The formal specification of abstract data types and their implementation in Fortran 90: Implementation issues concerning the use of pointers

<p>In this paper we continue our investigation into the development of computational-science software based on the identification and formal specification of Abstract Data Types (ADTs) and their implementation in Fortran 90. In particular, we consider the consequences of using pointers when implementing a formally specified ADT in Fortran 90. Our aim is to highlight the resulting conflict between the goal of information hiding, which is central to the ADT methodology, and the space efficiency of the implementation. We show that the issue of storage recovery cannot be avoided by the ADT user, and present a range of implementations of a simple ADT to illustrate various approaches towards satisfactory storage management. Finally, we propose a set of guidelines for implementing ADTs using pointers in Fortran 90. These guidelines offer a way gracefully to provide disposal operations in Fortran 90. Such an approach is desirable since Fortran 90 does not provide automatic garbage collection which is offered by many object-oriented languages including Eiffel, Java, Smalltalk, and Simula.p>

Electron excitation of Ca XVII

Electron-excitation collision strengths have been calculated for transitions between the ten lowest levels of Ca XVII (2sS, 2s2p P, 2s2p P, 2pP 2p D, 2pS ). At high impact energies, where all the channels are open, the calculation was carried out in the LS-coupling approximation by means of the R-matrix method. Transitions between the fine structure levels were then determined by application of a unitary transformation to the LS-coupled K-matrices. At low impact energies, where some of the channels may be closed, an extension of the R-matrix method was employed to take account of relativistic effects directly in the scattering equations. In general, results are in good agreement with recent distorted-wave calculations. Electron-excitation rates are given for a range of electron temperatures.

Element-specific depth profile of magnetism and stoichiometry at the La0.67Sr0.33MnO3/BiFeO3 interface

Depth-sensitive magnetic, structural and chemical characterization is important in the understanding and optimization of novel physical phenomena emerging at interfaces of transition metal oxide heterostructures. In a simultaneous approach we have used polarized neutron and resonant X-ray reflectometry to determine the magnetic profile across atomically sharp interfaces of ferromagnetic La0.67Sr0.33MnO3 / multiferroic BiFeO3 bi-layers with sub-nanometer resolution. In particular, the X-ray resonant magnetic reflectivity measurements at the Fe and Mn resonance edges allowed us to determine the element specific depth profile of the ferromagnetic moments in both the La0.67Sr0.33MnO3 and BiFeO3 layers. Our measurements indicate a magnetically diluted interface layer within the La0.67Sr0.33MnO3 layer, in contrast to previous observations on inversely deposited layers. Additional resonant X-ray reflection measurements indicate a region of an altered Mn- and O-content at the interface, with a thickness matching that of the magnetic diluted layer, as origin of the reduction of the magnetic moment.

Characterizing wear processes on orthopaedic materials using scanning probe microscopy

<p>The operational lifetime of hip replacement prostheses can be severely limited due to the occurrence of excessive wear at the load-bearing interfaces. The aim of this study was to investigate how the surface topography of articulating counterfaces evolves over the duration of a laboratory wear run. It was observed that modular stainless steel femoral heads wearing against ultrahigh molecular weight polyethylene (UHMWPE) can themselves be subject to wearing. A comparison with retrieved in vivo-aged femoral heads shows many topographical similarities: in a qualitative sense, scratching and pitting are evident on laboratory and in vivo-worn femoral heads; quantitatively, roughness comparisons between the new and worn devices are seen to increase typically by a factor of 4 after laboratory wearing. The observations suggest that a particular wear mode, namely third-body wear, is responsible for the increased roughness. It is conjectured that third bodies might arise through surface fatigue wear on the metal counterface, Wear debris is also observed to have been generated from the polymer surface, creating rounded debris with sizes predominantly in the range 0.4-0.8 microns: dimensions that are comparable to values previously reported for in vivo generated debris.p>

IRIDE:Interdisciplinary research infrastructure based on dual electron linacs and lasers

