Programming with time : cyber-physical programming with Impromptu

The act of computer programming is generally considered to be temporally removed from a computer program's execution. In this paper we discuss the idea of programming as an activity that takes place within the temporal bounds of a real-time computational process and its interactions with the physical world. We ground these ideas within the con- text of livecoding -- a live audiovisual performance practice. We then describe how the development of the programming environment "Impromptu" has addressed our ideas of programming with time and the notion of the programmer as an agent in a cyber-physical system.

A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Monitoring user activity on smart mobile devices

The invention relates to a method for monitoring user activity on a mobile device, comprising an input and an output unit, comprising the following steps preferably in the following order: detecting and / or logging user activity on said input unit, identifying a foreground running application, hashing of a user-interface-element management list of the foreground running application, and creating a screenshot comprising items displayed on said input unit. The invention also relates to a method for analyzing user activity at a server, comprising the following step: obtaining at least one of an information about detected and / or logged user activity, an information about a foreground running application, a hashed user-interface-element management list and a screenshot from a mobile device. Further, a computer program product is provided, comprising one or more computer readable media having computer executable instructions for performing the steps of at least one of the aforementioned methods.

Heterogeneity evidence and linkage studies on Charcot-Marie-Tooth disease

Charcot-Marie-Tooth neuropathy type 1 (CMT1) is an autosomal dominant disorder originally localized to chromosome 1 by linkage to the Duffy blood group. Studies have since shown that the disorder may be heterogeneous, as not all families show this linkage. We tested genetic heterogeneity by the HOMOG computer program in 15 CMT1 pedigrees informative for Duffy. We detected no evidence for heterogeneity in this sample, but when we combined results with previously published lod scores, heterogeneity was statistically significant. Twelve of the 15 families studied did not show linkage to Duffy. We found six of these families to be informative for a chromosome 19 marker, apolipoprotein CII(ApoC2). Despite a previous report showing probable linkage of a non-Duffy-linked CMT1 pedigree to two chromosome 19 markers, we did not detect significant linkage of ApoC2 to CMT1 in these families.

Rapid match-searching for gene silencing assessment

Motivation: Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G-U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.Results: The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives. © The Author 2010. Published by Oxford University Press. All rights reserved.

A time-based quantitative approach for selecting lean strategies for manufacturing organisations

Lean strategies have been developed to eliminate or reduce waste and thus improve operational efficiency in a manufacturing environment. However, in practice, manufacturers encounter difficulties to select appropriate lean strategies within their resource constraints and to quantitatively evaluate the perceived value of manufacturing waste reduction. This paper presents a methodology developed to quantitatively evaluate the contribution of lean strategies selected to reduce manufacturing wastes within the manufacturers’ resource (time) constraints. A mathematical model has been developed for evaluating the perceived value of lean strategies to manufacturing waste reduction and a step-by-step methodology is provided for selecting appropriate lean strategies to improve the manufacturing performance within their resource constraints. A computer program is developed in MATLAB for finding the optimum solution. With the help of a case study, the proposed methodology and developed model has been validated. A ‘lean strategy-wastes’ correlation matrix has been proposed to establish the relationship between the manufacturing wastes and lean strategies. Using the correlation matrix and applying the proposed methodology and developed mathematical model, authors came out with optimised perceived value of reduction of a manufacturer's wastes by implementing appropriate lean strategies within a manufacturer's resources constraints. Results also demonstrate that the perceived value of reduction of manufacturing wastes can significantly be changed based on policies and product strategy taken by a manufacturer. The proposed methodology can also be used in dynamic situations by changing the input in the programme developed in MATLAB. By identifying appropriate lean strategies for specific manufacturing wastes, a manufacturer can better prioritise implementation efforts and resources to maximise the success of implementing lean strategies in their organisation.

