FADTTSter: Accelerating hypothesis testing with functional analysis of diffusion tensor tract statistics

Functional Analysis of Diffusion Tensor Tract Statistics (FADTTS) is a toolbox for analysis of white matter (WM) fiber tracts. It allows associating diffusion properties along major WM bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these WM tract properties. However, to use this toolbox, a user must have an intermediate knowledge in scripting languages (MATLAB). FADTTSter was created to overcome this issue and make the statistical analysis accessible to any non-technical researcher. FADTTSter is actively being used by researchers at the University of North Carolina. FADTTSter guides non-technical users through a series of steps including quality control of subjects and fibers in order to setup the necessary parameters to run FADTTS. Additionally, FADTTSter implements interactive charts for FADTTS' outputs. This interactive chart enhances the researcher experience and facilitates the analysis of the results. FADTTSter's motivation is to improve usability and provide a new analysis tool to the community that complements FADTTS. Ultimately, by enabling FADTTS to a broader audience, FADTTSter seeks to accelerate hypothesis testing in neuroimaging studies involving heterogeneous clinical data and diffusion tensor imaging. This work is submitted to the Biomedical Applications in Molecular, Structural, and Functional Imaging conference. The source code of this application is available in NITRC

A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing

This work was supported by the United Kingdom Food Standards Agency [grant number FS101013]; the Wellcome Trust [grant numbers 087622 to M.C.J.M., 072782MA to N.D.M.]; and National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at the University of Oxford in partnership with Public Health England (PHE). The views expressed are those of the author(s) and not necessarily those of the FSA, NHS, the NIHR, the Department of Health or Public Health England.Peer reviewedPublisher PD

White matter fiber-based analysis of T1w/T2w ratio map

Purpose: To develop, test, evaluate and apply a novel tool for the white matter fiber-based analysis of T1w/T2w ratio maps quantifying myelin content. Background: The cerebral white matter in the human brain develops from a mostly non-myelinated state to a nearly fully mature white matter myelination within the first few years of life. High resolution T1w/T2w ratio maps are believed to be effective in quantitatively estimating myelin content on a voxel-wise basis. We propose the use of a fiber-tract-based analysis of such T1w/T2w ratio data, as it allows us to separate fiber bundles that a common regional analysis imprecisely groups together, and to associate effects to specific tracts rather than large, broad regions. Methods: We developed an intuitive, open source tool to facilitate such fiber-based studies of T1w/T2w ratio maps. Via its Graphical User Interface (GUI) the tool is accessible to non-technical users. The framework uses calibrated T1w/T2w ratio maps and a prior fiber atlas as an input to generate profiles of T1w/T2w values. The resulting fiber profiles are used in a statistical analysis that performs along-tract functional statistical analysis. We applied this approach to a preliminary study of early brain development in neonates. Results: We developed an open-source tool for the fiber based analysis of T1w/T2w ratio maps and tested it in a study of brain development

Paleomagnetic and paleoenvironmental implications of magnetofossil occurrences in late Miocene marine sediments from the Guadalquivir Basin, SW Spain.

Although recent studies have revealed more widespread occurrences of magnetofossils in pre-Quaternary sediments than have been previously reported, their significance for paleomagnetic and paleoenvironmental studies is not fully understood. We present a paleo- and rock-magnetic study of late Miocene marine sediments recovered from the Guadalquivir Basin (SW Spain). Well-defined paleomagnetic directions provide a robust magnetostratigraphic chronology for the two studied sediment cores. Rock magnetic results indicate the dominance of intact magnetosome chains throughout the studied sediments. These results provide a link between the highest-quality paleomagnetic directions and higher magnetofossil abundances. We interpret that bacterial magnetite formed in the surface sediment mixed layer and that these magnetic particles gave rise to a paleomagnetic signal in the same way as detrital grains. They, therefore, carry a magnetization that is essentially identical to a post-depositional remanent magnetization, which we term a bio-depositional remanent magnetization. Some studied polarity reversals record paleomagnetic directions with an apparent 60-70 kyr recording delay. Magnetofossils in these cases are interpreted to carry a biogeochemical remanent magnetization that is locked in at greater depth in the sediment column. A sharp decrease in magnetofossil abundance toward the middle of the studied boreholes coincides broadly with a major rise in sediment accumulation rates near the onset of the Messinian salinity crisis (MSC), an event caused by interruption of the connection between the Mediterranean Sea and the Atlantic Ocean. This correlation appears to have resulted from dilution of magnetofossils by enhanced terrigenous inputs that were driven, in turn, by sedimentary changes triggered in the basin at the onset of the MSC. Our results highlight the importance of magnetofossils as carriers of high-quality paleomagnetic and paleoenvironmental signals even in dominantly terrigenous sediments

