A comprehensive phylogeny helps clarify the evolutionary history of host breadth and lure response in the Australian Dacini fruit flies (Diptera: Tephritidae)

The tribe Dacini (Diptera: Tephritidae) contains over 930 recognised species and has been widely studied due to the economic importance of some taxa, such as the Oriental fruit fly Bactrocera dorsalis. Despite the attention this group has received, very few phylogenetic reconstructions have comprehensively sampled taxa from a single biogeographic region, thereby limiting our capacity to address more targeted evolutionary questions. To study the evolution of diet breadth and male lure response, two key traits fundamental to understanding dacine diversity and the biology of pest taxa, we analysed 273 individuals representing 144 described species from Australia (80% continental coverage), the Pacific, and select close relatives from South-east Asia to estimate a dated molecular phylogenetic reconstruction of the Dacini. We utilised seven loci with a combined total of 4,332 nucleotides, to estimate both Bayesian and Maximum Likelihood phylogenies of the tribe. Consistent with other molecular phylogenies of the tribe, there was a high level of disagreement between the placement of species in the phylogeny and their current subgeneric and species-complex level taxonomies. The Australian fauna exhibit high levels of endemism, with radiations of both exclusively Australian clades, and clades that originate elsewhere (e.g. the Bactrocera dorsalis species group). Bidirectional movement of species has occurred between Papua New Guinea and Australia, with evidence for multiple incursions over evolutionary time. The Bactrocera aglaiae species group emerged sister to all other Bactrocera species examined. Divergence time estimates were ∼ 30 my younger than previously reported for this group, with the tribe diverging from its most recent common ancestor ∼ 43 mya. Ancestral trait reconstruction and tests for trait phylogenetic signal revealed a strong signal for the evolution of male lure response across the tree, with cue-lure/raspberry ketone lure response the ancestral trait. Methyl eugenol response has arisen on multiple, independent occasions. The evolution of host breadth exhibited a weaker signal; yet, basal groups were more likely to be host specialists. Both the evolution of lure response and host fruit use provide predictive information for the outbreak management of understudied pest fruit flies for which direct inference of these features may be lacking. Our results, which parallel those of earlier research into the closely-related African Dacus spp., demonstrate how geographically focussed taxon coverage allows Dacini phylogenetics to more explicitly test evolutionary hypotheses, thereby progressing our understanding of the evolution of this highly diverse and recently-radiated group of flies.

Fad, Food, or Feed: Alternative Seafood and Its Contribution to Food Systems

Aquatic foods, or “seafood”, are an integral part of the global food system that contribute significantly to many dimensions of human wellbeing, including livelihoods and food and nutrition security. Fish, molluscs, crustaceans, algae and other aquatic foods are of particular importance in low- and middle-income countries as a source of employment, income, and nutrition for many poor and vulnerable people, including women. Global concern over the ability of fisheries and aquaculture to sustainably meet future seafood demand is driving improvements in technology and management. It has also inspired the emergence of plant-based and cell-based seafood, collectively termed “alternative seafood”. Growing investment, consumer demand, and participation by major food companies in the alternative seafood sector necessitate an evaluation of potential opportunities and challenges alternative seafood poses to food systems. This paper explores key economic, social, and environmental implications associated with production, distribution, and consumption of alternative seafood and its interactions with fisheries and aquaculture over the next decade, with specific emphasis on low- and middle-income countries. Available data on current supply and projected growth suggest that alternative seafood may account for almost eight percent of global seafood supplies destined for human consumption in 2030. Assuming current production techniques and expected technological development, the sector has potential for reduced environmental impacts relative to the existing fisheries and aquaculture sectors. However, its potential to impact livelihoods, food and nutrition security, and the environment remains largely a matter of conjecture due to the lack of robust data. Mechanistically, it is believed that growth of alternative seafood supplies will lessen demand for “conventional” seafood and/or meat, a scenario with implications for livelihoods, food and nutrition security, and the environment. Such changes are contingent on technological development, human and institutional behavior, market forces, and ecological linkages and as such, remain speculative. Nevertheless, as a novel sector, new food, and potential alternative to conventional seafood and/or meat, society has an opportunity to shape the growth of alternative seafood and its contribution to national and global development goals. This paper identifies knowledge gaps that require further research to inform inclusive, equitable, and sustainable development and governance of the emerging alternative seafood sector.

Compound climate risks threaten aquatic food system benefits

Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and cultures of billions of people worldwide, but climate-related hazards may compromise their ability to provide these benefits. Here, we estimate national-level aquatic food system climate risk using an integrative food systems approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes. We show that without mitigation, climate hazards pose high risks to nutritional, social, economic and environmental outcomes worldwide-especially for wild-capture fisheries in Africa, South and Southeast Asia, and Small Island Developing States. For countries projected to experience compound climate risks, reducing societal vulnerabilities can lower climate risk by margins similar to meeting Paris Agreement mitigation targets. System-level interventions addressing dimensions such as governance, gender equity and poverty are needed to enhance aquatic and terrestrial food system resilience and provide investments with large co-benefits towards meeting the Sustainable Development Goals.

Recurrent thrombosis in patients with antiphospholipid antibodies and an initial venous or arterial thromboembolic event: A systematic review and meta-analysis

BACKGROUND

Patients with antiphospholipid antibodies (aPL) and thromboembolism (TE) are at risk for recurrent TE. Few studies, however, distinguish patients based on the initial event.

OBJECTIVES

We performed a systematic review and meta-analysis to investigate patients with aPL and venous TE (VTE), provoked or unprovoked, and patients with arterial TE (ATE).

