Segmenting root systems in X-ray computed tomography images using level sets

The segmentation of plant roots from soil and other growing media in X-ray computed tomography images is needed to effectively study the root system architecture without excavation. However, segmentation is a challenging problem in this context because the root and non-root regions share similar features. In this paper, we describe a method based on level sets and specifically adapted for this segmentation problem. In particular, we deal with the issues of using a level sets approach on large image volumes for root segmentation, and track active regions of the front using an occupancy grid. This method allows for straightforward modifications to a narrow-band algorithm such that excessive forward and backward movements of the front can be avoided, distance map computations in a narrow band context can be done in linear time through modification of Meijster et al.'s distance transform algorithm, and regions of the image volume are iteratively used to estimate distributions for root versus non-root classes. Results are shown of three plant species of different maturity levels, grown in three different media. Our method compares favorably to a state-of-the-art method for root segmentation in X-ray CT image volumes.Comment: 11 page

Concurrent CO2 Control and O2 Generation for Advanced Life Support

The electrochemical reduction of carbon dioxide (CO2) using ceramic oxygen generators (COGs) is well known and widely studied, however, conventional devices using yttria-stabilized zirconia (YSZ) electrolytes operate at temperatures greater than 700 C. Operating at such high temperatures increases system mass compared to lower temperature systems because of increased energy overhead to get the COG up to operating temperature and the need for heavier insulation and/or heat exchangers to reduce the COG oxygen (O2) output temperature for comfortable inhalation. Recently, the University of Florida developed novel ceramic oxygen generators employing a bilayer electrolyte of gadolinia-doped ceria and erbia-stabilized bismuth for NASA's future exploration of Mars. To reduce landed mass and operation expenditures during the mission, in-situ resource utilization was proposed using these COGs to obtain both lifesupporting oxygen and oxidant/propellant fuel, by converting CO2 from the Mars atmosphere. The results showed that oxygen could be reliably produced from CO2 at temperatures as low as 400 C. These results indicate that this technology could be adapted to CO2 removal from a spacesuit and other applications in which CO2 removal was an issue. The strategy proposed for CO2 removal for advanced life support systems employs a catalytic layer combined with a COG so that it is reduced all the way to solid carbon and oxygen. Hence, a three-phased approach was used for the development of a viable low weight COG for CO2 removal. First, to reduce the COG operating temperature a high oxide ion conductivity electrolyte was developed. Second, to promote full CO2 reduction while avoiding the problem of carbon deposition on the COG cathode, novel cathodes and a removable catalytic carbon deposition layer were designed. Third, to improve efficiency, a pre-stage for CO2 absorption was used to concentrate CO2 from the exhalate before sending it to the COG. These subsystems were then integrated into a single CO2 removal system. This paper describes our progress to date on these tasks

Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

Funding: The Rowett Institute receives funding from SG-RESAS (Scottish Government Rural and Environmental Science and Analysis Service). Visit of M.V. was supported by research grants from FEMS and Slovene human resources development and scholarship funds. Parts of this work were funded by grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel – BSF Energy Research grant to E.A.B. and B.A.W. and Regular BSF Research grants to R.L. and B.A.W. – and by the Israel Science Foundation (grant nos 966/09 and 159/07 291/08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure

Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonisation, disease, antimicrobial resistance, and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30,976 genomes and contextual data for carriage and disease pneumococci recovered between 1916-2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1,222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds, and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme, and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen. Impact statement Many thousands of pneumococcal genomes are available in the public domain, and this creates opportunities for the scientific community to re-use existing data; however, these data are most useful when the contextual data (provenance and phenotype) are also linked to the genomes. Therefore, we created a curated, open-access database in PubMLST that contained nearly 31,000 published pneumococcal genomes and the corresponding contextual data for each genome. This large and diverse pneumococcal database was used to create a novel cgMLST scheme and multilevel clustering method to define genetic lineages with high resolution and a standardised nomenclature. These are open-access resources for all to use and provide a unified framework for the characterisation of global pneumococcal populations

Simulation of metallic nanostructures for emission of THz radiation using the lateral photo-Dember effect

A 2D simulation for the lateral photo-Dember effect is used to calculate the THz emission of metallic nanostructures due to ultrafast diffusion of carriers in order to realize a series of THz emitters.Comment: Corrected version of a paper given at 2011 36th International Conference on Infrared, Millimeter and Terahertz Waves (IRMMW-THz

Does mode of administration affect health-related quality-of-life outcomes after stroke?

Telephone interviews and postal surveys may be a resource-efficient way of assessing health-related quality-of-life post-stroke, if they produce data equivalent to face-to-face interviews. This study explored whether telephone interviews and postal surveys of the Stroke and Aphasia Quality of Life Scale (SAQOL-39g) yielded similar results to face-to-face interviews. Participants included people with aphasia and comprised two groups: group one (n =22) were 3-6 months post-stroke; group two (n =26) were ≥1 year post-stroke. They completed either a face-to-face and a telephone interview or a face-to-face interview and a postal survey of the SAQOL-39g. Response rates were higher for group two (87%) than for group one (72-77%). There were no significant differences between respondents and non-respondents on demographics, co-morbidities, stroke severity, or communication impairment. Concordance between face-to-face and telephone administrations (.90-.98) was excellent; and very good-excellent between face-to-face and postal administrations (.84-.96), although scores in postal administrations were lower (significant for psychosocial domain and overall SAQOL-39g in group two). These findings suggest that the SAQOL-39g yields similar results in different modes of administration. Researchers and clinicians may employ alternative modes, particularly in the longer term post-stroke, in order to reduce costs or facilitate clients with access difficulties

Protocolised non-invasive compared with invasive weaning from mechanical ventilation for adults in intensive care : the Breathe RCT

Background: Invasive mechanical ventilation (IMV) is a life-saving intervention. Following resolution of the condition that necessitated IMV, a spontaneous breathing trial (SBT) is used to determine patient readiness for IMV discontinuation. In patients who fail one or more SBTs, there is uncertainty as to the optimum management strategy. Objective: To evaluate the clinical effectiveness and cost-effectiveness of using non-invasive ventilation (NIV) as an intermediate step in the protocolised weaning of patients from IMV. Design: Pragmatic, open-label, parallel-group randomised controlled trial, with cost-effectiveness analysis. Setting: A total of 51 critical care units across the UK. Participants: Adult intensive care patients who had received IMV for at least 48 hours, who were categorised as ready to wean from ventilation, and who failed a SBT. Interventions: Control group (invasive weaning): patients continued to receive IMV with daily SBTs. A weaning protocol was used to wean pressure support based on the patient’s condition. Intervention group (non-invasive weaning): patients were extubated to NIV. A weaning protocol was used to wean inspiratory positive airway pressure, based on the patient’s condition. Main outcome measures: The primary outcome measure was time to liberation from ventilation. Secondary outcome measures included mortality, duration of IMV, proportion of patients receiving antibiotics for a presumed respiratory infection and health-related quality of life. Results: A total of 364 patients (invasive weaning, n = 182; non-invasive weaning, n = 182) were randomised. Groups were well matched at baseline. There was no difference between the invasive weaning and non-invasive weaning groups in median time to liberation from ventilation {invasive weaning 108 hours [interquartile range (IQR) 57–351 hours] vs. non-invasive weaning 104.3 hours [IQR 34.5–297 hours]; hazard ratio 1.1, 95% confidence interval [CI] 0.89 to 1.39; p = 0.352}. There was also no difference in mortality between groups at any time point. Patients in the non-invasive weaning group had fewer IMV days [invasive weaning 4 days (IQR 2–11 days) vs. non-invasive weaning 1 day (IQR 0–7 days); adjusted mean difference –3.1 days, 95% CI –5.75 to –0.51 days]. In addition, fewer non-invasive weaning patients required antibiotics for a respiratory infection [odds ratio (OR) 0.60, 95% CI 0.41 to 1.00; p = 0.048]. A higher proportion of non-invasive weaning patients required reintubation than those in the invasive weaning group (OR 2.00, 95% CI 1.27 to 3.24). The within-trial economic evaluation showed that NIV was associated with a lower net cost and a higher net effect, and was dominant in health economic terms. The probability that NIV was cost-effective was estimated at 0.58 at a cost-effectiveness threshold of £20,000 per quality-adjusted life-year. Conclusions: A protocolised non-invasive weaning strategy did not reduce time to liberation from ventilation. However, patients who underwent non-invasive weaning had fewer days requiring IMV and required fewer antibiotics for respiratory infections. Future work: In patients who fail a SBT, which factors predict an adverse outcome (reintubation, tracheostomy, death) if extubated and weaned using NIV? Trial registration: Current Controlled Trials ISRCTN15635197. Funding: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 23, No. 48. See the NIHR Journals Library website for further project information

