data transformation and attribute subset selection: do they help make differences in software failure prediction?

IEEE, IEEE Comp Soc, Tech Council Software Engn

Cross-species chromosome painting in the Perissodactyla: delimitation of homologous regions in Burchell's zebra (Equus burchellii) and the white (Ceratotherium simum) and black rhinoceros (Diceros bicornis)

Conserved chromosomal segments in the black rhinoceros, Diceros bicornis (DB1, 2n = 84), and its African sister-species the white rhinoceros, Ceratotherim simum (CSI, 2n = 82), were detected using Burchell's zebra (Equus burchellii, EBU, 2n = 44) chromosome-specific painting probes supplemented by a subset of those developed for the horse (Equus caballus, ECA, 2n = 64). In total 41 and 42 conserved autosomal segments were identified in C simum and D. bicornis respectively. Only 21 rearrangements (20 fissions and I fusion) are necessary to convert the Burchell's zebra karyotype into that of the white rhinoceros. One fission distinguishes the D. bicornis and C simum karyotypes which, excluding hetero- chromatic differences, are identical in all respects at this level of resolution. Most Burchell's zebra chromosomes correspond to two rhinoceros chromosomes although in four instances (EBU 18, 19, 20 and 21) whole chromosome synteny has been retained among these species. In contrast, one rhinoceros chromosome (DBI1, CSI1) comprises two separate Burchell's zebra chromosomes (EBU11 and EBU17). In spite of the high diploid numbers of the two rhinoceros species their karyotypes are surprisingly conserved offering a glimpse of the putative ancestral perissodactyl condition and a broader understanding of genome organization in mammals. Copyright (C) 2003 S. Karger AG, Base

Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: Implications for the peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen fo

POSTSYNAPTIC ALPHA-2 RECEPTOR STIMULATION IMPROVES MEMORY IN AGED MONKEYS - INDIRECT EFFECTS OF YOHIMBINE VERSUS DIRECT EFFECTS OF CLONIDINE

Very low doses (0.00001 mg/kg) of the alpha-2 adrenergic antagonist, yohimbine, improved working memory performance in a subset of aged monkeys. Improvement appeared to result from increased norepinephrine (NE) release onto postsynaptic alpha-2 adrenoceptors, as the response was blocked by the ''postsynaptic'' alpha-2 antagonist, SKF104078. Cognitive-enhancing effects of low dose yohimbine treatment may depend on aged animals retaining an intact, endogenous NE system. In contrast to yohimbine, the alpha-2 agonist, clonidine, has improved working memory in air aged animals examined. In the present study, clonidine's beneficial effects were also blocked by the postsynaptic antagonists SKF104078 and SKF104856, suggesting that clonidine acts by directly stimulating postsynaptic alpha-2 adrenoceptors. Beneficial doses of clonidine (0.01 mg/kg) and yohimbine (0.00001 mg/kg) were combined to see if they would produce additive effects on memory enhancement. This strategy was successful in young monkeys with intact NE systems but was not effective in the aged monkeys. These findings demonstrate that drugs that indirectly stimulate postsynaptic alpha-2 receptors by increasing NE release are not as reliable in aged monkeys as directly acting agonists that can replace NE at postsynaptic alpha-2 receptors.

DOPAMINE D-1 RECEPTOR MECHANISMS IN THE COGNITIVE PERFORMANCE OF YOUNG-ADULT AND AGED MONKEYS

Dopamine (DA) D-1 receptor compounds were examined in monkeys for effects on the working memory functions of the prefrontal cortex and on the fine motor abilities of the primary motor cortex. The D-1 antagonist, SCH23390, the partial D-1 agonist, SKF38393, and the full D-1 agonist, dihydrexidine, were characterized in young control monkeys, and in aged monkeys with naturally occurring catecholamine depletion. In addition, SKF38393 was tested in young monkeys experimentally depleted of catecholamines with chronic reserpine treatment. Injections of SCH23390 significantly impaired the memory performance of young control monkeys, but did not impair aged monkeys with presumed catecholamine depletion. Conversely, the partial agonist, SKF38393, improved the depleted monkeys (aged or reserpine-treated) but did not improve young control animals. The full agonist, dihydrexidine, did improve memory performance in young control monkeys, as well as in a subset of aged monkeys. Consistent with D, receptor mechanisms, agonist-induced improvements were blocked by SCH23390. Drug effects on memory performance occurred independently of effects on fine motor performance. These results underscore the importance of DA D-1 mechanisms in cognitive function, and provide functional evidence of DA system degeneration in aged monkeys. Finally, high doses of D-1 agonists impaired memory performance in aged monkeys, suggesting that excessive D-1 stimulation may be deleterious to cognitive function.

Identification and expression analysis of two IFN-inducible genes in crucian carp (Carassius auratus L.)

