Highly accurate model for prediction of lung nodule malignancy with CT scans

Computed tomography (CT) examinations are commonly used to predict lung nodule malignancy in patients, which are shown to improve noninvasive early diagnosis of lung cancer. It remains challenging for computational approaches to achieve performance comparable to experienced radiologists. Here we present NoduleX, a systematic approach to predict lung nodule malignancy from CT data, based on deep learning convolutional neural networks (CNN). For training and validation, we analyze >1000 lung nodules in images from the LIDC/IDRI cohort. All nodules were identified and classified by four experienced thoracic radiologists who participated in the LIDC project. NoduleX achieves high accuracy for nodule malignancy classification, with an AUC of ~0.99. This is commensurate with the analysis of the dataset by experienced radiologists. Our approach, NoduleX, provides an effective framework for highly accurate nodule malignancy prediction with the model trained on a large patient population. Our results are replicable with software available at http://bioinformatics.astate.edu/NoduleX

Incubation Energetics of the Laysan Albatross

The energy expenditure of incubating and foraging Laysan Albatross (Diomedea immutabilis, mean body weight 3.07 kg) was estimated by means of the doubly-la- belled water technique. During incubation, the energy expenditure was similar to that of resting birds that were not incubating an egg. The energy expenditure of foraging albatross (2072 kJ/day) was 2.6 times that of resting birds. It was concluded that the energy expenditure of the tropical Laysan Albatross was not less than that of species foraging over cold, high-latitude oceans. An energy budget compiled for an incubating pair of albatross revealed that the energy expenditure of the female was greater than that of the male bird, during the incubation perio

Assessing Coral Reef Fish Population and Community Changes in Response to Marine Reserves in the Dry Tortugas, Florida, USA

The efficacy of no-take marine reserves (NTMRs) to enhance and sustain regional coral reef fisheries was assessed in Dry Tortugas, Florida, through 9 annual fishery-independent research surveys spanning 2 years before and 10 years after NTMR implementation. A probabilistic sampling design produced precise estimates of population metrics of more than 250 exploited and non-target reef fishes. During the survey period more than 8100 research dives utilizing SCUBA Nitrox were optimally allocated using stratified random sampling. The survey domain covered 326 km2, comprised of eight reef habitats in four management areas that offered different levels of resource protection: the Tortugas North Ecological Reserve (a NTMR), Dry Tortugas National Park (recreational angling only), Dry Tortugas National Park Research Natural Area (a NTMR), and southern Tortugas Bank (open to all types of fishing). Surveys detected significant changes in population occupancy, density, and abundance within management zones for a suite of exploited and non-target species. Increases in size, adult abundance, and occupancy rates were detected for many principal exploited species in protected areas, which harbored a disproportionately greater number of adult spawning fishes. In contrast, density and occupancy rates for aquaria and non-target reef fishes fluctuated above and below baseline levels in each management zone. Observed decreases in density of exploited species below baseline levels only occurred at the Tortugas Bank area open to all fishing. Our findings indicate that these NTMRs, in conjunction with traditional fishery management control strategies, are helping to build sustainable fisheries while protecting the fundamental ecological dynamics of the Florida Keys coral-reef ecosystem

Schmallenberg virus pathogenesis, tropism and interaction with the innate immune system of the host

Schmallenberg virus (SBV) is an emerging orthobunyavirus of ruminants associated with outbreaks of congenital malformations in aborted and stillborn animals. Since its discovery in November 2011, SBV has spread very rapidly to many European countries. Here, we developed molecular and serological tools, and an experimental in vivo model as a platform to study SBV pathogenesis, tropism and virus-host cell interactions. Using a synthetic biology approach, we developed a reverse genetics system for the rapid rescue and genetic manipulation of SBV. We showed that SBV has a wide tropism in cell culture and “synthetic” SBV replicates in vitro as efficiently as wild type virus. We developed an experimental mouse model to study SBV infection and showed that this virus replicates abundantly in neurons where it causes cerebral malacia and vacuolation of the cerebral cortex. These virus-induced acute lesions are useful in understanding the progression from vacuolation to porencephaly and extensive tissue destruction, often observed in aborted lambs and calves in naturally occurring Schmallenberg cases. Indeed, we detected high levels of SBV antigens in the neurons of the gray matter of brain and spinal cord of naturally affected lambs and calves, suggesting that muscular hypoplasia observed in SBV-infected lambs is mostly secondary to central nervous system damage. Finally, we investigated the molecular determinants of SBV virulence. Interestingly, we found a biological SBV clone that after passage in cell culture displays increased virulence in mice. We also found that a SBV deletion mutant of the non-structural NSs protein (SBVΔNSs) is less virulent in mice than wild type SBV. Attenuation of SBV virulence depends on the inability of SBVΔNSs to block IFN synthesis in virus infected cells. In conclusion, this work provides a useful experimental framework to study the biology and pathogenesis of SBV

Gas retention in irradiated beryllium

Helium (an inert gas) with low solubility in beryllium is trapped in irradiated beryllium at low temperatures ( 1 MeV). In these samples the calculated helium generated was {approximately} 14,000 appm. They are described in terms of swelling, annealing, microstructure, and helium bubble behavior (size, density and mobility). A second sample was irradiated to {approximately}5 {times} 10{sup 22} n/cm{sup 2} (E > 1 MeV). In that one the calculated helium and tritium generated were {approximately}24,000 appm He and {approximately}3720 appm, and tritium content was examined in a dissolution experiment. Most of the tritium was released as gas to the glovebox indicating the generated tritium was retained in the helium bubbles. In a third set of experiments a specimen was examined by annealing at a succession of temperatures to more than 600{degree}C for tritium release. In the temperature range of 300--500{degree}C little release (0.01--0.4%) occurred, but there was a massive release at just over 600{degree}C. Theories of swelling appear to adequately describe bubble behavior with breakaway release occurring at high helium contents and at large bubble diameters. 8 refs., 6 figs

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Troubling identities: teacher education students` constructions of class and ethnicity

Working with diverse student populations productively depends on teachers and teacher educators recognizing and valuing difference. Too often, in teacher education programs, when markers of identity such as gender, ethnicity, \u27race\u27, or social class are examined, the focus is on developing student teachers\u27 understandings of how these discourses shape learner identities and rarely on how these also shape teachers\u27 identities. This article reports on a research project that explored how student teachers understand ethnicity and socio-economic status. In a preliminary stage of the research, we asked eight Year 3 teacher education students who had attended mainly Anglo-Australian, middle class schools as students and as student teachers, to explore their own ethnic and classed identities. The complexities of identity are foregrounded in both the assumptions we made in selecting particular students for the project and in the ways they constructed their own identities around ethnicity and social class. In this article we draw on these findings to interrogate how categories of identity are fluid, shifting and ongoing processes of negotiation, troubling and complex. We also consider the implications for teacher education.<br /

Studies of tritiated co-deposited Layers in TFTR

Plasma facing components in TFTR contain an important record of plasma wall interactions in reactor grade DT plasmas. Tiles, flakes, wall coupons, a stainless steel shutter and dust samples have been retrieved from the TFTR vessel for analysis. Selected samples have been baked to release tritium and assay the tritium content. The in-vessel tritium inventory is estimated to be 0.56 g and is consistent with the in-vessel tritium inventory derived from the difference between tritium fueling and tritium exhaust. The distribution of tritium on the limiter and vessel wall showed complex patterns of co-deposition. Relatively high concentrations of tritium were found at the top and bottom of the bumper limiter, as predicted by earlier BBQ modeling