Application of Streptococcus uberis Multilocus Sequence Typing: Analysis of the Population Structure Detected among Environmental and Bovine Isolates from New Zealand and the United Kingdom

We recently developed a multilocus sequence typing (MLST) scheme to differentiate S. uberis isolates and facilitate an understanding of the population biology of this pathogen. The scheme was initially used to study a collection of 160 bovine milk isolates from the United Kingdom and showed that the majority of isolates were from one clonal complex (designated the ST-5 complex). Here we describe the MLST analysis of a collection of New Zealand isolates. These were obtained from diverse sources, including bovine milk, other bovine anatomical sites, and environmental sources. The complete allelic profiles of 253 isolates were determined. The collection was highly diverse and included 131 different sequence types (STs). The New Zealand and United Kingdom populations were distinct, since none of the 131 STs were represented within the previously studied collection of 160 United Kingdom S. uberis isolates. However, seven of the STs were members of the ST-5 clonal complex, the major complex within the United Kingdom collection. Two new clonal complexes were identified: ST-143 and ST-86. All three major complexes were isolated from milk, other bovine sites, and the environment. Carriage of the hasA gene, which is necessary for capsule formation, correlated with clonal complex and isolation from clinical cases of mastitis.     

Application of Streptococcus uberis multilocus sequence typing: analysis of the population structure detected among environmental and bovine isolates from New Zealand and the United Kingdom

We recently developed a multilocus sequence typing (MLST) scheme to differentiate S. uberis isolates and facilitate an understanding of the population biology of this pathogen. The scheme was initially used to study a collection of 160 bovine milk isolates from the United Kingdom and showed that the majority of isolates were from one clonal complex (designated the ST-5 complex). Here we describe the MLST analysis of a collection of New Zealand isolates. These were obtained from diverse sources, including bovine milk, other bovine anatomical sites, and environmental sources. The complete allelic profiles of 253 isolates were determined. The collection was highly diverse and included 131 different sequence types (STs). The New Zealand and United Kingdom populations were distinct, since none of the 131 STs were represented within the previously studied collection of 160 United Kingdom S. uberis isolates. However, seven of the STs were members of the ST-5 clonal complex, the major complex within the United Kingdom collection. Two new clonal complexes were identified: ST-143 and ST-86. All three major complexes were isolated from milk, other bovine sites, and the environment. Carriage of the hasA gene, which is necessary for capsule formation, correlated with clonal complex and isolation from clinical cases of mastitis.     

Of Clues and Signs: The Dead Body and Its Evidential Traces

ABSTRACT   Taking the conflict over the remains of Ned Kelly as a starting point, in this article I trace the various conceptions of the, body as evidence within the intertwined histories of anthropology, criminology, and medicine to explore how anthropological practice brings the dead into being through exhumation and analysis. I outline the popular rhetorical tropes within which evidentiary claims are situated, exploring how the agency of people after death is understood within the framework of present-day forensic anthropological practice and how this is underwritten by a particular heritage of anatomical analysis. [Keywords: archaeology, forensic anthropology, materiality, semiotics of the body]     

‘Habitat’ Suitability Index Mapping for Industrial Symbiosis Planning

By ‘working with the willing’, the National Industrial Symbiosis Programme (NISP) has successfully facilitated industrial symbiosis throughout the United Kingdom and, in the process, delivered significant economic and environmental benefits for both Programme members and the country as a whole. One of the keys to NISP's success is that, unlike failed attempts to plan and construct eco‐industrial systems from scratch, the Programme works largely with existing companies who have already settled in, developed, and successfully operate within a given locale. This article argues that existing and mature industrial systems provide the best prospects for identifying opportunities for, and ultimately facilitating, industrial symbiosis. Due to levels of diversification and operational fundamental niches that, in the fullness of time, develop within all industrial systems, industrially mature areas are deemed to be industrial symbiosis ‘conducive environments’. Building on the conservation biology concept of a habitat suitability index, the article presents a methodology for comparing a potential site for eco‐industrial development to a known baseline industrial ‘habitat’ already identified as being highly conducive to industrial symbiosis. The suitability index methodology is further developed and applied to a multi‐criteria evaluation geographic information system to produce a ‘habitat’ suitability map that allows practitioners to quickly identify potential industrial symbiosis hotspots (the methodology is illustrated for England). The article concludes by providing options for the development of symbiosis suitability indices and how they can be used to support the facilitation of industrial symbiosis and regional resource efficiency.     

Variation in two phases of post‐winter development of a butterfly

The temporal aspects of life cycle characteristics, such as diapause development, are under strong selection in seasonal environments. Fine‐tuning of the life cycle may be particularly important to match the phenology of potential mates and resources as well as for optimizing abiotic conditions at eclosion. Here, we experimentally study the spring phenology of the orange tip butterfly, Anthocharis cardamines, by analysing post‐winter pupal development in three populations along a latitudinal cline in each of Sweden and the United Kingdom. These countries differ substantially in their seasonal temperature profile. By repeatedly recording pupal weights, we established that post‐winter development has two separate phases, with a more rapid weight loss in the second phase than in the first, likely corresponding to a ramping up of the rate of development. Variation in the duration of the first phase contributed more strongly than the second phase to the differences in phenology between the localities and sexes. We found that insects from Sweden had a faster overall rate of development than those from the United Kingdom, which is consistent with countergradient variation, as Sweden is colder during the spring than the United Kingdom. Similar trends were not observed at the within‐country scale, however. A cogradient pattern was found within Sweden, with populations from the north developing more slowly, and there was no clear latitudinal trend within the United Kingdom. In all localities, males developed faster than females. Our results point to the importance of variation in the progression of post‐winter development for spring phenology.     

Forensic uncertainty,fragile remains,and DNA as a panacea: an ethnographic observation of the challenges in twenty-first-century Disaster Victim Identification

This is an account of ethnographic research examining the specialist scientific processes known as ‘Disaster Victim Identification’ (DVI) in three settings: Québec, the United States, and the United Kingdom. In cases of multiple deaths, a series of actions accompanied by a plethora of tools are often invoked, housed at a disaster scene, forensic laboratories, a family assistance centre, and a mortuary. In this article, I examine a process dedicated to connecting the biological remains of the deceased with a confirmed validation of personhood. I describe a situation where responders/scientists will attempt multiple testing and re-testing of human remains, often pushing boundaries of available science. I argue that the search for certainty in identification lies at the heart of the activation of DVI processes, particularly when it is connected to DNA testing. Observing intimate forensic settings and the bricolage of the forensic anthropologist's labour has allowed me to track the production of the science of identity. I then reflect on the wider implications of these observations for affected communities and the responding scientists. Finally, I argue that there is complexity and ambivalence surrounding the increased use of technologies when applied to identification of victims.     

Evaluating "payback" on biomedical research from papers cited in clinical guidelines: applied bibliometric study

ObjectivesTo develop a methodology for evaluating the impact of research on health care, and to characterise the papers cited on clinical guidelines.DesignThe bibliographic details of the papers cited in 15 clinical guidelines, developed in and for the United Kingdom, were collated and analysed with applied bibliometric techniques.ResultsThe median age of papers cited in clinical guidelines was eight years; most papers were published by authors living in either the United States (36%) or the United Kingdom (25%)—this is two and a half times more than expected as about 10% of all biomedical outputs are published in the United Kingdom; and clinical guidelines do not cite basic research papers.ConclusionAnalysis of the evidence base of clinical guidelines may be one way of tracking the flow of knowledge from the laboratory to the clinic. Moreover, such analysis provides a useful, clinically relevant method for evaluating research outcomes and different strategies in research and development.     

Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis

Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.     

Labs and slabs: Television crime drama and the quest for forensic realism

This essay examines how crime dramas produced during, and since, the 1990s became marked by the quest for ‘forensic realism’. In particular, the essay traces a landmark shift in the development of forensic realism in the form of the ground-breaking British police drama Prime Suspect in 1991. It is argued that this television series not only represents a turning point in television history, but that it also constitutes a key text in the broader cultural turn towards forensic fascination. Prime Suspect vividly revealed and displayed corpses, crime scenes and post-mortem photos in an unprecedented fashion for television. This essay shows how in the process it established new standards and expectations regarding the aesthetics and thematic content of the perceived ‘realism’ of the crime genre. Through an analysis of the reception and impact of Prime Suspect the essay also demonstrates how crime drama’s increasing fascination with forensic realism has driven debate over just what kinds of stories and images constitute acceptable or appropriate subject matter for popular entertainment, and for the medium of television itself.     

