Flexible Interface Research Articles

SOCCOMAS: A Self-Describing and Content-Independent Application for Semantic Ontology-Controlled Web-Content-Management-Systems

Ontologies are usually utilized for representing knowledge. Here, we extend this use and demonstrate that ontologies also can be used for describing and controlling semantic Web-Content-Management-Systems (WCMS). We call the resulting application SOCCOMAS: a self-describing and content-independent application for semantic ontology-controlled Web-Content-Management-Systems (http://escience.biowikifarm.net/wiki/SOCCOMAS). SOCCOMAS manages the contents of its WCMS through a corresponding knowledge base that is stored in a tuple store. It makes its contents accessible via a flexible and interactive graphical user interface (GUI), utilizing the JavaScript framework AngularJS. Central to SOCCOMAS is a set of application ontologies and a Java middleware, both of which have been developed by us. The ontologies contain the descriptions that control the behavior of the WCMS and the Java middleware interprets these descriptions as an operation-language with commands, attributes and variables. This language is used for describing and therewith defining the function and design of the GUI of the WCMS, including all its user interactions, the underlying data schemes and representations, and all workflow processes of the WCMS. The core application implements a set of default features, such as versioning, provenance and access rights management. These features will be available in all semantic WCMS instances that are based on SOCCOMAS. Because of the ontology-controlled design, SOCCOMAS allows easy customization with a minimum of technical programming background required. Thereby, each WCMS can have its own particular data views, input forms and workflows. The morphological data repository Morph∙D∙Base serves as a first use-case for SOCCOMAS, for which we are implementing ontology-based specimen and media entry representations as well as a new module for the generation of ontology-based morphological descriptions with semantic image annotation.

Precise tuning of single-photon frequency using an optical single sideband modulator

Frequency translation of single photons while preserving their quantum characteristics is an important technology for flexible networking of photonic quantum communication systems. Here we demonstrate a flexible scheme to interface different-color photons using an optical single sideband (OSSB) modulator. By changing the radio-frequency signal that drives the modulators, we can easily shift and precisely tune the frequency of single photons. Using the OSSB modulator, we successfully erased the frequency distinguishability of non-degenerated photon pairs to obtain the Hong-Ou-Mandel interference with a visibility exceeding 90%. We also demonstrated that the level of distinguishability can be precisely controlled by the OSSB modulator. We expect that the OSSB modulator will provide a simple and flexible photonic interface for realizing advanced quantum information systems.

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4

Like all members of the Toll-like receptor (TLR) family, TLR4 comprises of a large ectodomain (ECD) involved in ligand recognition at the cell-surface, and a cytosolic Toll/interleukin-1 receptor (TIR) signalling domain, linked by a lipid membrane-anchored transmembrane (TM) domain (TMD). Binding of immunostimulatory pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide (LPS) to myeloid differentiation factor 2 (MD-2) coreceptor-complexed TLR4 leads to its dimerization, resulting in productive juxtaposition of TIR domains and the initiation of pro-inflammatory innate immune responses. Whilst the process of PAMP recognition is relatively well understood, thanks to numerous high-resolution crystallographic structures of ECDs, the mechanism by which such recognition is translated into TMD dimerization and activating conformational changes is less clear. Based on available biophysical and biochemical experimental data, ab initio modelling, and multiscale molecular dynamics (MD) simulations entailing a total of >13μs and >200μs of atomistic and coarse-grained sampling, respectively, we investigate the structural basis for TLR4 TMD dimerization within a biologically relevant lipid membrane environment. A key polar-xx-polar (637SxxS640) motif is shown to drive association of the TLR4 TMDs, and to maintain a flexible interface, which may be disrupted by selected point mutations. Furthermore, MD simulations of various TMD+ECD constructs have been used to investigate the coupling between domains, revealing that flexible linkers abrogate dimerization via aggregation of ECDs at the membrane surface, explaining previous biochemical observations. These results improve our understanding of the assembly and signalling mechanisms of TLR4, and pave the way for rational structure-based development of membrane-associated immunomodulatory molecules.

