Advanced Information Retrieval Within Blogosphere and Micro-Blogosphere

Social media gain worldwide popularity and their volumes are in rapid growth. Blogs and microblogs are two typical types of social media. By February 2011, there had been over 156 million public blogs in existence and the volume of blogosphere is predicted to double about every 5.5 months. Twitter, a microblogging service, has a daily volume of over 340 million tweets by 2012. With such an overwhelming amount of information in blogosphere and micro-blogosphere, advanced information retrieval techniques are needed. In this thesis, I tackle two advanced information retrieval problems: faceted blog distillation over blogosphere and real-time tweet ad-hoc retrieval over micro-blogosphere. For faceted blog distillation, users aim at retrieving the blogs that are not only relevant to queries but also exhibit some qualities. Six aspects of quality (called facets) are considered: opinionated vs. factual, personal vs. official and in-depth vs. shallow. Opinionated blogs provide the blog posts that contain relevant opinions to queries while factual blogs consist of the posts that describe the topics of queries without opinionated contents. The posts in personal blogs depict the topics related to the personal experiences of bloggers while those in official blogs deliver commercial purposes of bloggers. In-depth blogs provide deep analysis about the topics of interest while the posts in shallow blogs simply mention the topics, without analyzing the implications of the provided information. Faceted blog distillation consists of three sub-problems: opinionated and factual blog distillation, personal and official blog distillation, and in-depth and shallow blog distillation. For opinionated and factual blog distillation, I propose a classification-based method to identify the opinions relevant to queries in terms of syntax and semantics. For personal and official blog distillation, I propose two categories of methods: classification based and topic modeling based. All proposed methods effectively differentiate personal blog posts from official blog posts. For in-depth and shallow blog distillation, I propose a measurement to compute the query-oriented depth of blog posts. I also discuss the relationships among facets. The proposed techniques are evaluated by using 220 TREC 2006-2010 queries over two TREC collections: Blogs06 and Blogs08. The proposed methods significantly outperform the best known results for faceted blog distillation. For real-time tweet ad-hoc retrieval, users wish to see the tweets that are not only relevant to queries but also be most recent ones. I propose a two-phase approach to address this problem. Tweets can be categorized into two types. One type consists of short messages not containing any URL of a web page. The other type has at least one URL of a web page in addition to a short message. These two types of tweets have different structures. In the first phase, I propose a learning-to-rank method to rank tweets using the divide-and-conquer strategy to address the structural difference of tweets. In the second phase, I propose three novel categorizations of queries in terms of their temporal sensitivities; then I propose to calculate the time-related relevance scores of tweets according to the classified types of queries; finally I combine the time scores with the IR scores from the first phase to produce a ranking of tweets. Experimental results achieved by using the TREC 2011 and TREC 2012 queries over the TREC Tweets2011 collection show that the proposed divide-and-conquer method of ranking tweets yields better retrieval effectiveness than ranking them simultaneously and the proposed incorporation of temporal information into retrieval process yields further improvements. The method also compares favorably with state-of-the-art methods in retrieval effectiveness

Table_4_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.xlsx

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Table_2_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.xls

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Table_1_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.xls

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Data_Sheet_1_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.PDF

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Data_Sheet_2_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.PDF

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Table_3_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.xls

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

Data_Sheet_3_Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq.PDF

Tonotopic differences in the structure and physiological function, e.g., synapse number, membrane properties, Ca2+ channels, Ca2+ dependence of exocytosis and vesicle pool replenishment of inner hair cells (IHCs) along the longitudinal cochlear axis have recently been discovered, suggesting different gene expression patterns of IHCs. To determine whether IHCs present different gene expression patterns along the longitudinal cochlear axis, apical and basal IHCs were collected separately using the suction pipette technique from adult mouse cochleae for RNA-seq and genome-wide transcriptome analysis. We found 689 annotated genes showed more than 2-fold increase in expression. Interestingly, 93.4% of the differentially expressed genes (DEGs) was upregulated in apical IHCs. Although a subset of genes that related to IHC machinery and deafness were found to be differentially expressed, a gradient of gene expression was indeed detected in Ocm, Pvalb, Prkd1, Fbxo32, Nme2, and Sncg, which may play putative roles in the Ca2+ buffering and survival regulation. The expression of these genes was validated by real-time quantitative PCR (RT-qPCR) or immunostaining. We conclude that IHCs from different mouse cochlear longitudinal position have different gene expression profiles. Our data might serve as a valuable resource for exploring the molecular mechanisms underlying different biological properties as well as the survival regulation of IHCs.</p

DHA resulted in proliferation inhibition and migration, and induced apoptosis in HNSCC cells.

<p>(A) FaDu, Cal-27, and Hep-2 cells were treated with indicated concentrations of DHA for 24 or 48h, and cell viability was tested via MTT assay. IC50 values of DHA were calculated for the three cell lines. (B) DHA induced apoptosis in HNSCC cell. Three HNSCC cell lines were incubated with indicated concentrations of DHA for 24 h, followed by flow cytometric analysis with Annexin V-FITC and propidium iodide (PI) labeling. (C)DHA induced inhibition of migration of HNSCC cells. Cells were incubated with 40μM (FaDu) or 20μM (Cal-27and Hep-2) DHA or DMSO. The wound healing capacity was measured at 0, 12, 24, and 48 h. Data were expressed as means ± SD (left and middle panels). Simultaneous determination of levels of MMP-2, MMP-9 and p-STAT3 was conducted (right panel). (D) Effects of STAT3 inhibition by DHA on expression of downstream proteinsMcl-1, Bcl-xl, Cyclin-D1 and VEGF in HNSCC cells as determined by Western blotting. All experiments were performed in triplicates.</p

DHA synergistically potentiated cisplatin-induced proliferation inhibition and produced G0/G1 phase cell cycle arrest in HNSCC cells.

<p>(A) Fadu, Cal-27 and Hep-2 cells were treated with either DHA (10 and 20 μM), cisplatin (1, 5, and 10 μM), or a combination of both for 24 h. Proliferation inhibition was determined by MTT assay. Data expressed as means ± SD, **p<0.01. (B) Antiproliferative effects of drug synergy were determined by the CalcuSyn software (version 1.0). Combinations: point 1, DHA 10 μM and cisplatin (DDP) 1 μM; point 2, DHA 10 μM and cisplatin 5 μM; point 3, DHA 10 μM and cisplatin 10 μM; point 4, DHA 20 μM and cisplatin 1 μM; point 5, DHA 20 μM and cisplatin 5 μM; point 6, DHA 20 μM and cisplatin 10 μM. All experiments were performed in triplicates. (C) Cell cycle distribution patterns of FaDu, Cal-27 and Hep-2 cells were determined by flow cytometry after exposure to various concentrations of DHA for 24h. The proportions of cells in G1 were calculated. Data were expressed as means ± SD, *p<0.05, **p<0.01. All experiments were performed in triplicates.</p