Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

BACKGROUND: Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among different studies involving patients with the same disease. Therefore, it is of great interest and challenge to merge data sets from multiple studies to increase the sample size, which may in turn increase the power of statistical inferences. In this study, we combined two lung cancer studies using micorarray GeneChip(®), employed two gene shaving methods and a two-step survival test to identify genes with expression patterns that can distinguish diseased from normal samples, and to indicate patient survival, respectively. RESULTS: In addition to common data transformation and normalization procedures, we applied a distribution transformation method to integrate the two data sets. Gene shaving (GS) methods based on Random Forests (RF) and Fisher's Linear Discrimination (FLD) were then applied separately to the joint data set for cancer gene selection. The two methods discovered 13 and 10 marker genes (5 in common), respectively, with expression patterns differentiating diseased from normal samples. Among these marker genes, 8 and 7 were found to be cancer-related in other published reports. Furthermore, based on these marker genes, the classifiers we built from one data set predicted the other data set with more than 98% accuracy. Using the univariate Cox proportional hazard regression model, the expression patterns of 36 genes were found to be significantly correlated with patient survival (p < 0.05). Twenty-six of these 36 genes were reported as survival-related genes from the literature, including 7 known tumor-suppressor genes and 9 oncogenes. Additional principal component regression analysis further reduced the gene list from 36 to 16. CONCLUSION: This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy

A Broad-Spectrum Sweet Taste Sensor Based on Ni(OH)2/Ni Electrode

A broad-spectrum sweet taste sensor based on Ni(OH)2/Ni electrode was fabricated by the cyclic voltammetry technique. This sensor can be directly used to detect natural sweet substances in 0.1 M NaOH solution by chronoamperometry method. The current value measured by the sensor shows a linear relationship with the concentration of glucose, sucrose, fructose, maltose, lactose, xylitol, sorbitol, and erythritol (R2 = 0.998, 0.983, 0.999, 0.989, 0.985, 0.990, 0.991, and 0.985, respectively). Moreover, the characteristic value of this sensor is well correlated with the concentration and relative sweetness of eight sweet substances. The good correlation between the characteristic value of six fruit samples measured by the sensor and human sensory sweetness measured by sensory evaluation (correlation coefficient = 0.95) indicates that it can reflect the sweetness of fruits containing several sweet substances. In addition, the sensor also exhibits good long-term stability over 40 days (signal ratio fluctuation ranges from 91.5% to 116.2%). Thus, this broad-spectrum sensor is promising for sweet taste sensory application

Developmental characteristics of fractures in deep tight sandstone reservoirs in the second Member of the Xujiahe Formation of Zhongjiang Gas Field

The development characteristics, scale and control factors of fractures are the core subjects of reservoir sweet spot prediction. The sandstone reservoir of the TX2 gas reservoir in the Zhongjiang Gas Field is a typical low porosity and low permeability tight reservoir with strong heterogeneity, but relatively high-quality reservoirs can be found in different well areas and well segments. In this paper, taking the second Member of the Xujiahe Formation (TX2) as an example, the control factors of fractures were systemically investigated via core observation, thin section, logging data, and fracture logging identifications. The results show that shear fractures are mainly developed in the cores, and they generally have high filling rate and poor effectiveness; microfractures can be found based on the vitrinite and cast thin section results. The intersection diagram (semi-quantitative) and the principal component and BP comprehensive identification (quantitative) methods can effectively identify different types of fractures. The combined application of principal component and BP comprehensive identification methods results in an 83.3 % fracture identification probability. Finally, we found that the development of fractures in TX2 is comprehensively affected by lithology, rock thickness, porosity, and faults

Mechanistic Insight into Ketone α‑Alkylation with Unactivated Olefins via C–H Activation Promoted by Metal–Organic Cooperative Catalysis (MOCC): Enriching the MOCC Chemistry

Metal–organic cooperative catalysis (MOCC) has been successfully applied for hydroacylation of olefins with aldehydes via directed C­(sp²)–H functionalization. Most recently, it was reported that an elaborated MOCC system, containing Rh­(I) catalyst and 7-azaindoline (<b>L1</b>) cocatalyst, could even catalyze ketone α-alkylation with unactivated olefins via C­(sp³)–H activation. Herein we present a density functional theory study to understand the mechanism of the challenging ketone α-alkylation. The transformation uses IMesRh­(I)­Cl­(<b>L1</b>)­(CH₂CH₂) as an active catalyst and proceeds via sequential seven steps, including ketone condensation with <b>L1</b>, giving enamine <b>1b</b>; <b>1b</b> coordination to Rh­(I) active catalyst, generating Rh­(I)–<b>1b</b> intermediate; C­(sp²)–H oxidative addition, leading to a Rh­(III)–H hydride; olefin migratory insertion into Rh­(III)–H bond; reductive elimination, generating Rh­(I)–<b>1c</b>(alkylated <b>1b</b>) intermediate; decoordination of <b>1c</b>, liberating <b>1c</b> and regenerating Rh­(I) active catalyst; and hydrolysis of <b>1c</b>, furnishing the final α-alkylation product <b>1d</b> and regenerating <b>L1</b>. Among the seven steps, reductive elimination is the rate-determining step. The C–H bond preactivation via agostic interaction is crucial for the bond activation. The mechanism rationalizes the experimental puzzles: why only <b>L1</b> among several candidates performed perfectly, whereas others failed, and why Wilkinson’s catalyst commonly used in MOCC systems performed poorly. Based on the established mechanism and stimulated by other relevant experimental reactions, we attempted to enrich MOCC chemistry computationally, exemplifying how to develop new organic catalysts and proposing <b>L7</b> to be an alternative for <b>L1</b> and demonstrating the great potential of expanding the hitherto exclusive use of Rh­(I)/Rh­(III) manifold to Co(0)/Co­(II) redox cycling in developing MOCC systems

