Use of verbal autopsy and social autopsy in humanitarian crises

Data sharing statement Qualitative information is stored at a University of Aberdeen managed file-space. Data can be available upon prior permission from the University and the corresponding author can be contacted for further communication. Participants gave informed consent for data sharing. The research presented in this paper is supported by a programme grant as part of the Health Systems Research Initiative from the Department for International Development (DFID)/Medical Research Council (MRC)/Wellcome Trust/ Economic and Social Research Council (ESRC) (MR/P014844/1).Peer reviewedPublisher PD

Attempting to break the chain: Reimaging Inclusive Pedagogy and Decolonising the Curriculum within the Academy

Anti-racist education within the Academy holds the potential to truly reflect the cultural hybridity of our diverse, multi-cultural society through the canons of knowledge that educators celebrate, proffer and embody. The centrality of Whiteness as an instrument of power and privilege ensures that particular types of knowledge continue to remain omitted from our curriculums. The monopoly and proliferation of dom- inant White European canons does comprise much of our existing cur- riculum; consequently, this does impact on aspects of engagement, inclusivity and belonging particularly for Black, Asian and Minority Ethnic (BAME) learners. This paper explores the impact of a dominant Eurocentric curriculum and the Decolonising the Curriculum agenda within higher education and its influence upon navigating factors such as BAME attainment, engagement and belonging within the Academy. This paper draws on a Critical Race Theory (CRT) theoretical framework to centralize the marginalized voices of fifteen BAME students and three academics of colour regarding this phenomena. Aspects examined con- sider the impact of a narrow and restrictive curriculum on BAME students and staff and how the omission of diverse histories and multi- cultural knowledge canons facilitates marginalization and discrimin- atory cultures

Verbal Autopsy in Health Policy and Systems : A Literature Review

The research presented in this paper is funded by the Health Systems Research Initiative from the Department for International Development (DFID)/ Medical Research Council (MRC)/Wellcome Trust/Economic and Social Research Council (ESRC) (MR/P014844/1).Peer reviewedPublisher PD

Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation

AbstractAs the number of electronic biomedical textual resources increases, it becomes harder for physicians to find useful answers at the point of care. Information retrieval applications provide access to databases; however, little research has been done on using automatic summarization to help navigate the documents returned by these systems. After presenting a semantic abstraction automatic summarization system for MEDLINE citations, we concentrate on evaluating its ability to identify useful drug interventions for 53 diseases. The evaluation methodology uses existing sources of evidence-based medicine as surrogates for a physician-annotated reference standard. Mean average precision (MAP) and a clinical usefulness score developed for this study were computed as performance metrics. The automatic summarization system significantly outperformed the baseline in both metrics. The MAP gain was 0.17 (p<0.01) and the increase in the overall score of clinical usefulness was 0.39 (p<0.05)

Loss of APC induces polyploidy as a result of a combination of defects in mitosis and apoptosis

Mutations in the adenomatous polyposis coli (APC) tumor suppressor gene initiate a majority of colorectal cancers. Acquisition of chromosomal instability is an early event in these tumors. We provide evidence that the loss of APC leads to a partial loss of interkinetochore tension at metaphase and alters mitotic progression. Furthermore, we show that inhibition of APC in U2OS cells compromises the mitotic spindle checkpoint. This is accompanied by a decrease in the association of the checkpoint proteins Bub1 and BubR1 with kinetochores. Additionally, APC depletion reduced apoptosis. As expected from this combination of defects, tetraploidy and polyploidy are consequences of APC inhibition in vitro and in vivo. The removal of APC produced the same defects in HCT116 cells that have constitutively active β-catenin. These data show that the loss of APC immediately induces chromosomal instability as a result of a combination of mitotic and apoptotic defects. We suggest that these defects amplify each other to increase the incidence of tetra- and polyploidy in early stages of tumorigenesis

Functional Domains of the Fatty Acid Transport Proteins: Studies Using Protein Chimeras

