Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Stall warning by blade pressure signature analysis

At low mass flow rates axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past - primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focussed on the level of irregularity in the blade passing signature in the rotor tip region. In general, this irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of the flow irregularity, but little effort has been made to characterise the irregularity, or to understand its underlying causes. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity which accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether this irregularity observed in the pre-stall flow field is due to random turbulence, or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity will not be viable in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. Copyright © 2011 by ASME.

Stall Warning by Blade Pressure Signature Analysis

At low mass flow rates, axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past---primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focused on the level of irregularity in the blade passing signature in the rotor tip region. In general, the irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of flow irregularity, but little effort has been made to characterize the irregularity itself, or to understand its underlying cause. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance size and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity that accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether the irregularity observed in the prestall flow field is due to random turbulence or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity would be difficult to implement in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. © 2013 American Society of Mechanical Engineers.

A body force-based method for prediction of multiple-pure-tone noise: Validation

Emissions, fuel burn, and noise are the main drivers for innovative aircraft design. Embedded propulsion systems, such as for example used in hybrid-wing body aircraft, can offer fuel burn and noise reduction benefits but the impact of inlet flow distortion on the generation and propagation of turbomachinery noise has yet to be assessed. A novel approach is used to quantify the effects of non-uniform flow on the creation and propagation of multiple pure tone (MPT) noise. The ultimate goal is to conduct a parametric study of S-duct inlets to quantify the effects of inlet design parameters on the acoustic signature. The key challenge is that the effects of distortion transfer, noise source generation and propagation through the non-uniform flow field are inherently coupled such that a simultaneous computation of the aerodynamics and acoustics is required to capture the mechanisms at play. The technical approach is based on a body force description of the fan blade row that is able to capture the distortion transfer and the blade-to-blade flow variations that cause the MPT noise while reducing computational cost. A single, 3-D full-wheel CFD simulation, in which the Euler equations are solved to second-order spatial and temporal accuracy, simultaneously computes the MPT noise generation and its propagation in distorted inlet flow. A new method of producing the blade-to-blade variations in the body force field for MPT noise generation has been developed and validated. The numerical dissipation inherent to the solver is quantified and used to correct for non-physical attenuation in the far-field noise spectra. Source generation, acoustic propagation and acoustic energy transfer between modes is examined in detail. The new method is validated on NASA's Source Diagnostic Test fan and inlet, showing good agreement with experimental data for aerodynamic performance, acoustic source generation, and far-field noise spectra. The next steps involve the assessment of MPT noise in serpentine inlet ducts and the development of a reduced order formulation suitable for incorporation into NASA's ANOPP framework. © 2010 by Jeff Defoe, Alex Narkaj & Zoltan Spakovszky.

Determining vibration signature of a defective planet bearing in a wind turbine epicyclic gearbox

Planet bearings of wind turbine epicyclic gearboxes are considered as one of the most critical components due to their high failure rate. In order to develop effective vibration based detection algorithms for these bearings, a thorough understanding of their vibration signature is required. In this paper, we investigate the vibration behaviour of an epicyclic gearbox in the presence of a defective planet bearing both theoretically and experimentally. We also identify different sources of modulation sidebands using an analytical model which includes ring gear flexibility and planet bearing defects. The findings from this work will help engineers to develop more effective fault detection algorithms.

Microfluidics-based acoustic microbubble biosensor

This paper proposes a chip-scale microbubble-based biosensing platform. An encapsulated microbubble oscillates acoustically in liquid when exposed to an ultrasound field with its resonant frequency set by shell parameters. Changes in the resonant frequency of the microbubble can be used to monitor analyte-binding events on the shell. A device concept is proposed where ultrasonic transducers are integrated within a microfluidic channel, inside which electrodes are patterned for differential measurements of microbubble impedance. This device enables simultaneous measurements of the acoustic and electrical response of the microbubble, from which both mechanical and electrical parameters can be extracted. These parameters are used to provide a signature of the analyte. This paper presents acoustic and electrical models of the microbubbles, with the effect of shell parameters being thoroughly discussed. © 2013 IEEE.

Low-spin signature inversion in the pi h(9/2)circle times nu i(13/2) oblate band

Excited states in Tl-188,Tl-190 have been studied experimentally by means of in-beam gamma spectroscopy techniques, and resulted in the identification of a strongly coupled band based on the pi h(9/2) circle times nu i(13/2) configuration with oblate deformation. The oblate band in doubly odd Tl nuclei shows low-spin signature inversion. It is the first experimental observation of low-spin signature inversion for a band associated with the oblate pi h(9/2) circle times nu i(13/2) configuration.

Signature inversion in pi h(9/2) circle times nu i(13/2) oblate band of Tl-188

High-spin Level structure of Tl-188 has been studied via Gd-157 (Cl-35,4n) fusion-evaporation reaction at beam energy of 170MeV. A rotational band built on the pi h(9/2) circle times nu i(13/2) configuration with oblate deformation has been established. Spin values have been proposed to the pi h(9/2) circle times nu i(13/2) oblate band based on the similarities between the oblate band of Tl-188 and those in odd-odd Tl190-200. With the spin assignments, the low-spin signature inversion has been revealed for the pi h(9/2) circle times nu i(13/2) oblate band of Tl-188. The low-spin signature inversion can be interpreted qualitatively in the framework of the quasi-particles plus rotor model including a J dependent p-n residual interaction.

PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

Secure architectures for pairing based public key cryptography

Along with the growing demand for cryptosystems in systems ranging from large servers to mobile devices, suitable cryptogrophic protocols for use under certain constraints are becoming more and more important. Constraints such as calculation time, area, efficiency and security, must be considered by the designer. Elliptic curves, since their introduction to public key cryptography in 1985 have challenged established public key and signature generation schemes such as RSA, offering more security per bit. Amongst Elliptic curve based systems, pairing based cryptographies are thoroughly researched and can be used in many public key protocols such as identity based schemes. For hardware implementions of pairing based protocols, all components which calculate operations over Elliptic curves can be considered. Designers of the pairing algorithms must choose calculation blocks and arrange the basic operations carefully so that the implementation can meet the constraints of time and hardware resource area. This thesis deals with different hardware architectures to accelerate the pairing based cryptosystems in the field of characteristic two. Using different top-level architectures the hardware efficiency of operations that run at different times is first considered in this thesis. Security is another important aspect of pairing based cryptography to be considered in practically Side Channel Analysis (SCA) attacks. The naively implemented hardware accelerators for pairing based cryptographies can be vulnerable when taking the physical analysis attacks into consideration. This thesis considered the weaknesses in pairing based public key cryptography and addresses the particular calculations in the systems that are insecure. In this case, countermeasures should be applied to protect the weak link of the implementation to improve and perfect the pairing based algorithms. Some important rules that the designers must obey to improve the security of the cryptosystems are proposed. According to these rules, three countermeasures that protect the pairing based cryptosystems against SCA attacks are applied. The implementations of the countermeasures are presented and their performances are investigated.

Surveillance during pregnancy: methods and response rates from a hospital based pilot study of the Pregnancy Risk Assessment Monitoring System in Ireland

Background: Many European countries including Ireland lack high quality, on-going, population based estimates of maternal behaviours and experiences during pregnancy. PRAMS is a CDC surveillance program which was established in the United States in 1987 to generate high quality, population based data to reduce infant mortality rates and improve maternal and infant health. PRAMS is the only on-going population based surveillance system of maternal behaviours and experiences that occur before, during and after pregnancy worldwide.Methods: The objective of this study was to adapt, test and evaluate a modified CDC PRAMS methodology in Ireland. The birth certificate file which is the standard approach to sampling for PRAMS in the United States was not available for the PRAMS Ireland study. Consequently, delivery record books for the period between 3 and 5 months before the study start date at a large urban obstetric hospital [8,900 births per year] were used to randomly sample 124 women. Name, address, maternal age, infant sex, gestational age at delivery, delivery method, APGAR score and birth weight were manually extracted from records. Stillbirths and early neonatal deaths were excluded using APGAR scores and hospital records. Women were sent a letter of invitation to participate including option to opt out, followed by a modified PRAMS survey, a reminder letter and a final survey.Results: The response rate for the pilot was 67%. Two per cent of women refused the survey, 7% opted out of the study and 24% did not respond. Survey items were at least 88% complete for all 82 respondents. Prevalence estimates of socially undesirable behaviours such as alcohol consumption during pregnancy were high [>50%] and comparable with international estimates.Conclusion: PRAMS is a feasible and valid method of collecting information on maternal experiences and behaviours during pregnancy in Ireland. PRAMS may offer a potential solution to data deficits in maternal health behaviour indicators in Ireland with further work. This study is important to researchers in Europe and elsewhere who may be interested in new ways of tailoring an established CDC methodology to their unique settings to resolve data deficits in maternal health.

Use of 16S ribosomal RNA gene analyses to characterize the bacterial signature associated with poor oral health in West Virginia.

