FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome.

Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome. It uses a novel probabilistic generative model based on k-mer profiles to quantify the exon-inclusion ratios at the genome scale and an efficient expectation-maximization algorithm based on a divide-and-conquer strategy and ultrafast conjugate gradient projection descent method to solve the model. We compare FreePSI with the existing methods on simulated and real RNA-seq data in terms of both accuracy and efficiency and show that it is able to achieve very good performance even though a reference transcriptome is not provided. Our results suggest that FreePSI may have important applications in performing alternative splicing analysis for organisms that do not have quality reference transcriptomes. FreePSI is implemented in C++ and freely available to the public on GitHub

Best Practices of Liberal Arts Education: Curricula in Liberal Arts Colleges

As the primary example of best practice of liberal arts education, curricula in American liberal arts college have some distinctive features. Guided by the principle of integrating curriculum breadth and depth, both general education and major courses in liberal arts colleges may develop in a balanced way. Even the curriculum implementation at liberal arts colleges is fully reflective of the idea of liberal arts education. Small class sizes enhance students’ participation and promote intimate relations between faculty and students, and teachers’ investment in teaching occupies most of their time, which provides the conditions for high quality teaching. With the full cooperation of faculty, interdisciplinary curricula and majors are being developed continuously. All of these factors contribute to the nature of liberal arts education in liberal arts colleges’ curricula.This research is supported by The National Social Science Fund of China (Education) for young scholars (CIA160216)

Compact Heat Exchanger for Veno-Venous Perfusion-Induced Systemic Hyperthermia Systems

A compact heat exchanger for vena-venous perfusion-induced hyperthermia includes an integral pneumatic pump and a hollow tubule heat exchange array. A vena-venous perfusion-induced hyperthermia system incorporating the compact heat exchanger is described. The heat exchanger provides a compact, efficient design allowing a lesser heat exchanging surface area and lesser required pumping power compared to conventional systems. In turn, the system provides a shorter blood circuit compared to conventional systems, allowing maintaining a lower blood temperature than such conventional systems while supplying sufficiently heated blood to patient visceral organs to provide a therapeutic effect, such as in supplementing chemotherapy drugs

Even Perfusion Pump-Integrated Blood Oxygenator

A blood oxygenator includes an integral pneumatic pump disposed substantially within a housing thereof, an inlet blood flow redirector, and an outflow blood collector. An atrium provided at an inlet of the oxygenator promotes even delivery of blood to the oxygenator. In use, the oxygenator provides an even dispersion of blood therethrough, establishing even perfusion and reducing areas of stagnant blood flow

Axial-Centrifugal Flow Catheter Pump for Cavopulmonary Assistance

An axial-centrifugal flow catheter pump for cavopulmonary assistance is provided, incorporating a rotor providing both an axial fluid flow and a centrifugal fluid flow. The rotor includes a first terminal impeller configured to provide a centrifugal and axial fluid flow in a first direction, a second terminal impeller configured to provide a centrifugal and axial fluid flow in a second direction opposite to the first direction, and a central impeller configured to provide a predominantly centrifugal fluid flow. The first and second terminal impellers each include blade arrangements configured to provide a centrifugal and axial fluid flow directed toward the rotor central impeller. Cavopulmonary assistance devices are provided including the axial-centrifugal flow catheter pump

Coupling system of silver carbonate nanoparticles and bismuth oxyiodide nanosheets with enhanced photocatalytic properties

274-284In this work, silver carbonate nanoparticles and BiOI nanosheets have been prepared separately and binary Ag2CO3/BiOI composite are synthesized via a facile solvo thermal method. The as-prepared materials have been well characterized using techniques covering X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), High-resolution transmission electron microscopy (HRTEM), ultraviolet-visible (UV-vis) diffuse reflectance spectroscopy, X-ray photoelectron spectroscopy (XPS), Photoluminescence (PL) emission spectroscopy. The photocatalytic activity of the as-synthesized materials has been evaluated for degrading various model pollutants (methyl orange, phenol and p-nitroaniline). It has been found that the incorporation of co-catalyst BiOI could promote the catalytic activity of Ag2CO3 and suppress the serious photocorrosion of Ag2CO3. Thus the Ag2CO3/BiOI composite showed excellent catalytic recycling stability. Moreover, the underlying mechanism has been investigated through radical trapping experiments. The results demonstrate that photoinduced holes are the main active species. The improvement in activity of Ag2CO3/BiOI could be attributed to the charge transfer between the heterojunction. Also, its good stability and reusability establish its promising potential for catalytic applications