Fatty acid transport proteins (FATP) function in fatty acid trafficking pathways, several of which have been shown to participate in the transport of exogenous fatty acids into the cell. Members of this protein family also function as acyl CoA synthetases with specificity towards very long chain fatty acids or bile acids. These proteins have two identifying sequence motifs: The ATP/AMP motif, an approximately 100 amino acid segment required for ATP binding and common to members of the adenylate-forming super family of proteins, and the FATP/VLACS motif that consists of approximately 50 amino acid residues and is restricted to members of the FATP family. This latter motif has been implicated in fatty acid transport in the yeast FATP orthologue Fat1p. In the present studies using a yeast strain containing deletions in FAT1 (encoding Fat1p) and FAA1 (encoding the major acyl CoA synthetase (Acsl) Faa1p) as an experimental platform, the phenotypic and functional properties of specific murine FATP1-FATP4 and FATP6-FATP4 protein chimeras were evaluated in order to define elements within these proteins that further distinguish the fatty acid transport and activation functions. As expected from previous work FATP1 and FATP4 were functional in the fatty acid transport pathway, while and FATP6 was not. All three isoforms were able to activate the very long chain fatty acids arachidonate (C20:4) and lignocerate (C24:0), but with distinguishing activities between saturated and highly unsaturated ligands. A 73 amino acid segment common to FATP1 and FATP4 and between the ATP/AMP and FATP/VLACS motifs was identified by studying the chimeras, which is hypothesized to contribute to the transport function

Functional Domains of the Fatty Acid Transport Proteins: Studies Using Protein Chimeras

Fatty acid transport proteins (FATP) function in fatty acid trafficking pathways, several of which have been shown to participate in the transport of exogenous fatty acids into the cell. Members of this protein family also function as acyl CoA synthetases with specificity towards very long chain fatty acids or bile acids. These proteins have two identifying sequence motifs: The ATP/AMP motif, an approximately 100 amino acid segment required for ATP binding and common to members of the adenylate-forming super family of proteins, and the FATP/VLACS motif that consists of approximately 50 amino acid residues and is restricted to members of the FATP family. This latter motif has been implicated in fatty acid transport in the yeast FATP orthologue Fat1p. In the present studies using a yeast strain containing deletions in FAT1 (encoding Fat1p) and FAA1 (encoding the major acyl CoA synthetase (Acsl) Faa1p) as an experimental platform, the phenotypic and functional properties of specific murine FATP1-FATP4 and FATP6-FATP4 protein chimeras were evaluated in order to define elements within these proteins that further distinguish the fatty acid transport and activation functions. As expected from previous work FATP1 and FATP4 were functional in the fatty acid transport pathway, while and FATP6 was not. All three isoforms were able to activate the very long chain fatty acids arachidonate (C20:4) and lignocerate (C24:0), but with distinguishing activities between saturated and highly unsaturated ligands. A 73 amino acid segment common to FATP1 and FATP4 and between the ATP/AMP and FATP/VLACS motifs was identified by studying the chimeras, which is hypothesized to contribute to the transport function

Algorithms for Reconstructing DDoS Attack Graphs using Probabilistic Packet Marking

DoS and DDoS attacks are widely used and pose a constant threat. Here we explore Probability Packet Marking (PPM), one of the important methods for reconstructing the attack-graph and detect the attackers. We present two algorithms. Differently from others, their stopping time is not fixed a priori. It rather depends on the actual distance of the attacker from the victim. Our first algorithm returns the graph at the earliest feasible time, and turns out to guarantee high success probability. The second algorithm enables attaining any predetermined success probability at the expense of a longer runtime. We study the performance of the two algorithms theoretically, and compare them to other algorithms by simulation. Finally, we consider the order in which the marks corresponding to the various edges of the attack graph are obtained by the victim. We show that, although edges closer to the victim tend to be discovered earlier in the process than farther edges, the differences are much smaller than previously thought.Comment: 30 pages, 4 figures, 4 table

Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins