Approaching Visual Search in Photo-Realistic Scenes

Visual search is extended from the domain of polygonal figures presented on a uniform background to scenes in which search is for a photo-realistic object in a dense, naturalistic background. Scene generation for these displays relies on a powerful solid modeling program to define the three dimensional forms, surface properties, relative positions, and illumination of the objects and a rendering program to produce an image. Search in the presented experiments is for a rock with specific properties among other, similar rocks, although the method described can be generalized to other situations. Using this technique we explore the effects of illumination and shadows in aiding search for a rock in front of and closer to the viewer than other rocks in the scene. For these scenes, shadows of two different contrast levels can significantly deet·ease reaction times for displays in which target rocks are similar to distractor rocks. However, when the target rock is itself easily distinguishable from dis tractors on the basis of form, the presence or absence of shadows has no discernible effect. To relate our findings to those for earlier polygonal displays, we simplified the non-shadow displays so that only boundary information remained. For these simpler displays, search slopes (the reaction time as a function of the number of distractors) were significantly faster, indicating that the more complex photo-realistic objects require more time to process for visual search. In contrast with several previous experiments involving polygonal figures, we found no evidence for an effect of illumination direction on search times

SoK: Cryptographically Protected Database Search

Protected database search systems cryptographically isolate the roles of reading from, writing to, and administering the database. This separation limits unnecessary administrator access and protects data in the case of system breaches. Since protected search was introduced in 2000, the area has grown rapidly; systems are offered by academia, start-ups, and established companies. However, there is no best protected search system or set of techniques. Design of such systems is a balancing act between security, functionality, performance, and usability. This challenge is made more difficult by ongoing database specialization, as some users will want the functionality of SQL, NoSQL, or NewSQL databases. This database evolution will continue, and the protected search community should be able to quickly provide functionality consistent with newly invented databases. At the same time, the community must accurately and clearly characterize the tradeoffs between different approaches. To address these challenges, we provide the following contributions: 1) An identification of the important primitive operations across database paradigms. We find there are a small number of base operations that can be used and combined to support a large number of database paradigms. 2) An evaluation of the current state of protected search systems in implementing these base operations. This evaluation describes the main approaches and tradeoffs for each base operation. Furthermore, it puts protected search in the context of unprotected search, identifying key gaps in functionality. 3) An analysis of attacks against protected search for different base queries. 4) A roadmap and tools for transforming a protected search system into a protected database, including an open-source performance evaluation platform and initial user opinions of protected search.Comment: 20 pages, to appear to IEEE Security and Privac

Epidemiological evidence that garden birds are a source of human salmonellosis in England and Wales

The importance of wild bird populations as a reservoir of zoonotic pathogens is well established. Salmonellosis is a frequently diagnosed infectious cause of mortality of garden birds in England and Wales, predominantly caused by Salmonella enterica subspecies enterica serovar Typhimurium definitive phage types 40, 56(v) and 160. In Britain, these phage types are considered highly host-adapted with a high degree of genetic similarity amongst isolates, and in some instances are clonal. Pulsed field gel electrophoresis, however, demonstrated minimal variation amongst matched DT40 and DT56(v) isolates derived from passerine and human incidents of salmonellosis across England in 2000-2007. Also, during the period 1993-2012, similar temporal and spatial trends of infection with these S. Typhimurium phage types occurred in both the British garden bird and human populations; 1.6% of all S. Typhimurium (0.2% of all Salmonella) isolates from humans in England and Wales over the period 2000-2010. These findings support the hypothesis that garden birds act as the primary reservoir of infection for these zoonotic bacteria. Most passerine salmonellosis outbreaks identified occurred at and around feeding stations, which are likely sites of public exposure to sick or dead garden birds and their faeces. We, therefore, advise the public to practise routine personal hygiene measures when feeding wild birds and especially when handling sick wild birds

Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus).

(c) 2009 Teacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower F(ST)) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year

Spatio-temporal dynamics and aetiology of proliferative leg skin lesions in wild British finches

Proliferative leg skin lesions have been described in wild finches in Europe although there have been no large-scale studies of their aetiology or epizootiology to date. Firstly, disease surveillance, utilising public reporting of observations of live wild finches was conducted in Great Britain (GB) and showed proliferative leg skin lesions in chaffinches (Fringilla coelebs) to be widespread. Seasonal variation was observed, with a peak during the winter months. Secondly, pathological investigations were performed on a sample of 39 chaffinches, four bullfinches (Pyrrhula pyrrhula), one greenfinch (Chloris chloris) and one goldfinch (Carduelis carduelis) with proliferative leg skin lesions and detected Cnemidocoptes sp. mites in 91% (41/45) of affected finches and from all species examined. Fringilla coelebs papillomavirus (FcPV1) PCR was positive in 74% (23/31) of birds tested: a 394 base pair sequence was derived from 20 of these birds, from all examined species, with 100% identity to reference genomes. Both mites and FcPV1 DNA were detected in 71% (20/28) of birds tested for both pathogens. Histopathological examination of lesions did not discriminate the relative importance of mite or FcPV1 infection as their cause. Development of techniques to localise FcPV1 within lesions is required to elucidate the pathological significance of FcPV1 DNA detection.We thank the members of the public and BTO Garden BirdWatch participants who reported garden bird morbidity and mortality incidents and our colleagues, Katie Beckmann, Shaheed Macgregor, Ricardo Castro Cesar de Sa, Lydia Franklinos and Tim Hopkins from the Zoological Society of London; Kirsi Peck from the Royal Society for the Protection of Birds; BTO staff members in the Garden BirdWatch team; the staff at Abbey Veterinary Services and the Animal & Plant Health Agency (Daniel Hicks, Richard Irvine, Alejandro Núñez and Scott Reid) for their assistance with this investigation. This work was financially supported by the following organisations; Birdcare Standards Association, British Trust for Ornithology, British Veterinary Association Animal Welfare Foundation, CJ Wildbird Foods, Cranswick Pet Products, UK Department for the Environment Food & Rural Affairs and Welsh Government through the Animal & Plant Health Agency’s Diseases of Wildlife Scheme Scanning Surveillance Programme (Project ED1600), Esmée Fairbairn Foundation, Gardman Ltd, Institute of Zoology, Royal Society for the Protection of Birds and the Universities Federation for Animal Welfare. RAJW was supported by the Moncloa of Excellence PICATA programme and Crafoord Foundation Sweden (grant number 20160971). Molecular and sequencing costs were funded by the Spanish Ministry of Science and Innovation, (Ref: CGL2013-41642-P/BOS)

Bovine Spongiform Encephalopathy Infectivity in Greater Kudu (Tragelaphus strepsiceros)

Of all the species exposed naturally to the bovine spongiform encephalopathy (BSE) agent, the greater kudu (Tragelaphus strepsiceros), a nondomesticated bovine from Africa, appears to be the most susceptible to the disease. We present the results of mouse bioassay studies to show that, contrary to findings in cattle with BSE in which the tissue distribution of infectivity is the most limited recorded for any of the transmissible spongiform encephalopathies (TSE), infectivity in greater kudu with BSE is distributed in as wide a range of tissues as occurs in any TSE. BSE agent was also detected in skin, conjunctiva, and salivary gland, tissues in which infectivity has not previously been reported in any naturally occurring TSE. The distribution of infectivity in greater kudu with BSE suggests possible routes for transmission of the disease and highlights the need for further research into the distribution of TSE infectious agents in other host species

B cell priming for extrafollicular antibody responses requires Bcl-6 expression by T cells

Bcl-6 expression in CD4+ T cells is required to generate extrafollicular antibody responses

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

Peer reviewedPublisher PD

ABCB1 (MDR1) polymorphisms and ovarian cancer progression and survival: A comprehensive analysis from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas

<b>Objective</b> <i>ABCB1</i> encodes the multi-drug efflux pump P-glycoprotein (P-gp) and has been implicated in multi-drug resistance. We comprehensively evaluated this gene and flanking regions for an association with clinical outcome in epithelial ovarian cancer (EOC).<p></p> <b>Methods</b> The best candidates from fine-mapping analysis of 21 <i>ABCB1</i> SNPs tagging C1236T (rs1128503), G2677T/A (rs2032582), and C3435T (rs1045642) were analysed in 4616 European invasive EOC patients from thirteen Ovarian Cancer Association Consortium (OCAC) studies and The Cancer Genome Atlas (TCGA). Additionally we analysed 1,562 imputed SNPs around ABCB1 in patients receiving cytoreductive surgery and either ‘standard’ first-line paclitaxel–carboplatin chemotherapy (n = 1158) or any first-line chemotherapy regimen (n = 2867). We also evaluated ABCB1 expression in primary tumours from 143 EOC patients.<p></p> <b>Result</b> Fine-mapping revealed that rs1128503, rs2032582, and rs1045642 were the best candidates in optimally debulked patients. However, we observed no significant association between any SNP and either progression-free survival or overall survival in analysis of data from 14 studies. There was a marginal association between rs1128503 and overall survival in patients with nil residual disease (HR 0.88, 95% CI 0.77–1.01; p = 0.07). In contrast, <i>ABCB1</i> expression in the primary tumour may confer worse prognosis in patients with sub-optimally debulked tumours.<p></p> <b>Conclusion</b> Our study represents the largest analysis of <i>ABCB1</i> SNPs and EOC progression and survival to date, but has not identified additional signals, or validated reported associations with progression-free survival for rs1128503, rs2032582, and rs1045642. However, we cannot rule out the possibility of a subtle effect of rs1128503, or other SNPs linked to it, on overall survival.<p></p&gt