Magnetobiochronology of lower Pliocene marine sediments from the lower Guadalquivir Basin: insights into the tectonic evolution of the Strait of Gibraltar area

The Gibraltar Arc is a complex tectonic region, and several competing models have been proposed to explain its evolution. We studied the sedimentary fill of the Guadalquivir Basin to identify tectonic processes that were occurring when the reopening of the Strait of Gibraltar led to the reestablishment of Mediterranean outflow. We present a chronostratigraphic framework for the Lower Pliocene sediments from the lower Guadalquivir Basin (SW Spain). The updated chronology is based on magnetobiostratigraphic data from several boreholes. Our results show that the studied interval in the La Matilla core is in the early Pliocene section, providing better constraints on the sedimentary evolution of the basin during that period. Migrating depositional facies led to a younger onset of sandy deposition basinward. At the northwestern passive margin, a 0.7 m.y. period of sedimentary bypass related to a sharp decrease in sedimentation rates and lower sea levels resulted from the tectonic uplift of the forebulge. In contrast, high sedimentation rates with continuous deep-marine sedimentation are recorded at the basin center due to continuous tectonic subsidence and west-southwestward progradation of axial depositional systems. The marginal forebulge uplift, continuous tectonic basinal subsidence, and southward progradation of clinoforms in the early Pliocene can be explained by the pull of a lithospheric slab beneath the Gibraltar Arc as the Strait of Gibraltar opened. These findings are, to our knowledge, the first reported sedimentary expression of slab pull beneath the Betics related to the opening of the Strait of Gibraltar after the Messinian salinity crisis

Multiorder coherent Raman scattering of a quantum probe field

We study the multiorder coherent Raman scattering of a quantum probe field in a far-off-resonance medium with a prepared coherence. Under the conditions of negligible dispersion and limited bandwidth, we derive a Bessel-function solution for the sideband field operators. We analytically and numerically calculate various quantum statistical characteristics of the sideband fields. We show that the multiorder coherent Raman process can replicate the statistical properties of a single-mode quantum probe field into a broad comb of generated Raman sidebands. We also study the mixing and modulation of photon statistical properties in the case of two-mode input. We show that the prepared Raman coherence and the medium length can be used as control parameters to switch a sideband field from one type of photon statistics to another type, or from a non-squeezed state to a squeezed state and vice versa.Comment: 12 pages, 7 figures, to be published in Phys. Rev.

Validation of plasma proteomic biomarkers relating to brain amyloid burden in the EMIF-Alzheimer's disease multimodal biomarker discovery cohort

We have previously investigated, discovered, and replicated plasma protein biomarkers for use to triage potential trials participants for PET or cerebrospinal fluid measures of Alzheimer's disease (AD) pathology. This study sought to undertake validation of these candidate plasma biomarkers in a large, multi-center sample collection. Targeted plasma analyses of 34 proteins with prior evidence for prediction of in vivo pathology were conducted in up to 1,000 samples from cognitively healthy elderly individuals, people with mild cognitive impairment, and in patients with AD-type dementia, selected from the EMIF-AD catalogue. Proteins were measured using Luminex xMAP, ELISA, and Meso Scale Discovery assays. Seven proteins replicated in their ability to predict in vivo amyloid pathology. These proteins form a biomarker panel that, along with age, could significantly discriminate between individuals with high and low amyloid pathology with an area under the curve of 0.74. The performance of this biomarker panel remained consistent when tested in apolipoprotein E ϵ4 non-carrier individuals only. This blood-based panel is biologically relevant, measurable using practical immunocapture arrays, and could significantly reduce the cost incurred to clinical trials through screen failure

The Sudbury Neutrino Observatory

The Sudbury Neutrino Observatory is a second generation water Cherenkov detector designed to determine whether the currently observed solar neutrino deficit is a result of neutrino oscillations. The detector is unique in its use of D2O as a detection medium, permitting it to make a solar model-independent test of the neutrino oscillation hypothesis by comparison of the charged- and neutral-current interaction rates. In this paper the physical properties, construction, and preliminary operation of the Sudbury Neutrino Observatory are described. Data and predicted operating parameters are provided whenever possible.Comment: 58 pages, 12 figures, submitted to Nucl. Inst. Meth. Uses elsart and epsf style files. For additional information about SNO see http://www.sno.phy.queensu.ca . This version has some new reference