Genome characterization of a new strain of peanut chlorotic streak virus causing chlorotic vein banding disease of groundnut (Arachis hypogaea L.) in India

The double-stranded DNA of the chlorotic vein banding isolate of peanut chlorotic streak caulimovirus (PC1SV-CVB), isolated from purified virus, resolved into circular and linear molecules similar to those of other caulimoviruses. A physical map of viral DNA was constructed, which showed the PCLSV-CVB DNA to be circular and composed of approximately 8.2 kbp. A number of restriction sites were found to be shared with a similar caulimovirus, PCLSV. Nevertheless, several differences between physical maps of the 2 viruses suggested that PCLSV-CVB should be considered as a distinct strain of PCLSV. Bam HI-cleaved PCLSV-CVB DNA was cloned into pUC 118 and was infectious when cleaved from the cloning vector and inoculated onto Vigna unguiculata [cowpeas]

Ultra-rapid, sensitive and specific digital diagnosis of HIV with a dual-channel SAW biosensor in a pilot clinical study

Despite widened access to HIV testing, around half of those infected worldwide are unaware of their HIV-positive status and linkage to care remains a major challenge. Current rapid HIV tests are typically analogue risking incorrect interpretation, no facile electronic data capture, poor linkage to care and data loss for public health. Smartphone-connected diagnostic devices have potential to dramatically improve access to testing and patient retention with electronic data capture and wireless connectivity. We report a pilot clinical study of surface acoustic wave biosensors based on low-cost components found in smartphones to diagnose HIV in 133 patient samples. We engineered a small, portable, laboratory prototype and dual-channel biochips, with in-situ reference control coating and miniaturised configuration, requiring only 6 µL plasma. The dual-channel biochips were functionalized by ink-jet printing with capture coatings to detect either anti-p24 or anti-gp41 antibodies, and a reference control. Biochips were tested with 31 plasma samples from patients with HIV, and 102 healthy volunteers. SH-SAW biosensors showed excellent sensitivity, specificity, low sample volumes and rapid time to result, and were benchmarked to commercial rapid HIV tests. Testing for individual biomarkers found sensitivities of 100% (anti-gp41) and 64.5% (anti-p24) (combined sensitivity of 100%) and 100% specificity, within 5 min. All positive results were recorded within 60 s of sample addition with an electronic readout. Next steps will focus on a smartphone-connected device prototype and user-friendly app interface for larger scale evaluation and field studies, towards our ultimate goal of a new generation of affordable, connected point-of-care HIV tests

Cancer mortality and morbidity among plutonium workers at the Sellafield plant of British Nuclear Fuels

The mortality of all 14 319 workers employed at the Sellafield plant of British Nuclear Fuels between 1947 and 1975 was studied up to the end of 1992, and cancer incidence was examined from 1971 to 1986, in relation to their exposures to plutonium and to external radiation. The cancer mortality rate was 5% lower than that of England and Wales and 3% less than that of Cumbria. The significant excesses of deaths from cancer of the pleura and thyroid found in an earlier study persist with further follow-up (14 observed, 4.0 expected for pleura; 6 observed, 2.2 expected for thyroid). All of the deaths from pleural cancer were among radiation workers. For neither site was there a significant association between the risk of the cancer and accumulated radiation dose. There were significant deficits of deaths from cancers of mouth and pharynx, liver and gall bladder, and larynx and leukaemia when compared with the national rates. Among all radiation workers, there was a significant positive association between accumulated external radiation dose and mortality from cancers of ill-defined and secondary sites (10-year lag, P = 0.04), leukaemia (no lag, P = 0.03; 2-year lag, P = 0.05), multiple myeloma (20-year lag, P = 0.02), all lymphatic and haematopoietic cancers (20-year lag, P = 0.03) and all causes of death combined (20-year lag, P = 0.008). Among plutonium workers, there were significant excesses of deaths from cancer of the breast (6 observed, 2.6 expected) and ill-defined and secondary cancers (29 observed, 20.1 expected). No significant positive trends were observed between the risk of deaths from cancers of any specific site, or all cancers combined, and cumulative plutonium and external radiation doses. For no cancer site was there a significant excess of cancer registrations compared with rates for England and Wales. Analysis of trends in cancer incidence showed significant increases in risk with cumulative plutonium plus external radiation doses for all lymphatic and haematopoietic neoplasms for 0-, 10- and 20-year lag periods. Taken as a whole, our findings do not suggest that workers at Sellafield who have been exposed to plutonium are at an overall significantly increased risk of cancer compared with other radiation workers. © 1999 Cancer Research Campaig

Emerging Infectious Disease leads to Rapid Population Decline of Common British Birds

Emerging infectious diseases are increasingly cited as threats to wildlife, livestock and humans alike. They can threaten geographically isolated or critically endangered wildlife populations; however, relatively few studies have clearly demonstrated the extent to which emerging diseases can impact populations of common wildlife species. Here, we report the impact of an emerging protozoal disease on British populations of greenfinch Carduelis chloris and chaffinch Fringilla coelebs, two of the most common birds in Britain. Morphological and molecular analyses showed this to be due to Trichomonas gallinae. Trichomonosis emerged as a novel fatal disease of finches in Britain in 2005 and rapidly became epidemic within greenfinch, and to a lesser extent chaffinch, populations in 2006. By 2007, breeding populations of greenfinches and chaffinches in the geographic region of highest disease incidence had decreased by 35% and 21% respectively, representing mortality in excess of half a million birds. In contrast, declines were less pronounced or absent in these species in regions where the disease was found in intermediate or low incidence. Also, populations of dunnock Prunella modularis, which similarly feeds in gardens, but in which T. gallinae was rarely recorded, did not decline. This is the first trichomonosis epidemic reported in the scientific literature to negatively impact populations of free-ranging non-columbiform species, and such levels of mortality and decline due to an emerging infectious disease are unprecedented in British wild bird populations. This disease emergence event demonstrates the potential for a protozoan parasite to jump avian host taxonomic groups with dramatic effect over a short time period

