A New Approach for Automatic Removal of Movement Artifacts in Near-Infrared Spectroscopy Time Series by Means of Acceleration Data

Abstract: Near-infrared spectroscopy (NIRS) enables the non-invasive measurement of changes in hemodynamics and oxygenation in tissue. Changes in light-coupling due to movement of the subject can cause movement artifacts (MAs) in the recorded signals. Several methods have been developed so far that facilitate the detection and reduction of MAs in the data. However, due to fixed parameter values (e.g., global threshold) none of these methods are perfectly suitable for long-term (i.e., hours) recordings or were not time-effective when applied to large datasets. We aimed to overcome these limitations by automation, i.e., data adaptive thresholding specifically designed for long-term measurements, and by introducing a stable long-term signal reconstruction. Our new technique (“acceleration-based movement artifact reduction algorithm”, AMARA) is based on combining two methods: the “movement artifact reduction algorithm” (MARA, Scholkmann et al. Phys. Meas. 2010, 31, 649–662), and the “accelerometer-based motion artifact removal” (ABAMAR, Virtanen et al. J. Biomed. Opt. 2011, 16, 087005). We describe AMARA in detail and report about successful validation of the algorithm using empirical NIRS data, measured over the prefrontal cortex in adolescents during sleep. In addition, we compared the performance of AMARA to that of MARA and ABAMAR based on validation data.

A fixed-links modeling approach to assess individual differences in the attentional blink: Analysis of behavioral and psychophysiological data

The attentional blink (AB) is a fundamental limitation of the ability to select relevant information from irrelevant information. It can be observed with the detection rate in an AB task as well as with the corresponding P300 amplitude of the event-related potential. In previous research, however, correlations between these two levels of observation were weak and rather inconsistent. A possible explanation of this finding might be that multiple processes underlie the AB and, thus, obscure a possible relationship between AB-related detection rate and the corresponding P300 amplitude. The present study investigated this assumption by applying a fixed-links modeling approach to represent behavioral individual differences in the AB as a latent variable. Concurrently, this approach enabled us to control for additional sources of variance in AB performance by deriving two additional latent variables. The correlation between the latent variable reflecting behavioral individual differences in AB magnitude and a corresponding latent variable derived from the P300 amplitude was high (r=.70). Furthermore, this correlation was considerably stronger than the correlations of other behavioral measures of the AB magnitude with their psychophysiological counterparts (all rs<.40). Our findings clearly indicate that the systematic disentangling of various sources of variance by utilizing the fixed-links modeling approach is a promising tool to investigate behavioral individual differences in the AB and possible psychophysiological correlates of these individual differences.

Longitudinal categorical data analysis: A continuous -time Markov chain approach

In this dissertation, we propose a continuous-time Markov chain model to examine the longitudinal data that have three categories in the outcome variable. The advantage of this model is that it permits a different number of measurements for each subject and the duration between two consecutive time points of measurements can be irregular. Using the maximum likelihood principle, we can estimate the transition probability between two time points. By using the information provided by the independent variables, this model can also estimate the transition probability for each subject. The Monte Carlo simulation method will be used to investigate the goodness of model fitting compared with that obtained from other models. A public health example will be used to demonstrate the application of this method. ^

Apatite fission track analytical data for samples from ODP Leg 152

We test a new approach to understanding the tectonic evolution of passive margins by using fission-track analysis on detrital apatites from sediments deposited offshore East Greenland. These apatites have not undergone postdepositional track annealing and therefore reflect provenance. The apatites preserve a component of the source rocks' thermal history that otherwise may not be retained within the present-day outcrop. Fission-track derived denudational histories from samples at Ocean Drilling Program drill sites offshore East Greenland at lat 63°N are compared with data from the onshore Singertat Complex. Previous apatite fission-track studies and geomorphic mapping of the East Greenland coast have shown that locally up to 6 km of denudation may have occurred, implying significant tectonic or magmatic activity starting as much as 30 m.y. after breakup at 56 Ma. In contrast, apatite fission-track data presented here record <2 km of Cenozoic denudation in southeast Greenland, probably driven by magmatic underplating at the time of breakup. Large-magnitude, postrift denudation of East Greenland is restricted to the area around Kangerdlugssuaq (68°N). The timing (<40-50 Ma) and magnitude are in accord with revised plume track models suggesting that the Iceland plume crossed the margin here during the late Eocene.

Icebergs in the Amundsen Sea (Antarctica) determined from ENVISAT ASAR WSM data using object-based image analysis approach, link to ESRI GDB files

ENVISAT ASAR WSM images with pixel size 150 × 150 m, acquired in different meteorological, oceanographic and sea ice conditions were used to determined icebergs in the Amundsen Sea (Antarctica). An object-based method for automatic iceberg detection from SAR data has been developed and applied. The object identification is based on spectral and spatial parameters on 5 scale levels, and was verified with manual classification in four polygon areas, chosen to represent varying environmental conditions. The algorithm works comparatively well in freezing temperatures and strong wind conditions, prevailing in the Amundsen Sea during the year. The detection rate was 96% which corresponds to 94% of the area (counting icebergs larger than 0.03 km**2), for all seasons. The presented algorithm tends to generate errors in the form of false alarms, mainly caused by the presence of ice floes, rather than misses. This affects the reliability since false alarms were manually corrected post analysis.

