Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

Some new bounds on eigenvalues of the Hadamard product and the Fan product of matrices

Let A and B be nonsingular M-matrices. A lower bound on the minimum eigenvalue q(B circle A(-1)) for the Hadamard product of A(-1) and B, and a lower bound on the minimum eigenvalue q(A star B) for the Fan product of A and B are given. In addition, an upper bound on the spectral radius rho(A circle B) of nonnegative matrices A and B is also obtained. These bounds improve several existing results in some cases and the estimating formulas are easier to calculate for they are only depending on the entries of matrices A and B. (C) 2009 Elsevier Inc. All rights reserved.

Pitfalls in the analysis of ancient human mtDNA

The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

Bibliometric analysis of biological invasions research during the period of 1991 to 2007

The objective of this study is to conduct a bibliometric analysis of all biological invasions-related publications in the Science Citation Index (SCI) from 1991 to 2007. The indicator citation per publication (CPP) was used to evaluate the impact of articles, journals, and institutions. In the 3323 articles published in 521 journals, 7261 authors from 1905 institutions of 100 countries participated. As the most productive country of biological invasions research, the US will benefit from more collaboration between institutions, countries, and continents. In addition, analysis of keywords was applied to reveal research trends.

Heavy metals in plants and phytoremediation - A state-of-the-art report with special reference to literature published in Chinese journals

Goal, Scope and Background. In some cases, soil, water and food are heavily polluted by heavy metals in China. To use plants to remediate heavy metal pollution would be an effective technique in pollution control. The accumulation of heavy metals in plants and the role of plants in removing pollutants should be understood in order to implement phytoremediation, which makes use of plants to extract, transfer and stabilize heavy metals from soil and water. Methods. The information has been compiled from Chinese publications stemming mostly from the last decade, to show the research results on heavy metals in plants and the role of plants in controlling heavy metal pollution, and to provide a general outlook of phytoremediation in China. Related references from scientific journals and university journals are searched and summarized in sections concerning the accumulation of heavy metals in plants, plants for heavy metal purification and phytoremediation techniques. Results and Discussion. Plants can take up heavy metals by their roots, or even via their stems and leaves, and accumulate them in their organs. Plants take up elements selectively. Accumulation and distribution of heavy metals in the plant depends on the plant species, element species, chemical and bioavailiability, redox, pH, cation exchange capacity, dissolved oxygen, temperature and secretion of roots. Plants are employed in the decontamination of heavy metals from polluted water and have demonstrated high performances in treating mineral tailing water and industrial effluents. The purification capacity of heavy metals by plants are affected by several factors, such as the concentration of the heavy metals, species of elements, plant species, exposure duration, temperature and pH. Conclusions. Phytoremediation, which makes use of vegetation to remove, detoxify, or stabilize persistent pollutants, is a green and environmentally-friendly tool for cleaning polluted soil and water. The advantage of high biomass productive and easy disposal makes plants most useful to remediate heavy metals on site. Recommendations and Outlook. Based on knowledge of the heavy metal accumulation in plants, it is possible to select those species of crops and pasturage herbs, which accumulate fewer heavy metals, for food cultivation and fodder for animals; and to select those hyperaccumulation species for extracting heavy metals from soil and water. Studies on the mechanisms and application of hyperaccumulation are necessary in China for developing phytoremediation.

Computational information geometry and its applications

Digitization is the main feature of modern Information Science. Conjoining the digits and the coordinates, the relation between Information Science and high-dimensional space is consanguineous, and the information issues are transformed to the geometry problems in some high-dimensional spaces. From this basic idea, we propose Computational Information Geometry (CIG) to make information analysis and processing. Two kinds of applications of CIG are given, which are blurred image restoration and pattern recognition. Experimental results are satisfying. And in this paper, how to combine with groups of simple operators in some 2D planes to implement the geometrical computations in high-dimensional space is also introduced. Lots of the algorithms have been realized using software.

STUDIES FOR THE EQUATION OF STATE IN THE ISOSPIN ASYMMETRICAL NUCLEAR INTERACTIONS

In order to determine the equation of state in the isospin asymmetrical nuclear interactions, we have found the observables for extracting the information of them within the isospin-dependent quantum molecular dynamics in recent years. The several sensitive probes for extracting the information of the in-medium nucleon-nucleon cross section and the symmetry potential have found; meanwhile, their mechanisms are investigated in more details. The main point in this paper gives the summary for above probes and their outlook in the future.

A discrete square global grid system based on the parallels plane projection

Knowledge Innovation Project of Chinese Academy of Sciences [KZCX3-SW-347]; National Science Fund for Distinguished Young Scholar [40225004]

A discrete square global grid system based on the parallels plane projection

We developed a direct partitioning method to construct a seamless discrete global grid system (DGGS) with any resolution based on a two-dimensional projected plane and the earth ellipsoid. This DGGS is composed of congruent square grids over the projected plane and irregular ellipsoidal quadrilaterals on the ellipsoidal surface. A new equal area projection named the parallels plane (PP) projection derived from the expansion of the central meridian and parallels has been employed to perform the transformation between the planar squares and the corresponding ellipsoidal grids. The horizontal sides of the grids are parts of the parallel circles and the vertical sides are complex ellipsoidal curves, which can be obtained by the inverse expression of the PP projection. The partition strategies, transformation equations, geometric characteristics and distortions for this DGGS have been discussed. Our analysis proves that the DGGS is area-preserving while length distortions only occur on the vertical sides off the central meridian. Angular and length distortions positively correlate to the increase in latitudes and the spanning of longitudes away from a chosen central meridian. This direct partition only generates a small number of broken grids that can be treated individually.

Land use and water quality response in the northern region of Changxing County

In this paper, taking the northern region of Changxing County for example, with ammonia nitrogen as a pollution assessment index, we used an improved export coefficient method for estimate polluting load of non-point source pollution (NSP) and the social pollution survey data in the study area to estimate point source pollution. By comparing the total pollution output and the national surface water environmental quality standards find that the whole study area achieves the second water quality standard. However, Jiapu Township exceeds the water quality standards seriously because of the superfluous point source pollution. The water quality of other Townships is good. Further analysis showed that different types of land use and proportions in the northern region of Changxing County have a significant impact on the non-point source pollution, the general law is farmland contributes the largest share of the non-point source pollution output, followed by residential area and bare land, besides, with the increase in the proportion of forest and the decrease of farmland and residential area, the non-point source pollution reduces gradually. © 2010 IEEE.

Recent progress in the studies of endohedral metallofullerenes

This overview presents the recent progress in the area of endohedral metallofullerenes in the past several years. The important results have been summarized as follows: (1) Many metals including Group 3 metals, most of the lanthanide series elements, and Group 2 metals have been encapsulated into a fullerene cage to form mono-, di-, and trimetallofullerenes by using the arc-evaporation technique. (2) Some endohedral metallofullerenes such as Group 3 metals, most of the lanthanide series elements, Group 2 metals, and some of their isomers have been successfully isolated and purified by a two-step or several-step HPLC technique. By using high-temperature and high-pressure extraction with pyridine, Ln@C-80, Ln@C-82, and Ln2@C-80 for most rare-earth metals have been selectively extracted in high yield (about 1% of the saw soot) from fullerenes and other size metallofullerenes. (3) The endohedral nature of metallofullerenes such as Y@C-82, Sc2@C-84, and Sc@C-82 has been finally confirmed by synchrotron X-ray powder diffraction. The symmetries and the structures of metallofullerenes such as Ca@C-82(III), La-2@C-80(I-h), Sc-2@C-84(D-2d), and Sc-2@C-84(C-s) have been confirmed by NMR measurements. (Lb) The information on the electronic structures and properties of endohedral metallofullerenes has been obtained by various spectrometric means Such as EPR, W-vis-MR, XPS, CV. It is generally accepted that three-electron transfer is favorable when M = Y, La, Ce, Pr, Nd, Gd, Tb, Dy, Ho, Er, Lu but Sc, Eu, Sm, Yb, Tm, Ca, Sr, Ba prefer to donate two electrons to the fullerene cages. (5) Several chemical reactions of endohedral metallofullerenes have been reported in which reagents are disilacyclopropane, digermacyclopropane, diphenyldiazomethane, and trifluoroacetic acid. (6) Mass spectrometry provided the crucial evidence that led to the discovery of metallofullerenes in 1985 and has always played a key role in their identification and characterization, Ion-mobility measurements of gas-phase ions have obtained the information of structures and the formation mechanism of endohedral metallofullerenes. till Theoretical calculations on the endohedral metallofullerenes have made an important contribution to the studies on the symmetry of the cage, the position of metal atom(s) inside the cage, the number of electronic transfer between metal atom(s) and fullerene cage, etc. (C) 2000 Elsevier Science S.A. All rights reserved.

Characteristic infrared spectroscopic patterns in the protein bands of human breast cancer tissue

Infrared (IR) spectra of normal, hyperplasia, fibroadenoma and carcinoma tissues of human breast obtained from 96 patients have been determined and analyzed statistically. Several spectral differences were detected in the frequency regions of N-H stretching, amide I, II and III bands: (1) the bands in the region 3000-3600cm-1 shifted to lower frequencies for the carcinomatous tissue; (2) the A(3300)/A(3075) absorbance ratio was significantly higher for the fibroadenoma than for the other types of tissues; (3) the frequency of the a-helix amide I band decreased for the malignant tissue, while the corresponding beta -sheet amide I band frequency increased; (4) the A(1657)/A(1635) and A(1553)/A(1540) absorbance ratios were the highest for fibroadenoma and carcinoma tissues; (5) the A(1680)/A(1657) absorbance ratio decreased significantly in the order of normal > hyperplasia > fibroadenoma > carcinoma; (6) the A(1651)/A(1545) absorbance ratio increased slightly for the fibroadenoma and the carcinoma tissues; (7) the bands at 1204 and 1278 cm(-1), assigned to the vibrational modes of the collagen, did not appear in the original spectra as resolved peaks and were distinctly stronger in the deconvoluted spectra of the carcinoma tissue and (8) the A(1657)/A(1204) and A(1657)/A(1278) absorbance ratios, both yielding information on the relative content of collagen, increased in the order of normal < hyperplasia < carcinoma < fibroadenoma. The said differences imply that the information is useful for the diagnosis of breast cancer and malignant breast abnormalities, and may serve as a basis for further studies on conformational changes in tissue proteins during carcinogenesis. (C) 2001 Elsevier Science B.V. All rights reserved.