BACKGROUND: West Virginia has the worst oral health in the United States, but the reasons for this are unclear. This pilot study explored the etiology of this disparity using culture-independent analyses to identify bacterial species associated with oral disease. METHODS: Bacteria in subgingival plaque samples from twelve participants in two independent West Virginia dental-related studies were characterized using 16S rRNA gene sequencing and Human Oral Microbe Identification Microarray (HOMIM) analysis. Unifrac analysis was used to characterize phylogenetic differences between bacterial communities obtained from plaque of participants with low or high oral disease, which was further evaluated using clustering and Principal Coordinate Analysis. RESULTS: Statistically different bacterial signatures (P<0.001) were identified in subgingival plaque of individuals with low or high oral disease in West Virginia based on 16S rRNA gene sequencing. Low disease contained a high frequency of Veillonella and Streptococcus, with a moderate number of Capnocytophaga. High disease exhibited substantially increased bacterial diversity and included a large proportion of Clostridiales cluster bacteria (Selenomonas, Eubacterium, Dialister). Phylogenetic trees constructed using 16S rRNA gene sequencing revealed that Clostridiales were repeated colonizers in plaque associated with high oral disease, providing evidence that the oral environment is somehow influencing the bacterial signature linked to disease. CONCLUSIONS: Culture-independent analyses identified an atypical bacterial signature associated with high oral disease in West Virginians and provided evidence that the oral environment influenced this signature. Both findings provide insight into the etiology of the oral disparity in West Virginia.

A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2.

There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and limitations of traditional pathogen-based testing for suspected upper respiratory viral infection. We inoculated human volunteers with either influenza A (A/Brisbane/59/2007 (H1N1) or A/Wisconsin/67/2005 (H3N2)), and assayed the peripheral blood transcriptome every 8 hours for 7 days. Of 41 inoculated volunteers, 18 (44%) developed symptomatic infection. Using unbiased sparse latent factor regression analysis, we generated a gene signature (or factor) for symptomatic influenza capable of detecting 94% of infected cases. This gene signature is detectable as early as 29 hours post-exposure and achieves maximal accuracy on average 43 hours (p = 0.003, H1N1) and 38 hours (p-value = 0.005, H3N2) before peak clinical symptoms. In order to test the relevance of these findings in naturally acquired disease, a composite influenza A signature built from these challenge studies was applied to Emergency Department patients where it discriminates between swine-origin influenza A/H1N1 (2009) infected and non-infected individuals with 92% accuracy. The host genomic response to Influenza infection is robust and may provide the means for detection before typical clinical symptoms are apparent.

Effect of lesion morphology on microwave signature in 2-D ultra-wideband breast imaging

This paper studies the possibility of distinguishing between benign and malignant masses by exploiting the morphology-dependent temporal and spectral characteristics of their microwave backscatter response in ultra-wideband breast cancer detection. The spiculated border profiles of 2-D breast masses are generated by modifying the baseline elliptical rings based upon the irregularity of their peripheries. Furthermore, the single- and multilayer lesion models are used to characterize a distinct mass region followed by a sharp transition to background, and a blurred mass border exhibiting a gradual transition to background, respectively. Subsequently, the complex natural resonances (CNRs) of the backscatter microwave signature can be derived from the late-time target response and reveal diagnostically useful information. The fractional sequence CLEAN algorithm is proposed to estimate the lesions' delay intervals and identify the late-time responses. Finally, it is shown through numerical examples that the locations of dominant CNRs are dependent on the lesion morphologies, where 2-D computational breast phantoms with single and multiple lesions are investigated. The analysis is of potential use for discrimination between benign and malignant lesions, where the former usually possesses a better-defined, more compact shape as opposed to the latter.

Unlinked vital events in census-based longitudinal studies can bias subsequent analysis

Objective: To examine the potential biases arising from the nonlinkage of census records and vital events in longitudinal studies.
Study Design and Setting: A total of 56,396 deaths of residents of Northern Ireland in the 4 years after the 2001 Census were linked to the 2001 Census records. The characteristics of matched and nonmatched death records were compared using multivariate logistic regression. Subject attributes were as recorded on the death certificate.
Results: In total, 3,392 (6.0%) deaths could not be linked to a census record. Linkage rates were lowest in young adults, males, the unmarried, people living in communal establishments, or living in areas that were more deprived or had recorded low census enumeration. For those aged less than 65 years at census, this linkage would exclude from analysis 20.2% of suicides and 19.7% of deaths by external causes.
Conclusion: The nonlinkage of census and death records is a combination of nonenumeration at census and deficient information about the deceased recorded at the time of death. Unmatched individuals may have been more disadvantaged or socially isolated, and analysis based on the linked data set may therefore show some bias and perhaps understate true social gradients.