRICS countries (Brazil, Russia, India, China, and South Africa) and that for the USA during the period 1988-2012. Results of Granger causality tests show that military expenditures influence economic growth in the United States, economic growth influence military expenditures in both Brazil and India, a feedback between military expenditures and economic growth in Russia, and no causal relation exists between military expenditures and economic growth in China and South Africa. The findings of this study can provide important policy implications for the BRICS countries and also for the United States.http://www.tandfonline.com/loi/gdpe202017-08-31hb2016Economic