Networks in Archaeology: Phenomena, Abstraction, Representation

The application of method and theory from network science to archaeology has dramatically increased over the last decade. In this article, we document this growth over time, discuss several of the important concepts that are used in the application of network approaches to archaeology, and introduce the other articles in this special issue on networks in archaeology. We argue that the suitability and contribution of network science techniques within particular archaeological research contexts can be usefully explored by scrutinizing the past phenomena under study, how these are abstracted into concepts, and how these in turn are represented as network data. For this reason, each of the articles in this special issue is discussed in terms of the phenomena that they seek to address, the abstraction in terms of concepts that they use to study connectivity, and the representations of network data that they employ in their analyses. The approaches currently being used are diverse and interdisciplinary, which we think are evidence of a healthy exploratory stage in the application of network science in archaeology. To facilitate further innovation, application, and collaboration, we also provide a glossary of terms that are currently being used in network science and especially those in the applications to archaeological case studies

Identification and characterization of a novel non-structural protein of bluetongue virus

Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77–79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell

Enrollee Characteristics in an Intensive Tobacco Dependence Treatment Program: The Relationship of Race and Sex to Demographic Factors and Tobacco Use Patterns

Intensive tobacco treatment programs offer many advantages relative to other treatment options, particularly for more complex patients, e.g., highly nicotine dependent, or those with medical and psychiatric symptoms and disorders. Efforts to better understand those who choose to enroll in these programs, particularly regarding the characteristics they possess known to mediate outcomes, are important considerations in tailoring available services. In this study, we examined how participants differed on key descriptive and tobacco use variables within race (i.e., African-American, Caucasian) and sex subgroups. Baseline characteristics from a large group of consecutive program enrollees were examined across targeted subgroups. Strong racial effects and some sex effects were noted for marital status, education, employment and health insurance status, alcohol consumption, presence of medical and psychiatric disorders, as well as participant tobacco use patterns and tobacco use rates of family, friends and coworkers. The differences in participant tobacco use measures across race and sex factors remained significant after adjusting for the confounding effects of all other covariates. These findings have implications for characterizing key patient subgroups who present at tobacco treatment clinics. Such information may contribute to options for tailoring treatment regimens

Early Warning Signals of Social Transformation: A Case Study from the US Southwest

abstract: Recent research in ecology suggests that generic indicators, referred to as early warning signals (EWS), may occur before significant transformations, both critical and non-critical, in complex systems. Up to this point, research on EWS has largely focused on simple models and controlled experiments in ecology and climate science. When humans are considered in these arenas they are invariably seen as external sources of disturbance or management. In this article we explore ways to include societal components of socio-ecological systems directly in EWS analysis. Given the growing archaeological literature on ‘collapses,’ or transformations, in social systems, we investigate whether any early warning signals are apparent in the archaeological records of the build-up to two contemporaneous cases of social transformation in the prehistoric US Southwest, Mesa Verde and Zuni. The social transformations in these two cases differ in scope and severity, thus allowing us to explore the contexts under which warning signals may (or may not) emerge. In both cases our results show increasing variance in settlement size before the transformation, but increasing variance in social institutions only before the critical transformation in Mesa Verde. In the Zuni case, social institutions appear to have managed the process of significant social change. We conclude that variance is of broad relevance in anticipating social change, and the capacity of social institutions to mitigate transformation is critical to consider in EWS research on socio-ecological systems.The article is published at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.016368

Blood Pressure Management in the Very Preterm Infant:More than Just Millimetres

Despite significant advances in many areas of care, the management of low blood pressure and circulatory compromise in the preterm infant continues to be based on quite limited evidence. Deciding when to intervene, and with what to intervene, remains a conundrum at the bedside. In this chapter we explore the aetiology of low blood pressure, we review assessment strategies including new monitoring modalities that may provide a better understanding of the underlying problem and hence direct more appropriate treatments. The evidence for current therapies is reviewed, including the newer inodilators. The future will see a paradigm shift in our current approach to haemodynamic instability and management.</p

Pressure support versus thermal broadening in the Lyman alpha forest - I. Effects of the equation of state on longitudinal structure