Foot massage versus quiet presence on agitation and mood in people with dementia : a randomised controlled trial

Background There is increasing interest in using complementary and alternative treatments to manage behavioural and psychological symptoms of dementia such as agitation, aggression and depressed mood. Objective To compare the effect of foot massage (intervention) and quiet presence (control) on agitation and mood in people with dementia. Design A randomised controlled trial using a within-subjects, crossover design. Settings Five long-term care facilities in Brisbane, Australia. The primary outcome was the Cohen-Mansfield Agitation Inventory (CMAI) and the secondary outcome was the Observed Emotion Rating Scale (OERS). The screening and data collection research assistants, families, and care staff were blinded to participant allocation. Participants Participants of the study were 55 long-term care residents aged 74–103 years (mean age 86.5), with moderate to severe dementia and a history of agitated behaviour according to the Pittsburgh Agitation Scale. A computer-program randomised participants to 10-min foot massage (intervention) or quiet presence (control), every weekday for 3 weeks. Results A carry-over effect was identified in the data, and so the data was treated as a parallel groups RCT. The mean total CMAI increased in both groups (reflecting an increase in agitation) with this increase greater in the quiet presence group than the foot massage group (p=0.03). There was a trend towards a difference on OERS General Alertness, with a positive change in alertness for participants in the foot massage group (indicating reduced alertness) and a negative change for participants in the quiet presence group (indicating increased alertness) (F(1,51)=3.88, p=0.05, partial ή2=0.07). Conclusions The findings highlight the need for further research on the specific conditions under which massage might promote relaxation and improve mood for people with dementia. The unfamiliar research assistants and variations in usual activity may have contributed to the increase in agitation and this needs further research.

Foot massage and physiological stress in people with dementia : a randomized controlled trial

Background There is increasing interest in using complementary and alternative treatments to manage behavioural and psychological symptoms of dementia such as agitation, aggression and depressed mood. Objective To compare the effect of foot massage (intervention) and quiet presence (control) on agitation and mood in people with dementia. Design A randomised controlled trial using a within-subjects, crossover design. Settings Five long-term care facilities in Brisbane, Australia. The primary outcome was the Cohen-Mansfield Agitation Inventory (CMAI) and the secondary outcome was the Observed Emotion Rating Scale (OERS). The screening and data collection research assistants, families, and care staff were blinded to participant allocation. Participants Participants of the study were 55 long-term care residents aged 74–103 years (mean age 86.5), with moderate to severe dementia and a history of agitated behaviour according to the Pittsburgh Agitation Scale. A computer-program randomised participants to 10-min foot massage (intervention) or quiet presence (control), every weekday for 3 weeks. Results A carry-over effect was identified in the data, and so the data was treated as a parallel groups RCT. The mean total CMAI increased in both groups (reflecting an increase in agitation) with this increase greater in the quiet presence group than the foot massage group (p=0.03). There was a trend towards a difference on OERS General Alertness, with a positive change in alertness for participants in the foot massage group (indicating reduced alertness) and a negative change for participants in the quiet presence group (indicating increased alertness) (F(1,51)=3.88, p=0.05, partial ή2=0.07). Conclusions The findings highlight the need for further research on the specific conditions under which massage might promote relaxation and improve mood for people with dementia. The unfamiliar research assistants and variations in usual activity may have contributed to the increase in agitation and this needs further research.

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity - past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control. © 2014 Nguyen et al.

SECA: SNP effect concordance analysis using genome-wide association summary results

The genomics era provides opportunities to assess the genetic overlap across phenotypes at the measured genotype level; however, current approaches require individual-level genome-wide association (GWA) single nucleotide polymorphism (SNP) genotype data in one or both of a pair of GWA samples. To facilitate the discovery of pleiotropic effects and examine genetic overlap across two phenotypes, I have developed a user-friendly web-based application called SECA to perform SNP effect concordance analysis using GWA summary results. The method is validated using publicly available summary data from the Psychiatric Genomics Consortium.