Working at the intersection of context, culture, and technology: Provider perspectives on antimicrobial stewardship in the emergency department using electronic health record clinical decision support

Antibiotic stewardship programs (ASPs) have not been fully developed for the emergency department (ED), in part the result of the barriers characteristic of this setting. Electronic health record-based clinical decision support (EHR CDS) represents a promising strategy to implement ASPs in the ED. We aimed to determine the cultural beliefs and structural barriers and facilitators to implementation of antimicrobial stewardship in the pediatric ED using EHR CDS. Interviews and focus groups were conducted with hospital and ED leadership, attending ED physicians, nurse practitioners, physician assistants, and residents at a single health system in Colorado. We reviewed and coded the data using constant comparative analysis and framework analysis until a final set of themes emerged. Two dominant perceptions shaped providers' perspectives on ASPs in the ED and EHR CDS: (1) maintaining workflow efficiency and (2) constrained decision-making autonomy. Clinicians identified structural barriers to ASPs, such as pace of the ED, and various beliefs that shaped patterns of practice, including accommodating the prescribing decisions of other providers and managing parental expectations. Recommendations to enhance uptake focused on designing a simple yet flexible user interface, providing clinicians with performance data, and on-boarding clinicians to enhance buy-in. Developing a successful ED-based ASP using EHR CDS should attend to technologic needs, the institutional context, and the cultural beliefs of practice associated with providers' antibiotic prescribing.

A novel pneumatic stimulator for the investigation of noise-enhanced proprioception.

Executing coordinated movements requires that motor and sensory systems cooperate to achieve a motor goal. Impairment of either system may lead to unstable and/or inaccurate movements. In rehabilitation training, however, most approaches have focused on the motor aspects of the control loop. We are examining mechanisms that may enhance the sensory system to improve motor control. More precisely, the effects of stochastic subliminal vibratory tactile stimulation on wrist proprioception. We developed a device - based on a novel soft pneumatic actuator skin technology - to stimulate multiple sites simultaneously and independently. This device applies vibratory stimulation (amplitude < 0.50 mm, bandwidth 20-120 Hz) to the skin overlaying the tendons of a joint to target the receptors in charge of position and movement encoding. It achieves high spatial resolution (< 1 mm2), uses a soft and flexible interface, and has the potential to be used in combination with additional rehabilitation interventions. We conducted a feasibility study with 16 healthy subjects (11 younger - 6 females; 5 older - 2 females) in which a robotic manipulandum moved the subject's wrist to defined positions that had to be matched with a gauge. Comparing trials with and without stimulation we found that stochastic stimulation influenced joint position sense. The device we developed can be readily used in psycho-physical experiments, and subsequently benefit physiotherapy and rehabilitation treatments.

PulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.

Metabolic labelling of RNA is a well-established and powerful method to estimate RNA synthesis and decay rates. The pulseR R package simplifies the analysis of RNA-seq count data that emerge from corresponding pulse-chase experiments. The pulseR package provides a flexible interface and readily accommodates numerous different experimental designs. To our knowledge, it is the first publicly available software solution that models count data with the more appropriate negative-binomial model. Moreover, pulseR handles labelled and unlabelled spike-in sets in its workflow and accounts for potential labeling biases (e.g. number of uridine residues). The pulseR package is freely available at https://github.com/dieterich-lab/pulseR under the GPLv3.0 licence. a.uvarovskii@uni-heidelberg.de or christoph.dieterich@uni-heidelberg.de. Supplementary data are available at Bioinformatics online.

Waveform contenders for 5G: Description, analysis and comparison

5G will have to cope with a high degree of heterogeneity in terms of services and requirements. Among these latter, flexible and efficient use of all available non-contiguous spectra for different network deployment scenarios is one challenge for the future 5G. To maximize spectrum efficiency, a flexible 5G air interface technology capable of mapping various services to the best suitable combinations of frequency and radio resources will also be required. In this work, a fair comparison of several 5G waveform candidates (UFMC, FBMC-OQAM, and FBMC-QAM) is proposed under a common framework. Spectral efficiency, power spectral density, peak to average power ratio and performance in terms of bit error rate under various realistic channel conditions are assessed. The waveforms are then compared in an asynchronous multi-user uplink transmission. Based on these results, in order to increase the spectral efficiency, a bit loading algorithm is proposed to cope with the non-uniform distribution of the interference across the carriers. The benefits of these new waveforms for the foreseen 5G use cases are clearly highlighted. It is also stressed that some concepts still need to be improved to achieve the full range of expected benefits of 5G.

