Characterization of the human ESC transcriptome by hybrid sequencing

Although transcriptional and posttranscriptional events are detected in RNA-Seq data from second-generation sequencing, fulllength mRNA isoforms are not captured. On the other hand, thirdgeneration sequencing, which yields much longer reads, has current limitations of lower raw accuracy and throughput. Here, we combine second-generation sequencing and third-generation sequencing with a custom-designed method for isoform identification and quantification to generate a high-confidence isoform dataset for human embryonic stem cells (hESCs). We report 8,084 RefSeq-annotated isoforms detected as full-length and an additional 5,459 isoforms predicted through statistical inference. Over one-third of these are novel isoforms, including 273 RNAs from gene loci that have not previously been identified. Further characterization of the novel loci indicates that a subset is expressed in pluripotent cells but not in diverse fetal and adult tissues; moreover, their reduced expression perturbs the network of pluripotency- associated genes. Results suggest that gene identification, even in well-characterized human cell lines and tissues, is likely far from complete

Computational efficiency improvement for analyzing bending and tensile behavior of woven fabric using strain smoothing method

The tensile and bending behavior of woven fabrics are among the most important characteristics in complex deformation analysis and modelling of textile fabrics and they govern many aesthetics and performance aspects such as wrinkle/buckle, hand and drape. In this paper, a numerical method for analyzing of the tensile and bending behavior of plain-woven fabric structure was developed. The formulated model is based on the first-order shear deformation theory (FSDT) for a four-node quadrilateral element (Q4) and a strain smoothing method in finite elements, referred as a cell-based smoothed finite element method (CS-FEM). The physical and low-stress mechanical parameters of the fabric were obtained through the fabric objective measurement technology (FOM) using the Kawabata evaluation system for fabrics (KES-FB). The results show that the applied numerical method provides higher efficiency in computation in terms of central processing unit (CPU) time than the conventional finite element method (FEM) because the evaluation of compatible strain fields of Q4 element in CS-FEM model is constants, and it was also appropriated for numerical modelling and simulation of mechanical deformation behavior such as tensile and bending of woven fabric.The author (UMINHO/BPD/9/2017) and co-authors acknowledge the FCT funding from FCT – Foundation for Science and Technology within the scope of the project “PEST UID/CTM/00264; POCI-01-0145-FEDER-007136”

Manganese Oxide Particles as Cytoprotective, Oxygen Generating Agents

Cell culture and cellular transplant therapies are adversely affected by oxidative species and radicals. Herein, we present the production of bioactive manganese oxide nanoparticles for the purpose of radical scavenging and cytoprotection. Manganese comprises the core active structure of somatic enzymes that perform the same function, in vivo. Formulated nanoparticles were characterized structurally and surveyed for maximal activity (superoxide scavenging, hydrogen peroxide scavenging with resultant oxygen generation) and minimal cytotoxicity (48-h direct exposure to titrated manganese oxide concentrations). Cytoprotective capacity was tested using cell exposure to hydrogen peroxide in the presence or absence of the nanoparticles. Several ideal compounds were manufactured and utilized that showed complete disproportionation of superoxide produced by the xanthine/xanthine oxidase reaction. Further, the nanoparticles showed catalase–like activity by completely converting hydrogen peroxide into the corresponding concentration of oxygen. Finally, the particles protected cells (murine β-cell insulinoma) against insult from hydrogen peroxide exposure. Based on these observed properties, these particles could be utilized to combat oxidative stress and inflammatory response in a variety of cell therapy applications

Stimating and optimizing safety factors of retaining wall through neural network and bee colony techniques

An important task of geotechnical engineering is a suitable design of safety factor (SF) of retaining wall under both static and dynamic conditions. This paper presents the advantages of both prediction and optimization of retaining wall SF through artificial neural network (ANN) and artificial bee colony (ABC), respectively. These techniques were selected because of their capability in predicting and optimizing science and engineering problems. To gain purpose of this research, a comprehensive database consisted of 2880 datasets of wall height, wall width, wall mass, soil mass and internal angle of friction as input parameters and SF of retaining wall as output was prepared. In fact, SF is considered as a function of the mentioned parameters. At the first step of modeling, several ANN models were constructed and the best one among them was selected. The coefficient of determination (R2) value of 0.998 for both training and testing datasets was obtained for the best ANN model which indicates an excellent accuracy level in predicting SF values. In the next step of modeling, the results of selected ANN model were used as an input for the optimization technique of ABC. In general, 11 models of ABC optimization with different strategies were built. As a result, by decreasing wall height value from 10 m to 8 m and 5.628 m and using almost constant values for the other input parameters, SF values were obtained as 2.142 and 5.628, respectively. Results of (8.003, 0.794, 0.667, 1800 and 2800) and (5.628, 0.763, 0.660, 1735 and 2679) were obtained for wall height, wall width, internal friction angle, soil mass and wall mass of the best models with 2.142 and 5.628 SF values, respectively

