Processing Artifacts Research Articles

A Semi-Open Loop GNSS Carrier Tracking Algorithm for Monitoring Strong Equatorial Scintillation

Strong equatorial ionospheric scintillation of radio signals is often associated with simultaneous deep amplitude fading and rapid random carrier phase fluctuations. It poses a challenge for satellite navigation receiver carrier phase tracking loop operation. This paper presents a semi-open loop algorithm that utilizes the known position of a stationary receiver and satellite orbit information to estimate carrier phase variations during deep signal fading. Strong GPS scintillation data collected on Ascension Island in March 2013 are processed to reveal fast phase changes of half and full cycles over tens of milliseconds on all three GPS frequencies. Simulated signals are used to validate the algorithm and confirm that the fast phase changes are true scintillation effects rather than receiver processing artifacts. The algorithm performance is demonstrated through comparison with several closed-loop implementations. Potential errors associated with receiver clock bias and other environmental factors are also analyzed. A statistical summary of the concurrent fast phase changes and deep fades based on the processing results of the Ascension Island data is presented.

CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing

BackgroundLong-read nanopore sequencing technology is of particular significance for taxonomic identification at or below the species level. For many environmental samples, the total extractable DNA is far below the current input requirements of nanopore sequencing, preventing “sample to sequence” metagenomics from low-biomass or recalcitrant samples.ResultsHere we address this problem by employing carrier sequencing, a method to sequence low-input DNA by preparing the target DNA with a genomic carrier to achieve ideal library preparation and sequencing stoichiometry without amplification. We then use CarrierSeq, a sequence analysis workflow to identify the low-input target reads from the genomic carrier. We tested CarrierSeq experimentally by sequencing from a combination of 0.2 ng Bacillus subtilis ATCC 6633 DNA in a background of 1000 ng Enterobacteria phage λ DNA. After filtering of carrier, low quality, and low complexity reads, we detected target reads (B. subtilis), contamination reads, and “high quality noise reads” (HQNRs) not mapping to the carrier, target or known lab contaminants. These reads appear to be artifacts of the nanopore sequencing process as they are associated with specific channels (pores).ConclusionBy treating sequencing as a Poisson arrival process, we implement a statistical test to reject data from channels dominated by HQNRs while retaining low-input target reads.

Deconstructing spatial-numerical associations

Spatial-numerical associations (SNAs) have been studied extensively in the past two decades, always requiring either explicit magnitude processing or explicit spatial-directional processing. This means that the typical finding of an association of small numbers with left or bottom space and of larger numbers with right or top space could be due to these requirements and not the conceptual representation of numbers. The present study compares explicit and implicit magnitude processing in an implicit spatial-directional task and identifies SNAs as artefacts of either explicit magnitude processing or explicit spatial- directional processing; they do not reveal spatial-conceptual links. This finding requires revision of current accounts of the relationship between numbers and space.

A porous crystal plasticity constitutive model for ductile deformation and failure in porous single crystals

This work presents a porous crystal plasticity model which incorporates the necessary mechanisms of deformation and failure in single crystalline porous materials. Such models can play a significant role in better understanding the behaviour of inherently porous materials which could be an artefact of manufacturing process viz. 3D metal printing. The presented model is an extension of the conventional crystal plasticity model. The proposed model includes the effect of mechanics-based quantities, such as stress triaxiality, initial porosity, crystal orientation, void growth and coalescence, on the deformation and failure of a single crystalline material. A detailed parametric assessment of the model has been presented to assess the model behaviour for different material parameters. The model is validated using uniaxial data taken from literature. Lastly, model predictions have been presented to demonstrate the model’s ability in predicting deformation and failure in polycrystalline sheet materials.

Synchronised visualisation of software process and product artefacts: Concept, design and prototype implementation

ContextMost prior software visualisation (SV) research has focused primarily on making aspects of intangible software product artefacts more evident. While undoubtedly useful, this focus has meant that software process visualisation has received far less attention. ObjectiveThis paper presents Conceptual Visualisation, a novel SV approach that builds on the well-known CodeCity metaphor by situating software code artefacts alongside their software development processes, in order to link and synchronise these typically separate components. MethodWhile the majority of prior SV research has focused on re-presenting what is already available in the code (i.e., the implementation) or information derived from it (i.e., various metrics), the presented approach instead makes the design concepts and original developers’ intentions – both significant sources of information in terms of software development and maintenance – readily and contextually available in a visualisation environment that tightly integrates the code artefacts with their original functional requirements and development activity. ResultsOur approach has been implemented in a prototype tool called ScrumCity with the proof of concept being demonstrated using six real-world open source systems. A preliminary case study has further been carried out with real world data. ConclusionConceptual Visualisation, as implemented in ScrumCity, shows early promise in enabling developers and managers (and potentially other stakeholders) to traverse and explore multiple aspects of software product and process artefacts in a synchronised manner, achieving traceability between the two.