On the internal interfaces in finite-difference schemes

Implementing sharp internal interfaces in finite-difference schemes with high spatial accuracy is challenging. The propagation of fields in a locally homogeneous part of a model can be performed with spectral accuracy. The implementations of interfaces are generally considered accurate to, at best, second order. This situation can be improved by a proper band limitation of the simulation grid. Interfaces can be located anywhere on the grid; however, the fine detail information regarding the interface location must be imprinted correctly in the coarse simulation grid. This can be done by starting out with a representation of a sharp material jump in the wavenumber domain and limiting the highest wavenumber to the maximum wavenumber allowed for the simulation grid. The resulting wavenumber representation is then transformed to the space domain. An alternative procedure is to create a fine grid model that is low-pass filtered to remove wavenumbers above the maximum wavenumber allowed for the coarse simulation grid. The fine grid is thereafter sampled at the required coordinates for the coarse simulation grid. An accurate and flexible interface implementation is a requisite for reducing staircase diffractions in higher dimensional finite-difference simulations. Our strategy achieves this. The frequency content of the source must be constrained to a level in which the spatial sampling is at approximately four to five grid points per shortest wavelength. Simulation results indicate that the implementation of the interface is accurate to at least the sixth order for large contrasts. Our method can be used for all systems of partial differential equations that formally can be expressed as a material parameter times a dynamic field on one side of the equal sign and with spatial derivatives on the other side of the equal sign. For geophysical simulations, the most important cases will be the Maxwell equations and the acoustic and elastic wave equations.

Development of Drought Indices for Semi-Arid Region Using Drought Indices Calculator (DrinC) – A Case Study from Madurai District, a Semi-Arid Region in India

Drought is considered as a major natural hazard/ disaster, affecting several sectors of the economy and the environment worldwide. Drought, a complex phenomenon can be characterised by its severity, duration, and areal extent. Drought indices for the characterization and the monitoring of drought simplify the complex climatic functions and can quantify climatic anomalies for their severity, duration, and frequency. With this as background drought indices were worked out for Madurai district of Tamil Nadu using DrinC (Drought Indices Calculator) software. DrinC calculates the drought indices viz., deciles, Standard Precipitation Index (SPI), Reconnaissance Drought Index (RDI), Streamflow Drought Index (SDI) by providing a simple, though flexible interface by considering all the factors. The drought of 3, 6 and 9 months as time series can also be estimated. The results showed that drought index of Madurai region by decile method revealed that among the 100 years, 20 years were affected by drought and it is cyclic in nature and occurring almost every 3 to 7 years once repeatedly, except for some continuous period, i.e., 1923, 1924 and 1985, 1986, etc. During the last five decades, the incidence is higher with 13 events, whereas in the first five decades it was only 7. The SPI and RDI index also followed the similar trend of deciles. However, under SPI and RDI, the severely dry and extremely dry category was only seven years and all other drought years of deciles were moderately dry. Our study indicated that SPI is a better indicator than deciles since here severity can be understood. SDI did not follow the trend similar to SPI or RDI. Regression analysis showed that the SPI and RDI are significantly correlated and if 1st 3 months rainfall data is available one can predict yearly RDI drought index. The results demonstrated that these approaches could be useful for developing preparedness plan to combat the consequences of drought. Findings from such studies are useful tools for devising strategic preparedness plans to combat droughts and mitigate their effects on the activities in the various sectors of the economy.

BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology.

The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

Flexible Optoelectric Neural Interface Integrated Wire-Bonding $\mu$ LEDs and Microelectrocorticography for Optogenetics

As an advanced brain–computer interface, the flexible surface electrode array has been used for spatiotemporal localization of neural interactions by recording electrocorticography (ECoG) signals over brain cortical areas. Compared with the electrical stimulation, optogenetics provides a potentially ideal way to stimulate the genetically modified brain tissue by light. In this paper, we developed an optoelectric neural interface combining a micro ECoG ( $\mu $ ECoG) recording electrode array and a microlight-emitting diode ( $\mu $ LED) array. Three $\mu $ LED chips were connected to a flexible polyimide substrate by a unique wire bonding method, and their light-emitting surfaces were downward and in the same plane with the substrate’s lower surface, which allowed blue light directly going through the aligned holes on substrate with barely no loss. In addition, the recording electrodes were modified with electroplated platinum black or activated iridium oxide, and their stability was proved well after repetitive pressures. Mechanical strength and conformality of two $\mu $ ECoG arrays with 5 and $10~\mu \text{m}$ thicknesses were tested. Finally, this bidirectional neural interface was proved to be effective by an acute in vivo experiment performed by attaching two devices with varied thicknesses to the cortical surface of a mouse expressing Channelrhodopsin-2.