<p>This paper describes the scientific aims and potentials as well as the preliminary technical design of IRIDE, an innovative tool for multi-disciplinary investigations in a wide field of scientific, technological and industrial applications. IRIDE will be a high intensity "particles factory", based on a combination of high duty cycle radio-frequency superconducting electron linacs and of high energy lasers. Conceived to provide unique research possibilities for particle physics, for condensed matter physics, chemistry and material science, for structural biology and industrial applications, IRIDE will open completely new research possibilities and advance our knowledge in many branches of science and technology. IRIDE is also supposed to be realized in subsequent stages of development depending on the assigned priorities. © 2013 Elsevier B.V.p>

Transmit Antenna Selection in Cognitive MIMO Relaying with Multiple Primary Transceivers

We consider transmit antenna selection (TAS) in cognitive multiple-input multiple-output (MIMO) relay networks, as an interference-aware design for secondary users (SUs) to ensure power and interference constraints of multiple primary users (PUs). In doing so, we derive new exact and asymptotic expressions for the outage probability of TAS with maximal ratio combining (TAS/MRC) and with selection combining (TAS/SC) over Rayleigh fading. The proposed analysis and simulations highlight that TAS/MRC and TAS/SC with decode-and-forward relaying achieve the same diversity order in cognitive MIMO networks, which scales with the minimum number of antennas at the SUs. Furthermore, we accurately characterize the outage gap between TAS/MRC and TAS/SC relaying as a concise ratio of their array gains.

DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach

<p>BACKGROUND: Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.p><p>METHODS: The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.p><p>RESULTS: A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.p><p>CONCLUSIONS: High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.p>

“A quiet still voice that just touches”: music’s relevance for adults living with life-threatening cancer diagnoses.

Purpose
Music has historically aided health and loss-adaptation, however, cancer patients’ experience of music for self-care is not well understood. This study examines adult cancer patients’ views about music’s role before and after diagnosis.
Methods
Constructivist approach, with grounded theory informed design using convenience, snowball and theoretical sampling. Patients from Australian metropolitan cancer and hospice settings completed demographic questionnaires and participated in semi-structured interviews. Qualitative inter-rater reliability was applied.
Results
Fifty-two patients reported comparable time spent experiencing music pre-post diagnosis. Music may remain incidental; however, many patients adapt music usage to ameliorate cancer’s aversive effects. Patients often draw from their musical lives and explore unfamiliar music to: remain connected with pre-illness identities; strengthen capacity for enduring treatment, ongoing survival (even when knowing “you’re going to die”), or facing death; reframe upended worlds; and live enriched lives. Patients can ascribe human or physical properties to music when describing its transformative effects. Familiar lyrics maybe reinterpreted, and patients’ intensified emotional reactions to music can reflect their threatened mortality. Sometimes music becomes inaccessible, elusive, and/or intensifies distress and is avoided. Families’, friends’ and professionals’ recognition of patients’ altered musical lives and music-based suggestions can extend patients’ use of music for self-care.
Conclusion
Health professionals can support patients by inquiring about their music behaviours and recognising that altered music usage may signify vulnerability. Although commonly recommended, hospital concerts and music broadcasts need sensitive delivery. Patients’ preferred music should be available in diagnostic, treatment and palliative settings because it can promote endurance and life enrichment.

Polymorphisms near TBX5 and GDF7 are associated with increased risk for Barrett's esophagus

<p>BACKGROUND &amp; AIMS: Barrett's esophagus (BE) increases the risk of esophageal adenocarcinoma (EAC). We found the risk to be BE has been associated with single nucleotide polymorphisms (SNPs) on chromosome 6p21 (within the HLA region) and on 16q23, where the closest protein-coding gene is FOXF1. Subsequently, the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) identified risk loci for BE and esophageal adenocarcinoma near CRTC1 and BARX1, and within 100 kb of FOXP1. We aimed to identify further SNPs that increased BE risk and to validate previously reported associations.p><p>METHODS: We performed a genome-wide association study (GWAS) to identify variants associated with BE and further analyzed promising variants identified by BEACON by genotyping 10,158 patients with BE and 21,062 controls.p><p>RESULTS: We identified 2 SNPs not previously associated with BE: rs3072 (2p24.1; odds ratio [OR] = 1.14; 95% CI: 1.09-1.18; P = 1.8 × 10(-11)) and rs2701108 (12q24.21; OR = 0.90; 95% CI: 0.86-0.93; P = 7.5 × 10(-9)). The closest protein-coding genes were respectively GDF7 (rs3072), which encodes a ligand in the bone morphogenetic protein pathway, and TBX5 (rs2701108), which encodes a transcription factor that regulates esophageal and cardiac development. Our data also supported in BE cases 3 risk SNPs identified by BEACON (rs2687201, rs11789015, and rs10423674). Meta-analysis of all data identified another SNP associated with BE and esophageal adenocarcinoma: rs3784262, within ALDH1A2 (OR = 0.90; 95% CI: 0.87-0.93; P = 3.72 × 10(-9)).p><p>CONCLUSIONS: We identified 2 loci associated with risk of BE and provided data to support a further locus. The genes we found to be associated with risk for BE encode transcription factors involved in thoracic, diaphragmatic, and esophageal development or proteins involved in the inflammatory response.p>

