Automatic Music Composition using Answer Set Programming

Music composition used to be a pen and paper activity. These these days music is often composed with the aid of computer software, even to the point where the computer compose parts of the score autonomously. The composition of most styles of music is governed by rules. We show that by approaching the automation, analysis and verification of composition as a knowledge representation task and formalising these rules in a suitable logical language, powerful and expressive intelligent composition tools can be easily built. This application paper describes the use of answer set programming to construct an automated system, named ANTON, that can compose melodic, harmonic and rhythmic music, diagnose errors in human compositions and serve as a computer-aided composition tool. The combination of harmonic, rhythmic and melodic composition in a single framework makes ANTON unique in the growing area of algorithmic composition. With near real-time composition, ANTON reaches the point where it can not only be used as a component in an interactive composition tool but also has the potential for live performances and concerts or automatically generated background music in a variety of applications. With the use of a fully declarative language and an "off-the-shelf" reasoning engine, ANTON provides the human composer a tool which is significantly simpler, more compact and more versatile than other existing systems. This paper has been accepted for publication in Theory and Practice of Logic Programming (TPLP).Comment: 31 pages, 10 figures. Extended version of our ICLP2008 paper. Formatted following TPLP guideline

Genetic dissection of essential hypertension and familial intracranial aneurysm

The studies of hypertension, described herein, combined complementary strategies to examine the relevance of human chromosome 5q31.1-qter to blood pressure as a quantitative trait, and hypertension as a qualitative trait. This distal region of chromosome 5 was focused upon due to its implication by other human and animal model studies and the cluster of cardiovascular candidate genes located there. Eleven microsatellites across 55 cM of 5q31.1 to qter were genotyped in 212 hypertensive nuclear families of the Silesian Hypertension Study. Two-point and multipoint analyses showed linkage of a 7 cM region to both hypertensive status and blood pressure phenotypes. A maximal multipoint Z-score of 2.2 for systolic blood pressure (SBP) was obtained proximal to the marker D5s1480. In light of the debate regarding significance in linkage studies, this quantitative trait locus (QTL) was confirmed in a second sample derived from the Scottish population. Genotyping of the same markers was done for 1,469 individuals from sibships of the MIDSPAN Family Study. Two-point and multipoint analyses confirmed a reproducible 7 cM QTL with a maximum multipoint logarithm of odds (LOD) score of 1.8 obtained for mean arterial pressure. Several putative candidate genes were located within the QTL including the b2-adrenergic receptor gene, ADRB2, which is known to have a major role in cardiovascular physiology. Three functional loci, Arg16Gly, Gln27Glu and Thr164Ile, were genotyped within the ADRB2 gene using the Silesian sample. Single locus and haplotype analyses using transmission disequilibrium tests and family-based association methods showed no association to hypertension status (P>0.05), effectively excluding this gene in the Silesian sample. The fibroblast growth factor 1 gene, FGF1, is located at the centre of the QTL. This gene had previously been cited as a putative blood pressure candidate gene in the 5q region but not studied in humans. With roles in endothelial cell proliferation, possible oxidative stress defence and proven direct effects on blood pressure in rodent models, we considered it a possible novel candidate. Coding regions and 3’ UTR were sequenced and family-based association analyses performed for three polymorphisms which were discovered in the 3’ UTR. Association of SBP (P=0.045), pulse pressure (P=0.019) and hypertension status (P=0.038) was demonstrated to the most proximal locus. Association of hypertension to a three-locus haplotype was also shown (P=0.020). The work on essential hypertension demonstrated the merit of confirming linkage in independent populations, implicating a 7 cM region of 5q31.1-q33 linked to blood pressure. Subsequent candidate gene studies utilised the added value of haplotype analyses, excluding the ADRB2 locus but showing interesting data to implicate the novel FGF1 locus as a putative positional candidate. Further fine mapping strategies are now underway to define, more clearly, the haplotype tag across the FGF1 locus

Area Postrema

This report contains a gene expression summary of the area postrema (AP), derived from the "Allen Brain Atlas":http://www.brain-map.org/welcome.do;jsessionid=EDE40ADC940845D169DE378ADC9B71BD (ABA) in-situ hybridization (ISH) mouse data set. The structure’s location and morphological characteristics in the mouse brain are described using the Nissl data found in the "Allen Reference Atlas":http://www.brain-map.org/mouse/atlas/coronal/legend.html. Using an established algorithm, the expression values of the AP were compared to the values of the macro/parent-structure, in this case the medulla, for the purpose of extracting regionally specific gene expression data. The highest ranking ratios were then manually curated and verified. The 50 Select Genes were compiled for expression characterization. The experimental data for each gene may be accessed via the links provided; complementary sagittal data may also be accessed using the "ABA":http://www.brain-map.org/welcome.do. Correlation between gene expression in the AP and the rest of the brain, across all genes in the coronal dataset (~4300 genes), were derived computationally and are presented below. A gene ontology table (derived from DAVID Bioinformatics Resources 2007) is also included, highlighting possible functions of these 50 Select Genes. 
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In vivo evaluation of chemical biopersistence of nonfibrous inorganic particles.

