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Full-Text Articles in Life Sciences

Computational Approaches For Predicting Biomedical Research Collaborations, Qing Zhang, Hong Yu Nov 2014

Computational Approaches For Predicting Biomedical Research Collaborations, Qing Zhang, Hong Yu

Open Access Articles

Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity ...


Peptidylarginine Deiminases: Novel Drug Targets For Prevention Of Neuronal Damage Following Hypoxic Ischemic Insult (Hi) In Neonates., Sigrun Lange, Eridan Rocha-Ferreira, Laura Thei, Priyanka Mawjee, Kate Bennett, Paul R. Thompson, Venkataraman Subramanian, Anthony P. Nicholas, Donald Peebles, Mariya Hristova, Gennadij Raivich Aug 2014

Peptidylarginine Deiminases: Novel Drug Targets For Prevention Of Neuronal Damage Following Hypoxic Ischemic Insult (Hi) In Neonates., Sigrun Lange, Eridan Rocha-Ferreira, Laura Thei, Priyanka Mawjee, Kate Bennett, Paul R. Thompson, Venkataraman Subramanian, Anthony P. Nicholas, Donald Peebles, Mariya Hristova, Gennadij Raivich

Thompson Lab Publications

Neonatal hypoxic ischaemic (HI) injury frequently causes neural impairment in surviving infants. Our knowledge of the underlying molecular mechanisms is still limited. Protein deimination is a post-translational modification caused by Ca(+2) -regulated peptidylarginine deiminases (PADs), a group of five isozymes that display tissue-specific expression and different preference for target proteins. Protein deimination results in altered protein conformation and function of target proteins, and is associated with neurodegenerative diseases, gene regulation and autoimmunity. In this study, we used the neonatal HI and HI/infection [lipopolysaccharide (LPS) stimulation] murine models to investigate changes in protein deimination. Brains showed increases in deiminated ...


A Deterministic Model Predicts The Properties Of Stochastic Calcium Oscillations In Airway Smooth Muscle Cells, Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J. Sanderson, James Sneyd Aug 2014

A Deterministic Model Predicts The Properties Of Stochastic Calcium Oscillations In Airway Smooth Muscle Cells, Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J. Sanderson, James Sneyd

Open Access Articles

The inositol trisphosphate receptor ([Formula: see text]) is one of the most important cellular components responsible for oscillations in the cytoplasmic calcium concentration. Over the past decade, two major questions about the [Formula: see text] have arisen. Firstly, how best should the [Formula: see text] be modeled? In other words, what fundamental properties of the [Formula: see text] allow it to perform its function, and what are their quantitative properties? Secondly, although calcium oscillations are caused by the stochastic opening and closing of small numbers of [Formula: see text], is it possible for a deterministic model to be a reliable ...


Modulation Of Calcium-Induced Cell Death In Human Neural Stem Cells By The Novel Peptidylarginine Deiminase-Aif Pathway., Kin Pong U, Venkataraman Subramanian, Antony P. Nicholas, Paul R. Thompson, Patrizia Ferretti Jun 2014

Modulation Of Calcium-Induced Cell Death In Human Neural Stem Cells By The Novel Peptidylarginine Deiminase-Aif Pathway., Kin Pong U, Venkataraman Subramanian, Antony P. Nicholas, Paul R. Thompson, Patrizia Ferretti

Thompson Lab Publications

PADs (peptidylarginine deiminases) are calcium-dependent enzymes that change protein-bound arginine to citrulline (citrullination/deimination) affecting protein conformation and function. PAD up-regulation following chick spinal cord injury has been linked to extensive tissue damage and loss of regenerative capability. Having found that human neural stem cells (hNSCs) expressed PAD2 and PAD3, we studied PAD function in these cells and investigated PAD3 as a potential target for neuroprotection by mimicking calcium-induced secondary injury responses. We show that PAD3, rather than PAD2 is a modulator of cell growth/death and that PAD activity is not associated with caspase-3-dependent cell death, but is required ...


Structure-Centered Portal For Child Psychiatry Research, Pallavi Rane, Christian Haselgrove, Steven M. Hodge, Jean A. Frazier, David N. Kennedy Apr 2014

Structure-Centered Portal For Child Psychiatry Research, Pallavi Rane, Christian Haselgrove, Steven M. Hodge, Jean A. Frazier, David N. Kennedy

Psychiatry Publications

The real world needs of the clinical community require a domain-specific solution to integrate disparate information available from various web-based resources for data, materials, and tools into routine clinical and clinical research setting. We present a child-psychiatry oriented portal as an effort to deliver a knowledge environment wrapper that provides organization and integration of multiple information and data sources. Organized semantically by resource context, the portal groups information sources by context type, and permits the user to interactively "narrow" or "broaden" the scope of the information resources that are available and relevant to the specific context. The overall objective of ...


Learning To Rank Figures Within A Biomedical Article, Feifan Liu, Hong Yu Mar 2014

Learning To Rank Figures Within A Biomedical Article, Feifan Liu, Hong Yu

University of Massachusetts Medical School Faculty Publications

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. This ever-increasing sheer volume has made it difficult for scientists to effectively and accurately access figures of their interest, the process of which is crucial for validating research facts and for formulating or testing novel research hypotheses. Current figure search applications can't fully meet this challenge as the "bag of figures" assumption doesn't take into account the relationship among figures. In our previous study, hundreds of biomedical researchers have annotated articles in which they serve as corresponding authors. They ranked each figure in ...