Research Progress in Biological Control of Soft Rot of Amorphophallus konjac

In this paper, the main control methods of soft rot of Amorphophallus konjac are reviewed, with a focus on the current research status of using plant growth promoting rhizobacteria for biological control of soft rot of A. konjac, and future research directions are looked forward to

Research Progress in Biological Control of Soft Rot of Amorphophallus konjac

In this paper, the main control methods of soft rot of Amorphophallus konjac are reviewed, with a focus on the current research status of using plant growth promoting rhizobacteria for biological control of soft rot of A. konjac, and future research directions are looked forward to

Two-Dimensional Hexagonal Transition-Metal Oxide for Spintronics

Two-dimensional materials have been the hot subject of studies due to their great potential in applications. However, their applications in spintronics have been blocked by the difficulty in producing ordered spin structures in 2D structures. Here we demonstrated that the ultrathin films of recently experimentally realized wurtzite MnO can automatically transform into a stable graphitic structure with ordered spin arrangement via density functional calculation, and the stability of graphitic structure can be enhanced by external strain. Moreover, the antiferromagnetic ordering of graphitic MnO single layer can be switched into half-metallic ferromagnetism by small hole-doping, and the estimated Curie temperature is higher than 300 K. Thus, our results highlight a promising way toward 2D magnetic materials

KCTD10 is involved in the cardiovascular system and Notch signaling during early embryonic development.

As a member of the polymerase delta-interacting protein 1 (PDIP1) gene family, potassium channel tetramerisation domain-containing 10 (KCTD10) interacts with proliferating cell nuclear antigen (PCNA) and polymerase δ, participates in DNA repair, DNA replication and cell-cycle control. In order to further investigate the physiological functions of KCTD10, we generated the KCTD10 knockout mice. The heterozygous KCTD10(+/-) mice were viable and fertile, while the homozygous KCTD10(-/-) mice showed delayed growth from E9.0, and died at approximately E10.5, which displayed severe defects in angiogenesis and heart development. Further study showed that VEGF induced the expression of KCTD10 in a time- and dose-dependent manner. Quantitative real-time PCR and western blotting results revealed that several key members in Notch signaling were up-regulated either in KCTD10-deficient embryos or in KCTD10-silenced HUVECs. Meanwhile, the endogenous immunoprecipitation (IP) analysis showed that KCTD10 interacted with Cullin3 and Notch1 simultaneously, by which mediating Notch1 proteolytic degradation. Our studies suggest that KCTD10 plays crucial roles in embryonic angiogenesis and heart development in mammalians by negatively regulating the Notch signaling pathway

Growth of Uniform Monolayer Graphene Using Iron-Group Metals via the Formation of an Antiperovskite Layer

It has been generally accepted that iron-group metals (iron, cobalt, nickel) consistently show the highest catalytic activity for the growth of carbon nanomaterials, including carbon nanotubes (CNTs) and graphene. However, it still remains a challenge for them to obtain uniform graphene, because of their high carbon solubility, which can be attributed to an uncontrollable precipitation in cooling process. The quality and uniformity of the graphene grown on low-cost iron-group metals determine whether graphene can be put into the mass productions or not. Here, we develop a novel strategy to form an antiperovskite layer using ambient-pressure chemical vapor deposition (APCVD), which, so far, is the only known way for iron-group metals to prepare uniform monolayer graphene with 100% surface coverage. Our strategy utilizes liquid metal (e.g., gallium) to assist iron-group metals to form an antiperovskite layer that is chemically stable throughout the high-temperature growth process and then to seal the passageway of carbon segregation from the metal bulk during cooling. With the advantage of forming antiperovskite structure, the uniform monolayer graphene can always be obtained under the variations of experimental conditions. Our strategy solves the problem about how to get uniform graphene film on high-solubility carbon substrate, to utilize the high catalytic activity of low-cost iron-group metals and to realize low-temperature growth by chemical vapor deposition

Generation of KCTD10^−/− mice.

<p>(A), the genomic DNA of <i>Kctd10</i> gene includes 7 exons and 6 introns. The genetic manipulation of <i>Kctd10</i> was designed to delete exon 2, the first loxP was inserted into intron 2, and the second loxP together with neomycin-resistant gene flanked by FRT sites was inserted into intron 3. (B–D), Gene disruption was confirmed using Southern blotting in positive ES cells. (E), Genotyping strategy of the mutant mouse, there is only a 670 bp band in KCTD10^−/− mice, two bands (670 bp and 306 bp) in the KCTD10^+/− mice, and only a 306 bp in the wild type mice. (F–G), RT-PCR and western blotting results indicate that the deletion is successful. (F), embryos with the same genotype were collected, and total RNA was extracted separately, reverse transcripted into cDNA and real-time PCR was performed to determine the KCTD10 mRNA levels. (G), embryos with the same genotype were collected, and total protein was extracted separately and immunoblotted by anti-KCTD10 antibody.</p