Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells

The retinal vascular endothelium is essential for angiogenesis and is involved in maintaining barrier selectivity and vascular tone. The aim of this study was to identify and quantify microRNAs and other small regulatory non-coding RNAs (ncRNAs) which may regulate these crucial functions. Primary bovine retinal microvascular endothelial cells (RMECs) provide a well-characterized in vitro system for studying angiogenesis. RNA extracted from RMECs was used to prepare a small RNA library for deep sequencing (Illumina Genome Analyzer). A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). In many cases, the most frequent isomiR differed from the sequence reported in miRBase. In addition, five novel microRNAs, 13 novel bovine orthologs of known human microRNAs and multiple new members of the miR-2284/2285 family were detected. Several similar to 30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one-third of all mapped reads. Inhibition of miR-21 with an LNA inhibitor significantly reduced proliferation, migration, and tube-forming capacity of RMECs. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Knockdown of miR-21 suggests a role for this microRNA in regulation of angiogenesis in the retinal microvasculature. J. Cell. Biochem. 113: 20982111, 2012. (C) 2012 Wiley Periodicals, Inc.

Deep-sea chitons from sunken wood in the West Pacific (Mollusca: Polyplacophora: Lepidopleurida): taxonomy, distribution, and seven new species

Natural deposits of sunken wood provide an important habitat for deep-sea invertebrates. Deep-sea chitons in the primitive order Lepidopleurida are typically collected rarely and as single specimens. However, these animals have been recovered in large densities associated with sunken wood in the tropical West Pacific, in groups of up to 50 individuals. Four deep- sea expeditions in the West Pacific, to the Philippines, Solomon Islands, and Vanuatu, recovered a large number of poly- placophorans. We have examined the morphology as well as the range and distribution of these species, based on the larg- est collection ever examined (more than 1300 individuals). These species show potentially adapted characters associated with exploitation of sunken wood as habitat, such as protruding caps on sensory shell pores (aesthetes) and large interseg- mental bristles with potential sensory function. In this study we investigated the twenty-two species recovered, including seven newly described here (Leptochiton consimilis n. sp., L. angustidens n. sp., L. dykei n. sp., L. samadiae n. sp., L. longisetosus n. sp., L. clarki n. sp., L. schwabei n. sp.), and provide the first identification key to the 34 lepidopleuran chitons known from sunken wood worldwide.

Ultrahigh-intensity laser-produced plasmas as a compact heavy ion injection source

The possibility of using high-intensity laser-produced plasmas as a source of energetic ions for heavy ion accelerators is addressed. Experiments have shown that neon ions greater than 6 MeV can be produced from gas jet plasmas, and well-collimated proton beams greater than 20 MeV have been produced from high-intensity Laser solid interactions. The proton beams from the back of thin targets appear to be more collimated and reproducible than are high-energy ions generated in the ablated plasma at the front of the target and may be more suitable for ion injection applications. Lead ions have been produced at energies up to 430 MeV.

Numerical simulation of a patent technology for sealing of deep-sea oil wells using nonlinear finite element method

For over 50 years bridge plugs and cement have been used for well abandonment and work over and are still the material of choice. However the failures of cement abandonments using bridge plugs has been reported on many occasions, some of which have resulted in fatal consequences. A new patented product is designed to address the shortcomings associated with using bridge plugs and cement. The new developed tools use an alloy based on bismuth that is melted in situ using Thermite reaction. The tool uses the expansion properties of bismuth to seal the well. Testing the new technology in real field under more than 2 km deep sea water can be expensive. Virtual simulation of the new device under simulated thermal and mechanical environment can be achieved using nonlinear finite element method to validate the product and reduce cost. Experimental testing in the lab is performed to measure heat generated due to thermite reaction. Then, a sequential thermal mechanical explicit/implicit finite element solver is used to simulate the device under both testing lab and deep water conditions.

The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Control of intraocular pressure after deep sclerectomy

Aim: To study the long-term outcome of deep sclerectomy in patients with open angle glaucoma. Methods: Prospective consecutive series of 43 eyes (38 patients) with medically uncontrolled open-angle glaucoma undergoing deep sclerectomy. All patients underwent clinical assessment before and after surgery at day 7 and at months 1, 3, 6, 12, 18, 24, 36. Surgical success was considered if the patient's intraocular pressure (IOP)>22 mmHg and the IOP was lowered by more than 20% without the use of any medication. Kaplan-Meier survival curves were used to evaluate the success rate. Results: The mean follow-up time was 28.1±8.2 months. Mean IOP decreased significantly from a preoperative value of 24.6±5.5 mmHg to a postoperative value of 18.5±4.6 mmHg at 36 months (P>0.001). Microperforation of TDM occurred in three cases (7.0%) and ciliary body prolapse in one case (2.3%) but did not prevent completion of the operation. Postoperatively, hyphaema was detected in one case and shallow anterior chamber in another case and both were treated conservatively. Bleb encapsulation with elevation of IOP occurred in two cases (4.7%) and was treated with 5-fluorouracil subconjunctival injection. Goniopuncture with neodymium : YAG laser was performed in two cases (4.7%). There were no other late complications with the exception of failure of the operation. On the life-table analysis the success rate at 12, 24, and 30 months were 61.4, 36.6, and 18.9%, respectively. Conclusion: Deep sclerectomy reduced the IOP temporarily while minimising the risk of postoperative complications commonly encountered with standard trabeculectomy. However, after long-term follow-up surgery failed to maintain a low IOP. © 2006 Nature Publishing Group. All rights reserved.

