scholarly journals Phylogenetic Relationships Within Chrysogorgia (Alcyonacea: Octocorallia), a Morphologically Diverse Genus of Octocoral, Revealed Using a Target Enrichment Approach

2021 ◽  
Vol 7 ◽  
Author(s):  
Candice Bobby Untiedt ◽  
Andrea M. Quattrini ◽  
Catherine S. McFadden ◽  
Phil A. Alderslade ◽  
Eric Pante ◽  
...  
Keyword(s):  
Benthic Communities ◽  
A Priori ◽  
Integrative Approach ◽  
Nominal Species ◽  
Large Set ◽  
Museum Specimens ◽  
Target Enrichment ◽  
Specimen Collection ◽  
Wide Range ◽  
Taxonomic Examination

The octocoral genus Chrysogorgia (Duchassaing and Michelotti, 1864) contains 81 nominal species that are ecologically important components of benthic communities. Taxonomic examination of a large set of samples revealed many provisional new species, exhibiting a wide range of morphological variation. We established nine, distinct morphological groups of Chrysogorgia s.l. that were hypothesized to represent distinct genera. Here, we applied a recently developed universal target enrichment bait method for octocoral exons and ultraconserved elements (UCEs) on 96 specimens varying in morphology, collection ages and DNA quality and quantity to determine whether there was genetic support for these morphologically defined groups. Following Illumina sequencing and SPAdes assembly we recovered 1,682 of 1,700 targeted exon loci and 1,333 of 1,340 targeted UCE loci. Locus recovery per sample was highly variable and significantly correlated with time since specimen collection (2–60 years) and DNA quantity and quality. Phylogenetically informative sites in UCE and exon loci were ∼35% for 50% and 75% taxon-occupancy matrices. Maximum likelihood analyses recovered highly resolved trees with topologies supporting the recognition of 11 candidate genera, corresponding with morphological groups assigned a priori, nine of which are novel. Our results also demonstrate that this target-enrichment approach can be successfully applied to degraded museum specimens of up to 60 years old. This study shows that an integrative approach consisting of molecular and morphological methods will be essential to a proper revision of Chrysogorgia taxonomy and to understand regional diversity of these ecologically important corals.

Selected Contribution: Long-lived Drosophila melanogaster lines exhibit normal metabolic rates

2003 ◽  
Vol 95 (6) ◽  
pp. 2605-2613 ◽  
Author(s):  
Wayne A. Van Voorhies ◽  
Aziz A. Khazaeli ◽  
James W. Curtsinger
Keyword(s):  
Drosophila Melanogaster ◽  
Metabolic Rate ◽  
A Priori ◽  
Model Organisms ◽  
Large Set ◽  
Metabolic Rates ◽  
Powerful Method ◽  
Wide Range ◽  
The Relationship ◽  
Average Adult

The use of model organisms, such as Drosophila melanogaster, provides a powerful method for studying mechanisms of aging. Here we report on a large set of recombinant inbred (RI) D. melanogaster lines that exhibit approximately a fivefold range of average adult longevities. Understanding the factors responsible for the differences in longevity, particularly the characteristics of the longest-lived lines, can provide fundamental insights into the mechanistic correlates of aging. In ectothermic organisms, longevity is often inversely correlated with metabolic rate, suggesting the a priori hypothesis that long-lived lines will have low resting metabolic rates. We conducted ∼6,000 measurements of CO2 production in individual male flies aged 5, 16, 29, and 47 days postemergence and simultaneously measured the weight of individual flies and life spans in populations of each line. Even though there was a wide range of longevities, there was no evidence of an inverse relationship between the variables. The increased longevity of long-lived lines is not mediated through reduction of metabolic activity. In Drosophila, it is possible to both maintain a normal metabolic rate and achieve long life. These results are evaluated in the context of 100 years of research on the relationship between metabolic rate and life span.