Interferon (IFN) exerts its antiviral effects mainly through activation of a subset of IFN-stimulated genes (ISG), but relatively few of fish ISGs have been isolated and characterized so far. Here, we report two fish ISGs, termed CaIF158 and CaIF156, cloned from a subtractive cDNA library constructed with mRNAs obtained from crucian carp (Carassius auratus L.) blastulae embryonic (CAB) cells infected by UV-inactivated GCHV and mock-infected cells. Database search revealed that both ISGs had a high-level homology with all members of a well conserved gene family with multiple tetratricopeptide repeat (TPR) motifs, including human IF160, IF158, IF156, IFI54 and their homologues in some other mammalian species. The transcripts of CaIF158 and CaIF156 were undetectable in CAB cells but could be induced by active GCHV, UV-inactivated GCHV or CAB IFN. Analysis of expression difference between them and IFN signal factors, CaSTAT1 and CaIRF7, indicated that their transcriptions were mediated possibly through JAK-STAT signal pathway, which was further supported by the induction analysis in UV-inactivated GCHV infected, IFN-treated and untreated cells in the presence or absence of cycloheximide (CHX), a potent inhibitor of protein synthesis. In addition, a pufferfish (Fugu rubrides) DNA sequence representing putative FrIFI56 was also revealed when CalF158 and CalF156 were used to search the pufferfish genome database. Phylogenetic analysis showed that these fish ISGs form a unique clad independent of mammalian homologues, reflecting a distant evolutionary relationship from mammals. These studies identified the first teleost IFI56 and IFI58 orthologues. (C) 2003 Elsevier B.V All rights reserved.

Structure of macrozoobenthos of the East Dongting nature reserve, with emphasis on relationships with environmental variables

Ecological survey of macrozoobenthos assemblages was carried out at 32 sites in the East Dongting Nature Reserve, located in the northern region of the East Dongting Lake in the middle basin of the Yangtze River, China. All total 51 taxa including 18 oligochaetes, 15 mollusks, 14 insects and four other animals were recorded. Mollusks composed the dominant group and accounted for more than 70% of the total abundance. Assemblages were composed mainly of scrapers (66.7%) and collector-gatherers (nearly 20%), and to a lesser extent collector-filterers (roughly 12%), predators (ca. 7%), and shredders (ca. 6%). Two-way indicator species analysis, detrended correspondence, and canonical correspondence analysis (CCA) were employed to identify the relationships between macrozoobenthos assemblages and environmental variables. Thirty-two sites were separated into four site groups based on composition and relative abundance of benthic macroinvertebrates. CCA detected that water depth, pH, conductivity, SiO2, total nitrogen, total phosphorus, alkalinity, hardness, and Ca2+, were significant environmental factors influencing the pattern of macozoobenthos. In this minimal subset, water depth, pH, alkalinity and hardness were the most influential variables.

Distribution of epilithic algae in the Xiangxi River system and their relationships with environmental factors

The spatial pattern of epilithic algae in the Xiangxi River system was studied in relation to several environmental factors by two-way indictor species analysis (TWINSPAN), detrended correspondence analysis (DCA), and canonical correspondence analysis (CCA). Eighty-nine taxa including diatoms, green algae, and blue-green algae were observed. Diatoms were dominant, and Cocconeis placentula, Cymbella minuta, Diatoma vulgare, and Gomphonema angustatum appeared in most of sampling sites. By TWINSPAN and DCA, thirty-one sites were divided into three groups based on composition and relative richness of benthic algae. CCA indicated that SiO2, pH, total phosphorus, Ca2+, velocity, elevation, and Cl- were significant environmental factors affecting the distribution of algae communities. In this minimal subset, SiO2 and pH were the most influential variables.

Cognitive models in biomimetic pattern cognition

We describe a new model which is based on the concept of cognizing theory. The method identifies subsets of the data which are embedded in arbitrary oriented lower dimensional space. We definite k-mean covering, and study its property. Covering subsets of points are repeatedly sampled to construct trial geometry space of various dimensions. The sampling corresponding to the feature space having the best cognition ability between a mode near zero and the rest is selected and the data points are partitioned on the basis of the best cognition ability. The repeated sampling then continues recursively on each block of the data. We propose this algorithm based on cognition models. The experimental results for face recognition demonstrate that the correct rejection rate of the test samples excluded in the classes of training samples is very high and effective.

