Establishment of a viable cell detection system for microorganisms in wine based on ethidium monoazide and quantitative PCR

Fermentability and contamination level of wine can be assessed through the detection of viable fermentation-related and spoilage-related microorganisms. Ethidium monoazide in combination with quantitative PCR (EMA-qPCR) has been considered as a promising method to enumerate viable cells. Milling for 80 s by O 500-mu m glass beads is demonstrated to be optimal for DNA extraction from yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) in wine to be used as a template for PCR. EMA-qPCR results from experiments using DNA extracted by this method correlate well with the results of a plating assay (R-2 > 0.99), and a PCR efficiency between 96% and 105% was obtained. Moreover, for all of these microorganisms, EMA treatment of pure cultures at a low concentration (10 mu g/mL) for 20 min photoactivation resulted in effective differentiation between viable and non-viable cells and had no effect on viable cells. Due to sublethal injury to some cells, underestimation of cell counts was found in most of the wine samples tested using the EMA-qPCR method, and a 40-min incubation in recovery medium could completely offset this error. Our results suggest an optimal glass-bead DNA extraction method and EMA treatment suitable for all of the main microorganisms in wine. The EMA-qPCR method was successfully applied to quantify yeasts. Saccharomyces cerevisiae (S. cerevisiae), LAB, non-Oenococcus oeni LAB (non-O. oeni LAB) and AAB in wine samples. (C) 2012 Elsevier Ltd. All rights reserved

Aspewentins A-C, Norditerpenes from a Cryptic Pathway in an Algicolous Strain of Aspergillus wentii

Through addition of suberoylanilide hydroxamic acid, two new aromatic norditerpenes, aspewentins A (1) and B (2), along with an oxygenated derivative, aspewentin C (3), were obtained from the culture of an Aspergillus wentii strain (na-3) isolated from the tissue of the brown alga Sargassum fusiforme. The structures and absolute configurations were unambiguously elucidated by spectroscopic analyses and quantum chemical calculations. Aspewentins A-C were produced before sporulation and exhibited potent bioactivities against some marine-derived organisms.Through addition of suberoylanilide hydroxamic acid, two new aromatic norditerpenes, aspewentins A (1) and B (2), along with an oxygenated derivative, aspewentin C (3), were obtained from the culture of an Aspergillus wentii strain (na-3) isolated from the tissue of the brown alga Sargassum fusiforme. The structures and absolute configurations were unambiguously elucidated by spectroscopic analyses and quantum chemical calculations. Aspewentins A-C were produced before sporulation and exhibited potent bioactivities against some marine-derived organisms

A flow cytometer based protocol for quantitative analysis of bloom-forming cyanobacteria (Microcystis) in lake sediments

A quantitative protocol for the rapid analysis of Microcystis cells and colonies in lake sediment was developed using a modified flow cytometer, the CytoSense. For cell enumeration, diluted sediment samples containing Microcystis were processed with sonication to disintegrate colonies into single cells. An optimized procedure suggested that 5 mg dw (dry weight)/mL dilution combined with 200 W x 2 min sonication yielded the highest counting efficiency. Under the optimized determination conditions, the quantification limit of this protocol was 3.3x10(4) cells/g dw. For colony analysis, Microcystis were isolated from the sediment by filtration. Colony lengths measured by flow cytometry were similar to those measured by microscopy for the size range of one single cell to almost 400 mu m in length. Moreover, the relationship between colony size and cell number was determined for three Microcystis species, including Microcystis flos-aquae, M. aeruginosa and M. wessenbergii. Regression formulas were used to calculate the cell numbers in different-sized colonies. The developed protocol was applied to field sediment samples from Lake Taihu. The results indicated the potential and applicability of flow cytometry as a tool for the rapid analysis of benthic Microcystis. This study provided a new capability for the high frequency monitoring of benthic overwintering and population dynamics of this bloom-forming cyanobacterium.A quantitative protocol for the rapid analysis of Microcystis cells and colonies in lake sediment was developed using a modified flow cytometer, the CytoSense. For cell enumeration, diluted sediment samples containing Microcystis were processed with sonication to disintegrate colonies into single cells. An optimized procedure suggested that 5 mg dw (dry weight)/mL dilution combined with 200 W x 2 min sonication yielded the highest counting efficiency. Under the optimized determination conditions, the quantification limit of this protocol was 3.3x10(4) cells/g dw. For colony analysis, Microcystis were isolated from the sediment by filtration. Colony lengths measured by flow cytometry were similar to those measured by microscopy for the size range of one single cell to almost 400 mu m in length. Moreover, the relationship between colony size and cell number was determined for three Microcystis species, including Microcystis flos-aquae, M. aeruginosa and M. wessenbergii. Regression formulas were used to calculate the cell numbers in different-sized colonies. The developed protocol was applied to field sediment samples from Lake Taihu. The results indicated the potential and applicability of flow cytometry as a tool for the rapid analysis of benthic Microcystis. This study provided a new capability for the high frequency monitoring of benthic overwintering and population dynamics of this bloom-forming cyanobacterium