Visible-Wavelength Survey of Jupiter-Family Cometary Nuclei as Part of SEPPCoN

We present observations of a statistically-significant number of Jupiter-family cometary nuclei as part of SEPPCoN (Survey of the Ensemble Physical Properties of Cometary Nuclei). We present preliminary results on distributions of albedos and shapes.

Spitzer observations of the asteroid-comet transition object and potential spacecraft target 107P (4015) Wilson-Harrington

Context: Near-Earth asteroid-comet transition object 107P/ (4015) Wilson-Harrington is a possible target of the joint European Space Agency (ESA) and Japanese Aerospace Exploration Agency (JAXA) Marco Polo sample return mission. Physical studies of this object are relevant to this mission, and also to understanding its asteroidal or cometary nature. Aims: Our aim is to obtain significant new constraints on the surface thermal properties of this object. Methods: We present mid-infrared photometry in two filters (16 and 22 μm) obtained with NASA's Spitzer Space Telescope on February 12, 2007, and results from the application of the Near Earth Asteroid Thermal Model (NEATM). We obtained high S/N in two mid-IR bands allowing accurate measurements of its thermal emission. Results: We obtain a well constrained beaming parameter (η = 1.39±0.26) and obtain a diameter and geometric albedo of D = 3.46±0.32 km, and pV = 0.059±0.011. We also obtain similar results when we apply this best-fitting thermal model to single-band mid-IR photometry reported by Campins et al. (1995, P&amp;SS, 43, 733), Kraemer et al. (2005, AJ, 130, 2363) and Reach et al. (2007, Icarus, 191, 298). Conclusions: The albedo of 4015 Wilson-Harrington is low, consistent with those of comet nuclei and primitive C-, P-, D-type asteorids. We establish a rough lower limit for the thermal inertia of W-H of 60 Jm-2s-0.5 K-1 when it is at r = 1 AU, which is slightly over the limit of 30 Jm-2 s-0.5 K-1 derived by Groussin et al. (2009, Icarus, 199, 568) for the thermal inertia of the nucleus of comet 22P/Kopff.

A Hundred Comets: The Visual-Wavelength Observations of the Survey of Ensemble Physical Properties of Cometary Nuclei (SEPPCoN)

We present new results from SEPPCoN, a Survey of Ensemble Physical Properties of Cometary Nuclei. This project is currently surveying 100 Jupiter-family comets (JFCs) to measure the mid-infrared thermal emission and visible reflected sunlight of the nuclei. The scientific goal is to determine the distributions of radius, geometric albedo, thermal inertia, axial ratio, and color among the JFC nuclei. In the past we have presented results from the completed mid-IR observations of our sample [1]; here we present preliminary results from ongoing, broadband visible-wavelength observations of nuclei obtained from a variety of ground-based facilities (Mauna Kea, Cerro Pachon, La Silla, La Palma, Apache Point, Table Mtn., and Palomar Mtn.), including contributions from the Near Earth Asteroid Telescope project (NEAT) archive. The nuclei were observed at high heliocentric distance (usually over 4 AU) and so many comets show either no or little contamination from dust coma. While several nuclei have been observed as snapshots, we have multiepoch photometry for many of our targets. With our datasets we are building a large database of photometry, and such a database is essential to the derivation of albedo and shape of a large number of nuclei, and to the understanding of biases in the survey. Support for this work was provided by NSF and the NASA Planetary Astronomy program. Reference: [1] Fernandez, Y.R., et al. 2007, BAAS 39, 827.