Indonesian security responses to resurgent Papuan separatism : an open source intelligence case study

Simplistic but commonly held beliefs about State security functions would hold that the State manages an exclusive supply of the best possible quality of information, to which the public can only become privy via scandalous 'leaks'. Whether conducting counter-insurgencies, or intelligence collection and analysis of such operations, a State's special apparatus is often accorded an intelligence mystique, and its functions assumed to be specially endowed with 'the real story', far removed from 'low grade' information available to journalists, NGOs and other non-State actors and agents. In challenging such views, this paper sets out to detail various aspects of the Indonesian counter-insurgency in Irian Jaya/Papua, with a view to two distinct goals. The first objective is to attain an overview of the counter-insurgency's political context and some of its implications for regional security. The second is to assert the rich, though seemingly neglected, intelligence value of public domain information as evident in the Papua case. Reliance is placed upon a critical appraisal of many sources, especially Indonesian press reporting, in the discussion heading towards both destinations. Maps, tables and appendices are used to present the most specific and detailed aspects of the research made during the drafting of this paper. It must be emphasised that this study uses only information that has already been revealed in the public domain. Any analysis and opinion by the author is entirely his own, and made in a private capacity

PPD v1.0—an integrated, web-accessible database of experimentally determined protein pK(a) values

The Protein pK(a) Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pK(a) values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pK(a) archive and as a source of data that allows for the development and improvement of pK(a) prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL:

Assessment of maximum aerobic capacity and anaerobic threshold of elite ballet dancers

An athlete’s cardiorespiratory profile, maximal aerobic capacity and anaerobic threshold, is affected by their training regimen and competition demands. The purpose of the present study is to ascertain whether there are company rank differences in maximal aerobic capacity and anaerobic threshold in elite classical ballet dancers. Seventy-four volunteers (M=34, F=40) were recruited from two full-time professional classical ballet companies. All participants completed a continuous incremental treadmill protocol with a 1 km.h-1 speed increase at the end of each 1-minute stage until termination criteria had been achieved (e.g. voluntary cessation, RER <1.15, heart rate ±5b.min-1 of estimated HRmax). Peak VO2 (5-breathe smooth) was recorded and anaerobic threshold calculated using ventilatory curve and ventilatory equivalents methods. Statistical analysis reported between-subject effects for gender (F1,67=35.18; p<0.001) and rank (F1,67=8.67; p<0.001); post hoc tests reported soloists (39.5 ±5.15 ml.kg-1.min-1) as having significantly lower VO2 peak than artists (45.9 ±5.75 ml.kg-1.min-1, p<0.001) and principal dancers (48.07 ±3.24 ml.kg-1.min-1, p<0.001). Significant differences in anaerobic threshold were reported for age (F1,67=7.68; p=0.008), rank (F1,67=3.56; p=0.034); post hoc tests reported artists (75.8 ±5.45%) having significantly lower %AT than soloists (80.9 ±5.71, p<0.01) and principals (84.1 ±4.84%, p<0.001). The observed differences in VO2 peak and anaerobic threshold between the ranks in ballet companies is probably due to their different rehearsal and performance demands

Large Scale Structure traced by Molecular Gas at High Redshift

We present observations of redshifted CO(1-0) and CO(2-1) in a field containing an overdensity of Lyman break galaxies (LBGs) at z=5.12. Our Australia Telescope Compact Array observations were centered between two spectroscopically-confirmed z=5.12 galaxies. We place upper limits on the molecular gas masses in these two galaxies of M(H_2) <1.7 x 10^10 M_sun and <2.9 x 10^9 M_sun (2 sigma), comparable to their stellar masses. We detect an optically-faint line emitter situated between the two LBGs which we identify as warm molecular gas at z=5.1245 +/- 0.0001. This source, detected in the CO(2-1) transition but undetected in CO(1-0), has an integrated line flux of 0.106 +/- 0.012 Jy km/s, yielding an inferred gas mass M(H_2)=(1.9 +/- 0.2) x 10^10 M_sun. Molecular line emitters without detectable counterparts at optical and infrared wavelengths may be crucial tracers of structure and mass at high redshift.Comment: 4 pages, accepted for publication in ApJ Letter

Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens

GPCRTree: online hierarchical classification of GPCR function

Background: G protein-coupled receptors (GPCRs) play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings: Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion: A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree

To What Extent is Blood a Reasonable Surrogate for Brain in Gene Expression Studies: Estimation from Mouse Hippocampus and Spleen

Microarrays are designed to measure genome-wide differences in gene expression. In cases where a tissue is not accessible for analysis (e.g. human brain), it is of interest to determine whether a second, accessible tissue could be used as a surrogate for transcription profiling. Surrogacy has applications in the study of behavioural and neurodegenerative disorders. Comparison between hippocampus and spleen mRNA obtained from a mouse recombinant inbred panel indicates a high degree of correlation between the tissues for genes that display a high heritability of expression level. This correlation is not limited to apparent expression differences caused by sequence polymorphisms in the target sequences and includes both cis and trans genetic effects. A tissue such as blood could therefore give surrogate information on expression in brain for a subset of genes, in particular those co-expressed between the two tissues, which have heritably varying expression

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics

Delusional beliefs and reason giving

Delusions are often regarded as irrational beliefs, but their irrationality is not sufficient to explain what is pathological about them. In this paper we ask whether deluded subjects have the capacity to support the content of their delusions with reasons, that is, whether they can author their delusional states. The hypothesis that delusions are characterised by a failure of authorship, which is a dimension of self knowledge, deserves to be empirically tested because (a) it has the potential to account for the distinction between endorsing a delusion and endorsing a framework belief; (b) it contributes to a philosophical analysis of the relationship between rationality and self knowledge; and (c) it informs diagnosis and therapy in clinical psychiatry. However, authorship cannot provide a demarcation criterion between delusions and other irrational belief states

Constraining the Thermal Dust Content of Lyman-Break Galaxies in an Overdense Field at z~5

We have carried out 870 micron observations in the J1040.7-1155 field, known to host an overdensity of Lyman break galaxies at z=5.16 +/- 0.05. We do not detect any individual source at the S(870)=3.0 mJy/beam (2 sigma) level. A stack of nine spectroscopically confirmed z>5 galaxies also yields a non-detection, constraining the submillimeter flux from a typical galaxy at this redshift to S(870)<0.85 mJy, which corresponds to a mass limit M(dust)<1.2x10^8 M_sun (2 sigma). This constrains the mass of thermal dust in distant Lyman break galaxies to less than one tenth of their typical stellar mass. We see no evidence for strong submillimeter galaxies associated with the ultraviolet-selected galaxy overdensity, but cannot rule out the presence of fainter, less massive sources.Comment: 5 pages, 2 figures. MNRAS in pres