Rapid Progressing Allele HLA-B35 Px Restricted Anti-HIV-1 CD8+ T Cells Recognize Vestigial CTL Epitopes

BACKGROUND: The HLA-B*35-Px allele has been associated with rapid disease progression in HIV-1 infection, in contrast to the HLA-B*35-Py allele. METHODOLOGY/PRINCIPAL FINDINGS: Immune responses to two HLA-B*35 restricted HIV-1 specific CTL epitopes and their variants were followed longitudinally during early HIV-1 infection in 16 HLA-B*35+ individuals. Subjects expressing HLA-B*35-Px alleles showed no difference in response to the consensus epitopes compared to individuals with HLA-B*35-Py alleles. Surprisingly, all the HLA-B*35-Px+ individuals responded to epitope-variants even in the absence of a consensus response. Sequencing of the viral population revealed no evidence of variant virus in any of the individuals. CONCLUSIONS/SIGNIFICANCE: This demonstrates a novel phenomenon that distinguishes individuals with the HLA-B*35-Px rapid progressing allele and those with the HLA-B*35-Py slower progressing allele

Canadian Hydrogen Intensity Mapping Experiment (CHIME) Pathfinder

A pathfinder version of CHIME (the Canadian Hydrogen Intensity Mapping Experiment) is currently being commissioned at the Dominion Radio Astrophysical Observatory (DRAO) in Penticton, BC. The instrument is a hybrid cylindrical interferometer designed to measure the large scale neutral hydrogen power spectrum across the redshift range 0.8 to 2.5. The power spectrum will be used to measure the baryon acoustic oscillation (BAO) scale across this poorly probed redshift range where dark energy becomes a significant contributor to the evolution of the Universe. The instrument revives the cylinder design in radio astronomy with a wide field survey as a primary goal. Modern low-noise amplifiers and digital processing remove the necessity for the analog beamforming that characterized previous designs. The Pathfinder consists of two cylinders 37\,m long by 20\,m wide oriented north-south for a total collecting area of 1,500 square meters. The cylinders are stationary with no moving parts, and form a transit instrument with an instantaneous field of view of $\sim$100\,degrees by 1-2\,degrees. Each CHIME Pathfinder cylinder has a feedline with 64 dual polarization feeds placed every $\sim$30\,cm which Nyquist sample the north-south sky over much of the frequency band. The signals from each dual-polarization feed are independently amplified, filtered to 400-800\,MHz, and directly sampled at 800\,MSps using 8 bits. The correlator is an FX design, where the Fourier transform channelization is performed in FPGAs, which are interfaced to a set of GPUs that compute the correlation matrix. The CHIME Pathfinder is a 1/10th scale prototype version of CHIME and is designed to detect the BAO feature and constrain the distance-redshift relation.Comment: 20 pages, 12 figures. submitted to Proc. SPIE, Astronomical Telescopes + Instrumentation (2014