Fish for the city: meta-analysis of archaeological cod remains and the growth of London’s northern trade

The growth of medieval cities in Northern Europe placed new demands on food supply, and led to the import of fish from increasingly distant fishing grounds. Quantitative analysis of cod remains from London provides revealing insight into the changing patterns of supply that can be related to known historical events and circumstances. In particular it identifies a marked increase in imported cod from the thirteenth century AD. That trend continued into the fifteenth and sixteenth centuries, after a short downturn, perhaps attributable to the impact of the Black Death, in the mid fourteenth century. The detailed pattern of fluctuating abundance illustrates the potential of archaeological information that is now available from the high-quality urban excavations conducted in London and similar centres during recent decades

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

There is a high prevalence of coronary artery disease (CAD) in patients with left bundle branch block (LBBB); however there are many other causes for this electrocardiographic abnormality. Non-invasive assessment of these patients remains difficult, and all commonly used modalities exhibit several drawbacks. This often leads to these patients undergoing invasive coronary angiography which may not have been necessary. In this review, we examine the uses and limitations of commonly performed non-invasive tests for diagnosis of CAD in patients with LBBB

Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures

Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus. We present a structural comparison of several members of the Caliciviridae, showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures. Furthermore, at intermediate resolutions we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera, such as sapovirus and rabbit haemorrhagic disease virus. Phylogenetic analysis confirms vesivirus 2117 as a vesivirus closely related to canine vesiviruses. We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage

Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal

Between the Danube and the Deep Blue Sea : zooarchaeological meta-analysis reveals variability in the spread and development of Neolithic farming across the western Balkans

The first spread of farming practices into Europe in the Neolithic period involves two distinct 'streams', respectively around the Mediterranean littoral and along the Danube corridor to central Europe. In this paper we explore variation in Neolithic animal use practices within and between these streams, focusing on the first region in which they are clearly distinct (and yet still in close proximity): the western Balkans. We employ rigorous and reproducible meta-analysis of all available zooarchaeological data from the region to test hypotheses (a) that each stream featured a coherent 'package' of herding and hunting practices in the earliest Neolithic, and (b) that these subsequently diverged in response to local conditions and changing cultural preferences. The results partially uphold these hypotheses, while underlining that Neolithisation was a complex and varied process. A coherent, stable, caprine-based 'package' is seen in the coastal stream, albeit with some diversification linked to expansion northwards and inland. Accounting for a severe, systematic bias in bone recovery methodology between streams, we show that sheep and goats also played a major role across the continental stream in the earliest Neolithic (c.6100-5800 BC). This was followed by a geographically staggered transition over c.500 years to an economy focused on cattle, with significant levels of hunting in some areas – a pattern we interpret in terms of gradual adaptation to local conditions, perhaps mediated by varying degrees of cultural conservatism. Subsequent westward expansion carried with it elements of this new pattern, which persisted through the middle and late Neolithic

Stories from the city, stories from the sea

In an ingenious study that draws on decades of excavation, archaeologists asked what bones might tell us about past cod consumption in London. The result is a striking insight into medieval fish trade and the globalisation of the city’s food suppl

You Have to Send the Right Message: Examining the Influence of Protective Action Guidance on Message Perception Outcomes across Prior Hazard Warning Experience to Three Hazards

A long-term goal for warning message designers is to determine the most effective type of message that can instruct individuals to act quickly and prevent loss of life and/or injury when faced with an imminent threat. One likely way to increase an individual’s behavioral intent to act when they are faced with risk information is to provide protective action information or guidance. This study investigated participant perceptions (understanding, believing, personalizing, deciding, milling, self-efficacy, and response-efficacy) in response to the National Weather Service’s experimental product Twitter messages for three hazard types (tornado, snow squall, dust storm), with each message varying by inclusion and presentation of protective action information placed in the tweet text and the visual graphic. We also examine the role of prior hazard warning experience on message perception outcomes. To examine the effects, the experiment used a between-subjects design where participants were randomly assigned to one hazard type and received one of four warning messages. Participants then took a post-test measuring message perceptions, efficacy levels, prior hazard warning experience, and demographics. The results showed that for each hazard and prior hazard experience level, messages with protective action guidance in both the text and graphic increase their understanding, belief, ability to decide, self-, and response-efficacy. These results reinforce the idea that well-designed messages, that include protective action guidance, work well regardless of hazard type or hazard warning experience