Rock magnetic, element, and color data of three sediment cores along the Senegalese continental margin

We present a suite of new high-resolution records (0-135 ka) representing pulses of aeolian, fluvial, and biogenic sedimentation along the Senegalese continental margin. A multiproxy approach based on rock magnetic, element, and color data was applied on three cores enclosing the present-day northern limit of the ITCZ. A strong episodic aeolian contribution driven by stronger winds and dry conditions and characterized by high hematite and goethite input was revealed north of 13°N. These millennial-scale dust fluxes are synchronous with North Atlantic Heinrich stadials. Fluvial clay input driven by the West African monsoon predominates at 12°N and varies at Dansgaard-Oeschger time scales while marine productivity is strongly enhanced during the African humid periods and marine isotope stage 5. From latitudinal signal variations, we deduce that the last glacial ITCZ summer position was located between core positions at 12°26' and 13°40'N. Furthermore, this work also shows that submillennial periods of aridity over northwest Africa occurred more frequently and farther south than previously thought.

Physical oceanography, current meter data, and microstructure measurements 180 km downstream of Denmark Strait sill during Maria S. Merian cruise MSM21/1b

The main objectives of the cruise MSM21/1b were to characterize the spatio-temporal variability of the Denmark Strait overflow and to identify processes responsible for the exchange of the overflow plume with ambient water downstream of Denmark Strait. A multi-platform approach was taken to achieve the goals, based on moorings, an autonomous underwater vehicle (AUV), as well as lowered and vessel-mounted observations. From these platforms, measurements of temperature, salinity, dissolved oxygen, current velocity, dissipation of turbulent kinetic energy, and bottom pressure were obtained.

(Appendix 1) Crustal helium-4 abundance and flux data for ODP Hole 130-806B

The mass accumulation rates (MARs) of aeolian dust in the ocean basins provide an important record of climate in the continental source regions of atmospheric dust and of the prevailing wind patterns responsible for dust transport in the geologic past. The incorporation of other terrigenous components such as volcanic ashes in seafloor sediments, however, often obscures the aeolian dust record. We describe a new approach which uses the delivery rate of crustal 4He to seafloor sediments as a proxy for the mass accumulation rate of old continental dust which is unaffected by the addition of other terrigenous components. We have determined the flux of crustal 4He delivered to the seafloor of the Ontong Java Plateau (OJP) in the western equatorial Pacific over the last 1.9 Myrs. Crustal 4He fluxes vary between 7.7 and 30 ncc/cm**2/kyr and show excellent correlation with global climate as recorded by oxygen isotopes, with high crustal 4He fluxes associated with glacial periods over the entire interval studied. Furthermore, the onset of strong 100 kyr glacial-interglacial climate cycling is clearly seen in the 4He flux record about 700 kyrs ago. These data record variations in the supply of Asian dust in response to climate driven changes in the aridity of the Asian dust sources, consistent with earlier work on Asian dust flux to the northern Pacific Ocean. However, in contrast to previous studies of sites in the central and eastern equatorial Pacific Ocean, there is no evidence that the Inter Tropical Convergence Zone (an effective rainfall barrier to the southward transport of northern hemisphere dust across the equator in the central and eastern Pacific) has influenced the delivery of Asian dust to the OJP. The most likely carrier phase for crustal helium in these sediments is zircon, which can reasonably account for all the 4He observed in the samples. As a first order estimate, these results suggest that the mass accumulation rate of Asian dust on the OJP over the last 1.9 Myrs varied from about 4 to 15 mg/ cm**2/kyr. In contrast, previous studies show that over the same interval the total MAR of terrigenous dust (i.e. Asian dust plus local volcanics) on OJP varied between about 34 and 90 mg/ cm**2/kyr.

Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.

Determinants of inbound tourists in Cambodia : a dynamic panel data approach

Understanding the determinants of tourism demand is crucial for the tourism sector. This paper develops a dynamic panel model to examine the determinants of inbound tourists to Siem Reap airport, Phnom Penh airport, and land and waterway borders in Cambodia. Consistent with the consumer theory of tourism consumption, a 10% increase in the origin country GDP per capita is predicted to increase the number of tourist visits to Siem Reap airport by 5.8%. A 10% increase in the real exchange rate between the origin country and Cambodia is predicted to decrease the number of tourist visits by 0.89%. In contrast, the number of foreign tourists in a previous period has little effect on the number of foreign tourists in the current period. Additionally, the determinants are different by the mode of entry to Cambodia.

A new approach for publishing workflows: abstractions, standards, and linked data

In recent years, a variety of systems have been developed that export the workflows used to analyze data and make them part of published articles. We argue that the workflows that are published in current approaches are dependent on the specific codes used for execution, the specific workflow system used, and the specific workflow catalogs where they are published. In this paper, we describe a new approach that addresses these shortcomings and makes workflows more reusable through: 1) the use of abstract workflows to complement executable workflows to make them reusable when the execution environment is different, 2) the publication of both abstract and executable workflows using standards such as the Open Provenance Model that can be imported by other workflow systems, 3) the publication of workflows as Linked Data that results in open web accessible workflow repositories. We illustrate this approach using a complex workflow that we re-created from an influential publication that describes the generation of 'drugomes'.