A novel approach to minimize false discovery rate in genome-wide data analysis

BACKGROUND: High-throughput technologies, such as DNA microarray, have significantly advanced biological and biomedical research by enabling researchers to carry out genome-wide screens. One critical task in analyzing genome-wide datasets is to control the false discovery rate (FDR) so that the proportion of false positive features among those called significant is restrained. Recently a number of FDR control methods have been proposed and widely practiced, such as the Benjamini-Hochberg approach, the Storey approach and Significant Analysis of Microarrays (SAM). METHODS: This paper presents a straight-forward yet powerful FDR control method termed miFDR, which aims to minimize FDR when calling a fixed number of significant features. We theoretically proved that the strategy used by miFDR is able to find the optimal number of significant features when the desired FDR is fixed. RESULTS: We compared miFDR with the BH approach, the Storey approach and SAM on both simulated datasets and public DNA microarray datasets. The results demonstrated that miFDR outperforms others by identifying more significant features under the same FDR cut-offs. Literature search showed that many genes called only by miFDR are indeed relevant to the underlying biology of interest. CONCLUSIONS: FDR has been widely applied to analyzing high-throughput datasets allowed for rapid discoveries. Under the same FDR threshold, miFDR is capable to identify more significant features than its competitors at a compatible level of complexity. Therefore, it can potentially generate great impacts on biological and biomedical research. AVAILABILITY: If interested, please contact the authors for getting miFDR

An improved BRDF method for 3D textile simulation

There are some methods suggested by researchers were used to simulate one or two characteristics of textile in the past few years. With 3D geometry models, most of these methods are somewhat complex, and it is difficult to simulate fabric attributes. This paper represents a method for textile simulation based on improved BRDF illumination models. As one simple type of BRDF model, Phong illumination model can be used to simulate fabric 3D geometry model. The more complex BRDF illumination model may be used to simulate fabric 3D structure. The pixel color values, derived from simulating fabric 3D structure, is taken as the parameters to be entered into Phong illumination model. And thus both the fabric 3D geometry model and structure can be achieved, based on which the textile can be simulated successfully and obtain a perfect display effect

Rapid Remission in Peripheral T-Cell Lymphoma of the Nasal Type by the Bortezomib plus CHOP Therapy

Peripheral T-cell lymphoma (PTCL) is rare and difficult to treat for its high relapse rate. The authors report a case of PTCL of the skin, regarding which clinical and pathological features, treatment, and prognosis were discussed. A 66-year-old woman was admitted with complaints of enlarging erythematous noduloplaques on the right anterior tibial skin for one year and similar lesions on the left for 6 months. Surgical resection of right leg lesion and biopsy of enlarged inguinal lymph nodes histologically indicated a PTCL of the nasal type. The patient was treated by CHOP plus bortezomib, reached complete remission just after two courses of chemotherapy and then received another two as consolidation. The patient remained in remission for 11 months until local relapse. As for cutaneous lesions, detailed lymph node examination and prompt tissue biopsy are judicious choices prior to any medical management. The chemotherapy consisting of bortezomib and CHOP is safe and efficient in PTCL of the skin

Three Essays on Public Policies in R&D Growth Models

Ph.DDOCTOR OF PHILOSOPH

1,25-hydroxyvitamin D relieves colitis in rats via downregulation of toll-like receptor 9 expression

Aim To investigate the therapeutic and immunoregulatory effects of 1,25-dihydroxyvitamin D (1,25(OH)D3) on 2,4,6- trinitrobenzenesulfonic acid (TNBS) -induced colitis in rats. Methods Experimental colitis induced by enema administration of TNBS plus ethanol was treated with 5-aminosalicylic acid (5-ASA) and/or 1,25(OH)D3. Disease activity was measured using the disease activation index (DAI), colon macroscopic damage index (CMDI), histological colonic damage score, and myeloperoxidase (MPO) activity. The expression of toll-like receptor 9 (TLR9) in the colon was determined by reverse transcription-polymerase chain reaction and immunohistochemistry. Results Rats with TNBS-induced colitis had significantly elevated DAI, CMDI, histological colonic damage score, and MPO activity (all P < 0.001) compared to rats without colitis. Treatment with 5-ASA or 1,25(OH)D3 ameliorated colitis by lowering CMDI (P = 0.049, P = 0.040, respectively), histological colonic damage score (P = 0.010, P = 0.005, respectively), and MPO activity (P = 0.0003, P = 0.0013, respectively) compared with the TNBS group. Combined treatment with 5-ASA and 1,25(OH)D3 significantly decreased MPO activity (P = 0.003). 1,25(OH)D3 attenuated colitis without causing hypercalcemia or renal insufficiency. TNBS significantly increased the number of TLR9 positive cells compared to control (P < 0.010), while 5-ASA, 1,25(OH)D3, and combined treatment with 5-ASA and 1,25(OH)D3 significantly decreased it compared to TNBS group (all P < 0.010). In TNBS group a moderate correlation was observed between MPO activity and the number of TLR9-positive cells (r = 0.654, P < 0.001). Conclusion TLR9 expression correlates with the extent of inflammation in TNBS-induced colitis. 1,25(OH)D3 relieves this inflammation possibly by decreasing TLR9 expression