A Morphing Technique Applied to Lung Motions in Radiotherapy: Preliminary Results

Organ motion leads to dosimetric uncertainties during a patient’s treatment. Much work has been done to quantify the dosimetric effects of lung movement during radiation treatment. There is a particular need for a good description and prediction of organ motion. To describe lung motion more precisely, we have examined the possibility of using a computer technique: a morphing algorithm. Morphing is an iterative method which consists of blending one image into another image. To evaluate the use of morphing, Four Dimensions Computed Tomography (4DCT) acquisition of a patient was performed. The lungs were automatically segmented for different phases, and morphing was performed using the end-inspiration and the end-expiration phase scans only. Intermediate morphing files were compared with 4DCT intermediate images. The results showed good agreement between morphing images and 4DCT images: fewer than 2 % of the 512 by 256 voxels were wrongly classified as belonging/not belonging to a lung section. This paper presents preliminary results, and our morphing algorithm needs improvement. We can infer that morphing offers considerable advantages in terms of radiation protection of the patient during the diagnosis phase, handling of artifacts, definition of organ contours and description of organ motion

An Instruction to Accelerate Software Caches

In this paper we propose an instruction to accelerate software caches. While DMAs are very efficient for predictable data sets that can be fetched before they are needed, they introduce a large latency overhead for computations with unpredictable access behavior. Software caches are advantageous when the data set is not predictable but exhibits locality. However, software caches also incur a large overhead. Because the main overhead is in the access function, we propose an instruction that replaces the look-up function of the software cache. This instruction is evaluated using the Multidimensional Software Cache and two multimedia kernels, GLCM and H.264 Motion Compensation. The results show that the proposed instruction accelerates the software cache access time by a factor of 2.6. This improvement translates to a 2.1 speedup for GLCM and 1.28 for MC, when compared with the IBM software cache

Brønsted Acid Catalysis—Structural Preferences and Mobility in Imine/Phosphoric Acid Complexes

Despite the huge success of enantioselective Bronsted acid catalysis, experimental data about structures and activation modes of substrate/catalyst complexes in solution are very rare. Here, for the first time, detailed insights into the structures of imine/Bronsted acid catalyst complexes are presented on the basis of NMR data and underpinned by theoretical calculations. The chiral Bronsted acid catalyst R-TRIP (3,3'-bis(2,4,6-triisopropylphenyl)-1,1'-binaphthyl-2,2'-diyl hydrogen phosphate) was investigated together with six aromatic imines. For each investigated system, an E-imine/R-TRIP complex and a Z-imine/R-TRIP complex were observed. Each of these complexes consists of two structures, which are in fast exchange on the NMR time scale; i.e., overall four structures were found. Both identified E-imine/R-TRIP structures feature a strong hydrogen bond but differ in the orientation of the imine relative to the catalyst. The exchange occurs by tilting the imine inside the complex and thereby switching the oxygen that constitutes the hydrogen bond. A similar situation is observed for all investigated Z-imine/R-TRIP complexes. Here, an additional exchange pathway is opened via rotation of the imine. For all investigated imine/R-TRIP complexes, the four core structures are highly preserved. Thus, these core structures are independent of electron density and substituent modulations of the aromatic imines. Overall, this study reveals that the absolute structural space of binary imine/TRIP complexes is large and the variations of the four core structures are small. The high mobility is supposed to promote reactivity, while the preservation of the core structures in conjunction with extensive pi-pi and CH-pi interactions leads to high enantioselectivities and tolerance of different substrates

Technology use, adoption and behaviour in older adults: results from the iStoppFalls Project

Technology use is a common constituent of modern life. However, little is known about older adults’ use of technology. This article presents a subset of data collected via the technology deployed in the iStoppFalls randomized control trial. The primary focus lies on questions about digital device/Internet use, ownership, length, and frequency as well as social networking. Data was collected from participants aged 65 years or older. Seventy-eight participants completed a specifically developed technology survey as part of the baseline assessment. Results showed that the majority of subjects owned a computer with men being its main user. Participants used technological devices on a daily basis for more than 1 year. The main reason for using technology was e-mail communication, search engines, text processing, and online shopping. Only a few participants used social network applications, with Google+ and Facebook being the most popular ones. Future work should consider an in-depth qualitative approach to further increase understanding of technology use in older adults

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. Results: We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. Availability: The R package absfilter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

