Distance-based local linear regression for functional predictors

The problem of nonparametrically predicting a scalar response variable from a functional predictor is considered. A sample of pairs (functional predictor and response) is observed. When predicting the response for a new functional predictor value, a semi-metric is used to compute the distances between the new and the previously observed functional predictors. Then each pair in the original sample is weighted according to a decreasing function of these distances. A Weighted (Linear) Distance-Based Regression is fitted, where the weights are as above and the distances are given by a possibly different semi-metric. This approach can be extended to nonparametric predictions from other kinds of explanatory variables (e.g., data of mixed type) in a natural way.     

To Score or Not to Score? Tripling Insights for Participatory Design

For evaluating visual-analytics tools, many studies confine to scoring user insights into data. For participatory design of those tools, we propose a three-level methodology to make more out of users' insights. The Relational Insight Organizer (RIO) helps to understand how insights emerge and build on one each other.     

Semantics-driven annotation of patient-specific 3D data: a step to assist diagnosis and treatment of rheumatoid arthritis

In the digital era, patient-specific 3D models (3D-PSMs) are becoming increasingly relevant in computer-assisted diagnosis, surgery training on digital models, or implant design. While advanced imaging and reconstruction techniques can create accurate and detailed 3D models of patients’ anatomy, software tools that are able to fully exploit the potential of 3D-PSMs are still far from being satisfactory. In particular, there is still a lack of integrated approaches for extracting, coding, sharing and retrieving medically relevant information from 3D-PSMs and use it concretely as a support to diagnosis and treatment. In this article, we propose the SemAnatomy3D framework, which demonstrates how the ontology-driven annotation of 3D-PSMs and of their anatomically relevant features (parts of relevance) can assist clinicians to document more effectively pathologies and their evolution. We exemplify the idea in the context of the diagnosis of rheumatoid arthritis of the hand district, and show how feature extraction tools and semantic 3D annotation can provide a rich characterization of anatomical landmarks (e.g., articular facets, prominent features, ligament attachments) and pathological markers (erosions, bone loss). The core contributions are an ontology-driven part-based annotation method for the 3D-PSMs and a novel automatic localization of erosion and quantification of the OMERACT RAMRIS erosion score. Finally, our results have been compared against a medical ground truth.     

The Early Bird Gets the Worm,But the Second Mouse Gets the Cheese: Non‐Technological Innovation in Creative Industries

In the context of economic turmoil, firms in the creative industries (CIs) must make fast decisions as to when to break through with innovations. This paper discusses non‐technological, organizational innovation of early‐adopters, first movers and early followers in order to overcome persistent economic decline, and the implication of different strategies for innovation success. The strategic principle of the pioneer's advantage rests on pre‐emption – the premise that ‘the early bird gets the worm’ and this often applies to business model innovation (BMI). ‘But the second mouse gets the cheese’ points at early followers who may have a more systematic, strategic approach towards innovation. Greater understanding of the advantages of each strategic approach and their significance for innovation performance is critical for CIs where unpredictability and the accelerating pace of change pervade the decisions concerning innovation. Drawing on five exemplary cases of archaeological firms in Spain, this paper explores different innovation process dynamics. The study develops a contingency model where pioneers who challenge their current business model, may be outperformed by early followers who incorporate complementary management innovation (MI) initiatives into the BMI.     

Spiral-shaped inertial stem cell device for high-throughput enrichment of iPSC-derived neural stem cells

Stem cell enrichment plays a critical role in both research and clinical applications. The typical method for stem cell enrichment may use invasive processes and takes a long period of time. Spiral-shaped microfluidic devices, which combine lift and Dean drag forces to direct cells of different sizes into separate trajectories, can be used to noninvasively process samples at a rate of milliliters per minute. This paper presents a simple 2-loop spiral-shaped inertial microfluidic devices with the aid of sheath flow to enrich neural stem cells (NSCs), derived from induced pluripotent stem cells. NSCs and spontaneously differentiated non-neural cells were mixed and flowed through the spiral-shaped devices. Samples collected at the outlets were analyzed for purity and recovery. It was found that the device focused the NSCs into a narrow trajectory, which could then be collected in two out of the eight outlets. The device was tested at different flow rates and found that the most highly enriched fractions (2.1×) with NSCs recovery 93% were achieved at the flow rate (3 ml/min). Next, we extended our investigation from 2-loop design to 10-loop design to eliminate the use of sheath flow. NSCs were enriched to 2.5×, but only 38% of the NSCs were recovered from the most enriched fractions. Spiral-shaped microfluidic devices are capable of rapid, label-free enrichment of target stem cells, and have great potential in point-of-care tissue preparation.     

XtalOpt version r7: An open-source evolutionary algorithm for crystal structure prediction

A new version of XtalOpt, a user-friendly GPL-licensed evolutionary algorithm for crystal structure prediction, is available for download from the CPC library or the XtalOpt website, http://xtalopt.openmolecules.net. The new version now supports four external geometry optimization codes (VASP, GULP, PWSCF, and CASTEP), as well as three queuing systems: PBS, SGE, SLURM, and “Local”. The local queuing system allows the geometry optimizations to be performed on the user?s workstation if an external computational cluster is unavailable. Support for the Windows operating system has been added, and a Windows installer is provided. Numerous bugfixes and feature enhancements have been made in the new release as well.

