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On adopting Ontology Alignment techniques within the Phenotype Acquisition Process
The work presented in this paper is framed within the context of the BigMed project, aproject funded by the Norwegian Research Council. One of the objectives of BigMed isto enhance the phenotype acquisition process in newborns with a monogenetic disorder,one of the four patient groups studied in the project. The use of the Human PhenotypeOntology (HPO) [1] to tag phenotypes and systems like PhenoTips have substantiallycontributed to the overall phenotype acquisition workflow. PhenoTips [2] is a systemfor the acquisition of phenotypic information in patients with a genetic disease. Phe-noTips also suggests, given a selected set of HPO terms, candidate diagnoses usingOMIM (Online Mendelian Inheritance in Man) codes, and related genes for a subse-quent genetic test. Although PhenoTips represents a fantastic effort, we believe it couldbe extended with suitable Semantic Web solutions. In this paper, we present the firststeps to adopt ontology alignment techniques to contribute to the diagnostic process
Multibeam bathymetric surveys of submarine volcanoes and mega-pockmarks on the Chatham Rise, New Zealand
Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Taylor & Francis for personal use, not for redistribution. The definitive version was published in New Zealand Journal of Geology and Geophysics 54 (2011): 329-339, doi:10.1080/00288306.2011.589860.Multibeam bathymetric surveys east of the South Island of New Zealand present images of submarine volcanoes and pockmarks west of Urry Knolls on the Chatham Rise, and evidence of submarine erosion on the southern margin of the Chatham Rise. Among numerous volcanic cones, diameters of the largest reach ~2000 m, and some stand as high as 400 m above the surrounding seafloor. The tops of most of the volcanic cones are flat, with hints of craters, and some with asymmetric shapes may show flank collapses. There are hints of both northeast-southwest and northwest-southeast alignments of volcanoes, but no associated faulting is apparent. Near and to the west of these volcanoes, huge pockmarks, some more than ~1 km in diameter, disrupt bottom topography. Pockmarks in this region seem to be confined to sea floor shallower than ~1200 m, but we see evidence of deeper pockmarks at water depths of up to 2100 m on profiles crossing the Bounty Trough. The pockmark field on the Chatham Rise seems to be bounded on the south by a trough near 1200 m depth; like others, we presume that contour currents have eroded the margin and created the trough.This research was supported by the National Science Foundation under grants EAR-0409564, EAR-0409609, and EAR-0409835.2012-08-3
Robot-assisted laparoscopic prostatectomy in a 68-year-old patient with previous heart transplantation and pelvic irradiation
We report the case of a 68-year-old man who had previously undergone heart transplantation and pelvic irradiation for Hodgkinâs lymphoma and who was under active surveillance for prostate cancer. In response to his increased prostate-specific antigen levels and elevated Gleason score, he was offered robot-assisted laparoscopic prostatectomy
Keck Interferometer Nuller Data Reduction and On-Sky Performance
We describe the Keck Interferometer nuller theory of operation, data reduction, and on-sky performance, particularly as it applies to the nuller exozodiacal dust key science program that was carried out between 2008 February and 2009 January. We review the nuller implementation, including the detailed phasor processing involved in implementing the null-peak mode used for science data and the sequencing used for science observing. We then describe the Level 1 reduction to convert the instrument telemetry streams to raw null leakages, and the Level 2 reduction to provide calibrated null leakages. The Level 1 reduction uses conservative, primarily linear processing, implemented consistently for science and calibrator stars. The Level 2 processing is more flexible, and uses diameters for the calibrator stars measured contemporaneously with the interferometerâs K-band cophasing system in order to provide the requisite accuracy. Using the key science data set of 462 total scans, we assess the instrument performance for sensitivity and systematic error. At 2.0 Jy we achieve a photometrically-limited null leakage uncertainty of 0.25% rms per 10 minutes of integration time in our broadband channel. From analysis of the Level 2 reductions, we estimate a systematic noise floor for bright stars of ~0.2% rms null leakage uncertainty per observing cluster in the broadband channel. A similar analysis is performed for the narrowband channels. We also provide additional information needed for science reduction, including details on the instrument beam pattern and the basic astrophysical response of the system, and references to the data reduction and modeling tools
Automated derivation of the adjoint of high-level transient finite element programs
In this paper we demonstrate a new technique for deriving discrete adjoint
and tangent linear models of finite element models. The technique is
significantly more efficient and automatic than standard algorithmic
differentiation techniques. The approach relies on a high-level symbolic
representation of the forward problem. In contrast to developing a model
directly in Fortran or C++, high-level systems allow the developer to express
the variational problems to be solved in near-mathematical notation. As such,
these systems have a key advantage: since the mathematical structure of the
problem is preserved, they are more amenable to automated analysis and
manipulation. The framework introduced here is implemented in a freely
available software package named dolfin-adjoint, based on the FEniCS Project.