Physical properties of a new Deep Eutectic Solvent based on lithium bis[(trifluoromethyl)sulfonyl]imide and N-methylacetamide as superionic suitable electrolyte for lithium ion batteries and electric double layer capacitors

Herein we present a study on the physical/chemical properties of a new Deep Eutectic Solvent (DES) based on N-methylacetamide (MAc) and lithium bis[(trifluoromethyl)sulfonyl]imide (LiTFSI). Due to its interesting properties, such as wide liquid-phase range from -60°C to 280°C, low vapor pressure, and high ionic conductivity up to 28.4mScm at 150°C and at x=1/4, this solution can be practically used as electrolyte for electrochemical storage systems such as electric double-layer capacitors (EDLCs) and/or lithium ion batteries (LiBs). Firstly, relationships between its transport properties (conductivity and viscosity) as a function of composition and temperature were discussed through Arrhenius' Law and Vogel-Tamman-Fulcher (VTF) equations, as well as by using the Walden classification. From this investigation, it appears that this complex electrolyte possesses a number of excellent transport properties, like a superionic character for example. Based on which, we then evaluated its electrochemical performances as electrolyte for EDLCs and LiBs applications by using activated carbon (AC) and lithium iron phosphate (LiFePO) electrodes, respectively. These results demonstrate that this electrolyte has a good compatibility with both electrodes (AC and LiFePO) in each testing cell driven also by excellent electrochemical properties in specific capacitance, rate and cycling performances, indicating that the LiTFSI/MAc DES can be a promising electrolyte for EDLCs and LiBs applications especially for those requiring high safety and stability. © 2013 Elsevier Ltd.

Intellectual Property and the EU’s Deep Trade Agenda

The EU is considered to be one of the main proponents of what has been called the deep trade agenda—that is, the push for further trade liberalization with an emphasis on the removal of domestic non-tariff regulatory measures affecting trade, as opposed to the traditional focus on the removal of trade barriers at borders. As negotiations on the Doha Development Round have stalled, the EU has attempted to achieve these aims by entering into comprehensive free trade agreements (FTAs) that are not only limited exclusively to tariffs but also extend to non-tariff barriers, including services, intellectual property rights (IPRs), competition, and investment. These FTAs place great emphasis on regulatory convergence as a means to secure greater market openings. The paper examines the EU's current external trade policy in the area of IP, particularly its attempts to promote its own regulatory model for the protection of IP rights through trade agreements. By looking at the IP enforcement provisions of such agreements, the article also examines how the divisive issues that are currently hindering the progress of negotiations at WTO level, including the demands from developing countries to maintain a degree of autonomy in the area of IP regulation as well as the need to balance IP protection with human rights protection, are being dealt with in recent EU FTAs.

Deep separation of benzene from cyclohexane by liquid extraction using ionic liquids as the solvent

Separation of benzene and cyclohexane is one of the most important and difficult processes in the petrochemical industry, especially for low benzene concentration. In this work, three ionic liquids (ILs), [Bmim][BF ₄], [Bpy][BF ₄], and [Bmim][SCN], were investigated as the solvent in the extraction of benzene from cyclohexane. The corresponding ternary liquid-liquid equilibria (LLE) were experimentally determined at T = 298.15 K and atmospheric pressure. The LLE data were correlated with the nonrandom two-liquid model, and the parameters were fitted. The separation capabilities of the ILs were evaluated in terms of the benzene distribution coefficient and solvent selectivity. The effect of the IL structure on the separation was explained based on a well-founded physical model, COSMO-RS. Finally, the extraction processes were defined, and the operation parameters were analyzed. It shows that the ILs studied are suitable solvents for the extractive separation of benzene and cyclohexane, and their separation efficiency can be generally ranked as [Bmim][BF ₄] > [Bpy][BF ₄] > [Bmim][SCN]. The extraction process for a feed with 15 mol % benzene was optimized. High product purity (cyclohexane 0.997) and high recovery efficiency (cyclohexane 96.9% and benzene 98.1%) can be reached. © 2012 American Chemical Society.