New version program summary

Program title:XtalOptCatalogue identifier: AEGX_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 125 383No. of bytes in distributed program, including test data, etc.: 11 607 415Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: Linux, MS WindowsClassification: 7.7External routines: Qt [2], Open Babel [3], Avogadro [4], and one of: VASP [5], PWSCF [6], GULP [7], CASTEP [8]Catalogue identifier of previous version: AEGX_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 372Does the new version supersede the previous version?: YesNature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum of a crystalline structure on its potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available for use and collaboration under the GNU Public License. See the original publication on XtalOpt?s implementation [11] for more information on the method.Reasons for new version: Since XtalOpt?s initial release in June 2010, support for additional optimizers, queuing systems, and an operating system has been added. XtalOpt can now use VASP, GULP, PWSCF, or CASTEP to perform local geometry optimizations. The queue submission code has been rewritten, and now supports running any of the above codes on ssh-accessible computer clusters that use the Portable Batch System (PBS), Sun Grid Engine (SGE), or SLURM queuing systems for managing the optimization jobs. Alternatively, geometry optimizations may be performed on the user?s workstation using the new internal “Local” queuing system if high performance computing resources are unavailable. XtalOpt has been built and tested on the Microsoft Windows operating system (XP or later) in addition to Linux, and a Windows installer is provided. The installer includes a development version of Avogadro that contains expanded crystallography support [12] that is not available in the mainline Avogadro releases. Other notable new developments include:

• • 

  LIBSSH [10] is distributed with the XtalOpt sources and used for communication with the remote clusters, eliminating the previous requirement to set up public-key authentication;

• • 

  Plotting enthalpy (or energy) vs. structure number in the plot tab will trace out the history of the most stable structure as the search progresses A read-only mode has been added to allow inspection of previous searches through the user interface without connecting to a cluster or submitting new jobs;

• • 

  The tutorial [13] has been rewritten to reflect the changes to the interface and the newly supported codes. Expanded sections on optimizations schemes and save/resume have been added;

• • 

  The included version of SPGLIB has been updated. An option has been added to set the Cartesian tolerance of the space group detection. A new option has been added to the Progress table?s right-click menu that copies the selected structure?s POSCAR formatted representation to the clipboard;

• • 

  Numerous other small bugfixes/enhancements.

Summary of revisions: See “Reasons for new version” above.Running time: User dependent. The program runs until stopped by the user.References:

•  [1] 

  http://www.gnu.org/licenses/gpl.html.

•  [2] 

  http://www.trolltech.com/.

•  [3] 

  http://openbabel.org/.

•  [4] 

  http://avogadro.openmolecules.net.

•  [5] 

  http://cms.mpi.univie.ac.at/vasp.

•  [6] 

  http://www.quantum-espresso.org.

•  [7] 

  https://www.ivec.org/gulp.

•  [8] 

  http://www.castep.org.

•  [9] 

  http://spglib.sourceforge.net.

• [10] 

  http://www.libssh.org.

• [11] 

  D. Lonie, E. Zurek, Comp. Phys. Comm. 182 (2011) 372–387, doi:10.1016/j.cpc.2010.07.048.

• [12] 

  http://davidlonie.blogspot.com/2011/03/new-avogadro-crystallography-extension.html.

• [13] 

  http://xtalopt.openmolecules.net/globalsearch/docs/tut-xo.html.

     

XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Program summary

Program title:XtalOptCatalogue identifier: AEGX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 36 849No. of bytes in distributed program, including test data, etc.: 1 149 399Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: LinuxClassification: 7.7External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7].Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available to the scientific community for use and collaboration under the GNU Public License.Running time: User dependent. The program runs until stopped by the user.References:

• [1] 

  http://www.gnu.org/licenses/gpl.html.

• [2] 

  http://www.trolltech.com/.

• [3] 

  http://openbabel.org/.

• [4] 

  http://avogadro.openmolecules.net.

• [5] 

  http://cms.mpi.univie.ac.at/vasp.

• [6] 

  http://www.quantum-espresso.org.

• [7] 

  https://www.ivec.org/gulp.

• [8] 

  http://spglib.sourceforge.net.

     

Remotely sensed surface water extent as an indicator of short-term changes in ecohydrological processes in sub-Saharan Western Africa

The highly variable rainfall in the arid and semi-arid regions of sub-Saharan Western Africa drives both surface water availability and vegetation cover. Recent studies have established linkages between rainfall and vegetation cover at local to regional scales, but no study related yet remote sensing derived rainfall and vegetation cover to the available surface water. A new dataset based on SPOT VEGETATION (VGT) represents surface water bodies (SWB) in the arid and semi-arid regions of sub-Saharan Western Africa. Water bodies represent the integrated hydrological response of a catchment, and changes in their spatial extent involve complex interactions at the catchment scale. We analyzed time series of remotely sensed vegetation cover, rainfall and surface water extent for the period 1999–2008, and could detect and statistically demonstrate the links between these biophysical variables. Our findings for two regions in Mali and Burkina Faso suggest that vegetation cover is positively related to the amount of available surface water for those catchments that are mainly covered by annual plants. The observed relationships between remotely sensed variables allow developing ecological indicators that can indicate short-term changes in arid and semi-arid ecosystems at local to regional scales.