Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization

© 2015 Elsevier Ltd. All rights reserved. Random walk on heterogeneous networks is a recently emerging approach to effective disease gene prioritization. Laplacian normalization is a technique capable of normalizing the weight of edges in a network. We use this technique to normalize the gene matrix and the phenotype matrix before the construction of the heterogeneous network, and also use this idea to define the transition matrices of the heterogeneous network. Our method has remarkably better performance than the existing methods for recovering known gene-phenotype relationships. The Shannon information entropy of the distribution of the transition probabilities in our networks is found to be smaller than the networks constructed by the existing methods, implying that a higher number of top-ranked genes can be verified as disease genes. In fact, the most probable gene-phenotype relationships ranked within top 3 or top 5 in our gene lists can be confirmed by the OMIM database for many cases. Our algorithms have shown remarkably superior performance over the state-of-the-art algorithms for recovering gene-phenotype relationships. All Matlab codes can be available upon email request

AFLP analysis on genetic diversity and population structure of small yellow croaker Larimichthys polyactis

The population genetic structure and diversity of small yellow croaker Larimichthys polyactis in the Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism(AFLP). Ninety-one individuals were collected from six locations representing three stocks of small yellow croaker. A total of 218 putative loci were detected by 3 primer combinations, 148 of which were polymorphic (67.89%). The proportion of polymorphic loci and Nei’s genetic diversity for six populations ranged from 55.34 - 60.09%, and from 0.1244 - 0.1378. AMOVA analysis and pairwise FST revealedsignificant genetic differentiation among the three groups based on the breeding migration routes and over-wintering grounds, supporting separate stocks in this species. The result shows the migratorybehavior might be an important factor which influences the genetic structure of this species. The UPGMA tree also revealed the significant geographic structure in this species. Pattern of isolation bydistance was observed in this species, indicating that significant genetic differentiation among localities of small yellow croaker might be due to the geographic distance

Chemical characterization of water-soluble organic carbon aerosols at a rural site in the Pearl River Delta, China, in the summer of 2006

Online measurements of water-soluble organic carbon (WSOC) aerosols were made using a particle-into-liquid sampler (PILS) combined with a total organic carbon (TOC) analyzer at a rural site in the Pearl River Delta region, China, in July 2006. A macroporous nonionic (DAX-8) resin was used to quantify hydrophilic and hydrophobic WSOC, which are defined as the fractions of WSOC that penetrated through and retained on the DAX-8 column, respectively. Laboratory calibrations showed that hydrophilic WSOC (WSOCHPI) included low-molecular aliphatic dicarboxylic acids and carbonyls, saccharides, and amines, while hydrophobic WSOC (WSOCHPO) included longer-chain aliphatic dicarboxylic acids and carbonyls, aromatic acids, phenols, organic nitrates, cyclic acids, and fulvic acids. On average, total WSOC (TWSOC) accounted for 60% of OC, and WSOCHPO accounted for 60% of TWSOC. Both WSOC HIP and WSOCHPO increased with photochemical aging determined from the NOx/NOy ratio. In particular, the average WSOCHPO mass was found to increase by a factor of five within a timescale of ∼10 hours, which was substantially larger than that of WSOCHPI (by a factor of 2-3). The total increase in OC mass with photochemical aging was associated with the large increase in WSOCHPO mass. These results, combined with the laboratory calibrations, suggest that significant amounts of hydrophobic organic compounds (likely containing large carbon numbers) were produced by photochemical processing. By contrast, water-insoluble OC (WIOC) mass did not exhibit significant changes with photochemical aging, suggesting that chemical transformation of WIOC to WSOC was not a dominant process for the production of WSOC during the study period. Copyright 2009 by the American Geophysical Union

Mobility of primary health care workers in China

© 2009 Meng et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Ancient Chinese medicine and mechanistic evidence of acupuncture physiology

Acupuncture has been widely used in China for three millennia as an art of healing. Yet, its physiology is not yet understood. The current interest in acupuncture started in 1971. Soon afterward, extensive research led to the concept of neural signaling with possible involvement of opioid peptides, glutamate, adenosine and identifying responsive parts in the central nervous system. In the last decade scientists began investigating the subject with anatomical and molecular imaging. It was found that mechanical movements of the needle, ignored in the past, appear to be central to the method and intracellular calcium ions may play a pivotal role. In this review, we trace the technique of clinical treatment from the first written record about 2,200 years ago to the modern time. The ancient texts have been used to introduce the concepts of yin, yang, qi, de qi, and meridians, the traditional foundation of acupuncture. We explore the sequence of the physiological process, from the turning of the needle, the mechanical wave activation of calcium ion channel to beta-endorphin secretion. By using modern terminology to re-interpret the ancient texts, we have found that the 2nd century b.c. physiologists were meticulous investigators and their explanation fits well with the mechanistic model derived from magnetic resonance imaging (MRI) and confocal microscopy. In conclusion, the ancient model appears to have withstood the test of time surprisingly well confirming the popular axiom that the old wine is better than the new

Fabrication of surface-patterned ZnO thin films using sol-gel methods and nanoimprint lithography

Surface-patterned ZnO thin films were fabricated by direct imprinting on ZnO sol and subsequent annealing process. The polymer-based ZnO sols were deposited on various substrates for the nanoimprint lithography and converted to surface-patterned ZnO gel films during the thermal curing nanoimprint process. Finally, crystalline ZnO films were obtained by subsequent annealing of the patterned ZnO gel films. The optical characterization indicates that the surface patterning of ZnO thin films can lead to an enhanced transmittance. Large-scale ZnO thin films with different patterns can be fabricated by various easy-made ordered templates using this combination of sol-gel and nanoimprint lithography techniques.Comment: 17 pages, 5 figures; Published in Journal of Sol-Gel Science and Technology, 201

Quantum-Dot Light-Emitting Diodes with Nitrogen-Doped Carbon Nanodot Hole Transport and Electronic Energy Transfer Layer

Electroluminescence efficiency is crucial for the application of quantum-dot light-emitting diodes (QD-LEDs) in practical devices. We demonstrate that nitrogen-doped carbon nanodot (N-CD) interlayer improves electrical and luminescent properties of QD-LEDs. The N-CDs were prepared by solution-based bottom up synthesis and were inserted as a hole transport layer (HTL) between other multilayer HTL heterojunction and the red-QD layer. The QD-LEDs with N-CD interlayer represented superior electrical rectification and electroluminescent efficiency than those without the N-CD interlayer. The insertion of N-CD layer was found to provoke the Forster resonance energy transfer (FRET) from N-CD to QD layer, as confirmed by time-integrated and - resolved photoluminescence spectroscopy. Moreover, hole-only devices (HODs) with N-CD interlayer presented high hole transport capability, and ultraviolet photoelectron spectroscopy also revealed that the N-CD interlayer reduced the highest hole barrier height. Thus, more balanced carrier injection with sufficient hole carrier transport feasibly lead to the superior electrical and electroluminescent properties of the QD-LEDs with N-CD interlayer. We further studied effect of N-CD interlayer thickness on electrical and luminescent performances for high-brightness QD-LEDs. The ability of the N-CD interlayer to improve both the electrical and luminescent characteristics of the QD-LEDs would be readily exploited as an emerging photoactive material for high-efficiency optoelectronic devices.ope

Electrochemical synthesis of zinc complexes and preparation of nano-sized ZnO

Zinc complexes were directly prepared by using zinc metal as sacrificing anode in a cell without separating the cathode and anode spaces. The products were characterized by using FT-IR, NMR and Raman spectroscopy. The influence of temperature and conductive additives on product yield was also investigated. The study shows that direct electrochemical preparation of zinc complexes such as Zn(acac)(2), Zn(OEt)(2) (acac)(2) and Zn(OBu)(2)(acac)(2) has high current efficiency and electrolysis yield than that of Zn(OR)(2). Furthermore, these zinc complexes have high purity and can be directly used as sol-gel precursor for preparation of nanometer ZnO. Experimental results show that controlling temperature in the range of 50 similar to 60 degreesC, selecting R4NBr as conductive additives and preventing zinc anode from being covered by electrochemical products can improve product yield. The study also shows that nano-sized ZnO prepared by this method has monoclinic structure with a narrow size distribution of 5-10 nm

Finite element analysis and calculation method of residual flexural capacity of post-fire RC beams

Fire tests and subsequent bending tests of fourreinforced concrete (RC) beamswere performed. Based on these tests, the post-fire performance of RCbeams was further studied using finite element simulation through reasonable selection of suitable thermal and thermodynamic parameters of steel and concrete materials. A thermodynamic model of RC beams with three sides under fire was built using finite element analysis(FEA)software ABAQUS. The FEA model was validated with the results of fire tests. Different factors were taken into account for further parametric studies in fire using the proposed FE model.The results show that the main factors affecting the fire resistance of the beamsare the thickness of the concretecover, reinforcement ratio of longitudinal steel,the fire exposure timeandthe fire exposure sides. Based on the strength reduction formula at high temperature of steel and concrete, animproved section method was proposed to develop a calculation formula to calculate the flexural capacity of RC beams after fire. The theoretical calculation method proposed in this paper shows good agreement with FEA results, which can be used to calculate the flexuralcapacity of RC beams after fire

A novel tumor suppressor gene ECRG4 interacts directly with TMPRSS11A (ECRG1) to inhibit cancer cell growth in esophageal carcinoma

<p>Abstract</p> <p>Background</p> <p>The esophageal carcinoma related gene 4 (ECRG4) was initially identified and cloned from human normal esophageal epithelium in our laboratory (GenBank accession no.<ext-link ext-link-id="AF325503" ext-link-type="gen">AF325503</ext-link>). ECRG4 has been described as a novel tumor suppressor gene associated with prognosis in esophageal squamous cell carcinoma (ESCC).</p> <p>Methods</p> <p>In this study, binding affinity assay in vitro and co-immunoprecipitation experiment in vivo were utilized to verify the physical interaction between ECRG4 and transmembrane protease, serine 11A (TMPRSS11A, also known as ECRG1, GenBank accession no. <ext-link ext-link-id="AF 071882" ext-link-type="gen">AF 071882</ext-link>). Then, p21 protein expression, cell cycle and cell proliferation regulations were examined after ECRG4 and ECRG1 co-transfection in ESCC cells.</p> <p>Results</p> <p>We revealed for the first time that ECRG4 interacted directly with ECRG1 to inhibit cancer cell proliferation and induce cell cycle G1 phase block in ESCC. Binding affinity and co-immunoprecipitation assays demonstrated that ECRG4 interacted directly with ECRG1 in ESCC cells. Furthermore, the ECRG4 and ECRG1 co-expression remarkably upregulatd p21 protein level by Western blot (P < 0.001), induced cell cycle G1 phase block by flow cytometric analysis (P < 0.001) and suppressed cell proliferation by MTT and BrdU assay (both P < 0.01) in ESCC cells.</p> <p>Conclusions</p> <p>ECRG4 interacts directly with ECRG1 to upregulate p21 protein expression, induce cell cycle G1 phase block and inhibit cancer cells proliferation in ESCC.</p