Landscapes of Urbanisation and De-urbanisation: Integrating Site Location Datasets from Northwest India to Investigate Changes in the Indus Civilisation’s Settlement Distribution

Archaeological survey data plays a fundamental role in studies of long-term socio-cultural change, particularly those that examine the emergence of social complexity and urbanism. Re-evaluating survey datasets reveals lacunae in survey coverage, encourages the reconsideration of existing interpretations, and makes it possible to integrate the results of multiple projects into large scale analyses that address a broad range of research questions. This paper re-evaluates settlement site location reports that relate to the major phases of the Indus civilisation, whose Mature Harappan period (c. 2600-1900 B.C.) is characterised by numerous village settlements and a small number of larger urban centres. By the end of the Mature Harappan period, people appear to have left these cities, and a de-nucleated pattern of settlement is evident in the subsequent Late Harappan period. Survey data from the plains of northwest India are key to understanding this process of de-urbanisation, as it has been argued that there was an increase in the region’s settlement density as the cities declined. Assembling site locations from multiple surveys into an integrated relational database makes it possible to conduct geographical information systems (GIS)-based analyses at larger scales. This paper finds that the number of settlements on the plains of northwest India increased between c.1900 and 700 B.C., and that some settings within this region were favoured for settlement, resulting in new landscapes of de-urbanisation. These results lay the foundation for future research that will ask whether this shift in settlement location occurred at the expense of alternative social processes, such as movement to highland areas, fortification of nodes of long distance exchange, and political consolidation. More broadly, investigating the Indus civilisation’s landscapes has the potential to reshape models of social complexity by revealing how it emerged and transformed across extensive and varied environmental settings

Arsenite oxidase in complex with antimonite and arsenite oxyanions - insights into the catalytic mechanism

Arsenic contamination of groundwater is among one of the biggest health threats affecting millions of people in the world. There is an urgent need for efficient arsenic biosensors where the use of arsenic metabolizing enzymes can be explored. In this work we have solved the crystal structures of four complexes of arsenite oxidase (Aio) obtained in complex with arsenic and antimony oxyanions and the structures determined correspond to intermediate states of the enzymatic mechanism. These structural data were complemented with DFT calculations providing a unique view of the molybdenum active site at different time points that, together with mutagenesis data, enabled to clarify the enzymatic mechanism and the molecular determinants for the oxidation of As(III) to the less toxic As(V) species

Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

Changing insurance company claims handling processes improves some outcomes for people injured in road traffic crashes

<p>Abstract</p> <p>Background</p> <p>Regaining good health and returning to work are important for people injured in road traffic crashes and for society. The handling of claims by insurance companies may play an important role in the rate at which health recovers and return to work is actually attained.</p> <p>Methods</p> <p>A novel approach towards claims handling for people injured in road traffic accidents was compared to the standard approach. The setting was a large insurance company (NRMA Insurance) in the state of New South Wales, Australia. The new approach involved communicating effectively with injured people, early intervention, screening for adverse prognostic factors and focusing on early return to work and usual activities. Demographic and injury data, health outcomes, return to work and usual activities were collected at baseline and 7 months post-injury.</p> <p>Results</p> <p>Significant differences were found 7 months post-injury on 'caseness' of depression (<it>p </it>= 0.04), perceived health limitation on activities (<it>p </it>= 0.03), and self-reported return to usual activities (<it>p </it>= 0.01) with the intervention group scoring better. Baseline general health was a significant predictor for general health at 7 months (OR 11.6, 95% CI 2.7-49.4) and for return to usual activities (OR 4.6, 95% CI 2.3-9.3).</p> <p>Conclusion</p> <p>We found a few positive effects on health from a new claims handling method by a large insurance company. It may be most effective to target people who report low general health and low expectations for their health recovery when they file their claim.</p

Extreme Food-Plant Specialisation in Megabombus Bumblebees as a Product of Long Tongues Combined with Short Nesting Seasons

© 2015 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/ The attached file is the published version of the article

No evidence of Zika, dengue, or chikungunya virus infection in field-caught mosquitoes from the Recife Metropolitan Region, Brazil, 2015.

Background: The Recife Metropolitan Region (RMR), north-eastern Brazil, was the epicentre of the 2015 Zika virus (ZIKV) epidemic, which was followed by a 2016 chikungunya virus (CHIKV) epidemic. It historically has amongst the highest incidence of dengue virus (DENV) infections and is the only remaining focus of lymphatic filariasis (LF) in Brazil. In early 2015, a molecular xenomonitoring surveillance project focused on Culex (Cx.) quinquefasciatus commenced to inform LF elimination activities. Aedes (Ae.) aegypti mosquitoes were also collected, concurrent with the first microcephaly cases detected in the RMR. In terms of the 2015 ZIKV epidemic, these are the earliest known field-collected mosquitoes, preserved for potential RNA virus detection, when ZIKV was known to be circulating locally. Methods:   Adult mosquitoes were collected in two sites (0.4 km 2) of Sítio Novo, Olinda, RMR, from July 22 to August 21, 2015. Mosquitoes were morphologically identified, sorted by physiological status, and pooled (up to 10 mosquitoes per house per day or week). RNA was extracted, reverse transcribed and the cDNA tested by real-time PCR. Results: A total of 10,139 adult female Cx. quinquefasciatus and 939 adult female Ae. aegypti were captured. All female Ae. aegypti specimens were included within 156 pools and screened for ZIKV, DENV and CHIKV. In addition, a sub-set of 1,556 Cx. quinquefasciatus adult females in 182 pools were screened for ZIKV. No evidence of infection with any of the three arboviruses was found. Conclusions: The absence of arbovirus detection may have been expected given the extremely restricted geographic area and collection of mosquitoes during a very short time period of peak mosquito abundance (July-September), but low arbovirus circulation (November-March).  However, this study demonstrates the potential to retrospectively screen for additional unexpected pathogens in situations of rapid emergence, such as occurred during the outbreak of ZIKV in the RMR

Understanding valuation of travel time changes: are preferences different under different stated choice design settings?

Stated choice (SC) experiments are the most popular method to estimate the value of travel time changes (VTTC) of a population. In the simplest VTTC experiment, the SC design variables are time changes and cost changes. The levels of these variables create a particular setting from which preferences are inferred. This paper tries to answer the question “do preferences vary with SC settings?”. For this, we investigate the role of the variables used in the SC experiment on the estimation of the set of VTTC (i.e. mean and covariates). Ideally, one would like to observe the same individuals completing different SC experiments. Since that option is not available, an alternative approach is to use a large dataset of responses, and split it according to different levels of the variable of interest. We refer to this as partial data analysis. The estimation of the same model on each sub-sample provides insights into potential effects of the variable of interest. This approach is applied in relation to three design variables on the data for the last national VTTC study in the UK, using state-of-the-art model specifications. The results show several ways in which the estimated set of VTTC can be affected by the levels of SC design variables. We conclude that model estimates (including the VTTC and covariates) are different in different settings. Hence by focussing the survey on specific settings, sample level results will be affected accordingly. Our findings have implications for appraisal and can inform the construction of future SC experiments

Evo-devo of human adolescence: beyond disease models of early puberty

Despite substantial heritability in pubertal development, much variation remains to be explained, leaving room for the influence of environmental factors to adjust its phenotypic trajectory in the service of fitness goals. Utilizing evolutionary development biology (evo-devo), we examine adolescence as an evolutionary life-history stage in its developmental context. We show that the transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, other environmental cues, social needs of adolescence and maturation toward youth and adulthood. Using the evolutionary theory of socialization, we show that familial psychosocial stress fosters a fast life history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. Here we explore implications of an evolutionary-developmental-endocrinological-anthropological framework for theory building, while illuminating new directions for research

Feasibility of trial procedures for a randomised controlled trial of a community based group exercise intervention for falls prevention for visually impaired older people: the VIOLET study

Background Visually impaired older people (VIOP) have a higher risk of falling than their sighted peers, and are likely to avoid physical activity. The aim was to adapt the existing Falls Management Exercise (FaME) programme for VIOP, delivered in the community, and to investigate the feasibility of conducting a definitive randomised controlled trial (RCT) of this adapted intervention. Methods Two-centre randomised mixed methods pilot trial and economic evaluation of the adapted group-based FaME programme for VIOP versus usual care. A one hour exercise programme ran weekly over 12 weeks at the study sites (Newcastle and Glasgow), delivered by third sector (voluntary and community) organisations. Participants were advised to exercise at home for an additional two hours over the week. Those randomised to the usual activities group received no intervention. Outcome measures were completed at baseline, 12 and 24 weeks. The potential primary outcome was the Short Form Falls Efficacy Scale – International (SFES-I). Participants’ adherence was assessed by reviewing attendance records and self-reported compliance to the home exercises. Adherence with the course content (fidelity) by instructors was assessed by a researcher. Adverse events were collected in a weekly phone call. Results Eighteen participants, drawn from community-living VIOP were screened; 68 met the inclusion criteria; 64 participants were randomised with 33 allocated to the intervention and 31 to the usual activities arm. 94% of participants provided data at the 12 week visit and 92% at 24 weeks. Adherence was high. The intervention was found to be safe with 76% attending nine or more classes. Median time for home exercise was 50 min per week. There was little or no evidence that fear of falling, balance and falls risk, physical activity, emotional, attitudinal or quality of life outcomes differed between trial arms at follow-up. Conclusions The intervention, FaME, was implemented successfully for VIOP and all progression criteria for a main trial were met. The lack of difference between groups on fear of falling was unsurprising given it was a pilot study but there may have been other contributory factors including suboptimal exercise dose and apparent low risk of falls in participants. These issues need addressing for a future trial