Combined hardware–software multi-parallel prefiltering on the Convey HC-1 for fast homology detection

Protein databases used in research are huge and still grow at a fast pace. Many comparisons need to be done when searching similar (homologous) sequences for a given query sequence in these databases. Comparing a query sequence against all sequences of a huge database using the well-known Smith–Waterman algorithm is very time-consuming. Hidden Markov Models pose an opportunity for reducing the number of entries of a database and also enable to find distantly homologous sequences. Fewer entries are achieved by clustering similar sequences in a Hidden Markov Model. Such an approach is used by the bioinformatics tool HHblits. To further reduce the runtime, HHblits uses two-level prefiltering to reduce the number of time-consuming Viterbi comparisons. Still, prefiltering is very time-consuming. Highly parallel architectures and huge bandwidth are required for processing and transferring the massive amounts of data. In this article, we present an approach exploiting the reconfigurable, hybrid computer architecture Convey HC-1 for migrating the most time-consuming part. The Convey HC-1 with four FPGAs and high memory bandwidth of up to 76.8 GB/s serves as the platform of choice. Other bioinformatics applications have already been successfully supported by the HC-1. Limited by FPGA size only, we present a design that calculates four first-level prefiltering scores per FPGA concurrently, i.e. 16 calculations in total. This score calculation for the query profile against database sequences is done by a modified Smith–Waterman scheme that is internally parallelized 128 times in contrast to the original Streaming ‘Single Instruction Multiple Data (SIMD)’ Extensions (SSE)-supported implementation where only 16-fold parallelism can be exploited and where memory bandwidth poses the limiting factor. Preloading the query profile, we are able to transform the memory-bound implementation to a compute- and resource-bound FPGA design. We tightly integrated the FPGA-based coprocessor into the hybrid computing system by employing task-parallelism for the two-level prefiltering. Despite much lower clock rates, the FPGAs outperform SSE-based execution for the calculation of the prefiltering scores by a factor of 7.9.     

Rapid detection of viable Bacillus cereus emetic and enterotoxic strains in food by coupling propidium monoazide and multiplex PCR (PMA-mPCR)

Bacillus cereus can cause emetic and diarrheal food poisoning. It is widespread in nature and therefore, considered a major foodborne pathogen. To develop a sensitive and reliable assay for detecting enterotoxin genes (nheA, entFM, hblD, cytK) and emetic toxin (ces), specific primers each targeting one individual gene were designed. Propidium monoazide (PMA) was coupled with the developed multiplex PCR (mPCR) for the detection of viable B. cereus. The inclusivity and exclusivity of the PMA-mPCR was confirmed using a panel of 44 strains including 17 emetic and 9 enterotoxic B. cereus reference strains and 18 non-target strains. The limit of detection (LOD) without PMA treatment in pure DNA was 2 pg/reaction tube. The LOD of mPCR assay in pure heat-killed dead bacteria was 4.0 × 10² CFU/mL. Also, the LOD on the viable bacteria with or without PMA treatment was similar (3.8 × 10² CFU/mL) showing that the PMA treatment did not significantly decrease sensitivity. Finally, the newly developed PMA-mPCR successfully detected 4.8 × 10³ and 3.6 × 10³ CFU/g of viable B. cereus F4810/72 (emetic) and B. cereus ATCC 12480 (enterotoxic) reference strains, respectively, in food samples. Hence, this study combines PMA and mPCR to detect viable B. cereus with a wide range of toxin detection (5 toxins). Thus, the novel PMA-mPCR assay developed in this study is a rapid and efficient diagnostic tool for the monitoring of viable B. cereus in food samples and potentially other samples via appropriate DNA extraction.     

Hydrocarbon-based electrode ionomer for proton exchange membrane fuel cells

The electrode ionomer is a key factor that significantly affects the catalyst layer morphology and fuel cell performance. Herein, sulfonated poly(arylene ether sulfone)-based electrode ionomers with polymers of various molecular weights and alcohol/water mixtures were prepared, and those comprising the alcohol/water mixture showed a higher performance than the ones prepared using higher boiling solvents, such as dimethylacetamide; this is owing to the formation of the uniformly dispersed ionomer catalyst layer. The relation between ionomer molecular weight for the same polymer structure and the sulfonation degree was investigated. Because the chain length of polymer varies with molecular weight and chain entanglement degree, its molecular weight affects the electrode morphology. As the ionomer covered the catalyst, the agglomerates formed were of different morphologies according to their molecular weight, which could be deduced indirectly through dynamic light scattering and scanning electron microscopy. Additionally, the fuel cell performance was confirmed in the current-voltage curve.     

