Using Unsupervised Patterns to Extract Gene Regulation Relationships for Network Construction

BACKGROUND: The gene expression is usually described in the literature as a transcription factor X that regulates the target gene Y. Previously, some studies discovered gene regulations by using information from the biomedical literature and most of them require effort of human annotators to build the training dataset. Moreover, the large amount of textual knowledge recorded in the biomedical literature grows very rapidly, and the creation of manual patterns from literatures becomes more difficult. There is an increasing need to automate the process of establishing patterns. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we describe an unsupervised pattern generation method called AutoPat. It is a gene expression mining system that can generate unsupervised patterns automatically from a given set of seed patterns. The high scalability and low maintenance cost of the unsupervised patterns could help our system to extract gene expression from PubMed abstracts more precisely and effectively. CONCLUSIONS/SIGNIFICANCE: Experiments on several regulators show reasonable precision and recall rates which validate AutoPat's practical applicability. The conducted regulation networks could also be built precisely and effectively. The system in this study is available at http://ikmbio.csie.ncku.edu.tw/AutoPat/

The Microbiome and Hematopoietic Cell Transplantation: Past, Present, and Future

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Constraints on SUSY Gluonic Dipole Interaction from B\to K\pi Decays

In low energy SUSY theories exchange of gluino and squark with left-right mixing can produce a large gluonic dipole interaction. In this paper we study the effects of this interaction on $B\to K \pi$ using QCD improved factorization method. The Standard Model predicts a smaller branching ratio for $B^0 \to \bar K^0 \pi^0$ than experimental measured one. We find that within the parameter space allowed from $B\to \gamma X_s$ constraint, the SUSY dipole interaction can enhance this branching ratio to agree with the experimental measurement. Combining recent data for all the four $\bar B^0 \to K^- \pi^+, \bar K^0 \pi^0$ and $B^- \to K^- \pi^0, \bar K^0 \pi^-$ decay modes, we find that the allowed parameter space is reduced significantly compared with that using $B\to X_s \gamma$ data alone. It is found that even with these constraints, the predictions for CP violation in these modes can be dramatically different from those of the SM predictions.Comment: 22 pages, 22 figures. Major revise for B to K pi correctio

When does poor subjective financial position hurt the elderly? Testing the interaction with educational attainment using a national representative longitudinal survey

<p>Abstract</p> <p>Background</p> <p>Several studies have demonstrated that perceived financial status has a significant impact on health status among the elderly. However, little is known about whether such a subjective perception interacts with objective socioeconomic status (SES) measures such as education that affect the individual's health.</p> <p>Methods</p> <p>This research used data from the Survey of Health and Living Status of the Middle Age and Elderly in Taiwan (SHLS) conducted by the Bureau of Health Promotion, Department of Health in Taiwan. Waves 1996, 1999 and 2003 were used. The sample consisted of 2,387 elderly persons. The interactive effects of self-rated satisfaction with financial position and educational attainment were estimated. Self-rated health (SRH), depressive symptom (measured by CES-D) and mortality were used to measure health outcomes.</p> <p>Results</p> <p>Significant interaction effect was found for depressive symptoms. Among those who were dissatisfied with their financial position, those who were illiterate had an odds ratio (OR) of 8.3 (95% CI 4.9 to 14.0) for having depressive symptoms compared with those who were very satisfied with their financial position. The corresponding OR for those with college or above was only 2.7 (95% CI 1.0 to 7.3). No significant interaction effect was found for SRH and mortality.</p> <p>Conclusions</p> <p>Although poor financial satisfaction was found to be related to poorer health, the strongest association for this effect was observed among those with low educational attainment, and this is especially true for depressive symptoms. Subjective financial status among the elderly should be explored in conjunction with traditional measures of SES.</p

Aurora-A overexpression enhances cell-aggregation of Ha-ras transformants through the MEK/ERK signaling pathway

