A bootstrap-based regression method for comprehensive discovery of differential gene expressions: An application to the osteoporosis study

A common purpose of microarray experiments is to study the variation in gene expression across the categories of an experimental factor such as tissue types and drug treatments. However, it is not uncommon that the studied experimental factor is a quantitative variable rather than categorical variable. Loss of information would occur by comparing gene-expression levels between groups that are factitiously defined according to the quantitative threshold values of an experimental factor. Additionally, lack of control for some sensitive clinical factors may bring serious false positive or negative findings.In the present study, we described a bootstrap-based regression method for analyzing gene-expression data from the non-categorical microarray experiments. To illustrate the utility of this method, we applied it to our recent gene-expression study of circulating monocytes in subjects with a wide range of variations in bone mineral density (BMD). This method allows a comprehensive discovery of gene expressions associated with osteoporosis-related traits while controlling other common confounding factors such as height, weight and age. Several genes identified in our study are involved in osteoblast and osteoclast functions and bone remodeling and/or menopause-associated estrogen-dependent pathways, which provide important clues to understand the etiology of osteoporosis. Availability: SAS code is available from the authors upon request. © 2011 Elsevier Masson SAS.postprin

Inhibitory mechanism of 3-hydroxypropionaldehyde accumulation in 1,3-propanediol synthesis with Klebsiella pneumoniae

3-Hydroxypropionaldehyde accumulation may cause the cessation of 1,3-propanediol sustained production with glycerol by Klebsiella pneumoniae. The impeller tip speed shift from higher to lower speed at glycerol excess or the pulsed glycerol feeding could lead to an abrupt increase of the 3- hydroxypropionaldehyde concentration (up to 10 mmol/l) in 10 min. The intracellular consequence of the 3-hydroxypropionaldehyde accumulation has not yet been elucidated. The rapid accumulation of 3- hydroxypropionaldehyde relying on the impeller tip speed shift was employed to investigate the influences of 3-hydroxypropionaldehyde to the activities of nine key enzymes related to glycerol metabolism, CO2 and O2 levels in off-gas, cell growth and 1,3-propanediol synthesis. Compared with that at 1.19 mmol/l 3-hydroxypropionaldehyde in broth, the residual enzymatic activities of the nine key enzymes ranged from 9.44 to 74.68% in the cultures at 7.5 mmol/l 3-hydroxypropionaldehyde in broth. The inhibitions of cell growth and the 1,3-propanediol synthesis were unnoticeable at the low level of 3- hydroxypropionaldehyde. By contrast, the CO2 and O2 levels changes in off-gas response to the 3- hydroxypropionaldehyde accumulation were less than 15 min. These results suggest that 3- hydroxypropionaldehyde inhibited the growth and metabolism of K. pneumoniae in a more complicated manner.Keywords: Fermentation, glycerol, 3-hydroxypropionaldehyde, Klebsiella pneumoniae, 1,3-propanediol

Study on GMZ bentonite-sand mixture by undrained triaxial tests

© 2016 The Authors. It is particularly necessary to study the deformation, strength and the changes of pore water pressure of bentonite-based buffer/backfill materials under the undrained condition. A series of isotropic compression tests and triaxial shear tests under undrained conditions were conducted on the compacted saturated/unsaturated GMZ bentonite-sand mixtures with dry mass ratio of bentonite/sand of 30:70. During the tests, the images of the sample were collected by photographic equipment and subsequently were cropped, binarized and centroids marked by image processing technique. Based on identification of the variation of the position of marked centroids, the deformation of the sample can be determined automatically in real-time. Finally, the hydro-mechanical behaviour of saturated and unsaturated bentonite-sand mixtures under the undrained condition can be obtained. From results of triaxial shear tests on unsaturated samples under constant water content, inflated volumetric deformation transforms to contractive volumetric deformation due to the increase of the confining pressure and lateral expansion deformation are observed due to the increase in the shearing stress. Moreover, the net mean stress affects the initial stiffness, undrained shear strength and deformation of the sample during the undrained shear tests

Effects of swim training on the expression of gastrocnemius’ iron transport proteins in rats

2004-2005 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Influence of exercise on iron metabolism

2004-2005 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Superderivations for Modular Graded Lie Superalgebras of Cartan-type

Superderivations for the eight families of finite or infinite dimensional graded Lie superalgebras of Cartan-type over a field of characteristic $p>3$ are completely determined by a uniform approach: The infinite dimensional case is reduced to the finite dimensional case and the latter is further reduced to the restrictedness case, which proves to be far more manageable. In particular, the outer superderivation algebras of those Lie superalgebras are completely determined

Electrical Conductivity Studies on Individual Conjugated Polymer Nanowires: Two-Probe and Four-Probe Results

<p>Abstract</p> <p>Two- and four-probe electrical measurements on individual conjugated polymer nanowires with different diameters ranging from 20 to 190 nm have been performed to study their conductivity and nanocontact resistance. The two-probe results reveal that all the measured polymer nanowires with different diameters are semiconducting. However, the four-probe results show that the measured polymer nanowires with diameters of 190, 95&#8211;100, 35&#8211;40 and 20&#8211;25 nm are lying in the insulating, critical, metallic and insulting regimes of metal&#8211;insulator transition, respectively. The 35&#8211;40 nm nanowire displays a metal&#8211;insulator transition at around 35 K. In addition, it was found that the nanocontact resistance is in the magnitude of 10⁴&#937; at room temperature, which is comparable to the intrinsic resistance of the nanowires. These results demonstrate that four-probe electrical measurement is necessary to explore the intrinsic electronic transport properties of isolated nanowires, especially in the case of metallic nanowires, because the metallic nature of the measured nanowires may be coved by the nanocontact resistance that cannot be excluded by a two-probe technique.</p

Insufficient activity of MAPK pathway is a key monitor of Kidney-Yang Deficiency Syndrome.

OBJECTIVE: To explore the genetic characteristics and molecular regulator of Kidney-Yang Deficiency Syndrome (KDS). DESIGN: A typical KDS family was collected using a questionnaire of cold feeling and a 40-item scoring table of KDS based on Traditional Chinese Medicine (TCM), by single-blind method repeated annually over three years. Their transcriptomes were assayed by microarray and validated by RT-PCR and ELISA. Simultaneously, 10 healthy volunteers were recruited as controls and the same protocols were performed. RESULTS: This typical KDS family has 35 members, of whom 11 were evaluated as having severe KDS and 6 as having common KDS. Results of the cDNA microarray revealed that there were 420 genes/expressed sequence tags differentially expressed in KDS transcriptomes, indicating a global functional impairment in the mass-energy-information carrying network of KDS patients, involving energy metabolism, signal transduction, development, cell cycle, and immunity. Pathway analysis by gene set enrichment assay (GSEA) and other tools demonstrated that mitogenic activated protein kinase (MAPK) is among the most insufficiently activated pathways, while the oxidative phosphorylation and glycolysis/gluconeogenesis pathways, the two main pathways relevant to ATP synthesis, were among the most excessively activated pathways in KDS patients. Results of RT-PCR and ELISA confirmed the status of insufficient activity of the MAPK pathway. CONCLUSION: KDS patients undergo overall attenuated functions in the mass-energy-information carrying network. The marked low level of energy output in KDS may be primarily attributed to the insufficient activity of the MAPK pathway, which may be a key monitor for the abnormal energy metabolism and other impaired activities in KDS.published_or_final_versio