HER2 testing in breast cancer: Opportunities and challenges

Human epidermal growth factor receptor 2 (HER2) is overexpressed in 15-25% of breast cancers, usually as a result of HER2 gene amplification. Positive HER2 status is considered to be an adverse prognostic factor. Recognition of the role of HER2 in breast cancer growth has led to the development of anti-HER2 directed therapy, with the humanized monoclonal antibody trastuzumab (Herceptin (R)) having been approved for the therapy of HER2-positive metastatic breast cancer. Clinical studies have further suggested that HER2 status can provide important information regarding success or failure of certain hormonal therapies or chemotherapies. As a result of these developments, there has been increasing demand to perform HER2 testing on current and archived breast cancer specimens. This article reviews the molecular background of HER2 function, activation and inhibition as well as current opinions concerning its role in chemosensitivity and interaction with estrogen receptor biology. The different tissue-based assays used to detect HER2 amplification and overexpression are discussed with respect to their advantages and disadvantages, when to test (at initial diagnosis or pre-treatment), where to test (locally or centralized) and the need for quality assurance to ensure accurate and valid testing results

Facile C=O Bond Splitting of Carbon Dioxide Induced by Metal-Ligand Cooperativity in a Phosphinine Iron(0) Complex

New iron complexes [Cp*FeL](-) (1-sigma and 1-pi, Cp*=C5Me5) containing the chelating phosphinine ligand 2-(2 '-pyridyl)-4,6-diphenylphosphinine (L) have been prepared, and found to undergo facile reaction with CO2 under ambient conditions. The outcome of this reaction depends on the coordination mode of the versatile ligand L. Interaction of CO2 with the isomer 1-pi, in which L binds to Fe through the phosphinine moiety in an eta(5) fashion, leads to the formation of 3-pi, in which CO2 has undergone electrophilic addition to the phosphinine group. In contrast, interaction with 1-sigma-in which L acts as a sigma-chelating [P,N] ligand-leads to product 3-sigma in which one C=O bond has been completely broken. Such CO2 cleavage reactions are extremely rare for late 3d metals, and this represents the first such example mediated by a single Fe centre

Change Patterns in Use: A Critical Evaluation

Process model quality has been an area of considerable research efforts. In this context, the correctness-by-construction principle of change patterns provides promising perspectives. However, using change patterns for model creation imposes a more structured way of modeling. While the process of process modeling (PPM) based on change primitives has been investigated, little is known about this process based on change patterns. To obtain a better understanding of the PPM when using change patterns, the arising challenges, and the subjective perceptions of process designers, we conduct an exploratory study. The results indicate that process designers face little problems as long as control-flow is simple, but have considerable problems with the usage of change patterns when complex, nested models have to be created. Finally, we outline how effective tool support for change patterns should be realized.This research is supported by Austrian Science Fund (FWF): P23699-N23.Weber, B.; Pinggera, J.; Torres Bosch, MV.; Reichert, M. (2013). Change Patterns in Use: A Critical Evaluation. En Enterprise, Business-Process and Information Systems Modeling, BPMDS 2013. Springer Verlag. 261-276. https://doi.org/11007/978-3-642-38484-4_19S26127

The design of a purpose-built exergame for fall prediction and prevention for older people

Background Falls in older people represent a major age-related health challenge facing our society. Novel methods for delivery of falls prevention programs are required to increase effectiveness and adherence to these programs while containing costs. The primary aim of the Information and Communications Technology-based System to Predict and Prevent Falls (iStoppFalls) project was to develop innovative home-based technologies for continuous monitoring and exercise-based prevention of falls in community-dwelling older people. The aim of this paper is to describe the components of the iStoppFalls system. Methods The system comprised of 1) a TV, 2) a PC, 3) the Microsoft Kinect, 4) a wearable sensor and 5) an assessment and training software as the main components. Results The iStoppFalls system implements existing technologies to deliver a tailored home-based exercise and education program aimed at reducing fall risk in older people. A risk assessment tool was designed to identify fall risk factors. The content and progression rules of the iStoppFalls exergames were developed from evidence-based fall prevention interventions targeting muscle strength and balance in older people. Conclusions The iStoppFalls fall prevention program, used in conjunction with the multifactorial fall risk assessment tool, aims to provide a comprehensive and individualised, yet novel fall risk assessment and prevention program that is feasible for widespread use to prevent falls and fall-related injuries. This work provides a new approach to engage older people in home-based exercise programs to complement or provide a potentially motivational alternative to traditional exercise to reduce the risk of falling

Enhancing modeling and change support for process families through change patterns

The increasing adoption of process-aware information systems (PAISs), together with the variability of business processes (BPs), has resulted in large collections of related process model variants (i.e., process families). To effectively deal with process families, several proposals (e.g., C-EPC, Provop) exist that extend BP modeling languages with variability-specific constructs. While fostering reuse and reducing modeling efforts, respective constructs imply additional complexity and demand proper support for process designers when creating and modifying process families. Recently, generic and language independent adaptation patterns were successfully introduced for creating and evolving single BP models. However, they are not sufficient to cope with the specific needs for modeling and evolving process families. This paper suggests a complementary set of generic and language-independent change patterns specifically tailored to the needs of process families. 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