Our approach to automated adjoint derivation relies on run-time annotation of
the temporal structure of the model, and employs the FEniCS finite element form
compiler to automatically generate the low-level code for the derived models.
The approach requires only trivial changes to a large class of forward models,
including complicated time-dependent nonlinear models. The adjoint model
automatically employs optimal checkpointing schemes to mitigate storage
requirements for nonlinear models, without any user management or intervention.
Furthermore, both the tangent linear and adjoint models naturally work in
parallel, without any need to differentiate through calls to MPI or to parse
OpenMP directives. The generality, applicability and efficiency of the approach
are demonstrated with examples from a wide range of scientific applications
The dusty AGB star RS CrB: first mid-infrared interferometric observations with the Keck Telescopes
We report interferometric observations of the semi-regular variable star RS
CrB, a red giant with strong silicate emission features. The data were among
the first long baseline mid-infrared stellar fringes obtained between the Keck
telescopes, using parts of the new nulling beam combiner. The light was
dispersed by a low-resolution spectrometer, allowing simultaneous measurement
of the source visibility and intensity spectra from 8 to 12 microns. The
interferometric observations allow a non-ambiguous determination of the dust
shell spatial scale and relative flux contribution. Using a simple
spherically-symmetric model, in which a geometrically thin shell surrounds the
stellar photosphere, we find that ~30% to ~70% of the overall mid-infrared flux
- depending on the wavelength - originates from 7-8 stellar radii. The derived
shell opacity profile shows a broad peak around 11 microns (tau ~ 0.06),
characteristic of Mg-rich silicate dust particles.Comment: Accepted for publication in ApJ Letter
More than a century of bathymetric observations and present-day shallow sediment characterization in Belfast Bay, Maine, USA: implications for pockmark field longevity
This paper is not subject to U.S. copyright. The definitive version was published in Geo-Marine Letters 31 (2011): 237-248, doi:10.1007/s00367-011-0228-0.Mechanisms and timescales responsible for
pockmark formation and maintenance remain uncertain,
especially in areas lacking extensive thermogenic fluid
deposits (e.g., previously glaciated estuaries). This study
characterizes seafloor activity in the Belfast Bay, Maine
nearshore pockmark field using (1) three swath bathymetry
datasets collected between 1999 and 2008, complemented
by analyses of shallow box-core samples for radionuclide
activity and undrained shear strength, and (2) historical
bathymetric data (report and smooth sheets from 1872,
1947, 1948). In addition, because repeat swath bathymetry
surveys are an emerging data source, we present a selected
literature review of recent studies using such datasets for
seafloor change analysis. This study is the first to apply the
method to a pockmark field, and characterizes macro-scale
(>5 m) evolution of tens of square kilometers of highly
irregular seafloor. Presence/absence analysis yielded no
change in pockmark frequency or distribution over a 9-year
period (1999â2008). In that time pockmarks did not
detectably enlarge, truncate, elongate, or combine. Historical
data indicate that pockmark chains already existed in
the 19th century. Despite the lack of macroscopic changes
in the field, near-bed undrained shear-strength values of
less than 7 kPa and scattered downcore 137Cs signatures
indicate a highly disturbed setting. Integrating these
findings with independent geophysical and geochemical
observations made in the pockmark field, it can be
concluded that (1) large-scale sediment resuspension and
dispersion related to pockmark formation and failure do not
occur frequently within this field, and (2) pockmarks can
persevere in a dynamic estuarine setting that exhibits
minimal modern fluid venting. Although pockmarks are
conventionally thought to be long-lived features maintained
by a combination of fluid venting and minimal sediment
