Reordering Hierarchical Tree Based on Bilateral Symmetric Distance

BACKGROUND: In microarray data analysis, hierarchical clustering (HC) is often used to group samples or genes according to their gene expression profiles to study their associations. In a typical HC, nested clustering structures can be quickly identified in a tree. The relationship between objects is lost, however, because clusters rather than individual objects are compared. This results in a tree that is hard to interpret. METHODOLOGY/PRINCIPAL FINDINGS: This study proposes an ordering method, HC-SYM, which minimizes bilateral symmetric distance of two adjacent clusters in a tree so that similar objects in the clusters are located in the cluster boundaries. The performance of HC-SYM was evaluated by both supervised and unsupervised approaches and compared favourably with other ordering methods. CONCLUSIONS/SIGNIFICANCE: The intuitive relationship between objects and flexibility of the HC-SYM method can be very helpful in the exploratory analysis of not only microarray data but also similar high-dimensional data

An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks

<p>Abstract</p> <p>Background</p> <p>Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of <it>time </it>(<it>e.g.</it>, <it>retention time </it>of chemicals on a chromatographic column), a <it>spectral value </it>(<it>e.g., mass-to-charge ratio </it>of ions derived from chemicals), and the <it>analytical run number</it>. They also must rely on data preprocessing techniques. In particular, inter-run variance in the retention time of chemical species poses a significant hurdle that must be cleared before feature extraction, data reduction, and knowledge discovery can ensue. <it>Alignment methods</it>, for calibrating retention reportedly (and in our experience) can misalign matching chemicals, falsely align distinct ones, be unduly sensitive to chosen values of input parameters, and result in distortions of peak shape and area.</p> <p>Results</p> <p>We present an iterative block-shifting approach for retention-time calibration that detects chromatographic features and qualifies them by retention time, spectrum, and the effect of their inclusion on the quality of alignment itself. Mass chromatograms are aligned pairwise to one selected as a reference. In tests using a 45-run GC-MS experiment, block-shifting reduced the absolute deviation of retention by greater than 30-fold. It compared favourably to COW and XCMS with respect to alignment, and was markedly superior in preservation of peak area.</p> <p>Conclusion</p> <p>Iterative block-shifting is an attractive method to align GC-MS mass chromatograms that is also generalizable to other two-dimensional techniques such as HPLC-MS.</p

A fast VLSI architecture for full-search variable block size motion estimation in MPEG--4 AVC/H.264

We describe a fast VLSI architecture for full-search motion estimation for the blocks with 7 different sizes in MPEG-4 AVC/H.264. The proposed variable block size motion estimation (VBSME) architecture consists of a 16x16 PE array, an adder tree and comparators to find all 41 motion vectors and their minimum SADs for the blocks of 16x16, 16x8, 8x16, 8x8, 8x4, 4x8 and 4x4. It employs a 2-D datapath and its control of the search area data is simple and regular. The proposed VBSME can achieve 100% PE utilization by employing a preload register and a search data buffer inside each PE and allow real-time processing of 4CIF(704x576) video with 15 fps at 100 Mhz for a search range of [-32~+31]

Potential Explosion Risk Comparison between SMR and DMR Liquefaction Processes at Conceptual Design Stage of FLNG

An FLNG (floating liquefied natural gas) or LNG FPSO (floating production, storage and offloading) unit is a notable offshore unit with the increasing demand for LNG. The liquefaction process on an FLNG unit is the most important process because it determines the economic feasibility, but would be a hazard source because of the large quantity of hydrocarbons. While a high efficiency process such as C3MR has been preferred for onshore liquefaction processes, a relatively simple process such as the SMR (single mixed refrigerant) or DMR (dual mixed refrigerant) liquefaction process has been selected for offshore units because they require a more compact size, lighter weight, and higher safety due to their space limitation for facilities and long distance from shore. It is known that an SMR has the advantages of a simple configuration, small footprint, and lower risk. However, with an increased production rate, the inherent safety of SMR needs to be evaluated because of its small train capacity. In this study, the potential explosion risks of the SMR and DMR liquefaction processes were evaluated at the conceptual design stage. The results showed that an SMR has a lower overpressure than a DMR at the same frequency, only with a small production capacity of 0.9 MTPA. With increased capacity, the overpressure of the SMR was higher than that of the DMR. The increased number of trains increased the frequency in spite of the small amount of equipment per train. This showed that the inherent risk of an SMR is not always lower than that of a DMR, and an additional risk management strategy is recommended when an SMR is selected as the concept for an FLNG liquefaction process compared to the DMR liquefaction process

Antioxidant mitoquinone suppresses benign prostatic hyperplasia by regulating the AR–NLRP3 pathway

Mitoquinone (MitoQ), a mitochondria-targeted antioxidant, has been used to treat several diseases. The present study aimed to investigate the therapeutic effects of MitoQ in benign prostatic hyperplasia (BPH) models and their underlying molecular mechanisms. In this study, we determined that MitoQ inhibited dihydrotestosterone (DHT)-induced cell proliferation and mitochondrial ROS by inhibiting androgen receptor (AR) and NOD-like receptor family pyrin domain-containing 3 (NLRP3) signaling in prostate epithelial cells. Molecular modeling revealed that DHT may combine with AR and NLRP3, and that MitoQ inhibits both AR and NLRP3. AR and NLRP3 downregulation using siRNA showed the linkage among AR, NLRP3, and MitoQ. MitoQ administration alleviated pathological prostate enlargement and exerted anti-proliferative and antioxidant effects by suppressing the AR and NLRP3 signaling pathways in rats with BPH. Hence, our findings demonstrated that MitoQ is an inhibitor of NLPR3 and AR and a therapeutic agent for BPH treatment

Mn-Cr Layered Structure Catalysts for Low Temperature NH3 Selective Catalytic Reduction

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