基于空气质量模拟的江苏省大气污染物排放清单比较研究

大气污染物排放清单是空气质量模拟和空气污染治理的重要依据.本研究比较分析了两套覆盖江苏省的2017年大气污染物排放清单，即分别由上海市环境科学研究院、江苏省环境科学研究院编制的"长三角清单"和"江苏省清单"，并结合区域空气质量模型CMAQ评估不同清单对长三角地区2017年1、4、7、10月的空气质量模拟的影响.清单比较结果表明，除二氧化硫（SO₂）以外，江苏省清单估算的各污染物排放量较长三角清单低.通过与观测数据比较，发现两套清单对SO₂、氮氧化物（NO_x）、臭氧（O₃）和细颗粒物（PM_2.5）的模型模拟性能均较好.江苏省清单与长三角清单两者的模拟结果空间分布接近，其中江苏省清单模拟的PM_2.5和O₃在长三角多数地区略低于长三角清单的模拟结果（1月O₃除外）.江苏省清单与长三角清单均能够用于空气质量模式模拟，可为江苏地区的细颗粒物和光化学烟雾污染的控制策略制定提供参考.     

Formulation of sage essential oil (Salvia officinalis,L.) monoterpenes into chitosan hydrogels and permeation study with GC-MS analysis

This study deals with the formulation of natural drugs into hydrogels. For the first time, compounds from the sage essential oil were formulated into chitosan hydrogels. A sample preparation procedure for hydrophobic volatile analytes present in a hydrophilic water matrix along with an analytical method based on the gas chromatography coupled with the mass spectrometry (GC-MS) was developed and applied for the evaluation of the identity and quantity of essential oil components in the hydrogels and saline samples. The experimental results revealed that the chitosan hydrogels are suitable for the formulation of sage essential oil. The monoterpene release can be effectively controlled by both chitosan and caffeine concentration in the hydrogels. Permeation experiment, based on a hydrogel with the optimized composition [3.5% (w/w) sage essential oil, 2.0% (w/w) caffeine, 2.5% (w/w) chitosan and 0.1% (w/w) Tween-80] in donor compartment, saline solution in acceptor compartment, and semi-permeable cellophane membrane, demonstrated the useful permeation selectivity. Here, (according to lipophilicity) an enhanced permeation of the bicyclic monoterpenes with antiflogistic and antiseptic properties (eucalyptol, camphor and borneol) and, at the same time, suppressed permeation of toxic thujone (not exceeding its permitted applicable concentration) was observed. These properties highlight the pharmaceutical importance of the developed chitosan hydrogel formulating sage essential oil in the dermal applications.     

Simultaneous synthesis of a heat exchanger network with multiple utilities using utility substages

Heat exchanger network synthesis (HENS) has progressed by using mathematical programming-based simultaneous methodology. Although various considerations such as non-isothermal mixing and bypass streams are applied to consider real world alternatives in modeling phase, many challenges are faced because of its properties within non-convex mixed-integer nonlinear programming (MINLP). We propose a modified superstructure, which contains a utility substage for use in considering multiple utilities in a simultaneous MINLP model. To improve model size and convergence, fixed utility locations according to temperature and series connections between utilities are suggested. The numbers of constraints, discrete, and continuous variables show that overall model size decreases compared with previous research. Thus, it is possible to expand the feasible search area for reaching the nearest global solution. The model's effectiveness and applications are exemplified by several literature problems, where it is used to deduce a network superior to that of any other reported methodology.     

