Molecular Descriptor Subset Selection in Theoretical Peptide Quantitative Structure–Retention Relationship Model Development Using Nature-Inspired Optimization Algorithms

Z0c,uvela, Petar,Liu, J. Jay,Macur, Katarzyna,Bą,czek, Tomasz American Chemical Society 2015 ANALYTICAL CHEMISTRY - Vol.87 No.19

<P>In this work, performance of five nature-inspired optimization algorithms, genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly algorithm (FA), and flower pollination algorithm (EPA), was compared in molecular descriptor selection for development of quantitative structure retention relationship (QSRR) models for 83 peptides that originate from eight model proteins. The matrix with 423 descriptors was used as input, and QSRR models based on selected descriptors were built using partial least squares (PLS), whereas root mean square error of prediction (RMSEP) was used as a fitness function for their selection. Three performance criteria, prediction accuracy, computational cost, and the number of selected descriptors, were used to evaluate the developed QSRR models. The results show that all five variable selection methods outperform interval PLS (iPLS), sparse PLS (sPLS), and the full PLS model, whereas GA is superior because of its lowest computational cost and higher accuracy (RMSEP of 5.534%) with a smaller number of variables (nine descriptors). The GA-QSRR model was validated initially through Y-randomization. In addition, it was successfully validated with an external testing set out of 102 peptides originating from Bacillus subtilis proteomes (RMSEP of 22.030%). Its applicability domain was defined, from which it was evident that the developed GA-QSRR exhibited strong robustness. All the sources of the model's error were identified, thus allowing for further application of the developed methodology in proteomics.</P>

Study of broad bandwidth vibrational energy harvesting system with optimum thickness of PET substrate

C.T. Pan,Z.H. Liu,Y.C. Chen 한국물리학회 2012 Current Applied Physics Vol.12 No.3

In this paper, we present the development of a flexible PET-based (polyethylene terephthalate; PET)vibrational energy harvesting system with broad bandwidth. This broad bandwidth harvesting system comprises of four units of individual ZnO (zinc oxide) piezoelectric harvester in the form of a cantilever structure connected in parallel, and rectifying circuit with storage module. This system has ability to convert mechanical energy into electrical energy from the varying ambient vibration. The design and simulation of a piezoelectric cantilever plate was described by using commercial software ANSYS FEA (Finite Element Analysis) to determine the optimum thickness of PET substrate, internal stress distribution,operation frequency and electric potential. With the optimum thickness predicted by developed accurate analytical formula analysis, the one-way mechanical strain that is efficient to enhance the induced electric potential can be controlled within the piezoelectric ZnO layer. In addition, the relationship among the model solution of piezoelectric cantilever plate equation, vibration-induced electric potential and electric power was realized. An individual piezoelectric harvester consists of flexible PET substrate, piezoelectric ZnO thin film with (002) c-axis preferred orientation, and selectively deposited UV-curable resin lump structure which is used to change the resonant frequency of the harvester. In combination with multi-harvesters and rectifying with storage module together, an energy harvesting system with broad bandwidth can be fabricated. One individual harvester achieves a maximum OCV (open-circuit voltage) up to 4 V with power density of 1.247 mW/cm3. So far, we succeeded in accomplishing a broad bandwidth system with operating frequency range within 100 Hze450 Hz to enhance powering efficiency. When the DC voltage (direct current voltage) across a storage module is charged up to 1.55 V after rectification, a flash LED (light emitting diode) is driven.