Fracture Characteristics and Damage Evolution of Coating Systems Under Four-Point Bending

The fracture and damage behaviors of ceramic coating/alloy substrate systems under four-point bending were investigated using a scanning electron microscope to observe insitu tests. Both the thin and thick coatings fractured by tensile instability at the pure bending sections, and multiple transverse cracks that were vertical to the interface occurred in the coatings. The average crack spacing was greater for the thick coatings than for the thin ones. A catastrophic failure model was developed to explain the damage evolution behavior of the coatings. The damage was found to increase sharply near the failure point

Nonlinear spectral-like schemes for hybrid schemes

In spectral-like resolution-WENO hybrid schemes, if the switch function takes more grid points as discontinuity points, the WENO scheme is often turned on, and the numerical solutions may be too dissipative. Conversely, if the switch function takes less grid points as discontinuity points, the hybrid schemes usually are found to produce oscillatory solutions or just to be unstable. Even if the switch function takes less grid points as discontinuity points, the final hybrid scheme is inclined to be more stable, provided the spectral-like resolution scheme in the hybrid scheme has moderate shock-capturing capability. Following this idea, we propose nonlinear spectral-like schemes named weighted group velocity control (WGVC) schemes. These schemes show not only high-resolution for short waves but also moderate shock capturing capability. Then a new class of hybrid schemes is designed in which the WGVC scheme is used in smooth regions and the WENO scheme is used to capture discontinuities. These hybrid schemes show good resolution for small-scales structures and fine shock-capturing capabilities while the switch function takes less grid points as discontinuity points. The seven-order WGVC-WENO scheme has also been applied successfully to the direct numerical simulation of oblique shock wave-turbulent boundary layer interaction

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Best-Worst Method: Inconsistency, Uncertainty, Consensus, and Range Sensitivity

It is our choices that make us who we are. To lead a better life, we have to make better decisions. Nowadays, decisions are increasingly made in complex contexts, in a host of different application domains. Because of that, we need more reliable decision analysis methodologies to improve our decisions. The ability to deal with multi-dimensionality is one of the critical requirements of the decision analysis methods that help us make better decisions. Multi-Criteria Decision-Making (MCDM) is one of the most popular approaches when it comes to formulating and solving decision-making problems, best-known for its ability to handle problems where a multitude of, often conflicting, criteria arise. As one of the latest MCDM methods, the Best-Worst Method (BWM) has been studied substantially and applied increasingly to various fields since its introduction, thanks to its simplicity, flexibility and general applicability. Despite its popularity, some significant issues of BWM have not yet been systematically investigated in existing literature, including: (i) the inconsistency in the preferences provided by Decision-Makers (DMs), (ii) the uncertain information embedded in the DMs’ judgements, (iii) problems in reaching a consensus in group decision-making, and (iv) the range sensitivity in an MCDM problem that is not taken into account in BWM. The main objective of this thesis is to develop an approach to measure, check and improve inconsistency, to develop an approach to incorporate judgments uncertainty, to develop a method to reach consensus and to incorporate range sensitivity in the BWM.Transport and Logistic

Off-site Construction Study for Potential Application in Bandung

The housing shortage in Bandung has been an acute problem for long, which requires to be solved urgently; however, the affordability of housing blocks people away from improving their living condition. This paper is trying to focus on the rapid and repeatable off-site construction system which could be the possible option to accommodate the housing shortage in a short period. The comparative analysis of different off-site construction methods and materials as well would be introduced in this paper to figure out the preferable solution for the context of Bandung. Also, the off-site construction industry and its workflow would be would be discussed in this paper. This research paper is part of my graduation project and would be beneficial to the future bio-based off-site construction design project.Architecture, Urbanism and Building Science