PATIENTS/METHODS

We conducted searches in PubMed, CINAHL, Cochrane, and EMBASE. Inclusion criteria were prospective trials or cohort studies investigating patients with aPL and ATE or VTE. Excluded studies did not provide estimated recurrence rates, did not specify whether the incident event was ATE or VTE, included patients with multiple events, or included <10 patients. Two-year summary proportions were estimated using a random effects model.

RESULTS

Ten studies described patients with VTE, 2 with ATE, and 5 with VTE or ATE. The 2-year proportion for recurrent TE in patients with VTE who were taking anticoagulant therapy was 0.054 (95% confidence interval [CI], 0.037-0.079); the 2-year proportion for patients not taking anticoagulant therapy was 0.178 (95% CI, 0.150-0.209). Most studies did not distinguish whether VTE were provoked or unprovoked. The 2-year proportion for recurrent TE in patients with ATE who were taking anticoagulant therapy was 0.220 (95% CI, 0.149-0.311); the 2-year proportion for patients taking antiplatelet therapy was 0.216 (95% CI, 0.177-0.261).

CONCLUSIONS

Patients with aPL and ATE may benefit from a different antithrombotic approach than patients with aPL and VTE. Prospective studies with well-defined cohorts with aPL and TE are necessary to determine optimal antithrombotic strategies.

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the F_ST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

Vulnerabilities in aquatic animal production

The role of aquatic animals in global food and nutrition security is increasingly recognised. The global demand for fish is increasing, leading to a need to significantly increase its supply. Securing future fish supplies through sustainable production is a challenge as major resources such as fresh water and land are becoming limited worldwide. Aquaculture and capture fisheries face various threats from both human-mediated and natural environmental change, including climate change. Aquaculture systems and practices are vulnerable to such changes. Moreover, aquatic animal diseases are currently considered one of the most important constraints to sustainable global fish production. The need to increase global production, combined with climate change, may increase losses due to diseases. This paper examines key vulnerabilities, their impacts and management to achieve increased and sustainable global fish production. The authors focus on the need to apply international standards, and to develop biosecurity and capacity in aquatic animal health to improve global fish health. Research needed to underpin the development of improved detection and control of fish diseases is also discussed.

A Dose Ranging Study to Evaluate Dermatan Sulphate in Preventing Deep Vein Thrombosis following Total Hip Arthroplasty

Dermatan sulphate catalyses thrombin inhibition by heparin cofactor II; it has a lower haemorrhagic to antithrombotic ratio than that of heparin in animal models. Consecutive patients aged forty years or more, electively undergoing total hip replacement under general anaesthesia, were randomly allocated to one of three dosage regimens of dermatan sulphate (MF701, Mediolanum Farmaceutici) given intramuscularly. These were 200 mg once daily (n = 50), 200 mg twice daily (n = 52) and 300 mg twice daily (n = 51), administered from twenty-four hours pre-operatively until the tenth postoperative day. The overall incidence of DVT assessed by bilateral venography was 53%, 51% and 34% respectively (Chi-square test for trend p = 0.06). The incidence of major proximal DVT was 10.6%, 8.5% and 2.1% respectively. Pulmonary embolism (PE) and bleeding were assessed in all 153 patients. There was one case of PE in each dose group. The incidence of bleeding episodes, volume of blood lost and blood transfusion requirements were low and showed no increase with increasing dose. The patients were followed up 4-8 weeks after discharge.

We conclude that the two lower doses were subtherapeutic in this population, however dermatan sulphate given 300 mg twice daily, proved to be efficacious with an incidence of proximal major DVT of 2.1% and a low incidence of bleeding complications. A trial of dermatan sulphate 300 mg twice daily compared to standard prophylactic agents is needed.

Research standardization tools: pregnancy measures in the PhenX Toolkit

Only through concerted and well-executed research endeavors can we gain the requisite knowledge to advance pregnancy care and have a positive impact on maternal and newborn health. Yet the heterogeneity inherent in individual studies limits our ability to compare and synthesize study results, thus impeding the capacity to draw meaningful conclusions that can be trusted to inform clinical care. The PhenX Toolkit (http://www.phenxtoolkit.org), supported since 2007 by the National Institutes of Health, is a web-based catalog of standardized protocols for measuring phenotypes and exposures relevant for clinical research. In 2016, a working group of pregnancy experts recommended 15 measures for the PhenX Toolkit that are highly relevant to pregnancy research. The working group followed the established PhenX consensus process to recommend protocols that are broadly validated, well established, nonproprietary, and have a relatively low burden for investigators and participants. The working group considered input from the pregnancy experts and the broader research community and included measures addressing the mode of conception, gestational age, fetal growth assessment, prenatal care, the mode of delivery, gestational diabetes, behavioral and mental health, and environmental exposure biomarkers. These pregnancy measures complement the existing measures for other established domains in the PhenX Toolkit, including reproductive health, anthropometrics, demographic characteristics, and alcohol, tobacco, and other substances. The preceding domains influence a woman's health during pregnancy. For each measure, the PhenX Toolkit includes data dictionaries and data collection worksheets that facilitate incorporation of the protocol into new or existing studies. The measures within the pregnancy domain offer a valuable resource to investigators and clinicians and are well poised to facilitate collaborative pregnancy research with the goal to improve patient care. To achieve this aim, investigators whose work includes the perinatal population are encouraged to utilize the PhenX Toolkit in the design and implementation of their studies, thus potentially reducing heterogeneity in data measures across studies. Such an effort will enhance the overall impact of individual studies, increasing the ability to draw more meaningful conclusions that can then be translated into clinical practice.