On a Certain Algebraic Property of Block Ciphers

This is a study on a certain group theoretic property of the set of encryption functions of a block cipher. We have shown how to construct a subset which has this property in a given symmetric group by a computer algebra software GAP4.2 (Groups, Algorithms, and Programming, Version 4.2). These observations on group structures of block ciphers suggest us that we may be able to set a trapdoor based on meet-in-the-middle attack on block ciphers.

practical type checking of functions defined on context-free languages

A type checking method for the functional language LFC is presented. A distinct feature of LFC is that it uses Context-Free (CF) languages as data types to represent compound data structures. This makes LFC a dynamically typed language. To improve efficiency, a practical type checking method is presented, which consists of both static and dynamic type checking. Although the inclusion relation of CF.languages is not decidable,a special subset of the relation is decidable, i.e., the sentential form relation, which can be statically checked.Moreover, most of the expressions in actual LFC programs appear to satisfy this relation according to the statistic data of experiments. So, despite that the static type checking is not complete, it undertakes most of the type checking task. Consequently the run-time efficiency is effectively improved. Another feature of the type checking is that it converts the expressions with implicit structures to structured representation. Structure reconstruction technique is presented.

cDNA cloning and mRNA expression of heat shock protein 90 gene in the haemocytes of Zhikong scallop Chlamys farreri

Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone contributing to the folding, maintenance of structural integrity and proper regulation of a subset of cytosolic proteins. The full-length cDNA of Zhikong scallop Chlamysfarreri HSP90 (designated CfHSP90) was cloned by EST and rapid RACE techniques. It was of 2710 bp, including an open reading frame (ORF) of 2181 bp encoding a polypeptide of 726 amino acids with all the five HSP90 family signatures. BLAST analysis revealed that the CfHSP90 gene shared high similarity with other known HSP90 genes. Fluorescent real-time quantitative RT-PCR was used to examine the expression pattern of CfHSP90 mRNA in haemocytes of scallops exposed to Cd2+, Pb2+ and Cu2+ for 10 and 20 days, respectively. All the three heavy metals could induce CfHSP90 expression. There was a clear dose-dependent expression pattern of CfHSP90 after heavy metals exposure for 10 days or 20 days. Different concentrations of the same metal resulted in different effects on CfHSP90 expression. The results indicated that CfHSP90 responded to various heavy metal stresses with a dose-dependent expression pattern as well as exposure time effect, and could be used as a molecular biomarker in a heavy metal polluted environment. (c) 2007 Elsevier Inc. All rights reserved.

Molecular cloning, characterization and expression of heat shock protein 90 gene in the haemocytes of bay scallop Argopecten irradians

Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that plays key roles in the folding, maintenance of structural integrity and regulation of a subset of cytosolic proteins. In the present study, the cDNA of Argopecten irradians HSP90 (designated AiHSP90) was cloned by the combination of homology cloning and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of AiHSP90 was of 2669 bp, including an open reading frame (ORF) of 2175 bp encoding a polypeptide of 724 amino acids with predicted molecular weight of 83.08 kDa and theoretical isoelectric point of 4.81. BLAST analysis revealed that AiHSP90 shared high similarity with other known HSP90s, and the five conserved amino acid blocks defined as HSP90 protein family signatures were also identified in AiHSP90, which indicated that AiHSP90 should be a cytosolic member of the HSP90 family. Fluorescent real-time quantitative PCR was employed to examine the expression pattern of AiHSP90 mRNA in haemocytes of scallops challenged by Gram-negative bacteria Vibrio anguillarum and Gram-positive bacteria Micrococcus luteus. In both bacterial challenged groups, the relative expression level of AiHSP90 transcript was up-regulated and reached maximal. level at 9 h after injection, and then dropped progressively to the original level at about 48 h post challenge. The results indicated that AiHSP90 was potentially involved in the immune responses against bacteria challenge in scallop A. irradian. (c) 2007 Elsevier Ltd. All rights reserved.

Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system

Large-insert bacterial artificial chromosome (BAC) libraries are necessary for advanced genetics and genomics research. To facilitate gene cloning and characterization, genome analysis, and physical mapping of scallop, two BAC libraries were constructed from nuclear DNA of Zhikong scallop, Chlamys farreri Jones et Preston. The libraries were constructed in the BamHI and MboI sites of the vector pECBAC1, respectively. The BamHI library consists of 73,728 clones, and approximately 99% of the clones contain scallop nuclear DNA inserts with an average size of 110 kb, covering 8.0x haploid genome equivalents. Similarly, the MboI library consists of 7680 clones, with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1x. The combined libraries collectively contain a total of 81,408 BAC clones arrayed in 212 384-well microtiter plates, representing 9.1x haploid genome equivalents and having a probability of greater than 99% of discovering at least one positive clone with a single-copy sequence. High-density clone filters prepared from a subset of the two libraries were screened with nine pairs of Overgos designed from the cDNA or DNA sequences of six genes involved in the innate immune system of mollusks. Positive clones were identified for every gene, with an average of 5.3 BAC clones per gene probe. These results suggest that the two scallop BAC libraries provide useful tools for gene cloning, genome physical mapping, and large-scale sequencing in the species.