Mapping Step Research Articles

Studying the Global Bifurcation Involving Wada Boundary Metamorphosis by a Method of Generalized Cell Mapping with Sampling-Adaptive Interpolation

In this paper, a new method of Generalized Cell Mapping with Sampling-Adaptive Interpolation (GCMSAI) is presented in order to enhance the efficiency of the computation of one-step probability transition matrix of the Generalized Cell Mapping method (GCM). Integrations with one mapping step are replaced by sampling-adaptive interpolations of third order. An explicit formula of interpolation error is derived for a sampling-adaptive control to switch on integrations for the accuracy of computations with GCMSAI. By applying the proposed method to a two-dimensional forced damped pendulum system, global bifurcations are investigated with observations of boundary metamorphoses including full to partial and partial to partial as well as the birth of fully Wada boundary. Moreover GCMSAI requires a computational time of one thirtieth up to one fiftieth compared to that of the previous GCM.

Cost-Efficient Scheduling for Deadline Constrained Grid Workflows

Cost optimization for workflow scheduling while meeting deadline is one of the fundamental problems in utility computing. In this paper, a two-phase cost-efficient scheduling algorithm called critical chain is presented. The proposed algorithm uses the concept of slack time in both phases. The first phase is deadline distribution over all tasks existing in the workflow which is done considering critical path properties of workflow graphs. Critical chain uses slack time to iteratively select most critical sequence of tasks and then assigns sub-deadlines to those tasks. In the second phase named mapping step, it tries to allocate a server to each task considering task's sub-deadline. In the mapping step, slack time priority in selecting ready task is used to reduce deadline violation. Furthermore, the algorithm tries to locally optimize the computation and communication costs of sequential tasks exploiting dynamic programming. After proposing the scheduling algorithm, three measures for the superiority of a scheduling algorithm are introduced, and the proposed algorithm is compared with other existing algorithms considering the measures. Results obtained from simulating various systems show that the proposed algorithm outperforms four well-known existing workflow scheduling algorithms.

Building Sense Tagged Corpus Using Wikipedia for Supervised Word Sense Disambiguation

Building of sense-tagged data is a main challenge for supervised techniques that achieved promising results in word sense disambiguation. The manual building of sense-tagged data is a labor and a time-consuming task because each ambiguous word has to be labeled in collected contexts by linguistic experts. Therefore, this paper proposes a knowledge-based method for building the Arabic sense-tagged corpus from Wikipedia. The method starts with mapping Arabic WordNet and Wikipedia to select the Wikipedia article for the corresponding sense in WordNet. In this mapping step, the cross-lingual method is used to measure the similarity between features of a Wikipedia article and a WordNet sense separately. Then, the incoming-links of Wikipedia articles are exploited to extract instances for the sense of each ambiguous word in WordNet. For handling the lack of instances of some articles in Wikipedia, the multiword-based technique is proposed to increase a number of instances for each concept. Experimental results show that the cross-lingual method outperforms monolingual method that is based on Arabic features only. The sense-tagged corpus is created for 50 ambiguous words yielding 148 senses with 30,961 instances.

Map of the terminal moraine of the Werenskioldbreen glacier (South-West Spitsbergen) from 2015

The first direct field measurement of the entire terminal moraine of the Werenskioldbreen glacier on Spitsbergen took place at the end of July and the beginning of August 2015. The results of the measurements were the basis for the development of the large-scale terminal moraine map. The article presents the stages of map creation and editing based on measurement points established by the GNSS method. The map editing required knowledge of the morphologically complex terrain. Key documentation was field notes and documentary photographs, enabling the cartographic interpretation of the varied topographic features of the terrain's surface. Based on the documentation, the water bodies on the moraine were located, the outline of the structure and the boundary points were executed and the latter were excluded from the triangulation process. The glacial river was also excluded from triangulation, which allowed a DTM to be developed. An important step in point cloud mapping was to generate a topologically correct digital elevation model of satisfactory accuracy. On the basis of the DTM, contour lines were generated showing the topographic features of the terrain's surface. The printable resultant map's scale is 1: 5000; it is in the UTM coordinate system, in the 33X zone. Complementing the content of the map, a grid of geographic coordinates, a kilometer grid, and map key descriptions were added.