Is That Dog a Pit Bull? A Cross-Country Comparison of Perceptions of Shelter Workers Regarding Breed Identification

Bull breeds are commonly kept as companion animals, but the pit bull terrier is restricted by breed-specific legislation (BSL) in parts of the United States and throughout the United Kingdom. Shelter workers must decide which breed(s) a dog is. This decision may influence the dog's fate, particularly in places with BSL. In this study, shelter workers in the United States and United Kingdom were shown pictures of 20 dogs and were asked what breed each dog was, how they determined each dog's breed, whether each dog was a pit bull, and what they expected the fate of each dog to be. There was much variation in responses both between and within the United States and United Kingdom. UK participants frequently labeled dogs commonly considered by U.S. participants to be pit bulls as Staffordshire bull terriers. UK participants were more likely to say their shelters would euthanize dogs deemed to be pit bulls. Most participants noted using dogs' physical features to determine breed, and 41% affected by BSL indicated they would knowingly mislabel a dog of a restricted breed, presumably to increase the dog's adoption chances.     

The Zagreb Skull Collection—The unique identified collection of human skulls from fetuses to centenarians

Skull anatomy and development have been extensively studied due to their significance in evolutionary biology, forensic anthropology, and clinical medicine. Bone collections are an indispensable resource for conducting such anthropological and anatomical studies. However, worldwide there are only few skull collections containing specimens covering the entire fetal and postnatal period. Herein we describe the Zagreb Skull Collection, an identified collection comprising more than 1100 skulls and skull bone sets from the early fetal period to centenarians. The Zagreb Skull Collection consists of two main parts: the unique Collection of Skull Bones containing 386 sets of separated skull bones from the early fetal period to adulthood and the Collection of Skulls containing 742 skulls (age range 4–101 years). The collection was the core source for numerous anatomical studies on the development, postnatal changes, and anatomical variations of the skull. However, the Zagreb Skull Collection is still an underexploited resource for anthropological, forensic, and anatomical studies with translatability to contemporary clinical practice.     

The qualitative and time-dependent character of spatial relations in biomedical ontologies

MOTIVATION: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently. RESULTS: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ). AVAILABILITY: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.     

Establishing the robustness of short-tandem-repeat statistics for forensic applications.

Before the introduction of a four-locus multiplex short-tandem-repeat (STR) system into casework, an extensive series of tests were carried out to determine robust procedures for assessing the evidential value of a match between crime and suspect samples. Twelve databases were analyzed from the three main ethnic groups encountered in casework in the United Kingdom: Caucasians, Afro-Caribbeans, and Asians from the Indian subcontinent. Independence tests resulted in a number of significant results, and the impact that these might have on forensic casework was investigated. It is demonstrated that previously published methods provide a simple procedure for correcting allele frequencies--and that this leads to conservative casework estimates of evidential value.     

工业化国家的环境问题—中、英生态学会联合学术讨论会论文

中英两国有着完全不同的历史。在英国,工业发展始于18世纪,随着财富的积累,迅速席卷了英伦三岛。由于对因此而造成的环境破坏没有得到重视,污染物不可避免地沉积下来,当时流行的一句话是“哪有烟尘,哪就有金钱”。尽管在某种程度上也曾提出过早期的     

Object-oriented methods for habitat mapping at multiple scales – Case studies from Northern Germany and Wye Downs, UK

This paper presents an application of object-oriented techniques for habitat classification based on remotely sensed images and ancillary data. The study reports the results of habitat mapping at multiple scales using Earth Observation (EO) data at various spatial resolutions and multi temporal acquisition dates. We investigate the role of object texture and context in classification as well as the value of integrating knowledge from ancillary data sources. Habitat maps were produced at regional and local scales in two case studies; Schleswig-Holstein, Germany and Wye Downs, United Kingdom. At the regional scale, the main task was the development of a consistent object-oriented classification scheme that is transferable to satellite images for other years. This is demonstrated for a time series of Landsat TM/ETM+ scenes. At the local scale, investigations focus on the development of appropriate object-oriented rule networks for the detailed mapping of habitats, e.g. dry grasslands and wetlands using very high resolution satellite and airborne scanner images. The results are evaluated using statistical accuracy assessment and visual comparison with traditional field-based habitat maps. Whereas the application of traditional pixel-based classification result in a pixelised (salt and pepper) representation of land cover, the object-based classification technique result in solid habitat objects allowing easy integration into a vector-GIS for further analysis. The level of detail obtained at the local scale is comparable to that achieved by visual interpretation of aerial photographs or field-based mapping and also retains spatially explicit, fine scale information such as scrub encroachment or ecotone patterns within habitats.     