External modulation method for generating accurate linear optical FMCW

Frequency modulation continuous wave (FMCW) lasers are key components in modern optical imaging. However, current intracavity modulation lasers do not exhibit low-frequency jitter rate and high linearity due to the inherent relaxation oscillations. Although this may be compensated in a direct modulation laser diode using an optoelectronic feedback loop, the available sweep speed is moderately small. In this letter, a special external modulation method is developed to improve the performance of FMCW. Since only the first sideband optical field is used during the entire generation process, phase noise is kept to a minimum and is also independent of the sweep speed. We demonstrate that the linearity and jitter rates do not deteriorate appreciably when the sweep speed is changed over three orders of magnitude, even up to the highest sweep speed of 2.5 GHz/ μs

An extracellular protein expression system in Escherichia coli implies potential application

Escherichia coli is commonly used as a host for the extracellular production of proteins. However, its secretion capacity is often limited to a frustratingly low level compared with other expression hosts, because E. coli has a complex cell envelope with two layers. We recently identified the catalytic domain of a cellulase (Cel-CD) from Bacillus sp. that can be secreted into the medium from recombinant E. coli in large quantities without its native signal peptide. By subcellular location analysis, we verified that the secretion was a two-step process via the SecB-dependent pathway through the inner membrane and an unknown pathway through the outer membrane. However, the N-terminal region of Cel-CD is polar and hydrophilic, which showed no similarities to other typical signal sequences. Random mutagenesis experiment suggested that the N-terminal sequence is a compromising result of transportation through inner and outer membranes. This is the first report that a non-classical signal peptide can guide recombinant proteins out of the cells from cytoplasm. Both the Cel-CD and its N-terminal sequence can serve as carriers for efficient extracellular production of select target proteins with a concentration from 101 to 691 mg/L in flask cultivation. This protein can degrading cellulose efficiently in the culture medium indicating a great potential. Therefore, a recombinant E.coli that can directly utilize cellulose as sole carbon source by fusion Cel-CD with a b-glucosidase was constructed. Recombinant strains were confirmed to use the amorphous cellulose as well as cellobiose as the sole carbon source for growth. Furthermore, both strains were engineered with poly (3-hydroxybutyrate) (PHB) synthesis pathway to demonstrate the production of biodegradable polyesters directly from cellulose materials without exogenously added cellulases. The results suggested that this system has a potential application in lignocellulosic biomass degradation and biochemical biofuel production. These guidelines have been prepared in the format that should be used for the abstract submission. Authors should replace the text of this template in order to prepare their abstracts. Fonts, sizes and spacing should be used as they are used in this document. Page size is US 8.5 inch x 11 inch, top and bottom margin 0.8 inches, left and right margin 0.8 inches. Body text should be written in Arial, 10 pt, single spacing. The Abstract, in English, should introduce the proposed paper’s subject, summarize its contents, explain any unique aspects, and clearly indicate the specific relevance to the themes of the Conference. Do not sub-divide the text into separate sections. References may be included at the bottom. Reference Exploring the N-terminal role of a heterologous protein in secreting out of Escherichia coli, Biotechnol Bioeng. 2016 Dec;113(12):2561-2567. doi: 10.1002/bit.26028. Epub 2016 Jun 14. Construction of cellulose-utilizing Escherichia coli based on a secretable cellulose, Microb Cell Fact. 2015 Oct 9;14:159. doi: 10.1186/s12934-015-0349-7