Current Status on Stem Cells and Cancers of the Gastric Epithelium

Gastric cancer is still a leading cause of cancer-related mortality worldwide in spite of declining incidence. Gastric cancers are, essentially, adenocarcinomas and one of the strongest risk factors is still infection with Helicobacter pylori. Within the last years, it became clear that gastric self-renewal and carcinogenesis are intimately linked, particularly during chronic inflammatory conditions. Generally, gastric cancer is now regarded as a disease resulting from dysregulated differentiation of stem and progenitor cells, mainly due to an inflammatory environment. However, the situation in the stomach is rather complex, consisting of two types of gastric units which show bidirectional self-renewal from an unexpectedly large variety of progenitor/stem cell populations. As in many other tumors, cancer stem cells have also been characterized for gastric cancer. This review focuses on the various gastric epithelial stem cells, how they contribute to self-renewal and which routes are known to gastric adenocarcinomas, including their stem cells.     

Parallel chaos optimization algorithm with migration and merging operation

Chaos optimization algorithm (COA) utilizes the chaotic maps to generate the pseudo-random sequences mapped as the decision variables for global optimization applications. A kind of parallel chaos optimization algorithm (PCOA) has been proposed in our former studies to improve COA. The salient feature of PCOA lies in its pseudo-parallel mechanism. However, all individuals in the PCOA search independently without utilizing the fitness and diversity information of the population. In view of the limitation of PCOA, a novel PCOA with migration and merging operation (denoted as MMO-PCOA) is proposed in this paper. Specifically, parallel individuals are randomly selected to be conducted migration and merging operation with the so far parallel solutions. Both migration and merging operation exchange information within population and produce new candidate individuals, which are different from those generated by stochastic chaotic sequences. Consequently, a good balance between exploration and exploitation can be achieved in the MMO-PCOA. The impacts of different one-dimensional maps and parallel numbers on the MMO-PCOA are also discussed. Benchmark functions and parameter identification problems are used to test the performance of the MMO-PCOA. Simulation results, compared with other optimization algorithms, show the superiority of the proposed MMO-PCOA algorithm.     

Impact behavior and fractographic study of carbon nanotubes grafted carbon fiber-reinforced epoxy matrix multi-scale hybrid composites

Carbon nanotubes are the most promising reinforcement for high performance composites. Multiwall carbon nanotubes were directly grown onto the carbon fiber surface by catalytic thermal chemical vapor deposition technique. Multi-scale hybrid composites were fabricated using the carbon nanotubes grown fibers with epoxy matrix. Morphology of the grown carbon nanotubes was investigated using field emission scanning electron microscopy and transmission electron microscopy. The fabricated composites were subjected to impact tests which showed 48.7% and 42.2% higher energy absorption in Charpy and Izod impact tests respectively. Fractographic analysis of the impact tested specimens revealed the presence of carbon nanotubes both at the fiber surface and within the matrix which explained the reason for improved energy absorption capability of these composites. Carbon nanotubes presence at various cracks formed during loading provided a direct evidence of micro crack bridging. Thus the enhanced fracture strength of these composites is attributed to stronger fiber–matrix interfacial bonding and simultaneous matrix strengthening due to the grown carbon nanotubes.     

Direct Injection of CRISPR/Cas9-Related mRNA into Cytoplasm of Parthenogenetically Activated Porcine Oocytes Causes Frequent Mosaicism for Indel Mutations

Some reports demonstrated successful genome editing in pigs by one-step zygote microinjection of mRNA of CRISPR/Cas9-related components. Given the relatively long gestation periods and the high cost of housing, the establishment of a single blastocyst-based assay for rapid optimization of the above system is required. As a proof-of-concept, we attempted to disrupt a gene (GGTA1) encoding the α-1,3-galactosyltransferase that synthesizes the α-Gal epitope using parthenogenetically activated porcine oocytes. The lack of α-Gal epitope expression can be monitored by staining with fluorescently labeled isolectin BS-I-B₄ (IB4), which binds specifically to the α-Gal epitope. When oocytes were injected with guide RNA specific to GGTA1 together with enhanced green fluorescent protein (EGFP) and human Cas9 mRNAs, 65% (24/37) of the developing blastocysts exhibited green fluorescence, although almost all (96%, 23/24) showed a mosaic fluorescent pattern. Staining with IB4 revealed that the green fluorescent area often had a reduced binding activity to IB4. Of the 16 samples tested, six (five fluorescent and one non-fluorescent blastocysts) had indel mutations, suggesting a correlation between EGFP expression and mutation induction. Furthermore, it is suggested that zygote microinjection of mRNAs might lead to the production of piglets with cells harboring various mutation types.