Electronic properties of graphene on the C-decorated Si(111) surface:An ab initio study

J. Liu,C.Y. He,W. Wang,N. Jiao,C.X. Zhang,L.Z. Sun 한국물리학회 2013 Current Applied Physics Vol.13 No.7

First principles calculations based on the density functional theory are performed to study electronic structures of graphene adsorbed on clean or C-decorated Si(111) surface. Two types of surface reconstructions,2 x 2 and ffiffiffi 3p x 3p , are considered to be decorated by carbon atoms with different concentrations. We find that graphene adsorbed on ideal clean Si(111) surface tends to induce a 2 x 1reconstruction, and its electronic dispersion characteristics are preserved. Moreover, the decoration of carbon atoms on the Si(111) surface can effectively passivate the Si dangling bonds on the surface. Such decoration effects make the carbon deco

Deletion of the Lmna Gene Induces Growth Delay and Serum Biochemical Changes in C57BL/6 Mice

Ruan, J.,Liu, X.G.,Zheng, H.L.,Li, J.B.,Xiong, X.D.,Zhang, C.L.,Luo, C.Y.,Zhou, Z.J.,Shi, Q.,Weng, Y.G. Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.1

The A-type lamin deficient mouse line ($Lmna^{-/-}$) has become one of the most frequently used models for providing insights into many different aspects of A-type lamin function. To elucidate the function of Lmna in the growth and metabolism of mice, tissue growth and blood biochemistry were monitored in Lmna-deficient mice, heterozygous ($Lmna^{+/-}$) and wide-type ($Lmna^{+/+}$) backcrossed to C57BL/6 background. At 4 weeks after birth, the weight of various organs of the $Lmna^{-/-}$, $Lmna^{+/-}$ and $Lmna^{+/+}$ mice was measured. A panel of biochemical analyses consisting of 15 serological tests was examined. The results showed that Lmna deficient mice had significantly decreased body weight and increased the ratio of organ to body weight in most of tissues. Compared with $Lmna^{+/+}$ and $Lmna^{+/-}$ mice, $Lmna^{-/-}$ mice exhibited lower levels of ALP (alkaline phosphatase), Chol (cholesterol), CR (creatinine), GLU (glucose), HDL (high-density lipoprotein cholesterol) and higher levels of ALT (alanine aminotransferase) (p<0.05). $Lmna^{-/-}$ mice displayed higher AST (aspartate aminotransferase) values and lower LDL (lowdensity lipoprotein cholesterol), CK-MB (creatine kinase-MB) levels than $Lmna^{+/+}$ mice (p<0.05). There were no significant differences among the three groups of mice with respect to BUN (blood urea nitrogen), CK (creatine kinase), Cyc C (cystatin C), TP (total protein), TG (triacylglycerols) and UA (uric acid) levels (p>0.05). These changes of serological parameters may provide an experimental basis for the elucidation of Lmna gene functions.

Polymorphisms in the Promoter Region of the Chinese Bovine PPARGC1A Gene

Li, M.J.,Liu, M.,Liu, D.,Lan, X.Y.,Lei, C.Z.,Yang, D.Y.,Chen, H. Asian Australasian Association of Animal Productio 2013 Animal Bioscience Vol.26 No.4

The peroxisome proliferator-activated receptor gamma coactivator-1 alpha protein, encoded by the PPARGC1A gene, plays an important role in energy homeostasis. The genetic variations within the PPARGC1A gene promoter region were scanned in 808 Chinese native bovines belonging to three cattle breeds and yaks. A total of 6 SNPs and one 4 bp insertion variation in the promoter region of the bovine PPARGC1A gene were identified: SNP -259 T>A, -301_-298insCTTT, -915 A>G, -1175 T>G, -1590 C>T, -1665 C>T and -1690 G>A, which are in the binding sites of some important transcription factors: sex-determining region Y (SRY), myeloid-specific zinc finger-1 (MZF-1) and octamer factor 1(Oct-1). It is expected that these polymorphisms may regulate PPARGC1A gene transcription and might have consequences at a regulatory level.

Radiation damage in helium ion – irradiated reduced activation ferritic/martensitic steel

L.D. Xia,W.B. Liu,H.P. Liu,J.H. Zhang,H. Chen,Z.G. Yang,C. Zhang 한국원자력학회 2018 Nuclear Engineering and Technology Vol.50 No.1

Nanocrystalline reduced activation ferritic/martensitic (RAFM) steel samples were prepared using surfacemechanical attrition treatment (SMAT). Un-SMATed and SMATed reduced activation ferritic/martensitic samples were irradiated by helium ions at 200 C and 350 C with 2 dpa and 8 dpa, respectively,to investigate the effects of grain boundaries (GBs) and temperature on the formation of Hebubbles during irradiation. Experimental results show that He bubbles are preferentially trapped at GBsin all the irradiated samples. Bubble denuded zones are clearly observed near the GBs at 350 C, whereasthe bubble denuded zones are not obvious in the samples irradiated at 200 C. The average bubble sizeincreases and the bubble density decreases with an increasing irradiation temperature from 200 C to350 C. Both the average size and density of the bubbles increase with an increasing irradiation dose from2 dpa to 8 dpa. Bubbles with smaller size and lower density were observed in the SMATed samples butnot in the un-SMATed samples irradiated in the same conditions, which indicate t

Fabricating Ultrathin Plate-Like WC Grains in WC–8Co Hardmetals by Increasing Discharge Intensity During Plasma-Assisted Ball Milling

M. Q. Zeng,J. L. Tu,M. Zhu,W. Wang,J. W. Liu,Z. C. Lu 대한금속·재료학회 2020 METALS AND MATERIALS International Vol.26 No.9

The effects of plasma discharge intensity on the microstructure evolution of ball-milled tungsten (W)–carbon (C)–cobalt (Co)mixtures and the formation mechanism of ultrathin plate-like tungsten carbide (WC) grains prepared by ball milling with andwithout plasma discharge were investigated. It was found that increasing the plasma discharge intensity during ball millingobviously promoted the formation of a thin flake-like W phase because of the electroplasticity effect and simultaneouslylowered the carburization temperature between W and C. A combination of high hardness and transverse rupture strength of92.9 HRA and 3659 MPa, respectively, was obtained for the WC–8Co alloy fabricated by plasma milling at a gas pressure of5 × 103 Pa with a dielectric barrier discharge layer thickness of 3 mm. These properties were mainly attributed to the markedlylowered activation energy of the WC phase and generation of highly oriented ultrathin plate-like WC grains by plasma milling. The combination of the flake-like structure of the plasma-milled W aggregate and high specific interfacial area and shortdiffusion distance of W/C were readily inherited by the ultrathin plate-like WC grains in the sintered WC–Co hardmetals.

Novel anti-apoptotic mechanism of A20 through targeting ASK1 to suppress TNF-induced JNK activation

Won, M,Park, K A,Byun, H S,Sohn, K-C,Kim, Y-R,Jeon, J,Hong, J H,Park, J,Seok, J H,Kim, J M,Yoon, W-H,Jang, I-S,Shen, H M,Liu, Z G,Hur, G M Macmillan Publishers Limited 2010 CELL DEATH AND DIFFERENTIATION Vol.17 No.12

The zinc-finger protein A20 has crucial physiological functions as a dual inhibitor of nuclear factor-κB (NF-κB) activation and apoptosis in tumor necrosis factor (TNF) receptor 1 signaling pathway. Although the molecular basis for the anti-NF-κB function of A20 has been well elucidated, the anti-apoptotic function of A20 is largely unknown. Here, we report a novel mechanism underlying the anti-apoptotic function of A20: A20 blocks TNF-induced apoptosis through suppression of c-jun N-terminal kinase (JNK) by targeting apoptosis signal-regulating kinase1 (ASK1). First, the ectopic expression of A20 drastically inhibits TNF-induced JNK activation and apoptosis in multiple cell types including those deficient of NF-κB activation. Unexpectedly, the blunting effect of A20 on TNF-induced JNK activation is not mediated by affecting the TNFR1 signaling complex formation. Instead, A20 interacts with ASK1, an important MAPKK kinase in the JNK signaling cascade. More importantly, overexpression of wild-type A20, but not of mutant A20 (ZnF4; C624A, C627A), promotes degradation of the ASK1 through the ubiquitin-proteasome system. Taken together, the results from this study reveal a novel anti-apoptotic mechanism of A20 in TNF signaling pathway: A20 binds to ASK1 and mediates ASK1 degradation, leading to suppression of JNK activation and eventually blockage of apoptosis.

