BOLD Noise Assumptions in fMRI

This paper discusses the assumption of Gaussian noise in the blood-oxygenation-dependent (BOLD) contrast for functional MRI (fMRI). In principle, magnitudes in MRI images follow a Rice distribution. We start by reviewing differences between Rician and Gaussian noise. An analytic expression is derived for the null (resting-state) distribution of the difference between two Rician distributed images. This distribution is shown to be symmetric, and an exact expression for its standard deviation is derived. This distribution can be well approximated by a Gaussian, with very high precision for high SNR, and high precision for lower SNR. Tests on simulated and real MR images show that subtracting the time-series mean in fMRI yields asymmetrically distributed temporal noise. Subtracting a resting-state time series from the first results in symmetric and nearly Gaussian noise. This has important consequences for fMRI analyses using standard statistical tests

Dictionary Learning and Sparse Coding-based Denoising for High-Resolution Task Functional Connectivity MRI Analysis

We propose a novel denoising framework for task functional Magnetic Resonance Imaging (tfMRI) data to delineate the high-resolution spatial pattern of the brain functional connectivity via dictionary learning and sparse coding (DLSC). In order to address the limitations of the unsupervised DLSC-based fMRI studies, we utilize the prior knowledge of task paradigm in the learning step to train a data-driven dictionary and to model the sparse representation. We apply the proposed DLSC-based method to Human Connectome Project (HCP) motor tfMRI dataset. Studies on the functional connectivity of cerebrocerebellar circuits in somatomotor networks show that the DLSC-based denoising framework can significantly improve the prominent connectivity patterns, in comparison to the temporal non-local means (tNLM)-based denoising method as well as the case without denoising, which is consistent and neuroscientifically meaningful within motor area. The promising results show that the proposed method can provide an important foundation for the high-resolution functional connectivity analysis, and provide a better approach for fMRI preprocessing.Comment: 8 pages, 3 figures, MLMI201

Larval performance and adult attraction of Delia platura (Diptera: Anthomyiidae) in a native and an introduced crop

Delia platura Meigen is an important pest in crops around the world. Its host range includes almost 50 species and it can develop in soil organic matter. In Ecuador, D. platura is a serious problem for the crop, Lupinus mutabilis Sweet (Chocho) and it also attacks broccoli (Brassica oleracea). After broccoli is harvested, crop residue is mixed with soil or collected and stored close to Chocho fields. The objectives of this study were to determine the adaptive responses of larvae reared on different hosts and whether D. platura females are preferentially attracted to germinating L. mutabilis seeds or broccoli residue. Accordingly, larval performance and attraction of female D. platura reared on broccoli residue and L. mutabilis seeds were evaluated. The number of larvae, pupae and adults were higher when reared on broccoli. Conversely, pupal weight was higher and time from larva to pupa, pupa to adult and total life cycle were longer in flies reared on L. mutabilis. Although D. platura developed more quickly on broccoli, L. mutabilis was also a good host since pupae were heavier compared with flies reared on broccoli. Delia platura females reared on broccoli preferred broccoli residue to L. mutabilis in an olfactometer. Volatiles from broccoli residue in soil may attract D. platura females and stimulate oviposition on L. mutabilis seeds. Environmentally benign production of L. mutabilis crops with minimal insecticide applications may require the elimination of fresh broccoli residue as fertilizer in soils where L. mutabilis is cultivated

Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease.

Tokovenko B, Rückert C, Kalinowski J, et al. Complete Draft Genome Sequence of the Actinobacterium Nocardiopsis sinuspersici UTMC102 (DSM 45277T), Which Produces Serine Protease. Genome Announc. 2017;5(20): e00362-17.The genome sequence of alkalohalophilic actinobacterium Nocardiopsis sinuspersici UTMC102 is provided. N. sinuspersici UTMC102 produces a highly active serine alkaline protease, and contains at least 11 gene clusters encoding the biosynthesis of secondary metabolites. The N. sinuspersici UTMC102 genome was assembled into a single chromosomal scaffold

A high throughput microscopy toxicity pathway reporter platform for chemical safety assessment