Sri Lanka Pilot Study to Examine Respiratory Health Effects and Personal PM2.5 Exposures from Cooking Indoors

A pilot study of indoor air pollution produced by biomass cookstoves was conducted in 53 homes in Sri Lanka to assess respiratory conditions associated with stove type ("Anagi" or "Traditional"), kitchen characteristics (e.g., presence of a chimney in the home, indoor cooking area), and concentrations of personal and indoor particulate matter less than 2.5 micrometers in diameter (PM2.5). Each primary cook reported respiratory conditions for herself (cough, phlegm, wheeze, or asthma) and for children (wheeze or asthma) living in her household. For cooks, the presence of at least one respiratory condition was significantly associated with 48-h log-transformed mean personal PM2.5 concentration (PR = 1.35; p < 0.001). The prevalence ratio (PR) was significantly elevated for cooks with one or more respiratory conditions if they cooked without a chimney (PR = 1.51, p = 0.025) and non-significantly elevated if they cooked in a separate but poorly ventilated building (PR = 1.51, p = 0.093). The PRs were significantly elevated for children with wheeze or asthma if a traditional stove was used (PR = 2.08, p = 0.014) or if the cooking area was not partitioned from the rest of the home (PR = 2.46, p = 0.012). For the 13 children for whom the cooking area was not partitioned from the rest of the home, having a respiratory condition was significantly associated with log-transformed indoor PM2.5 concentration (PR = 1.51; p = 0.014).

Overexpression of Fibrinogen-Like Protein 2 Promotes Tolerance in a Fully Mismatched Murine Model of Heart Transplantation

Fibrinogen-like protein 2 (FGL2) is an immunomodulatory protein that is expressed by regulatory T cells (Tregs). The objective of this study was to determine if recombinant FGL2 (rFGL2) treatment or constitutive FGL2 overexpression could promote transplant tolerance in mice. Although rFGL2 treatment prevented rejection of fully mismatched cardiac allografts, all grafts were rejected after stopping treatment. Next, we generated FGL2 transgenic mice (fgl2(Tg) ) that ubiquitously overexpressed FGL2. These mice developed normally and had no evidence of the autoimmune glomerulonephritis seen in fgl2(-/-) mice. Immune characterization showed fgl2(Tg) T cells were hypoproliferative to stimulation with alloantigens or anti-CD3 and anti-CD28 stimulation, and fgl2(Tg) Tregs had increased immunosuppressive activity compared with fgl2(+/+) Tregs. To determine if FGL2 overexpression can promote tolerance, we transplanted fully mismatched cardiac allografts into fgl2(Tg) recipients. Fifty percent of cardiac grafts were accepted indefinitely in fgl2(Tg) recipients without any immunosuppression. Tolerant fgl2(Tg) grafts had increased numbers and proportions of Tregs and tolerant fgl2(Tg) mice had reduced proliferation to donor but not third party antigens. These data show that tolerance in fgl2(Tg) recipients involves changes in Treg and T cell activity that contribute to a higher intragraft Treg-to-T cell ratio and acceptance of fully mismatched allografts.

Meeting the food and nutrition needs of the poor: the role of fish and the opportunities and challenges emerging from the rise of aquaculture

People who are food and nutrition insecure largely reside in Asia and Sub-Saharan Africa and for many, fish represents a rich source of protein, micronutrients and essential fatty acids. The contribution of fish to household food and nutrition security depends upon availability, access and cultural and personal preferences. Access is largely determined by location, seasonality and price but at the individual level it also depends upon a person's physiological and health status and how fish is prepared, cooked and shared among household members. The sustained and rapid expansion of aquaculture over the past 30 years has resulted in >40% of all fish now consumed being derived from farming. While aquaculture produce increasingly features in the diets of many Asians, it is much less apparent among those living in Sub-Saharan Africa. Here, per capita fish consumption has grown little and despite the apparently strong markets and adequate biophysical conditions, aquaculture has yet to develop. The contribution of aquaculture to food and nutrition security is not only just an issue of where aquaculture occurs but also of what is being produced and how and whether the produce is as accessible as that from capture fisheries. The range of fish species produced by an increasingly globalized aquaculture industry differs from that derived from capture fisheries. Farmed fishes are also different in terms of their nutrient content, a result of the species being grown and of rearing methods. Farmed fish price affects access by poor consumers while the size at which fish is harvested influences both access and use. This paper explores these issues with particular reference to Asia and Africa and the technical and policy innovations needed to ensure that fish farming is able to fulfil its potential to meet the global population's food and nutrition needs.

Physical activity and physical fitness: standardizing assessment with the PhenX Toolkit

The focus of the PhenX (Phenotypes and eXposures) Toolkit is to provide researchers whose expertise lies outside a particular area with key measures identified by experts for uniform use in large-scale genetic studies and other extensive epidemiologic efforts going forward. The current paper specifically addresses the PhenX Toolkit research domain of physical activity and physical fitness (PA/PF), which are often associated with health outcomes. A Working Group (WG) of content experts completed a 6-month consensus process in which they identified a set of 14 high-priority, low-burden, and scientifically supported measures. During this process, the WG considered self-reported and objective measures that included the latest technology (e.g., accelerometers, pedometers, and heart-rate monitors). They also sought the input of measurement experts and other members of the research community during their deliberations. A majority of the measures include protocols for children (or adolescents), adults, and older adults or are applicable to all ages. Measures from the PA/PF domain and 20 other domains are publicly available and found at the PhenX Toolkit website, www.phenxtoolkit.org. The use of common measures and protocols across large studies enhances the capacity to combine or compare data across studies, benefiting both PA/PF experts and non-experts. Use of these common measures by the research community should increase statistical power and enhance the ability to answer scientific questions that previously might have gone unanswered.

Using PhenX measures to identify opportunities for cross-study analysis

The PhenX Toolkit provides researchers with recommended, well-established, low-burden measures suitable for human subject research. The database of Genotypes and Phenotypes (dbGaP) is the data repository for a variety of studies funded by the National Institutes of Health, including genome-wide association studies. The dbGaP requires that investigators provide a data dictionary of study variables as part of the data submission process. Thus, dbGaP is a unique resource that can help investigators identify studies that share the same or similar variables. As a proof of concept, variables from 16 studies deposited in dbGaP were mapped to PhenX measures. Soon, investigators will be able to search dbGaP using PhenX variable identifiers and find comparable and related variables in these 16 studies. To enhance effective data exchange, PhenX measures, protocols, and variables were modeled in Logical Observation Identifiers Names and Codes (LOINC® ). PhenX domains and measures are also represented in the Cancer Data Standards Registry and Repository (caDSR). Associating PhenX measures with existing standards (LOINC® and caDSR) and mapping to dbGaP study variables extends the utility of these measures by revealing new opportunities for cross-study analysis.

A rapid and reliable PCR method for detecting clonal T cell populations

Aims-To establish a reverse transcription polymerase chain reaction (RT-PCR) for the detection of clonal T cell populations, and to evaluate the sensitivity and reliability of the technique.Methods-After reverse transcription of the target RNA with a consensus T cell receptor (TCR) beta constant (C) region primer, consensus C, variable (V), diversity (D) and joining (J) region primers were used to amplify across various portions of the TCRbeta V-D-J-C junction.Results-In normal T cells the polyclonal rearrangements produce a ladder of PCR bands representing the different sized junction fragments. The presence of a T cell clone leads to over-representation of one junction fragment, hence a disproportionately brighter band in the PCR ladder. In a series of 16 patients the RT-PCR detected nine of nine shown to have a clonal TCRbeta rearrangement by Southern blotting and for six of seven patients, it confirmed the presence of a clone indicated by histology or immunophenotyping with FACS analysis, but which was undetectable (five patients) or not investigated (two patients) by Southern blotting. Investigations mixing RNA from normal lymphocytes and the Jurkat TCR-Vbeta8 T cell line suggested that the method was more sensitive than Southern blotting.Conclusions-All PCR methods are faster and easier than Southern blotting, but RT-PCR also improves detection of clonal T cell populations, is reliable and produces results that are easy to interpret.

A novel prognostic model for malignant mesothelioma incorporating quantitative FDG-PET imaging with clinical parameters

PURPOSE

Existing prognostic systems for malignant pleural mesothelioma do not incorporate imaging information. We aimed to identify the contribution of quantitative fluorodeoxyglucose positron emission tomography (FDG-PET) analysis to other prognostic variables in this disease.

EXPERIMENTAL DESIGN

Patients with malignant pleural mesothelioma underwent helical thoracoabdominal computed tomography and FDG-PET scans at baseline. Patients were treated as clinically indicated and followed for survival. FDG-PET variables derived included total glycolytic volume, a composite of tumor volume and glycolytic activity.

RESULTS

Ninety-three patients were accrued from 2003 to 2006. Of 89 eligible assessable patients, 28 had undergone pleurodesis before enrolment. Seventeen patients remained alive at analysis; median survival is 15.4 months. On univariate analysis, significant prognostic factors were: total glycolytic volume on FDG-PET (P = 0.003), sarcomatoid histology (P < 0.0005), weight loss (P = 0.031), computed tomography stage (P = 0.015), and European Organization for Research and Treatment of Cancer good prognostic score (P = 0.049). In patients with epithelioid or biphasic histology, baseline total glycolytic volume remained predictive of survival in patients with (P = 0.01) or without (P = 0.018) previous pleurodesis. In multivariate analysis, no variable other than histology contributed to the model in patients with sarcomatoid histology; total glycolytic volume and weight loss contributed to the models in patients with nonsarcomatoid histology. computed tomography-assessed tumor-node-metastasis stage did not contribute to the model. A nomogram, which incorporates quantitative PET parameters and pleurodesis into prognostic information, is presented.

CONCLUSIONS

Sarcomatoid histology remains the strongest prognostic factor. In patients with non sarcomatoid disease, volumetric FDG-PET parameters are more predictive of survival than tumor-node-metastasis staging, suggesting that tumor volume and glycolytic activity may be more important determinants of prognosis in malignant pleural mesothelioma than anatomic extent of disease.

Wigner surmise for Hermitian and non-Hermitian chiral random matrices

We use the idea of a Wigner surmise to compute approximate distributions of the first eigenvalue in chiral random matrix theory, for both real and complex eigenvalues. Testing against known results for zero and maximal non-Hermiticity in the microscopic large- N limit, we find an excellent agreement valid for a small number of exact zero eigenvalues. Compact expressions are derived for real eigenvalues in the orthogonal and symplectic classes and at intermediate non-Hermiticity for the unitary and symplectic classes. Such individual Dirac eigenvalue distributions are a useful tool in lattice gauge theory, and we illustrate this by showing that our results can describe data from two-color quantum chromodynamics simulations with chemical potential in the symplectic class.

Managing obstruction of the central airways

Lung cancer is the most common cause of cancer death in Australia, Europe and the USA. Up to 20-30% of these cancers eventually affect the central airways and result in reduced quality of life, dyspnoea, haemoptysis, post-obstructive pneumonia and ultimately death. Non-malignant processes may also lead to central airway obstruction and can have similar symptoms. With the development of newer technologies, the last 20 years have seen the emergence of the field of interventional pulmonology to deal specifically with the diagnosis and management of thoracic malignancy, including obstruction of the central airways. This review discusses the pathology, pre-procedure work-up and management options for obstructing central airway lesions. Several treatment modalities exist for dealing with endobronchial pathology with local availability and expertise guiding choice of treatment. While the literature lacks large, multicentre, randomized studies defining the optimal management strategy for a given problem, there is growing evidence from numerous case studies of improved physiology, of quality of life and possibly of survival with modern interventional techniques.

Quantifying tracheobronchial tree dimensions: methods, limitations and emerging techniques

The ability to measure airway dimensions is important for clinicians, interventional bronchoscopists and researchers in order to accurately quantify structural abnormalities and track their changes over time or in response to treatment. Most quantitative airway measurements are based on X-ray computed tomography and, more recently, on multidetector computed tomography. Quantitative bronchoscopic techniques have also been developed, although these are less widely employed. Emerging techniques, including magnetic resonance imaging, endoscopic optical coherence tomography, endobronchial ultrasound and confocal endomicroscopy, provide new research tools with potential clinical applications. An understanding of issues related to the acquisition, processing and analysis of images, and how such issues impact on imaging the tracheobronchial tree, is essential in order to assess measurement accuracy and to make effective use of the newer methods. This article contributes to this understanding by providing a comprehensive review of current and emerging techniques for quantifying airway dimensions.

Simultaneous analysis of cell surface antigens and DNA content by flow cytometry

Cells obtained from the blood or bone marrow of patients with haematological malignancies can both be stained with fluorescent labelled monoclonal antibodies to determine an immunophenotype and permeabilized with 30% ethanol then stained with propidium iodide for simultaneous DNA analysis. In the technique described here, no evidence of selective depletion of the malignant cell population was demonstrated and decreases in the mean fluorescence intensity of the surface markers were insufficient to affect the sensitivity of flow cytometric analysis. The combined method is simple and robust enough to allow incorporation of DNA analysis into routine immunophenotyping of leukaemia and lymphoma cells.

A GIS-based method for household recruitment in a prospective pesticide exposure study

BACKGROUND

Recent advances in GIS technology and remote sensing have provided new opportunities to collect ecologic data on agricultural pesticide exposure. Many pesticide studies have used historical or records-based data on crops and their associated pesticide applications to estimate exposure by measuring residential proximity to agricultural fields. Very few of these studies collected environmental and biological samples from study participants. One of the reasons for this is the cost of identifying participants who reside near study fields and analyzing samples obtained from them. In this paper, we present a cost-effective, GIS-based method for crop field selection and household recruitment in a prospective pesticide exposure study in a remote location. For the most part, our multi-phased approach was carried out in a research facility, but involved two brief episodes of fieldwork for ground truthing purposes. This method was developed for a larger study designed to examine the validity of indirect pesticide exposure estimates by comparing measured exposures in household dust, water and urine with records-based estimates that use crop location, residential proximity and pesticide application data. The study focused on the pesticide atrazine, a broadleaf herbicide used in corn production and one of the most widely-used pesticides in the U.S.

RESULTS

We successfully used a combination of remotely-sensed data, GIS-based methods and fieldwork to select study fields and recruit participants in Illinois, a state with high corn production and heavy atrazine use. Our several-step process consisted of the identification of potential study fields and residential areas using aerial photography; verification of crop patterns and land use via site visits; development of a GIS-based algorithm to define recruitment areas around crop fields; acquisition of geocoded household-level data within each recruitment area from a commercial vendor; and confirmation of final participant household locations via ground truthing. The use of these procedures resulted in a sufficient sample of participants from 14 recruitment areas in seven Illinois counties.

CONCLUSION

One of the challenges in pesticide research is the identification and recruitment of study participants, which is time consuming and costly, especially when the study site is in a remote location. We have demonstrated how GIS-based processes can be used to recruit participants, increase efficiency and enhance accuracy. The method that we used ultimately made it possible to collect biological samples from a specific demographic group within strictly defined exposure areas, with little advance knowledge of the location or population.

Farm-level plans and husbandry measures for aquatic animal disease emergencies

Disease is one of the gravest threats to the sustainability of the aquaculture industry. A good understanding of biosecurity and disease causation is essential for developing and implementing farm-level plans and husbandry measures to respond to disease emergencies. Using epidemiological approaches, it is possible to identify pond- and farm-level risk factors for disease outbreaks and develop intervention strategies. Better management practices (BMPs) should be simple, science-based, cost-effective and appropriate to their context if farmers are to adopt and implement them. As part of a regional initiative by the Network of Aquaculture Centres in Asia-Pacific (NACA) to control aquatic animal diseases, effective extension approaches to promote the widespread adoption of BMPs have been developed in India, Indonesia, Vietnam and Thailand, and have proved their worth. A highly successful programme, which addresses rising concerns about the effect of disease on the sustainability of shrimp farming in India, is now in its seventh year. In this paper, the authors present a brief insight into the details of the programme, its outcomes and impact, the lessons learned and the way forward.

Two mouse retinal degenerations caused by missense mutations in the beta-subunit of rod cGMP phosphodiesterase gene