Injection moulding process optimization for microstructured parts production

Ao longo das últimas décadas, a micromoldação (u-moldação) por injeção de termoplásticos ganhou um lugar de destaque no mercado de equipamentos eletrónicos e de uma ampla gama de componentes mecânicos. No entanto, quando o tamanho do componente diminui, os pressupostos geralmente aceites na moldação por injeção convencional deixam de ser válidos para descrever o comportamento reológico e termomecânico do polímero na microimpressão. Por isso, a compreensão do comportamento dinâmico do polímero à escala micro bem como da sua caraterização, análise e previsão das propriedades mecânicas exige uma investigação mais alargada. O objetivo principal deste programa doutoral passa por uma melhor compreensão do fenómeno físico intrínseco ao processo da μ-moldação por injeção. Para cumprir com o objetivo estabelecido, foi efetuado um estudo paramétrico do processo de μ-moldação por injeção, cujos resultados foram comparados com os resultados obtidos por simulação numérica. A caracterização dinâmica mecânica das μ-peças foi efetuada com o objetivo de recolher os dados necessários para a previsão do desempenho mecânico das mesmas, a longo prazo. Finalmente, depois da calibração do modelo matemático do polímero, foram realizadas análises estruturais com o intuito de prever o desempenho mecânico das μ-peças no longo prazo. Verificou-se que o desempenho mecânico das μ-peças pode ser significativamente afetado pelas tensões residuais de origem mecânica e térmica. Estas últimas, resultantes do processo de fabrico e das condições de processamento, por isso, devem ser consideradas na previsão do desempenho mecânico e do tempo de serviço das u-moldações.

Citrate selective electrodes for the flow injection analysis of soft drinks, beers and pharmaceutical products

Aiming the establishment of simple and accurate readings of citric acid (CA) in complex samples, citrate (CIT) selective electrodes with tubular configuration and polymeric membranes plus a quaternary ammonium ion exchanger were constructed. Several selective membranes were prepared for this purpose, having distinct mediator solvents (with quite different polarities) and, in some cases, p-tert-octylphenol (TOP) as additive. The latter was used regarding a possible increase in selectivity. The general working characteristics of all prepared electrodes were evaluated in a low dispersion flow injection analysis (FIA) manifold by injecting 500µl of citrate standard solutions into an ionic strength (IS) adjuster carrier (10−2 mol l−1) flowing at 3ml min−1. Good potentiometric response, with an average slope and a repeatability of 61.9mV per decade and ±0.8%, respectively, resulted from selective membranes comprising additive and bis(2-ethylhexyl)sebacate (bEHS) as mediator solvent. The same membranes conducted as well to the best selectivity characteristics, assessed by the separated solutions method and for several chemical species, such as chloride, nitrate, ascorbate, glucose, fructose and sucrose. Pharmaceutical preparations, soft drinks and beers were analyzed under conditions that enabled simultaneous pH and ionic strength adjustment (pH = 3.2; ionic strength = 10−2 mol l−1), and the attained results agreed well with the used reference method (relative error < 4%). The above experimental conditions promoted a significant increase in sensitivity of the potentiometric response, with a supra-Nernstian slope of 80.2mV per decade, and allowed the analysis of about 90 samples per hour, with a relative standard deviation <1.0%.

A comparative analysis of fault injection methods via enhanced on-chip debug infrastructures

On-chip debug (OCD) features are frequently available in modern microprocessors. Their contribution to shorten the time-to-market justifies the industry investment in this area, where a number of competing or complementary proposals are available or under development, e.g. NEXUS, CJTAG, IJTAG. The controllability and observability features provided by OCD infrastructures provide a valuable toolbox that can be used well beyond the debugging arena, improving the return on investment rate by diluting its cost across a wider spectrum of application areas. This paper discusses the use of OCD features for validating fault tolerant architectures, and in particular the efficiency of various fault injection methods provided by enhanced OCD infrastructures. The reference data for our comparative study was captured on a workbench comprising the 32-bit Freescale MPC-565 microprocessor, an iSYSTEM IC3000 debugger (iTracePro version) and the Winidea 2005 debugging package. All enhanced OCD infrastructures were implemented in VHDL and the results were obtained by simulation within the same fault injection environment. The focus of this paper is on the comparative analysis of the experimental results obtained for various OCD configurations and debugging scenarios.

European guidelines for sclerotherapy in chronic venous disorders.