Toxicolog

Pearling: stroke segmentation with crusted pearl strings

We introduce a novel segmentation technique, called Pearling, for the semi-automatic extraction of idealized models of networks of strokes (variable width curves) in images. These networks may for example represent roads in an aerial photograph, vessels in a medical scan, or strokes in a drawing. The operator seeds the process by selecting representative areas of good (stroke interior) and bad colors. Then, the operator may either provide a rough trace through a particular path in the stroke graph or simply pick a starting point (seed) on a stroke and a direction of growth. Pearling computes in realtime the centerlines of the strokes, the bifurcations, and the thickness function along each stroke, hence producing a purified medial axis transform of a desired portion of the stroke graph. No prior segmentation or thresholding is required. Simple gestures may be used to trim or extend the selection or to add branches. The realtime performance and reliability of Pearling results from a novel disk-sampling approach, which traces the strokes by optimizing the positions and radii of a discrete series of disks (pearls) along the stroke. A continuous model is defined through subdivision. By design, the idealized pearl string model is slightly wider than necessary to ensure that it contains the stroke boundary. A narrower core model that fits inside the stroke is computed simultaneously. The difference between the pearl string and its core contains the boundary of the stroke and may be used to capture, compress, visualize, or analyze the raw image data along the stroke boundary

High-content imaging-based BAC-GFP toxicity pathway reporters to assess chemical adversity liabilities.

Adaptive cellular stress responses are paramount in the healthy control of cell and tissue homeostasis and generally activated during toxicity in a chemical-specific manner. Here, we established a platform containing a panel of distinct adaptive stress response reporter cell lines based on BAC-transgenomics GFP tagging in HepG2 cells. Our current panel of eleven BAC-GFP HepG2 reporters together contains (1) upstream sensors, (2) downstream transcription factors and (3) their respective target genes, representing the oxidative stress response pathway (Keap1/Nrf2/Srxn1), the unfolded protein response in the endoplasmic reticulum (Xbp1/Atf4/BiP/Chop) and the DNA damage response (53bp1/p53/p21). Using automated confocal imaging and quantitative single-cell image analysis, we established that all reporters allowed the time-resolved, sensitive and mode-of-action-specific activation of the individual BAC-GFP reporter cell lines as defined by a panel of pathway-specific training compounds. Implementing the temporal pathway activity information increased the discrimination of training compounds. For a set of >30 hepatotoxicants, the induction of Srxn1, BiP, Chop and p21 BAC-GFP reporters correlated strongly with the transcriptional responses observed in cryopreserved primary human hepatocytes. Together, our data indicate that a phenotypic adaptive stress response profiling platform will allow a high throughput and time-resolved classification of chemical-induced stress responses, thus assisting in the future mechanism-based safety assessment of chemicals.Toxicolog

Expansion of W 3(OH)

A direct measurement of the expansion of W 3(OH) is made by comparing Very Large Array images taken about 10 yr apart. The expansion is anisotropic with a typical speed of 3 to 5 km/s, indicating a dynamical age of only 2300 yr. These observations are inconsistent with either the freely expanding shell model or a simple bow shock model. The most favored model is a slowly expanding shell-like HII region, with either a fast rarefied flow or another less massive diffuse ionized region moving towards the observer. There is also a rapidly evolving source near the projected center of emission, perhaps related to the central star.Comment: LaTeX file, 28 pages, includes 8 figures. To appear in ApJ in December 10 (1998) issue. Also available at http://www.submm.caltech.edu/~kawamura/w3oh_pp.p

Having Fun in Learning Formal Specifications

There are many benefits in providing formal specifications for our software. However, teaching students to do this is not always easy as courses on formal methods are often experienced as dry by students. This paper presents a game called FormalZ that teachers can use to introduce some variation in their class. Students can have some fun in playing the game and, while doing so, also learn the basics of writing formal specifications in the form of pre- and post-conditions. Unlike existing software engineering themed education games such as Pex and Code Defenders, FormalZ takes the deep gamification approach where playing gets a more central role in order to generate more engagement. This short paper presents our work in progress: the first implementation of FormalZ along with the result of a preliminary users' evaluation. This implementation is functionally complete and tested, but the polishing of its user interface is still future work