Pulse shaping design for OFDM systems

Spectrally contained OFDM-based waveforms are considered key enablers for a flexible air interface design to support a broad range of services and frequencies as envisaged for 5G mobile systems. By allowing for the flexible configuration of physical layer parameters in response to diverse requirements, these waveforms enable the in-band coexistence of different services. One candidate from this category of waveforms is pulse-shaped OFDM, which follows the idea of subcarrier filtering while fully maintaining the compatibility with CP-OFDM. In this paper, we provide an overview of pulse shaping methods in OFDM systems and propose a new pulse-shaped design method with arbitrary length constraint and good time-frequency localization property. Based on the pulse design, we discuss different receiver realizations and present a criterion for pulse shape evaluation. In addition, the parameterizations of OFDM system to address diverse requirements of the services envisaged for the 5G systems are described. Link and system performance results for selected scenarios show that a proper design of the OFDM numerologies and pulse shapes could substantially improve the performance under time and frequency distortions. Furthermore, pulse-shaped OFDM is able to support asynchronous transmissions and reduce the signal sensitivity to Doppler distortions, rendering it beneficial for various applications from the context of vehicular communications and the Internet-of-things.

Bovine and degenerated human annulus fibrosus: a microstructural and micromechanical comparison

The complex structure of the annulus fibrosus is strongly related to its mechanical properties. Recent work showed that it is possible to observe the relative movement of fibre bundles in loaded cow tail annulus; the aim of this work was to describe and quantify annulus fibrosus micromechanics in degenerated human disc, and compare it with cow tail annulus, an animal model often used in the literature. Second harmonic generation was used to image the collagen matrix in twenty strips of annulus fibrosus harvested from intervertebral disc of seven patients undergoing surgery. Samples were loaded to 6% tensile strain in 1% steps. Elastic modulus was calculated from loading curves, and micromechanical strains were calculated from the images using custom software. The same protocol was applied to twenty strips of annulus harvested from cow tail discs. Significant morphological differences were found between human and cow tail samples, the most striking being the lack of collagen fibre crimp in the former. Fibres were also observed bending and running from one lamella to the other, forming a strong flexible interface. Interdigitation of fibre bundles was also present at this interface. Quantitative results show complex patterns of inter-bundle and inter-lamellar behaviour, with inter-bundle sliding being the main strain mechanism. Elastic modulus was similar between species, and it was not affected by the degree of degeneration. This work gives an insight into the complex structure and mechanical function of the annulus fibrosus, which should be accounted for in disc numerical modelling.

Synergy-Based Bilateral Port: A Universal Control Module for Tele-Manipulation Frameworks Using Asymmetric Master-Slave Systems.

Endowing tele-manipulation frameworks with the capability to accommodate a variety of robotic hands is key to achieving high performances through permitting to flexibly interchange the end-effector according to the task considered. This requires the development of control policies that not only cope with asymmetric master–slave systems but also whose high-level components are designed in a unified space in abstraction from the devices specifics. To address this dual challenge, a novel synergy port is developed that resolves the kinematic, sensing, and actuation asymmetries of the considered system through generating motion and force feedback references in the hardware-independent hand postural synergy space. It builds upon the concept of the Cartesian-based synergy matrix, which is introduced as a tool mapping the fingertips Cartesian space to the directions oriented along the grasp principal components. To assess the effectiveness of the proposed approach, the synergy port has been integrated into the control system of a highly asymmetric tele-manipulation framework, in which the 3-finger hand exoskeleton HEXOTRAC is used as a master device to control the SoftHand, a robotic hand whose transmission system relies on a single motor to drive all joints along a soft synergistic path. The platform is further enriched with the vision-based motion capture system Optitrack to monitor the 6D trajectory of the user’s wrist, which is used to control the robotic arm on which the SoftHand is mounted. Experiments have been conducted with the humanoid robot COMAN and the KUKA LWR robotic manipulator. Results indicate that this bilateral interface is highly intuitive and allows users with no prior experience to reach, grasp, and transport a variety of objects exhibiting very different shapes and impedances. In addition, the hardware and control solutions proved capable of accommodating users with different hand kinematics. Finally, the proposed control framework offers a universal, flexible, and intuitive interface allowing for the performance of effective tele-manipulations.

Pseudogapping as Pseudo-VP-Ellipsis

In this article, we propose an analysis of pseudogapping in Hybrid Type-Logical Categorial Grammar (Hybrid TLCG; Kubota 2010 ; Kubota and Levine 2012 ). Pseudogapping poses a particularly challenging problem for previous analyses in both the transformational and the nontransformational literature. We argue that the flexible syntax-semantics interface of Hybrid TLCG enables an analysis of pseudogapping that synthesizes the key insights of both transformational and nontransformational approaches, at the same time overcoming the major difficulties of each type of approach.