Visualising the 3D microstructure of stained and native intervertebral discs using X-ray microtomography

Intervertebral disc degeneration (IVDD) is linked to low back pain. Microstructural changes during degeneration have previously been imaged using 2D sectioning techniques and 3D methods which are limited to small specimens and prone to inducing artefacts from sample preparation. This study explores micro computed X-ray tomography (microCT) methods with the aim of resolving IVD 3D microstructure whilst minimising sample preparation artefacts. Low X-ray absorption contrast in non-mineralised tissue can be enhanced using staining and phase contrast techniques. A step-wise approach, including comparing three stains, was used to develop microCT for bovine tail IVD using laboratory and synchrotron sources. Staining successfully contrasted collagenous structures; however not all regions were stained and the procedure induced macroscopic structural changes. Phase contrast microCT of chemically fixed yet unstained samples resolved the nucleus pulposus, annulus fibrosus and constituent lamellae, and finer structures including collagen bundles and cross-bridges. Using the same imaging methods native tissue scans were of slightly lower contrast but free from sample processing artefacts. In the future these methods may be used to characterise structural remodelling in soft (non-calcified) tissues and to conduct in situ studies of native loaded tissues and constructs to characterise their 3D mechanical properties.

Cutting-edge microangio-CT: new dimensions in vascular imaging and kidney morphometry.

In the last decades, the contrast-enhanced micro-computed tomography (micro-CT) imaging of a whole animal kidney became increasingly important. The visualization was mainly limited to middle-sized vessels. Since modern desktop micro-CT scanners provide the necessary detail resolution, we developed an approach for rapid visualization and consistent assessment of kidney vasculature and glomeruli number. This method is based on μAngiofil, a new polymerizing contrast agent with homogenous X-ray absorption, which provides continuous filling of the complete vasculature and enables correlative imaging approaches. For rapid and reliable kidney morphometry, the microangio-CT (µaCT) data sets from glial cell line-derived neurotrophic factor (GDNF)+/- mice and their wild-type littermates were used. The results were obtained much faster compared with the current gold standard, histology-based stereology, and without processing artifacts. The histology-based morphometry was done afterward on the same kidneys. Both approaches revealed that the GDNF+/- male mice had about 40% fewer glomeruli. Furthermore, our approach allows for the definition of sites of interest for further histological investigation, i.e., correlative morphology. The polymerized μAngiofil stays in perfused vessels and is autofluorescent, which is what greatly facilitates the matching of histological sections with µaCT data. The presented approach is a time-efficient, reliable, qualitative, and quantitative methodology. Besides glomerular morphometry, the µaCT data can be used for qualitative and quantitative analysis of the kidney vasculature and correlative morphology.

A spatial approach to transformational change

PurposeThe purpose of this paper is to explore how strategic alignment of the corporations’ real estate with the organisational strategy may be used to facilitate change within an organisation’s collaborative culture. The focus is on the interconnectedness between spatial and behavioural artefacts in the transition process to a new workplace concept.Design/methodology/approachThe discussion builds on observational studies and semi-structured interviews with 65 employees in a Norwegian organisation.FindingsThe findings indicate that the physical change, when supported by behavioural artefacts as change management actions, paved way for a cultural change towards increased collaboration between employees and across hierarchical levels. However, misalignments between the new workplace concept and existing behavioural artefacts and cultural constructs also restricted the organisation in fully achieving the intended ends.Research limitations/implicationsApplying a socio-material perspective with explicit focus on issues such as management and culture in workplace studies is important to develop better models for strategic use of a corporations’ real estate.Originality/valueWhen new workplace concepts are implemented with the aim of effecting organisational change they require support of a focused change management process where both spatial and behavioural artefacts are designed to support employee adaptation to the new concept. By conducting the change as a continuous iterative process, extending beyond the moving process itself, the corporate real estate management (CREM) may add to the success by guiding and steering the organisation in the right direction.

