Bridges Structural Health Monitoring and Deterioration Detection Synthesis of Knowledge and Technology

INE/AUTC 10.0

Nanoenhanced Materials for Reclamation of Mine Lands and Other Degraded Soils: A Review

Successful mine soil reclamation facilitates ecosystem recovery, minimizes adverse environmental impacts, creates additional lands for agricultural or forestry uses, and enhances the carbon (C) sequestration. Nanoparticles with extremely high reactivity and deliverability can be applied as amendments to improve soil quality, mitigate soil contaminations, ensure safe land–application of the conventional amendment materials (e.g., manures and biosolids), and enhance soil erosion control. However, there is no report on using nanoenhanced materials for mine soil reclamation. Through reviewing the up-to-date research results on using environment-friendly nanoparticles for agricultural soil quality improvement and for contaminated soil remediation, this paper synthesizes that these nanomaterials with high potentials for mine soil reclamation include zeolites, zero-valent iron nanoparticles, iron oxide nanoparticles, phosphate-based nanoparticles, iron sulfide nanoparticles and C nanotubes. Transport of these particles in the environment and their possible ecotoxicological effects are also discussed. Additionally, this article proposes a practical and economical approach to applying nanotechnology for mine soil reclamation: adding small amounts of nanoparticles to the conventional soil amendment materials and then applying the mixtures for soil quality improvements. Hence the cost of using nanoparticles is reduced and the benefits of both nanoparticles and the conventional amendment materials are harnessed

Development of Mining Technology and Equipment for Seafloor Massive Sulfide Deposits

Seafloor massive sulfide(SMS) deposits which consist of Au, Ag, Cu, and other metal elements, have been a target of commercial mining in recent decades. The demand for established and reliable commercial mining system for SMS deposits is increasing within the marine mining industry. The current status and progress of mining technology and equipment for SMS deposits are introduced. First, the mining technology and other recent developments of SMS deposits are comprehensively explained and analyzed. The seafloor production tools manufactured by Nautilus Minerals and similar mining tools from Japan for SMS deposits are compared and discussed in turn. Second, SMS deposit mining technology research being conducted in China is described, and a new SMS deposits mining tool is designed according to the environmental requirement. Finally, some new trends of mining technology of SMS deposits are summarized and analyzed. All of these conclusions and results have reference value and guiding significance for the research of SMS deposit mining in China

Circulating MicroRNA Expression Profiles in Patients with Stable and Unstable Angina

OBJECTIVES: High incidence and case fatality of unstable angina (UA) is, to a large extent, a consequence of the lack of highly sensitive and specific non-invasive markers. Circulating microRNAs (miRNAs) have been widely recommended as potential biomarkers for numerous diseases. In the present study, we characterized distinctive miRNA expression profiles in patients with stable angina (SA), UA, and normal coronary arteries (NCA), and identified promising candidates for UA diagnosis. METHODS: Serum was collected from patients with SA, UA, and NCA who visited the Department of Cardiovascular Diseases of the Meizhou People’s Hospital. Small RNA sequencing was carried out on an Illumina HiSeq 2500 platform. miRNA expression in different groups of patients was profiled and then confirmed based on that in an independent set of patients. Functions of differentially expressed miRNAs were predicted using gene ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis. RESULTS: Our results indicated that circulating miRNA expression profiles differed between SA, UA, and NCA patients. A total of 36 and 161 miRNAs were dysregulated in SA and UA patients, respectively. miRNA expression was validated by reverse transcription quantitative polymerase chain reaction. CONCLUSION: The results suggest that circulating miRNAs are potential biomarkers of UA

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Global systematic review with meta-analysis shows that warming effects on terrestrial plant biomass allocation are influenced by precipitation and mycorrhizal association

Biomass allocation in plants is fundamental for understanding and predicting terrestrial carbon storage. Yet, our knowledge regarding warming effects on root: shoot ratio (R/S) remains limited. Here, we present a meta-analysis encompassing more than 300 studies and including angiosperms and gymnosperms as well as different biomes (cropland, desert, forest, grassland, tundra, and wetland). The meta-analysis shows that average warming of 2.50 °C (median = 2 °C) significantly increases biomass allocation to roots with a mean increase of 8.1% in R/S. Two factors associate significantly with this response to warming: mean annual precipitation and the type of mycorrhizal fungi associated with plants. Warming-induced allocation to roots is greater in drier habitats when compared to shoots (+15.1% in R/S), while lower in wetter habitats (+4.9% in R/S). This R/S pattern is more frequent in plants associated with arbuscular mycorrhizal fungi, compared to ectomycorrhizal fungi. These results show that precipitation variability and mycorrhizal association can affect terrestrial carbon dynamics by influencing biomass allocation strategies in a warmer world, suggesting that climate change could influence belowground C sequestration

TreeFam: a curated database of phylogenetic trees of animal gene families

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at and

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.published_or_final_versio