EBASIS (Bioactive Substances in Food Information Systems) and Bioactive Intakes: Major Updates of the Bioactive Compound Composition and Beneficial Bioeffects Database and the Development of a Probabilistic Model to Assess Intakes in Europe.

eBASIS (Bioactive Substances in Food Information Systems), a web-based database that contains compositional and biological effects data for bioactive compounds of plant origin, has been updated with new data on fruits and vegetables, wheat and, due to some evidence of potential beneficial effects, extended to include meat bioactives. eBASIS remains one of only a handful of comprehensive and searchable databases, with up-to-date coherent and validated scientific information on the composition of food bioactives and their putative health benefits. The database has a user-friendly, efficient, and flexible interface facilitating use by both the scientific community and food industry. Overall, eBASIS contains data for 267 foods, covering the composition of 794 bioactive compounds, from 1147 quality-evaluated peer-reviewed publications, together with information from 567 publications describing beneficial bioeffect studies carried out in humans. This paper highlights recent updates and expansion of eBASIS and the newly-developed link to a probabilistic intake model, allowing exposure assessment of dietary bioactive compounds to be estimated and modelled in human populations when used in conjunction with national food consumption data. This new tool could assist small- and medium-sized enterprises (SMEs) in the development of food product health claim dossiers for submission to the European Food Safety Authority (EFSA).

The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design.

The task of epitope discovery and vaccine design is increasingly reliant on bioinformatics analytic tools and access to depositories of curated data relevant to immune reactions and specific pathogens. The Immune Epitope Database and Analysis Resource (IEDB) was indeed created to assist biomedical researchers in the development of new vaccines, diagnostics, and therapeutics. The Analysis Resource is freely available to all researchers and provides access to a variety of epitope analysis and prediction tools. The tools include validated and benchmarked methods to predict MHC class I and class II binding. The predictions from these tools can be combined with tools predicting antigen processing, TCR recognition, and B cell epitope prediction. In addition, the resource contains a variety of secondary analysis tools that allow the researcher to calculate epitope conservation, population coverage, and other relevant analytic variables. The researcher involved in vaccine design and epitope discovery will also be interested in accessing experimental published data, relevant to the specific indication of interest. The database component of the IEDB contains a vast amount of experimentally derived epitope data that can be queried through a flexible user interface. The IEDB is linked to other pathogen-specific and immunological database resources.

Highly Flexible and Self-Healable Thermal Interface Material Based on Boron Nitride Nanosheets and a Dual Cross-Linked Hydrogel

The booming growth of flexible and stretchable electronic devices with increasing power and multifunctionalities calls for novel highly efficient thermal interface materials (TIMs) with versatile functions, such as high deformability and self-healing ability, whereas traditional metallic-based or grease-based ones could hardly provide. Herein, we report a highly flexible and self-healable dual-cross-linked hydrogel-based nanocomposite filled with hexagonal boron nitride (h-BN) nanosheets fabricated by in situ polymerization of acrylic acid (AA). The thermal conductivity of the composites can be tuned by adjusting both fraction of BNNSs and water content. Although a solid, the highly flexible characteristic of the developed TIMs enables a perfect ability to replicate the texture of a rough surface, which may greatly enhance thermal transfer between adjacent surfaces. By increasing the water content to soften the material, it can be recycled and reused for different kinds of rough surface. In addition, benefiting from the dual-cross-linked structure, the composites are capable of recovering both mechanical strength and thermal conductivity even from severe structural breakdowns, for example, three consecutive cutting and healing cycles. This study may pave the way to fabrication of multifunctional highly flexible TIMs, which may promote the development of heat dissipation materials.

Programmable Neuron Array Based on a 2-Transistor Multiplier Using Organic Floating-Gate for Intelligent Sensors

Artificial neurons are introduced for local data processing in a large area sensor device, thereby reducing multiple sensor outputs to 1-bit digital output. To reduce the area overhead and layout complexity due to the artificial neuron array, a 2-transistor multiplier using organic floating-gate pFET is proposed. Each artificial neuron has multiple organic floating-gate pFETs embedded in it. A virtual scalable floating-gate based memory architecture is realized for selective programming of each floating-gate pFET. Threshold voltage tuning is utilized to realize both of the positive and the negative weight values for a neuron. A flexible interface pressure monitoring device with pressure-sensitive rubber sheet is developed for pressure ulcer prevention to show the feasibility of our concept. A 50 mm2 organic sheet integrating $2\times 2$ neuron array is fabricated with 2-V organic CMOS transistors. Selective floating-gate programming and neuron operation are successfully demonstrated.