<p>Abstract</p> <p>Background</p> <p>Overexpression of Aurora-A and mutant Ras (Ras^V12) together has been detected in human bladder cancer tissue. However, it is not clear whether this phenomenon is a general event or not. Although crosstalk between Aurora-A and Ras signaling pathways has been reported, the role of these two genes acting together in tumorigenesis remains unclear.</p> <p>Methods</p> <p>Real-time PCR and sequence analysis were utilized to identify Ha- and Ki-<it>ras </it>mutation (Gly -> Val). Immunohistochemistry staining was used to measure the level of Aurora-A expression in bladder and colon cancer specimens. To reveal the effect of overexpression of the above two genes on cellular responses, mouse NIH3T3 fibroblast derived cell lines over-expressing either Ras^V12and wild-type Aurora-A (designated WT) or Ras^V12and kinase-inactivated Aurora-A (KD) were established. MTT and focus formation assays were conducted to measure proliferation rate and focus formation capability of the cells. Small interfering RNA, pharmacological inhibitors and dominant negative genes were used to dissect the signaling pathways involved.</p> <p>Results</p> <p>Overexpression of wild-type Aurora-A and mutation of Ras^V12were detected in human bladder and colon cancer tissues. Wild-type Aurora-A induces focus formation and aggregation of the Ras^V12transformants. Aurora-A activates Ral A and the phosphorylation of AKT as well as enhances the phosphorylation of MEK, ERK of WT cells. Finally, the Ras/MEK/ERK signaling pathway is responsible for Aurora-A induced aggregation of the Ras^V12transformants.</p> <p>Conclusion</p> <p>Wild-type-Aurora-A enhances focus formation and aggregation of the Ras^V12transformants and the latter occurs through modulating the Ras/MEK/ERK signaling pathway.</p

Ceacam1 separates graft-versus-host-disease from graft-versus-tumor activity after experimental allogeneic bone marrow transplantation.

BACKGROUND: Allogeneic bone marrow transplantation (allo-BMT) is a potentially curative therapy for a variety of hematologic diseases, but benefits, including graft-versus-tumor (GVT) activity are limited by graft-versus-host-disease (GVHD). Carcinoembryonic antigen related cell adhesion molecule 1 (Ceacam1) is a transmembrane glycoprotein found on epithelium, T cells, and many tumors. It regulates a variety of physiologic and pathological processes such as tumor biology, leukocyte activation, and energy homeostasis. Previous studies suggest that Ceacam1 negatively regulates inflammation in inflammatory bowel disease models. METHODS: We studied Ceacam1 as a regulator of GVHD and GVT after allogeneic bone marrow transplantation (allo-BMT) in mouse models. In vivo, Ceacam1(-/-) T cells caused increased GVHD mortality and GVHD of the colon, and greater numbers of donor T cells were positive for activation markers (CD25(hi), CD62L(lo)). Additionally, Ceacam1(-/-) CD8 T cells had greater expression of the gut-trafficking integrin α(4)β(7), though both CD4 and CD8 T cells were found increased numbers in the gut post-transplant. Ceacam1(-/-) recipients also experienced increased GVHD mortality and GVHD of the colon, and alloreactive T cells displayed increased activation. Additionally, Ceacam1(-/-) mice had increased mortality and decreased numbers of regenerating small intestinal crypts upon radiation exposure. Conversely, Ceacam1-overexpressing T cells caused attenuated target-organ and systemic GVHD, which correlated with decreased donor T cell numbers in target tissues, and mortality. Finally, graft-versus-tumor survival in a Ceacam1(+) lymphoma model was improved in animals receiving Ceacam1(-/-) vs. control T cells. CONCLUSIONS: We conclude that Ceacam1 regulates T cell activation, GVHD target organ damage, and numbers of donor T cells in lymphoid organs and GVHD target tissues. In recipients of allo-BMT, Ceacam1 may also regulate tissue radiosensitivity. Because of its expression on both the donor graft and host tissues, this suggests that targeting Ceacam1 may represent a potent strategy for the regulation of GVHD and GVT after allogeneic transplantation

A Conditioning Lesion Provides Selective Protection in a Rat Model of Amyotrophic Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is neurodegenerative disease characterized by muscle weakness and atrophy due to progressive motoneuron loss. The death of motoneuron is preceded by the failure of neuromuscular junctions (NMJs) and axonal retraction. Thus, to develop an effective ALS therapy you must simultaneously preserve motoneuron somas, motor axons and NMJs. A conditioning lesion has the potential to accomplish this since it has been shown to enhance neuronal survival and recovery from trauma in a variety of contexts. rats that received a conditioning lesion was delayed and less severe. These improvements in motor function corresponded to greater motoneuron survival, reduced motor axonopathy, and enhanced NMJ maintenance at disease end-stage. Furthermore, the increased NMJ maintenance was selective for muscle compartments innervated by the most resilient (slow) motoneuron subtypes, but was absent in muscle compartments innervated by the most vulnerable (fast fatigable) motoneuron subtypes.These findings support the development of strategies aimed at mimicking the conditioning lesion effect to treat ALS as well as underlined the importance of considering the heterogeneity of motoneuron sub-types when evaluating prospective ALS therapeutics