First Results of the SkyMapper Transient Survey

AbstractThe SkyMapper Transient survey (SMT) is exploring variability in the southern sky by performing (a) a rolling search to discover and study supernovæ, and (b) a Target of Opportunity programme that uses the robotic SkyMapper Telescope at Siding Spring Observatory. The supernova survey is obtaining a non-targeted sample of Type Ia supernovæ (SNe Ia) at low redshifts, z < 0.1, and studying other interesting transients found with the search strategy. We have a Target of Opportunity programme with an automatic response mechanism to search for optical counterparts to gravitational-wave and fast radio-burst events; it benefits from SkyMapper’s large field of view of 5.7 sq. deg. and a rapid data reduction pipeline.We present first results of the SMT survey. The SMT pipeline can process and obtain potential candidates within 12 hours of observation. It disentangles real transients from processing artefacts using a machine-learning algorithm. To date, SMT has discovered over 60 spectroscopically confirmed supernovæ, several peculiar objects, and over 40 SNe Ia including one (SNIa 2016hhd) which was found within the first few days of explosion. We have also participated in searches for optical counterparts of gravitational waves, fast radio bursts and other transients, and have published observations of the optical counterpart of the gravitational-wave event GW170817. We also participate in coordinated observations with the Deeper Wider Faster programme, and the Kepler K2 cosmology project.

Inconsistency Detection of Model and Code via Critic-Based Approach

Model Driven Software Engineering (MDSE) has become the state of the art in software abstraction and increasingly popular in industry and academia. MDSE concerns the use of models as first-class artifacts of software development process. The MDSE has been seen as a way to manage the increasing of software complexity. However, one of the challenges in MDSE is to generate a consistent model-implementation mapping between design model and source code. Source code is also an important software development artifact as it represents the executable system. Detecting inconsistencies between design models and source code is hard because both artifacts normally will have some changes or modifications. Several researchers have introduced various methods in managing the inconsistency of model-code. In this paper, we propose a critic-based approach to detect the inconsistencies between design model and source code. The critic-based approach will provide instant feedback that point out the inconsistencies between model and code.

Plane-wave Sobel attribute for discontinuity enhancement in seismic images

Discontinuity enhancement attributes are commonly used to facilitate the interpretation process by enhancing edges in seismic images and providing a quantitative measure of the significance of discontinuous features. These attributes require careful preprocessing to maintain geologic features and suppress acquisition and processing artifacts, which may be artificially detected as a geologic edge. We have developed the plane-wave Sobel attribute, a modification of the classic Sobel filter, by orienting the filter along seismic structures using plane-wave destruction and plane-wave shaping. The plane-wave Sobel attribute can be applied directly to a seismic image to efficiently and effectively enhance discontinuous features or to a coherence image to create a sharper and more detailed image. Two field benchmark data examples with many faults and channel features from offshore New Zealand and offshore Nova Scotia demonstrate the effectiveness of this method compared with conventional coherence attributes. The results are reproducible using the Madagascar software package.

The fast transient sky with Gaia

The ESA Gaia satellite scans the whole sky with a temporal sampling ranging from seconds and hours to months. Each time a source passes within the Gaia field of view, it moves over 10 CCDs in 45 s and a lightcurve with 4.5 s sampling (the crossing time per CCD) is registered. Given that the 4.5 s sampling represents a virtually unexplored parameter space in optical time domain astronomy, this data set potentially provides a unique opportunity to open up the fast transient sky. We present a method to start mining the wealth of information in the per CCD Gaia data. We perform extensive data filtering to eliminate known on-board and data processing artefacts, and present a statistical method to identify sources that show transient brightness variations on ~2 hours timescales. We illustrate that by using the Gaia photometric CCD measurements, we can detect transient brightness variations down to an amplitude of 0.3 mag on timescales ranging from 15 seconds to several hours. We search an area of ~23.5 square degrees on the sky, and find four strong candidate fast transients. Two candidates are tentatively classified as flares on M-dwarf stars, while one is probably a flare on a giant star and one potentially a flare on a solar type star. These classifications are based on archival data and the timescales involved. We argue that the method presented here can be added to the existing Gaia Science Alerts infrastructure for the near real-time public dissemination of fast transient events.