A Koiter-Newton arclength method for buckling-sensitive structures

Thin-walled structures, when properly designed, possess a high strength-to-weight and stiffness-to-weight ratio, and therefore are used as the primary components in some weight critical structural applications, such as aerospace and marine engineering. These structures are prone to be limited in their load carrying capability by buckling, while staying in the linear elastic range of the material. Buckling of thinwalled structures is an inherently nonlinear phenomena. When the material stays within its linear elastic range, the source of the nonlinearity is purely geometric. Thus, the analysis of nonlinear response of structures, especially thin-walled structures which are buckling sensitive, is important for determining their load carrying capability. For this reason, structural geometric nonlinearities are increasingly taken into account in engineering design. Nowadays, with the expanding computational power of modern computers nonlinear finite element analysis using commercial software is becoming the standard technique used to obtain the nonlinear response of complex structures, however, the repeated analyses that are needed in the design phase are still computationally intensive, in terms of the computation time required to run large models, even for modern computers. For this reason, reduced order techniques that reduce the problem size are attractive whenever repetitive analyses are required, such as in design optimization. Research on reduced order modeling of the nonlinear response of structures has attracted much attention from researchers. Some analytic techniques constitute very powerful tools for reducing the number of degrees of freedom (DOFs) in a nonlinear system, such as the Rayleigh-Ritz techniques and perturbation techniques. These two reduced basis techniques can be implemented in both analytical and numerical contexts, and due to the modeling versatility of the finite element method (FEM), most researchers prefer to reconstruct them within the FEM context, referred to as reduction methods. There are two families of reduction methods which can be recognized. The first family consists the path-following reduction methods which are based on some analytic techniques to reduce the number of DOFs in the full model and are able to trace the entire nonlinear equilibrium path of structures automatically, while they may find difficulties in the presence of buckling. Koiter reduction methods belong to the second family, and they are very good at handling the buckling sensitive cases due to the use of Koiter’s classical initial postbuckling theory, but the Koiter perturbation approach also limits the validity of these methods to a small range around the bifurcation point. The focus of the research reported in this thesis therefore is to find ways to synthesize the advantages of current reduction methods and obtain a new reduced basis path-following approach. In this thesis, a new approach called the Koiter-Newton (K-N) is presented for the numerical solution of a class of elastic nonlinear structural analysis problems. The method combines ideas from Koiter’s initial post-buckling analysis and Newton arclength methods to obtain an algorithm that is accurate over the entire equilibrium path of structures and efficient in the presence of buckling and/or imperfection sensitivity. The proposed approach is performed in a step by step manner to trace the entire equilibrium path, as is commonly used in the classical Newton arc-length method. In every expansion step, the approach works by combining a prediction step using a nonlinear reduced order model (ROM) based on Koiter’s initial postbuckling expansion with a Newton arc-length correction procedure. This nonlinear prediction provided by the reduced order model is much better compared to linear predictors used by the classical Newton-Raphson method, thus allowing the algorithm to use fairly large step sizes. The basic premise behind the proposed approach is the use of Koiter’s asymptotic expansion from the beginning rather than using it only at the bifurcation point in contrast to the traditional Koiter approaches. In each asymptotic expansion, the force space is reduced by the span of a set of perturbation loads that are chosen to excite the possible buckling branches. According to the stability of the equilibrium point, at which the asymptotic expansion is applied, different ways for selecting the perturbation loads are proposed. The proposed selection rules guarantee that the expansion step of the proposed approach can be applied at any point along the equilibrium path. The proposed technique requires derivatives of the element load vectors with respect to the degrees of freedom up to the third order. This is two orders more than what is traditionally needed for Newton’s method. To facilitate differentiation, nonlinear elements based on the element independent co-rotational frame are applied in the Koiter-Newton analysis. Automatic differentiation is used to find the derivatives of the co-rotational frame with respect to element degrees of freedom. In this way, full nonlinear kinematics are taken into account when constructing the reduced order model. In some cases, the nonlinear in-plane rotations of structures can be neglected, although the rotations of the normals to the mid-surface are finite. In such cases, Von Karman kinematics, which ignore some nonlinear items in the Green’s staindisplacement relations, possess an acceptable accuracy compared with the full nonlinear kinematics. Hence, the Koiter-Newton approach is also implemented based on Von Karman kinematics to achieve a better computational efficiency. Various numerical examples of beam and shell models are presented and used to evaluate the performance of the method. The Koiter-Newton analyses using the corotational kinematics and the Von K´arm´an kinematics are accurate and more computational efficient, compared with the results obtained using ABAQUS which adopts a full nonlinear analysis. The improved efficiency demonstrated by the Koiter-Newton technique will open the door to the direct use of detailed nonlinear finite element models in the design optimization of next generation flight and launch vehicles.Aerospace Structures and Computational MechanicsAerospace Engineerin

Re-public City: A strategic planning of public space for local people in the context of globalization in Shanghai Lujiazui Finance & Trade Zone

complex cityUrbanismArchitectur