The lung's response to deposited particles may depend upon the physical-chemical properties of the particles, the amount initially deposited, and the persistence of the particles. Clearance involves mucociliary transport as well as the action of phagocytic cells in nonciliated regions of the lung. Depending on the animal species studied, particle type, and particle load, inorganic materials are ingested by macrophages on alveolar surfaces with half-times of 0.6 to 7 hr. Particle-laden macrophages may migrate to airways, but we believe that an important mechanism of clearance is the dissolution of particles within alveolar macrophages and the subsequent translocation of dissolved materials to the blood. Particle dissolution in situ has long been recognized but was often thought to be carried out extracellularly in the alveolar lining layer, airway mucus, or interstitial fluid. However, many particles such as cobalt oxide or iron oxide which dissolve very little in simulated lung fluid, are solubilized more rapidly within alveolar macrophages. Clearance of particles from the lungs can be followed by a number of techniques, both invasive and noninvasive. The approaches vary in expense and resolution, and can be directed toward quantifying mechanical removal of particles versus their intracellular dissolution. Noninvasive methods permit repeated measurements of particle retention in the lungs of the same animal or human and thus allow replications and serial measurements. Greater precision with respect to the sites of retention and redistribution is achieved with quantitative morphometric methods that utilize fixation followed by physically dividing the respiratory tract into individual pieces. Microwave drying or slam-freezing can eliminate the possibility of significant particle redistribution or loss of particles and dissolved elements during tissue processing. Detection of particles and therefore evidence of clearance can rely upon any distinctive property of the aerosol. Particles may be radioactive, fluorescent, or magnetic, or may have a characteristic visual appearance. Detection techniques include radiography, analyses of radioactivity, magnetometry, and microscopic approaches such as fluorescence and confocal microscopy, X-ray emission analysis, and electron energy loss spectrometry (EELS). Using these approaches, considerable evidence has been accumulated to conclude that particle dissolution in situ within alveolar macrophages and subsequent absorption by the circulation, rather than bulk transport, is the dominant mechanism for the long-term clearance of many insoluble minerals from the lungs

Focal Ca2+ Transient Detection in Smooth Muscle

Ca2+ imaging of smooth muscle provides insight into cellular mechanisms that may not result in changes of membrane potential, such as the release of Ca2+ from internal stores, and allows multiple cells to be monitored simultaneously to assess, for example, coupling in syncytial tissue. Subcellular Ca2+ transients are common in smooth muscle, yet are difficult to measure accurately because of the problems caused by their stochastic occurrence, over an often wide field of view, in an organ that it prone to contract. To overcome this problem, we've developed a series of imaging protocols and analysis routines to acquire and then analyse, in an automated fashion, the frequency, location and amplitude of such events. While this approach may be applied in other contexts, our own work involves the detection of local purinergic Ca2+ transients for locating transmitter release with submicron resolution

Linked-List-Based Multibody Dynamics (MBDyn) Engine

This new release of MBDyn is a software engine that calculates the dynamics states of kinematic, rigid, or flexible multibody systems. An MBDyn multibody system may consist of multiple groups of articulated chains, trees, or closed-loop topologies. Transient topologies are handled through conservation of energy and momentum. The solution for rigid-body systems is exact, and several configurable levels of nonlinear term fidelity are available for flexible dynamics systems. The algorithms have been optimized for efficiency and can be used for both non-real-time (NRT) and real-time (RT) simulations. Interfaces are currently compatible with NASA's Trick Simulation Environment. This new release represents a significant advance in capability and ease of use. The two most significant new additions are an application programming interface (API) that clarifies and simplifies use of MBDyn, and a link-list infrastructure that allows a single MBDyn instance to propagate an arbitrary number of interacting groups of multibody top ologies. MBDyn calculates state and state derivative vectors for integration using an external integration routine. A Trickcompatible interface is provided for initialization, data logging, integration, and input/output

Use of mobile devices to help cancer patients meet their information needs in non-inpatient settings: systematic review

Background: The shift from inpatient to outpatient cancer care means that patients are now required to manage their condition at home, away from regular supervision by clinicians. Subsequently, research has consistently reported that many patients with cancer have unmet information needs during their illness. Mobile devices, such as mobile phones and tablet computers, provide an opportunity to deliver information to patients remotely. To date, no systematic reviews have evaluated how mobile devices have been used specifically to help patients meet to their information needs. Objective: A systematic review was conducted to identify studies that describe the use of mobile interventions to enable patients with cancer to meet their cancer-related information needs in non-inpatient settings, and to describe the effects and feasibility of these interventions. Methods: MEDLINE EMBASE and PsychINFO databases were searched up until January 2017. Search terms related to ‘mobile devices’, ‘information needs’ and ‘cancer’. There were no restrictions on study type in order to be as inclusive as possible. Study participants were patients with cancer undergoing treatment. Interventions had to be delivered by a mobile or handheld device, attempt to meet patients’ cancer-related information needs, and be for use in non-inpatient settings. Critical Appraisal Skills Programme (CASP) checklists were used to assess the methodological quality of included studies. A narrative synthesis was performed and findings were organised by common themes found across studies. Results: The initial search yielded 1020 results. Twenty-three articles describing 20 studies were included. Interventions aimed to improve the monitoring and management of treatment-related symptoms (n=17, 85%), directly increase patients’ knowledge related to their condition (n=2, 10%) and improve communication of symptoms to clinicians in consultations (n=1, 5%). Studies were of adult (n=17; age range 24-87 years) and adolescent (n=3; age range 8-18 years) patients. Sample sizes ranged from 4-125, with 13 studies consisting of 25 participants or less. Most studies were conducted in the UK (n=12, 52%) or US (n=7, 30%). Of the 23 articles included, twelve were of medium quality, nine were of poor quality and two were of good quality. Overall, interventions were reported to be acceptable and were perceived as useful and easy to use. Few technical problems were encountered. Adherence was generally consistent and high (periods ranged from 5 days to 6 months), however there was considerable variation in use of intervention components within and between studies. Reported benefits of the interventions included improved symptom management, patient empowerment and improved clinician-patient communication, although mixed findings were reported for patients’ health-related quality of life and anxiety. Conclusions: The current review highlighted that mobile interventions for patients with cancer are only meeting treatment or symptom-related information needs. There were no interventions designed to meet patients’ full range of cancer-related information needs, from information on psychological support to how to manage finances during cancer, and the long-term effects of treatment. More comprehensive interventions are required for patients to meet their information needs when managing their condition in non-inpatient settings. Controlled evaluations are needed to further determine the effectiveness of these types of intervention

Evolution of Flexible Multibody Dynamics for Simulation Applications Supporting Human Spaceflight

During the course of transition from the Space Shuttle and International Space Station programs to the Orion and Journey to Mars exploration programs, a generic flexible multibody dynamics formulation and associated software implementation has evolved to meet an ever changing set of requirements at the NASA Johnson Space Center (JSC). Challenging problems related to large transitional topologies and robotic free-flyer vehicle capture/ release, contact dynamics, and exploration missions concept evaluation through simulation (e.g., asteroid surface operations) have driven this continued development. Coupled with this need is the requirement to oftentimes support human spaceflight operations in real-time. Moreover, it has been desirable to allow even more rapid prototyping of on-orbit manipulator and spacecraft systems, to support less complex infrastructure software for massively integrated simulations, to yield further computational efficiencies, and to take advantage of recent advances and availability of multi-core computing platforms. Since engineering analysis, procedures development, and crew familiarity/training for human spaceflight is fundamental to JSC's charter, there is also a strong desire to share and reuse models in both the non-realtime and real-time domains, with the goal of retaining as much multibody dynamics fidelity as possible. Three specific enhancements are reviewed here: (1) linked list organization to address large transitional topologies, (2) body level model order reduction, and (3) parallel formulation/implementation. This paper provides a detailed overview of these primary updates to JSC's flexible multibody dynamics algorithms as well as a comparison of numerical results to previous formulations and associated software

Challenges in decomposing encodings of verification problems

Modern program verifiers use logic-based encodings of the verification problem that are discharged by a back end reasoning engine. However, instances of such encodings for large programs can quickly overwhelm these back end solvers. Hence, we need techniques to make the solving process scale to large systems, such as partitioning (divide-and-conquer) and abstraction. In recent work, we showed how decomposing the formula encoding of a termination analysis can significantly increase efficiency. The analysis generates a sequence of logical formulas with existentially quantified predicates that are solved by a synthesis-based program analysis engine. However, decomposition introduces abstractions in addition to those required for finding the unknown predicates in the formula, and can hence deteriorate precision. We discuss the challenges associated with such decompositions and their interdependencies with the solving process