The Management of Post-Tonsillectomy Morbidity in Patients With Sleep Apnoea

2019 ◽  
Vol 70 (10) ◽  
pp. 3738-3740
Keyword(s):  
Day Surgery ◽  
Sleep Apnoea ◽  
Integrative Approach ◽  
Multicenter Studies ◽  
Therapeutic Modalities ◽  
Advantages And Disadvantages ◽  
Obstructive Sleep ◽  
Wide Range ◽  
The Impact ◽  
Surgery Center

The Tonsillectomy in children or adults is an intervention commonly encountered in the ENT (Ear Nose and Throat) and Head and Neck surgeon practice. The current tendency is to perform this type of surgery in major ambulatory surgery centers. Two objectives are thus pursued: first of all, the increase of the patient quality of life through the reintegration into the family as quickly as possible and secondly, the expenses associated with continuous hospitalization are reduced. Any tertiary (multidisciplinary) sleep center must ensure the complete diagnosis and treatment (including surgery) of sleep respiratory disorders. Under these conditions the selection of patients and especially the implementation of the specific protocols in order to control the postoperative complications it becomes essential. The present paper describes our experience of tonsillectomy as treatment for selected patients with chronic rhonchopathy (snoring) and mild to moderate obstructive sleep apnoea. It was presented the impact of antibiotics protocols in reducing the main morbid outcomes following tonsillectomy, in our day surgery center. The obtained results can also be a prerequisite for the integrative approach of the patients with sleep apnoea who were recommended surgical treatment. Considering the wide range of therapeutic modalities used in sleep apnoea, each with its specific advantages and disadvantages, more extensive and multicenter studies are needed. Keywords: post-tonsillectomy morbidity, day surgery center, sleep disorders

Web-based Tools for Drug Repurposing: Successful Examples of Collaborative Research

2020 ◽  
Vol 28 (1) ◽  
pp. 181-195
Author(s):  
Quentin Vanhaelen
Keyword(s):  
User Interfaces ◽  
Collaborative Research ◽  
Meta Analysis ◽  
A Priori ◽  
Drug Repurposing ◽  
Data Access ◽  
Estimation Methods ◽  
Large Set ◽  
Computational Tools ◽  
Web Based

: Computational approaches have been proven to be complementary tools of interest in identifying potential candidates for drug repurposing. However, although the methods developed so far offer interesting opportunities and could contribute to solving issues faced by the pharmaceutical sector, they also come with their constraints. Indeed, specific challenges ranging from data access, standardization and integration to the implementation of reliable and coherent validation methods must be addressed to allow systematic use at a larger scale. In this mini-review, we cover computational tools recently developed for addressing some of these challenges. This includes specific databases providing accessibility to a large set of curated data with standardized annotations, web-based tools integrating flexible user interfaces to perform fast computational repurposing experiments and standardized datasets specifically annotated and balanced for validating new computational drug repurposing methods. Interestingly, these new databases combined with the increasing number of information about the outcomes of drug repurposing studies can be used to perform a meta-analysis to identify key properties associated with successful drug repurposing cases. This information could further be used to design estimation methods to compute a priori assessment of the repurposing possibilities.

scholarly journals A Systematic Review and Qualitative Synthesis Resulting in a Typology of Elementary Classroom Movement Integration Interventions

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Spyridoula Vazou ◽  
Collin A. Webster ◽  
Gregory Stewart ◽  
Priscila Candal ◽  
Cate A. Egan ◽  
...  
Keyword(s):  
Physical Activity ◽  
Teacher Collaboration ◽  
A Priori ◽  
Real Life ◽  
Dose Intensity ◽  
Routine Practice ◽  
Qualitative Synthesis ◽  
Wide Range ◽  
Meta Analyses ◽  
Movement Integration

Abstract Background/Objective Movement integration (MI) involves infusing physical activity into normal classroom time. A wide range of MI interventions have succeeded in increasing children’s participation in physical activity. However, no previous research has attempted to unpack the various MI intervention approaches. Therefore, this study aimed to systematically review, qualitatively analyze, and develop a typology of MI interventions conducted in primary/elementary school settings. Subjects/Methods Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed to identify published MI interventions. Irrelevant records were removed first by title, then by abstract, and finally by full texts of articles, resulting in 72 studies being retained for qualitative analysis. A deductive approach, using previous MI research as an a priori analytic framework, alongside inductive techniques were used to analyze the data. Results Four types of MI interventions were identified and labeled based on their design: student-driven, teacher-driven, researcher-teacher collaboration, and researcher-driven. Each type was further refined based on the MI strategies (movement breaks, active lessons, other: opening activity, transitions, reward, awareness), the level of intrapersonal and institutional support (training, resources), and the delivery (dose, intensity, type, fidelity). Nearly half of the interventions were researcher-driven, which may undermine the sustainability of MI as a routine practice by teachers in schools. An imbalance is evident on the MI strategies, with transitions, opening and awareness activities, and rewards being limitedly studied. Delivery should be further examined with a strong focus on reporting fidelity. Conclusions There are distinct approaches that are most often employed to promote the use of MI and these approaches may often lack a minimum standard for reporting MI intervention details. This typology may be useful to effectively translate the evidence into practice in real-life settings to better understand and study MI interventions.