We report the chromosomal localization, mutant gene identification, ophthalmic appearance, histology, and functional analysis of two new hereditary mouse models of retinal degeneration not having the Pde6brd1("r", "rd", or "rodless") mutation. One strain harbors an autosomal recessive mutation that maps to mouse chromosome 5. Sequence analysis showed that the retinal degeneration is caused by a missense point mutation in exon 13 of the beta-subunit of the rod cGMP phosphodiesterase (beta-PDE) gene (Pde6b). The gene symbol for this strain was set as Pde6brd10, abbreviated rd10 hereafter. Mice homozygous for the rd10 mutation showed histological changes at postnatal day 16 (P16) of age and sclerotic retinal vessels at four weeks of age, consistent with retinal degeneration. Retinal sections were highly positive for TUNEL and activated caspase-3 immunoreactivity, specifically in the outer nuclear layer (ONL). ERGs were never normal, but rod and cone ERG a- and b-waves were easily measured at P18 and steadily declined over 90% by two months of age. Protein extracts from rd10 retinas were positive for beta-PDE immunoreactivity starting at about the same time as wild-type (P10), though signal averaged less than 40% of wild-type. Interestingly, rearing rd10 mice in total darkness delayed degeneration for at least a week, after which morphological and functional loss progressed irregularly. With the second strain, a complementation test with rd1 mice revealed that the retinal degeneration phenotype observed represents a possible new allele of Pde6b. Sequencing demonstrated a missense point mutation in exon 16 of the beta-subunit of rod phosphodiesterase gene, different from the point mutations in rd1 and rd10. The gene symbol for this strain was set as Pde6bnmf137, abbreviated nmf137 hereafter. Mice homozygous for this mutation showed retinal degeneration with a mottled retina and white retinal vessels at three weeks of age. The exon 13 missense mutation (rd10) is the first known occurrence of a second mutant allele spontaneously arising in the Pde6b gene in mice and may provide a model for studying the pathogenesis of autosomal recessive retinitis pigmentosa (arRP) in humans. It may also provide a better model for experimental pharmaceutical-based therapy for RP because of its later onset and milder retinal degeneration than rd1 and nmf137.

Communication and networking in a regional organisation

Access to accurate information and technical expertise is a pre-requisite for informed decision making. The Network of Aquaculture Centres in Asia-Pacific (NACA), an intergovernmental organization of 17 governments in Asia-Pacific, works on the principle of cooperation and collaboration with the intention of sharing regional resources amongst the stakeholders within the network: governments, institutions and individuals. Networking, communication and project implementation coordinated by NACA in collaboration with partner organizations and donor agencies has been instrumental in facilitating the flow of science and provision of technical assistance to relevant stakeholders in Member Countries. Development and adoption of the FAO/NACA's Asia regional technical guidelines (TG) for the responsible movement of live aquatic animals by 21 Asia-Pacific governments is a major outcome of networking and communication that had been facilitated by the NACA, from 1999 to 2001. Since then, the implementation of key elements of the TG has remained the focus of NACA's regional aquatic animal health programme. The present paper provides some examples of past and ongoing activities that highlight the role of networking and communication in a regional organization in strengthening aquatic animal health capacity and biosecurity in the Asia-Pacific region.

Control of disinfection and halogenated disinfection byproducts by the electrochemical process

The aim of this study was to investigate some aspects of the performance of electrochemical process as an alternative disinfection strategy, while minimising DBPs, for water purification. The study of electrochemical processes has shown free chlorine to be produced, but smaller amounts of stronger oxidants, such as ozone, hydrogen peroxide and OH radicals (*OH), were also generated. The formation of mixed oxidants increased with increasing electric conductivity, but was limited at conductivities greater than 0.6 mS/cm. Using several microorganisms, such as E. coli and MS2 bacteriophage, inactivation kinetic studies were performed. With the exception of free chlorine, the role of mixed oxidants, especially OH radicals, was investigated for enhancement of the inactivation rate. Additionally, the formation and reduction of DBPs was studied by monitoring the concentration of haloacetic acids (HAAs) during the process.

Existing Delays Following the Presentation of Ruptured Abdominal Aortic Aneurysm Allow Sufficient Time to Assess Patients for Endovascular Repair

OBJECTIVES

The greatest benefit of endovascular AAA repair (EVAR) may be in the management of rupture (RAAA). However, the detailed anatomical assessment required for EVAR has lead to concerns of surgical delay and death during cross-sectional imaging. In this study, we prospectively assessed patients with RAAA and correlated time of hospital arrival with time of surgery or death to ascertain whether these concerns are justified.

METHODS

All patients presenting with RAAA between October 2000 and December 2002 were included. The hospital arrival time, onset of surgery or time of death, were recorded, as were demographic and physiological parameters.

RESULTS

One hundred consecutive patients were studied, median age 75 years (range 54-94). Seventy-nine patients underwent attempted conventional surgical repair and 21 were palliated. The median delay from arrival to operation was 159 min (range 16-1450 min). Mortality in the surgical group was not affected by the length of delay (p = 1.0) or by CT scanning (p = 0.34). The median time from arrival to death in the non-surgical group was 435 min (15 min-6 days).

CONCLUSIONS

Most patients who present with ruptured AAA experience a significant delay prior to surgery. This study suggests it is safe to assess the majority of RAAA patients for EVAR.

Neuroprotective effect of subretinal implants in the RCS rat

PURPOSE

Retinal prosthetics have been designed to interface with the neural retina by electrically stimulating the remaining retinal circuits after photoreceptor degeneration. However, the electrical stimulation provided by the subretinal implant may also stimulate neurotrophic factors that provide neuroprotection to the retina. This study was undertaken to determine whether electrical stimulation from a subretinal photodiode-based implant has a neuroprotective effect on photoreceptors in the RCS rat, a model of photoreceptor degeneration.

METHODS

Eyes of RCS rats were implanted with an active or inactive device or underwent sham surgery before photoreceptor degeneration. Outer retinal function was assessed with electroretinogram (ERG) recordings weekly until 8 weeks after surgery, at which time retinal tissue was collected and processed for morphologic assessment, including photoreceptor cell counts and retinal layer thickness.

RESULTS

At 4 to 6 weeks after surgery, the ERG responses in the active-implant eyes were 30% to 70% greater in b-wave amplitude than the responses from eyes implanted with inactive devices, those undergoing sham surgery, or the nonsurgical control eyes. At 8 weeks after surgery the ERG responses from active-implant eyes were not significantly different from the control groups. However, the number of photoreceptors in eyes implanted with the active or inactive device was significantly greater in the regions over and around the implant versus sham-surgical and nonsurgical control eyes.