A Forensically Sound Adversary Model for Mobile Devices

In this paper, we propose an adversary model to facilitate forensic investigations of mobile devices (e.g. Android, iOS and Windows smartphones) that can be readily adapted to the latest mobile device technologies. This is essential given the ongoing and rapidly changing nature of mobile device technologies. An integral principle and significant constraint upon forensic practitioners is that of forensic soundness. Our adversary model specifically considers and integrates the constraints of forensic soundness on the adversary, in our case, a forensic practitioner. One construction of the adversary model is an evidence collection and analysis methodology for Android devices. Using the methodology with six popular cloud apps, we were successful in extracting various information of forensic interest in both the external and internal storage of the mobile device.     

Subdivision meshes for organizing spatial biomedical data

As biomedical images and volumes are being collected at an increasing speed, there is a growing demand for efficient means to organize spatial information for comparative analysis. In many scenarios, such as determining gene expression patterns by in situ hybridization, the images are collected from multiple subjects over a common anatomical region, such as the brain. A fundamental challenge in comparing spatial data from different images is how to account for the shape variations among subjects, which make direct image-to-image comparisons meaningless. In this paper, we describe subdivision meshes as a geometric means to efficiently organize 2D images and 3D volumes collected from different subjects for comparison. The key advantages of a subdivision mesh for this purpose are its light-weight geometric structure and its explicit modeling of anatomical boundaries, which enable efficient and accurate registration. The multi-resolution structure of a subdivision mesh also allows development of fast comparison algorithms among registered images and volumes.     

Modelling distributional trends to inform conservation strategies for an endangered species

Aim Species loss has increased significantly over the last 1000 years and is ultimately attributed to the direct and indirect consequences of increased human population growth across the planet. A growing number of species are becoming endangered and require human intervention to prevent their local extirpation or complete extinction. Management strategies aimed at mitigating a species loss can benefit greatly from empirical approaches that indicate the rate of decline of a species providing objective information on the need for immediate conservation actions, e.g. captive breeding; however, this is rarely employed. The current study used a novel method to examine the distributional trends of a model endangered species, the freshwater pearl mussel, Margaritifera margaritifera (L.). Location United Kingdom and Republic of Ireland. Methods Using species presence data within 10‐km grid squares since records began three‐parameter logistic regression curves were fitted to extrapolate an estimated date of regional extinction. Results This study has shown that freshwater pearl mussel distribution has contracted since known historical records and outlier populations were lost first. Within the United Kingdom and Republic of Ireland, distribution loss has been greatest in Scotland, Northern Ireland, Wales and England, respectively, with the Republic of Ireland containing the highest relative proportion of M. margaritifera distribution, in 1998. Main conclusions This study provides empirical evidence that this species could become extinct throughout countries within the United Kingdom within 170 years under the current trends and emphasizes that regionally specific management strategies need to be implemented to prevent extirpation of this species.     

Regression equations for the estimation of stature and body mass using a Greek documented skeletal collection

Body size is an important variable in bioarchaeological and forensic studies, making the accurate calculation of stature and body mass imperative. Given that anatomical and morphometric approaches offer accurate results but require a particularly good preservation of the skeletal material, whereas mathematical and mechanical methods are more easily applicable but they are largely population-specific, the present paper uses a ‘hybrid’ approach in order to generate regression equations for the prediction of stature and body mass in a modern Greek sample. Specifically, anatomical and morphometric methods were used to calculate the stature and body mass of the individuals and regression equations using the Ordinary Least Squares and Reduced Major Axis methods were generated with long bone lengths and femoral head breadth as predictors. The obtained equations exhibit low random and directional error and perform better than existing equations designed using different samples from the United States, Europe, and the Balkans. Therefore, these equations are more appropriate for modern Greek material.     

国外生物经济规模测算方法分析及对我国的启示

生物经济的概念自提出以来,美国、欧盟、英国、日本等都积极开展路线图规划和实施相关项目部署,以培育国内新的经济增长点,掌握未来国际竞争的主动权。近年来,生物科技领域创新与产业飞速发展,生物经济有望在国民经济中发挥更加凸显的作用和贡献,主导引领经济形态的新一次轮换。为了更好的掌握全球生物经济的发展现状和规模,对美国、欧盟和日本等几个具有代表性的国家/地区的生物经济测算方式开展了比较分析。在此基础上结合生物经济的定义,提出我国生物经济测算框架并得到初步测算结果,为我国生物经济发展决策提供科学的数据支撑。最后,对我国生物经济未来发展规模做出展望,同时也对我国生物经济测算框架的下一步改进进行了讨论。