How fast planar maps get swallowed by a peeling process

The peeling process is an algorithmic procedure that discovers a random planar map step by step. In generic cases such as the UIPT or the UIPQ, it is known [15] that any peeling process will eventually discover the whole map. In this paper we study the probability that the origin is not swallowed by the peeling process until time $n$ and show it decays at least as $n^{-2c/3}$ where \[ c \approx 0.1283123514178324542367448657387285493314266204833984375... \] is defined via an integral equation derived using the Lamperti representation of the spectrally negative $3/2$-stable Lévy process conditioned to remain positive [12] which appears as a scaling limit for the perimeter process. As an application we sharpen the upper bound of the sub-diffusivity exponent for random walk of [4].

Pengembangan Potensi Ekowisata Sungai Pekalen Atas, Desa Ranu Gedang, Kecamatan Tiris, Kabupaten Probolinggo

River ecosystem is a potential resource for ecotourism development necessary to job creation for the local community and river conservation support. The aims of this research are to depict the ecotourism attraction potentials, to prepare ecotourism product designs, to evaluate tourist’s preferences regarding ecotourism objects and attractions, and to develop a typology of tourism products prospectively developed along the Pekalen Atas River. This study was completed from October 2016 to March 2017 in Pekalen Atas River, Ranu Gedang Village, Tiris Subdistrict, Probolinggo Regency. This research covered object identification and mapping steps along the riverbank, and then followed by respondent preferences testing toward the ecotourism objects required to the making of ecotourism product development’s classification and ranking. This product was also developed by taking stakeholders’ feedback into account during the Focus Group Discussion (FGD). The result reveals that the Pekalen Atas Riverbank consists of 26 rapids, three waterfalls, three fields, three caves and 11 animal species. The potential objects could be classified into rafting and non-rafting. Based on tourists’ perceptions, the non-rafting objects are considered “attractive” so that their further developments should meet the principles of sustainable natural resources utilization compliance. The FGD results confirmed three types of ecotourism products that could be developed along the Pekalen Atas Riverbank, i.e. low-, medium-and hard-level product.

Development of the Social Network-Based Intervention "Powerful Together with Diabetes" Using Intervention Mapping.

This article describes the development of the social network-based intervention Powerful Together with Diabetes which aims to improve diabetes self-management (DSM) among patients with type 2 diabetes living in socioeconomically deprived neighborhoods by stimulating social support for DSM and diminishing social influences hindering DSM (e.g., peer pressure and social norms). The intervention was specifically developed for patients with Dutch, Turkish, Moroccan, and Surinamese backgrounds. The intervention was developed according to Intervention Mapping. This article describes the first four steps of Intervention Mapping: (1) the needs assessment; (2) development of performance and change objectives; (3) selection of theory-based methods and strategies; and (4) the translation of these into an organized program. These four steps resulted in Powerful Together with Diabetes, a 10-month group-based intervention consisting of 24 meetings, 6 meetings for significant others, and 2 meetings for participants and their spouses. The IM method resulted in a tailored approach with a specific focus on the social networks of its participants. This article concludes that the IM method helped our planning team to tailor the intervention to the needs of our target population and facilitated our evaluation design. However, in hindsight, the intervention could have been improved by investing more in participatory planning and community involvement.

Point cloud registration from local feature correspondences-Evaluation on challenging datasets.

Registration of laser scans, or point clouds in general, is a crucial step of localization and mapping with mobile robots or in object modeling pipelines. A coarse alignment of the point clouds is generally needed before applying local methods such as the Iterative Closest Point (ICP) algorithm. We propose a feature-based approach to point cloud registration and evaluate the proposed method and its individual components on challenging real-world datasets. For a moderate overlap between the laser scans, the method provides a superior registration accuracy compared to state-of-the-art methods including Generalized ICP, 3D Normal-Distribution Transform, Fast Point-Feature Histograms, and 4-Points Congruent Sets. Compared to the surface normals, the points as the underlying features yield higher performance in both keypoint detection and establishing local reference frames. Moreover, sign disambiguation of the basis vectors proves to be an important aspect in creating repeatable local reference frames. A novel method for sign disambiguation is proposed which yields highly repeatable reference frames.

Increase in taxonomic assignment efficiency of viral reads in metagenomic studies

Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms. Here, based on published and original metagenomic datasets coming from virus-like particle enriched samples, we present and quantify the improvement of viral taxonomic assignment that is achievable with a new similarity-based approach. Indeed, prior to any use of similarity based taxonomic assignment methods, we propose assembling contigs from short reads as is currently routinely done in metagenomic studies, but then to further map unassembled reads to the assembled contigs. This additional mapping step increases significantly the proportions of taxonomically assignable sequence reads from a variety –plant, insect and environmental (estuary, lakes, soil, feces) – of virome studies.