Is it harder to know or to reason? Analyzing two-tier science assessment items using the Rasch measurement model

Two-tier multiple-choice (TTMC) items are used to assess students’ knowledge of a scientific concept for tier 1 and their reasoning about this concept for tier 2. But are the knowledge and reasoning involved in these tiers really distinguishable? Are the tiers equally challenging for students? The answers to these questions influence how we use and interpret TTMC instruments. We apply the Rasch measurement model on TTMC items to see if the items are distinguishable according to different traits (represented by the tier), or according to different content sub-topics within the instrument, or to both content and tier. Two TTMC data sets are analyzed: data from Singapore and Korea on the Light Propagation Diagnostic Instrument (LPDI), data from the United States on the Classroom Test of Scientific Reasoning (CTSR). Findings for LPDI show that tier-2 reasoning items are more difficult than tier-1 knowledge items, across content sub-topics. Findings for CTSR do not show a consistent pattern by tier or by content sub-topic. We conclude that TTMC items cannot be assumed to have a consistent pattern of difficulty by tier—and that assessment developers and users need to consider how the tiers operate when administering TTMC items and interpreting results. Researchers must check the tiers’ difficulties empirically during validation and use. Though findings from data in Asian contexts were more consistent, further study is needed to rule out differences between the LPDI and CTSR instruments

Dental management considerations for the patient with an acquired coagulopathy. Part 1: Coagulopathies from systemic disease

Current teaching suggests that many patients are at risk for prolonged bleeding during and following invasive dental procedures, due to an acquired coagulopathy from systemic disease and/or from medications. However, treatment standards for these patients often are the result of long-standing dogma with little or no scientific basis. The medical history is critical for the identification of patients potentially at risk for prolonged bleeding from dental treatment. Some time-honoured laboratory tests have little or no use in community dental practice. Loss of functioning hepatic, renal, or bone marrow tissue predisposes to acquired coagulopathies through different mechanisms, but the relationship to oral haemostasis is poorly understood. Given the lack of established, science-based standards, proper dental management requires an understanding of certain principles of pathophysiology for these medical conditions and a few standard laboratory tests. Making changes in anticoagulant drug regimens are often unwarranted and/or expensive, and can put patients at far greater risk for morbidity and mortality than the unlikely outcome of postoperative bleeding. It should be recognised that prolonged bleeding is a rare event following invasive dental procedures, and therefore the vast majority of patients with suspected acquired coagulopathies are best managed in the community practice setting

Testing foundations of quantum mechanics with photons

The foundational ideas of quantum mechanics continue to give rise to counterintuitive theories and physical effects that are in conflict with a classical description of Nature. Experiments with light at the single photon level have historically been at the forefront of tests of fundamental quantum theory and new developments in photonics engineering continue to enable new experiments. Here we review recent photonic experiments to test two foundational themes in quantum mechanics: wave-particle duality, central to recent complementarity and delayed-choice experiments; and Bell nonlocality where recent theoretical and technological advances have allowed all controversial loopholes to be separately addressed in different photonics experiments.Comment: 10 pages, 5 figures, published as a Nature Physics Insight review articl

Age, extent and carbon storage of the central Congo Basin peatland complex

Peatlands are carbon-rich ecosystems that cover just three per cent of Earth's land surface, but store one-third of soil carbon. Peat soils are formed by the build-up of partially decomposed organic matter under waterlogged anoxic conditions. Most peat is found in cool climatic regions where unimpeded decomposition is slower, but deposits are also found under some tropical swamp forests. Here we present field measurements from one of the world's most extensive regions of swamp forest, the Cuvette Centrale depression in the central Congo Basin. We find extensive peat deposits beneath the swamp forest vegetation (peat defined as material with an organic matter content of at least 65 per cent to a depth of at least 0.3 metres). Radiocarbon dates indicate that peat began accumulating from about 10,600 years ago, coincident with the onset of more humid conditions in central Africa at the beginning of the Holocene. The peatlands occupy large interfluvial basins, and seem to be largely rain-fed and ombrotrophic-like (of low nutrient status) systems. Although the peat layer is relatively shallow (with a maximum depth of 5.9 metres and a median depth of 2.0 metres), by combining in situ and remotely sensed data, we estimate the area of peat to be approximately 145,500 square kilometres (95 per cent confidence interval of 131,900-156,400 square kilometres), making the Cuvette Centrale the most extensive peatland complex in the tropics. This area is more than five times the maximum possible area reported for the Congo Basin in a recent synthesis of pantropical peat extent. We estimate that the peatlands store approximately 30.6 petagrams (30.6 × 10(15) grams) of carbon belowground (95 per cent confidence interval of 6.3-46.8 petagrams of carbon)-a quantity that is similar to the above-ground carbon stocks of the tropical forests of the entire Congo Basin. Our result for the Cuvette Centrale increases the best estimate of global tropical peatland carbon stocks by 36 per cent, to 104.7 petagrams of carbon (minimum estimate of 69.6 petagrams of carbon; maximum estimate of 129.8 petagrams of carbon). This stored carbon is vulnerable to land-use change and any future reduction in precipitation