Imagined Homelands

A ground-breaking study of nineteenth-century British colonial poetry.Imagined Homelands chronicles the emerging cultures of nineteenth-century British settler colonialism, focusing on poetry as a genre especially equipped to reflect colonial experience. Jason Rudy argues that the poetry of Victorian-era Australia, New Zealand, South Africa, and Canada—often disparaged as derivative and uncouth—should instead be seen as vitally engaged in the social and political work of settlement. The book illuminates cultural pressures that accompanied the unprecedented growth of British emigration across the nineteenth century. It also explores the role of poetry as a mediator between familiar British ideals and new colonial paradigms within emerging literary markets from Sydney and Melbourne to Cape Town and Halifax. Rudy focuses on the work of poets both canonical—including Tennyson, Browning, Longfellow, and Hemans—and relatively obscure, from Adam Lindsay Gordon, Susanna Moodie, and Thomas Pringle to Henry Kendall and Alexander McLachlan. He examines in particular the nostalgic relations between home and abroad, core and periphery, whereby British emigrants used both original compositions and canonical British works to imagine connections between their colonial experiences and the lives they left behind in Europe.Drawing on archival work from four continents, Imagined Homelands insists on a wider geographic frame for nineteenth-century British literature. From lyrics printed in newspapers aboard emigrant ships heading to Australia and South Africa, to ballads circulating in New Zealand and Canadian colonial journals, poetry was a vibrant component of emigrant life. In tracing the histories of these poems and the poets who wrote them, this book provides an alternate account of nineteenth-century British poetry and, more broadly, of settler colonial culture

Discrimination Task Reveals Differences in Neural Bases of Tinnitus and Hearing Impairment

We investigated auditory perception and cognitive processing in individuals with chronic tinnitus or hearing loss using functional magnetic resonance imaging (fMRI). Our participants belonged to one of three groups: bilateral hearing loss and tinnitus (TIN), bilateral hearing loss without tinnitus (HL), and normal hearing without tinnitus (NH). We employed pure tones and frequency-modulated sweeps as stimuli in two tasks: passive listening and active discrimination. All subjects had normal hearing through 2 kHz and all stimuli were low-pass filtered at 2 kHz so that all participants could hear them equally well. Performance was similar among all three groups for the discrimination task. In all participants, a distributed set of brain regions including the primary and non-primary auditory cortices showed greater response for both tasks compared to rest. Comparing the groups directly, we found decreased activation in the parietal and frontal lobes in the participants with tinnitus compared to the HL group and decreased response in the frontal lobes relative to the NH group. Additionally, the HL subjects exhibited increased response in the anterior cingulate relative to the NH group. Our results suggest that a differential engagement of a putative auditory attention and short-term memory network, comprising regions in the frontal, parietal and temporal cortices and the anterior cingulate, may represent a key difference in the neural bases of chronic tinnitus accompanied by hearing loss relative to hearing loss alone

Elucidating Nature’s Solutions to Heart, Lung, and Blood Diseases and Sleep Disorders

Evolution has provided a number of animal species with extraordinary phenotypes. Several of these phenotypes allow species to survive and thrive in environmental conditions that mimic disease states in humans. The study of evolved mechanisms that responsible for these phenotypes may provide insights into the basis of human disease and guide the design of new therapeutic approaches. Examples include species that tolerate acute or chronic hypoxemia like deep-diving mammals and high-altitude inhabitants, as well as those that hibernate and interrupt their development when exposed to adverse environments. The evolved traits exhibited by these animal species involve modifications of common biological pathways that affect metabolic regulation, organ function, antioxidant defenses, and oxygen transport. In 2006, the National Heart, Lung, and Blood Institute (NHLBI) released a funding opportunity announcement to support studies that were designed to elucidate the natural molecular and cellular mechanisms of adaptation in species that tolerate extreme environmental conditions. The rationale for this funding opportunity is detailed in this Special Article, and the specific evolved mechanisms examined in the supported research are described. Also highlighted are past medical advances achieved through the study of animal species that have evolved extraordinary phenotypes as well as the expectations for new understanding of nature’s solutions to heart, lung, blood, and sleep disorders through future research in this area

Elucidating Nature’s Solutions to Heart, Lung, and Blood Diseases and Sleep Disorders

Evolution has provided a number of animal species with extraordinary phenotypes. Several of these phenotypes allow species to survive and thrive in environmental conditions that mimic disease states in humans. The study of evolved mechanisms that responsible for these phenotypes may provide insights into the basis of human disease and guide the design of new therapeutic approaches. Examples include species that tolerate acute or chronic hypoxemia like deep-diving mammals and high-altitude inhabitants, as well as those that hibernate and interrupt their development when exposed to adverse environments. The evolved traits exhibited by these animal species involve modifications of common biological pathways that affect metabolic regulation, organ function, antioxidant defenses, and oxygen transport. In 2006, the National Heart, Lung, and Blood Institute (NHLBI) released a funding opportunity announcement to support studies that were designed to elucidate the natural molecular and cellular mechanisms of adaptation in species that tolerate extreme environmental conditions. The rationale for this funding opportunity is detailed in this Special Article, and the specific evolved mechanisms examined in the supported research are described. Also highlighted are past medical advances achieved through the study of animal species that have evolved extraordinary phenotypes as well as the expectations for new understanding of nature’s solutions to heart, lung, blood, and sleep disorders through future research in this area