A Noninterpolated Estimate of Horizontal Spatial Covariance from Nonorthogonally and Irregularly Sampled Scalar Velocities

AbstractThis paper presents a least squares method to estimate the horizontal (isotropic or anisotropic) spatial covariance of two-dimensional orthogonal vector components, without introducing an intervening mapping step and biases, from the spatial covariance of the nonorthogonally and irregularly sampled raw scalar velocities. The field is assumed to be locally homogeneous in space and sampled in an ensemble so the unknown spatial covariance is a function of spatial lag only. The transformation between the irregular grid on which nonorthogonal scalar projections of the vector are sampled and the regular orthogonal grid on which they will be mapped is created using the geometry of the problem. The spatial covariance of the orthogonal velocity components of the field is parameterized by either the energy (power) spectrum in the wavenumber domain or the lagged covariance in the spatial domain. The energy spectrum is constrained to be nonnegative definite as part of the solution of the inverse problem. This approach is applied to three example sets of data, using nonorthogonally and irregularly sampled radial velocity data obtained from 1) a simple spectral model, 2) a regional numerical model, and 3) an array of high-frequency radars. In tests where the true covariance is known, the proposed direct approaches fitting to parameterizations of the nonorthogonally and irregularly sampled raw data in the wavenumber domain and spatial domain outperform methods that map the data to a regular grid before estimating the covariance.

QTLepi Mapping in Arabidopsis thaliana.

While DNA sequence variation is known to be a major driver of phenotypic divergence, epigenetic variation has long been disregarded. One reason for that was the lack of suitable tools. The creation of epigenetically divergent but otherwise largely isogenic Arabidopsis populations has now alleviated some of these constraints. Epigenetic recombinant inbred line (epiRIL) populations allow for examining the effects of epigenetic variation on phenotypes. In addition, epiRILs enabled the development of epigenetic quantitative trait locus (QTLepi) mapping, an approach to identify causal epigenetic factors. Here, we describe the successive steps of QTLepi mapping in a broad sense, from the creation of epigenetically divergent populations to the identification of causal genes underlying particular phenotypes in Arabidopsis.

FV 15 Non-invasive high-gamma mapping in an optimized EEG lab

High-gamma mapping is still viewed by many as an exclusive privilege of intracranial EEG. In contrast we routinely perform non-invasive high-gamma mapping in our EEG lab. Here we present our high-gamma optimized EEG lab and complement the description by results from 4 studies showing clear high-gamma activity in EEG. The key elements of the setup are an electromagnetically shielded cabin (DC – 10 kHz: −30 dB to −50 dB) to attenuate powerline noise, coupled with high-resolution (24 bits/sample) and low-noise ( μ V RMS 0.16–200 Hz, μ V RMS 0.16–3500 Hz) biosignal amplifiers to record non-invasive EEG. These are complemented by high-frequency (500 Hz), high-resolution (RMS Study 1: Time-frequency analysis revealed significant high-gamma increases between 60 and 90 Hz, strongest at electrodes contralateral to the side of finger movement in single subjects and over the group. Study 2: Time-frequency analysis revealed significant high-gamma increases from 60 Hz up to 200 Hz with a focal distribution around the vertex in single subjects and over the group. Study 3: The movement-related non-invasive high-gamma band is most informative between 66 and 86 Hz. 100% decoding accuracy were achieved in both right/left hand vs feet classifications in 3 subjects for bands 1–11 Hz, 11–21 Hz, 16–26 Hz, 71–81 Hz and 76–86 Hz. Inverted CSP filters show functionally plausible patterns. Study 4: High-gamma increases (60–90 Hz) significantly stronger in erroneous responses and is strongest at fronto-central sites. We show that it is possible to reliably record non-invasive high-gamma brain activity in different EEG paradigms. Saccade-related spike potentials, which are often mistakenly taken for high-gamma brain activity, were distributed frontopolar and centroparietal and were temporally and spatially distinct from brain-related high-gamma. As the hardware is commercially available for clinically affordable prices (total ∼ 200 k€) non-invasive mapping of high-gamma using EEG is within reach of clinical routine. To further push for the clinical adoption of non-invasive high-gamma mapping steps shall be undertaken to narrow down the setup to its critical components.

Using Intervention Mapping for Program Design and Production of iCHAMPSS: An Online Decision Support System to Increase Adoption, Implementation, and Maintenance of Evidence-Based Sexual Health Programs.

In Texas and across the United States, unintended pregnancy, HIV, and sexually transmitted infections (STIs) among adolescents remain serious public health issues. Sexual risk-taking behaviors, including early sexual initiation, contribute to these public health problems. Over 35 sexual health evidence-based programs (EBPs) have been shown to reduce sexual risk behaviors and/or prevent teen pregnancies or STIs. Because more than half of these EBPs are designed for schools, they could reach and impact a considerable number of adolescents if implemented in these settings. Most schools across the U.S. and in Texas, however, do not implement these programs. U.S. school districts face many barriers to the successful dissemination (i.e., adoption, implementation, and maintenance) of sexual health EBPs, including lack of knowledge about EBPs and where to find them, perceived lack of support from school administrators and parents, lack of guidance regarding the adoption process, competing priorities, and lack of specialized training on sexual health. Therefore, this paper describes how we used intervention mapping (Steps 3 and 4, in particular), a systematic design framework that uses theory, empirical evidence, and input from the community to develop CHoosing And Maintaining Effective Programs for Sex Education in Schools (iCHAMPSS), an online decision support system to help school districts adopt, implement, and maintain sexual health EBPs. Guided by this systematic intervention design approach, iCHAMPSS has the potential to increase dissemination of sexual health EBPs in school settings.

LRCstats, a tool for evaluating long reads correction methods

Third-generation sequencing (TGS) platforms that generate long reads, such as PacBio and Oxford Nanopore technologies, have had a dramatic impact on genomics research. However, despite recent improvements, TGS reads suffer from high-error rates and the development of read correction methods is an active field of research. This motivates the need to develop tools that can evaluate the accuracy of noisy long reads correction tools. We introduce LRCstats, a tool that measures the accuracy of long reads correction tools. LRCstats takes advantage of long reads simulators that provide each simulated read with an alignment to the reference genome segment they originate from, and does not rely on a step of mapping corrected reads onto the reference genome. This allows for the measurement of the accuracy of the correction while being consistent with the actual errors introduced in the simulation process used to generate noisy reads. We illustrate the usefulness of LRCstats by analyzing the accuracy of four hybrid correction methods for PacBio long reads over three datasets. https://github.com/cchauve/lrcstats. laseanl@sfu.ca or cedric.chauve@sfu.ca. Supplementary data are available at Bioinformatics online.

Implementation of a health information exchange into community pharmacy workflow

ObjectivesTo explore the feasibility and report preliminary outcomes of the integration of a health information exchange (HIE) into community pharmacy workflow clinical service delivery. SettingIndependent pharmacy in eastern Tennessee. Practice descriptionThe pharmacy offers medication reconciliation services via HIE access, as well as other clinical pharmacy services. The average number of prescriptions filled weekly is 1900, and staffing included 3.5 full-time-equivalent (FTE) pharmacists, and 7 FTE technicians. Practice innovationHIE integration within the workflow of the pharmacy was used to enhance existing patient care services, such as medication distribution, drug use review, medication therapy management, and immunizations, as well as to implement a novel transitional care service. EvaluationA mixed-methods design was used to explore HIE workflow. Data collection included a pharmacist and pharmacy technician perceptions survey, mapping steps involved in HIE use in workflow via a think-aloud protocol, and quantitatively reporting the number and type of discordant medications found on medication reconciliation. ResultsIn total, 25 patients qualified for the medication reconciliation intervention and data collection. All 25 patients (100%) had at least 1 discordant medication. HIE access was used for 60% of patients. Community pharmacists were confident in their abilities to perform medication reconciliation and were able to perform the medication reconciliation with the use of the HIE within their workflow, albeit with some reported barriers. The average time spent per patient for HIE-facilitated transitional care was 21 minutes. ConclusionIntegration and utilization of an HIE within the workflow for the purposes of patient care service delivery in the community pharmacy is feasible, but not without limitations. Such HIE utilization and extended access to the patient’s clinical picture may represent a scalable method to enhance currently delivered pharmacist services.

Use of Radiology Procedure Codes in Health Care: The Need for Standardization and Structure.