Mineralogical and Ash Geochemical Studies of Coal-mine Shale and its Hydrocarbon Potential: A Case Study of Shale from Makum Coalfield, Northeast India

ABSTRACT The mineralogy and geochemical studies of the coal-mine shale collected from the Tirap opencast coal-mine (Makum coalfield, Northeast India) are reported in this paper. Thermo-chemical conversion (pyrolysis) of coal-mine shale has been studied to see its hydrocarbon potential. A combined approach using X-Ray diffraction (LTA-XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) equipped with an energy-dispersive X-ray spectrophotometer (EDS), X-ray fluorescence spectrometry (XRF), thermogravimetry-derivative and differential thermogravimetric (TG-DTG and DTA) analysis is made to obtain new information on the mineralogical and geochemical studies of a coal-mine shale (CMS) sample. Gas chromatography-mass spectrometry (GC-MS) analysis is performed to evaluate the quality of the liquid fraction (tar) obtained after pyrolysis at 600°C. The shale sample is dominated by quartz, clay minerals (kaolinite and illite), sulphate bearing phase like gypsum with minor proportion of anatase, probably as artifacts of the plasma-ashing process. GC-MS analysis illustrates the presence of highly oxygenated organic components (M.W. around 94-108) and high molecular weight (M.W. 256) cyclic sulphur (e.g. octathiocane with molecular formula S8) compounds along with the complex N-containing organic sulphur compounds (M.W. around 255-486) in the tar produced.

Improved signal recovery for flow cytometry based on ‘spatially modulated emission’

Recently, the technique of ‘spatially modulated emission’ has been introduced (Baßler et al 2008 US Patent 0080181827A1; Kiesel et al 2009 Appl. Phys. Lett. 94 041107; Kiesel et al 2011 Cytometry A 79A 317–24) improving the signal-to-noise ratio (SNR) for detecting bio-particles in the field of flow cytometry. Based on this concept, we developed two advanced signal processing methods which further enhance the SNR and selectivity for cell detection. The improvements are achieved by adapting digital filtering methods from RADAR technology and mainly address inherent offset elimination, increased signal dynamics and moreover reduction of erroneous detections due to processing artifacts. We present a comprehensive theory on SNR gain and provide experimental results of our concepts.

Performance of an automated algorithm to process artefacts for quantitative EEG analysis during a simultaneous driving simulator performance task

BackgroundArtefact removal from noisy EEG signals is cumbersome, and often requires manual intervention. We tested the performance of an automated method to detect and remove artefacts from EEG recorded during a driving simulation task. MethodsFive patients with obstructive sleep apnea (OSA) and five healthy controls were randomly selected from 17 participants undergoing a 40-h extended wakefulness study with 2-hourly 30-minute simulated driving tasks with simultaneous EEG. Two EEG recordings from each individual were studied. EEG data was first processed by independent component analysis (ICA). The accuracy of the automated algorithm (AA) to detect residual EEG artefact was evaluated against a reference-standard (RS) of visually identified artefact-contaminated epochs. EEG spectral power was calculated using 1) the RS method, 2) the AA, and 3) raw data without any artefact rejection (ICA only). ResultsThe algorithm showed good sensitivity (median: 83.9%), excellent specificity (91.1%), and high accuracy (87.0%) to detect noisy epochs. Cohen's κ indicated a substantial agreement between the two methods (0.72). EEG spectral power calculated using the RS and the AA did not differ significantly, while the power of the raw signal was significantly higher than those produced by any artefact rejection method. Increased EEG delta and theta power were significantly correlated with poorer driving performance. ConclusionsThese preliminary findings demonstrate an effective automated method to process EEG artefact recorded during driving simulation. This approach may facilitate the routine application of quantitative EEG analyses in future studies and identify new markers of impaired driving performance associated with sleep disorders.

Peristaltic-Like Motion of the Human Fetal Right Ventricle and its Effects on Fluid Dynamics and Energy Dynamics.

In both adult human and canine, the cardiac right ventricle (RV) is known to exhibit a peristaltic-like motion, where RV sinus (inflow region) contracts first and the infundibulum (outflow region) later, in a wave-like contraction motion. The delay in contraction between the sinus and infundibulum averaged at 15% of the cardiac cycle and was estimated to produce an intra-ventricular pressure difference of 15mmHg. However, whether such a contractile motion occurs in human fetuses as well, its effects on hemodynamics remains unknown, and are the subject of the current study. Hemodynamic studies of fetal hearts are important as previous works showed that healthy cardiac development is sensitive to fluid mechanical forces. We performed 4D clinical ultrasound imaging on eight 20-weeks old human fetuses. In five fetal RVs, peristaltic-like contractile motion from the sinus to infundibulum ("forward peristaltic-like motion") was observed, but in one RV, peristaltic-like motion was observed from the infundibulum to sinus ("reversed peristaltic-like motion"), and two RVs contraction delay could not be determined due to poor regression fit. Next, we performed dynamic-mesh computational fluid dynamics simulations with varying extents of peristaltic-like motions for three of the eight RVs. Results showed that the peristaltic-like motion did not affect flow patterns significantly, but had significant influence on energy dynamics: increasing extent of forward peristaltic-like motion reduced the energy required for movement of fluid out of the heart during systolic ejection, while increasing extent of reversed peristaltic-like motion increased the required energy. It is currently unclear whether the peristaltic-like motion is an adaptation to reduce physiological energy expenditure, or merely an artefact of the cardiac developmental process.

