An analysis of extensible modelling for functional genomics data

BACKGROUND: Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time. RESULTS: In this paper we review the data formats that exist in functional genomics, some of which have become de facto or de jure standards, with a particular focus on how each domain has been modelled, and how each format allows extensions. We describe the tasks that are frequently performed over data formats and analyse how well each task is supported by a particular modelling structure. CONCLUSION: From our analysis, we make recommendations as to the types of modelling structure that are most suitable for particular types of experimental annotation. There are several standards currently under development that we believe could benefit from systematically following a set of guidelines

Improvi ng Federal Informati on Systems Management: Technological Opportunityes and Social Constraints

The management of data processing systems in the Federal government is rapidly approaching a state of crisis.1 The Federal information systems inventory is a collection of outdated hardware as well as software techniques and systems which were abandoned 1 ong ago in the private sector. Projects have such long lead times that when systems are finally devel oped they are outmoded or no 1 onger meet current requi rements. A number of sol uti ons have been proposed which range from new rul es and procedures to i ncreased use of private contractors in delivering EDP resources. Many of the proposed solutions have more to do with the political philosophy of the proposers than with the realities of data processing management or the underlying political processes which make EDP management so complex in the government sector. This paper examines the causes of Federal FDP management problems and the political questions that must be resolved for any proposed solutions to succeed

Perinatal and paediatric post-mortem magnetic resonance imaging (PMMR): sequences and technique

As post-mortem MRI (PMMR) becomes more widely used for investigation following perinatal and paediatric deaths, the best possible images should be acquired. In this article, we review the most widely used published PMMR sequences, together with outlining our acquisition protocol and sequence parameters for foetal, perinatal and paediatric PMMR. We give examples of both normal and abnormal appearances, so that the reader can understand the logic behind each acquisition step before interpretation, as a useful day-to-day reference guide to performing PMMR

UK military doctors; stigma, mental health and help-seeking: a comparative cohort study

Introduction Studies suggest that medical doctors can suffer from substantial levels of mental ill-health. Little is known about military doctors’ mental health and well-being; we therefore assessed attitudes to mental health, self-stigma, psychological distress and help-seeking among UK Armed Forces doctors. Methods Six hundred and seventy-eight military doctors (response rate 59%) completed an anonymous online survey. Comparisons were made with serving and ex-military personnel (n=1448, response rate 84.5%) participating in a mental health-related help-seeking survey. Basic sociodemographic data were gathered, and participants completed measures of mental health-related stigmatisation, perceived barriers to care and the 12-Item General Health Questionnaire. All participants were asked if in the last three years they had experienced stress, emotional, mental health, alcohol, family or relationship problems, and whether they had sought help from formal sources. Results Military doctors reported fewer mental disorder symptoms than the comparison groups. They endorsed higher levels of stigmatising beliefs, negative attitudes to mental healthcare, desire to self-manage and self-stigmatisation than each of the comparison groups. They were most concerned about potential negative effects of and peer perceptions about receiving a mental disorder diagnosis. Military doctors reporting historical and current relationship, and alcohol or mental health problems were significantly and substantially less likely to seek help than the comparison groups. Conclusions Although there are a number of study limitations, outcomes suggest that UK military doctors report lower levels of mental disorder symptoms, higher levels of stigmatising beliefs and a lower propensity to seek formal support than other military reference group

Association of Systemic Inflammation With Retinal Vascular Caliber in Patients With AIDS.

