A wavelet-based feature vector model for DNA clustering.

DNA data are important in the bioinformatic domain. To extract useful information from the enormous collection of DNA sequences, DNA clustering is often adopted to efficiently deal with DNA data. The alignment-free method is a very popular way of creating feature vectors from DNA sequences, which are then used to compare DNA similarities. This paper proposes a wavelet-based feature vector (WFV) model, which is also an alignment-free method. From the perspective of signal processing, a DNA sequence is a sequence of digital signals. However, most traditional alignment-free models only extract features in the time domain. The WFV model uses discrete wavelet transform to adaptively yield feature vectors with a fixed dimension based on the features in both the time and frequency domains. The level of wavelet transform is adjusted according to the length of the DNA sequence rather than a fixed manually set value. The WFV model prefers a 32-dimension feature vector, which greatly promotes system performance. We compared the WFV model with the other five alignment-free models, i.e., k-tuple, DMK, TSM, AMI, and CV, on several large-scale DNA datasets on the DNA clustering application by means of the K-means algorithm. The experimental results showed that the WFV model outperformed the other models in terms of both the clustering results and the running time.

Visfatin: a potential therapeutic target for rheumatoid arthritis.

Rheumatoid arthritis (RA) is usually a chronic, systemic inflammatory disorder primarily targeting the synovium and articular cartilage. It is incurable, costly and responds poorly to treatment. Methotrexate alone or in combination with conventional and/or biological disease-modifying antirheumatic drugs (DMARDs) is often used to induce remission of active disease. The effectiveness of treatment is, however, limited and most patients develop chronic disability and require total knee arthroplasty or total hip replacement. Emerging therapies targeting specific cytokines and growth factors in the RA inflammatory cascade offer potent new means of modifying disease activity. Recently, increased concentrations of adipokines, including visfatin, mainly produced by adipocytes in serum and joint synovial fluid, were found in RA patients. Visfatin has important pro-inflammatory and catabolic roles in RA pathogenesis and is now being studied as a potential therapeutic target for RA. Here we discuss the relationship between visfatin and RA and its potential as a therapeutic target for RA.

Pilot study on the relationship between male stomach and liver cancer death and mutagenicity of drinking water in the Huangpu River area.

A quasi-historical cohort study method was used to collect the data of male stomach and liver cancer death from 1984 to 1988 in male residents (> or = 30 years old) of three tap-water-drinking communities at the upper, middle and lower reaches of the Huangpu River. Total person-years observed are 184,645. The result shows that the world standard population standardized cut-off mortalities (> or = 30 years old) of male stomach and liver cancer increase gradually from the upper to lower reaches. The mortalities from the upper to the lower reaches are 62.7, 86.2 and 146.0/100,000 person-years for male stomach cancer and 56.9, 67.7 and 81.3/100,000 person-years for male liver cancer, respectively. This trend is consistent with the change of the rate of positive Ames Test results of drinking water from the upper to lower reaches (0, 70, 100%). It suggests that a causal correlation may exist between the two. The distribution of other possible risk factors in the three communities is also described.

Effects of drinking water from the lower reaches of the Huangpu River on the risk of male stomach and liver cancer death.

A quasi-historical cohort study method was used to collect the data of male stomach and liver cancer death and the data of exposure to relevant risk factors from 1984 to 1988 in male tap-water- and raw-water-drinking cohorts (> or = 30 years old) at both the upper and lower reaches of the Huangpu River. Total person-years observed are 172,448. The Odds Ratios of drinking water from the lower reaches for male stomach cancer and liver cancer death are 2.021 (p < 0.01) and 1.851 (p < 0.01), respectively, in unconditional logistic regression analysis after controlling possible confounding factors. The result shows that drinking water from the lower reaches of the Huangpu River is one of the important risk factors for male stomach and liver cancer death in local areas.