In the low-density intergalactic medium that gives rise to the Lyman α (Lyα) forest, gas temperature and density are tightly correlated. The velocity scale of thermal broadening and the Hubble flow across the gas Jeans scale are of similar magnitude (HλJ∼σth). To separate the effects of gas pressure support and thermal broadening on the Lyα forest, we compare spectra extracted from two smoothed particle hydrodynamics simulations evolved with different photoionization heating rates (and thus different Jeans scales) and from the pressureless dark matter distribution, imposing different temperature–density relations on the evolved particle distributions. The dark matter spectra are similar but not identical to those created from the full gas distributions, showing that thermal broadening sets the longitudinal (line-of-sight) scale of the Lyα forest. The turnover scales in the flux power spectrum and flux autocorrelation function are determined mainly by thermal broadening rather than pressure. However, the insensitivity to pressure arises partly from a cancellation effect with a sloped temperature–density relation (T∝ρ0.6 in our simulations): the high-density peaks in the colder, lower pressure simulation are less smoothed by pressure support than in the hotter simulation, and it is this higher density gas that experiences the strongest thermal broadening. Changes in thermal broadening and pressure support have comparably important effects on the flux probability distribution, which responds directly to the gas overdensity distribution rather than the scale on which it is smooth. Tests on a lower resolution simulation (2 × 1443 versus 2 × 2883 particles in a 12.5 h−1 Mpc comoving box) show that our statistical results are converged even at this lower resolution. While thermal broadening generally dominates the longitudinal structure in the Lyα forest, we show in Peeples et al. that pressure support determines the transverse coherence of the forest observed towards close quasar pairs

Albumin binding as a potential biomarker of exposure to moderately low levels of organophosphorus pesticides

We have evaluated the potential of plasma albumin to provide a sensitive biomarker of exposure to commonly used organophosphorus pesticides in order to complement the widely used measure of acetylcholinesterase (AChE) inhibition. Rat or human plasma albumin binding by tritiated-diisopropylfluorophosphate ((3)H-DFP) was quantified by retention of albumin on glass microfibre filters. Preincubation with unlabelled pesticide in vitro or dosing of F344 rats with pesticide in vivo resulted in a reduction in subsequent albumin radiolabelling with (3)H-DFP, the decrease in which was used to quantify pesticide binding. At pesticide exposures producing approximately 30% inhibition of AChE, rat plasma albumin binding in vitro by azamethiphos (oxon), chlorfenvinphos (oxon), chlorpyrifos-oxon, diazinon-oxon and malaoxon was reduced from controls by 9+/-1%, 67+/-2%, 56+/-2%, 54+/-2% and 8+/-1%, respectively. After 1 h of incubation with 19 microM (3)H-DFP alone, the level of binding to rat or human plasma albumins reached 0.011 or 0.039 moles of DFP per mole of albumin, respectively. This level of binding could be further increased by raising the concentration of (3)H-DFP, increasing the (3)H-DFP incubation time, or by substitution of commercial albumins for native albumin. Pesticide binding to albumin was presumed covalent since it survived 24 h dialysis. After dosing rats with pirimiphos-methyl (dimethoxy) or chlorfenvinphos (oxon) (diethoxy) pesticides, the resultant albumin binding were still significant 7 days after dosing. As in vitro, dosing of rats with malathion did not result in significant albumin binding in vivo. Our results suggest albumin may be a useful additional biomonitor for moderately low-level exposures to several widely used pesticides, and that this binding differs markedly between pesticides

HUMAN LIVER PLASMA MEMBRANES CONTAIN RECEPTORS FOR THE HEPATITIS B VIRUS PRE S1 REGION AND, VIA POLYMERIZED HUMAN SERUM ALBUMIN, FOR THE PRES2 REGION

Hepatitis B virus particles contain three related viral envelope proteins, the small, middle, and large S (surface) proteins. All three proteins contain the small S amino acid sequence at their carboxyl terminus. It is not clear which of these S proteins functions as the viral attachment protein, binding to a target cell receptor and initiating infection. In this report, recombinant hepatitis B surface antigen (rHBsAg) particles, which contain only virus envelope proteins, were radioactively labeled, and their attachment to human liver membranes was examined. Only the rHBsAg particles containing the large S protein were capable of directly attaching to liver plasma membranes. The attachment was saturable and could be prevented by competition with unlabeled particles or by a monoclonal antibody specific for the large S protein. In the presence of polymerized human serum albumin, both large and middle S protein-containing rHBsAg particles were capable of attaching to the liver plasma membranes. Small S protein-containing rHBsAg particles were not able to attach even in the presence of polymerized human serum albumin. These results indicate that the large S protein may be the viral attachment protein for hepatocytes, binding directly to liver plasma membranes by its unique amino-terminal (pre-S1) sequence. These results also indicate that polymerized human serum albumin or a similar molecule could act as an intermediate receptor, attaching to liver plasma membranes and to the amino acid sequence (pre-S2) shared by the middle and large S proteins but not contained in the small S protein