CONCLUSIONS

These results suggest that subretinal electrical stimulation provides temporary preservation of retinal function in the RCS rat. In addition, implantation of an active or inactive device into the subretinal space causes morphologic preservation of photoreceptors in the RCS rat until 8 weeks after surgery. Further studies are needed to determine whether the correlation of neuropreservation with subretinal implantation is due to electrical stimulation and/or a mechanical presence of the implant in the subretinal space.

Possible sources of neuroprotection following subretinal silicon chip implantation in RCS rats

Current retinal prosthetics are designed to stimulate existing neural circuits in diseased retinas to create a visual signal. However, implantation of retinal prosthetics may create a neurotrophic environment that also leads to improvements in visual function. Possible sources of increased neuroprotective effects on the retina may arise from electrical activity generated by the prosthetic, mechanical injury due to surgical implantation, and/or presence of a chronic foreign body. This study evaluates these three neuroprotective sources by implanting Royal College of Surgeons (RCS) rats, a model of retinitis pigmentosa, with a subretinal implant at an early stage of photoreceptor degeneration. Treatment groups included rats implanted with active and inactive devices, as well as sham-operated. These groups were compared to unoperated controls. Evaluation of retinal function throughout an 18 week post-implantation period demonstrated transient functional improvements in eyes implanted with an inactive device at 6, 12 and 14 weeks post-implantation. However, the number of photoreceptors located directly over or around the implant or sham incision was significantly increased in eyes implanted with an active or inactive device or sham-operated. These results indicate that in the RCS rat localized neuroprotection of photoreceptors from mechanical injury or a chronic foreign body may provide similar results to subretinal electrical stimulation at the current output evaluated here.

Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous

Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.

Predicting Outcome in Ruptured Abdominal Aortic Aneurysm: A Prospective Study of 100 Consecutive Cases

OBJECTIVES

Case selection for surgery in patients presenting with ruptured abdominal aortic aneurysms (RAAA) is often difficult. A previous retrospective review identified five pre-operative risk factors associated with mortality [J Vasc Surg 23 (1996) 123]. In this study we aimed to identify whether these criteria could be usefully applied prospectively in patients presenting with RAAA.

METHODS

All patients presenting with RAAA from October 2000 to December 2002 were included. The criteria were recorded with the time they were available and the time surgery commenced. The decision to operate was made on clinical grounds and no patient was refused surgery on the basis of these criteria.

RESULTS

One hundred consecutive patients were studied, median age 75 (range 54-94). The operative mortality was 32.9% (26/79 patients). Surgical mortality increased with the number of positive criteria and was 8% (2/24), 24% (7/29), 55% (11/20) and 100% (6/6) for scores, 0, 1, 2 and > or =3, respectively. Age and conscious level were available in every patient. However, an ECG, haemoglobin and creatinine results were only available in 94, 81, and 69%, respectively.

CONCLUSIONS

The scoring system accurately predicted operative mortality. The score was available in the majority of cases and may help the surgeon give informed consent to patients and relatives prior to surgical intervention.

Synthesis and characterization of nano-biomaterials with potential osteological applications

The manufacture of high-surface area, un-agglomerated nano-sized (1-100 nm) bioceramic particles are of interest for many applications including injectable/controlled setting bone cements, high strength porous/non-porous synthetic bone grafts, and the reinforcing phase in nano-composites that attempt to mimic the complex structure and superior mechanical properties of bone. In the present study, we report on the manufacture of nano-particle hydroxyapatite powders by several wet chemical methods, which incorporate a freeze-drying step. In particular, it was found that the emulsion-based syntheses yielded powders with high surface areas and small primary particle sizes. Freeze drying rather than oven drying of powders prepared by conventional wet chemical synthesis yielded a nano-sized powder with a comparatively higher surface area of 113 m(2)/g. All powders were calcined in air in a furnace at 900 degrees C to investigate the effects of synthesis method on phase purity and surface area. The materials were characterized by a range of analytical methods including Fourier-transform infrared spectroscopy employing the photo acoustic (PAS-FTIR) sampling technique, BET surface area analysis, X-ray powder diffraction (XRD), and the particles were examined using a transmission electron microscope (TEM).

C-reactive protein is elevated in symptomatic compared with asymptomatic patients with carotid artery disease

OBJECTIVES

to investigate the level of inflammatory markers between symptomatic and asymptomatic carotid stenosis patients.

DESIGN

cross-sectional study.

MATERIALS AND METHODS

a prospective study of 137 consecutive patients, admitted electively for carotid endarterectomy during 1997-2000, was conducted. 125 patients had cerebrovascular symptoms: either stroke (neurological deficit >24 h), Transient ischaemic attack (neurological deficit<24 h) or amaurosis fugax. Twelve patients were asymptomatic. A medical history and a fasting venous blood sample were taken from each patient around 6 weeks before surgery. The plasma concentrations of cholesterol and of inflammatory markers; (high sensitivity C-reactive protein (hs-CRP), sICAM-1, sVCAM-1, sE-selectin) were determined.

RESULTS

the concentration of hs-CRP in the symptomatic group (3.9 mg/L) was significantly higher than in the asymptomatic group (2.1 mg/L; p = 0.04). These concentrations were within normal range (<10 mg/L). sICAM-1, sVCAM-1, sE-selectin and total cholesterol concentrations were not different between the two groups.

CONCLUSION

plasma hs-CRP was elevated in symptomatic compared to asymptomatic patients with carotid artery disease. High sensitivity C-reactive protein has been shown to be of prognostic value in a number of cardiovascular conditions and this study suggests it may be of value to identify patient at high risk of developing neurological deficits.