PurposeTo evaluate relationships among retinal vascular caliber and biomarkers of systemic inflammation in patients with AIDS.MethodsA total of 454 participants with AIDS had retinal vascular caliber (central retinal artery equivalent and central retinal vein equivalent) determined from enrollment retinal photographs by reading center graders masked to clinical and biomarker information. Cryopreserved plasma specimens were assayed for inflammatory biomarkers, including C-reactive protein (CRP), IL-6, interferon-γ inducible protein (IP)-10, kynurenine/tryptophan (KT) ratio, and intestinal fatty acid binding protein (I-FABP).ResultsIn the simple linear regression of retinal vascular caliber on plasma biomarkers, elevated CRP, IL-6, and IP-10 were associated with retinal venular dilation, and elevated KT ratio with retinal arteriolar narrowing. In the multiple linear regression, including baseline characteristics and plasma biomarkers, AMD was associated with dilation of retinal arterioles (mean difference: 9.1 μm; 95% confidence interval [CI] 5.2, 12.9; P < 0.001) and venules (mean difference, 10.9 μm; 95% CI, 5.3, 16.6; P < 0.001), as was black race (P < 0.001). Hyperlipidemia was associated with retinal venular narrowing (mean difference, -7.5 μm; 95% CI, -13.7, -1.2; P = 0.02); cardiovascular disease with arteriolar narrowing (mean difference, -5.2 μm; 95% CI, -10.3, -0.1; P = 0.05); age with arteriolar narrowing (slope, -0.26 μm/year; 95% CI, -0.46, -0.06; P = 0.009); and IL-6 with venular dilation (slope, 5.3 μm/standard deviation log10[plasma IL-6 concentration]; 95% CI, 2.7, 8.0; P < 0.001).ConclusionsThese data suggest that retinal vascular caliber is associated with age, race, AMD, hyperlipidemia, cardiovascular disease, and selected biomarkers of systemic inflammation

3D Simulations of MHD Jet Propagation Through Uniform and Stratified External Environments

We present a set of high-resolution 3D MHD simulations of steady light, supersonic jets, exploring the influence of jet Mach number and the ambient medium on jet propagation and energy deposition over long distances. The results are compared to simple self-similar scaling relations for the morphological evolution of jet-driven structures and to previously published 2D simulations. For this study we simulated the propagation of light jets with internal Mach numbers 3 and 12 to lengths exceeding 100 initial jet radii in both uniform and stratified atmospheres. The propagating jets asymptotically deposit approximately half of their energy flux as thermal energy in the ambient atmosphere, almost independent of jet Mach number or the external density gradient. Nearly one-quarter of the jet total energy flux goes directly into dissipative heating of the ICM, supporting arguments for effective feedback from AGNs to cluster media. The remaining energy resides primarily in the jet and cocoon structures. Despite having different shock distributions and magnetic field features, global trends in energy flow are similar among the different models. As expected the jets advance more rapidly through stratified atmospheres than uniform environments. The asymptotic head velocity in King-type atmospheres shows little or no deceleration. This contrasts with jets in uniform media with heads that are slowed as they propagate. This suggests that the energy deposited by jets of a given length and power depends strongly on the structure of the ambient medium. While our low-Mach jets are more easily disrupted, their cocoons obey evolutionary scaling relations similar to the high-Mach jets.Comment: Accepted in ApJ, 32 pages, 18 figures, animations available from: http://www.msi.umn.edu/Projects/twj/newsite/projects/radiojets/movies

Electrical model of carbon fibre reinforced polymers for the development of electrical protection systems for more-electric aircraft

Carbon fibre reinforced polymers (CFRP) are increasingly used for structures on aircraft due to their superior mechanical properties compared to traditional materials, such as aluminium. Additionally, in order to improve aircraft performance, there is a continued trend for electrically driven loads on aircraft, increasing the on-board electrical power generation capacity and complexity of the electrical power system, including a desire to increase voltage levels and move towards DC distribution systems. Central to the reliable operation of an electrical power system is the development of an appropriate protection and fault management strategy. If an electrical earth fault occurs on a composite more-electric aircraft then the CFRP may form part of the route to ground. In order to develop an appropriate protection system and thus to understand the effects on engine generators it is necessary to investigate the fault response of this network. Hence a suitable electrical model of the CFRP material is required, which will enable CFRP to be included in a computationally-intensive systems-level simulation study of a more-electric aircraft (MEA) with fully switching power electronic converter models. This paper presents an experimentally validated impedance model of CFRP at an appropriate level of fidelity for use in systems level simulation platforms, enabling appropriate protection methods to be developed. The validated model considers the impact of the electrical bonding to ground, including the impedance added by a metallic frame that a CFRP panel may be mounted in. The simplicity of the model results in a less complex process to determine the expected impedance of the CFRP material, enabling a focus on the fault response of the system and subsequent development of appropriate protection solutions

