Two Islamophobias? Racism and religion as distinct but mutually supportive dimensions of anti-Muslim prejudice.

Debates about Islamophobia have been blighted by the question of whether the prejudice can be defined as a form of racism or as hostility to religion (or a combination of the two). This paper sheds light on this debate by presenting the findings of a new nationally representative survey, focused on the UK, that contrasts perceptions of Muslims not only with perceptions of other ethnic and religious minorities but also with perceptions of Islam as a religious tradition. We find that prejudice against Muslims is higher than for any other group examined other than Travellers. We also find contrasting demographic drivers of prejudice towards Muslims and towards Islam. Across most prejudice measures we analyse, intolerant views are generally significantly associated with being male, voting Conservative and being older, although not with Anglican identity. We find, however, that class effects vary depending on the question's focus. Anti-immigration sentiment - including support for a 'Muslim ban' - is significantly correlated with being working-class. However, prejudice towards Islam as a body of teachings (tested using a question measuring perceptions of religious literalism) is significantly correlated with being middle-class, as is negative sentiment towards Travellers. Using these findings, the paper makes an argument for supplementing recent scholarship on the associations between racism and Islamophobia with analyses focusing on misperceptions of belief.

The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast United States.

Microbial ecology studies have proven to be important resources for improving infectious disease response and outbreak prevention. Vibrio parahaemolyticus is an ongoing source of shellfish-borne food illness in the Northeast United States, and there is keen interest in understanding the environmental conditions that coincide with V. parahaemolyticus disease risk, in order to aid harvest management and prevent further illness. Zooplankton and chitinous phytoplankton are associated with V. parahaemolyticus dynamics elsewhere; however, this relationship is undetermined for the Great Bay estuary (GBE), an important emerging shellfish growing region in the Northeast United States. A comprehensive evaluation of the microbial ecology of V. parahaemolyticus associated with plankton was conducted in the GBE using 3 years of data regarding plankton community, nutrient concentration, water quality, and V. parahaemolyticus concentration in plankton. The concentrations of V. parahaemolyticus associated with plankton were highly seasonal, and the highest concentrations of V. parahaemolyticus cultured from zooplankton occurred approximately 1 month before the highest concentrations of V. parahaemolyticus from phytoplankton. The two V. parahaemolyticus peaks corresponded with different water quality variables and a few highly seasonal plankton taxa. Importantly, V. parahaemolyticus concentrations and plankton community dynamics were poorly associated with nutrient concentrations and chlorophyll a, commonly applied proxy variables for assessing ecological health risks and human health risks from harmful plankton and V. parahaemolyticus elsewhere. Together, these statistical associations (or lack thereof) provide valuable insights to characterize the plankton-V. parahaemolyticus dynamic and inform approaches for understanding the potential contribution of plankton to human health risks from V. parahaemolyticus for the Northeast United States. IMPORTANCE The Vibrio-plankton interaction is a focal relationship in Vibrio disease research; however, little is known about this dynamic in the Northeast United States, where V. parahaemolyticus is an established public health issue. We integrated phototactic plankton separation with seasonality analysis to determine the dynamics of the plankton community, water quality, and V. parahaemolyticus concentrations. Distinct bimodal peaks in the seasonal timing of V. parahaemolyticus abundance from phyto- versus zooplankton and differing associations with water quality variables and plankton taxa indicate that monitoring and forecasting approaches should consider the source of exposure when designing predictive methods for V. parahaemolyticus. Helicotheca tamensis has not been previously reported in the GBE. Its detection during this study provides evidence of the changes occurring in the ecology of regional estuaries and potential mechanisms for changes in V. parahaemolyticus populations. The Vibrio monitoring approaches can be translated to aid other areas facing similar public health challenges.

Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands.

Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States. This change coincided with a bacterial population shift toward human-pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43, and ST636) to nearshore areas off the Atlantic coast of the Northeast United States. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human-pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI). These VPaI differ from each other and bear little resemblance to hemolysin-containing VPaI from isolates of the pandemic clonal complex. Clade I ST631 isolates either harbored no hemolysins or contained a chromosome I-inserted island we call VPaIß that encodes a type 3 secretion system (T3SS2ß) typical of Trh hemolysin producers. The more clinically prevalent and clonal ST631 clade II had an island we call VPaIγ that encodes both tdh and trh and that was inserted in chromosome II. VPaIγ was derived from VPaIß but with some additional acquired elements in common with VPaI carried by pandemic isolates, exemplifying the mosaic nature of pathogenicity islands. Genomics comparisons and amplicon assays identified VPaIγ-type islands containing tdh inserted adjacent to the ure cluster in the three introduced Pacific and most other emergent lineages that collectively cause 67% of infections in the Northeast United States as of 2016.IMPORTANCE The availability of three different hemolysin genotypes in the ST631 lineage provided a unique opportunity to employ genome comparisons to further our understanding of the processes underlying pathogen evolution. The fact that two different pathogenic clades arose in parallel from the same potentially benign lineage by independent VPaI acquisition is surprising considering the historically low prevalence of community members harboring VPaI in waters along the Northeast U.S. coast that could serve as the source of this material. This illustrates a possible predisposition of some lineages to not only acquire foreign DNA but also become human pathogens. Whereas the underlying cause for the expansion of V. parahaemolyticus lineages harboring VPaIγ along the U.S. Atlantic coast and spread of this element to multiple lineages that underlies disease emergence is not known, this work underscores the need to define the environment factors that favor bacteria harboring VPaI in locations of emergent disease.

Governing through Prevent? Regulation and Contested Practice in State-Muslim Engagement.

In this article, we consider the implications of the 'Prevent' strand of the government's counter-terrorism strategy for the UK state's engagement with Muslims. We argue that the logics of Prevent have been highly problematic for state-Muslim engagement. Nevertheless, we suggest that the characterisation of state approaches to engaging Muslims as a form of discipline is incomplete without an analysis of: first, differences in practices, habits and perspectives across governance domains; second, variations in approach and implementation between levels of governance; and third, the agency of Muslims who engage with the state. Through this approach we show how attention to the situated practices of governance reveals the contested nature of governing through Prevent.

Use of Whole-Genome Phylogeny and Comparisons for Development of a Multiplex PCR Assay To Identify Sequence Type 36 Vibrio parahaemolyticus.

Vibrio parahaemolyticus sequence type 36 (ST36) strains that are native to the Pacific Ocean have recently caused multistate outbreaks of gastroenteritis linked to shellfish harvested from the Atlantic Ocean. Whole-genome comparisons of 295 genomes of V. parahaemolyticus, including several traced to northeastern U.S. sources, were used to identify diagnostic loci, one putatively encoding an endonuclease (prp), and two others potentially conferring O-antigenic properties (cps and flp). The combination of all three loci was present in only one clade of closely related strains of ST36, ST59, and one additional unknown sequence type. However, each locus was also identified outside this clade, with prp and flp occurring in only two nonclade isolates and cps in four. Based on the distribution of these loci in sequenced genomes, prp identified clade strains with >99% accuracy, but the addition of one more locus increased accuracy to 100%. Oligonucleotide primers targeting prp and cps were combined in a multiplex PCR method that defines species using the tlh locus and determines the presence of both the tdh and trh hemolysin-encoding genes, which are also present in ST36. Application of the method in vitro to a collection of 94 clinical isolates collected over a 4-year period in three northeastern U.S. states and 87 environmental isolates revealed that the prp and cps amplicons were detected only in clinical isolates identified as belonging to the ST36 clade and in no environmental isolates from the region. The assay should improve detection and surveillance, thereby reducing infections.

Parameterization of H2SO4 and organic contributions to volatile PM in aircraft plumes at ground idle.

Volatile Particulate Matter (vPM) emissions are challenging to measure and quantify, since they are not present in the condensed form at the engine exit plane and they evolve to first form in the aircraft plume and then continue to grow and change as they mix and dilute in the ambient atmosphere. To better understand the issues associated with the initial formation and growth of vPM, a modeling study has been undertaken to examine several key parameters that affect the formation and properties of the vPM that is created in the initial cooling and dilution of the aircraft exhaust. A modeling tool (Aerosol Dynamic Simulation Code, ADSC) that was developed and enhanced over a series of past research projects supported by NASA, DoD's SERDP/ESTCP, and FAA was used to perform a parametric analysis of vPM. The parameters of fuel sulfur content (FSC), emitted condensable hydrocarbon (HC) concentrations, and the species profile of the HCs were used to construct a computational matrix that framed a wide range of expected parameter values. This computational matrix was executed for two representative commercial aircraft engines at ground idle and results were obtained for distances of 250 m and 1000 m downstream. From prior results, the most significant vPM emissions occur at the lowest power settings, so an engine power condition of 7% rated thrust was used. A primary goal of the parametric study is to develop an updated vPM modeling methodology and also to help interpret data collected in experimental campaigns. The parameterization proposed here allows the vPM emission composition and particle numbers to be estimated in greater detail than current methods. The aim is to provide additional understanding on how the vPM properties vary with fuel and engine parameters to increase the utility of vPM predictions.Implications: Volatile Particulate Matter (vPM) is an important contribution to the total PM emitted by aviation engines. While vPM is not currently a part of engine emissions certification regulations, vPM is used in aviation environmental impact assessments and for air quality modeling in and around airports. Current methods in use, such as FOA, were developed before many recent advances in experimental data acquisition and in understanding of vPM processes. The parameterization proposed here allows the vPM emission composition and particle numbers to be estimated in greater detail than current methods. These estimates can be used to develop inventories and provide a better estimate of total emission for most aviation engines. Its use in international regulatory tools can inform possible future regulatory actions regarding vPM.

Complete genome sequence of Vibrio parahaemolyticus ST36 strain MAVP-26, a clinical isolate from an oyster-borne human gastric infection.

A Pacific native lineage of Vibrio parahaemolyticus ST36 serotype O4:K12 was introduced into the Atlantic, which increased local source illnesses. To identify genetic determinants of virulence and ecological resiliency and track their transfer into endemic populations, we constructed a complete genome of a 2013 Atlantic-traced clinical isolate by hybrid assembly.

Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus.

IMPORTANCE: An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.

Influence of seasonality on the genetic diversity of Vibrio parahaemolyticus in New Hampshire shellfish waters as determined by multilocus sequence analysis.

Risk of gastric infection with Vibrio parahaemolyticus increases with favorable environmental conditions and population shifts that increase prevalence of infective strains. Genetic analysis of New Hampshire strains revealed a unique population with some isolates similar to outbreak-causing strains and high-level diversity that increased as waters warmed.

Mercury sources and fate in the Gulf of Maine.

Most human exposure to mercury (Hg) in the United States is from consuming marine fish and shellfish. The Gulf of Maine is a complex marine ecosystem comprising twelve physioregions, including the Bay of Fundy, coastal shelf areas and deeper basins that contain highly productive fishing grounds. Here we review available data on spatial and temporal Hg trends to better understand the drivers of human and biological exposures. Atmospheric Hg deposition from U.S. and Canadian sources has declined since the mid-1990s in concert with emissions reductions and deposition from global sources has increased. Oceanographic circulation is the dominant source of total Hg inputs to the entire Gulf of Maine region (59%), followed by atmospheric deposition (28%), wastewater/industrial sources (8%) and rivers (5%). Resuspension of sediments increases MeHg inputs to overlying waters, raising concerns about benthic trawling activities in shelf regions. In the near coastal areas, elevated sediment and mussel Hg levels are co-located in urban embayments and near large historical point sources. Temporal patterns in sentinel species (mussels and birds) have in some cases declined in response to localized point source mercury reductions but overall Hg trends do not show consistent declines. For example, levels of Hg have either declined or remained stable in eggs from four seabird species collected in the Bay of Fundy since 1972. Quantitatively linking Hg exposures from fish harvested from the Gulf of Maine to human health risks is challenging at this time because no data are available on the geographic origin of seafood consumed by coastal residents. In addition, there is virtually no information on Hg levels in commercial species for offshore regions of the Gulf of Maine where some of the most productive fisheries are located. Both of these data gaps should be priorities for future research.

Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types.

Introduction: Gastrointestinal illnesses associated with the consumption of shellfish contaminated with Vibrio parahaemolyticus have a negative impact on the shellfish industry due to recalls and loss of consumer confidence in products. This bacterial pathogen is very diverse and specific sequence types (STs), ST631 and ST36, have emerged as prevalent causes of Vibrio foodborne disease outbreaks in the US, though other STs have been implicated in sporadic cases. We investigated whether bacteriophages could be used as a proxy to monitor for the presence of distinct V. parahaemolyticus STs in coastal waters. Methods: For this purpose, bacteriophages infecting V. parahaemolyticus were isolated from water samples collected on the Northeast Atlantic coast. The isolated phages were tested against a collection of 29 V. parahaemolyticus isolates representing 18 STs, including six clonal complexes (CC). Four distinct phages were identified based on their ability to infect different sets of V. parahaemolyticus isolates. Results and Discussion: Overall, the 29 bacterial isolates segregated into one of eight patterns of susceptibility, ranging from resistance to all four phages to susceptibility to any number of phages. STs represented by more than one bacterial isolate segregated within the same pattern of susceptibility except for one V. parahaemolyticus ST. Other patterns of susceptibility included exclusively clinical isolates represented by distinct STs. Overall, this study suggests that phages populating coastal waters could be exploited to monitor for the presence of V. parahaemolyticus STs known to cause foodborne outbreaks.

Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates.

Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.

Comparison of the pathogenic potentials of environmental and clinical vibrio parahaemolyticus strains indicates a role for temperature regulation in virulence.

Although the presence of pathogenic Vibrio spp. in estuarine environments of northern New England has been known for some time (C. H. Bartley and L. W. Slanetz, Appl. Microbiol. 21: 965-966, 1971, and K. R. O'Neil, S. H. Jones, and D. J. Grimes, FEMS Microbiol. Lett. 60:163-167, 1990), their virulence and the relative threat they may pose to human health has yet to be evaluated. In this study, the virulence potential of 33 Vibrio parahaemolyticus isolates collected from the Great Bay Estuary of New Hampshire was assessed in comparison to that of clinical strains. The environmental isolates lack thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), which are encoded by tdh and trh, respectively. Though not hemolytic, they do possess putative virulence factors, such type III secretion system 1, and are highly cytotoxic to human gastrointestinal cells. The expression of known and putative virulence-associated traits, including hemolysin, protease, motility, biofilm formation, and cytotoxicity, by clinical reference isolates correlated with increased temperature from 28°C to 37°C. In contrast, the environmental isolates did not induce their putative virulence-associated traits in response to a temperature of 37°C. We further identified a significant correlation between hemolytic activity and growth phase among clinical strains, whereby hemolysin production decreases with increasing cell density. The introduction of a tdh::gfp promoter fusion into the environmental strains revealed that they regulate this virulence-associated gene appropriately in response to temperature, indicating that their existing regulatory mechanisms are primed to manage newly acquired virulence genes.

What science means to me: Understanding personal identification with (evolutionary) science using the sociology of (non)religion.

Within science and technology studies, there is an established tradition of examining publics' knowledge of, trust in, access to and engagement with science, but less attention has been paid to whether and why publics identify with science. While this is understandable given the field's interest in bridging gaps between publics and producers of scientific knowledge, it leaves unanswered questions about how science forms part of people's worldviews and fits into cultural politics and conflict. Based on 123 interviews and 16 focus groups with mixed religious and nonreligious publics and scientists in the United Kingdom and Canada, this article utilises approaches from the sociology of (non)religion to delineate varieties of science identification. It maps out 'practical', 'norm-based', 'civilisational' and 'existential' identifications and explores how these interrelate with people's social characteristics. The article illustrates how science identification is typically dependent on a constellation of cultural/political influences rather than just emerging out of interest in science.

Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire.

Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Both types of sediment contained many unclassified bacterial sequences, including the mollusk pathogen Perkinsus marinus, and detectable xenobiotic degradation and nitrogen transformation genes.

Detecting water quality patterns in New Hampshire's estuaries using National Coastal Assessment probability-based survey data.

Between 2000 and 2006, the New Hampshire Department of Environmental Services and the University of New Hampshire collected water quality samples at 25 to 40 stations per year in a 56.5-km(2) estuary as part of the Environmental Protection Agency's National Coastal Assessment program. Due to the high density of stations, probabilistic statistics for the estuary could be calculated with low uncertainty. The proportions of the estuary exceeding thresholds in each year were calculated for temperature, salinity, dissolved oxygen, chlorophyll a, nitrogen as nitrate and nitrite, nitrogen as ammonium, phosphorus as orthophosphate, total suspended solids, and fecal coliform bacteria. These values were tested for trends over time and correlations with climate variables. The same statistical tests were applied to monthly grab sample data from a representative station in the estuary. The outcomes of the statistical tests on the two datasets were compared to determine if they provided similar information to coastal managers. Trends and correlations were equally likely to be detected using the probability-based data and the fixed station data, but the results were different for the two datasets. The differences were likely due to the distributed nature of the probability-based sampling design, which places stations in all sections of the estuary. In addition, expressing the probabilistic datasets as estimated proportions reduced variability in volatile parameters, such as bacteria, relative to the grab sample dataset. It will be important to develop tools to rectify trends from probability-based surveys with fixed station monitoring to provide clear information to managers.

Forecasting Seasonal Vibrio parahaemolyticus Concentrations in New England Shellfish.

Seafood-borne Vibrio parahaemolyticus illness is a global public health issue facing resource managers and the seafood industry. The recent increase in shellfish-borne illnesses in the Northeast United States has resulted in the application of intensive management practices based on a limited understanding of when and where risks are present. We aim to determine the contribution of factors that affect V. parahaemolyticus concentrations in oysters (Crassostrea virginica) using ten years of surveillance data for environmental and climate conditions in the Great Bay Estuary of New Hampshire from 2007 to 2016. A time series analysis was applied to analyze V. parahaemolyticus concentrations and local environmental predictors and develop predictive models. Whereas many environmental variables correlated with V. parahaemolyticus concentrations, only a few retained significance in capturing trends, seasonality and data variability. The optimal predictive model contained water temperature and pH, photoperiod, and the calendar day of study. The model enabled relatively accurate seasonality-based prediction of V. parahaemolyticus concentrations for 2014-2016 based on the 2007-2013 dataset and captured the increasing trend in extreme values of V. parahaemolyticus concentrations. The developed method enables the informative tracking of V. parahaemolyticus concentrations in coastal ecosystems and presents a useful platform for developing area-specific risk forecasting models.

Varying Success of Relaying To Reduce Vibrio parahaemolyticus Levels in Oysters ( Crassostrea virginica).

Vibrio parahaemolyticus is the leading cause of seafood-borne human infections in the United States, and many of these illnesses are associated with consumption of raw molluscan shellfish. V. parahaemolyticus levels in shellfish vary temporally and spatially with environmental conditions in and around production areas. The objective of this study was to study the potential for reducing levels of V. parahaemolyticus in live oysters by relaying them during higher-risk warm weather to a site with elevated salinity and consistently low V. parahaemolyticus levels. The effectiveness of relaying was assessed by analyzing oyster samples collected on days 0, 2, 7, 10, and 14 for V. parahaemolyticus levels using a three-tube most-probable-number enrichment method in conjunction with genetic marker-based quantitative PCR. The salinity at the relay site was always higher than the salinity at the harvest site, with the difference between the two sites ranging from 3.4 to 19.1 ppt (average, 12 ppt) during 2011 to 2014. Oysters relayed during June, July, and August in 2011 and 2012 showed consistently reduced V. parahaemolyticus levels after 14 days, whereas relaying was less successful and V. parahaemolyticus populations changed to include trh-positive strains during 2013. When effective, relay required at least 10 days to reduce V. parahaemolyticus levels. A sample of oysters collected in August 2012, which was temperature abused to increase initial V. parahaemolyticus levels, showed a 4.5-log decrease in V. parahaemolyticus levels after 14 days of relay. These results suggest that relaying oysters to reduce V. parahaemolyticus levels holds promise, but that both microbial community and environmental conditions at relay sites can affect relay success. Further investigation to discover key factors that affect V. parahaemolyticus levels in relayed oysters may aid in developing a consistent approach for reducing V. parahaemolyticus in oysters to eliminate the risk of illness for oyster consumers.