title: Learning a concept-based document similarity measure

authors: Huang, Lan

subjects: content analysis

abstract: Document similarity measures are crucial components of many text-analysis tasks, including information retrieval, document classification, and document clustering. Conventional measures are brittle: They estimate the surface overlap between documents based on the words they mention and ignore deeper semantic connections. We propose a new measure that assesses similarity at both the lexical and semantic levels, and learns from human judgments how to combine them by using machine-learning techniques. Experiments show that the new measure produces values for documents that are more consistent with people's judgments than people are with each other. We also use it to classify and cluster large document sets covering different genres and topics, and find that it improves both classification and clustering performance.

text: Learning a concept-based document similarity measure Document similarity measures are crucial components of many text-analysis tasks, including information retrieval, document classification, and document clustering. Conventional measures are brittle: They estimate the surface overlap between documents based on the words they mention and ignore deeper semantic connections. We propose a new measure that assesses similarity at both the lexical and semantic levels, and learns from human judgments how to combine them by using machine-learning techniques. Experiments show that the new measure produces values for documents that are more consistent with people's judgments than people are with each other. We also use it to classify and cluster large document sets covering different genres and topics, and find that it improves both classification and clustering performance.

year: 2012

title: The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection

authors: Summers, Emma Louise

subjects: Science & Technology

abstract: Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNAbinding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal crosslinking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 A˚ resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß–ß–a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel b-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

text: The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNAbinding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal crosslinking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 A˚ resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß–ß–a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel b-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

year: 2012-06-13

title: Enacting Kaitiakitanga Challenges and Complexities in the Governance and Ownership of Rongoā Research Information.

authors: Boulton, Amohia

subjects: Indigenous

abstract: This article explores the tensions one research team has faced in securing appropriate governance or stewardship (which we refer to as kaitiakitanga) of research data. Whilst ethical and regulatory frameworks exist which provide a minimum standard for researchers to meet when working with Māori, what our experience has highlighted is there is currently a “governance” gap in terms of who should hold stewardship of research data collected from Māori individuals or collectives. In the case of a project undertaken in the traditional healing space, the organisation best placed to fulfil this governance role receives no funding or support to take on such a responsibility; consequently by default, this role is being borne by the research team until such time as capacity can be built and adequate resourcing secured. In addition, we have realised that the tensions played out in this research project have implications for the broader issue of how we protect traditional knowledge in a modern intellectual property law context, and once again how we adequately support those, often community-based organisations, who work at the interface between Indigenous knowledge and the Western world.

text: Enacting Kaitiakitanga Challenges and Complexities in the Governance and Ownership of Rongoā Research Information. This article explores the tensions one research team has faced in securing appropriate governance or stewardship (which we refer to as kaitiakitanga) of research data. Whilst ethical and regulatory frameworks exist which provide a minimum standard for researchers to meet when working with Māori, what our experience has highlighted is there is currently a “governance” gap in terms of who should hold stewardship of research data collected from Māori individuals or collectives. In the case of a project undertaken in the traditional healing space, the organisation best placed to fulfil this governance role receives no funding or support to take on such a responsibility; consequently by default, this role is being borne by the research team until such time as capacity can be built and adequate resourcing secured. In addition, we have realised that the tensions played out in this research project have implications for the broader issue of how we protect traditional knowledge in a modern intellectual property law context, and once again how we adequately support those, often community-based organisations, who work at the interface between Indigenous knowledge and the Western world.

year: 2014