Determining chemical exchange rate constants in nanoemulsions using nuclear magnetic resonance

In this work, the second-order kinetics of molecules exchanging between chemically distinct microenvironments, such as those found in nanoemulsions, is studied using nuclear magnetic resonance (NMR). A unique aspect of NMR exchange studies in nanoemulsions is that the difference in molecular resonance frequencies between the two phases, which determines whether the exchange is fast, intermediate, or slow on the NMR timescale, can depend upon the emulsion droplet composition, which is also determined by the kinetic exchange constants themselves. Within the fast-exchange regime, changes in resonance frequencies and line widths with dilution were used to extract the exchange rate constants from the NMR spectra in a manner analogous to determining the kinetic parameters in NMR ligand binding experiments. As a demonstration, the kinetic exchange parameters of isoflurane release from an emulsification of isoflurane and perflurotributylamine (FC43) were determined using NMR dilution and diffusion studies

Reverse-dialysis can be misleading for drug release studies in emulsions as demonstrated by NMR dilution experiments

[Display omitted] Emulsions are an important class of carriers for the delivery of hydrophobic drugs. While knowledge of drug release kinetics is critical to optimizing drug carrying emulsions, there remain many open questions about the validity of standard characterization methods such as the commonly used reverse-dialysis. In this paper, the kinetic parameters of isoflurane release in perfluorotributylamine emulsions determined from both reverse-dialysis and nuclear magnetic resonance (NMR) dilution experiments are compared. The NMR-determined kinetic parameters of isoflurane release were found to be approximately seven orders of magnitude larger than those determined from conventional reverse-dialysis and were also shown to be consistent with prior in vivo observations of the anesthetization of rats

Rapid quantification of isoflurane in anesthetic nanoemulsions using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR)

There is increased research into pharmaceutical nanoemulsions where the timing of quantification of active components can dictate continuous manufacturing production cost and consistency. The goal of this study was development of a rapid quantification method for isoflurane nanoemulsions using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR). Isoflurane was quantified by ATR-FTIR and High-Performance Liquid Chromatography (HPLC). Correlation and agreement between methods was determined to validate the ATR-FTIR procedure. Evaporation rate studies from the nanoemulsions and pure isoflurane were performed. ATR-FTIR values were in agreement and correlated with (HPLC) measurements (calculated Pearson R of 0.99; 99 % confidence interval; P < 0.001). ∼97 % of the values fell within the upper and lower limits of agreement in Bland Altman plot analysis. ATR-FTIR values were obtained within 1 min compared to 25 min for comparable triplicate measurements using HPLC. Evaporative loss from open nanoemulsions was 80x less than that from containers of pure isoflurane. The reformulation of isoflurane into nanoemulsions lowers risk of exposure for clinical staff, demonstrated by the evaporative loss studies. This method could prevent expensive errors in large-scale continuous manufacture and could be used in the production of other nanoemulsified drug formulations

Stable perfluorocarbon emulsions for the delivery of halogenated ether anesthetics

[Display omitted] •Stability of anesthetic emulsions is related to boiling point of perfluorocarbon.•Emulsions of FC-43 and isoflurane are stable for 1.5 years.•Anesthetic emulsions have consistent and reproducible action in induction trials.•Anesthetic induction with emulsions casues no observed pathological changes. Research into injectable volatile anesthetics has been ongoing for approximately 40 years, with limited success, in an attempt to address the deficiencies of inhalational anesthesia. The purpose of this work was to formulate and optimize volatile anesthetic carrier emulsions based on our prior work in perfluorocarbon emulsions. Perfluorocarbons were screened for their volatilty and emulsion stability. Optimal anesthetic emulsions were manufactured by high pressure homogenization of a select, clinically relevant perfluorocarbon, isoflurane and a surfactant-containing aqueous phase. Longitudinal particle size, polydispersity and isoflurane content analysis was performed. Observational studies of in vivo efficacy and safety were performed in 225–300 g Lewis Rats (n = 34) with blood chemistry and post study tissue pathology analysis. Emulsion particle size and isolflurane content in select emulsions were stable at room temperature greater than 300 days. This stability was depedent on perfluorocarbon molecular weight and boiling point. in vivo, emulsions demonstrated a rapid onset and offset. Variability in onset metrics (loss of righting reflex, pain reflexes and time to recovery) was less than 40% amongst individual emulsion preparations (n = 9) utilized in induction trials. No adverse effects due to the intravenous administration of emulsions were observed in blood chemistry results or post-study pathological examination. These formulations showed stability, safety and efficacy. In addition to induction and general anesthesia, these emulsions could have utility in global health or in military applications where equipment and resources are limited