A prospective, randomized, multicenter comparative study of clinafloxacin versus a ceftriaxone-based regimen in the treatment of hospitalized patients with community-acquired pneumonia

In an open-label, phase 3, randomized, multicenter study, clinafloxacin (200 mg/d) was compared to ceftriaxone (2 g/d; with or without erythromycin) in 527 patients with acute community-acquired bacterial pneumonia (CAP). Primary efficacy parameters were clinical cure rate and microbiologic eradication rates (by pathogen and by patient) determined 5-9 d post-therapy (test of cure; TOC). Clinical cure rates at TOC for the 2 treatment groups were equivalent in the intention-to-treat (clinafloxacin 79.3, ceftriaxone 78.6%), clinically evaluable (clinafloxacin 88.1, ceftriaxone 85.0%), modified intention-to-treat (clinafloxacin 82.6, ceftriaxone 86.9%) and microbiologically evaluable populations (clinafloxacin 86.2, ceftriaxone 86.2%). Microbiologic eradication rates were similar in the 2 treatment groups. Both drugs were tolerated. Treatment of hospitalized CAP patients with clinafloxacin is a reasonable choice, especially when a resistant pathogen is anticipated.

Serotonin, testosterone and alcohol in the etiology of domestic violence

In a previous study we administered the panicogenic agent sodium lactate to a select group of perpetrators of domestic violence and comparison groups. Results of that study showed that perpetrators exhibited exaggerated lactate-induced fear, panic and rage. In this current study, we compared the cerebral spinal fluid (CSF) concentrations of 5-hydroxyindoleacetic acid (5-HIAA) and testosterone obtained from perpetrators of domestic violence and a group of healthy comparison subjects. All subjects were assessed for DSM-III-R diagnoses. Perpetrators with alcohol dependence (DV-ALC) (n=13), perpetrators without alcohol dependence (DV-NALC) (n=10) and healthy comparison subjects (HCS) (n=20) were clinically assessed using the Spielberger Trait Anxiety, Brown-Goodwin Aggression Scale, Buss Durkee Hostility Inventory and Straus Conflict Tactics. Following an overnight fast and bed rest, subjects received a lumbar puncture to obtain CSF concentrations of 5-HIAA and testosterone. Perpetrators scored significantly higher on measures of aggression than HCS. DV-NALC had significantly lower concentrations of CSF 5-HIAA and higher Straus Conflict Tactics (CT) physical violence scores than DV-ALC and HCS. DV-ALC had significantly higher concentrations of CSF testosterone than DV-NALC. DV-ALC also had significantly higher Straus CT physical violence scores than HCS. DV-NALC and DV-ALC differed on 5-HIAA concentrations, testosterone concentrations, Straus CT physical violence scores and alcohol dependence. These results suggest that DV-NALC and DV-ALC groups could have different biological mechanisms mediating domestic violence.

Estimation from censored data with incomplete information

Phillips and Sweeting [J. R. Statist. Soc. B 58 (1996) 775-783.] considered estimation of the parameter of the exponential distribution with censored failure time data when there is incomplete knowledge of the censoring times. It was shown that, under particular models for the censoring mechanism and censoring errors, it will usually be safe to ignore such errors provided they are not expected to be too large. A flexible model is introduced which includes the extreme cases of no censoring errors and no information on the censoring values. The effect of alternative assumptions about knowledge of the censoring values on the estimation of failure rate is investigated.

Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials

Recent molecular analyses suggest that the position of bandicoots is the major difficulty in determining the root of the tree of extant marsupials. To resolve this, we analyse mitochondrial genome sequences of a bandicoot (Isoodon macrourus) and a brushtail possum (Trichosurus vulpecula) together with the previously available marsupial mitochondrial genomes, the Virginia opossum (Didelphis virginiana) and the wallaroo (Macropus robustus). Analyses of mitochondrial protein-coding and RNA genes strongly support the bandicoot as sister to the wallaroo and the brushtail possum. This result, combined with other recent molecular analyses, confirms the monophyly of Australidelphia (Australasian marsupials plus Dromiciops from South America). Further, RY coding was found to nullify AGCT coding nucleotide composition bias.

Targeted inactivation of sister of P-glycoprotein gene (spgp) in mice results in nonprogressive but persistent intrahepatic cholestasis

Mutations in the sister of P-glycoprotein (Spgp) or bile salt export pump (BSEP) are associated with Progressive Familial Intrahepatic Cholestasis (PFIC2). Spgp is predominantly expressed in the canalicular membranes of liver. Consistent with in vitro evidence demonstrating the involvement of Spgp in bile salt transport, PFIC2 patients secrete less than 1% of biliary bile salts compared with normal infants. The disease rapidly progresses to hepatic failure requiring liver transplantation before adolescence. In this study, we show that the knockout of spgp gene in mice results in intrahepatic cholestasis, but with significantly less severity than PFIC2 in humans. Some unexpected characteristics are observed. Notably, although the secretion of cholic acid in mutant mice is greatly reduced (6% of wild-type), total bile salt output in mutant mice is about 30% of wild-type. Also, secretion of an unexpectedly large amount of tetra-hydroxylated bile acids (not detected in wild-type) is observed. These results suggest that hydroxylation and an alternative canalicular transport mechanism for bile acids compensate for the absence of Spgp function and protect the mutant mice from severe cholestatic damage. In addition, the spgp(-/-) mice display a significant increase in the secretion of cholesterol and phospholipids into the bile. This latter observation in spgp(-/-) mice suggests that intrahepatic, rather than intracanalicular, bile salts are the major driving force for the biliary lipid secretion. The spgp(-/-) mice thus provide a unique model for gaining new insights into therapeutic intervention for intrahepatic cholestasis and understanding mechanisms associated with lipid homeostasis.