On Combining Morphological Component Analysis and Concentric Morphology Model for Mammographic Mass Detection

Mammographic mass detection is an important task for the early diagnosis of breast cancer. However, it is difficult to distinguish masses from normal regions because of their abundant morphological characteristics and ambiguous margins. To improve the mass detection performance, it is essential to effectively preprocess mammogram to preserve both the intensity distribution and morphological characteristics of regions. In this paper, morphological component analysis is first introduced to decompose a mammogram into a piecewise-smooth component and a texture component. The former is utilized in our detection scheme as it effectively suppresses both structural noises and effects of blood vessels. Then, we propose two novel concentric layer criteria to detect different types of suspicious regions in a mammogram. The combination is evaluated based on the Digital Database for Screening Mammography, where 100 malignant cases and 50 benign cases are utilized. The sensitivity of the proposed scheme is 99% in malignant, 88% in benign, and 95.3% in all types of cases. The results show that the proposed detection scheme achieves satisfactory detection performance and preferable compromises between sensitivity and false positive rates.

Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry

Since protein phosphorylation is a dominant mechanism of information transfer in cells, there is a great need for methods capable of accurately elucidating sites of phosphorylation. In recent years mass spectrometry has become an increasingly viable alternative to more traditional methods of phosphorylation analysis. The present study used immobilized metal affinity chromatography (IMAC coupled with a linear ion trap mass spectrometer to analyze phosphorylated proteins in mouse liver. A total of 26 peptide sequences defining 26 sites of phosphorylation were determined. Although this number of identified phosphoproteins is not large, the approach is still of interest because a series of conservative criteria were adopted in data analysis. We note that, although the binding of non-phosphorylated peptides to the IMAC column was apparent, the improvements in high-speed scanning and quality of MS/MS spectra provided by the linear ion trap contributed to the phosphoprotein identification. Further analysis demonstrated that MS/MS/MS analysis was necessary to exclude the false-positive matches resulting from the MS/MS experiments, especially for multiphosphorylated peptides. The use of the linear ion trap considerably enabled exploitation of nanoflow-HPLC/MS/MS, and in addition MS/MS/MS has great potential in phosphoproteome research of relatively complex samples. Copyright (C) 2004 John Wiley Sons, Ltd.

Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns. (C) 2003 Elsevier Ltd. All rights reserved.

Density-dependent effects on seston dynamics and rates of filtering and biodeposition of the suspension-cultured scallop Chlamys farreri in a eutrophic bay (northern China): An experimental study in semi-in situ flow-through systems

Effects of stocking density on seston dynamics and filtering and biodeposition by the suspension-cultured Zhikong scallop Chlamys farreri Jones et Preston in a eutrophic bay (Sishili Bay, northern China), were determined in a 3-month semi-field experiment with continuous flow-through seawater from the bay. Results showed that the presence of the scallops could strongly decrease seston and chlorophyll a concentrations in the water column. Moreover, in a limited water column, increasing scallop density could cause seston depletion due to scallop's filtering and biodeposition process, and impair scallop growth. Both filtration rate and biodeposition rate of C. farreri showed significant negative correlation with their density and positive relationship with seston concentration. Calculation predicts that the daily removal of suspended matter from water column by the scallops in Sishili Bay ecosystem can be as high as 45% of the total suspended matter; and the daily production of biodeposits by the scallops in early summer in farming zone may amount to 7.78 g m(-2), with daily C, N and P biodeposition rates of 3.06 x 10(-1), 3.86 x 10(-2) and 9.80 x 10(-3) g m(-2), respectively. The filtering and biodeposition by suspension-cultured scallops could substantially enhance the deposition of total suspended particulate material, suppress accumulation of particulate organic matter in water column, and increase the flux of C, N and P to benthos, strongly enhancing pelagic-benthic coupling. It was suggested that the filtering-biodeposition process by intensively suspension-cultured bivalve filter-feeders could exert strong top-down control on phytoplankton biomass and other suspended particulate material in coastal ecosystems. This study also indicated that commercially suspension-cultured bivalves may simultaneously and potentially aid in mitigating eutrophication pressures on coastal ecosystems subject to anthropogenic N and P loadings, serving as a eutrophic-environment bioremediator. The ecological services (e.g. filtering capacity, top-down control, and benthic-pelagic coupling) functioned by extractive bivalve aquaculture should be emphasized in coastal ecosystems. (c) 2005 Elsevier B.V. All rights reserved.

Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes

Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide. Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.