Association between Melatonin Receptor 1A Gene and Expression of Reproductive Seasonality in Sheep

Chu, M.X.,Cheng, D.X.,Liu, W.Z.,Fang, L.,Ye, S.C. Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.8

To determine whether a link exists between reproductive seasonality and the structure of the melatonin receptor 1A (MTNR1A) gene, the latter was studied in nonseasonal estrous breeds (Small Tail Han and Hu ewes) and seasonal estrous breeds (Dorset, Suffolk and German Mutton Merino ewes). A large fragment of the exon 2 of the MTNR1A gene was amplified and a uniform fragment of 824 bp was obtained in 239 ewes of five breeds. The 824 bp PCR product was digested with restriction endonucleases Mnl I and Rsa I, and checked for the presence of restriction sites. The presence (allele M) or absence (allele m) of an Mnl I site at base position 605 led to three genotypes MM (236 bp/236 bp), Mm (236 bp/303 bp) and mm (303 bp/303 bp) in five sheep breeds. The presence (allele R) or absence (allele r) of a Rsa I site at base position 604 led to three genotypes RR (267 bp/267 bp), Rr (267 bp/290 bp) and rr (290 bp/290 bp) in five sheep breeds. Frequencies of MM and RR genotypes were obviously higher, and frequencies of mm and rr genotypes were obviously lower in nonseasonal estrous sheep breeds than in seasonal estrous sheep breeds. Sequencing revealed four mutations (G453T, G612A, G706A, C891T) in mm genotype compared to MM genotype and one mutation (C606T) in rr genotype compared to RR genotype. For polymorphic Mnl I and Rsa I cleavage sites, the differences of genotype distributions were very highly significant (p<0.01) between Small Tail Han ewes and seasonal estrous sheep breeds. In each group, no significant difference (p>0.05) was detected. These results preliminarily showed an association between MM, RR genotypes and nonseasonal estrus in ewes and an association between mm, rr genotypes and seasonal estrus in ewes.

Association Analyses with Carcass Traits in the Porcine KIAA1717 and HUMMLC2B Genes

Xu, D.Q.,Xiong, Y.Z.,Liu, M.,Lan, J.,Ling, X.F.,Deng, C.Y.,Jiang, S.W. Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.11

By screening a subtracted cDNA library constructed with mRNA obtained from the longissimus dorsi muscles of F1 hybrids Landrace${\times}$Yorkshire and their Yorkshire female parents, we isolated two partial sequences coding for the H3-K4-specific methyltransferase (KIAA1717) and skeletal muscle myosin regulatory light chain (HUMMLC2B) genes. In the present work we investigated two SNPs, one (C1354T) at the 3' untranslated region (UTR) of KIAA1717 and one (A345G) at the SINE (PRE-1) element of HUMMLC2B, in a resource population derived from crossing Chinese Meishan and Large White pig. The selected pigs were genotyped by means of a PCR-RFLP protocol. Significant associations were observed for the KIAA1717 C1354T polymorphic site with thorax-waist backfat thickness (p<0.05), buttock backfat thickness (p<0.05), average backfat thickness (p<0.05), loin eye height (p<0.05), loin eye area (p<0.05), carcass length to 1$^{st}$ spondyle (p<0.01) and carcass length to 1st rib (p<0.01). HUMMLC2B A345G were significantly associated with loin eye width (p<0.05), loin eye area (p<0.05). Further studies are needed to confirm these preliminary results.