An artificial neural network system to identify alleles in reference electropherograms

Electropherograms are produced in great numbers in forensic DNA laboratories as part of everyday criminal casework. Before the results of these electropherograms can be used they must be scrutinised by analysts to determine what the identified data tells them about the underlying DNA sequences and what is purely an artefact of the DNA profiling process. This process of interpreting the electropherograms can be time consuming and is prone to subjective differences between analysts. Recently it was demonstrated that artificial neural networks could be used to classify information within an electropherogram as allelic (i.e. representative of a DNA fragment present in the DNA extract) or as one of several different categories of artefactual fluorescence that arise as a result of generating an electropherogram. We extend that work here to demonstrate a series of algorithms and artificial neural networks that can be used to identify peaks on an electropherogram and classify them. We demonstrate the functioning of the system on several profiles and compare the results to a leading commercial DNA profile reading system.

Unintended consequences: institutional artefacts, closure mechanisms and the performance gap

ABSTRACTRenewable technologies often feature in policies to improve the energy efficiency of buildings. Designers introduce predicted energy values for specific technologies, but are surprised when the technologies fail to perform as expected. Three building projects are used to explore the effect of construction processes on the energy performance of building-integrated photovoltaic (BIPV) technology. In two cases BIPV failed to deliver expected energy generation, while in the third, dramatic changes in project processes and technical specifications were needed to achieve the specified output. A social construction of technology (SCOT) analysis documents how the energy generation of BIPV disappeared from view at certain points as actors focused on building features. A contribution is made to the theoretical development of SCOT by responding to two issues: privileging of cognitive closure mechanisms and the neglect of institutional analysis. The concept of inflection mechanisms is introduced as a second type of closure mechanism. More specifically, the role of institutional artefacts (e.g. planning requirements and schedules) in the construction process is found to contribute to the performance gap. To reduce the ‘performance gap’, practitioners need to focus on the distribution of design responsibility, sequencing of work and the location of expertise.

3D histopathological grading of osteochondral tissue using contrast-enhanced micro-computed tomography.

SummaryObjectiveHistopathological grading of osteochondral (OC) tissue is widely used in osteoarthritis (OA) research, and it is relatively common in post-surgery in vitro diagnostics. However, relying on thin tissue section, this approach includes a number of limitations, such as: (1) destructiveness, (2) sample processing artefacts, (3) 2D section does not represent spatial 3D structure and composition of the tissue, and (4) the final outcome is subjective. To overcome these limitations, we recently developed a contrast-enhanced μCT (CEμCT) imaging technique to visualize the collagenous extracellular matrix (ECM) of articular cartilage (AC). In the present study, we demonstrate that histopathological scoring of OC tissue from CEμCT is feasible. Moreover, we establish a new, semi-quantitative OA μCT grading system for OC tissue.ResultsPathological features were clearly visualized in AC and subchondral bone (SB) with μCT and verified with histology, as demonstrated with image atlases. Comparison of histopathological grades (OARSI or severity (0–3)) across the characterization approaches, CEμCT and histology, excellent (0.92, 95% CI = [0.84, 0.96], n = 30) or fair (0.50, 95% CI = [0.16, 0.74], n = 27) intra-class correlations (ICC), respectively. A new μCT grading system was successfully established which achieved an excellent cross-method (μCT vs histology) reader-to-reader intra-class correlation (0.78, 95% CI = [0.58, 0.89], n = 27).ConclusionsWe demonstrated that histopathological information relevant to OA can reliably be obtained from CEμCT images. This new grading system could be used as a reference for 3D imaging and analysis techniques intended for volumetric evaluation of OA pathology in research and clinical applications.

Establishing the True Structure of the Sorbicillinoid-Derived Isolate Rezishanone C by Total Synthesis.

The enantiomer, ent-4, of the true structure, 4, of the sorbicillinoid rezishanone C (sorbivinetone) has been synthesized from a homochiral cis-1,2-dihydrocatechol that is itself generated through the whole-cell biotransformation of toluene. These studies together with dispersion-corrected DFT calculations support the proposal that rezishanone C is an artefact of the isolation process and arises through a Diels-Alder reaction between ethyl vinyl ether and sorbicillinol (3).