AIM: Sclerotherapy is the targeted chemical ablation of varicose veins by intravenous injection of a liquid or foamed sclerosing drug. The treated veins may be intradermal, subcutaneous, and/or transfascial as well as superficial and deep in venous malformations. The aim of this guideline is to give evidence-based recommendations for liquid and foam sclerotherapy. METHODS: This guideline was drafted on behalf of 23 European Phlebological Societies during a Guideline Conference on 7-10 May 2012 in Mainz. The conference was organized by the German Society of Phlebology. These guidelines review the present state of knowledge as reflected in published medical literature. The regulatory situation of sclerosant drugs differs from country to country but this has not been considered in this document. The recommendations of this guideline are graded according to the American College of Chest Physicians Task Force recommendations on Grading Strength of Recommendations and Quality of Evidence in Clinical Guidelines. RESULTS: This guideline focuses on the two sclerosing drugs which are licensed in the majority of the European countries, polidocanol and sodium tetradecyl sulphate. Other sclerosants are not discussed in detail. The guideline gives recommendations concerning indications, contraindications, side-effects, concentrations, volumes, technique and efficacy of liquid and foam sclerotherapy of varicose veins and venous malformations.

Gas chromatographic electron capture negative ionization mass spectrometric (GC/ECNI/MS) determination of unique fluorinated compounds in the sediments of Lake Ontario and the effect of high-boiling alcohols (as injection solvents) on chromatographic behaviour of polycyclic aromatic hydrocarbons in gas chromatography

Part I - Fluorinated Compounds A method has been developed for the extraction, concentration, and determination of two unique fluorinated compounds from the sediments of Lake Ontario. These compounds originated from a common industrial landfill, and have been carried to Lake Ontario by the Niagara River. Sediment samples from the Mississauga basin of Lake Ontario have been evaluated for these compounds and a depositional trend was established. The sediments were extracted by accelerated solvent extraction (ASE) and then underwent clean-up, fractionation, solvent exchange, and were concentrated by reduction under nitrogen gas. The concentrated extracts were analyzed by gas chromatography - electron capture negative ionization - mass spectrometry. The depositional profile determined here is reflective of the operation of the landfill and shows that these compounds are still found at concentrations well above background levels. These increased levels have been attributed to physical disturbances of previously deposited contaminated sediments, and probable continued leaching from the dumpsite. Part II - Polycyclic Aromatic Hydrocarbons Gas chromatography/mass spectrometry is the most common method for the determination of polycyclic aromatic hydrocarbons (PAHs) from various matrices. Mass discrimination of high-boiling compounds in gas chromatographic methods is well known. The use of high-boiling injection solvents shows substantial increase in the response of late-eluting peaks. These solvents have an increased efficiently in the transfer of solutes from the injector to the analytical column. The effect of I-butanol, I-pentanol, cyclopentanol, I-hexanol, toluene and n-octane, as injection solvents, was studied. Higher-boiling solvents yield increased response for all PAHs. I -Hexanol is the best solvent, in terms of P AH response, but in this solvent P AHs were more susceptible to chromatographic problems such as peak splitting and tailing. Toluene was found to be the most forgiving solvent in terms of peak symmetry and response. It offered the smallest discrepancies in response, and symmetry over a wide range of initial column temperatures.

Training deep convolutional architectures for vision

Les tâches de vision artificielle telles que la reconnaissance d’objets demeurent irrésolues à ce jour. Les algorithmes d’apprentissage tels que les Réseaux de Neurones Artificiels (RNA), représentent une approche prometteuse permettant d’apprendre des caractéristiques utiles pour ces tâches. Ce processus d’optimisation est néanmoins difficile. Les réseaux profonds à base de Machine de Boltzmann Restreintes (RBM) ont récemment été proposés afin de guider l’extraction de représentations intermédiaires, grâce à un algorithme d’apprentissage non-supervisé. Ce mémoire présente, par l’entremise de trois articles, des contributions à ce domaine de recherche. Le premier article traite de la RBM convolutionelle. L’usage de champs réceptifs locaux ainsi que le regroupement d’unités cachées en couches partageant les même paramètres, réduit considérablement le nombre de paramètres à apprendre et engendre des détecteurs de caractéristiques locaux et équivariant aux translations. Ceci mène à des modèles ayant une meilleure vraisemblance, comparativement aux RBMs entraînées sur des segments d’images. Le deuxième article est motivé par des découvertes récentes en neurosciences. Il analyse l’impact d’unités quadratiques sur des tâches de classification visuelles, ainsi que celui d’une nouvelle fonction d’activation. Nous observons que les RNAs à base d’unités quadratiques utilisant la fonction softsign, donnent de meilleures performances de généralisation. Le dernière article quand à lui, offre une vision critique des algorithmes populaires d’entraînement de RBMs. Nous montrons que l’algorithme de Divergence Contrastive (CD) et la CD Persistente ne sont pas robustes : tous deux nécessitent une surface d’énergie relativement plate afin que leur chaîne négative puisse mixer. La PCD à "poids rapides" contourne ce problème en perturbant légèrement le modèle, cependant, ceci génère des échantillons bruités. L’usage de chaînes tempérées dans la phase négative est une façon robuste d’adresser ces problèmes et mène à de meilleurs modèles génératifs.