Partial epilepsy syndrome in a Gypsy family linked to 5q31.3-q32

PURPOSE The restricted genetic diversity and homogeneous molecular basis of Mendelian disorders in isolated founder populations have rarely been explored in epilepsy research. Our long-term goal is to explore the genetic basis of epilepsies in one such population, the Gypsies. The aim of this report is the clinical and genetic characterization of a Gypsy family with a partial epilepsy syndrome. METHODS Clinical information was collected using semistructured interviews with affected subjects and informants. At least one interictal electroencephalography (EEG) recording was performed for each patient and previous data obtained from records. Neuroimaging included structural magnetic resonance imaging (MRI). Linkage and haplotype analysis was performed using the Illumina IVb Linkage Panel, supplemented with highly informative microsatellites in linked regions and Affymetrix SNP 5.0 array data. RESULTS We observed an early-onset partial epilepsy syndrome with seizure semiology strongly suggestive of temporal lobe epilepsy (TLE), with mild intellectual deficit co-occurring in a large proportion of the patients. Psychiatric morbidity was common in the extended pedigree but did not cosegregate with epilepsy. Linkage analysis definitively excluded previously reported loci, and identified a novel locus on 5q31.3-q32 with an logarithm of the odds (LOD) score of 3 corresponding to the expected maximum in this family. DISCUSSION The syndrome can be classified as familial temporal lobe epilepsy (FTLE) or possibly a new syndrome with mild intellectual deficit. The linked 5q region does not contain any ion channel-encoding genes and is thus likely to contribute new knowledge about epilepsy pathogenesis. Identification of the mutation in this family and in additional patients will define the full phenotypic spectrum.

Software simulation of the EEG

The literature contains many examples of digital procedures for the analytical treatment of electroencephalograms, but there is as yet no standard by which those techniques may be judged or compared. This paper proposes one method of generating an EEG, based on a computer program for Zetterberg's simulation. It is assumed that the statistical properties of an EEG may be represented by stationary processes having rational transfer functions and achieved by a system of software fillers and random number generators.The model represents neither the neurological mechanism response for generating the EEG, nor any particular type of EEG record; transient phenomena such as spikes, sharp waves and alpha bursts also are excluded. The basis of the program is a valid ‘partial’ statistical description of the EEG; that description is then used to produce a digital representation of a signal which if plotted sequentially, might or might not by chance resemble an EEG, that is unimportant. What is important is that the statistical properties of the series remain those of a real EEG; it is in this sense that the output is a simulation of the EEG. There is considerable flexibility in the form of the output, i.e. its alpha, beta and delta content, which may be selected by the user, the same selected parameters always producing the same statistical output. The filtered outputs from the random number sequences may be scaled to provide realistic power distributions in the accepted EEG frequency bands and then summed to create a digital output signal, the ‘stationary EEG’. It is suggested that the simulator might act as a test input to digital analytical techniques for the EEG, a simulator which would enable at least a substantial part of those techniques to be compared and assessed in an objective manner. The equations necessary to implement the model are given. The program has been run on a DEC1090 computer but is suitable for any microcomputer having more than 32 kBytes of memory; the execution time required to generate a 25 s simulated EEG is in the region of 15 s.

A computerized methodology for structural synthesis of kinematic chains: Part 1- Formulation

In an effort to develop a fully computerized approach for structural synthesis of kinematic chains the steps involved in the method of structural synthesis based on transformation of binary chains [38] have been recast in a format suitable for implementation on a digital computer. The methodology thus evolved has been combined with the algebraic procedures for structural analysis [44] to develop a unified computer program for structural synthesis and analysis of simple jointed kinematic chains with a degree of freedom 0. Applications of this program are presented in the succeeding parts of the paper.

A computerized methodology for structural synthesis of kinematic chains: Part 2 - Application to several fully or partially known cases

The reliability of the computer program for structural synthesis and analysis of simple-jointed kinematic chains developed in Part 1 has been established by applying it to several cases for whuch solutions are either fully or partially available in the literature, such as 7-link, zero-freedom chains; 8- and 10-link, single-freedom chains; 12-link, single-freedom binary chains; and 9-link, two-freedom chains. In the process some discrepancies in the results reported in previous literature have been brought to light.

A computerized methodology for structural synthesis of kinematic chains: Part 3 - application to the new case of 10-link, three- freedom chains

The unified computer program for structural synthesis and analysis developed in Part 1 has been employed to derive the new and complete collection of 97 10-link, three-freedom simple-jointed kinematic chains. The program shows that of these chains, 3 have total freedom, 70 have partial freedom and the remaining 24 have fractionated freedom and that the 97 chains yield a total of 676 distinct mechanisms.