accumulation, this suggests that other mechanisms may be
equally active in maintaining such irregular seafloor
morphology. One such mechanism could be upwelling
within pockmarks induced by near-bed currents.Graduate support for Brothers came from a
Maine Economic Improvement Fund Dissertation Fellowship
Milliarcsecond N-Band Observations of the Nova RS Ophiuchi: First Science with the Keck Interferometer Nuller
We report observations of the nova RS Ophiuchi (RS Oph) using the Keck
Interferometer Nuller (KIN), approximately 3.8 days following the most recent
outburst that occurred on 2006 February 12. These observations represent the
first scientific results from the KIN, which operates in N-band from 8 to 12.5
microns in a nulling mode. By fitting the unique KIN data, we have obtained an
angular size of the mid-infrared continuum of 6.2, 4.0, or 5.4 mas for a disk
profile, gaussian profile (FWHM), and shell profile respectively. The data show
evidence of enhanced neutral atomic hydrogen emission and atomic metals
including silicon located in the inner spatial regime near the white dwarf (WD)
relative to the outer regime. There are also nebular emission lines and
evidence of hot silicate dust in the outer spatial region, centered at ! 17 AU
from the WD, that are not found in the inner regime. Our evidence suggests that
these features have been excited by the nova flash in the outer spatial regime
before the blast wave reached these regions. These identifications support a
model in which the dust appears to be present between outbursts and is not
created during the outburst event. We further discuss the present results in
terms of a unifying model of the system that includes an increase in density in
the plane of the orbit of the two stars created by a spiral shock wave caused
by the motion of the stars through the cool wind of the red giant star. These
data show the power and potential of the nulling technique which has been
developed for the detection of Earth-like planets around nearby stars for the
Terrestrial Planet Finder Mission and Darwin missions.Comment: 41 pages, 10 figure
Geophysical and geochemical survey of a large marine pockmark on the Malin Shelf, Ireland
Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q01011, doi:10.1029/2011GC003787.Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub-bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.We wish to thank the Geological Survey of Ireland, the
INtegrated Mapping FOr the Sustainable Development of Irelandâs MArine Resource (INFOMAR) program, the Irish
Environmental Protection Agency, Science Foundation of
Ireland, QUESTOR (Queens University Belfast) and the Irish
Council for Science, engineering and technology for funding
this research. AJS thanks NSERC, (Strategic and Discovery
Programs), the Canada Foundation for Innovation (CFI), and
the Ministry of Research and Innovation (MRI) for providing
Canadian funding. The survey data utilized in the research has
been coâfunded by the Geological Survey of Ireland and the Offshore
Irish Petroleum Infrastructure Programme (PIP; Ref. No:
IS05/16 Malin Basin EM).2012-07-1
Cyber security fear appeals:unexpectedly complicated
Cyber security researchers are starting to experiment with fear appeals, with a wide variety of designs and reported efficaciousness. This makes it hard to derive recommendations for designing and deploying these interventions. We thus reviewed the wider fear appeal literature to arrive at a set of guidelines to assist cyber security researchers. Our review revealed a degree of dissent about whether or not fear appeals are indeed helpful and advisable. Our review also revealed a wide range of fear appeal experimental designs, in both cyber and other domains, which confirms the need for some standardized guidelines to inform practice in this respect. We propose a protocol for carrying out fear appeal experiments, and we review a sample of cyber security fear appeal studies, via this lens, to provide a snapshot of the current state of play. We hope the proposed experimental protocol will prove helpful to those who wish to engage in future cyber security fear appeal research
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