Radiology procedure codes are a fundamental part of most radiology workflows, such as ordering, scheduling, billing, and image interpretation. Nonstandardized unstructured procedure codes have typically been used in radiology departments. Such codes may be sufficient for specific purposes, but they offer limited support for interoperability. As radiology workflows and the various forms of clinical data exchange have become more sophisticated, the need for more advanced interoperability with use of standardized structured codes has increased. For example, structured codes facilitate the automated identification of relevant prior imaging studies and the collection of data for radiation dose tracking. The authors review the role of imaging procedure codes in radiology departments and across the health care enterprise. Standards for radiology procedure coding are described, and the mechanisms of structured coding systems are reviewed. In particular, the structure of the RadLex™ Playbook coding system and examples of the use of this system are described. Harmonization of the RadLex Playbook system with the Logical Observation Identifiers Names and Codes standard, which is currently in progress, also is described. The benefits and challenges of adopting standardized codes-especially the difficulties in mapping local codes to standardized codes-are reviewed. Tools and strategies for mitigating these challenges, including the use of billing codes as an intermediate step in mapping, also are reviewed. In addition, the authors describe how to use the RadLex Playbook Web service application programming interface for partial automation of code mapping. © RSNA, 2017.

An Application of Intervention Mapping as a Phased Approach in Developing a Family-centred Programme to Reduce Violence in the Family

Aim:To describe the application of intervention mapping in the development of a family-centred approach to reduce violence in the family.Methods:Development towards a family-centred approach is described, in which only the first three steps of the five intervention mapping steps have been detailed. These three steps are unpacked as phases. Phase I, a family violence needs assessment which includes a policy analysis. Phase II determines appropriate theoretical and practical approaches through systematic reviews and lastly, Phase III as a Delphi study.Results:Intervention mapping as a form of programme development is inclusive of all relevant stakeholders and allows diverse engagement with family-centred information through its structured development process.Conclusion:Family violence should be seen as a holistic phenomenon which affects all members of the family and future interventions must be mindful of this to address family violence effectively.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

BackgroundThe analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function.ResultsWe have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic.ConclusionUb-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/.

Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain

Background field removal is an important MR phase preprocessing step for quantitative susceptibility mapping (QSM). It separates the local field induced by tissue magnetic susceptibility sources from the background field generated by sources outside a region of interest, e.g. brain, such as air-tissue interface. In the vicinity of air-tissue boundary, e.g. skull and paranasal sinuses, where large susceptibility variations exist, present background field removal methods are usually insufficient and these regions often need to be excluded by brain mask erosion at the expense of losing information of local field and thus susceptibility measures in these regions. In this paper, we propose an extension to the variable-kernel sophisticated harmonic artifact reduction for phase data (V-SHARP) background field removal method using a region adaptive kernel (R-SHARP), in which a scalable spherical Gaussian kernel (SGK) is employed with its kernel radius and weights adjustable according to an energy “functional” reflecting the magnitude of field variation. Such an energy functional is defined in terms of a contour and two fitting functions incorporating regularization terms, from which a curve evolution model in level set formation is derived for energy minimization. We utilize it to detect regions of with a large field gradient caused by strong susceptibility variation. In such regions, the SGK will have a small radius and high weight at the sphere center in a manner adaptive to the voxel energy of the field perturbation. Using the proposed method, the background field generated from external sources can be effectively removed to get a more accurate estimation of the local field and thus of the QSM dipole inversion to map local tissue susceptibility sources. Numerical simulation, phantom and in vivo human brain data demonstrate improved performance of R-SHARP compared to V-SHARP and RESHARP (regularization enabled SHARP) methods, even when the whole paranasal sinus regions are preserved in the brain mask. Shadow artifacts due to strong susceptibility variations in the derived QSM maps could also be largely eliminated using the R-SHARP method, leading to more accurate QSM reconstruction.

Soundscapes, social media, and big data: The next step in strategic noise mapping

The current state-of-the art in noise assessment involves the development of a strategic noise map to identify areas with excessive noise levels, expressed in terms of a single time-averaged noise indicator. While noise maps yield important information regarding sound pressure levels in a particular space, they do not give any representation of the overall sound quality in that space. A more human-centered approach to noise assessment could be achieved by developing soundscapes as a complementary tool to noise mapping. However, most soundscape studies traditionally use surveys or interviews to assess general sentiment toward the acoustic environment, and as such are generally restricted to small geographic areas, compared to the entire cities considered in noise mapping. Instead of using traditional assessment techniques, this project aims to harness the potential of big data, including, for example noise complaint data or social media chatter related to noise, to better assess public sentiments towards s...