Quasiparticle Interactions for f2^2-Impurity Anderson Model with Crystalline-Electric-Field: Numerical Renormalization Group Study

The aspect of the quasiparticle interaction of a local Fermi liquid, the impurity version of f$^2$-based heavy fermions, is studied by the Wilson numerical renormalization group method. In particular, the case of the f$^2$-singlet crystalline-electric-field ground state is investigated assuming the case of UPt$_3$ with the hexagonal symmetry. It is found that the interorbital interaction becomes larger than the intraorbital one in contrast to the case of the bare Coulomb interaction for the parameters relevant to UPt$_3$. This result offers us a basis to construct a microscopic theory of the superconductivity of UPt$_3$ where the interorbital interactions are expected to play important roles.Comment: 9 pages, 5 figure

The Cluster and Field Galaxy AGN Fraction at z = 1 to 1.5: Evidence for a Reversal of the Local Anticorrelation Between Environment and AGN Fraction

The fraction of cluster galaxies that host luminous AGN is an important probe of AGN fueling processes, the cold ISM at the centers of galaxies, and how tightly black holes and galaxies co-evolve. We present a new measurement of the AGN fraction in a sample of 13 clusters of galaxies (M >= 10^{14} Msun) at 1<z<1.5 selected from the Spitzer/IRAC Shallow Cluster Survey, as well as the field fraction in the immediate vicinity of these clusters, and combine these data with measurements from the literature to quantify the relative evolution of cluster and field AGN from the present to z~3. We estimate that the cluster AGN fraction at 1<z<1.5 is f_A = 3.0^{+2.4}_{-1.4}% for AGN with a rest-frame, hard X-ray luminosity greater than L_{X,H} >= 10^{44} erg/s. This fraction is measured relative to all cluster galaxies more luminous than M*_{3.6}(z)+1, where M*_{3.6}(z) is the absolute magnitude of the break in the galaxy luminosity function at the cluster redshift in the IRAC 3.6um bandpass. The cluster AGN fraction is 30 times greater than the 3sigma upper limit on the value for AGN of similar luminosity at z~0.25, as well as more than an order of magnitude greater than the AGN fraction at z~0.75. AGN with L_{X,H} >= 10^{43} erg/s exhibit similarly pronounced evolution with redshift. In contrast with the local universe, where the luminous AGN fraction is higher in the field than in clusters, the X-ray and MIR-selected AGN fractions in the field and clusters are consistent at 1<z<1.5. This is evidence that the cluster AGN population has evolved more rapidly than the field population from z~1.5 to the present. This environment-dependent AGN evolution mimics the more rapid evolution of star-forming galaxies in clusters relative to the field.Comment: ApJ Accepted. 16 pages, 8 figures in emulateapj forma

Surface-acoustic-wave-driven luminescence from a lateral p-n junction

The authors report surface-acoustic-wave-driven luminescence from a lateral p-n junction formed by molecular beam epitaxy regrowth of a modulation doped GaAs/AlGaAs quantum well on a patterned GaAs substrate. Surface-acoustic-wave-driven transport is demonstrated by peaks in the electrical current and light emission from the GaAs quantum well at the resonant frequency of the transducer. This type of junction offers high carrier mobility and scalability. The demonstration of surface-acoustic-wave luminescence is a significant step towards single-photon applications in quantum computation and quantum cryptography.Comment: 4 pages, 3 figure