scholarly journals A developmentally descriptive method for quantifying shape in gastropod shells

2020 ◽  
Vol 17 (163) ◽  
pp. 20190721
Author(s):  
J. Larsson ◽  
A. M. Westram ◽  
S. Bengmark ◽  
T. Lundh ◽  
R. K. Butlin
Keyword(s):  
Empirical Studies ◽  
Three Dimensional ◽  
Shell Shape ◽  
Large Set ◽  
Littorina Saxatilis ◽  
Shape Variation ◽  
Gastropod Shell ◽  
Geometric Morphometric ◽  
Wide Range ◽  
Descriptive Method

The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.

Applications of 3D printing in critical care medicine: A scoping review

2021 ◽  
pp. 0310057X2097665
Author(s):  
Natasha Abeysekera ◽  
Kirsty A Whitmore ◽  
Ashvini Abeysekera ◽  
George Pang ◽  
Kevin B Laupland
Keyword(s):  
Critical Care ◽  
Scoping Review ◽  
A Priori ◽  
Three Dimensional ◽  
Critical Care Medicine ◽  
Future Research ◽  
Care Practice ◽  
Three Dimensional Printing ◽  
Wide Range ◽  
Dimensional Printing

Although a wide range of medical applications for three-dimensional printing technology have been recognised, little has been described about its utility in critical care medicine. The aim of this review was to identify three-dimensional printing applications related to critical care practice. A scoping review of the literature was conducted via a systematic search of three databases. A priori specified themes included airway management, procedural support, and simulation and medical education. The search identified 1544 articles, of which 65 were included. Ranging across many applications, most were published since 2016 in non – critical care discipline-specific journals. Most studies related to the application of three-dimensional printed models of simulation and reported good fidelity; however, several studies reported that the models poorly represented human tissue characteristics. Randomised controlled trials found some models were equivalent to commercial airway-related skills trainers. Several studies relating to the use of three-dimensional printing model simulations for spinal and neuraxial procedures reported a high degree of realism, including ultrasonography applications three-dimensional printing technologies. This scoping review identified several novel applications for three-dimensional printing in critical care medicine. Three-dimensional printing technologies have been under-utilised in critical care and provide opportunities for future research.

Using CFD to Enhance the Preliminary Design of High-Pressure Steam Turbines

2013 ◽  
Author(s):  
Juri Bellucci ◽  
Federica Sazzini ◽  
Filippo Rubechini ◽  
Andrea Arnone ◽  
Lorenzo Arcangeli ◽  
...  
Keyword(s):  
High Pressure ◽  
Steam Turbine ◽  
Design Tool ◽  
Tip Clearance ◽  
Large Set ◽  
Preliminary Design ◽  
Steam Turbines ◽  
High Pressure Steam ◽  
Wide Range ◽  
Pressure Steam

This paper focuses on the use of the CFD for improving a steam turbine preliminary design tool. Three-dimensional RANS analyses were carried out in order to independently investigate the effects of profile, secondary flow and tip clearance losses, on the efficiency of two high-pressure steam turbine stages. The parametric study included geometrical features such as stagger angle, aspect ratio and radius ratio, and was conducted for a wide range of flow coefficients to cover the whole operating envelope. The results are reported in terms of stage performance curves, enthalpy loss coefficients and span-wise distribution of the blade-to-blade exit angles. A detailed discussion of these results is provided in order to highlight the different aerodynamic behavior of the two geometries. Once the analysis was concluded, the tuning of a preliminary steam turbine design tool was carried out, based on a correlative approach. Due to the lack of a large set of experimental data, the information obtained from the post-processing of the CFD computations were applied to update the current correlations, in order to improve the accuracy of the efficiency evaluation for both stages. Finally, the predictions of the tuned preliminary design tool were compared with the results of the CFD computations, in terms of stage efficiency, in a broad range of flow coefficients and in different real machine layouts.

scholarly journals Hierarchical Matching and Regression with Application to Photometric Redshift Estimation

2016 ◽  
Vol 12 (S325) ◽  
pp. 145-155
Author(s):  
Fionn Murtagh
Keyword(s):  
Information Structure ◽  
Data Analytics ◽  
A Priori ◽  
Sloan Digital Sky Survey ◽  
Photometric Redshifts ◽  
Merging Galaxies ◽  
Photometric Redshift ◽  
Sky Survey ◽  
Wide Range ◽  
Regression Problems

AbstractThis work emphasizes that heterogeneity, diversity, discontinuity, and discreteness in data is to be exploited in classification and regression problems. A global a priori model may not be desirable. For data analytics in cosmology, this is motivated by the variety of cosmological objects such as elliptical, spiral, active, and merging galaxies at a wide range of redshifts. Our aim is matching and similarity-based analytics that takes account of discrete relationships in the data. The information structure of the data is represented by a hierarchy or tree where the branch structure, rather than just the proximity, is important. The representation is related to p-adic number theory. The clustering or binning of the data values, related to the precision of the measurements, has a central role in this methodology. If used for regression, our approach is a method of cluster-wise regression, generalizing nearest neighbour regression. Both to exemplify this analytics approach, and to demonstrate computational benefits, we address the well-known photometric redshift or ‘photo-z’ problem, seeking to match Sloan Digital Sky Survey (SDSS) spectroscopic and photometric redshifts.

scholarly journals A Consistent Track-to-Track Fusion Method Based on Copula Theory

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Kelin Lu ◽  
K. C. Chang ◽  
Rui Zhou
Keyword(s):  
Probability Distributions ◽  
A Priori ◽  
Joint Probability ◽  
Network Connectivity ◽  
Consistent Estimate ◽  
Fusion Algorithm ◽  
Copula Theory ◽  
Wide Range ◽  
Primary Advantage ◽  
Joint Probability Distributions

This paper addresses the problem of distributed fusion when the conditional independence assumptions on sensor measurements or local estimates are not met. A new data fusion algorithm called Copula fusion is presented. The proposed method is grounded on Copula statistical modeling and Bayesian analysis. The primary advantage of the Copula-based methodology is that it could reveal the unknown correlation that allows one to build joint probability distributions with potentially arbitrary underlying marginals and a desired intermodal dependence. The proposed fusion algorithm requires no a priori knowledge of communications patterns or network connectivity. The simulation results show that the Copula fusion brings a consistent estimate for a wide range of process noises.

scholarly journals Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Katherine L. James ◽  
Thushan I. de Silva ◽  
Katherine Brown ◽  
Hilton Whittle ◽  
Stephen Taylor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Blood Plasma ◽  
De Novo ◽  
A Priori ◽  
Pcr Amplification ◽  
Hiv Vaccine ◽  
Whole Genome ◽  
Plasma Samples ◽  
Target Enrichment ◽  
Rna Seq

ABSTRACTAccurate determination of the genetic diversity present in the HIV quasispecies is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in coinfected subjects. The majority of traditional and next-generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Additionally, target enrichment through PCR requiresa priorisequence knowledge, which is lacking for HIV-2. Therefore, a target enrichment free method of library preparation would be valuable for the field. We applied an RNA shotgun sequencing (RNA-Seq) method without PCR amplification to cultured viral stocks and patient plasma samples from HIV-2-infected individuals. Libraries generated from total plasma RNA were analyzed with a two-step pipeline: (i)de novogenome assembly, followed by (ii) read remapping. By this approach, whole-genome sequences were generated with a 28× to 67× mean depth of coverage. Assembled reads showed a low level of GC bias, and comparison of the genome diversities at the intrahost level showed low diversity in the accessory genevpxin all patients. Our study demonstrates that RNA-Seq is a feasible full-genomede novosequencing method for blood plasma samples collected from HIV-2-infected individuals.IMPORTANCEAn accurate picture of viral genetic diversity is critical for the development of a globally effective HIV vaccine. However, sequencing strategies are often complicated by target enrichment prior to sequencing, introducing biases that can distort variant frequencies, which are not easily corrected for in downstream analyses. Additionally, detaileda priorisequence knowledge is needed to inform robust primer design when employing PCR amplification, a factor that is often lacking when working with tropical diseases localized in developing countries. Previous work has demonstrated that direct RNA shotgun sequencing (RNA-Seq) can be used to circumvent these issues for hepatitis C virus (HCV) and norovirus. We applied RNA-Seq to total RNA extracted from HIV-2 blood plasma samples, demonstrating the applicability of this technique to HIV-2 and allowing us to generate a dynamic picture of genetic diversity over the whole genome of HIV-2 in the context of low-bias sequencing.

Sign in / Sign up

Export Citation Format

Share Document