The LOFAR Transients Pipeline

Current and future astronomical survey facilities provide a remarkably rich opportunity for transient astronomy, combining unprecedented fields of view with high sensitivity and the ability to access previously unexplored wavelength regimes. This is particularly true of LOFAR, a recently-commissioned, low-frequency radio interferometer, based in the Netherlands and with stations across Europe. The identification of and response to transients is one of LOFAR's key science goals. However, the large data volumes which LOFAR produces, combined with the scientific requirement for rapid response, make automation essential. To support this, we have developed the LOFAR Transients Pipeline, or TraP. The TraP ingests multi-frequency image data from LOFAR or other instruments and searches it for transients and variables, providing automatic alerts of significant detections and populating a lightcurve database for further analysis by astronomers. Here, we discuss the scientific goals of the TraP and how it has been designed to meet them. We describe its implementation, including both the algorithms adopted to maximize performance as well as the development methodology used to ensure it is robust and reliable, particularly in the presence of artefacts typical of radio astronomy imaging. Finally, we report on a series of tests of the pipeline carried out using simulated LOFAR observations with a known population of transients.Comment: 30 pages, 11 figures; Accepted for publication in Astronomy & Computing; Code at https://github.com/transientskp/tk

Coordinated X-Ray, Ultraviolet, Optical, and Radio Observations of the PSR J1023+0038 System in a Low-mass X-Ray Binary State

The PSR J1023+0038 binary system hosts a neutron star and a low-mass, main-sequence-like star. It switches on year timescales between states as an eclipsing radio millisecond pulsar and a low-mass X-ray binary (LMXB). We present a multi-wavelength observational campaign of PSR J1023+0038 in its most recent LMXB state. Two long XMM-Newton observations reveal that the system spends ~70% of the time in a ≈3 × 10^(33) erg s^(−1) X-ray luminosity mode, which, as shown in Archibald et al., exhibits coherent X-ray pulsations. This emission is interspersed with frequent lower flux mode intervals with ≈5 x 10^(32) erg s^(−1) and sporadic flares reaching up to ≈10^(34) erg s^(−1), with neither mode showing significant X-ray pulsations. The switches between the three flux modes occur on timescales of order 10 s. In the UV and optical, we observe occasional intense flares coincident with those observed in X-rays. Our radio timing observations reveal no pulsations at the pulsar period during any of the three X-ray modes, presumably due to complete quenching of the radio emission mechanism by the accretion flow. Radio imaging detects highly variable, flat-spectrum continuum radiation from PSR J1023+0038, consistent with an origin in a weak jet-like outflow. Our concurrent X-ray and radio continuum data sets do not exhibit any correlated behavior. The observational evidence we present bears qualitative resemblance to the behavior predicted by some existing "propeller" and "trapped" disk accretion models although none can account for key aspects of the rich phenomenology of this system

Accretion-powered Pulsations in an Apparently Quiescent Neutron Star Binary

Accreting millisecond X-ray pulsars (AMXPs) are an important subset of low-mass X-ray binaries (LMXBs) in which coherent X-ray pulsations can be observed during occasional, bright outbursts (X-ray luminosity ). These pulsations show that matter is being channeled onto the neutron star's magnetic poles. However, such sources spend most of their time in a low-luminosity, quiescent state (L_X ≲ 10^(34) erg s^(-1)), where the nature of the accretion flow onto the neutron star (if any) is not well understood. Here we report that the millisecond pulsar/LMXB transition object PSR J1023+0038 intermittently shows coherent X-ray pulsations at luminosities nearly 100 times fainter than observed in any other AMXP. We conclude that in spite of its low luminosity, PSR J1023+0038 experiences episodes of channeled accretion, a discovery that challenges existing models for accretion onto magnetized neutron stars

High-throughput gene discovery in the rat

The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3′ ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to ∼50,000 rat UniGene clusters. We have identified, arrayed, and derived 5′ ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI

Empirical comparison of cross-platform normalization methods for gene expression data

<p>Abstract</p> <p>Background</p> <p>Simultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the combination and comparison of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, software for the selected method must be obtained and incorporated into a data analysis workflow.</p> <p>Results</p> <p>Using two publicly available cross-platform testing data sets, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data. Scatter and ROC-like plots are produced and new statistics based on those plots are introduced to measure the effectiveness of each method. Bootstrapping is employed to obtain distributions for those statistics. The consistency of platform effects across studies is explored theoretically and with respect to the testing data sets.</p> <p>Conclusions</p> <p>Our comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. We provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. The package can be downloaded at <url>http://alborz.sdsu.edu/conor</url> and is available from CRAN.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead