A performance analysis of dense stereo correspondence algorithms and error reduction techniques

Abstract: Dense stereo correspondence has been intensely studied and there exists a wide variety of proposed solutions in the literature. Different datasets have been constructed to test stereo algorithms, however, their ground truth formation and scene types vary. In this paper, state-of-the-art algorithms are compared using a number of datasets captured under varied conditions, with accuracy and density metrics forming the basis of a performance evaluation. Pre- and post-processing disparity map error reduction techniques are quantified

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus

Background: The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3–16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. Results: In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Conclusions: Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear

Silicon-mediated mitigation of wounding stress acts by up-regulating the rice antioxidant system

Silicon (Si) is essential for normal growth and development in plants and is also beneficial for their responses to wounding. However, the mechanisms by which Si acts to mitigate the effects of wounding is not fully understood. This effect possibly occurs through a reduction in the oxidative stresses associated with wounding. Here, we tested this possibility by investigating the effects of applying different concentrations of Si (0,5 and 1,0 mM) to rice plants under wounding stress for a period of 6 and 12 h. We found that a higher uptake of Si was signifiacntly associated with an increase in leaf chlorophyll contet. In response to wounding induced oxidative stress, the extent of lipid bilayer peroxidation was reduced in a dose-dependent manner by Si application for 6 or 12 h. Activity of the catalase enzyme was initially lowered by Si treatment; however, at 1.0 mM Si, catalase activity increased significantly after 12h of wounding stress. A similar response was also observed for a peroxidase enzyme. Polyphenol oxidase showed a significant reduction in activity. We conclude that Si application does not only improve leaf chlorophyll content but can also overcome the oxidative stress due wounds or physical injuries

Accurate measurement of gene copy number for human alpha-defensin DEFA1A3

Background: Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. Results: In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. Conclusions: We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis

The novel design of an energy efficient superconductor-based series reactor for installation at a grid connected research site

This paper proposes the development of a superconducting series reactor (SSR) as an alternative to traditionally employed technologies and superconducting fault current limiters when managing fault levels on the electrical power grid. By utilizing superconducting tape, which has negligible resistance, in the construction of a series reactor, it is proposed that fault level mitigation could be achieved in a more energy efficient manner. Once constructed the SSR will be installed and tested at a grid-connected power engineering research site, and the proposed impact of this installation is firstly simulated using Reticmaster® power system simulation software. Design parameters for the prototype SSR are then calculated enabling the total cost of the modifications and prototype SSR to be determined. A desktop SSR was also constructed and tested as a pre-cursor to the prototype construction to confirm functionality and design and was found to be up to four times more energy efficient as the equivalent copper reactor. Finally, the calorimetric method of power loss determination was investigated and experimentally shown to be a viable alternative to the traditional electrical method of power loss determination. In the past, the relatively cheap cost of electricity in South Africa had favoured the installation of poor power efficiency devices that required a lower initial capital investment. With increasing energy costs and a focus on carbon emission reductions, the development of the SSR augurs a new era in power system engineering in which designs are proposed considering both total lifecycle costs and energy efficiency. Design proposal for the first superconducting power device in Africa Alternative to less efficient fault current management technologies currently employed Construction and testing of a desktop superconducting series reactor Verification of the calorimetric method for power loss determination

Folded Three-Spin String Solutions in AdS_5 x S^5

We construct a spinning closed string solution in AdS_5 x S^5 which is folded in the radial direction and has two equal spins in AdS_5 and a spin in S^5. The energy expression of the three-spin solution specified by the folding and winding numbers for the small S^5 spin shows a logarithmic behavior and a one-third power behavior of the large total AdS_5 spin, in the long string and in the short string located near the boundary of AdS_5 respectively. It exhibits the non-regular expansion in the 't Hooft coupling constant, while it takes the regular one when the S^5 spin becomes large.Comment: 14 pages, LaTeX, no figures, a reference adde

Screening of Exosomal MicroRNAs From Colorectal Cancer Cells

BACKGROUND: Cells release extracellular membrane vesicles including microvesicles known as exosomes. Exosomes contain microRNAs (miRNAs) however the full range within colorectal cancer cell secreted exosomes is unknown. OBJECTIVE: To identify the full range of exosome encapsulated miRNAs secreted from 2 colorectal cancer cell lines and to investigate engineering of exosomes over-expressing miRNAs. METHODS: Exosomes were isolated from HCT-116 and HT-29 cell lines. RNA was extracted from exosomes and microRNA array performed. Cells were engineered to express miR-379 (HCT-116-379) or a non-targeting control (HCT-116-NTC) and functional effects were determined. Exosomes secreted by engineered cells were transferred to recipient cells and the impact examined. RESULTS: Microvesicles 40-100 nm in size secreted by cell lines were visualised and confirmed to express exosomal protein CD63. HT-29 exosomes contained 409 miRNAs, HCT-116 exosomes contained 393, and 338 were common to exosomes from both cell lines. Selected targets were validated. HCT-116-379 cells showed decreased proliferation (12-15% decrease, p \u3c 0.001) and decreased migration (32-86% decrease, p \u3c 0.001) compared to controls. HCT-116-379 exosomes were enriched for miR-379. Confocal microscopy visualised transfer of HCT-116-379 exosomes to recipient cells. CONCLUSIONS: Colorectal cancer cells secrete a large number of miRNAs within exosomes. miR-379 decreases cell proliferation and migration, and miR-379 enriched exosomes can be engineered

Haloperidol and Ziprasidone for Treatment of Delirium in Critical Illness

BACKGROUND: There are conflicting data on the effects of antipsychotic medications on delirium in patients in the intensive care unit (ICU). METHODS: In a randomized, double-blind, placebo-controlled trial, we assigned patients with acute respiratory failure or shock and hypoactive or hyperactive delirium to receive intravenous boluses of haloperidol (maximum dose, 20 mg daily), ziprasidone (maximum dose, 40 mg daily), or placebo. The volume and dose of a trial drug or placebo was halved or doubled at 12-hour intervals on the basis of the presence or absence of delirium, as detected with the use of the Confusion Assessment Method for the ICU, and of side effects of the intervention. The primary end point was the number of days alive without delirium or coma during the 14-day intervention period. Secondary end points included 30-day and 90-day survival, time to freedom from mechanical ventilation, and time to ICU and hospital discharge. Safety end points included extrapyramidal symptoms and excessive sedation. RESULTS: Written informed consent was obtained from 1183 patients or their authorized representatives. Delirium developed in 566 patients (48%), of whom 89% had hypoactive delirium and 11% had hyperactive delirium. Of the 566 patients, 184 were randomly assigned to receive placebo, 192 to receive haloperidol, and 190 to receive ziprasidone. The median duration of exposure to a trial drug or placebo was 4 days (interquartile range, 3 to 7). The median number of days alive without delirium or coma was 8.5 (95% confidence interval [CI], 5.6 to 9.9) in the placebo group, 7.9 (95% CI, 4.4 to 9.6) in the haloperidol group, and 8.7 (95% CI, 5.9 to 10.0) in the ziprasidone group (P=0.26 for overall effect across trial groups). The use of haloperidol or ziprasidone, as compared with placebo, had no significant effect on the primary end point (odds ratios, 0.88 [95% CI, 0.64 to 1.21] and 1.04 [95% CI, 0.73 to 1.48], respectively). There were no significant between-group differences with respect to the secondary end points or the frequency of extrapyramidal symptoms. CONCLUSIONS: The use of haloperidol or ziprasidone, as compared with placebo, in patients with acute respiratory failure or shock and hypoactive or hyperactive delirium in the ICU did not significantly alter the duration of delirium. (Funded by the National Institutes of Health and the VA Geriatric Research Education and Clinical Center; MIND-USA ClinicalTrials.gov number, NCT01211522 .)